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 WFIKKN2 124857 broad.mit.edu 37 17 48917574 48917580 + Frame_Shift_Del DEL CAGGCTG CAGGCTG - TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr17:48917574_48917580delCAGGCTG ENST00000311378.4 + 2 1453_1459 c.925_931delCAGGCTG c.(925-933)caggctgcafs p.QAA309fs WFIKKN2_ENST00000426127.1_Frame_Shift_Del_p.QAA216fs|RP11-506D12.5_ENST00000572491.2_RNA NM_175575.5 NP_783165.1 Q8TEU8 WFKN2_HUMAN WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2 p.A311S(1) 29 BRCA - Breast invasive adenocarcinoma(22;1.09e-08) CAGGGGTCATCAGGCTGCAGCCACCTC 0.657000 1 Substitution - Missense(1) SO:0001589 frameshift_variant ENST00000311378.4 1 1 hg19 CCDS11575.1 TCGA-3A-A9I9-01A-11D-A38G-08 WFIKKN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000368358.1 1 0 0 25 294 0 122 0 0 0 0 0 0 0 0 0 0 0 0 1 0.363067 36 302 7 128 30 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.053906 0 0.300000 1.870000 0.304175 0.530000 0.350000 1.000000 0.530000 0.552593 0.530000 0 4.300000e-01 6.500000e-01 MUC16 94025 broad.mit.edu 37 19 9086442 9086457 + Frame_Shift_Del DEL GCTGGACTCTGTCCTT GCTGGACTCTGTCCTT - TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr19:9086442_9086457delGCTGGACTCTGTCCTT ENST00000397910.4 - 1 5561_5576 c.5358_5373delAAGGACAGAGTCCAGC c.(5356-5373)gcaaggacagagtccagcfs p.ARTESS1786fs NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 590 GGGTAGCTGAGCTGGACTCTGTCCTTGCTGAAGACT 0.468000 0 SO:0001589 frameshift_variant ENST00000397910.4 0 1 hg19 CCDS54212.1 TCGA-3A-A9I9-01A-11D-A38G-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 1 0 0 30 359 0 67 0 0 0 0 0 0 0 0 0 0 0 0 1 0.490149 63 388 3 69 36 0 0 0 0 0 0 -9.043442 1 1 0 0 1 0 0 0 2.018298 0 0.300000 1.870000 0.291498 0.500000 0.350000 0.690000 0.500000 0.518962 0.500000 0 4.200000e-01 6.000000e-01 PDCD11 22984 broad.mit.edu 37 10 105158241 105158241 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr10:105158241G>C ENST00000369797.3 + 2 152 c.58G>C c.(58-60)Gag>Cag p.E20Q USMG5_ENST00000369825.1_5'Flank|USMG5_ENST00000369815.1_5'Flank|USMG5_ENST00000369811.1_5'Flank|USMG5_ENST00000337003.4_5'Flank|USMG5_ENST00000309579.3_5'Flank NM_014976.1 NP_055791.1 Q14690 RRP5_HUMAN programmed cell death 11 64 Colorectal(252;0.0747)|Breast(234;0.128) CCACAAACCAGAGAAAGCTTT 0.418000 0 SO:0001583 missense ENST00000369797.3 1 1 hg19 CCDS31276.1 . . . . . . . . . . G 14.19 2.462398 0.43736 . . ENSG00000148843 ENST00000369797;ENST00000543503 T 0.13420 2.59 5.3 5.3 0.74995 . 0.452187 0.25628 N 0.029371 T 0.17619 0.0423 M 0.69523 2.12 0.26868 N 0.967807 B 0.32620 0.378 B 0.36289 0.221 T 0.11842 -1.0571 10 0.29301 T 0.29 -23.9668 9.3697 0.38246 0.1602:0.0:0.8398:0.0 . 20 Q14690 RRP5_HUMAN Q 20 ENSP00000358812:E20Q ENSP00000358812:E20Q E + 1 0 PDCD11 105148231 1.000000 0.71417 1.000000 0.80357 0.904000 0.53231 4.614000 0.61183 2.499000 0.84300 0.555000 0.69702 GAG TCGA-3A-A9I9-01A-11D-A38G-08 PDCD11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050151.1 1 0 1 34 175 0 81 0 6.090767e-01 1 11 0 81 2 0 0 0 0 0 2 1 1.000000 34 171 0 81 2 0 0 0 0 81 2 -20.000000 1 1 0 0 1 1 2 3 2.064640 0 0.300000 1.870000 0.305211 0.990000 0.780000 1.000000 1.000000 0.973968 0.990000 1 9.300000e-01 1 MKI67 4288 broad.mit.edu 37 10 129903384 129903384 + Missense_Mutation SNP C C G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr10:129903384C>G ENST00000368654.3 - 13 7095 c.6720G>C c.(6718-6720)aaG>aaC p.K2240N MKI67_ENST00000368653.3_Missense_Mutation_p.K1880N NM_002417.4 NP_002408.3 P46013 KI67_HUMAN marker of proliferation Ki-67 159 all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203) TGAGACTTCTCTTGGACTGTG 0.498000 0 SO:0001583 missense ENST00000368654.3 1 1 hg19 CCDS7659.1 . . . . . . . . . . C 12.85 2.061815 0.36373 . . ENSG00000148773 ENST00000368654;ENST00000368653;ENST00000537609 T;T 0.03635 3.86;3.86 3.07 2.15 0.27550 . 0.672301 0.12961 N 0.425010 T 0.12433 0.0302 M 0.68952 2.095 0.09310 N 1 D;D;D 0.76494 0.991;0.992;0.999 P;D;D 0.72982 0.8;0.921;0.979 T 0.12066 -1.0562 10 0.30078 T 0.28 . 8.7284 0.34483 0.0:0.8779:0.0:0.1221 . 2239;1880;2240 F5H4V4;P46013-2;P46013 .;.;KI67_HUMAN N 2240;1880;2239 ENSP00000357643:K2240N;ENSP00000357642:K1880N ENSP00000357642:K1880N K - 3 2 MKI67 129793374 0.000000 0.05858 0.002000 0.10522 0.003000 0.03518 0.058000 0.14301 1.716000 0.51395 0.561000 0.74099 AAG TCGA-3A-A9I9-01A-11D-A38G-08 MKI67-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000050999.1 1 0 1 226 1167 0 335 1 7.578585e-01 8 8 0 335 2 0 0 0 0 0 2 1 1.000000 219 1126 0 325 2 0 0 0 0 335 2 -20.000000 1 1 0 0 1 0 0 0 2.005016 0 0.300000 1.870000 0.287169 0.990000 0.930000 1.000000 1.000000 0.994600 0.990000 1 9.900000e-01 1 ARHGAP21 57584 broad.mit.edu 37 10 24908567 24908567 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr10:24908567G>A ENST00000396432.2 - 9 2743 c.2257C>T c.(2257-2259)Cat>Tat p.H753Y ARHGAP21_ENST00000320481.6_Missense_Mutation_p.H540Y NM_020824.3 NP_065875.3 Q5T5U3 RHG21_HUMAN Rho GTPase activating protein 21 78 TAAGACTGATGCCTTAAAGGC 0.473000 0 SO:0001583 missense ENST00000396432.2 1 1 hg19 CCDS7144.2 . . . . . . . . . . G 22.6 4.307576 0.81247 . . ENSG00000107863 ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703 T;T;T;T 0.49139 0.79;0.79;0.79;0.79 5.1 5.1 0.69264 . 0.162808 0.53938 D 0.000044 T 0.64560 0.2609 M 0.70595 2.14 0.42876 D 0.994156 D;D 0.64830 0.989;0.994 P;P 0.57152 0.814;0.656 T 0.67925 -0.5544 10 0.54805 T 0.06 . 18.8879 0.92387 0.0:0.0:1.0:0.0 . 743;752 F8W9U9;Q5T5U3 .;RHG21_HUMAN Y 753;540;743;753;588 ENSP00000379709:H753Y;ENSP00000365604:H540Y;ENSP00000365592:H743Y;ENSP00000405018:H753Y ENSP00000365604:H540Y H - 1 0 ARHGAP21 24948573 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.340000 0.97038 2.509000 0.84616 0.655000 0.94253 CAT TCGA-3A-A9I9-01A-11D-A38G-08 ARHGAP21-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047229.4 1 0 1 75 482 0 162 1 4.970817e-01 4 8 0 162 2 0 0 0 0 0 2 1 1.000000 72 468 0 160 2 0 0 0 0 162 2 -20.000000 1 1 121412 1 31 1 0 1 1 2.031517 0 0.300000 1.870000 0.297894 0.890000 0.710000 1.000000 1.000000 0.891799 0.890000 1 7.900000e-01 9.900000e-01 CDH23 64072 broad.mit.edu 37 10 73377087 73377087 + Silent SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr10:73377087C>T ENST00000224721.6 + 10 1091 c.1086C>T c.(1084-1086)atC>atT p.I362I CDH23_ENST00000461841.3_Silent_p.I402I|CDH23_ENST00000398809.4_Silent_p.I357I|CDH23_ENST00000299366.7_Silent_p.I402I|CDH23_ENST00000398842.3_Silent_p.I357I NM_022124.5 NP_071407.4 Q9H251 CAD23_HUMAN cadherin-related 23 133 GCGTGGCCATCACTGAGCTGG 0.557000 0 SO:0001819 synonymous_variant ENST00000224721.6 0 1 hg19 TCGA-3A-A9I9-01A-11D-A38G-08 CDH23-001 PUTATIVE basic|appris_principal protein_coding protein_coding OTTHUMT00000051227.4 0 0 0 4 178 0 97 0 0 0 1 0 97 2 0 0 0 0 0 2 1 0.881827 4 171 0 96 2 0 0 0 0 97 2 -5.855426 1 1 121318 1 34 1 1 2 3 2.064640 0 0.300000 1.870000 0.305211 0.160000 0.050000 1.000000 0.150000 0.211375 0.160000 0 9.000000e-02 2.700000e-01 CDH23 64072 broad.mit.edu 37 10 73545428 73545428 + Missense_Mutation SNP G G A rs115113440 by1000genomes TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr10:73545428G>A ENST00000224721.6 + 43 5773 c.5768G>A c.(5767-5769)cGg>cAg p.R1923Q NM_022124.5 NP_071407.4 Q9H251 CAD23_HUMAN cadherin-related 23 133 GACCGCGAGCGGATCCCAGAG 0.597000 0 SO:0001583 missense ENST00000224721.6 1 1 hg19 6 0.0027472527472527475 6 0.012195121951219513 0 0.0 0 0.0 0 0.0 G 12.73 2.024660 0.35701 0.004271 0.0 ENSG00000107736 ENST00000398860;ENST00000398855;ENST00000224721 . . . 5.2 2.33 0.28932 Cadherin (4);Cadherin-like (1); 0.074456 0.53938 D 0.000048 T 0.18173 0.0436 N 0.05510 -0.035 0.80722 D 1 B 0.22683 0.073 B 0.18871 0.023 T 0.03287 -1.1052 9 0.15499 T 0.54 . 5.4098 0.16342 0.2787:0.0:0.592:0.1293 . 1918 Q9H251 CAD23_HUMAN Q 1923;1918;1921 . ENSP00000224721:R1923Q R + 2 0 CDH23 73215434 0.999000 0.42202 0.991000 0.47740 0.646000 0.38490 0.633000 0.24598 0.208000 0.20626 -0.380000 0.06706 CGG TCGA-3A-A9I9-01A-11D-A38G-08 CDH23-001 PUTATIVE basic|appris_principal protein_coding protein_coding OTTHUMT00000051227.4 1 0 1 11 63 0 44 0 2.665755e-02 0 2 0 44 2 0 0 0 0 0 2 1 0.998438 11 60 0 44 2 0 0 0 0 44 2 -3.883401 1 1 121044 68 46 1 1 2 3 2.064640 0 0.300000 1.870000 0.305211 0.990000 0.550000 1.000000 1.000000 0.910611 0.990000 1 7.600000e-01 1 SYNPO2L 79933 broad.mit.edu 37 10 75407582 75407582 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr10:75407582G>C ENST00000394810.2 - 4 1977 c.1828C>G c.(1828-1830)Cgc>Ggc p.R610G SYNPO2L_ENST00000372873.4_Missense_Mutation_p.R386G NM_001114133.1 NP_001107605.1 Q9H987 SYP2L_HUMAN synaptopodin 2-like 26 Prostate(51;0.0112) CGCTGCTCGCGAGCGCTGGGG 0.706000 0 SO:0001583 missense ENST00000394810.2 1 1 hg19 CCDS44438.1 . . . . . . . . . . G 15.34 2.805525 0.50315 . . ENSG00000166317 ENST00000372873;ENST00000394810 T;T 0.27402 1.67;1.98 5.02 3.05 0.35203 . 0.000000 0.85682 D 0.000000 T 0.45935 0.1367 L 0.50333 1.59 0.43608 D 0.995978 D;D 0.89917 1.0;1.0 D;D 0.79784 0.98;0.993 T 0.31696 -0.9934 10 0.33141 T 0.24 -16.451 12.8585 0.57899 0.0:0.0:0.4834:0.5165 . 610;386 Q9H987;Q9H987-2 SYP2L_HUMAN;. G 386;610 ENSP00000361964:R386G;ENSP00000378289:R610G ENSP00000361964:R386G R - 1 0 SYNPO2L 75077588 0.221000 0.23642 0.834000 0.33040 0.795000 0.44927 0.966000 0.29331 1.313000 0.45069 0.549000 0.68633 CGC TCGA-3A-A9I9-01A-11D-A38G-08 SYNPO2L-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316562.2 1 0 0 51 252 0 145 0 0 0 0 145 2 0 0 0 0 0 2 1 1.000000 48 247 0 142 2 0 0 0 0 145 2 -20.000000 1 1 0 0 1 1 2 3 2.064640 0 0.300000 1.870000 0.305211 0.990000 0.860000 1.000000 1.000000 0.988590 0.990000 1 9.900000e-01 1 TECTA 7007 broad.mit.edu 37 11 121028674 121028674 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr11:121028674G>A ENST00000392793.1 + 14 4701 c.4430G>A c.(4429-4431)cGc>cAc p.R1477H TECTA_ENST00000264037.2_Missense_Mutation_p.R1477H O75443 TECTA_HUMAN tectorin alpha TECTA/TBCEL(2) 135 all_hematologic(175;0.208) Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112) AACGGGGTGCGCGGCTGCTTC 0.687000 0 SO:0001583 missense ENST00000392793.1 1 1 hg19 CCDS8434.1 . . . . . . . . . . G 23.3 4.397066 0.83120 . . ENSG00000109927 ENST00000392793;ENST00000264037 T;T 0.04970 3.52;3.52 5.69 5.69 0.88448 von Willebrand factor, type D domain (1);VWC out (1); 0.000000 0.85682 D 0.000000 T 0.16385 0.0394 L 0.31926 0.97 0.58432 D 0.999991 D 0.89917 1.0 D 0.91635 0.999 T 0.17137 -1.0379 10 0.14656 T 0.56 . 19.8006 0.96506 0.0:0.0:1.0:0.0 . 1477 O75443 TECTA_HUMAN H 1477 ENSP00000376543:R1477H;ENSP00000264037:R1477H ENSP00000264037:R1477H R + 2 0 TECTA 120533884 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 9.508000 0.98000 2.687000 0.91594 0.462000 0.41574 CGC TCGA-3A-A9I9-01A-11D-A38G-08 TECTA-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313850.1 1 0 1 39 247 0 123 0 0 0 1 0 123 2 0 0 0 0 0 2 1 1.000000 39 239 0 121 2 0 0 0 0 123 2 -20.000000 1 1 121338 5 36 1 1 2 3 2.118814 0 0.300000 1.870000 0.314398 0.940000 0.680000 1.000000 1.000000 0.918206 0.940000 1 8.000000e-01 1 UBASH3B 84959 broad.mit.edu 37 11 122667631 122667631 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr11:122667631G>A ENST00000284273.5 + 9 1622 c.1247G>A c.(1246-1248)cGc>cAc p.R416H NM_032873.4 NP_116262.2 Q8TF42 UBS3B_HUMAN ubiquitin associated and SH3 domain containing B 26 Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104) CGCTACATACGCACCAACCTG 0.473000 0 SO:0001583 missense ENST00000284273.5 1 1 hg19 CCDS31694.1 . . . . . . . . . . G 28.0 4.881504 0.91740 . . ENSG00000154127 ENST00000284273 T 0.07567 3.18 6.05 5.14 0.70334 Histidine phosphatase superfamily, clade-1 (1); 0.000000 0.85682 D 0.000000 T 0.31702 0.0805 M 0.80332 2.49 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.10660 -1.0620 10 0.72032 D 0.01 -25.6525 15.3314 0.74215 0.0666:0.0:0.9334:0.0 . 416 Q8TF42 UBS3B_HUMAN H 416 ENSP00000284273:R416H ENSP00000284273:R416H R + 2 0 UBASH3B 122172841 1.000000 0.71417 1.000000 0.80357 0.866000 0.49608 9.368000 0.97152 1.577000 0.49804 0.650000 0.86243 CGC TCGA-3A-A9I9-01A-11D-A38G-08 UBASH3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387499.1 1 0 1 73 281 0 90 1 6.947207e-01 2 9 0 90 2 0 0 0 0 0 2 1 1.000000 72 275 0 90 2 0 0 0 0 90 2 -3.454717 1 1 0 0 1 1 2 3 2.118814 0 0.300000 1.870000 0.314398 0.990000 0.990000 1.000000 1.000000 0.999961 0.990000 1 9.900000e-01 1 OR4B1 119765 broad.mit.edu 37 11 48238701 48238701 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr11:48238701G>A ENST00000309562.2 + 1 358 c.340G>A c.(340-342)Gtg>Atg p.V114M NM_001005470.1 NP_001005470.1 Q8NGF8 OR4B1_HUMAN olfactory receptor, family 4, subfamily B, member 1 p.V114L(1) 28 CCTTTTGATTGTGGTGATGGC 0.443000 1 Substitution - Missense(1) SO:0001583 missense ENST00000309562.2 1 1 hg19 CCDS31485.1 . . . . . . . . . . G 13.82 2.350283 0.41599 . . ENSG00000175619 ENST00000309562 T 0.00502 6.95 5.24 0.588 0.17445 GPCR, rhodopsin-like superfamily (1); 0.647154 0.13543 N 0.380012 T 0.00637 0.0021 L 0.33710 1.025 0.09310 N 1 P 0.42248 0.774 P 0.52909 0.713 T 0.53830 -0.8383 10 0.56958 D 0.05 . 8.0126 0.30361 0.4392:0.0:0.5608:0.0 . 114 Q8NGF8 OR4B1_HUMAN M 114 ENSP00000311605:V114M ENSP00000311605:V114M V + 1 0 OR4B1 48195277 0.000000 0.05858 0.407000 0.26434 0.736000 0.42039 -0.124000 0.10595 0.199000 0.20427 0.385000 0.25706 GTG TCGA-3A-A9I9-01A-11D-A38G-08 OR4B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390554.1 1 0 1 104 590 0 147 0 0 0 0 147 2 0 0 0 0 0 2 1 1.000000 102 577 0 143 2 0 0 0 0 147 2 -20.000000 1 0 0 0 1 0 0 0 2.030180 0 0.300000 1.870000 0.295775 0.980000 0.820000 1.000000 1.000000 0.962266 0.980000 1 9.000000e-01 1 SMTNL1 219537 broad.mit.edu 37 11 57311123 57311123 + Silent SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr11:57311123G>A ENST00000399154.2 + 3 648 c.648G>A c.(646-648)caG>caA p.Q216Q SMTNL1_ENST00000527972.1_Silent_p.Q253Q|SMTNL1_ENST00000457912.1_Silent_p.Q271Q A8MU46 SMTL1_HUMAN smoothelin-like 1 8 GCGAAGAGCAGGAGCAGGACG 0.607000 0 SO:0001819 synonymous_variant ENST00000399154.2 1 1 hg19 TCGA-3A-A9I9-01A-11D-A38G-08 SMTNL1-201 KNOWN basic|appris_candidate protein_coding protein_coding 1 0 1 12 65 0 32 0 7.572668e-02 0 3 0 32 2 0 0 0 0 0 2 1 0.999266 12 63 0 30 2 0 0 0 0 32 2 -19.976210 1 1 120812 2 18 1 0 0 0 2.030180 0 0.300000 1.870000 0.295775 0.990000 0.580000 1.000000 1.000000 0.922032 0.990000 1 7.800000e-01 1 DAGLA 747 broad.mit.edu 37 11 61508664 61508664 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr11:61508664G>A ENST00000257215.5 + 19 2130 c.2014G>A c.(2014-2016)Gct>Act p.A672T NM_006133.2 NP_006124.1 Q9Y4D2 DGLA_HUMAN diacylglycerol lipase, alpha 43 GGGGAAGACCGCTCTGCTCTC 0.637000 0 SO:0001583 missense ENST00000257215.5 1 1 hg19 CCDS31578.1 . . . . . . . . . . G 17.07 3.295157 0.60086 . . ENSG00000134780 ENST00000257215 T 0.29655 1.56 3.73 3.73 0.42828 . 0.056336 0.64402 D 0.000001 T 0.43986 0.1272 L 0.34521 1.04 0.58432 D 0.999999 D 0.76494 0.999 D 0.72625 0.978 T 0.42949 -0.9421 10 0.48119 T 0.1 -13.0611 16.4468 0.83936 0.0:0.0:1.0:0.0 . 672 Q9Y4D2 DGLA_HUMAN T 672 ENSP00000257215:A672T ENSP00000257215:A672T A + 1 0 DAGLA 61265240 1.000000 0.71417 0.852000 0.33557 0.619000 0.37552 9.441000 0.97557 2.039000 0.60335 0.456000 0.33151 GCT TCGA-3A-A9I9-01A-11D-A38G-08 DAGLA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398516.1 1 0 1 44 258 0 134 0 1.614848e-01 0 5 0 134 2 0 0 0 0 0 2 1 1.000000 41 253 0 132 2 0 0 0 0 134 2 -19.949590 1 1 0 0 1 0 0 0 2.026767 0 0.300000 1.870000 0.295775 0.960000 0.720000 1.000000 1.000000 0.931834 0.960000 1 8.300000e-01 1 CAPN5 726 broad.mit.edu 37 11 76833726 76833726 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr11:76833726C>T ENST00000278559.3 + 12 1897 c.1708C>T c.(1708-1710)Cgc>Tgc p.R570C CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000529629.1_Missense_Mutation_p.R570C|CAPN5_ENST00000456580.2_Missense_Mutation_p.R610C NM_004055.4 NP_004046.2 O15484 CAN5_HUMAN calpain 5 30 CATCTTCTACCGCAAGAAGCT 0.567000 0 SO:0001583 missense ENST00000278559.3 1 1 hg19 CCDS8248.1 . . . . . . . . . . C 20.4 3.988182 0.74589 . . ENSG00000149260 ENST00000278559;ENST00000360841;ENST00000529629;ENST00000456580 T;T;T 0.71103 -0.54;-0.54;-0.54 4.93 4.93 0.64822 C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1); 0.050653 0.85682 D 0.000000 T 0.81074 0.4747 M 0.62016 1.91 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 1.0;0.996;0.995;1.0 T 0.82692 -0.0331 10 0.87932 D 0 . 12.5828 0.56399 0.1658:0.8341:0.0:0.0 . 608;610;610;570 Q59GM2;E7EV01;Q6ZRM8;O15484 .;.;.;CAN5_HUMAN C 570;610;570;610 ENSP00000278559:R570C;ENSP00000432332:R570C;ENSP00000409996:R610C ENSP00000278559:R570C R + 1 0 CAPN5 76511374 1.000000 0.71417 1.000000 0.80357 0.902000 0.53008 2.941000 0.49011 2.428000 0.82296 0.655000 0.94253 CGC TCGA-3A-A9I9-01A-11D-A38G-08 CAPN5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382564.2 1 0 1 31 191 0 121 1 9.999971e-01 54 74 0 121 2 0 0 0 0 0 2 1 1.000000 30 186 0 120 2 0 0 0 0 121 2 -2.381871 0 1 121412 18 43 1 0 0 0 2.026767 0 0.300000 1.870000 0.295775 0.920000 0.650000 1.000000 1.000000 0.901151 0.920000 1 7.700000e-01 1 NOS1 4842 broad.mit.edu 37 12 117693813 117693813 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr12:117693813C>T ENST00000338101.4 - 16 2565 c.2561G>A c.(2560-2562)cGt>cAt p.R854H NOS1_ENST00000317775.6_Intron|NOS1_ENST00000344089.3_Intron Q8WY41 NANO1_HUMAN nitric oxide synthase 1 (neuronal) 117 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) AGGCCCTTTACGGGGAAAGAA 0.602000 Esophageal Squamous(162;1748 2599 51982 52956) 0 SO:0001583 missense ENST00000338101.4 1 1 hg19 CCDS55890.1 1 4.578754578754579E-4 0 0.0 1 0.0027624309392265192 0 0.0 0 0.0 C 24.6 4.549961 0.86127 5.71E-4 5.02E-4 ENSG00000089250 ENST00000338101;ENST00000544320 T 0.01388 4.95 5.93 5.93 0.95920 . . . . . T 0.02455 0.0075 N 0.24115 0.695 0.80722 D 1 . . . . . . T 0.73132 -0.4079 7 0.29301 T 0.29 -6.7644 15.854 0.78960 0.0:1.0:0.0:0.0 . . . . H 854;20 ENSP00000337459:R854H ENSP00000337459:R854H R - 2 0 NOS1 116178196 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 3.549000 0.53681 2.826000 0.97356 0.655000 0.94253 CGT TCGA-3A-A9I9-01A-11D-A38G-08 NOS1-002 NOVEL basic|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000268053.1 1 0 1 61 387 0 131 0 0 0 0 131 2 0 0 0 0 0 2 1 1.000000 61 373 0 131 2 0 0 0 0 131 2 -3.075786 1 1 116018 62 50 1 0 0 0 2.026697 0 0.300000 1.870000 0.295775 0.890000 0.700000 1.000000 1.000000 0.895737 0.890000 1 7.900000e-01 1 POLE 5426 broad.mit.edu 37 12 133240667 133240667 + Missense_Mutation SNP C C G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr12:133240667C>G ENST00000320574.5 - 23 2672 c.2629G>C c.(2629-2631)Gtc>Ctc p.V877L POLE_ENST00000535270.1_Missense_Mutation_p.V850L NM_006231.2 NP_006222.2 Q07864 DPOE1_HUMAN polymerase (DNA directed), epsilon, catalytic subunit 89 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0416) Cladribine(DB00242) GTCTTGAAGACAAAATTTTCT 0.517000 DNA polymerases (catalytic subunits) 0 SO:0001583 missense ENST00000320574.5 1 1 hg19 CCDS9278.1 . . . . . . . . . . C 13.84 2.357675 0.41801 . . ENSG00000177084 ENST00000320574;ENST00000455752;ENST00000535270;ENST00000539006;ENST00000376577 T;T;T;T 0.13778 4.22;4.22;4.22;2.56 5.57 5.57 0.84162 DNA-directed DNA polymerase, family B, multifunctional domain (1); 0.000000 0.85682 D 0.000000 T 0.18593 0.0446 L 0.42245 1.32 0.58432 D 0.999996 P;B 0.36959 0.575;0.261 B;B 0.39876 0.312;0.243 T 0.00912 -1.1517 10 0.49607 T 0.09 . 19.5987 0.95551 0.0:1.0:0.0:0.0 . 850;877 F5H1D6;Q07864 .;DPOE1_HUMAN L 877;888;850;657;812 ENSP00000322570:V877L;ENSP00000406383:V888L;ENSP00000445753:V850L;ENSP00000442519:V657L ENSP00000322570:V877L V - 1 0 POLE 131750740 1.000000 0.71417 0.997000 0.53966 0.025000 0.11179 4.943000 0.63554 2.640000 0.89533 0.638000 0.83543 GTC TCGA-3A-A9I9-01A-11D-A38G-08 POLE-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397689.2 1 0 1 40 218 0 123 1 7.347366e-01 4 12 0 123 2 0 0 0 0 0 2 1 1.000000 40 214 0 122 2 0 0 0 0 123 2 -19.860310 1 1 0 0 1 0 0 0 2.026697 0 0.300000 1.870000 0.295775 0.990000 0.750000 1.000000 1.000000 0.957505 0.990000 1 8.800000e-01 1 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C G C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr12:25398285C>G ENST00000256078.4 - 2 97 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|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) CCTACGCCACCAGCTCCAACT 0.348000 G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE) 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 5144 Substitution - Missense(5142)|Insertion - In frame(2) GRCh37 CM076251 KRAS M rs121913530 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 28.6 4.930538 0.92389 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78246 -1.16;-1.16;-1.16;-1.16 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.84893 0.5573 M 0.84082 2.675 0.80722 D 1 P;P 0.43287 0.802;0.741 B;P 0.47941 0.36;0.562 D 0.86658 0.1902 10 0.66056 D 0.02 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN R 12 ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R ENSP00000256078:G12R G - 1 0 KRAS 25289552 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-A9I9-01A-11D-A38G-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 36 286 0 106 0 1.335233e-02 1 1 0 106 2 1 1 40 282 0 222 2 1 1.000000 36 282 0 106 2 1 1 2031 5987 0 106 2 -14.467220 1 1 0 0 1 0 1 1 1.744959 1 0.300000 1.870000 0.176471 0.620000 0.450000 0.820000 0.620000 0.637571 0.620000 0 5.300000e-01 7.300000e-01 FGF6 2251 broad.mit.edu 37 12 4554454 4554454 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr12:4554454C>T ENST00000228837.2 - 1 326 c.283G>A c.