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 EFEMP2 30008 broad.mit.edu 37 11 65636030 65636030 + Silent SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr11:65636030G>A ENST00000307998.6 - 8 1028 c.798C>T c.(796-798)tcC>tcT p.S266S EFEMP2_ENST00000528176.1_Silent_p.S266S NM_016938.4 NP_058634.4 O95967 FBLN4_HUMAN EGF containing fibulin-like extracellular matrix protein 2 266 EGF-like 5; calcium-binding (Potential). blood coagulation basement membrane|membrane calcium ion binding|extracellular matrix structural constituent|protein binding|transmembrane receptor activity cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1) 21 READ - Rectum adenocarcinoma(159;0.169) GGCAGTGGCAGGAGAAACGGC 0.622000 3 64 0 0 0.115264 0 0 ZNF521 25925 broad.mit.edu 37 18 22805082 22805082 + Missense_Mutation SNP C C T TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr18:22805082C>T ENST00000361524.3 - 4 2948 c.2800G>A c.(2800-2802)Gtg>Atg p.V934M ZNF521_ENST00000584787.1_Missense_Mutation_p.V714M|ZNF521_ENST00000538137.2_Missense_Mutation_p.V934M NM_015461.2 NP_056276.1 Q96K83 ZN521_HUMAN zinc finger protein 521 934 cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein domain specific binding|zinc ion binding NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2) 149 all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991) CGAGAGCACACGTTGCACTTG 0.507000 T PAX5 ALL 22 106 0 0 0.667858 0 0 DLGAP4 22839 broad.mit.edu 37 20 35125295 35125295 + Silent SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr20:35125295G>A ENST00000373913.3 + 8 2316 c.1836G>A c.(1834-1836)ctG>ctA p.L612L DLGAP4_ENST00000475894.1_3'UTR|DLGAP4_ENST00000340491.4_Silent_p.L73L|DLGAP4_ENST00000401952.2_Silent_p.L612L|DLGAP4_ENST00000339266.5_Silent_p.L612L|DLGAP4_ENST00000373907.2_Silent_p.L612L Q9Y2H0 DLGP4_HUMAN discs, large (Drosophila) homolog-associated protein 4 612 cell-cell signaling membrane protein binding breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1) 37 Breast(12;0.0192) Myeloproliferative disorder(115;0.00878) CGGACAGCCTGGACAGCAGTA 0.632000 3 96 0 0 0.115264 0 0 GALNT12 79695 broad.mit.edu 37 9 101597558 101597558 + Silent SNP T T C TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr9:101597558T>C ENST00000375011.3 + 5 945 c.945T>C c.(943-945)ttT>ttC p.F315F NM_024642.4 NP_078918.3 Q8IXK2 GLT12_HUMAN UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12) 315 Catalytic subdomain B. Golgi membrane|integral to membrane polypeptide N-acetylgalactosaminyltransferase activity|sugar binding breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1) 17 Acute lymphoblastic leukemia(62;0.0559) GTGGGCTGTTTGCTGTGAGTA 0.393000 75 76 0 0 0.870114 0 0 ITGA8 8516 broad.mit.edu 37 10 15655758 15655758 + Missense_Mutation SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr10:15655758G>A ENST00000378076.3 - 15 1807 c.1454C>T c.(1453-1455)cCg>cTg p.P485L NM_003638.1 NP_003629.1 P53708 ITA8_HUMAN integrin, alpha 8 485 cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development integrin complex receptor activity NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3) 96 AGTCACAACCGGTCTTGCTCT 0.463000 3 102 0 0 0.115264 0 0 ABCA1 19 broad.mit.edu 37 9 107562200 107562200 + Missense_Mutation SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr9:107562200G>A ENST00000374736.3 - 36 5237 c.4843C>T c.(4843-4845)Cgg>Tgg p.R1615W NM_005502.3 NP_005493.2 O95477 ABCA1_HUMAN ATP-binding cassette, sub-family A (ABC1), member 1 1615 R -> Q (associated with reduced plasma HDL cholesterol). Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 115 OV - Ovarian serous cystadenocarcinoma(323;0.023) Adenosine triphosphate(DB00171)|Glibenclamide(DB01016) AGGTTGGCCCGGAGAATGGCA 0.468000 3 121 0 0 0.115264 0 0 GBP2 2634 broad.mit.edu 37 1 89579760 89579760 + Missense_Mutation SNP A A G TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr1:89579760A>G ENST00000370466.3 - 7 1356 c.1088T>C c.