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 TBP 6908 broad.mit.edu 37 6 170871040 170871040 + Silent SNP A A G rs10592950 TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr6:170871040A>G ENST00000392092.2 + 3 495 c.216A>G c.(214-216)caA>caG p.Q72Q TBP_ENST00000230354.6_Silent_p.Q72Q|TBP_ENST00000540980.1_Silent_p.Q52Q NM_003194.4 NP_003185.1 P20226 TBP_HUMAN TATA box binding protein 72 Poly-Gln. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding p.Q72del(3) breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1) 26 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) agcagcagcaacagcaacagc 0.567000 5 95 0 0 1 0 0 APOB 338 broad.mit.edu 37 2 21228468 21228468 + Missense_Mutation SNP C C A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr2:21228468C>A ENST00000233242.1 - 26 11399 c.11272G>T c.(11272-11274)Gtt>Ttt p.V3758F NM_000384.2 NP_000375.2 P04114 APOB_HUMAN apolipoprotein B 3758 cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6) 305 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) Atorvastatin(DB01076) CACGATGGAACCTGAAGATCT 0.388000 28 138 2.4375e-19 2.90178e-19 1 1 0 RGPD3 653489 broad.mit.edu 37 2 107049631 107049631 + Silent SNP C C T TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr2:107049631C>T ENST00000409886.3 - 16 2403 c.2316G>A c.(2314-2316)gcG>gcA p.A772A RGPD3_ENST00000304514.7_Silent_p.A772A NM_001144013.1 NP_001137485.1 A6NKT7 RGPD3_HUMAN RANBP2-like and GRIP domain containing 3 772 intracellular transport binding p.A772A(4) breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2) 71 TTTCTGAATCCGCATTTCGCA 0.373000 4 175 0 0 1 0 0 PI15 51050 broad.mit.edu 37 8 75756325 75756325 + Missense_Mutation SNP G G A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr8:75756325G>A ENST00000260113.2 + 3 562 c.383G>A c.(382-384)cGc>cAc p.R128H RP11-758M4.4_ENST00000523860.1_RNA|RP11-758M4.4_ENST00000518128.1_RNA|PI15_ENST00000523773.1_Missense_Mutation_p.R128H NM_015886.3 NP_056970.1 O43692 PI15_HUMAN peptidase inhibitor 15 128 extracellular region peptidase inhibitor activity p.R128H(1) breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|skin(1) 30 Breast(64;0.137) BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118) CTATCTGTACGCACTGGAAGG 0.408000 14 149 0 0 1 0 0 PCLO 27445 broad.mit.edu 37 7 82583285 82583285 + Silent SNP G G A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr7:82583285G>A ENST00000423517.2 - 5 7321 c.6984C>T c.(6982-6984)gcC>gcT p.A2328A PCLO_ENST00000333891.8_Silent_p.A2328A NM_014510.2 NP_055325.2 Q9Y6V0 PCLO_HUMAN piccolo presynaptic cytomatrix protein 2259 Pro-rich. cytoskeleton organization|synaptic vesicle exocytosis cell junction|cytoskeleton|synaptic vesicle calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity p.A2328A(2)|p.A2259A(1) 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 TTGTTCGTTCGGCCTCCAACT 0.413000 22 135 0 0 1 0 0 KRTAP4-11 653240 broad.mit.edu 37 17 39274415 39274415 + Silent SNP C C T rs425487 by1000genomes TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr17:39274415C>T ENST00000391413.2 - 1 191 c.153G>A c.(151-153)agG>agA p.R51R NM_033059.3 NP_149048.2 Q9BYQ6 KR411_HUMAN keratin associated protein 4-11 51 27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC]. Missing (in allele KAP4.14). keratin filament p.R51R(6) endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1) 33 Breast(137;0.000496) STAD - Stomach adenocarcinoma(17;0.000371) AGCACTGGGGCCTGCAGCAGC 0.667000 5 108 0 0 1 0 0 RP11-24M17.5 0 broad.mit.edu 37 15 76074431 76074431 + RNA SNP C C T rs149323153 by1000genomes TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr15:76074431C>T ENST00000395215.3 + 0 610 p.S190L(2) CTCCAGTCCTCGAGCTGCAGA 0.547000 4 23 0 0 1 0 0 RFX2 5990 broad.mit.edu 37 19 6013017 6013017 + Silent SNP C C T TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr19:6013017C>T ENST00000303657.5 - 8 1028 c.879G>A c.