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 TAB3 257397 broad.mit.edu 37 X 30877655 30877655 + Silent SNP T T C TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chrX:30877655T>C ENST00000378933.1 - 2 228 c.51A>G c.(49-51)cgA>cgG p.R17R TAB3_ENST00000378932.2_Silent_p.R17R|TAB3_ENST00000378930.3_Silent_p.R17R|TAB3_ENST00000288422.2_Silent_p.R17R NM_152787.3 NP_690000.2 Q8N5C8 TAB3_HUMAN TGF-beta activated kinase 1/MAP3K7 binding protein 3 17 CUE. activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|endosome membrane|plasma membrane protein binding|zinc ion binding NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1) 27 GGAAACGTTGTCGAAGATCAT 0.448000 4 22 0 0 1 0 0 TDRD9 122402 broad.mit.edu 37 14 104473169 104473169 + Missense_Mutation SNP T T C TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr14:104473169T>C ENST00000409874.4 + 18 2042 c.1994T>C c.(1993-1995)gTt>gCt p.V665A TDRD9_ENST00000339063.5_Missense_Mutation_p.V665A NM_153046.2 NP_694591.2 Q8NDG6 TDRD9_HUMAN tudor domain containing 9 665 cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis nucleus|piP-body ATP binding|ATP-dependent helicase activity|nucleic acid binding breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1) 33 all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768) ATTGCACTTGTTGAGGCATTT 0.358000 4 10 0 0 1 0 0 ARHGAP30 257106 broad.mit.edu 37 1 161039405 161039405 + Missense_Mutation SNP G G A rs149081252 TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr1:161039405G>A ENST00000368013.3 - 1 330 c.10C>T c.(10-12)Cgg>Tgg p.R4W ARHGAP30_ENST00000368015.1_Intron|ARHGAP30_ENST00000368016.3_Missense_Mutation_p.R4W NM_001025598.1|NM_181720.2 NP_001020769.1|NP_859071.2 Q7Z6I6 RHG30_HUMAN Rho GTPase activating protein 30 4 regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction cytosol GTPase activator activity breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2) 37 all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.00122) CCTTTCTGCCGAGACTTCATG 0.637000 6 66 0 0 1 0 0 ATXN2 6311 broad.mit.edu 37 12 111894043 111894043 + Silent SNP G G A TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr12:111894043G>A ENST00000377617.3 - 23 3695 c.3534C>T c.(3532-3534)gcC>gcT p.A1178A ATXN2_ENST00000535949.1_Silent_p.A871A|ATXN2_ENST00000389153.4_Silent_p.A915A|ATXN2_ENST00000550104.1_3'UTR|ATXN2_ENST00000542287.2_Silent_p.A913A NM_002973.3 NP_002964.3 Q99700 ATX2_HUMAN ataxin 2 1178 cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network protein C-terminus binding|RNA binding NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1) 37 GAGCCTGGGCGGCCTGGTGCT 0.552000 10 103 0 0 1 0 0 IRF9 10379 broad.mit.edu 37 14 24633826 24633826 + Missense_Mutation SNP A A G TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr14:24633826A>G ENST00000396864.3 + 7 940 c.653A>G c.(652-654)tAc>tGc p.Y218C RP11-468E2.4_ENST00000558468.1_3'UTR|IRF9_ENST00000557894.1_Missense_Mutation_p.Y116C NM_006084.4 NP_006075.3 Q00978 IRF9_HUMAN interferon regulatory factor 9 218 interferon-gamma-mediated signaling pathway|response to virus|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway cytosol|nucleoplasm DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity NS(1)|breast(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2) 16 GBM - Glioblastoma multiforme(265;0.00853) TCCCCAGACTACTCACTGCTG 0.642000 16 100 0 0 1 0 0 LCT 3938 broad.mit.edu 37 2 136564823 136564823 + Missense_Mutation SNP C C T TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr2:136564823C>T ENST00000264162.2 - 9 4058 c.4048G>A c.