(283-285)Ggc>Agc p.G95S NM_020996.1 NP_066276.2 P10767 FGF6_HUMAN fibroblast growth factor 6 20 Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229) AGGTGAAAGCCGATGCCCACG 0.652000 0 SO:0001583 missense ENST00000228837.2 1 1 hg19 CCDS8527.1 . . . . . . . . . . C 34 5.310723 0.95629 . . ENSG00000111241 ENST00000228837 D 0.82526 -1.62 5.3 5.3 0.74995 . 0.000000 0.85682 D 0.000000 D 0.92166 0.7516 M 0.85462 2.755 0.80722 D 1 D 0.76494 0.999 D 0.74348 0.983 D 0.93036 0.6453 10 0.87932 D 0 . 19.3285 0.94273 0.0:1.0:0.0:0.0 . 95 P10767 FGF6_HUMAN S 95 ENSP00000228837:G95S ENSP00000228837:G95S G - 1 0 FGF6 4424715 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.776000 0.85560 2.636000 0.89361 0.655000 0.94253 GGC TCGA-3A-A9I9-01A-11D-A38G-08 FGF6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398939.1 1 0 1 38 181 0 98 0 0 0 0 98 2 0 0 0 0 0 2 1 1.000000 37 178 0 98 2 0 0 0 0 98 2 -20.000000 1 1 0 0 1 0 2 2 2.055419 1 0.300000 1.870000 0.300000 0.990000 0.840000 1.000000 1.000000 0.986820 0.990000 1 9.900000e-01 1 C1S 716 broad.mit.edu 37 12 7172426 7172426 + Missense_Mutation SNP C C A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr12:7172426C>A ENST00000406697.1 + 9 1168 c.540C>A c.(538-540)ttC>ttA p.F180L C1S_ENST00000328916.3_Missense_Mutation_p.F180L|C1S_ENST00000360817.5_Missense_Mutation_p.F180L|C1S_ENST00000402681.3_Missense_Mutation_p.F13L P09871 C1S_HUMAN complement component 1, s subcomponent 33 Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072) GGGATGTATTCACTGCACTGA 0.428000 GBM(156;750 1943 12971 24779 31015) 0 SO:0001583 missense ENST00000406697.1 1 1 hg19 CCDS31735.1 . . . . . . . . . . C 21.8 4.195206 0.78902 . . ENSG00000182326 ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000402681;ENST00000542978 T;T;T;T;T 0.15603 2.41;2.41;2.41;2.41;2.41 6.17 3.05 0.35203 CUB (5); 0.000000 0.44483 D 0.000450 T 0.17152 0.0412 L 0.28054 0.825 0.36787 D 0.884655 P 0.39551 0.678 P 0.51777 0.679 T 0.18555 -1.0333 10 0.13853 T 0.58 . 8.1984 0.31411 0.0:0.6461:0.0:0.3539 . 180 P09871 C1S_HUMAN L 180;180;180;169;13;13 ENSP00000385035:F180L;ENSP00000328173:F180L;ENSP00000354057:F180L;ENSP00000384171:F13L;ENSP00000442298:F13L ENSP00000328173:F180L F + 3 2 C1S 7042687 1.000000 0.71417 0.972000 0.41901 0.871000 0.50021 0.473000 0.22132 0.941000 0.37499 0.655000 0.94253 TTC TCGA-3A-A9I9-01A-11D-A38G-08 C1S-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317481.1 1 0 1 72 454 0 100 0 1 0 239 0 100 2 0 0 0 0 0 2 1 1.000000 71 445 0 97 2 0 0 0 0 100 2 -20.000000 1 1 0 0 1 0 3 3 2.377243 1 0.300000 1.870000 0.391304 0.990000 0.830000 1.000000 1.000000 0.977571 0.990000 1 9.300000e-01 1 C1RL 51279 broad.mit.edu 37 12 7254607 7254607 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr12:7254607C>T ENST00000266542.4 - 3 469 c.377G>A c.(376-378)aGg>aAg p.R126K C1RL_ENST00000545280.1_Missense_Mutation_p.G50R|C1RL_ENST00000544702.1_Missense_Mutation_p.R126K|C1RL_ENST00000545337.1_Missense_Mutation_p.R126K NM_016546.2 NP_057630.2 Q9NZP8 C1RL_HUMAN complement component 1, r subcomponent-like 16 TACAAACTCCCTCTGACCAGG 0.607000 0 SO:0001583 missense ENST00000266542.4 1 1 hg19 CCDS8573.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 3.321|3.321 -0.138671|-0.138671 0.06669|0.06669 .|. .|. ENSG00000139178|ENSG00000139178 ENST00000545280|ENST00000266542;ENST00000396661;ENST00000544702;ENST00000543933;ENST00000545337 .|T;T;T;T .|0.16597 .|2.33;2.33;2.33;2.33 3.76|3.76 0.896|0.896 0.19253|0.19253 .|CUB (5); .|0.544302 .|0.17177 .|N .|0.184060 T|T 0.05547|0.05547 0.0146|0.0146 N|N 0.05574|0.05574 -0.02|-0.02 0.28959|0.28959 N|N 0.889922|0.889922 .|B;B;B .|0.23990 .|0.095;0.004;0.001 .|B;B;B .|0.20184 .|0.028;0.007;0.003 T|T 0.37753|0.37753 -0.9692|-0.9692 5|10 .|0.07030 .|T .|0.85 .|. 3.4791|3.4791 0.07595|0.07595 0.1981:0.5841:0.0:0.2179|0.1981:0.5841:0.0:0.2179 .|. .|126;126;126 .|F5GWF3;F5H7C8;Q9NZP8 .|.;.;C1RL_HUMAN R|K 50|126 .|ENSP00000266542:R126K;ENSP00000441885:R126K;ENSP00000437398:R126K;ENSP00000442611:R126K .|ENSP00000266542:R126K G|R -|- 1|2 0|0 C1RL|C1RL 7145883|7145883 0.033000|0.033000 0.19621|0.19621 0.979000|0.979000 0.43373|0.43373 0.888000|0.888000 0.51559|0.51559 -0.382000|-0.382000 0.07408|0.07408 0.183000|0.183000 0.20059|0.20059 0.462000|0.462000 0.41574|0.41574 GGG|AGG TCGA-3A-A9I9-01A-11D-A38G-08 C1RL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398367.1 1 0 1 112 588 0 289 1 9.859088e-01 2 35 0 289 2 0 0 0 0 0 2 1 1.000000 112 580 0 289 2 0 0 0 0 289 2 -2.507496 1 1 0 0 1 0.300000 1.870000 0 0 TPP2 7174 broad.mit.edu 37 13 103301346 103301346 + Silent SNP T T A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr13:103301346T>A ENST00000376065.4 + 22 2754 c.2718T>A c.(2716-2718)ctT>ctA p.L906L TPP2_ENST00000376052.3_Silent_p.L906L NM_003291.2 NP_003282.2 P29144 TPP2_HUMAN tripeptidyl peptidase II 52 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184) TTAAAGACCTTCCATTTATTG 0.338000 0 SO:0001819 synonymous_variant ENST00000376065.4 1 1 hg19 CCDS9502.1 TCGA-3A-A9I9-01A-11D-A38G-08 TPP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045683.2 1 0 1 65 482 0 88 1 7.066586e-01 2 18 0 88 2 0 0 0 0 0 2 1 1.000000 64 471 0 87 2 0 0 0 0 88 2 -20.000000 1 1 0 0 1 1 2 3 2.353886 1 0.300000 1.870000 0.391304 0.900000 0.710000 1.000000 1.000000 0.904532 0.900000 1 8.000000e-01 1 EML1 2009 broad.mit.edu 37 14 100374050 100374050 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr14:100374050G>C ENST00000262233.6 + 10 1223 c.1084G>C c.(1084-1086)Gaa>Caa p.E362Q EML1_ENST00000327921.9_Missense_Mutation_p.E350Q|EML1_ENST00000334192.4_Missense_Mutation_p.E381Q NM_004434.2 NP_004425.2 O00423 EMAL1_HUMAN echinoderm microtubule associated protein like 1 42 Melanoma(154;0.0879)|all_epithelial(191;0.216) GCAGAAAGAAGAAAAACTAGC 0.468000 0 SO:0001583 missense ENST00000262233.6 1 1 hg19 CCDS32155.1 . . . . . . . . . . G 15.70 2.911712 0.52439 . . ENSG00000066629 ENST00000554479;ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138 T;T;T;T 0.46451 5.01;0.87;0.87;0.87 4.99 4.09 0.47781 WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1); 0.049952 0.85682 D 0.000000 T 0.44201 0.1282 N 0.25890 0.77 0.50813 D 0.999899 D;P;B;D;D 0.59767 0.975;0.911;0.029;0.986;0.957 P;B;B;P;B 0.57846 0.648;0.363;0.011;0.828;0.445 T 0.19712 -1.0297 10 0.21014 T 0.42 -24.9371 14.9443 0.71016 0.0:0.0:0.8557:0.1443 . 350;350;362;381;381 F8W717;B7Z650;O00423;O00423-3;B3KXA3 .;.;EMAL1_HUMAN;.;. Q 349;350;362;381;381 ENSP00000451346:E349Q;ENSP00000327384:E350Q;ENSP00000262233:E362Q;ENSP00000334314:E381Q ENSP00000262233:E362Q E + 1 0 EML1 99443803 1.000000 0.71417 0.042000 0.18584 0.901000 0.52897 7.832000 0.86757 1.206000 0.43276 0.655000 0.94253 GAA TCGA-3A-A9I9-01A-11D-A38G-08 EML1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000413943.1 1 0 1 41 230 0 97 0 5.666489e-01 0 12 0 97 2 0 0 0 0 0 2 1 1.000000 41 225 0 97 2 0 0 0 0 97 2 -3.152586 1 1 0 0 1 1 2 3 2.045233 0 0.300000 1.870000 0.302094 0.990000 0.740000 1.000000 1.000000 0.952594 0.990000 1 8.700000e-01 1 VTI1B 10490 broad.mit.edu 37 14 68118129 68118129 + Silent SNP A A C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr14:68118129A>C ENST00000554659.1 - 6 1013 c.672T>G c.(670-672)gtT>gtG p.V224V ARG2_ENST00000261783.3_3'UTR NM_006370.2 NP_006361.1 Q9UEU0 VTI1B_HUMAN vesicle transport through interaction with t-SNAREs 1B 5 ATTTGTAGTAAACCAGGCCTC 0.453000 0 SO:0001819 synonymous_variant ENST00000554659.1 1 1 hg19 CCDS9786.1 . . . . . . . . . . A 6.515 0.463167 0.12402 . . ENSG00000100568 ENST00000554636 . . . 6.17 -2.23 0.06930 . . . . . T 0.50343 0.1610 . . . 0.80722 D 1 . . . . . . T 0.43376 -0.9395 4 . . . . 6.4943 0.22133 0.3206:0.2838:0.3956:0.0 . . . . C 102 . . F - 2 0 VTI1B 67187882 0.962000 0.33011 0.993000 0.49108 0.998000 0.95712 0.084000 0.14891 -0.288000 0.09051 0.533000 0.62120 TTT TCGA-3A-A9I9-01A-11D-A38G-08 VTI1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412558.2 1 0 0 47 263 0 67 1 1 89 307 0 67 2 0 0 0 0 0 2 1 1.000000 46 259 0 67 2 0 0 0 0 67 2 -20.000000 1 1 0 0 1 1 2 3 2.045233 0 0.300000 1.870000 0.302094 0.990000 0.760000 1.000000 1.000000 0.956621 0.990000 1 8.800000e-01 1 MAP3K9 4293 broad.mit.edu 37 14 71200060 71200060 + Splice_Site SNP C C G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr14:71200060C>G ENST00000554752.2 - 11 2026 c.e11-1 MAP3K9_ENST00000553414.1_Splice_Site|MAP3K9_ENST00000554146.1_Splice_Site|MAP3K9_ENST00000381250.4_Splice_Site|MAP3K9_ENST00000555993.2_Splice_Site NM_001284230.1 NP_001271159.1 P80192 M3K9_HUMAN mitogen-activated protein kinase kinase kinase 9 46 tcctcatcctctgtgaagatg 0.542000 GBM(114;411 1587 13539 28235 50070) 0 SO:0001630 splice_region_variant ENST00000554752.2 0 1 hg19 . . . . . . . . . . C 18.23 3.578227 0.65878 . . ENSG00000006432 ENST00000542284 . . . 4.77 4.77 0.60923 . . . . . T 0.73892 0.3645 . . . 0.80722 D 1 . . . . . . T 0.73366 -0.4005 4 . . . . 17.9928 0.89174 0.0:1.0:0.0:0.0 . . . . Q 392 . . E - 1 0 MAP3K9 70269813 1.000000 0.71417 1.000000 0.80357 0.927000 0.56198 5.862000 0.69560 2.478000 0.83669 0.561000 0.74099 GAG TCGA-3A-A9I9-01A-11D-A38G-08 MAP3K9-001 KNOWN basic protein_coding protein_coding OTTHUMT00000412550.2 0 0 1 11 68 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.998740 11 68 0 34 2 0 0 0 0 36 2 -19.378620 1 1 0 0 1 1 2 3 2.045233 0 0.300000 1.870000 0.302094 0.940000 0.510000 1.000000 1.000000 0.879021 0.940000 1 7.000000e-01 1 THBS1 7057 broad.mit.edu 37 15 39876541 39876541 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr15:39876541C>T ENST00000260356.5 + 6 1109 c.944C>T c.(943-945)cCt>cTt p.P315L NM_003246.2 NP_003237.2 P07996 TSP1_HUMAN thrombospondin 1 53 all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223) CTGAGGCGGCCTCCCCTATGC 0.483000 0 SO:0001583 missense ENST00000260356.5 1 1 hg19 CCDS32194.1 . . . . . . . . . . C 16.97 3.268480 0.59540 . . ENSG00000137801 ENST00000260356 T 0.77620 -1.11 5.88 5.88 0.94601 . 0.224139 0.22966 N 0.053490 T 0.78091 0.4229 M 0.61703 1.905 0.47214 D 0.999351 B 0.15141 0.012 B 0.14023 0.01 T 0.72883 -0.4157 10 0.59425 D 0.04 -2.5851 19.2015 0.93713 0.0:1.0:0.0:0.0 . 315 P07996 TSP1_HUMAN L 315 ENSP00000260356:P315L ENSP00000260356:P315L P + 2 0 THBS1 37663833 0.032000 0.19561 0.123000 0.21794 0.901000 0.52897 2.941000 0.49011 2.786000 0.95864 0.655000 0.94253 CCT TCGA-3A-A9I9-01A-11D-A38G-08 THBS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257831.2 1 0 1 47 244 0 119 1 9.999759e-01 3 82 0 119 2 0 0 0 0 0 2 1 1.000000 47 240 0 117 2 0 0 0 0 119 2 -20.000000 1 1 0 0 1 1 2 3 2.050126 0 0.300000 1.870000 0.302094 0.990000 0.810000 1.000000 1.000000 0.977355 0.990000 1 9.400000e-01 1 RNF111 54778 broad.mit.edu 37 15 59359283 59359283 + Splice_Site SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr15:59359283G>C ENST00000557998.1 + 6 1973 c.e6+1 RNF111_ENST00000559209.1_Splice_Site|RNF111_ENST00000348370.4_Splice_Site|RNF111_ENST00000561186.1_Splice_Site|RNF111_ENST00000434298.1_Splice_Site NM_001270530.1 NP_001257459.1 Q6ZNA4 RN111_HUMAN ring finger protein 111 35 TCATGAACAGGTATGTGGAAT 0.468000 NSCLC(72;983 1365 10746 34387 47081) 0 SO:0001630 splice_region_variant ENST00000557998.1 1 1 hg19 CCDS58366.1 . . . . . . . . . . G 20.5 4.008992 0.75046 . . ENSG00000157450 ENST00000348370;ENST00000434298 . . . 5.14 5.14 0.70334 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 17.5984 0.88018 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . RNF111 57146575 1.000000 0.71417 1.000000 0.80357 0.881000 0.50899 8.279000 0.89901 2.398000 0.81561 0.462000 0.41574 . TCGA-3A-A9I9-01A-11D-A38G-08 RNF111-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000416012.1 1 0 1 43 221 0 99 0 0 0 0 99 2 0 0 0 0 0 2 1 1.000000 42 217 0 99 2 0 0 0 0 99 2 -20.000000 1 0 0 0 1 0 1 1 1.733808 1 0.300000 1.870000 0.176471 0.870000 0.660000 0.990000 0.910000 0.865874 0.870000 1 7.600000e-01 9.600000e-01 PKD1 5310 broad.mit.edu 37 16 2165466 2165466 + Silent SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr16:2165466C>T ENST00000262304.4 - 10 2218 c.2010G>A c.(2008-2010)acG>acA p.T670T RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Silent_p.T670T NM_001009944.2 NP_001009944 P98161 PKD1_HUMAN polycystic kidney disease 1 (autosomal dominant) 72 CTGGCCCTGACGTGCAGCCAT 0.711000 0 SO:0001819 synonymous_variant ENST00000262304.4 0 1 hg19 CCDS32369.1 . . . . . . . . . . . 5.400 0.259040 0.10239 . . ENSG00000008710 ENST00000306101 . . . 4.65 -6.53 0.01866 . . . . . . . . . . . 0.09310 N 1 . . . . . . . . . . . . . . 7.5936 0.28035 0.0:0.3152:0.2329:0.4519 . . . . . -1 . . . - . . PKD1 2105467 0.000000 0.05858 0.000000 0.03702 0.059000 0.15707 -1.318000 0.02705 -1.032000 0.03304 -0.259000 0.10710 . TCGA-3A-A9I9-01A-11D-A38G-08 PKD1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000341688.1 0 0 0 3 56 0 32 0 1.685428e-01 0 11 0 32 2 0 0 0 0 0 2 1 0.763344 3 48 0 35 2 0 0 0 0 32 2 -7.064841 1 0 119366 4 27 1 1 2 3 2.286804 1 0.300000 1.870000 0.384886 0.460000 0.130000 1.000000 1.000000 0.513348 0.460000 0 2.600000e-01 7.900000e-01 ITFG3 83986 broad.mit.edu 37 16 313364 313364 + Missense_Mutation SNP A A T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr16:313364A>T ENST00000399932.3 + 9 1526 c.1075A>T c.(1075-1077)Acg>Tcg p.T359S ITFG3_ENST00000442458.2_Missense_Mutation_p.T359S|ITFG3_ENST00000450082.2_Missense_Mutation_p.T359S|ITFG3_ENST00000301679.2_Missense_Mutation_p.T359S|ITFG3_ENST00000600536.1_Missense_Mutation_p.T359S|ITFG3_ENST00000301678.3_Missense_Mutation_p.T359S NM_001284497.1 NP_001271426.1 Q9H0X4 ITFG3_HUMAN integrin alpha FG-GAP repeat containing 3 16 all_cancers(16;0.000129)|all_epithelial(16;0.000206)|Hepatocellular(16;0.00264)|Lung NSC(18;0.0626)|all_lung(18;0.13) GCAGGAGCTGACGCCTCGCTG 0.652000 0 SO:0001583 missense ENST00000399932.3 1 1 hg19 CCDS10402.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 2.312|2.312 -0.357614|-0.357614 0.05138|0.05138 .|. .|. ENSG00000167930|ENSG00000167930 ENST00000399932;ENST00000301679;ENST00000442458;ENST00000301678;ENST00000450082|ENST00000424016 T;T;T;T;T|. 0.56611|. 0.45;0.45;0.45;0.45;0.45|. 4.23|4.23 -3.04|-3.04 0.05412|0.05412 Quinonprotein alcohol dehydrogenase-like (1);|. 1.032930|. 0.07604|. N|. 0.924179|. T|. 0.35068|. 0.0919|. L|L 0.47716|0.47716 1.5|1.5 0.09310|0.09310 N|N 1|1 B;B|. 0.27559|. 0.181;0.181|. B;B|. 0.26693|. 0.072;0.072|. T|. 0.39663|. -0.9603|. 10|. 0.12430|. T|. 0.62|. -19.7556|-19.7556 6.642|6.642 0.22914|0.22914 0.5895:0.1307:0.2798:0.0|0.5895:0.1307:0.2798:0.0 .|. 359;359|. Q9H0X4-2;Q9H0X4|. .;ITFG3_HUMAN|. S|C 359|50 ENSP00000382814:T359S;ENSP00000301679:T359S;ENSP00000397477:T359S;ENSP00000301678:T359S;ENSP00000411394:T359S|. ENSP00000301678:T359S|. T|X +|+ 1|3 0|0 ITFG3|ITFG3 253365|253365 0.000000|0.000000 0.05858|0.05858 0.001000|0.001000 0.08648|0.08648 0.036000|0.036000 0.12997|0.12997 -0.408000|-0.408000 0.07169|0.07169 -0.463000|-0.463000 0.06973|0.06973 0.459000|0.459000 0.35465|0.35465 ACG|TGA TCGA-3A-A9I9-01A-11D-A38G-08 ITFG3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000134227.2 1 0 1 26 238 0 109 1 9.999998e-01 38 206 0 109 2 0 0 0 0 0 2 1 1.000000 26 232 0 107 2 0 0 0 0 109 2 -20.000000 1 1 0 0 1 1 2 3 2.286804 1 0.300000 1.870000 0.384886 0.760000 0.510000 1.000000 1.000000 0.776855 0.760000 0 6.200000e-01 9.500000e-01 ABCC11 85320 broad.mit.edu 37 16 48248799 48248799 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr16:48248799G>A ENST00000394747.1 - 8 1590 c.1241C>T c.(1240-1242)gCg>gTg p.A414V ABCC11_ENST00000353782.5_Missense_Mutation_p.A414V|ABCC11_ENST00000394748.1_Missense_Mutation_p.A414V|ABCC11_ENST00000537808.1_Missense_Mutation_p.A414V|ABCC11_ENST00000356608.2_Missense_Mutation_p.A414V NM_033151.3 NP_149163.2 Q96J66 ABCCB_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 11 83 all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166) Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032) TACCATTGACGCTGTGAGTTT 0.493000 0 SO:0001583 missense ENST00000394747.1 1 1 hg19 CCDS10732.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 12.39 1.924986 0.34002 . . ENSG00000121270 ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808 D;D;D;D;D 0.92299 -3.01;-3.01;-3.01;-3.01;-3.01 4.95 2.93 0.34026 ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1); 0.956055 0.08704 N 0.905962 D 0.88112 0.6349 L 0.42744 1.35 0.09310 N 1 B;B 0.15719 0.003;0.014 B;B 0.16722 0.001;0.016 T 0.76680 -0.2870 10 0.48119 T 0.1 0.4302 7.1914 0.25828 0.2178:0.0:0.7822:0.0 . 414;414 Q96J66-2;Q96J66 .;ABCCB_HUMAN V 414 ENSP00000311326:A414V;ENSP00000349017:A414V;ENSP00000378231:A414V;ENSP00000378230:A414V;ENSP00000438530:A414V ENSP00000311326:A414V A - 2 0 ABCC11 46806300 0.016000 0.18221 0.000000 0.03702 0.001000 0.01503 2.029000 0.41098 0.454000 0.26884 0.650000 0.86243 GCG TCGA-3A-A9I9-01A-11D-A38G-08 ABCC11-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000429984.1 1 0 1 27 179 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 1.000000 26 179 0 54 2 0 0 0 0 55 2 -13.606940 1 1 121412 8 39 1 0 0 0 2.030203 0 0.300000 1.870000 0.295775 0.860000 0.590000 1.000000 1.000000 0.860423 0.860000 1 7.200000e-01 1 C16orf70 80262 broad.mit.edu 37 16 67166803 67166803 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr16:67166803C>T ENST00000219139.3 + 6 627 c.439C>T c.(439-441)Cca>Tca p.P147S C16orf70_ENST00000569600.1_Missense_Mutation_p.P147S|C16orf70_ENST00000569683.1_3'UTR NM_025187.3 NP_079463.2 Q9BSU1 CP070_HUMAN chromosome 16 open reading frame 70 17 Ovarian(137;0.192) GACTGAGGCTCCAAAGTATGA 0.512000 0 SO:0001583 missense ENST00000219139.3 1 1 hg19 CCDS10828.1 . . . . . . . . . . C 17.07 3.294667 0.60086 . . ENSG00000125149 ENST00000219139 . . . 6.05 6.05 0.98169 . 0.000000 0.85682 D 0.000000 T 0.52901 0.1763 N 0.10874 0.06 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.998 T 0.45425 -0.9262 9 0.09084 T 0.74 -10.8823 18.1025 0.89510 0.0:1.0:0.0:0.0 . 222;147 Q9BSU1-2;Q9BSU1 .;CP070_HUMAN S 147 . ENSP00000219139:P147S P + 1 0 C16orf70 65724304 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 7.624000 0.83124 2.866000 0.98385 0.650000 0.86243 CCA TCGA-3A-A9I9-01A-11D-A38G-08 C16orf70-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268829.2 1 0 1 109 673 0 313 0 4.690778e-01 1 10 0 313 2 0 0 0 0 0 2 1 1.000000 107 656 0 311 2 0 0 0 0 313 2 -20.000000 1 1 0 0 1 0 0 0 2.020615 0 0.300000 1.870000 0.291498 0.910000 0.760000 1.000000 1.000000 0.913527 0.910000 1 8.300000e-01 1 FAM65A 79567 broad.mit.edu 37 16 67576517 67576517 + Missense_Mutation SNP C C G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr16:67576517C>G ENST00000379312.3 + 13 1961 c.1840C>G c.(1840-1842)Cat>Gat p.H614D CTD-2012K14.3_ENST00000563083.1_RNA|CTD-2012K14.4_ENST00000564717.1_RNA|CTD-2012K14.2_ENST00000567122.1_RNA|FAM65A_ENST00000042381.4_Missense_Mutation_p.H610D|FAM65A_ENST00000422602.2_Missense_Mutation_p.H630D|FAM65A_ENST00000540839.3_Missense_Mutation_p.H630D|FAM65A_ENST00000428437.2_Missense_Mutation_p.H624D NM_001193522.1|NM_024519.3 NP_001180451.1|NP_078795.2 Q6ZS17 FA65A_HUMAN family with sequence similarity 65, member A 39 Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563) AAGCCCTACCCATACCACAGC 0.547000 0 SO:0001583 missense ENST00000379312.3 1 1 hg19 CCDS54028.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. c|c 14.90|14.90 2.672180|2.672180 0.47781|0.47781 .|. .|. ENSG00000039523|ENSG00000039523 ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839|ENST00000428437 T;T;T|. 0.14640|. 2.49;2.49;2.49|. 4.72|4.72 1.63|1.63 0.23807|0.23807 .|. 1.276350|. 0.05009|. N|. 0.470630|. T|T 0.16769|0.16769 0.0403|0.0403 N|N 0.08118|0.08118 0|0 0.09310|0.09310 N|N 1|1 B;B;B;B|. 0.26400|. 0.039;0.039;0.039;0.148|. B;B;B;B|. 0.19946|. 0.007;0.007;0.007;0.027|. T|T 0.28267|0.28267 -1.0049|-1.0049 10|5 0.42905|. T|. 0.14|. 0.0019|0.0019 6.4361|6.4361 0.21825|0.21825 0.0:0.6759:0.1505:0.1737|0.0:0.6759:0.1505:0.1737 .|. 624;630;614;630|. B4DIM2;E9PBS3;Q6ZS17;B4DEQ9|. .;.;FA65A_HUMAN;.