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 AHNAK 79026 broad.mit.edu 37 11 62287998 62287998 + Missense_Mutation SNP C C A TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr11:62287998C>A ENST00000378024.4 - 5 14165 c.13891G>T c.(13891-13893)Gac>Tac p.D4631Y AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron NM_001620.1 NP_001611.1 Q09666 AHNK_HUMAN AHNAK nucleoprotein 4631 D -> G (in dbSNP:rs12801123). RD -> KG (in Ref. 2; AAA69898). nervous system development nucleus protein binding NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6) 268 Melanoma(852;0.155) ACTTTGGGGTCCCTGATGTCA 0.522000 100 338 2.6645e-62 3.34771e-62 0.139131 1 0 LGI1 9211 broad.mit.edu 37 10 95557106 95557106 + Missense_Mutation SNP G G A TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr10:95557106G>A ENST00000371418.4 + 8 1480 c.1220G>A c.(1219-1221)cGt>cAt p.R407H LGI1_ENST00000542308.1_Missense_Mutation_p.R359H|LGI1_ENST00000371413.3_Intron NM_005097.2 NP_005088.1 O95970 LGI1_HUMAN leucine-rich, glioma inactivated 1 407 axon guidance|cell proliferation|positive regulation of cell growth|positive regulation of synaptic transmission cell junction|extracellular space|synapse receptor binding central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1) 29 Colorectal(252;0.124) AGTTCCCAGCGTCCTGTAATT 0.433000 113 82 0 0 0.139131 0 0 CMA1 1215 broad.mit.edu 37 14 24976583 24976583 + Missense_Mutation SNP G G A rs13306251 by1000genomes TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr14:24976583G>A ENST00000250378.3 - 2 217 c.188C>T c.(187-189)aCg>aTg p.T63M RP11-80A15.1_ENST00000555109.1_Intron|CMA1_ENST00000206446.4_Intron NM_001836.3 NP_001827.1 P23946 CMA1_HUMAN chymase 1, mast cell 63 Peptidase S1. interleukin-1 beta biosynthetic process|proteolysis extracellular region serine-type endopeptidase activity kidney(1)|lung(8)|pancreas(1)|prostate(1) 11 GBM - Glioblastoma multiforme(265;0.0271) ATGAGCAGCCGTCAGCACAAA 0.488000 83 163 0 0 0.139131 0 0 NEBL 10529 broad.mit.edu 37 10 21097515 21097515 + Silent SNP G G A rs140245727 byFrequency TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr10:21097515G>A ENST00000377122.4 - 26 3081 c.2685C>T c.(2683-2685)gaC>gaT p.D895D NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron NM_006393.2 NP_006384.1 O76041 NEBL_HUMAN nebulette 895 Linker. regulation of actin filament length actin binding|structural constituent of muscle NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2) 70 CTGACCTGTCGTCTCCGAGAC 0.458000 7 331 0 0 0.038147 0 0 FYCO1 79443 broad.mit.edu 37 3 46014621 46014621 + Silent SNP C C T rs149291592 byFrequency TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr3:46014621C>T ENST00000296137.2 - 6 703 c.498G>A c.(496-498)tcG>tcA p.S166S FYCO1_ENST00000535325.1_Silent_p.S166S NM_024513.3 NP_078789.2 Q9BQS8 FYCO1_HUMAN FYVE and coiled-coil domain containing 1 166 RUN. transport integral to membrane metal ion binding|protein binding NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1) 54 BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323) CAAAGCCCCTCGACGCCAGGT 0.483000 26 74 0 0 0.091800 0 0 CNGA1 1259 broad.mit.edu 37 4 47938995 47938995 + Missense_Mutation SNP T T A TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr4:47938995T>A ENST00000402813.3 - 10 1865 c.1723A>T c.(1723-1725)Att>Ttt p.I575F CNGA1_ENST00000358519.4_Missense_Mutation_p.I506F|CNGA1_ENST00000544810.1_Missense_Mutation_p.I506F|CNGA1_ENST00000420489.2_Missense_Mutation_p.I506F|CNGA1_ENST00000514170.1_Missense_Mutation_p.I506F P29973 CNGA1_HUMAN cyclic nucleotide gated channel alpha 1 506 response to stimulus|visual perception integral to plasma membrane cGMP binding|ion channel activity central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1) 28 TTCTTGCAAATATAATCTCCA 0.438000 16 283 0 0 0.160694 0 0 AKNA 80709 broad.mit.edu 37 9 117139492 117139492 + Missense_Mutation SNP T T C TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr9:117139492T>C ENST00000307564.4 - 3 756 c.595A>G c.