Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_file Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Role FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values ACHILLES_Lineage_Results_Top_Genes CGC_CancerGermlineMut CGC_CancerMolecularGenetics CGC_CancerSomaticMut CGC_CancerSyndrome CGC_Chr CGC_ChrBand CGC_GeneID CGC_Name CGC_OtherGermlineMut CGC_TissueType COSMIC_n_overlapping_mutations COSMIC_overlapping_mutation_descriptions ClinVar_ASSEMBLY ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_rs Ensembl_so_accession Ensembl_so_term Familial_Cancer_Genes_Reference Familial_Cancer_Genes_Synonym annotation_transcript bcgsc broad build ccds_id dbNSFP_1000Gp1_AC dbNSFP_1000Gp1_AF dbNSFP_1000Gp1_AFR_AC dbNSFP_1000Gp1_AFR_AF dbNSFP_1000Gp1_AMR_AC dbNSFP_1000Gp1_AMR_AF dbNSFP_1000Gp1_ASN_AC dbNSFP_1000Gp1_ASN_AF dbNSFP_1000Gp1_EUR_AC dbNSFP_1000Gp1_EUR_AF dbNSFP_Ancestral_allele dbNSFP_CADD_phred dbNSFP_CADD_raw dbNSFP_CADD_raw_rankscore dbNSFP_ESP6500_AA_AF dbNSFP_ESP6500_EA_AF dbNSFP_Ensembl_geneid dbNSFP_Ensembl_transcriptid dbNSFP_FATHMM_pred dbNSFP_FATHMM_rankscore dbNSFP_FATHMM_score dbNSFP_GERP_NR dbNSFP_GERP_RS dbNSFP_GERP_RS_rankscore dbNSFP_Interpro_domain dbNSFP_LRT_Omega dbNSFP_LRT_converted_rankscore dbNSFP_LRT_pred dbNSFP_LRT_score dbNSFP_LR_pred dbNSFP_LR_rankscore dbNSFP_LR_score dbNSFP_MutationAssessor_pred dbNSFP_MutationAssessor_rankscore dbNSFP_MutationAssessor_score dbNSFP_MutationTaster_converted_rankscore dbNSFP_MutationTaster_pred dbNSFP_MutationTaster_score dbNSFP_Polyphen2_HDIV_pred dbNSFP_Polyphen2_HDIV_rankscore dbNSFP_Polyphen2_HDIV_score dbNSFP_Polyphen2_HVAR_pred dbNSFP_Polyphen2_HVAR_rankscore dbNSFP_Polyphen2_HVAR_score dbNSFP_RadialSVM_pred dbNSFP_RadialSVM_rankscore dbNSFP_RadialSVM_score dbNSFP_Reliability_index dbNSFP_SIFT_converted_rankscore dbNSFP_SIFT_pred dbNSFP_SIFT_score dbNSFP_SLR_test_statistic dbNSFP_SiPhy_29way_logOdds dbNSFP_SiPhy_29way_logOdds_rankscore dbNSFP_SiPhy_29way_pi dbNSFP_UniSNP_ids dbNSFP_Uniprot_aapos dbNSFP_Uniprot_acc dbNSFP_Uniprot_id dbNSFP_aaalt dbNSFP_aapos dbNSFP_aapos_FATHMM dbNSFP_aapos_SIFT dbNSFP_aaref dbNSFP_cds_strand dbNSFP_codonpos dbNSFP_folddegenerate dbNSFP_genename dbNSFP_hg18_pos1coor dbNSFP_phastCons100way_vertebrate dbNSFP_phastCons100way_vertebrate_rankscore dbNSFP_phastCons46way_placental dbNSFP_phastCons46way_placental_rankscore dbNSFP_phastCons46way_primate dbNSFP_phastCons46way_primate_rankscore dbNSFP_phyloP100way_vertebrate dbNSFP_phyloP100way_vertebrate_rankscore dbNSFP_phyloP46way_placental dbNSFP_phyloP46way_placental_rankscore dbNSFP_phyloP46way_primate dbNSFP_phyloP46way_primate_rankscore dbNSFP_refcodon entrez_gene_id external_id_capture gencode_transcript_name gencode_transcript_status gencode_transcript_tags gencode_transcript_type gene_type havana_transcript hgsc igv_bad ucsc t_alt_count t_ref_count n_alt_count n_ref_count validation_judgement_rna validation_power_rna validation_tumor_alt_count_rna validation_tumor_ref_count_rna validation_normal_alt_count_rna validation_normal_ref_count_rna min_val_count_rna validation_judgement_targeted validation_power_targeted validation_tumor_alt_count_targeted validation_tumor_ref_count_targeted validation_normal_alt_count_targeted validation_normal_ref_count_targeted min_val_count_targeted validation_judgement_localAssembly validation_power_localAssembly t_alt_count_localAssembly t_ref_count_localAssembly n_alt_count_localAssembly n_ref_count_localAssembly min_val_count_localAssembly validation_judgement_KRAS validation_power_KRAS t_alt_count_KRAS t_ref_count_KRAS n_alt_count_KRAS n_ref_count_KRAS min_val_count_KRAS pon_loglike pon_pass_loglike localAssembly_detected ExAC_AN ExAC_AC ExAC_LQ passExAC SCNA_NA SCNA_NB SCNA_q_hat SCNA_tau IS_SCNA purity ploidy dna_fraction_in_tumor CCF_hat CCF_CI95_low CCF_CI95_high CCF_mode CCF_mean CCF_median clonal CCF_CI_low CCF_CI_high PEX12 5193 broad.mit.edu 37 17 33902992 33902993 + Frame_Shift_Del DEL AG AG - rs61752110 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr17:33902992_33902993delAG ENST00000225873.4 - 3 1495_1496 c.888_889delCT c.(886-891)ctcttafs p.LL296fs RP11-1094M14.11_ENST00000592381.1_lincRNA|SNORD7_ENST00000384567.1_RNA NM_000286.2 NP_000277.1 O00623 PEX12_HUMAN peroxisomal biogenesis factor 12 18 ATTTTGGGTAAGAGGGGAGAAT 0.470000 0 GRCh37 CD982877 PEX12 D SO:0001589 frameshift_variant ENST00000225873.4 1 1 hg19 CCDS11296.1 TCGA-OE-A75W-01A-12D-A32N-08 PEX12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256489.2 1 0 0 45 413 0 77 1 3.026300e-01 2 9 0 77 2 0 1.879608e-13 0 1 0 0 2 1 0.929685 54 411 3 77 34 0 0 0 0 0 0 -3.318794 1 0 0 0 1 0 0 0 2.108319 0 0.570000 1.770000 0.565041 0.330000 2.500000e-01 0.440000 0.340000 0.346295 0.330000 0 2.900000e-01 3.900000e-01 LUZP1 7798 broad.mit.edu 37 1 23420152 23420159 + Frame_Shift_Del DEL ATTCAAGT ATTCAAGT - TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:23420152_23420159delATTCAAGT ENST00000302291.4 - 4 1397_1404 c.596_603delACTTGAAT c.(595-603)tacttgaatfs p.YLN199fs LUZP1_ENST00000314174.5_Frame_Shift_Del_p.YLN199fs|LUZP1_ENST00000418342.1_Frame_Shift_Del_p.YLN199fs|LUZP1_ENST00000374623.3_Frame_Shift_Del_p.YLN199fs Q86V48 LUZP1_HUMAN leucine zipper protein 1 31 Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255) TCTCCTTTTCATTCAAGTATTTTCTCTC 0.351000 0 SO:0001589 frameshift_variant ENST00000302291.4 1 1 hg19 CCDS30628.1 TCGA-OE-A75W-01A-12D-A32N-08 LUZP1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000008900.3 1 0 0 39 200 0 55 0 0 0 55 0 0 0 0 1 1.000000 55 214 0 55 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 0 0 2.104551 0 0.570000 1.770000 0.565041 0.560000 4.100000e-01 0.730000 0.570000 0.573884 0.560000 0 4.800000e-01 6.500000e-01 CCDC147 0 broad.mit.edu 37 10 106118265 106118265 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr10:106118265G>A ENST00000369704.3 + 2 310 c.176G>A c.(175-177)cGt>cAt p.R59H CCDC147_ENST00000312902.5_5'UTR NM_001008723.1 NP_001008723.1 Q5T655 CC147_HUMAN 52 Colorectal(252;0.103)|Breast(234;0.122) AATGAAAAGCGTCTGATGGCC 0.423000 0 SO:0001583 missense ENST00000369704.3 1 1 hg19 CCDS31282.1 . . . . . . . . . . G 22.4 4.288041 0.80803 . . ENSG00000120051 ENST00000369704 T 0.37058 1.22 5.57 5.57 0.84162 . 0.000000 0.85682 D 0.000000 T 0.51024 0.1650 M 0.91090 3.175 0.80722 D 1 P 0.46020 0.871 B 0.42214 0.38 T 0.62718 -0.6795 10 0.52906 T 0.07 -6.117 15.0736 0.72059 0.0699:0.0:0.9301:0.0 . 59 Q5T655 CC147_HUMAN H 59 ENSP00000358718:R59H ENSP00000358718:R59H R + 2 0 CCDC147 106108255 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 6.732000 0.74790 2.785000 0.95823 0.655000 0.94253 CGT TCGA-OE-A75W-01A-12D-A32N-08 CCDC147-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050216.1 1 0 0 24 291 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 1.000000 24 289 0 51 2 0 0 0 0 52 2 -20.000000 1 1 121412 1 31 1 1 2 3 2.213635 0 0.570000 1.770000 0.577229 0.270000 1.700000e-01 1.000000 0.270000 0.314576 0.270000 0 2.200000e-01 3.500000e-01 ATRNL1 26033 broad.mit.edu 37 10 117154220 117154220 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr10:117154220G>A ENST00000355044.3 + 20 3353 c.3227G>A c.(3226-3228)tGt>tAt p.C1076Y ATRNL1_ENST00000303745.7_5'UTR|ATRNL1_ENST00000423111.2_Missense_Mutation_p.C127Y NM_207303.2 NP_997186.1 Q5VV63 ATRN1_HUMAN attractin-like 1 95 all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234) ACAGGAAAATGTTTCTGCACA 0.343000 0 SO:0001583 missense ENST00000355044.3 1 1 hg19 CCDS7592.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 20.4|20.4 3.976281|3.976281 0.74360|0.74360 .|. .|. ENSG00000107518|ENSG00000107518 ENST00000355044;ENST00000423111|ENST00000526373 T;T|. 0.62105|. 0.05;0.05|. 5.61|5.61 5.61|5.61 0.85477|0.85477 EGF-like, laminin (1);|. 0.087453|. 0.85682|. D|. 0.000000|. D|D 0.86531|0.86531 0.5955|0.5955 H|H 0.94222|0.94222 3.51|3.51 0.80722|0.80722 D|D 1|1 D;D|. 0.71674|. 0.998;0.998|. D;D|. 0.78314|. 0.991;0.991|. D|D 0.89807|0.89807 0.3979|0.3979 10|5 0.87932|. D|. 0|. -20.6284|-20.6284 15.1377|15.1377 0.72583|0.72583 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 127;1076|. B4DH41;Q5VV63|. .;ATRN1_HUMAN|. Y|I 1076;127|159 ENSP00000347152:C1076Y;ENSP00000409624:C127Y|. ENSP00000347152:C1076Y|. C|M +|+ 2|3 0|0 ATRNL1|ATRNL1 117144210|117144210 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.996000|0.996000 0.88848|0.88848 7.632000|7.632000 0.83247|0.83247 2.640000|2.640000 0.89533|0.89533 0.655000|0.655000 0.94253|0.94253 TGT|ATG TCGA-OE-A75W-01A-12D-A32N-08 ATRNL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050507.3 1 0 1 79 194 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 1.000000 76 193 0 41 2 0 0 0 0 41 2 -20.000000 1 1 0 0 1 1 2 3 2.213635 0 0.570000 1.770000 0.577229 0.990000 8.400000e-01 1.000000 1.000000 0.977569 0.990000 1 9.300000e-01 1 KIAA1217 56243 broad.mit.edu 37 10 24825794 24825794 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr10:24825794G>A ENST00000376454.3 + 17 3536 c.3506G>A c.(3505-3507)gGc>gAc p.G1169D KIAA1217_ENST00000307544.6_Missense_Mutation_p.G852D|KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000396445.1_Missense_Mutation_p.G852D|KIAA1217_ENST00000376451.2_Missense_Mutation_p.G852D|KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000458595.1_Missense_Mutation_p.G1134D|KIAA1217_ENST00000376452.3_Missense_Mutation_p.G1133D NM_019590.3 NP_062536.2 Q5T5P2 SKT_HUMAN KIAA1217 70 ACTAGGTCGGGCGCCACAGTG 0.512000 0 SO:0001583 missense ENST00000376454.3 0 1 hg19 CCDS31165.1 . . . . . . . . . . G 15.37 2.814941 0.50527 . . ENSG00000120549 ENST00000458595;ENST00000442879;ENST00000376454;ENST00000376452;ENST00000307544;ENST00000450158;ENST00000396445;ENST00000376451 T;T;T;T;T;T 0.56275 1.1;1.47;1.08;0.54;0.47;0.97 5.62 4.66 0.58398 . 0.130328 0.51477 D 0.000091 T 0.66684 0.2814 M 0.68593 2.085 0.45662 D 0.998584 D;D;D;D;D;D 0.89917 0.996;1.0;0.999;0.999;0.968;0.999 P;D;D;D;P;D 0.75020 0.9;0.974;0.985;0.963;0.733;0.964 T 0.66736 -0.5848 10 0.51188 T 0.08 . 10.0223 0.42051 0.0:0.1282:0.6268:0.2451 . 1134;1133;852;852;852;1169 Q5T5P2-7;A6NLF3;Q5T5P2-8;Q5T5P2-3;Q5T5P2-6;Q5T5P2 .;.;.;.;.;SKT_HUMAN D 1134;852;1169;1133;852;852;852;852 ENSP00000392625:G1134D;ENSP00000365637:G1169D;ENSP00000365635:G1133D;ENSP00000302343:G852D;ENSP00000379722:G852D;ENSP00000365634:G852D ENSP00000302343:G852D G + 2 0 KIAA1217 24865800 1.000000 0.71417 1.000000 0.80357 0.154000 0.21943 4.623000 0.61247 2.646000 0.89796 0.655000 0.94253 GGC TCGA-OE-A75W-01A-12D-A32N-08 KIAA1217-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047223.2 0 0 0 6 318 0 56 0 1.847927e-01 0 36 0 56 2 0 0 0 0 0 2 1 0.964333 5 316 0 56 2 0 0 0 0 56 2 -6.807801 1 1 0 0 1 1 2 3 2.192967 0 0.570000 1.770000 0.576041 0.060000 2.000000e-02 1.000000 0.060000 0.111334 0.060000 0 4.000000e-02 1.100000e-01 ERCC6 2074 broad.mit.edu 37 10 50678629 50678629 + Missense_Mutation SNP T T C TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr10:50678629T>C ENST00000355832.5 - 18 3455 c.3377A>G c.(3376-3378)aAt>aGt p.N1126S ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000542458.1_Missense_Mutation_p.N496S NM_000124.2 NP_000115.1 Q03468 ERCC6_HUMAN excision repair cross-complementation group 6 64 ACATTCCCCATTTCCACTAAT 0.393000 Direct reversal of damage;Nucleotide excision repair (NER) 0 SO:0001583 missense ENST00000355832.5 0 1 hg19 CCDS7229.1 . . . . . . . . . . T 10.92 1.486713 0.26686 . . ENSG00000225830 ENST00000355832;ENST00000374129;ENST00000542458 D;T 0.82344 -1.6;-1.33 5.95 2.33 0.28932 . . . . . T 0.71290 0.3322 L 0.38175 1.15 0.09310 N 1 B;B 0.11235 0.004;0.0 B;B 0.06405 0.002;0.001 T 0.51474 -0.8701 9 0.11794 T 0.64 -1.9129 8.1179 0.30955 0.0:0.2339:0.0:0.7661 . 1126;503 Q03468;Q59FF6 ERCC6_HUMAN;. S 1126;503;496 ENSP00000348089:N1126S;ENSP00000445134:N496S ENSP00000348089:N1126S N - 2 0 ERCC6 50348635 0.007000 0.16637 0.006000 0.13384 0.404000 0.30871 1.437000 0.34991 0.152000 0.19188 0.533000 0.62120 AAT TCGA-OE-A75W-01A-12D-A32N-08 ERCC6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047990.1 0 0 0 13 604 0 101 0 3.171501e-03 0 4 0 101 2 0 0 0 0 0 2 1 0.999501 12 598 0 100 2 0 0 0 0 101 2 -2.893971 1 1 0 0 1 1 2 3 2.192118 0 0.570000 1.770000 0.576041 0.070000 3.000000e-02 1.000000 0.080000 0.115310 0.070000 0 5.000000e-02 1.100000e-01 PCDH15 65217 broad.mit.edu 37 10 55570351 55570351 + Missense_Mutation SNP C C A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr10:55570351C>A ENST00000373965.2 - 35 4862 c.4468G>T c.(4468-4470)Gtt>Ttt p.V1490F PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000409834.1_Missense_Mutation_p.W1117C|PCDH15_ENST00000395438.1_Missense_Mutation_p.W1506C|PCDH15_ENST00000395445.1_Missense_Mutation_p.V1490F|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000414778.1_Missense_Mutation_p.V1487F NM_001142771.1|NM_001142772.1 NP_001136243.1|NP_001136244.1 Q96QU1 PCD15_HUMAN protocadherin-related 15 237 Melanoma(3;0.117)|Lung SC(717;0.238) GCTTCACCAACCACCTCACCA 0.373000 HNSCC(58;0.16) 0 SO:0001583 missense ENST00000373965.2 1 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 15.19|15.19 2.760384|2.760384 0.49468|0.49468 .|. .|. ENSG00000150275|ENSG00000150275 ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395445|ENST00000395438;ENST00000409834 T;T;T|T;T 0.63096|0.58358 0.03;0.14;-0.02|0.38;0.34 6.16|6.16 4.3|4.3 0.51218|0.51218 .|. .|. .|. .|. .|. T|T 0.31796|0.31796 0.0808|0.0808 N|N 0.08118|0.08118 0|0 0.80722|0.80722 D|D 1|1 B;B;B;B|B 0.34103|0.02656 0.437;0.437;0.437;0.437|0.0 B;B;B;B|B 0.26770|0.04013 0.073;0.073;0.073;0.073|0.001 T|T 0.06698|0.06698 -1.0812|-1.0812 9|9 0.62326|0.45353 D|T 0.03|0.12 .|. 10.6203|10.6203 0.45476|0.45476 0.0:0.7929:0.134:0.0731|0.0:0.7929:0.134:0.0731 .|. 1488;1490;1481;1487|1506 C6ZEF5;A2A3E2;C6ZEF7;C9J4F3|A2A3E3 .;.;.;.|. F|C 1490;1487;1483;1490|1506;1117 ENSP00000363076:V1490F;ENSP00000410304:V1487F;ENSP00000378832:V1490F|ENSP00000378826:W1506C;ENSP00000386693:W1117C ENSP00000363076:V1490F|ENSP00000378826:W1506C V|W -|- 1|3 0|0 PCDH15|PCDH15 55240357|55240357 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.989000|0.989000 0.77384|0.77384 1.440000|1.440000 0.35024|0.35024 0.907000|0.907000 0.36646|0.36646 0.650000|0.650000 0.86243|0.86243 GTT|TGG TCGA-OE-A75W-01A-12D-A32N-08 PCDH15-008 NOVEL not_organism_supported|basic protein_coding protein_coding OTTHUMT00000291336.1 0 0 1 126 473 0 106 0 0 0 0 106 2 0 0 0 0 0 2 1 1.000000 123 464 0 103 2 0 0 0 0 106 2 -20.000000 1 1 0 0 1 1 2 3 2.192118 0 0.570000 1.770000 0.576041 0.740000 6.300000e-01 1.000000 0.750000 0.760549 0.740000 0 6.800000e-01 8.200000e-01 TMEM26 219623 broad.mit.edu 37 10 63170318 63170318 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr10:63170318G>A ENST00000399298.3 - 6 1237 c.869C>T c.(868-870)gCc>gTc p.A290V TMEM26_ENST00000507507.1_5'UTR NM_178505.6 NP_848600.2 Q6ZUK4 TMM26_HUMAN transmembrane protein 26 18 Prostate(12;0.0112) GTTCTTCGCGGCAAAGAACAC 0.502000 0 SO:0001583 missense ENST00000399298.3 0 1 hg19 CCDS41530.1 . . . . . . . . . . G 27.5 4.834333 0.91036 . . ENSG00000196932 ENST00000399298 . . . 5.95 5.95 0.96441 . 0.109707 0.64402 D 0.000011 T 0.66177 0.2763 L 0.33189 0.99 0.80722 D 1 D 0.63046 0.992 P 0.59012 0.85 T 0.66732 -0.5849 9 0.66056 D 0.02 -2.1204 20.3967 0.98985 0.0:0.0:1.0:0.0 . 290 Q6ZUK4 TMM26_HUMAN V 290 . ENSP00000382237:A290V A - 2 0 TMEM26 62840324 1.000000 0.71417 0.967000 0.41034 0.382000 0.30200 9.416000 0.97383 2.829000 0.97493 0.655000 0.94253 GCC TCGA-OE-A75W-01A-12D-A32N-08 TMEM26-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359121.1 0 0 0 5 247 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 0.938156 5 247 0 41 2 0 0 0 0 41 2 -2.806305 1 1 0 0 1 1 2 3 2.192118 0 0.570000 1.770000 0.576041 0.070000 2.000000e-02 1.000000 0.070000 0.118609 0.070000 0 4.000000e-02 1.200000e-01 CYP2C8 1558 broad.mit.edu 37 10 96802653 96802653 + Silent SNP G G T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr10:96802653G>T ENST00000371270.3 - 7 1237 c.1143C>A c.(1141-1143)atC>atA p.I381I CYP2C8_ENST00000539050.1_Silent_p.I295I|CYP2C8_ENST00000535898.1_Silent_p.I279I NM_000770.3|NM_001198853.1|NM_001198855.1 NP_000761.3|NP_001185782.1|NP_001185784.1 P10632 CP2C8_HUMAN cytochrome P450, family 2, subfamily C, polypeptide 8 21 Colorectal(252;0.0397) Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198) TTACCTTGGGGATGAGGTAGT 0.453000 0 SO:0001819 synonymous_variant ENST00000371270.3 1 1 hg19 CCDS7438.1 TCGA-OE-A75W-01A-12D-A32N-08 CYP2C8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049499.2 0 0 0 14 407 0 84 0 5.775729e-02 0 11 0 84 2 0 0 0 0 0 2 1 0.999747 14 403 0 84 2 0 0 0 0 84 2 -3.858464 1 1 0 0 1 1 2 3 2.213635 0 0.570000 1.770000 0.577229 0.120000 6.000000e-02 1.000000 0.120000 0.167360 0.120000 0 8.000000e-02 1.700000e-01 KIAA1377 57562 broad.mit.edu 37 11 101833633 101833633 + Missense_Mutation SNP A A T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr11:101833633A>T ENST00000263468.8 + 6 2137 c.1867A>T c.(1867-1869)Att>Ttt p.I623F KIAA1377_ENST00000537689.1_Missense_Mutation_p.I424F NM_020802.2 NP_065853.2 Q9P2H0 K1377_HUMAN KIAA1377 53 all_epithelial(12;0.0104) Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931) AGGTGCAGAAATTCCAAAGAC 0.318000 0 SO:0001583 missense ENST00000263468.8 1 1 hg19 CCDS31658.1 . . . . . . . . . . A 12.49 1.953067 0.34471 . . ENSG00000110318 ENST00000263468;ENST00000537689 T;T 0.08807 3.05;3.05 5.42 4.26 0.50523 . 0.353806 0.27206 N 0.020421 T 0.19446 0.0467 M 0.68317 2.08 0.33432 D 0.581278 D 0.53151 0.958 P 0.54312 0.748 T 0.22556 -1.0213 10 0.48119 T 0.1 -7.3063 12.5825 0.56397 0.8611:0.1389:0.0:0.0 . 623 Q9P2H0 K1377_HUMAN F 623;424 ENSP00000263468:I623F;ENSP00000443184:I424F ENSP00000263468:I623F I + 1 0 KIAA1377 101338843 0.995000 0.38212 0.784000 0.31847 0.115000 0.19883 3.384000 0.52478 0.952000 0.37798 0.459000 0.35465 ATT TCGA-OE-A75W-01A-12D-A32N-08 KIAA1377-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394140.1 1 0 1 55 149 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 1.000000 54 147 0 28 2 0 0 0 0 28 2 -20.000000 1 1 0 0 1 1 2 3 2.161715 0 0.570000 1.770000 0.571222 0.940000 7.400000e-01 1.000000 1.000000 0.928787 0.940000 1 8.300000e-01 1 ELMOD1 55531 broad.mit.edu 37 11 107506439 107506439 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr11:107506439G>A ENST00000265840.7 + 6 633 c.368G>A c.(367-369)cGt>cAt p.R123H ELMOD1_ENST00000531234.1_Missense_Mutation_p.R117H|ELMOD1_ENST00000443271.2_Missense_Mutation_p.R123H NM_018712.3 NP_061182.3 Q8N336 ELMD1_HUMAN ELMO/CED-12 domain containing 1 19 Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104) GAAAAACTGCGTAGAGAGGCC 0.433000 0 SO:0001583 missense ENST00000265840.7 0 1 hg19 CCDS44723.1 . . . . . . . . . . G 34 5.318541 0.95682 . . ENSG00000110675 ENST00000531234;ENST00000265840;ENST00000443271 T;T;T 0.33865 1.39;1.39;1.39 5.57 5.57 0.84162 Engulfment/cell motility, ELMO (1); 0.000000 0.85682 D 0.000000 T 0.65154 0.2664 M 0.81614 2.55 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.83275 0.996;0.993 T 0.66337 -0.5949 10 0.56958 D 0.05 . 19.918 0.97070 0.0:0.0:1.0:0.0 . 123;123 Q8N336;G5E9S5 ELMD1_HUMAN;. H 117;123;123 ENSP00000433232:R117H;ENSP00000265840:R123H;ENSP00000412257:R123H ENSP00000265840:R123H R + 2 0 ELMOD1 107011649 1.000000 0.71417 1.000000 0.80357 0.976000 0.68499 8.989000 0.93506 2.785000 0.95823 0.591000 0.81541 CGT TCGA-OE-A75W-01A-12D-A32N-08 ELMOD1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000389406.1 0 0 0 7 258 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 0.980738 7 257 0 52 2 0 0 0 0 53 2 -3.405233 1 1 120828 1 37 1 1 2 3 2.161715 0 0.570000 1.770000 0.571222 0.090000 3.000000e-02 0.190000 0.100000 0.105137 0.090000 0 6.000000e-02 1.400000e-01 ACRV1 56 broad.mit.edu 37 11 125548083 125548083 + Silent SNP A A G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr11:125548083A>G ENST00000533904.1 - 2 504 c.162T>C c.(160-162)gcT>gcC p.A54A ACRV1_ENST00000445562.1_Intron|ACRV1_ENST00000425431.1_Intron|ACRV1_ENST00000315608.3_Silent_p.A54A|ACRV1_ENST00000453509.1_Intron|ACRV1_ENST00000345274.1_Intron|ACRV1_ENST00000530048.1_Intron|ACRV1_ENST00000353070.1_Intron|ACRV1_ENST00000348856.3_Intron|ACRV1_ENST00000527795.1_Intron P26436 ASPX_HUMAN acrosomal vesicle protein 1 6 all_hematologic(175;0.177) Breast(109;0.0021)|all_lung(97;0.0179)|Lung NSC(97;0.0185)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) TCTCATATAAAGCCTCAGCAT 0.463000 0 SO:0001819 synonymous_variant ENST00000533904.1 1 1 hg19 CCDS8460.1 TCGA-OE-A75W-01A-12D-A32N-08 ACRV1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000386722.1 1 0 1 79 224 0 65 0 0 0 0 65 2 0 0 0 0 0 2 1 1.000000 79 224 0 63 2 0 0 0 0 65 2 -20.000000 1 1 0 0 1 1 2 3 2.161715 0 0.570000 1.770000 0.571222 0.910000 7.400000e-01 1.000000 1.000000 0.911286 0.910000 1 8.200000e-01 1 PTDSS2 81490 broad.mit.edu 37 11 473950 473950 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr11:473950G>A ENST00000308020.5 + 3 516 c.340G>A c.(340-342)Gac>Aac p.D114N PTDSS2_ENST00000530087.1_3'UTR NM_030783.1 NP_110410.1 Q9BVG9 PTSS2_HUMAN phosphatidylserine synthase 2 9 all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) Phosphatidylserine(DB00144) ACAAGCTAAAGACGGGCCATT 0.483000 0 SO:0001583 missense ENST00000308020.5 1 1 hg19 CCDS7696.1 . . . . . . . . . . G 22.4 4.281337 0.80692 . . ENSG00000174915 ENST00000308020 . . . 5.12 5.12 0.69794 . 0.059306 0.64402 D 0.000003 T 0.33147 0.0853 N 0.11341 0.13 0.58432 D 0.999999 P 0.38617 0.64 B 0.32465 0.146 T 0.20107 -1.0285 9 0.30078 T 0.28 -23.8077 17.6882 0.88262 0.0:0.0:1.0:0.0 . 114 Q9BVG9 PTSS2_HUMAN N 114 . ENSP00000308258:D114N D + 1 0 PTDSS2 463950 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 8.943000 0.92975 2.545000 0.85829 0.462000 0.41574 GAC TCGA-OE-A75W-01A-12D-A32N-08 PTDSS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000239301.2 1 0 1 168 485 0 114 1 9.830410e-01 3 18 0 114 2 0 0 0 0 0 2 1 1.000000 165 471 0 111 2 0 0 0 0 114 2 -20.000000 1 1 0 0 1 0 0 0 2.095420 0 0.570000 1.770000 0.559967 0.870000 7.600000e-01 0.990000 0.880000 0.882983 0.870000 1 8.100000e-01 9.400000e-01 OR51A2 401667 broad.mit.edu 37 11 4976514 4976514 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr11:4976514C>T ENST00000380371.1 - 1 429 c.430G>A c.(430-432)Gcc>Acc p.A144T MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron NM_001004748.1 NP_001004748.1 Q8NGJ7 O51A2_HUMAN olfactory receptor, family 51, subfamily A, member 2 17 Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086) CCTATTTGGGCAACTCTGACA 0.423000 0 SO:0001583 missense ENST00000380371.1 1 1 hg19 CCDS31368.1 . . . . . . . . . . - 9.509 1.105347 0.20632 . . ENSG00000205496 ENST00000380371 T 0.37752 1.18 3.13 -4.86 0.03132 GPCR, rhodopsin-like superfamily (1); . . . . T 0.23054 0.0557 L 0.43598 1.365 0.09310 N 1 B 0.19583 0.037 B 0.24006 0.05 T 0.28996 -1.0026 9 0.28530 T 0.3 . 3.2793 0.06909 0.4379:0.2384:0.0:0.3237 . 144 Q8NGJ7 O51A2_HUMAN T 144 ENSP00000369729:A144T ENSP00000369729:A144T A - 1 0 OR51A2 4933090 0.000000 0.05858 0.000000 0.03702 0.003000 0.03518 -6.391000 0.00068 -1.068000 0.03156 0.395000 0.25975 GCC TCGA-OE-A75W-01A-12D-A32N-08 OR51A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000142809.1 1 0 0 73 1053 0 224 0 0 0 0 224 2 0 0 0 0 0 2 1 1.000000 58 903 0 259 2 0 0 0 0 224 2 -12.040710 1 1 0 0 1 0 0 0 2.141750 0 0.570000 1.770000 0.570000 0.220000 1.700000e-01 0.280000 0.220000 0.230016 0.220000 0 1.900000e-01 2.600000e-01 SHANK2 22941 broad.mit.edu 37 11 70333392 70333392 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr11:70333392G>A ENST00000423696.2 - 15 1905 c.1869C>T c.(1867-1869)gtC>gtT p.V623V SHANK2_ENST00000338508.4_Silent_p.V1003V|SHANK2_ENST00000449833.2_Silent_p.V407V|SHANK2_ENST00000409161.1_Silent_p.V406V Q9UPX8 SHAN2_HUMAN SH3 and multiple ankyrin repeat domains 2 62 LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071) GCTTGGCGGGGACGTAGACGG 0.617000 0 SO:0001819 synonymous_variant ENST00000423696.2 0 1 hg19 TCGA-OE-A75W-01A-12D-A32N-08 SHANK2-203 KNOWN basic protein_coding protein_coding 0 0 0 11 1090 0 251 0 0 0 0 251 2 0 0 0 0 0 2 1 0.998174 11 1073 0 248 2 0 0 0 0 251 2 -3.075588 1 1 0 0 1 1 2 3 2.161715 0 0.570000 1.770000 0.571222 0.030000 0 0.070000 0.040000 0.038887 0.030000 0 2.000000e-02 5.000000e-02 NADSYN1 55191 broad.mit.edu 37 11 71194032 71194032 + Missense_Mutation SNP C C T rs149234649 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr11:71194032C>T ENST00000319023.2 + 14 1476 c.1288C>T c.(1288-1290)Cgg>Tgg p.R430W NADSYN1_ENST00000526039.2_3'UTR|NADSYN1_ENST00000530055.1_Missense_Mutation_p.R59W|NADSYN1_ENST00000539574.1_Missense_Mutation_p.R170W NM_018161.4 NP_060631.2 Q6IA69 NADE_HUMAN NAD synthetase 1 p.R430M(1) 25 L-Glutamine(DB00130) GACGTGCACCCGGGCCAGAGA 0.607000 Ovarian(79;763 1781 6490 50276) 1 Substitution - Missense(1) SO:0001583 missense ENST00000319023.2 1 1 hg19 CCDS8201.1 . . . . . . . . . . C 13.99 2.400419 0.42613 0.0 3.49E-4 ENSG00000172890 ENST00000319023;ENST00000539574;ENST00000529840;ENST00000530055 T;T;T;T 0.44083 0.93;0.93;0.93;0.93 4.06 -1.88 0.07713 NAD/GMP synthase (1);Rossmann-like alpha/beta/alpha sandwich fold (1); 0.000000 0.85682 D 0.000000 T 0.69061 0.3069 H 0.94808 3.585 0.49798 D 0.999826 D;D 0.89917 1.0;1.0 D;D 0.91635 0.977;0.999 T 0.73780 -0.3875 10 0.87932 D 0 -26.347 12.5193 0.56050 0.3856:0.6144:0.0:0.0 . 170;430 B3KUU4;Q6IA69 .;NADE_HUMAN W 430;170;59;59 ENSP00000326424:R430W;ENSP00000443718:R170W;ENSP00000437172:R59W;ENSP00000431820:R59W ENSP00000326424:R430W R + 1 2 NADSYN1 70871680 0.927000 0.31430 0.007000 0.13788 0.216000 0.24613 0.660000 0.25009 -0.610000 0.05716 -0.397000 0.06425 CGG TCGA-OE-A75W-01A-12D-A32N-08 NADSYN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394356.1 1 0 0 39 359 0 80 1 9.999999e-01 41 187 0 80 2 0 0 0 0 0 2 1 1.000000 39 356 0 79 2 0 0 0 0 80 2 -2.598634 1 1 121412 22 46 1 1 2 3 2.161715 0 0.570000 1.770000 0.571222 0.340000 2.400000e-01 0.460000 0.340000 0.351215 0.340000 0 2.900000e-01 4.000000e-01 ME3 10873 broad.mit.edu 37 11 86158183 86158183 + Missense_Mutation SNP C C T rs15926 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr11:86158183C>T ENST00000393324.3 - 11 1557 c.1304G>A c.(1303-1305)cGc>cAc p.R435H ME3_ENST00000543262.1_Missense_Mutation_p.R435H|ME3_ENST00000359636.2_Missense_Mutation_p.R435H|RP11-317J19.1_ENST00000524610.1_RNA NM_001014811.1 NP_001014811.1 Q16798 MAON_HUMAN malic enzyme 3, NADP(+)-dependent, mitochondrial 27 Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252) GATGATAGGGCGCTCGTGGAA 0.622000 0 SO:0001583 missense ENST00000393324.3 1 1 hg19 CCDS8277.1 . . . . . . . . . . C 12.73 2.025030 0.35701 . . ENSG00000151376 ENST00000359636;ENST00000543262;ENST00000393324;ENST00000524826 T;T;T;T 0.48522 0.81;0.81;0.81;0.81 5.38 3.42 0.39159 Malic enzyme, NAD-binding (2);NAD(P)-binding domain (1); 0.098256 0.64402 N 0.000002 T 0.48926 0.1527 M 0.81802 2.56 0.80722 D 1 B 0.19331 0.035 B 0.21546 0.035 T 0.43343 -0.9397 9 . . . . 11.3629 0.49655 0.0:0.845:0.0:0.155 . 435 Q16798 MAON_HUMAN H 435 ENSP00000352657:R435H;ENSP00000440246:R435H;ENSP00000376998:R435H;ENSP00000431182:R435H . R - 2 0 ME3 85835831 1.000000 0.71417 0.997000 0.53966 0.096000 0.18686 3.210000 0.51129 0.683000 0.31428 -0.355000 0.07637 CGC TCGA-OE-A75W-01A-12D-A32N-08 ME3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393767.2 1 0 1 103 195 0 59 1 1 19 37 0 59 2 0 0 0 0 0 2 1 1.000000 103 195 0 58 2 0 0 0 0 59 2 -20.000000 1 1 0 0 1 1 2 3 2.161715 0 0.570000 1.770000 0.571222 0.990000 9.900000e-01 1.000000 1.000000 0.999676 0.990000 1 9.900000e-01 1 TBX5 6910 broad.mit.edu 37 12 114839668 114839668 + Missense_Mutation SNP C C T rs104894377 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:114839668C>T ENST00000310346.4 - 3 871 c.205G>A c.(205-207)Gaa>Aaa p.E69K TBX5_ENST00000552726.1_5'UTR|TBX5_ENST00000405440.2_Missense_Mutation_p.E69K|TBX5_ENST00000349716.5_Missense_Mutation_p.E19K|TBX5_ENST00000526441.1_Missense_Mutation_p.E69K NM_000192.3 NP_000183.2 Q99593 TBX5_HUMAN T-box 5 p.E69K(1) 56 Medulloblastoma(191;0.163)|all_neural(191;0.178) GTGCCCACTTCGTGGAATTTT 0.463000 NSCLC(152;1358 1980 4050 23898 40356) 1 Substitution - Missense(1) GRCh37 CM971436 TBX5 M rs104894377 SO:0001583 missense ENST00000310346.4 1 1 hg19 CCDS9173.1 . . . . . . . . . . C 14.80 2.642376 0.47153 . . ENSG00000089225 ENST00000349716;ENST00000310346;ENST00000405440;ENST00000526441 D;D;D;D 0.89617 -2.54;-2.54;-2.54;-2.54 5.07 5.07 0.68467 Transcription factor, T-box, conserved site (1);p53-like transcription factor, DNA-binding (1); 0.105066 0.64402 D 0.000005 T 0.79678 0.4487 N 0.20401 0.57 0.80722 D 1 B;B 0.18310 0.027;0.013 B;B 0.17098 0.017;0.004 T 0.73681 -0.3906 10 0.22706 T 0.39 . 11.0049 0.47629 0.0:0.9151:0.0:0.0849 . 69;69 Q99593-2;Q99593 .;TBX5_HUMAN K 19;69;69;69 ENSP00000337723:E19K;ENSP00000309913:E69K;ENSP00000384152:E69K;ENSP00000433292:E69K ENSP00000309913:E69K E - 1 0 TBX5 113324051 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 5.914000 0.69964 2.359000 0.80004 0.561000 0.74099 GAA TCGA-OE-A75W-01A-12D-A32N-08 TBX5-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000388297.1 1 0 1 77 241 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 1.000000 76 235 0 74 2 0 0 0 0 74 2 -4.668860 1 1 0 0 1 0 0 0 2.012138 0 0.570000 1.770000 0.541235 0.790000 6.400000e-01 0.950000 0.800000 0.799297 0.790000 0 7.100000e-01 8.800000e-01 MORN3 283385 broad.mit.edu 37 12 122091031 122091031 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:122091031C>T ENST00000355329.3 - 4 768 c.598G>A c.(598-600)Gac>Aac p.D200N NM_173855.4 NP_776254.3 Q6PF18 MORN3_HUMAN MORN repeat containing 3 p.D200Y(1) 9 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) CGGCCAAAGTCGATCATCGTC 0.607000 1 Substitution - Missense(1) SO:0001583 missense ENST00000355329.3 0 1 hg19 CCDS31917.1 . . . . . . . . . . C 28.5 4.929149 0.92389 . . ENSG00000139714 ENST00000355329 T 0.74315 -0.83 4.86 4.86 0.63082 . 0.053142 0.64402 D 0.000001 D 0.83059 0.5172 L 0.52573 1.65 0.80722 D 1 D 0.89917 1.0 D 0.81914 0.995 D 0.83861 0.0268 10 0.52906 T 0.07 . 17.952 0.89056 0.0:1.0:0.0:0.0 . 200 Q6PF18 MORN3_HUMAN N 200 ENSP00000347486:D200N ENSP00000347486:D200N D - 1 0 MORN3 120575414 1.000000 0.71417 1.000000 0.80357 0.813000 0.45954 5.215000 0.65241 2.422000 0.82143 0.561000 0.74099 GAC TCGA-OE-A75W-01A-12D-A32N-08 MORN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402154.1 0 0 0 5 179 0 36 0 2.826317e-02 0 8 0 36 2 0 0 0 0 0 2 1 0.937510 5 178 0 35 2 0 0 0 0 36 2 -7.134443 1 1 121410 1 22 1 0 0 0 2.012138 0 0.570000 1.770000 0.541235 0.090000 3.000000e-02 0.190000 0.090000 0.105605 0.090000 0 5.000000e-02 1.500000e-01 CLIP1 6249 broad.mit.edu 37 12 122825973 122825973 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:122825973G>A ENST00000540338.1 - 10 1819 c.1778C>T c.