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 C18orf8 29919 broad.mit.edu 37 18 21098885 21098887 + In_Frame_Del DEL CAT CAT - TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 CAT - CAT CAT Valid Somatic Phase_I WXS RNA Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr18:21098885_21098887delCAT ENST00000269221.3 + 8 795_797 c.685_687delCAT c.(685-687)catdel p.H230del C18orf8_ENST00000590868.1_In_Frame_Del_p.H182del NM_013326.3 NP_037458.3 Q96DM3 MIC1_HUMAN chromosome 18 open reading frame 8 21 all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127) CTTCTTGAGGCATCATTCTCGGA 0.424000 0 SO:0001651 inframe_deletion ENST00000269221.3 1 1 hg19 CCDS32803.1 TCGA-3A-A9IB-01A-21D-A397-08 C18orf8-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445386.1 1 0 0 70 306 0 57 1 9.998735e-01 16 44 0 57 2 0 0 0 0 0 0 1 1.000000 84 314 0 56 2 0 0 0 0 0 0 -20.000000 1 0 0 0 1 0 2 2 1.872751 1 0.380000 1.970000 0.380000 0.990000 7.800000e-01 1.000000 1.000000 0.956841 0.990000 1 0.880000 1.000000 TNFRSF10A 8797 broad.mit.edu 37 8 23054679 23054701 + Frame_Shift_Del DEL CAGCCTCCTCCTCTGAGACCCTT CAGCCTCCTCCTCTGAGACCCTT - TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr8:23054679_23054701delCAGCCTCCTCCTCTGAGACCCTT ENST00000221132.3 - 9 1095_1117 c.1031_1053delAAGGGTCTCAGAGGAGGAGGCTG c.(1030-1053)gaagggtctcagaggaggaggctgfs p.EGSQRRRL344fs NM_003844.3 NP_003835.3 O00220 TR10A_HUMAN tumor necrosis factor receptor superfamily, member 10a 16 Prostate(55;0.0421)|Breast(100;0.14) CTGGAACCAGCAGCCTCCTCCTCTGAGACCCTTCAGCTTCTGC 0.556000 0 SO:0001589 frameshift_variant ENST00000221132.3 1 1 hg19 CCDS6039.1 TCGA-3A-A9IB-01A-21D-A397-08 TNFRSF10A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000215133.2 0 0 0 17 372 0 102 0 6.688081e-01 0 51 0 102 2 0 0 0 0 0 0 1 0.775461 47 400 1 103 16 0 0 0 0 0 0 -4.112441 1 1 0 0 1 0 1 1 1.694817 1 0.380000 1.970000 0.243441 0.180000 1.100000e-01 0.290000 0.190000 0.196979 0.180000 0 0.140000 0.240000 SEC31B 25956 broad.mit.edu 37 10 102267770 102267770 + Silent SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr10:102267770C>T ENST00000370345.3 - 6 631 c.534G>A c.(532-534)cgG>cgA p.R178R SEC31B_ENST00000535773.1_Silent_p.R21R|NDUFB8_ENST00000531258.1_3'UTR|SEC31B_ENST00000451524.1_Silent_p.R178R|NDUFB8_ENST00000557395.1_3'UTR|SEC31B_ENST00000370329.5_Silent_p.R181R NM_015490.3 NP_056305.1 Q9NQW1 SC31B_HUMAN SEC31 homolog B (S. cerevisiae) 36 Colorectal(252;0.117) GTTGGGCTTGCCGGTTCCAAG 0.517000 0 SO:0001819 synonymous_variant ENST00000370345.3 0 1 hg19 CCDS7495.1 TCGA-3A-A9IB-01A-21D-A397-08 SEC31B-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051198.1 0 0 0 6 507 0 50 0 3.017397e-03 0 6 0 50 2 0 0 0 0 0 2 1 0.964087 6 502 0 50 2 0 0 0 0 0 2 -1.972706 0 1 0 0 1 1 2 3 2.071752 0 0.380000 1.970000 0.390424 0.060000 2.000000e-02 1.000000 0.060000 0.139997 0.060000 0 0.040000 0.110000 CHST15 51363 broad.mit.edu 37 10 125805512 125805512 + Missense_Mutation SNP G G A rs145631200 TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr10:125805512G>A ENST00000346248.5 - 2 859 c.217C>T c.(217-219)Cgc>Tgc p.R73C CHST15_ENST00000421115.1_Missense_Mutation_p.R73C|CHST15_ENST00000435907.1_Missense_Mutation_p.R73C|CHST15_ENST00000462406.1_5'Flank NM_015892.4 NP_056976.2 Q7LFX5 CHSTF_HUMAN carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15 26 TTTTTGAAGCGCAAAAACCCA 0.453000 0 SO:0001583 missense ENST00000346248.5 0 1 hg19 CCDS7638.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 G 7.620 0.676663 0.14841 6.81E-4 0.0 ENSG00000182022 ENST00000346248;ENST00000435907;ENST00000434607;ENST00000546346;ENST00000421115 . . . 5.67 4.77 0.60923 . 0.253960 0.41294 N 0.000904 T 0.20740 0.0499 N 0.04508 -0.205 0.31534 N 0.660833 B;B 0.25007 0.116;0.071 B;B 0.19391 0.025;0.011 T 0.13469 -1.0508 9 0.44086 T 0.13 -28.6264 9.5674 0.39407 0.1996:0.0:0.8004:0.0 . 73;73 Q7LFX5-2;Q7LFX5 .;CHSTF_HUMAN C 73 . ENSP00000333947:R73C R - 1 0 CHST15 125795502 0.905000 0.30787 0.951000 0.38953 0.262000 0.26303 1.908000 0.39907 1.415000 0.47037 -0.219000 0.12488 CGC TCGA-3A-A9IB-01A-21D-A397-08 CHST15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050856.1 0 0 0 6 414 0 87 0 3.192314e-01 0 70 0 87 2 0 0 0 0 0 2 1 0.964184 6 409 0 86 2 0 0 0 0 0 2 -2.478128 0 1 121412 10 43 1 1 2 3 2.071752 0 0.380000 1.970000 0.390424 0.080000 2.000000e-02 1.000000 0.080000 0.154757 0.080000 0 0.050000 0.140000 MMP13 4322 broad.mit.edu 37 11 102822878 102822878 + Missense_Mutation SNP G G A rs147544761 TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr11:102822878G>A ENST00000260302.3 - 5 690 c.662C>T c.(661-663)gCg>gTg p.A221V MMP13_ENST00000340273.4_Missense_Mutation_p.A221V NM_002427.3 NP_002418.1 P45452 MMP13_HUMAN matrix metallopeptidase 13 (collagenase 3) 27 all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967) Marimastat(DB00786) GAACTCATGCGCAGCAACAAG 0.423000 0 SO:0001583 missense ENST00000260302.3 0 1 hg19 CCDS8324.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 G 36 5.655859 0.96724 6.81E-4 0.0 ENSG00000137745 ENST00000260302;ENST00000546012;ENST00000340273 T;T 0.21543 2.0;2.0 5.75 5.75 0.90469 Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1); 0.093477 0.64402 D 0.000001 T 0.48277 0.1491 M 0.67700 2.07 0.80722 D 1 D 0.89917 1.0 D 0.78314 0.991 T 0.32955 -0.9887 10 0.59425 D 0.04 . 20.312 0.98644 0.0:0.0:1.0:0.0 . 221 P45452 MMP13_HUMAN V 221 ENSP00000260302:A221V;ENSP00000339672:A221V ENSP00000260302:A221V A - 2 0 MMP13 102328088 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 7.946000 0.87746 2.866000 0.98385 0.650000 0.86243 GCG TCGA-3A-A9IB-01A-21D-A397-08 MMP13-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000386648.1 0 0 0 7 521 0 63 0 0 0 1 0 63 2 0 0 0 0 0 2 1 0.980200 7 517 0 63 2 0 0 0 0 0 2 -2.447729 0 1 121412 17 46 1 1 2 3 2.044609 0 0.380000 1.970000 0.385835 0.070000 2.000000e-02 1.000000 0.070000 0.114902 0.070000 0 0.040000 0.110000 MMP13 4322 broad.mit.edu 37 11 102826101 102826101 + Missense_Mutation SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr11:102826101C>T ENST00000260302.3 - 2 270 c.242G>A c.(241-243)gGc>gAc p.G81D MMP13_ENST00000340273.4_Missense_Mutation_p.G81D NM_002427.3 NP_002418.1 P45452 MMP13_HUMAN matrix metallopeptidase 13 (collagenase 3) 27 all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967) Marimastat(DB00786) GTCAAGTTTGCCAGTCACCTC 0.473000 0 SO:0001583 missense ENST00000260302.3 0 1 hg19 CCDS8324.1 . . . . . . . . . . C 27.6 4.846161 0.91277 . . ENSG00000137745 ENST00000260302;ENST00000546012;ENST00000340273 D;D 0.90197 -2.63;-2.63 5.77 5.77 0.91146 Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1); 0.000000 0.85682 D 0.000000 D 0.97111 0.9056 H 0.95816 3.725 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.97478 1.0045 10 0.87932 D 0 . 20.3627 0.98863 0.0:1.0:0.0:0.0 . 81 P45452 MMP13_HUMAN D 81 ENSP00000260302:G81D;ENSP00000339672:G81D ENSP00000260302:G81D G - 2 0 MMP13 102331311 1.000000 0.71417 0.995000 0.50966 0.870000 0.49936 7.776000 0.85560 2.885000 0.99019 0.655000 0.94253 GGC TCGA-3A-A9IB-01A-21D-A397-08 MMP13-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000386648.1 0 0 0 7 692 0 75 0 0 0 1 0 75 2 0 0 0 0 0 2 1 0.980570 7 691 0 74 2 0 0 0 0 0 2 -1.929216 0 1 0 0 1 1 2 3 2.044609 0 0.380000 1.970000 0.385835 0.050000 1.000000e-02 1.000000 0.060000 0.096228 0.050000 0 0.030000 0.090000 SLC5A12 159963 broad.mit.edu 37 11 26743035 26743035 + Missense_Mutation SNP C C T rs142065702 TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr11:26743035C>T ENST00000396005.3 - 1 536 c.227G>A c.(226-228)cGc>cAc p.R76H SLC5A12_ENST00000280467.6_Missense_Mutation_p.R76H NM_178498.3 NP_848593.2 Q1EHB4 SC5AC_HUMAN solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12 p.R76L(2) 35 TGCCCCAAAGCGGTAGACTTC 0.512000 2 Substitution - Missense(2) SO:0001583 missense ENST00000396005.3 1 1 hg19 CCDS7860.2 . . . . . . . . . . C 17.76 3.467643 0.63625 2.27E-4 0.0 ENSG00000148942 ENST00000396005;ENST00000280467 D;D 0.87966 -2.32;-2.32 5.59 5.59 0.84812 . 0.000000 0.85682 D 0.000000 D 0.89567 0.6752 M 0.73962 2.25 0.53688 D 0.99997 B;P 0.50617 0.227;0.937 B;P 0.47015 0.082;0.534 D 0.88612 0.3157 10 0.35671 T 0.21 . 19.5898 0.95506 0.0:1.0:0.0:0.0 . 76;76 Q1EHB4-2;Q1EHB4 .;SC5AC_HUMAN H 76 ENSP00000379326:R76H;ENSP00000280467:R76H ENSP00000280467:R76H R - 2 0 SLC5A12 26699611 0.985000 0.35326 1.000000 0.80357 0.898000 0.52572 2.683000 0.46943 2.643000 0.89663 0.585000 0.79938 CGC TCGA-3A-A9IB-01A-21D-A397-08 SLC5A12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319681.1 1 0 1 50 221 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 1.000000 50 220 0 46 2 0 0 0 0 0 2 -20.000000 1 1 121412 4 39 1 1 2 3 2.044609 0 0.380000 1.970000 0.385835 0.980000 7.500000e-01 1.000000 1.000000 0.945417 0.980000 1 0.860000 1.000000 RTN3 10313 broad.mit.edu 37 11 63449189 63449189 + Silent SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr11:63449189C>T ENST00000377819.5 + 1 235 c.81C>T c.(79-81)ggC>ggT p.G27G RTN3_ENST00000354497.4_Silent_p.G27G|RTN3_ENST00000538995.1_3'UTR|RTN3_ENST00000540798.1_Silent_p.G27G|RTN3_ENST00000537981.1_Silent_p.G27G|RTN3_ENST00000356000.3_Silent_p.G27G|RTN3_ENST00000339997.4_Silent_p.G27G|RTN3_ENST00000341307.2_Silent_p.G27G NM_001265589.1 NP_001252518.1 O95197 RTN3_HUMAN reticulon 3 20 CGCCCGGCGGCGGCGGGAGCC 0.746000 0 SO:0001819 synonymous_variant ENST00000377819.5 1 1 hg19 CCDS58141.1 TCGA-3A-A9IB-01A-21D-A397-08 RTN3-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000397846.1 1 0 0 31 125 0 50 1 1 73 134 0 50 2 0 0 0 0 0 2 1 1.000000 30 123 0 48 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.044609 0 0.380000 1.970000 0.385835 0.990000 7.500000e-01 1.000000 1.000000 0.963169 0.990000 1 0.890000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 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-3A-A9IB-01A-21D-A397-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 66 244 0 65 1 9.876195e-01 13 15 0 65 2 1 1 75 311 0 223 2 1 1.000000 66 243 0 64 2 1 1 2089 5927 19 7994 31 -20.000000 1 1 121404 2 44 1 1 2 3 2.053135 0 0.380000 1.970000 0.408115 0.990000 9.400000e-01 1.000000 1.000000 0.996734 0.990000 1 0.990000 1.000000 KRT85 3891 broad.mit.edu 37 12 52760836 52760836 + Silent SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr12:52760836G>A ENST00000257901.3 - 1 429 c.354C>T c.