(877-879)caG>caA p.Q293Q RFX2_ENST00000592546.1_Silent_p.Q268Q|RFX2_ENST00000359161.3_Silent_p.Q293Q|CTC-232P5.1_ENST00000587836.1_RNA NM_000635.3 NP_000626.2 P48378 RFX2_HUMAN regulatory factor X, 2 (influences HLA class II expression) 293 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1) 21 GGTGCATGGGCTGCTGCCGCA 0.612000 34 160 0 0 1 0 0 CDH8 1006 broad.mit.edu 37 16 61891032 61891032 + Missense_Mutation SNP G G A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr16:61891032G>A ENST00000577390.1 - 4 1612 c.658C>T c.(658-660)Cct>Tct p.P220S CDH8_ENST00000584337.1_Missense_Mutation_p.P220S|CDH8_ENST00000577730.1_Missense_Mutation_p.P220S|CDH8_ENST00000299345.6_Missense_Mutation_p.P220S NM_001796.4 NP_001787.2 P55286 CADH8_HUMAN cadherin 8, type 2 220 Cadherin 2. adherens junction organization|cell junction assembly|homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4) 112 Ovarian(137;0.0799)|Melanoma(118;0.16) UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249) CCTGTTTCAGGCTCAATGGAA 0.393000 28 45 0 0 1 0 0 TBP 6908 broad.mit.edu 37 6 170871046 170871046 + Silent SNP A A G rs10592951 TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr6:170871046A>G ENST00000392092.2 + 3 501 c.222A>G c.(220-222)caA>caG p.Q74Q TBP_ENST00000230354.6_Silent_p.Q74Q|TBP_ENST00000540980.1_Silent_p.Q54Q NM_003194.4 NP_003185.1 P20226 TBP_HUMAN TATA box binding protein 74 Poly-Gln. cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction transcription factor TFIIA complex|transcription factor TFIID complex repressing transcription factor binding|transcription regulatory region DNA binding breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1) 26 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591) agcaacagcaacagcagcagc 0.567000 6 90 0 0 1 0 0 SDHAP1 0 broad.mit.edu 37 3 195711423 195711423 + RNA SNP A A G TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr3:195711423A>G ENST00000427841.1 - 0 524 NR_003264.2 CTCTTGTACTAGAAACAGACC 0.552000 3 63 0 0 1 0 0 EPHB4 2050 broad.mit.edu 37 7 100421497 100421497 + Silent SNP C C A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr7:100421497C>A ENST00000358173.3 - 3 648 c.180G>T c.(178-180)gtG>gtT p.V60V EPHB4_ENST00000477446.1_5'UTR|EPHB4_ENST00000360620.3_Silent_p.V60V NM_004444.4 NP_004435.3 P54760 EPHB4_HUMAN EPH receptor B4 60 cell proliferation|organ morphogenesis|regulation of angiogenesis cell surface|integral to plasma membrane ATP binding|ephrin receptor activity breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3) 47 Lung NSC(181;0.041)|all_lung(186;0.0581) GCACGTCACACACTTCGTAGG 0.682000 10 34 2.17888e-05 2.31795e-05 1 1 0 FBXW7 0 broad.mit.edu 37 4 153244137 153244137 + Missense_Mutation SNP G G A rs140856583 byFrequency TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr4:153244137G>A ENST00000281708.4 - 12 3249 c.2020C>T c.(2020-2022)Cgg>Tgg p.R674W FBXW7_ENST00000603548.1_Missense_Mutation_p.R674W|FBXW7_ENST00000603841.1_Missense_Mutation_p.R674W|FBXW7_ENST00000393956.3_Missense_Mutation_p.R498W|FBXW7_ENST00000263981.5_Missense_Mutation_p.R594W|FBXW7_ENST00000296555.5_Missense_Mutation_p.R556W NM_033632.3 NP_361014.1 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase 674 interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development nucleolus|nucleoplasm|SCF ubiquitin ligase complex protein binding p.?(1) NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6) 462 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) GCTCTGATCCGCCACACAACT 0.493000 """Mis, N, D, F""" """colorectal, endometrial, T-ALL""" 49 109 0 0 1 0 0 ITGB4 3691 broad.mit.edu 37 17 73736512 73736512 + Silent SNP C C T TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr17:73736512C>T ENST00000200181.3 + 21 2707 c.2520C>T c.