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 RP11-69H14.6 0 broad.mit.edu 37 15 22332570 22332570 + RNA SNP T T C TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr15:22332570T>C ENST00000558896.1 + 0 377 CCCATGCTCATCTGCTCCAAT 0.398000 4 194 0 0 1 0 0 ATP2B4 493 broad.mit.edu 37 1 203671203 203671203 + Missense_Mutation SNP C C G TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr1:203671203C>G ENST00000357681.5 + 7 2056 c.933C>G c.(931-933)aaC>aaG p.N311K ATP2B4_ENST00000367218.3_Missense_Mutation_p.N311K|ATP2B4_ENST00000367219.3_Intron|ATP2B4_ENST00000341360.2_Missense_Mutation_p.N311K|ATP2B4_ENST00000391954.2_Missense_Mutation_p.N311K NM_001684.4 NP_001675.3 P23634 AT2B4_HUMAN ATPase, Ca++ transporting, plasma membrane 4 311 ATP biosynthetic process|platelet activation integral to plasma membrane ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3) 56 all_cancers(21;0.071)|all_epithelial(62;0.228) BRCA - Breast invasive adenocarcinoma(75;0.109) AAAATCGCAACAAAGGTAACC 0.418000 OREG0014124 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 16 29 0 0 1 0 0 UBBP4 0 broad.mit.edu 37 17 21731144 21731144 + Missense_Mutation SNP T T G rs149119138 by1000genomes TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr17:21731144T>G ENST00000584755.1 + 2 843 c.446T>G c.(445-447)cTg>cGg p.L149R UBBP4_ENST00000584398.1_3'UTR|UBBP4_ENST00000578713.1_Missense_Mutation_p.L149R|UBBP4_ENST00000583708.1_3'UTR p.L149R(18) endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4) 24 GTCCTGCGTCTGAGAGGTGGT 0.542000 4 92 0 0 1 0 0 COPA 1314 broad.mit.edu 37 1 160261696 160261696 + Silent SNP G G A TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr1:160261696G>A ENST00000241704.7 - 30 3400 c.3171C>T c.(3169-3171)tgC>tgT p.C1057C COPA_ENST00000368069.3_Silent_p.C1066C NM_001098398.1|NM_004371.3 NP_001091868.1|NP_004362.2 P53621 COPA_HUMAN coatomer protein complex, subunit alpha 1057 COPI coating of Golgi vesicle|intracellular protein transport|pancreatic juice secretion|retrograde vesicle-mediated transport, Golgi to ER COPI vesicle coat|cytosol|extracellular space|microsome|soluble fraction hormone activity|structural molecule activity central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2) 46 all_cancers(52;8.15e-18)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.111) TGTACTCACGGCAAATGGTGA 0.522000 OREG0013929 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 5 266 0 0 1 0 0 PLA2G15 23659 broad.mit.edu 37 16 68289778 68289778 + Silent SNP G G A TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr16:68289778G>A ENST00000219345.5 + 5 695 c.612G>A c.(610-612)acG>acA p.T204T PLA2G15_ENST00000566188.1_Intron|PLA2G15_ENST00000444212.2_Intron|PLA2G15_ENST00000413021.2_Intron NM_012320.3 NP_036452.1 Q8NCC3 PAG15_HUMAN phospholipase A2, group XV 204 fatty acid catabolic process extracellular region|lysosome lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1) 12 ACATGTACACGCTCTACTTTC 0.637000 30 36 0 0 1 0 0 LRRC19 64922 broad.mit.edu 37 9 26999613 26999613 + Splice_Site SNP C C G TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr9:26999613C>G ENST00000380055.5 - 2 190 c.81_splice c.e2+1 p.R27_splice IFT74_ENST00000380062.5_Intron|IFT74_ENST00000433700.1_Intron|IFT74_ENST00000429045.2_Intron|IFT74_ENST00000443698.1_Intron NM_022901.2 NP_075052.1 Q9H756 LRC19_HUMAN leucine rich repeat containing 19 27 integral to membrane breast(1)|endometrium(2)|kidney(1)|lung(2) 6 all_neural(11;1.81e-09) Lung(218;1.06e-05)|LUSC - Lung squamous cell carcinoma(38;0.0001) AAAACTTACTCTTTTAGAAGA 0.303000 8 13 0 0 1 0 0 RBP1 5947 broad.mit.edu 37 3 139258330 139258330 + Silent SNP C C T TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr3:139258330C>T ENST00000483943.2 - 1 231 c.231G>A c.