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 UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_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 t_alt_count t_ref_count validation_alt_allele validation_method validation_status validation_tumor_sample pox qox pox_cutoff isArtifactMode oxoGCut COMMD1 150684 broad.mit.edu 37 2 62132935 62132935 + Missense_Mutation SNP C C A TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr2:62132935C>A ENST00000311832.5 + 1 154 c.122C>A c.(121-123)cCa>cAa p.P41Q COMMD1_ENST00000472729.1_Intron|COMMD1_ENST00000538736.1_Missense_Mutation_p.P41Q NM_152516.2 NP_689729.1 Q8N668 COMD1_HUMAN copper metabolism (Murr1) domain containing 1 41 copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus copper ion binding|protein homodimerization activity large_intestine(1)|liver(2)|lung(5)|ovary(1) 9 Lung NSC(7;0.035)|all_lung(7;0.0691) LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934) CAGCTATATCCAGAGGTGCCA 0.597000 3 49 1 1 1 1 0 AC008103.5 0 broad.mit.edu 37 22 18846029 18846029 + RNA SNP C C T rs148762447 by1000genomes TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr22:18846029C>T ENST00000412938.1 + 0 3387 TTGAAGGCTGCCTTCAGTGCC 0.647000 5 52 0 0 1 0 0 HOXD12 3238 broad.mit.edu 37 2 176964720 176964720 + Missense_Mutation SNP C C T TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr2:176964720C>T ENST00000406506.2 + 1 263 c.191C>T c.(190-192)gCg>gTg p.A64V HOXD12_ENST00000404162.2_Missense_Mutation_p.A64V P35452 HXD12_HUMAN homeobox D12 64 QPA -> TC (in Ref. 1; AAF79044). nuclear chromosome sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1) 10 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678) GCGCAGCCTGCGGGCGCCACT 0.751000 2 1 0 0 1 0 0 NEIL3 55247 broad.mit.edu 37 4 178283471 178283471 + Missense_Mutation SNP A A G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr4:178283471A>G ENST00000264596.3 + 10 1782 c.1664A>G c.(1663-1665)aAc>aGc p.N555S NM_018248.2 NP_060718.2 Q8TAT5 NEIL3_HUMAN nei endonuclease VIII-like 3 (E. coli) 555 base-excision repair|nucleotide-excision repair nucleus bubble DNA binding|damaged DNA binding|DNA N-glycosylase activity|DNA-(apurinic or apyrimidinic site) lyase activity|double-stranded DNA binding|single-stranded DNA binding|zinc ion binding breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 29 Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164) all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191) CCATTCTGCAACCATGGCAAG 0.388000 Base excision repair (BER), DNA glycosylases 15 73 0 0 1 0 0 CDK5RAP1 51654 broad.mit.edu 37 20 31981850 31981850 + Missense_Mutation SNP G G A TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr20:31981850G>A ENST00000357886.4 - 4 584 c.431C>T c.(430-432)aCa>aTa p.T144I CDK5RAP1_ENST00000346416.2_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000544843.1_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000339269.5_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000452723.3_Missense_Mutation_p.T54I|CDK5RAP1_ENST00000473997.1_5'UTR Q96SZ6 CK5P1_HUMAN CDK5 regulatory subunit associated protein 1 144 CDK5 activation inhibition.|MTTase N-terminal. brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification cytoplasm 4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1) 26 GATAGAGCATGTGACAAGGAG 0.403000 5 87 0 0 1 0 0 POLR1A 25885 broad.mit.edu 37 2 86297188 86297188 + Missense_Mutation SNP C C T TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr2:86297188C>T ENST00000263857.6 - 13 2197 c.1819G>A c.(1819-1821)Gag>Aag p.E607K POLR1A_ENST00000409681.1_Missense_Mutation_p.E607K O95602 RPA1_HUMAN polymerase (RNA) I polypeptide A, 194kDa 607 termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter DNA-directed RNA polymerase I complex|nucleoplasm DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5) 63 ACGTAGGCCTCGGCCCGGCCC 0.572000 19 15 0 0 1 0 0 TP53BP1 7158 broad.mit.edu 37 15 43738684 43738684 + Missense_Mutation SNP C C A TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr15:43738684C>A ENST00000263801.3 - 14 3178 c.2926G>T c.