(2518-2520)tgC>tgT p.C840C ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000579662.1_Silent_p.C840C|ITGB4_ENST00000450894.3_Silent_p.C840C|ITGB4_ENST00000449880.2_Silent_p.C840C|ITGB4_ENST00000339591.3_Silent_p.C840C NM_000213.3 NP_000204.3 P16144 ITB4_HUMAN integrin, beta 4 840 cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding cell leading edge|cell surface|hemidesmosome|integrin complex protein binding|receptor activity breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1) 43 all_cancers(13;1.5e-07) all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154) CTCGGGAGTGCGCCCAGCTGC 0.662000 4 66 0 0 1 0 0 KCNQ3 3786 broad.mit.edu 37 8 133192522 133192522 + Missense_Mutation SNP T T C TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr8:133192522T>C ENST00000388996.4 - 4 1079 c.659A>G c.(658-660)aAt>aGt p.N220S KCNQ3_ENST00000521134.1_Missense_Mutation_p.N100S|KCNQ3_ENST00000519445.1_Missense_Mutation_p.N220S NM_004519.3 NP_004510.1 O43525 KCNQ3_HUMAN potassium voltage-gated channel, KQT-like subfamily, member 3 220 axon guidance|synaptic transmission voltage-gated potassium channel complex voltage-gated potassium channel activity NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 70 Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.000311) GGCCAGAACATTGCCTTGGTT 0.597000 11 123 0 0 1 0 0 USP44 84101 broad.mit.edu 37 12 95914959 95914959 + Nonsense_Mutation SNP G G A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr12:95914959G>A ENST00000258499.3 - 5 2041 c.1753C>T c.(1753-1755)Cga>Tga p.R585* USP44_ENST00000393091.2_Nonsense_Mutation_p.R585*|USP44_ENST00000552440.1_Intron|USP44_ENST00000537435.2_Nonsense_Mutation_p.R585* NM_001278393.1|NM_032147.2 NP_001265322.1|NP_115523.2 Q9H0E7 UBP44_HUMAN ubiquitin specific peptidase 44 585 anaphase|cell division|mitosis|negative regulation of mitotic anaphase-promoting complex activity|protein deubiquitination|regulation of spindle checkpoint|ubiquitin-dependent protein catabolic process nucleus protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1) 36 ATCTTCTCTCGGTTATTACGT 0.423000 18 55 0 0 1 0 0 IDH1 3417 broad.mit.edu 37 2 209113112 209113112 + Missense_Mutation SNP C C T rs121913500 TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr2:209113112C>T ENST00000415913.1 - 4 776 c.395G>A c.(394-396)cGt>cAt p.R132H IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_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 5 40 0 0 1 0 0 CROCCP2 0 broad.mit.edu 37 1 16946407 16946407 + RNA SNP T T G rs10796418 by1000genomes TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr1:16946407T>G ENST00000412962.1 - 0 1112 AGCAATCTCCTCACTCAGCTG 0.672000 5 31 0 0 1 0 0 SH3BP2 6452 broad.mit.edu 37 4 2834097 2834097 + Missense_Mutation SNP T T A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr4:2834097T>A ENST00000442312.2 + 11 1709 c.1530T>A c.(1528-1530)gaT>gaA p.D510E SH3BP2_ENST00000452765.2_Missense_Mutation_p.D482E|SH3BP2_ENST00000356331.5_Missense_Mutation_p.D482E|SH3BP2_ENST00000435136.2_Missense_Mutation_p.D482E|SH3BP2_ENST00000511747.1_Missense_Mutation_p.D482E|SH3BP2_ENST00000503393.2_Missense_Mutation_p.D539E NM_001145855.1 NP_001139327.1 P78314 3BP2_HUMAN SH3-domain binding protein 2 482 SH2. signal transduction SH3 domain binding|SH3/SH2 adaptor activity NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2) 20 UCEC - Uterine corpus endometrioid carcinoma (64;0.164) AGCCCCAGGATGGACTCTACT 0.592000 Cherubism 7 178 0 0 1 0 0 APLNR 187 broad.mit.edu 37 11 57003704 57003704 + Missense_Mutation SNP G G T TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr11:57003704G>T ENST00000606794.1 - 1 971 c.775C>A c.