(595-597)Agg>Ggg p.R199G AKNA_ENST00000312033.3_Missense_Mutation_p.R199G|AKNA_ENST00000374088.3_Missense_Mutation_p.R199G|AKNA_ENST00000374075.5_Missense_Mutation_p.R118G NM_030767.4 NP_110394.3 Q7Z591 AKNA_HUMAN AT-hook transcription factor 199 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2) 51 CTCCAGGACCTTGCCGGGCTG 0.612000 87 61 0 0 0.139131 0 0 PKHD1 5314 broad.mit.edu 37 6 51513908 51513908 + Missense_Mutation SNP G G T TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr6:51513908G>T ENST00000371117.3 - 62 11560 c.11285C>A c.(11284-11286)cCa>cAa p.P3762Q NM_138694.3 NP_619639.3 P08F94 PKHD1_HUMAN polycystic kidney and hepatic disease 1 (autosomal recessive) 3762 cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5) 304 Lung NSC(77;0.0605) TACCAATTGTGGCTGCACTGG 0.413000 82 132 1.55521e-42 1.85866e-42 0.139131 1 0 KLF11 8462 broad.mit.edu 37 2 10188340 10188340 + Silent SNP G G T TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr2:10188340G>T ENST00000535335.1 + 3 1041 c.825G>T c.(823-825)gtG>gtT p.V275V KLF11_ENST00000305883.1_Silent_p.V292V|KLF11_ENST00000540845.1_Silent_p.V275V NM_001177718.1 NP_001171189.1 O14901 KLF11_HUMAN Kruppel-like factor 11 292 apoptosis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|regulation of transcription involved in S phase of mitotic cell cycle nucleus sequence-specific DNA binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 16 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228) TGATCCCTGTGACTGGACAAA 0.537000 OREG0014425 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 8 195 0.0381472 0.038942 0.038147 1 0 PHF3 23469 broad.mit.edu 37 6 64356551 64356551 + Missense_Mutation SNP A A G TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr6:64356551A>G ENST00000262043.3 + 2 435 c.95A>G c.(94-96)gAg>gGg p.E32G PHF3_ENST00000393387.1_Missense_Mutation_p.E32G|PHF3_ENST00000509330.1_Missense_Mutation_p.E32G Q92576 PHF3_HUMAN PHD finger protein 3 32 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6) 75 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) GAAGTCTGTGAGGATTTTAGT 0.393000 49 143 0 0 0.139131 0 0 PAX6 5080 broad.mit.edu 37 11 31815341 31815341 + Missense_Mutation SNP A A G TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr11:31815341A>G ENST00000419022.1 - 11 1285 c.817T>C c.(817-819)Tct>Cct p.S273P PAX6_ENST00000379132.3_Missense_Mutation_p.S259P|PAX6_ENST00000379115.4_Missense_Mutation_p.S273P|PAX6_ENST00000379107.2_Missense_Mutation_p.S273P|PAX6_ENST00000379129.2_Missense_Mutation_p.S273P|PAX6_ENST00000379111.2_Missense_Mutation_p.S259P|PAX6_ENST00000241001.8_Missense_Mutation_p.S259P|PAX6_ENST00000379123.5_Missense_Mutation_p.S259P NM_001127612.1|NM_001258462.1|NM_001258463.1 NP_001121084.1|NP_001245391.1|NP_001245392.1 P26367 PAX6_HUMAN paired box 6 259 blood vessel development|central nervous system development|cornea development in camera-type eye|glucose homeostasis|iris morphogenesis|negative regulation of neurogenesis|neuron fate commitment|pancreatic A cell development|positive regulation of transcription, DNA-dependent|response to wounding|visual perception cytoplasm|nuclear chromatin R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|ubiquitin-protein ligase activity central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2) 35 Lung SC(675;0.225) CTTCGATTAGAAAACCATACC 0.522000 Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation 78 5 0 0 0.139131 0 0 MAN2A2 4122 broad.mit.edu 37 15 91450665 91450665 + Missense_Mutation SNP G G A TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr15:91450665G>A ENST00000360468.3 + 7 1154 c.1136G>A c.