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 CHEK2 11200 broad.mit.edu 37 22 29091787 29091787 + Nonsense_Mutation SNP G G C TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr22:29091787G>C ENST00000544772.1 - 12 1943 c.507C>G c.(505-507)taC>taG p.Y169* CHEK2_ENST00000403642.1_Nonsense_Mutation_p.Y299*|CHEK2_ENST00000405598.1_Nonsense_Mutation_p.Y390*|CHEK2_ENST00000348295.3_Nonsense_Mutation_p.Y361*|CHEK2_ENST00000402731.1_Nonsense_Mutation_p.Y361*|CHEK2_ENST00000382580.2_Nonsense_Mutation_p.Y433*|CHEK2_ENST00000382578.1_Nonsense_Mutation_p.Y299*|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000328354.6_Nonsense_Mutation_p.Y390*|CHEK2_ENST00000404276.1_Nonsense_Mutation_p.Y390* NM_001257387.1 NP_001244316.1 O96017 CHK2_HUMAN checkpoint kinase 2 390 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 central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2) 50 CAGGCGCCAAGTAGGTGGGGG 0.423000 F breast Direct reversal of damage;Other conserved DNA damage response genes 8 95 0 0 0.335167 0 0 SP140 11262 broad.mit.edu 37 2 231135315 231135315 + Missense_Mutation SNP G G A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr2:231135315G>A ENST00000392045.3 + 15 1573 c.1459G>A c.(1459-1461)Gca>Aca p.A487T SP140_ENST00000417495.3_Missense_Mutation_p.A373T|SP140_ENST00000486687.2_Missense_Mutation_p.A411T|SP140_ENST00000420434.3_Missense_Mutation_p.A460T|SP140_ENST00000350136.5_Missense_Mutation_p.A356T|SP140_ENST00000343805.6_Missense_Mutation_p.A427T NM_007237.4 NP_009168.4 Q13342 LY10_HUMAN SP140 nuclear body protein 487 defense response cytoplasm|nuclear envelope|nucleolus|nucleoplasm DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1) 12 Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167) Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942) TGTGGATATTGCAAACAACTC 0.308000 12 141 0 0 0.500413 0 0 RP11-69H14.6 0 broad.mit.edu 37 15 22332570 22332570 + RNA SNP T T C TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr15:22332570T>C ENST00000558896.1 + 0 377 CCCATGCTCATCTGCTCCAAT 0.398000 4 239 0 0 0.150653 0 0 GYS1 2997 broad.mit.edu 37 19 49488755 49488755 + Silent SNP G G A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr19:49488755G>A ENST00000323798.3 - 5 982 c.786C>T c.(784-786)acC>acT p.T262T GYS1_ENST00000540532.1_Silent_p.T182T|GYS1_ENST00000541188.1_Silent_p.T182T|GYS1_ENST00000263276.6_Silent_p.T198T|GYS1_ENST00000544287.1_Intron NM_002103.4 NP_002094.2 P13807 GYS1_HUMAN glycogen synthase 1 (muscle) 262 glucose metabolic process|glycogen biosynthetic process cytosol glycogen (starch) synthase activity|protein binding breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 22 all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286) CCTCGATGGCGGTGATCTGGG 0.582000 3 74 0 0 0.115264 0 0 PSMB7 5695 broad.mit.edu 37 9 127177679 127177679 + Missense_Mutation SNP G G A rs143961480 TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr9:127177679G>A ENST00000536392.1 - 1 42 c.26C>T c.(25-27)cCa>cTa p.P9L PSMB7_ENST00000259457.3_Missense_Mutation_p.P9L Q99436 PSB7_HUMAN proteasome (prosome, macropain) subunit, beta type, 7 9 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction cytoplasm|nucleus|proteasome core complex threonine-type endopeptidase activity breast(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1) 5 TCCAACTGGTGGAGCATACAC 0.607000 OREG0019476 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 3 76 0 0 0.115264 0 0 XRN2 22803 broad.mit.edu 37 20 21346221 21346221 + Missense_Mutation SNP G G A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr20:21346221G>A ENST00000377191.3 + 26 2430 c.2335G>A c.