(352-354)tgC>tgT p.C118C KRT85_ENST00000544265.1_5'Flank NM_002283.3 NP_002274.1 P78386 KRT85_HUMAN keratin 85 36 Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088) CCTGCTTCACGCACTGTGCGT 0.632000 0 SO:0001819 synonymous_variant ENST00000257901.3 1 1 hg19 CCDS8824.1 TCGA-3A-A9IB-01A-21D-A397-08 KRT85-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405184.1 1 0 1 129 606 0 182 0 0 0 0 182 2 0 0 0 0 0 2 1 1.000000 123 584 0 205 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.053135 0 0.380000 1.970000 0.408115 0.980000 8.200000e-01 1.000000 1.000000 0.960504 0.980000 1 0.890000 1.000000 ERBB3 2065 broad.mit.edu 37 12 56495712 56495712 + Missense_Mutation SNP A A G TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr12:56495712A>G ENST00000267101.3 + 28 4342 c.3902A>G c.(3901-3903)cAg>cGg p.Q1301R PA2G4_ENST00000552766.1_5'Flank|ERBB3_ENST00000450146.2_Missense_Mutation_p.Q658R|RP11-603J24.17_ENST00000548595.1_RNA|ERBB3_ENST00000549832.1_Missense_Mutation_p.Q421R|PA2G4_ENST00000303305.6_5'Flank|RP11-603J24.9_ENST00000548861.1_Intron|ERBB3_ENST00000553131.1_Missense_Mutation_p.Q542R|ERBB3_ENST00000415288.2_Missense_Mutation_p.Q1242R NM_001982.3 NP_001973.2 P21860 ERBB3_HUMAN v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3 8 OV - Ovarian serous cystadenocarcinoma(18;0.112) CCTGGACATCAGGCCCCCCAT 0.537000 0 SO:0001583 missense ENST00000267101.3 0 1 hg19 CCDS31833.1 . . . . . . . . . . A 7.897 0.733645 0.15574 . . ENSG00000065361 ENST00000267101;ENST00000450146;ENST00000415288;ENST00000550070;ENST00000553131;ENST00000549832 T;T;T;T;T 0.78003 -1.0;-0.92;-0.99;-1.14;-0.88 5.39 4.26 0.50523 . 0.563354 0.17890 N 0.158548 T 0.56093 0.1962 N 0.14661 0.345 0.23855 N 0.996651 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.01281 0.0;0.0;0.0 T 0.37454 -0.9705 10 0.07482 T 0.82 . 8.109 0.30903 0.8379:0.0:0.1621:0.0 . 1242;421;1301 P21860-4;B3KWG5;P21860 .;.;ERBB3_HUMAN R 1301;658;1242;424;542;421 ENSP00000267101:Q1301R;ENSP00000399178:Q658R;ENSP00000408340:Q1242R;ENSP00000449129:Q542R;ENSP00000448729:Q421R ENSP00000267101:Q1301R Q + 2 0 ERBB3 54781979 0.059000 0.20769 0.807000 0.32361 0.337000 0.28794 0.589000 0.23939 1.069000 0.40788 0.533000 0.62120 CAG TCGA-3A-A9IB-01A-21D-A397-08 ERBB3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407619.3 0 0 0 6 717 0 140 0 5.702678e-01 1 210 0 140 2 0 0 0 0 0 2 1 0.964309 6 712 0 139 2 0 0 0 0 0 2 -2.336163 0 1 0 0 1 1 2 3 2.053135 0 0.380000 1.970000 0.408115 0.050000 0 1.000000 0.050000 0.222902 0.050000 0 0.020000 1.000000 LRP1 4035 broad.mit.edu 37 12 57594247 57594247 + Missense_Mutation SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr12:57594247G>A ENST00000243077.3 + 63 10503 c.10037G>A c.(10036-10038)tGc>tAc p.C3346Y NM_002332.2 NP_002323.2 Q07954 LRP1_HUMAN low density lipoprotein receptor-related protein 1 184 Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) AACGACAAGTGCATCCCCTTC 0.617000 0 SO:0001583 missense ENST00000243077.3 1 1 hg19 CCDS8932.1 . . . . . . . . . . G 18.57 3.652311 0.67472 . . ENSG00000123384 ENST00000243077 D 0.99919 -8.0 4.56 4.56 0.56223 Low-density lipoprotein (LDL) receptor class A, conserved site (1);Growth factor, receptor (1); 0.000000 0.85682 D 0.000000 D 0.99943 0.9975 H 0.97491 4.015 0.80722 D 1 D 0.76494 0.999 D 0.87578 0.998 D 0.96047 0.9028 10 0.59425 D 0.04 . 16.3322 0.83039 0.0:0.0:1.0:0.0 . 3346 Q07954 LRP1_HUMAN Y 3346 ENSP00000243077:C3346Y ENSP00000243077:C3346Y C + 2 0 LRP1 55880514 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 7.765000 0.85310 2.386000 0.81285 0.555000 0.69702 TGC TCGA-3A-A9IB-01A-21D-A397-08 LRP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412772.2 1 0 0 72 216 0 51 1 1 64 203 0 51 2 0 0 0 0 0 2 1 1.000000 71 213 0 51 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.053135 0 0.380000 1.970000 0.408115 0.990000 9.900000e-01 1.000000 1.000000 0.999948 0.990000 1 0.990000 1.000000 B4GALNT3 283358 broad.mit.edu 37 12 662878 662878 + Missense_Mutation SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr12:662878G>A ENST00000266383.5 + 14 1802 c.1789G>A c.(1789-1791)Gca>Aca p.A597T NM_173593.3 NP_775864.3 Q6L9W6 B4GN3_HUMAN beta-1,4-N-acetyl-galactosaminyl transferase 3 26 all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215) OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262) GGTGGCGGCCGCAGGCCAGGA 0.617000 0 SO:0001583 missense ENST00000266383.5 0 1 hg19 CCDS8504.1 . . . . . . . . . . G 7.395 0.631635 0.14322 . . ENSG00000139044 ENST00000266383;ENST00000322843 T;T 0.32515 3.46;1.45 5.63 2.78 0.32641 . 0.762765 0.12432 N 0.469495 T 0.23886 0.0578 L 0.47716 1.5 0.09310 N 1 B;B 0.14438 0.01;0.002 B;B 0.08055 0.003;0.001 T 0.30357 -0.9981 10 0.18276 T 0.48 -0.4872 7.5465 0.27770 0.0673:0.2194:0.601:0.1124 . 500;597 E9PHD9;Q6L9W6 .;B4GN3_HUMAN T 597;500 ENSP00000266383:A597T;ENSP00000322953:A500T ENSP00000266383:A597T A + 1 0 B4GALNT3 533139 0.000000 0.05858 0.000000 0.03702 0.004000 0.04260 0.620000 0.24403 0.309000 0.22966 -1.332000 0.01269 GCA TCGA-3A-A9IB-01A-21D-A397-08 B4GALNT3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251406.2 0 0 0 4 230 0 41 0 1.752873e-01 0 35 0 41 2 0 0 0 0 0 2 1 0.884931 4 224 0 40 2 0 0 0 0 0 2 -5.106352 1 1 121392 8 41 1 1 2 3 2.053135 0 0.380000 1.970000 0.408115 0.110000 3.000000e-02 1.000000 0.090000 0.274625 0.110000 0 0.060000 1.000000 MYO16 23026 broad.mit.edu 37 13 109779895 109779895 + Missense_Mutation SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr13:109779895G>A ENST00000357550.2 + 30 4023 c.3982G>A c.(3982-3984)Gaa>Aaa p.E1328K MYO16_ENST00000356711.2_Missense_Mutation_p.E1328K|MYO16_ENST00000457511.2_Missense_Mutation_p.E840K NM_001198950.1 NP_001185879.1 myosin XVI 121 all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104) BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201) AGCGGCCAACGAAGGTCAGCC 0.662000 0 SO:0001583 missense ENST00000357550.2 1 1 hg19 CCDS32008.1 . . . . . . . . . . G 16.54 3.151349 0.57151 . . ENSG00000041515 ENST00000356711;ENST00000357550;ENST00000457511 T;T;T 0.42900 0.96;0.96;0.96 5.09 5.09 0.68999 . 0.000000 0.38605 U 0.001637 T 0.50394 0.1613 M 0.67953 2.075 0.48571 D 0.999678 D;D 0.59767 0.986;0.985 P;B 0.47705 0.555;0.41 T 0.53330 -0.8454 9 . . . . 17.5095 0.87756 0.0:0.0:1.0:0.0 . 840;1328 F8W883;Q9Y6X6 .;MYO16_HUMAN K 1328;1328;840 ENSP00000349145:E1328K;ENSP00000350160:E1328K;ENSP00000401633:E840K . E + 1 0 MYO16 108577896 1.000000 0.71417 0.922000 0.36590 0.090000 0.18270 5.411000 0.66386 2.367000 0.80283 0.563000 0.77884 GAA TCGA-3A-A9IB-01A-21D-A397-08 MYO16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045746.1 1 0 1 18 114 0 28 0 0 0 1 0 28 2 0 0 0 0 0 2 1 0.999987 16 114 0 26 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 2 2 4 2.246067 1 0.380000 1.970000 0.445339 0.870000 5.200000e-01 1.000000 1.000000 0.848516 0.870000 1 0.670000 1.000000 FBN1 2200 broad.mit.edu 37 15 48707785 48707785 + Missense_Mutation SNP C C T rs149062442 TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr15:48707785C>T ENST00000316623.5 - 64 8454 c.7999G>A c.(7999-8001)Gag>Aag p.E2667K FBN1_ENST00000561429.1_5'UTR NM_000138.4 NP_000129 P35555 FBN1_HUMAN fibrillin 1 139 all_lung(180;0.00279) TAACCGCCCTCGGTATTGGAA 0.542000 0 SO:0001583 missense ENST00000316623.5 1 1 hg19 CCDS32232.1 . . . . . . . . . . C 14.83 2.651521 0.47362 2.27E-4 1.16E-4 ENSG00000166147 ENST00000316623 D 0.87412 -2.25 5.81 5.81 0.92471 EGF-like calcium-binding, conserved site (1);Growth factor, receptor (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1); 0.155020 0.64402 D 0.000019 T 0.74329 0.3702 N 0.16266 0.395 0.80722 D 1 P 0.44090 0.826 B 0.34452 0.183 T 0.76063 -0.3096 10 0.06099 T 0.92 . 18.8343 0.92155 0.0:1.0:0.0:0.0 . 2667 P35555 FBN1_HUMAN K 2667 ENSP00000325527:E2667K ENSP00000325527:E2667K E - 1 0 FBN1 46495077 1.000000 0.71417 0.988000 0.46212 0.657000 0.38888 4.893000 0.63199 2.745000 0.94114 0.655000 0.94253 GAG TCGA-3A-A9IB-01A-21D-A397-08 FBN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000417355.1 1 0 1 82 242 0 53 1 1 14 376 0 53 2 0 0 0 0 0 2 1 1.000000 81 242 0 52 2 0 0 0 0 0 2 -5.014298 1 1 121412 4 37 1 0 1 1 1.871649 1 0.380000 1.970000 0.317782 0.990000 9.800000e-01 1.000000 1.000000 0.998822 0.990000 1 0.990000 1.000000 NKD1 85407 broad.mit.edu 37 16 50664178 50664178 + Missense_Mutation SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr16:50664178C>T ENST00000268459.3 + 7 768 c.544C>T c.(544-546)Cgg>Tgg p.R182W NM_033119.4 NP_149110.1 Q969G9 NKD1_HUMAN naked cuticle homolog 1 (Drosophila) 23 all_cancers(37;0.229) CAAGATGCTGCGGGTAAAGCT 0.592000 0 SO:0001583 missense ENST00000268459.3 0 1 hg19 CCDS10743.1 . . . . . . . . . . C 15.01 2.707405 0.48412 0.0 1.16E-4 ENSG00000140807 ENST00000268459 T 0.72505 -0.66 4.88 3.91 0.45181 . 0.000000 0.85682 D 0.000000 D 0.84306 0.5443 M 0.83603 2.65 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.86778 0.1977 10 0.87932 D 0 -22.9129 14.0418 0.64681 0.2725:0.7275:0.0:0.0 . 182 Q969G9 NKD1_HUMAN W 182 ENSP00000268459:R182W ENSP00000268459:R182W R + 1 2 NKD1 49221679 1.000000 0.71417 1.000000 0.80357 0.103000 0.19146 3.134000 0.50538 1.151000 0.42436 0.655000 0.94253 CGG TCGA-3A-A9IB-01A-21D-A397-08 NKD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256873.1 1 0 0 29 334 1 63 0 1.429727e-01 0 16 1 63 3 0 0 0 0 0 2 1 0.947125 28 333 1 63 19 0 0 0 0 0 2 -3.142702 1 1 121412 2 35 1 1 2 3 2.248531 1 0.380000 1.970000 0.441542 0.500000 3.200000e-01 1.000000 0.470000 0.601661 0.500000 0 0.400000 1.000000 PMFBP1 83449 broad.mit.edu 37 16 72163043 72163043 + Missense_Mutation SNP C C G TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr16:72163043C>G ENST00000237353.10 - 13 2133 c.1872G>C c.(1870-1872)aaG>aaC p.K624N PMFBP1_ENST00000537465.1_Missense_Mutation_p.K629N|PMFBP1_ENST00000355636.6_Missense_Mutation_p.K479N NM_031293.2 NP_112583.2 Q8TBY8 PMFBP_HUMAN polyamine modulated factor 1 binding protein 1 45 Ovarian(137;0.179) CTTTGCTCTTCTTCAACTGCT 0.468000 0 SO:0001583 missense ENST00000237353.10 1 1 hg19 CCDS32483.1 . . . . . . . . . . C 5.334 0.246930 0.10130 . . ENSG00000118557 ENST00000537465;ENST00000237353;ENST00000355636 T;T;T 0.13538 2.58;2.59;2.58 4.31 2.09 0.27110 . 0.129090 0.35646 N 0.003070 T 0.09291 0.0229 L 0.29908 0.895 0.23449 N 0.997656 B;P;B 0.39250 0.447;0.665;0.447 B;B;B 0.41088 0.147;0.347;0.147 T 0.19844 -1.0293 10 0.26408 T 0.33 -18.0873 5.1417 0.14963 0.0:0.2541:0.0:0.7459 . 