(1087-1089)aTt>aCt p.I363T GBP2_ENST00000463660.1_5'UTR NM_004120.3 NP_004111.2 P32456 GBP2_HUMAN guanylate binding protein 2, interferon-inducible 363 interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway plasma membrane GTP binding|GTPase activity endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1) 20 Lung NSC(277;0.0908) all cancers(265;0.0151)|Epithelial(280;0.0284) GAAGACTTCAATGGCCTCTCT 0.493000 42 108 0 0 0.870114 0 0 WDR59 79726 broad.mit.edu 37 16 74990380 74990380 + Missense_Mutation SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr16:74990380G>A ENST00000262144.6 - 3 363 c.233C>T c.(232-234)gCg>gTg p.A78V WDR59_ENST00000562331.1_5'UTR NM_030581.3 NP_085058.3 Q6PJI9 WDR59_HUMAN WD repeat domain 59 78 breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1) 27 CACCGAAGCCGCAAAATAGTG 0.488000 3 78 0 0 0.115264 0 0 GTPBP1 9567 broad.mit.edu 37 22 39112749 39112749 + Missense_Mutation SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr22:39112749G>A ENST00000216044.5 + 4 811 c.578G>A c.(577-579)cGc>cAc p.R193H NM_004286.4 NP_004277.2 O00178 GTPB1_HUMAN GTP binding protein 1 193 immune response|positive regulation of mRNA catabolic process|signal transduction cytoplasmic exosome (RNase complex)|cytosol GTP binding|GTPase activity p.R193H(1) endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1) 18 Melanoma(58;0.04) GGCTTTGCCCGCCAGAAACTC 0.557000 3 55 0 0 0.115264 0 0 VDAC1 7416 broad.mit.edu 37 5 133311612 133311612 + Missense_Mutation SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr5:133311612G>A ENST00000265333.3 - 7 896 c.652C>T c.(652-654)Cgc>Tgc p.R218C VDAC1_ENST00000395044.3_Missense_Mutation_p.R218C|VDAC1_ENST00000395047.2_Missense_Mutation_p.R218C NM_003374.2 NP_003365.1 P21796 VDAC1_HUMAN voltage-dependent anion channel 1 218 apoptosis|interspecies interaction between organisms mitochondrial nucleoid|mitochondrial outer membrane|plasma membrane|pore complex porin activity|protein binding|voltage-gated anion channel activity endometrium(1)|large_intestine(1)|lung(1)|skin(1) 4 KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02) Dihydroxyaluminium(DB01375) ATTCCGAAGCGCGTGTTACTG 0.522000 56 215 0 0 0.870114 0 0 AP4M1 9179 broad.mit.edu 37 7 99704048 99704048 + Missense_Mutation SNP C C A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr7:99704048C>A ENST00000429084.1 + 14 1227 c.1069C>A c.(1069-1071)Cca>Aca p.P357T AP4M1_ENST00000422582.1_Missense_Mutation_p.P222T|AP4M1_ENST00000359593.4_Missense_Mutation_p.P350T|AP4M1_ENST00000421755.1_Missense_Mutation_p.P350T O00189 AP4M1_HUMAN adaptor-related protein complex 4, mu 1 subunit 350 MHD. intracellular protein transport|vesicle-mediated transport clathrin adaptor complex|coated pit|Golgi trans cisterna transporter activity breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1) 17 Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439) GCTGAGCAGCCCAGAGCAGAA 0.607000 3 80 0.115264 0.133855 0.115264 1 0 DAAM1 23002 broad.mit.edu 37 14 59797945 59797945 + Missense_Mutation SNP A A G TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr14:59797945A>G ENST00000395125.1 + 13 1602 c.1579A>G c.(1579-1581)Atc>Gtc p.I527V DAAM1_ENST00000360909.3_Missense_Mutation_p.I527V|DAAM1_ENST00000351081.1_Missense_Mutation_p.I527V NM_014992.2 NP_055807.1 Q9Y4D1 DAAM1_HUMAN dishevelled associated activator of morphogenesis 1 527 actin cytoskeleton organization cytoplasm|plasma membrane actin binding|Rho GTPase binding breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1) 37 OV - Ovarian serous cystadenocarcinoma(108;0.165) CTGTGCTTCAATCCCAGGTGG 0.502000 17 179 0 0 0.500413 0 0 ZW10 9183 broad.mit.edu 37 11 113631247 113631247 + Missense_Mutation SNP C C A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr11:113631247C>A ENST00000200135.3 - 4 552 c.408G>T c.