(1135-1137)cGc>cAc p.R379H MAN2A2_ENST00000431652.2_5'UTR|MAN2A2_ENST00000559717.1_Missense_Mutation_p.R379H NM_006122.2 NP_006113.2 P49641 MA2A2_HUMAN mannosidase, alpha, class 2A, member 2 379 mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine Golgi membrane|integral to membrane alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1) 47 Lung NSC(78;0.0771)|all_lung(78;0.137) Lung(145;0.229) CCTGGTGGGCGCATCAACTGC 0.567000 5 184 0 0 0.014758 0 0 STK3 6788 broad.mit.edu 37 8 99779474 99779474 + Missense_Mutation SNP T T C TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr8:99779474T>C ENST00000523601.1 - 5 716 c.317A>G c.(316-318)gAc>gGc p.D106G STK3_ENST00000419617.2_Missense_Mutation_p.D78G NM_001256312.1 NP_001243241.1 Q13188 STK3_HUMAN serine/threonine kinase 3 78 Protein kinase. apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis cytoplasm|nucleus ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1) 17 Breast(36;2.4e-06) Breast(495;0.106) OV - Ovarian serous cystadenocarcinoma(57;0.0382) KIRC - Kidney renal clear cell carcinoma(542;9.44e-06) TTCATACCTGTCACATTGCTG 0.313000 54 60 0 0 0.139131 0 0 NAT8 9027 broad.mit.edu 37 2 73868641 73868641 + Missense_Mutation SNP G G C TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr2:73868641G>C ENST00000272425.3 - 2 264 c.115C>G c.(115-117)Ctg>Gtg p.L39V NM_003960.3|NM_016347.2 NP_003951.3|NP_057431.2 Q9UHE5 NAT8_HUMAN N-acetyltransferase 8 (GCN5-related, putative) 39 gastrulation with mouth forming second|response to drug integral to membrane N-acetyltransferase activity breast(1)|endometrium(2)|kidney(2)|lung(2)|ovary(1)|prostate(1) 9 GTTCGAGGCAGCTTCAGCAAT 0.622000 63 209 0 0 0.139131 0 0 ALMS1 7840 broad.mit.edu 37 2 73718168 73718168 + Missense_Mutation SNP T T G TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr2:73718168T>G ENST00000264448.6 + 10 9190 c.9079T>G c.(9079-9081)Tgt>Ggt p.C3027G ALMS1_ENST00000409009.1_Missense_Mutation_p.C2985G NM_015120.4 NP_055935.4 Q8TCU4 ALMS1_HUMAN Alstrom syndrome 1 3027 G2/M transition of mitotic cell cycle centrosome|cilium|cytosol|microtubule basal body|spindle pole breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2) 147 CCCAAATCACTGTACATTAGC 0.378000 64 195 0 0 0.139131 0 0 CHAT 1103 broad.mit.edu 37 10 50901834 50901834 + Nonstop_Mutation SNP G G T TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr10:50901834G>T ENST00000455728.2 + 15 1748 c.1638G>T c.(1636-1638)taG>taT p.*546Y C10orf53_ENST00000374111.3_Missense_Mutation_p.D38Y|C10orf53_ENST00000374112.3_Missense_Mutation_p.D38Y|C10orf53_ENST00000374113.3_Missense_Mutation_p.D38Y|C10orf53_ENST00000535836.1_Missense_Mutation_p.D38Y P28329 CLAT_HUMAN choline O-acetyltransferase 0 neurotransmitter biosynthetic process|neurotransmitter secretion cytosol|nucleus choline O-acetyltransferase activity central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1) 56 all_neural(218;0.107) GBM - Glioblastoma multiforme(2;0.000585) Choline(DB00122) GTTGGCCATAGATGGACATGA 0.463000 12 127 2.27111e-07 2.52919e-07 0.093190 1 0 PCSK5 5125 broad.mit.edu 37 9 78965754 78965754 + Silent SNP G G A TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr9:78965754G>A ENST00000545128.1 + 35 5434 c.4896G>A c.(4894-4896)gcG>gcA p.A1632A NM_001190482.1 NP_001177411.1 Q92824 PCSK5_HUMAN proprotein convertase subtilisin/kexin type 5 797 anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release extracellular space|Golgi lumen|stored secretory granule peptide binding|serine-type endopeptidase activity NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3) 55 GAAAAGGAGCGTTGAATTGTT 0.448000 129 128 0 0 0.139131 0 0 COL25A1 84570 broad.mit.edu 37 4 109765700 109765700 + Missense_Mutation SNP C C T TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr4:109765700C>T ENST00000399132.1 - 30 2134 c.1604G>A c.