(229-231)gaG>gaA p.E77E RBP1_ENST00000492918.1_Silent_p.E77E|RP11-319G6.1_ENST00000515247.1_RNA|RBP1_ENST00000232219.2_Silent_p.E77E NM_001130993.1 NP_001124465.1 P09455 RET1_HUMAN retinol binding protein 1, cellular 15 cytoplasm retinal binding|retinol binding|transporter activity endometrium(1)|large_intestine(2)|lung(1)|prostate(1) 5 Vitamin A(DB00162) CCTCGAAATTCTCGTTGACCA 0.667000 10 19 0 0 1 0 0 BRD3 8019 broad.mit.edu 37 9 136901310 136901310 + Missense_Mutation SNP G G A TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr9:136901310G>A ENST00000303407.7 - 10 1965 c.1780C>T c.(1780-1782)Cgg>Tgg p.R594W BRD3_ENST00000473349.1_5'UTR|BRD3_ENST00000371834.2_3'UTR NM_007371.3 NP_031397.1 Q15059 BRD3_HUMAN bromodomain containing 3 594 nucleus protein binding BRD3/C15orf55(3) kidney(1)|skin(1)|stomach(4) 6 OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07) TGCACTACCCGGCCCAGCTTC 0.582000 T C15orf55 lethal midline carcinoma of young people 6 66 0 0 1 0 0 MEFV 4210 broad.mit.edu 37 16 3293676 3293676 + Missense_Mutation SNP G G A TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr16:3293676G>A ENST00000219596.1 - 10 1850 c.1811C>T c.(1810-1812)gCa>gTa p.A604V MEFV_ENST00000541159.1_3'UTR|MEFV_ENST00000339854.4_Missense_Mutation_p.A424V|MEFV_ENST00000536379.1_Missense_Mutation_p.A393V NM_000243.2 NP_000234.1 O15553 MEFV_HUMAN Mediterranean fever 604 B30.2/SPRY. inflammatory response cytoplasm|microtubule|microtubule associated complex|nucleus actin binding|zinc ion binding NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6) 50 Colchicine(DB01394) AGCGGTTTCTGCATCCAGAAT 0.488000 10 298 0 0 1 0 0 RNF40 9810 broad.mit.edu 37 16 30780529 30780529 + Missense_Mutation SNP A A C TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr16:30780529A>C ENST00000324685.6 + 16 2705 c.2270A>C c.(2269-2271)gAg>gCg p.E757A RNF40_ENST00000357890.5_Missense_Mutation_p.E657A|RNF40_ENST00000563683.1_Missense_Mutation_p.E717A|RNF40_ENST00000402121.3_Missense_Mutation_p.E449A NM_001207033.1|NM_014771.3 NP_001193962.1|NP_055586.1 O75150 BRE1B_HUMAN ring finger protein 40, E3 ubiquitin protein ligase 757 histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process nucleus|synaptosome|ubiquitin ligase complex protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2) 30 Colorectal(24;0.198) CTGCTCTCAGAGATGGATGTG 0.547000 6 135 0 0 1 0 0 CHEK2 11200 broad.mit.edu 37 22 29091841 29091841 + Silent SNP G G A rs146546850 byFrequency TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr22:29091841G>A ENST00000544772.1 - 12 1889 c.453C>T c.(451-453)tcC>tcT p.S151S CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000328354.6_Silent_p.S372S NM_001257387.1 NP_001244316.1 O96017 CHK2_HUMAN checkpoint kinase 2 372 FHA. cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence PML body ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity p.S372S(8) central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2) 50 CCAAAATCTTGGAGTGCCCAA 0.413000 F breast Direct reversal of damage;Other conserved DNA damage response genes 4 69 0 0 1 0 0 FGR 2268 broad.mit.edu 37 1 27943448 27943448 + Missense_Mutation SNP C C T TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr1:27943448C>T ENST00000374005.3 - 7 890 c.602G>A c.(601-603)cGc>cAc p.R201H FGR_ENST00000374004.1_Missense_Mutation_p.R201H|FGR_ENST00000545953.1_Missense_Mutation_p.R135H|FGR_ENST00000399173.1_Missense_Mutation_p.R201H NM_005248.2 NP_005239.1 P09769 FGR_HUMAN feline Gardner-Rasheed sarcoma viral oncogene homolog 201 SH2. platelet activation|response to virus cytosol ATP binding|non-membrane spanning protein tyrosine kinase activity breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4) 16 all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419) GTCCAGTTTGCGGATCTTGTA 0.557000 4 140 0 0 1 0 0 DMXL1 1657 broad.mit.edu 37 5 118533558 118533558 + Missense_Mutation SNP A A C TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr5:118533558A>C ENST00000311085.8 + 32 7732 c.7652A>C c.