(1777-1779)aCc>aTc p.T593I CLIP1_ENST00000361654.4_Missense_Mutation_p.T547I|CLIP1_ENST00000545889.1_Missense_Mutation_p.T283I|CLIP1_ENST00000537178.1_Missense_Mutation_p.T547I|CLIP1_ENST00000302528.7_Missense_Mutation_p.T582I|CLIP1_ENST00000358808.2_Missense_Mutation_p.T582I P30622 CLIP1_HUMAN CAP-GLY domain containing linker protein 1 60 all_neural(191;0.0837)|Medulloblastoma(191;0.163) TTCCGTGGCGGTATACAGAGC 0.458000 0 SO:0001583 missense ENST00000540338.1 0 1 hg19 CCDS58285.1 . . . . . . . . . . G 7.866 0.727207 0.15439 . . ENSG00000130779 ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304 T;T;T;T;T;T 0.61627 2.74;0.69;0.69;0.7;0.69;0.09 5.37 0.13 0.14746 . 0.766493 0.13191 N 0.406706 T 0.23965 0.0580 N 0.01352 -0.895 0.09310 N 1 B;B;B;B 0.02656 0.0;0.0;0.0;0.0 B;B;B;B 0.04013 0.001;0.001;0.001;0.001 T 0.18116 -1.0347 10 0.44086 T 0.13 3.1754 5.4745 0.16688 0.372:0.1308:0.4972:0.0 . 283;547;582;593 F5H0N7;P30622-2;P30622-1;P30622 .;.;.;CLIP1_HUMAN I 283;582;582;427;547;593;516 ENSP00000438743:T283I;ENSP00000303585:T582I;ENSP00000351665:T582I;ENSP00000445531:T547I;ENSP00000439093:T593I;ENSP00000437786:T516I ENSP00000303585:T582I T - 2 0 CLIP1 121391926 0.848000 0.29623 0.000000 0.03702 0.566000 0.35808 2.612000 0.46343 0.033000 0.15463 0.561000 0.74099 ACC TCGA-OE-A75W-01A-12D-A32N-08 CLIP1-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000401625.1 0 0 0 8 857 1 185 0 1.165960e-03 0 5 1 185 2 0 0 0 0 0 2 0 0.049530 8 848 1 185 17 0 0 0 1 185 2 -2.212927 0 1 0 0 1 0 0 0 2.012138 0 0.570000 1.770000 0.541235 0.020000 0 0.060000 0.030000 0.034060 0.020000 0 1.000000e-02 5.000000e-02 LRP6 4040 broad.mit.edu 37 12 12300383 12300383 + Missense_Mutation SNP A A G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:12300383A>G ENST00000261349.4 - 15 3390 c.3314T>C c.(3313-3315)aTt>aCt p.I1105T LRP6_ENST00000543091.1_Missense_Mutation_p.I1105T NM_002336.2 NP_002327.2 O75581 LRP6_HUMAN low density lipoprotein receptor-related protein 6 85 Prostate(47;0.0865) GGCTAAAGCAATTGGTTTACT 0.453000 0 SO:0001583 missense ENST00000261349.4 1 1 hg19 CCDS8647.1 . . . . . . . . . . A 7.457 0.643887 0.14451 . . ENSG00000070018 ENST00000261349;ENST00000543091 D;D 0.95588 -3.75;-3.75 5.69 5.69 0.88448 Six-bladed beta-propeller, TolB-like (1); 0.519638 0.17309 U 0.178962 D 0.84338 0.5450 N 0.00569 -1.365 0.50171 D 0.999857 B;B 0.15141 0.007;0.012 B;B 0.23419 0.046;0.036 T 0.81077 -0.1096 10 0.11182 T 0.66 . 15.9477 0.79806 1.0:0.0:0.0:0.0 . 1105;1105 F5H7J9;O75581 .;LRP6_HUMAN T 1105 ENSP00000261349:I1105T;ENSP00000442472:I1105T ENSP00000261349:I1105T I - 2 0 LRP6 12191650 0.964000 0.33143 0.960000 0.40013 0.960000 0.62799 8.962000 0.93254 2.179000 0.69175 0.460000 0.39030 ATT TCGA-OE-A75W-01A-12D-A32N-08 LRP6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400137.1 1 0 1 180 491 0 124 0 0 0 0 124 2 0 0 0 1 0 0 2 1 1.000000 180 489 0 121 2 0 0 0 0 124 2 -20.000000 1 1 0 0 1 0 0 0 2.051268 0 0.570000 1.770000 0.552130 0.890000 7.800000e-01 1.000000 0.900000 0.903579 0.890000 1 8.400000e-01 9.600000e-01 PITPNM2 57605 broad.mit.edu 37 12 123470864 123470864 + Nonsense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:123470864G>A ENST00000542749.1 - 24 3823 c.3760C>T c.(3760-3762)Cag>Tag p.Q1254* PITPNM2_ENST00000280562.5_Nonsense_Mutation_p.Q1248*|PITPNM2_ENST00000320201.4_Nonsense_Mutation_p.Q1254*|PITPNM2_ENST00000392428.1_Nonsense_Mutation_p.Q975* Q9BZ72 PITM2_HUMAN phosphatidylinositol transfer protein, membrane-associated 2 39 all_neural(191;0.101)|Medulloblastoma(191;0.163) TACTTCAGCTGCGCCAGGTGG 0.726000 0 SO:0001587 stop_gained ENST00000542749.1 0 1 hg19 CCDS9242.1 . . . . . . . . . . G 41 8.645874 0.98899 . . ENSG00000090975 ENST00000280562;ENST00000320201;ENST00000392428;ENST00000542749 . . . 4.8 4.8 0.61643 . 0.071076 0.56097 D 0.000021 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.08179 T 0.78 -33.4146 18.4084 0.90542 0.0:0.0:1.0:0.0 . . . . X 1248;1254;975;1254 . ENSP00000280562:Q1248X Q - 1 0 PITPNM2 122036817 1.000000 0.71417 1.000000 0.80357 0.707000 0.40811 7.611000 0.82962 2.664000 0.90586 0.561000 0.74099 CAG TCGA-OE-A75W-01A-12D-A32N-08 PITPNM2-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401342.1 0 0 0 4 74 0 18 0 0 0 0 18 2 0 0 0 0 0 2 1 0.885999 4 72 0 18 2 0 0 0 0 18 2 -8.464021 1 1 0 0 1 0 0 0 2.012138 0 0.570000 1.770000 0.541235 0.180000 6.000000e-02 0.390000 0.170000 0.203342 0.180000 0 1.100000e-01 2.900000e-01 GUCY2C 2984 broad.mit.edu 37 12 14766211 14766211 + Missense_Mutation SNP C C T rs118078831 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:14766211C>T ENST00000261170.3 - 27 3198 c.3062G>A c.(3061-3063)cGt>cAt p.R1021H RP11-695J4.2_ENST00000545424.1_RNA|RP11-695J4.2_ENST00000542401.1_RNA NM_004963.3 NP_004954.2 P25092 GUC2C_HUMAN guanylate cyclase 2C (heat stable enterotoxin receptor) 51 Linaclotide(DB08890) TGCTTGCAAACGCTGTTGATT 0.413000 0 SO:0001583 missense ENST00000261170.3 0 1 hg19 CCDS8664.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 C 14.52 2.560274 0.45590 2.27E-4 1.16E-4 ENSG00000070019 ENST00000261170 D 0.81659 -1.52 5.85 4.78 0.61160 . 0.209202 0.48767 D 0.000168 T 0.73265 0.3565 L 0.39147 1.195 0.58432 D 0.999994 B 0.25272 0.122 B 0.20955 0.032 T 0.70346 -0.4897 10 0.42905 T 0.14 . 14.7732 0.69696 0.0:0.8799:0.0:0.1201 . 1021 P25092 GUC2C_HUMAN H 1021 ENSP00000261170:R1021H ENSP00000261170:R1021H R - 2 0 GUCY2C 14657478 0.984000 0.35163 0.979000 0.43373 0.997000 0.91878 2.584000 0.46102 2.773000 0.95371 0.655000 0.94253 CGT TCGA-OE-A75W-01A-12D-A32N-08 GUCY2C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400835.1 0 0 0 7 707 0 143 0 1.394695e-04 0 2 0 143 2 0 0 0 0 0 2 1 0.980171 7 702 0 142 2 0 0 0 0 143 2 -2.806187 1 1 121406 22 50 1 0 0 0 2.051268 0 0.570000 1.770000 0.552130 0.030000 0 0.070000 0.040000 0.037489 0.030000 0 1.000000e-02 5.000000e-02 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-OE-A75W-01A-12D-A32N-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 30 63 0 18 1 9.601079e-01 6 8 0 18 2 1 1 67 264 0 304 2 1 1.000000 30 63 0 18 2 1 1 2553 5469 0 18 2 -20.000000 1 1 121404 2 44 1 0 0 0 2.051268 0 0.570000 1.770000 0.552130 0.990000 7.800000e-01 1.000000 1.000000 0.972074 0.990000 1 9.200000e-01 1 PPFIBP1 8496 broad.mit.edu 37 12 27832529 27832529 + Missense_Mutation SNP G G C TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:27832529G>C ENST00000318304.8 + 19 2024 c.1741G>C c.(1741-1743)Gat>Cat p.D581H PPFIBP1_ENST00000537927.1_Missense_Mutation_p.D428H|PPFIBP1_ENST00000542629.1_Missense_Mutation_p.D550H|PPFIBP1_ENST00000228425.6_Missense_Mutation_p.D575H NM_001198916.1|NM_177444.2 NP_001185845.1|NP_803193 Q86W92 LIPB1_HUMAN PTPRF interacting protein, binding protein 1 (liprin beta 1) PPFIBP1/ALK(3) 32 Lung SC(9;0.0873) TCCATCTCCAGATTCCAAAAA 0.443000 0 SO:0001583 missense ENST00000318304.8 0 1 hg19 CCDS55812.1 . . . . . . . . . . G 27.2 4.808956 0.90707 . . ENSG00000110841 ENST00000540114;ENST00000537927;ENST00000318304;ENST00000542629;ENST00000228425 T;T;T;T;T 0.77750 -1.12;-1.12;-1.12;-1.12;-1.12 5.8 5.8 0.92144 . 0.000000 0.35096 U 0.003459 D 0.87030 0.6076 L 0.59436 1.845 0.80722 D 1 D;D;D;P;D 0.89917 0.999;1.0;0.999;0.886;0.996 D;D;D;P;D 0.91635 0.981;0.999;0.928;0.847;0.967 D 0.87005 0.2119 10 0.66056 D 0.02 -23.4066 19.6581 0.95851 0.0:0.0:1.0:0.0 . 428;412;581;575;550 Q86W92-3;F5GZP6;Q86W92;Q86W92-2;Q86W92-4 .;.;LIPB1_HUMAN;.;. H 412;428;581;550;575 ENSP00000444304:D412H;ENSP00000445425:D428H;ENSP00000314724:D581H;ENSP00000443442:D550H;ENSP00000228425:D575H ENSP00000228425:D575H D + 1 0 PPFIBP1 27723796 1.000000 0.71417 1.000000 0.80357 0.968000 0.65278 7.039000 0.76544 2.735000 0.93741 0.655000 0.94253 GAT TCGA-OE-A75W-01A-12D-A32N-08 PPFIBP1-007 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000402877.1 0 0 0 9 660 0 112 0 0 0 0 112 2 0 0 0 0 0 2 1 0.993808 9 649 0 111 2 0 0 0 0 112 2 -2.667391 1 1 0 0 1 0 0 0 2.051268 0 0.570000 1.770000 0.552130 0.040000 1.000000e-02 0.080000 0.040000 0.050245 0.040000 0 2.000000e-02 7.000000e-02 NELL2 4753 broad.mit.edu 37 12 45169879 45169879 + Missense_Mutation SNP T T A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:45169879T>A ENST00000429094.2 - 8 1321 c.817A>T c.(817-819)Act>Tct p.T273S NELL2_ENST00000437801.2_Missense_Mutation_p.T323S|NELL2_ENST00000549027.1_Missense_Mutation_p.T272S|NELL2_ENST00000452445.2_Missense_Mutation_p.T273S|NELL2_ENST00000395487.2_Missense_Mutation_p.T272S|NELL2_ENST00000333837.4_Missense_Mutation_p.T296S|NELL2_ENST00000551601.1_Missense_Mutation_p.T272S NM_001145108.1 NP_001138580.1 Q99435 NELL2_HUMAN NEL-like 2 (chicken) 65 Lung SC(27;0.192) Lung NSC(34;0.144) ATGGTGCAAGTCCTTTCACAA 0.458000 0 SO:0001583 missense ENST00000429094.2 1 1 hg19 CCDS8746.1 . . . . . . . . . . T 12.43 1.935303 0.34189 . . ENSG00000184613 ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801;ENST00000543684;ENST00000550462;ENST00000552993 T;T;T;T;T;T;T;T;T 0.63417 -0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04 5.61 5.61 0.85477 von Willebrand factor, type C (1); 0.050756 0.85682 D 0.000000 T 0.38878 0.1057 N 0.13003 0.285 0.52099 D 0.999945 B;B;B;B;B;B 0.30824 0.01;0.296;0.045;0.036;0.027;0.185 B;B;B;B;B;B 0.24006 0.003;0.05;0.038;0.012;0.017;0.034 T 0.34428 -0.9829 10 0.10111 T 0.7 -16.8894 10.9681 0.47424 0.1394:0.0:0.0:0.8606 . 296;323;272;273;273;272 B7Z2U7;B7Z9U3;F8VVB6;B3KTI3;Q99435;Q96JS2 .;.;.;.;NELL2_HUMAN;. S 272;273;272;273;272;296;323;272;46;273 ENSP00000378866:T272S;ENSP00000390680:T273S;ENSP00000449332:T272S;ENSP00000394612:T273S;ENSP00000447927:T272S;ENSP00000327988:T296S;ENSP00000416341:T323S;ENSP00000450102:T46S;ENSP00000447085:T273S ENSP00000327988:T296S T - 1 0 NELL2 43456146 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.818000 0.69236 2.137000 0.66172 0.528000 0.53228 ACT TCGA-OE-A75W-01A-12D-A32N-08 NELL2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404180.1 1 0 1 65 211 0 44 0 0 0 1 0 44 2 0 0 0 0 0 2 1 1.000000 64 207 0 44 2 0 0 0 0 44 2 -20.000000 1 1 0 0 1 0 0 0 2.051268 0 0.570000 1.770000 0.552130 0.780000 6.200000e-01 0.960000 0.790000 0.797052 0.780000 0 7.000000e-01 8.800000e-01 ANO6 196527 broad.mit.edu 37 12 45814920 45814920 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:45814920C>T ENST00000320560.8 + 18 2486 c.2284C>T c.(2284-2286)Cct>Tct p.P762S ANO6_ENST00000425752.2_Missense_Mutation_p.P762S|ANO6_ENST00000435642.1_Missense_Mutation_p.P762S|ANO6_ENST00000441606.2_Missense_Mutation_p.P744S|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000423947.3_Missense_Mutation_p.P783S NM_001025356.2 NP_001020527.2 Q4KMQ2 ANO6_HUMAN anoctamin 6 46 CTTCTCCGTCCCTCCCTACGG 0.473000 0 SO:0001583 missense ENST00000320560.8 1 1 hg19 CCDS31782.1 . . . . . . . . . . C 11.84 1.759155 0.31137 . . ENSG00000177119 ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606 T;T;T;T;T 0.69435 -0.4;-0.27;-0.4;-0.26;-0.26 5.05 5.05 0.67936 . 0.319688 0.35151 N 0.003416 T 0.55784 0.1942 L 0.34521 1.04 0.46798 D 0.999205 B;B;B;B 0.27068 0.008;0.055;0.167;0.006 B;B;B;B 0.23018 0.019;0.02;0.031;0.043 T 0.51718 -0.8670 10 0.13853 T 0.58 . 19.2834 0.94061 0.0:1.0:0.0:0.0 . 744;783;762;762 E9PB30;B9EGG0;E9PCT2;Q4KMQ2 .;.;.;ANO6_HUMAN S 762;783;762;762;744 ENSP00000391417:P762S;ENSP00000409126:P783S;ENSP00000413840:P762S;ENSP00000320087:P762S;ENSP00000413137:P744S ENSP00000320087:P762S P + 1 0 ANO6 44101187 0.996000 0.38824 0.803000 0.32268 0.219000 0.24729 3.992000 0.56980 2.717000 0.92951 0.650000 0.86243 CCT TCGA-OE-A75W-01A-12D-A32N-08 ANO6-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000404822.1 1 0 1 133 307 0 77 0 9.197120e-02 0 2 0 77 2 0 0 0 0 0 2 1 1.000000 132 303 0 77 2 0 0 0 0 77 2 -9.600790 1 0 0 0 1 0 0 0 2.051268 0 0.570000 1.770000 0.552130 0.990000 8.700000e-01 1.000000 1.000000 0.979368 0.990000 1 9.400000e-01 1 RAPGEF3 10411 broad.mit.edu 37 12 48134500 48134500 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:48134500G>A ENST00000449771.2 - 21 2244 c.2156C>T c.(2155-2157)gCc>gTc p.A719V RAPGEF3_ENST00000548919.1_Missense_Mutation_p.A628V|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.A719V|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.A677V|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.A677V|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.A677V O95398 RPGF3_HUMAN Rap guanine nucleotide exchange factor (GEF) 3 25 Lung SC(27;0.192) CAGCTCGGTGGCCACCCAGTA 0.652000 0 SO:0001583 missense ENST00000449771.2 0 1 hg19 CCDS41775.1 . . . . . . . . . . G 14.16 2.452324 0.43531 . . ENSG00000079337 ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919 T;T;T;T;T;T 0.32272 1.46;1.46;1.46;1.46;1.46;1.46 3.82 2.9 0.33743 Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1); 0.148106 0.44688 D 0.000440 T 0.16342 0.0393 N 0.16368 0.405 0.35502 D 0.799909 B 0.33841 0.428 B 0.38106 0.265 T 0.14144 -1.0483 10 0.02654 T 1 . 9.7478 0.40457 0.1057:0.0:0.8943:0.0 . 719 O95398 RPGF3_HUMAN V 677;719;366;677;677;677;719;682;628 ENSP00000384521:A677V;ENSP00000395708:A719V;ENSP00000448619:A677V;ENSP00000171000:A677V;ENSP00000373864:A719V;ENSP00000448480:A628V ENSP00000171000:A677V A - 2 0 RAPGEF3 46420767 1.000000 0.71417 1.000000 0.80357 0.914000 0.54420 1.182000 0.32029 1.870000 0.54199 0.561000 0.74099 GCC TCGA-OE-A75W-01A-12D-A32N-08 RAPGEF3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000257848.1 0 0 0 5 354 0 81 0 9.433103e-02 0 30 0 81 2 0 0 0 0 0 2 1 0.934678 4 348 0 80 2 0 0 0 0 81 2 -5.074177 1 0 0 0 1 0 0 0 2.051268 0 0.570000 1.770000 0.552130 0.040000 1.000000e-02 0.100000 0.050000 0.055832 0.040000 0 2.000000e-02 8.000000e-02 GALNT6 11226 broad.mit.edu 37 12 51749736 51749736 + Missense_Mutation SNP C C G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:51749736C>G ENST00000543196.2 - 10 1814 c.1609G>C c.(1609-1611)Gag>Cag p.E537Q GALNT6_ENST00000356317.3_Missense_Mutation_p.E537Q Q8NCL4 GALT6_HUMAN polypeptide N-acetylgalactosaminyltransferase 6 27 GTTGTGTACTCAAAGTACTGG 0.547000 0 SO:0001583 missense ENST00000543196.2 0 1 hg19 CCDS8813.1 . . . . . . . . . . C 18.94 3.729653 0.69074 . . ENSG00000139629 ENST00000543196;ENST00000356317;ENST00000546163 T;T 0.26810 1.71;1.71 3.92 3.92 0.45320 Ricin B-related lectin (1);Ricin B lectin (3); 0.000000 0.85682 D 0.000000 T 0.52933 0.1765 M 0.84585 2.705 0.80722 D 1 D 0.89917 1.0 D 0.78314 0.991 T 0.54629 -0.8265 10 0.27082 T 0.32 . 15.908 0.79445 0.0:1.0:0.0:0.0 . 537 Q8NCL4 GALT6_HUMAN Q 537;537;518 ENSP00000444171:E537Q;ENSP00000348668:E537Q ENSP00000348668:E537Q E - 1 0 GALNT6 50036003 1.000000 0.71417 1.000000 0.80357 0.384000 0.30261 7.378000 0.79679 2.485000 0.83878 0.655000 0.94253 GAG TCGA-OE-A75W-01A-12D-A32N-08 GALNT6-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000469735.1 0 0 0 7 416 0 67 0 2.617245e-02 0 13 0 67 2 0 0 0 0 0 2 1 0.980470 7 414 0 67 2 0 0 0 0 67 2 -2.650283 1 1 0 0 1 0 0 0 2.051268 0 0.570000 1.770000 0.552130 0.050000 1.000000e-02 0.110000 0.060000 0.063322 0.050000 0 3.000000e-02 9.000000e-02 HOXC11 3227 broad.mit.edu 37 12 54367152 54367152 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:54367152G>A ENST00000546378.1 + 1 243 c.127G>A c.(127-129)Gag>Aag p.E43K HOTAIR_ENST00000455246.1_RNA|HOXC11_ENST00000243082.4_Missense_Mutation_p.E43K|HOTAIR_ENST00000424518.1_RNA O43248 HXC11_HUMAN homeobox C11 2 CTACATGCCCGAGTTCTCCAC 0.642000 T NUP98 AML Dom yes 12 12q13.3 3227 homeo box C11 L 0 SO:0001583 missense ENST00000546378.1 0 1 hg19 CCDS8867.1 . . . . . . . . . . G 23.6 4.433131 0.83776 . . ENSG00000123388 ENST00000546378;ENST00000243082 T;T 0.49432 0.78;0.78 4.47 4.47 0.54385 Domain of unknown function DUF3528, homeobox protein, eukaryotic (1); 0.052375 0.85682 D 0.000000 T 0.55955 0.1953 L 0.54323 1.7 0.58432 D 0.999998 P 0.51791 0.948 P 0.51999 0.687 T 0.61569 -0.7036 10 0.72032 D 0.01 . 16.4268 0.83817 0.0:0.0:1.0:0.0 . 43 O43248 HXC11_HUMAN K 43 ENSP00000446680:E43K;ENSP00000243082:E43K ENSP00000243082:E43K E + 1 0 HOXC11 52653419 1.000000 0.71417 0.999000 0.59377 0.948000 0.59901 9.227000 0.95236 2.471000 0.83476 0.561000 0.74099 GAG TCGA-OE-A75W-01A-12D-A32N-08 HOXC11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000358869.2 0 0 0 16 828 0 156 0 0 0 0 156 2 0 0 0 0 0 2 1 0.999919 16 810 0 153 2 0 0 0 0 156 2 -2.410515 0 1 0 0 1 0 0 0 2.020472 0 0.570000 1.770000 0.544008 0.060000 2.000000e-02 0.100000 0.060000 0.066415 0.060000 0 4.000000e-02 8.000000e-02 NTF3 4908 broad.mit.edu 37 12 5603958 5603958 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:5603958C>T ENST00000331010.6 + 1 661 c.578C>T c.(577-579)aCg>aTg p.T193M NTF3_ENST00000535299.1_Intron|NTF3_ENST00000423158.3_Missense_Mutation_p.T206M NM_002527.4 NP_002518.1 P20783 NTF3_HUMAN neurotrophin 3 22 TTTTATGAAACGCGATGTAAG 0.507000 GBM(194;1104 2182 8339 9578 18493) 0 SO:0001583 missense ENST00000331010.6 1 1 hg19 CCDS8538.1 . . . . . . . . . . C 21.5 4.155349 0.78114 . . ENSG00000185652 ENST00000423158;ENST00000331010 T;T 0.73681 -0.77;-0.77 5.45 5.45 0.79879 Nerve growth factor-related (5); 0.000000 0.85682 D 0.000000 D 0.87665 0.6234 M 0.84326 2.69 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 D 0.89132 0.3510 10 0.87932 D 0 -33.1613 18.2818 0.90101 0.0:1.0:0.0:0.0 . 193;206 P20783;B7Z1T5 NTF3_HUMAN;. M 206;193 ENSP00000397297:T206M;ENSP00000328738:T193M ENSP00000328738:T193M T + 2 0 NTF3 5474219 1.000000 0.71417 0.997000 0.53966 0.980000 0.70556 7.818000 0.86416 2.583000 0.87209 0.650000 0.86243 ACG TCGA-OE-A75W-01A-12D-A32N-08 NTF3-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000400486.1 1 0 0 28 271 0 62 0 4.990021e-02 0 4 0 62 2 0 0 0 0 0 2 1 1.000000 27 268 0 61 2 0 0 0 0 62 2 -1.750592 0 1 0 0 1 0 0 0 2.055069 0 0.570000 1.770000 0.552130 0.310000 2.100000e-01 0.430000 0.320000 0.323689 0.310000 0 2.600000e-01 3.800000e-01 LRIG3 121227 broad.mit.edu 37 12 59267907 59267907 + Silent SNP T T A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:59267907T>A ENST00000320743.3 - 18 3331 c.3045A>T c.(3043-3045)ctA>ctT p.L1015L LRIG3_ENST00000379141.4_Silent_p.L955L NM_153377.4 NP_700356.2 Q6UXM1 LRIG3_HUMAN leucine-rich repeats and immunoglobulin-like domains 3 LRIG3/ROS1(2) 48 GBM - Glioblastoma multiforme(1;1.17e-18) AGGACTTGTTTAGACACAGAT 0.408000 T ROS1 NSCLC Dom yes 12 12q14.1 121227 leucine-rich repeats and immunoglobulin-like domains 3 E 0 SO:0001819 synonymous_variant ENST00000320743.3 1 1 hg19 CCDS8960.1 . . . . . . . . . . T 7.635 0.679659 0.14907 . . ENSG00000139263 ENST00000550825 . . . 5.63 -9.02 0.00741 . . . . . . . . . . . 0.26728 N 0.97065 . . . . . . . . . . . . . . 10.2731 0.43493 0.0:0.3257:0.4744:0.1999 . . . . X 117 . . K - 1 0 LRIG3 57554174 0.386000 0.25180 0.082000 0.20525 0.229000 0.25112 -0.728000 0.04925 -2.026000 0.00934 -0.417000 0.06048 AAA TCGA-OE-A75W-01A-12D-A32N-08 LRIG3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406623.1 1 0 0 15 313 0 60 0 9.828050e-01 0 142 0 60 2 0 0 0 0 0 2 1 0.999881 15 313 0 59 2 0 0 0 0 60 2 -16.762910 1 1 0 0 1 0 0 0 2.020472 0 0.570000 1.770000 0.544008 0.150000 8.000000e-02 0.240000 0.150000 0.160017 0.150000 0 1.100000e-01 2.000000e-01 MGAT4C 25834 broad.mit.edu 37 12 86374022 86374022 + Missense_Mutation SNP G G A rs140499591 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr12:86374022G>A ENST00000604798.1 - 8 1686 c.482C>T c.(481-483)gCg>gTg p.A161V MGAT4C_ENST00000549405.2_Missense_Mutation_p.A161V|MGAT4C_ENST00000548651.1_Missense_Mutation_p.A161V|MGAT4C_ENST00000552435.2_Intron|MGAT4C_ENST00000552808.2_Missense_Mutation_p.A161V|MGAT4C_ENST00000332156.1_Missense_Mutation_p.A161V|MGAT4C_ENST00000393205.2_Missense_Mutation_p.A190V Q9UBM8 MGT4C_HUMAN MGAT4 family, member C 41 AATATGGTGCGCAAATTTCTG 0.403000 0 SO:0001583 missense ENST00000604798.1 0 1 hg19 CCDS9030.1 . . . . . . . . . . G 13.63 2.293358 0.40594 2.27E-4 1.16E-4 ENSG00000182050 ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651;ENST00000547225 D;D;D;D;D;D 0.85861 -2.04;-2.04;-2.04;-2.04;-2.04;-2.04 5.58 3.67 0.42095 . 0.272302 0.36134 N 0.002770 D 0.88916 0.6567 M 0.66939 2.045 0.32647 N 0.519858 D;D 0.69078 0.997;0.997 P;P 0.62560 0.904;0.904 D 0.89173 0.3538 10 0.26408 T 0.33 -7.7201 12.7018 0.57038 0.0:0.1257:0.7434:0.1309 . 190;161 B4DRH2;Q9UBM8 .;MGT4C_HUMAN V 161;190;161;161;161;161;161 ENSP00000331664:A161V;ENSP00000376900:A190V;ENSP00000449022:A161V;ENSP00000446647:A161V;ENSP00000447253:A161V;ENSP00000449172:A161V ENSP00000331664:A161V A - 2 0 MGAT4C 84898153 1.000000 0.71417 0.635000 0.29338 0.003000 0.03518 6.447000 0.73465 1.321000 0.45227 0.655000 0.94253 GCG TCGA-OE-A75W-01A-12D-A32N-08 MGAT4C-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406212.2 0 0 0 5 477 0 83 0 0 0 0 83 2 0 0 0 0 0 2 1 0.937840 6 476 0 82 2 0 0 0 0 83 2 -2.060875 0 1 121410 4 38 1 1 2 3 2.170025 0 0.570000 1.770000 0.572437 0.030000 0 0.090000 0.040000 0.052728 0.030000 0 1.000000e-02 6.000000e-02 MPHOSPH8 54737 broad.mit.edu 37 13 20221309 20221309 + Missense_Mutation SNP C C G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr13:20221309C>G ENST00000361479.5 + 3 1164 c.1096C>G c.(1096-1098)Caa>Gaa p.Q366E MPHOSPH8_ENST00000414242.2_Missense_Mutation_p.Q366E NM_017520.3 NP_059990.2 Q99549 MPP8_HUMAN M-phase phosphoprotein 8 16 all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367) GCAGAGGAATCAAGACAGAAG 0.502000 0 SO:0001583 missense ENST00000361479.5 1 1 hg19 CCDS9287.1 . . . . . . . . . . C 8.005 0.756354 0.15846 . . ENSG00000196199 ENST00000414242;ENST00000361479;ENST00000538024 T;T 0.35048 1.34;1.33 5.61 5.61 0.85477 . 1.796160 0.02353 N 0.076114 T 0.48077 0.1480 L 0.58101 1.795 0.41991 D 0.990848 P;B;P;B 0.41131 0.739;0.435;0.571;0.435 B;B;B;B 0.40782 0.34;0.15;0.225;0.152 T 0.49341 -0.8950 10 0.25106 T 0.35 . 19.6274 0.95684 0.0:1.0:0.0:0.0 . 366;366;366;366 F5H8H9;Q99549;Q99549-2;B3KS10 .;MPP8_HUMAN;.;. E 366 ENSP00000414663:Q366E;ENSP00000355388:Q366E ENSP00000355388:Q366E Q + 1 0 MPHOSPH8 19119309 1.000000 0.71417 0.852000 0.33557 0.180000 0.23129 4.294000 0.59043 2.634000 0.89283 0.585000 0.79938 CAA TCGA-OE-A75W-01A-12D-A32N-08 MPHOSPH8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044028.2 1 0 1 39 115 0 32 1 9.991951e-01 16 20 0 32 2 0 0 0 0 0 2 1 1.000000 36 115 0 32 2 0 0 0 0 32 2 -20.000000 1 1 0 0 1 0 0 0 2.141106 0 0.570000 1.770000 0.570000 0.880000 6.600000e-01 1.000000 1.000000 0.881290 0.880000 1 7.600000e-01 1 SPG20 23111 broad.mit.edu 37 13 36886315 36886315 + Missense_Mutation SNP A A G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr13:36886315A>G ENST00000451493.1 - 8 1917 c.1700T>C c.(1699-1701)gTt>gCt p.V567A SPG20_ENST00000438666.2_Missense_Mutation_p.V567A|SPG20_ENST00000355182.4_Missense_Mutation_p.V567A|SPG20_ENST00000494062.2_Missense_Mutation_p.V567A NM_001142295.1 NP_001135767.1 Q8N0X7 SPG20_HUMAN spastic paraplegia 20 (Troyer syndrome) 27 Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) TTCTGCTGAAACATTGTTAAC 0.323000 0 SO:0001583 missense ENST00000451493.1 1 1 hg19 CCDS9356.1 . . . . . . . . . . A 27.8 4.862134 0.91511 . . ENSG00000133104 ENST00000438666;ENST00000355182;ENST00000451493;ENST00000423217 D;D;D 0.89617 -2.54;-2.54;-2.54 5.86 5.86 0.93980 Senescence/spartin-associated (1); 0.000000 0.85682 D 0.000000 D 0.93268 0.7855 M 0.61703 1.905 0.58432 D 0.999999 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 D 0.92473 0.5987 10 0.37606 T 0.19 -22.1858 16.2644 0.82568 1.0:0.0:0.0:0.0 . 567;567 A8K6Q9;Q8N0X7 .;SPG20_HUMAN A 567 ENSP00000406061:V567A;ENSP00000347314:V567A;ENSP00000414147:V567A ENSP00000347314:V567A V - 2 0 SPG20 35784315 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 6.703000 0.74633 2.244000 0.73946 0.528000 0.53228 GTT TCGA-OE-A75W-01A-12D-A32N-08 SPG20-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044494.2 1 0 1 74 258 0 49 0 9.746497e-01 0 23 0 49 2 0 0 0 0 0 2 1 1.000000 74 254 0 48 2 0 0 0 0 49 2 -20.000000 1 1 0 0 1 0 0 0 2.112994 0 0.570000 1.770000 0.565041 0.760000 6.200000e-01 0.930000 0.770000 0.777012 0.760000 0 6.900000e-01 8.500000e-01 SMAD9 4093 broad.mit.edu 37 13 37453546 37453546 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr13:37453546C>T ENST00000399275.2 - 1 420 c.281G>A c.(280-282)cGc>cAc p.R94H SMAD9_ENST00000483941.1_5'Flank|SMAD9_ENST00000379826.4_Missense_Mutation_p.R94H|SMAD9_ENST00000350148.5_Missense_Mutation_p.R94H O15198 SMAD9_HUMAN SMAD family member 9 18 Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184) GCGCCACACGCGACAGTAAAT 0.627000 0 SO:0001583 missense ENST00000399275.2 0 1 hg19 CCDS45032.1 . . . . . . . . . . C 21.4 4.140955 0.77775 . . ENSG00000120693 ENST00000399275;ENST00000350148;ENST00000379826 D;D;D 0.82255 -1.59;-1.59;-1.59 5.53 5.53 0.82687 MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2); 0.000000 0.85682 D 0.000000 D 0.92506 0.7620 M 0.88512 2.96 0.80722 D 1 D;D 0.76494 0.992;0.999 P;D 0.70716 0.801;0.97 D 0.93576 0.6908 10 0.87932 D 0 . 18.4517 0.90705 0.0:1.0:0.0:0.0 . 94;94 O15198-2;O15198 .;SMAD9_HUMAN H 94 ENSP00000382216:R94H;ENSP00000239885:R94H;ENSP00000369154:R94H ENSP00000239885:R94H R - 2 0 SMAD9 36351546 1.000000 0.71417 0.962000 0.40283 0.019000 0.09904 6.034000 0.70933 2.599000 0.87857 0.563000 0.77884 CGC TCGA-OE-A75W-01A-12D-A32N-08 SMAD9-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000044525.2 0 0 0 7 221 0 60 0 0 0 0 60 2 0 0 0 0 0 2 1 0.980783 7 220 0 57 2 0 0 0 0 60 2 -8.859226 1 1 121410 1 31 1 0 0 0 2.112994 0 0.570000 1.770000 0.565041 0.110000 4.000000e-02 0.210000 0.100000 0.120249 0.110000 0 7.000000e-02 1.600000e-01 NOVA1 4857 broad.mit.edu 37 14 26917998 26917998 + Nonsense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr14:26917998G>A ENST00000539517.2 - 5 1008 c.691C>T c.(691-693)Cga>Tga p.R231* NOVA1_ENST00000267422.7_Nonsense_Mutation_p.R109*|NOVA1_ENST00000465357.2_Nonsense_Mutation_p.R207* NM_002515.2 NP_002506.2 P51513 NOVA1_HUMAN neuro-oncological ventral antigen 1 40 ACAGCTTTTCGGTTTTGTTCA 0.473000 0 SO:0001587 stop_gained ENST00000539517.2 0 1 hg19 CCDS32061.1 . . . . . . . . . . G 38 6.801762 0.97849 . . ENSG00000139910 ENST00000465357;ENST00000539517;ENST00000267422;ENST00000449198;ENST00000347476 . . . 5.73 5.73 0.89815 . 0.000000 0.64402 D 0.000005 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.20046 T 0.44 -3.4817 19.8956 0.96956 0.0:0.0:1.0:0.0 . . . . X 207;231;109;190;85 . ENSP00000267422:R109X R - 1 2 NOVA1 25987838 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.824000 0.99380 2.708000 0.92522 0.563000 0.77884 CGA TCGA-OE-A75W-01A-12D-A32N-08 NOVA1-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000073261.3 0 0 0 6 546 0 92 0 0 0 0 92 2 0 0 0 0 0 2 1 0.964745 6 544 0 92 2 0 0 0 0 92 2 -2.172289 0 1 0 0 1 0 0 0 2.122520 0 0.570000 1.770000 0.567535 0.030000 0 0.080000 0.040000 0.043886 0.030000 0 2.000000e-02 6.000000e-02 EXOC5 10640 broad.mit.edu 37 14 57698379 57698379 + Missense_Mutation SNP C C G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr14:57698379C>G ENST00000413566.2 - 11 1352 c.993G>C c.(991-993)caG>caC p.Q331H EXOC5_ENST00000340918.7_Missense_Mutation_p.Q266H NM_006544.3 NP_006535.1 O00471 EXOC5_HUMAN exocyst complex component 5 22 ACAAGAAAGTCTGTTTATCAG 0.343000 0 SO:0001583 missense ENST00000413566.2 0 1 hg19 CCDS45111.1 . . . . . . . . . . C 13.45 2.240468 0.39598 . . ENSG00000070367 ENST00000413566;ENST00000340918 T;T 0.44482 0.92;0.92 5.62 5.62 0.85841 . 0.048260 0.85682 D 0.000000 T 0.23766 0.0575 N 0.02539 -0.55 0.51767 D 0.999934 B;B 0.06786 0.001;0.0 B;B 0.04013 0.001;0.001 T 0.08617 -1.0713 10 0.33940 T 0.23 -8.6151 20.0333 0.97547 0.0:1.0:0.0:0.0 . 266;331 F8W9B8;O00471 .;EXOC5_HUMAN H 331;266 ENSP00000389934:Q331H;ENSP00000342100:Q266H ENSP00000342100:Q266H Q - 3 2 EXOC5 56768132 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.013000 0.57138 2.810000 0.96702 0.585000 0.79938 CAG TCGA-OE-A75W-01A-12D-A32N-08 EXOC5-001 KNOWN upstream_uORF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412905.1 0 0 0 5 271 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.935682 5 267 0 36 2 0 0 0 0 36 2 -4.106622 1 1 0 0 1 0 0 0 2.142545 0 0.570000 1.770000 0.570000 0.060000 2.000000e-02 0.140000 0.060000 0.075501 0.060000 0 3.000000e-02 1.000000e-01 SIPA1L1 26037 broad.mit.edu 37 14 72055518 72055518 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr14:72055518C>T ENST00000555818.1 + 2 1277 c.929C>T c.(928-930)tCa>tTa p.S310L SIPA1L1_ENST00000381232.3_Missense_Mutation_p.S310L|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.S310L NM_001284247.1|NM_015556.1 NP_001271176.1|NP_056371.1 O43166 SI1L1_HUMAN signal-induced proliferation-associated 1 like 1 78 CTTGGGAAGTCATCAGATCTT 0.418000 0 SO:0001583 missense ENST00000555818.1 0 1 hg19 CCDS9807.1 . . . . . . . . . . C 11.17 1.558807 0.27827 . . ENSG00000197555 ENST00000381232;ENST00000555818;ENST00000358550 T;T;T 0.43688 0.94;0.94;0.94 6.07 6.07 0.98685 . 0.428174 0.28161 N 0.016373 T 0.46698 0.1406 L 0.39898 1.24 0.80722 D 1 B;P;B 0.37500 0.074;0.597;0.001 B;B;B 0.43990 0.01;0.438;0.001 T 0.15752 -1.0426 10 0.36615 T 0.2 -11.6329 20.6593 0.99626 0.0:1.0:0.0:0.0 . 310;310;310 A6H8W6;O43166-2;O43166 .;.;SI1L1_HUMAN L 310 ENSP00000370630:S310L;ENSP00000450832:S310L;ENSP00000351352:S310L ENSP00000351352:S310L S + 2 0 SIPA1L1 71125271 0.983000 0.35010 0.378000 0.26068 0.087000 0.18053 2.677000 0.46892 2.885000 0.99019 0.655000 0.94253 TCA TCGA-OE-A75W-01A-12D-A32N-08 SIPA1L1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412806.1 0 0 0 6 321 0 45 0 1.519339e-03 0 3 0 45 2 0 0 0 0 0 2 1 0.963994 6 317 0 45 2 0 0 0 0 45 2 -6.530284 1 0 0 0 1 0 0 0 2.142545 0 0.570000 1.770000 0.570000 0.060000 2.000000e-02 0.130000 0.060000 0.074481 0.060000 0 4.000000e-02 1.000000e-01 SIPA1L1 26037 broad.mit.edu 37 14 72055521 72055521 + Nonsense_Mutation SNP C C A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr14:72055521C>A ENST00000555818.1 + 2 1280 c.932C>A c.(931-933)tCa>tAa p.S311* SIPA1L1_ENST00000381232.3_Nonsense_Mutation_p.S311*|SIPA1L1_ENST00000358550.2_Nonsense_Mutation_p.S311* NM_001284247.1|NM_015556.1 NP_001271176.1|NP_056371.1 O43166 SI1L1_HUMAN signal-induced proliferation-associated 1 like 1 78 GGGAAGTCATCAGATCTTGAA 0.413000 0 SO:0001587 stop_gained ENST00000555818.1 0 1 hg19 CCDS9807.1 . . . . . . . . . . C 42 9.477020 0.99181 . . ENSG00000197555 ENST00000381232;ENST00000555818;ENST00000358550 . . . 6.07 6.07 0.98685 . 0.378699 0.30869 N 0.008709 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -11.9733 20.6593 0.99626 0.0:1.0:0.0:0.0 . . . . X 311 . ENSP00000351352:S311X S + 2 0 SIPA1L1 71125274 1.000000 0.71417 0.271000 0.24616 0.037000 0.13140 7.575000 0.82447 2.885000 0.99019 0.655000 0.94253 TCA TCGA-OE-A75W-01A-12D-A32N-08 SIPA1L1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412806.1 0 0 0 6 314 0 44 0 1.585379e-03 0 3 0 44 2 0 0 0 0 0 2 1 0.964327 6 311 0 44 2 0 0 0 0 44 2 -4.039786 1 0 0 0 1 0 0 0 2.142545 0 0.570000 1.770000 0.570000 0.060000 2.000000e-02 0.140000 0.060000 0.076095 0.060000 0 4.000000e-02 1.000000e-01 NIPA2 81614 broad.mit.edu 37 15 23006789 23006789 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr15:23006789C>T ENST00000337451.3 - 8 1127 c.515G>A c.