(406-408)caG>caT p.Q136H NM_004724.3 NP_004715.1 O43264 ZW10_HUMAN zw10 kinetochore protein 136 Interaction with RINT1. cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole centromeric DNA binding|protein binding central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1) 18 all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425) BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786) CTTCCAGACGCTGAGCACCAG 0.323000 81 223 7.0969e-38 8.80995e-38 0.870114 1 0 TCHP 84260 broad.mit.edu 37 12 110353299 110353299 + Missense_Mutation SNP C C G TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr12:110353299C>G ENST00000312777.5 + 12 1626 c.1412C>G c.(1411-1413)gCc>gGc p.A471G TCHP_ENST00000405876.4_Missense_Mutation_p.A471G NM_032300.4 NP_115676.1 Q9BT92 TCHP_HUMAN trichoplein, keratin filament binding 471 Glu-rich.|Interaction with keratin proteins. apoptosis|negative regulation of cell growth apical cortex|centrosome|keratin filament|mitochondrion|plasma membrane protein binding NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2) 22 CTCTCAGATGCCCTGCTGCAG 0.637000 25 21 0 0 0.729181 0 0 RBL2 5934 broad.mit.edu 37 16 53504454 53504454 + Missense_Mutation SNP C C G TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr16:53504454C>G ENST00000262133.6 + 16 2542 c.2405C>G c.(2404-2406)cCt>cGt p.P802R RBL2_ENST00000544545.1_Intron|RBL2_ENST00000379935.4_3'UTR NM_005611.3 NP_005602.3 Q08999 RBL2_HUMAN retinoblastoma-like 2 (p130) 802 Pocket; binds E1A.|Spacer. cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleolus DNA binding|protein binding breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 45 TTGCAAGTCCCTGGTCAAGTG 0.552000 5 105 0 0 0.184627 0 0 RUNDC1 146923 broad.mit.edu 37 17 41141502 41141502 + Nonsense_Mutation SNP G G T TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr17:41141502G>T ENST00000361677.1 + 3 814 c.802G>T c.(802-804)Gag>Tag p.E268* NM_173079.2 NP_775102.2 Q96C34 RUND1_HUMAN RUN domain containing 1 268 breast(1)|large_intestine(2)|lung(4)|prostate(1) 8 Breast(137;0.00499) BRCA - Breast invasive adenocarcinoma(366;0.161) ACAGTTGGTTGAGCAACTGAA 0.493000 28 85 2.09667e-21 2.516e-21 0.788014 1 0 ADPRH 141 broad.mit.edu 37 3 119305412 119305412 + Silent SNP A A G TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr3:119305412A>G ENST00000478399.1 + 3 1984 c.579A>G c.(577-579)aaA>aaG p.K193K ADPRH_ENST00000357003.3_Silent_p.K193K|ADPRH_ENST00000478927.1_Silent_p.K193K|ADPRH_ENST00000465513.1_Silent_p.K193K|ADPRH_ENST00000471850.1_3'UTR P54922 ADPRH_HUMAN ADP-ribosylarginine hydrolase 193 protein de-ADP-ribosylation ADP-ribosylarginine hydrolase activity|magnesium ion binding breast(1)|kidney(1)|lung(10)|ovary(1) 13 Lung NSC(201;0.0977) GBM - Glioblastoma multiforme(114;0.23) AGTGGGGAAAAGGACTGATGG 0.512000 3 107 0 0 0.115264 0 0 NCOA6 23054 broad.mit.edu 37 20 33345744 33345744 + Silent SNP C C T TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr20:33345744C>T ENST00000374796.2 - 8 3377 c.807G>A c.(805-807)caG>caA p.Q269Q NCOA6_ENST00000359003.2_Silent_p.Q269Q Q14686 NCOA6_HUMAN nuclear receptor coactivator 6 269 CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region. brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter transcription factor complex chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding p.Q269Q(15) NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1) 107 gctgctgctgctgttgttgtt 0.537000 4 36 0 0 0.150653 0 0 EFCAB1 79645 broad.mit.edu 37 8 49643961 49643961 + Nonsense_Mutation SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr8:49643961G>A ENST00000262103.3 - 2 240 c.160C>T c.