(7651-7653)tAt>tCt p.Y2551S DMXL1_ENST00000539542.1_Missense_Mutation_p.Y2551S NM_005509.4 NP_005500.4 Q9Y485 DMXL1_HUMAN Dmx-like 1 2551 breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1) 86 all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231) OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243) CCTCAAAATTATATCGCAAGT 0.443000 4 161 0 0 1 0 0 ANKRD35 148741 broad.mit.edu 37 1 145562072 145562072 + Missense_Mutation SNP G G C TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr1:145562072G>C ENST00000355594.4 + 10 1847 c.1760G>C c.(1759-1761)aGg>aCg p.R587T NM_144698.3 NP_653299.3 Q8N283 ANR35_HUMAN ankyrin repeat domain 35 587 NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1) 47 all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786) AAGGAGAAAAGGGTTCCTGGG 0.582000 39 50 0 0 1 0 0 MSH5-SAPCD1 0 broad.mit.edu 37 6 31727947 31727947 + Missense_Mutation SNP T T A TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr6:31727947T>A ENST00000493662.2 + 19 1873 c.1817T>A c.(1816-1818)gTc>gAc p.V606D MSH5_ENST00000431848.2_Missense_Mutation_p.V288D|MSH5_ENST00000375755.3_Missense_Mutation_p.V589D|MSH5_ENST00000375703.3_Missense_Mutation_p.V589D|MSH5_ENST00000534153.4_Missense_Mutation_p.V606D|MSH5_ENST00000375740.3_Missense_Mutation_p.V606D|MSH5_ENST00000375742.3_Missense_Mutation_p.V606D|MSH5_ENST00000375750.3_Missense_Mutation_p.V589D|MSH5_ENST00000395853.1_Missense_Mutation_p.V263D AGGGTCAAAGTCATCACTGGA 0.567000 51 75 0 0 1 0 0 ADAMTSL1 92949 broad.mit.edu 37 9 18817126 18817126 + Silent SNP G G A TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr9:18817126G>A ENST00000380548.4 + 21 4164 c.3825G>A c.(3823-3825)acG>acA p.T1275T NM_001040272.5 NP_001035362.3 Q8N6G6 ATL1_HUMAN ADAMTS-like 1 1275 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) TAGTGAAAACGTCACGAATGA 0.448000 5 8 0 0 1 0 0 KCNH1 3756 broad.mit.edu 37 1 210971076 210971076 + Missense_Mutation SNP C C T TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr1:210971076C>T ENST00000367007.4 - 9 1777 c.1608G>A c.(1606-1608)atG>atA p.M536I KCNH1_ENST00000271751.4_Missense_Mutation_p.M563I NM_002238.3|NM_172362.2 NP_002229.1|NP_758872.1 O95259 KCNH1_HUMAN potassium voltage-gated channel, subfamily H (eag-related), member 1 563 myoblast fusion|regulation of transcription, DNA-dependent voltage-gated potassium channel complex calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 68 OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185) TGTCGGCTCTCATGTCCTTGG 0.597000 17 36 0 0 1 0 0 PLEKHH1 57475 broad.mit.edu 37 14 68053956 68053956 + Missense_Mutation SNP T T C TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr14:68053956T>C ENST00000417684.2 + 12 1511 c.923T>C c.(922-924)aTt>aCt p.I308T PLEKHH1_ENST00000329153.5_3'UTR Q9ULM0 PKHH1_HUMAN pleckstrin homology domain containing, family H (with MyTH4 domain) member 1 0 cytoskeleton binding endometrium(2)|kidney(4)|lung(12)|urinary_tract(1) 19 all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011) GCTGTGAATATTTCTCCTACC 0.517000 44 50 0 0 1 0 0 TRIM26 7726 broad.mit.edu 37 6 30153814 30153814 + Missense_Mutation SNP G G A TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr6:30153814G>A ENST00000454678.2 - 10 1895 c.1459C>T c.(1459-1461)Cgg>Tgg p.R487W TRIM26_ENST00000453195.1_Missense_Mutation_p.R487W|TRIM26_ENST00000437089.1_Missense_Mutation_p.R487W NM_003449.4 NP_003440.1 Q12899 TRI26_HUMAN tripartite motif containing 26 487 B30.2/SPRY. DNA binding|zinc ion binding lung(1)|ovary(2) 3 CCCACTCTCCGGGGCCGCAGT 0.642000 11 7 0 0 1 0 0 ALLC 55821 broad.mit.edu 37 2 3749214 3749214 + Silent SNP T T A TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr2:3749214T>A ENST00000252505.3 + 11 1125 c.963T>A c.