629;624;629 Q8TBY8;Q8TBY8-2;G3V1Q7 PMFBP_HUMAN;.;. N 629;624;479 ENSP00000443817:K629N;ENSP00000237353:K624N;ENSP00000347854:K479N ENSP00000237353:K624N K - 3 2 PMFBP1 70720544 0.996000 0.38824 0.994000 0.49952 0.049000 0.14656 0.330000 0.19715 0.458000 0.26988 -0.302000 0.09304 AAG TCGA-3A-A9IB-01A-21D-A397-08 PMFBP1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000396473.2 1 0 1 321 953 0 179 0 0 0 0 179 2 0 0 0 0 0 2 1 1.000000 314 946 0 174 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.232757 1 0.380000 1.970000 0.432806 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 RHOT2 89941 broad.mit.edu 37 16 721954 721954 + Missense_Mutation SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr16:721954G>A ENST00000315082.4 + 13 1163 c.1049G>A c.(1048-1050)cGc>cAc p.R350H NM_138769.2 NP_620124.1 Q8IXI1 MIRO2_HUMAN ras homolog family member T2 13 Hepatocellular(780;0.0218) CGCACAGTCCGCACAGAGGCC 0.692000 0 SO:0001583 missense ENST00000315082.4 0 1 hg19 CCDS10417.1 . . . . . . . . . . G 13.71 2.319598 0.41096 . . ENSG00000140983 ENST00000315082 T 0.10099 2.91 5.31 2.09 0.27110 EF hand associated, type-1 (1); 0.488085 0.25897 N 0.027587 T 0.10380 0.0254 N 0.22421 0.69 0.20403 N 0.999906 P 0.44006 0.824 P 0.44477 0.451 T 0.10497 -1.0627 10 0.44086 T 0.13 -4.7154 15.1832 0.72975 0.0:0.4165:0.5835:0.0 . 350 Q8IXI1 MIRO2_HUMAN H 350 ENSP00000321971:R350H ENSP00000321971:R350H R + 2 0 RHOT2 661955 0.971000 0.33674 0.002000 0.10522 0.006000 0.05464 1.740000 0.38228 0.186000 0.20125 0.456000 0.33151 CGC TCGA-3A-A9IB-01A-21D-A397-08 RHOT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000241617.1 0 0 0 6 486 0 151 0 5.650552e-01 0 141 0 151 2 0 0 0 0 0 2 1 0.963824 6 480 0 148 2 0 0 0 0 0 2 -2.445671 0 1 120846 11 41 1 1 2 3 2.254564 1 0.380000 1.970000 0.448153 0.080000 2.000000e-02 1.000000 0.080000 0.285007 0.080000 0 0.050000 1.000000 FANCA 2175 broad.mit.edu 37 16 89842201 89842201 + Missense_Mutation SNP G G C TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr16:89842201G>C ENST00000389301.3 - 21 1879 c.1849C>G c.(1849-1851)Ctg>Gtg p.L617V FANCA_ENST00000568369.1_Missense_Mutation_p.L617V|FANCA_ENST00000567284.2_5'UTR NM_000135.2 NP_000126.2 O15360 FANCA_HUMAN Fanconi anemia, complementation group A 47 Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194) GTGGAGTACAGAGATGGGGGG 0.443000 D, Mis, N, F, S AML, leukemia Involved in tolerance or repair of DNA crosslinks Fanconi Anemia yes Rec Fanconi anaemia A 16 16q24.3 2175 Fanconi anemia, complementation group A L 0 SO:0001583 missense Familial Cancer Database Pancytopenia Dysmelia, FA (several complementation groups) ENST00000389301.3 1 1 hg19 CCDS32515.1 . . . . . . . . . . G 10.09 1.255899 0.22965 . . ENSG00000187741 ENST00000389301 D 0.85411 -1.98 5.03 -0.755 0.11061 . 0.494987 0.16475 N 0.212816 T 0.77246 0.4102 M 0.71581 2.175 0.09310 N 1 B;B 0.29909 0.261;0.261 B;B 0.20184 0.028;0.016 T 0.67898 -0.5551 10 0.66056 D 0.02 -1.1651 1.6061 0.02684 0.3053:0.1378:0.4164:0.1405 . 617;617 B4DRI7;O15360 .;FANCA_HUMAN V 617 ENSP00000373952:L617V ENSP00000373952:L617V L - 1 2 FANCA 88369702 0.000000 0.05858 0.008000 0.14137 0.759000 0.43091 -0.464000 0.06688 -0.023000 0.13963 0.650000 0.86243 CTG TCGA-3A-A9IB-01A-21D-A397-08 FANCA-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000421927.1 1 0 0 13 109 0 25 0 2.712908e-01 1 8 0 25 2 0 0 0 0 0 2 1 0.999633 13 109 0 25 2 0 0 0 0 0 2 -3.320514 1 1 0 0 1 1 2 3 2.232757 1 0.380000 1.970000 0.432806 0.690000 3.700000e-01 1.000000 0.610000 0.727917 0.690000 0 0.500000 1.000000 TAOK1 57551 broad.mit.edu 37 17 27869675 27869675 + Missense_Mutation SNP G G C TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr17:27869675G>C ENST00000261716.3 + 20 3160 c.2641G>C c.(2641-2643)Gaa>Caa p.E881Q TAOK1_ENST00000536202.1_Missense_Mutation_p.E733Q NM_020791.2 NP_065842.1 Q7L7X3 TAOK1_HUMAN TAO kinase 1 28 Colorectal(6;0.198) TTTTGACTCTGAAAGCATGAG 0.473000 0 SO:0001583 missense ENST00000261716.3 1 1 hg19 CCDS32601.1 . . . . . . . . . . G 25.6 4.650537 0.87958 . . ENSG00000160551 ENST00000261716;ENST00000536202 T;T 0.57752 0.38;0.38 5.57 5.57 0.84162 Protein kinase-like domain (1); 0.000000 0.85682 D 0.000000 T 0.77226 0.4099 M 0.86178 2.8 0.27873 N 0.939969 D;D 0.89917 0.981;1.0 D;D 0.85130 0.932;0.997 T 0.73304 -0.4025 10 0.72032 D 0.01 . 19.5531 0.95330 0.0:0.0:1.0:0.0 . 733;881 B7ZLV6;Q7L7X3 .;TAOK1_HUMAN Q 881;733 ENSP00000261716:E881Q;ENSP00000438819:E733Q ENSP00000261716:E881Q E + 1 0 TAOK1 24893801 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.809000 0.99208 2.623000 0.88846 0.561000 0.74099 GAA TCGA-3A-A9IB-01A-21D-A397-08 TAOK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447790.1 0 0 1 92 499 0 129 1 5.317937e-01 5 6 0 129 2 0 0 0 0 0 2 1 1.000000 92 493 0 129 2 0 0 0 0 0 2 -20.000000 1 0 0 0 1 1 2 3 2.071362 0 0.380000 1.970000 0.390424 0.830000 6.800000e-01 1.000000 0.830000 0.848375 0.830000 0 0.750000 0.940000 TMEM132E 124842 broad.mit.edu 37 17 32953589 32953589 + Missense_Mutation SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr17:32953589C>T ENST00000321639.5 + 2 839 c.511C>T c.(511-513)Cgg>Tgg p.R171W NM_207313.1 NP_997196.1 Q6IEE7 T132E_HUMAN transmembrane protein 132E 57 GCATGCCTTCCGGGATGCCCG 0.711000 0 SO:0001583 missense ENST00000321639.5 1 1 hg19 CCDS11283.1 . . . . . . . . . . c 18.86 3.713777 0.68730 . . ENSG00000181291 ENST00000321639 T 0.13420 2.59 5.17 1.84 0.25277 . 0.120858 0.56097 D 0.000034 T 0.24812 0.0602 L 0.48877 1.53 0.31168 N 0.703569 D 0.89917 1.0 D 0.67548 0.952 T 0.07790 -1.0754 10 0.56958 D 0.05 -14.7201 9.9255 0.41489 0.2791:0.5861:0.1348:0.0 . 171 Q6IEE7 T132E_HUMAN W 171 ENSP00000316532:R171W ENSP00000316532:R171W R + 1 2 TMEM132E 29977702 0.999000 0.42202 0.993000 0.49108 0.971000 0.66376 0.741000 0.26202 0.545000 0.28902 -0.294000 0.09567 CGG TCGA-3A-A9IB-01A-21D-A397-08 TMEM132E-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256440.2 1 0 0 17 75 0 25 0 3.829787e-02 0 2 0 25 2 0 0 0 0 0 2 1 0.999980 16 75 0 25 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.071362 0 0.380000 1.970000 0.390424 0.990000 6.200000e-01 1.000000 1.000000 0.925301 0.990000 1 0.800000 1.000000 CRHR1 1394 broad.mit.edu 37 17 43907805 43907805 + Missense_Mutation SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr17:43907805C>T ENST00000398285.3 + 8 665 c.665C>T c.(664-666)gCc>gTc p.A222V CRHR1_ENST00000314537.5_Missense_Mutation_p.A193V|CRHR1_ENST00000293493.7_Missense_Mutation_p.A18V|CRHR1_ENST00000339069.5_Missense_Mutation_p.A92V|CRHR1_ENST00000577353.1_Missense_Mutation_p.A193V|CRHR1_ENST00000352855.5_Missense_Mutation_p.A153V NM_001145146.1 NP_001138618.1 P34998 CRFR1_HUMAN corticotropin releasing hormone receptor 1 24 Colorectal(2;0.0416) TTGGTGACAGCCGCCTACAAC 0.632000 Ovarian(110;57 1568 10207 38216 49865) 0 SO:0001583 missense ENST00000398285.3 0 1 hg19 CCDS45712.1 . . . . . . . . . . C 15.16 2.750172 0.49257 . . ENSG00000120088 ENST00000293493;ENST00000339069;ENST00000398285;ENST00000314537;ENST00000347197;ENST00000352855 T;T;T;T;T 0.39406 1.19;1.08;1.19;1.19;1.19 5.27 5.27 0.74061 GPCR, family 2-like (1); 0.099034 0.64402 D 0.000001 T 0.25938 0.0632 N 0.04297 -0.235 0.50467 D 0.999875 B;B;B;P;B;B 0.42871 0.268;0.201;0.122;0.792;0.268;0.268 B;B;B;P;B;B 0.46419 0.26;0.088;0.082;0.516;0.135;0.192 T 0.06935 -1.0799 10 0.23891 T 0.37 . 9.92 0.41459 0.0:0.9073:0.0:0.0927 . 193;222;92;92;153;193 P34998-4;P34998;B3TIK8;B4DMR5;P34998-3;P34998-2 .;CRFR1_HUMAN;.;.;.;. V 18;92;222;193;193;153 ENSP00000293493:A18V;ENSP00000340522:A92V;ENSP00000381333:A222V;ENSP00000326060:A193V;ENSP00000344068:A153V ENSP00000293493:A18V A + 2 0 CRHR1 41263586 1.000000 0.71417 0.993000 0.49108 0.950000 0.60333 6.091000 0.71406 2.462000 0.83206 0.561000 0.74099 GCC TCGA-3A-A9IB-01A-21D-A397-08 CRHR1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000441241.3 0 0 0 5 364 0 76 0 0 0 1 0 76 2 0 0 0 0 0 2 1 0.937054 6 361 0 75 2 0 0 0 0 0 2 -2.697745 1 1 0 0 1 1 2 3 2.071362 0 0.380000 1.970000 0.390424 0.080000 2.000000e-02 1.000000 0.070000 0.152653 0.080000 0 0.040000 0.140000 TP53 7157 broad.mit.edu 37 17 7578190 7578190 + Missense_Mutation SNP T T C rs121912666 TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 T C T T Valid Somatic Phase_I WXS targeted Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr17:7578190T>C ENST00000269305.4 - 6 848 c.659A>G c.(658-660)tAt>tGt p.Y220C TP53_ENST00000445888.2_Missense_Mutation_p.Y220C|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.Y220C|TP53_ENST00000420246.2_Missense_Mutation_p.Y220C|TP53_ENST00000359597.4_Missense_Mutation_p.Y220C|TP53_ENST00000413465.2_Missense_Mutation_p.Y220C 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.Y220C(278)|p.Y127C(24)|p.Y220S(12)|p.?(11)|p.0?(8)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y127S(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) AGGCGGCTCATAGGGCACCAC 0.557000 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 343 Substitution - Missense(315)|Unknown(11)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(3)|Insertion - Frameshift(1) GRCh37 CM015378|CM951227 TP53 M rs121912666 SO:0001583 missense 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 1 1 hg19 CCDS11118.1 . . . . . . . . . . T 22.1 4.248510 0.80024 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944 D;D;D;D;D;D;D;D 0.99840 -7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08 5.28 5.28 0.74379 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99822 0.9921 M 0.89287 3.02 0.80722 D 1 D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D 0.97110 1.0;0.998;0.996;1.0;0.999;0.998;1.0 D 0.96735 0.9542 10 0.87932 D 0 -1.87 13.4753 0.61306 0.0:0.0:0.0:1.0 . 181;220;220;127;220;220;220 B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. C 220;220;220;220;220;220;209;127;88;127 ENSP00000410739:Y220C;ENSP00000352610:Y220C;ENSP00000269305:Y220C;ENSP00000398846:Y220C;ENSP00000391127:Y220C;ENSP00000391478:Y220C;ENSP00000425104:Y88C;ENSP00000423862:Y127C ENSP00000269305:Y220C Y - 2 0 TP53 7518915 1.000000 0.71417 0.585000 0.28666 0.993000 0.82548 6.232000 0.72313 2.128000 0.65567 0.460000 0.39030 TAT TCGA-3A-A9IB-01A-21D-A397-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 41 94 0 34 1 9.999921e-01 21 26 0 34 2 1 1 231 668 0 518 2 1 1.000000 40 93 0 34 2 0 0 0 0 0 2 -20.000000 1 1 121412 3 37 1 0 1 1 1.688645 1 0.380000 1.970000 0.238142 0.970000 8.200000e-01 1.000000 1.000000 0.959510 0.970000 1 0.900000 1.000000 ZNF175 7728 broad.mit.edu 37 19 52090881 52090881 + Missense_Mutation SNP A A G TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr19:52090881A>G ENST00000262259.2 + 5 1655 c.1297A>G c.