(775-777)Ctg>Atg p.L259M NM_005161.4 NP_005152.1 P35414 APJ_HUMAN apelin receptor 259 integral to plasma membrane G-protein coupled receptor activity breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1) 32 ATCCAGCACAGGGCAAAGGTC 0.612000 7 66 2.0095e-06 2.18424e-06 1 1 0 SIPA1 6494 broad.mit.edu 37 11 65408860 65408860 + Silent SNP G G A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr11:65408860G>A ENST00000394224.3 + 2 764 c.468G>A c.(466-468)tcG>tcA p.S156S SIPA1_ENST00000534313.1_Silent_p.S156S|SIPA1_ENST00000394227.3_Silent_p.S156S|SIPA1_ENST00000527525.1_Silent_p.S156S NM_153253.29 NP_694985.29 Q96FS4 SIPA1_HUMAN signal-induced proliferation-associated 1 156 cell proliferation|cytoskeleton organization|intracellular signal transduction|negative regulation of cell adhesion|negative regulation of cell cycle|negative regulation of cell growth cytosol|endomembrane system|membrane|perinuclear region of cytoplasm Rap GTPase activator activity cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1) 10 CTGCCAGCTCGGACCTGCTGC 0.667000 33 83 0 0 1 0 0 FLG 2312 broad.mit.edu 37 1 152282080 152282080 + Missense_Mutation SNP C C T TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr1:152282080C>T ENST00000368799.1 - 3 5317 c.5282G>A c.(5281-5283)cGt>cAt p.R1761H FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA NM_002016.1 NP_002007.1 P20930 FILA_HUMAN filaggrin 1761 Ser-rich. keratinocyte differentiation cytoplasmic membrane-bounded vesicle|intermediate filament calcium ion binding|structural molecule activity autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12) 424 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) AGACCCTGAACGTCCAGACCT 0.602000 Ichthyosis 36 394 0 0 1 0 0 PCNX 22990 broad.mit.edu 37 14 71443880 71443880 + Nonsense_Mutation SNP A A T TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr14:71443880A>T ENST00000304743.2 + 6 1272 c.826A>T c.(826-828)Aaa>Taa p.K276* PCNX_ENST00000238570.5_Nonsense_Mutation_p.K276*|PCNX_ENST00000439984.3_Nonsense_Mutation_p.K276* NM_014982.2 NP_055797.2 Q96RV3 PCX1_HUMAN pecanex homolog (Drosophila) 276 integral to membrane NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1) 87 KIRC - Kidney renal clear cell carcinoma(12;0.206) all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417) CTCTTATAGAAAAGACCACCG 0.493000 19 55 0 0 1 0 0 MUC1 4582 broad.mit.edu 37 1 155161799 155161799 + Missense_Mutation SNP T T G TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr1:155161799T>G ENST00000368395.1 - 2 405 c.334A>C c.(334-336)Acc>Ccc p.T112P MUC1_ENST00000462215.1_Intron|MUC1_ENST00000457295.2_Intron|MUC1_ENST00000438413.1_Intron|MUC1_ENST00000368390.3_Intron|MUC1_ENST00000368389.2_Intron|MUC1_ENST00000342482.4_Intron|MUC1_ENST00000338684.5_Intron|MUC1_ENST00000337604.5_Intron|MUC1_ENST00000368392.3_Intron|MUC1_ENST00000368393.3_Intron|MUC1_ENST00000368396.4_Intron|MUC1_ENST00000368398.3_Intron|MUC1_ENST00000343256.5_Intron NM_001204285.1|NM_001204286.1 NP_001191214.1|NP_001191215.1 P15941 MUC1_HUMAN mucin 1, cell surface associated 892 apical plasma membrane|cell surface|cytoplasm|extracellular region|integral to plasma membrane|nucleus protein binding breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|skin(2) 10 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) GCTGGCGGGGTGGTGGAGCCC 0.711000 T IGH@ B-NHL 11 17 0 0 1 0 0 TP53 7157 broad.mit.edu 37 17 7577094 7577094 + Missense_Mutation SNP G G A rs28934574 TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr17:7577094G>A ENST00000420246.2 - 8 976 c.844C>T c.(844-846)Cgg>Tgg p.R282W TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000269305.4_Missense_Mutation_p.R282W|TP53_ENST00000455263.2_Missense_Mutation_p.R282W NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 282 Interaction with AXIN1 (By similarity).|Interaction with E4F1.