(4048-4050)Gcc>Acc p.A1350T NM_002299.2 NP_002290.2 P09848 LPH_HUMAN lactase 1350 4 X approximate repeats. carbohydrate metabolic process|polysaccharide digestion apical plasma membrane|integral to plasma membrane|membrane fraction cation binding|glycosylceramidase activity|lactase activity breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4) 124 BRCA - Breast invasive adenocarcinoma(221;0.169) CTGGCGGAGGCTCTTGCTGTG 0.517000 7 61 0 0 1 0 0 COLGALT2 23127 broad.mit.edu 37 1 183914685 183914685 + Missense_Mutation SNP T T G TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr1:183914685T>G ENST00000361927.4 - 9 1521 c.1150A>C c.(1150-1152)Agc>Cgc p.S384R COLGALT2_ENST00000546159.1_Missense_Mutation_p.S384R|COLGALT2_ENST00000367520.3_Missense_Mutation_p.S121R|COLGALT2_ENST00000367521.1_5'UTR NM_015101.2 NP_055916.1 collagen beta(1-O)galactosyltransferase 2 TTCAGCTGGCTTGTGTTGAGT 0.488000 41 56 0 0 1 0 0 TBP 6908 broad.mit.edu 37 6 170871058 170871058 + Silent SNP G G A rs113440919 TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr6:170871058G>A ENST00000392092.2 + 3 513 c.234G>A c.(232-234)caG>caA p.Q78Q TBP_ENST00000230354.6_Silent_p.Q78Q|TBP_ENST00000540980.1_Silent_p.Q58Q NM_003194.4 NP_003185.1 P20226 TBP_HUMAN TATA box binding protein 78 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) agcagcagcagcagcagcagc 0.577000 3 28 0 0 1 0 0 SLC12A8 84561 broad.mit.edu 37 3 124854521 124854521 + Missense_Mutation SNP G G A TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr3:124854521G>A ENST00000423114.2 - 6 814 c.815C>T c.(814-816)gCg>gTg p.A272V SLC12A8_ENST00000393469.4_Missense_Mutation_p.A243V|SLC12A8_ENST00000469902.1_Missense_Mutation_p.A243V|SLC12A8_ENST00000314584.7_5'UTR A0AV02 S12A8_HUMAN solute carrier family 12, member 8 243 potassium ion transport integral to membrane symporter activity endometrium(2)|kidney(2)|lung(12) 16 ACCTGTAGCCGCTGGGAAGAA 0.448000 4 12 0 0 1 0 0 KBTBD2 25948 broad.mit.edu 37 7 32910344 32910344 + Missense_Mutation SNP G G A TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr7:32910344G>A ENST00000304056.4 - 4 1184 c.485C>T c.(484-486)gCt>gTt p.A162V AVL9_ENST00000404479.1_Intron NM_015483.2 NP_056298.2 Q8IY47 KBTB2_HUMAN kelch repeat and BTB (POZ) domain containing 2 162 endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|urinary_tract(1) 17 GBM - Glioblastoma multiforme(11;0.0499) ATGATACACAGCAGTGAACTT 0.398000 9 73 0 0 1 0 0 FGD6 55785 broad.mit.edu 37 12 95604019 95604019 + Missense_Mutation SNP G G C TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr12:95604019G>C ENST00000343958.4 - 2 1264 c.1041C>G c.(1039-1041)agC>agG p.S347R FGD6_ENST00000546711.1_Missense_Mutation_p.S347R|FGD6_ENST00000549499.1_Missense_Mutation_p.S347R NM_018351.3 NP_060821.3 Q6ZV73 FGD6_HUMAN FYVE, RhoGEF and PH domain containing 6 347 Poly-Ser. actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape cytoskeleton|Golgi apparatus|lamellipodium|ruffle metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 56 GACAGGAAGAGCTACTGTCTG 0.418000 35 46 0 0 1 0 0 RYR1 6261 broad.mit.edu 37 19 38976754 38976754 + Missense_Mutation SNP G G A TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr19:38976754G>A ENST00000355481.4 + 34 5590 c.5459G>A c.