(2926-2928)Ggg>Tgg p.G976W TP53BP1_ENST00000450115.2_Missense_Mutation_p.G981W|TP53BP1_ENST00000382039.3_Missense_Mutation_p.G981W|TP53BP1_ENST00000382044.4_Missense_Mutation_p.G981W NM_005657.2 NP_005648.1 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 976 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3) 72 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) GGGGCAGCCCCAGAATCCCCT 0.473000 Other conserved DNA damage response genes 84 87 1.02218e-41 1.27773e-41 1 1 0 PIDD 55367 broad.mit.edu 37 11 799816 799816 + Splice_Site SNP G G A TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr11:799816G>A ENST00000347755.5 - 15 2614 c.2474_splice c.e15+1 p.R825_splice PIDD_ENST00000411829.2_Splice_Site_p.R808_splice NM_145886.3|NM_145887.3 NP_665893.2|NP_665894.2 Q9HB75 PIDD_HUMAN p53-induced death domain protein 825 Death. apoptosis|signal transduction cytoplasm|nucleus death receptor binding GAGCCTCACCGGAACTCGTGC 0.687000 2 0 0 0 1 0 0 PRPF40B 25766 broad.mit.edu 37 12 50027256 50027256 + Missense_Mutation SNP G G A TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr12:50027256G>A ENST00000261897.1 + 7 973 c.422G>A c.(421-423)gGc>gAc p.G141D PRPF40B_ENST00000548825.2_Missense_Mutation_p.G169D|PRPF40B_ENST00000380281.1_Missense_Mutation_p.G147D Q6NWY9 PR40B_HUMAN PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) 147 WW 2. mRNA processing|RNA splicing nuclear speck breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1) 34 TCGGACACAGGCAAACCTTAT 0.552000 5 319 0 0 1 0 0 AFF1 4299 broad.mit.edu 37 4 88055713 88055713 + Missense_Mutation SNP T T G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr4:88055713T>G ENST00000307808.6 + 19 3798 c.3378T>G c.(3376-3378)agT>agG p.S1126R AFF1_ENST00000544085.1_Missense_Mutation_p.S765R|AFF1_ENST00000395146.4_Missense_Mutation_p.S1134R NM_005935.2 NP_005926.1 P51825 AFF1_HUMAN AF4/FMR2 family, member 1 1126 nucleus sequence-specific DNA binding transcription factor activity breast(1)|large_intestine(2) 3 Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;0.000233) TGGGGAGCAGTGGGGTGGCTG 0.567000 10 179 0 0 1 0 0 AC004466.1 0 broad.mit.edu 37 12 48179336 48179336 + Silent SNP C C T TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr12:48179336C>T ENST00000599515.1 + 1 631 c.420C>T c.(418-420)ttC>ttT p.F140F HDAC7_ENST00000354334.3_Intron|HDAC7_ENST00000552960.1_Intron|HDAC7_ENST00000427332.2_Intron|HDAC7_ENST00000380610.4_Intron|HDAC7_ENST00000080059.7_Intron CCCCAGCCTTCTAGCCACAAG 0.577000 7 12 0 0 1 0 0 SEZ6L 23544 broad.mit.edu 37 22 26743742 26743742 + Missense_Mutation SNP C C A TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr22:26743742C>A ENST00000529632.2 + 11 2466 c.2270C>A c.(2269-2271)aCc>aAc p.T757N SEZ6L_ENST00000404234.3_Missense_Mutation_p.T757N|SEZ6L_ENST00000360929.3_Missense_Mutation_p.T757N|SEZ6L_ENST00000343706.4_Missense_Mutation_p.T757N|SEZ6L_ENST00000403121.1_Missense_Mutation_p.T530N|SEZ6L_ENST00000411842.2_5'UTR|SEZ6L_ENST00000402979.1_Missense_Mutation_p.T530N|SEZ6L_ENST00000248933.6_Missense_Mutation_p.T757N NM_001184774.1|NM_001184775.1|NM_001184777.1 NP_001171703.1|NP_001171704.1|NP_001171706.1 Q9BYH1 SE6L1_HUMAN seizure related 6 homolog (mouse)-like 757 Sushi 3. endoplasmic reticulum membrane|integral to membrane breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 80 GGCTGGAAAACCACTTCTCAC 0.532000 5 66 0.0293803 0.0303131 1 1 0 NEIL3 55247 broad.mit.edu 37 4 178283471 178283471 + Missense_Mutation SNP A A G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr4:178283471A>G ENST00000264596.3 + 10 1782 c.1664A>G c.