|Interaction with HIPK1 (By similarity). DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934574). 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.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(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) TCTGTGCGCCGGTCTCTCCCA 0.557000 111 """Mis, N, F""" """breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types""" """breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types""" Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) 44 14 0 0 1 0 0 OR4A15 81328 broad.mit.edu 37 11 55136013 55136013 + Silent SNP C C A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr11:55136013C>A ENST00000314706.3 + 1 654 c.654C>A c.(652-654)acC>acA p.T218T NM_001005275.1 NP_001005275.1 Q8NGL6 O4A15_HUMAN olfactory receptor, family 4, subfamily A, member 15 218 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1) 71 TTGCTTGCACCAATACCTATG 0.413000 4 84 1 1 1 1 0 CDH4 1002 broad.mit.edu 37 20 60503304 60503304 + Missense_Mutation SNP G G A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr20:60503304G>A ENST00000360469.5 + 12 1916 c.1828G>A c.(1828-1830)Gac>Aac p.D610N CDH4_ENST00000543233.1_Missense_Mutation_p.D536N NM_001794.3 NP_001785.2 P55283 CADH4_HUMAN cadherin 4, type 1, R-cadherin (retinal) 610 Cadherin 4. adherens junction organization|cell junction assembly calcium ion binding NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1) 74 BRCA - Breast invasive adenocarcinoma(19;2.36e-08) TGACATCAACGACAACGCCCC 0.622000 10 286 0 0 1 0 0 THSD4 79875 broad.mit.edu 37 15 72040864 72040864 + Silent SNP G G A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr15:72040864G>A ENST00000355327.3 + 14 2480 c.2346G>A c.(2344-2346)ccG>ccA p.P782P THSD4_ENST00000357769.4_Silent_p.P422P|THSD4_ENST00000261862.6_Silent_p.P782P|THSD4_ENST00000567838.1_3'UTR Q6ZMP0 THSD4_HUMAN thrombospondin, type I, domain containing 4 782 TSP type-1 3. proteinaceous extracellular matrix metalloendopeptidase activity breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 42 AGCTCCGGCCGAATGACATTG 0.597000 12 49 0 0 1 0 0 CGREF1 10669 broad.mit.edu 37 2 27325300 27325300 + Splice_Site SNP T T C TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr2:27325300T>C ENST00000402394.1 - 4 415 c.e4-2 CGREF1_ENST00000405600.1_Splice_Site|CGREF1_ENST00000260595.5_Splice_Site|CGREF1_ENST00000402550.1_Splice_Site|CGREF1_ENST00000312734.4_Splice_Site|CGREF1_ENST00000452318.2_Splice_Site|CGREF1_ENST00000404694.3_Splice_Site NM_006569.5 NP_006560.3 Q99674 CGRE1_HUMAN cell growth regulator with EF-hand domain 1 cell adhesion|cell cycle arrest|negative regulation of cell proliferation|response to stress extracellular region calcium ion binding kidney(1)|lung(4)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1) 10 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) TGCAGAAGTCTGTCAGAAAAG 0.617000 4 55 0 0 1 0 0 POLN 353497 broad.mit.edu 37 4 2073954 2073954 + Missense_Mutation SNP G G A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr4:2073954G>A ENST00000511885.2 - 26 2943 c.2590C>T c.(2590-2592)Cct>Tct p.P864S POLN_ENST00000382865.1_Missense_Mutation_p.P864S Q7Z5Q5 DPOLN_HUMAN polymerase (DNA directed) nu 864 DNA repair|DNA replication nucleus DNA binding|DNA-directed DNA polymerase activity kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2) 28 OV - Ovarian serous cystadenocarcinoma(23;0.0955) CCTGGCGGAGGGCCCCAGGCC 0.692000 DNA polymerases (catalytic subunits) 8 64 0 0 1 0 0 TUBB8P7 0 broad.mit.edu 37 16 90160999 90160999 + RNA SNP C C T TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr16:90160999C>T ENST00000567960.1 + 0 229 TUBB8P7_ENST00000564451.1_RNA GGACTCCGTGCGCTCGGGGCC 0.687000 19 116 0 0 1 0 0 OR2M2 391194 broad.mit.edu 37 1 248343709 248343709 + Missense_Mutation SNP G G T TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr1:248343709G>T ENST00000359682.2 + 1 422 c.422G>T c.