(961-963)ctT>ctA p.L321L ALLC_ENST00000471711.1_3'UTR NM_018436.3 NP_060906.3 Q8N6M5 ALLC_HUMAN allantoicase 340 allantoicase activity breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1) 30 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088) all_cancers(51;0.24) OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206) AACCACTGCTTCCAGTGACCA 0.488000 HNSCC(21;0.051) 9 13 0 0 1 0 0 CHEK2 11200 broad.mit.edu 37 22 29091840 29091840 + Missense_Mutation SNP T T C rs142470496 byFrequency TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr22:29091840T>C ENST00000544772.1 - 12 1890 c.454A>G c.(454-456)Aag>Gag p.K152E CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E NM_001257387.1 NP_001244316.1 O96017 CHK2_HUMAN checkpoint kinase 2 373 FHA. cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence PML body ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity p.K373E(9) central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2) 50 CCCAAAATCTTGGAGTGCCCA 0.418000 F breast Direct reversal of damage;Other conserved DNA damage response genes 4 70 0 0 1 0 0 VPS53 55275 broad.mit.edu 37 17 556535 556535 + Missense_Mutation SNP C C T TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr17:556535C>T ENST00000437048.2 - 7 750 c.604G>A c.(604-606)Gaa>Aaa p.E202K VPS53_ENST00000401468.3_Intron|VPS53_ENST00000576149.1_Intron|VPS53_ENST00000291074.5_Missense_Mutation_p.E173K|VPS53_ENST00000446250.2_5'UTR|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000571805.1_Missense_Mutation_p.E202K NM_001128159.2 NP_001121631.1 Q5VIR6 VPS53_HUMAN vacuolar protein sorting 53 homolog (S. cerevisiae) 202 protein transport endosome membrane|Golgi apparatus breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1) 19 UCEC - Uterine corpus endometrioid carcinoma (25;0.0265) GTTTACCTTTCGGAAAGCTGC 0.483000 5 185 0 0 1 0 0 U2AF1 7307 broad.mit.edu 37 21 44513235 44513235 + Missense_Mutation SNP G G A TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr21:44513235G>A ENST00000459639.1 - 7 1505 c.481C>T c.(481-483)Cgt>Tgt p.R161C U2AF1_ENST00000398137.1_Missense_Mutation_p.R161C|U2AF1_ENST00000291552.4_Missense_Mutation_p.R234C|U2AF1_ENST00000380276.2_Missense_Mutation_p.R234C Q01081 U2AF1_HUMAN U2 small nuclear RNA auxiliary factor 1 234 mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription Cajal body|catalytic step 2 spliceosome|nuclear speck nucleotide binding|RNA binding|zinc ion binding breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(111)|large_intestine(2)|lung(7)|prostate(2)|skin(1) 126 GATCTTTCACGATCTCTCGAC 0.552000 Mis """CLL, MDS""" 6 84 0 0 1 0 0 USP9X 8239 broad.mit.edu 37 X 41043349 41043349 + Missense_Mutation SNP C C G TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chrX:41043349C>G ENST00000324545.7 + 22 3880 c.3247C>G c.(3247-3249)Cct>Gct p.P1083A USP9X_ENST00000378308.2_Missense_Mutation_p.P1083A NM_001039590.2|NM_001039591.2 NP_001034679.2|NP_001034680.2 Q93008 USP9X_HUMAN ubiquitin specific peptidase 9, X-linked 1083 BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process cytoplasm co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 87 TTTCTTTGGTCCTTCAGCCTC 0.353000 9 70 0 0 1 0 0 FBN3 84467 broad.mit.edu 37 19 8168496 8168496 + Missense_Mutation SNP C C T TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr19:8168496C>T ENST00000600128.1 - 39 5303 c.4889G>A c.(4888-4890)tGt>tAt p.C1630Y FBN3_ENST00000601739.1_Missense_Mutation_p.C1630Y|FBN3_ENST00000270509.2_Missense_Mutation_p.C1630Y Q75N90 FBN3_HUMAN fibrillin 3 1630 EGF-like 25; calcium-binding. proteinaceous extracellular matrix calcium ion binding|extracellular matrix structural constituent NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2) 132 AGGGCAGACACAGGTGTAGTT 0.562000 41 45 0 0 1 0 0 BRAF 673 broad.mit.edu 37 7 140453136 140453136 + Missense_Mutation SNP A A T rs121913377 TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr7:140453136A>T ENST00000288602.6 - 15 1859 c.1799T>A c.