(1663-1665)aAc>aGc p.N555S NM_018248.2 NP_060718.2 Q8TAT5 NEIL3_HUMAN nei endonuclease VIII-like 3 (E. coli) 555 base-excision repair|nucleotide-excision repair nucleus bubble DNA binding|damaged DNA binding|DNA N-glycosylase activity|DNA-(apurinic or apyrimidinic site) lyase activity|double-stranded DNA binding|single-stranded DNA binding|zinc ion binding breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 29 Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164) all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191) CCATTCTGCAACCATGGCAAG 0.388000 Base excision repair (BER), DNA glycosylases 15 73 0 0 1 0 0 CDK5RAP1 51654 broad.mit.edu 37 20 31981850 31981850 + Missense_Mutation SNP G G A TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr20:31981850G>A ENST00000357886.4 - 4 584 c.431C>T c.(430-432)aCa>aTa p.T144I CDK5RAP1_ENST00000346416.2_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000339269.5_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000473997.1_5'UTR|CDK5RAP1_ENST00000544843.1_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000452723.3_Missense_Mutation_p.T54I Q96SZ6 CK5P1_HUMAN CDK5 regulatory subunit associated protein 1 144 CDK5 activation inhibition.|MTTase N-terminal. brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification cytoplasm 4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1) 26 GATAGAGCATGTGACAAGGAG 0.403000 5 87 0 0 1 0 0 LINC00969 0 broad.mit.edu 37 3 195410627 195410627 + RNA SNP A A G rs6583272 by1000genomes TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr3:195410627A>G ENST00000445430.1 + 0 1824 CCTCAGGTGCAGATTGATGAG 0.473000 3 13 0 0 1 0 0 ANKRD32 84250 broad.mit.edu 37 5 94014548 94014548 + Silent SNP A A G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr5:94014548A>G ENST00000265140.5 + 15 2282 c.1863A>G c.(1861-1863)ggA>ggG p.G621G NM_032290.3 NP_115666.2 Q9BQI6 ANR32_HUMAN ankyrin repeat domain 32 621 p.G621G(4) NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1) 13 all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152) all cancers(79;3.88e-18) TATTGGCTGGAATTCTTGGAG 0.308000 34 34 0 0 1 0 0 PIDD 55367 broad.mit.edu 37 11 799816 799816 + Splice_Site SNP G G A TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr11:799816G>A ENST00000347755.5 - 15 2614 c.2474_splice c.e15+1 p.R825_splice PIDD_ENST00000411829.2_Splice_Site_p.R808_splice NM_145886.3|NM_145887.3 NP_665893.2|NP_665894.2 Q9HB75 PIDD_HUMAN p53-induced death domain protein 825 Death. apoptosis|signal transduction cytoplasm|nucleus death receptor binding GAGCCTCACCGGAACTCGTGC 0.687000 2 0 0 0 1 0 0 MXRA5 25878 broad.mit.edu 37 X 3228358 3228358 + Missense_Mutation SNP A A C TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chrX:3228358A>C ENST00000217939.6 - 7 8040 c.7886T>G c.(7885-7887)gTc>gGc p.V2629G NM_015419.3 NP_056234.2 Q9NR99 MXRA5_HUMAN matrix-remodelling associated 5 2629 Ig-like C2-type 10. extracellular region NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2) 157 all_lung(23;0.00031)|Lung NSC(23;0.000946) CTTCAGGGAGACCAGCCTCTC 0.612000 6 30 0 0 1 0 0 COMMD1 150684 broad.mit.edu 37 2 62132935 62132935 + Missense_Mutation SNP C C A TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr2:62132935C>A ENST00000311832.5 + 1 154 c.122C>A c.(121-123)cCa>cAa p.P41Q COMMD1_ENST00000472729.1_Intron|COMMD1_ENST00000538736.1_Missense_Mutation_p.P41Q NM_152516.2 NP_689729.1 Q8N668 COMD1_HUMAN copper metabolism (Murr1) domain containing 1 41 copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus copper ion binding|protein homodimerization activity large_intestine(1)|liver(2)|lung(5)|ovary(1) 9 Lung NSC(7;0.035)|all_lung(7;0.0691) LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934) CAGCTATATCCAGAGGTGCCA 0.597000 3 49 1 1 1 1 0 POLR2B 5431 broad.mit.edu 37 4 57876368 57876368 + Splice_Site SNP T T G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr4:57876368T>G