(421-423)tGt>tTt p.C141F NM_001004688.1 NP_001004688.1 Q96R28 OR2M2_HUMAN olfactory receptor, family 2, subfamily M, member 2 141 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3) 70 all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0245) CCTAAAATTTGTGGACTTATG 0.423000 12 283 2.27111e-07 2.52346e-07 1 1 0 TTN 7273 broad.mit.edu 37 2 179430063 179430063 + Silent SNP A A T TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr2:179430063A>T ENST00000589042.1 - 326 81020 c.80796T>A c.(80794-80796)gcT>gcA p.A26932A TTN_ENST00000359218.5_Silent_p.A17992A|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000460472.2_Silent_p.A17867A|TTN_ENST00000591111.1_Silent_p.A25291A|TTN_ENST00000342175.6_Silent_p.A18059A|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Silent_p.A24364A|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000419746.1_RNA NM_001267550.1 NP_001254479.1 Q8WZ42 TITIN_HUMAN titin 25291 Fibronectin type-III 96. ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26) 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CAGTTGAGGTAGCTGTTTCTT 0.398000 4 127 0 0 1 0 0 OR5M11 219487 broad.mit.edu 37 11 56310051 56310051 + Missense_Mutation SNP T T C TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr11:56310051T>C ENST00000528616.2 - 1 706 c.683A>G c.(682-684)aAa>aGa p.K228R NM_001005245.1 NP_001005245.1 Q96RB7 OR5MB_HUMAN olfactory receptor, family 5, subfamily M, member 11 228 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14) 18 CTCTGCTGATTTGATCCGGAG 0.498000 28 62 0 0 1 0 0 ZNF814 730051 broad.mit.edu 37 19 58385546 58385546 + Missense_Mutation SNP G G T TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr19:58385546G>T ENST00000435989.2 - 3 1446 c.1212C>A c.(1210-1212)gaC>gaA p.D404E ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron NM_001144989.1 NP_001138461.1 B7Z6K7 ZN814_HUMAN zinc finger protein 814 404 regulation of transcription, DNA-dependent intracellular nucleic acid binding|zinc ion binding p.D404E(10) NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3) 25 AATGTTTTTTGTCAGTGTGAA 0.393000 3 21 0.115264 0.117616 1 1 0 PRG4 10216 broad.mit.edu 37 1 186276640 186276640 + Missense_Mutation SNP A A C TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr1:186276640A>C ENST00000445192.2 + 7 1834 c.1789A>C c.(1789-1791)Acc>Ccc p.T597P PRG4_ENST00000367485.4_Missense_Mutation_p.T504P|PRG4_ENST00000367486.3_Missense_Mutation_p.T554P|PRG4_ENST00000367483.4_Missense_Mutation_p.T556P|PRG4_ENST00000367484.3_Intron NM_005807.3 NP_005798.2 Q92954 PRG4_HUMAN proteoglycan 4 597 59 X 8 AA repeats of K-X-P-X-P-T-T-X. cell proliferation|immune response extracellular region polysaccharide binding|protein binding|scavenger receptor activity p.T597P(1) NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1) 102 ACCCACCACCACCAAGAAGCC 0.652000 8 146 0 0 1 0 0 ABCA4 24 broad.mit.edu 37 1 94480119 94480119 + Nonsense_Mutation SNP C C A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr1:94480119C>A ENST00000370225.3 - 38 5526 c.5440G>T c.(5440-5442)Gaa>Taa p.E1814* ABCA4_ENST00000536513.1_Nonsense_Mutation_p.E84* NM_000350.2 NP_000341.2 P78363 ABCA4_HUMAN ATP-binding cassette, sub-family A (ABC1), member 4 1814 phototransduction, visible light|visual perception integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of substances NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2) 147 all_lung(203;0.000757)|Lung NSC(277;0.00335) all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171) TCAAATAATTCCAAGATGAAG 0.438000 32 169 6.00712e-18 6.82628e-18 1 1 0 ABCA4 24 broad.mit.edu 37 1 94480120 94480120 + Missense_Mutation SNP C C A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr1:94480120C>A ENST00000370225.3 - 38 5525 c.5439G>T c.