(1297-1299)Aca>Gca p.T433A ZNF175_ENST00000436511.2_Intron NM_007147.2 NP_009078.1 Q9Y473 ZN175_HUMAN zinc finger protein 175 24 all_neural(266;0.0299) CCAGAAGTCAACACTCAGCTT 0.473000 0 SO:0001583 missense ENST00000262259.2 1 1 hg19 CCDS12837.1 . . . . . . . . . . A 7.325 0.617711 0.14129 . . ENSG00000105497 ENST00000262259 T 0.35421 1.31 2.39 -1.01 0.10169 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.11537 0.0281 N 0.03238 -0.38 0.09310 N 0.999998 B 0.02656 0.0 B 0.04013 0.001 T 0.30650 -0.9971 9 0.08381 T 0.77 . 3.2726 0.06887 0.3719:0.0:0.4173:0.2107 . 433 Q9Y473 ZN175_HUMAN A 433 ENSP00000262259:T433A ENSP00000262259:T433A T + 1 0 ZNF175 56782693 0.000000 0.05858 0.677000 0.29947 0.993000 0.82548 -1.388000 0.02533 -0.348000 0.08286 -0.290000 0.09829 ACA TCGA-3A-A9IB-01A-21D-A397-08 ZNF175-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396205.1 1 0 1 44 175 0 26 0 5.045139e-01 0 8 0 26 2 0 0 0 0 0 2 1 1.000000 43 174 0 25 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.052867 0 0.380000 1.970000 0.386988 0.990000 8.000000e-01 1.000000 1.000000 0.975252 0.990000 1 0.930000 1.000000 ZNF528 84436 broad.mit.edu 37 19 52919334 52919334 + Missense_Mutation SNP G G C TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr19:52919334G>C ENST00000360465.3 + 7 1655 c.1229G>C c.(1228-1230)gGa>gCa p.G410A ZNF528_ENST00000391788.2_3'UTR NM_032423.2 NP_115799.2 Q3MIS6 ZN528_HUMAN zinc finger protein 528 39 AGACCTTATGGATGCAGTCAG 0.403000 0 SO:0001583 missense ENST00000360465.3 1 1 hg19 CCDS33091.1 . . . . . . . . . . G 7.716 0.696068 0.15106 . . ENSG00000167555 ENST00000360465 T 0.35048 1.33 2.08 0.998 0.19857 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.09949 0.0244 N 0.00637 -1.305 0.09310 N 1 B 0.30709 0.291 B 0.29663 0.105 T 0.17806 -1.0357 9 0.44086 T 0.13 . 3.0495 0.06165 0.5844:0.2488:0.1668:0.0 . 410 Q3MIS6 ZN528_HUMAN A 410 ENSP00000353652:G410A ENSP00000353652:G410A G + 2 0 ZNF528 57611146 0.000000 0.05858 0.002000 0.10522 0.001000 0.01503 -0.943000 0.03917 0.074000 0.16767 -0.302000 0.09304 GGA TCGA-3A-A9IB-01A-21D-A397-08 ZNF528-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344336.1 1 0 1 58 286 0 62 0 2.948477e-02 0 2 0 62 2 0 0 0 0 0 2 1 1.000000 57 283 0 60 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.049780 0 0.380000 1.970000 0.386988 0.900000 7.000000e-01 1.000000 1.000000 0.897071 0.900000 1 0.790000 1.000000 MUC16 94025 broad.mit.edu 37 19 9090831 9090831 + Silent SNP A A G TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr19:9090831A>G ENST00000397910.4 - 1 1187 c.984T>C c.(982-984)ccT>ccC p.P328P NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 590 TCATGGAAAAAGGGATAGCTG 0.522000 0 SO:0001819 synonymous_variant ENST00000397910.4 0 1 hg19 CCDS54212.1 TCGA-3A-A9IB-01A-21D-A397-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 0 0 0 4 278 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 0.888528 4 275 0 39 2 0 0 0 0 0 2 -2.334638 0 1 0 0 1 1 2 3 2.043449 0 0.380000 1.970000 0.385835 0.080000 2.000000e-02 1.000000 0.080000 0.127432 0.080000 0 0.040000 0.140000 AMPD2 271 broad.mit.edu 37 1 110172959 110172959 + Silent SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr1:110172959G>A ENST00000256578.3 + 16 2610 c.2250G>A c.(2248-2250)ccG>ccA p.P750P AMPD2_ENST00000393688.3_Silent_p.P631P|RP5-1160K1.6_ENST00000369843.3_RNA|AMPD2_ENST00000528454.1_Silent_p.P632P|AMPD2_ENST00000528667.1_Silent_p.P750P|AMPD2_ENST00000526301.1_3'UTR|AMPD2_ENST00000358729.4_Silent_p.P675P|AMPD2_ENST00000342115.4_Silent_p.P669P NM_004037.7 NP_004028.3 Q01433 AMPD2_HUMAN adenosine monophosphate deaminase 2 7 all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244) ATCCGCTACCGGAGTACCTGT 0.617000 0 SO:0001819 synonymous_variant ENST00000256578.3 1 1 hg19 CCDS805.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. g|g 6.875|6.875 0.530795|0.530795 0.13127|0.13127 .|. .|. ENSG00000116337|ENSG00000116337 ENST00000369840|ENST00000476688 .|. .|. .|. 4.66|4.66 -4.93|-4.93 0.03066|0.03066 .|. .|. .|. .|. .|. T|T 0.17959|0.17959 0.0431|0.0431 .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|. .|. .|. .|. .|. .|. T|T 0.38735|0.38735 -0.9647|-0.9647 4|4 .|. .|. .|. -21.0222|-21.0222 0.507|0.507 0.00589|0.00589 0.205:0.284:0.2159:0.2951|0.205:0.284:0.2159:0.2951 .|. .|. .|. .|. R|Q 721|139 .|. .|. G|R +|+ 1|2 0|0 AMPD2|AMPD2 109974482|109974482 0.000000|0.000000 0.05858|0.05858 0.630000|0.630000 0.29268|0.29268 0.705000|0.705000 0.40729|0.40729 -3.213000|-3.213000 0.00555|0.00555 -1.228000|-1.228000 0.02568|0.02568 -2.079000|-2.079000 0.00380|0.00380 GGA|CGG TCGA-3A-A9IB-01A-21D-A397-08 AMPD2-011 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000390615.1 0 0 0 125 539 0 158 1 1 37 92 0 158 2 0 0 0 0 0 2 1 1.000000 125 539 0 153 2 0 0 0 0 0 2 -2.891062 1 1 0 0 1 0 0 0 1.996625 0 0.380000 1.970000 0.375252 0.970000 8.200000e-01 1.000000 1.000000 0.960572 0.970000 1 0.900000 1.000000 GPR161 23432 broad.mit.edu 37 1 168066276 168066276 + Missense_Mutation SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr1:168066276G>A ENST00000367838.1 - 5 882 c.569C>T c.(568-570)gCc>gTc p.A190V GPR161_ENST00000537209.1_Missense_Mutation_p.A210V|GPR161_ENST00000367836.1_Missense_Mutation_p.A58V|GPR161_ENST00000539777.1_Missense_Mutation_p.A112V|GPR161_ENST00000361697.2_Missense_Mutation_p.A190V|GPR161_ENST00000367835.1_Missense_Mutation_p.A190V|GPR161_ENST00000271357.5_Missense_Mutation_p.A190V|GPR161_ENST00000546300.1_Missense_Mutation_p.A76V NM_001267611.1|NM_153832.2 NP_001254540.1|NP_722561.1 Q8N6U8 GP161_HUMAN G protein-coupled receptor 161 26 all_hematologic(923;0.215) CTGCCAGAAGGCCGTGTAGCC 0.592000 0 SO:0001583 missense ENST00000367838.1 1 1 hg19 CCDS1268.1 . . . . . . . . . . G 12.75 2.032295 0.35893 . . ENSG00000143147 ENST00000367838;ENST00000271357;ENST00000367836;ENST00000367835;ENST00000546300;ENST00000539777;ENST00000537209;ENST00000361697 T;T;T;T;T;T;T;T 0.69306 -0.39;-0.39;-0.39;-0.39;-0.39;-0.39;-0.39;-0.39 5.07 4.14 0.48551 GPCR, rhodopsin-like superfamily (1); 0.102442 0.64402 N 0.000003 T 0.30665 0.0772 N 0.16098 0.37 0.38353 D 0.944394 B;B;B;B;B;B 0.13145 0.001;0.007;0.006;0.002;0.001;0.001 B;B;B;B;B;B 0.17722 0.003;0.019;0.018;0.006;0.001;0.005 T 0.08146 -1.0736 9 0.30078 T 0.28 -16.4128 12.5826 0.56399 0.0834:0.0:0.9166:0.0 . 210;76;112;210;190;190 F5GXD6;B7Z5E8;F5H6J7;B7Z5Z6;Q8N6U8-2;Q8N6U8 .;.;.;.;.;GP161_HUMAN V 190;190;58;190;76;112;210;190 ENSP00000356812:A190V;ENSP00000271357:A190V;ENSP00000356810:A58V;ENSP00000356809:A190V;ENSP00000444348:A76V;ENSP00000437576:A112V;ENSP00000441039:A210V;ENSP00000355194:A190V ENSP00000271357:A190V A - 2 0 GPR161 166332900 1.000000 0.71417 0.922000 0.36590 0.974000 0.67602 4.756000 0.62205 1.242000 0.43836 0.561000 0.74099 GCC TCGA-3A-A9IB-01A-21D-A397-08 GPR161-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083829.1 1 0 1 24 114 0 21 1 7.286607e-01 2 12 0 21 2 0 0 0 0 0 2 1 1.000000 24 111 0 21 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 1.989927 0 0.380000 1.970000 0.375252 0.900000 6.100000e-01 1.000000 1.000000 0.885921 0.900000 1 0.750000 1.000000 EPHX1 2052 broad.mit.edu 37 1 226032215 226032215 + Missense_Mutation SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr1:226032215G>A ENST00000366837.4 + 8 1253 c.1057G>A c.(1057-1059)Gac>Aac p.D353N RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_Missense_Mutation_p.D353N NM_000120.3 NP_000111.1 P07099 HYEP_HUMAN epoxide hydrolase 1, microsomal (xenobiotic) 28 Breast(184;0.197) CTCCCTGGACGACCTGCTGAC 0.552000 0 SO:0001583 missense ENST00000366837.4 1 1 hg19 CCDS1547.1 . . . . . . . . . . G 29.1 4.973433 0.92919 . . ENSG00000143819 ENST00000272167;ENST00000366837 T;T 0.75704 -0.96;-0.96 5.37 5.37 0.77165 Alpha/beta hydrolase fold-1 (1); 0.000000 0.85682 D 0.000000 D 0.88400 0.6426 M 0.90814 3.15 0.80722 D 1 D 0.60160 0.987 P 0.62649 0.905 D 0.90256 0.4297 10 0.72032 D 0.01 -22.9316 19.464 0.94931 0.0:0.0:1.0:0.0 . 353 P07099 HYEP_HUMAN N 353 ENSP00000272167:D353N;ENSP00000355802:D353N ENSP00000272167:D353N D + 1 0 EPHX1 224098838 1.000000 0.71417 0.800000 0.32199 0.506000 0.33950 7.817000 0.86213 2.686000 0.91538 0.561000 0.74099 GAC TCGA-3A-A9IB-01A-21D-A397-08 EPHX1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000092064.1 1 0 1 53 237 0 56 1 1 95 234 0 56 2 0 0 0 0 0 2 1 1.000000 53 234 0 54 2 0 0 0 0 0 2 -20.000000 1 1 121412 3 35 1 0 0 0 1.989927 0 0.380000 1.970000 0.375252 0.950000 7.300000e-01 1.000000 1.000000 0.930073 0.950000 1 0.830000 1.000000 SLC32A1 140679 broad.mit.edu 37 20 37356232 37356232 + Silent SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr20:37356232C>T ENST00000217420.1 + 2 791 c.528C>T c.(526-528)gaC>gaT p.D176D NM_080552.2 NP_542119.1 Q9H598 VIAAT_HUMAN solute carrier family 32 (GABA vesicular transporter), member 1 38 Myeloproliferative disorder(115;0.00878) Glycine(DB00145) AGAATGAAGACGGCGAGGTGG 0.647000 0 SO:0001819 synonymous_variant ENST00000217420.1 1 1 hg19 CCDS13307.1 TCGA-3A-A9IB-01A-21D-A397-08 SLC32A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079206.1 1 0 1 48 191 0 72 0 0 0 0 72 2 0 0 0 0 0 2 1 1.000000 48 191 0 72 2 0 0 0 0 0 2 -20.000000 1 1 121408 1 31 1 0 2 2 2.053610 1 0.380000 1.970000 0.380000 0.990000 8.000000e-01 1.000000 1.000000 0.972440 0.990000 1 0.920000 1.000000 RBM38 55544 broad.mit.edu 37 20 55966783 55966783 + Nonsense_Mutation SNP C C A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr20:55966783C>A ENST00000356208.5 + 1 321 c.146C>A c.(145-147)tCg>tAg p.S49* RBM38_ENST00000440234.2_Nonsense_Mutation_p.S49*|RP4-800J21.3_ENST00000417346.1_RNA|RBM38_ENST00000371219.2_5'Flank NM_017495.5 NP_059965.2 Q9H0Z9 RBM38_HUMAN RNA binding motif protein 38 9 Lung NSC(12;0.00242)|all_lung(29;0.00767)|Melanoma(10;0.242) BRCA - Breast invasive adenocarcinoma(4;1.55e-12)|Epithelial(14;9.49e-09)|all cancers(14;5.01e-08) ACCGACGCCTCGCTCAGGAAG 0.677000 0 SO:0001587 stop_gained ENST00000356208.5 0 1 hg19 CCDS46617.1 . . . . . . . . . . C 22.7 4.322144 0.81580 . . ENSG00000132819 ENST00000356208;ENST00000440234 . . . 3.49 3.49 0.39957 . 0.000000 0.85682 U 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -9.6071 13.737 0.62824 0.0:1.0:0.0:0.0 . . . . X 49 . ENSP00000343718:S49X S + 2 0 RBM38 55400189 1.000000 0.71417 1.000000 0.80357 0.033000 0.12548 1.488000 0.35551 1.500000 0.48636 0.442000 0.29010 TCG TCGA-3A-A9IB-01A-21D-A397-08 RBM38-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079843.4 1 0 0 8 32 0 23 0 9.098666e-01 1 19 0 23 2 0 0 0 0 0 2 1 0.991943 8 32 0 22 2 0 0 0 0 0 2 -16.818390 1 1 0 0 1 0 2 2 2.053610 1 0.380000 1.970000 0.380000 0.990000 5.200000e-01 1.000000 1.000000 0.913715 0.990000 1 0.760000 1.000000 ISX 91464 broad.mit.edu 37 22 35463185 35463185 + Silent SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr22:35463185G>A ENST00000308700.6 + 1 1057 c.105G>A c.