(1603-1605)gGt>gAt p.G535D COL25A1_ENST00000399126.1_Missense_Mutation_p.G535D|COL25A1_ENST00000399127.1_Missense_Mutation_p.G508D NM_198721.2 NP_942014.1 Q9BXS0 COPA1_HUMAN collagen, type XXV, alpha 1 535 collagen|extracellular space beta-amyloid binding|heparin binding NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1) 49 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.000173) gccatggggacctggtgggcc 0.433000 48 100 0 0 0.139131 0 0 ETAA1 54465 broad.mit.edu 37 2 67631847 67631847 + Missense_Mutation SNP A A G TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr2:67631847A>G ENST00000272342.5 + 5 2163 c.2033A>G c.(2032-2034)aAc>aGc p.N678S ETAA1_ENST00000462772.1_Intron NM_019002.3 NP_061875.2 Q9NY74 ETAA1_HUMAN Ewing tumor-associated antigen 1 678 cytoplasm|nucleus autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1) 33 GGAGCCAAAAACATGTTTGCT 0.363000 90 110 0 0 0.139131 0 0 MMP19 4327 broad.mit.edu 37 12 56233333 56233333 + Missense_Mutation SNP C C T rs138516871 TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr12:56233333C>T ENST00000322569.4 - 5 804 c.713G>A c.(712-714)cGg>cAg p.R238Q MMP19_ENST00000409200.3_Intron|MMP19_ENST00000548629.1_Missense_Mutation_p.R215Q NM_002429.4 NP_002420.1 Q99542 MMP19_HUMAN matrix metallopeptidase 19 238 angiogenesis|cell differentiation|collagen catabolic process|proteolysis proteinaceous extracellular matrix calcium ion binding|metalloendopeptidase activity|zinc ion binding endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2) 26 AAAGTGGGGCCGGTAGCCCTC 0.617000 18 63 0 0 0.043863 0 0 KIAA1407 57577 broad.mit.edu 37 3 113761686 113761686 + Silent SNP C C T TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr3:113761686C>T ENST00000295878.3 - 4 425 c.279G>A c.(277-279)gaG>gaA p.E93E KIAA1407_ENST00000545063.1_5'UTR|KIAA1407_ENST00000480588.1_5'UTR NM_020817.1 NP_065868.1 Q8NCU4 K1407_HUMAN KIAA1407 93 endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1) 40 CATTGACCAGCTCCTGAGCTA 0.333000 48 137 0 0 0.139131 0 0 GBP3 2635 broad.mit.edu 37 1 89486247 89486247 + Missense_Mutation SNP T T C TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr1:89486247T>C ENST00000370481.4 - 2 378 c.158A>G c.(157-159)tAc>tGc p.Y53C GBP3_ENST00000475853.2_5'UTR NM_018284.2 NP_060754.2 Q9H0R5 GBP3_HUMAN guanylate binding protein 3 53 integral to membrane GTP binding|GTPase activity breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1) 26 Lung NSC(277;0.123) all cancers(265;0.0103)|Epithelial(280;0.0293) GTTCATCAGGTAGGATTTTCC 0.517000 30 159 0 0 0.116897 0 0 OSGIN1 29948 broad.mit.edu 37 16 83994303 83994303 + Missense_Mutation SNP C C T TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr16:83994303C>T ENST00000343939.2 + 5 966 c.583C>T c.(583-585)Cgg>Tgg p.R195W OSGIN1_ENST00000361711.3_Missense_Mutation_p.R112W|OSGIN1_ENST00000393306.1_Missense_Mutation_p.R112W|OSGIN1_ENST00000565123.1_Missense_Mutation_p.R112W Q9UJX0 OSGI1_HUMAN oxidative stress induced growth inhibitor 1 195 cell differentiation|multicellular organismal development|negative regulation of cell growth growth factor activity autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1) 12 CTGGAAGCACCGGAAGGAGCA 0.657000 21 101 0 0 0.069288 0 0 IDH1 3417 broad.mit.edu 37 2 209113112 209113112 + Missense_Mutation SNP C C T rs121913500 TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr2:209113112C>T ENST00000415913.1 - 4 776 c.395G>A c.(394-396)cGt>cAt p.R132H IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H O75874 IDHC_HUMAN isocitrate dehydrogenase 1 (NADP+), soluble 132 R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). 