(2335-2337)Gca>Aca p.A779T XRN2_ENST00000430571.2_Missense_Mutation_p.A703T|XRN2_ENST00000539513.1_Missense_Mutation_p.A725T NM_012255.3 NP_036387.2 Q9H0D6 XRN2_HUMAN 5'-3' exoribonuclease 2 779 cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent nucleolus 5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5) 39 AAAGCCAGCAGCAGTACTGAA 0.438000 3 103 0 0 0.115264 0 0 TSSC2 0 broad.mit.edu 37 11 3427845 3427845 + RNA SNP C C T TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr11:3427845C>T ENST00000529482.1 + 0 962 CTTCAAGTGGCAGGAGCAGAA 0.587000 4 67 0 0 0.150653 0 0 GON4L 54856 broad.mit.edu 37 1 155796629 155796629 + Splice_Site SNP C C T TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr1:155796629C>T ENST00000437809.1 - 3 818 c.697_splice c.e3+1 p.M232_splice GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000361040.5_Splice_Site_p.M232_splice|GON4L_ENST00000271883.5_Splice_Site_p.M232_splice|GON4L_ENST00000368331.1_Splice_Site_p.M232_splice Q3T8J9 GON4L_HUMAN gon-4-like (C. elegans) 232 regulation of transcription, DNA-dependent cytoplasm|nucleus DNA binding NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1) 45 Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195) AAAGCCTACCCATTGGAATGA 0.383000 5 77 0 0 0.217242 0 0 PTCH1 5727 broad.mit.edu 37 9 98229625 98229625 + Missense_Mutation SNP G G A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr9:98229625G>A ENST00000430669.2 - 15 2720 c.2135C>T c.(2134-2136)aCg>aTg p.T712M PTCH1_ENST00000429896.2_Missense_Mutation_p.T627M|PTCH1_ENST00000421141.1_Missense_Mutation_p.T627M|PTCH1_ENST00000375274.2_Missense_Mutation_p.T777M|PTCH1_ENST00000418258.1_Missense_Mutation_p.T627M|PTCH1_ENST00000437951.1_Missense_Mutation_p.T712M|PTCH1_ENST00000331920.6_Missense_Mutation_p.T778M Q13635 PTC1_HUMAN patched 1 778 embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway integral to plasma membrane hedgehog receptor activity p.T778M(2)|p.T777M(1) NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1) 490 Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136) TACAATGTCCGTAAGGTCCAG 0.473000 4 152 0 0 0.150653 0 0 E2F3 1871 broad.mit.edu 37 6 20402610 20402610 + Silent SNP C C T TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr6:20402610C>T ENST00000346618.3 + 1 213 c.147C>T c.(145-147)gcC>gcT p.A49A NM_001949.4 NP_001940.1 O00716 E2F3_HUMAN E2F transcription factor 3 49 Poly-Ala. G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter transcription factor complex DNA binding|protein binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3) 7 all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148) OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562) ccgccgccgccgctgccgccg 0.741000 3 75 0 0 0.115264 0 0 SNHG14 0 broad.mit.edu 37 15 25230184 25230184 + RNA SNP G G A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr15:25230184G>A ENST00000551631.2 + 0 887 SNHG14_ENST00000551361.1_RNA NR_001293.1 ACTATCTGCAGGAATTTATTT 0.373000 3 61 0 0 0.115264 0 0 NRAS 4893 broad.mit.edu 37 1 115256529 115256529 + Missense_Mutation SNP T T C rs11554290 TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr1:115256529T>C ENST00000369535.4 - 3 435 c.182A>G c.(181-183)cAa>cGa p.Q61R NM_002524.4 NP_002515.1 P01111 RASN_HUMAN neuroblastoma RAS viral (v-ras) oncogene homolog 61 Q -> K (in neuroblastoma cell).|Q -> R (in lung carcinoma cell and melanoma; dbSNP:rs11554290). activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction Golgi membrane|plasma membrane GTP binding|GTPase activity p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1) NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13) 3085 all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211) all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133) GTACTCTTCTTGTCCAGCTGT 0.458000 Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID) 50 Mis """melanoma, MM, AML, thyroid""" Noonan syndrome TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6) 85 172 0 0 0.870114 0 0 DIRAS2 0 broad.mit.edu 37 9 93375575 93375575 + Missense_Mutation SNP C C A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr9:93375575C>A ENST00000375765.3 - 2 923 c.535G>T c.(535-537)Gac>Tac p.D179Y NM_017594.3 NP_060064.2 Q96HU8 DIRA2_HUMAN DIRAS family, GTP-binding RAS-like 2 179 small GTPase mediated signal transduction intracellular|plasma membrane GTP binding|GTPase activity p.D179N(1) kidney(1)|large_intestine(6)|lung(3)|skin(2) 12 TTTTTCCCGTCGATCTGGAGA 0.547000 3 58 0.115264 0.123123 0.115264 1 0 PCDHGB4 0 broad.mit.edu 37 5 140768722 140768722 + Missense_Mutation SNP A A G TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr5:140768722A>G ENST00000519479.1 + 1 1271 c.1271A>G c.