(103-105)gcG>gcA p.A35A RP1-272J12.1_ENST00000448318.4_RNA|ISX_ENST00000404699.2_Silent_p.A35A NM_001008494.1 NP_001008494.1 Q2M1V0 ISX_HUMAN intestine-specific homeobox 26 CCATTGAGGCGATCCTAAAGA 0.602000 0 SO:0001819 synonymous_variant ENST00000308700.6 0 1 hg19 CCDS33640.1 TCGA-3A-A9IB-01A-21D-A397-08 ISX-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320662.1 1 0 0 18 69 0 8 0 0 0 0 8 2 0 0 0 0 0 2 1 0.999992 19 69 0 8 2 0 0 0 0 0 2 -20.000000 1 1 121394 3 31 1 1 2 3 2.018648 1 0.380000 1.970000 0.411318 0.990000 7.500000e-01 1.000000 1.000000 0.974937 0.990000 1 0.950000 1.000000 BUB1 699 broad.mit.edu 37 2 111425242 111425242 + Missense_Mutation SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr2:111425242C>T ENST00000302759.6 - 8 779 c.661G>A c.(661-663)Gtg>Atg p.V221M BUB1_ENST00000535254.1_Missense_Mutation_p.V201M|BUB1_ENST00000409311.1_Missense_Mutation_p.V221M NM_004336.3 NP_004327.1 O43683 BUB1_HUMAN BUB1 mitotic checkpoint serine/threonine kinase p.V221_S227>S(1) 45 Ovarian(717;0.0822) GATGAGTGCACAGAATATTCT 0.368000 1 Complex - deletion inframe(1) SO:0001583 missense ENST00000302759.6 1 1 hg19 CCDS33273.1 . . . . . . . . . . C 15.32 2.797928 0.50208 . . ENSG00000169679 ENST00000535254;ENST00000409311;ENST00000302759;ENST00000541432 T;T;T 0.32272 2.2;1.46;2.46 5.72 0.743 0.18347 . 1.042200 0.07470 N 0.902057 T 0.32496 0.0831 L 0.40543 1.245 0.09310 N 1 P;D;P 0.54047 0.955;0.964;0.874 P;P;B 0.53593 0.73;0.547;0.346 T 0.16571 -1.0398 10 0.32370 T 0.25 0.1037 3.7315 0.08495 0.293:0.4713:0.0:0.2356 . 201;221;221 F5GXI5;E9PC26;O43683 .;.;BUB1_HUMAN M 201;221;221;221 ENSP00000441013:V201M;ENSP00000386701:V221M;ENSP00000302530:V221M ENSP00000302530:V221M V - 1 0 BUB1 111141713 0.020000 0.18652 0.002000 0.10522 0.926000 0.56050 0.091000 0.15046 -0.140000 0.11394 0.650000 0.86243 GTG TCGA-3A-A9IB-01A-21D-A397-08 BUB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000331925.1 1 0 1 68 347 0 70 1 4.520284e-01 3 6 0 70 2 0 0 0 0 0 2 1 1.000000 68 347 0 70 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.037772 0 0.380000 1.970000 0.384676 0.860000 6.800000e-01 1.000000 1.000000 0.872973 0.860000 1 0.770000 0.980000 SCN3A 6328 broad.mit.edu 37 2 165950907 165950907 + Missense_Mutation SNP G G C TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr2:165950907G>C ENST00000360093.3 - 26 5004 c.4513C>G c.(4513-4515)Cag>Gag p.Q1505E SCN3A_ENST00000540861.1_5'Flank|SCN3A_ENST00000465043.1_5'Flank|SCN3A_ENST00000283254.7_Missense_Mutation_p.Q1505E|SCN3A_ENST00000409101.3_Missense_Mutation_p.Q1456E 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) ATGGGTTTCTGAGGTTTCTTG 0.388000 0 SO:0001583 missense ENST00000360093.3 1 1 hg19 . . . . . . . . . . G 16.64 3.178549 0.57692 . . ENSG00000153253 ENST00000360093;ENST00000283254;ENST00000409101 D;D;D 0.96104 -3.91;-3.91;-3.84 4.71 4.71 0.59529 . 0.000000 0.64402 D 0.000001 D 0.97192 0.9082 H 0.94808 3.585 0.80722 D 1 P;P;B 0.47841 0.901;0.502;0.005 P;B;B 0.45881 0.496;0.118;0.019 D 0.98609 1.0662 10 0.72032 D 0.01 . 18.2045 0.89850 0.0:0.0:1.0:0.0 . 1456;1456;1505 Q9NY46-2;Q9NY46-4;Q9NY46-3 .;.;. E 1505;1505;1456 ENSP00000353206:Q1505E;ENSP00000283254:Q1505E;ENSP00000386726:Q1456E ENSP00000283254:Q1505E Q - 1 0 SCN3A 165659153 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.556000 0.98127 2.613000 0.88420 0.655000 0.94253 CAG TCGA-3A-A9IB-01A-21D-A397-08 SCN3A-201 KNOWN basic|appris_candidate_longest protein_coding protein_coding 1 0 1 147 778 0 167 0 0 0 0 167 2 0 0 0 0 0 2 1 1.000000 146 766 0 164 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 1.981250 0 0.380000 1.970000 0.370431 0.810000 7.000000e-01 0.940000 0.820000 0.825914 0.810000 0 0.750000 0.890000 LRP2 4036 broad.mit.edu 37 2 170115538 170115538 + Missense_Mutation SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr2:170115538G>A ENST00000263816.3 - 17 2795 c.2510C>T c.(2509-2511)gCc>gTc p.A837V LRP2_ENST00000443831.1_Missense_Mutation_p.A700V NM_004525.2 NP_004516.2 P98164 LRP2_HUMAN low density lipoprotein receptor-related protein 2 315 """Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)" CACTTACCCGGCAAAAGGATG 0.403000 0 SO:0001583 missense ENST00000263816.3 0 1 hg19 CCDS2232.1 . . . . . . . . . . G 9.483 1.098743 0.20552 . . ENSG00000081479 ENST00000263816;ENST00000443831 D;D 0.91295 -2.82;-2.82 5.77 3.73 0.42828 Six-bladed beta-propeller, TolB-like (1); 0.770796 0.12440 N 0.468797 D 0.86239 0.5885 M 0.67953 2.075 0.27234 N 0.959321 B;B 0.29552 0.248;0.209 B;B 0.28553 0.091;0.035 T 0.75777 -0.3198 10 0.33141 T 0.24 . 1.5273 0.02528 0.4359:0.0:0.2681:0.296 . 700;837 E9PC35;P98164 .;LRP2_HUMAN V 837;700 ENSP00000263816:A837V;ENSP00000409813:A700V ENSP00000263816:A837V A - 2 0 LRP2 169823784 0.999000 0.42202 0.452000 0.26994 0.191000 0.23601 3.640000 0.54350 0.669000 0.31146 0.591000 0.81541 GCC TCGA-3A-A9IB-01A-21D-A397-08 LRP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255231.2 0 0 0 5 447 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 0.935277 5 440 0 52 2 0 0 0 0 0 2 -2.141562 0 1 121402 2 32 1 0 0 0 1.981250 0 0.380000 1.970000 0.370431 0.050000 1.000000e-02 0.130000 0.060000 0.068237 0.050000 0 0.030000 0.090000 OSR1 130497 broad.mit.edu 37 2 19552943 19552943 + Nonsense_Mutation SNP G G T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr2:19552943G>T ENST00000272223.2 - 2 968 c.624C>A c.(622-624)tgC>tgA p.C208* OSR1_ENST00000536433.1_Nonsense_Mutation_p.C208* NM_145260.2 NP_660303.1 Q8TAX0 OSR1_HUMAN odd-skipped related transciption factor 1 8 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197) Acute lymphoblastic leukemia(84;0.221) AGGCTTTGTGGCAGATGTCAC 0.597000 0 SO:0001587 stop_gained ENST00000272223.2 0 1 hg19 CCDS1694.1 . . . . . . . . . . G 39 7.611580 0.98390 . . ENSG00000143867 ENST00000272223;ENST00000536433 . . . 6.04 4.19 0.49359 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . . . . -22.081 8.9124 0.35561 0.2346:0.0:0.7654:0.0 . . . . X 208 . . C - 3 2 OSR1 19416424 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 1.198000 0.32223 0.838000 0.34948 0.650000 0.86243 TGC TCGA-3A-A9IB-01A-21D-A397-08 OSR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000201432.2 0 0 0 6 336 0 107 0 4.975124e-02 0 17 0 107 2 0 0 0 0 0 2 1 0.963700 6 331 0 107 2 0 0 0 0 0 2 -3.368486 1 1 0 0 1 1 2 3 2.037772 0 0.380000 1.970000 0.384676 0.090000 3.000000e-02 1.000000 0.100000 0.133105 0.090000 0 0.060000 0.150000 PTPRN 5798 broad.mit.edu 37 2 220162054 220162054 + Silent SNP G G A rs17847405 byFrequency TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr2:220162054G>A ENST00000295718.2 - 14 2229 c.1989C>T c.(1987-1989)gaC>gaT p.D663D PTPRN_ENST00000497977.1_5'Flank|AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000423636.2_Silent_p.D573D|PTPRN_ENST00000409251.3_Silent_p.D634D NM_002846.3 NP_002837.1 Q16849 PTPRN_HUMAN protein tyrosine phosphatase, receptor type, N 65 Renal(207;0.0474) CCTGGGCTGCGTCGCTGAACT 0.652000 0 SO:0001819 synonymous_variant ENST00000295718.2 1 0 hg19 CCDS2440.1 TCGA-3A-A9IB-01A-21D-A397-08 PTPRN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256819.2 0 0 1 72 336 0 120 0 4.932440e-01 0 9 0 120 2 0 0 0 0 0 2 1 1.000000 72 333 0 118 2 0 0 0 0 0 2 -2.124767 0 1 121412 4133 69 1 0 1 1 2.010617 0 0.380000 1.970000 0.378820 0.920000 7.400000e-01 1.000000 1.000000 0.916653 0.920000 1 0.820000 1.000000 LTBP1 4052 broad.mit.edu 37 2 33487847 33487847 + Missense_Mutation SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr2:33487847C>T ENST00000404816.2 + 14 2830 c.2477C>T c.(2476-2478)tCt>tTt p.S826F LTBP1_ENST00000407925.1_Missense_Mutation_p.S500F|LTBP1_ENST00000390003.4_Missense_Mutation_p.S500F|LTBP1_ENST00000404525.1_Missense_Mutation_p.S447F|LTBP1_ENST00000402934.1_Missense_Mutation_p.S447F|LTBP1_ENST00000354476.3_Missense_Mutation_p.S826F|LTBP1_ENST00000418533.2_Missense_Mutation_p.S500F Q14766 LTBP1_HUMAN latent transforming growth factor beta binding protein 1 108 all_hematologic(175;0.115) Medulloblastoma(90;0.215) CCCCAGCTGTCTCCAGGCATT 0.398000 0 SO:0001583 missense ENST00000404816.2 0 1 hg19 CCDS33177.2 . . . . . . . . . . C 23.1 4.372043 0.82573 . . ENSG00000049323 ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000413303;ENST00000468091 D;T;T;T;T;T;T;T;T 0.81659 -1.52;-1.48;-1.42;-1.39;-1.4;-1.39;-1.4;1.66;0.2 5.29 5.29 0.74685 . . . . . D 0.87030 0.6076 L 0.50333 1.59 0.80722 D 1 D;D;D;D;D;D 0.89917 0.999;1.0;0.995;1.0;1.0;1.0 D;D;D;D;D;D 0.91635 0.979;0.999;0.947;0.999;0.999;0.999 D 0.85468 0.1171 9 0.35671 T 0.21 . 18.0174 0.89246 0.0:1.0:0.0:0.0 . 826;500;447;500;500;826 Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4 LTBP1_HUMAN;.;.;.;.;. F 826;826;500;500;447;447;500;154;143 ENSP00000386043:S826F;ENSP00000346467:S826F;ENSP00000374653:S500F;ENSP00000393057:S500F;ENSP00000384373:S447F;ENSP00000385359:S447F;ENSP00000384091:S500F;ENSP00000415412:S154F;ENSP00000417591:S143F ENSP00000346467:S826F S + 2 0 LTBP1 33341351 1.000000 0.71417 1.000000 0.80357 0.932000 0.56968 6.160000 0.71862 2.490000 0.84030 0.650000 0.86243 TCT TCGA-3A-A9IB-01A-21D-A397-08 LTBP1-014 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000326227.2 1 0 1 23 164 0 18 1 9.999971e-01 20 137 0 18 2 0 0 0 0 0 2 1 1.000000 23 163 0 18 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.037772 0 0.380000 1.970000 0.384676 0.660000 4.300000e-01 1.000000 0.650000 0.676794 0.660000 0 0.530000 0.810000 GPAT2 150763 broad.mit.edu 37 2 96690527 96690527 + Silent SNP A A G TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr2:96690527A>G ENST00000434632.1 - 15 1881 c.1422T>C c.(1420-1422)caT>caC p.H474H GPAT2_ENST00000453542.1_Silent_p.H403H|GPAT2_ENST00000359548.4_Silent_p.H474H|FAHD2CP_ENST00000607780.1_RNA|GPAT2_ENST00000377137.3_Silent_p.H474H Q6NUI2 GPAT2_HUMAN glycerol-3-phosphate acyltransferase 2, mitochondrial 16 CTACCTTCTGATGCTTGAAGA 0.652000 0 SO:0001819 synonymous_variant ENST00000434632.1 1 1 hg19 CCDS42714.1 TCGA-3A-A9IB-01A-21D-A397-08 GPAT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000338786.1 0 0 0 25 677 0 163 0 6.138825e-02 0 11 0 163 2 0 0 0 0 0 2 1 1.000000 23 663 0 157 2 0 0 0 0 0 2 -19.995140 1 1 0 0 1 1 2 3 2.037772 0 0.380000 1.970000 0.384676 0.180000 1.200000e-01 1.000000 0.190000 0.218568 0.180000 0 0.150000 0.240000 CNGA3 1261 broad.mit.edu 37 2 99012788 99012788 + Missense_Mutation SNP C C G TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr2:99012788C>G ENST00000272602.2 + 7 1194 c.1155C>G c.