|. D|R 614;610;630;624|604 ENSP00000368614:H614D;ENSP00000042381:H610D;ENSP00000400099:H630D|. ENSP00000042381:H610D|. H|P +|+ 1|2 0|0 FAM65A|FAM65A 66134018|66134018 0.000000|0.000000 0.05858|0.05858 0.001000|0.001000 0.08648|0.08648 0.112000|0.112000 0.19704|0.19704 0.853000|0.853000 0.27777|0.27777 0.178000|0.178000 0.19917|0.19917 0.436000|0.436000 0.28706|0.28706 CAT|CCA TCGA-3A-A9I9-01A-11D-A38G-08 FAM65A-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000268866.3 1 0 1 122 1066 0 586 1 9.966956e-01 13 62 0 586 2 0 0 0 0 0 2 1 1.000000 118 1022 0 570 2 0 0 0 0 586 2 -3.221883 1 1 0 0 1 0 0 0 2.020615 0 0.300000 1.870000 0.291498 0.670000 0.560000 0.790000 0.670000 0.679413 0.670000 0 6.100000e-01 7.400000e-01 DHX38 9785 broad.mit.edu 37 16 72138480 72138480 + Silent SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr16:72138480C>T ENST00000268482.3 + 15 2615 c.2106C>T c.(2104-2106)ttC>ttT p.F702F DHX38_ENST00000536867.1_Intron NM_014003.3 NP_054722.2 Q92620 PRP16_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 38 48 Ovarian(137;0.125) TCCCCATCTTCCACATCCCTG 0.537000 Melanoma(97;711 1442 7855 13832 28836) 0 SO:0001819 synonymous_variant ENST00000268482.3 1 1 hg19 CCDS10907.1 TCGA-3A-A9I9-01A-11D-A38G-08 DHX38-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269004.3 1 0 1 67 409 0 189 1 9.916134e-01 8 39 0 189 2 0 0 0 0 0 2 1 1.000000 67 396 0 187 2 0 0 0 0 189 2 -20.000000 1 1 0 0 1 0 0 0 2.020615 0 0.300000 1.870000 0.291498 0.920000 0.730000 1.000000 1.000000 0.915230 0.920000 1 8.200000e-01 1 CDYL2 124359 broad.mit.edu 37 16 80718735 80718735 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr16:80718735G>A ENST00000570137.2 - 2 471 c.316C>T c.(316-318)Cgg>Tgg p.R106W CDYL2_ENST00000563890.1_Missense_Mutation_p.R106W|CDYL2_ENST00000562753.1_5'UTR|CDYL2_ENST00000566173.1_Missense_Mutation_p.R106W|CDYL2_ENST00000562812.1_Missense_Mutation_p.R106W NM_152342.2 NP_689555.2 Q8N8U2 CDYL2_HUMAN chromodomain protein, Y-like 2 21 ATTCGCTTCCGTTTATGGGAG 0.557000 0 SO:0001583 missense ENST00000570137.2 1 1 hg19 CCDS32493.1 . . . . . . . . . . G 17.19 3.327533 0.60743 2.27E-4 0.0 ENSG00000166446 ENST00000299564 T 0.59364 0.27 5.23 4.24 0.50183 . 0.412335 0.23696 N 0.045479 T 0.64394 0.2594 L 0.29908 0.895 0.49130 D 0.999755 D 0.89917 1.0 D 0.81914 0.995 T 0.67126 -0.5749 10 0.87932 D 0 . 13.7029 0.62620 0.0:0.0:0.7712:0.2288 . 106 Q8N8U2 CDYL2_HUMAN W 106 ENSP00000299564:R106W ENSP00000299564:R106W R - 1 2 CDYL2 79276236 0.995000 0.38212 1.000000 0.80357 0.702000 0.40608 0.199000 0.17237 2.713000 0.92767 0.655000 0.94253 CGG TCGA-3A-A9I9-01A-11D-A38G-08 CDYL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000434727.2 1 0 1 53 224 0 96 0 3.801843e-02 0 2 0 96 2 0 0 0 0 0 2 1 1.000000 51 219 0 95 2 0 0 0 0 96 2 -20.000000 1 1 121412 2 36 1 0 0 0 2.020615 0 0.300000 1.870000 0.291498 0.990000 0.970000 1.000000 1.000000 0.998014 0.990000 1 9.900000e-01 1 ZNF778 197320 broad.mit.edu 37 16 89294771 89294771 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr16:89294771G>A ENST00000433976.2 + 6 2323 c.1991G>A c.(1990-1992)gGa>gAa p.G664E RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Missense_Mutation_p.G622E NM_001201407.1|NM_182531.3 NP_001188336.1|NP_872337.2 Q96MU6 ZN778_HUMAN zinc finger protein 778 24 CATAAACATGGAAGAATTCAC 0.403000 0 SO:0001583 missense ENST00000433976.2 0 1 hg19 CCDS45550.1 . . . . . . . . . . G 9.055 0.993026 0.19043 . . ENSG00000170100 ENST00000433976;ENST00000306502 T;T 0.07327 3.2;3.2 1.21 -2.43 0.06522 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.02494 0.0076 N 0.01424 -0.875 0.09310 N 1 B;B 0.06786 0.001;0.001 B;B 0.10450 0.003;0.005 T 0.40590 -0.9555 9 0.56958 D 0.05 . 2.2348 0.04005 0.3511:0.0:0.2421:0.4068 . 622;664 Q96MU6-2;Q96MU6 .;ZN778_HUMAN E 664;622 ENSP00000405289:G664E;ENSP00000305203:G622E ENSP00000305203:G622E G + 2 0 ZNF778 87822272 0.000000 0.05858 0.000000 0.03702 0.039000 0.13416 -1.083000 0.03397 -1.203000 0.02652 -0.534000 0.04291 GGA TCGA-3A-A9I9-01A-11D-A38G-08 ZNF778-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000430383.1 0 0 0 4 128 0 53 0 3.785154e-02 1 7 0 53 2 0 0 0 0 0 2 1 0.889744 4 127 0 53 2 0 0 0 0 53 2 -6.914200 1 1 121306 1 25 1 0 0 0 1.968406 0 0.300000 1.870000 0.273859 0.210000 0.070000 0.450000 0.190000 0.235020 0.210000 0 1.200000e-01 3.300000e-01 KIAA0100 9703 broad.mit.edu 37 17 26971150 26971150 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr17:26971150G>C ENST00000528896.2 - 2 198 c.124C>G c.(124-126)Cta>Gta p.L42V KIAA0100_ENST00000389003.3_5'UTR|KIAA0100_ENST00000544884.1_5'UTR NM_014680.3 NP_055495.2 Q14667 K0100_HUMAN KIAA0100 68 Lung NSC(42;0.00431) CCAATCTTTAGCTCCGCCTGC 0.473000 OREG0024280 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000528896.2 1 1 hg19 CCDS32595.1 . . . . . . . . . . G 12.07 1.828801 0.32329 . . ENSG00000007202 ENST00000005905;ENST00000389003;ENST00000528896 T 0.23552 1.9 5.32 1.1 0.20463 FMP27, N-terminal (1); 0.000000 0.64402 D 0.000001 T 0.32971 0.0847 L 0.34521 1.04 0.80722 D 1 D;D 0.89917 1.0;0.997 D;D 0.83275 0.996;0.992 T 0.01591 -1.1317 10 0.31617 T 0.26 . 8.9329 0.35682 0.3431:0.0:0.6569:0.0 . 42;42 F6XS94;Q14667 .;K0100_HUMAN V 42 ENSP00000436773:L42V ENSP00000005905:L42V L - 1 2 KIAA0100 23995277 1.000000 0.71417 0.919000 0.36401 0.996000 0.88848 2.540000 0.45727 0.062000 0.16340 0.655000 0.94253 CTA TCGA-3A-A9I9-01A-11D-A38G-08 KIAA0100-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390571.3 1 0 1 85 511 0 278 0 2.664808e-01 0 7 0 278 2 0 0 0 0 0 2 1 1.000000 82 503 0 277 2 0 0 0 0 278 2 -20.000000 1 1 0 0 1 1 2 3 2.068952 0 0.300000 1.870000 0.306244 0.960000 0.770000 1.000000 1.000000 0.943171 0.960000 1 8.600000e-01 1 CDC27 996 broad.mit.edu 37 17 45206848 45206848 + Missense_Mutation SNP T T A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 T A T T Valid Somatic Phase_I WXS targeted Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr17:45206848T>A ENST00000066544.3 - 16 2164 c.2071A>T c.(2071-2073)Acc>Tcc p.T691S CDC27_ENST00000531206.1_Missense_Mutation_p.T697S|CDC27_ENST00000527547.1_Missense_Mutation_p.T690S|CDC27_ENST00000446365.2_Missense_Mutation_p.T630S NM_001114091.1|NM_001256.3 NP_001107563.1|NP_001247.3 P30260 CDC27_HUMAN cell division cycle 27 90 TTGTTTAGGGTATCCAAAGCC 0.338000 0 SO:0001583 missense ENST00000066544.3 1 1 hg19 CCDS11509.1 . . . . . . . . . . T 28.0 4.878527 0.91740 . . ENSG00000004897 ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547 T;T;T;T 0.61980 0.06;0.06;0.06;0.06 5.68 5.68 0.88126 Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1); 0.000000 0.85682 D 0.000000 T 0.78755 0.4333 M 0.79258 2.445 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.85130 0.997;0.988;0.988;0.993 T 0.80074 -0.1534 10 0.49607 T 0.09 -10.4546 13.8853 0.63704 0.0:0.0:0.0:1.0 . 630;690;697;691 B4DL80;G5EA36;G3V1C4;P30260 .;.;.;CDC27_HUMAN S 691;697;630;690 ENSP00000066544:T691S;ENSP00000434614:T697S;ENSP00000392802:T630S;ENSP00000437339:T690S ENSP00000066544:T691S T - 1 0 CDC27 42561847 1.000000 0.71417 1.000000 0.80357 0.981000 0.71138 8.032000 0.88838 2.156000 0.67533 0.460000 0.39030 ACC TCGA-3A-A9I9-01A-11D-A38G-08 CDC27-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000389742.2 0 0 0 16 463 0 149 0 1.213277e-01 0 17 0 149 2 1 9.963055e-01 9 257 0 204 2 1 0.999927 16 456 0 147 2 0 0 0 0 149 2 -15.042200 1 1 0 0 1 1 2 3 2.053906 0 0.300000 1.870000 0.304175 0.220000 0.130000 1.000000 0.220000 0.257897 0.220000 0 1.700000e-01 3.000000e-01 SCRN2 90507 broad.mit.edu 37 17 45916852 45916852 + Silent SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr17:45916852G>A ENST00000290216.9 - 4 639 c.514C>T c.(514-516)Ctg>Ttg p.L172L SCRN2_ENST00000407215.3_Silent_p.L172L|SCRN2_ENST00000584123.1_Silent_p.L180L NM_001145023.1|NM_138355.3 NP_001138495.1|NP_612364.2 Q96FV2 SCRN2_HUMAN secernin 2 14 GCTGTCTCCAGCACCCACGCC 0.622000 0 SO:0001819 synonymous_variant ENST00000290216.9 1 1 hg19 CCDS11519.1 TCGA-3A-A9I9-01A-11D-A38G-08 SCRN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000441383.1 1 0 0 51 302 0 171 1 9.999312e-01 17 69 0 171 2 0 0 0 0 0 2 1 1.000000 50 297 0 169 2 0 0 0 0 171 2 -20.000000 1 0 0 0 1 1 2 3 2.053906 0 0.300000 1.870000 0.304175 0.970000 0.740000 1.000000 1.000000 0.938756 0.970000 1 8.400000e-01 1 PHOSPHO1 162466 broad.mit.edu 37 17 47301945 47301945 + Missense_Mutation SNP C C A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr17:47301945C>A ENST00000310544.4 - 3 594 c.467G>T c.(466-468)gGa>gTa p.G156V PHOSPHO1_ENST00000514112.1_Missense_Mutation_p.G181V|PHOSPHO1_ENST00000413580.1_Missense_Mutation_p.G181V Q8TCT1 PHOP1_HUMAN phosphatase, orphan 1 Epithelial(5;8.1e-06)|all cancers(6;7.71e-05) Choline(DB00122) AGCCAGCAGTCCCCGCGCATC 0.701000 0 SO:0001583 missense ENST00000310544.4 1 1 hg19 CCDS11547.1 . . . . . . . . . . C 25.3 4.626389 0.87560 . . ENSG00000173868 ENST00000310544;ENST00000413580;ENST00000514112;ENST00000511066 T;T;T;T 0.72725 -0.68;-0.68;-0.68;-0.68 5.38 4.38 0.52667 HAD-like domain (2); 0.000000 0.85682 D 0.000000 D 0.86468 0.5940 M 0.90082 3.085 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.89151 0.3523 10 0.66056 D 0.02 . 15.7956 0.78407 0.0:0.864:0.136:0.0 . 156;181 Q8TCT1;E9PAM0 PHOP1_HUMAN;. V 156;181;181;156 ENSP00000311925:G156V;ENSP00000406909:G181V;ENSP00000427694:G181V;ENSP00000426095:G156V ENSP00000311925:G156V G - 2 0 PHOSPHO1 44656944 1.000000 0.71417 1.000000 0.80357 0.946000 0.59487 7.292000 0.78731 2.510000 0.84645 0.462000 0.41574 GGA TCGA-3A-A9I9-01A-11D-A38G-08 PHOSPHO1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000364467.2 1 0 0 7 27 0 14 0 0 0 1 0 14 2 0 0 0 0 0 2 1 0.978381 6 25 0 14 2 0 0 0 0 14 2 -18.729430 1 0 0 0 1 1 2 3 2.053906 0 0.300000 1.870000 0.304175 0.990000 0.650000 1.000000 1.000000 0.966608 0.990000 1 9.500000e-01 1 MBTD1 54799 broad.mit.edu 37 17 49272667 49272667 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr17:49272667C>T ENST00000586178.1 - 13 1623 c.1280G>A c.(1279-1281)gGa>gAa p.G427E MBTD1_ENST00000415868.1_Missense_Mutation_p.G427E|MBTD1_ENST00000376381.2_Intron NM_017643.2 NP_060113.2 Q05BQ5 MBTD1_HUMAN mbt domain containing 1 12 BRCA - Breast invasive adenocarcinoma(22;1.54e-08) CCAGTCAGATCCGTCTGCTGC 0.428000 0 SO:0001583 missense ENST00000586178.1 1 1 hg19 CCDS11581.2 . . . . . . . . . . C 34 5.328880 0.95733 . . ENSG00000011258 ENST00000405860;ENST00000415868 T 0.40476 1.03 5.36 5.36 0.76844 . 0.105548 0.64402 D 0.000004 T 0.60818 0.2298 L 0.48218 1.51 0.80722 D 1 D;D 0.89917 1.0;0.999 D;D 0.91635 0.999;0.999 T 0.62267 -0.6890 10 0.87932 D 0 . 19.4315 0.94772 0.0:1.0:0.0:0.0 . 427;263 Q05BQ5;Q05BQ5-3 MBTD1_HUMAN;. E 427 ENSP00000403946:G427E ENSP00000386072:G427E G - 2 0 MBTD1 46627666 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 6.033000 0.70925 2.665000 0.90641 0.643000 0.83706 GGA TCGA-3A-A9I9-01A-11D-A38G-08 MBTD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318124.1 1 0 1 43 336 0 150 0 1.471241e-01 0 6 0 150 2 0 0 0 0 0 2 1 1.000000 41 330 0 150 2 0 0 0 0 150 2 -20.000000 1 1 0 0 1 1 2 3 2.053906 0 0.300000 1.870000 0.304175 0.760000 0.560000 1.000000 0.760000 0.775394 0.760000 0 6.500000e-01 8.900000e-01 UTP18 51096 broad.mit.edu 37 17 49353296 49353296 + Missense_Mutation SNP C C A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr17:49353296C>A ENST00000225298.7 + 6 838 c.781C>A c.(781-783)Ccc>Acc p.P261T NM_016001.2 NP_057085.2 Q9Y5J1 UTP18_HUMAN UTP18 small subunit (SSU) processome component homolog (yeast) 16 BRCA - Breast invasive adenocarcinoma(22;2.09e-07) GCAGTTCCATCCCGGTGCACA 0.383000 0 SO:0001583 missense ENST00000225298.7 0 1 hg19 CCDS42362.1 . . . . . . . . . . C 25.6 4.656868 0.88154 . . ENSG00000011260 ENST00000225298;ENST00000508506 T 0.25414 1.8 6.07 6.07 0.98685 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.000000 0.85682 D 0.000000 T 0.58278 0.2111 M 0.85945 2.785 0.80722 D 1 D 0.89917 1.0 D 0.77004 0.989 T 0.61510 -0.7048 10 0.87932 D 0 -16.6136 18.8399 0.92180 0.0:1.0:0.0:0.0 . 261 Q9Y5J1 UTP18_HUMAN T 261;237 ENSP00000225298:P261T ENSP00000225298:P261T P + 1 0 UTP18 46708295 1.000000 0.71417 0.997000 0.53966 0.912000 0.54170 6.329000 0.72920 2.885000 0.99019 0.655000 0.94253 CCC TCGA-3A-A9I9-01A-11D-A38G-08 UTP18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000368654.1 0 0 0 7 420 0 123 0 1.749805e-01 0 40 0 123 2 0 0 0 0 0 2 1 0.978365 7 406 0 123 2 0 0 0 0 123 2 -3.226472 1 1 0 0 1 1 2 3 2.053906 0 0.300000 1.870000 0.304175 0.110000 0.040000 1.000000 0.110000 0.149601 0.110000 0 7.000000e-02 1.700000e-01 TP53 7157 broad.mit.edu 37 17 7577548 7577548 + Missense_Mutation SNP C C T rs28934575 TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr17:7577548C>T ENST00000269305.4 - 7 922 c.733G>A c.(733-735)Ggc>Agc p.G245S TP53_ENST00000445888.2_Missense_Mutation_p.G245S|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.G245S|TP53_ENST00000420246.2_Missense_Mutation_p.G245S|TP53_ENST00000359597.4_Missense_Mutation_p.G245S|TP53_ENST00000413465.2_Missense_Mutation_p.G245S 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.G245S(304)|p.G245C(59)|p.G245R(10)|p.G152S(8)|p.0?(8)|p.?(5)|p.G152C(4)|p.G244_M246>V(3)|p.G245N(2)|p.G245fs*2(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.G245fs*22(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.M243fs*18(1)|p.G151_M153>V(1)|p.G245del(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*16(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) CGGTTCATGCCGCCCATGCAG 0.577000 G245S(LS1034_LARGE_INTESTINE)|G245S(NUGC2_STOMACH)|G245S(PANC0403_PANCREAS)|G245S(SKLMS1_SOFT_TISSUE)|G245S(SKMEL2_SKIN) 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 420 Substitution - Missense(390)|Deletion - Frameshift(8)|Whole gene deletion(8)|Complex - deletion inframe(5)|Unknown(5)|Deletion - In frame(3)|Insertion - Frameshift(1) GRCh37 CM010463|CM900210|CM920674 TP53 M rs28934575 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 . . . . . . . . . . C 33 5.259904 0.95368 0.0 1.16E-4 ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944 D;D;D;D;D;D;D;D 0.99894 -7.58;-7.58;-7.58;-7.58;-7.58;-7.58;-7.58;-7.58 4.62 4.62 0.57501 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 0.99878 0.9942 M 0.84585 2.705 0.80722 D 1 D;D;D;D;D;D 0.89917 1.0;0.999;1.0;1.0;1.0;1.0 D;D;D;D;D;D 0.97110 0.999;0.976;0.992;0.999;0.999;1.0 D 0.96039 0.9023 10 0.87932 D 0 -19.4293 15.3618 0.74483 0.0:1.0:0.0:0.0 rs28934575 245;245;152;245;245;245 P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;P53_HUMAN;.;. S 245;245;245;245;245;245;234;152;113;152 ENSP00000410739:G245S;ENSP00000352610:G245S;ENSP00000269305:G245S;ENSP00000398846:G245S;ENSP00000391127:G245S;ENSP00000391478:G245S;ENSP00000425104:G113S;ENSP00000423862:G152S ENSP00000269305:G245S G - 1 0 TP53 7518273 1.000000 0.71417 0.965000 0.40720 0.974000 0.67602 7.609000 0.82925 2.564000 0.86499 0.462000 0.41574 GGC TCGA-3A-A9I9-01A-11D-A38G-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 28 203 0 131 1 9.365487e-01 8 28 0 131 2 1 1 91 609 1 689 6 1 1.000000 27 198 0 129 2 0 0 0 0 131 2 -2.599063 1 1 121412 1 39 1 0 1 1 1.730853 1 0.300000 1.870000 0.176471 0.670000 0.460000 0.910000 0.670000 0.688017 0.670000 0 5.600000e-01 8.000000e-01 RNF213 57674 broad.mit.edu 37 17 78324169 78324169 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr17:78324169G>A ENST00000582970.1 + 31 10300 c.10157G>A c.(10156-10158)cGt>cAt p.R3386H CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.R3435H|RNF213_ENST00000336301.6_Missense_Mutation_p.R1459H NM_001256071.1 NP_001243000.1 Q63HN8 RN213_HUMAN ring finger protein 213 130 all_neural(118;0.0538) BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057) GATGGAATCCGTAGCGCCCAG 0.353000 0 SO:0001583 missense ENST00000582970.1 1 1 hg19 CCDS58606.1 . . . . . . . . . . g 5.030 0.191195 0.09547 . . ENSG00000173821 ENST00000508628;ENST00000411702;ENST00000336301 T 0.17528 2.27 5.0 -1.62 0.08372 . 0.947517 0.08876 N 0.880757 T 0.06325 0.0163 N 0.02736 -0.51 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.42565 -0.9444 10 0.22109 T 0.4 . 7.9091 0.29780 0.4707:0.0:0.4235:0.1057 . 1459 Q63HN8 RN213_HUMAN H 3386;3435;1459 ENSP00000338218:R1459H ENSP00000338218:R1459H R + 2 0 RNF213 75938764 0.000000 0.05858 0.000000 0.03702 0.188000 0.23474 0.460000 0.21924 -0.543000 0.06240 -0.285000 0.09966 CGT TCGA-3A-A9I9-01A-11D-A38G-08 RNF213-020 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000443298.1 1 0 0 21 325 0 156 1 2.923285e-01 3 14 0 156 2 1 9.996228e-01 17 349 1 342 6 1 0.999998 21 323 0 154 2 0 0 0 0 156 2 -6.340543 1 1 121410 1 32 1 0 1 1 1.736465 1 0.300000 1.870000 0.176471 0.340000 0.210000 0.500000 0.340000 0.353417 0.340000 0 2.700000e-01 4.200000e-01 PCYT2 5833 broad.mit.edu 37 17 79866869 79866869 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr17:79866869C>T ENST00000538936.2 - 3 331 c.223G>A c.(223-225)Gag>Aag p.E75K PCYT2_ENST00000570391.1_Missense_Mutation_p.E43K|PCYT2_ENST00000538721.2_Missense_Mutation_p.E75K|PCYT2_ENST00000570388.1_5'UTR|PCYT2_ENST00000571105.1_Missense_Mutation_p.E75K|PCYT2_ENST00000331285.3_5'UTR NM_001256435.1|NM_002861.3 NP_001243364.1|NP_002852.1 Q99447 PCY2_HUMAN phosphate cytidylyltransferase 2, ethanolamine 8 all_neural(118;0.0878)|Ovarian(332;0.12) BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382) Lamivudine(DB00709) TTGTATCTCTCCTCCTGAGTG 0.592000 0 SO:0001583 missense ENST00000538936.2 1 1 hg19 CCDS11791.1 . . . . . . . . . . C 33 5.206311 0.95033 . . ENSG00000185813 ENST00000538721;ENST00000538936 D;D 0.97256 -4.31;-4.31 4.25 4.25 0.50352 Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);Cytidyltransferase-related (1); 0.000000 0.85682 D 0.000000 D 0.98704 0.9565 M 0.91140 3.18 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 1.0;1.0;0.999;1.0 D 0.99793 1.1032 10 0.87932 D 0 -43.1461 16.8397 0.85965 0.0:1.0:0.0:0.0 . 43;43;75;75 B7Z4W6;B7ZAS0;F5H8B1;Q99447 .;.;.;PCY2_HUMAN K 75 ENSP00000442050:E75K;ENSP00000439245:E75K ENSP00000442050:E75K E - 1 0 PCYT2 77460161 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 5.330000 0.65899 2.197000 0.70478 0.561000 0.74099 GAG TCGA-3A-A9I9-01A-11D-A38G-08 PCYT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000439939.1 1 0 1 34 212 0 144 1 9.787827e-01 22 19 0 144 2 0 0 0 0 0 2 1 1.000000 33 208 0 143 2 0 0 0 0 144 2 -2.923902 1 1 0 0 1 0 1 1 1.736465 1 0.300000 1.870000 0.176471 0.760000 0.550000 0.970000 0.770000 0.771686 0.760000 0 6.500000e-01 8.800000e-01 MYH10 4628 broad.mit.edu 37 17 8398511 8398511 + Missense_Mutation SNP C C A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr17:8398511C>A ENST00000269243.4 - 29 4045 c.3907G>T c.(3907-3909)Ggt>Tgt p.G1303C MYH10_ENST00000360416.3_Missense_Mutation_p.G1334C|MYH10_ENST00000396239.1_Missense_Mutation_p.G1324C|MYH10_ENST00000379980.4_Missense_Mutation_p.G1319C NM_005964.3 NP_005955.3 P35580 MYH10_HUMAN myosin, heavy chain 10, non-muscle 52 AATTTAATACCCTTCTTCTCT 0.408000 0 SO:0001583 missense ENST00000269243.4 1 1 hg19 CCDS11144.1 . . . . . . . . . . C 13.04 2.118677 0.37436 . . ENSG00000133026 ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980 T;T;T;T 0.77620 -1.11;-1.11;-1.11;-1.11 4.88 4.88 0.63580 Myosin tail (1); 0.051033 0.85682 D 0.000000 T 0.66416 0.2787 N 0.13098 0.295 0.58432 D 0.999996 B;B;B 0.06786 0.001;0.001;0.001 B;B;B 0.10450 0.005;0.003;0.005 T 0.63514 -0.6620 10 0.62326 D 0.03 . 18.5819 0.91174 0.0:1.0:0.0:0.0 . 1312;1334;1303 B2RWP9;F8VTL3;P35580 .;.;MYH10_HUMAN C 1303;1334;1324;1319 ENSP00000269243:G1303C;ENSP00000353590:G1334C;ENSP00000379539:G1324C;ENSP00000369315:G1319C ENSP00000269243:G1303C G - 1 0 MYH10 8339236 0.212000 0.23540 0.973000 0.42090 0.977000 0.68977 0.960000 0.29253 2.688000 0.91661 0.655000 0.94253 GGT TCGA-3A-A9I9-01A-11D-A38G-08 MYH10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000227001.2 0 0 0 11 222 1 152 0 2.909272e-01 1 20 1 152 2 0 0 0 0 0 2 1 0.812692 11 218 1 150 8 0 0 0 1 152 2 -2.654036 1 1 0 0 1 0 1 1 1.730853 1 0.300000 1.870000 0.176471 0.270000 0.140000 0.440000 0.260000 0.283587 0.270000 0 1.900000e-01 3.600000e-01 DLGAP1 9229 broad.mit.edu 37 18 3879577 3879577 + Silent SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr18:3879577G>A ENST00000315677.3 - 4 1087 c.492C>T c.(490-492)aaC>aaT p.N164N DLGAP1-AS3_ENST00000577649.1_RNA|DLGAP1_ENST00000515196.2_Silent_p.N164N|DLGAP1_ENST00000581527.1_Silent_p.N164N|DLGAP1_ENST00000584874.1_Silent_p.N164N NM_004746.3 NP_004737.2 O14490 DLGP1_HUMAN discs, large (Drosophila) homolog-associated protein 1 56 Colorectal(8;0.0257) CCTTGCCCCCGTTGACGCTGC 0.711000 0 SO:0001819 synonymous_variant ENST00000315677.3 1 1 hg19 CCDS11836.1 TCGA-3A-A9I9-01A-11D-A38G-08 DLGAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254394.4 1 0 1 97 401 0 252 0 0 0 0 252 2 0 0 0 0 0 2 1 1.000000 96 392 0 244 2 0 0 0 0 252 2 -20.000000 1 1 0 0 1 1 2 3 2.081949 0 0.300000 1.870000 0.308300 0.990000 0.990000 1.000000 1.000000 0.999931 0.990000 1 9.900000e-01 1 FCGBP 8857 broad.mit.edu 37 19 40408807 40408807 + Silent SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr19:40408807G>A ENST00000221347.6 - 8 4039 c.4032C>T c.