(514-516)cGc>cAc p.R172H NIPA2_ENST00000398013.3_Missense_Mutation_p.R172H|NIPA2_ENST00000359727.4_Missense_Mutation_p.R153H|NIPA2_ENST00000539711.2_Missense_Mutation_p.R153H|NIPA2_ENST00000398014.2_Missense_Mutation_p.R172H NM_030922.6 NP_112184.4 Q8N8Q9 NIPA2_HUMAN non imprinted in Prader-Willi/Angelman syndrome 2 15 all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488) CTGTCCATGGCGAGGACCCAC 0.468000 0 SO:0001583 missense ENST00000337451.3 1 1 hg19 CCDS10010.1 . . . . . . . . . . C 16.35 3.097751 0.56075 . . ENSG00000140157 ENST00000337451;ENST00000398014;ENST00000359727;ENST00000539711;ENST00000398013 D;D;D 0.91740 -2.9;-2.9;-2.9 5.65 3.79 0.43588 . 0.047323 0.85682 D 0.000000 D 0.91646 0.7360 M 0.81614 2.55 0.80722 D 1 P;P 0.38020 0.615;0.562 B;B 0.37888 0.17;0.26 D 0.90560 0.4515 10 0.59425 D 0.04 -18.3833 12.5884 0.56430 0.0:0.8679:0.0:0.1321 . 153;172 F8W7Y8;Q8N8Q9 .;NIPA2_HUMAN H 172;172;153;172;153 ENSP00000337618:R172H;ENSP00000381096:R172H;ENSP00000352762:R153H ENSP00000337618:R172H R - 2 0 NIPA2 20558230 1.000000 0.71417 1.000000 0.80357 0.804000 0.45430 4.882000 0.63121 0.871000 0.35750 -0.768000 0.03414 CGC TCGA-OE-A75W-01A-12D-A32N-08 NIPA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251137.1 1 0 1 113 113 0 41 1 1 54 12 0 41 2 0 0 0 0 0 2 1 1.000000 109 112 0 41 2 0 0 0 0 41 2 -20.000000 1 1 121412 8 39 1 0 2 2 2.275188 1 0.570000 1.770000 0.570000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 TJP1 7082 broad.mit.edu 37 15 30001114 30001114 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr15:30001114G>A ENST00000346128.6 - 25 4973 c.4499C>T c.(4498-4500)cCc>cTc p.P1500L TJP1_ENST00000356107.6_Missense_Mutation_p.P1500L|TJP1_ENST00000545208.2_Missense_Mutation_p.P1420L|TJP1_ENST00000400011.2_Missense_Mutation_p.P1424L NM_003257.3|NM_175610.2 NP_003248.3|NP_783297.2 Q07157 ZO1_HUMAN tight junction protein 1 68 all_lung(180;7.48e-11)|Breast(32;0.000153) ACTTTTCTGGGGATAGAAAGC 0.438000 Melanoma(77;681 1843 6309 6570) 0 SO:0001583 missense ENST00000346128.6 0 1 hg19 CCDS42007.1 . . . . . . . . . . G 17.37 3.371619 0.61624 . . ENSG00000104067 ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107 T;T 0.59083 0.29;0.29 5.61 5.61 0.85477 . 0.111909 0.64402 D 0.000008 T 0.63593 0.2524 L 0.50333 1.59 0.80722 D 1 B;B;B;P 0.45827 0.005;0.001;0.009;0.867 B;B;B;P 0.48030 0.009;0.002;0.016;0.564 T 0.65747 -0.6093 10 0.87932 D 0 . 19.8945 0.96949 0.0:0.0:1.0:0.0 . 1493;1420;1500;1424 A9CQZ8;Q07157-2;Q07157;G5E9E7 .;.;ZO1_HUMAN;. L 1500;1424;1500;1420;1420 ENSP00000281537:P1500L;ENSP00000382890:P1424L ENSP00000281537:P1500L P - 2 0 TJP1 27788406 1.000000 0.71417 0.902000 0.35471 0.988000 0.76386 9.263000 0.95617 2.937000 0.99478 0.650000 0.86243 CCC TCGA-OE-A75W-01A-12D-A32N-08 TJP1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000268237.3 0 0 0 8 859 0 132 0 1.947290e-02 0 20 0 132 2 0 0 0 0 0 2 1 0.989130 8 854 0 130 2 0 0 0 0 132 2 -2.276977 0 1 0 0 1 0 2 2 2.275188 1 0.570000 1.770000 0.570000 0.030000 0 1.000000 0.040000 0.089759 0.030000 0 1.000000e-02 5.000000e-02 VPS18 57617 broad.mit.edu 37 15 41192857 41192857 + Nonsense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr15:41192857G>A ENST00000220509.5 + 4 2180 c.1841G>A c.(1840-1842)tGg>tAg p.W614* VPS18_ENST00000558474.1_Intron NM_020857.2 NP_065908.1 Q9P253 VPS18_HUMAN vacuolar protein sorting 18 homolog (S. cerevisiae) 28 all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946) GTAGATGCCTGGATTGAGATG 0.637000 0 SO:0001587 stop_gained ENST00000220509.5 0 1 hg19 CCDS10069.1 . . . . . . . . . . G 40 8.369804 0.98781 . . ENSG00000104142 ENST00000220509 . . . 5.84 5.84 0.93424 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -22.9768 20.1278 0.97990 0.0:0.0:1.0:0.0 . . . . X 614 . ENSP00000220509:W614X W + 2 0 VPS18 38980149 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 9.869000 0.99810 2.768000 0.95171 0.561000 0.74099 TGG TCGA-OE-A75W-01A-12D-A32N-08 VPS18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252443.2 0 0 0 21 504 1 118 0 1.427688e-01 2 29 1 118 3 0 0 0 0 0 2 1 0.835106 21 500 1 117 16 0 0 0 1 118 2 -2.927596 1 1 0 0 1 0 2 2 2.243088 1 0.570000 1.770000 0.570000 0.140000 8.000000e-02 1.000000 0.140000 0.170823 0.140000 0 1.100000e-01 1.800000e-01 SEMA6D 80031 broad.mit.edu 37 15 48060897 48060897 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr15:48060897G>A ENST00000316364.5 + 18 2324 c.1885G>A c.(1885-1887)Gat>Aat p.D629N SEMA6D_ENST00000355997.3_Intron|SEMA6D_ENST00000358066.4_Intron|SEMA6D_ENST00000389428.3_Intron|SEMA6D_ENST00000389433.2_Missense_Mutation_p.D610N|SEMA6D_ENST00000537942.1_Intron|SEMA6D_ENST00000389432.2_Intron|SEMA6D_ENST00000536845.2_Missense_Mutation_p.D629N|SEMA6D_ENST00000558816.1_Intron|SEMA6D_ENST00000558014.1_Intron|SEMA6D_ENST00000354744.4_Intron NM_153618.1 NP_705871.1 Q8NFY4 SEM6D_HUMAN sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D 77 all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18) AGTTCAAGATGATCCAAACAC 0.433000 0 SO:0001583 missense ENST00000316364.5 1 1 hg19 CCDS32225.1 . . . . . . . . . . G 15.93 2.979420 0.53827 . . ENSG00000137872 ENST00000536845;ENST00000316364;ENST00000389433 T;T;T 0.17854 2.25;2.25;2.27 5.49 5.49 0.81192 . 0.490778 0.22255 N 0.062495 T 0.11110 0.0271 N 0.08118 0 0.80722 D 1 B 0.23058 0.079 B 0.23018 0.043 T 0.26916 -1.0089 10 0.17832 T 0.49 . 19.7433 0.96241 0.0:0.0:1.0:0.0 . 629 Q8NFY4 SEM6D_HUMAN N 629;629;610 ENSP00000446152:D629N;ENSP00000324857:D629N;ENSP00000374084:D610N ENSP00000324857:D629N D + 1 0 SEMA6D 45848189 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.466000 0.80914 2.733000 0.93635 0.655000 0.94253 GAT TCGA-OE-A75W-01A-12D-A32N-08 SEMA6D-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416868.1 0 0 0 12 407 0 62 0 0 0 0 62 2 0 0 0 0 0 2 1 0.999078 12 402 0 61 2 0 0 0 0 62 2 -3.625637 1 1 0 0 1 0 2 2 2.243088 1 0.570000 1.770000 0.570000 0.100000 5.000000e-02 1.000000 0.100000 0.133806 0.100000 0 7.000000e-02 1.400000e-01 CYP19A1 1588 broad.mit.edu 37 15 51504611 51504611 + Missense_Mutation SNP T T C TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr15:51504611T>C ENST00000396402.1 - 9 1322 c.1169A>G c.(1168-1170)aAg>aGg p.K390R CYP19A1_ENST00000559878.1_Missense_Mutation_p.K390R|CYP19A1_ENST00000396404.4_Missense_Mutation_p.K390R|RP11-108K3.1_ENST00000559909.1_lincRNA|CYP19A1_ENST00000260433.2_Missense_Mutation_p.K390R NM_000103.3 NP_000094.2 P11511 CP19A_HUMAN cytochrome P450, family 19, subfamily A, polypeptide 1 33 Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072) GTTTGTCCCCTTTTTCACTGG 0.413000 Melanoma(142;1016 1807 39614 48966 51721) 0 SO:0001583 missense ENST00000396402.1 0 1 hg19 CCDS10139.1 . . . . . . . . . . T 15.74 2.922211 0.52653 . . ENSG00000137869 ENST00000396402;ENST00000260433;ENST00000396404 T;T;T 0.73575 -0.76;-0.76;-0.76 6.06 2.13 0.27403 . 0.084915 0.85682 N 0.000000 T 0.69691 0.3139 L 0.58354 1.805 0.46279 D 0.998961 B 0.15141 0.012 B 0.27262 0.078 T 0.66152 -0.5995 10 0.52906 T 0.07 -23.6398 10.5475 0.45068 0.0:0.2114:0.0:0.7886 . 390 P11511 CP19A_HUMAN R 390 ENSP00000379683:K390R;ENSP00000260433:K390R;ENSP00000379685:K390R ENSP00000260433:K390R K - 2 0 CYP19A1 49291903 1.000000 0.71417 1.000000 0.80357 0.919000 0.55068 3.131000 0.50515 0.541000 0.28827 0.533000 0.62120 AAG TCGA-OE-A75W-01A-12D-A32N-08 CYP19A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254669.1 0 0 0 6 630 0 107 0 0 0 0 107 2 0 0 0 0 0 2 1 0.964585 7 626 0 106 2 0 0 0 0 107 2 -1.959807 0 1 0 0 1 0 2 2 2.243088 1 0.570000 1.770000 0.570000 0.030000 0 1.000000 0.040000 0.065686 0.030000 0 1.000000e-02 6.000000e-02 LMAN1L 79748 broad.mit.edu 37 15 75116728 75116728 + Missense_Mutation SNP C C A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr15:75116728C>A ENST00000309664.5 + 13 1499 c.1360C>A c.(1360-1362)Ccc>Acc p.P454T LMAN1L_ENST00000379709.3_Missense_Mutation_p.P442T|RP11-414J4.2_ENST00000564823.1_RNA|CPLX3_ENST00000395018.4_5'Flank NM_021819.2 NP_068591.2 Q9HAT1 LMA1L_HUMAN lectin, mannose-binding, 1 like 19 ACCTGGCCAGCCCCCAAGGGC 0.602000 0 SO:0001583 missense ENST00000309664.5 1 1 hg19 CCDS10270.1 . . . . . . . . . . C 9.098 1.003432 0.19121 . . ENSG00000140506 ENST00000309664;ENST00000379709 T;T 0.45276 1.06;0.9 4.95 -3.18 0.05186 . 4.451500 0.00424 N 0.000078 T 0.27205 0.0667 L 0.29908 0.895 0.09310 N 1 B;B 0.17038 0.02;0.001 B;B 0.19391 0.025;0.002 T 0.05194 -1.0900 10 0.26408 T 0.33 . 1.6489 0.02767 0.1359:0.32:0.1328:0.4113 . 442;454 Q9HAT1-3;Q9HAT1 .;LMA1L_HUMAN T 454;442 ENSP00000310431:P454T;ENSP00000369031:P442T ENSP00000310431:P454T P + 1 0 LMAN1L 72903781 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.646000 0.05403 -0.565000 0.06061 -1.288000 0.01363 CCC TCGA-OE-A75W-01A-12D-A32N-08 LMAN1L-001 KNOWN upstream_ATG|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000286397.4 1 0 1 252 679 0 177 0 0 0 0 177 2 0 0 0 0 0 2 1 1.000000 248 666 0 176 2 0 0 0 0 177 2 -20.000000 1 1 121406 1 32 1 0 2 2 2.243088 1 0.570000 1.770000 0.570000 0.940000 8.400000e-01 1.000000 1.000000 0.947453 0.940000 1 8.900000e-01 1 ACAN 176 broad.mit.edu 37 15 89402244 89402244 + Missense_Mutation SNP G G C TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr15:89402244G>C ENST00000561243.1 + 11 6428 c.6428G>C c.(6427-6429)aGa>aCa p.R2143T ACAN_ENST00000559004.1_Missense_Mutation_p.R2143T|ACAN_ENST00000352105.7_Missense_Mutation_p.R2143T|ACAN_ENST00000439576.2_Missense_Mutation_p.R2143T P16112 PGCA_HUMAN aggrecan 93 Lung NSC(78;0.0392)|all_lung(78;0.077) BRCA - Breast invasive adenocarcinoma(143;0.146) AACCTTGAGAGATCCTCTGGC 0.577000 0 SO:0001583 missense ENST00000561243.1 0 1 hg19 CCDS53970.1 . . . . . . . . . . G 0.001 -3.123810 0.00031 . . ENSG00000157766 ENST00000439576;ENST00000352105;ENST00000268134 T;T 0.01804 4.8;4.63 4.78 0.0257 0.14146 . 1.021840 0.07884 N 0.969992 T 0.00875 0.0029 N 0.03608 -0.345 0.09310 N 1 B;B 0.22346 0.041;0.068 B;B 0.17433 0.018;0.018 T 0.48479 -0.9032 10 0.13108 T 0.6 2.0912 4.3001 0.10920 0.1066:0.5139:0.2441:0.1353 . 2143;2143 E7ENV9;E7EX88 .;. T 2143;2143;2029 ENSP00000387356:R2143T;ENSP00000341615:R2143T ENSP00000268134:R2029T R + 2 0 ACAN 87203248 0.000000 0.05858 0.010000 0.14722 0.065000 0.16274 -0.708000 0.05035 0.410000 0.25675 0.555000 0.69702 AGA TCGA-OE-A75W-01A-12D-A32N-08 ACAN-006 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416267.2 0 0 0 8 564 0 134 0 2.624323e-03 0 5 0 134 2 0 0 0 0 0 2 1 0.989142 8 560 0 134 2 0 0 0 0 134 2 -3.147050 1 1 0 0 1 0 2 2 2.243088 1 0.570000 1.770000 0.570000 0.040000 1.000000e-02 1.000000 0.050000 0.082215 0.040000 0 3.000000e-02 8.000000e-02 RCCD1 91433 broad.mit.edu 37 15 91500894 91500894 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr15:91500894G>A ENST00000394258.2 + 4 820 c.618G>A c.(616-618)gcG>gcA p.A206A AC068831.6_ENST00000553321.1_RNA|RCCD1_ENST00000556774.1_Intron|RCCD1_ENST00000555155.1_Silent_p.A206A|RCCD1_ENST00000556618.1_Silent_p.A206A NM_001017919.1|NM_033544.2 NP_001017919.1|NP_291022.2 A6NED2 RCCD1_HUMAN RCC1 domain containing 1 4 Lung NSC(78;0.0987)|all_lung(78;0.175) Lung(145;0.189) TGTTGGAGGCGTTGCAGGGCC 0.607000 0 SO:0001819 synonymous_variant ENST00000394258.2 0 1 hg19 CCDS32333.1 TCGA-OE-A75W-01A-12D-A32N-08 RCCD1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000414748.1 0 0 0 6 476 0 106 0 8.256143e-02 0 32 0 106 2 0 0 0 0 0 2 1 0.961869 6 463 0 104 2 0 0 0 0 106 2 -2.919649 1 1 121406 1 30 1 0 2 2 2.243088 1 0.570000 1.770000 0.570000 0.040000 0 1.000000 0.040000 0.077956 0.040000 0 2.000000e-02 7.000000e-02 IFT140 9742 broad.mit.edu 37 16 1657152 1657152 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr16:1657152G>A ENST00000426508.2 - 3 479 c.116C>T c.(115-117)tCa>tTa p.S39L IFT140_ENST00000439987.2_5'UTR|LA16c-395F10.2_ENST00000563162.1_RNA NM_014714.3 NP_055529.2 Q96RY7 IF140_HUMAN intraflagellar transport 140 53 Hepatocellular(780;0.219) GCTGCCTGTTGAGGTTGTGCT 0.522000 0 SO:0001583 missense ENST00000426508.2 0 1 hg19 CCDS10439.1 . . . . . . . . . . G 7.782 0.709735 0.15239 . . ENSG00000187535 ENST00000397417;ENST00000426508;ENST00000439987 T;T 0.65178 -0.14;-0.14 5.53 3.52 0.40303 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.614492 0.17548 N 0.170274 T 0.50922 0.1644 L 0.49126 1.545 0.09310 N 1 B 0.11235 0.004 B 0.08055 0.003 T 0.39313 -0.9620 10 0.31617 T 0.26 . 6.0312 0.19681 0.1449:0.0:0.7042:0.1509 . 39 Q96RY7 IF140_HUMAN L 39 ENSP00000380562:S39L;ENSP00000406012:S39L ENSP00000380562:S39L S - 2 0 IFT140 1597153 0.000000 0.05858 0.006000 0.13384 0.029000 0.11900 0.693000 0.25497 0.653000 0.30826 0.655000 0.94253 TCA TCGA-OE-A75W-01A-12D-A32N-08 IFT140-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250438.2 0 0 0 10 655 0 134 0 0 0 0 134 2 0 0 0 0 0 2 1 0.996638 10 644 0 133 2 0 0 0 0 134 2 -2.405791 0 1 0 0 1 0 0 0 2.054168 0 0.570000 1.770000 0.552130 0.040000 1.000000e-02 0.090000 0.050000 0.055501 0.040000 0 3.000000e-02 7.000000e-02 MYLK3 91807 broad.mit.edu 37 16 46781922 46781922 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr16:46781922G>A ENST00000394809.4 - 1 299 c.184C>T c.(184-186)Cgg>Tgg p.R62W MYLK3_ENST00000536476.1_Intron NM_182493.2 NP_872299.2 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 p.R62W(2) 37 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) TGCAGGCCCCGCTCCAGGTGG 0.652000 2 Substitution - Missense(2) SO:0001583 missense ENST00000394809.4 1 1 hg19 CCDS10723.2 . . . . . . . . . . G 11.63 1.694724 0.30052 2.27E-4 1.16E-4 ENSG00000140795 ENST00000394809 T 0.73152 -0.72 5.09 1.66 0.24008 . 0.248315 0.21157 N 0.079230 T 0.61022 0.2314 L 0.29908 0.895 0.09310 N 0.999997 D 0.63880 0.993 P 0.47470 0.548 T 0.55854 -0.8075 10 0.72032 D 0.01 . 9.4835 0.38915 0.0:0.1113:0.4457:0.443 . 62 Q32MK0 MYLK3_HUMAN W 62 ENSP00000378288:R62W ENSP00000378288:R62W R - 1 2 MYLK3 45339423 0.991000 0.36638 0.963000 0.40424 0.003000 0.03518 0.984000 0.29565 0.466000 0.27193 -0.500000 0.04577 CGG TCGA-OE-A75W-01A-12D-A32N-08 MYLK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255743.2 1 0 1 65 169 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 1.000000 64 166 0 48 2 0 0 0 0 48 2 -20.000000 1 1 121412 11 40 1 0 0 0 2.119491 0 0.570000 1.770000 0.567535 0.960000 7.700000e-01 1.000000 1.000000 0.943995 0.960000 1 8.600000e-01 1 GPR97 222487 broad.mit.edu 37 16 57714440 57714440 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr16:57714440G>A ENST00000333493.4 + 8 953 c.792G>A c.(790-792)acG>acA p.T264T GPR97_ENST00000450388.3_Silent_p.T144T|RP11-405F3.4_ENST00000563062.1_RNA|GPR97_ENST00000327655.6_Silent_p.T54T NM_170776.4 NP_740746.4 Q86Y34 GPR97_HUMAN G protein-coupled receptor 97 p.T264T(1) 30 ACCAGTCCACGGTGCATATCC 0.587000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000333493.4 1 1 hg19 CCDS10786.1 TCGA-OE-A75W-01A-12D-A32N-08 GPR97-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257333.2 1 0 1 67 191 0 40 0 0 0 0 40 2 0 0 0 0 0 2 1 1.000000 67 188 0 40 2 0 0 0 0 40 2 -4.695790 1 1 0 0 1 0 0 0 2.115270 0 0.570000 1.770000 0.565041 0.890000 7.200000e-01 1.000000 1.000000 0.896346 0.890000 1 8.000000e-01 1 CES3 23491 broad.mit.edu 37 16 67006386 67006386 + Silent SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr16:67006386C>T ENST00000303334.4 + 11 1490 c.1419C>T c.(1417-1419)ctC>ctT p.L473L CES3_ENST00000543856.1_Silent_p.L112L|CES3_ENST00000394037.1_Silent_p.L473L NM_024922.5 NP_079198.2 Q6UWW8 EST3_HUMAN carboxylesterase 3 24 Ovarian(137;0.0563) GTCCCTTCCTCATGGACGAGA 0.592000 0 SO:0001819 synonymous_variant ENST00000303334.4 0 1 hg19 CCDS10826.1 TCGA-OE-A75W-01A-12D-A32N-08 CES3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000268848.1 0 0 0 12 580 0 131 0 1.499770e-01 1 30 0 131 2 0 0 0 0 0 2 1 0.999061 12 573 0 130 2 0 0 0 0 131 2 -2.595096 1 1 0 0 1 0 0 0 2.115270 0 0.570000 1.770000 0.565041 0.060000 3.000000e-02 0.120000 0.070000 0.075811 0.060000 0 4.000000e-02 1.000000e-01 ESRP2 80004 broad.mit.edu 37 16 68265495 68265495 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr16:68265495G>A ENST00000565858.1 - 11 1518 c.1432C>T c.(1432-1434)Cgc>Tgc p.R478C RP11-96D1.11_ENST00000571197.1_RNA|ESRP2_ENST00000473183.2_Missense_Mutation_p.R468C NM_024939.2 NP_079215.2 Q9H6T0 ESRP2_HUMAN epithelial splicing regulatory protein 2 16 CCTCGGAGGCGTACACAGTCC 0.622000 0 SO:0001583 missense ENST00000565858.1 0 1 hg19 . . . . . . . . . . G 20.6 4.012624 0.75161 . . ENSG00000103067 ENST00000473183 T 0.09163 3.01 5.93 5.93 0.95920 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1); 0.000000 0.85682 D 0.000000 T 0.52500 0.1738 H 0.97291 3.975 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 T 0.69105 -0.5233 10 0.87932 D 0 -15.6647 20.3437 0.98782 0.0:0.0:1.0:0.0 . 478;468 Q9H6T0;Q9H6T0-2 ESRP2_HUMAN;. C 468 ENSP00000418748:R468C ENSP00000418748:R468C R - 1 0 ESRP2 66822996 1.000000 0.71417 0.999000 0.59377 0.909000 0.53808 6.459000 0.73513 2.815000 0.96918 0.561000 0.74099 CGC TCGA-OE-A75W-01A-12D-A32N-08 ESRP2-004 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000433083.1 0 0 0 4 275 0 82 0 2.322939e-01 0 51 0 82 2 0 0 0 0 0 2 1 0.890207 4 274 0 81 2 0 0 0 0 82 2 -4.970394 1 0 0 0 1 0 0 0 2.115270 0 0.570000 1.770000 0.565041 0.050000 1.000000e-02 0.120000 0.050000 0.061450 0.050000 0 2.000000e-02 9.000000e-02 NF1 4763 broad.mit.edu 37 17 29652851 29652851 + Nonsense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr17:29652851C>T ENST00000358273.4 + 37 5232 c.4849C>T c.(4849-4851)Caa>Taa p.Q1617* NF1_ENST00000581113.2_3'UTR|NF1_ENST00000356175.3_Nonsense_Mutation_p.Q1596* NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 p.0?(8)|p.?(3) NF1/ACCN1(2) 599 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) CAAAACTGGTCAAATCAATGG 0.323000 D, Mis, N, F, S, O neurofibroma, glioma neurofibroma, glioma Neurofibromatosis, type 1 TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088) yes Rec yes Neurofibromatosis type 1 17 17q12 4763 neurofibromatosis type 1 gene O 11 Whole gene deletion(8)|Unknown(3) SO:0001587 stop_gained Familial Cancer Database NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome ENST00000358273.4 0 1 hg19 CCDS42292.1 . . . . . . . . . . C 47 13.673406 0.99756 . . ENSG00000196712 ENST00000358273;ENST00000356175;ENST00000456735 . . . 5.67 5.67 0.87782 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.30854 T 0.27 . 18.7588 0.91842 0.0:1.0:0.0:0.0 . . . . X 1617;1596;1262 . ENSP00000348498:Q1596X Q + 1 0 NF1 26676977 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 7.456000 0.80751 2.697000 0.92050 0.655000 0.94253 CAA TCGA-OE-A75W-01A-12D-A32N-08 NF1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256351.2 0 0 0 5 381 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 0.937502 5 380 0 44 2 0 0 0 0 44 2 -3.083064 1 1 0 0 1 0 0 0 2.108319 0 0.570000 1.770000 0.565041 0.040000 0 0.100000 0.040000 0.053452 0.040000 0 2.000000e-02 7.000000e-02 NF1 4763 broad.mit.edu 37 17 29665118 29665118 + Silent SNP T T G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr17:29665118T>G ENST00000358273.4 + 45 7163 c.6780T>G c.(6778-6780)tcT>tcG p.S2260S NF1_ENST00000444181.2_Silent_p.S53S|NF1_ENST00000356175.3_Silent_p.S2239S|NF1_ENST00000417592.2_Intron NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 p.0?(8)|p.?(3) NF1/ACCN1(2) 599 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) AACGAGTGTCTCATGGGCAGA 0.403000 D, Mis, N, F, S, O neurofibroma, glioma neurofibroma, glioma Neurofibromatosis, type 1 TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088) yes Rec yes Neurofibromatosis type 1 17 17q12 4763 neurofibromatosis type 1 gene O 11 Whole gene deletion(8)|Unknown(3) SO:0001819 synonymous_variant Familial Cancer Database NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome ENST00000358273.4 1 1 hg19 CCDS42292.1 TCGA-OE-A75W-01A-12D-A32N-08 NF1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256351.2 1 0 0 61 716 0 143 0 0 0 0 143 2 0 0 0 0 0 2 1 1.000000 61 712 0 140 2 0 0 0 0 143 2 -13.762360 1 1 0 0 1 0 0 0 2.108319 0 0.570000 1.770000 0.565041 0.260000 2.000000e-01 0.340000 0.270000 0.275802 0.260000 0 2.300000e-01 3.100000e-01 LIG3 3980 broad.mit.edu 37 17 33318808 33318808 + Missense_Mutation SNP T T A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr17:33318808T>A ENST00000378526.4 + 6 1293 c.1160T>A c.(1159-1161)cTc>cAc p.L387H LIG3_ENST00000262327.5_Missense_Mutation_p.L387H NM_013975.3 NP_039269.2 P49916 DNLI3_HUMAN ligase III, DNA, ATP-dependent 31 Ovarian(249;0.17) Bleomycin(DB00290) CTGTCCAAGCTCACCAAGGAG 0.552000 Other BER factors 0 SO:0001583 missense ENST00000378526.4 0 1 hg19 CCDS11284.2 . . . . . . . . . . T 24.0 4.480006 0.84747 . . ENSG00000005156 ENST00000378526;ENST00000262327 T;T 0.21191 2.02;2.02 5.5 5.5 0.81552 DNA ligase, ATP-dependent, N-terminal (3); 0.064354 0.64402 D 0.000004 T 0.46444 0.1393 M 0.78049 2.395 0.80722 D 1 D;D;D 0.76494 0.999;0.999;0.999 D;D;D 0.70935 0.971;0.971;0.957 T 0.38090 -0.9677 10 0.36615 T 0.2 -20.8443 14.9457 0.71029 0.0:0.0:0.0:1.0 . 387;387;387 E5KLB5;P49916;E5KLB6 .;DNLI3_HUMAN;. H 387 ENSP00000367787:L387H;ENSP00000262327:L387H ENSP00000262327:L387H L + 2 0 LIG3 30342921 1.000000 0.71417 1.000000 0.80357 0.795000 0.44927 7.672000 0.83956 2.308000 0.77769 0.533000 0.62120 CTC TCGA-OE-A75W-01A-12D-A32N-08 LIG3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250330.3 0 0 0 8 287 0 68 0 2.975820e-03 0 3 0 68 2 0 0 0 0 0 2 1 0.989335 8 285 0 64 2 0 0 0 0 68 2 -9.291851 1 1 0 0 1 0 0 0 2.108319 0 0.570000 1.770000 0.565041 0.090000 4.000000e-02 0.180000 0.100000 0.104841 0.090000 0 6.000000e-02 1.400000e-01 SMARCE1 6605 broad.mit.edu 37 17 38787103 38787103 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr17:38787103C>T ENST00000348513.6 - 10 1670 c.890G>A c.(889-891)cGc>cAc p.R297H SMARCE1_ENST00000578044.1_Missense_Mutation_p.R227H|SMARCE1_ENST00000544009.1_Missense_Mutation_p.R227H|SMARCE1_ENST00000377808.4_Missense_Mutation_p.R262H|KRT222_ENST00000476049.1_3'UTR|SMARCE1_ENST00000580419.1_Missense_Mutation_p.R262H|SMARCE1_ENST00000400122.3_Missense_Mutation_p.R227H|SMARCE1_ENST00000431889.2_Missense_Mutation_p.R279H NM_003079.4 NP_003070.3 Q969G3 SMCE1_HUMAN SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 p.R297H(1) 1 Breast(137;0.000812) CTGCCTTTTGCGGGCCTGTTC 0.507000 1 Substitution - Missense(1) SO:0001583 missense ENST00000348513.6 1 1 hg19 CCDS11370.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 17.53|17.53 3.412636|3.412636 0.62511|0.62511 .|. .|. ENSG00000073584|ENSG00000073584 ENST00000400122|ENST00000348513;ENST00000544009;ENST00000431889;ENST00000377808;ENST00000447024 .|T;T;T .|0.20598 .|2.07;2.06;2.3 5.47|5.47 5.47|5.47 0.80525|0.80525 .|. .|0.048290 .|0.85682 .|D .|0.000000 T|T 0.44993|0.44993 0.1320|0.1320 L|L 0.54323|0.54323 1.7|1.7 0.80722|0.80722 D|D 1|1 .|D;D;D .|0.76494 .|0.999;0.999;0.999 .|D;D;D .|0.76071 .|0.987;0.98;0.98 T|T 0.28332|0.28332 -1.0047|-1.0047 5|10 .|0.72032 .|D .|0.01 .|. 19.7017|19.7017 0.96057|0.96057 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|262;262;297 .|C0IMW5;C0IMW4;Q969G3 .|.;.;SMCE1_HUMAN T|H 123|297;227;279;262;91 .|ENSP00000323967:R297H;ENSP00000445370:R279H;ENSP00000367039:R262H .|ENSP00000323967:R297H A|R -|- 1|2 0|0 SMARCE1|SMARCE1 36040629|36040629 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.872000|0.872000 0.50106|0.50106 6.978000|6.978000 0.76147|0.76147 2.724000|2.724000 0.93272|0.93272 0.561000|0.561000 0.74099|0.74099 GCA|CGC TCGA-OE-A75W-01A-12D-A32N-08 SMARCE1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257203.1 1 0 0 125 365 0 93 1 1 108 252 0 93 2 0 0 0 0 0 2 1 1.000000 122 360 0 93 2 0 0 0 0 93 2 -5.881682 1 1 0 0 1 0 0 0 2.108319 0 0.570000 1.770000 0.565041 0.870000 7.500000e-01 1.000000 1.000000 0.885355 0.870000 1 8.100000e-01 9.500000e-01 VPS25 84313 broad.mit.edu 37 17 40925889 40925889 + Missense_Mutation SNP G G T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr17:40925889G>T ENST00000253794.2 + 2 232 c.192G>T c.(190-192)aaG>aaT p.K64N NM_032353.2 NP_115729.1 Q9BRG1 VPS25_HUMAN vacuolar protein sorting 25 homolog (S. cerevisiae) 5 Breast(137;0.00104) ACAACGTCAAGCTACAGCGTA 0.607000 0 SO:0001583 missense ENST00000253794.2 1 1 hg19 CCDS11438.1 . . . . . . . . . . G 14.05 2.419314 0.42918 . . ENSG00000131475 ENST00000253794 T 0.45276 0.9 5.64 4.67 0.58626 ESCRT-II complex, Vps25 subunit, N-terminal winged helix (1); 0.048195 0.85682 D 0.000000 T 0.30572 0.0769 L 0.41124 1.26 0.58432 D 0.999997 B 0.27117 0.168 B 0.25759 0.063 T 0.10359 -1.0633 10 0.30854 T 0.27 -27.0428 7.0885 0.25272 0.1496:0.0:0.7087:0.1416 . 64 Q9BRG1 VPS25_HUMAN N 64 ENSP00000253794:K64N ENSP00000253794:K64N K + 3 2 VPS25 38179415 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.207000 0.42788 1.383000 0.46405 0.655000 0.94253 AAG TCGA-OE-A75W-01A-12D-A32N-08 VPS25-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452383.1 1 0 1 66 197 0 35 1 1 53 127 0 35 2 0 0 0 0 0 2 1 1.000000 64 194 0 34 2 0 0 0 0 35 2 -20.000000 1 1 0 0 1 0 0 0 2.108319 0 0.570000 1.770000 0.565041 0.860000 6.900000e-01 1.000000 1.000000 0.870295 0.860000 1 7.700000e-01 9.600000e-01 TP53 7157 broad.mit.edu 37 17 7577022 7577022 + Nonsense_Mutation SNP G G A rs121913344 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr17:7577022G>A ENST00000269305.4 - 8 1105 c.916C>T c.(916-918)Cga>Tga p.R306* TP53_ENST00000445888.2_Nonsense_Mutation_p.R306*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.R306*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R306*|TP53_ENST00000359597.4_Nonsense_Mutation_p.R306*|TP53_ENST00000413465.2_Intron NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.R306*(133)|p.0?(8)|p.?(3)|p.R306fs*39(2)|p.K305fs*1(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) TGCTTACCTCGCTTAGTGCTC 0.562000 R306*(HCC1937_BREAST)|R306*(JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(MFE296_ENDOMETRIUM)|R306*(MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(RCM1_LARGE_INTESTINE) 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 147 Substitution - Nonsense(133)|Whole gene deletion(8)|Unknown(3)|Deletion - Frameshift(2)|Insertion - Frameshift(1) GRCh37 CM971506 TP53 M rs121913344 SO:0001587 stop_gained Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 0 1 hg19 CCDS11118.1 . . . . . . . . . . G 26.9 4.782988 0.90282 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 . . . 5.26 3.21 0.36854 . 1.348720 0.05032 N 0.474808 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 10.4785 0.44678 0.0:0.0:0.6334:0.3666 . . . . X 306;306;306;306;306;295;174 . ENSP00000269305:R306X R - 1 2 TP53 7517747 1.000000 0.71417 0.970000 0.41538 0.345000 0.29048 2.280000 0.43443 0.735000 0.32537 0.561000 0.74099 CGA TCGA-OE-A75W-01A-12D-A32N-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 120 174 1 74 1 9.879044e-01 2 11 1 74 2 1 1 253 344 1 960 6 1 1.000000 120 174 2 72 20 0 0 0 1 74 2 -20.000000 1 1 0 0 1 0 1 1 1.562258 1 0.570000 1.770000 0.398601 0.950000 8.500000e-01 1.000000 0.990000 0.953260 0.950000 1 9.000000e-01 9.900000e-01 CHD3 1107 broad.mit.edu 37 17 7797171 7797171 + Missense_Mutation SNP G G A rs139173826 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr17:7797171G>A ENST00000330494.7 + 6 992 c.842G>A c.(841-843)cGc>cAc p.R281H CHD3_ENST00000358181.4_Missense_Mutation_p.R281H|CHD3_ENST00000380358.4_Missense_Mutation_p.R340H NM_001005273.2 NP_001005273.1 Q12873 CHD3_HUMAN chromodomain helicase DNA binding protein 3 65 Prostate(122;0.202) CCTGATGGACGCAAGAAGCTT 0.542000 0 SO:0001583 missense ENST00000330494.7 0 1 hg19 CCDS32554.1 . . . . . . . . . . G 11.21 1.571999 0.28092 0.0 1.16E-4 ENSG00000170004 ENST00000380358;ENST00000358181;ENST00000330494 D;D;D 0.90504 -2.68;-2.63;-2.62 5.29 5.29 0.74685 . 0.000000 0.44688 D 0.000423 T 0.80529 0.4640 N 0.22421 0.69 0.34035 D 0.654297 P;P;P 0.46220 0.871;0.874;0.874 B;B;B 0.35550 0.205;0.101;0.145 D 0.85691 0.1307 10 0.62326 D 0.03 -6.0171 7.7325 0.28796 0.0868:0.1663:0.7469:0.0 . 281;281;340 Q12873-2;Q12873;E9PG89 .;CHD3_HUMAN;. H 340;281;281 ENSP00000369716:R340H;ENSP00000350907:R281H;ENSP00000332628:R281H ENSP00000332628:R281H R + 2 0 CHD3 7737896 0.981000 0.34729 1.000000 0.80357 0.987000 0.75469 1.600000 0.36762 2.480000 0.83734 0.650000 0.86243 CGC TCGA-OE-A75W-01A-12D-A32N-08 CHD3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000318050.1 0 0 0 6 645 0 167 0 0 0 1 0 167 2 0 0 0 0 0 2 1 0.963730 6 637 0 167 2 0 0 0 0 167 2 -2.038208 0 1 121412 10 45 1 0 1 1 1.562258 1 0.570000 1.770000 0.398601 0.020000 0 0.050000 0.020000 0.026824 0.020000 0 1.000000e-02 4.000000e-02 ARHGEF15 22899 broad.mit.edu 37 17 8221919 8221919 + Missense_Mutation SNP G G A rs143720339 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr17:8221919G>A ENST00000361926.3 + 11 1921 c.1811G>A c.(1810-1812)cGc>cAc p.R604H ARHGEF15_ENST00000421050.1_Missense_Mutation_p.R604H|AC135178.7_ENST00000458568.1_RNA NM_173728.3 NP_776089.2 O94989 ARHGF_HUMAN Rho guanine nucleotide exchange factor (GEF) 15 37 GAGGTGGGGCGCATGAAGCAG 0.612000 0 SO:0001583 missense ENST00000361926.3 0 1 hg19 CCDS11139.1 . . . . . . . . . . g 23.0 4.358370 0.82243 2.27E-4 0.0 ENSG00000198844 ENST00000361926;ENST00000455564;ENST00000421050 T;T 0.32515 1.45;1.45 5.29 5.29 0.74685 Dbl homology (DH) domain (1); 0.059270 0.64402 D 0.000004 T 0.51160 0.1658 L 0.59436 1.845 0.46113 D 0.998873 D;D 0.89917 1.0;1.0 D;D 0.66979 0.948;0.948 T 0.49679 -0.8914 10 0.54805 T 0.06 -18.0429 16.4339 0.83864 0.0:0.0:1.0:0.0 . 604;604 D3DTR7;O94989 .;ARHGF_HUMAN H 604;394;604 ENSP00000355026:R604H;ENSP00000412505:R604H ENSP00000355026:R604H R + 2 0 ARHGEF15 8162644 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.368000 0.59505 2.470000 0.83445 0.555000 0.69702 CGC TCGA-OE-A75W-01A-12D-A32N-08 ARHGEF15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000226993.2 0 0 0 4 194 0 73 0 2.187084e-03 0 3 0 73 2 0 0 0 0 0 2 1 0.890036 4 193 0 73 2 0 0 0 0 73 2 -3.072909 1 1 121412 2 29 1 0 1 1 1.562258 1 0.570000 1.770000 0.398601 0.050000 1.000000e-02 0.120000 0.050000 0.062232 0.050000 0 3.000000e-02 9.000000e-02 SMCHD1 23347 broad.mit.edu 37 18 2739500 2739500 + Missense_Mutation SNP G G C TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr18:2739500G>C ENST00000320876.6 + 27 3834 c.3496G>C c.(3496-3498)Gag>Cag p.E1166Q SMCHD1_ENST00000261598.8_Missense_Mutation_p.E1166Q|RP11-703M24.5_ENST00000583546.1_RNA NM_015295.2 NP_056110.2 A6NHR9 SMHD1_HUMAN structural maintenance of chromosomes flexible hinge domain containing 1 45 GATGGGCCAAGAGCTTCAAGG 0.338000 0 SO:0001583 missense ENST00000320876.6 1 1 hg19 CCDS45822.1 . . . . . . . . . . G 18.01 3.527477 0.64860 . . ENSG00000101596 ENST00000320876;ENST00000261598 T;T 0.23552 1.9;1.91 5.61 5.61 0.85477 . 