(1153-1155)ttC>ttG p.F385L CNGA3_ENST00000393504.1_Missense_Mutation_p.F385L|CNGA3_ENST00000409937.1_Missense_Mutation_p.F389L|CNGA3_ENST00000436404.2_Missense_Mutation_p.F367L Q16281 CNGA3_HUMAN cyclic nucleotide gated channel alpha 3 49 TCGTAGACTTCTTGGTGGGTG 0.498000 0 SO:0001583 missense ENST00000272602.2 1 1 hg19 CCDS2034.1 . . . . . . . . . . C 11.74 1.727449 0.30593 . . ENSG00000144191 ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937 D;D;D;D 0.98493 -4.96;-4.96;-4.96;-4.96 5.05 5.05 0.67936 Ion transport (1); 0.000000 0.85682 D 0.000000 D 0.97021 0.9027 M 0.73598 2.24 0.58432 D 0.999997 B;B;B 0.31752 0.091;0.338;0.203 B;B;B 0.38194 0.147;0.267;0.255 D 0.94382 0.7605 10 0.32370 T 0.25 . 7.4961 0.27490 0.0:0.8252:0.0:0.1748 . 389;367;385 E9PF93;Q4VAP7;Q16281 .;.;CNGA3_HUMAN L 385;367;385;389 ENSP00000377140:F385L;ENSP00000410070:F367L;ENSP00000272602:F385L;ENSP00000386761:F389L ENSP00000272602:F385L F + 3 2 CNGA3 98379220 0.995000 0.38212 1.000000 0.80357 0.983000 0.72400 0.525000 0.22956 2.620000 0.88729 0.563000 0.77884 TTC TCGA-3A-A9IB-01A-21D-A397-08 CNGA3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000252986.1 1 0 1 72 234 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 1.000000 71 231 0 40 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.037772 0 0.380000 1.970000 0.384676 0.990000 9.900000e-01 1.000000 1.000000 0.999159 0.990000 1 0.990000 1.000000 FBXO40 51725 broad.mit.edu 37 3 121341863 121341863 + Silent SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr3:121341863G>A ENST00000338040.4 + 3 2001 c.1587G>A c.(1585-1587)ggG>ggA p.G529G NM_016298.3 NP_057382.2 Q9UH90 FBX40_HUMAN F-box protein 40 46 GTCCCCCAGGGCAAAAGGCAA 0.498000 0 SO:0001819 synonymous_variant ENST00000338040.4 0 1 hg19 CCDS33835.1 TCGA-3A-A9IB-01A-21D-A397-08 FBXO40-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000355158.1 0 0 0 5 273 0 39 0 0 0 0 39 2 0 0 0 0 0 2 1 0.936305 5 270 0 37 2 0 0 0 0 0 2 -2.988766 1 1 0 0 1 1 2 3 2.443204 1 0.380000 1.970000 0.478992 0.120000 4.000000e-02 0.250000 0.120000 0.133683 0.120000 0 0.070000 0.190000 TMCC1 23023 broad.mit.edu 37 3 129370592 129370592 + Missense_Mutation SNP T T A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr3:129370592T>A ENST00000393238.3 - 6 2034 c.1694A>T c.(1693-1695)cAg>cTg p.Q565L TMCC1_ENST00000329333.5_Missense_Mutation_p.Q386L|TMCC1_ENST00000426664.2_Missense_Mutation_p.Q451L|TMCC1_ENST00000432054.2_Missense_Mutation_p.Q241L NM_001017395.3 NP_001017395.2 O94876 TMCC1_HUMAN transmembrane and coiled-coil domain family 1 PLXND1/TMCC1(4) 25 CTGCTGCTGCTGCAGCTCCAT 0.572000 0 SO:0001583 missense ENST00000393238.3 0 1 hg19 CCDS33855.1 . . . . . . . . . . T 20.6 4.009576 0.75046 . . ENSG00000172765 ENST00000432054;ENST00000393238;ENST00000426664;ENST00000329333 T;T;T;T 0.50001 0.76;0.76;0.76;0.76 5.16 5.16 0.70880 . 0.000000 0.85682 D 0.000000 T 0.61261 0.2333 L 0.46614 1.455 0.80722 D 1 D;D 0.67145 0.996;0.985 D;D 0.85130 0.997;0.973 T 0.58278 -0.7664 10 0.33940 T 0.23 -18.4911 15.1509 0.72696 0.0:0.0:0.0:1.0 . 386;565 B4DE04;O94876 .;TMCC1_HUMAN L 241;565;451;386 ENSP00000404711:Q241L;ENSP00000376930:Q565L;ENSP00000389892:Q451L;ENSP00000327349:Q386L ENSP00000327349:Q386L Q - 2 0 TMCC1 130853282 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 7.735000 0.84939 2.172000 0.68678 0.533000 0.62120 CAG TCGA-3A-A9IB-01A-21D-A397-08 TMCC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356418.2 0 0 0 5 413 0 54 0 2.343875e-01 0 64 0 54 2 0 0 0 0 0 2 1 0.942391 4 426 0 56 2 0 0 0 0 0 2 -2.081405 0 1 0 0 1 1 2 3 2.443204 1 0.380000 1.970000 0.478992 0.070000 1.000000e-02 0.170000 0.080000 0.089162 0.070000 0 0.040000 0.120000 ACAP2 23527 broad.mit.edu 37 3 195027329 195027329 + Missense_Mutation SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr3:195027329C>T ENST00000326793.6 - 13 1257 c.1027G>A c.(1027-1029)Gca>Aca p.A343T NM_012287.5 NP_036419.3 Q15057 ACAP2_HUMAN ArfGAP with coiled-coil, ankyrin repeat and PH domains 2 27 TCGGAATCTGCCTGGAGCATG 0.403000 0 SO:0001583 missense ENST00000326793.6 1 1 hg19 CCDS33924.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 32|32 5.136760|5.136760 0.94517|0.94517 .|. .|. ENSG00000114331|ENSG00000114331 ENST00000326793|ENST00000439758 T|. 0.78126|. -1.15|. 5.68|5.68 5.68|5.68 0.88126|0.88126 Pleckstrin homology-type (1);Pleckstrin homology domain (3);|. 0.000000|. 0.85682|. D|. 0.000000|. D|D 0.84552|0.84552 0.5497|0.5497 M|M 0.89095|0.89095 3.005|3.005 0.80722|0.80722 D|D 1|1 D|. 0.89917|. 1.0|. D|. 0.91635|. 0.999|. D|D 0.86482|0.86482 0.1792|0.1792 10|5 0.87932|. D|. 0|. .|. 18.7846|18.7846 0.91949|0.91949 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 343|. Q15057|. ACAP2_HUMAN|. T|D 343|217 ENSP00000324287:A343T|. ENSP00000324287:A343T|. A|G -|- 1|2 0|0 ACAP2|ACAP2 196508618|196508618 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.988000|0.988000 0.76386|0.76386 7.818000|7.818000 0.86416|0.86416 2.662000|2.662000 0.90505|0.90505 0.609000|0.609000 0.83330|0.83330 GCA|GGC TCGA-3A-A9IB-01A-21D-A397-08 ACAP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342126.2 1 0 0 48 486 0 63 1 4.663170e-01 2 15 0 63 2 0 0 0 0 0 2 1 1.000000 48 485 0 63 2 0 0 0 0 0 2 -13.516650 1 1 0 0 1 1 2 3 2.443204 1 0.380000 1.970000 0.478992 0.560000 4.200000e-01 0.720000 0.570000 0.571402 0.560000 0 0.480000 0.650000 LRCH3 84859 broad.mit.edu 37 3 197562598 197562598 + Missense_Mutation SNP G G C TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr3:197562598G>C ENST00000425562.2 + 9 1156 c.1156G>C c.(1156-1158)Gag>Cag p.E386Q LRCH3_ENST00000536618.1_5'UTR|LRCH3_ENST00000334859.4_Missense_Mutation_p.E386Q|LRCH3_ENST00000438796.2_Missense_Mutation_p.E386Q|LRCH3_ENST00000414675.2_Missense_Mutation_p.E386Q|LRCH3_ENST00000441090.2_Missense_Mutation_p.E260Q Q96II8 LRCH3_HUMAN leucine-rich repeats and calponin homology (CH) domain containing 3 29 all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976) Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07) CGCAGAGGAAGAGGAGGCCGA 0.502000 0 SO:0001583 missense ENST00000425562.2 1 1 hg19 . . . . . . . . . . G 24.0 4.481581 0.84747 . . ENSG00000186001 ENST00000438796;ENST00000441090;ENST00000414675;ENST00000334859;ENST00000425562 T;T;T;T;T 0.38401 1.89;1.14;1.91;2.14;1.91 5.27 5.27 0.74061 . 0.057940 0.64402 D 0.000004 T 0.40222 0.1108 L 0.34521 1.04 0.80722 D 1 D;D;P;B 0.60160 0.987;0.958;0.817;0.27 P;P;P;B 0.52424 0.698;0.697;0.686;0.398 T 0.04621 -1.0938 10 0.16420 T 0.52 -10.8516 19.2996 0.94138 0.0:0.0:1.0:0.0 . 260;386;386;386 E9PD99;B4E0T7;Q96II8-2;Q96II8-3 .;.;.;. Q 386;260;386;386;386 ENSP00000399751:E386Q;ENSP00000394609:E260Q;ENSP00000394965:E386Q;ENSP00000334375:E386Q;ENSP00000393579:E386Q ENSP00000334375:E386Q E + 1 0 LRCH3 199046995 1.000000 0.71417 0.957000 0.39632 0.888000 0.51559 8.533000 0.90617 2.642000 0.89623 0.644000 0.83932 GAG TCGA-3A-A9IB-01A-21D-A397-08 LRCH3-006 KNOWN basic protein_coding protein_coding OTTHUMT00000339965.1 1 0 0 37 402 0 58 1 8.759212e-01 3 39 0 58 2 0 0 0 0 0 2 1 1.000000 35 399 0 57 2 0 0 0 0 0 2 -3.017764 1 1 0 0 1 1 2 3 2.436954 1 0.380000 1.970000 0.478158 0.520000 3.700000e-01 0.710000 0.530000 0.537485 0.520000 0 0.440000 0.620000 CCDC149 91050 broad.mit.edu 37 4 24839847 24839847 + Silent SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr4:24839847G>A ENST00000389609.4 - 6 563 c.420C>T c.(418-420)atC>atT p.I140I CCDC149_ENST00000428116.2_Intron|CCDC149_ENST00000502801.1_Intron|CCDC149_ENST00000504487.1_Silent_p.I140I NM_173463.4 NP_775734.2 Q6ZUS6 CC149_HUMAN coiled-coil domain containing 149 7 Breast(46;0.173) GTCGCACGCCGATTGCTTCGT 0.483000 0 SO:0001819 synonymous_variant ENST00000389609.4 0 1 hg19 CCDS33967.2 TCGA-3A-A9IB-01A-21D-A397-08 CCDC149-002 PUTATIVE basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000360157.1 0 0 0 5 472 0 92 0 3.120933e-02 0 21 0 92 2 0 0 0 0 0 2 0 0.004322 5 465 1 88 18 0 0 0 0 0 2 -2.237863 0 1 121412 6 42 1 0 1 1 1.760189 1 0.380000 1.970000 0.238142 0.040000 1.000000e-02 0.100000 0.050000 0.053294 0.040000 0 0.020000 0.070000 CHRNA9 55584 broad.mit.edu 37 4 40351405 40351405 + Missense_Mutation SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr4:40351405C>T ENST00000310169.2 + 4 1011 c.872C>T c.(871-873)cCg>cTg p.P291L NM_017581.3 NP_060051.2 Q9UGM1 ACHA9_HUMAN cholinergic receptor, nicotinic, alpha 9 (neuronal) 33 Galantamine(DB00674)|Nicotine(DB00184) GAAATCATGCCGGCCTCAGAA 0.512000 Esophageal Squamous(115;1297 1602 22235 25158 43327) 0 SO:0001583 missense ENST00000310169.2 0 1 hg19 CCDS3459.1 . . . . . . . . . . C 22.9 4.355172 0.82243 . . ENSG00000174343 ENST00000310169 D 0.99382 -5.8 5.6 5.6 0.85130 Neurotransmitter-gated ion-channel transmembrane domain (2); 0.000000 0.85682 D 0.000000 D 0.99722 0.9892 H 0.98295 4.195 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.97219 0.9876 10 0.87932 D 0 . 19.6143 0.95626 0.0:1.0:0.0:0.0 . 291 Q9UGM1 ACHA9_HUMAN L 291 ENSP00000312663:P291L ENSP00000312663:P291L P + 2 0 CHRNA9 40046162 1.000000 0.71417 0.979000 0.43373 0.662000 0.39071 7.818000 0.86416 2.640000 0.89533 0.561000 0.74099 CCG TCGA-3A-A9IB-01A-21D-A397-08 CHRNA9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000216822.1 0 0 0 5 436 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 0.937128 6 433 0 67 2 0 0 0 0 0 2 -2.456322 0 1 121398 1 36 1 0 1 1 1.725719 1 0.380000 1.970000 0.234568 0.040000 1.000000e-02 0.110000 0.050000 0.057306 0.040000 0 0.020000 0.080000 UBA6 55236 broad.mit.edu 37 4 68501258 68501258 + Silent SNP T T C TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr4:68501258T>C ENST00000322244.5 - 20 1814 c.1755A>G c.(1753-1755)ctA>ctG p.L585L NM_018227.5 NP_060697.4 A0AVT1 UBA6_HUMAN ubiquitin-like modifier activating enzyme 6 44 AAAGAGGCCTTAGATTTGCTA 0.358000 0 SO:0001819 synonymous_variant ENST00000322244.5 0 1 hg19 CCDS3516.1 TCGA-3A-A9IB-01A-21D-A397-08 UBA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251429.2 0 0 0 4 327 0 87 0 1.280853e-01 0 40 0 87 2 0 0 0 0 0 2 1 0.890272 4 326 0 86 2 0 0 0 0 0 2 -5.101528 1 0 0 0 1 1 2 3 2.063709 0 0.380000 1.970000 0.411318 0.080000 2.000000e-02 1.000000 0.070000 0.260391 0.080000 0 0.040000 1.000000 PCDHB7 56129 broad.mit.edu 37 5 140554443 140554443 + Missense_Mutation SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr5:140554443C>T ENST00000231137.3 + 1 2201 c.2027C>T c.