(5458-5460)cGc>cAc p.R1820H RYR1_ENST00000359596.3_Missense_Mutation_p.R1820H|RYR1_ENST00000360985.3_Missense_Mutation_p.R1820H NM_000540.2|NM_001042723.1 NP_000531.2|NP_001036188.1 P21817 RYR1_HUMAN ryanodine receptor 1 (skeletal) 1820 6 X approximate repeats. muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7) 285 all_cancers(60;7.91e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) Dantrolene(DB01219) GAGGCGGTGCGCGACGGTGGG 0.706000 10 77 0 0 1 0 0 MYO5C 55930 broad.mit.edu 37 15 52488561 52488561 + Missense_Mutation SNP G G A TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr15:52488561G>A ENST00000261839.7 - 39 5101 c.4940C>T c.(4939-4941)aCa>aTa p.T1647I RP11-430B1.2_ENST00000560518.1_lincRNA NM_018728.3 NP_061198.2 Q9NQX4 MYO5C_HUMAN myosin VC 1647 Dilute. myosin complex actin binding|ATP binding|calmodulin binding|motor activity breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 66 all cancers(107;0.0137) ATCACTGTCTGTGGTCTTCTT 0.512000 7 42 0 0 1 0 0 SEC14L5 9717 broad.mit.edu 37 16 5057420 5057420 + Missense_Mutation SNP C C T TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr16:5057420C>T ENST00000251170.7 + 13 1685 c.1505C>T c.(1504-1506)aCg>aTg p.T502M NM_014692.1 NP_055507.1 O43304 S14L5_HUMAN SEC14-like 5 (S. cerevisiae) 502 integral to membrane|intracellular transporter activity NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1) 29 CAGGAGCACACGGACCAGCTG 0.647000 12 14 0 0 1 0 0 ASTL 431705 broad.mit.edu 37 2 96789863 96789863 + Missense_Mutation SNP T T A TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr2:96789863T>A ENST00000342380.2 - 9 1021 c.1022A>T c.(1021-1023)gAg>gTg p.E341V NM_001002036.3 NP_001002036.3 Q6HA08 ASTL_HUMAN astacin-like metallo-endopeptidase (M12 family) 341 proteolysis metalloendopeptidase activity|zinc ion binding endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2) 30 ATGTGGGCTCTCCCCAGGCCC 0.652000 4 75 0 0 1 0 0 FBXL20 84961 broad.mit.edu 37 17 37420555 37420555 + Missense_Mutation SNP A A G TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr17:37420555A>G ENST00000264658.6 - 14 1336 c.1076T>C c.(1075-1077)aTt>aCt p.I359T FBXL20_ENST00000577399.1_Missense_Mutation_p.I361T|FBXL20_ENST00000394294.3_Missense_Mutation_p.I327T|FBXL20_ENST00000583610.1_Missense_Mutation_p.I359T NM_032875.2 NP_116264.2 Q96IG2 FXL20_HUMAN F-box and leucine-rich repeat protein 20 359 cytoplasm breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1) 22 LUAD - Lung adenocarcinoma(14;0.146) GTCCAGCTCAATCACCTCCAG 0.522000 7 36 0 0 1 0 0 RLTPR 146206 broad.mit.edu 37 16 67680391 67680391 + Missense_Mutation SNP C C T TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr16:67680391C>T ENST00000334583.6 + 6 765 c.437C>T c.(436-438)tCg>tTg p.S146L RLTPR_ENST00000545661.1_Missense_Mutation_p.S146L NM_001013838.1 NP_001013860.1 Q6F5E8 LR16C_HUMAN RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing 146 breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2) 18 Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192) OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232) AGCAGCCCCTCGGAGTCCACT 0.652000 4 63 0 0 1 0 0 FOXM1 2305 broad.mit.edu 37 12 2970493 2970493 + Missense_Mutation SNP A A G TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr12:2970493A>G ENST00000342628.2 - 9 1465 c.1352T>C c.