(160-162)Cga>Tga p.R54* EFCAB1_ENST00000523092.1_Intron|EFCAB1_ENST00000521002.1_Intron|EFCAB1_ENST00000433756.1_Intron NM_024593.3 NP_078869.1 Q9HAE3 EFCB1_HUMAN EF-hand calcium binding domain 1 54 calcium ion binding endometrium(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(2) 14 all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464) AGGATGTTTCGAAATGCATTA 0.393000 29 88 0 0 0.740014 0 0 ROBO2 6092 broad.mit.edu 37 3 77623657 77623657 + Missense_Mutation SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr3:77623657G>A ENST00000461745.1 + 14 2879 c.1979G>A c.(1978-1980)cGc>cAc p.R660H ROBO2_ENST00000487694.3_Missense_Mutation_p.R676H|ROBO2_ENST00000332191.8_Missense_Mutation_p.R660H NM_002942.4 NP_002933.1 Q9HCK4 ROBO2_HUMAN roundabout, axon guidance receptor, homolog 2 (Drosophila) 660 Fibronectin type-III 2. apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development axolemma|cell surface|integral to membrane axon guidance receptor activity|identical protein binding NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1) 117 Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103) CAGGTTGATCGCCAACCCCAG 0.423000 24 48 0 0 0.706142 0 0 HOOK3 84376 broad.mit.edu 37 8 42873627 42873627 + Missense_Mutation SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr8:42873627G>A ENST00000307602.4 + 22 2343 c.2143G>A c.(2143-2145)Gcc>Acc p.A715T RP11-598P20.5_ENST00000534420.1_Missense_Mutation_p.A21T NM_032410.3 NP_115786.1 Q86VS8 HOOK3_HUMAN hook microtubule-tethering protein 3 715 Required for association with Golgi.|Required for interaction with MSR1. cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport cis-Golgi network|FHF complex|microtubule|pericentriolar material identical protein binding|microtubule binding NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2) 31 Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184) all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129) Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114) CGTGCAGCCGGCCACAGCAAG 0.537000 T RET papillary thyroid 4 129 0 0 0.184627 0 0 SLC6A10P 0 broad.mit.edu 37 16 32890622 32890622 + RNA SNP T T G TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr16:32890622T>G ENST00000330048.5 - 0 3176 NR_003083.2 CGTTGGTGTTTTTGTAGACCA 0.617000 4 50 0 0 0.248553 0 0 CNNM1 26507 broad.mit.edu 37 10 101120670 101120670 + Missense_Mutation SNP C C T TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr10:101120670C>T ENST00000356713.4 + 3 2085 c.1796C>T c.(1795-1797)aCg>aTg p.T599M CNNM1_ENST00000446890.1_Missense_Mutation_p.T528M|CNNM1_ENST00000370534.4_Missense_Mutation_p.T234M|CNNM1_ENST00000370528.3_Missense_Mutation_p.T528M NM_020348.2 NP_065081.2 Q9NRU3 CNNM1_HUMAN cyclin M1 599 ion transport integral to membrane|plasma membrane NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1) 25 Colorectal(252;0.234) Epithelial(162;6.82e-10)|all cancers(201;5.62e-08) CTTTCGGACACGGAGATGCGG 0.542000 4 121 0 0 0.150653 0 0 PHKA1 5255 broad.mit.edu 37 X 71864258 71864258 + Silent SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chrX:71864258G>A ENST00000373545.3 - 14 1851 c.1413C>T c.(1411-1413)atC>atT p.I471I PHKA1_ENST00000541944.1_Silent_p.I471I|PHKA1_ENST00000373539.3_Silent_p.I471I|PHKA1_ENST00000373542.4_Silent_p.I471I|PHKA1_ENST00000339490.3_Silent_p.I471I P46020 KPB1_HUMAN phosphorylase kinase, alpha 1 (muscle) 471 glucose metabolic process|glycogen catabolic process cytosol|plasma membrane calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1) 52 Renal(35;0.156) GTTGTACTCTGATGGGGTATA 0.433000 18 51 0 0 0.575678 0 0 DMC1 11144 broad.mit.edu 37 22 38951410 38951410 + Silent SNP A A G TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr22:38951410A>G ENST00000216024.2 - 6 607 c.331T>C c.(331-333)Tta>Cta p.L111L DMC1_ENST00000428462.2_Silent_p.L111L NM_007068.2 NP_008999.2 Q14565 DMC1_HUMAN DNA meiotic recombinase 1 111 reciprocal meiotic recombination condensed nuclear chromosome ATP binding|DNA binding|DNA-dependent ATPase activity|protein binding large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(1) 11 Melanoma(58;0.0286) CCTCCTAGTAACTTACTGGAA 0.303000 Homologous recombination 4 106 0 0 0.184627 0 0 FOXP2 93986 broad.mit.edu 37 7 114270000 114270000 + Silent SNP G G A TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr7:114270000G>A ENST00000393500.3 + 11 1132 c.312G>A c.