2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle cytosol|peroxisomal matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1) NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1) 4887 Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136) ATAAGCATGACGACCTATGAT 0.393000 Mis gliobastoma 107 83 0 0 0.139131 0 0 RPS6KA1 6195 broad.mit.edu 37 1 26898350 26898350 + Missense_Mutation SNP G G T TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr1:26898350G>T ENST00000374168.2 + 19 1917 c.1763G>T c.(1762-1764)cGc>cTc p.R588L RPS6KA1_ENST00000374162.2_Missense_Mutation_p.R496L|RPS6KA1_ENST00000531382.1_Missense_Mutation_p.R597L|RPS6KA1_ENST00000374166.4_Missense_Mutation_p.R577L|RPS6KA1_ENST00000526792.1_Missense_Mutation_p.R496L|RPS6KA1_ENST00000530003.1_Missense_Mutation_p.R572L NM_002953.3 NP_002944.2 Q15418 KS6A1_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 1 588 Protein kinase 2. axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity lung(1) 1 all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234) GTGCTGAAGCGCCAGGGCTAC 0.627000 27 35 3.00307e-07 3.27001e-07 0.134883 1 0 EPHA3 2042 broad.mit.edu 37 3 89448615 89448615 + Nonsense_Mutation SNP G G T TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr3:89448615G>T ENST00000336596.2 + 7 1804 c.1579G>T c.(1579-1581)Gaa>Taa p.E527* EPHA3_ENST00000452448.2_Nonsense_Mutation_p.E527*|EPHA3_ENST00000494014.1_Nonsense_Mutation_p.E527* NM_005233.5 NP_005224.2 P29320 EPHA3_HUMAN EPH receptor A3 527 Fibronectin type-III 2. extracellular region|integral to plasma membrane ATP binding NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5) 139 all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612) Lung NSC(201;0.0782) LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942) GTTTGAGTTTGAAACTAGTCC 0.448000 TSP Lung(6;0.00050) 30 92 1.57351e-24 1.79307e-24 0.064281 1 0 ALKBH6 84964 broad.mit.edu 37 19 36501795 36501795 + Splice_Site SNP C C T TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr19:36501795C>T ENST00000486389.1 - 4 1016 c.e4+1 ALKBH6_ENST00000252984.7_Splice_Site|ALKBH6_ENST00000378875.3_Splice_Site|ALKBH6_ENST00000485128.1_Splice_Site|ALKBH6_ENST00000495116.2_Intron|AC002116.8_ENST00000473572.2_RNA Q3KRA9 ALKB6_HUMAN alkB, alkylation repair homolog 6 (E. coli) cytoplasm|nucleus metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1) 9 all_lung(56;1.35e-06)|Lung NSC(56;2.15e-06)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.06) TGTGTGGTTACCATGATGCCC 0.592000 35 88 0 0 0.183431 0 0 DPAGT1 1798 broad.mit.edu 37 11 118971495 118971495 + Missense_Mutation SNP G G A TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr11:118971495G>A ENST00000409993.2 - 5 1892 c.341C>T c.(340-342)gCg>gTg p.A114V DPAGT1_ENST00000432443.2_Missense_Mutation_p.A7V|DPAGT1_ENST00000445653.1_5'UTR|DPAGT1_ENST00000354202.4_Missense_Mutation_p.A114V Q9H3H5 GPT_HUMAN dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase) 114 dolichol biosynthetic process|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|protein oligomerization integral to endoplasmic reticulum membrane|microsome phospho-N-acetylmuramoyl-pentapeptide-transferase activity|transferase activity, transferring glycosyl groups|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2) 17 all_hematologic(175;0.0977) Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;7.55e-05) TACATCATCCGCAAAGCCCAG 0.567000 OREG0021396 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 4 115 0 0 0.150653 0 0 CSMD3 114788 broad.mit.edu 37 8 113988170 113988170 + Missense_Mutation SNP T T C TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr8:113988170T>C ENST00000297405.5 - 7 1482 c.1238A>G c.(1237-1239)gAc>gGc p.D413G CSMD3_ENST00000352409.3_Missense_Mutation_p.D413G|CSMD3_ENST00000343508.3_Missense_Mutation_p.D373G|CSMD3_ENST00000455883.2_Intron NM_198123.1 NP_937756.1 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 413 integral to membrane|plasma membrane breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7) 646 AGAGAGCCCGTCCTTGGACGT 0.478000 HNSCC(6;0.00088)|TCGA Ovarian(7;0.080) 73 265 0 0 0.139131 0 0 ANKRD36 375248 broad.mit.edu 37 2 97875420 97875420 + Missense_Mutation SNP T T G TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr2:97875420T>G ENST00000420699.2 + 55 3512 c.3268T>G c.