0.195294 0.46758 D 0.000274 T 0.32526 0.0832 L 0.51422 1.61 0.39011 D 0.959543 P 0.45044 0.849 P 0.45377 0.478 T 0.03157 -1.1066 10 0.32370 T 0.25 -17.716 18.627 0.91344 0.0:0.0:1.0:0.0 . 1166 A6NHR9 SMHD1_HUMAN Q 1166 ENSP00000326603:E1166Q;ENSP00000261598:E1166Q ENSP00000261598:E1166Q E + 1 0 SMCHD1 2729500 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 6.796000 0.75145 2.642000 0.89623 0.650000 0.86243 GAG TCGA-OE-A75W-01A-12D-A32N-08 SMCHD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000441082.2 1 0 0 5 133 0 24 0 0 0 0 24 2 0 0 0 0 0 2 1 0.936303 5 131 0 24 2 0 0 0 0 24 2 -7.731958 1 1 0 0 1 0 1 1 1.551594 1 0.570000 1.770000 0.403358 0.090000 3.000000e-02 0.200000 0.090000 0.107223 0.090000 0 6.000000e-02 1.500000e-01 LPHN1 22859 broad.mit.edu 37 19 14266197 14266197 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:14266197C>T ENST00000340736.6 - 19 3580 c.3283G>A c.(3283-3285)Gtc>Atc p.V1095I CTB-55O6.12_ENST00000588658.1_RNA|LPHN1_ENST00000361434.3_Missense_Mutation_p.V1090I|CTB-55O6.12_ENST00000592086.1_RNA|CTB-55O6.12_ENST00000588387.1_RNA NM_001008701.2 NP_001008701.1 O94910 LPHN1_HUMAN latrophilin 1 p.V1095I(1) 32 CAGTGAAAGACGAAGATGAAG 0.587000 1 Substitution - Missense(1) SO:0001583 missense ENST00000340736.6 1 1 hg19 CCDS32928.1 . . . . . . . . . . C 5.280 0.237123 0.10023 . . ENSG00000072071 ENST00000340736;ENST00000361434 T;T 0.41065 1.01;1.01 5.21 4.18 0.49190 GPCR, family 2-like (1);GPCR, family 2, secretin-like, conserved site (1); 0.070788 0.56097 D 0.000027 T 0.13200 0.0320 N 0.01529 -0.815 0.40998 D 0.984908 B;B 0.10296 0.003;0.003 B;B 0.12837 0.008;0.001 T 0.18808 -1.0325 10 0.02654 T 1 . 7.6688 0.28447 0.0:0.8111:0.0:0.1889 . 1090;1095 O94910-2;O94910 .;LPHN1_HUMAN I 1095;1090 ENSP00000340688:V1095I;ENSP00000355328:V1090I ENSP00000340688:V1095I V - 1 0 LPHN1 14127197 0.986000 0.35501 0.984000 0.44739 0.998000 0.95712 2.344000 0.44010 1.184000 0.42957 0.561000 0.74099 GTC TCGA-OE-A75W-01A-12D-A32N-08 LPHN1-001 KNOWN overlapping_uORF|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000459696.1 1 0 0 188 365 0 166 1 9.819391e-01 3 12 0 166 2 0 0 0 0 0 2 1 1.000000 185 364 0 163 2 0 0 0 0 166 2 -20.000000 1 1 121412 2 41 1 0 1 1 1.945463 1 0.570000 1.770000 0.493492 0.990000 8.900000e-01 1.000000 1.000000 0.981856 0.990000 1 9.400000e-01 1 NOTCH3 4854 broad.mit.edu 37 19 15271827 15271827 + Silent SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:15271827C>T ENST00000263388.2 - 33 6687 c.6612G>A c.(6610-6612)ccG>ccA p.P2204P NM_000435.2 NP_000426.2 Q9UM47 NOTC3_HUMAN notch 3 93 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) GCCGCTCCTGCGGGGAGACGG 0.741000 0 SO:0001819 synonymous_variant ENST00000263388.2 1 1 hg19 CCDS12326.1 TCGA-OE-A75W-01A-12D-A32N-08 NOTCH3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465714.1 1 0 0 6 33 0 20 0 9.959318e-01 0 66 0 20 2 0 0 0 0 0 2 1 0.966505 6 32 0 18 2 0 0 0 0 20 2 -13.643960 1 1 116512 1 21 1 0 1 1 1.923758 0 0.570000 1.770000 0.525360 0.500000 2.200000e-01 0.890000 0.480000 0.529496 0.500000 0 3.400000e-01 7.000000e-01 SPPL2B 56928 broad.mit.edu 37 19 2341000 2341000 + RNA SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:2341000G>A ENST00000452401.2 + 0 1021 Q8TCT7 SPP2B_HUMAN signal peptide peptidase like 2B Hepatocellular(1079;0.137) GGCGTCTTCCGCAACGAGGAC 0.701000 0 ENST00000452401.2 0 1 hg19 . . . . . . . . . . G 18.35 3.604692 0.66445 . . ENSG00000005206 ENST00000452401;ENST00000382189 . . . 4.47 4.47 0.54385 . 0.000000 0.85682 D 0.000000 T 0.79845 0.4516 . . . 0.51767 D 0.999931 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.84965 0.0879 7 0.87932 D 0 -33.5577 15.6943 0.77481 0.0:0.0:1.0:0.0 . 315;314 Q8TCT7;C9JFE6 PSL1_HUMAN;. H 314;303 . ENSP00000371624:R303H R + 2 0 AC004410.1 2292000 1.000000 0.71417 0.983000 0.44433 0.048000 0.14542 9.152000 0.94680 2.041000 0.60428 0.561000 0.74099 CGC TCGA-OE-A75W-01A-12D-A32N-08 SPPL2B-202 KNOWN basic processed_transcript processed_transcript 0 0 0 7 230 0 53 1 6.651939e-01 4 69 0 53 2 0 0 0 0 0 2 1 0.979864 7 226 0 52 2 0 0 0 0 53 2 -8.207476 1 1 121324 1 25 1 0 1 1 1.954477 0 0.570000 1.770000 0.532710 0.090000 4.000000e-02 0.190000 0.100000 0.107680 0.090000 0 6.000000e-02 1.400000e-01 ATP4A 495 broad.mit.edu 37 19 36043993 36043993 + Silent SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:36043993C>T ENST00000262623.3 - 18 2725 c.2697G>A c.(2695-2697)gcG>gcA p.A899A NM_000704.2 NP_000695.2 P20648 ATP4A_HUMAN ATPase, H+/K+ exchanging, alpha polypeptide 53 all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129) CCTCCCACTGCGCCCGCAGCC 0.647000 0 SO:0001819 synonymous_variant ENST00000262623.3 0 1 hg19 CCDS12467.1 TCGA-OE-A75W-01A-12D-A32N-08 ATP4A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109470.2 0 0 0 9 758 0 163 0 0 0 0 163 2 0 0 0 0 0 2 1 0.994034 9 752 0 159 2 0 0 0 0 163 2 -2.665716 1 1 121412 2 39 1 0 0 0 2.108690 0 0.570000 1.770000 0.565041 0.030000 0 0.080000 0.040000 0.045314 0.030000 0 2.000000e-02 6.000000e-02 ARHGAP33 115703 broad.mit.edu 37 19 36271129 36271129 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:36271129G>A ENST00000007510.4 + 7 662 c.518G>A c.(517-519)cGg>cAg p.R173Q ARHGAP33_ENST00000314737.5_Missense_Mutation_p.R173Q|ARHGAP33_ENST00000378944.5_Missense_Mutation_p.R37Q O14559 RHG33_HUMAN Rho GTPase activating protein 33 p.R173Q(1) 37 AATCACGGCCGGCGACTGCTC 0.592000 1 Substitution - Missense(1) SO:0001583 missense ENST00000007510.4 0 1 hg19 . . . . . . . . . . G 25.0 4.590020 0.86851 . . ENSG00000004777 ENST00000007510;ENST00000314737;ENST00000378944 T;T;T 0.11930 3.08;2.73;3.15 4.84 3.8 0.43715 . 0.305936 0.23487 N 0.047642 T 0.21267 0.0512 L 0.49126 1.545 0.30529 N 0.767663 D;D 0.71674 0.998;0.974 P;P 0.58721 0.844;0.466 T 0.04537 -1.0944 10 0.54805 T 0.06 . 5.6018 0.17357 0.2761:0.0:0.7239:0.0 . 37;173 O14559-10;O14559-11 .;. Q 173;173;37 ENSP00000007510:R173Q;ENSP00000320038:R173Q;ENSP00000368227:R37Q ENSP00000007510:R173Q R + 2 0 ARHGAP33 40962969 1.000000 0.71417 1.000000 0.80357 0.979000 0.70002 5.552000 0.67281 2.227000 0.72691 0.561000 0.74099 CGG TCGA-OE-A75W-01A-12D-A32N-08 ARHGAP33-201 KNOWN basic protein_coding protein_coding 0 0 0 5 545 0 98 0 0 0 1 0 98 2 0 0 0 0 0 2 1 0.936292 5 540 0 96 2 0 0 0 0 98 2 -2.673527 1 1 121412 1 37 1 0 0 0 2.108690 0 0.570000 1.770000 0.565041 0.030000 0 0.070000 0.040000 0.037151 0.030000 0 1.000000e-02 5.000000e-02 PRODH2 58510 broad.mit.edu 37 19 36303061 36303061 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:36303061G>A ENST00000301175.3 - 4 730 c.713C>T c.(712-714)aCg>aTg p.T238M NM_021232.1 NP_067055.1 Q9UF12 PROD2_HUMAN proline dehydrogenase (oxidase) 2 21 all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) GGTCAGCGCCGTCACCTTCAG 0.687000 0 SO:0001583 missense ENST00000301175.3 1 1 hg19 CCDS12478.1 . . . . . . . . . . G 21.7 4.186150 0.78789 . . ENSG00000250799 ENST00000301175 T 0.41065 1.01 4.85 4.85 0.62838 . . . . . T 0.62986 0.2473 M 0.73962 2.25 0.80722 D 1 D 0.89917 1.0 D 0.65987 0.94 T 0.66925 -0.5800 9 0.66056 D 0.02 . 15.5053 0.75735 0.0:0.0:1.0:0.0 . 238 Q9UF12 PROD2_HUMAN M 238 ENSP00000301175:T238M ENSP00000301175:T238M T - 2 0 PRODH2 40994901 1.000000 0.71417 0.997000 0.53966 0.859000 0.49053 7.408000 0.80041 2.531000 0.85337 0.655000 0.94253 ACG TCGA-OE-A75W-01A-12D-A32N-08 PRODH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452552.2 1 0 0 23 482 0 90 0 0 0 0 90 2 0 0 0 0 0 2 1 0.999999 22 478 0 89 2 0 0 0 0 90 2 -3.213168 1 1 121412 1 35 1 0 0 0 2.108690 0 0.570000 1.770000 0.565041 0.150000 9.000000e-02 0.230000 0.160000 0.163953 0.150000 0 1.200000e-01 2.000000e-01 SIPA1L3 23094 broad.mit.edu 37 19 38682812 38682812 + Silent SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:38682812C>T ENST00000222345.6 + 17 4967 c.4458C>T c.(4456-4458)gtC>gtT p.V1486V NM_015073.1 NP_055888.1 O60292 SI1L3_HUMAN signal-induced proliferation-associated 1 like 3 59 Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292) CCAAAAATGTCTTTGGGCAAC 0.522000 0 SO:0001819 synonymous_variant ENST00000222345.6 1 1 hg19 CCDS33007.1 TCGA-OE-A75W-01A-12D-A32N-08 SIPA1L3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000156294.2 1 0 1 58 234 0 50 1 8.951679e-01 4 14 0 50 2 0 0 0 0 0 2 1 1.000000 58 228 0 50 2 0 0 0 0 50 2 -20.000000 1 1 0 0 1 0 0 0 2.108690 0 0.570000 1.770000 0.565041 0.680000 5.300000e-01 0.850000 0.690000 0.694280 0.680000 0 6.000000e-01 7.700000e-01 RYR1 6261 broad.mit.edu 37 19 39075614 39075614 + Missense_Mutation SNP G G A rs118192151 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:39075614G>A ENST00000359596.3 + 102 14678 c.14678G>A c.(14677-14679)cGg>cAg p.R4893Q RYR1_ENST00000360985.3_Missense_Mutation_p.R4888Q|RYR1_ENST00000355481.4_Missense_Mutation_p.R4888Q P21817 RYR1_HUMAN ryanodine receptor 1 (skeletal) 285 all_cancers(60;7.91e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786) GTGGGTGTCCGGGCTGGCGGA 0.572000 0 GRCh37 CM030713|CM061940 RYR1 M rs118192151 SO:0001583 missense ENST00000359596.3 1 1 hg19 CCDS33011.1 . . . . . . . . . . G 20.3 3.959539 0.74016 . . ENSG00000196218 ENST00000359596;ENST00000355481;ENST00000360985 D;D;D 0.94457 -3.43;-3.43;-3.43 5.08 5.08 0.68730 Ion transport (1); 0.000000 0.64402 U 0.000015 D 0.98086 0.9369 M 0.94142 3.5 0.52501 D 0.999954 D;D 0.76494 0.999;0.999 D;D 0.80764 0.99;0.994 D 0.99081 1.0837 10 0.87932 D 0 . 18.3248 0.90250 0.0:0.0:1.0:0.0 . 4888;4893 P21817-2;P21817 .;RYR1_HUMAN Q 4893;4888;4888 ENSP00000352608:R4893Q;ENSP00000347667:R4888Q;ENSP00000354254:R4888Q ENSP00000347667:R4888Q R + 2 0 RYR1 43767454 1.000000 0.71417 1.000000 0.80357 0.975000 0.68041 9.656000 0.98514 2.658000 0.90341 0.449000 0.29647 CGG TCGA-OE-A75W-01A-12D-A32N-08 RYR1-010 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000462137.1 1 0 1 37 262 0 65 0 1.630327e-02 0 2 0 65 2 0 0 0 0 0 2 1 1.000000 35 259 0 64 2 0 0 0 0 65 2 -2.559263 1 1 0 0 1 0 0 0 2.108690 0 0.570000 1.770000 0.565041 0.420000 3.000000e-01 0.560000 0.430000 0.436794 0.420000 0 3.600000e-01 5.000000e-01 CYP2A6 1548 broad.mit.edu 37 19 41351245 41351245 + Missense_Mutation SNP C C T rs145036049 by1000genomes TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:41351245C>T ENST00000301141.5 - 7 1135 c.1115G>A c.(1114-1116)cGc>cAc p.R372H CTC-490E21.12_ENST00000601627.1_Intron NM_000762.5 NP_000753 P11509 CP2A6_HUMAN cytochrome P450, family 2, subfamily A, polypeptide 6 37 LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959) Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495) TTTGACTCTGCGGGCCAAACT 0.572000 0 SO:0001583 missense ENST00000301141.5 0 1 hg19 CCDS12568.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 - 0.014 -1.595383 0.00857 2.27E-4 0.0 ENSG00000255974 ENST00000301141 T 0.77877 -1.13 2.76 0.567 0.17325 . 0.199062 0.42821 N 0.000649 T 0.50871 0.1641 N 0.02973 -0.45 0.09310 N 1 B;B 0.32693 0.105;0.38 B;B 0.43413 0.046;0.419 T 0.55885 -0.8070 10 0.02654 T 1 . 4.58 0.12253 0.0:0.4325:0.0:0.5675 . 372;372 Q13120;P11509 .;CP2A6_HUMAN H 372 ENSP00000301141:R372H ENSP00000301141:R372H R - 2 0 CYP2A6 46043085 0.000000 0.05858 0.056000 0.19401 0.181000 0.23173 -1.136000 0.03222 0.446000 0.26666 0.379000 0.24179 CGC TCGA-OE-A75W-01A-12D-A32N-08 CYP2A6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000463259.1 0 0 0 6 765 0 133 0 0 0 0 133 2 0 0 0 0 0 2 1 0.963015 6 751 0 133 2 0 0 0 0 133 2 -1.531743 0 1 121308 20 46 1 0 0 0 2.108690 0 0.570000 1.770000 0.565041 0.020000 0 0.060000 0.020000 0.030430 0.020000 0 1.000000e-02 4.000000e-02 EXOSC5 56915 broad.mit.edu 37 19 41903139 41903139 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:41903139G>A ENST00000221233.4 - 1 245 c.95C>T c.(94-96)gCc>gTc p.A32V BCKDHA_ENST00000269980.2_5'Flank|BCKDHA_ENST00000457836.2_5'Flank|CTC-435M10.10_ENST00000598988.1_RNA|CTC-435M10.3_ENST00000540732.1_Intron|BCKDHA_ENST00000595085.1_Intron|EXOSC5_ENST00000596905.1_Missense_Mutation_p.A32V|CTC-435M10.3_ENST00000604424.1_Intron NM_020158.3 NP_064543.3 Q9NQT4 EXOS5_HUMAN exosome component 5 7 CTGTTCGCAGGCAAAGTGCCG 0.582000 0 SO:0001583 missense ENST00000221233.4 0 1 hg19 CCDS12580.1 . . . . . . . . . . G 15.39 2.819174 0.50633 . . ENSG00000077348 ENST00000221233 T 0.63580 -0.05 5.55 4.52 0.55395 Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1); 0.159578 0.53938 N 0.000054 T 0.36963 0.0986 N 0.05351 -0.065 0.38224 D 0.940854 B 0.26547 0.152 B 0.17098 0.017 T 0.32322 -0.9911 10 0.31617 T 0.26 -17.2989 8.2921 0.31963 0.1727:0.0:0.8273:0.0 . 32 Q9NQT4 EXOS5_HUMAN V 32 ENSP00000221233:A32V ENSP00000221233:A32V A - 2 0 EXOSC5 46594979 0.997000 0.39634 0.992000 0.48379 0.964000 0.63967 2.911000 0.48774 1.579000 0.49836 0.590000 0.80494 GCC TCGA-OE-A75W-01A-12D-A32N-08 EXOSC5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000463492.1 0 0 0 7 740 0 127 0 2.728728e-01 0 96 0 127 2 0 0 0 0 0 2 1 0.979893 6 733 0 125 2 0 0 0 0 127 2 -2.148347 0 1 0 0 1 0 0 0 2.108690 0 0.570000 1.770000 0.565041 0.030000 0 0.070000 0.040000 0.036700 0.030000 0 1.000000e-02 5.000000e-02 TNFAIP8L1 126282 broad.mit.edu 37 19 4652052 4652052 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:4652052G>A ENST00000536716.1 + 2 317 c.171G>A c.(169-171)caG>caA p.Q57Q TNFAIP8L1_ENST00000327473.4_Silent_p.Q57Q|AC005339.2_ENST00000598070.1_RNA NM_001167942.1 NP_001161414.1 Q8WVP5 TP8L1_HUMAN tumor necrosis factor, alpha-induced protein 8-like 1 1 AGGAGGCCCAGAAGATGCTCA 0.662000 0 SO:0001819 synonymous_variant ENST00000536716.1 1 1 hg19 CCDS12132.1 TCGA-OE-A75W-01A-12D-A32N-08 TNFAIP8L1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000458662.1 1 0 1 24 74 0 36 1 4.631738e-01 2 4 0 36 2 0 0 0 0 0 2 1 1.000000 23 73 0 35 2 0 0 0 0 36 2 -20.000000 1 1 0 0 1 0 1 1 1.954477 0 0.570000 1.770000 0.532710 0.780000 5.400000e-01 1.000000 1.000000 0.794521 0.780000 0 6.500000e-01 9.300000e-01 CD33 945 broad.mit.edu 37 19 51728379 51728379 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:51728379C>T ENST00000262262.4 + 1 26 c.5C>T c.(4-6)cCg>cTg p.P2L CD33_ENST00000421133.2_Missense_Mutation_p.P2L|CD33_ENST00000436584.2_Missense_Mutation_p.P2L|CD33_ENST00000391796.3_Missense_Mutation_p.P2L NM_001772.3 NP_001763.3 P20138 CD33_HUMAN CD33 molecule 24 all_neural(266;0.0199) Gemtuzumab ozogamicin(DB00056) TCAGACATGCCGCTGCTGCTA 0.652000 0 SO:0001583 missense ENST00000262262.4 1 1 hg19 CCDS33084.1 . . . . . . . . . . . 5.629 0.300790 0.10678 . . ENSG00000105383 ENST00000436584;ENST00000262262;ENST00000421133;ENST00000391796 T;T;T;T 0.39592 1.07;2.53;1.38;2.41 3.75 -4.49 0.03504 . . . . . T 0.11793 0.0287 N 0.02192 -0.645 0.09310 N 1 B;B;B 0.12630 0.006;0.0;0.0 B;B;B 0.04013 0.001;0.0;0.0 T 0.28106 -1.0054 9 0.02654 T 1 . 5.3402 0.15979 0.0:0.2105:0.3616:0.4279 . 2;2;2 C9JEN7;F8WAL2;P20138 .;.;CD33_HUMAN L 2 ENSP00000403331:P2L;ENSP00000262262:P2L;ENSP00000410126:P2L;ENSP00000375673:P2L ENSP00000262262:P2L P + 2 0 CD33 56420191 0.000000 0.05858 0.000000 0.03702 0.003000 0.03518 -2.283000 0.01155 -1.134000 0.02899 -1.099000 0.02127 CCG TCGA-OE-A75W-01A-12D-A32N-08 CD33-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000464199.2 1 0 1 20 205 0 29 0 8.926501e-03 0 2 0 29 2 0 0 0 0 0 2 1 0.999995 21 198 0 29 2 0 0 0 0 29 2 -20.000000 1 1 0 0 1 1 2 3 2.233574 0 0.570000 1.770000 0.579585 0.320000 2.000000e-01 1.000000 0.310000 0.373980 0.320000 0 2.600000e-01 4.200000e-01 KIR3DL2 3812 broad.mit.edu 37 19 55363669 55363669 + Missense_Mutation SNP G G A rs148964687 byFrequency TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:55363669G>A ENST00000326321.3 + 3 320 c.287G>A c.(286-288)cGg>cAg p.R96Q KIR3DL2_ENST00000270442.5_Missense_Mutation_p.R96Q|KIR3DL1_ENST00000402254.2_Intron NM_006737.3 NP_006728.2 P43630 KI3L2_HUMAN killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2 p.R96Q(1) 23 TACAGATGTCGGGGTTCACGC 0.582000 1 Substitution - Missense(1) SO:0001583 missense ENST00000326321.3 1 0 hg19 CCDS12906.1 . . . . . . . . . . g 8.265 0.812014 0.16537 . . ENSG00000240403 ENST00000326321;ENST00000270442 T;T 0.13657 2.57;2.57 1.03 -0.701 0.11269 Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1); 5.841140 0.01572 U 0.020616 T 0.18425 0.0442 M 0.73372 2.23 0.09310 N 1 D;P 0.59357 0.985;0.938 B;B 0.43386 0.418;0.343 T 0.27191 -1.0081 10 0.66056 D 0.02 . 3.417 0.07380 0.5147:0.0:0.4853:0.0 . 96;96 Q95366;P43630 .;KI3L2_HUMAN Q 96 ENSP00000325525:R96Q;ENSP00000270442:R96Q ENSP00000270442:R96Q R + 2 0 KIR3DL2 60055481 0.000000 0.05858 0.001000 0.08648 0.050000 0.14768 -1.794000 0.01753 -0.237000 0.09739 0.184000 0.17185 CGG TCGA-OE-A75W-01A-12D-A32N-08 KIR3DL2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000141241.1 1 0 0 51 421 0 85 0 0 0 0 85 2 0 0 0 0 0 2 1 1.000000 49 389 0 106 2 0 0 0 0 85 2 -2.665581 1 1 115524 252 55 1 1 2 3 2.233574 0 0.570000 1.770000 0.579585 0.390000 2.900000e-01 1.000000 0.390000 0.432148 0.390000 0 3.300000e-01 4.600000e-01 NLRP9 338321 broad.mit.edu 37 19 56243922 56243922 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:56243922G>A ENST00000332836.2 - 2 1302 c.1275C>T c.(1273-1275)ggC>ggT p.G425G NM_176820.2 NP_789790.2 Q7RTR0 NALP9_HUMAN NLR family, pyrin domain containing 9 74 Colorectal(82;0.000133)|Ovarian(87;0.133) CCCACATCACGCCCTCAGACT 0.473000 0 SO:0001819 synonymous_variant ENST00000332836.2 1 1 hg19 CCDS12934.1 TCGA-OE-A75W-01A-12D-A32N-08 NLRP9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000453653.1 1 0 1 186 495 0 110 0 0 0 0 110 2 0 0 0 0 0 2 1 1.000000 185 487 0 109 2 0 0 0 0 110 2 -9.029628 1 1 0 0 1 1 2 3 2.233574 0 0.570000 1.770000 0.579585 0.980000 8.500000e-01 1.000000 1.000000 0.967244 0.980000 1 9.100000e-01 1 ZNF471 57573 broad.mit.edu 37 19 57036821 57036821 + Missense_Mutation SNP A A T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:57036821A>T ENST00000308031.5 + 5 1518 c.1385A>T c.(1384-1386)aAg>aTg p.K462M ZNF471_ENST00000591537.1_3'UTR|ZNF471_ENST00000593197.1_Intron NM_020813.2 NP_065864.2 Q9BX82 ZN471_HUMAN zinc finger protein 471 36 Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157) TATGAATGCAAGGAATGTGGG 0.378000 Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211) 0 SO:0001583 missense ENST00000308031.5 1 1 hg19 CCDS12945.1 . . . . . . . . . . A 12.94 2.089753 0.36855 . . ENSG00000196263 ENST00000308031 T 0.08193 3.12 3.66 2.64 0.31445 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.19446 0.0467 M 0.68317 2.08 0.09310 N 0.999999 D 0.69078 0.997 P 0.62649 0.905 T 0.09015 -1.0694 9 0.56958 D 0.05 . 4.605 0.12372 0.6982:0.1949:0.1069:0.0 . 462 Q9BX82 ZN471_HUMAN M 462 ENSP00000309161:K462M ENSP00000309161:K462M K + 2 0 ZNF471 61728633 0.000000 0.05858 0.954000 0.39281 0.962000 0.63368 -1.500000 0.02283 0.496000 0.27904 0.379000 0.24179 AAG TCGA-OE-A75W-01A-12D-A32N-08 ZNF471-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000458405.1 1 0 0 37 546 0 109 0 0 0 1 0 109 2 0 0 0 0 0 2 1 1.000000 37 543 0 108 2 0 0 0 0 109 2 -8.202811 1 1 0 0 1 1 2 3 2.233574 0 0.570000 1.770000 0.579585 0.220000 1.600000e-01 1.000000 0.230000 0.282187 0.220000 0 1.900000e-01 2.800000e-01 FBN3 84467 broad.mit.edu 37 19 8190815 8190815 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr19:8190815C>T ENST00000600128.1 - 22 3106 c.2692G>A c.(2692-2694)Gag>Aag p.E898K FBN3_ENST00000601739.1_Missense_Mutation_p.E898K|FBN3_ENST00000270509.2_Missense_Mutation_p.E898K Q75N90 FBN3_HUMAN fibrillin 3 132 ATCAGGCCCTCTGGACACTCA 0.622000 0 SO:0001583 missense ENST00000600128.1 1 1 hg19 CCDS12196.1 . . . . . . . . . . c 4.459 0.085024 0.08583 . . ENSG00000142449 ENST00000270509 D 0.92348 -3.02 4.0 -8.0 0.01126 EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1); 0.296672 0.32884 N 0.005521 T 0.77315 0.4112 N 0.17564 0.495 0.09310 N 1 B 0.22146 0.065 B 0.18561 0.022 T 0.62515 -0.6838 10 0.33940 T 0.23 . 4.9192 0.13862 0.084:0.3077:0.4089:0.1993 . 898 Q75N90 FBN3_HUMAN K 898 ENSP00000270509:E898K ENSP00000270509:E898K E - 1 0 FBN3 8096815 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.712000 0.05013 -2.657000 0.00421 -1.887000 0.00540 GAG TCGA-OE-A75W-01A-12D-A32N-08 FBN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461428.2 0 0 0 10 297 0 59 0 0 0 0 59 2 0 0 0 0 0 2 1 0.996854 10 294 0 58 2 0 0 0 0 59 2 -10.576320 1 1 0 0 1 0 1 1 1.950536 0 0.570000 1.770000 0.528328 0.100000 5.000000e-02 0.180000 0.100000 0.113542 0.100000 0 7.000000e-02 1.500000e-01 CELF3 11189 broad.mit.edu 37 1 151680404 151680404 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:151680404G>A ENST00000290583.4 - 6 1287 c.494C>T c.(493-495)tCg>tTg p.S165L CELF3_ENST00000290585.4_Missense_Mutation_p.S165L|RIIAD1_ENST00000326413.3_5'Flank|CELF3_ENST00000392706.3_5'Flank|AL589765.1_ENST00000442233.2_5'Flank|RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000470688.1_5'UTR NM_001172648.1|NM_007185.4 NP_001166119.1|NP_009116.3 Q5SZQ8 CELF3_HUMAN CUGBP, Elav-like family member 3 21 CAGGCTGGACGAGGCACCCTG 0.647000 0 SO:0001583 missense ENST00000290583.4 1 1 hg19 CCDS1002.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. 24.9|24.9 4.582586|4.582586 0.86748|0.86748 .|. .|. ENSG00000159409|ENSG00000159409 ENST00000420342|ENST00000290585;ENST00000290583;ENST00000368833 .|T;T .|0.06449 .|3.3;3.3 3.75|3.75 3.75|3.75 0.43078|0.43078 .|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2); .|0.000000 .|0.64402 .|D .|0.000001 T|T 0.10165|0.10165 0.0249|0.0249 L|L 0.43152|0.43152 1.355|1.355 0.80722|0.80722 D|D 1|1 .|D;D;D;D;D .|0.89917 .|0.998;1.0;0.999;0.999;0.998 .|P;D;D;P;P .|0.64877 .|0.834;0.93;0.918;0.887;0.819 T|T 0.04078|0.04078 -1.0979|-1.0979 5|10 .|0.87932 .|D .|0 -4.7861|-4.7861 14.6626|14.6626 0.68882|0.68882 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|165;165;164;165;164 .|Q5SZQ7;Q5SZQ8-2;F8W6B7;Q5SZQ8;Q5SZQ8-3 .|.;.;.;CELF3_HUMAN;. C|L 166|165;165;164 .|ENSP00000290585:S165L;ENSP00000290583:S165L .|ENSP00000290583:S165L R|S -|- 1|2 0|0 CELF3|CELF3 149947028|149947028 1.000000|1.000000 0.71417|0.71417 0.985000|0.985000 0.45067|0.45067 0.999000|0.999000 0.98932|0.98932 9.566000|9.566000 0.98157|0.98157 2.098000|2.098000 0.63641|0.63641 0.655000|0.655000 0.94253|0.94253 CGT|TCG TCGA-OE-A75W-01A-12D-A32N-08 CELF3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000036663.2 1 0 1 42 127 0 46 0 0 0 1 0 46 2 0 0 0 0 0 2 1 1.000000 42 125 0 46 2 0 0 0 0 46 2 -20.000000 1 1 0 0 1 1 2 3 2.165351 0 0.570000 1.770000 0.572437 0.870000 6.600000e-01 1.000000 1.000000 0.874227 0.870000 1 7.600000e-01 1 PGLYRP3 114771 broad.mit.edu 37 1 153271680 153271680 + Silent SNP C C A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:153271680C>A ENST00000290722.1 - 6 808 c.756G>T c.(754-756)gtG>gtT p.V252V NM_052891.1 NP_443123.1 Q96LB9 PGRP3_HUMAN peptidoglycan recognition protein 3 28 all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.171) CCCCTTCATACACGCCACCAT 0.458000 0 SO:0001819 synonymous_variant ENST00000290722.1 1 1 hg19 CCDS1035.1 TCGA-OE-A75W-01A-12D-A32N-08 PGLYRP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039488.1 1 0 1 40 85 0 31 0 0 0 0 31 2 0 0 0 1 0 0 2 1 1.000000 39 85 0 30 2 0 0 0 0 31 2 -20.000000 1 1 0 0 1 1 2 3 2.165351 0 0.570000 1.770000 0.572437 0.990000 8.500000e-01 1.000000 1.000000 0.986701 0.990000 1 9.800000e-01 1 OR10J1 26476 broad.mit.edu 37 1 159410194 159410194 + Missense_Mutation SNP G G T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:159410194G>T ENST00000423932.3 + 1 683 c.646G>T c.(646-648)Gtg>Ttg p.V216L RP11-550P17.5_ENST00000431862.1_RNA NM_012351.2 NP_036483.2 P30954 O10J1_HUMAN olfactory receptor, family 10, subfamily J, member 1 25 all_hematologic(112;0.0429) CAGTGTGCTGGTGCTTGTTGT 0.453000 0 SO:0001583 missense ENST00000423932.3 1 1 hg19 CCDS1185.1 . . . . . . . . . . G 15.51 2.855739 0.51376 . . ENSG00000196184 ENST00000423932 T 0.00036 8.86 4.42 3.49 0.39957 GPCR, rhodopsin-like superfamily (1); 0.000000 0.37437 N 0.002096 T 0.00073 0.0002 N 0.25245 0.725 0.09310 N 1 D 0.55385 0.971 P 0.58577 0.841 T 0.04440 -1.0951 10 0.45353 T 0.12 . 6.6645 0.23032 0.0986:0.1797:0.7217:0.0 . 216 P30954 O10J1_HUMAN L 216 ENSP00000399078:V216L ENSP00000399078:V216L V + 1 0 OR10J1 157676818 0.000000 0.05858 0.028000 0.17463 0.974000 0.67602 -0.144000 0.10280 1.155000 0.42497 0.650000 0.86243 GTG TCGA-OE-A75W-01A-12D-A32N-08 OR10J1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059020.1 1 0 1 161 411 0 107 0 0 0 0 107 2 0 0 0 0 0 2 1 1.000000 161 409 0 107 2 0 0 0 0 107 2 -20.000000 1 1 0 0 1 1 2 3 2.165351 0 0.570000 1.770000 0.572437 0.980000 8.600000e-01 1.000000 1.000000 0.970913 0.980000 1 9.200000e-01 1 CACNA1E 777 broad.mit.edu 37 1 181724500 181724500 + Missense_Mutation SNP C C G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:181724500C>G ENST00000367573.2 + 28 3956 c.3956C>G c.(3955-3957)aCg>aGg p.T1319R CACNA1E_ENST00000367567.4_Missense_Mutation_p.T926R|CACNA1E_ENST00000526775.1_Missense_Mutation_p.T1300R|CACNA1E_ENST00000360108.3_Missense_Mutation_p.T1300R|CACNA1E_ENST00000358338.5_Missense_Mutation_p.T1251R|CACNA1E_ENST00000357570.5_Missense_Mutation_p.T1270R|CACNA1E_ENST00000367570.1_Missense_Mutation_p.T1319R NM_001205293.1 NP_001192222.1 Q15878 CAC1E_HUMAN calcium channel, voltage-dependent, R type, alpha 1E subunit 204 TTTTATTGCACGGACAGTTCC 0.453000 0 SO:0001583 missense ENST00000367573.2 0 1 hg19 CCDS55664.1 . . . . . . . . . . C 26.1 4.707504 0.89018 . . ENSG00000198216 ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573 D;D;D;D;D;D;D 0.98474 -4.95;-4.95;-4.95;-4.95;-4.95;-4.95;-4.95 5.29 5.29 0.74685 Ion transport (1); 0.000000 0.85682 D 0.000000 D 0.98893 0.9625 M 0.78637 2.42 0.80722 D 1 D;D;D 0.89917 1.0;0.999;1.0 D;D;D 0.87578 0.998;0.982;0.998 D 0.99882 1.1115 10 0.87932 D 0 . 18.524 0.90965 0.0:1.0:0.0:0.0 . 1300;1319;1319 Q15878-2;Q15878;Q15878-3 .;CAC1E_HUMAN;. R 1319;1300;1270;1251;926;1300;1319 ENSP00000356542:T1319R;ENSP00000434814:T1300R;ENSP00000350183:T1270R;ENSP00000351101:T1251R;ENSP00000356539:T926R;ENSP00000353222:T1300R;ENSP00000356545:T1319R ENSP00000350183:T1270R T + 2 0 CACNA1E 179991123 1.000000 0.71417 0.934000 0.37439 0.977000 0.68977 7.676000 0.84012 2.468000 0.83385 0.650000 0.86243 ACG TCGA-OE-A75W-01A-12D-A32N-08 CACNA1E-003 KNOWN non_canonical_U12|basic|CCDS protein_coding protein_coding OTTHUMT00000090793.2 0 0 0 11 676 0 149 0 0 0 0 149 2 0 0 0 0 0 2 1 0.998205 11 667 0 147 2 0 0 0 0 149 2 -2.512174 1 1 0 0 1 1 2 3 2.165351 0 0.570000 1.770000 0.572437 0.050000 2.000000e-02 0.110000 0.060000 0.070560 0.050000 0 3.000000e-02 8.000000e-02 RGS16 6004 broad.mit.edu 37 1 182569575 182569575 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:182569575G>A ENST00000367558.5 - 5 609 c.461C>T c.(460-462)gCg>gTg p.A154V NM_002928.3 NP_002919.3 O15492 RGS16_HUMAN regulator of G-protein signaling 16 11 CCCCTGAGCCGCATCAAAGCA 0.602000 0 SO:0001583 missense ENST00000367558.5 0 1 hg19 CCDS1348.1 . . . . . . . . . . G 0.008 -1.927175 0.00493 . . ENSG00000143333 ENST00000367558 T 0.01998 4.51 5.38 -2.44 0.06502 Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1); 1.166690 0.05992 N 0.646171 T 0.01320 0.0043 N 0.13198 0.31 0.09310 N 1 B 0.06786 0.001 B 0.04013 0.001 T 0.47086 -0.9144 10 0.06891 T 0.86 . 5.0723 0.14613 0.4925:0.0:0.2363:0.2712 . 154 O15492 RGS16_HUMAN V 154 ENSP00000356529:A154V ENSP00000356529:A154V A - 2 0 RGS16 180836198 0.000000 0.05858 0.065000 0.19835 0.001000 0.01503 -0.510000 0.06328 -0.202000 0.10268 -1.223000 0.01593 GCG TCGA-OE-A75W-01A-12D-A32N-08 RGS16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000085188.1 0 0 0 6 564 0 98 0 4.601121e-01 0 132 0 98 2 0 0 0 0 0 2 1 0.963570 6 556 0 97 2 0 0 0 0 98 2 -1.819585 0 1 121412 1 28 1 1 2 3 2.165351 0 0.570000 1.770000 0.572437 0.030000 0 0.090000 0.040000 0.052300 0.030000 0 1.000000e-02 6.000000e-02 HMCN1 83872 broad.mit.edu 37 1 186120449 186120449 + Missense_Mutation SNP G G A rs148097981 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:186120449G>A ENST00000271588.4 + 94 14955 c.14726G>A c.(14725-14727)cGt>cAt p.R4909H HMCN1_ENST00000367492.2_Missense_Mutation_p.R4909H NM_031935.2 NP_114141.2 Q96RW7 HMCN1_HUMAN hemicentin 1 308 AGAATAATACGTGCCAAAATT 0.318000 0 SO:0001583 missense ENST00000271588.4 1 1 hg19 CCDS30956.1 . . . . . . . . . . G 8.309 0.821570 0.16678 0.0 4.65E-4 ENSG00000143341 ENST00000271588;ENST00000367492 T;T 0.29397 1.57;1.57 5.13 -0.313 0.12754 G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1); 0.353337 0.33272 N 0.005100 T 0.11452 0.0279 N 0.11201 0.11 0.27937 N 0.937675 B 0.02656 0.0 B 0.04013 0.001 T 0.26326 -1.0106 10 0.13853 T 0.58 . 5.0568 0.14537 0.6639:0.0:0.2126:0.1235 . 4909 Q96RW7 HMCN1_HUMAN H 4909 ENSP00000271588:R4909H;ENSP00000356462:R4909H ENSP00000271588:R4909H R + 2 0 HMCN1 184387072 1.000000 0.71417 0.714000 0.30535 0.586000 0.36452 3.507000 0.53371 -0.275000 0.09219 -1.311000 0.01308 CGT TCGA-OE-A75W-01A-12D-A32N-08 HMCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131848.1 1 0 1 89 249 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 1.000000 89 247 0 71 2 0 0 0 0 71 2 -20.000000 1 1 121412 23 44 1 1 2 3 2.165351 0 0.570000 1.770000 0.572437 0.920000 7.600000e-01 1.000000 1.000000 0.922361 0.920000 1 8.400000e-01 1 UBR4 23352 broad.mit.edu 37 1 19420503 19420503 + Missense_Mutation SNP C C G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:19420503C>G ENST00000375254.3 - 95 13904 c.13877G>C c.(13876-13878)gGa>gCa p.G4626A UBR4_ENST00000375217.2_Missense_Mutation_p.G4619A|UBR4_ENST00000543981.1_Missense_Mutation_p.G290A|UBR4_ENST00000375267.2_Missense_Mutation_p.G4626A|UBR4_ENST00000429347.2_Missense_Mutation_p.G149A|UBR4_ENST00000375226.2_Missense_Mutation_p.G4602A|UBR4_ENST00000375224.1_Missense_Mutation_p.G333A|UBR4_ENST00000467272.2_5'UTR NM_020765.2 NP_065816.2 Q5T4S7 UBR4_HUMAN ubiquitin protein ligase E3 component n-recognin 4 171 Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256) CTCCACCTCTCCAAAGGAAAG 0.468000 0 SO:0001583 missense ENST00000375254.3 0 1 hg19 CCDS189.1 . . . . . . . . . . C 32 5.134565 0.94517 . . ENSG00000127481 ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000375224;ENST00000429347;ENST00000543981 T;T;T;T;T;T;T 0.44881 0.91;0.91;0.91;0.91;0.91;0.91;0.91 5.87 5.87 0.94306 . 0.000000 0.85682 D 0.000000 T 0.71896 0.3394 M 0.88450 2.955 0.80722 D 1 D;D;D;D 0.76494 0.999;0.999;0.999;0.999 D;D;D;D 0.85130 0.995;0.995;0.997;0.992 T 0.76146 -0.3066 10 0.72032 D 0.01 . 18.7785 0.91922 0.0:1.0:0.0:0.0 . 