(1798-1800)gTg>gAg p.V600E NM_004333.4 NP_004324.2 P15056 BRAF_HUMAN v-raf murine sarcoma viral oncogene homolog B 600 Protein kinase. V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis). activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission cytosol|nucleus|plasma membrane ATP binding|metal ion binding p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1) SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2) NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3) 27380 Melanoma(164;0.00956) Sorafenib(DB00398) TCGAGATTTCACTGTAGCTAG 0.368000 V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN) 61 """Mis, T, O""" """AKAP9, KIAA1549""" """melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma""" Cardio-facio-cutaneous syndrome Cardiofaciocutaneous syndrome 33 52 0 0 1 0 0 PLCD1 5333 broad.mit.edu 37 3 38051629 38051629 + Missense_Mutation SNP G G C TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr3:38051629G>C ENST00000463876.1 - 7 1546 c.1193C>G c.(1192-1194)gCc>gGc p.A398G PLCD1_ENST00000334661.4_Missense_Mutation_p.A377G NM_001130964.1 NP_001124436.1 P51178 PLCD1_HUMAN phospholipase C, delta 1 377 PI-PLC X-box. intracellular signal transduction|lipid catabolic process|phospholipid metabolic process cytoplasm calcium ion binding|GTPase activating protein binding|phosphatidylinositol phospholipase C activity|signal transducer activity breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1) 24 KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653) CACCTTGAAGGCATAGTCCCG 0.607000 30 45 0 0 1 0 0 BAGE2 85319 broad.mit.edu 37 21 11058168 11058168 + RNA SNP A A T TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr21:11058168A>T ENST00000470054.1 - 0 479 B melanoma antigen family, member 2 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) TACATCTTTCAGGAGCTTGGT 0.388000 5 88 0 0 1 0 0 TAF1B 9014 broad.mit.edu 37 2 9989571 9989571 + Frame_Shift_Del DEL A A - TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr2:9989571delA ENST00000263663.5 + 3 375 c.187delA c.(187-189)aafs p.K65fs TAF1B_ENST00000396242.3_5'UTR|TAF1B_ENST00000402170.1_3'UTR NM_005680.2 NP_005671.2 Q53T94 TAF1B_HUMAN TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa 65 termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter nucleoplasm DNA binding|sequence-specific DNA binding transcription factor activity breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1) 14 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) CCGGGGGCTTAAAAAAAAAAA 0.333 2 4 --- --- --- --- GPR123 84435 broad.mit.edu 37 10 134895345 134895345 + Frame_Shift_Del DEL A A - TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr10:134895345delA ENST00000607359.1 + 5 988 c.988delA c.(988-990)ccfs p.T330fs Q86SQ6 GP123_HUMAN G protein-coupled receptor 123 481 integral to membrane|plasma membrane G-protein coupled receptor activity endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3) 14 all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203) OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05) CTCTGGCAGGACCCCCTGGAG 0.662 2 4 --- --- --- --- HNRNPKP3 0 broad.mit.edu 37 11 43283606 43283606 + RNA DEL A A - TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chr11:43283606delA ENST00000511537.1 - 0 1329 NR_033868.1 AAGCAAATGTAAAAAAAAAAA 0.388 4 6 --- --- --- --- TXLNG2P 0 broad.mit.edu 37 Y 21758004 21758005 + RNA DEL AG AG - TCGA-L6-A4EQ-01A-11D-A257-08 TCGA-L6-A4EQ-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 247b1c50-5882-4714-b26e-8059705de3f2 bef85d8f-bfee-493e-a438-2465d603b02a g.chrY:21758004_21758005delAG ENST00000253320.4 + 0 3085_3086 Q9BZA5 CY15A_HUMAN haematopoietic_and_lymphoid_tissue(1) 1 GAAAGACATCAGAGAGAGAGAG 0.347 3 6 --- --- --- ---