(3268-3270)Tct>Gct p.S1090A ANKRD36_ENST00000461153.2_Missense_Mutation_p.S1090A NM_001164315.1 NP_001157787.1 A6QL64 AN36A_HUMAN ankyrin repeat domain 36 1090 endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1) 23 CTTTTCAGTGTCTTCTCGGAA 0.358000 14 95 0 0 0.043863 0 0 TP53 7157 broad.mit.edu 37 17 7578550 7578550 + Missense_Mutation SNP G G T TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr17:7578550G>T ENST00000420246.2 - 5 512 c.380C>A c.(379-381)tCc>tAc p.S127Y TP53_ENST00000269305.4_Missense_Mutation_p.S127Y|TP53_ENST00000455263.2_Missense_Mutation_p.S127Y|TP53_ENST00000359597.4_Missense_Mutation_p.S127Y|TP53_ENST00000413465.2_Missense_Mutation_p.S127Y|TP53_ENST00000445888.2_Missense_Mutation_p.S127Y NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 127 Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Required for interaction with FBXO42. S -> C (in a sporadic cancer; somatic mutation).|S -> F (in sporadic cancers; somatic mutation).|S -> P (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.S127F(23)|p.0?(8)|p.S127Y(8)|p.S127C(7)|p.Y126_K132delYSPALNK(6)|p.A129fs*20(3)|p.Y126_N131delYSPALN(3)|p.S34C(2)|p.P128fs*42(2)|p.V73fs*9(1)|p.S127fs*36(1)|p.P128fs*18(1)|p.Y126fs*11(1)|p.S127_Q136del10(1)|p.P13fs*18(1)|p.?(1)|p.S34F(1)|p.A36fs*20(1)|p.S127fs*42(1)|p.Y126fs*18(1) NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) GAGGGCAGGGGAGTACTGTAG 0.552000 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) 44 0 1.00001e-27 1.16667e-27 0.111260 1 0 RINT1 60561 broad.mit.edu 37 7 105189063 105189063 + Missense_Mutation SNP C C A TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr7:105189063C>A ENST00000257700.2 + 7 1133 c.902C>A c.(901-903)tCt>tAt p.S301Y NM_021930.4 NP_068749.3 Q6NUQ1 RINT1_HUMAN RAD50 interactor 1 301 RINT1/TIP20. cell cycle|G2/M transition DNA damage checkpoint|protein transport|vesicle-mediated transport endoplasmic reticulum membrane protein binding central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 22 GCCTCCCCTTCTGTCATCCTG 0.443000 98 347 9.15355e-43 1.12131e-42 0.139131 1 0 ABCB10 23456 broad.mit.edu 37 1 229685030 229685030 + Silent SNP C C G TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr1:229685030C>G ENST00000344517.4 - 2 711 c.669G>C c.(667-669)ctG>ctC p.L223L NM_012089.2 NP_036221.2 Q9NRK6 ABCBA_HUMAN ATP-binding cassette, sub-family B (MDR/TAP), member 10 223 ABC transmembrane type-1. integral to mitochondrial membrane|mitochondrial inner membrane ATP binding|oligopeptide-transporting ATPase activity breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2) 31 Breast(184;0.143)|Ovarian(103;0.249) Prostate(94;0.167) CAGCACCACACAGAAACACGG 0.522000 15 68 0 0 0.062417 0 0 EIF2AK4 440275 broad.mit.edu 37 15 40258023 40258023 + Silent SNP G G A TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr15:40258023G>A ENST00000263791.5 + 8 1039 c.996G>A c.(994-996)aaG>aaA p.K332K EIF2AK4_ENST00000559624.1_Silent_p.K332K|EIF2AK4_ENST00000382727.2_Silent_p.K332K NM_001013703.2 NP_001013725.2 Q9P2K8 E2AK4_HUMAN eukaryotic translation initiation factor 2 alpha kinase 4 332 Protein kinase 1. translation cytosolic ribosome aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1) 40 all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119) GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616) AAAAAGAGAAGATTGATAAGT 0.443000 37 115 0 0 0.069456 0 0 ATRX 546 broad.mit.edu 37 X 76814313 76814313 + Nonsense_Mutation SNP G G A TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chrX:76814313G>A ENST00000373344.5 - 29 6545 c.6331C>T c.