(5437-5439)ttG>ttT p.L1813F ABCA4_ENST00000536513.1_Missense_Mutation_p.L83F NM_000350.2 NP_000341.2 P78363 ABCA4_HUMAN ATP-binding cassette, sub-family A (ABC1), member 4 1813 phototransduction, visible light|visual perception integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of substances NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2) 147 all_lung(203;0.000757)|Lung NSC(277;0.00335) all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171) CAAATAATTCCAAGATGAAGG 0.438000 32 172 6.00712e-18 6.82628e-18 1 1 0 ADAMTSL1 92949 broad.mit.edu 37 9 18829917 18829917 + Silent SNP G G A TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr9:18829917G>A ENST00000380548.4 + 23 4530 c.4191G>A c.(4189-4191)gtG>gtA p.V1397V ADAMTSL1_ENST00000380545.5_Silent_p.V98V NM_001040272.5 NP_001035362.3 Q8N6G6 ATL1_HUMAN ADAMTS-like 1 1397 Ig-like C2-type 4. proteinaceous extracellular matrix metallopeptidase activity|zinc ion binding breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 42 GBM - Glioblastoma multiforme(50;1.29e-17) TTCCTTCAGTGCTGACGTCTC 0.572000 6 46 0 0 1 0 0 LRIT2 340745 broad.mit.edu 37 10 85984831 85984832 + Frame_Shift_Ins INS - - G TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr10:85984831_85984832insG ENST00000372113.4 - 2 154_155 c.149_150insC c.(148-150)cggfs p.R50fs LRIT2_ENST00000538192.1_Frame_Shift_Ins_p.R50fs NM_001017924.2 NP_001017924.1 A6NDA9 LRIT2_HUMAN leucine-rich repeat, immunoglobulin-like and transmembrane domains 2 50 LRRNT. integral to membrane central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1) 32 AAAGGTTCCCAGGGATCTTTCC 0.455 18 76 --- --- --- --- ARRDC4 91947 broad.mit.edu 37 15 98504133 98504133 + Frame_Shift_Del DEL G G - TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr15:98504133delG ENST00000268042.6 + 1 206 c.42delG c.(40-42)gafs p.E14fs ARRDC4_ENST00000538249.1_Intron NM_183376.2 NP_899232.2 Q8NCT1 ARRD4_HUMAN arrestin domain containing 4 14 signal transduction breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|skin(3) 16 Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222) OV - Ovarian serous cystadenocarcinoma(32;0.0417) TGGGTGCCGAGGGCCGCGTGA 0.741 2 4 --- --- --- --- TNRC6C 57690 broad.mit.edu 37 17 76047335 76047335 + Frame_Shift_Del DEL G G - TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chr17:76047335delG ENST00000335749.4 + 3 2761 c.2192delG c.(2191-2193)tgfs p.W731fs TNRC6C_ENST00000301624.4_Frame_Shift_Del_p.W731fs|TNRC6C_ENST00000588847.1_Frame_Shift_Del_p.W731fs|TNRC6C_ENST00000544502.1_Frame_Shift_Del_p.W731fs|TNRC6C_ENST00000541771.1_Frame_Shift_Del_p.W731fs|TNRC6C_ENST00000588061.1_Frame_Shift_Del_p.W731fs NM_001142640.1 NP_001136112.1 Q9HCJ0 TNR6C_HUMAN trinucleotide repeat containing 6C 731 Sufficient for interaction with argonaute family proteins. gene silencing by RNA|regulation of translation nucleotide binding|RNA binding NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1) 40 BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973) ACCTCAGCTTGGGGGGACCCA 0.507 2 4 --- --- --- --- ATRX 546 broad.mit.edu 37 X 76939387 76939387 + Frame_Shift_Del DEL T T - TCGA-HT-A618-01A-11D-A29Q-08 TCGA-HT-A618-10A-01D-A29Q-08 Untested Somatic Phase_I WXS none Illumina GAIIx 49fd71af-f8af-43dd-a5d6-caa20d4f82e4 193f9709-5167-4fb6-a1dd-b1c102d01e77 g.chrX:76939387delT ENST00000373344.5 - 9 1575 c.1361delA c.(1360-1362)agfs p.K455fs ATRX_ENST00000395603.3_Frame_Shift_Del_p.K417fs|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 455 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.?(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) AATATCCTTCTTTTCCAAAGC 0.343 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 97 98 --- --- --- ---