(4030-4032)aaC>aaT p.N1344N NM_003890.2 NP_003881.2 Q9Y6R7 FCGBP_HUMAN Fc fragment of IgG binding protein 165 all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06) Epithelial(26;6.25e-23)|all cancers(26;1.13e-20) GGATCTGGCCGTTGGCCAGCA 0.587000 0 SO:0001819 synonymous_variant ENST00000221347.6 0 1 hg19 CCDS12546.1 TCGA-3A-A9I9-01A-11D-A38G-08 FCGBP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462507.1 1 0 0 19 114 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 0.999762 12 75 0 76 2 0 0 0 0 71 2 -20.000000 1 1 121330 21 39 1 0 0 0 2.011623 0 0.300000 1.870000 0.289340 0.930000 0.590000 1.000000 1.000000 0.896457 0.930000 1 7.500000e-01 1 MEGF8 1954 broad.mit.edu 37 19 42848986 42848986 + Splice_Site SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr19:42848986G>C ENST00000251268.6 + 12 2097 c.e12+1 MEGF8_ENST00000334370.4_Splice_Site NM_001271938.1 NP_001258867.1 Q7Z7M0 MEGF8_HUMAN multiple EGF-like-domains 8 50 Prostate(69;0.00682) GCCTGACAAGGTGGGTAGGAG 0.542000 0 SO:0001630 splice_region_variant ENST00000251268.6 1 1 hg19 . . . . . . . . . . g 16.72 3.201977 0.58234 . . ENSG00000105429 ENST00000334370;ENST00000251268 . . . 4.93 4.93 0.64822 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 15.638 0.76970 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . MEGF8 47540826 1.000000 0.71417 1.000000 0.80357 0.552000 0.35366 8.593000 0.90832 2.288000 0.76882 0.457000 0.33378 . TCGA-3A-A9I9-01A-11D-A38G-08 MEGF8-002 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000463854.1 1 0 0 32 373 0 226 1 1.911386e-02 2 1 0 226 2 0 0 0 0 0 2 1 1.000000 30 365 0 223 2 0 0 0 0 226 2 -20.000000 1 1 0 0 1 0 0 0 2.011623 0 0.300000 1.870000 0.289340 0.510000 0.360000 0.700000 0.520000 0.529211 0.510000 0 4.300000e-01 6.100000e-01 PSG6 5675 broad.mit.edu 37 19 43420449 43420449 + Silent SNP G G A rs73934315 byFrequency TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr19:43420449G>A ENST00000292125.2 - 2 299 c.255C>T c.(253-255)caC>caT p.H85H PSG6_ENST00000187910.2_Silent_p.H85H|PSG6_ENST00000601833.1_Silent_p.H14H|PSG6_ENST00000402603.4_Silent_p.H85H NM_002782.4 NP_002773.1 Q00889 PSG6_HUMAN pregnancy specific beta-1-glycoprotein 6 44 Prostate(69;0.00899) TAATTTGACCGTGTACTACAT 0.443000 0 SO:0001819 synonymous_variant ENST00000292125.2 1 0 hg19 CCDS12613.1 TCGA-3A-A9I9-01A-11D-A38G-08 PSG6-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000321436.1 1 0 0 246 1430 0 460 0 0 0 0 460 2 0 0 0 0 0 2 1 1.000000 245 1405 0 456 2 0 0 0 0 460 2 -10.636750 1 1 121320 246 62 1 0 0 0 2.011623 0 0.300000 1.870000 0.289340 0.950000 0.850000 1.000000 1.000000 0.955519 0.950000 1 9.000000e-01 1 PPP2R1A 5518 broad.mit.edu 37 19 52709296 52709296 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr19:52709296G>C ENST00000322088.6 + 3 308 c.250G>C c.(250-252)Gag>Cag p.E84Q PPP2R1A_ENST00000462990.1_5'UTR|PPP2R1A_ENST00000473455.2_3'UTR|PPP2R1A_ENST00000444322.2_Intron NM_014225.5 NP_055040.2 P30153 2AAA_HUMAN protein phosphatase 2, regulatory subunit A, alpha 135 GGGAGGCCCAGAGTACGTGCA 0.607000 Mis clear cell ovarian carcinoma Dom? yes 19 19q13.41 5518 protein phosphatase 2, regulatory subunit A, alpha E 0 SO:0001583 missense ENST00000322088.6 1 1 hg19 CCDS12849.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 8.630|8.630 0.893441|0.893441 0.17613|0.17613 .|. .|. ENSG00000105568|ENSG00000105568 ENST00000454220;ENST00000423369;ENST00000322088|ENST00000391791 T;T|. 0.35048|. 1.33;1.33|. 3.23|3.23 2.2|2.2 0.27929|0.27929 Armadillo-like helical (1);Armadillo-type fold (1);|. 0.225700|. 0.30455|. N|. 0.009598|. T|T 0.62792|0.62792 0.2457|0.2457 M|M 0.62723|0.62723 1.935|1.935 0.80722|0.80722 D|D 1|1 B;B|. 0.15719|. 0.014;0.014|. B;B|. 0.10450|. 0.005;0.005|. T|T 0.64597|0.64597 -0.6370|-0.6370 10|6 0.48119|0.87932 T|D 0.1|0 -26.2108|-26.2108 8.5769|8.5769 0.33603|0.33603 0.1188:0.0:0.8812:0.0|0.1188:0.0:0.8812:0.0 .|. 84;84|. A8K7B7;P30153|. .;2AAA_HUMAN|. Q|H 124;84;84|62 ENSP00000391905:E124Q;ENSP00000324804:E84Q|. ENSP00000324804:E84Q|ENSP00000375668:Q62H E|Q +|+ 1|3 0|2 PPP2R1A|PPP2R1A 57401108|57401108 1.000000|1.000000 0.71417|0.71417 0.672000|0.672000 0.29872|0.29872 0.515000|0.515000 0.34225|0.34225 8.178000|8.178000 0.89690|0.89690 0.948000|0.948000 0.37687|0.37687 -0.339000|-0.339000 0.08088|0.08088 GAG|CAG TCGA-3A-A9I9-01A-11D-A38G-08 PPP2R1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000267967.2 1 0 0 11 267 0 75 1 9.926215e-01 7 199 0 75 2 0 0 0 0 0 2 1 0.998184 11 260 0 75 2 0 0 0 0 75 2 -3.139827 1 1 0 0 1 1 2 3 2.352969 1 0.300000 1.870000 0.391304 0.310000 0.160000 0.510000 0.300000 0.326736 0.310000 0 2.200000e-01 4.100000e-01 FBN3 84467 broad.mit.edu 37 19 8190867 8190867 + Silent SNP A A G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr19:8190867A>G ENST00000600128.1 - 22 3054 c.2640T>C c.(2638-2640)tgT>tgC p.C880C FBN3_ENST00000601739.1_Silent_p.C880C|FBN3_ENST00000270509.2_Silent_p.C880C Q75N90 FBN3_HUMAN fibrillin 3 132 GCCCGTTGGGACAGACTCCCG 0.637000 0 SO:0001819 synonymous_variant ENST00000600128.1 1 1 hg19 CCDS12196.1 TCGA-3A-A9I9-01A-11D-A38G-08 FBN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461428.2 1 0 1 29 185 0 103 0 0 0 0 103 2 0 0 0 0 0 2 1 1.000000 28 183 0 102 2 0 0 0 0 103 2 -20.000000 1 1 0 0 1 0 0 0 2.018298 0 0.300000 1.870000 0.291498 0.890000 0.620000 1.000000 1.000000 0.878375 0.890000 1 7.400000e-01 1 FBXL12 54850 broad.mit.edu 37 19 9921950 9921950 + Silent SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr19:9921950G>A ENST00000247977.4 - 3 844 c.603C>T c.(601-603)ctC>ctT p.L201L FBXL12_ENST00000591009.1_Silent_p.L148L|FBXL12_ENST00000586651.1_3'UTR|FBXL12_ENST00000585379.1_Silent_p.L148L|FBXL12_ENST00000588922.1_3'UTR|FBXL12_ENST00000589626.1_3'UTR NM_017703.1 NP_060173.1 Q9NXK8 FXL12_HUMAN F-box and leucine-rich repeat protein 12 10 GCAGATAGCTGAGCTCCTGCA 0.667000 0 SO:0001819 synonymous_variant ENST00000247977.4 1 1 hg19 CCDS12218.1 TCGA-3A-A9I9-01A-11D-A38G-08 FBXL12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000450265.1 1 0 1 30 167 0 99 1 9.927314e-01 7 39 0 99 2 0 0 0 0 0 2 1 1.000000 30 162 0 97 2 0 0 0 0 99 2 -20.000000 1 1 0 0 1 0 0 0 2.018298 0 0.300000 1.870000 0.291498 0.990000 0.700000 1.000000 1.000000 0.940338 0.990000 1 8.400000e-01 1 CLCC1 23155 broad.mit.edu 37 1 109477302 109477302 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr1:109477302G>A ENST00000369971.2 - 11 1775 c.1646C>T c.(1645-1647)cCc>cTc p.P549L CLCC1_ENST00000482889.1_Intron|CLCC1_ENST00000415331.1_Missense_Mutation_p.P499L|CLCC1_ENST00000369970.3_Missense_Mutation_p.P499L|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000356970.2_Missense_Mutation_p.P549L|CLCC1_ENST00000369976.1_Intron|CLCC1_ENST00000369968.2_Missense_Mutation_p.P364L|CLCC1_ENST00000302500.4_Missense_Mutation_p.P428L|CLCC1_ENST00000348264.2_Missense_Mutation_p.P364L|CLCC1_ENST00000369969.2_Missense_Mutation_p.P428L NM_001048210.1 NP_001041675.1 Q96S66 CLCC1_HUMAN chloride channel CLIC-like 1 14 all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626) CTAGCCACAGGGGCTGCTGAC 0.547000 0 SO:0001583 missense ENST00000369971.2 1 1 hg19 CCDS41362.1 . . . . . . . . . . G 25.1 4.604243 0.87157 . . ENSG00000121940 ENST00000356970;ENST00000369971;ENST00000415331;ENST00000369969;ENST00000369968;ENST00000369970;ENST00000348264;ENST00000302500 T;T;T;T;T;T;T;T 0.46451 0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87 5.81 1.51 0.23008 . 0.372474 0.23454 N 0.048004 T 0.15652 0.0377 L 0.51422 1.61 0.34281 D 0.682164 B;B;B;B 0.17667 0.008;0.008;0.023;0.01 B;B;B;B 0.16289 0.011;0.011;0.009;0.015 T 0.02868 -1.1100 10 0.72032 D 0.01 -0.2661 3.6445 0.08180 0.2808:0.0:0.5081:0.2112 . 364;428;499;549 Q96S66-4;Q96S66-3;Q96S66-2;Q96S66 .;.;.;CLCC1_HUMAN L 549;549;499;428;364;499;364;428 ENSP00000349456:P549L;ENSP00000358988:P549L;ENSP00000411591:P499L;ENSP00000358986:P428L;ENSP00000358985:P364L;ENSP00000358987:P499L;ENSP00000337243:P364L;ENSP00000306552:P428L ENSP00000306552:P428L P - 2 0 CLCC1 109278825 0.063000 0.20901 0.224000 0.23877 0.685000 0.39939 0.037000 0.13840 0.392000 0.25172 0.655000 0.94253 CCC TCGA-3A-A9I9-01A-11D-A38G-08 CLCC1-203 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032405.1 0 0 1 56 327 1 153 1 9.973308e-01 16 65 1 153 4 0 0 0 0 0 2 1 1.000000 56 324 1 150 11 0 0 0 1 153 2 -19.999980 1 1 0 0 1 1 2 3 2.046472 0 0.300000 1.870000 0.302094 0.970000 0.750000 1.000000 1.000000 0.943968 0.970000 1 8.600000e-01 1 WDR3 10885 broad.mit.edu 37 1 118477263 118477263 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr1:118477263G>C ENST00000349139.5 + 3 386 c.339G>C c.(337-339)ttG>ttC p.L113F WDR3_ENST00000369441.3_3'UTR|WDR3_ENST00000471680.1_3'UTR NM_006784.2 NP_006775.1 Q9UNX4 WDR3_HUMAN WD repeat domain 3 49 Esophageal squamous(2;0.162) all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244) TCACTACCTTGAAGTATGATC 0.478000 0 SO:0001583 missense ENST00000349139.5 1 1 hg19 CCDS898.1 . . . . . . . . . . G 19.07 3.756898 0.69648 . . ENSG00000065183 ENST00000349139 T 0.64803 -0.12 5.76 1.42 0.22433 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.169045 0.50627 D 0.000118 T 0.66426 0.2788 M 0.87758 2.905 0.80722 D 1 D 0.65815 0.995 D 0.65987 0.94 T 0.66712 -0.5854 10 0.72032 D 0.01 -9.5395 3.4483 0.07488 0.1398:0.2421:0.4916:0.1265 . 113 Q9UNX4 WDR3_HUMAN F 113 ENSP00000308179:L113F ENSP00000308179:L113F L + 3 2 WDR3 118278786 1.000000 0.71417 0.937000 0.37676 0.873000 0.50193 0.594000 0.24014 0.406000 0.25560 -0.150000 0.13652 TTG TCGA-3A-A9I9-01A-11D-A38G-08 WDR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033720.2 1 0 0 26 399 0 121 0 1.082232e-01 1 8 0 121 2 0 0 0 0 0 2 1 1.000000 24 388 0 119 2 0 0 0 0 121 2 -6.782391 1 1 0 0 1 1 2 3 2.046472 0 0.300000 1.870000 0.302094 0.410000 0.270000 0.610000 0.410000 0.426193 0.410000 0 3.300000e-01 5.000000e-01 CFH 3075 broad.mit.edu 37 1 196695962 196695962 + Missense_Mutation SNP T T C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr1:196695962T>C ENST00000367429.4 + 14 2368 c.2128T>C c.(2128-2130)Tac>Cac p.Y710H NM_000186.3 NP_000177.2 P08603 CFAH_HUMAN complement factor H 101 CCCTCCTTATTACTATGGAGA 0.393000 0 SO:0001583 missense ENST00000367429.4 1 1 hg19 CCDS1385.1 . . . . . . . . . . T 1.622 -0.521227 0.04171 . . ENSG00000000971 ENST00000367429 T 0.64085 -0.08 5.8 1.14 0.20703 Complement control module (2);Sushi/SCR/CCP (3); . . . . T 0.29882 0.0747 N 0.01003 -1.06 0.09310 N 0.999999 B 0.02656 0.0 B 0.04013 0.001 T 0.23476 -1.0187 9 0.39692 T 0.17 . 8.5839 0.33646 0.0:0.6377:0.0:0.3623 . 710 P08603 CFAH_HUMAN H 710 ENSP00000356399:Y710H ENSP00000356399:Y710H Y + 1 0 CFH 194962585 0.017000 0.18338 0.468000 0.27192 0.386000 0.30323 -0.083000 0.11286 0.318000 0.23185 -0.250000 0.11733 TAC TCGA-3A-A9I9-01A-11D-A38G-08 CFH-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086412.2 1 0 1 68 365 0 59 0 9.855184e-01 0 38 0 59 2 0 0 0 0 0 2 1 1.000000 68 356 0 59 2 0 0 0 0 59 2 -20.000000 1 0 0 0 1 1 2 3 2.044382 0 0.300000 1.870000 0.301048 0.990000 0.830000 1.000000 1.000000 0.976072 0.990000 1 9.300000e-01 1 LAMB3 3914 broad.mit.edu 37 1 209799171 209799171 + Missense_Mutation SNP C C G rs35794952 TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr1:209799171C>G ENST00000356082.4 - 14 1932 c.1798G>C c.(1798-1800)Ggt>Cgt p.G600R LAMB3_ENST00000391911.1_Missense_Mutation_p.G600R|LAMB3_ENST00000367030.3_Missense_Mutation_p.G600R|MIR4260_ENST00000583107.1_RNA NM_000228.2 NP_000219.2 Q13751 LAMB3_HUMAN laminin, beta 3 45 CGGAGTCTACCAAAGCGCAGG 0.632000 0 SO:0001583 missense ENST00000356082.4 1 1 hg19 CCDS1487.1 . . . . . . . . . . C 3.231 -0.157369 0.06544 . . ENSG00000196878 ENST00000391911;ENST00000356082;ENST00000367030 T;T;T 0.34667 1.35;1.35;1.35 5.14 -3.05 0.05396 . 1.305210 0.04711 N 0.417607 T 0.17408 0.0418 N 0.08118 0 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.23297 -1.0192 10 0.14656 T 0.56 . 8.4291 0.32746 0.0:0.4658:0.1106:0.4235 . 600 Q13751 LAMB3_HUMAN R 600 ENSP00000375778:G600R;ENSP00000348384:G600R;ENSP00000355997:G600R ENSP00000348384:G600R G - 1 0 LAMB3 207865794 0.000000 0.05858 0.000000 0.03702 0.378000 0.30076 -1.769000 0.01792 -0.858000 0.04110 0.456000 0.33151 GGT TCGA-3A-A9I9-01A-11D-A38G-08 LAMB3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000088525.2 1 0 1 29 166 0 78 1 9.999999e-01 75 80 0 78 2 0 0 0 0 0 2 1 1.000000 27 160 0 75 2 0 0 0 0 78 2 -3.092606 1 1 0 0 1 0 1 1 2.038281 0 0.300000 1.870000 0.298948 0.980000 0.680000 1.000000 1.000000 0.933940 0.980000 1 8.200000e-01 1 OBSCN 84033 broad.mit.edu 37 1 228562337 228562337 + Missense_Mutation SNP A A G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr1:228562337A>G ENST00000422127.1 + 97 22591 c.22547A>G c.(22546-22548)aAg>aGg p.K7516R OBSCN_ENST00000366707.4_Missense_Mutation_p.K5150R|OBSCN_ENST00000570156.2_Missense_Mutation_p.K8473R NM_001098623.2 NP_001092093.2 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF 223 Prostate(94;0.0405) GCCACCCTCAAGAACTTCCAG 0.622000 0 SO:0001583 missense ENST00000422127.1 1 1 hg19 CCDS58065.1 . . . . . . . . . . A 28.8 4.954837 0.92726 . . ENSG00000154358 ENST00000422127;ENST00000366707 D;D 0.82526 -1.62;-1.62 5.16 5.16 0.70880 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.220098 0.36628 N 0.002485 D 0.84624 0.5513 N 0.21282 0.65 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 D 0.84121 0.0406 10 0.33141 T 0.24 . 15.0022 0.71483 1.0:0.0:0.0:0.0 . 7516 Q5VST9 OBSCN_HUMAN R 7516;5150 ENSP00000409493:K7516R;ENSP00000355668:K5150R ENSP00000355668:K5150R K + 2 0 OBSCN 226628960 1.000000 0.71417 1.000000 0.80357 0.746000 0.42486 5.428000 0.66489 1.960000 0.56953 0.459000 0.35465 AAG TCGA-3A-A9I9-01A-11D-A38G-08 OBSCN-204 KNOWN basic|CCDS protein_coding protein_coding 1 0 1 67 458 0 281 0 1.283174e-01 0 5 0 281 2 0 0 0 0 0 2 1 1.000000 67 440 0 278 2 0 0 0 0 281 2 -20.000000 1 1 0 0 1 0 1 1 2.038281 0 0.300000 1.870000 0.298948 0.840000 0.660000 1.000000 1.000000 0.851633 0.840000 0 7.500000e-01 9.500000e-01 OR2B11 127623 broad.mit.edu 37 1 247614391 247614391 + Silent SNP A A G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr1:247614391A>G ENST00000318749.6 - 1 917 c.894T>C c.(892-894)aaT>aaC p.N298N NM_001004492.1 NP_001004492.1 Q5JQS5 OR2BB_HUMAN olfactory receptor, family 2, subfamily B, member 11 60 all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.241) OV - Ovarian serous cystadenocarcinoma(106;0.0188) TCATATCTTTATTTCTCAGGG 0.473000 0 SO:0001819 synonymous_variant ENST00000318749.6 1 1 hg19 CCDS31090.1 TCGA-3A-A9I9-01A-11D-A38G-08 OR2B11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097620.1 1 0 1 217 1031 0 521 0 0 0 0 521 2 0 0 0 0 0 2 1 1.000000 215 1009 0 515 2 0 0 0 0 521 2 -20.000000 1 1 0 0 1 0 1 1 2.038281 0 0.300000 1.870000 0.298948 0.990000 0.990000 1.000000 1.000000 0.999748 0.990000 1 9.900000e-01 1 PUM1 9698 broad.mit.edu 37 1 31409636 31409636 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr1:31409636C>T ENST00000257075.5 - 21 3376 c.3283G>A c.(3283-3285)Gct>Act p.A1095T PUM1_ENST00000423018.2_Missense_Mutation_p.A953T|PUM1_ENST00000424085.2_Missense_Mutation_p.A853T|PUM1_ENST00000373747.3_Missense_Mutation_p.A1098T|PUM1_ENST00000373741.4_Missense_Mutation_p.A1133T|PUM1_ENST00000440538.2_Missense_Mutation_p.A1071T|PUM1_ENST00000426105.2_Missense_Mutation_p.A1097T|SNORD103A_ENST00000363284.1_RNA|PUM1_ENST00000373742.2_Missense_Mutation_p.A1036T NM_014676.2 NP_055491.1 Q14671 PUM1_HUMAN pumilio RNA-binding family member 1 48 Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123) ATGAGCACAGCGCGCTCCGTA 0.507000 0 SO:0001583 missense ENST00000257075.5 1 1 hg19 CCDS338.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 22.2|22.2 4.261608|4.261608 0.80358|0.80358 0.0|0.0 1.16E-4|1.16E-4 ENSG00000134644|ENSG00000134644 ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742;ENST00000529846|ENST00000525843;ENST00000498419 T;T;T;T;T;T;T;T;T|T;T 0.13538|0.17213 2.58;2.58;2.58;2.58;2.58;2.58;2.58;2.58;2.58|2.29;2.29 5.78|5.78 5.78|5.78 0.91487|0.91487 Armadillo-like helical (1);Armadillo-type fold (1);|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.33847|0.33847 0.0877|0.0877 L|L 0.48877|0.48877 1.53|1.53 0.80722|0.80722 D|D 1|1 P;B;B;P;P;B;P;B|. 0.39250|. 0.643;0.326;0.185;0.665;0.643;0.185;0.643;0.257|. B;B;B;B;B;B;B;B|. 0.26614|. 0.065;0.032;0.015;0.071;0.065;0.007;0.065;0.065|. T|T 0.00847|0.00847 -1.1542|-1.1542 10|7 0.39692|0.87932 T|D 0.17|0 -7.352|-7.352 20.0137|20.0137 0.97470|0.97470 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 1036;953;1133;1071;1095;1097;1098;1097|. B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5|. .;.;.;.;PUM1_HUMAN;.;.;.|. T|H 853;1095;1098;835;1097;1071;1133;953;1036;206|1033;808 ENSP00000400141:A853T;ENSP00000257075:A1095T;ENSP00000362852:A1098T;ENSP00000391723:A1097T;ENSP00000401777:A1071T;ENSP00000362846:A1133T;ENSP00000399440:A953T;ENSP00000362847:A1036T;ENSP00000431213:A206T|ENSP00000435825:R1033H;ENSP00000433850:R808H ENSP00000257075:A1095T|ENSP00000433850:R808H A|R -|- 1|2 0|0 PUM1|PUM1 31182223|31182223 1.000000|1.000000 0.71417|0.71417 0.986000|0.986000 0.45419|0.45419 0.705000|0.705000 0.40729|0.40729 7.818000|7.818000 0.86416|0.86416 2.734000|2.734000 0.93682|0.93682 0.563000|0.563000 0.77884|0.77884 GCT|CGC TCGA-3A-A9I9-01A-11D-A38G-08 PUM1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000010671.1 1 0 0 11 201 0 103 0 7.459652e-01 0 50 0 103 2 0 0 0 0 0 2 1 0.998338 11 198 0 103 2 0 0 0 0 103 2 -3.074004 1 1 121412 1 35 1 0 1 1 1.742108 1 0.300000 1.870000 0.176471 0.290000 0.150000 0.480000 0.290000 0.310791 0.290000 0 2.100000e-01 3.900000e-01 THRAP3 9967 broad.mit.edu 37 1 36752630 36752630 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr1:36752630C>T ENST00000354618.5 + 4 1023 c.799C>T c.(799-801)Cct>Tct p.P267S THRAP3_ENST00000469141.2_Missense_Mutation_p.P267S NM_005119.3 NP_005110.2 Q9Y2W1 TR150_HUMAN thyroid hormone receptor associated protein 3 37 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) GTCACCCCGTCCTAGCCCCGT 0.617000 T USP6 aneurysmal bone cysts Pancreas(129;785 1795 20938 23278 32581) Dom yes 1 1p34.3 9967 thyroid hormone receptor associated protein 3 (TRAP150) M 0 SO:0001583 missense ENST00000354618.5 1 1 hg19 CCDS405.1 . . . . . . . . . . C 19.54 3.846324 0.71603 . . ENSG00000054118 ENST00000354618;ENST00000469141 T;T 0.12879 2.64;2.64 5.85 5.85 0.93711 . 0.000000 0.64402 D 0.000001 T 0.34454 0.0898 L 0.56769 1.78 0.54753 D 0.999988 D 0.89917 1.0 D 0.87578 0.998 T 0.00883 -1.1528 10 0.20046 T 0.44 -12.8835 19.1531 0.93496 0.0:1.0:0.0:0.0 . 267 Q9Y2W1 TR150_HUMAN S 267 ENSP00000346634:P267S;ENSP00000433825:P267S ENSP00000346634:P267S P + 1 0 THRAP3 36525217 0.987000 0.35691 1.000000 0.80357 0.998000 0.95712 3.482000 0.53186 2.753000 0.94483 0.655000 0.94253 CCT TCGA-3A-A9I9-01A-11D-A38G-08 THRAP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000021688.2 1 0 1 90 390 0 175 1 9.796036e-01 3 26 0 175 2 0 0 0 0 0 2 1 1.000000 89 383 0 170 2 0 0 0 0 175 2 -20.000000 1 1 0 0 1 1 2 3 2.084625 0 0.300000 1.870000 0.309324 0.990000 0.990000 1.000000 1.000000 0.999707 0.990000 1 9.900000e-01 1 THRAP3 9967 broad.mit.edu 37 1 36752631 36752631 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr1:36752631C>T ENST00000354618.5 + 4 1024 c.800C>T c.(799-801)cCt>cTt p.P267L THRAP3_ENST00000469141.2_Missense_Mutation_p.P267L NM_005119.3 NP_005110.2 Q9Y2W1 TR150_HUMAN thyroid hormone receptor associated protein 3 37 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) TCACCCCGTCCTAGCCCCGTG 0.617000 T USP6 aneurysmal bone cysts Pancreas(129;785 1795 20938 23278 32581) Dom yes 1 1p34.3 9967 thyroid hormone receptor associated protein 3 (TRAP150) M 0 SO:0001583 missense ENST00000354618.5 1 1 hg19 CCDS405.1 . . . . . . . . . . C 20.3 3.962964 0.74016 . . ENSG00000054118 ENST00000354618;ENST00000469141 T;T 0.12879 2.64;2.64 5.85 5.85 0.93711 . 0.000000 0.64402 D 0.000001 T 0.33876 0.0878 L 0.45581 1.43 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 T 0.00589 -1.1656 10 0.59425 D 0.04 -12.8835 19.1531 0.93496 0.0:1.0:0.0:0.0 . 267 Q9Y2W1 TR150_HUMAN L 267 ENSP00000346634:P267L;ENSP00000433825:P267L ENSP00000346634:P267L P + 2 0 THRAP3 36525218 0.987000 0.35691 1.000000 0.80357 0.998000 0.95712 3.482000 0.53186 2.753000 0.94483 0.655000 0.94253 CCT TCGA-3A-A9I9-01A-11D-A38G-08 THRAP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000021688.2 1 0 1 91 401 0 173 1 9.781006e-01 3 26 0 173 2 0 0 0 0 0 2 1 1.000000 90 394 0 168 2 0 0 0 0 173 2 -3.121901 1 1 0 0 1 1 2 3 2.084625 0 0.300000 1.870000 0.309324 0.990000 0.990000 1.000000 1.000000 0.999589 0.990000 1 9.900000e-01 1 BLCAP 10904 broad.mit.edu 37 20 36147320 36147320 + Missense_Mutation SNP C C G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr20:36147320C>G ENST00000373537.2 - 2 571 c.257G>C c.