(6331-6333)Cga>Tga p.R2111* ATRX_ENST00000395603.3_Nonsense_Mutation_p.R2073*|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 2111 Helicase C-terminal. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding p.R2111*(1)|p.?(1) bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 145 Phosphatidylserine(DB00144) ATAAATAATCGTCCTCTGAAA 0.274000 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 69 1 0 0 0.139131 0 0 PLEC 5339 broad.mit.edu 37 8 145007212 145007212 + Missense_Mutation SNP C C T TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr8:145007212C>T ENST00000322810.4 - 14 2066 c.1897G>A c.(1897-1899)Gtg>Atg p.V633M PLEC_ENST00000357649.2_Missense_Mutation_p.V500M|PLEC_ENST00000345136.3_Missense_Mutation_p.V496M|PLEC_ENST00000527096.1_Missense_Mutation_p.V519M|PLEC_ENST00000398774.2_Missense_Mutation_p.V464M|PLEC_ENST00000354589.3_Missense_Mutation_p.V496M|PLEC_ENST00000436759.2_Missense_Mutation_p.V523M|PLEC_ENST00000354958.2_Missense_Mutation_p.V474M|PLEC_ENST00000356346.3_Missense_Mutation_p.V482M NM_201380.2 NP_958782.1 Q15149 PLEC_HUMAN plectin 633 Globular 1. cellular component disassembly involved in apoptosis|hemidesmosome assembly cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma actin binding|structural constituent of muscle NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10) 137 GGGGCCGCCACGCCTGCCTTC 0.662000 3 4 0 0 0.069234 0 0 MAP3K5 4217 broad.mit.edu 37 6 136932510 136932510 + Missense_Mutation SNP T T C TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr6:136932510T>C ENST00000359015.4 - 18 2791 c.2431A>G c.(2431-2433)Att>Gtt p.I811V MAP3K5_ENST00000355845.4_Missense_Mutation_p.I58V NM_005923.3 NP_005914.1 Q99683 M3K5_HUMAN mitogen-activated protein kinase kinase kinase 5 811 Protein kinase. activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4) 58 Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569) TAGGTATTAATCAACACATTG 0.368000 7 123 0 0 0.029380 0 0 KCNJ13 3769 broad.mit.edu 37 2 233633140 233633140 + Missense_Mutation SNP A A G TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr2:233633140A>G ENST00000233826.3 - 3 983 c.844T>C c.(844-846)Tgc>Cgc p.C282R GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000373563.4_Intron|GIGYF2_ENST00000452341.2_Intron|KCNJ13_ENST00000409779.1_3'UTR|GIGYF2_ENST00000373566.3_Intron|GIGYF2_ENST00000409451.3_Intron|GIGYF2_ENST00000409480.1_Intron|KCNJ13_ENST00000410029.1_Missense_Mutation_p.C282R|GIGYF2_ENST00000409547.1_Intron NM_002242.4 NP_002233.2 O60928 IRK13_HUMAN potassium inwardly-rectifying channel, subfamily J, member 13 282 voltage-gated potassium channel complex inward rectifier potassium channel activity endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1) 9 Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908) Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617) CTCCTTTGGCATATTTCTCCA 0.433000 131 120 0 0 0.139131 0 0 HECW2 57520 broad.mit.edu 37 2 197298053 197298053 + Missense_Mutation SNP G G A TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr2:197298053G>A ENST00000260983.2 - 2 277 c.95C>T c.(94-96)gCc>gTc p.A32V NM_020760.1 NP_065811.1 Q9P2P5 HECW2_HUMAN HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 32 protein ubiquitination involved in ubiquitin-dependent protein catabolic process cytoplasm ubiquitin-protein ligase activity biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2) 113 GCTCTGGGCGGCAAGGCTCTG 0.602000 5 231 0 0 0.014758 0 0 C3orf52 79669 broad.mit.edu 37 3 111835572 111835572 + Frame_Shift_Del DEL G G - TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr3:111835572delG ENST00000431717.2 + 4 553 c.480delG c.