(2026-2028)gCg>gTg p.A676V PCDHB8_ENST00000239444.2_5'Flank NM_018940.2 NP_061763.1 Q9Y5E2 PCDB7_HUMAN protocadherin beta 7 119 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) CTCCCGGAGGCGGCCCCGGAC 0.692000 0 SO:0001583 missense ENST00000231137.3 1 1 hg19 CCDS4249.1 . . . . . . . . . . C 4.037 0.004475 0.07866 . . ENSG00000113212 ENST00000231137 T 0.51817 0.69 3.77 -3.6 0.04570 . . . . . T 0.17704 0.0425 N 0.10707 0.03 0.09310 N 1 B 0.15473 0.013 B 0.10450 0.005 T 0.31641 -0.9936 9 0.02654 T 1 . 4.7814 0.13204 0.0:0.2545:0.3902:0.3553 . 676 Q9Y5E2 PCDB7_HUMAN V 676 ENSP00000231137:A676V ENSP00000231137:A676V A + 2 0 PCDHB7 140534627 0.000000 0.05858 0.077000 0.20336 0.306000 0.27790 -0.419000 0.07071 -0.428000 0.07339 0.449000 0.29647 GCG TCGA-3A-A9IB-01A-21D-A397-08 PCDHB7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251803.2 1 0 1 72 566 0 259 1 1.436596e-01 2 4 0 259 2 0 0 0 0 2 2 1 1.000000 72 562 0 252 2 0 0 0 0 0 2 -3.318794 1 1 0 0 1 1 2 3 2.051129 0 0.380000 1.970000 0.386988 0.600000 4.700000e-01 1.000000 0.600000 0.624188 0.600000 0 0.530000 0.690000 GEMIN5 25929 broad.mit.edu 37 5 154292538 154292538 + Missense_Mutation SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr5:154292538G>A ENST00000285873.7 - 14 1991 c.1916C>T c.(1915-1917)aCg>aTg p.T639M NM_001252156.1|NM_015465.4 NP_001239085.1|NP_056280.2 Q8TEQ6 GEMI5_HUMAN gem (nuclear organelle) associated protein 5 38 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.147) KIRC - Kidney renal clear cell carcinoma(527;0.00112) AATCTTGGCCGTATGCCCTGA 0.522000 0 SO:0001583 missense ENST00000285873.7 0 1 hg19 CCDS4330.1 . . . . . . . . . . G 19.12 3.766113 0.69878 . . ENSG00000082516 ENST00000285873 T 0.65549 -0.16 5.37 5.37 0.77165 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.000000 0.85682 D 0.000000 T 0.80742 0.4681 M 0.78637 2.42 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 T 0.82647 -0.0354 10 0.87932 D 0 -17.564 19.0919 0.93229 0.0:0.0:1.0:0.0 . 638;639 B7ZLC9;Q8TEQ6 .;GEMI5_HUMAN M 639 ENSP00000285873:T639M ENSP00000285873:T639M T - 2 0 GEMIN5 154272731 1.000000 0.71417 1.000000 0.80357 0.298000 0.27526 8.881000 0.92415 2.667000 0.90743 0.561000 0.74099 ACG TCGA-3A-A9IB-01A-21D-A397-08 GEMIN5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252507.1 0 0 0 5 307 0 55 0 5.492174e-02 0 19 0 55 2 0 0 0 0 0 2 1 0.935895 5 303 0 54 2 0 0 0 0 0 2 -2.742634 1 1 121412 5 34 1 1 2 3 2.051129 0 0.380000 1.970000 0.386988 0.090000 3.000000e-02 1.000000 0.080000 0.143414 0.090000 0 0.050000 0.150000 DOCK2 1794 broad.mit.edu 37 5 169446049 169446049 + Silent SNP C C A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr5:169446049C>A ENST00000256935.8 + 33 3398 c.3318C>A c.(3316-3318)gcC>gcA p.A1106A DOCK2_ENST00000520908.1_Silent_p.A598A|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Silent_p.A167A NM_004946.2 NP_004937.1 Q92608 DOCK2_HUMAN dedicator of cytokinesis 2 160 Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337) Medulloblastoma(196;0.0399)|all_neural(177;0.0966) Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) TCCGGAAAGCCACCATACCAA 0.453000 0 SO:0001819 synonymous_variant ENST00000256935.8 1 1 hg19 CCDS4371.1 TCGA-3A-A9IB-01A-21D-A397-08 DOCK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252828.2 1 0 1 148 750 0 113 0 7.667690e-01 0 16 0 113 2 0 0 0 0 0 2 1 1.000000 148 746 0 108 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.051129 0 0.380000 1.970000 0.386988 0.870000 7.400000e-01 1.000000 0.880000 0.884334 0.870000 1 0.810000 0.960000 CDHR2 54825 broad.mit.edu 37 5 176003158 176003158 + Missense_Mutation SNP T T A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr5:176003158T>A ENST00000510636.1 + 12 1440 c.1166T>A c.(1165-1167)cTc>cAc p.L389H CDHR2_ENST00000506348.1_Missense_Mutation_p.L389H|CDHR2_ENST00000261944.5_Missense_Mutation_p.L389H NM_001171976.1 NP_001165447.1 Q9BYE9 CDHR2_HUMAN cadherin-related family member 2 56 ATCGATGACCTCACCATGGTG 0.667000 0 SO:0001583 missense ENST00000510636.1 1 1 hg19 CCDS34297.1 . . . . . . . . . . T 19.26 3.792906 0.70452 . . ENSG00000074276 ENST00000510636;ENST00000261944;ENST00000506348 T;T;T 0.63255 -0.03;-0.03;-0.03 4.54 4.54 0.55810 Cadherin (2);Cadherin-like (1); . . . . T 0.79879 0.4522 M 0.91972 3.26 0.53688 D 0.999978 D 0.67145 0.996 P 0.60345 0.873 D 0.84655 0.0703 9 0.87932 D 0 -24.7678 12.2853 0.54789 0.0:0.0:0.0:1.0 . 389 Q9BYE9 CDHR2_HUMAN H 389 ENSP00000424565:L389H;ENSP00000261944:L389H;ENSP00000421078:L389H ENSP00000261944:L389H L + 2 0 CDHR2 175935764 1.000000 0.71417 0.971000 0.41717 0.555000 0.35460 4.560000 0.60802 1.910000 0.55303 0.448000 0.29417 CTC TCGA-3A-A9IB-01A-21D-A397-08 CDHR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372201.1 1 0 1 39 218 0 65 1 1 83 88 0 65 2 0 0 0 0 0 2 1 1.000000 37 215 0 65 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.051129 0 0.380000 1.970000 0.386988 0.810000 5.900000e-01 1.000000 1.000000 0.821819 0.810000 0 0.690000 0.960000 AKAP12 9590 broad.mit.edu 37 6 151671524 151671524 + Silent SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr6:151671524G>A ENST00000253332.1 + 3 2187 c.1998G>A c.(1996-1998)ccG>ccA p.P666P AKAP12_ENST00000402676.2_Silent_p.P666P|AKAP12_ENST00000359755.5_Silent_p.P561P|AKAP12_ENST00000354675.6_Silent_p.P568P Q02952 AKA12_HUMAN A kinase (PRKA) anchor protein 12 68 Ovarian(120;0.125) BRCA - Breast invasive adenocarcinoma(37;0.175) AGCCAAAGCCGGAAGAACCAA 0.493000 Melanoma(141;1616 1805 10049 24534 51979) 0 SO:0001819 synonymous_variant ENST00000253332.1 0 1 hg19 CCDS5229.1 TCGA-3A-A9IB-01A-21D-A397-08 AKAP12-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000042712.1 0 0 0 4 223 0 46 0 4.490937e-01 0 73 0 46 2 0 0 0 0 0 2 1 0.889062 4 221 0 46 2 0 0 0 0 0 2 -2.965700 1 1 121412 4 37 1 0 1 1 1.896966 1 0.380000 1.970000 0.339864 0.090000 2.000000e-02 0.210000 0.090000 0.107006 0.090000 0 0.050000 0.150000 FNDC1 84624 broad.mit.edu 37 6 159646578 159646578 + Missense_Mutation SNP T T C TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 T C T T Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr6:159646578T>C ENST00000297267.9 + 8 1096 c.896T>C c.(895-897)gTg>gCg p.V299A FNDC1_ENST00000480856.1_3'UTR|FNDC1_ENST00000340366.6_Missense_Mutation_p.V299A NM_032532.2 NP_115921.2 Q4ZHG4 FNDC1_HUMAN fibronectin type III domain containing 1 93 Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195) CAGTACACCGTGCGCTATCGA 0.463000 0 SO:0001583 missense ENST00000297267.9 1 1 hg19 CCDS47512.1 . . . . . . . . . . T 21.1 4.101834 0.76983 . . ENSG00000164694 ENST00000297267;ENST00000340366 T;T 0.68624 -0.34;-0.34 5.84 5.84 0.93424 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 T 0.81083 0.4749 M 0.86028 2.79 0.53688 D 0.999972 D;D 0.89917 1.0;1.0 D;D 0.87578 0.997;0.998 D 0.84681 0.0717 10 0.87932 D 0 -20.4318 16.2108 0.82158 0.0:0.0:0.0:1.0 . 299;299 Q4ZHG4-2;Q4ZHG4 .;FNDC1_HUMAN A 299 ENSP00000297267:V299A;ENSP00000342460:V299A ENSP00000297267:V299A V + 2 0 FNDC1 159566566 1.000000 0.71417 1.000000 0.80357 0.951000 0.60555 7.603000 0.82811 2.232000 0.73038 0.533000 0.62120 GTG TCGA-3A-A9IB-01A-21D-A397-08 FNDC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042897.3 1 0 1 139 493 0 148 0 1 0 109 0 148 2 0 0 0 0 0 2 1 1.000000 138 490 0 148 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.896966 1 0.380000 1.970000 0.339864 0.990000 9.200000e-01 1.000000 1.000000 0.994605 0.990000 1 0.990000 1.000000 NUP153 9972 broad.mit.edu 37 6 17669530 17669530 + Silent SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr6:17669530C>T ENST00000262077.2 - 7 1007 c.1008G>A c.(1006-1008)ctG>ctA p.L336L NUP153_ENST00000537253.1_Silent_p.L336L NM_005124.2 NP_005115.2 P49790 NU153_HUMAN nucleoporin 153kDa 53 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) TTACAGAATTCAGAGGAGAAG 0.328000 0 SO:0001819 synonymous_variant ENST00000262077.2 1 1 hg19 CCDS4541.1 TCGA-3A-A9IB-01A-21D-A397-08 NUP153-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039953.1 1 0 1 85 361 0 74 1 9.274229e-01 3 18 0 74 2 0 0 0 0 0 2 1 1.000000 84 354 0 73 2 0 0 0 0 0 2 -3.393051 1 1 0 0 1 0 0 0 1.948105 0 0.380000 1.970000 0.358045 0.960000 7.800000e-01 1.000000 1.000000 0.946405 0.960000 1 0.870000 1.000000 TAP1 6890 broad.mit.edu 37 6 32818230 32818230 + Missense_Mutation SNP G G A rs147332077 TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr6:32818230G>A ENST00000354258.4 - 5 1456 c.1295C>T c.(1294-1296)tCg>tTg p.S432L PSMB9_ENST00000395330.1_Intron|TAP1_ENST00000425148.2_Missense_Mutation_p.S171L NM_000593.5 NP_000584.2 Q03518 TAP1_HUMAN transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) 21 Lapatinib(DB01259) AGGCATGGCCGACAGAGCCTC 0.532000 0 SO:0001583 missense ENST00000354258.4 0 1 hg19 CCDS4758.1 0 0.0 0 0.0 0 0.0 0 0.0 0 0.0 G 35 5.420836 0.96111 0.001362 0.0 ENSG00000168394 ENST00000354258;ENST00000425148 D;D 0.91068 -2.78;-2.78 5.72 5.72 0.89469 ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1); 0.000000 0.38436 N 0.001686 D 0.92734 0.7690 M 0.79805 2.47 0.80722 D 1 P 0.52842 0.956 P 0.52189 0.692 D 0.93356 0.6722 10 0.72032 D 0.01 -5.2332 17.381 0.87405 0.0:0.0:1.0:0.0 . 432 Q03518 TAP1_HUMAN L 432;171 ENSP00000346206:S432L;ENSP00000401919:S171L ENSP00000346206:S432L S - 2 0 TAP1 32926208 1.000000 0.71417 0.994000 0.49952 0.935000 0.57460 5.503000 0.66962 2.706000 0.92434 0.643000 0.83706 TCG TCGA-3A-A9IB-01A-21D-A397-08 TAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076087.2 0 0 0 4 207 0 39 0 9.810162e-01 0 412 0 39 2 0 0 0 0 0 2 1 0.891188 4 207 0 38 2 0 0 0 0 0 2 -3.333864 1 1 121412 14 42 1 0 0 0 1.948105 0 0.380000 1.970000 0.358045 0.100000 3.000000e-02 0.230000 0.100000 0.118308 0.100000 0 0.060000 0.170000 DDX43 55510 broad.mit.edu 37 6 74115486 74115486 + Silent SNP C C T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr6:74115486C>T ENST00000370336.4 + 6 893 c.735C>T c.(733-735)gaC>gaT p.D245D DDX43_ENST00000539829.1_3'UTR NM_018665.2 NP_061135.2 Q9NXZ2 DDX43_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 24 CATTTGATGACGCCTTTCAAT 0.353000 0 SO:0001819 synonymous_variant ENST00000370336.4 1 1 hg19 CCDS4977.1 TCGA-3A-A9IB-01A-21D-A397-08 DDX43-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041219.3 1 0 0 43 181 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 1.000000 43 179 0 34 2 0 0 0 0 0 2 -20.000000 1 1 121412 1 35 1 0 0 0 1.948105 0 0.380000 1.970000 0.358045 0.970000 7.200000e-01 1.000000 1.000000 0.937276 0.970000 1 0.840000 1.000000 TTK 7272 broad.mit.edu 37 6 80720617 80720617 + Missense_Mutation SNP A A T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr6:80720617A>T ENST00000369798.2 + 5 667 c.556A>T c.