ENST00000510355.1 + 1 28 c.e1+2 POLR2B_ENST00000381227.1_Intron|POLR2B_ENST00000441246.2_Intron|POLR2B_ENST00000431623.2_Intron|POLR2B_ENST00000314595.5_Intron P30876 RPB2_HUMAN polymerase (RNA) II (DNA directed) polypeptide B, 140kDa mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction DNA-directed RNA polymerase II, core complex DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1) 52 Glioma(25;0.08)|all_neural(26;0.181) AAGTGGCAGGTAAGTTAAAGT 0.353000 5 9 0 0 1 0 0 EPG5 57724 broad.mit.edu 37 18 43487997 43487997 + Missense_Mutation SNP C C T TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr18:43487997C>T ENST00000282041.5 - 24 4289 c.4255G>A c.(4255-4257)Gga>Aga p.G1419R EPG5_ENST00000585906.1_5'UTR NM_020964.2 NP_066015.2 Q9HCE0 EPG5_HUMAN ectopic P-granules autophagy protein 5 homolog (C. elegans) 1419 autophagy NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2) 95 TAGGTATCTCCTTTTTGAAAA 0.313000 9 89 0 0 1 0 0 SCMH1 22955 broad.mit.edu 37 1 41514523 41514523 + Missense_Mutation SNP T T G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr1:41514523T>G ENST00000402904.2 - 11 1483 c.1115A>C c.(1114-1116)cAc>cCc p.H372P SCMH1_ENST00000361191.5_Missense_Mutation_p.H311P|SCMH1_ENST00000361705.3_Missense_Mutation_p.H325P|SCMH1_ENST00000337495.5_Missense_Mutation_p.H382P|SCMH1_ENST00000326197.7_Missense_Mutation_p.H372P|SCMH1_ENST00000456518.2_Missense_Mutation_p.H214P|SCMH1_ENST00000397171.2_Missense_Mutation_p.H311P|SCMH1_ENST00000397174.2_Missense_Mutation_p.H352P|SCMH1_ENST00000372595.1_Missense_Mutation_p.H311P|SCMH1_ENST00000372596.1_Missense_Mutation_p.H311P|SCMH1_ENST00000372597.1_Missense_Mutation_p.H325P NM_001031694.2 NP_001026864.1 Q96GD3 SCMH1_HUMAN sex comb on midleg homolog 1 (Drosophila) 372 anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent DNA binding|sequence-specific DNA binding transcription factor activity breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1) 15 Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162) Myeloproliferative disorder(586;0.0393) CTTATCTAAGTGGGGGCCTGT 0.498000 9 102 0 0 1 0 0 TP53BP1 7158 broad.mit.edu 37 15 43738684 43738684 + Missense_Mutation SNP C C A TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr15:43738684C>A ENST00000263801.3 - 14 3178 c.2926G>T c.(2926-2928)Ggg>Tgg p.G976W TP53BP1_ENST00000382039.3_Missense_Mutation_p.G981W|TP53BP1_ENST00000450115.2_Missense_Mutation_p.G981W|TP53BP1_ENST00000382044.4_Missense_Mutation_p.G981W NM_005657.2 NP_005648.1 Q12888 TP53B_HUMAN tumor protein p53 binding protein 1 976 double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter condensed chromosome kinetochore|cytoplasm|nucleoplasm p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3) 72 all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728) GBM - Glioblastoma multiforme(94;1.59e-06) GGGGCAGCCCCAGAATCCCCT 0.473000 Other conserved DNA damage response genes 84 87 1.02218e-41 1.30278e-41 1 1 0 PRPF40B 25766 broad.mit.edu 37 12 50027256 50027256 + Missense_Mutation SNP G G A TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr12:50027256G>A ENST00000261897.1 + 7 973 c.422G>A c.(421-423)gGc>gAc p.G141D PRPF40B_ENST00000548825.2_Missense_Mutation_p.G169D|PRPF40B_ENST00000380281.1_Missense_Mutation_p.G147D Q6NWY9 PR40B_HUMAN PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) 147 WW 2. mRNA processing|RNA splicing nuclear speck breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1) 34 TCGGACACAGGCAAACCTTAT 0.552000 5 319 0 0 1 0 0 GPR160 26996 broad.mit.edu 37 3 169802316 169802316 + Missense_Mutation SNP T T G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr3:169802316T>G ENST00000355897.5 + 4 1164 c.556T>G c.