(478-480)cafs p.Q160fs C3orf52_ENST00000467942.2_3'UTR|C3orf52_ENST00000264848.5_3'UTR|C3orf52_ENST00000430855.1_Intron NM_001171747.1 NP_001165218.1 Q5BVD1 TTMP_HUMAN chromosome 3 open reading frame 52 0 endoplasmic reticulum membrane|integral to membrane endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1) 4 CTGTTTTGCAGAAAAGATTCT 0.458 7 8 --- --- --- --- CTD-2533K21.4 0 broad.mit.edu 37 5 26740947 26740949 + RNA DEL TTT TTT - TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr5:26740947_26740949delTTT ENST00000506032.1 - 0 125 AATCttcttcttttttttttttt 0.478 2 4 --- --- --- --- RP11-436D23.1 0 broad.mit.edu 37 6 98715362 98715377 + RNA DEL TCCTTCCTTCCTTCCT TCCTTCCTTCCTTCCT - rs59041540 TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr6:98715362_98715377delTCCTTCCTTCCTTCCT ENST00000607823.1 + 0 352 AAAGAttctctccttccttccttccttccttccttc 0.375 3 5 --- --- --- --- CTB-104F4.2 0 broad.mit.edu 37 7 91341460 91341461 + RNA INS - - A rs13246112 TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr7:91341460_91341461insA ENST00000454222.1 - 0 159 aaggaaggaaggaaagaaagaa 0.302 2 4 --- --- --- --- RP11-677M14.7 0 broad.mit.edu 37 11 124672250 124672251 + RNA DEL GT GT - rs60473155 TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr11:124672250_124672251delGT ENST00000499143.2 + 0 981 RP11-677M14.7_ENST00000529392.1_RNA CCAAAGAGGGgtgtgtgtgtgt 0.460 3 3 --- --- --- --- RP11-314D7.1 0 broad.mit.edu 37 12 73525130 73525130 + RNA DEL A A - TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr12:73525130delA ENST00000551135.1 - 0 104 accctgtctgaaaaaaaaaga 0.443 3 6 --- --- --- --- DYNLL1 8655 broad.mit.edu 37 12 120935907 120935908 + Frame_Shift_Ins INS - - TT rs142458935 by1000genomes TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr12:120935907_120935908insTT ENST00000392509.2 + 3 425_426 c.164_165insTT c.(163-165)ctgfs p.L55fs DYNLL1_ENST00000392508.2_Frame_Shift_Ins_p.L55fs|DYNLL1_ENST00000242577.6_Frame_Shift_Ins_p.L55fs|DYNLL1_ENST00000552870.1_Intron|DYNLL1_ENST00000552316.1_3'UTR|DYNLL1_ENST00000548342.1_Frame_Shift_Ins_p.L55fs|DYNLL1_ENST00000549989.1_Frame_Shift_Ins_p.L55fs NM_001037494.1 NP_001032583.1 P63167 DYL1_HUMAN dynein, light chain, LC8-type 1 55 actin cytoskeleton organization|activation of pro-apoptotic gene products|anatomical structure morphogenesis|female gamete generation|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|microtubule-based process|negative regulation of phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transport centrosome|cytoplasmic dynein complex|cytosol|microtubule|mitochondrion|nucleus|plasma membrane motor activity|protein binding all_neural(191;0.0804)|Medulloblastoma(191;0.0922) CCCACCTGGCATTGCATCGTGG 0.426 35 58 --- --- --- --- TPTE2P1 0 broad.mit.edu 37 13 25525716 25525716 + RNA DEL A A - TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr13:25525716delA ENST00000429698.1 - 0 282 TGGAAGAAACAAAAAAAAGAA 0.383 6 3 --- --- --- --- GSE1 23199 broad.mit.edu 37 16 85682289 85682290 + Frame_Shift_Ins INS - - C TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chr16:85682289_85682290insC ENST00000253458.7 + 3 534_535 c.358_359insC c.(358-360)cccfs p.P120fs GSE1_ENST00000405402.2_Frame_Shift_Ins_p.P16fs|GSE1_ENST00000393243.1_Frame_Shift_Ins_p.P47fs NM_014615.2 NP_055430.1 Gse1 coiled-coil protein p.V123fs*2(1) CGTGCCCAGCACCCCCCCCGTG 0.688 8 197 --- --- --- --- IRS4 8471 broad.mit.edu 37 X 107977802 107977803 + Frame_Shift_Ins INS - - C TCGA-E1-5304-01A-01D-1468-08 TCGA-E1-5304-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx e6b925bf-a091-4254-ad24-d1581fa66cb1 81f4e278-bb3d-4621-886b-5e03e7205291 g.chrX:107977802_107977803insC ENST00000372129.2 - 1 1848_1849 c.1772_1773insG c.(1771-1773)gaafs p.E591fs NM_003604.2 NP_003595.1 O14654 IRS4_HUMAN insulin receptor substrate 4 591 plasma membrane insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1) 78 CTGAGCCTTTGCCCCCCCCAGA 0.545 8 421 --- --- --- ---