290;149;4626;4602 B4DYV5;B4DPF6;Q5T4S7;Q5T4S7-3 .;.;UBR4_HUMAN;. A 4626;4626;4619;4602;333;149;290 ENSP00000364403:G4626A;ENSP00000364416:G4626A;ENSP00000364365:G4619A;ENSP00000364374:G4602A;ENSP00000364372:G333A;ENSP00000394173:G149A;ENSP00000444070:G290A ENSP00000364365:G4619A G - 2 0 UBR4 19293090 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.278000 0.78587 2.785000 0.95823 0.591000 0.81541 GGA TCGA-OE-A75W-01A-12D-A32N-08 UBR4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000007085.1 0 0 0 4 158 0 41 0 1.612476e-01 1 22 0 41 2 0 0 0 0 0 2 1 0.888428 4 156 0 41 2 0 0 0 0 41 2 -6.078562 1 1 0 0 1 0 0 0 2.104551 0 0.570000 1.770000 0.565041 0.090000 2.000000e-02 0.200000 0.080000 0.105247 0.090000 0 5.000000e-02 1.500000e-01 UBR4 23352 broad.mit.edu 37 1 19464627 19464627 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:19464627G>A ENST00000375254.3 - 60 8807 c.8780C>T c.(8779-8781)cCg>cTg p.P2927L UBR4_ENST00000375217.2_Missense_Mutation_p.P2920L|UBR4_ENST00000375267.2_Missense_Mutation_p.P2927L|UBR4_ENST00000375226.2_Missense_Mutation_p.P2903L NM_020765.2 NP_065816.2 Q5T4S7 UBR4_HUMAN ubiquitin protein ligase E3 component n-recognin 4 171 Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256) TGGTCCAGCCGGATGCCCCTC 0.542000 0 SO:0001583 missense ENST00000375254.3 0 1 hg19 CCDS189.1 . . . . . . . . . . G 15.55 2.867697 0.51588 . . ENSG00000127481 ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000425413;ENST00000417040 T;T;T;T 0.27256 1.74;1.74;1.68;1.7 5.83 4.89 0.63831 . 0.056992 0.64402 D 0.000001 T 0.25158 0.0611 L 0.57536 1.79 0.80722 D 1 P 0.36768 0.569 B 0.29663 0.105 T 0.05053 -1.0909 10 0.42905 T 0.14 . 15.9733 0.80036 0.0:0.0:0.8646:0.1354 . 2927 Q5T4S7 UBR4_HUMAN L 2927;2927;2920;2903;535;1613 ENSP00000364403:P2927L;ENSP00000364416:P2927L;ENSP00000364365:P2920L;ENSP00000364374:P2903L ENSP00000364365:P2920L P - 2 0 UBR4 19337214 1.000000 0.71417 0.967000 0.41034 0.793000 0.44817 7.308000 0.78929 2.770000 0.95276 0.655000 0.94253 CCG TCGA-OE-A75W-01A-12D-A32N-08 UBR4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000007085.1 0 0 0 4 152 0 19 0 0 0 0 19 2 0 0 0 0 0 2 1 0.888342 4 150 0 19 2 0 0 0 0 19 2 -3.150066 1 1 121410 5 34 1 0 0 0 2.104551 0 0.570000 1.770000 0.565041 0.090000 2.000000e-02 0.210000 0.090000 0.109226 0.090000 0 5.000000e-02 1.500000e-01 CR1 1378 broad.mit.edu 37 1 207790017 207790017 + Silent SNP C C T rs55775404 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:207790017C>T ENST00000367049.4 + 41 6759 c.6759C>T c.(6757-6759)tgC>tgT p.C2253C CR1_ENST00000367051.1_Silent_p.C1803C|CR1_ENST00000367052.1_Silent_p.C1803C|CR1_ENST00000367053.1_Silent_p.C1803C|CR1_ENST00000400960.2_Silent_p.C1803C NM_000651.4 NP_000642.3 P17927 CR1_HUMAN complement component (3b/4b) receptor 1 (Knops blood group) 82 CTTACGCATGCGACACCCACC 0.498000 0 SO:0001819 synonymous_variant ENST00000367049.4 0 1 hg19 CCDS44308.1 . . . . . . . . . . C 0.030 -1.342195 0.01277 . . ENSG00000203710 ENST00000529814 . . . 4.15 -1.35 0.09114 . . . . . T 0.31327 0.0793 . . . 0.20638 N 0.999873 . . . . . . T 0.33007 -0.9885 4 . . . . 8.0389 0.30511 0.0:0.5164:0.0:0.4836 rs55775404 . . . V 426 . . A + 2 0 CR1 205856640 0.319000 0.24607 0.014000 0.15608 0.037000 0.13140 -0.190000 0.09615 -0.233000 0.09797 -0.320000 0.08662 GCG TCGA-OE-A75W-01A-12D-A32N-08 CR1-012 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382527.1 0 0 0 6 686 0 122 0 0 0 0 122 2 0 0 0 0 0 2 1 0.963962 6 679 0 121 2 0 0 0 0 122 2 -2.014208 0 1 120864 4 41 1 1 2 3 2.165351 0 0.570000 1.770000 0.572437 0.020000 0 0.070000 0.040000 0.044310 0.020000 0 1.000000e-02 5.000000e-02 HSPG2 3339 broad.mit.edu 37 1 22186350 22186350 + Silent SNP G G A rs138980184 by1000genomes TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:22186350G>A ENST00000374695.3 - 41 5239 c.5160C>T c.(5158-5160)agC>agT p.S1720S NM_005529.5 NP_005520.4 P98160 PGBM_HUMAN heparan sulfate proteoglycan 2 127 Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) Palifermin(DB00039) GCTGGGTGCCGCTGGGCACAG 0.662000 0 SO:0001819 synonymous_variant ENST00000374695.3 0 1 hg19 CCDS30625.1 TCGA-OE-A75W-01A-12D-A32N-08 HSPG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000007598.1 0 0 0 4 101 0 26 0 0 0 1 0 26 2 0 0 0 0 0 2 1 0.891773 4 101 0 24 2 0 0 0 0 26 2 -6.996568 1 1 121094 98 47 1 0 0 0 2.104551 0 0.570000 1.770000 0.565041 0.140000 4.000000e-02 0.310000 0.140000 0.160914 0.140000 0 8.000000e-02 2.300000e-01 ARF1 375 broad.mit.edu 37 1 228285699 228285699 + Silent SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:228285699C>T ENST00000541182.1 + 5 793 c.531C>T c.(529-531)ctC>ctT p.L177L C1orf35_ENST00000472617.1_5'Flank|ARF1_ENST00000540651.1_Silent_p.L177L|ARF1_ENST00000272102.5_Silent_p.L177L|ARF1_ENST00000478424.1_3'UTR|MIR3620_ENST00000584469.1_RNA NM_001024227.1|NM_001024228.1 NP_001019398.1|NP_001019399.1 P84077 ARF1_HUMAN ADP-ribosylation factor 1 10 Prostate(94;0.0405) CCAATCAGCTCCGGAACCAGA 0.602000 0 SO:0001819 synonymous_variant ENST00000541182.1 1 1 hg19 CCDS1565.1 TCGA-OE-A75W-01A-12D-A32N-08 ARF1-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000091650.1 1 0 1 23 260 0 54 1 1 113 676 0 54 2 0 0 0 0 0 2 1 0.999999 22 249 0 53 2 0 0 0 0 54 2 -20.000000 1 1 0 0 1 1 2 3 2.165351 0 0.570000 1.770000 0.572437 0.280000 1.800000e-01 0.430000 0.290000 0.303269 0.280000 0 2.300000e-01 3.600000e-01 ZC3H12A 80149 broad.mit.edu 37 1 37948876 37948876 + Silent SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:37948876C>T ENST00000373087.6 + 6 1580 c.1464C>T c.(1462-1464)ggC>ggT p.G488G NM_025079.2 NP_079355.2 zinc finger CCCH-type containing 12A 21 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) CTGCCTTTGGCCGGGCCATGG 0.662000 0 SO:0001819 synonymous_variant ENST00000373087.6 0 1 hg19 CCDS417.1 TCGA-OE-A75W-01A-12D-A32N-08 ZC3H12A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000012154.2 0 0 0 6 578 0 189 0 3.360051e-01 0 102 0 189 2 0 0 0 0 0 2 1 0.963605 6 570 0 185 2 0 0 0 0 189 2 -1.790340 0 1 0 0 1 0 1 1 1.593368 1 0.570000 1.770000 0.403358 0.020000 0 0.050000 0.030000 0.030143 0.020000 0 1.000000e-02 4.000000e-02 MAST2 23139 broad.mit.edu 37 1 46491369 46491369 + Silent SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:46491369C>T ENST00000361297.2 + 16 2084 c.1801C>T c.(1801-1803)Ctg>Ttg p.L601L MAST2_ENST00000372009.2_Silent_p.L531L NM_015112.2 NP_055927.2 microtubule associated serine/threonine kinase 2 11 Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184) TGCCACTCTGCTGAAGAATAT 0.547000 0 SO:0001819 synonymous_variant ENST00000361297.2 1 1 hg19 CCDS41326.1 TCGA-OE-A75W-01A-12D-A32N-08 MAST2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000021977.1 1 0 0 124 154 0 69 0 8.896811e-01 1 6 0 69 2 0 0 0 0 0 2 1 1.000000 122 154 0 67 2 0 0 0 0 69 2 -20.000000 1 1 0 0 1 0 1 1 1.593368 1 0.570000 1.770000 0.403358 0.990000 9.100000e-01 1.000000 1.000000 0.984168 0.990000 1 9.500000e-01 1 ZCCHC11 23318 broad.mit.edu 37 1 52927392 52927392 + Missense_Mutation SNP C C A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:52927392C>A ENST00000371544.3 - 17 3381 c.3119G>T c.(3118-3120)aGa>aTa p.R1040I ZCCHC11_ENST00000257177.4_Missense_Mutation_p.R1040I|ZCCHC11_ENST00000371541.1_5'Flank NM_001009881.2|NM_015269.2 NP_001009881.1|NP_056084.1 Q5TAX3 TUT4_HUMAN zinc finger, CCHC domain containing 11 58 ACCTGGATGTCTCTTAAGAAT 0.214000 0 SO:0001583 missense ENST00000371544.3 0 1 hg19 CCDS30716.1 . . . . . . . . . . C 18.81 3.703685 0.68501 . . ENSG00000134744 ENST00000257177;ENST00000371544;ENST00000528642;ENST00000484723 T;T;T;T 0.46063 0.88;0.88;0.88;0.88 5.45 4.53 0.55603 Nucleotidyl transferase domain (1); 0.053333 0.64402 D 0.000001 T 0.49712 0.1573 L 0.49640 1.575 0.80722 D 1 B;D 0.63046 0.112;0.992 B;D 0.67382 0.18;0.951 T 0.53201 -0.8472 10 0.56958 D 0.05 . 3.6343 0.08143 0.229:0.5995:0.0:0.1715 . 799;1040 E9PKX1;Q5TAX3 .;TUT4_HUMAN I 1040;1040;969;799 ENSP00000257177:R1040I;ENSP00000360599:R1040I;ENSP00000433486:R969I;ENSP00000435256:R799I ENSP00000257177:R1040I R - 2 0 ZCCHC11 52699980 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.468000 0.60162 2.550000 0.86006 0.585000 0.79938 AGA TCGA-OE-A75W-01A-12D-A32N-08 ZCCHC11-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000022462.1 1 0 1 9 21 0 9 0 1.041667e-01 1 1 0 9 2 0 0 0 0 0 2 1 0.996000 9 20 0 9 2 0 0 0 0 9 2 -19.907490 1 1 0 0 1 0 1 1 1.593368 1 0.570000 1.770000 0.403358 0.710000 3.900000e-01 0.990000 1.000000 0.717604 0.710000 0 5.400000e-01 8.900000e-01 SSBP3 23648 broad.mit.edu 37 1 54708959 54708959 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr1:54708959C>T ENST00000371320.3 - 10 1075 c.665G>A c.(664-666)gGc>gAc p.G222D SSBP3_ENST00000326956.7_5'UTR|SSBP3_ENST00000357475.4_Missense_Mutation_p.G202D|SSBP3_ENST00000371319.3_Missense_Mutation_p.G195D|SSBP3_ENST00000417664.2_Missense_Mutation_p.G112D NM_145716.2 NP_663768.1 Q9BWW4 SSBP3_HUMAN single stranded DNA binding protein 3 11 TGGTCTCATGCCGCTGCCGTA 0.562000 0 SO:0001583 missense ENST00000371320.3 0 1 hg19 CCDS591.1 . . . . . . . . . . c 25.8 4.676502 0.88445 . . ENSG00000157216 ENST00000417664;ENST00000371320;ENST00000371319;ENST00000357475;ENST00000444533;ENST00000525990 . . . 3.94 3.94 0.45596 . 0.000000 0.85682 U 0.000000 T 0.78717 0.4327 M 0.75085 2.285 0.80722 D 1 D;P;P 0.89917 1.0;0.951;0.866 D;P;P 0.97110 1.0;0.743;0.686 T 0.81534 -0.0889 9 0.59425 D 0.04 -1.6526 17.3039 0.87189 0.0:1.0:0.0:0.0 . 195;202;222 Q9BWW4-2;Q9BWW4-3;Q9BWW4 .;.;SSBP3_HUMAN D 112;222;195;202;53;85 . ENSP00000350067:G202D G - 2 0 SSBP3 54481547 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 6.969000 0.76092 2.493000 0.84123 0.479000 0.44913 GGC TCGA-OE-A75W-01A-12D-A32N-08 SSBP3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000022721.1 0 0 0 6 924 0 296 0 8.153054e-02 0 61 0 296 2 0 0 0 0 0 2 1 0.961700 6 898 0 296 2 0 0 0 0 296 2 -1.725707 0 1 0 0 1 0 1 1 1.593368 1 0.570000 1.770000 0.403358 0.010000 0 0.040000 0.020000 0.018688 0.010000 0 0 3.000000e-02 TASP1 55617 broad.mit.edu 37 20 13514683 13514683 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr20:13514683C>T ENST00000337743.4 - 9 901 c.781G>A c.(781-783)Ggg>Agg p.G261R TASP1_ENST00000539805.1_Intron|TASP1_ENST00000480436.1_5'UTR NM_017714.2 NP_060184.2 Q9H6P5 TASP1_HUMAN taspase, threonine aspartase, 1 31 CCAACTCTCCCCGGATGTTTC 0.463000 0 SO:0001583 missense ENST00000337743.4 1 1 hg19 CCDS13116.1 . . . . . . . . . . C 29.1 4.976123 0.92982 . . ENSG00000089123 ENST00000378157;ENST00000337743;ENST00000455532 D;D 0.97529 -4.42;-4.42 5.66 5.66 0.87406 . 0.000000 0.85682 D 0.000000 D 0.99180 0.9716 H 0.97829 4.085 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.98931 1.0787 10 0.87932 D 0 -9.528 19.3476 0.94372 0.0:1.0:0.0:0.0 . 261;238 Q9H6P5;Q5JWM4 TASP1_HUMAN;. R 238;261;238 ENSP00000338624:G261R;ENSP00000400580:G238R ENSP00000338624:G261R G - 1 0 TASP1 13462683 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 7.031000 0.76491 2.666000 0.90696 0.563000 0.77884 GGG TCGA-OE-A75W-01A-12D-A32N-08 TASP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078041.2 1 0 0 39 548 0 108 0 9.930690e-02 0 8 0 108 2 0 0 0 0 0 2 1 1.000000 38 542 0 105 2 0 0 0 0 108 2 -2.690403 1 1 0 0 1 0 0 0 2.102693 0 0.570000 1.770000 0.565041 0.220000 1.600000e-01 0.310000 0.230000 0.235261 0.220000 0 1.900000e-01 2.700000e-01 CBFA2T2 9139 broad.mit.edu 37 20 32232202 32232202 + Missense_Mutation SNP A A T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr20:32232202A>T ENST00000346541.3 + 12 2102 c.1565A>T c.(1564-1566)aAt>aTt p.N522I CBFA2T2_ENST00000397800.1_Missense_Mutation_p.N493I|CBFA2T2_ENST00000543126.1_Missense_Mutation_p.N70I|CBFA2T2_ENST00000342704.6_Missense_Mutation_p.N513I|CBFA2T2_ENST00000492345.1_Missense_Mutation_p.N493I|CBFA2T2_ENST00000359606.3_Missense_Mutation_p.N532I|CBFA2T2_ENST00000375279.2_Missense_Mutation_p.N522I NM_005093.3 NP_005084.1 O43439 MTG8R_HUMAN core-binding factor, runt domain, alpha subunit 2; translocated to, 2 20 AGTGGCTGCAATATCGCGCGA 0.602000 Esophageal Squamous(174;142 1955 14837 21276 28041) 0 SO:0001583 missense ENST00000346541.3 1 1 hg19 CCDS13221.1 . . . . . . . . . . A 31 5.091645 0.94149 . . ENSG00000078699 ENST00000397803;ENST00000375279;ENST00000342704;ENST00000346541;ENST00000397800;ENST00000359606;ENST00000543126 T;T;T;T;T 0.51325 0.71;0.72;0.71;0.72;1.3 5.79 5.79 0.91817 Zinc finger, MYND-type (3); 0.000000 0.85682 D 0.000000 T 0.70325 0.3211 M 0.76838 2.35 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.997 T 0.74518 -0.3639 10 0.87932 D 0 -4.7166 16.1193 0.81336 1.0:0.0:0.0:0.0 . 522;513 O43439;F8W6D7 MTG8R_HUMAN;. I 296;522;513;522;493;532;70 ENSP00000364428:N522I;ENSP00000345810:N513I;ENSP00000262653:N522I;ENSP00000380902:N493I;ENSP00000352622:N532I ENSP00000345810:N513I N + 2 0 CBFA2T2 31695863 1.000000 0.71417 0.996000 0.52242 0.903000 0.53119 9.339000 0.96797 2.201000 0.70794 0.533000 0.62120 AAT TCGA-OE-A75W-01A-12D-A32N-08 CBFA2T2-201 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000078708.2 1 0 1 125 367 0 105 1 9.998292e-01 13 27 0 105 2 0 0 0 0 0 2 1 1.000000 124 362 0 104 2 0 0 0 0 105 2 -20.000000 1 1 0 0 1 0 0 0 2.102693 0 0.570000 1.770000 0.565041 0.870000 7.400000e-01 1.000000 0.880000 0.881970 0.870000 1 8.000000e-01 9.500000e-01 CDH4 1002 broad.mit.edu 37 20 60448850 60448850 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr20:60448850G>A ENST00000360469.5 + 7 1032 c.944G>A c.(943-945)cGg>cAg p.R315Q CDH4_ENST00000543233.1_Missense_Mutation_p.R241Q NM_001794.3 NP_001785.2 P55283 CADH4_HUMAN cadherin 4, type 1, R-cadherin (retinal) 74 BRCA - Breast invasive adenocarcinoma(19;2.36e-08) GGGATGGTGCGGTACCGGATC 0.612000 0 SO:0001583 missense ENST00000360469.5 0 1 hg19 CCDS13488.1 . . . . . . . . . . G 20.2 3.949030 0.73787 0.0 1.16E-4 ENSG00000179242 ENST00000360469;ENST00000536643;ENST00000543233 T;T 0.53206 0.63;0.63 4.92 3.97 0.46021 Cadherin (4);Cadherin-like (1); 0.230798 0.40640 N 0.001048 T 0.45816 0.1361 L 0.58354 1.805 0.36334 D 0.859075 D 0.53745 0.962 P 0.46208 0.507 T 0.54886 -0.8226 9 . . . . 8.4155 0.32668 0.0789:0.0:0.7685:0.1527 . 315 P55283 CADH4_HUMAN Q 315;223;241 ENSP00000353656:R315Q;ENSP00000443301:R241Q . R + 2 0 CDH4 59882245 1.000000 0.71417 0.967000 0.41034 0.735000 0.41995 6.559000 0.73946 1.068000 0.40764 0.585000 0.79938 CGG TCGA-OE-A75W-01A-12D-A32N-08 CDH4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079965.2 0 0 0 5 602 0 116 0 0 0 0 116 2 0 0 0 0 0 2 1 0.937501 5 601 0 116 2 0 0 0 0 116 2 -2.515517 1 1 121410 5 39 1 0 0 0 2.102693 0 0.570000 1.770000 0.565041 0.020000 0 0.070000 0.030000 0.033465 0.020000 0 1.000000e-02 5.000000e-02 COL6A2 1292 broad.mit.edu 37 21 47532333 47532333 + Silent SNP C C A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr21:47532333C>A ENST00000300527.4 + 3 660 c.556C>A c.(556-558)Cgg>Agg p.R186R COL6A2_ENST00000357838.4_Silent_p.R186R|COL6A2_ENST00000397763.1_Silent_p.R186R|COL6A2_ENST00000310645.5_Silent_p.R186R|COL6A2_ENST00000409416.1_Silent_p.R186R|COL6A2_ENST00000460886.1_3'UTR NM_001849.3 NP_001840.3 P12110 CO6A2_HUMAN collagen, type VI, alpha 2 43 Breast(49;0.245) GGAGGGCATCCGGCTCTTCGC 0.701000 0 SO:0001819 synonymous_variant ENST00000300527.4 0 1 hg19 CCDS13728.1 TCGA-OE-A75W-01A-12D-A32N-08 COL6A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206971.1 0 0 0 4 82 0 43 0 9.997067e-01 0 519 0 43 2 0 0 0 0 0 2 1 0.892036 4 82 0 41 2 0 0 0 0 43 2 -7.546148 1 1 0 0 1 0 1 1 1.552496 1 0.570000 1.770000 0.398601 0.120000 4.000000e-02 0.270000 0.120000 0.140065 0.120000 0 7.000000e-02 2.000000e-01 DGCR8 54487 broad.mit.edu 37 22 20096497 20096497 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr22:20096497G>A ENST00000351989.3 + 13 2638 c.2209G>A c.(2209-2211)Gag>Aag p.E737K AC006547.8_ENST00000412713.1_RNA|DGCR8_ENST00000407755.1_Missense_Mutation_p.E704K|DGCR8_ENST00000383024.2_Missense_Mutation_p.E704K NM_022720.6 NP_073557.3 Q8WYQ5 DGCR8_HUMAN DGCR8 microprocessor complex subunit 22 Colorectal(54;0.0993) CAAGCTCCAAGAGGAGATGAA 0.577000 0 SO:0001583 missense ENST00000351989.3 0 1 hg19 CCDS13773.1 . . . . . . . . . . G 32 5.181797 0.94885 . . ENSG00000128191 ENST00000351989;ENST00000383024;ENST00000407755 T;T;T 0.33216 1.42;1.51;1.51 5.22 5.22 0.72569 . 0.048942 0.85682 D 0.000000 T 0.45115 0.1326 L 0.34521 1.04 0.80722 D 1 D;D 0.67145 0.996;0.99 D;P 0.76071 0.987;0.824 T 0.21314 -1.0249 10 0.33141 T 0.24 -10.5121 17.5395 0.87843 0.0:0.0:1.0:0.0 . 704;737 Q8WYQ5-3;Q8WYQ5 .;DGCR8_HUMAN K 737;704;704 ENSP00000263209:E737K;ENSP00000372488:E704K;ENSP00000384726:E704K ENSP00000263209:E737K E + 1 0 DGCR8 18476497 1.000000 0.71417 1.000000 0.80357 0.928000 0.56348 9.096000 0.94182 2.428000 0.82296 0.462000 0.41574 GAG TCGA-OE-A75W-01A-12D-A32N-08 DGCR8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318654.1 0 0 0 9 351 0 70 0 1.836840e-01 0 28 0 70 2 0 0 0 0 0 2 1 0.994142 8 349 0 70 2 0 0 0 0 70 2 -3.591107 1 1 0 0 1 2 2 4 2.275507 0 0.570000 1.770000 0.595370 0.090000 4.000000e-02 1.000000 0.090000 0.182554 0.090000 0 6.000000e-02 1.500000e-01 ZNF70 7621 broad.mit.edu 37 22 24086056 24086056 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr22:24086056G>A ENST00000341976.3 - 2 1732 c.1272C>T c.(1270-1272)tgC>tgT p.C424C NM_021916.2 NP_068735.1 Q9UC06 ZNF70_HUMAN zinc finger protein 70 21 AGGACTTGCCGCACAGATTGC 0.547000 0 SO:0001819 synonymous_variant ENST00000341976.3 0 1 hg19 CCDS13812.1 TCGA-OE-A75W-01A-12D-A32N-08 ZNF70-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319881.1 0 0 0 6 857 1 181 0 0 0 1 181 2 0 0 0 0 0 2 0 0.015404 8 844 1 179 17 0 0 0 1 181 2 -1.930780 0 1 121412 1 33 1 0.570000 1.770000 0 0 CRYBB1 1414 broad.mit.edu 37 22 27003917 27003917 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr22:27003917C>T ENST00000215939.2 - 4 498 c.368G>A c.(367-369)cGc>cAc p.R123H NM_001887.3 NP_001878.1 P53674 CRBB1_HUMAN crystallin, beta B1 31 TGTGTTCCAGCGAGGGTACTC 0.592000 0 SO:0001583 missense ENST00000215939.2 1 1 hg19 CCDS13840.1 . . . . . . . . . . C 24.9 4.582400 0.86748 . . ENSG00000100122 ENST00000215939 T 0.76060 -0.99 4.4 3.36 0.38483 Beta/gamma crystallin (5);Gamma-crystallin-related (1); 0.105598 0.64402 D 0.000003 T 0.82157 0.4976 L 0.56199 1.76 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 D 0.83373 0.0008 10 0.66056 D 0.02 . 13.3936 0.60836 0.0:0.8408:0.1592:0.0 . 123 P53674 CRBB1_HUMAN H 123 ENSP00000215939:R123H ENSP00000215939:R123H R - 2 0 CRYBB1 25333917 1.000000 0.71417 0.995000 0.50966 0.995000 0.86356 2.906000 0.48735 1.041000 0.40125 0.585000 0.79938 CGC TCGA-OE-A75W-01A-12D-A32N-08 CRYBB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320767.1 1 0 1 52 215 0 56 0 3.911439e-02 0 2 0 56 2 0 0 0 0 0 2 1 1.000000 51 212 0 56 2 0 0 0 0 56 2 -20.000000 1 1 0 0 1 0 1 1 1.977177 0 0.570000 1.770000 0.529798 0.620000 4.700000e-01 0.780000 0.620000 0.630119 0.620000 0 5.400000e-01 7.000000e-01 L3MBTL2 83746 broad.mit.edu 37 22 41625557 41625557 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr22:41625557G>A ENST00000216237.5 + 16 2060 c.1902G>A c.(1900-1902)ccG>ccA p.P634P CHADL_ENST00000216241.9_3'UTR NM_031488.4 NP_113676.2 Q969R5 LMBL2_HUMAN l(3)mbt-like 2 (Drosophila) 24 AAAGAATCCCGCCCACTAAGA 0.542000 0 SO:0001819 synonymous_variant ENST00000216237.5 1 1 hg19 CCDS14011.1 TCGA-OE-A75W-01A-12D-A32N-08 L3MBTL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320613.1 1 0 1 62 130 0 44 1 1 31 62 0 44 2 0 0 0 0 0 2 1 1.000000 62 129 0 44 2 0 0 0 0 44 2 -20.000000 1 1 121410 1 31 1 0 1 1 1.977177 0 0.570000 1.770000 0.529798 0.990000 8.200000e-01 1.000000 1.000000 0.973512 0.990000 1 9.200000e-01 1 ALG12 79087 broad.mit.edu 37 22 50303671 50303671 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr22:50303671C>T ENST00000330817.6 - 5 808 c.535G>A c.(535-537)Gcc>Acc p.A179T NM_024105.3 NP_077010.1 Q9BV10 ALG12_HUMAN ALG12, alpha-1,6-mannosyltransferase 12 all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164) ACGATGATGGCGAAGGCTGAC 0.637000 0 SO:0001583 missense ENST00000330817.6 1 1 hg19 CCDS14081.1 . . . . . . . . . . C 15.80 2.939391 0.52972 . . ENSG00000182858 ENST00000330817 T 0.64991 -0.13 4.44 3.42 0.39159 . 0.161366 0.53938 D 0.000044 T 0.65729 0.2719 L 0.58302 1.8 0.42474 D 0.992838 D 0.54772 0.968 P 0.51079 0.658 T 0.66559 -0.5893 10 0.35671 T 0.21 -16.6342 13.9771 0.64279 0.0:0.9236:0.0:0.0764 . 179 Q9BV10 ALG12_HUMAN T 179 ENSP00000333813:A179T ENSP00000333813:A179T A - 1 0 ALG12 48689675 0.995000 0.38212 0.008000 0.14137 0.008000 0.06430 3.331000 0.52075 1.166000 0.42689 -0.205000 0.12727 GCC TCGA-OE-A75W-01A-12D-A32N-08 ALG12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317405.2 1 0 0 22 85 0 26 1 9.290455e-01 5 15 0 26 2 0 0 0 0 0 2 1 1.000000 22 85 0 26 2 0 0 0 0 26 2 -20.000000 1 1 0 0 1 0 1 1 1.977177 0 0.570000 1.770000 0.529798 0.650000 4.300000e-01 0.910000 0.650000 0.671167 0.650000 0 5.400000e-01 7.900000e-01 SCN3A 6328 broad.mit.edu 37 2 165997338 165997338 + Silent SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr2:165997338C>T ENST00000360093.3 - 13 2333 c.1842G>A c.(1840-1842)ccG>ccA p.P614P SCN3A_ENST00000283254.7_Silent_p.P614P|SCN3A_ENST00000409101.3_Silent_p.P614P NM_001081677.1 NP_001075146.1 Q9NY46 SCN3A_HUMAN sodium channel, voltage-gated, type III, alpha subunit 120 Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909) CATGTCTGTGCGGCACAAACA 0.507000 0 SO:0001819 synonymous_variant ENST00000360093.3 0 1 hg19 TCGA-OE-A75W-01A-12D-A32N-08 SCN3A-201 KNOWN basic|appris_candidate_longest protein_coding protein_coding 0 0 0 6 247 0 35 0 0 0 0 35 2 0 0 0 0 0 2 1 0.962825 6 241 0 34 2 0 0 0 0 35 2 -2.590124 1 1 121410 1 35 1 1 2 3 2.171289 0 0.570000 1.770000 0.572437 0.080000 3.000000e-02 0.190000 0.080000 0.105436 0.080000 0 5.000000e-02 1.300000e-01 NOSTRIN 115677 broad.mit.edu 37 2 169716142 169716142 + Missense_Mutation SNP G G C TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr2:169716142G>C ENST00000317647.7 + 13 1403 c.1174G>C c.(1174-1176)Gaa>Caa p.E392Q NOSTRIN_ENST00000397206.2_Missense_Mutation_p.E314Q|NOSTRIN_ENST00000445023.2_Missense_Mutation_p.E314Q|NOSTRIN_ENST00000421711.2_Missense_Mutation_p.E364Q|NOSTRIN_ENST00000397209.2_Missense_Mutation_p.E364Q|NOSTRIN_ENST00000444448.2_Missense_Mutation_p.E449Q|NOSTRIN_ENST00000458381.2_Missense_Mutation_p.E449Q NM_001039724.3 NP_001034813.2 Q8IVI9 NOSTN_HUMAN nitric oxide synthase trafficking 9 CAGGTGGAGGGAAAAGGTAAC 0.438000 0 SO:0001583 missense ENST00000317647.7 0 1 hg19 CCDS42771.1 . . . . . . . . . . G 21.3 4.127768 0.77549 . . ENSG00000163072 ENST00000458381;ENST00000444448;ENST00000317647;ENST00000445023;ENST00000397206;ENST00000397209;ENST00000421711 T;T;T;T;T;T;T 0.38560 1.3;1.3;1.13;1.32;1.32;1.33;1.33 5.3 5.3 0.74995 . 0.162747 0.53938 D 0.000056 T 0.59649 0.2209 M 0.75447 2.3 0.80722 D 1 D;D;D;D;D;D 0.64830 0.98;0.991;0.994;0.994;0.969;0.987 P;P;P;P;P;P 0.58331 0.663;0.837;0.798;0.783;0.599;0.776 T 0.56275 -0.8006 10 0.28530 T 0.3 -0.2101 16.7834 0.85568 0.0:0.0:1.0:0.0 . 364;314;449;286;392;449 Q8IVI9-2;Q8IVI9-3;B3KSF5;D3DPB9;Q8IVI9;E7EPT9 .;.;.;.;NOSTN_HUMAN;. Q 449;449;392;314;314;364;364 ENSP00000402140:E449Q;ENSP00000394051:E449Q;ENSP00000318921:E392Q;ENSP00000404413:E314Q;ENSP00000380390:E314Q;ENSP00000380392:E364Q;ENSP00000401316:E364Q ENSP00000318921:E392Q E + 1 0 NOSTRIN 169424388 1.000000 0.71417 1.000000 0.80357 0.775000 0.43874 6.770000 0.74990 2.630000 0.89119 0.655000 0.94253 GAA TCGA-OE-A75W-01A-12D-A32N-08 NOSTRIN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000333356.4 0 0 0 6 521 0 83 0 3.799201e-01 0 102 0 83 2 0 0 0 0 0 2 1 0.964109 6 516 0 81 2 0 0 0 0 83 2 -2.919711 1 1 0 0 1 1 2 3 2.171289 0 0.570000 1.770000 0.572437 0.030000 0 0.090000 0.040000 0.055877 0.030000 0 2.000000e-02 7.000000e-02 TTN 7273 broad.mit.edu 37 2 179412983 179412983 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr2:179412983C>T ENST00000591111.1 - 289 88671 c.88447G>A c.(88447-88449)Gat>Aat p.D29483N RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D28556N|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.D22059N|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.D31124N|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D22251N|TTN_ENST00000359218.5_Missense_Mutation_p.D22184N|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTGCTAGTATCAACAACATCA 0.483000 0 SO:0001583 missense ENST00000591111.1 0 1 hg19 . . . . . . . . . . C 19.66 3.869050 0.72065 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.56776 0.44;0.44;0.44;0.44 5.65 5.65 0.86999 Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.69860 0.3158 L 0.50919 1.6 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.999;0.999;0.999;0.999 T 0.71144 -0.4678 9 0.87932 D 0 . 19.7272 0.96168 0.0:1.0:0.0:0.0 . 22059;22184;22251;29483 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN N 28556;22059;22251;22184;22056 ENSP00000343764:D28556N;ENSP00000434586:D22059N;ENSP00000340554:D22251N;ENSP00000352154:D22184N ENSP00000340554:D22251N D - 1 0 TTN 179121229 1.000000 0.71417 0.980000 0.43619 0.745000 0.42441 7.818000 0.86416 2.646000 0.89796 0.655000 0.94253 GAT TCGA-OE-A75W-01A-12D-A32N-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 0 0 0 14 652 0 149 0 0 0 0 149 2 0 0 0 0 0 2 1 0.999731 13 645 0 148 2 0 0 0 0 149 2 -2.624656 1 1 0 0 1 0 0 0 2.059777 0 0.570000 1.770000 0.552130 0.060000 3.000000e-02 0.120000 0.070000 0.075555 0.060000 0 4.000000e-02 1.000000e-01 TTN 7273 broad.mit.edu 37 2 179597812 179597812 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr2:179597812C>T ENST00000591111.1 - 53 15364 c.15140G>A c.(15139-15141)cGc>cAc p.R5047H TTN_ENST00000342992.6_Missense_Mutation_p.R4120H|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.R5364H|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) ATCCACGTTGCGCAAGGGTTT 0.453000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . C 10.90 1.480091 0.26598 2.58E-4 0.0 ENSG00000155657 ENST00000342992 T 0.68331 -0.32 6.17 5.29 0.74685 Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.71576 0.3356 M 0.75884 2.315 0.80722 D 1 D 0.57571 0.98 P 0.48921 0.595 T 0.75557 -0.3276 9 0.87932 D 0 . 12.1123 0.53846 0.0:0.8742:0.0:0.1258 . 5047 Q8WZ42 TITIN_HUMAN H 4120 ENSP00000343764:R4120H ENSP00000343764:R4120H R - 2 0 TTN 179306057 1.000000 0.71417 1.000000 0.80357 0.638000 0.38207 3.216000 0.51176 2.941000 0.99782 0.655000 0.94253 CGC TCGA-OE-A75W-01A-12D-A32N-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 1 28 96 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 1.000000 28 93 0 28 2 0 0 0 0 30 2 -20.000000 1 1 120876 18 41 1 1 2 3 2.168169 0 0.570000 1.770000 0.572437 0.790000 5.600000e-01 1.000000 1.000000 0.804195 0.790000 0 6.700000e-01 9.400000e-01 TTN 7273 broad.mit.edu 37 2 179641336 179641336 + Missense_Mutation SNP C C T rs150737838 by1000genomes TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr2:179641336C>T ENST00000591111.1 - 28 5479 c.5255G>A c.(5254-5256)cGt>cAt p.R1752H TTN_ENST00000360870.5_Missense_Mutation_p.R1752H|RP11-88L24.4_ENST00000582038.2_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R1752H|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R1706H|TTN_ENST00000589042.1_Missense_Mutation_p.R1752H|TTN_ENST00000342175.6_Missense_Mutation_p.R1706H|TTN_ENST00000359218.5_Missense_Mutation_p.R1706H|TTN-AS1_ENST00000584485.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) ATTGATCATACGGAGCCTGTT 0.478000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 C 13.20 2.166946 0.38217 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870 T;T;T;T;T 0.68479 -0.33;-0.33;-0.33;-0.33;-0.33 5.05 5.05 0.67936 Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.76877 0.4049 L 0.41079 1.255 0.38775 D 0.954622 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.91635 0.999;0.999;0.999;0.999;0.999 T 0.80984 -0.1138 9 0.87932 D 0 . 18.3911 0.90484 0.0:1.0:0.0:0.0 . 1706;1706;1706;1752;1752 D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6 .;.;.;TITIN_HUMAN;. H 1752;1706;1706;1706;1706;1752 ENSP00000343764:R1752H;ENSP00000434586:R1706H;ENSP00000340554:R1706H;ENSP00000352154:R1706H;ENSP00000354117:R1752H ENSP00000340554:R1706H R - 2 0 TTN 179349581 1.000000 0.71417 0.980000 0.43619 0.972000 0.66771 4.864000 0.62990 2.363000 0.80096 0.561000 0.74099 CGT TCGA-OE-A75W-01A-12D-A32N-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 1 92 183 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 1.000000 91 182 0 70 2 0 0 0 0 71 2 -20.000000 1 1 121408 25 45 1 1 2 3 2.168169 0 0.570000 1.770000 0.572437 0.990000 9.800000e-01 1.000000 1.000000 0.998847 0.990000 1 9.900000e-01 1 MYT1L 23040 broad.mit.edu 37 2 1982980 1982980 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr2:1982980C>T ENST00000399161.2 - 8 856 c.109G>A c.(109-111)Gac>Aac p.D37N MYT1L_ENST00000428368.2_Missense_Mutation_p.D37N NM_015025.2 NP_055840.2 Q9UL68 MYT1L_HUMAN myelin transcription factor 1-like 97 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.037)|all_epithelial(98;0.241) CCACTGCCGTCACAGCCAGGG 0.512000 0 SO:0001583 missense ENST00000399161.2 1 1 hg19 . . . . . . . . . . C 20.1 3.935617 0.73442 . . ENSG00000186487 ENST00000399161;ENST00000295067;ENST00000428368 T;T 0.43688 0.94;0.94 5.18 5.18 0.71444 . 0.138574 0.46442 D 0.000293 T 0.52517 0.1739 N 0.24115 0.695 0.58432 D 0.999996 D;D 0.69078 0.997;0.996 D;D 0.77004 0.989;0.981 T 0.55749 -0.8092 10 0.51188 T 0.08 -38.9835 18.6852 0.91560 0.0:1.0:0.0:0.0 . 37;37 Q9UL68;Q9UL68-4 MYT1L_HUMAN;. N 37 ENSP00000382114:D37N;ENSP00000396103:D37N ENSP00000295067:D37N D - 1 0 MYT1L 1961987 1.000000 0.71417 0.999000 0.59377 0.994000 0.84299 6.604000 0.74150 2.405000 0.81733 0.655000 0.94253 GAC TCGA-OE-A75W-01A-12D-A32N-08 MYT1L-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000322493.1 1 0 1 31 59 0 15 0 0 0 0 15 2 0 0 0 0 0 2 1 1.000000 31 59 0 14 2 0 0 0 0 15 2 -20.000000 1 1 0 0 1 0 1 1 1.536997 1 0.570000 1.770000 0.398601 0.830000 6.100000e-01 0.990000 0.850000 0.829425 0.830000 0 7.200000e-01 9.300000e-01 NDUFB3 4709 broad.mit.edu 37 2 201943722 201943722 + Silent SNP A A G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 A G A A Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr2:201943722A>G ENST00000237889.4 + 2 440 c.117A>G c.(115-117)aaA>aaG p.K39K NDUFB3_ENST00000433898.1_Silent_p.K39K|RNU6-1206P_ENST00000516339.1_RNA|NDUFB3_ENST00000454214.1_Silent_p.K39K NM_001257102.1|NM_002491.2 NP_001244031.1|NP_002482.1 O43676 NDUB3_HUMAN NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3, 12kDa 3 TGGCTGCAAAAGGGCTAAGGG 0.393000 0 SO:0001819 synonymous_variant ENST00000237889.4 0 1 hg19 CCDS2336.1 TCGA-OE-A75W-01A-12D-A32N-08 NDUFB3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256277.1 0 0 0 4 215 0 29 0 9.979281e-01 1 817 0 29 2 0 0 0 0 0 2 1 0.885690 4 211 0 29 2 0 0 0 0 29 2 -2.995412 1 1 0 0 1 1 2 3 2.168169 0 0.570000 1.770000 0.572437 0.070000 1.000000e-02 0.170000 0.060000 0.088540 0.070000 0 3.000000e-02 1.200000e-01 NRP2 8828 broad.mit.edu 37 2 206581077 206581077 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr2:206581077C>T ENST00000357785.5 + 3 443 c.412C>T c.