(256-258)gGc>gCc p.G86A BLCAP_ENST00000397131.1_Missense_Mutation_p.G86A|BLCAP_ENST00000397135.1_Missense_Mutation_p.G86A|BLCAP_ENST00000414542.2_Missense_Mutation_p.G86A|NNAT_ENST00000346199.2_5'Flank|BLCAP_ENST00000397137.1_Missense_Mutation_p.G86A|BLCAP_ENST00000397134.1_Missense_Mutation_p.G86A|NNAT_ENST00000062104.2_5'Flank NM_001167823.1|NM_006698.3 NP_001161295.1|NP_006689.1 P62952 BLCAP_HUMAN bladder cancer associated protein 5 Myeloproliferative disorder(115;0.00878) CCGTTAGGTGCCCACAACGCC 0.552000 0 SO:0001583 missense ENST00000373537.2 1 1 hg19 CCDS13295.1 . . . . . . . . . . C 20.8 4.050067 0.75846 . . ENSG00000166619 ENST00000373537;ENST00000397137;ENST00000414542;ENST00000397135;ENST00000397134;ENST00000397131;ENST00000432507 . . . 4.95 4.95 0.65309 . 0.000000 0.85682 D 0.000000 T 0.76870 0.4048 . . . 0.80722 D 1 D 0.67145 0.996 D 0.63033 0.91 T 0.80108 -0.1520 8 0.87932 D 0 . 15.7067 0.77588 0.0:1.0:0.0:0.0 . 86 P62952 BLCAP_HUMAN A 86 . ENSP00000362637:G86A G - 2 0 BLCAP 35580734 1.000000 0.71417 1.000000 0.80357 0.949000 0.60115 5.842000 0.69417 2.554000 0.86153 0.585000 0.79938 GGC TCGA-3A-A9I9-01A-11D-A38G-08 BLCAP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079113.2 1 0 1 39 243 0 109 1 9.998603e-01 19 67 0 109 2 0 0 0 0 0 2 1 1.000000 39 240 0 108 2 0 0 0 0 109 2 -3.320611 1 1 0 0 1 0 1 1 2.032123 0 0.300000 1.870000 0.297894 0.910000 0.670000 1.000000 1.000000 0.901667 0.910000 1 7.800000e-01 1 KCNK15 60598 broad.mit.edu 37 20 43374752 43374752 + Silent SNP C C A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr20:43374752C>A ENST00000372861.3 + 1 332 c.201C>A c.(199-201)ctC>ctA p.L67L RP11-445H22.4_ENST00000445420.1_RNA|RP11-445H22.4_ENST00000427303.1_RNA NM_022358.3 NP_071753.2 Q9H427 KCNKF_HUMAN potassium channel, subfamily K, member 15 10 Myeloproliferative disorder(115;0.0122) GCCTGGCGCTCCAGGCTGAGC 0.692000 0 SO:0001819 synonymous_variant ENST00000372861.3 1 1 hg19 CCDS13337.1 TCGA-3A-A9I9-01A-11D-A38G-08 KCNK15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079378.2 1 0 0 34 86 0 41 1 9.747446e-01 4 14 0 41 2 0 0 0 0 0 2 1 1.000000 33 86 0 41 2 0 0 0 0 41 2 -20.000000 1 1 0 0 1 1 2 3 2.305382 1 0.300000 1.870000 0.382444 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 DIDO1 11083 broad.mit.edu 37 20 61512310 61512310 + Silent SNP G G T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr20:61512310G>T ENST00000266070.4 - 16 5323 c.4998C>A c.(4996-4998)ggC>ggA p.G1666G DIDO1_ENST00000395343.1_Silent_p.G1666G NM_033081.2 NP_149072.2 Q9BTC0 DIDO1_HUMAN death inducer-obliterator 1 99 Breast(26;5.68e-08) GCTGCAGGGCGCCGCAAGGCG 0.726000 Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095) 0 SO:0001819 synonymous_variant ENST00000266070.4 1 1 hg19 CCDS33506.1 TCGA-3A-A9I9-01A-11D-A38G-08 DIDO1-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000080091.2 1 0 1 35 100 0 61 1 8.497495e-01 4 8 0 61 2 0 0 0 0 0 2 1 1.000000 34 99 0 61 2 0 0 0 0 61 2 -20.000000 1 1 0 0 1 1 2 3 2.305382 1 0.300000 1.870000 0.382444 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1 BRWD1 54014 broad.mit.edu 37 21 40571514 40571514 + Missense_Mutation SNP T T A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr21:40571514T>A ENST00000333229.2 - 40 5155 c.4828A>T c.(4828-4830)Aat>Tat p.N1610Y BRWD1_ENST00000342449.3_Missense_Mutation_p.N1610Y|BRWD1_ENST00000380800.3_Missense_Mutation_p.N1610Y NM_018963.4 NP_061836.2 Q9NSI6 BRWD1_HUMAN bromodomain and WD repeat domain containing 1 58 Prostate(19;8.44e-08)|all_epithelial(19;0.223) TCCAATGAATTGTTATCAGAA 0.373000 OREG0003861 type=REGULATORY REGION|Gene=BRWD1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay Melanoma(170;988 1986 4794 16843 39731) 0 SO:0001583 missense ENST00000333229.2 1 1 hg19 CCDS13662.1 . . . . . . . . . . T 17.94 3.510435 0.64522 . . ENSG00000185658 ENST00000333229;ENST00000342449;ENST00000380800 T;T;T 0.56103 0.48;0.52;0.6 5.19 4.01 0.46588 . 0.410373 0.22711 N 0.056578 T 0.59088 0.2168 M 0.64997 1.995 0.80722 D 1 P;P 0.49185 0.92;0.561 P;B 0.51135 0.66;0.128 T 0.60840 -0.7183 10 0.72032 D 0.01 -9.7638 11.0953 0.48141 0.0:0.0:0.1544:0.8456 . 1610;1610 Q9NSI6-2;Q9NSI6 .;BRWD1_HUMAN Y 1610 ENSP00000330753:N1610Y;ENSP00000344333:N1610Y;ENSP00000370178:N1610Y ENSP00000330753:N1610Y N - 1 0 BRWD1 39493384 1.000000 0.71417 0.928000 0.36995 0.993000 0.82548 1.889000 0.39718 0.783000 0.33636 0.460000 0.39030 AAT TCGA-3A-A9I9-01A-11D-A38G-08 BRWD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000141398.3 0 0 0 35 791 0 168 0 1.526921e-01 0 16 0 168 2 0 0 0 0 0 2 1 1.000000 36 775 0 167 2 0 0 0 0 168 2 -20.000000 1 1 0 0 1 1 4 5 2.681246 1 0.300000 1.870000 0.474869 0.390000 0.260000 1.000000 0.380000 0.499059 0.390000 0 3.200000e-01 1 KRTAP10-9 386676 broad.mit.edu 37 21 46047922 46047922 + Silent SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr21:46047922C>T ENST00000397911.3 + 1 883 c.834C>T c.(832-834)cgC>cgT p.R278R TSPEAR_ENST00000323084.4_Intron|KRTAP10-9_ENST00000484861.1_Intron NM_198690.2 NP_941963.2 P60411 KR109_HUMAN keratin associated protein 10-9 9 TGTGCTCCCGCCCGGCCTGCT 0.692000 0 SO:0001819 synonymous_variant ENST00000397911.3 1 1 hg19 CCDS42961.1 TCGA-3A-A9I9-01A-11D-A38G-08 KRTAP10-9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128040.1 1 0 1 70 338 0 241 0 0 0 0 241 2 0 0 0 0 0 2 1 1.000000 68 326 0 235 2 0 0 0 0 241 2 -3.257765 1 1 121344 1 32 1 0 1 1 1.684932 1 0.300000 1.870000 0.176471 0.910000 0.750000 1.000000 0.960000 0.907808 0.910000 1 8.300000e-01 9.800000e-01 CACNG2 10369 broad.mit.edu 37 22 36962506 36962506 + Silent SNP C C A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr22:36962506C>A ENST00000300105.6 - 3 1311 c.330G>T c.(328-330)ctG>ctT p.L110L NM_006078.3 NP_006069.1 Q9Y698 CCG2_HUMAN calcium channel, voltage-dependent, gamma subunit 2 18 GAATCACACTCAGGATTGGGA 0.552000 0 SO:0001819 synonymous_variant ENST00000300105.6 1 1 hg19 CCDS13931.1 TCGA-3A-A9I9-01A-11D-A38G-08 CACNG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000075500.2 1 0 1 41 233 0 140 0 0 0 0 140 2 0 0 0 0 0 2 1 1.000000 41 228 0 139 2 0 0 0 0 140 2 -3.326822 1 1 0 0 1 1 2 3 2.061585 0 0.300000 1.870000 0.305211 0.990000 0.740000 1.000000 1.000000 0.951366 0.990000 1 8.600000e-01 1 DPP10 57628 broad.mit.edu 37 2 116510788 116510788 + Missense_Mutation SNP C C A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:116510788C>A ENST00000410059.1 + 11 1469 c.989C>A c.(988-990)aCc>aAc p.T330N DPP10_ENST00000310323.8_Missense_Mutation_p.T323N|DPP10_ENST00000409163.1_Missense_Mutation_p.T280N|DPP10_ENST00000393147.2_Missense_Mutation_p.T334N NM_001178037.1|NM_020868.3 NP_001171508.1|NP_065919 Q8N608 DPP10_HUMAN dipeptidyl-peptidase 10 (non-functional) 101 GTAAGCAATACCAAGACTGTG 0.363000 0 SO:0001583 missense ENST00000410059.1 1 1 hg19 CCDS46400.1 . . . . . . . . . . C 21.7 4.190021 0.78789 . . ENSG00000175497 ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155 T;T;T;T 0.28454 1.61;1.61;1.61;1.61 5.1 5.1 0.69264 Peptidase S9B, dipeptidylpeptidase IV N-terminal (1); 0.000000 0.85682 D 0.000000 T 0.49270 0.1547 L 0.46614 1.455 0.80722 D 1 P;D;D;P 0.76494 0.883;0.999;0.963;0.904 P;D;P;P 0.85130 0.61;0.997;0.73;0.73 T 0.27773 -1.0064 10 0.33940 T 0.23 -11.7935 17.6852 0.88255 0.0:1.0:0.0:0.0 . 323;334;326;330 Q8N608-2;Q0GLB8;Q0GLB9;Q8N608 .;.;.;DPP10_HUMAN N 330;280;334;323;280 ENSP00000386565:T330N;ENSP00000387038:T280N;ENSP00000376855:T334N;ENSP00000309066:T323N ENSP00000309066:T323N T + 2 0 DPP10 116227258 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 7.299000 0.78831 2.660000 0.90430 0.650000 0.86243 ACC TCGA-3A-A9I9-01A-11D-A38G-08 DPP10-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000330580.4 1 0 1 37 257 0 61 0 0 0 1 0 61 2 0 0 0 0 0 2 1 1.000000 38 252 0 60 2 0 0 0 0 61 2 -20.000000 1 1 0 0 1 0 0 0 2.005415 0 0.300000 1.870000 0.287169 0.820000 0.590000 1.000000 1.000000 0.826766 0.820000 0 7.000000e-01 9.500000e-01 CCDC148 130940 broad.mit.edu 37 2 159077147 159077147 + Nonsense_Mutation SNP T T A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:159077147T>A ENST00000283233.5 - 11 1643 c.1330A>T c.(1330-1332)Aag>Tag p.K444* CCDC148-AS1_ENST00000412781.2_RNA|CCDC148_ENST00000409187.1_Nonsense_Mutation_p.K453* NM_138803.3 NP_620158.3 Q8NFR7 CC148_HUMAN coiled-coil domain containing 148 23 ATTAATTTCTTCAGTTCTTCT 0.328000 0 SO:0001587 stop_gained ENST00000283233.5 0 1 hg19 CCDS33304.1 . . . . . . . . . . T 38 7.213421 0.98139 . . ENSG00000153237 ENST00000283233;ENST00000409187 . . . 5.5 5.5 0.81552 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -19.6426 13.8506 0.63494 0.0:0.0:0.0:1.0 . . . . X 444;453 . ENSP00000283233:K444X K - 1 0 CCDC148 158785393 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 4.843000 0.62838 2.203000 0.70933 0.460000 0.39030 AAG TCGA-3A-A9I9-01A-11D-A38G-08 CCDC148-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000333270.1 1 0 1 41 317 0 69 0 7.013909e-02 1 3 0 69 2 0 0 0 0 0 2 1 1.000000 41 307 0 67 2 0 0 0 0 69 2 -20.000000 1 1 0 0 1 0 0 0 2.005415 0 0.300000 1.870000 0.287169 0.740000 0.550000 0.970000 0.750000 0.757564 0.740000 0 6.400000e-01 8.600000e-01 TTN 7273 broad.mit.edu 37 2 179456474 179456474 + Missense_Mutation SNP C C G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:179456474C>G ENST00000591111.1 - 253 55373 c.55149G>C c.(55147-55149)tgG>tgC p.W18383C TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.W17456C|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.W10959C|TTN_ENST00000589042.1_Missense_Mutation_p.W20024C|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.W11151C|TTN_ENST00000359218.5_Missense_Mutation_p.W11084C|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TAAATTTAATCCAGTCCTGGG 0.423000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . C 15.41 2.824565 0.50739 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.56776 0.44;0.44;0.44;0.44 6.16 6.16 0.99307 Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . D 0.85440 0.5697 H 0.98754 4.32 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.999;0.999;0.999;0.999 D 0.90151 0.4221 9 0.87932 D 0 . 20.8598 0.99761 0.0:1.0:0.0:0.0 . 10959;11084;11151;18383 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN C 17456;10959;11151;11084;10957 ENSP00000343764:W17456C;ENSP00000434586:W10959C;ENSP00000340554:W11151C;ENSP00000352154:W11084C ENSP00000340554:W11151C W - 3 0 TTN 179164720 1.000000 0.71417 1.000000 0.80357 0.827000 0.46813 7.770000 0.85390 2.937000 0.99478 0.650000 0.86243 TGG TCGA-3A-A9I9-01A-11D-A38G-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 0 0 0 11 484 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 0.998272 12 478 0 57 2 0 0 0 0 58 2 -3.060826 1 1 0 0 1 0 0 0 2.005415 0 0.300000 1.870000 0.287169 0.140000 0.070000 0.250000 0.150000 0.157273 0.140000 0 1.000000e-01 2.000000e-01 TTN 7273 broad.mit.edu 37 2 179638079 179638079 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:179638079C>T ENST00000591111.1 - 33 7836 c.7612G>A c.(7612-7614)Ggt>Agt p.G2538S TTN_ENST00000360870.5_Missense_Mutation_p.G2538S|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G2538S|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.G2492S|TTN_ENST00000589042.1_Missense_Mutation_p.G2538S|TTN_ENST00000342175.6_Missense_Mutation_p.G2492S|TTN_ENST00000359218.5_Missense_Mutation_p.G2492S|TTN-AS1_ENST00000584485.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCACGAAGACCTCTGATAATT 0.353000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . C 13.09 2.134330 0.37630 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870 T;T;T;T;T 0.65916 -0.18;-0.18;-0.18;-0.18;-0.18 5.82 5.82 0.92795 Immunoglobulin I-set (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.75079 0.3801 L 0.42581 1.335 0.28955 N 0.890175 D;D;D;D;D 0.76494 0.978;0.978;0.978;0.989;0.999 P;P;P;P;D 0.69479 0.871;0.871;0.871;0.871;0.964 T 0.70737 -0.4790 9 0.87932 D 0 . 20.1143 0.97922 0.0:1.0:0.0:0.0 . 2492;2492;2492;2538;2538 D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6 .;.;.;TITIN_HUMAN;. S 2538;2492;2492;2492;2492;2538 ENSP00000343764:G2538S;ENSP00000434586:G2492S;ENSP00000340554:G2492S;ENSP00000352154:G2492S;ENSP00000354117:G2538S ENSP00000340554:G2492S G - 1 0 TTN 179346324 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 4.965000 0.63708 2.765000 0.95021 0.650000 0.86243 GGT TCGA-3A-A9I9-01A-11D-A38G-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 1 52 279 0 72 0 0 0 0 72 2 0 0 0 0 0 2 1 1.000000 52 273 0 72 2 0 0 0 0 72 2 -3.233193 1 1 0 0 1 1 2 3 2.071217 0 0.300000 1.870000 0.326275 0.990000 0.840000 1.000000 1.000000 0.984592 0.990000 1 9.700000e-01 1 ITGA4 3676 broad.mit.edu 37 2 182347132 182347132 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:182347132G>C ENST00000397033.2 + 8 1316 c.886G>C c.(886-888)Gaa>Caa p.E296Q NM_000885.4 NP_000876.3 P13612 ITA4_HUMAN integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor) 58 OV - Ovarian serous cystadenocarcinoma(117;0.0593) Natalizumab(DB00108)|Tinzaparin(DB06822) TATCTTACATGAAATGAAAGG 0.308000 0 SO:0001583 missense ENST00000397033.2 1 1 hg19 CCDS42788.1 . . . . . . . . . . G 14.29 2.490462 0.44249 . . ENSG00000115232 ENST00000425522;ENST00000397033;ENST00000233573 T;T 0.14516 2.5;2.5 5.92 5.92 0.95590 . 0.000000 0.85682 D 0.000000 T 0.19805 0.0476 L 0.37697 1.125 0.52501 D 0.999957 B;D 0.54772 0.22;0.968 B;P 0.51016 0.109;0.656 T 0.02020 -1.1228 10 0.13108 T 0.6 . 20.327 0.98704 0.0:0.0:1.0:0.0 . 296;296 E7EP60;P13612 .;ITA4_HUMAN Q 296 ENSP00000380227:E296Q;ENSP00000233573:E296Q ENSP00000233573:E296Q E + 1 0 ITGA4 182055377 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 5.846000 0.69444 2.794000 0.96219 0.650000 0.86243 GAA TCGA-3A-A9I9-01A-11D-A38G-08 ITGA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000334427.1 1 0 0 18 396 0 64 0 6.351562e-03 0 3 0 64 2 0 0 0 0 0 2 1 0.999981 18 391 0 63 2 0 0 0 0 64 2 -4.641127 1 1 0 0 1 1 2 3 2.071217 0 0.300000 1.870000 0.326275 0.320000 0.180000 1.000000 0.300000 0.441090 0.320000 0 2.400000e-01 1 SLC11A1 6556 broad.mit.edu 37 2 219251895 219251895 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:219251895G>C ENST00000233202.6 + 6 853 c.513G>C c.(511-513)tgG>tgC p.W171C SLC11A1_ENST00000539932.1_Missense_Mutation_p.W53C NM_000578.3 NP_000569.3 P49279 NRAM1_HUMAN solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1 19 Renal(207;0.0474) TCCCACTCTGGGGTGGCGTCC 0.602000 0 SO:0001583 missense ENST00000233202.6 1 1 hg19 CCDS2415.1 . . . . . . . . . . G 19.64 3.866221 0.71949 . . ENSG00000018280 ENST00000233202;ENST00000539932 T;T 0.70516 -0.49;-0.49 5.18 5.18 0.71444 . 0.000000 0.85682 D 0.000000 D 0.88544 0.6465 M 0.93328 3.405 0.80722 D 1 D;D;D 0.89917 0.999;1.0;1.0 D;D;D 0.81914 0.971;0.995;0.995 D 0.91207 0.4996 10 0.87932 D 0 -12.7329 18.8984 0.92433 0.0:0.0:1.0:0.0 . 171;53;171 B4DQ73;C0H5Y3;P49279 .;.;NRAM1_HUMAN C 171;53 ENSP00000233202:W171C;ENSP00000443435:W53C ENSP00000233202:W171C W + 3 0 SLC11A1 218960139 1.000000 0.71417 1.000000 0.80357 0.752000 0.42762 6.007000 0.70731 2.694000 0.91930 0.655000 0.94253 TGG TCGA-3A-A9I9-01A-11D-A38G-08 SLC11A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195076.2 1 0 1 31 230 0 125 0 9.257395e-01 0 35 0 125 2 0 0 0 0 0 2 1 1.000000 31 228 0 125 2 0 0 0 0 125 2 -2.559266 1 1 121412 1 33 1 1 2 3 2.071217 0 0.300000 1.870000 0.326275 0.860000 0.580000 1.000000 1.000000 0.858611 0.860000 1 7.100000e-01 1 SLC11A1 6556 broad.mit.edu 37 2 219251897 219251897 + Missense_Mutation SNP G G T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:219251897G>T ENST00000233202.6 + 6 855 c.515G>T c.(514-516)gGt>gTt p.G172V SLC11A1_ENST00000539932.1_Missense_Mutation_p.G54V NM_000578.3 NP_000569.3 P49279 NRAM1_HUMAN solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1 19 Renal(207;0.0474) CCACTCTGGGGTGGCGTCCTC 0.602000 0 SO:0001583 missense ENST00000233202.6 1 1 hg19 CCDS2415.1 . . . . . . . . . . G 15.21 2.765423 0.49574 . . ENSG00000018280 ENST00000233202;ENST00000539932 T;T 0.66280 -0.2;-0.2 5.18 4.29 0.51040 . 0.066829 0.64402 D 0.000008 T 0.62307 0.2417 L 0.35341 1.055 0.80722 D 1 B;B;B 0.33739 0.016;0.422;0.422 B;P;B 0.46452 0.017;0.517;0.363 T 0.62774 -0.6783 10 0.41790 T 0.15 -6.105 14.3044 0.66375 0.0723:0.0:0.9277:0.0 . 172;54;172 B4DQ73;C0H5Y3;P49279 .;.;NRAM1_HUMAN V 172;54 ENSP00000233202:G172V;ENSP00000443435:G54V ENSP00000233202:G172V G + 2 0 SLC11A1 218960141 0.998000 0.40836 0.883000 0.34634 0.757000 0.42996 2.602000 0.46257 1.380000 0.46344 0.655000 0.94253 GGT TCGA-3A-A9I9-01A-11D-A38G-08 SLC11A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195076.2 1 0 1 30 235 0 131 0 8.945898e-01 0 33 0 131 2 0 0 0 0 0 2 1 1.000000 30 234 0 131 2 0 0 0 0 131 2 -12.816680 1 1 0 0 1 1 2 3 2.071217 0 0.300000 1.870000 0.326275 0.820000 0.550000 1.000000 1.000000 0.830988 0.820000 0 6.700000e-01 1 CRYBA2 1412 broad.mit.edu 37 2 219856841 219856841 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:219856841G>A ENST00000295728.2 - 2 522 c.286C>T c.(286-288)Cgg>Tgg p.R96W CRYBA2_ENST00000392096.2_Missense_Mutation_p.R96W|CRYBA2_ENST00000487181.1_5'Flank NM_057093.1 NP_476434.1 P53672 CRBA2_HUMAN crystallin, beta A2 5 Renal(207;0.0474) AGCACTGGCCGGAAGGACAGC 0.622000 0 SO:0001583 missense ENST00000295728.2 0 1 hg19 CCDS2429.1 . . . . . . . . . . G 17.09 3.299333 0.60195 . . ENSG00000163499 ENST00000392096;ENST00000295728;ENST00000453769 D;D;D 0.83163 -1.69;-1.69;-1.69 4.65 1.67 0.24075 Beta/gamma crystallin (4);Gamma-crystallin-related (1); 0.109256 0.56097 D 0.000022 D 0.92903 0.7742 M 0.94142 3.5 0.49798 D 0.999823 D 0.89917 1.0 D 0.87578 0.998 D 0.93478 0.6825 10 0.87932 D 0 . 14.747 0.69496 0.0:0.0:0.6235:0.3765 . 96 P53672 CRBA2_HUMAN W 96 ENSP00000375946:R96W;ENSP00000295728:R96W;ENSP00000395120:R96W ENSP00000295728:R96W R - 1 2 CRYBA2 219565085 1.000000 0.71417 0.998000 0.56505 0.987000 0.75469 1.688000 0.37690 -0.008000 0.14320 -0.808000 0.03180 CGG TCGA-3A-A9I9-01A-11D-A38G-08 CRYBA2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336424.1 0 0 0 4 137 0 75 0 1.604477e-01 0 20 0 75 2 0 0 0 0 0 2 1 0.882796 4 132 0 73 2 0 0 0 0 75 2 -6.352010 1 1 121396 14 37 1 1 2 3 2.071217 0 0.300000 1.870000 0.326275 0.240000 0.070000 1.000000 0.200000 0.379000 0.240000 0 1.400000e-01 1 CHPF 79586 broad.mit.edu 37 2 220406647 220406647 + Missense_Mutation SNP G G T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:220406647G>T ENST00000243776.6 - 2 827 c.579C>A c.(577-579)gaC>gaA p.D193E CHPF_ENST00000373891.2_Missense_Mutation_p.D193E|TMEM198_ENST00000373883.3_5'Flank|TMEM198_ENST00000344458.2_5'Flank|CHPF_ENST00000535926.1_Missense_Mutation_p.D31E NM_024536.5 NP_078812 Q8IZ52 CHSS2_HUMAN chondroitin polymerizing factor 21 Renal(207;0.0183) GGAAGAACCAGTCAAAGTCGT 0.672000 OREG0015229 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000243776.6 0 1 hg19 CCDS2443.1 . . . . . . . . . . G 22.5 4.294157 0.81025 . . ENSG00000123989 ENST00000243776;ENST00000535926;ENST00000373891 T;T 0.19394 2.15;2.44 4.41 1.63 0.23807 . 0.000000 0.85682 D 0.000000 T 0.33235 0.0856 L 0.49571 1.57 0.58432 D 0.999999 D;D 0.76494 0.999;0.999 D;D 0.91635 0.994;0.999 T 0.02603 -1.1135 10 0.23302 T 0.38 -31.7198 9.132 0.36850 0.2372:0.0:0.7628:0.0 . 193;193 F8W6H2;Q8IZ52 .;CHSS2_HUMAN E 193;31;193 ENSP00000243776:D193E;ENSP00000445571:D31E ENSP00000243776:D193E D - 3 2 CHPF 220114891 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.600000 0.61083 0.242000 0.21303 0.549000 0.68633 GAC TCGA-3A-A9I9-01A-11D-A38G-08 CHPF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000130268.1 0 0 0 4 87 0 53 1 9.687469e-01 9 142 0 53 2 0 0 0 0 0 2 1 0.889366 4 86 0 53 2 0 0 0 0 53 2 -7.811913 1 1 0 0 1 1 2 3 2.071217 0 0.300000 1.870000 0.326275 0.380000 0.120000 1.000000 0.310000 0.481176 0.380000 0 2.200000e-01 1 COL4A4 1286 broad.mit.edu 37 2 227875104 227875104 + Missense_Mutation SNP C C A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:227875104C>A ENST00000396625.3 - 46 4654 c.4447G>T c.(4447-4449)Ggc>Tgc p.G1483C COL4A4_ENST00000329662.7_Missense_Mutation_p.G1480C NM_000092.4 NP_000083.3 P53420 CO4A4_HUMAN collagen, type IV, alpha 4 98 Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242) CTGGGCATGCCCAGGGGGCAG 0.577000 0 SO:0001583 missense ENST00000396625.3 1 1 hg19 CCDS42828.1 . . . . . . . . . . C 17.39 3.378418 0.61735 . . ENSG00000081052 ENST00000396625;ENST00000329662 D;D 0.95412 -3.7;-3.7 5.69 4.82 0.62117 C-type lectin fold (1); . . . . D 0.98476 0.9492 H 0.96720 3.87 0.80722 D 1 D 0.89917 1.0 D 0.77557 0.99 D 0.99433 1.0936 9 0.87932 D 0 . 14.6375 0.68699 0.0:0.9302:0.0:0.0698 . 1483 P53420 CO4A4_HUMAN C 1483;1480 ENSP00000379866:G1483C;ENSP00000328553:G1480C ENSP00000328553:G1480C G - 1 0 COL4A4 227583348 1.000000 0.71417 0.985000 0.45067 0.807000 0.45602 7.745000 0.85046 1.418000 0.47098 -0.136000 0.14681 GGC TCGA-3A-A9I9-01A-11D-A38G-08 COL4A4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000313770.1 1 0 1 45 290 0 115 0 0 0 0 115 2 0 0 0 0 0 2 1 1.000000 45 281 0 113 2 0 0 0 0 115 2 -19.722120 1 1 0 0 1 1 2 3 2.071217 0 0.300000 1.870000 0.326275 0.960000 0.700000 1.000000 1.000000 0.928347 0.960000 1 8.200000e-01 1 THAP4 51078 broad.mit.edu 37 2 242572368 242572368 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:242572368C>T ENST00000407315.1 - 2 1635 c.1204G>A c.