(1351-1353)tTg>tCg p.L451S FOXM1_ENST00000361953.3_Intron|FOXM1_ENST00000359843.3_Intron NM_202002.2 NP_973731.1 Q08050 FOXM1_HUMAN forkhead box M1 422 cell cycle|embryo development|liver development|negative regulation of cell aging|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|positive regulation of cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell cycle arrest|regulation of cell growth|regulation of cell proliferation|regulation of oxygen and reactive oxygen species metabolic process|regulation of Ras protein signal transduction|regulation of reactive oxygen species metabolic process|regulation of sequence-specific DNA binding transcription factor activity|tissue development|transcription from RNA polymerase II promoter|vasculogenesis cytoplasm|transcription factor complex DNA bending activity|DNA binding|double-stranded DNA binding|promoter binding|protein binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|transcription factor binding breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3) 24 OV - Ovarian serous cystadenocarcinoma(31;0.000622) aaaattaaacaagctggtgat 0.363000 6 24 0 0 1 0 0 NPHS1 4868 broad.mit.edu 37 19 36333388 36333388 + Missense_Mutation SNP C C T rs146400394 TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr19:36333388C>T ENST00000378910.5 - 18 2398 c.2399G>A c.(2398-2400)cGc>cAc p.R800H NPHS1_ENST00000353632.6_Missense_Mutation_p.R800H NM_004646.3 NP_004637.1 O60500 NPHN_HUMAN nephrosis 1, congenital, Finnish type (nephrin) 800 Ig-like C2-type 7. cell adhesion|excretion|muscle organ development integral to plasma membrane p.R800H(1) NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1) 74 all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) AATCCGCAGGCGCCCCGTTGG 0.607000 6 105 0 0 1 0 0 HSD17B7P2 158160 broad.mit.edu 37 10 38654432 38654432 + RNA SNP A A G rs2257765 TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr10:38654432A>G ENST00000494540.1 + 0 599 NR_003086.1 TCATCTCGCAATGCAAGGAAA 0.453000 3 45 0 0 1 0 0 DGAT2 84649 broad.mit.edu 37 11 75509417 75509417 + Missense_Mutation SNP C C T TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr11:75509417C>T ENST00000228027.7 + 7 1215 c.955C>T c.(955-957)Ctc>Ttc p.L319F DGAT2_ENST00000376262.3_Missense_Mutation_p.L276F NM_032564.4 NP_115953.2 Q96PD7 DGAT2_HUMAN diacylglycerol O-acyltransferase 2 319 glycerol metabolic process|triglyceride biosynthetic process endoplasmic reticulum membrane|integral to membrane diacylglycerol O-acyltransferase activity endometrium(3)|large_intestine(5)|lung(5)|prostate(2)|skin(2) 17 Ovarian(111;0.103) TGGTCGAGGCCTCTTCTCCTC 0.587000 6 28 0 0 1 0 0 ARID2 196528 broad.mit.edu 37 12 46246107 46246107 + Missense_Mutation SNP A A C TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr12:46246107A>C ENST00000334344.6 + 15 4373 c.4201A>C c.(4201-4203)Atc>Ctc p.I1401L ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_Missense_Mutation_p.I9L|ARID2_ENST00000422737.1_Missense_Mutation_p.I1252L|ARID2_ENST00000444670.1_Missense_Mutation_p.I1011L NM_152641.2 NP_689854.2 Q68CP9 ARID2_HUMAN AT rich interactive domain 2 (ARID, RFX-like) 1401 chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding|zinc ion binding NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2) 116 Lung SC(27;0.192)|Renal(347;0.236) Lung NSC(34;0.106)|all_lung(34;0.22) OV - Ovarian serous cystadenocarcinoma(5;0.00691) GBM - Glioblastoma multiforme(48;0.0153) GACTTTAGATATCACTCAGCA 0.383000 """N, S, F""" hepatocellular carcinoma 7 50 0 0 1 0 0 PADI2 11240 broad.mit.edu 37 1 17395638 17395638 + Silent SNP G G A rs61731909 TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr1:17395638G>A ENST00000375486.4 - 16 1962 c.1899C>T c.