(556-558)Aat>Tat p.N186Y TTK_ENST00000509894.1_Missense_Mutation_p.N186Y|TTK_ENST00000230510.3_Missense_Mutation_p.N186Y NM_001166691.1|NM_003318.4 NP_001160163.1|NP_003309.2 P33981 TTK_HUMAN TTK protein kinase 53 all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2) TGCCCTGCGGAATTTAAACCT 0.363000 0 SO:0001583 missense ENST00000369798.2 1 1 hg19 CCDS4993.1 . . . . . . . . . . A 23.4 4.415177 0.83449 . . ENSG00000112742 ENST00000509894;ENST00000230510;ENST00000369798 D;D;D 0.89123 -2.47;-2.47;-2.47 4.95 4.95 0.65309 . 0.090404 0.85682 D 0.000000 D 0.92061 0.7484 M 0.68952 2.095 0.50171 D 0.999852 D;D 0.89917 1.0;1.0 D;D 0.77557 0.99;0.987 D 0.93268 0.6649 10 0.87932 D 0 . 14.0796 0.64912 1.0:0.0:0.0:0.0 . 186;186 P33981;A8K8U5 TTK_HUMAN;. Y 186 ENSP00000422936:N186Y;ENSP00000230510:N186Y;ENSP00000358813:N186Y ENSP00000230510:N186Y N + 1 0 TTK 80777336 1.000000 0.71417 0.899000 0.35326 0.986000 0.74619 8.060000 0.89464 1.982000 0.57802 0.459000 0.35465 AAT TCGA-3A-A9IB-01A-21D-A397-08 TTK-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000041316.2 1 0 1 60 427 0 90 1 3.118787e-01 3 6 0 90 2 0 0 0 0 0 2 1 1.000000 60 425 0 90 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 1.948105 0 0.380000 1.970000 0.358045 0.620000 4.800000e-01 0.780000 0.620000 0.631765 0.620000 0 0.550000 0.700000 DLD 1738 broad.mit.edu 37 7 107546792 107546792 + Silent SNP A A C TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr7:107546792A>C ENST00000205402.5 + 8 944 c.663A>C c.(661-663)gcA>gcC p.A221A DLD_ENST00000537148.1_Silent_p.A122A|DLD_ENST00000440410.1_Silent_p.A198A|DLD_ENST00000437604.2_Silent_p.A173A NM_000108.3 NP_000099.2 P09622 DLDH_HUMAN dihydrolipoamide dehydrogenase 20 Flavin adenine dinucleotide(DB03147) TTATTGGTGCAGGAGTAATAG 0.348000 0 SO:0001819 synonymous_variant ENST00000205402.5 1 1 hg19 CCDS5749.1 TCGA-3A-A9IB-01A-21D-A397-08 DLD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000337194.3 1 0 1 11 161 0 36 1 9.928027e-01 18 109 0 36 2 0 0 0 0 0 2 1 0.998403 11 159 0 35 2 0 0 0 0 0 2 -5.165075 1 1 0 0 1 1 2 3 2.067162 0 0.380000 1.970000 0.389283 0.360000 1.800000e-01 1.000000 0.330000 0.405996 0.360000 0 0.260000 0.500000 FOXP2 93986 broad.mit.edu 37 7 114303542 114303542 + Missense_Mutation SNP G G T TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr7:114303542G>T ENST00000393494.2 + 15 2086 c.1807G>T c.(1807-1809)Ggc>Tgc p.G603C FOXP2_ENST00000393500.3_3'UTR|FOXP2_ENST00000393498.2_Missense_Mutation_p.G582C|FOXP2_ENST00000350908.4_Missense_Mutation_p.G603C|FOXP2_ENST00000393491.3_Missense_Mutation_p.G418C|FOXP2_ENST00000403559.4_Missense_Mutation_p.G620C|FOXP2_ENST00000408937.3_Missense_Mutation_p.G628C|FOXP2_ENST00000393489.3_Missense_Mutation_p.G511C O15409 FOXP2_HUMAN forkhead box P2 52 TACCAGTTTAGGCTATGGAGC 0.303000 0 SO:0001583 missense ENST00000393494.2 0 1 hg19 CCDS5760.1 . . . . . . . . . . G 15.51 2.853517 0.51270 . . ENSG00000128573 ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000393489;ENST00000393491 D;D;D;D;D;D 0.92099 -2.71;-2.7;-2.71;-2.71;-2.79;-2.97 5.32 5.32 0.75619 . 0.000000 0.85682 D 0.000000 D 0.95001 0.8382 L 0.50333 1.59 0.80722 D 1 D;D;D;D;D 0.89917 1.0;1.0;0.999;1.0;1.0 D;D;D;D;D 0.87578 0.996;0.996;0.959;0.996;0.998 D 0.95345 0.8441 10 0.72032 D 0.01 . 19.0298 0.92952 0.0:0.0:1.0:0.0 . 602;620;418;603;628 B7ZLK5;B4DLD9;Q0PRL4;O15409;O15409-4 .;.;.;FOXP2_HUMAN;. C 603;628;620;603;580;511;418 ENSP00000377132:G603C;ENSP00000386200:G628C;ENSP00000385069:G620C;ENSP00000265436:G603C;ENSP00000377129:G511C;ENSP00000377130:G418C ENSP00000265436:G603C G + 1 0 FOXP2 114090778 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.624000 0.98398 2.486000 0.83907 0.650000 0.86243 GGC TCGA-3A-A9IB-01A-21D-A397-08 FOXP2-014 KNOWN alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317366.1 0 0 0 6 397 0 57 0 0 0 1 0 57 2 0 0 0 0 0 2 1 0.964709 6 395 0 55 2 0 0 0 0 0 2 -2.629297 1 1 0 0 1 1 2 3 2.067162 0 0.380000 1.970000 0.389283 0.080000 2.000000e-02 1.000000 0.080000 0.150415 0.080000 0 0.050000 0.140000 ZNF789 285989 broad.mit.edu 37 7 99084376 99084376 + Silent SNP C C G TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr7:99084376C>G ENST00000331410.5 + 5 813 c.543C>G c.(541-543)ccC>ccG p.P181P ZNF789_ENST00000493485.1_Intron|ZNF789_ENST00000494186.1_Intron|ZNF789_ENST00000448667.1_3'UTR NM_213603.2 NP_998768.2 Q5FWF6 ZN789_HUMAN zinc finger protein 789 11 all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166) ATGGCAAACCCTTCAATCAAA 0.428000 0 SO:0001819 synonymous_variant ENST00000331410.5 1 1 hg19 CCDS34693.1 TCGA-3A-A9IB-01A-21D-A397-08 ZNF789-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336266.1 0 0 0 11 454 0 71 0 3.867456e-02 0 12 0 71 2 0 0 0 0 0 2 1 0.998228 10 448 0 69 2 0 0 0 0 0 2 -2.669539 1 1 0 0 1 1 2 3 2.053263 0 0.380000 1.970000 0.386988 0.130000 6.000000e-02 1.000000 0.120000 0.176878 0.130000 0 0.090000 0.180000 GRHL2 79977 broad.mit.edu 37 8 102585988 102585988 + Missense_Mutation SNP A A G TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr8:102585988A>G ENST00000251808.3 + 6 1165 c.827A>G c.(826-828)tAt>tGt p.Y276C GRHL2_ENST00000395927.1_Missense_Mutation_p.Y260C NM_024915.3 NP_079191.2 Q6ISB3 GRHL2_HUMAN grainyhead-like 2 (Drosophila) 28 all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05) Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213) GGACAGTTCTATGCCATAACA 0.507000 0 SO:0001583 missense ENST00000251808.3 1 1 hg19 CCDS34931.1 . . . . . . . . . . A 24.2 4.501570 0.85176 . . ENSG00000083307 ENST00000251808;ENST00000395927;ENST00000395928 T;T 0.38401 1.14;1.14 5.7 5.7 0.88788 CP2 transcription factor (1); 0.000000 0.85682 D 0.000000 T 0.69441 0.3111 M 0.92412 3.305 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 0.999;1.0 T 0.78107 -0.2333 10 0.87932 D 0 -14.6055 15.9541 0.79871 1.0:0.0:0.0:0.0 . 276;276 B4DL28;Q6ISB3 .;GRHL2_HUMAN C 276;260;276 ENSP00000251808:Y276C;ENSP00000379260:Y260C ENSP00000251808:Y276C Y + 2 0 GRHL2 102655164 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 9.307000 0.96226 2.167000 0.68274 0.528000 0.53228 TAT TCGA-3A-A9IB-01A-21D-A397-08 GRHL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313882.1 1 0 1 133 148 0 45 1 1 42 2 0 45 2 0 0 0 0 0 2 1 1.000000 132 145 0 43 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 3 3 2.429079 1 0.380000 1.970000 0.478992 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 BHLHE22 27319 broad.mit.edu 37 8 65493724 65493724 + Missense_Mutation SNP G G C TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr8:65493724G>C ENST00000321870.1 + 1 911 c.377G>C c.(376-378)tGc>tCc p.C126S RP11-21C4.1_ENST00000517909.1_RNA NM_152414.4 NP_689627.1 Q8NFJ8 BHE22_HUMAN basic helix-loop-helix family, member e22 5 GCCGCCCTTTGCCTCAAGTAC 0.746000 Colon(113;104 1586 2865 9855 18065) 0 SO:0001583 missense ENST00000321870.1 0 1 hg19 CCDS6179.1 . . . . . . . . . . G 16.11 3.029659 0.54790 . . ENSG00000180828 ENST00000321870 D 0.98747 -5.11 3.19 3.19 0.36642 . 0.153691 0.43747 U 0.000527 D 0.98065 0.9362 L 0.29908 0.895 0.50039 D 0.999844 D 0.71674 0.998 D 0.73708 0.981 D 0.98433 1.0583 10 0.59425 D 0.04 . 14.4812 0.67585 0.0:0.0:1.0:0.0 . 126 Q8NFJ8 BHE22_HUMAN S 126 ENSP00000318799:C126S ENSP00000318799:C126S C + 2 0 BHLHE22 65656278 1.000000 0.71417 0.998000 0.56505 0.712000 0.41017 5.668000 0.68074 1.787000 0.52448 0.455000 0.32223 TGC TCGA-3A-A9IB-01A-21D-A397-08 BHLHE22-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378549.1 0 0 0 3 42 0 10 0 0 0 1 0 10 2 0 0 0 0 0 2 1 0.812618 3 42 0 10 2 0 0 0 0 0 2 -7.854897 1 1 0 0 1 0 3 3 2.422574 1 0.380000 1.970000 0.478992 0.470000 1.400000e-01 1.000000 1.000000 0.513552 0.470000 0 0.270000 0.750000 DOCK8 81704 broad.mit.edu 37 9 376273 376273 + Missense_Mutation SNP G G C TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chr9:376273G>C ENST00000453981.1 + 19 2285 c.2173G>C c.(2173-2175)Gaa>Caa p.E725Q DOCK8_ENST00000432829.2_Missense_Mutation_p.E657Q|DOCK8_ENST00000382331.1_Missense_Mutation_p.E27Q|DOCK8_ENST00000382329.1_Missense_Mutation_p.E192Q|DOCK8_ENST00000469391.1_Missense_Mutation_p.E657Q Q8NF50 DOCK8_HUMAN dedicator of cytokinesis 8 65 all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128) ATTTAATATTGAAGTGCAAGC 0.408000 0 SO:0001583 missense ENST00000453981.1 0 1 hg19 CCDS6440.2 . . . . . . . . . . G 21.6 4.176915 0.78564 . . ENSG00000107099 ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382331;ENST00000382329 T;T;T;T;T 0.47869 0.83;0.83;0.83;0.83;0.83 5.66 5.66 0.87406 . 0.000000 0.85682 D 0.000000 T 0.65069 0.2656 L 0.56769 1.78 0.80722 D 1 D;B;P;B 0.76494 0.999;0.255;0.534;0.361 D;B;B;B 0.66847 0.947;0.314;0.369;0.393 T 0.58059 -0.7703 10 0.27785 T 0.31 . 19.8078 0.96537 0.0:0.0:1.0:0.0 . 27;657;192;725 A2A370;E9PH09;A2A369;Q8NF50 .;.;.;DOCK8_HUMAN Q 725;725;657;657;27;192 ENSP00000408464:E725Q;ENSP00000394888:E657Q;ENSP00000419438:E657Q;ENSP00000371768:E27Q;ENSP00000371766:E192Q ENSP00000287364:E725Q E + 1 0 DOCK8 366273 1.000000 0.71417 1.000000 0.80357 0.979000 0.70002 9.675000 0.98638 2.661000 0.90470 0.650000 0.86243 GAA TCGA-3A-A9IB-01A-21D-A397-08 DOCK8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000171792.5 0 0 0 5 405 0 65 0 4.837524e-03 0 7 0 65 2 0 0 0 0 0 2 1 0.935876 5 400 0 64 2 0 0 0 0 0 2 -2.624229 1 1 0 0 1 0 1 1 1.677924 1 0.380000 1.970000 0.243441 0.050000 1.000000e-02 0.120000 0.050000 0.062334 0.050000 0 0.030000 0.090000 RPS6KA6 27330 broad.mit.edu 37 X 83319323 83319323 + Nonsense_Mutation SNP G G A TCGA-3A-A9IB-01A-21D-A397-08 TCGA-3A-A9IB-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8d01d1e0-82fd-4a98-a3ba-da1df31dafc6 45996250-51de-4620-9821-7944ed970774 g.chrX:83319323G>A ENST00000262752.2 - 22 2207 c.2200C>T c.(2200-2202)Cga>Tga p.R734* RPS6KA6_ENST00000543399.1_Nonsense_Mutation_p.R734* NM_014496.4 NP_055311.1 Q9UK32 KS6A6_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 6 46 ATGCTCCGTCGCTGGGCTAAG 0.458000 0 SO:0001587 stop_gained ENST00000262752.2 0 1 hg19 CCDS14451.1 . . . . . . . . . . G 34 5.373426 0.95923 . . ENSG00000072133 ENST00000262752;ENST00000543399 . . . 5.11 2.15 0.27550 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 13.2327 0.59953 0.0:0.0:0.5813:0.4187 . . . . X 734 . ENSP00000262752:R734X R - 1 2 RPS6KA6 83205979 1.000000 0.71417 0.994000 0.49952 0.988000 0.76386 3.126000 0.50477 0.011000 0.14865 0.600000 0.82982 CGA TCGA-3A-A9IB-01A-21D-A397-08 RPS6KA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057372.1 1 0 1 33 103 0 26 0 0 0 1 0 26 2 0 0 0 0 0 2 1 1.000000 33 103 0 25 2 0 0 0 0 0 2 -19.999960 1 1 0 0 1 0 1 1 0.380000 1.970000 0.380000 0.990000 9.200000e-01 1.000000 1.000000 0.995502 0.990000 1 0.990000 1.000000