(1204-1206)Gtc>Atc p.V402I NM_015963.5 NP_057047.4 Q8WY91 THAP4_HUMAN THAP domain containing 4 9 all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2) GGATAGGGGACGCTCACTCTC 0.627000 0 SO:0001583 missense ENST00000407315.1 1 1 hg19 CCDS2551.1 . . . . . . . . . . C 2.394 -0.339085 0.05243 . . ENSG00000176946 ENST00000407315;ENST00000512346 D 0.95554 -3.74 5.22 -10.4 0.00318 . . . . . T 0.81064 0.4745 N 0.03608 -0.345 0.24018 N 0.996156 B 0.02656 0.0 B 0.01281 0.0 T 0.71431 -0.4595 9 0.21540 T 0.41 -1.1688 1.6018 0.02675 0.138:0.3253:0.2302:0.3065 . 402 Q8WY91 THAP4_HUMAN I 402;77 ENSP00000385006:V402I ENSP00000385006:V402I V - 1 0 THAP4 242221041 0.234000 0.23783 0.000000 0.03702 0.462000 0.32619 -0.598000 0.05706 -3.708000 0.00117 -2.089000 0.00373 GTC TCGA-3A-A9I9-01A-11D-A38G-08 THAP4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257267.3 1 0 0 6 91 0 55 1 9.592442e-01 10 81 0 55 2 0 0 0 0 0 2 1 0.966557 6 91 0 55 2 0 0 0 0 55 2 -10.262600 1 1 121408 2 27 1 1 2 3 2.071217 0 0.300000 1.870000 0.326275 0.500000 0.200000 1.000000 0.430000 0.574896 0.500000 0 3.200000e-01 1 TMEM214 54867 broad.mit.edu 37 2 27261588 27261588 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:27261588G>C ENST00000238788.9 + 12 1374 c.1312G>C c.(1312-1314)Gaa>Caa p.E438Q TMEM214_ENST00000404032.3_Missense_Mutation_p.E393Q NM_017727.4 NP_060197.4 Q6NUQ4 TM214_HUMAN transmembrane protein 214 18 GTCTTTGCAAGAAACCATTCA 0.512000 0 SO:0001583 missense ENST00000238788.9 0 1 hg19 CCDS42664.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 22.1|22.1 4.239182|4.239182 0.79800|0.79800 .|. .|. ENSG00000119777|ENSG00000119777 ENST00000238788;ENST00000404032;ENST00000537397;ENST00000444135|ENST00000425720 T;T;T|. 0.46819|. 0.86;0.86;0.86|. 5.69|5.69 5.69|5.69 0.88448|0.88448 .|. 0.088644|. 0.85682|. D|. 0.000000|. T|T 0.74718|0.74718 0.3753|0.3753 M|M 0.71581|0.71581 2.175|2.175 0.58432|0.58432 D|D 0.999999|0.999999 D;D|. 0.67145|. 0.996;0.985|. P;D|. 0.63113|. 0.902;0.911|. T|T 0.73613|0.73613 -0.3927|-0.3927 10|5 0.40728|. T|. 0.16|. -12.2017|-12.2017 16.735|16.735 0.85444|0.85444 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 393;438|. Q6NUQ4-2;Q6NUQ4|. .;TM214_HUMAN|. Q|N 438;393;178;98|222 ENSP00000238788:E438Q;ENSP00000384417:E393Q;ENSP00000392442:E98Q|. ENSP00000238788:E438Q|. E|K +|+ 1|3 0|2 TMEM214|TMEM214 27115092|27115092 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.994000|0.994000 0.84299|0.84299 7.607000|7.607000 0.82883|0.82883 2.700000|2.700000 0.92200|0.92200 0.561000|0.561000 0.74099|0.74099 GAA|AAG TCGA-3A-A9I9-01A-11D-A38G-08 TMEM214-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324748.1 0 0 0 9 99 0 71 1 9.816753e-01 8 73 0 71 2 0 0 0 0 0 2 1 0.994403 9 97 0 69 2 0 0 0 0 71 2 -14.358330 1 1 0 0 1 0 1 1 1.715785 1 0.300000 1.870000 0.176471 0.470000 0.230000 0.780000 0.450000 0.492032 0.470000 0 3.400000e-01 6.300000e-01 PRKD3 23683 broad.mit.edu 37 2 37520399 37520399 + Missense_Mutation SNP A A C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:37520399A>C ENST00000379066.1 - 3 1066 c.304T>G c.(304-306)Ttc>Gtc p.F102V PRKD3_ENST00000234179.2_Missense_Mutation_p.F102V O94806 KPCD3_HUMAN protein kinase D3 33 all_hematologic(82;0.21) ATGCCAAAGAATCCACACTCT 0.333000 Melanoma(80;621 1355 8613 11814 51767) 0 SO:0001583 missense ENST00000379066.1 0 1 hg19 CCDS1789.1 . . . . . . . . . . A 22.2 4.260900 0.80246 . . ENSG00000115825 ENST00000379066;ENST00000234179 T;T 0.65549 -0.16;-0.16 5.32 4.13 0.48395 . 0.056727 0.64402 N 0.000001 T 0.62986 0.2473 L 0.47716 1.5 0.58432 D 0.999999 P;B 0.36633 0.562;0.427 P;B 0.45794 0.493;0.235 T 0.62553 -0.6830 10 0.49607 T 0.09 -12.2843 12.4041 0.55430 0.8592:0.1408:0.0:0.0 . 102;102 O94806-2;O94806 .;KPCD3_HUMAN V 102 ENSP00000368356:F102V;ENSP00000234179:F102V ENSP00000234179:F102V F - 1 0 PRKD3 37373903 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 9.287000 0.95975 0.914000 0.36822 0.533000 0.62120 TTC TCGA-3A-A9I9-01A-11D-A38G-08 PRKD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000218570.3 0 0 0 9 462 0 190 0 1.241830e-02 0 8 0 190 2 0 0 0 0 0 2 1 0.993406 8 448 0 186 2 0 0 0 0 190 2 -8.380415 1 1 0 0 1 0 1 1 1.726450 1 0.300000 1.870000 0.176471 0.100000 0.050000 0.190000 0.110000 0.118611 0.100000 0 7.000000e-02 1.500000e-01 SOCS5 9655 broad.mit.edu 37 2 46987120 46987120 + Missense_Mutation SNP T T C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:46987120T>C ENST00000306503.5 + 2 1623 c.1451T>C c.(1450-1452)cTg>cCg p.L484P SOCS5_ENST00000394861.2_Missense_Mutation_p.L484P NM_014011.4 NP_054730.1 O75159 SOCS5_HUMAN suppressor of cytokine signaling 5 22 all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175) LUSC - Lung squamous cell carcinoma(58;0.114) CCTTTTAGCCTGCAGTATATC 0.398000 0 SO:0001583 missense ENST00000306503.5 1 1 hg19 CCDS1830.1 . . . . . . . . . . T 18.08 3.543224 0.65198 . . ENSG00000171150 ENST00000306503;ENST00000394861 D;D 0.94497 -3.44;-3.44 5.43 5.43 0.79202 SOCS protein, C-terminal (4);SH2 motif (1); 0.000000 0.64402 D 0.000001 D 0.98229 0.9414 H 0.97023 3.925 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.99597 1.0977 10 0.87932 D 0 -13.9042 15.3001 0.73940 0.0:0.0:0.0:1.0 . 484 O75159 SOCS5_HUMAN P 484 ENSP00000305133:L484P;ENSP00000378330:L484P ENSP00000305133:L484P L + 2 0 SOCS5 46840624 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.868000 0.87116 2.279000 0.76181 0.533000 0.62120 CTG TCGA-3A-A9I9-01A-11D-A38G-08 SOCS5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250791.2 1 0 1 95 381 0 138 1 6.760566e-01 2 9 0 138 2 0 0 0 0 0 2 1 1.000000 91 376 0 138 2 0 0 0 0 138 2 -20.000000 1 1 0 0 1 0 1 1 1.726450 1 0.300000 1.870000 0.176471 0.960000 0.850000 1.000000 0.990000 0.958236 0.960000 1 9.100000e-01 9.900000e-01 SMEK2 57223 broad.mit.edu 37 2 55795477 55795477 + Silent SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr2:55795477C>T ENST00000345102.5 - 13 2089 c.1788G>A c.(1786-1788)cgG>cgA p.R596R SMEK2_ENST00000272313.5_Silent_p.R511R|SMEK2_ENST00000407823.3_Silent_p.R564R|SNORA12_ENST00000390873.1_RNA NM_001122964.1 NP_001116436 Q5MIZ7 P4R3B_HUMAN SMEK homolog 2, suppressor of mek1 (Dictyostelium) 16 LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132) GTCCAATTATCCGCCTCATAA 0.313000 0 SO:0001819 synonymous_variant ENST00000345102.5 1 1 hg19 CCDS46289.1 TCGA-3A-A9I9-01A-11D-A38G-08 SMEK2-002 NOVEL basic|CCDS protein_coding protein_coding OTTHUMT00000251483.1 1 0 1 57 285 0 96 1 9.949058e-01 6 37 0 96 2 0 0 0 0 0 2 1 1.000000 56 281 0 95 2 0 0 0 0 96 2 -3.250900 1 1 0 0 1 0 1 1 1.726450 1 0.300000 1.870000 0.176471 0.890000 0.710000 1.000000 0.930000 0.887821 0.890000 1 8.000000e-01 9.700000e-01 SIDT1 54847 broad.mit.edu 37 3 113320452 113320452 + Missense_Mutation SNP G G C rs138220562 TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr3:113320452G>C ENST00000264852.4 + 11 1789 c.1063G>C c.(1063-1065)Gca>Cca p.A355P SIDT1_ENST00000393830.3_Missense_Mutation_p.A355P NM_017699.2 NP_060169.2 Q9NXL6 SIDT1_HUMAN SID1 transmembrane family, member 1 50 AAATATGGTGGCATCTCATCC 0.413000 0 SO:0001583 missense ENST00000264852.4 1 1 hg19 CCDS2974.1 . . . . . . . . . . G 4.852 0.158347 0.09236 . . ENSG00000072858 ENST00000264852;ENST00000393830 T;T 0.23348 1.91;1.91 6.17 4.37 0.52481 . 0.722817 0.12743 N 0.442876 T 0.21468 0.0517 L 0.40543 1.245 0.09310 N 1 B;B 0.06786 0.001;0.001 B;B 0.09377 0.003;0.004 T 0.11591 -1.0581 10 0.33940 T 0.23 -4.7062 9.7877 0.40686 0.0667:0.0:0.6671:0.2661 . 355;355 Q9NXL6-2;Q9NXL6 .;SIDT1_HUMAN P 355 ENSP00000264852:A355P;ENSP00000377416:A355P ENSP00000264852:A355P A + 1 0 SIDT1 114803142 0.002000 0.14202 0.038000 0.18304 0.115000 0.19883 1.111000 0.31159 1.607000 0.50170 -0.181000 0.13052 GCA TCGA-3A-A9I9-01A-11D-A38G-08 SIDT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317564.1 1 0 0 10 223 0 61 0 0 0 1 0 61 2 0 0 0 0 0 2 1 0.996932 10 221 0 60 2 0 0 0 0 61 2 -4.333398 1 1 0 0 1 1 2 3 2.050663 0 0.300000 1.870000 0.302094 0.290000 0.150000 0.540000 0.290000 0.316662 0.290000 0 2.100000e-01 4.000000e-01 GRAMD1C 54762 broad.mit.edu 37 3 113595066 113595066 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr3:113595066C>T ENST00000358160.4 + 5 910 c.418C>T c.(418-420)Ctc>Ttc p.L140F GRAMD1C_ENST00000479212.1_3'UTR|GRAMD1C_ENST00000452134.2_5'UTR NM_017577.4 NP_060047.3 Q8IYS0 GRM1C_HUMAN GRAM domain containing 1C 26 AACTGCTCGACTCATCCCAAA 0.303000 0 SO:0001583 missense ENST00000358160.4 1 1 hg19 CCDS33826.1 1 4.578754578754579E-4 0 0.0 1 0.0027624309392265192 0 0.0 0 0.0 C 16.99 3.273860 0.59649 4.54E-4 0.0 ENSG00000178075 ENST00000358160 T 0.37584 1.19 5.2 4.33 0.51752 . 0.154190 0.40728 N 0.001026 T 0.39682 0.1087 M 0.79123 2.44 0.80722 D 1 B 0.25521 0.128 B 0.19666 0.026 T 0.37888 -0.9686 10 0.59425 D 0.04 . 11.6383 0.51217 0.0:0.9126:0.0:0.0874 . 140 Q8IYS0 GRM1C_HUMAN F 140 ENSP00000350881:L140F ENSP00000350881:L140F L + 1 0 GRAMD1C 115077756 0.996000 0.38824 1.000000 0.80357 0.997000 0.91878 2.219000 0.42899 1.331000 0.45412 0.655000 0.94253 CTC TCGA-3A-A9I9-01A-11D-A38G-08 GRAMD1C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354733.1 1 0 1 80 441 0 176 0 0 0 1 0 176 2 0 0 0 0 0 2 1 1.000000 79 428 0 175 2 0 0 0 0 176 2 -20.000000 1 1 121412 16 47 1 1 2 3 2.050663 0 0.300000 1.870000 0.302094 0.990000 0.820000 1.000000 1.000000 0.972261 0.990000 1 9.200000e-01 1 ARHGAP31 57514 broad.mit.edu 37 3 119121031 119121031 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr3:119121031C>T ENST00000264245.4 + 10 1964 c.1432C>T c.(1432-1434)Cgt>Tgt p.R478C NM_020754.2 NP_065805.2 Q2M1Z3 RHG31_HUMAN Rho GTPase activating protein 31 67 GCCCTCGCCGCGTAACCAGCG 0.587000 Pancreas(7;176 297 5394 51128 51241) 0 SO:0001583 missense ENST00000264245.4 1 1 hg19 CCDS43135.1 . . . . . . . . . . C 22.1 4.250570 0.80135 . . ENSG00000031081 ENST00000264245;ENST00000543280 T 0.12879 2.64 5.33 5.33 0.75918 . 0.000000 0.64402 D 0.000002 T 0.26882 0.0658 M 0.66939 2.045 0.80722 D 1 D 0.76494 0.999 P 0.53185 0.72 T 0.00544 -1.1679 10 0.87932 D 0 . 13.1802 0.59649 0.1592:0.8408:0.0:0.0 . 478 Q2M1Z3 RHG31_HUMAN C 478 ENSP00000264245:R478C ENSP00000264245:R478C R + 1 0 ARHGAP31 120603721 0.997000 0.39634 0.444000 0.26895 0.924000 0.55760 3.505000 0.53356 2.774000 0.95407 0.655000 0.94253 CGT TCGA-3A-A9I9-01A-11D-A38G-08 ARHGAP31-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354942.2 1 0 1 65 375 0 198 0 3.974105e-01 1 8 0 198 2 0 0 0 0 0 2 1 1.000000 64 367 0 197 2 0 0 0 0 198 2 -20.000000 1 1 121016 3 41 1 1 2 3 2.050663 0 0.300000 1.870000 0.302094 0.980000 0.770000 1.000000 1.000000 0.951941 0.980000 1 8.700000e-01 1 ZFYVE20 64145 broad.mit.edu 37 3 15116060 15116060 + Silent SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr3:15116060C>T ENST00000253699.3 - 14 2197 c.1584G>A c.(1582-1584)cgG>cgA p.R528R ZFYVE20_ENST00000476527.2_Silent_p.R528R NM_022340.2 NP_071735.2 Q9H1K0 RBNS5_HUMAN zinc finger, FYVE domain containing 20 26 GTTCCAACTCCCGTTCACGCA 0.597000 0 SO:0001819 synonymous_variant ENST00000253699.3 1 1 hg19 CCDS2623.1 TCGA-3A-A9I9-01A-11D-A38G-08 ZFYVE20-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252102.2 1 0 1 121 364 0 210 1 8.699429e-01 5 8 0 210 2 0 0 0 0 0 2 1 1.000000 120 353 0 207 2 0 0 0 0 210 2 -20.000000 1 1 0 0 1 1 2 3 2.361890 1 0.300000 1.870000 0.391304 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 DHX36 170506 broad.mit.edu 37 3 154032888 154032888 + Missense_Mutation SNP A A C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr3:154032888A>C ENST00000496811.1 - 3 630 c.550T>G c.(550-552)Tta>Gta p.L184V DHX36_ENST00000308361.6_Missense_Mutation_p.L184V|DHX36_ENST00000329463.5_Missense_Mutation_p.L184V|DHX36_ENST00000544526.1_Missense_Mutation_p.L184V NM_020865.2 NP_065916.2 Q9H2U1 DHX36_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 36 35 LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173) TCTTCCAATAATTTTTGGTCT 0.289000 0 SO:0001583 missense ENST00000496811.1 1 1 hg19 CCDS3171.1 . . . . . . . . . . A 12.16 1.854682 0.32791 . . ENSG00000174953 ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941 T;T;T;T;T 0.10192 2.9;2.9;2.9;2.9;2.9 5.64 2.36 0.29203 . 0.000000 0.64402 D 0.000001 T 0.08537 0.0212 L 0.36672 1.1 0.46774 D 0.999197 P;P;B 0.41313 0.573;0.745;0.251 B;B;B 0.37550 0.18;0.253;0.095 T 0.18116 -1.0347 10 0.51188 T 0.08 . 9.201 0.37258 0.2292:0.0:0.7708:0.0 . 184;184;184 Q9H2U1-2;Q9H2U1-3;Q9H2U1 .;.;DHX36_HUMAN V 184;184;184;184;98 ENSP00000417078:L184V;ENSP00000309296:L184V;ENSP00000444247:L184V;ENSP00000330113:L184V;ENSP00000419862:L98V ENSP00000309296:L184V L - 1 2 DHX36 155515582 0.980000 0.34600 0.395000 0.26283 0.968000 0.65278 1.368000 0.34216 0.114000 0.18032 0.472000 0.43445 TTA TCGA-3A-A9I9-01A-11D-A38G-08 DHX36-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353349.1 1 0 1 57 295 0 76 1 5.032503e-01 2 8 0 76 2 0 0 0 0 0 2 1 1.000000 55 288 0 73 2 0 0 0 0 76 2 -20.000000 1 1 0 0 1 1 2 3 2.050663 0 0.300000 1.870000 0.302094 0.990000 0.840000 1.000000 1.000000 0.981715 0.990000 1 9.500000e-01 1 GHSR 2693 broad.mit.edu 37 3 172165640 172165640 + Silent SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr3:172165640G>A ENST00000241256.2 - 1 606 c.564C>T c.(562-564)aaC>aaT p.N188N GHSR_ENST00000427970.1_Silent_p.N188N NM_198407.2 NP_940799.1 Q92847 GHSR_HUMAN growth hormone secretagogue receptor 33 Ovarian(172;0.00143)|Breast(254;0.197) Lung(28;3.93e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235) GGTCGGTGCCGTTCTCGTGCT 0.637000 Esophageal Squamous(93;641 1401 20883 29581 34638) 0 SO:0001819 synonymous_variant ENST00000241256.2 0 1 hg19 CCDS3218.1 TCGA-3A-A9I9-01A-11D-A38G-08 GHSR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346728.1 0 0 0 4 166 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 0.887104 4 163 0 65 2 0 0 0 0 66 2 -6.312351 1 1 121402 1 32 1 1 2 3 2.050663 0 0.300000 1.870000 0.302094 0.170000 0.050000 0.420000 0.160000 0.199669 0.170000 0 1.000000e-01 2.800000e-01 ETV5 2119 broad.mit.edu 37 3 185783686 185783686 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr3:185783686G>C ENST00000306376.5 - 8 1072 c.826C>G c.(826-828)Ccg>Gcg p.P276A ETV5_ENST00000537818.1_Missense_Mutation_p.P318A|ETV5_ENST00000480706.1_5'Flank|ETV5_ENST00000434744.1_Missense_Mutation_p.P276A NM_004454.2 NP_004445.1 P41161 ETV5_HUMAN ets variant 5 28 all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247) OV - Ovarian serous cystadenocarcinoma(80;1.62e-24) GGCATGCCCGGGACCCCATGT 0.552000 T TMPRSS2, SCL45A3 Prostate Dom yes 3 3q28 2119 ets variant gene 5 E 0 SO:0001583 missense ENST00000306376.5 1 1 hg19 CCDS33906.1 . . . . . . . . . . G 11.77 1.738599 0.30774 . . ENSG00000244405 ENST00000306376;ENST00000434744;ENST00000537818 T;T;T 0.24151 1.87;1.87;1.87 6.17 4.36 0.52297 PEA3-type ETS-domain transcription factor, N-terminal (1); 0.053049 0.85682 D 0.000000 T 0.16085 0.0387 N 0.19112 0.55 0.42954 D 0.994381 B;B 0.14438 0.01;0.008 B;B 0.16289 0.015;0.013 T 0.05321 -1.0892 10 0.37606 T 0.19 . 9.3211 0.37964 0.0734:0.0:0.7838:0.1428 . 276;318 P41161;B7Z7D7 ETV5_HUMAN;. A 276;276;318 ENSP00000306894:P276A;ENSP00000413755:P276A;ENSP00000441737:P318A ENSP00000306894:P276A P - 1 0 ETV5 187266380 1.000000 0.71417 1.000000 0.80357 0.479000 0.33129 3.446000 0.52928 0.907000 0.36646 0.655000 0.94253 CCG TCGA-3A-A9I9-01A-11D-A38G-08 ETV5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344947.1 1 0 0 24 422 0 141 0 7.084748e-02 0 8 0 141 2 0 0 0 0 0 2 1 1.000000 23 414 0 137 2 0 0 0 0 141 2 -5.194360 1 1 0 0 1 1 2 3 2.050663 0 0.300000 1.870000 0.302094 0.360000 0.230000 0.540000 0.360000 0.377370 0.360000 0 2.900000e-01 4.500000e-01 SCN5A 6331 broad.mit.edu 37 3 38671831 38671831 + Silent SNP C C G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr3:38671831C>G ENST00000333535.4 - 3 512 c.363G>C c.(361-363)cgG>cgC p.R121R SCN5A_ENST00000413689.1_Silent_p.R121R|SCN5A_ENST00000449557.2_Silent_p.R121R|SCN5A_ENST00000425664.1_Silent_p.R121R|SCN5A_ENST00000451551.2_Silent_p.R121R|SCN5A_ENST00000455624.2_Silent_p.R121R|SCN5A_ENST00000450102.2_Silent_p.R121R|SCN5A_ENST00000414099.2_Silent_p.R121R|SCN5A_ENST00000443581.1_Silent_p.R121R|SCN5A_ENST00000423572.2_Silent_p.R121R Q14524 SCN5A_HUMAN sodium channel, voltage-gated, type V, alpha subunit 107 Medulloblastoma(35;0.163) Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909) CAGCCGCTCTCCGGATGGGGT 0.557000 0 SO:0001819 synonymous_variant ENST00000333535.4 1 1 hg19 CCDS46796.1 TCGA-3A-A9I9-01A-11D-A38G-08 SCN5A-014 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000377958.1 1 0 1 46 307 0 145 0 0 0 0 145 2 0 0 0 0 0 2 1 1.000000 45 300 0 146 2 0 0 0 0 145 2 -2.921011 1 1 0 0 1 1 2 3 2.042112 0 0.300000 1.870000 0.301048 0.860000 0.650000 1.000000 1.000000 0.867573 0.860000 1 7.500000e-01 1 ZNF619 285267 broad.mit.edu 37 3 40529155 40529155 + Missense_Mutation SNP C C T rs139131960 by1000genomes TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr3:40529155C>T ENST00000314686.5 + 6 1511 c.1106C>T c.(1105-1107)tCg>tTg p.S369L ZNF619_ENST00000521353.1_Missense_Mutation_p.S425L|ZNF619_ENST00000447116.2_Missense_Mutation_p.S425L|ZNF619_ENST00000429348.2_Missense_Mutation_p.S385L|ZNF619_ENST00000520737.1_3'UTR|ZNF619_ENST00000522736.1_Missense_Mutation_p.S376L|ZNF619_ENST00000456778.1_Missense_Mutation_p.S341L|ZNF619_ENST00000432264.2_Missense_Mutation_p.S385L Q8N2I2 ZN619_HUMAN zinc finger protein 619 21 CACCGCAGTTCGGTATTTCTT 0.443000 0 SO:0001583 missense ENST00000314686.5 1 1 hg19 2 9.157509157509158E-4 2 0.0040650406504065045 0 0.0 0 0.0 0 0.0 C 7.811 0.715641 0.15306 4.54E-4 0.0 ENSG00000177873 ENST00000314686;ENST00000447116;ENST00000429348;ENST00000456778;ENST00000522736;ENST00000521353;ENST00000432264 T;T;T;T;T;T;T 0.17854 2.25;2.25;2.25;2.25;2.25;2.25;2.25 2.44 1.51 0.23008 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.26593 0.0650 M 0.81179 2.53 0.09310 N 1 D;P;P;D;P;P 0.67145 0.996;0.839;0.839;0.96;0.839;0.921 P;B;B;B;B;B 0.49683 0.619;0.071;0.071;0.394;0.098;0.118 T 0.14980 -1.0453 9 0.72032 D 0.01 . 4.6774 0.12719 0.2336:0.4962:0.2702:0.0 . 341;385;425;327;376;369 B4E271;C9JRN5;E9PCD9;B7Z9B3;Q17RW3;Q8N2I2 .;.;.;.;.;ZN619_HUMAN L 369;425;385;341;376;425;385 ENSP00000322529:S369L;ENSP00000411132:S425L;ENSP00000398024:S385L;ENSP00000397232:S341L;ENSP00000428004:S376L;ENSP00000430705:S425L;ENSP00000388710:S385L ENSP00000322529:S369L S + 2 0 ZNF619 40504159 0.000000 0.05858 0.001000 0.08648 0.014000 0.08584 -1.135000 0.03225 0.342000 0.23796 0.563000 0.77884 TCG TCGA-3A-A9I9-01A-11D-A38G-08 ZNF619-001 KNOWN basic protein_coding protein_coding OTTHUMT00000254180.2 0 0 0 54 265 0 82 1 3.402626e-01 2 5 0 82 2 0 0 0 0 0 2 1 1.000000 54 259 0 82 2 0 0 0 0 82 2 -4.363608 1 0 121412 37 46 1 1 2 3 2.042112 0 0.300000 1.870000 0.301048 0.990000 0.870000 1.000000 1.000000 0.988959 0.990000 1 9.900000e-01 1 TRAIP 10293 broad.mit.edu 37 3 49867474 49867474 + Silent SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr3:49867474C>T ENST00000331456.2 - 12 1178 c.1065G>A c.(1063-1065)aaG>aaA p.K355K TRAIP_ENST00000469027.1_Silent_p.K200K NM_005879.2 NP_005870.2 Q9BWF2 TRAIP_HUMAN TRAF interacting protein 24 CTTTGCATATCTTCTTGGGGA 0.532000 0 SO:0001819 synonymous_variant ENST00000331456.2 0 1 hg19 CCDS2806.1 TCGA-3A-A9I9-01A-11D-A38G-08 TRAIP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350518.1 0 0 0 8 495 0 174 0 2.044684e-03 0 4 0 174 2 0 0 0 0 0 2 1 0.988389 8 484 0 168 2 0 0 0 0 174 2 -3.333272 1 1 0 0 1 0 1 1 2.033341 0 0.300000 1.870000 0.297894 0.100000 0.040000 0.200000 0.100000 0.117900 0.100000 0 7.000000e-02 1.600000e-01 GPR27 2850 broad.mit.edu 37 3 71804286 71804286 + Silent SNP C C A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr3:71804286C>A ENST00000304411.2 + 1 1086 c.1086C>A c.(1084-1086)acC>acA p.T362T EIF4E3_ENST00000421769.2_5'Flank|EIF4E3_ENST00000448225.1_5'Flank|EIF4E3_ENST00000295612.3_5'Flank NM_018971.1 NP_061844.1 Q9NS67 GPR27_HUMAN G protein-coupled receptor 27 5 Prostate(10;0.00899) CCCGGACCACCCAGGCGACCC 0.647000 0 SO:0001819 synonymous_variant ENST00000304411.2 0 1 hg19 CCDS2915.1 TCGA-3A-A9I9-01A-11D-A38G-08 GPR27-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352303.1 0 0 0 4 67 0 30 0 1.542357e-01 0 10 0 30 2 0 0 0 0 0 2 1 0.885530 4 65 0 29 2 0 0 0 0 30 2 -8.481318 1 1 0 0 1 0 1 1 2.033341 0 0.300000 1.870000 0.297894 0.400000 0.140000 0.830000 0.360000 0.439490 0.400000 0 2.500000e-01 6.200000e-01 DAPP1 27071 broad.mit.edu 37 4 100784951 100784951 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr4:100784951G>C ENST00000512369.1 + 7 693 c.625G>C c.