(556-558)Tca>Gca p.S186A NM_014373.2 NP_055188.1 Q9UJ42 GP160_HUMAN G protein-coupled receptor 160 186 integral to membrane|plasma membrane G-protein coupled receptor activity breast(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2) 8 all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169) Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655) TTACTGGCTGTCATTTTTCAT 0.398000 9 45 0 0 1 0 0 PURG 29942 broad.mit.edu 37 8 30889322 30889322 + Missense_Mutation SNP T T G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr8:30889322T>G ENST00000475541.1 - 1 1909 c.977A>C c.(976-978)aAc>aCc p.N326T PURG_ENST00000339382.2_Intron NM_013357.2 NP_037489.1 Q9UJV8 PURG_HUMAN purine-rich element binding protein G 326 nucleus DNA binding endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|urinary_tract(1) 12 KIRC - Kidney renal clear cell carcinoma(542;0.0895)|Kidney(114;0.108) TTTATGGCTGTTGCAAATTTT 0.388000 3 1 0 0 1 0 0 MTHFR 4524 broad.mit.edu 37 1 11856448 11856448 + Missense_Mutation SNP T T G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr1:11856448T>G ENST00000376592.1 - 4 723 c.595A>C c.(595-597)Aaa>Caa p.K199Q MTHFR_ENST00000376590.3_Missense_Mutation_p.K199Q|MTHFR_ENST00000376583.3_Missense_Mutation_p.K240Q|MTHFR_ENST00000376585.1_Missense_Mutation_p.K240Q P42898 MTHR_HUMAN methylenetetrahydrofolate reductase (NAD(P)H) 199 blood circulation|folic acid metabolic process cytosol methylenetetrahydrofolate reductase (NADPH) activity|protein binding NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 33 Ovarian(185;0.249) Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649) Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116) GGGTGGCCTTTGGGGTAACCT 0.562000 7 96 0 0 1 0 0 HOXD12 3238 broad.mit.edu 37 2 176964720 176964720 + Missense_Mutation SNP C C T TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr2:176964720C>T ENST00000406506.2 + 1 263 c.191C>T c.(190-192)gCg>gTg p.A64V HOXD12_ENST00000404162.2_Missense_Mutation_p.A64V P35452 HXD12_HUMAN homeobox D12 64 QPA -> TC (in Ref. 1; AAF79044). nuclear chromosome sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1) 10 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678) GCGCAGCCTGCGGGCGCCACT 0.751000 2 1 0 0 1 0 0 FCRL1 115350 broad.mit.edu 37 1 157772382 157772382 + Missense_Mutation SNP A A C TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr1:157772382A>C ENST00000358292.3 - 4 443 c.392T>G c.(391-393)gTc>gGc p.V131G FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000368176.3_Missense_Mutation_p.V131G|FCRL1_ENST00000491942.1_Missense_Mutation_p.V131G NM_001159397.1 NP_001152869.1 Q96LA6 FCRL1_HUMAN Fc receptor-like 1 131 Ig-like C2-type 2. integral to membrane|plasma membrane receptor activity breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6) 42 all_hematologic(112;0.0378) LUSC - Lung squamous cell carcinoma(543;0.24) GCAGATGAGGACCAGCCTGTC 0.542000 5 23 0 0 1 0 0 POLR1A 25885 broad.mit.edu 37 2 86297188 86297188 + Missense_Mutation SNP C C T TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr2:86297188C>T ENST00000263857.6 - 13 2197 c.1819G>A c.(1819-1821)Gag>Aag p.E607K POLR1A_ENST00000409681.1_Missense_Mutation_p.E607K O95602 RPA1_HUMAN polymerase (RNA) I polypeptide A, 194kDa 607 termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter DNA-directed RNA polymerase I complex|nucleoplasm DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5) 63 ACGTAGGCCTCGGCCCGGCCC 0.572000 19 15 0 0 1 0 0 C1orf172 126695 broad.mit.edu 37 1 27276560 27276560 + Nonstop_Mutation SNP T T G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr1:27276560T>G ENST00000320567.5 - 4 1285 c.1197A>C c.(1195-1197)taA>taC p.*399Y NM_152365.2 NP_689578.2 Q8NAX2 CA172_HUMAN chromosome 1 open reading frame 172 0 NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 17 all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419) CTGGCAGGGGTTAGCAGTACA 0.602000 5 45 0 0 1 0 0 PADI2 11240 broad.mit.edu 37 1 17411155 17411155 + Frame_Shift_Del DEL G G - rs149752241 by1000genomes TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr1:17411155delG ENST00000375486.4 - 8 940 c.877delC c.