(1897-1899)gaC>gaT p.D633D PADI2_ENST00000444885.2_Silent_p.D517D|PADI2_ENST00000466151.1_5'UTR NM_007365.2 NP_031391.2 Q9Y2J8 PADI2_HUMAN peptidyl arginine deiminase, type II 633 peptidyl-citrulline biosynthetic process from peptidyl-arginine cytoplasm calcium ion binding|protein-arginine deiminase activity breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3) 29 Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201) L-Citrulline(DB00155) CAGAAATGTCGTCGATGAAGG 0.597000 16 53 0 0 1 0 0 FOXA2 3170 broad.mit.edu 37 20 22563313 22563313 + Missense_Mutation SNP G G C TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr20:22563313G>C ENST00000419308.2 - 2 751 c.549C>G c.(547-549)agC>agG p.S183R FOXA2_ENST00000377115.4_Missense_Mutation_p.S183R|FOXA2_ENST00000319993.4_Missense_Mutation_p.S189R NM_021784.4 NP_068556.2 Q9Y261 FOXA2_HUMAN forkhead box A2 183 cell differentiation in hindbrain|central nervous system myelin formation|chromatin modification|dorsal/ventral neural tube patterning|ectoderm formation|endocrine pancreas development|endoderm development|epithelial tube branching involved in lung morphogenesis|in utero embryonic development|lung epithelial cell differentiation|negative regulation of neuron differentiation|neuron fate specification|oligodendrocyte cell fate commitment|positive regulation of embryonic development|positive regulation of gastrulation|positive regulation of neuron differentiation|primitive streak formation|regulation of blood coagulation|regulation of sequence-specific DNA binding transcription factor activity|response to interleukin-6 cytoplasm|transcription factor complex DNA bending activity|double-stranded DNA binding|protein domain specific binding|RNA polymerase II core promoter proximal region 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 breast(1)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|urinary_tract(1) 22 Lung NSC(19;0.188) GGTAGATCTCGCTCAGCGTCA 0.587000 61 58 0 0 1 0 0 NF1 4763 broad.mit.edu 37 17 29556992 29556992 + Splice_Site SNP G G C TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr17:29556992G>C ENST00000358273.4 + 22 3373 c.2990_splice c.e22+1 p.R997_splice NF1_ENST00000356175.3_Splice_Site_p.R997_splice NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 997 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.0?(8)|p.?(4)|p.R997K(1) NF1/ACCN1(2) autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9) 599 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) AATCTGGTCAGGTAAGCATTC 0.353000 """D, Mis, N, F, S, O""" """neurofibroma, glioma""" """neurofibroma, glioma""" Neurofibromatosis, type 1 TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088) 37 11 0 0 1 0 0 MAGEC1 9947 broad.mit.edu 37 X 140994473 140994473 + Missense_Mutation SNP C C T TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chrX:140994473C>T ENST00000285879.4 + 4 1569 c.1283C>T c.(1282-1284)cCt>cTt p.P428L MAGEC1_ENST00000406005.2_Intron NM_005462.4 NP_005453.2 O60732 MAGC1_HUMAN melanoma antigen family C, 1 428 protein binding breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1) 127 Acute lymphoblastic leukemia(192;6.56e-05) CAGAGTTCTCCTGAGAGTGCT 0.448000 HNSCC(15;0.026) 7 184 0 0 1 0 0 LOC100288069 100288069 broad.mit.edu 37 1 700514 700514 + RNA DEL A A - TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr1:700514delA ENST00000428504.1 - 0 1039 NR_033908.1 actccatctcaaaaaaaaaaa 0.453 2 4 --- --- --- --- CSMD1 64478 broad.mit.edu 37 8 2815310 2815310 + Frame_Shift_Del DEL A A - TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr8:2815310delA ENST00000602557.1 - 64 10280 c.9725delT c.