(625-627)Gac>Cac p.D209H DAPP1_ENST00000296414.7_Missense_Mutation_p.D209H NM_014395.2 NP_055210.2 Q9UN19 DAPP1_HUMAN dual adaptor of phosphotyrosine and 3-phosphoinositides 6 TCGGATCCTAGACCTAACAGA 0.303000 0 SO:0001583 missense ENST00000512369.1 1 1 hg19 CCDS47112.1 . . . . . . . . . . G 20.7 4.032235 0.75504 . . ENSG00000070190 ENST00000296414;ENST00000512369 T;T 0.76709 -1.04;-1.04 5.72 4.88 0.63580 Pleckstrin homology-type (1);Pleckstrin homology domain (3); 0.045133 0.85682 D 0.000000 D 0.87341 0.6153 M 0.78916 2.43 0.58432 D 0.999999 D;D 0.89917 1.0;1.0 D;D 0.80764 0.985;0.994 D 0.88675 0.3198 10 0.72032 D 0.01 -19.8161 13.5784 0.61888 0.076:0.0:0.9239:0.0 . 209;209 Q9UN19-2;Q9UN19 .;DAPP1_HUMAN H 209 ENSP00000296414:D209H;ENSP00000423602:D209H ENSP00000296414:D209H D + 1 0 DAPP1 101003974 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 5.093000 0.64517 1.410000 0.46936 0.655000 0.94253 GAC TCGA-3A-A9I9-01A-11D-A38G-08 DAPP1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000363215.1 1 0 1 15 77 0 21 0 6.159777e-01 0 12 0 21 2 0 0 0 0 0 2 1 0.999896 15 74 0 21 2 0 0 0 0 21 2 -20.000000 1 1 0 0 1 0 1 1 2.035556 0 0.300000 1.870000 0.298948 0.990000 0.650000 1.000000 1.000000 0.946643 0.990000 1 8.500000e-01 1 AIMP1 9255 broad.mit.edu 37 4 107252827 107252827 + Splice_Site SNP A A G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr4:107252827A>G ENST00000442366.1 + 5 443 c.e5-1 AIMP1_ENST00000358008.3_Splice_Site|AIMP1_ENST00000394701.4_Splice_Site NM_001142415.1 NP_001135887.1 Q12904 AIMP1_HUMAN aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 11 AATACTTTTTAGGAGAGAAGA 0.358000 0 SO:0001630 splice_region_variant ENST00000442366.1 0 1 hg19 CCDS3674.1 . . . . . . . . . . A 13.06 2.124201 0.37533 . . ENSG00000164022 ENST00000510207;ENST00000442366;ENST00000432345;ENST00000358008;ENST00000394701 . . . 5.23 5.23 0.72850 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 15.1091 0.72340 1.0:0.0:0.0:0.0 . . . . . -1 . . . + . . AIMP1 107472276 1.000000 0.71417 1.000000 0.80357 0.374000 0.29953 5.339000 0.65953 1.979000 0.57680 0.528000 0.53228 . TCGA-3A-A9I9-01A-11D-A38G-08 AIMP1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253961.1 0 0 0 5 312 0 82 0 0 0 1 0 82 2 0 0 0 0 0 2 1 0.935921 5 308 0 82 2 0 0 0 0 82 2 -2.543142 1 1 0 0 1 0 1 1 2.035556 0 0.300000 1.870000 0.298948 0.110000 0.030000 0.230000 0.100000 0.124282 0.110000 0 6.000000e-02 1.700000e-01 NCAPG 64151 broad.mit.edu 37 4 17839269 17839269 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr4:17839269G>C ENST00000251496.2 + 16 2487 c.2311G>C c.(2311-2313)Gaa>Caa p.E771Q NM_022346.4 NP_071741.2 Q9BPX3 CND3_HUMAN non-SMC condensin I complex, subunit G 27 GGAATGCTTTGAAGAAGCTTT 0.358000 0 SO:0001583 missense ENST00000251496.2 1 1 hg19 CCDS3424.1 . . . . . . . . . . G 22.2 4.257970 0.80246 . . ENSG00000109805 ENST00000251496 T 0.31769 1.48 5.55 4.71 0.59529 Armadillo-type fold (1); 0.044582 0.85682 D 0.000000 T 0.54565 0.1866 M 0.76574 2.34 0.80722 D 1 D 0.76494 0.999 D 0.76575 0.988 T 0.56517 -0.7966 10 0.45353 T 0.12 -21.4946 14.1271 0.65228 0.0721:0.0:0.9279:0.0 . 771 Q9BPX3 CND3_HUMAN Q 771 ENSP00000251496:E771Q ENSP00000251496:E771Q E + 1 0 NCAPG 17448367 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 8.813000 0.91963 1.339000 0.45563 0.591000 0.81541 GAA TCGA-3A-A9I9-01A-11D-A38G-08 NCAPG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250375.1 1 0 1 109 643 0 126 1 5.826654e-01 5 8 0 126 2 0 0 0 0 0 2 1 1.000000 104 633 0 123 2 0 0 0 0 126 2 -20.000000 1 1 0 0 1 0 1 1 2.035556 0 0.300000 1.870000 0.298948 0.960000 0.800000 1.000000 1.000000 0.947308 0.960000 1 8.700000e-01 1 FAT1 2195 broad.mit.edu 37 4 187524664 187524664 + Silent SNP A A G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr4:187524664A>G ENST00000441802.2 - 19 11225 c.11016T>C c.(11014-11016)ggT>ggC p.G3672G NM_005245.3 NP_005236.2 Q14517 FAT1_HUMAN FAT atypical cadherin 1 228 TCCTCCTCACACCCAGGATGT 0.502000 HNSCC(5;0.00058) Colon(197;1040 2055 4143 4984 49344) 0 SO:0001819 synonymous_variant ENST00000441802.2 1 1 hg19 CCDS47177.1 TCGA-3A-A9I9-01A-11D-A38G-08 FAT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000360209.3 1 0 1 23 128 0 68 1 9.768967e-01 11 26 0 68 2 0 0 0 0 0 2 1 1.000000 23 125 0 68 2 0 0 0 0 68 2 -13.651160 1 1 0 0 1 0 1 1 1.794579 1 0.300000 1.870000 0.183673 0.830000 0.560000 1.000000 1.000000 0.826438 0.830000 0 6.900000e-01 9.600000e-01 FAM114A1 92689 broad.mit.edu 37 4 38933133 38933133 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr4:38933133C>T ENST00000358869.2 + 11 1399 c.1223C>T c.(1222-1224)gCa>gTa p.A408V FAM114A1_ENST00000515037.1_Missense_Mutation_p.A201V NM_138389.2 NP_612398.2 Q8IWE2 NXP20_HUMAN family with sequence similarity 114, member A1 20 GTAGATGTGGCAAAAGTGTCC 0.453000 0 SO:0001583 missense ENST00000358869.2 1 1 hg19 CCDS3447.1 . . . . . . . . . . C 7.958 0.746323 0.15710 . . ENSG00000197712 ENST00000515037;ENST00000358869;ENST00000355404 T;T 0.22743 1.94;2.92 6.07 3.04 0.35103 . 1.106540 0.06528 N 0.740982 T 0.18882 0.0453 L 0.57536 1.79 0.09310 N 1 B;B 0.10296 0.003;0.001 B;B 0.06405 0.002;0.002 T 0.45381 -0.9265 10 0.02654 T 1 -0.0049 7.2024 0.25889 0.1269:0.6457:0.0:0.2274 . 201;408 Q6MZV4;Q8IWE2 .;NXP20_HUMAN V 201;408;201 ENSP00000424115:A201V;ENSP00000351740:A408V ENSP00000347569:A201V A + 2 0 FAM114A1 38609528 0.600000 0.26899 0.002000 0.10522 0.268000 0.26511 1.217000 0.32455 0.907000 0.36646 0.655000 0.94253 GCA TCGA-3A-A9I9-01A-11D-A38G-08 FAM114A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250436.1 0 0 0 8 186 0 55 0 4.387243e-01 0 33 0 55 2 0 0 0 0 0 2 1 0.988671 8 181 0 53 2 0 0 0 0 55 2 -4.093351 1 1 0 0 1 0 1 1 2.035556 0 0.300000 1.870000 0.298948 0.280000 0.130000 0.500000 0.270000 0.301988 0.280000 0 1.900000e-01 3.900000e-01 MFSD7 84179 broad.mit.edu 37 4 678335 678335 + Missense_Mutation SNP G G C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 G C G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr4:678335G>C ENST00000404286.2 - 6 795 c.780C>G c.(778-780)atC>atG p.I260M MFSD7_ENST00000515118.1_Missense_Mutation_p.I163M|MFSD7_ENST00000322224.4_Missense_Mutation_p.I259M|MFSD7_ENST00000347950.5_Missense_Mutation_p.I141M|MFSD7_ENST00000503156.1_Missense_Mutation_p.I195M|MFSD7_ENST00000513740.1_5'Flank NM_032219.2 NP_115595.2 Q6UXD7 MFSD7_HUMAN major facilitator superfamily domain containing 7 11 CAGAGATCCCGATCATTCCCC 0.642000 OREG0016025 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000404286.2 1 1 hg19 . . . . . . . . . . G 9.541 1.113390 0.20795 . . ENSG00000169026 ENST00000347950;ENST00000322224;ENST00000404286;ENST00000515118;ENST00000503156;ENST00000507165 T;T;T;T;T;T 0.58358 0.34;0.45;0.45;0.34;0.45;0.45 4.73 -6.09 0.02145 Major facilitator superfamily domain, general substrate transporter (1); 0.365001 0.28011 N 0.016960 T 0.53334 0.1790 L 0.55103 1.725 0.09310 N 1 D;D;D;P;D 0.58970 0.98;0.984;0.968;0.906;0.975 P;P;P;P;P 0.59171 0.853;0.777;0.841;0.77;0.639 T 0.55147 -0.8186 10 0.42905 T 0.14 -14.7166 9.9496 0.41631 0.7043:0.1275:0.1682:0.0 . 195;163;141;260;259 D6RIZ6;D6R9R0;Q6UXD7-3;Q6UXD7;Q6UXD7-2 .;.;.;MFSD7_HUMAN;. M 141;259;260;163;195;196 ENSP00000307545:I141M;ENSP00000320234:I259M;ENSP00000384616:I260M;ENSP00000423204:I163M;ENSP00000425753:I195M;ENSP00000424556:I196M ENSP00000320234:I259M I - 3 3 MFSD7 668335 0.041000 0.20044 0.000000 0.03702 0.002000 0.02628 -0.702000 0.05069 -1.401000 0.02058 0.460000 0.39030 ATC TCGA-3A-A9I9-01A-11D-A38G-08 MFSD7-004 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000358585.1 1 0 1 75 427 0 225 0 9.935028e-01 0 46 0 225 2 0 0 0 0 0 2 1 1.000000 72 420 0 223 2 0 0 0 0 225 2 -20.000000 1 1 0 0 1 0 1 1 2.035556 0 0.300000 1.870000 0.298948 0.980000 0.790000 1.000000 1.000000 0.957387 0.980000 1 8.800000e-01 1 ALB 213 broad.mit.edu 37 4 74283893 74283893 + Missense_Mutation SNP T T C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 T C T T Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr4:74283893T>C ENST00000503124.1 + 10 1274 c.1067T>C c.(1066-1068)gTg>gCg p.V356A ALB_ENST00000401494.3_Missense_Mutation_p.V391A|ALB_ENST00000509063.1_Missense_Mutation_p.V506A|ALB_ENST00000415165.2_Missense_Mutation_p.V314A|ALB_ENST00000295897.4_Missense_Mutation_p.V506A|ALB_ENST00000505649.1_3'UTR Q8TES7 FBF1_HUMAN albumin 48 Breast(15;0.00102) Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154) GAATCCTTGGTGAACAGGCGA 0.448000 0 SO:0001583 missense ENST00000503124.1 1 1 hg19 . . . . . . . . . . T 0.009 -1.808861 0.00606 . . ENSG00000163631 ENST00000295897;ENST00000415165;ENST00000329326;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202 T;T;T;T;T 0.56776 0.44;0.44;0.44;0.44;0.44 5.94 2.26 0.28386 Serum albumin-like (1);Serum albumin, N-terminal (3); 0.507607 0.19058 N 0.123858 T 0.34048 0.0884 N 0.12471 0.22 0.28162 N 0.928932 B;B;B;B;B 0.23128 0.08;0.001;0.006;0.001;0.002 B;B;B;B;B 0.31495 0.131;0.034;0.069;0.017;0.034 T 0.33317 -0.9873 10 0.87932 D 0 -9.8227 7.1945 0.25845 0.0:0.3801:0.0:0.6199 . 391;314;356;506;506 B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768 .;.;.;.;ALBU_HUMAN A 506;314;293;356;506;391;515 ENSP00000295897:V506A;ENSP00000401820:V314A;ENSP00000421027:V356A;ENSP00000422784:V506A;ENSP00000384695:V391A ENSP00000295897:V506A V + 2 0 ALB 74502757 0.993000 0.37304 0.762000 0.31397 0.006000 0.05464 1.347000 0.33975 0.503000 0.28060 -0.297000 0.09499 GTG TCGA-3A-A9I9-01A-11D-A38G-08 ALB-011 PUTATIVE basic|exp_conf protein_coding protein_coding OTTHUMT00000365419.1 1 0 1 76 471 0 122 0 9.999999e-01 0 139 0 122 2 0 0 0 0 0 2 1 1.000000 75 465 0 121 2 0 0 0 0 122 2 -20.000000 1 1 121412 4 38 1 0 1 1 2.035556 0 0.300000 1.870000 0.298948 0.920000 0.730000 1.000000 1.000000 0.915333 0.920000 1 8.200000e-01 1 IBSP 3381 broad.mit.edu 37 4 88727301 88727301 + Nonsense_Mutation SNP G G T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr4:88727301G>T ENST00000226284.5 + 5 278 c.211G>T c.(211-213)Gga>Tga p.G71* NM_004967.3 NP_004958.2 P21815 SIAL_HUMAN integrin-binding sialoprotein 21 Hepatocellular(203;0.114) CGAAGAAAATGGAGATGACAG 0.348000 0 SO:0001587 stop_gained ENST00000226284.5 0 1 hg19 CCDS3624.1 . . . . . . . . . . G 36 5.856098 0.97030 . . ENSG00000029559 ENST00000226284 . . . 5.71 5.71 0.89125 . 0.190255 0.36932 N 0.002329 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.72032 D 0.01 . 16.9553 0.86257 0.0:0.0:1.0:0.0 . . . . X 71 . ENSP00000226284:G71X G + 1 0 IBSP 88946325 0.998000 0.40836 0.988000 0.46212 0.981000 0.71138 3.591000 0.53986 2.861000 0.98227 0.650000 0.86243 GGA TCGA-3A-A9I9-01A-11D-A38G-08 IBSP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253050.2 1 0 0 31 169 0 47 0 6.867288e-02 0 3 0 47 2 0 0 0 0 0 2 1 1.000000 31 165 0 47 2 0 0 0 0 47 2 -3.248383 1 1 0 0 1 0 1 1 2.035556 0 0.300000 1.870000 0.298948 0.990000 0.720000 1.000000 1.000000 0.952582 0.990000 1 8.600000e-01 1 PCDHB2 56133 broad.mit.edu 37 5 140475321 140475321 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr5:140475321C>T ENST00000194155.4 + 1 1095 c.947C>T c.(946-948)aCa>aTa p.T316I NM_018936.2 NP_061759.1 Q9Y5E7 PCDB2_HUMAN protocadherin beta 2 71 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) TCCATCCAGACATACACAGTA 0.423000 0 SO:0001583 missense ENST00000194155.4 1 1 hg19 CCDS4244.1 . . . . . . . . . . C 2.170 -0.390128 0.04932 . . ENSG00000112852 ENST00000194155 T 0.52057 0.68 5.38 0.0927 0.14474 Cadherin (5);Cadherin-like (1); . . . . T 0.31420 0.0796 L 0.38733 1.17 0.09310 N 1 B 0.22541 0.071 B 0.21546 0.035 T 0.22556 -1.0213 9 0.23302 T 0.38 . 4.5758 0.12232 0.3845:0.2605:0.2888:0.0662 . 316 Q9Y5E7 PCDB2_HUMAN I 316 ENSP00000194155:T316I ENSP00000194155:T316I T + 2 0 PCDHB2 140455505 0.000000 0.05858 0.135000 0.22099 0.049000 0.14656 -3.545000 0.00435 0.020000 0.15106 0.650000 0.86243 ACA TCGA-3A-A9I9-01A-11D-A38G-08 PCDHB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251801.2 1 0 1 47 301 0 146 1 4.063775e-01 5 5 0 146 2 0 0 0 0 0 2 1 1.000000 46 296 0 143 2 0 0 0 0 146 2 -19.938540 1 1 0 0 1 1 2 3 2.051815 0 0.300000 1.870000 0.302094 0.900000 0.680000 1.000000 1.000000 0.894446 0.900000 1 7.800000e-01 1 PCDHGC5 56097 broad.mit.edu 37 5 140869580 140869580 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr5:140869580G>A ENST00000252087.1 + 1 773 c.773G>A c.(772-774)gGt>gAt p.G258D PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA12_ENST00000252085.3_Intron NM_018929.2|NM_032403.2|NM_032407.1 NP_061752.1|NP_115779.1|NP_115783.1 Q9Y5F6 PCDGM_HUMAN protocadherin gamma subfamily C, 5 35 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GCACCCATTGGTACTCTGCTG 0.517000 0 SO:0001583 missense ENST00000252087.1 1 1 hg19 CCDS4263.1 . . . . . . . . . . G 11.44 1.638018 0.29157 . . ENSG00000240764 ENST00000252087 T 0.04454 3.62 6.08 6.08 0.98989 Cadherin (4);Cadherin-like (1); 0.000000 0.64402 D 0.000019 T 0.13286 0.0322 M 0.66506 2.035 0.58432 D 0.999995 B;P 0.48294 0.311;0.908 B;P 0.51777 0.334;0.679 T 0.00032 -1.2273 10 0.51188 T 0.08 . 13.4893 0.61386 0.0718:0.0:0.9282:0.0 . 258;258 Q9Y5F6-2;Q9Y5F6 .;PCDGM_HUMAN D 258 ENSP00000252087:G258D ENSP00000252087:G258D G + 2 0 PCDHGC5 140849764 1.000000 0.71417 0.569000 0.28460 0.003000 0.03518 5.776000 0.68924 2.890000 0.99128 0.655000 0.94253 GGT TCGA-3A-A9I9-01A-11D-A38G-08 PCDHGC5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251819.1 1 0 1 110 572 0 288 0 2.645613e-02 0 2 0 288 2 0 0 0 0 0 2 1 1.000000 107 557 0 282 2 0 0 0 0 288 2 -20.000000 1 1 0 0 1 1 2 3 2.051815 0 0.300000 1.870000 0.302094 0.990000 0.890000 1.000000 1.000000 0.990549 0.990000 1 9.800000e-01 1 PPARGC1B 133522 broad.mit.edu 37 5 149216585 149216585 + Missense_Mutation SNP C C G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr5:149216585C>G ENST00000309241.5 + 8 2599 c.2567C>G c.(2566-2568)tCt>tGt p.S856C PPARGC1B_ENST00000360453.4_Missense_Mutation_p.S817C|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.S856C|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.S792C NM_133263.3 NP_573570.3 Q86YN6 PRGC2_HUMAN peroxisome proliferator-activated receptor gamma, coactivator 1 beta 30 KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147) CGCTCAAGCTCTGGCTCTTCA 0.637000 0 SO:0001583 missense ENST00000309241.5 1 1 hg19 CCDS4298.1 . . . . . . . . . . C 20.6 4.013777 0.75161 . . ENSG00000155846 ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750 T;T;T;T 0.57107 0.42;0.42;0.42;0.42 5.8 5.8 0.92144 . 0.619197 0.15973 N 0.235681 T 0.72277 0.3440 M 0.62723 1.935 0.52501 D 0.999955 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.91635 0.999;0.997;0.999;0.998;0.999 T 0.71859 -0.4465 10 0.72032 D 0.01 -20.0049 18.2397 0.89963 0.0:1.0:0.0:0.0 . 835;835;817;856;856 Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3 .;.;.;PRGC2_HUMAN;. C 817;856;856;792 ENSP00000353638:S817C;ENSP00000377855:S856C;ENSP00000312649:S856C;ENSP00000384403:S792C ENSP00000312649:S856C S + 2 0 PPARGC1B 149196778 0.997000 0.39634 0.975000 0.42487 0.977000 0.68977 3.862000 0.56009 2.747000 0.94245 0.462000 0.41574 TCT TCGA-3A-A9I9-01A-11D-A38G-08 PPARGC1B-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000252334.1 1 0 1 62 419 0 224 0 0 0 0 224 2 0 0 0 0 0 2 1 1.000000 58 409 0 220 2 0 0 0 0 224 2 -3.142713 1 1 0 0 1 1 2 3 2.051815 0 0.300000 1.870000 0.302094 0.860000 0.670000 1.000000 1.000000 0.863893 0.860000 1 7.600000e-01 9.700000e-01 DRD1 1812 broad.mit.edu 37 5 174869707 174869707 + Missense_Mutation SNP C C G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr5:174869707C>G ENST00000393752.2 - 2 1388 c.396G>C c.(394-396)gaG>gaC p.E132D NM_000794.3 NP_000785.1 P21728 DRD1_HUMAN dopamine receptor D1 23 all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104) Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214) Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183) Acepromazine(DB01614)|Acetophenazine(DB01063)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Dopamine(DB00988)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Methylergometrine(DB00353)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Phenylpropanolamine(DB00397)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Ziprasidone(DB00246) TCATCTTTCTCTCATACCGGA 0.542000 0 SO:0001583 missense ENST00000393752.2 1 1 hg19 CCDS4393.1 . . . . . . . . . . C 13.22 2.172325 0.38315 . . ENSG00000184845 ENST00000393752;ENST00000329144 T 0.72505 -0.66 5.55 3.77 0.43336 GPCR, rhodopsin-like superfamily (1); 0.046619 0.85682 D 0.000000 T 0.81079 0.4748 M 0.82517 2.595 0.51233 D 0.999911 D 0.60575 0.988 P 0.61722 0.893 T 0.81150 -0.1064 10 0.62326 D 0.03 . 8.8539 0.35217 0.0:0.772:0.0:0.228 . 132 P21728 DRD1_HUMAN D 132 ENSP00000377353:E132D ENSP00000327652:E132D E - 3 2 DRD1 174802313 1.000000 0.71417 0.978000 0.43139 0.401000 0.30781 1.935000 0.40173 0.819000 0.34492 0.655000 0.94253 GAG TCGA-3A-A9I9-01A-11D-A38G-08 DRD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252982.2 0 0 1 57 298 1 132 0 0 0 1 132 2 0 0 0 0 0 2 1 1.000000 56 295 1 129 11 0 0 0 1 132 2 -2.821127 1 1 0 0 1 0 0 0 2.011166 0 0.300000 1.870000 0.289340 0.990000 0.810000 1.000000 1.000000 0.974269 0.990000 1 9.200000e-01 1 PDE8B 8622 broad.mit.edu 37 5 76646926 76646926 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr5:76646926G>A ENST00000264917.5 + 9 1099 c.1054G>A c.(1054-1056)Ggg>Agg p.G352R PDE8B_ENST00000333194.4_Missense_Mutation_p.G352R|PDE8B_ENST00000340978.3_Missense_Mutation_p.G305R|PDE8B_ENST00000346042.3_Intron|PDE8B_ENST00000342343.4_Missense_Mutation_p.G332R NM_003719.3 NP_003710.1 O95263 PDE8B_HUMAN phosphodiesterase 8B p.G352R(1) GMDS/PDE8B(2) 40 all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605) Caffeine(DB00201)|Ketotifen(DB00920) ACGGAAATCCGGGGACAGCAT 0.502000 1 Substitution - Missense(1) SO:0001583 missense ENST00000264917.5 1 1 hg19 CCDS4037.1 . . . . . . . . . . G 33 5.260123 0.95368 . . ENSG00000113231 ENST00000340978;ENST00000264917;ENST00000342343;ENST00000333194;ENST00000503963 D;D;D;D;T 0.87179 -2.22;-2.22;-2.22;-2.22;-0.39 5.39 5.39 0.77823 PAS (1);PAS fold (1); 0.588962 0.18116 N 0.151194 D 0.96021 0.8704 H 0.96889 3.9 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.79784 0.984;0.988;0.984;0.993 D 0.96973 0.9710 10 0.62326 D 0.03 . 17.9374 0.89017 0.0:0.0:1.0:0.0 . 305;352;332;352 O95263-6;O95263-3;O95263-4;O95263 .;.;.;PDE8B_HUMAN R 305;352;332;352;114 ENSP00000345446:G305R;ENSP00000264917:G352R;ENSP00000345646:G332R;ENSP00000331336:G352R;ENSP00000422861:G114R ENSP00000264917:G352R G + 1 0 PDE8B 76682682 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.494000 0.97962 2.528000 0.85240 0.563000 0.77884 GGG TCGA-3A-A9I9-01A-11D-A38G-08 PDE8B-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000220015.3 1 0 1 13 83 0 31 0 1.555184e-01 0 5 0 31 2 0 0 0 0 0 2 1 0.999610 13 81 0 31 2 0 0 0 0 31 2 -2.802626 1 1 0 0 1 0 1 1 1.745013 1 0.300000 1.870000 0.185099 0.740000 0.430000 1.000000 1.000000 0.747146 0.740000 0 5.700000e-01 9.200000e-01 TNFAIP3 7128 broad.mit.edu 37 6 138202266 138202266 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr6:138202266G>A ENST00000237289.4 + 9 2249 c.2183G>A c.(2182-2184)cGc>cAc p.R728H NM_001270507.1|NM_001270508.1|NM_006290.3 NP_001257436.1|NP_001257437.1|NP_006281.1 P21580 TNAP3_HUMAN tumor necrosis factor, alpha-induced protein 3 p.0?(25) 225 Breast(32;0.135)|Colorectal(23;0.24) CTGGCCTGCCGCAGCGAGGAG 0.657000 D, N, F marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma GBM(130;153 1739 22295 28918 47987) Rec yes 6 6q23 7128 tumor necrosis factor, alpha-induced protein 3 L 25 Whole gene deletion(25) SO:0001583 missense ENST00000237289.4 0 1 hg19 CCDS5187.1 . . . . . . . . . . G 36 5.621768 0.96660 . . ENSG00000118503 ENST00000237289;ENST00000535574 T 0.46819 0.86 5.67 5.67 0.87782 Zinc finger, A20-type (3); 0.253340 0.44902 D 0.000405 T 0.50786 0.1636 L 0.48642 1.525 0.53005 D 0.999965 D 0.58620 0.983 P 0.57283 0.817 T 0.50056 -0.8872 10 0.56958 D 0.05 -19.7323 17.9431 0.89031 0.0:0.0:1.0:0.0 . 728 P21580 TNAP3_HUMAN H 728 ENSP00000237289:R728H ENSP00000237289:R728H R + 2 0 TNFAIP3 138243959 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 6.069000 0.71209 2.673000 0.90976 0.563000 0.77884 CGC TCGA-3A-A9I9-01A-11D-A38G-08 TNFAIP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042414.1 0 0 0 6 379 0 190 0 1.553160e-01 0 38 0 190 2 0 0 0 0 0 2 1 0.961064 6 365 0 187 2 0 0 0 0 190 2 -2.865474 1 1 121412 4 38 1 0 1 1 1.734104 1 0.300000 1.870000 0.176471 0.090000 0.030000 0.180000 0.090000 0.101251 0.090000 0 5.000000e-02 1.400000e-01 RREB1 6239 broad.mit.edu 37 6 7231195 7231195 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr6:7231195G>A ENST00000349384.6 + 10 3177 c.2863G>A c.(2863-2865)Gaa>Aaa p.E955K RREB1_ENST00000379938.2_Missense_Mutation_p.E955K|RREB1_ENST00000334984.6_Missense_Mutation_p.E955K|RREB1_ENST00000379933.3_Missense_Mutation_p.E955K NM_001003698.3 NP_001003698.1 Q92766 RREB1_HUMAN ras responsive element binding protein 1 58 Ovarian(93;0.0398) all_hematologic(90;0.0384)|Prostate(151;0.191) CACTCCCAGCGAAGCCAAGAA 0.617000 0 SO:0001583 missense ENST00000349384.6 1 1 hg19 CCDS34336.1 . . . . . . . . . . G 10.63 1.404290 0.25378 . . ENSG00000124782 ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984 T;T;T;T 0.11604 2.88;2.87;2.88;2.76 4.75 3.88 0.44766 . 