(877-879)ggfs p.R293fs PADI2_ENST00000444885.2_Intron|PADI2_ENST00000375481.1_Frame_Shift_Del_p.R293fs NM_007365.2 NP_031391.2 Q9Y2J8 PADI2_HUMAN peptidyl arginine deiminase, type II 293 peptidyl-citrulline biosynthetic process from peptidyl-arginine cytoplasm calcium ion binding|protein-arginine deiminase activity breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3) 29 Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201) L-Citrulline(DB00155) GGAGCAATCCGGAATATCACG 0.577 2 4 --- --- --- --- RP11-453E17.1 0 broad.mit.edu 37 4 68632404 68632404 + RNA DEL C C - TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr4:68632404delC ENST00000500538.2 + 0 1905 RP11-453E17.1_ENST00000502758.1_RNA cacacacacacacacacacac 0.443 2 4 --- --- --- --- RP11-551L14.1 0 broad.mit.edu 37 12 31269189 31269190 + RNA INS - - ATCAT rs35880498 TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-10A-01D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 6f4ff365-ee63-40d0-8f71-ed062f755d22 g.chr12:31269189_31269190insATCAT ENST00000542490.1 - 0 165 central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(25)|prostate(3)|stomach(3)|urinary_tract(1) 41 CATGAGAACTCATTACCATGAT 0.351 6 8 --- --- --- --- PADI2 11240 broad.mit.edu 37 1 17411155 17411155 + Frame_Shift_Del DEL G G - rs149752241 by1000genomes TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr1:17411155delG ENST00000375486.4 - 8 940 c.877delC c.(877-879)ggfs p.R293fs PADI2_ENST00000444885.2_Intron|PADI2_ENST00000375481.1_Frame_Shift_Del_p.R293fs NM_007365.2 NP_031391.2 Q9Y2J8 PADI2_HUMAN peptidyl arginine deiminase, type II 293 peptidyl-citrulline biosynthetic process from peptidyl-arginine cytoplasm calcium ion binding|protein-arginine deiminase activity breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3) 29 Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201) L-Citrulline(DB00155) GGAGCAATCCGGAATATCACG 0.577 2 4 --- --- --- --- C2orf78 388960 broad.mit.edu 37 2 74043341 74043342 + Frame_Shift_Ins INS - - C rs74479148 by1000genomes TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr2:74043341_74043342insC ENST00000409561.1 + 3 2112_2113 c.1991_1992insC c.(1990-1992)acgfs p.T664fs NM_001080474.1 NP_001073943.1 A6NCI8 CB078_HUMAN chromosome 2 open reading frame 78 664 cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1) 34 AACACCCAAAACCGCCAGCCAT 0.495 13 48 --- --- --- --- AC073321.4 0 broad.mit.edu 37 2 217475031 217475032 + RNA INS - - AA rs71401156 TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr2:217475031_217475032insAA ENST00000441803.1 + 0 195 AATTTTATTTCAAAAAAAAAAA 0.376 3 5 --- --- --- --- RP11-453E17.1 0 broad.mit.edu 37 4 68632404 68632404 + RNA DEL C C - TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr4:68632404delC ENST00000500538.2 + 0 1905 RP11-453E17.1_ENST00000502758.1_RNA cacacacacacacacacacac 0.443 2 4 --- --- --- --- PCLO 27445 broad.mit.edu 37 7 82595145 82595146 + Frame_Shift_Ins INS - - G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr7:82595145_82595146insG ENST00000423517.2 - 4 4295_4296 c.3958_3959insC c.(3958-3960)gccfs p.A1320fs PCLO_ENST00000333891.8_Frame_Shift_Ins_p.A1320fs NM_014510.2 NP_055325.2 Q9Y6V0 PCLO_HUMAN piccolo presynaptic cytomatrix protein 1259 cytoskeleton organization|synaptic vesicle exocytosis cell junction|cytoskeleton|synaptic vesicle calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2) 259 TGGCTGTGGCTGTTCTTTTATT 0.406 9 150 --- --- --- --- ZAN 7455 broad.mit.edu 37 7 100352835 100352836 + RNA INS - - G rs145118358 by1000genomes TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr7:100352835_100352836insG ENST00000542585.1 + 0 3272 ZAN_ENST00000349350.6_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000348028.3_RNA|ZAN_ENST00000538115.1_RNA NM_003386.1 NP_003377.1 Q9Y493 ZAN_HUMAN zonadhesin (gene/pseudogene) binding of sperm to zona pellucida|cell-cell adhesion integral to membrane|plasma membrane NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3) 139 Lung NSC(181;0.041)|all_lung(186;0.0581) STAD - Stomach adenocarcinoma(171;0.19) TGACAGAGGCTGTTTTCCCCTT 0.545 16 199 --- --- --- --- PNPLA8 50640 broad.mit.edu 37 7 108155503 108155504 + Frame_Shift_Ins INS - - C TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr7:108155503_108155504insC ENST00000426128.2 - 2 557_558 c.432_433insG c.