(310-312)caG>caA p.Q104Q FOXP2_ENST00000393489.3_Silent_p.Q87Q|FOXP2_ENST00000360232.4_Silent_p.Q179Q|FOXP2_ENST00000408937.3_Silent_p.Q204Q|FOXP2_ENST00000378237.3_Silent_p.Q179Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393491.3_Silent_p.Q87Q|FOXP2_ENST00000403559.4_Silent_p.Q196Q|FOXP2_ENST00000390668.3_Silent_p.Q203Q|FOXP2_ENST00000393494.2_Silent_p.Q179Q|FOXP2_ENST00000393498.2_Silent_p.Q159Q|FOXP2_ENST00000350908.4_Silent_p.Q179Q O15409 FOXP2_HUMAN forkhead box P2 179 Gln-rich. camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning cytoplasm|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding p.Q204Q(1) breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 52 agcaacaacagcagcagcagc 0.498000 3 73 0 0 0.115264 0 0 RP11-417J8.6 0 broad.mit.edu 37 1 142699941 142699942 + RNA DEL TA TA - TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr1:142699941_142699942delTA ENST00000369381.2 - 0 2077 GAGGAAACACtatatatatata 0.248 4 3 --- --- --- --- SYN2 6854 broad.mit.edu 37 3 12046124 12046126 + RNA DEL AGC AGC - rs76272937 TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr3:12046124_12046126delAGC ENST00000432424.2 + 0 245_247 Q86VA8 Q86VA8_HUMAN synapsin II neurotransmitter secretion synaptic vesicle ATP binding|ligase activity breast(5)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1) 18 AGCCCCAGCAAGCGCCGAcgccg 0.764 3 5 --- --- --- --- RP11-377D9.3 0 broad.mit.edu 37 12 13174142 13174147 + RNA DEL AACAAC AACAAC - rs113537246 TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr12:13174142_13174147delAACAAC ENST00000543321.1 + 0 1025 ctgtctcaaaaacaacaacaacaaca 0.553 3 6 --- --- --- --- R3HDM2 22864 broad.mit.edu 37 12 57674205 57674207 + In_Frame_Del DEL TGC TGC - TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr12:57674205_57674207delTGC ENST00000402412.1 - 14 1668_1670 c.1278_1280delGCA c.(1276-1281)caa>ca p.QQ426del R3HDM2_ENST00000347140.3_In_Frame_Del_p.QQ412del|R3HDM2_ENST00000413953.2_In_Frame_Del_p.QQ139del|RP11-123K3.4_ENST00000548184.1_RNA|R3HDM2_ENST00000393811.2_In_Frame_Del_p.QQ139del|R3HDM2_ENST00000441731.2_In_Frame_Del_p.QQ73del|R3HDM2_ENST00000358907.2_In_Frame_Del_p.QQ412del|R3HDM2_ENST00000403821.2_In_Frame_Del_p.QQ412del Q9Y2K5 R3HD2_HUMAN R3H domain containing 2 412 Gln-rich. nucleus nucleic acid binding breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1) 22 AGCAGGAAGTtgctgctgctgct 0.576 11 172 --- --- --- --- SAMD15 161394 broad.mit.edu 37 14 77845094 77845094 + Frame_Shift_Del DEL A A - TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr14:77845094delA ENST00000216471.4 + 1 1619 c.1333delA c.(1333-1335)aafs p.K445fs SAMD15_ENST00000533095.2_Intron NM_001010860.1 NP_001010860.1 Q9P1V8 SAM15_HUMAN sterile alpha motif domain containing 15 445 breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 28 CCGTGAGCCTAAAAGAGGAAA 0.383 35 40 --- --- --- --- C20orf85 128602 broad.mit.edu 37 20 56735727 56735727 + Frame_Shift_Del DEL C C - TCGA-FY-A3I5-01B-11D-A21Z-08 TCGA-FY-A3I5-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2ede8763-643f-4e29-ba92-60bc5be02a3e f61f065c-bf04-454a-a292-a5178665ac29 g.chr20:56735727delC ENST00000371168.3 + 4 324 c.263delC c.(262-264)tcfs p.S88fs NM_178456.2 NP_848551.1 Q9H1P6 CT085_HUMAN chromosome 20 open reading frame 85 88 kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1) 13 all_epithelial(3;5.99e-14)|Lung NSC(12;0.000152)|all_lung(29;0.000518)|Melanoma(10;0.118) BRCA - Breast invasive adenocarcinoma(13;5.53e-12)|Epithelial(14;7.42e-08)|all cancers(14;7.19e-07) GTCTTTCCATCCCCCCCAGTC 0.582 7 82 --- --- --- ---