(9724-9726)tcfs p.F3242fs CSMD1_ENST00000602723.1_Frame_Shift_Del_p.F3065fs|CSMD1_ENST00000537824.1_Frame_Shift_Del_p.F3241fs|CSMD1_ENST00000520002.1_Frame_Shift_Del_p.F3242fs|CSMD1_ENST00000542608.1_Frame_Shift_Del_p.F3064fs|CSMD1_ENST00000400186.3_Frame_Shift_Del_p.F3065fs Q96PZ7 CSMD1_HUMAN CUB and Sushi multiple domains 1 3242 Sushi 27. integral to membrane breast(20)|large_intestine(5) 25 all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234) all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689) TCTGCACCTGAAAAAAACCGT 0.453 2 4 --- --- --- --- GPSM1 26086 broad.mit.edu 37 9 139235482 139235482 + Frame_Shift_Del DEL C C - TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr9:139235482delC ENST00000392945.3 + 9 1459 c.1239delC c.(1237-1239)ctfs p.L413fs GPSM1_ENST00000440944.1_Intron NM_015597.4 NP_056412.4 Q86YR5 GPSM1_HUMAN G-protein signaling modulator 1 0 Interaction with STK11/LKB1 (By similarity).|Mediates association with membranes (By similarity). cell differentiation|nervous system development|signal transduction cytosol|endoplasmic reticulum membrane|Golgi membrane|plasma membrane binding|GTPase activator activity biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1) 9 Myeloproliferative disorder(178;0.0821) OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06) GGGTCTTGCTCCCCACAGGCA 0.687 7 2 --- --- --- --- RP11-19N8.4 0 broad.mit.edu 37 16 33070154 33070154 + RNA DEL C C - TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr16:33070154delC ENST00000561541.1 - 0 291 CCTATCACATCCCATTCCAGC 0.488 3 6 --- --- --- --- BCAS3 54828 broad.mit.edu 37 17 59465991 59465992 + Frame_Shift_Ins INS - - A TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr17:59465991_59465992insA ENST00000589222.1 + 25 2740_2741 c.2672_2673insA c.(2671-2673)gaafs p.E891fs BCAS3_ENST00000588462.1_Intron|BCAS3_ENST00000390652.5_Intron|RP11-332H18.5_ENST00000585765.1_RNA|BCAS3_ENST00000585812.1_Intron|BCAS3_ENST00000407086.3_Intron|BCAS3_ENST00000408905.3_Intron|BCAS3_ENST00000585744.1_Intron|BCAS3_ENST00000588874.1_Intron Q9H6U6 BCAS3_HUMAN breast carcinoma amplified sequence 3 0 nucleus NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 44 BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06) AAAAAAAAAGGAAAAAAAAAAC 0.431 3 4 --- --- --- --- KCTD1 284252 broad.mit.edu 37 18 24128262 24128264 + In_Frame_Del DEL TCC TCC - TCGA-RT-A6YA-01A-12D-A35D-08 TCGA-RT-A6YA-10B-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 05227ee7-4ecf-4dd2-bbff-9e457664f858 5d7caf6d-3e44-48f0-96f4-0838b3c38d98 g.chr18:24128262_24128264delTCC ENST00000417602.1 - 1 236_238 c.237_239delGGA c.(235-240)gac>ga p.ED79del KCTD1_ENST00000317932.7_Intron|KCTD1_ENST00000408011.3_Intron|KCTD1_ENST00000579973.1_Intron NM_001142730.2 NP_001136202.1 Q719H9 KCTD1_HUMAN potassium channel tetramerization domain containing 1 0 BTB. negative regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus|voltage-gated potassium channel complex transcription corepressor activity|transcription factor binding|voltage-gated potassium channel activity endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(3) 12 all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848) Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05) cccacctccgtcctcctcctcct 0.690 3 3 --- --- --- ---