(430-435)tgtaaafs p.CK144fs PNPLA8_ENST00000453144.1_Frame_Shift_Ins_p.CK44fs|PNPLA8_ENST00000436062.1_Frame_Shift_Ins_p.CK144fs|PNPLA8_ENST00000388728.5_Frame_Shift_Ins_p.CK144fs|PNPLA8_ENST00000422087.1_Frame_Shift_Ins_p.CK144fs|PNPLA8_ENST00000257694.8_Frame_Shift_Ins_p.CK144fs|PNPLA8_ENST00000483879.1_Intron NM_001256009.1 NP_001242938.1 Q9NP80 PLPL8_HUMAN patatin-like phospholipase domain containing 8 144 fatty acid metabolic process|lipid catabolic process endoplasmic reticulum membrane|Golgi membrane|integral to membrane|membrane fraction|perinuclear region of cytoplasm|peroxisomal membrane ATP binding|calcium-independent phospholipase A2 activity|lysophospholipase activity breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3) 29 TTCTGTTTTAACCAGCCACTAT 0.327 8 92 --- --- --- --- PODXL 5420 broad.mit.edu 37 7 131195806 131195807 + Frame_Shift_Ins INS - - G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr7:131195806_131195807insG ENST00000541194.1 - 2 749_750 c.492_493insC c.(490-495)aggccafs p.RP164fs PODXL_ENST00000322985.9_Frame_Shift_Ins_p.RP162fs|PODXL_ENST00000378555.3_Frame_Shift_Ins_p.RP162fs|PODXL_ENST00000537928.1_Frame_Shift_Ins_p.RP162fs NM_001018111.2 NP_001018121.1 O00592 PODXL_HUMAN podocalyxin-like 162 Thr-rich. cell adhesion|epithelial tube formation|negative regulation of cell-cell adhesion|positive regulation of cell migration|positive regulation of cell-cell adhesion mediated by integrin|regulation of microvillus assembly actin cytoskeleton|apical plasma membrane|centrosome|filopodium|integral to plasma membrane|lamellipodium|membrane raft|microvillus membrane|nucleolus|ruffle NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1) 24 Melanoma(18;0.162) ACACTGTGGCTGCTTTTCCCCC 0.535 7 329 --- --- --- --- ADAM28 10863 broad.mit.edu 37 8 24207413 24207414 + Frame_Shift_Ins INS - - G rs139883608 by1000genomes TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr8:24207413_24207414insG ENST00000265769.4 + 19 2137_2138 c.2027_2028insG c.(2026-2028)ggtfs p.G676fs RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000397649.3_Frame_Shift_Ins_p.S425fs|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA NM_014265.4 NP_055080.2 Q9UKQ2 ADA28_HUMAN ADAM metallopeptidase domain 28 676 proteolysis|spermatogenesis extracellular region|integral to membrane|plasma membrane metalloendopeptidase activity|zinc ion binding p.A676V(1) central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 42 Prostate(55;0.0959) Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175) TTCCCAATGGCGGTCATTTTTG 0.505 8 140 --- --- --- --- FBN1 2200 broad.mit.edu 37 15 48704823 48704824 + Frame_Shift_Ins INS - - T TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr15:48704823_48704824insT ENST00000316623.5 - 65 8623_8624 c.8168_8169insA c.(8167-8169)tccfs p.S2723fs FBN1_ENST00000561429.1_5'UTR NM_000138.4 NP_000129.3 P35555 FBN1_HUMAN fibrillin 1 2723 heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development basement membrane|extracellular space|microfibril calcium ion binding|extracellular matrix structural constituent|protein binding NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2) 139 all_lung(180;0.00279) all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05) CCCGTTTGGGGTAGCCATTGAT 0.515 9 230 --- --- --- --- CNOT1 23019 broad.mit.edu 37 16 58633164 58633165 + Frame_Shift_Ins INS - - C TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr16:58633164_58633165insC ENST00000317147.5 - 2 409_410 c.77_78insG c.