(412-414)Cgc>Tgc p.R138C NRP2_ENST00000360409.3_Missense_Mutation_p.R138C|NRP2_ENST00000417189.1_Missense_Mutation_p.R138C|NRP2_ENST00000540841.1_Missense_Mutation_p.R138C|NRP2_ENST00000355117.4_Missense_Mutation_p.R138C|NRP2_ENST00000357118.4_Missense_Mutation_p.R138C|NRP2_ENST00000540178.1_Missense_Mutation_p.R138C|NRP2_ENST00000272849.3_Missense_Mutation_p.R138C|NRP2_ENST00000412873.2_Missense_Mutation_p.R138C Q99435 NELL2_HUMAN neuropilin 2 52 CTTCTCTCTGCGCTACGAGAT 0.617000 0 SO:0001583 missense ENST00000357785.5 0 1 hg19 CCDS46496.1 . . . . . . . . . . C 34 5.331934 0.95733 . . ENSG00000118257 ENST00000360409;ENST00000540178;ENST00000540841;ENST00000355117;ENST00000417189;ENST00000357118;ENST00000357785;ENST00000412873;ENST00000272849 T;T;T;T;T;T;T;T;T 0.19532 2.14;2.14;2.14;2.14;2.14;2.14;2.14;2.14;2.14 6.17 6.17 0.99709 CUB (5); 0.000000 0.85682 D 0.000000 T 0.59142 0.2172 M 0.91920 3.255 0.80722 D 1 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0 D;D;P;D;D;D 0.79108 0.983;0.983;0.9;0.992;0.992;0.971 T 0.65187 -0.6229 10 0.87932 D 0 -22.1386 20.8794 0.99867 0.0:1.0:0.0:0.0 . 138;138;138;138;138;138 O60462-2;O60462-3;O60462;O60462-4;O60462-5;E9PF66 .;.;NRP2_HUMAN;.;.;. C 138 ENSP00000353582:R138C;ENSP00000439658:R138C;ENSP00000439261:R138C;ENSP00000347238:R138C;ENSP00000387519:R138C;ENSP00000349632:R138C;ENSP00000350432:R138C;ENSP00000407626:R138C;ENSP00000272849:R138C ENSP00000272849:R138C R + 1 0 NRP2 206289322 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 7.818000 0.86416 2.941000 0.99782 0.655000 0.94253 CGC TCGA-OE-A75W-01A-12D-A32N-08 NRP2-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000336467.1 0 0 0 6 520 0 95 0 5.946687e-04 0 3 0 95 2 0 0 0 0 0 2 1 0.964106 6 515 0 91 2 0 0 0 0 95 2 -2.773521 1 1 121412 1 29 1 1 2 3 2.168169 0 0.570000 1.770000 0.572437 0.040000 0 0.090000 0.040000 0.055967 0.040000 0 2.000000e-02 7.000000e-02 CXCR1 3577 broad.mit.edu 37 2 219029099 219029099 + Missense_Mutation SNP C C T rs56030518 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr2:219029099C>T ENST00000295683.2 - 2 956 c.836G>A c.(835-837)cGc>cAc p.R279H NM_000634.2 NP_000625.1 P25024 CXCR1_HUMAN chemokine (C-X-C motif) receptor 1 13 Ketoprofen(DB01009) GTTGTTGCGGCGCTCACAGCT 0.572000 0 SO:0001583 missense ENST00000295683.2 1 1 hg19 CCDS2409.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 C 15.25 2.778988 0.49891 0.0 3.49E-4 ENSG00000163464 ENST00000295683;ENST00000421691 T 0.71934 -0.61 4.89 3.94 0.45596 GPCR, rhodopsin-like superfamily (1); 0.392430 0.28482 N 0.015186 T 0.65923 0.2738 M 0.62154 1.92 0.31690 N 0.641996 P 0.40083 0.702 B 0.37780 0.258 T 0.72276 -0.4341 10 0.33940 T 0.23 . 13.1692 0.59589 0.1603:0.8397:0.0:0.0 rs56030518 279 P25024 CXCR1_HUMAN H 279;223 ENSP00000295683:R279H ENSP00000295683:R279H R - 2 0 CXCR1 218737344 0.005000 0.15991 0.967000 0.41034 0.149000 0.21700 1.489000 0.35562 2.406000 0.81754 0.561000 0.74099 CGC TCGA-OE-A75W-01A-12D-A32N-08 CXCR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256773.2 1 0 1 116 312 0 90 0 0 0 0 90 2 0 0 0 0 0 2 1 1.000000 116 308 0 90 2 0 0 0 0 90 2 -3.017840 1 1 121412 23 46 1 1 2 3 2.168169 0 0.570000 1.770000 0.572437 0.950000 8.000000e-01 1.000000 1.000000 0.944854 0.950000 1 8.700000e-01 1 LRRTM1 347730 broad.mit.edu 37 2 80529763 80529763 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr2:80529763G>A ENST00000295057.3 - 2 1838 c.1182C>T c.(1180-1182)ctC>ctT p.L394L LRRTM1_ENST00000409148.1_Silent_p.L394L|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000541047.1_Intron NM_178839.4 NP_849161.2 Q86UE6 LRRT1_HUMAN leucine rich repeat transmembrane neuronal 1 63 CGCCGTCCGCGAGCGTGGTGG 0.716000 HNSCC(69;0.2) 0 SO:0001819 synonymous_variant ENST00000295057.3 0 1 hg19 CCDS1966.1 TCGA-OE-A75W-01A-12D-A32N-08 LRRTM1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313614.1 0 0 0 7 225 0 39 0 9.613978e-02 0 15 0 39 2 0 0 0 0 0 2 1 0.980165 7 222 0 39 2 0 0 0 0 39 2 -8.803212 1 1 0 0 1 0 0 0 2.138019 0 0.570000 1.770000 0.570000 0.100000 4.000000e-02 0.210000 0.100000 0.119552 0.100000 0 7.000000e-02 1.600000e-01 NCAPH 23397 broad.mit.edu 37 2 97007560 97007560 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr2:97007560G>A ENST00000240423.4 + 2 243 c.200G>A c.(199-201)cGg>cAg p.R67Q NCAPH_ENST00000455200.1_Missense_Mutation_p.R56Q|NCAPH_ENST00000427946.1_Intron NM_001281710.1|NM_001281711.1|NM_015341.3 NP_001268639.1|NP_001268640.1|NP_056156.2 Q15003 CND2_HUMAN non-SMC condensin I complex, subunit H 28 Ovarian(717;0.0221) CGGCTGCAGCGGAGGCGCTCG 0.592000 0 SO:0001583 missense ENST00000240423.4 1 1 hg19 CCDS2021.1 . . . . . . . . . . G 25.5 4.639751 0.87760 . . ENSG00000121152 ENST00000240423;ENST00000435975;ENST00000456906;ENST00000455200 T;T;T;T 0.56275 0.47;0.47;0.47;0.47 5.66 4.78 0.61160 . 0.106857 0.64402 N 0.000006 T 0.71467 0.3343 M 0.80183 2.485 0.48975 D 0.999732 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 1.0;1.0;1.0;1.0 T 0.74595 -0.3613 10 0.66056 D 0.02 -21.3725 10.5775 0.45235 0.0891:0.0:0.9109:0.0 . 43;56;56;67 B4DRG7;E9PHA2;C9J470;Q15003 .;.;.;CND2_HUMAN Q 67;56;67;56 ENSP00000240423:R67Q;ENSP00000405237:R56Q;ENSP00000401227:R67Q;ENSP00000407308:R56Q ENSP00000240423:R67Q R + 2 0 NCAPH 96371287 1.000000 0.71417 1.000000 0.80357 0.553000 0.35397 8.515000 0.90548 1.400000 0.46741 0.650000 0.86243 CGG TCGA-OE-A75W-01A-12D-A32N-08 NCAPH-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000252842.2 1 0 1 155 526 0 133 0 0 0 0 133 2 0 0 0 0 0 2 1 1.000000 155 514 0 131 2 0 0 0 0 133 2 -4.469609 1 1 121412 1 33 1 1 2 3 2.171444 0 0.570000 1.770000 0.572437 0.790000 6.900000e-01 0.930000 0.800000 0.807003 0.790000 0 7.400000e-01 8.600000e-01 GPR156 165829 broad.mit.edu 37 3 119886046 119886046 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:119886046G>A ENST00000464295.1 - 10 2723 c.2278C>T c.(2278-2280)Cgg>Tgg p.R760W GPR156_ENST00000461057.1_Missense_Mutation_p.R756W|GPR156_ENST00000315843.3_Missense_Mutation_p.R760W Q8NFN8 GP156_HUMAN G protein-coupled receptor 156 32 CAGTAGGGCCGGTGGCAGCGG 0.572000 0 SO:0001583 missense ENST00000464295.1 0 1 hg19 CCDS2997.1 . . . . . . . . . . G 19.69 3.874542 0.72180 . . ENSG00000175697 ENST00000464295;ENST00000315843;ENST00000461057 T;T;T 0.63417 -0.04;-0.04;-0.0 4.97 2.03 0.26663 . 0.000000 0.64402 D 0.000008 T 0.67069 0.2854 L 0.34521 1.04 0.58432 D 0.999991 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 T 0.62473 -0.6847 9 . . . -23.5143 13.1849 0.59675 0.0:0.0:0.4344:0.5656 . 756;760 E9PFZ4;Q8NFN8 .;GP156_HUMAN W 760;760;756 ENSP00000417261:R760W;ENSP00000324553:R760W;ENSP00000418758:R756W . R - 1 2 GPR156 121368736 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 1.382000 0.34374 0.318000 0.23185 0.561000 0.74099 CGG TCGA-OE-A75W-01A-12D-A32N-08 GPR156-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000355139.1 0 0 0 7 824 0 152 0 0 0 0 152 2 0 0 0 0 0 2 1 0.979777 6 815 0 151 2 0 0 0 0 152 2 -1.898680 0 1 121412 7 43 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.020000 0 0.060000 0.030000 0.031722 0.020000 0 1.000000e-02 5.000000e-02 IQCB1 9657 broad.mit.edu 37 3 121489398 121489398 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:121489398C>T ENST00000310864.6 - 15 1805 c.1591G>A c.(1591-1593)Gaa>Aaa p.E531K IQCB1_ENST00000349820.6_Missense_Mutation_p.E398K NM_001023570.2 NP_001018864.2 Q15051 IQCB1_HUMAN IQ motif containing B1 30 TCTTTCCCTTCTGCCTCCTTC 0.517000 0 SO:0001583 missense ENST00000310864.6 0 1 hg19 CCDS33837.1 . . . . . . . . . . C 10.30 1.312378 0.23908 . . ENSG00000173226 ENST00000310864;ENST00000349820 T;T 0.78595 -1.19;-1.19 5.34 3.4 0.38934 . 0.261904 0.42420 N 0.000712 T 0.58308 0.2113 N 0.25647 0.755 0.28325 N 0.922048 B;P 0.36837 0.002;0.571 B;B 0.36608 0.003;0.229 T 0.51268 -0.8727 10 0.08381 T 0.77 -4.0249 6.4099 0.21686 0.0:0.782:0.0:0.218 . 531;398 Q15051;Q15051-2 IQCB1_HUMAN;. K 531;398 ENSP00000311505:E531K;ENSP00000323756:E398K ENSP00000311505:E531K E - 1 0 IQCB1 122972088 0.999000 0.42202 1.000000 0.80357 0.902000 0.53008 1.277000 0.33167 1.482000 0.48325 0.650000 0.86243 GAA TCGA-OE-A75W-01A-12D-A32N-08 IQCB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250573.1 0 0 0 14 715 0 146 1 4.020814e-01 3 65 0 146 2 0 0 0 0 0 2 1 0.999739 14 709 0 145 2 0 0 0 0 146 2 -2.737766 1 1 0 0 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.060000 2.000000e-02 0.110000 0.060000 0.069054 0.060000 0 4.000000e-02 9.000000e-02 MUC13 56667 broad.mit.edu 37 3 124632520 124632520 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:124632520G>A ENST00000311075.3 - 7 1008 c.970C>T c.(970-972)Cgg>Tgg p.R324W NM_033049.3 NP_149038 Q9H3R2 MUC13_HUMAN mucin 13, cell surface associated p.R324W(1) 18 TAATCACACCGAAGGGTCACT 0.423000 1 Substitution - Missense(1) SO:0001583 missense ENST00000311075.3 0 1 hg19 . . . . . . . . . . G 11.76 1.733931 0.30684 . . ENSG00000173702 ENST00000311075 D 0.87491 -2.26 3.93 -4.04 0.04010 . 3.072470 0.01105 N 0.005470 D 0.89329 0.6684 L 0.48642 1.525 0.09310 N 1 D 0.76494 0.999 D 0.71184 0.972 T 0.79112 -0.1937 10 0.66056 D 0.02 0.2081 4.6867 0.12760 0.4045:0.0:0.3619:0.2336 . 324 Q9H3R2 MUC13_HUMAN W 324 ENSP00000312235:R324W ENSP00000312235:R324W R - 1 2 MUC13 126115210 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.076000 0.11412 -1.421000 0.02007 -2.157000 0.00329 CGG TCGA-OE-A75W-01A-12D-A32N-08 MUC13-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000355714.1 0 0 1 8 305 0 48 1 7.156202e-01 11 84 0 48 2 0 0 0 0 0 2 1 0.989189 6 304 0 48 2 0 0 0 0 48 2 -2.957200 1 1 121412 1 28 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.080000 3.000000e-02 0.160000 0.090000 0.095998 0.080000 0 5.000000e-02 1.300000e-01 CAND2 23066 broad.mit.edu 37 3 12858310 12858310 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:12858310C>T ENST00000456430.2 + 10 1920 c.1879C>T c.(1879-1881)Cgg>Tgg p.R627W CAND2_ENST00000295989.5_Missense_Mutation_p.R534W NM_001162499.1 NP_001155971.1 O75155 CAND2_HUMAN cullin-associated and neddylation-dissociated 2 (putative) p.R534W(1) 37 TGAGATCACCCGGCTGCCCGC 0.632000 GBM(43;676 868 1633 6395 37496) 1 Substitution - Missense(1) SO:0001583 missense ENST00000456430.2 0 1 hg19 CCDS54554.1 . . . . . . . . . . C 17.43 3.386485 0.61956 . . ENSG00000144712 ENST00000295989;ENST00000456430 T;T 0.71341 -0.56;-0.56 4.82 4.82 0.62117 Armadillo-like helical (1);Armadillo-type fold (1); 0.068282 0.56097 D 0.000033 D 0.87884 0.6290 M 0.93550 3.43 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.995 D 0.91089 0.4905 10 0.87932 D 0 -35.2501 15.7833 0.78281 0.0:1.0:0.0:0.0 . 627;534 O75155;O75155-2 CAND2_HUMAN;. W 534;627 ENSP00000295989:R534W;ENSP00000387641:R627W ENSP00000295989:R534W R + 1 2 CAND2 12833310 0.317000 0.24589 1.000000 0.80357 0.837000 0.47467 0.913000 0.28611 2.395000 0.81488 0.561000 0.74099 CGG TCGA-OE-A75W-01A-12D-A32N-08 CAND2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000339856.4 0 0 0 12 712 1 179 0 0 0 1 179 2 0 0 0 0 0 2 0 0.337077 12 704 1 176 15 0 0 0 1 179 2 -2.184270 0 1 121052 1 33 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.050000 2.000000e-02 0.100000 0.060000 0.060231 0.050000 0 3.000000e-02 8.000000e-02 CEP63 80254 broad.mit.edu 37 3 134278028 134278028 + Missense_Mutation SNP G G T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:134278028G>T ENST00000337090.3 + 14 1883 c.1710G>T c.(1708-1710)aaG>aaT p.K570N CEP63_ENST00000354446.3_Intron|CEP63_ENST00000383229.3_Intron|CEP63_ENST00000332047.5_Intron|CEP63_ENST00000513612.2_Missense_Mutation_p.K570N|CEP63_ENST00000606977.1_Missense_Mutation_p.K570N Q96MT8 CEP63_HUMAN centrosomal protein 63kDa 27 ATGGAATAAAGACTGAGCACT 0.423000 0 SO:0001583 missense ENST00000337090.3 1 1 hg19 CCDS3086.1 . . . . . . . . . . G 12.46 1.944889 0.34283 . . ENSG00000182923 ENST00000337090;ENST00000513612 T;T 0.18338 2.22;2.22 4.77 3.89 0.44902 . 0.724271 0.12624 N 0.452796 T 0.17238 0.0414 L 0.44542 1.39 0.32265 N 0.569604 P 0.44429 0.835 P 0.44990 0.466 T 0.02339 -1.1174 10 0.25751 T 0.34 -11.6316 8.2011 0.31426 0.1056:0.0:0.8944:0.0 . 570 Q96MT8 CEP63_HUMAN N 570 ENSP00000336524:K570N;ENSP00000426129:K570N ENSP00000336524:K570N K + 3 2 CEP63 135760718 1.000000 0.71417 0.880000 0.34516 0.885000 0.51271 1.319000 0.33655 2.611000 0.88343 0.650000 0.86243 AAG TCGA-OE-A75W-01A-12D-A32N-08 CEP63-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000470139.1 1 0 1 166 397 0 93 0 7.938119e-01 1 8 0 93 2 0 0 0 0 0 2 1 1.000000 165 391 0 93 2 0 0 0 0 93 2 -20.000000 1 1 0 0 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.980000 8.600000e-01 1.000000 1.000000 0.971125 0.980000 1 9.200000e-01 1 CEP63 80254 broad.mit.edu 37 3 134278030 134278030 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:134278030C>T ENST00000337090.3 + 14 1885 c.1712C>T c.(1711-1713)aCt>aTt p.T571I CEP63_ENST00000354446.3_Intron|CEP63_ENST00000383229.3_Intron|CEP63_ENST00000332047.5_Intron|CEP63_ENST00000513612.2_Missense_Mutation_p.T571I|CEP63_ENST00000606977.1_Missense_Mutation_p.T571I Q96MT8 CEP63_HUMAN centrosomal protein 63kDa 27 GGAATAAAGACTGAGCACTAC 0.428000 0 SO:0001583 missense ENST00000337090.3 1 1 hg19 CCDS3086.1 . . . . . . . . . . C 5.920 0.353755 0.11182 . . ENSG00000182923 ENST00000337090;ENST00000513612 T;T 0.18174 2.23;2.23 4.77 2.93 0.34026 . 1.163120 0.06370 N 0.713479 T 0.16769 0.0403 L 0.47716 1.5 0.25605 N 0.986555 B 0.06786 0.001 B 0.09377 0.004 T 0.29549 -1.0008 10 0.35671 T 0.21 -0.0211 6.73 0.23379 0.0:0.7252:0.1782:0.0966 . 571 Q96MT8 CEP63_HUMAN I 571 ENSP00000336524:T571I;ENSP00000426129:T571I ENSP00000336524:T571I T + 2 0 CEP63 135760720 1.000000 0.71417 0.646000 0.29493 0.835000 0.47333 0.453000 0.21811 0.677000 0.31305 -0.143000 0.13931 ACT TCGA-OE-A75W-01A-12D-A32N-08 CEP63-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000470139.1 1 0 1 168 403 0 99 0 8.403252e-01 1 9 0 99 2 0 0 0 0 0 2 1 1.000000 167 397 0 99 2 0 0 0 0 99 2 -20.000000 1 1 0 0 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.980000 8.600000e-01 1.000000 1.000000 0.970160 0.980000 1 9.200000e-01 1 SOX14 8403 broad.mit.edu 37 3 137483748 137483748 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:137483748G>A ENST00000306087.1 + 1 170 c.122G>A c.(121-123)cGc>cAc p.R41H NM_004189.3 NP_004180.1 O95416 SOX14_HUMAN SRY (sex determining region Y)-box 14 14 ATCAGCAAACGCCTAGGTGCC 0.597000 0 SO:0001583 missense ENST00000306087.1 1 1 hg19 CCDS3094.1 . . . . . . . . . . G 26.2 4.711362 0.89112 . . ENSG00000168875 ENST00000306087 D 0.98060 -4.69 5.08 5.08 0.68730 High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4); 0.000000 0.64402 D 0.000001 D 0.98343 0.9450 M 0.82630 2.6 0.80722 D 1 D 0.69078 0.997 P 0.55508 0.777 D 0.99338 1.0911 10 0.87932 D 0 . 18.2699 0.90064 0.0:0.0:1.0:0.0 . 41 O95416 SOX14_HUMAN H 41 ENSP00000305343:R41H ENSP00000305343:R41H R + 2 0 SOX14 138966438 1.000000 0.71417 1.000000 0.80357 0.900000 0.52787 9.597000 0.98273 2.653000 0.90120 0.511000 0.50034 CGC TCGA-OE-A75W-01A-12D-A32N-08 SOX14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357182.1 1 0 0 15 208 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 0.999877 15 205 0 45 2 0 0 0 0 46 2 -3.318794 1 1 0 0 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.220000 1.300000e-01 0.350000 0.220000 0.238689 0.220000 0 1.700000e-01 2.900000e-01 SLC25A36 55186 broad.mit.edu 37 3 140692616 140692616 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:140692616G>A ENST00000324194.6 + 6 679 c.511G>A c.(511-513)Gat>Aat p.D171N RP11-231L11.3_ENST00000513802.1_RNA|SLC25A36_ENST00000446041.2_Missense_Mutation_p.D171N|SLC25A36_ENST00000453248.2_Missense_Mutation_p.D145N Q96CQ1 S2536_HUMAN solute carrier family 25 (pyrimidine nucleotide carrier ), member 36 6 GTATCAGACAGATGGACTAAA 0.353000 0 SO:0001583 missense ENST00000324194.6 1 1 hg19 CCDS46927.1 . . . . . . . . . . G 22.9 4.347924 0.82022 . . ENSG00000114120 ENST00000446041;ENST00000324194;ENST00000453248 T;T;T 0.78816 -1.21;-1.21;-1.21 6.01 6.01 0.97437 Mitochondrial carrier domain (2); 0.042314 0.85682 D 0.000000 D 0.83718 0.5315 L 0.46157 1.445 0.80722 D 1 B;B;D 0.55800 0.417;0.215;0.973 B;B;P 0.60117 0.213;0.135;0.869 D 0.84345 0.0529 10 0.87932 D 0 -25.1645 18.015 0.89236 0.0:0.0:1.0:0.0 . 145;171;171 B4DL01;Q96CQ1-3;Q96CQ1 .;.;S2536_HUMAN N 171;171;145 ENSP00000401938:D171N;ENSP00000320688:D171N;ENSP00000391521:D145N ENSP00000320688:D171N D + 1 0 SLC25A36 142175306 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 9.869000 0.99810 2.861000 0.98227 0.650000 0.86243 GAT TCGA-OE-A75W-01A-12D-A32N-08 SLC25A36-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000359929.1 1 0 1 77 198 0 38 1 3.164734e-01 3 1 0 38 2 0 0 0 0 0 2 1 1.000000 76 196 0 37 2 0 0 0 0 38 2 -20.000000 1 1 0 0 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.930000 7.600000e-01 1.000000 1.000000 0.930055 0.930000 1 8.400000e-01 1 P2RY1 5028 broad.mit.edu 37 3 152553971 152553971 + Missense_Mutation SNP A A T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:152553971A>T ENST00000305097.3 + 1 1236 c.400A>T c.(400-402)Aac>Tac p.N134Y NM_002563.3 NP_002554.1 P47900 P2RY1_HUMAN purinergic receptor P2Y, G-protein coupled, 1 23 LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11) CTTTCATGTGAACCTCTATGG 0.507000 0 SO:0001583 missense ENST00000305097.3 0 1 hg19 CCDS3169.1 . . . . . . . . . . A 25.8 4.675868 0.88445 . . ENSG00000169860 ENST00000305097 T 0.38560 1.13 5.76 5.76 0.90799 GPCR, rhodopsin-like superfamily (1); 0.000000 0.85682 D 0.000000 T 0.71913 0.3396 M 0.91717 3.235 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.79165 -0.1916 10 0.87932 D 0 . 15.2728 0.73717 1.0:0.0:0.0:0.0 . 134 P47900 P2RY1_HUMAN Y 134 ENSP00000304767:N134Y ENSP00000304767:N134Y N + 1 0 P2RY1 154036661 1.000000 0.71417 0.998000 0.56505 0.995000 0.86356 9.210000 0.95106 2.186000 0.69663 0.533000 0.62120 AAC TCGA-OE-A75W-01A-12D-A32N-08 P2RY1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356943.1 0 0 0 5 343 0 78 0 0 0 0 78 2 0 0 0 0 0 2 1 0.937974 5 343 0 78 2 0 0 0 0 78 2 -5.871927 1 0 0 0 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.040000 1.000000e-02 0.110000 0.050000 0.057592 0.040000 0 2.000000e-02 8.000000e-02 MECOM 2122 broad.mit.edu 37 3 168845679 168845679 + Silent SNP C C T rs150481592 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:168845679C>T ENST00000464456.1 - 4 1419 c.219G>A c.(217-219)acG>acA p.T73T MECOM_ENST00000472280.1_Silent_p.T73T|MECOM_ENST00000392736.3_Silent_p.T73T|MECOM_ENST00000460814.1_Silent_p.T73T|MECOM_ENST00000494292.1_Silent_p.T261T|MECOM_ENST00000433243.2_Silent_p.T73T|MECOM_ENST00000264674.3_Silent_p.T137T|MECOM_ENST00000468789.1_Silent_p.T73T NM_001164000.1 NP_001157472.1 Q13465 MDS1_HUMAN MDS1 and EVI1 complex locus 85 ACTCCTGGATCGTGTGTATCT 0.388000 0 SO:0001819 synonymous_variant ENST00000464456.1 1 1 hg19 CCDS54669.1 TCGA-OE-A75W-01A-12D-A32N-08 MECOM-020 NOVEL basic|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000351519.1 1 0 1 203 536 0 139 1 1.855623e-01 2 1 0 139 2 0 0 0 0 0 2 1 1.000000 201 534 0 138 2 0 0 0 0 139 2 -20.000000 1 1 121412 4 43 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.920000 8.100000e-01 1.000000 1.000000 0.923864 0.920000 1 8.600000e-01 9.800000e-01 FXR1 8087 broad.mit.edu 37 3 180675681 180675681 + Missense_Mutation SNP G G C TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:180675681G>C ENST00000357559.4 + 10 1339 c.955G>C c.(955-957)Gaa>Caa p.E319Q FXR1_ENST00000445140.2_Missense_Mutation_p.E319Q|FXR1_ENST00000491062.1_Missense_Mutation_p.E270Q|FXR1_ENST00000480918.1_Missense_Mutation_p.E306Q|FXR1_ENST00000468861.1_Missense_Mutation_p.E234Q|FXR1_ENST00000305586.7_Missense_Mutation_p.E234Q NM_001013438.2|NM_005087.3 NP_001013456.1|NP_005078.2 P51114 FXR1_HUMAN fragile X mental retardation, autosomal homolog 1 26 all_cancers(143;6.07e-14)|Ovarian(172;0.0212) Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22) AGTGAGAATTGAAGGGGACAA 0.313000 0 SO:0001583 missense ENST00000357559.4 0 1 hg19 CCDS3238.1 . . . . . . . . . . G 29.2 4.985897 0.93044 . . ENSG00000114416 ENST00000357559;ENST00000305586;ENST00000491062;ENST00000468861;ENST00000445140;ENST00000480918 T;T;T;T;T;T 0.32272 1.46;1.46;1.46;1.46;1.46;1.46 5.44 5.44 0.79542 K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1); 0.000000 0.85682 D 0.000000 T 0.61999 0.2392 M 0.84219 2.685 0.80722 D 1 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;0.999;1.0;0.999 D;D;D;D;D;D 0.91635 0.999;0.999;0.999;0.974;0.99;0.993 T 0.66372 -0.5940 10 0.87932 D 0 -16.7507 19.6264 0.95679 0.0:0.0:1.0:0.0 . 306;270;234;234;319;319 B4DXZ6;E9PFF5;E7EU85;E7ERF5;P51114-2;P51114 .;.;.;.;.;FXR1_HUMAN Q 319;234;270;234;319;306 ENSP00000350170:E319Q;ENSP00000307633:E234Q;ENSP00000420643:E270Q;ENSP00000420515:E234Q;ENSP00000388828:E319Q;ENSP00000418097:E306Q ENSP00000307633:E234Q E + 1 0 FXR1 182158375 1.000000 0.71417 1.000000 0.80357 0.922000 0.55478 9.813000 0.99286 2.717000 0.92951 0.655000 0.94253 GAA TCGA-OE-A75W-01A-12D-A32N-08 FXR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350265.5 0 0 0 7 291 0 50 0 4.118954e-01 1 53 0 50 2 0 0 0 0 0 2 1 0.979241 6 285 0 49 2 0 0 0 0 50 2 -2.860373 1 1 0 0 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.080000 3.000000e-02 0.160000 0.080000 0.089589 0.080000 0 5.000000e-02 1.200000e-01 EIF4G1 1981 broad.mit.edu 37 3 184038482 184038482 + Missense_Mutation SNP G G A rs34838305 byFrequency TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:184038482G>A ENST00000346169.2 + 8 873 c.602G>A c.(601-603)cGc>cAc p.R201H EIF4G1_ENST00000411531.1_Missense_Mutation_p.R161H|EIF4G1_ENST00000352767.3_Missense_Mutation_p.R208H|EIF4G1_ENST00000392537.2_Missense_Mutation_p.R114H|EIF4G1_ENST00000382330.3_Missense_Mutation_p.R208H|EIF4G1_ENST00000427845.1_Missense_Mutation_p.R114H|EIF4G1_ENST00000350481.5_Missense_Mutation_p.R37H|EIF4G1_ENST00000434061.2_Missense_Mutation_p.R5H|EIF4G1_ENST00000435046.2_Missense_Mutation_p.R5H|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Missense_Mutation_p.R37H|EIF4G1_ENST00000342981.4_Missense_Mutation_p.R201H|EIF4G1_ENST00000414031.1_Missense_Mutation_p.R161H|EIF4G1_ENST00000319274.6_Missense_Mutation_p.R201H|EIF4G1_ENST00000424196.1_Missense_Mutation_p.R208H NM_198241.2 NP_937884 Q04637 IF4G1_HUMAN eukaryotic translation initiation factor 4 gamma, 1 75 all_cancers(143;1.06e-10)|Ovarian(172;0.0339) Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22) TCTGGGGCCCGCACTGCCTCC 0.547000 0 SO:0001583 missense ENST00000346169.2 0 1 hg19 CCDS3259.1 . . . . . . . . . . G 21.9 4.213090 0.79352 0.0 4.65E-4 ENSG00000114867 ENST00000346169;ENST00000414031;ENST00000392537;ENST00000444134;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000456033;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000428387;ENST00000434061;ENST00000427607;ENST00000457456;ENST00000435046 T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T 0.66460 1.11;1.11;1.11;0.19;1.11;1.11;1.11;1.11;3.39;1.11;1.11;1.11;1.11;1.11;1.11;1.11;1.95;3.37;0.07;3.31;-0.21;0.78;3.32 5.08 4.21 0.49690 . 0.062143 0.64402 N 0.000015 T 0.53626 0.1808 L 0.32530 0.975 0.53688 D 0.999978 B;B;B;B 0.19073 0.033;0.033;0.033;0.033 B;B;B;B 0.15052 0.012;0.012;0.012;0.007 T 0.47749 -0.9093 10 0.20519 T 0.43 -3.7867 13.5567 0.61763 0.0749:0.0:0.9251:0.0 rs34838305 208;201;201;208 E9PFM1;D3DNT2;Q04637;B2RU10 .;.;IF4G1_HUMAN;. H 201;161;114;5;201;208;208;142;37;208;114;201;201;208;151;161;37;37;5;5;5;5;5 ENSP00000316879:R201H;ENSP00000391935:R161H;ENSP00000376320:R114H;ENSP00000407244:R5H;ENSP00000391412:R201H;ENSP00000413159:R208H;ENSP00000371767:R208H;ENSP00000403269:R142H;ENSP00000317600:R37H;ENSP00000338020:R208H;ENSP00000407682:R114H;ENSP00000343450:R201H;ENSP00000323737:R201H;ENSP00000416255:R208H;ENSP00000415943:R151H;ENSP00000395974:R161H;ENSP00000398145:R37H;ENSP00000399858:R37H;ENSP00000411707:R5H;ENSP00000411826:R5H;ENSP00000409545:R5H;ENSP00000399969:R5H;ENSP00000404754:R5H ENSP00000323737:R201H R + 2 0 EIF4G1 185521176 1.000000 0.71417 0.996000 0.52242 0.999000 0.98932 7.439000 0.80444 1.377000 0.46286 0.655000 0.94253 CGC TCGA-OE-A75W-01A-12D-A32N-08 EIF4G1-007 NOVEL basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000345733.1 0 0 0 6 361 0 74 0 3.921854e-02 0 16 0 74 2 0 0 0 0 0 2 1 0.962842 6 353 0 74 2 0 0 0 0 74 2 -2.552329 1 1 121412 21 46 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.050000 1.000000e-02 0.110000 0.060000 0.063790 0.050000 0 3.000000e-02 9.000000e-02 SENP5 205564 broad.mit.edu 37 3 196612958 196612958 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:196612958G>A ENST00000323460.5 + 2 1155 c.906G>A c.(904-906)cgG>cgA p.R302R SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Silent_p.R302R NM_152699.4 NP_689912.2 Q96HI0 SENP5_HUMAN SUMO1/sentrin specific peptidase 5 32 all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135) Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06) CTTCTTGTCGGCATCAGCCGT 0.532000 Ovarian(47;891 1095 11174 13858 51271) 0 SO:0001819 synonymous_variant ENST00000323460.5 0 1 hg19 CCDS3322.1 TCGA-OE-A75W-01A-12D-A32N-08 SENP5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340524.1 0 0 0 5 466 0 79 0 1.873311e-04 0 2 0 79 2 0 0 0 0 0 2 0 0.002708 6 460 1 78 19 0 0 0 0 79 2 -2.383246 0 1 0 0 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.030000 0 0.080000 0.040000 0.042447 0.030000 0 1.000000e-02 6.000000e-02 SCN5A 6331 broad.mit.edu 37 3 38592068 38592068 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:38592068G>A ENST00000333535.4 - 28 5944 c.5795C>T c.(5794-5796)gCg>gTg p.A1932V SCN5A_ENST00000450102.2_Missense_Mutation_p.A1878V|SCN5A_ENST00000451551.2_Missense_Mutation_p.A1878V|SCN5A_ENST00000413689.1_Missense_Mutation_p.A1932V|SCN5A_ENST00000423572.2_Missense_Mutation_p.A1931V|SCN5A_ENST00000455624.2_Missense_Mutation_p.A1899V|SCN5A_ENST00000443581.1_Missense_Mutation_p.A1931V|SCN5A_ENST00000425664.1_Missense_Mutation_p.A1914V|SCN5A_ENST00000449557.2_Missense_Mutation_p.A1878V|SCN5A_ENST00000464652.1_5'Flank|SCN5A_ENST00000414099.2_Missense_Mutation_p.A1914V Q14524 SCN5A_HUMAN sodium channel, voltage-gated, type V, alpha subunit 107 Medulloblastoma(35;0.163) Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909) GCCGCTGCCCGCCTGCTGACG 0.622000 0 SO:0001583 missense ENST00000333535.4 1 1 hg19 CCDS46796.1 . . . . . . . . . . G 0.361 -0.939513 0.02322 2.42E-4 0.0 ENSG00000183873 ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557 D;D;D;D;D;D;D;D;D;D 0.95949 -3.77;-3.8;-3.8;-3.81;-3.8;-3.77;-3.8;-3.86;-3.81;-3.81 4.86 3.08 0.35506 . 0.586375 0.16484 N 0.212412 D 0.90157 0.6924 N 0.20685 0.6 0.09310 N 1 B;B;B;B;B;B 0.09022 0.0;0.001;0.0;0.001;0.002;0.001 B;B;B;B;B;B 0.12156 0.001;0.001;0.002;0.002;0.007;0.004 T 0.82226 -0.0562 10 0.52906 T 0.07 . 10.9373 0.47253 0.1517:0.0:0.8483:0.0 . 1878;1899;1914;1932;1931;1932 E9PEF3;E9PHB6;E9PG18;Q14524;Q14524-2;E9PEK2 .;.;.;SCN5A_HUMAN;.;. V 1914;1931;1932;1878;1931;1914;1932;1899;1878;1878 ENSP00000398962:A1914V;ENSP00000398266:A1931V;ENSP00000410257:A1932V;ENSP00000388797:A1878V;ENSP00000397915:A1931V;ENSP00000416634:A1914V;ENSP00000328968:A1932V;ENSP00000399524:A1899V;ENSP00000403355:A1878V;ENSP00000413996:A1878V ENSP00000328968:A1932V A - 2 0 SCN5A 38567072 0.004000 0.15560 0.104000 0.21259 0.085000 0.17905 1.632000 0.37102 0.662000 0.31006 -0.218000 0.12543 GCG TCGA-OE-A75W-01A-12D-A32N-08 SCN5A-014 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000377958.1 1 0 1 22 188 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 0.999999 22 183 0 46 2 0 0 0 0 46 2 -20.000000 1 1 121024 8 37 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.350000 2.200000e-01 0.500000 0.350000 0.364075 0.350000 0 2.800000e-01 4.300000e-01 FYCO1 79443 broad.mit.edu 37 3 45996750 45996750 + Missense_Mutation SNP G G A rs140583635 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:45996750G>A ENST00000296137.2 - 14 4140 c.3935C>T c.(3934-3936)gCg>gTg p.A1312V FYCO1_ENST00000535325.1_Missense_Mutation_p.A1312V|FYCO1_ENST00000438446.1_5'UTR NM_024513.3 NP_078789.2 Q9BQS8 FYCO1_HUMAN FYVE and coiled-coil domain containing 1 54 CTGTTCAGCCGCATTTGGGTC 0.498000 0 SO:0001583 missense ENST00000296137.2 0 1 hg19 CCDS2734.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. g|g 0.144|0.144 -1.099395|-1.099395 0.01843|0.01843 0.0|0.0 1.16E-4|1.16E-4 ENSG00000163820|ENSG00000163820 ENST00000296137;ENST00000535325|ENST00000433878 T;T|. 0.20598|. 2.06;2.13|. 5.82|5.82 3.37|3.37 0.38596|0.38596 .|. 1.153750|. 0.06193|. N|. 0.681750|. T|T 0.08088|0.08088 0.0202|0.0202 N|N 0.00436|0.00436 -1.5|-1.5 0.09310|0.09310 N|N 1|1 B;B|. 0.02656|. 0.0;0.0|. B;B|. 0.01281|. 0.0;0.0|. T|T 0.32955|0.32955 -0.9887|-0.9887 10|5 0.02654|. T|. 1|. -2.141|-2.141 9.5319|9.5319 0.39198|0.39198 0.8598:0.0:0.1402:0.0|0.8598:0.0:0.1402:0.0 .|. 1312;1312|. B7ZKT7;Q9BQS8|. .;FYCO1_HUMAN|. V|W 1312|101 ENSP00000296137:A1312V;ENSP00000441178:A1312V|. ENSP00000296137:A1312V|. A|R -|- 2|1 0|2 FYCO1|FYCO1 45971754|45971754 0.324000|0.324000 0.24652|0.24652 0.162000|0.162000 0.22713|0.22713 0.435000|0.435000 0.31806|0.31806 1.668000|1.668000 0.37481|0.37481 0.435000|0.435000 0.26365|0.26365 -0.285000|-0.285000 0.09966|0.09966 GCG|CGG TCGA-OE-A75W-01A-12D-A32N-08 FYCO1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257320.2 0 0 0 7 780 0 154 0 4.860049e-03 0 10 0 154 2 0 0 0 0 0 2 1 0.979168 7 764 0 152 2 0 0 0 0 154 2 -1.630981 0 1 121412 4 45 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.020000 0 0.060000 0.040000 0.033735 0.020000 0 1.000000e-02 5.000000e-02 NISCH 11188 broad.mit.edu 37 3 52523640 52523640 + Silent SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:52523640C>T ENST00000479054.1 + 18 3474 c.3402C>T c.(3400-3402)gtC>gtT p.V1134V NISCH_ENST00000345716.4_Silent_p.V1134V Q9Y2I1 NISCH_HUMAN nischarin 33 Tizanidine(DB00697) TCCGGCACGTCGCCAGCCTGC 0.672000 0 SO:0001819 synonymous_variant ENST00000479054.1 1 1 hg19 CCDS33767.1 TCGA-OE-A75W-01A-12D-A32N-08 NISCH-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351357.1 1 0 1 70 452 0 141 1 9.980640e-01 11 51 0 141 2 0 0 0 0 0 2 1 1.000000 68 445 0 140 2 0 0 0 0 141 2 -3.221905 1 1 121276 7 40 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.440000 3.500000e-01 0.550000 0.450000 0.455748 0.440000 0 3.900000e-01 5.000000e-01 NSUN3 63899 broad.mit.edu 37 3 93783283 93783283 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr3:93783283G>A ENST00000314622.4 + 2 226 c.15G>A c.