0.198485 0.34025 N 0.004340 T 0.03959 0.0111 L 0.40543 1.245 0.30128 N 0.805065 P;P;D 0.56035 0.954;0.956;0.974 B;B;P 0.47251 0.374;0.27;0.542 T 0.11792 -1.0573 10 0.07325 T 0.83 -13.4013 12.3157 0.54955 0.0:0.0:0.6923:0.3077 . 955;955;955 Q92766-3;Q92766;Q92766-2 .;RREB1_HUMAN;. K 955 ENSP00000369265:E955K;ENSP00000369270:E955K;ENSP00000305560:E955K;ENSP00000335574:E955K ENSP00000335574:E955K E + 1 0 RREB1 7176194 0.988000 0.35896 0.020000 0.16555 0.182000 0.23217 2.986000 0.49370 1.194000 0.43101 0.655000 0.94253 GAA TCGA-3A-A9I9-01A-11D-A38G-08 RREB1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000352985.1 0 0 1 17 86 1 66 1 4.675654e-01 3 6 1 66 2 0 0 0 0 0 2 1 0.991139 17 85 1 64 7 0 0 0 1 66 2 -20.000000 1 1 121410 2 26 1 1 2 3 2.043999 0 0.300000 1.870000 0.301048 0.990000 0.680000 1.000000 1.000000 0.955398 0.990000 1 8.700000e-01 1 EPHB4 2050 broad.mit.edu 37 7 100421350 100421350 + Silent SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr7:100421350C>T ENST00000358173.3 - 3 795 c.327G>A c.(325-327)gaG>gaA p.E109E RN7SL750P_ENST00000582814.1_RNA|EPHB4_ENST00000360620.3_Silent_p.E109E|EPHB4_ENST00000477446.1_5'UTR NM_004444.4 NP_004435.3 P54760 EPHB4_HUMAN EPH receptor B4 47 Lung NSC(181;0.041)|all_lung(186;0.0581) CGGTGAAGGTCTCCTTGCAGG 0.667000 GBM(200;2113 3072 25865 52728) 0 SO:0001819 synonymous_variant ENST00000358173.3 1 1 hg19 CCDS5706.1 TCGA-3A-A9I9-01A-11D-A38G-08 EPHB4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347222.1 1 0 1 44 317 0 149 1 9.268978e-01 6 28 0 149 2 0 0 0 0 0 2 1 1.000000 42 307 0 147 2 0 0 0 0 149 2 -3.318817 1 1 0 0 1 1 2 3 2.359084 1 0.300000 1.870000 0.391304 0.930000 0.690000 1.000000 1.000000 0.915356 0.930000 1 8.000000e-01 1 RELN 5649 broad.mit.edu 37 7 103234836 103234836 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr7:103234836C>T ENST00000428762.1 - 26 3802 c.3643G>A c.(3643-3645)Gat>Aat p.D1215N RELN_ENST00000343529.5_Missense_Mutation_p.D1215N|RELN_ENST00000424685.2_Missense_Mutation_p.D1215N NM_005045.3 NP_005036.2 P78509 RELN_HUMAN reelin 227 ATGATGTCATCGACTGCCCAC 0.517000 NSCLC(146;835 1944 15585 22231 52158) 0 SO:0001583 missense ENST00000428762.1 1 1 hg19 CCDS47680.1 . . . . . . . . . . C 32 5.144229 0.94603 . . ENSG00000189056 ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171 T;T;T 0.38560 1.13;1.13;1.13 5.75 5.75 0.90469 . 0.000000 0.85682 D 0.000000 T 0.67951 0.2948 M 0.79475 2.455 0.80722 D 1 D;D 0.89917 0.999;1.0 D;D 0.73708 0.952;0.981 T 0.70392 -0.4884 10 0.87932 D 0 . 19.9347 0.97133 0.0:1.0:0.0:0.0 . 1215;1215 P78509-2;P78509 .;RELN_HUMAN N 1215 ENSP00000392423:D1215N;ENSP00000345694:D1215N;ENSP00000388446:D1215N ENSP00000345694:D1215N D - 1 0 RELN 103022072 1.000000 0.71417 0.960000 0.40013 0.990000 0.78478 7.267000 0.78462 2.707000 0.92482 0.591000 0.81541 GAT TCGA-3A-A9I9-01A-11D-A38G-08 RELN-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000348148.1 1 0 1 176 1186 0 284 0 0 0 0 284 2 0 0 0 0 0 2 1 1.000000 173 1165 0 280 2 0 0 0 0 284 2 -20.000000 1 1 0 0 1 1 2 3 2.359084 1 0.300000 1.870000 0.391304 0.980000 0.850000 1.000000 1.000000 0.968529 0.980000 1 9.100000e-01 1 ZNF746 155061 broad.mit.edu 37 7 149171720 149171720 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr7:149171720G>A ENST00000340622.3 - 7 1970 c.1690C>T c.(1690-1692)Cgg>Tgg p.R564W ZNF746_ENST00000458143.2_Missense_Mutation_p.R565W Q6NUN9 ZN746_HUMAN zinc finger protein 746 34 Melanoma(164;0.165) OV - Ovarian serous cystadenocarcinoma(82;0.00358) GTGAAGGGCCGCACGCCCGTG 0.672000 0 SO:0001583 missense ENST00000340622.3 1 1 hg19 CCDS5897.1 . . . . . . . . . . G 18.58 3.654521 0.67472 . . ENSG00000181220 ENST00000340622;ENST00000458143 T;T 0.15139 2.45;2.45 5.58 4.67 0.58626 Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.46758 D 0.000277 T 0.43010 0.1228 M 0.84082 2.675 0.36220 D 0.851953 D;D 0.89917 1.0;1.0 D;D 0.78314 0.917;0.991 T 0.55891 -0.8069 10 0.87932 D 0 -24.6663 11.729 0.51726 0.0:0.0:0.6974:0.3026 . 565;564 Q6NUN9-2;Q6NUN9 .;ZN746_HUMAN W 564;565 ENSP00000345140:R564W;ENSP00000395007:R565W ENSP00000345140:R564W R - 1 2 ZNF746 148802653 0.497000 0.26067 1.000000 0.80357 0.991000 0.79684 0.576000 0.23744 2.630000 0.89119 0.462000 0.41574 CGG TCGA-3A-A9I9-01A-11D-A38G-08 ZNF746-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000352730.1 1 0 0 9 102 0 46 1 7.360498e-01 5 26 0 46 2 0 0 0 0 0 2 1 0.993899 9 98 0 46 2 0 0 0 0 46 2 -13.836400 1 1 0 0 1 1 2 3 2.376325 1 0.300000 1.870000 0.391304 0.640000 0.320000 1.000000 1.000000 0.661786 0.640000 0 4.600000e-01 8.600000e-01 AMPH 273 broad.mit.edu 37 7 38502605 38502605 + Silent SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr7:38502605G>A ENST00000356264.2 - 10 1073 c.858C>T c.(856-858)ccC>ccT p.P286P AMPH_ENST00000428293.2_Silent_p.P286P|AMPH_ENST00000325590.5_Silent_p.P286P NM_001635.3 NP_001626.1 P49418 AMPH_HUMAN amphiphysin 62 GTGCTGGTGCGGGAGACGCAG 0.547000 0 SO:0001819 synonymous_variant ENST00000356264.2 1 1 hg19 CCDS5456.1 . . . . . . . . . . G 7.801 0.713694 0.15306 0.0 1.16E-4 ENSG00000078053 ENST00000441628 . . . 6.17 -4.56 0.03431 . . . . . T 0.36386 0.0965 . . . 0.80722 D 1 . . . . . . T 0.37502 -0.9703 4 . . . -16.034 1.5039 0.02482 0.2196:0.2615:0.324:0.1949 . . . . C 37 . . R - 1 0 AMPH 38469130 0.005000 0.15991 0.968000 0.41197 0.560000 0.35617 -1.526000 0.02229 -0.560000 0.06102 -1.202000 0.01658 CGC TCGA-3A-A9I9-01A-11D-A38G-08 AMPH-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000226953.2 0 0 1 66 378 1 139 0 0 0 1 1 139 2 0 0 0 0 0 2 1 1.000000 67 367 1 137 12 0 0 0 1 139 2 -2.151298 0 1 121386 3 40 1 0 0 0 2.030441 0 0.300000 1.870000 0.295775 0.980000 0.770000 1.000000 1.000000 0.950309 0.980000 1 8.700000e-01 1 PKD1L1 168507 broad.mit.edu 37 7 47842826 47842826 + Silent SNP G G T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr7:47842826G>T ENST00000289672.2 - 53 7994 c.7944C>A c.(7942-7944)ccC>ccA p.P2648P C7orf69_ENST00000258776.4_Intron|C7orf69_ENST00000418326.2_Intron NM_138295.3 NP_612152.1 Q8TDX9 PK1L1_HUMAN polycystic kidney disease 1 like 1 BBS9/PKD1L1(2) 142 CAAAGATGCTGGGGAGTGAGT 0.463000 0 SO:0001819 synonymous_variant ENST00000289672.2 1 1 hg19 CCDS34633.1 TCGA-3A-A9I9-01A-11D-A38G-08 PKD1L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340974.1 1 0 1 32 251 0 97 0 0 0 1 0 97 2 0 0 0 0 0 2 1 1.000000 31 248 0 93 2 0 0 0 0 97 2 -2.744790 1 1 0 0 1 0 0 0 2.030441 0 0.300000 1.870000 0.295775 0.740000 0.520000 1.000000 1.000000 0.758838 0.740000 0 6.300000e-01 8.800000e-01 ATAD2 29028 broad.mit.edu 37 8 124348628 124348628 + Missense_Mutation SNP C C G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr8:124348628C>G ENST00000287394.5 - 22 3303 c.3196G>C c.(3196-3198)Gat>Cat p.D1066H ATAD2_ENST00000521903.1_Missense_Mutation_p.D384H NM_014109.3 NP_054828.2 Q6PL18 ATAD2_HUMAN ATPase family, AAA domain containing 2 p.D1066Y(1) 48 Lung NSC(37;1.25e-09)|Ovarian(258;0.00838) STAD - Stomach adenocarcinoma(47;0.00288) GGATCTCTATCTGGATTGTAT 0.373000 1 Substitution - Missense(1) SO:0001583 missense ENST00000287394.5 1 1 hg19 CCDS6343.1 . . . . . . . . . . C 20.9 4.066390 0.76187 . . ENSG00000156802 ENST00000287394;ENST00000521903 T;T 0.29917 1.55;1.55 5.89 5.89 0.94794 Bromodomain (5); 0.507344 0.17654 U 0.166599 T 0.55641 0.1933 M 0.78223 2.4 0.58432 D 0.999999 D 0.55385 0.971 P 0.56398 0.797 T 0.56992 -0.7887 10 0.72032 D 0.01 -27.5249 20.2576 0.98430 0.0:1.0:0.0:0.0 . 1066 Q6PL18 ATAD2_HUMAN H 1066;384 ENSP00000287394:D1066H;ENSP00000429213:D384H ENSP00000287394:D1066H D - 1 0 ATAD2 124417809 1.000000 0.71417 1.000000 0.80357 0.475000 0.33008 7.541000 0.82084 2.783000 0.95769 0.655000 0.94253 GAT TCGA-3A-A9I9-01A-11D-A38G-08 ATAD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381766.2 1 0 1 57 337 0 103 1 4.919688e-01 5 6 0 103 2 0 0 0 0 0 2 1 1.000000 56 327 0 101 2 0 0 0 0 103 2 -3.319915 1 1 0 0 1 1 2 3 2.042262 0 0.300000 1.870000 0.301048 0.960000 0.740000 1.000000 1.000000 0.937391 0.960000 1 8.400000e-01 1 NCOA2 10499 broad.mit.edu 37 8 71082538 71082538 + Missense_Mutation SNP A A G TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr8:71082538A>G ENST00000452400.2 - 6 621 c.440T>C c.(439-441)cTa>cCa p.L147P NM_006540.2 NP_006531.1 Q15596 NCOA2_HUMAN nuclear receptor coactivator 2 PAX3/NCOA2(4)|HEY1/NCOA2(10) 60 Breast(64;0.201) Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606) GTTATACCTTAGATACTGTGT 0.418000 T RUNXBP2, HEY1 AML, Chondrosarcoma Dom yes 8 8q13.1 10499 nuclear receptor coactivator 2 (TIF2) L 0 SO:0001583 missense ENST00000452400.2 0 1 hg19 CCDS47872.1 . . . . . . . . . . A 24.8 4.567322 0.86439 . . ENSG00000140396 ENST00000452400 T 0.24908 1.83 5.49 5.49 0.81192 PAS (2);PAS fold (1); 0.000000 0.85682 D 0.000000 T 0.66761 0.2822 H 0.97214 3.96 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.80125 -0.1513 10 0.87932 D 0 . 15.5729 0.76354 1.0:0.0:0.0:0.0 . 147 Q15596 NCOA2_HUMAN P 147 ENSP00000399968:L147P ENSP00000399968:L147P L - 2 0 NCOA2 71245092 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 9.335000 0.96500 2.074000 0.62210 0.528000 0.53228 CTA TCGA-3A-A9I9-01A-11D-A38G-08 NCOA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000379696.1 1 0 1 12 78 0 15 1 2.066883e-01 2 4 0 15 2 0 0 0 0 0 2 1 0.999292 11 78 0 15 2 0 0 0 0 15 2 -8.687685 1 1 0 0 1 0 1 1 2.033253 0 0.300000 1.870000 0.297894 0.890000 0.500000 1.000000 1.000000 0.856378 0.890000 1 6.700000e-01 1 MATN2 4147 broad.mit.edu 37 8 99019798 99019798 + Silent SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr8:99019798C>T ENST00000520016.1 + 9 1666 c.1542C>T c.(1540-1542)caC>caT p.H514H MATN2_ENST00000522025.2_Silent_p.H230H|MATN2_ENST00000521689.1_Silent_p.H514H|MATN2_ENST00000524308.1_Silent_p.H473H|MATN2_ENST00000254898.5_Silent_p.H514H O00339 MATN2_HUMAN matrilin 2 31 Breast(36;1.43e-06) OV - Ovarian serous cystadenocarcinoma(57;0.244) CTGAGGGACACGTGCTCCGCA 0.567000 0 SO:0001819 synonymous_variant ENST00000520016.1 1 1 hg19 CCDS55264.1 . . . . . . . . . . C 0.079 -1.186741 0.01620 . . ENSG00000132561 ENST00000518154 . . . 5.65 -7.32 0.01436 . . . . . T 0.41073 0.1143 . . . 0.18873 N 0.999988 . . . . . . T 0.41270 -0.9518 4 . . . -16.2738 16.4012 0.83641 0.0:0.2847:0.0:0.7153 . . . . C 297 . . R + 1 0 MATN2 99088974 0.000000 0.05858 0.037000 0.18230 0.086000 0.17979 -1.867000 0.01646 -1.505000 0.01807 -1.553000 0.00894 CGT TCGA-3A-A9I9-01A-11D-A38G-08 MATN2-004 KNOWN non_canonical_conserved|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000380332.1 1 0 0 64 296 0 137 1 9.996553e-01 12 45 0 137 2 0 0 0 0 0 2 1 1.000000 62 283 0 135 2 0 0 0 0 137 2 -20.000000 1 1 0 0 1 1 2 3 2.042262 0 0.300000 1.870000 0.301048 0.990000 0.930000 1.000000 1.000000 0.996225 0.990000 1 9.900000e-01 1 ENTPD8 377841 broad.mit.edu 37 9 140330612 140330612 + Silent SNP G G T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr9:140330612G>T ENST00000472938.1 - 6 919 c.903C>A c.(901-903)ctC>ctA p.L301L ENTPD8_ENST00000371506.2_Silent_p.L301L|ENTPD8_ENST00000344119.2_Silent_p.L301L Q5MY95 ENTP8_HUMAN ectonucleoside triphosphate diphosphohydrolase 8 7 all_cancers(76;0.0926) GGTTCTGGGGGAGGCTCAGCG 0.642000 0 SO:0001819 synonymous_variant ENST00000472938.1 1 1 hg19 CCDS43913.1 TCGA-3A-A9I9-01A-11D-A38G-08 ENTPD8-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000355991.1 1 0 1 38 225 0 118 1 5.409179e-01 5 7 0 118 2 0 0 0 0 0 2 1 1.000000 38 219 0 117 2 0 0 0 0 118 2 -18.638740 1 1 0 0 1 0 0 0 2.015732 0 0.300000 1.870000 0.289340 0.940000 0.690000 1.000000 1.000000 0.919208 0.940000 1 8.100000e-01 1 TLN1 7094 broad.mit.edu 37 9 35700280 35700280 + Missense_Mutation SNP C C T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr9:35700280C>T ENST00000314888.9 - 49 6921 c.6568G>A c.(6568-6570)Gtt>Att p.V2190I TLN1_ENST00000540444.1_Missense_Mutation_p.V2078I NM_006289.3 NP_006280.3 Q9Y490 TLN1_HUMAN talin 1 85 all_epithelial(49;0.167) Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194) CCAGCAGCAACGGCCTTGGCG 0.547000 0 SO:0001583 missense ENST00000314888.9 1 1 hg19 CCDS35009.1 . . . . . . . . . . C 34 5.358745 0.95854 . . ENSG00000137076 ENST00000314888;ENST00000540444 T;T 0.74421 -0.84;-0.83 5.2 5.2 0.72013 . 0.000000 0.85682 D 0.000000 T 0.77942 0.4206 M 0.85859 2.78 0.80722 D 1 D 0.54207 0.965 B 0.39771 0.309 D 0.84352 0.0533 10 0.87932 D 0 -20.4308 18.3575 0.90362 0.0:1.0:0.0:0.0 . 2190 Q9Y490 TLN1_HUMAN I 2190;2078 ENSP00000316029:V2190I;ENSP00000442981:V2078I ENSP00000316029:V2190I V - 1 0 TLN1 35690280 1.000000 0.71417 0.788000 0.31933 0.938000 0.57974 7.747000 0.85070 2.436000 0.82500 0.655000 0.94253 GTT TCGA-3A-A9I9-01A-11D-A38G-08 TLN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052353.2 0 0 0 16 357 0 132 0 9.916581e-01 1 175 0 132 2 0 0 0 0 0 2 1 0.999927 16 350 0 132 2 0 0 0 0 132 2 -4.433175 1 1 121412 4 36 1 0 1 1 2.032459 0 0.300000 1.870000 0.297894 0.280000 0.160000 0.440000 0.280000 0.299417 0.280000 0 2.200000e-01 3.700000e-01 FAM189A2 9413 broad.mit.edu 37 9 71951186 71951186 + Splice_Site SNP G G T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chr9:71951186G>T ENST00000257515.8 + 2 432 c.e2+1 FAM189A2_ENST00000455972.1_Splice_Site NM_004816.3 NP_004807.3 Q15884 F1892_HUMAN family with sequence similarity 189, member A2 12 GATACTCCTGGTATGTACTGA 0.333000 0 SO:0001630 splice_region_variant ENST00000257515.8 1 1 hg19 CCDS6629.1 . . . . . . . . . . G 17.18 3.323082 0.60634 . . ENSG00000135063 ENST00000455972;ENST00000257515 . . . 5.04 5.04 0.67666 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 14.2361 0.65927 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . FAM189A2 71141006 1.000000 0.71417 1.000000 0.80357 0.977000 0.68977 4.913000 0.63341 2.526000 0.85167 0.655000 0.94253 . TCGA-3A-A9I9-01A-11D-A38G-08 FAM189A2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052576.2 1 0 1 86 575 0 158 0 0 0 0 158 2 0 0 0 0 0 2 1 1.000000 85 563 0 156 2 0 0 0 0 158 2 -20.000000 1 1 0 0 1 1 2 3 2.051050 0 0.300000 1.870000 0.302094 0.860000 0.700000 1.000000 1.000000 0.872168 0.860000 1 7.800000e-01 9.600000e-01 GPR50 9248 broad.mit.edu 37 X 150345311 150345311 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chrX:150345311G>A ENST00000218316.3 + 1 187 c.118G>A c.(118-120)Gtt>Att p.V40I GPR50-AS1_ENST00000454196.1_RNA NM_004224.3 NP_004215.2 Q13585 MTR1L_HUMAN G protein-coupled receptor 50 38 Acute lymphoblastic leukemia(192;6.56e-05) TATCACCATCGTTGTAGACCT 0.512000 0 SO:0001583 missense ENST00000218316.3 1 1 hg19 CCDS44012.1 . . . . . . . . . . G 6.356 0.433766 0.12045 . . ENSG00000102195 ENST00000218316 T 0.37411 1.2 4.2 3.34 0.38264 . 0.154979 0.42821 N 0.000654 T 0.16257 0.0391 N 0.08118 0 0.30817 N 0.738223 B 0.24092 0.097 B 0.15870 0.014 T 0.09840 -1.0656 10 0.31617 T 0.26 -12.3268 7.0452 0.25042 0.1279:0.0:0.8721:0.0 . 40 Q13585 MTR1L_HUMAN I 40 ENSP00000218316:V40I ENSP00000218316:V40I V + 1 0 GPR50 150095969 0.914000 0.31030 0.782000 0.31804 0.022000 0.10575 1.373000 0.34272 0.789000 0.33779 0.292000 0.19580 GTT TCGA-3A-A9I9-01A-11D-A38G-08 GPR50-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060874.1 1 0 1 104 370 0 135 0 0 0 0 135 2 0 0 0 0 0 2 1 1.000000 102 361 0 134 2 0 0 0 0 135 2 -20.000000 1 1 0 0 1 0 1 1 0.300000 1.870000 0.300000 0.720000 0.600000 0.850000 0.730000 0.731677 0.720000 0 6.600000e-01 7.900000e-01 ZNF157 7712 broad.mit.edu 37 X 47272834 47272834 + Missense_Mutation SNP A A T TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chrX:47272834A>T ENST00000377073.3 + 4 1448 c.1362A>T c.(1360-1362)aaA>aaT p.K454N NM_003446.3 NP_003437.2 P51786 ZN157_HUMAN zinc finger protein 157 11 TCTATGTGAAAGTACGCCTCA 0.438000 0 SO:0001583 missense ENST00000377073.3 1 1 hg19 CCDS14278.1 . . . . . . . . . . A 7.389 0.630476 0.14322 . . ENSG00000147117 ENST00000377073 T 0.13778 2.56 3.37 2.2 0.27929 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.07818 0.0196 L 0.28054 0.825 0.09310 N 1 B 0.30482 0.281 B 0.24848 0.056 T 0.35895 -0.9770 9 0.26408 T 0.33 . 4.5131 0.11921 0.7149:0.0:0.2851:0.0 . 454 P51786 ZN157_HUMAN N 454 ENSP00000366273:K454N ENSP00000366273:K454N K + 3 2 ZNF157 47157778 0.000000 0.05858 0.678000 0.29963 0.998000 0.95712 -0.418000 0.07080 0.514000 0.28300 0.486000 0.48141 AAA TCGA-3A-A9I9-01A-11D-A38G-08 ZNF157-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056415.1 1 0 1 28 86 0 41 0 0 0 1 0 41 2 0 0 0 0 0 2 1 1.000000 27 84 0 41 2 0 0 0 0 41 2 -20.000000 1 0 0 0 1 0 1 1 0.300000 1.870000 0.300000 0.790000 0.560000 0.980000 0.800000 0.793811 0.790000 0 6.700000e-01 9.100000e-01 ELK1 2002 broad.mit.edu 37 X 47498346 47498346 + Missense_Mutation SNP G G A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chrX:47498346G>A ENST00000247161.3 - 3 701 c.602C>T c.(601-603)cCa>cTa p.P201L ELK1_ENST00000376983.3_Missense_Mutation_p.P201L|ELK1_ENST00000592066.1_Missense_Mutation_p.P147L|ELK1_ENST00000343894.4_Intron NM_005229.4 NP_005220.2 P19419 ELK1_HUMAN ELK1, member of ETS oncogene family 10 CAAGGGGCTTGGACTGGTGCT 0.632000 0 SO:0001583 missense ENST00000247161.3 0 1 hg19 CCDS14283.1 . . . . . . . . . . G 18.96 3.734656 0.69189 . . ENSG00000126767 ENST00000247161;ENST00000376983 T;T 0.44482 0.92;0.92 3.73 3.73 0.42828 . 0.322177 0.29355 N 0.012395 T 0.47395 0.1443 L 0.27053 0.805 0.80722 D 1 D 0.89917 1.0 D 0.80764 0.994 T 0.44651 -0.9314 10 0.52906 T 0.07 . 10.0463 0.42188 0.0:0.0:1.0:0.0 . 201 P19419 ELK1_HUMAN L 201 ENSP00000247161:P201L;ENSP00000366182:P201L ENSP00000247161:P201L P - 2 0 ELK1 47383290 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 3.925000 0.56484 2.122000 0.65172 0.529000 0.55759 CCA TCGA-3A-A9I9-01A-11D-A38G-08 ELK1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000056436.1 1 0 1 11 14 0 9 1 9.994712e-01 9 16 0 9 2 0 0 0 0 0 2 1 0.999115 11 12 0 9 2 0 0 0 0 9 2 -20.000000 1 1 0 0 1 0 1 1 0.300000 1.870000 0.300000 0.900000 0.620000 1.000000 0.990000 0.881637 0.900000 1 7.700000e-01 9.800000e-01 SHROOM4 57477 broad.mit.edu 37 X 50350791 50350791 + Silent SNP T T C TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 Untested Somatic Phase_I WXS none Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chrX:50350791T>C ENST00000289292.7 - 6 3634 c.3351A>G c.(3349-3351)gcA>gcG p.A1117A SHROOM4_ENST00000460112.3_Silent_p.A1001A|SHROOM4_ENST00000376020.2_Silent_p.A1117A Q9ULL8 SHRM4_HUMAN shroom family member 4 52 Ovarian(276;0.236) gctgctgGGCTGCACGAAAGA 0.577000 0 SO:0001819 synonymous_variant ENST00000289292.7 1 1 hg19 CCDS35277.1 TCGA-3A-A9I9-01A-11D-A38G-08 SHROOM4-001 KNOWN NMD_exception|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056564.4 1 0 1 13 91 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 0.999628 13 90 0 34 2 0 0 0 0 34 2 -20.000000 1 1 0 0 1 0 1 1 0.300000 1.870000 0.300000 0.410000 0.230000 0.640000 0.410000 0.430462 0.410000 0 3.100000e-01 5.300000e-01 MAGED2 10916 broad.mit.edu 37 X 54841940 54841940 + Missense_Mutation SNP C C A TCGA-3A-A9I9-01A-11D-A38G-08 TCGA-3A-A9I9-10A-01D-A38J-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx a00e940f-6021-454d-be90-a2fdebd8751d 6bf66319-97e4-4169-887d-b861913257f1 g.chrX:54841940C>A ENST00000375068.1 + 12 1879 c.1646C>A c.(1645-1647)aCt>aAt p.T549N MAGED2_ENST00000375060.1_Missense_Mutation_p.T464N|MAGED2_ENST00000396224.1_Missense_Mutation_p.T549N|MAGED2_ENST00000375062.4_Missense_Mutation_p.T464N|MAGED2_ENST00000375058.1_Missense_Mutation_p.T549N|SNORA11_ENST00000408789.1_RNA|MAGED2_ENST00000218439.4_Missense_Mutation_p.T549N|MAGED2_ENST00000347546.4_Missense_Mutation_p.T531N|MAGED2_ENST00000375053.2_Missense_Mutation_p.T549N Q9UNF1 MAGD2_HUMAN melanoma antigen family D, 2 26 agtgccagcactggtgccagt 0.597000 0 SO:0001583 missense ENST00000375068.1 1 1 hg19 CCDS14362.1 . . . . . . . . . . C 3.309 -0.141160 0.06669 . . ENSG00000102316 ENST00000375068;ENST00000375053;ENST00000347546;ENST00000343474;ENST00000375062;ENST00000218439;ENST00000375058;ENST00000375060;ENST00000396224 T;T;T;T;T;T;T;T;T 0.42513 4.04;4.04;4.1;4.01;0.97;4.04;4.04;0.97;4.04 4.21 2.36 0.29203 . 0.474225 0.17920 N 0.157539 T 0.27629 0.0679 N 0.24115 0.695 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.20472 -1.0274 10 0.59425 D 0.04 . 8.9422 0.35736 0.4:0.6:0.0:0.0 . 464;549 Q5H907;Q9UNF1 .;MAGD2_HUMAN N 549;549;493;531;464;549;549;464;549 ENSP00000364209:T549N;ENSP00000364193:T549N;ENSP00000336962:T493N;ENSP00000340290:T531N;ENSP00000364202:T464N;ENSP00000218439:T549N;ENSP00000364198:T549N;ENSP00000364200:T464N;ENSP00000379526:T549N ENSP00000218439:T549N T + 2 0 MAGED2 54858665 0.007000 0.16637 0.001000 0.08648 0.045000 0.14185 0.681000 0.25320 0.314000 0.23086 0.513000 0.50165 ACT TCGA-3A-A9I9-01A-11D-A38G-08 MAGED2-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000056821.2 1 0 1 9 22 0 13 1 1 96 400 0 13 2 0 0 0 0 0 2 1 0.995938 9 21 0 13 2 0 0 0 0 13 2 -19.885600 1 1 0 0 1 0 1 1 0.300000 1.870000 0.300000 0.800000 0.460000 0.990000 0.910000 0.789105 0.800000 0 6.300000e-01 9.400000e-01