(76-78)cgcfs p.R26fs CNOT1_ENST00000441024.2_Frame_Shift_Ins_p.R26fs|CNOT1_ENST00000569240.1_Frame_Shift_Ins_p.R26fs NM_001265612.1|NM_016284.4 NP_001252541.1|NP_057368.3 A5YKK6 CNOT1_HUMAN CCR4-NOT transcription complex, subunit 1 26 nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasmic mRNA processing body|cytosol breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2) 87 Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239) GCTGGCTGGCTCGGTAATTTTT 0.455 7 72 --- --- --- --- SYNRG 11276 broad.mit.edu 37 17 35914100 35914101 + Frame_Shift_Ins INS - - G rs147693241 by1000genomes TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr17:35914100_35914101insG ENST00000339208.6 - 14 1864_1865 c.1724_1725insC c.(1723-1725)agcfs p.S575fs SYNRG_ENST00000588194.1_5'UTR|SYNRG_ENST00000591288.1_Frame_Shift_Ins_p.S414fs|SYNRG_ENST00000585472.1_Frame_Shift_Ins_p.S496fs|SYNRG_ENST00000502449.2_Frame_Shift_Ins_p.S497fs|SYNRG_ENST00000345615.4_Frame_Shift_Ins_p.S497fs|SYNRG_ENST00000346661.4_Frame_Shift_Ins_p.S575fs|SYNRG_ENST00000394378.2_Frame_Shift_Ins_p.S497fs NM_001163544.1|NM_001163545.1|NM_007247.4 NP_001157016.1|NP_001157017.1|NP_009178.3 Q9UMZ2 SYNRG_HUMAN synergin, gamma 575 Interaction with A1P1G1 and A1P1G2. endocytosis|intracellular protein transport AP-1 adaptor complex calcium ion binding breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1) 36 CACTATCGGCTGTTTTAAAATC 0.401 40 156 --- --- --- --- RNF43 54894 broad.mit.edu 37 17 56435501 56435502 + Frame_Shift_Ins INS - - G rs144487242 by1000genomes TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr17:56435501_56435502insG ENST00000584437.1 - 8 3590_3591 c.1635_1636insC c.(1633-1638)tcgccafs p.P546fs RNF43_ENST00000583753.1_Frame_Shift_Ins_p.P505fs|RNF43_ENST00000577625.1_Frame_Shift_Ins_p.P419fs|RNF43_ENST00000407977.2_Frame_Shift_Ins_p.P546fs|RNF43_ENST00000500597.2_Frame_Shift_Ins_p.P505fs|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Frame_Shift_Ins_p.P546fs|RNF43_ENST00000581868.1_Frame_Shift_Ins_p.P419fs Q68DV7 RNF43_HUMAN ring finger protein 43 546 endoplasmic reticulum membrane|integral to membrane|nuclear envelope ligase activity|protein binding|zinc ion binding NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4) 60 Medulloblastoma(34;0.127)|all_neural(34;0.237) TGGACATGGCTGGAAACCTGGG 0.624 11 152 --- --- --- --- SIX5 147912 broad.mit.edu 37 19 46269225 46269226 + Frame_Shift_Ins INS - - G TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr19:46269225_46269226insG ENST00000317578.6 - 3 2134_2135 c.1753_1754insC c.(1753-1755)gccfs p.A585fs AC074212.5_ENST00000559756.1_RNA|SIX5_ENST00000560168.1_3'UTR NM_175875.4 NP_787071.2 Q8N196 SIX5_HUMAN SIX homeobox 5 585 cytoplasm|nucleus protein binding|sequence-specific DNA binding transcription factor activity endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1) 8 Ovarian(192;0.0308)|all_neural(266;0.112) OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235) CTTCAGTGGCAGGGCCAGGCCG 0.698 4 8 --- --- --- --- RSPH6A 81492 broad.mit.edu 37 19 46299147 46299149 + In_Frame_Del DEL CCT CCT - TCGA-DO-A1JZ-01A-11D-A13W-08 TCGA-DO-A1JZ-11A-11D-A13W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 7c622602-14bf-4377-bb3d-c6197a55a8cc 64f1b3b9-24c9-4715-b6ce-834b3443d46f g.chr19:46299147_46299149delCCT ENST00000221538.3 - 6 2274_2276 c.2132_2134delAGG c.(2131-2136)ggc>g p.EG711del RSPH6A_ENST00000597055.1_3'UTR|RSPH6A_ENST00000600188.1_In_Frame_Del_p.EG447del NM_030785.3 NP_110412.1 Q9H0K4 RSH6A_HUMAN radial spoke head 6 homolog A (Chlamydomonas) 711 Glu-rich. intracellular central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2) 32 GTctcctcgccctcctcctcctc 0.557 7 186 --- --- --- ---