(13-15)ctG>ctA p.L5L DHFRL1_ENST00000481631.1_5'Flank|DHFRL1_ENST00000314636.2_5'Flank|DHFRL1_ENST00000394221.2_5'Flank|NSUN3_ENST00000485793.1_3'UTR NM_022072.3 NP_071355.1 Q9H649 NSUN3_HUMAN NOP2/Sun domain family, member 3 18 CGTCATAGCTGAAAGCAAAAT 0.353000 0 SO:0001819 synonymous_variant ENST00000314622.4 1 1 hg19 CCDS2927.1 TCGA-OE-A75W-01A-12D-A32N-08 NSUN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352934.1 1 0 0 7 186 0 24 0 6.486699e-02 1 9 0 24 2 0 0 0 0 0 2 1 0.980841 7 185 0 24 2 0 0 0 0 24 2 -9.031901 1 1 0 0 1 0 0 0 2.052927 0 0.570000 1.770000 0.552130 0.120000 5.000000e-02 0.240000 0.120000 0.137628 0.120000 0 8.000000e-02 1.800000e-01 ZNF330 27309 broad.mit.edu 37 4 142150724 142150724 + Splice_Site SNP G G T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr4:142150724G>T ENST00000262990.4 + 6 519 c.e6-1 ZNF330_ENST00000421169.2_Splice_Site NM_014487.4 NP_055302.1 Q9Y3S2 ZN330_HUMAN zinc finger protein 330 14 all_hematologic(180;0.162) CTTGGTTACAGGGTGCAATAT 0.428000 0 SO:0001630 splice_region_variant ENST00000262990.4 0 1 hg19 CCDS3754.1 . . . . . . . . . . G 19.18 3.778159 0.70107 . . ENSG00000109445 ENST00000262990;ENST00000512809;ENST00000503649;ENST00000512738;ENST00000421169 . . . 5.93 5.93 0.95920 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 20.3437 0.98782 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . ZNF330 142370174 1.000000 0.71417 1.000000 0.80357 0.603000 0.37013 9.864000 0.99589 2.802000 0.96397 0.563000 0.77884 . TCGA-OE-A75W-01A-12D-A32N-08 ZNF330-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257271.2 0 0 0 7 749 0 180 0 0 0 0 180 2 0 0 0 0 0 2 1 0.978809 7 730 0 179 2 0 0 0 0 180 2 -1.838574 0 1 0 0 1 0 1 1 1.635240 1 0.570000 1.770000 0.410353 0.020000 0 0.050000 0.020000 0.026992 0.020000 0 1.000000e-02 4.000000e-02 MND1 84057 broad.mit.edu 37 4 154318479 154318479 + Nonsense_Mutation SNP G G T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr4:154318479G>T ENST00000504860.1 + 5 458 c.415G>T c.(415-417)Gaa>Taa p.E139* MND1_ENST00000240488.3_Nonsense_Mutation_p.E154* meiotic nuclear divisions 1 homolog (S. cerevisiae) 3 all_hematologic(180;0.093) AGTTGTGGAAGAAATACGTAA 0.373000 0 SO:0001587 stop_gained ENST00000504860.1 0 1 hg19 . . . . . . . . . . G 18.67 3.673305 0.67928 . . ENSG00000121211 ENST00000240488;ENST00000504860 . . . 5.44 5.44 0.79542 . 0.090339 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.10377 T 0.69 -33.0793 16.5451 0.84443 0.0:0.0:1.0:0.0 . . . . X 154;139 . ENSP00000240488:E154X E + 1 0 MND1 154537929 1.000000 0.71417 1.000000 0.80357 0.268000 0.26511 6.502000 0.73695 2.690000 0.91761 0.555000 0.69702 GAA TCGA-OE-A75W-01A-12D-A32N-08 MND1-002 PUTATIVE alternative_5_UTR|basic|exp_conf protein_coding protein_coding OTTHUMT00000365195.1 1 0 0 11 48 0 16 1 9.424177e-01 5 20 0 16 2 0 0 0 0 0 2 1 0.998868 11 48 0 16 2 0 0 0 0 16 2 -19.951880 1 1 0 0 1 0 1 1 1.635240 1 0.570000 1.770000 0.410353 0.470000 2.600000e-01 0.740000 0.470000 0.491266 0.470000 0 3.600000e-01 6.100000e-01 FBXL5 26234 broad.mit.edu 37 4 15629518 15629518 + Missense_Mutation SNP G G C TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr4:15629518G>C ENST00000341285.3 - 7 1155 c.1031C>G c.(1030-1032)tCc>tGc p.S344C FBXL5_ENST00000412094.2_Missense_Mutation_p.S327C|FBXL5_ENST00000382358.4_Missense_Mutation_p.S218C NM_001193534.1|NM_001193535.1|NM_012161.3 NP_001180463.1|NP_001180464.1|NP_036293.1 Q9UKA1 FBXL5_HUMAN F-box and leucine-rich repeat protein 5 13 CATTTTGCTGGAAACTGCAGA 0.338000 0 SO:0001583 missense ENST00000341285.3 0 1 hg19 CCDS3415.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 16.92|16.92 3.256719|3.256719 0.59321|0.59321 .|. .|. ENSG00000118564|ENSG00000118564 ENST00000513163|ENST00000341285;ENST00000412094;ENST00000382358 .|T;T;T .|0.20598 .|2.06;2.06;2.06 5.47|5.47 5.47|5.47 0.80525|0.80525 .|. .|0.103499 .|0.64402 .|D .|0.000002 T|T 0.28466|0.28466 0.0704|0.0704 M|M 0.67953|0.67953 2.075|2.075 0.80722|0.80722 D|D 1|1 .|B;B .|0.12630 .|0.006;0.003 .|B;B .|0.13407 .|0.009;0.004 T|T 0.05194|0.05194 -1.0900|-1.0900 5|10 .|0.87932 .|D .|0 -9.4228|-9.4228 17.5156|17.5156 0.87772|0.87772 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|327;344 .|Q9UKA1-2;Q9UKA1 .|.;FBXL5_HUMAN L|C 264|344;327;218 .|ENSP00000344866:S344C;ENSP00000408679:S327C;ENSP00000371795:S218C .|ENSP00000344866:S344C F|S -|- 3|2 2|0 FBXL5|FBXL5 15238616|15238616 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.990000|0.990000 0.78478|0.78478 8.856000|8.856000 0.92245|0.92245 2.570000|2.570000 0.86706|0.86706 0.460000|0.460000 0.39030|0.39030 TTC|TCC TCGA-OE-A75W-01A-12D-A32N-08 FBXL5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214235.2 0 0 0 5 211 0 38 0 3.267467e-02 0 10 0 38 2 0 0 0 0 0 2 1 0.938267 5 211 0 38 2 0 0 0 0 38 2 -6.545644 1 1 0 0 1 1 2 3 2.166255 0 0.570000 1.770000 0.572437 0.080000 2.000000e-02 0.200000 0.080000 0.105636 0.080000 0 5.000000e-02 1.400000e-01 FSTL5 56884 broad.mit.edu 37 4 162307378 162307378 + Missense_Mutation SNP A A T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr4:162307378A>T ENST00000306100.5 - 16 2501 c.2065T>A c.(2065-2067)Ttc>Atc p.F689I RP11-234O6.2_ENST00000508189.1_RNA|FSTL5_ENST00000379164.4_Missense_Mutation_p.F688I|FSTL5_ENST00000536695.1_Missense_Mutation_p.F688I|FSTL5_ENST00000427802.2_Missense_Mutation_p.F679I NM_001128427.2|NM_020116.4 NP_001121899.1|NP_064501.2 Q8N475 FSTL5_HUMAN follistatin-like 5 91 all_hematologic(180;0.24) TCACTATTGAACCCAATGACT 0.488000 0 SO:0001583 missense ENST00000306100.5 1 1 hg19 CCDS3802.1 . . . . . . . . . . A 14.06 2.422309 0.43020 . . ENSG00000168843 ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695 T;T;T;T 0.71817 -0.58;-0.56;-0.6;-0.56 5.55 4.38 0.52667 WD40/YVTN repeat-like-containing domain (1); 0.397737 0.31134 N 0.008186 T 0.48484 0.1502 N 0.08118 0 0.28959 N 0.889968 B;B;B 0.17268 0.021;0.007;0.01 B;B;B 0.20184 0.028;0.007;0.019 T 0.38112 -0.9676 10 0.22706 T 0.39 . 10.4916 0.44754 0.9243:0.0:0.0757:0.0 . 679;688;689 E9PCP6;F8VZ90;Q8N475 .;.;FSTL5_HUMAN I 689;688;679;688 ENSP00000305334:F689I;ENSP00000368462:F688I;ENSP00000389270:F679I;ENSP00000440409:F688I ENSP00000305334:F689I F - 1 0 FSTL5 162526828 1.000000 0.71417 0.663000 0.29738 0.888000 0.51559 3.708000 0.54845 0.952000 0.37798 0.533000 0.62120 TTC TCGA-OE-A75W-01A-12D-A32N-08 FSTL5-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000364773.2 1 0 1 76 146 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 1.000000 76 144 0 53 2 0 0 0 0 53 2 -20.000000 1 1 0 0 1 0 1 1 1.635240 1 0.570000 1.770000 0.410353 0.860000 7.100000e-01 1.000000 1.000000 0.869617 0.860000 1 7.800000e-01 9.500000e-01 HGFAC 3083 broad.mit.edu 37 4 3445871 3445871 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr4:3445871G>A ENST00000382774.3 + 5 696 c.581G>A c.(580-582)gGc>gAc p.G194D HGFAC_ENST00000511533.1_Missense_Mutation_p.G194D NM_001528.2 NP_001519.1 Q04756 HGFA_HUMAN HGF activator 22 GCCTTCACCGGCAAGGACTGC 0.687000 0 SO:0001583 missense ENST00000382774.3 0 1 hg19 CCDS3369.1 . . . . . . . . . . G 13.21 2.169872 0.38315 . . ENSG00000109758 ENST00000382774;ENST00000511533 D;D 0.99105 -5.43;-5.43 3.94 3.94 0.45596 EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1); 0.000000 0.85682 D 0.000000 D 0.99315 0.9760 M 0.90650 3.135 0.45239 D 0.998246 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.98698 1.0699 10 0.87932 D 0 . 13.5073 0.61491 0.0:0.0:1.0:0.0 . 194;194 D6RAR4;Q04756 .;HGFA_HUMAN D 194 ENSP00000372224:G194D;ENSP00000421801:G194D ENSP00000372224:G194D G + 2 0 HGFAC 3415669 0.004000 0.15560 0.189000 0.23252 0.168000 0.22595 0.771000 0.26633 2.023000 0.59567 0.313000 0.20887 GGC TCGA-OE-A75W-01A-12D-A32N-08 HGFAC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206607.3 0 0 0 5 113 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 0.934659 3 113 0 32 2 0 0 0 0 32 2 -8.403799 1 0 0 0 1 1 2 3 2.166255 0 0.570000 1.770000 0.572437 0.160000 5.000000e-02 0.360000 0.150000 0.183408 0.160000 0 1.000000e-01 2.500000e-01 FRAS1 80144 broad.mit.edu 37 4 79417989 79417989 + Missense_Mutation SNP G G T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr4:79417989G>T ENST00000264895.6 + 60 9429 c.8989G>T c.(8989-8991)Gac>Tac p.D2997Y NM_025074.6 NP_079350.5 Q86XX4 FRAS1_HUMAN Fraser extracellular matrix complex subunit 1 103 TATCCACGATGACTCCATGTT 0.448000 0 SO:0001583 missense ENST00000264895.6 0 1 hg19 CCDS54771.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 21.2|21.2 4.113120|4.113120 0.77210|0.77210 .|. .|. ENSG00000138759|ENSG00000138759 ENST00000264895|ENST00000512123 T|. 0.57107|. 0.42|. 5.38|5.38 5.38|5.38 0.77491|0.77491 .|. 0.000000|. 0.85682|. D|. 0.000000|. D|. 0.86661|. 0.5986|. M|M 0.92268|0.92268 3.29|3.29 0.80722|0.80722 D|D 1|1 D|. 0.89917|. 1.0|. D|. 0.97110|. 1.0|. D|. 0.89622|. 0.3849|. 10|. 0.87932|. D|. 0|. .|. 19.1434|19.1434 0.93455|0.93455 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 2997|. E9PHH6|. .|. Y|L 2997|1225 ENSP00000264895:D2997Y|. ENSP00000264895:D2997Y|. D|X +|+ 1|2 0|2 FRAS1|FRAS1 79637013|79637013 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.580000|0.580000 0.36256|0.36256 9.594000|9.594000 0.98254|0.98254 2.497000|2.497000 0.84241|0.84241 0.655000|0.655000 0.94253|0.94253 GAC|TGA TCGA-OE-A75W-01A-12D-A32N-08 FRAS1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 13 793 0 106 0 1.570166e-02 0 11 0 106 2 0 0 0 0 0 2 1 0.999500 13 785 0 105 2 0 0 0 0 106 2 -2.645963 1 1 0 0 1 1 2 3 2.648177 1 0.570000 1.770000 0.648204 0.070000 3.000000e-02 1.000000 0.080000 0.225336 0.070000 0 4.000000e-02 1 DGKQ 1609 broad.mit.edu 37 4 954958 954958 + Missense_Mutation SNP A A G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr4:954958A>G ENST00000273814.3 - 22 2679 c.2606T>C c.(2605-2607)aTc>aCc p.I869T DGKQ_ENST00000502309.1_5'Flank NM_001347.3 NP_001338.2 P52824 DGKQ_HUMAN diacylglycerol kinase, theta 110kDa 9 OV - Ovarian serous cystadenocarcinoma(23;0.0158) GGCAATCCGGATTCCGGAGCG 0.726000 Esophageal Squamous(17;537 645 4447 26373) 0 SO:0001583 missense ENST00000273814.3 1 1 hg19 CCDS3342.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 17.63|17.63 3.437655|3.437655 0.62955|0.62955 .|. .|. ENSG00000145214|ENSG00000145214 ENST00000273814;ENST00000515182|ENST00000509465 T;T|. 0.47177|. 0.85;0.85|. 5.29|5.29 5.29|5.29 0.74685|0.74685 Diacylglycerol kinase, accessory domain (2);|. 0.049071|. 0.85682|. D|. 0.000000|. T|T 0.57681|0.57681 0.2070|0.2070 L|L 0.39633|0.39633 1.23|1.23 0.58432|0.58432 D|D 0.999999|0.999999 D;D|. 0.89917|. 0.996;1.0|. D;D|. 0.77557|. 0.967;0.99|. T|T 0.55062|0.55062 -0.8199|-0.8199 10|5 0.44086|. T|. 0.13|. .|. 13.1628|13.1628 0.59554|0.59554 1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0 .|. 869;869|. E9KL49;P52824|. .;DGKQ_HUMAN|. T|P 869;84|803 ENSP00000273814:I869T;ENSP00000421756:I84T|. ENSP00000273814:I869T|. I|S -|- 2|1 0|0 DGKQ|DGKQ 944958|944958 1.000000|1.000000 0.71417|0.71417 0.997000|0.997000 0.53966|0.53966 0.825000|0.825000 0.46686|0.46686 5.430000|5.430000 0.66501|0.66501 2.008000|2.008000 0.58898|0.58898 0.454000|0.454000 0.30748|0.30748 ATC|TCC TCGA-OE-A75W-01A-12D-A32N-08 DGKQ-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000200888.1 1 0 0 35 156 0 39 1 8.806734e-01 4 15 0 39 2 0 0 0 0 0 2 1 1.000000 34 155 0 38 2 0 0 0 0 39 2 -20.000000 1 1 0 0 1 1 2 3 2.166255 0 0.570000 1.770000 0.572437 0.640000 4.600000e-01 0.880000 0.650000 0.659005 0.640000 0 5.500000e-01 7.600000e-01 FAM170A 340069 broad.mit.edu 37 5 118965470 118965470 + Nonsense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:118965470C>T ENST00000515256.1 + 1 179 c.7C>T c.(7-9)Cga>Tga p.R3* A1A519 F170A_HUMAN family with sequence similarity 170, member A 24 TATCATGAAACGACGACAAAA 0.458000 0 SO:0001587 stop_gained ENST00000515256.1 0 1 hg19 . . . . . . . . . . C 36 5.799191 0.96960 . . ENSG00000164334 ENST00000296787;ENST00000515256;ENST00000509264 . . . 4.24 3.36 0.38483 . 0.000000 0.42172 D 0.000747 . . . . . . 0.80722 A 1 . . . . . . . . . . . . . -6.6887 9.5633 0.39383 0.2093:0.7907:0.0:0.0 . . . . X 3 . . R + 1 2 FAM170A 118993369 0.821000 0.29204 0.659000 0.29680 0.781000 0.44180 1.696000 0.37773 1.368000 0.46115 0.561000 0.74099 CGA TCGA-OE-A75W-01A-12D-A32N-08 FAM170A-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000371126.1 0 0 0 7 716 1 165 0 0 0 1 165 2 0 0 0 0 0 2 0 0.041855 10 703 1 165 16 0 0 0 1 165 2 -2.715705 1 1 0 0 1 0 1 1 2.009754 0 0.570000 1.770000 0.541235 0.030000 0 0.070000 0.040000 0.036150 0.030000 0 1.000000e-02 5.000000e-02 KIF20A 10112 broad.mit.edu 37 5 137518869 137518869 + Nonsense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:137518869C>T ENST00000394894.3 + 8 1070 c.844C>T c.(844-846)Cga>Tga p.R282* KIF20A_ENST00000508792.1_Nonsense_Mutation_p.R264* NM_005733.2 NP_005724.1 O95235 KI20A_HUMAN kinesin family member 20A 27 KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109) AACAAGTCATCGATGGGCACA 0.498000 0 SO:0001587 stop_gained ENST00000394894.3 0 1 hg19 CCDS4199.1 . . . . . . . . . . C 17.11 3.306221 0.60305 . . ENSG00000112984 ENST00000394894;ENST00000508792 . . . 4.88 2.9 0.33743 . 0.709223 0.11400 N 0.567885 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.11182 T 0.66 0.0424 8.3654 0.32382 0.137:0.7029:0.0:0.1601 . . . . X 282;264 . ENSP00000378356:R282X R + 1 2 KIF20A 137546768 0.005000 0.15991 0.518000 0.27811 0.964000 0.63967 1.560000 0.36331 1.264000 0.44198 0.655000 0.94253 CGA TCGA-OE-A75W-01A-12D-A32N-08 KIF20A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251272.1 1 0 1 69 222 0 54 0 0 0 1 0 54 2 0 0 0 0 0 2 1 1.000000 69 221 0 54 2 0 0 0 0 54 2 -20.000000 1 1 121412 1 33 1 0 1 1 2.009754 0 0.570000 1.770000 0.541235 0.770000 6.200000e-01 0.940000 0.780000 0.783264 0.770000 0 6.900000e-01 8.600000e-01 PCDHA13 56136 broad.mit.edu 37 5 140263655 140263655 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:140263655C>T ENST00000289272.2 + 1 1802 c.1802C>T c.(1801-1803)tCg>tTg p.S601L PCDHA6_ENST00000529310.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.S601L|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA12_ENST00000398631.2_Intron NM_018904.2|NM_031865.1 NP_061727.1|NP_114071.1 Q9Y5I0 PCDAD_HUMAN protocadherin alpha 13 95 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GACGCCGATTCGGGCTACAAT 0.697000 Melanoma(147;1739 1852 5500 27947 37288) 0 SO:0001583 missense ENST00000289272.2 0 1 hg19 CCDS4240.1 . . . . . . . . . . C 16.83 3.230086 0.58777 . . ENSG00000239389 ENST00000409494;ENST00000289272 T;T 0.49432 0.78;0.78 4.21 4.21 0.49690 Cadherin (4);Cadherin-like (1); . . . . T 0.71643 0.3364 M 0.84773 2.715 0.38022 D 0.934879 D;D;D 0.89917 1.0;1.0;0.999 D;D;D 0.78314 0.966;0.991;0.99 T 0.80863 -0.1192 9 0.87932 D 0 . 16.3687 0.83346 0.0:1.0:0.0:0.0 . 601;601;601 Q9Y5I0;C9JA99;Q9Y5I0-2 PCDAD_HUMAN;.;. L 601 ENSP00000386821:S601L;ENSP00000289272:S601L ENSP00000289272:S601L S + 2 0 PCDHA13 140243839 0.000000 0.05858 0.966000 0.40874 0.123000 0.20343 0.579000 0.23788 2.144000 0.66660 0.655000 0.94253 TCG TCGA-OE-A75W-01A-12D-A32N-08 PCDHA13-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335000.1 0 0 0 6 658 0 158 0 0 0 0 158 2 0 0 0 0 0 2 1 0.964261 7 652 0 156 2 0 0 0 0 158 2 -2.591305 1 1 0 0 1 0 1 1 2.009754 0 0.570000 1.770000 0.541235 0.020000 0 0.060000 0.030000 0.034162 0.020000 0 1.000000e-02 5.000000e-02 PCDHB6 56130 broad.mit.edu 37 5 140531689 140531689 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:140531689G>A ENST00000231136.1 + 1 1851 c.1851G>A c.(1849-1851)gcG>gcA p.A617A PCDHB6_ENST00000543635.1_Silent_p.A481A NM_018939.2 NP_061762.1 Q9Y5E3 PCDB6_HUMAN protocadherin beta 6 84 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) GCGTGTGGGCGCACAATGGCG 0.672000 0 SO:0001819 synonymous_variant ENST00000231136.1 0 1 hg19 CCDS4248.1 TCGA-OE-A75W-01A-12D-A32N-08 PCDHB6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251818.2 0 0 0 5 346 0 97 0 0 0 0 97 2 0 0 0 0 0 2 1 0.902817 5 288 0 141 2 0 0 0 0 97 2 -2.722834 1 1 0 0 1 0 1 1 2.009754 0 0.570000 1.770000 0.541235 0.040000 1.000000e-02 0.100000 0.050000 0.055732 0.040000 0 2.000000e-02 8.000000e-02 PCDHB8 56128 broad.mit.edu 37 5 140558339 140558339 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:140558339G>A ENST00000239444.2 + 1 969 c.724G>A c.(724-726)Gaa>Aaa p.E242K PCDHB16_ENST00000361016.2_5'Flank NM_019120.3 NP_061993.2 Q9UN66 PCDB8_HUMAN protocadherin beta 8 83 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) TAATGCCCCTGAATTTGAGCA 0.502000 0 SO:0001583 missense ENST00000239444.2 1 1 hg19 CCDS4250.1 . . . . . . . . . . g 12.50 1.957802 0.34565 . . ENSG00000120322 ENST00000239444 T 0.61510 0.1 4.25 1.37 0.22104 Cadherin (2);Cadherin-like (1); . . . . T 0.36054 0.0953 N 0.16266 0.395 0.23126 N 0.998252 B 0.26876 0.162 B 0.27608 0.081 T 0.21211 -1.0252 9 0.25106 T 0.35 . 5.6828 0.17786 0.26:0.1488:0.5912:0.0 . 242 Q9UN66 PCDB8_HUMAN K 242 ENSP00000239444:E242K ENSP00000239444:E242K E + 1 0 PCDHB8 140538523 0.000000 0.05858 0.995000 0.50966 0.983000 0.72400 0.137000 0.15995 -0.038000 0.13624 0.585000 0.79938 GAA TCGA-OE-A75W-01A-12D-A32N-08 PCDHB8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251816.2 1 0 1 218 1305 0 282 0 0 0 0 282 2 0 0 0 1 0 0 2 1 1.000000 217 1291 0 282 2 0 0 0 0 282 2 -20.000000 1 1 0 0 1 0 1 1 2.009754 0 0.570000 1.770000 0.541235 0.460000 4.000000e-01 0.530000 0.470000 0.472024 0.460000 0 4.300000e-01 5.000000e-01 CLINT1 9685 broad.mit.edu 37 5 157232960 157232960 + Missense_Mutation SNP C C G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:157232960C>G ENST00000411809.2 - 7 1060 c.856G>C c.(856-858)Gat>Cat p.D286H CLINT1_ENST00000523908.1_Missense_Mutation_p.D286H|CLINT1_ENST00000523094.1_Missense_Mutation_p.D268H|CLINT1_ENST00000530742.1_Missense_Mutation_p.D268H|CLINT1_ENST00000296951.5_Missense_Mutation_p.D268H NM_014666.3 NP_055481.1 Q14677 EPN4_HUMAN clathrin interactor 1 21 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.138) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) GCTCCAAGATCAATGGTTTTG 0.483000 Colon(22;427 587 2170 6147 14291) 0 SO:0001583 missense ENST00000411809.2 0 1 hg19 CCDS47330.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 26.5|26.5 4.742679|4.742679 0.89573|0.89573 .|. .|. ENSG00000113282|ENSG00000113282 ENST00000523094;ENST00000530742;ENST00000411809;ENST00000296951;ENST00000523908|ENST00000521615 T;T;T;T;T|. 0.61040|. 0.14;0.14;0.25;0.14;0.22|. 5.63|5.63 5.63|5.63 0.86233|0.86233 .|. 0.000000|. 0.85682|. D|. 0.000000|. T|. 0.75591|. 0.3870|. M|M 0.68317|0.68317 2.08|2.08 0.80722|0.80722 D|D 1|1 D;D|. 0.89917|. 1.0;1.0|. D;D|. 0.97110|. 1.0;1.0|. T|. 0.73238|. -0.4046|. 10|. 0.72032|. D|. 0.01|. -18.413|-18.413 19.6818|19.6818 0.95967|0.95967 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 286;286|. B7Z6F8;Q14677|. .;EPN4_HUMAN|. H|S 268;268;286;268;286|2 ENSP00000429345:D268H;ENSP00000433419:D268H;ENSP00000388340:D286H;ENSP00000296951:D268H;ENSP00000429824:D286H|. ENSP00000296951:D268H|. D|X -|- 1|2 0|2 CLINT1|CLINT1 157165538|157165538 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.997000|0.997000 0.91878|0.91878 7.786000|7.786000 0.85741|0.85741 2.656000|2.656000 0.90262|0.90262 0.557000|0.557000 0.71058|0.71058 GAT|TGA TCGA-OE-A75W-01A-12D-A32N-08 CLINT1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000374001.1 0 0 0 7 323 0 70 0 2.500796e-02 1 9 0 70 2 0 0 0 0 0 2 1 0.978667 7 313 0 68 2 0 0 0 0 70 2 -3.075884 1 1 0 0 1 0 1 1 2.009754 0 0.570000 1.770000 0.541235 0.070000 2.000000e-02 0.140000 0.070000 0.079046 0.070000 0 4.000000e-02 1.100000e-01 SLIT3 6586 broad.mit.edu 37 5 168175367 168175367 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:168175367C>T ENST00000519560.1 - 20 2629 c.2210G>A c.(2209-2211)cGa>cAa p.R737Q SLIT3_ENST00000404867.3_Missense_Mutation_p.R737Q|SLIT3_ENST00000332966.8_Missense_Mutation_p.R737Q NM_001271946.1|NM_003062.2 NP_001258875.1|NP_003053 O75094 SLIT3_HUMAN slit homolog 3 (Drosophila) 100 Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392) Medulloblastoma(196;0.0399)|all_neural(177;0.0966) Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) GTTGCTGCATCGCACCACTGT 0.642000 Ovarian(29;311 847 10864 17279 24903) 0 SO:0001583 missense ENST00000519560.1 0 1 hg19 CCDS4369.1 . . . . . . . . . . c 36 5.620461 0.96660 . . ENSG00000184347 ENST00000519560;ENST00000332966;ENST00000404867 D;D;D 0.95918 -3.85;-3.85;-3.85 5.3 5.3 0.74995 Leucine-rich repeat-containing N-terminal (2); 0.167150 0.53938 D 0.000050 D 0.96442 0.8839 L 0.38692 1.165 0.80722 D 1 D 0.89917 1.0 D 0.77557 0.99 D 0.97301 0.9931 10 0.87932 D 0 . 19.0096 0.92868 0.0:1.0:0.0:0.0 . 737 O75094 SLIT3_HUMAN Q 737 ENSP00000430333:R737Q;ENSP00000332164:R737Q;ENSP00000384890:R737Q ENSP00000332164:R737Q R - 2 0 SLIT3 168107945 1.000000 0.71417 0.954000 0.39281 0.894000 0.52154 7.485000 0.81204 2.483000 0.83821 0.550000 0.68814 CGA TCGA-OE-A75W-01A-12D-A32N-08 SLIT3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252792.4 0 0 0 7 470 0 122 0 0 0 1 0 122 2 0 0 0 0 0 2 1 0.980171 7 466 0 121 2 0 0 0 0 122 2 -3.085984 1 1 0 0 1 0 1 1 2.009754 0 0.570000 1.770000 0.541235 0.040000 1.000000e-02 0.100000 0.050000 0.054862 0.040000 0 2.000000e-02 7.000000e-02 CDHR2 54825 broad.mit.edu 37 5 176008451 176008451 + Silent SNP C C G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:176008451C>G ENST00000510636.1 + 17 2200 c.1926C>G c.(1924-1926)ctC>ctG p.L642L CDHR2_ENST00000506348.1_Silent_p.L642L|CDHR2_ENST00000261944.5_Silent_p.L642L NM_001171976.1 NP_001165447.1 Q9BYE9 CDHR2_HUMAN cadherin-related family member 2 56 CAGGGCTCCTCAGAAACCTGG 0.627000 0 SO:0001819 synonymous_variant ENST00000510636.1 0 1 hg19 CCDS34297.1 TCGA-OE-A75W-01A-12D-A32N-08 CDHR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372201.1 0 0 0 4 257 0 68 1 2.275312e-01 2 45 0 68 2 0 0 0 0 0 2 1 0.887421 4 253 0 67 2 0 0 0 0 68 2 -5.167245 1 1 0 0 1 0 1 1 2.009754 0 0.570000 1.770000 0.541235 0.050000 1.000000e-02 0.120000 0.050000 0.062257 0.050000 0 2.000000e-02 9.000000e-02 F12 2161 broad.mit.edu 37 5 176831274 176831274 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:176831274G>A ENST00000253496.3 - 9 989 c.941C>T c.(940-942)cCa>cTa p.P314L F12_ENST00000514943.1_5'Flank NM_000505.3 NP_000496.2 P00748 FA12_HUMAN coagulation factor XII (Hageman factor) 12 all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) Ethanolamine Oleate(DB06689) GGGCATGAGTGGGACATGAAG 0.711000 Hereditary Angioedema OREG0017088 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense Familial Cancer Database HAE, type I-III, Hereditary Angioneurotic Edema, HANE, ENST00000253496.3 1 1 hg19 CCDS34302.1 . . . . . . . . . . G 8.380 0.837406 0.16891 . . ENSG00000131187 ENST00000253496 D 0.89050 -2.46 4.4 -4.43 0.03568 . 3.436950 0.00947 N 0.002906 T 0.72574 0.3477 N 0.05124 -0.11 0.09310 N 0.999993 B 0.02656 0.0 B 0.01281 0.0 T 0.67360 -0.5690 10 0.10377 T 0.69 . 5.3148 0.15850 0.486:0.0:0.374:0.14 . 314 P00748 FA12_HUMAN L 314 ENSP00000253496:P314L ENSP00000253496:P314L P - 2 0 F12 176763880 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.201000 0.09464 -0.948000 0.03668 -1.191000 0.01696 CCA TCGA-OE-A75W-01A-12D-A32N-08 F12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000373217.1 0 0 0 37 118 1 38 1 7.681109e-01 11 10 1 38 4 0 0 0 0 0 2 1 0.999885 37 117 1 38 14 0 0 0 1 38 2 -20.000000 1 1 0 0 1 0 1 1 2.009754 0 0.570000 1.770000 0.541235 0.780000 5.700000e-01 1.000000 1.000000 0.789892 0.780000 0 6.700000e-01 9.000000e-01 CLK4 57396 broad.mit.edu 37 5 178045614 178045614 + Missense_Mutation SNP C C G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:178045614C>G ENST00000316308.4 - 3 495 c.327G>C c.(325-327)agG>agC p.R109S RN7SKP70_ENST00000516655.1_RNA|CLK4_ENST00000522749.1_5'UTR NM_020666.2 NP_065717.1 Q9HAZ1 CLK4_HUMAN CDC-like kinase 4 21 all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918) all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GACTGCTTCTCCTGCTGCGGA 0.413000 0 SO:0001583 missense ENST00000316308.4 0 1 hg19 CCDS4437.1 . . . . . . . . . . C 12.13 1.845262 0.32606 . . ENSG00000113240 ENST00000316308;ENST00000536763 T 0.68479 -0.33 5.72 5.72 0.89469 . 0.111533 0.64402 D 0.000001 T 0.48390 0.1497 L 0.31578 0.945 0.80722 D 1 B;P;B;B;B 0.39782 0.002;0.688;0.006;0.293;0.293 B;B;B;B;B 0.31442 0.006;0.13;0.006;0.039;0.039 T 0.47548 -0.9109 10 0.15066 T 0.55 . 13.0251 0.58810 0.0:0.8381:0.1619:0.0 . 109;109;109;109;109 B7Z990;B7ZL31;Q4G0Z5;B9EG64;Q9HAZ1 .;.;.;.;CLK4_HUMAN S 109 ENSP00000316948:R109S ENSP00000316948:R109S R - 3 2 CLK4 177978220 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 1.230000 0.32612 2.700000 0.92200 0.563000 0.77884 AGG TCGA-OE-A75W-01A-12D-A32N-08 CLK4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253479.2 0 0 0 5 587 0 110 0 9.721886e-03 0 14 0 110 2 0 0 0 0 0 2 1 0.936942 5 584 0 108 2 0 0 0 0 110 2 -2.204181 0 1 0 0 1 0 1 1 2.009754 0 0.570000 1.770000 0.541235 0.020000 0 0.060000 0.030000 0.032673 0.020000 0 1.000000e-02 5.000000e-02 EGFLAM 133584 broad.mit.edu 37 5 38370412 38370412 + Missense_Mutation SNP A A T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:38370412A>T ENST00000354891.3 + 6 906 c.560A>T c.(559-561)aAg>aTg p.K187M EGFLAM_ENST00000322350.5_Missense_Mutation_p.K187M NM_001205301.1 NP_001192230.1 Q63HQ2 EGFLA_HUMAN EGF-like, fibronectin type III and laminin G domains 85 all_lung(31;0.000385) GATTTCGACAAGAAGTGGACC 0.448000 Colon(62;485 1295 3347 17454) 0 SO:0001583 missense ENST00000354891.3 1 1 hg19 CCDS56363.1 . . . . . . . . . . A 10.89 1.479053 0.26511 . . ENSG00000164318 ENST00000354891;ENST00000322350 T;T 0.57595 0.39;0.39 5.82 0.571 0.17352 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.578369 0.20260 N 0.095883 T 0.31071 0.0785 N 0.17922 0.545 0.45515 D 0.998477 B;B 0.18461 0.014;0.028 B;B 0.13407 0.009;0.008 T 0.06770 -1.0808 10 0.45353 T 0.12 -9.2271 5.5891 0.17291 0.325:0.4351:0.2399:0.0 . 187;187 Q63HQ2;Q63HQ2-2 EGFLA_HUMAN;. M 187 ENSP00000346964:K187M;ENSP00000313084:K187M ENSP00000313084:K187M K + 2 0 EGFLAM 38406169 1.000000 0.71417 0.897000 0.35233 0.776000 0.43924 0.897000 0.28390 0.462000 0.27095 -0.429000 0.05907 AAG TCGA-OE-A75W-01A-12D-A32N-08 EGFLAM-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000367323.1 1 0 1 88 230 0 55 0 0 0 1 0 55 2 0 0 0 0 0 2 1 1.000000 86 227 0 54 2 0 0 0 0 55 2 -20.000000 1 1 0 0 1 0 2 2 2.176816 1 0.570000 1.770000 0.570000 0.970000 8.000000e-01 1.000000 1.000000 0.955181 0.970000 1 8.800000e-01 1 NNT 23530 broad.mit.edu 37 5 43651892 43651892 + Missense_Mutation SNP A A G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:43651892A>G ENST00000264663.5 + 13 1990 c.1769A>G c.(1768-1770)gAc>gGc p.D590G NNT_ENST00000512996.2_Missense_Mutation_p.D459G|NNT_ENST00000344920.4_Missense_Mutation_p.D590G NM_012343.3 NP_036475.3 Q13423 NNTM_HUMAN nicotinamide nucleotide transhydrogenase 51 Lung NSC(6;2.58e-06) CGTCCCACTGACCCCCCAGAA 0.463000 0 SO:0001583 missense ENST00000264663.5 0 1 hg19 CCDS3949.1 . . . . . . . . . . A 27.7 4.854509 0.91355 . . ENSG00000112992 ENST00000542759;ENST00000264663;ENST00000344920;ENST00000512996 D;D;D 0.96459 -4.02;-4.02;-3.87 5.64 5.64 0.86602 . 0.000000 0.85682 D 0.000000 D 0.98220 0.9411 M 0.86651 2.83 0.80722 D 1 D 0.89917 1.0 D 0.72982 0.979 D 0.99285 1.0897 10 0.87932 D 0 -27.7305 15.8513 0.78934 1.0:0.0:0.0:0.0 . 590 Q13423 NNTM_HUMAN G 105;590;590;459 ENSP00000264663:D590G;ENSP00000343873:D590G;ENSP00000426343:D459G ENSP00000264663:D590G D + 2 0 NNT 43687649 1.000000 0.71417 0.816000 0.32577 0.983000 0.72400 8.962000 0.93254 2.152000 0.67230 0.533000 0.62120 GAC TCGA-OE-A75W-01A-12D-A32N-08 NNT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214026.1 0 0 0 9 954 1 154 0 3.137766e-03 0 8 1 154 2 0 0 0 0 0 2 0 0.018672 8 942 1 151 21 0 0 0 1 154 2 -1.787495 0 1 0 0 1 0 2 2 2.176816 1 0.570000 1.770000 0.570000 0.030000 0 1.000000 0.040000 0.136732 0.030000 0 1.000000e-02 6.000000e-02 CEP72 55722 broad.mit.edu 37 5 633946 633946 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:633946C>T ENST00000264935.5 + 5 665 c.575C>T c.(574-576)gCg>gTg p.A192V CEP72_ENST00000444221.1_Intron NM_018140.3 NP_060610.2 Q9P209 CEP72_HUMAN centrosomal protein 72kDa 20 Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863) GTCATGGATGCGGATGACGAG 0.612000 0 SO:0001583 missense ENST00000264935.5 0 1 hg19 CCDS34126.1 . . . . . . . . . . C 8.455 0.854063 0.17106 . . ENSG00000112877 ENST00000264935 T 0.09911 2.93 5.14 2.14 0.27477 . 0.406531 0.25458 N 0.030523 T 0.11410 0.0278 M 0.65975 2.015 0.29054 N 0.884302 B 0.15473 0.013 B 0.12837 0.008 T 0.09662 -1.0664 10 0.40728 T 0.16 -11.1821 6.2359 0.20762 0.4236:0.4884:0.0:0.088 . 192 Q9P209 CEP72_HUMAN V 192 ENSP00000264935:A192V ENSP00000264935:A192V A + 2 0 CEP72 686946 0.023000 0.18921 0.021000 0.16686 0.247000 0.25773 0.787000 0.26858 0.650000 0.30769 -0.355000 0.07637 GCG TCGA-OE-A75W-01A-12D-A32N-08 CEP72-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000365967.3 0 0 0 8 1020 0 228 0 2.269723e-03 0 8 0 228 2 0 0 0 0 0 2 1 0.989020 8 1013 0 227 2 0 0 0 0 228 2 -1.810234 0 1 121412 2 39 1 1 2 3 2.259955 0 0.570000 1.770000 0.589871 0.020000 0 1.000000 0.020000 0.158953 0.020000 0 1.000000e-02 6.000000e-02 RNF180 285671 broad.mit.edu 37 5 63509712 63509712 + Nonsense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:63509712C>T ENST00000389100.4 + 4 631 c.559C>T c.(559-561)Cga>Tga p.R187* RNF180_ENST00000381081.2_Intron|RNF180_ENST00000296615.6_Nonsense_Mutation_p.R187* NM_001113561.1 NP_001107033.1 Q86T96 RN180_HUMAN ring finger protein 180 20 Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234) CCTGGAGGTGCGACCAACATA 0.453000 0 SO:0001587 stop_gained ENST00000389100.4 0 1 hg19 CCDS47219.1 . . . . . . . . . . C 20.4 3.987398 0.74589 . . ENSG00000164197 ENST00000296615;ENST00000389100 . . . 6.08 3.21 0.36854 . 0.180087 0.38778 N 0.001574 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -3.0471 14.6552 0.68828 0.5204:0.4796:0.0:0.0 . . . . X 187 . ENSP00000296615:R187X R + 1 2 RNF180 63545468 0.452000 0.25713 0.552000 0.28243 0.998000 0.95712 0.245000 0.18142 0.381000 0.24851 0.655000 0.94253 CGA TCGA-OE-A75W-01A-12D-A32N-08 RNF180-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000368394.1 0 0 0 82 165 1 48 0 0 0 1 1 48 2 0 0 0 0 0 2 1 1.000000 82 163 1 48 17 0 0 0 1 48 2 -20.000000 1 1 121406 1 32 1 0 2 2 2.176816 1 0.570000 1.770000 0.570000 0.990000 9.600000e-01 1.000000 1.000000 0.998027 0.990000 1 9.900000e-01 1 HMGCR 3156 broad.mit.edu 37 5 74650437 74650437 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr5:74650437C>T ENST00000287936.4 + 12 1634 c.1478C>T c.(1477-1479)tCt>tTt p.S493F HMGCR_ENST00000511206.1_Missense_Mutation_p.S493F|HMGCR_ENST00000343975.5_Missense_Mutation_p.S493F NM_000859.2 NP_000850.1 P04035 HMDH_HUMAN 3-hydroxy-3-methylglutaryl-CoA reductase 20 all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174) Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641) CGTGGTGTATCTATTCGCCGA 0.408000 0 SO:0001583 missense ENST00000287936.4 0 1 hg19 CCDS4027.1 . . . . . . . . . . C 16.95 3.263447 0.59431 . . ENSG00000113161 ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975 T;T;T 0.44881 0.91;0.91;0.96 5.14 5.14 0.70334 Hydroxymethylglutaryl-CoA reductase, N-terminal (1);Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding (1); 0.166783 0.56097 D 0.000035 T 0.46946 0.1419 L 0.52905 1.665 0.46678 D 0.999152 B;P;B 0.42296 0.215;0.775;0.215 B;B;B 0.43274 0.102;0.414;0.102 T 0.50524 -0.8818 10 0.59425 D 0.04 -18.4228 18.978 0.92745 0.0:1.0:0.0:0.0 . 493;493;493 B2R649;P04035-2;P04035 .;.;HMDH_HUMAN F 493;424;493;493 ENSP00000426745:S493F;ENSP00000287936:S493F;ENSP00000340816:S493F ENSP00000287936:S493F S + 2 0 HMGCR 74686193 1.000000 0.71417 1.000000 0.80357 0.545000 0.35147 4.270000 0.58896 2.570000 0.86706 0.467000 0.42956 TCT TCGA-OE-A75W-01A-12D-A32N-08 HMGCR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219877.2 0 0 0 6 326 0 42 0 9.557913e-03 0 7 0 42 2 0 0 0 0 0 2 1 0.964681 6 324 0 40 2 0 0 0 0 42 2 -2.618065 1 1 0 0 1 1 2 3 2.675887 1 0.570000 1.770000 0.665370 0.080000 2.000000e-02 0.170000 0.090000 0.094380 0.080000 0 5.000000e-02 1.300000e-01 GRIK2 2898 broad.mit.edu 37 6 102516276 102516276 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr6:102516276C>T ENST00000421544.1 + 16 3107 c.2617C>T c.(2617-2619)Cgt>Tgt p.R873C GRIK2_ENST00000369138.1_3'UTR|GRIK2_ENST00000413795.1_3'UTR|GRIK2_ENST00000369137.3_Missense_Mutation_p.R797C|GRIK2_ENST00000369134.4_Missense_Mutation_p.R824C NM_021956.4 NP_068775.1 Q13002 GRIK2_HUMAN glutamate receptor, ionotropic, kainate 2 83 all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14) Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599) GAAGTGCCAGCGTCGGTTAAA 0.398000 0 SO:0001583 missense ENST00000421544.1 1 1 hg19 CCDS5048.1 . . . . . . . . . . C 27.0 4.795302 0.90453 . . ENSG00000164418 ENST00000421544;ENST00000369137;ENST00000369134 T;T;T 0.12147 2.71;2.87;2.72 5.79 5.79 0.91817 . 0.050411 0.85682 D 0.000000 T 0.20941 0.0504 L 0.54323 1.7 0.80722 D 1 D 0.71674 0.998 P 0.55260 0.772 T 0.00276 -1.1855 10 0.59425 D 0.04 . 20.0361 0.97558 0.0:1.0:0.0:0.0 . 873 Q13002 GRIK2_HUMAN C 873;797;824 ENSP00000397026:R873C;ENSP00000358133:R797C;ENSP00000358130:R824C ENSP00000358130:R824C R + 1 0 GRIK2 102622969 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 7.487000 0.81328 2.745000 0.94114 0.462000 0.41574 CGT TCGA-OE-A75W-01A-12D-A32N-08 GRIK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043718.1 1 0 1 71 131 0 51 0 0 0 0 51 2 0 0 0 0 0 2 1 1.000000 70 128 0 51 2 0 0 0 0 51 2 -20.000000 1 1 0 0 1 0 1 1 1.573763 1 0.570000 1.770000 0.398601 0.860000 7.100000e-01 0.990000 0.880000 0.866050 0.860000 1 7.800000e-01 9.400000e-01 KIAA0319 9856 broad.mit.edu 37 6 24580108 24580108 + Silent SNP C C T rs138756394 byFrequency TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr6:24580108C>T ENST00000378214.3 - 8 1874 c.1350G>A c.(1348-1350)acG>acA p.T450T KIAA0319_ENST00000430948.2_Silent_p.T405T|KIAA0319_ENST00000535378.1_Silent_p.T441T|KIAA0319_ENST00000543707.1_Silent_p.T450T|KIAA0319_ENST00000537886.1_Silent_p.T450T NM_001168375.1|NM_014809.3 NP_001161847.1|NP_055624.2 Q5VV43 K0319_HUMAN KIAA0319 53 TGAGGGCTGACGTCAAAGGCA 0.458000 0 SO:0001819 synonymous_variant ENST00000378214.3 0 0 hg19 CCDS34348.1 TCGA-OE-A75W-01A-12D-A32N-08 KIAA0319-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040009.1 1 0 1 11 54 0 12 0 0 0 0 12 2 0 0 0 0 0 2 1 0.998828 11 54 0 12 2 0 0 0 0 12 2 -19.693130 1 0 121334 27 42 1 1 2 3 2.152451 0 0.570000 1.770000 0.571222 0.600000 3.300000e-01 0.970000 0.590000 0.621773 0.600000 0 4.500000e-01 7.800000e-01 MOCS1 4337 broad.mit.edu 37 6 39881079 39881079 + Missense_Mutation SNP C C G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr6:39881079C>G ENST00000340692.5 - 6 742 c.739G>C c.(739-741)Gag>Cag p.E247Q MOCS1_ENST00000373175.4_Missense_Mutation_p.E218Q|MOCS1_ENST00000373195.3_Missense_Mutation_p.E160Q|MOCS1_ENST00000373186.4_Missense_Mutation_p.E247Q|MOCS1_ENST00000432280.2_Missense_Mutation_p.E218Q|MOCS1_ENST00000308559.7_Missense_Mutation_p.E247Q|MOCS1_ENST00000425303.2_Missense_Mutation_p.E247Q|MOCS1_ENST00000373188.2_Missense_Mutation_p.E247Q Q9NZB8 MOCS1_HUMAN molybdenum cofactor synthesis 1 21 Ovarian(28;0.0355)|Colorectal(47;0.196) GGCATATACTCTATGAAGCGC 0.582000 NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639) 0 SO:0001583 missense ENST00000340692.5 1 1 hg19 . . . . . . . . . . C 27.1 4.801911 0.90538 . . ENSG00000124615 ENST00000373186;ENST00000308559;ENST00000373175;ENST00000373188;ENST00000373195;ENST00000340692;ENST00000425303;ENST00000432280 D;D;D;D;D;D;D;D 0.98060 -4.69;-4.69;-4.69;-4.69;-4.69;-4.69;-4.69;-4.69 4.68 4.68 0.58851 Elongator protein 3/MiaB/NifB (1);Molybdenum cofactor synthesis C-terminal (1);Aldolase-type TIM barrel (1); 0.000000 0.85682 D 0.000000 D 0.99542 0.9836 H 0.99984 5.225 0.80722 D 1 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.91635 0.998;0.996;0.999;0.998;0.997 D 0.97279 0.9916 9 . . . -29.1172 17.2165 0.86945 0.0:1.0:0.0:0.0 . 247;247;247;247;247 Q9NZB8-2;Q9NZB8-5;Q9NZB8;Q9NZB8-8;Q9NZB8-6 .;.;MOCS1_HUMAN;.;. Q 247;247;218;247;160;247;247;218 ENSP00000362282:E247Q;ENSP00000309843:E247Q;ENSP00000362270:E218Q;ENSP00000362284:E247Q;ENSP00000362291:E160Q;ENSP00000344794:E247Q;ENSP00000416478:E247Q;ENSP00000410809:E218Q . E - 1 0 MOCS1 39989057 1.000000 0.71417 1.000000 0.80357 0.984000 0.73092 7.783000 0.85696 2.166000 0.68216 0.655000 0.94253 GAG TCGA-OE-A75W-01A-12D-A32N-08 MOCS1-005 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000040476.2 1 0 1 72 213 0 51 0 7.058376e-01 0 9 0 51 2 0 0 0 0 0 2 1 1.000000 72 211 0 51 2 0 0 0 0 51 2 -4.883959 1 1 0 0 1 1 2 3 2.167841 0 0.570000 1.770000 0.572437 0.880000 7.100000e-01 1.000000 1.000000 0.890290 0.880000 1 8.000000e-01 9.900000e-01 RREB1 6239 broad.mit.edu 37 6 7246974 7246974 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr6:7246974G>A ENST00000349384.6 + 11 4440 c.4126G>A c.(4126-4128)Gag>Aag p.E1376K RREB1_ENST00000379938.2_Missense_Mutation_p.E1431K|RREB1_ENST00000334984.6_Intron|RREB1_ENST00000379933.3_Missense_Mutation_p.E1376K NM_001003698.3 NP_001003698.1 Q92766 RREB1_HUMAN ras responsive element binding protein 1 58 Ovarian(93;0.0398) all_hematologic(90;0.0384)|Prostate(151;0.191) CAAGCTGGCGGAGGGCGACGG 0.687000 0 SO:0001583 missense ENST00000349384.6 0 1 hg19 CCDS34336.1 . . . . . . . . . . G 10.08 1.252018 0.22880 . . ENSG00000124782 ENST00000379933;ENST00000379938;ENST00000349384 T;T;T 0.11495 2.8;2.77;2.8 5.6 2.79 0.32731 . . . . . T 0.03390 0.0098 L 0.52573 1.65 0.42564 D 0.993153 P;P 0.39022 0.524;0.655 B;B 0.30855 0.095;0.121 T 0.46857 -0.9161 9 0.29301 T 0.29 -19.3632 10.5135 0.44876 0.0679:0.2532:0.6789:0.0 . 1376;1431 Q92766;Q92766-2 RREB1_HUMAN;. K 1376;1431;1376 ENSP00000369265:E1376K;ENSP00000369270:E1431K;ENSP00000305560:E1376K ENSP00000305560:E1376K E + 1 0 RREB1 7191973 1.000000 0.71417 0.020000 0.16555 0.035000 0.12851 3.103000 0.50298 0.297000 0.22615 0.655000 0.94253 GAG TCGA-OE-A75W-01A-12D-A32N-08 RREB1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000352985.1 0 0 0 8 30 0 9 0 0 0 1 0 9 2 0 0 0 0 0 2 1 0.992080 8 30 0 9 2 0 0 0 0 9 2 -17.555920 1 1 0 0 1 1 2 3 2.152451 0 0.570000 1.770000 0.571222 0.750000 3.700000e-01 1.000000 1.000000 0.754088 0.750000 0 5.400000e-01 1 DNAJC2 27000 broad.mit.edu 37 7 102960230 102960230 + Missense_Mutation SNP T T G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr7:102960230T>G ENST00000379263.3 - 11 1395 c.1145A>C c.(1144-1146)aAa>aCa p.K382T DNAJC2_ENST00000249270.7_Intron|PMPCB_ENST00000420236.2_Intron NM_014377.1 NP_055192.1 Q99543 DNJC2_HUMAN DnaJ (Hsp40) homolog, subfamily C, member 2 21 ATCACAAAGTTTTTCCACTTC 0.353000 0 SO:0001583 missense ENST00000379263.3 0 1 hg19 CCDS43628.1 . . . . . . . . . . T 24.0 4.487186 0.84854 . . ENSG00000105821 ENST00000379263 T 0.44482 0.92 5.87 5.87 0.94306 . 0.000000 0.85682 U 0.000000 T 0.60495 0.2273 M 0.62723 1.935 0.80722 D 1 D 0.76494 0.999 D 0.78314 0.991 T 0.55289 -0.8164 10 0.20046 T 0.44 -28.1622 16.2853 0.82717 0.0:0.0:0.0:1.0 . 382 Q99543 DNJC2_HUMAN T 382 ENSP00000368565:K382T ENSP00000368565:K382T K - 2 0 DNAJC2 102747466 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 7.665000 0.83852 2.236000 0.73375 0.528000 0.53228 AAA TCGA-OE-A75W-01A-12D-A32N-08 DNAJC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347891.1 0 0 0 8 739 0 116 0 3.579704e-01 0 106 0 116 2 0 0 0 0 0 2 1 0.988618 8 726 0 116 2 0 0 0 0 116 2 -3.318556 1 1 0 0 1 1 2 3 2.187475 0 0.570000 1.770000 0.574847 0.030000 0 1.000000 0.040000 0.070284 0.030000 0 2.000000e-02 6.000000e-02 GRM8 2918 broad.mit.edu 37 7 126410092 126410092 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr7:126410092G>A ENST00000339582.2 - 7 1992 c.1184C>T c.(1183-1185)tCt>tTt p.S395F GRM8_ENST00000405249.1_Missense_Mutation_p.S395F|GRM8_ENST00000358373.3_Missense_Mutation_p.S395F|GRM8_ENST00000444921.2_Missense_Mutation_p.S395F|GRM8_ENST00000480995.1_5'UTR O00222 GRM8_HUMAN glutamate receptor, metabotropic 8 125 Prostate(267;0.186) CTGTTCATAAGATGAATCCCG 0.388000 HNSCC(24;0.065) 0 SO:0001583 missense ENST00000339582.2 1 1 hg19 CCDS5794.1 . . . . . . . . . . G 8.134 0.783695 0.16189 . . ENSG00000179603 ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249 D;D;D;D 0.86432 -2.12;-2.12;-2.12;-2.12 5.88 5.88 0.94601 Extracellular ligand-binding receptor (1); 0.247838 0.38217 N 0.001768 D 0.82848 0.5126 L 0.29908 0.895 0.44247 D 0.997094 B;B;B 0.29378 0.243;0.141;0.037 B;B;B 0.35114 0.196;0.054;0.043 T 0.80455 -0.1375 10 0.46703 T 0.11 . 14.7788 0.69749 0.0:0.1438:0.8562:0.0 . 395;395;395 O00222-3;O00222-2;O00222 .;.;GRM8_HUMAN F 395 ENSP00000344173:S395F;ENSP00000409790:S395F;ENSP00000351142:S395F;ENSP00000385731:S395F ENSP00000344173:S395F S - 2 0 GRM8 126197328 0.998000 0.40836 0.781000 0.31783 0.040000 0.13550 2.992000 0.49417 2.769000 0.95229 0.655000 0.94253 TCT TCGA-OE-A75W-01A-12D-A32N-08 GRM8-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000059209.4 1 0 1 47 89 0 27 0 0 0 1 0 27 2 0 0 0 0 0 2 1 1.000000 47 89 0 27 2 0 0 0 0 27 2 -20.000000 1 1 0 0 1 1 2 3 2.187475 0 0.570000 1.770000 0.574847 0.990000 9.500000e-01 1.000000 1.000000 0.997232 0.990000 1 9.900000e-01 1 SSPO 23145 broad.mit.edu 37 7 149523658 149523658 + RNA SNP G G C TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr7:149523658G>C ENST00000378016.2 + 0 14572 A2VEC9 SSPO_HUMAN SCO-spondin Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) TGGCTGCCCTGGAGGGCAGGT 0.672000 0 ENST00000378016.2 0 1 hg19 TCGA-OE-A75W-01A-12D-A32N-08 SSPO-202 KNOWN basic processed_transcript processed_transcript 0 0 0 23 56 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 1.000000 23 53 0 22 2 0 0 0 0 23 2 -20.000000 1 1 0 0 1 0 0 0 2.086752 0 0.570000 1.770000 0.557385 0.980000 6.700000e-01 1.000000 1.000000 0.932000 0.980000 1 8.200000e-01 1 TMUB1 83590 broad.mit.edu 37 7 150779321 150779321 + Silent SNP G G T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr7:150779321G>T ENST00000392818.3 - 2 687 c.330C>A c.(328-330)ctC>ctA p.L110L TMUB1_ENST00000297533.4_Silent_p.L110L|FASTK_ENST00000482571.1_5'Flank|TMUB1_ENST00000482202.1_Silent_p.L110L|FASTK_ENST00000540185.1_5'Flank|TMUB1_ENST00000476627.1_Silent_p.L110L|TMUB1_ENST00000462940.1_Silent_p.L110L|FASTK_ENST00000297532.6_5'Flank|FASTK_ENST00000353841.2_5'Flank|FASTK_ENST00000489884.1_5'Flank NM_031434.3 NP_113622.1 Q9BVT8 TMUB1_HUMAN transmembrane and ubiquitin-like domain containing 1 2 OV - Ovarian serous cystadenocarcinoma(82;0.00989) CTGAATCATTGAGGAATTTCA 0.607000 0 SO:0001819 synonymous_variant ENST00000392818.3 0 1 hg19 CCDS5920.1 TCGA-OE-A75W-01A-12D-A32N-08 TMUB1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351485.1 0 0 0 12 1380 0 324 1 9.483590e-01 7 573 0 324 2 0 0 0 0 0 2 1 0.999024 10 1363 0 322 2 0 0 0 0 324 2 -2.329838 0 1 0 0 1 0 0 0 2.086752 0 0.570000 1.770000 0.557385 0.020000 0 0.050000 0.040000 0.031941 0.020000 0 1.000000e-02 4.000000e-02 SHH 6469 broad.mit.edu 37 7 155604784 155604784 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr7:155604784G>A ENST00000297261.2 - 1 183 c.33C>T c.(31-33)gtC>gtT p.V11V NM_000193.2 NP_000184.1 Q15465 SHH_HUMAN sonic hedgehog 14 all_neural(206;0.101) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00882) AGGAGACGAGGACTAGCAGCA 0.657000 0 SO:0001819 synonymous_variant ENST00000297261.2 0 1 hg19 CCDS5942.1 TCGA-OE-A75W-01A-12D-A32N-08 SHH-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000322327.1 0 0 0 10 523 0 119 0 8.852774e-03 0 7 0 119 2 0 0 0 0 0 2 1 0.996687 10 516 0 112 2 0 0 0 0 119 2 -8.265762 1 1 0 0 1 0 0 0 2.086752 0 0.570000 1.770000 0.557385 0.060000 2.000000e-02 0.110000 0.060000 0.069979 0.060000 0 4.000000e-02 9.000000e-02 SDK1 221935 broad.mit.edu 37 7 4089014 4089014 + Silent SNP A A G TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr7:4089014A>G ENST00000404826.2 + 18 2776 c.2637A>G c.(2635-2637)gaA>gaG p.E879E SDK1_ENST00000389531.3_Silent_p.E879E NM_152744.3 NP_689957.3 Q7Z5N4 SDK1_HUMAN sidekick cell adhesion molecule 1 153 all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194) TGCAGACGGAAGCCGTGAACT 0.582000 0 SO:0001819 synonymous_variant ENST00000404826.2 1 1 hg19 CCDS34590.1 TCGA-OE-A75W-01A-12D-A32N-08 SDK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323702.1 1 0 1 53 170 0 46 0 0 0 1 0 46 2 0 0 0 0 0 2 1 1.000000 53 169 0 44 2 0 0 0 0 46 2 -20.000000 1 1 0 0 1 1 2 3 2.187475 0 0.570000 1.770000 0.574847 0.840000 6.500000e-01 1.000000 1.000000 0.849883 0.840000 0 7.400000e-01 9.600000e-01 DDC 1644 broad.mit.edu 37 7 50595897 50595897 + Missense_Mutation SNP G G C rs150760434 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr7:50595897G>C ENST00000444124.2 - 6 852 c.652C>G c.(652-654)Cgt>Ggt p.R218G DDC_ENST00000431062.1_Intron|DDC_ENST00000380984.4_Missense_Mutation_p.R218G|DDC_ENST00000489162.1_5'UTR|DDC_ENST00000426377.1_Missense_Mutation_p.R140G|DDC_ENST00000357936.5_Missense_Mutation_p.R218G NM_001082971.1 NP_001076440 P20711 DDC_HUMAN dopa decarboxylase (aromatic L-amino acid decarboxylase) 40 Glioma(55;0.08)|all_neural(89;0.245) Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968) GCAGACGCACGCATGGCGAAG 0.532000 0 SO:0001583 missense ENST00000444124.2 1 1 hg19 CCDS5511.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 16.67|16.67 3.186512|3.186512 0.57909|0.57909 .|. .|. ENSG00000132437|ENSG00000132437 ENST00000430300|ENST00000357936;ENST00000426377;ENST00000444124;ENST00000380984 .|T;T;T;T .|0.38560 .|1.13;1.13;1.13;1.13 6.06|6.06 4.2|4.2 0.49525|0.49525 .|Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1); .|0.102551 .|0.64402 .|D .|0.000006 T|T 0.65186|0.65186 0.2667|0.2667 H|H 0.95187|0.95187 3.635|3.635 0.48632|0.48632 D|D 0.999681|0.999681 .|B;B .|0.33103 .|0.397;0.397 .|B;B .|0.43251 .|0.413;0.413 T|T 0.71807|0.71807 -0.4481|-0.4481 5|10 .|0.87932 .|D .|0 -7.8105|-7.8105 14.373|14.373 0.66854|0.66854 0.0:0.0:0.7221:0.2779|0.0:0.0:0.7221:0.2779 .|. .|218;218 .|Q53Y41;P20711 .|.;DDC_HUMAN W|G 98|218;140;218;218 .|ENSP00000350616:R218G;ENSP00000395069:R140G;ENSP00000403644:R218G;ENSP00000370371:R218G .|ENSP00000350616:R218G C|R -|- 3|1 2|0 DDC|DDC 50563391|50563391 1.000000|1.000000 0.71417|0.71417 0.906000|0.906000 0.35671|0.35671 0.564000|0.564000 0.35744|0.35744 1.378000|1.378000 0.34328|0.34328 0.826000|0.826000 0.34661|0.34661 0.650000|0.650000 0.86243|0.86243 TGC|CGT TCGA-OE-A75W-01A-12D-A32N-08 DDC-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342593.1 1 0 1 130 384 0 103 1 3.742986e-01 3 2 0 103 2 0 0 0 1 0 0 2 1 1.000000 130 380 0 102 2 0 0 0 0 103 2 -6.020745 1 1 121412 1 37 1 1 2 3 2.187475 0 0.570000 1.770000 0.574847 0.890000 7.600000e-01 1.000000 1.000000 0.900253 0.890000 1 8.200000e-01 9.800000e-01 RP1L1 94137 broad.mit.edu 37 8 10470667 10470667 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr8:10470667C>T ENST00000382483.3 - 4 1164 c.941G>A c.(940-942)cGc>cAc p.R314H NM_178857.5 NP_849188.4 Q8IWN7 RP1L1_HUMAN retinitis pigmentosa 1-like 1 148 CTCATTCATGCGGACCTTCTT 0.662000 0 SO:0001583 missense ENST00000382483.3 0 1 hg19 CCDS43708.1 . . . . . . . . . . C 11.27 1.589738 0.28357 . . ENSG00000183638 ENST00000382483 T 0.03745 3.82 4.82 -5.91 0.02269 . 1.397370 0.05168 N 0.499120 T 0.03136 0.0092 N 0.19112 0.55 0.09310 N 1 B 0.23058 0.079 B 0.12837 0.008 T 0.35822 -0.9773 10 0.21014 T 0.42 -0.1093 16.5366 0.84374 0.0:0.105:0.0:0.895 . 314 A6NKC6 . H 314 ENSP00000371923:R314H ENSP00000371923:R314H R - 2 0 RP1L1 10508077 0.003000 0.15002 0.013000 0.15412 0.915000 0.54546 0.048000 0.14078 -1.353000 0.02191 0.591000 0.81541 CGC TCGA-OE-A75W-01A-12D-A32N-08 RP1L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000375673.1 0 0 0 6 573 1 174 0 0 0 1 174 2 0 0 0 0 0 2 0 0.076678 6 565 1 174 13 0 0 0 1 174 2 -2.022498 0 1 121092 2 40 1 0 1 1 1.571413 1 0.570000 1.770000 0.400989 0.020000 0 0.050000 0.030000 0.030283 0.020000 0 1.000000e-02 4.000000e-02 WISP1 8840 broad.mit.edu 37 8 134233083 134233083 + Splice_Site SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr8:134233083C>T ENST00000250160.6 + 3 715 c.609C>T c.(607-609)ttC>ttT p.F203F WISP1_ENST00000517423.1_Intron|WISP1_ENST00000377863.2_Intron|WISP1_ENST00000519433.1_Intron|WISP1_ENST00000220856.6_Intron NM_003882.3 NP_003873.1 O95388 WISP1_HUMAN WNT1 inducible signaling pathway protein 1 p.F203F(1) 21 all_epithelial(106;5.39e-23)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.0107) CAGGAGCCTTCGGTGGGTGTG 0.632000 1 Substitution - coding silent(1) SO:0001630 splice_region_variant ENST00000250160.6 1 0 hg19 CCDS6371.1 TCGA-OE-A75W-01A-12D-A32N-08 WISP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378794.2 1 0 1 65 207 0 56 0 1.471406e-01 0 3 0 56 2 0 0 0 0 0 2 1 1.000000 63 204 0 56 2 0 0 0 0 56 2 -20.000000 1 1 120958 8 36 1 0 3 3 2.850194 1 0.570000 1.770000 0.665370 0.990000 8.500000e-01 1.000000 1.000000 0.984538 0.990000 1 9.600000e-01 1 PLEC 5339 broad.mit.edu 37 8 144993374 144993374 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr8:144993374G>A ENST00000322810.4 - 32 11195 c.11026C>T c.(11026-11028)Cgc>Tgc p.R3676C PLEC_ENST00000436759.2_Missense_Mutation_p.R3566C|PLEC_ENST00000354589.3_Missense_Mutation_p.R3539C|PLEC_ENST00000527096.1_Missense_Mutation_p.R3562C|PLEC_ENST00000357649.2_Missense_Mutation_p.R3543C|PLEC_ENST00000354958.2_Missense_Mutation_p.R3517C|PLEC_ENST00000345136.3_Missense_Mutation_p.R3539C|PLEC_ENST00000356346.3_Missense_Mutation_p.R3525C|PLEC_ENST00000398774.2_Missense_Mutation_p.R3507C NM_201380.2 NP_958782.1 Q15149 PLEC_HUMAN plectin 137 GGCAGAAGGCGCAAGCCCGTC 0.597000 0 SO:0001583 missense ENST00000322810.4 0 1 hg19 CCDS43772.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 2.854 -0.237549 0.05944 . . ENSG00000178209 ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096 T;T;T;T;T;T;T;T;T 0.69175 -0.38;-0.38;-0.38;-0.38;-0.38;-0.38;-0.38;-0.38;-0.38 4.72 2.67 0.31697 . 0.448841 0.19000 U 0.125371 T 0.36248 0.0960 N 0.03115 -0.41 0.40996 D 0.984897 B;B;B;B;B;B;B;B 0.06786 0.001;0.001;0.001;0.0;0.001;0.001;0.001;0.001 B;B;B;B;B;B;B;B 0.04013 0.0;0.0;0.0;0.0;0.0;0.001;0.0;0.0 T 0.26883 -1.0090 10 0.59425 D 0.04 . 2.1195 0.03723 0.3623:0.0:0.392:0.2457 . 3566;3525;3517;3676;3507;3539;3543;3539 Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4 .;.;.;PLEC_HUMAN;.;.;.;. C 3539;3543;3539;3507;3676;3517;3525;3566;3562 ENSP00000344848:R3539C;ENSP00000350277:R3543C;ENSP00000346602:R3539C;ENSP00000381756:R3507C;ENSP00000323856:R3676C;ENSP00000347044:R3517C;ENSP00000348702:R3525C;ENSP00000388180:R3566C;ENSP00000434583:R3562C ENSP00000323856:R3676C R - 1 0 PLEC 145065362 0.756000 0.28383 0.916000 0.36221 0.053000 0.15095 2.222000 0.42926 1.111000 0.41721 0.448000 0.29417 CGC TCGA-OE-A75W-01A-12D-A32N-08 PLEC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383281.1 0 0 0 9 1265 1 217 0 1.435946e-02 0 161 1 217 5 0 0 0 0 0 2 0 0.027185 9 1246 1 213 20 0 0 0 1 217 2 -2.025378 0 1 120920 20 47 1 0 3 3 2.850194 1 0.570000 1.770000 0.665370 0.020000 0 0.060000 0.030000 0.032847 0.020000 0 1.000000e-02 5.000000e-02 MURC 347273 broad.mit.edu 37 9 103340638 103340638 + Silent SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr9:103340638C>T ENST00000307584.5 + 1 278 c.213C>T c.(211-213)gaC>gaT p.D71D RN7SKP87_ENST00000364096.1_RNA NM_001018116.1 NP_001018126.1 Q5BKX8 MURC_HUMAN muscle-related coiled-coil protein 16 Acute lymphoblastic leukemia(62;0.0461) TCCAGATTGACCTGTTGAAGC 0.418000 0 SO:0001819 synonymous_variant ENST00000307584.5 0 1 hg19 CCDS35083.1 TCGA-OE-A75W-01A-12D-A32N-08 MURC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053419.2 0 0 0 12 482 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 0.999020 13 471 0 94 2 0 0 0 0 95 2 -3.020032 1 1 0 0 1 0 0 0 2.021774 0 0.570000 1.770000 0.544008 0.070000 3.000000e-02 0.140000 0.080000 0.086570 0.070000 0 5.000000e-02 1.100000e-01 TNC 3371 broad.mit.edu 37 9 117791711 117791711 + Missense_Mutation SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr9:117791711G>A ENST00000350763.4 - 25 6508 c.6097C>T c.(6097-6099)Cgc>Tgc p.R2033C TNC_ENST00000535648.1_Missense_Mutation_p.R1578C|TNC_ENST00000346706.3_Missense_Mutation_p.R1487C|TNC_ENST00000345230.3_Missense_Mutation_p.R1396C|TNC_ENST00000423613.2_Missense_Mutation_p.R1760C|TNC_ENST00000340094.3_Missense_Mutation_p.R1669C|TNC_ENST00000341037.4_Missense_Mutation_p.R1851C|TNC_ENST00000542877.1_Missense_Mutation_p.R1670C|TNC_ENST00000537320.1_Missense_Mutation_p.R1396C NM_002160.3 NP_002151.2 P24821 TENA_HUMAN tenascin C 120 AAGTTCTCGCGTCCGTTTTTG 0.463000 0 SO:0001583 missense ENST00000350763.4 0 1 hg19 CCDS6811.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 16.65|16.65 3.182544|3.182544 0.57800|0.57800 .|. .|. ENSG00000041982|ENSG00000041982 ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877|ENST00000544972 T;T;T;T;T;T;T;T;T|. 0.21031|. 2.03;2.03;2.03;2.03;2.03;2.03;2.03;2.03;2.03|. 5.48|5.48 4.53|4.53 0.55603|0.55603 Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);|. 0.340153|. 0.30401|. N|. 0.009704|. T|T 0.38054|0.38054 0.1026|0.1026 L|L 0.48362|0.48362 1.52|1.52 0.26177|0.26177 N|N 0.979773|0.979773 D;D|. 0.89917|. 1.0;0.999|. D;D|. 0.71414|. 0.973;0.93|. T|T 0.32107|0.32107 -0.9919|-0.9919 10|5 0.72032|. D|. 0.01|. .|. 3.7527|3.7527 0.08573|0.08573 0.0839:0.1325:0.5337:0.2499|0.0839:0.1325:0.5337:0.2499 .|. 1760;2033|. E9PC84;P24821|. .;TENA_HUMAN|. C|M 1669;1578;1487;1396;2033;1851;1760;1396;1670|595 ENSP00000344400:R1669C;ENSP00000438152:R1578C;ENSP00000344555:R1487C;ENSP00000345861:R1396C;ENSP00000265131:R2033C;ENSP00000339553:R1851C;ENSP00000411406:R1760C;ENSP00000443478:R1396C;ENSP00000442242:R1670C|. ENSP00000344400:R1669C|. R|T -|- 1|2 0|0 TNC|TNC 116831532|116831532 0.934000|0.934000 0.31675|0.31675 0.986000|0.986000 0.45419|0.45419 0.442000|0.442000 0.32017|0.32017 4.235000|4.235000 0.58666|0.58666 2.587000|2.587000 0.87381|0.87381 0.655000|0.655000 0.94253|0.94253 CGC|ACG TCGA-OE-A75W-01A-12D-A32N-08 TNC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055418.2 0 0 0 14 503 0 92 0 8.195302e-01 0 115 0 92 2 1 9.989375e-01 14 704 1 854 5 1 0.999735 13 497 0 91 2 0 0 0 0 92 2 -2.526147 1 1 121412 9 42 1 0 0 0 1.991791 0 0.570000 1.770000 0.538429 0.080000 4.000000e-02 0.140000 0.090000 0.094325 0.080000 0 6.000000e-02 1.200000e-01 OR1L4 254973 broad.mit.edu 37 9 125486388 125486388 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr9:125486388G>A ENST00000259466.1 + 1 120 c.120G>A c.(118-120)gcG>gcA p.A40A NM_001005235.1 NP_001005235.1 Q8NGR5 OR1L4_HUMAN olfactory receptor, family 1, subfamily L, member 4 p.A40A(1) 20 TACTCACTGCGGTGGGGAATG 0.517000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000259466.1 0 1 hg19 CCDS35129.1 TCGA-OE-A75W-01A-12D-A32N-08 OR1L4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053951.1 0 0 0 12 606 0 120 0 0 0 0 120 2 0 0 0 0 0 2 1 0.999004 12 593 0 118 2 0 0 0 0 120 2 -2.050768 0 1 0 0 1 0 0 0 1.991791 0 0.570000 1.770000 0.538429 0.060000 2.000000e-02 0.110000 0.070000 0.068434 0.060000 0 4.000000e-02 9.000000e-02 GOLGA1 2800 broad.mit.edu 37 9 127644234 127644234 + Splice_Site SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr9:127644234C>T ENST00000373555.4 - 21 2299 c.e21-1 NM_002077.3 NP_002068 Q92805 GOGA1_HUMAN golgin A1 20 GTCTGATTTTCTGAAAAACCA 0.493000 0 SO:0001630 splice_region_variant ENST00000373555.4 1 1 hg19 CCDS6860.1 . . . . . . . . . . C 25.4 4.633014 0.87660 . . ENSG00000136935 ENST00000373555 . . . 5.81 5.81 0.92471 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 19.051 0.93046 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . GOLGA1 126684055 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 3.772000 0.55325 2.745000 0.94114 0.655000 0.94253 . TCGA-OE-A75W-01A-12D-A32N-08 GOLGA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054049.1 1 0 1 27 215 0 41 0 0 1 0 0 41 2 0 0 0 0 0 2 1 1.000000 27 215 0 41 2 0 0 0 0 41 2 -20.000000 1 1 0 0 1 0 0 0 1.991791 0 0.570000 1.770000 0.538429 0.360000 2.400000e-01 0.500000 0.370000 0.373781 0.360000 0 3.000000e-01 4.400000e-01 NOTCH1 4851 broad.mit.edu 37 9 139412298 139412298 + Silent SNP G G A TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr9:139412298G>A ENST00000277541.6 - 8 1422 c.1347C>T c.(1345-1347)tgC>tgT p.C449C MIR4673_ENST00000584777.1_RNA NM_017617.3 NP_060087.3 P46531 NOTC1_HUMAN notch 1 1359 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) CGTCGATCTCGCATCGGGGGC 0.647000 T, Mis, O TRB@ T-ALL HNSCC(8;0.001) Dom yes 9 9q34.3 4851 Notch homolog 1, translocation-associated (Drosophila) (TAN1) L 0 SO:0001819 synonymous_variant ENST00000277541.6 1 1 hg19 CCDS43905.1 TCGA-OE-A75W-01A-12D-A32N-08 NOTCH1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055087.1 1 0 1 97 281 0 89 0 0 0 0 89 2 0 0 0 0 0 2 1 1.000000 97 279 0 87 2 0 0 0 0 89 2 -5.695908 1 1 0 0 1 0 0 0 1.991791 0 0.570000 1.770000 0.538429 0.830000 6.900000e-01 0.980000 0.830000 0.840585 0.830000 0 7.600000e-01 9.100000e-01 CDKN2A 1029 broad.mit.edu 37 9 21971111 21971111 + Missense_Mutation SNP G G A rs121913385 TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chr9:21971111G>A ENST00000304494.5 - 2 517 c.247C>T c.(247-249)Cac>Tac p.H83Y CDKN2A_ENST00000530628.2_Missense_Mutation_p.A97V|CDKN2A_ENST00000498124.1_Missense_Mutation_p.H83Y|CDKN2A_ENST00000579755.1_Missense_Mutation_p.A97V|CDKN2A_ENST00000494262.1_Missense_Mutation_p.H32Y|CDKN2A_ENST00000497750.1_Missense_Mutation_p.H32Y|CDKN2A_ENST00000578845.2_Missense_Mutation_p.H32Y|CDKN2A_ENST00000446177.1_Missense_Mutation_p.H83Y|CDKN2A_ENST00000361570.3_Missense_Mutation_p.A138V|CDKN2A_ENST00000498628.2_Missense_Mutation_p.H32Y|CDKN2A_ENST00000579122.1_Missense_Mutation_p.H83Y|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Missense_Mutation_p.H32Y NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.?(44)|p.H83Y(30)|p.A138V(2)|p.H83fs*2(2)|p.H83N(1)|p.V82fs*62(1)|p.0(1)|p.V82_G89>G(1)|p.E61_L94del(1)|p.R137fs*48(1)|p.A68fs*3(1)|p.P81_A85del(1)|p.R80fs*34(1)|p.V82_E88del(1) 4199 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) GCAGCGTCGTGCACGGGTCGG 0.741000 H83Y(CALU3_LUNG)|H83Y(HS944T_SKIN)|H83Y(JHH2_LIVER)|H83Y(OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|H83Y(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE) 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1403 Whole gene deletion(1316)|Unknown(44)|Substitution - Missense(33)|Deletion - Frameshift(6)|Deletion - In frame(3)|Complex - deletion inframe(1) GRCh37 CM053801|CM056557 CDKN2A M rs121913385 SO:0001583 missense ENST00000304494.5 1 1 hg19 CCDS6510.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 26.7|26.7 4.762523|4.762523 0.89932|0.89932 .|. .|. ENSG00000147889|ENSG00000147889 ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177 T;T|T;T 0.80393|0.71222 -1.37;-1.31|-0.55;-0.55 5.93|5.93 5.93|5.93 0.95920|0.95920 .|Ankyrin repeat-containing domain (4); 0.000000|. 0.37261|. N|. 0.002164|. T|T 0.77579|0.77579 0.4151|0.4151 L|L 0.27053|0.27053 0.805|0.805 0.46521|0.46521 D|D 0.999085|0.999085 P|D 0.47191|0.76494 0.891|0.999 B|D 0.44044|0.75484 0.439|0.986 T|T 0.79024|0.79024 -0.1972|-0.1972 10|9 0.62326|0.66056 D|D 0.03|0.02 -15.192|-15.192 19.1026|19.1026 0.93279|0.93279 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 138|83 Q8N726|P42771 CD2A2_HUMAN|CD2A1_HUMAN V|Y 138;97|83 ENSP00000355153:A138V;ENSP00000432664:A97V|ENSP00000307101:H83Y;ENSP00000394932:H83Y ENSP00000355153:A138V|ENSP00000307101:H83Y A|H -|- 2|1 0|0 CDKN2A|CDKN2A 21961111|21961111 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.915000|0.915000 0.54546|0.54546 8.665000|8.665000 0.91144|0.91144 2.803000|2.803000 0.96430|0.96430 0.650000|0.650000 0.86243|0.86243 GCA|CAC TCGA-OE-A75W-01A-12D-A32N-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 60 78 0 35 1 1 307 15 0 35 2 1 1 39 53 0 109 2 1 1.000000 54 67 0 30 2 0 0 0 0 35 2 -20.000000 1 1 0 0 1 0 1 1 1.541195 1 0.570000 1.770000 0.398601 0.950000 8.200000e-01 1.000000 0.990000 0.945383 0.950000 1 8.900000e-01 9.900000e-01 ARHGAP4 393 broad.mit.edu 37 X 153187163 153187163 + Missense_Mutation SNP C C T TCGA-OE-A75W-01A-12D-A32N-08 TCGA-OE-A75W-10A-01D-A32N-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx fcfcc363-8ced-4979-967d-b42dac3fac8b 86bdd531-09be-40db-b941-b7a4273bdf4e g.chrX:153187163C>T ENST00000350060.5 - 2 208 c.167G>A c.(166-168)cGc>cAc p.R56H ARHGAP4_ENST00000393721.1_Missense_Mutation_p.R56H|ARHGAP4_ENST00000370016.1_Missense_Mutation_p.R56H|ARHGAP4_ENST00000370028.3_Missense_Mutation_p.R56H|ARHGAP4_ENST00000537206.1_Missense_Mutation_p.R33H NM_001666.4 NP_001657.3 P98171 RHG04_HUMAN Rho GTPase activating protein 4 14 all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05) CACCTCAGCGCGGCGCCGCAT 0.697000 0 SO:0001583 missense ENST00000350060.5 0 1 hg19 CCDS14736.1 . . . . . . . . . . C 15.61 2.885319 0.51908 . . ENSG00000089820 ENST00000393721;ENST00000370028;ENST00000350060;ENST00000370016;ENST00000537206;ENST00000442262;ENST00000422091 T;T;T;T;T;T;T 0.54479 0.57;0.57;0.57;0.57;0.57;0.57;0.57 5.08 5.08 0.68730 Fps/Fes/Fer/CIP4 homology (3); 0.000000 0.41194 D 0.000933 T 0.64853 0.2636 L 0.60455 1.87 0.19775 N 0.99996 D;D 0.89917 1.0;1.0 D;D 0.85130 0.997;0.997 T 0.58702 -0.7590 10 0.87932 D 0 . 7.4388 0.27171 0.0:0.8068:0.0:0.1932 . 56;56 Q86UY3;P98171 .;RHG04_HUMAN H 56;56;56;56;33;33;33 ENSP00000377322:R56H;ENSP00000359045:R56H;ENSP00000203786:R56H;ENSP00000359033:R56H;ENSP00000444169:R33H;ENSP00000398259:R33H;ENSP00000413782:R33H ENSP00000203786:R56H R - 2 0 ARHGAP4 152840357 0.630000 0.27155 0.141000 0.22245 0.297000 0.27493 2.726000 0.47302 2.262000 0.75019 0.436000 0.28706 CGC TCGA-OE-A75W-01A-12D-A32N-08 ARHGAP4-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000061119.1 1 0 1 29 23 0 10 0 9.926918e-01 0 10 0 10 2 0 0 0 0 0 2 1 1.000000 29 23 0 10 2 0 0 0 0 10 2 -20.000000 1 1 120410 1 25 1 0 1 1 0.570000 1.770000 0.570000 0.900000 7.000000e-01 1.000000 0.970000 0.893053 0.900000 1 8.000000e-01 9.700000e-01