(1270-1272)gAt>gGt p.D424G PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron NM_003736.2|NM_018925.2|NM_032098.1 NP_003727.1|NP_061748.1|NP_115269.1 endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2) 37 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) ACGGCAACAGATCGGGGCAAG 0.448000 7 191 0 0 0.278610 0 0 KIAA0895L 653319 broad.mit.edu 37 16 67211930 67211930 + Silent SNP G G A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr16:67211930G>A ENST00000290881.7 - 7 2160 c.1234C>T c.(1234-1236)Ctg>Ttg p.L412L KIAA0895L_ENST00000561621.1_Silent_p.C408C|KIAA0895L_ENST00000563831.2_Intron|KIAA0895L_ENST00000561679.1_Silent_p.L257L|KIAA0895L_ENST00000563902.1_Silent_p.L412L Q68EN5 K895L_HUMAN KIAA0895-like 412 breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|skin(1) 17 AGTGAGGTCAGCAACGGGAAA 0.607000 3 88 0 0 0.115264 0 0 RANGAP1 5905 broad.mit.edu 37 22 41650402 41650402 + Silent SNP C C T TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr22:41650402C>T ENST00000455915.2 - 10 2639 c.1170G>A c.(1168-1170)gaG>gaA p.E390E RANGAP1_ENST00000356244.3_Silent_p.E390E|RANGAP1_ENST00000407260.4_Silent_p.E335E|RANGAP1_ENST00000405486.1_Silent_p.E390E P46060 RAGP1_HUMAN Ran GTPase activating protein 1 390 Asp/Glu-rich (highly acidic). mitotic prometaphase|signal transduction condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole protein binding|Ran GTPase activator activity p.E390E(1) breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1) 19 cctcctcctcctcttcttcct 0.562000 4 45 0 0 0.150653 0 0 PDE1A 0 broad.mit.edu 37 2 183387037 183387037 + Missense_Mutation SNP G G T TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr2:183387037G>T ENST00000435564.1 - 1 267 c.67C>A c.(67-69)Cag>Aag p.Q23K PDE1A_ENST00000536095.1_5'UTR|PDE1A_ENST00000358139.2_Missense_Mutation_p.Q23K|PDE1A_ENST00000331935.6_Missense_Mutation_p.Q23K|PDE1A_ENST00000456212.1_Missense_Mutation_p.Q23K|PDE1A_ENST00000410103.1_Missense_Mutation_p.Q23K NM_001258312.1|NM_005019.4 NP_001245241.1|NP_005010.2 P54750 PDE1A_HUMAN phosphodiesterase 1A, calmodulin-dependent 23 activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation cytosol 3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2) 35 OV - Ovarian serous cystadenocarcinoma(117;0.061) TTTTCAGTCTGTTCTCCTGTA 0.398000 23 123 5.61819e-17 6.77064e-17 0.693898 1 0 CROCCP2 0 broad.mit.edu 37 1 16957414 16957414 + RNA SNP C C T rs2296161 by1000genomes TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr1:16957414C>T ENST00000412962.1 - 0 264 AAGTGCAGGGCGGAGAGAATC 0.706000 3 27 0 0 0.115264 0 0 PRPF3 9129 broad.mit.edu 37 1 150307507 150307507 + Missense_Mutation SNP G G A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr1:150307507G>A ENST00000324862.6 + 7 995 c.830G>A c.(829-831)cGc>cAc p.R277H PRPF3_ENST00000414970.2_Missense_Mutation_p.R228H|PRPF3_ENST00000543398.1_Missense_Mutation_p.R142H|PRPF3_ENST00000467329.1_3'UTR NM_004698.2 NP_004689.1 O43395 PRPF3_HUMAN pre-mRNA processing factor 3 277 nuclear mRNA splicing, via spliceosome Cajal body|cytoplasm|nuclear speck|spliceosomal complex protein binding breast(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 21 Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171) LUSC - Lung squamous cell carcinoma(543;0.171) Colorectal(1306;0.0149) CTGACACACCGCATGCCTACT 0.458000 3 51 0 0 0.115264 0 0 PRPF38B 55119 broad.mit.edu 37 1 109235326 109235326 + Missense_Mutation SNP C C T TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr1:109235326C>T ENST00000370025.4 + 1 382 c.113C>T c.(112-114)gCg>gTg p.A38V PRPF38B_ENST00000370021.1_5'UTR|PRPF38B_ENST00000370022.5_Missense_Mutation_p.A38V|PRPF38B_ENST00000467302.1_3'UTR NM_018061.2 NP_060531.2 Q5VTL8 PR38B_HUMAN pre-mRNA processing factor 38B 38 mRNA processing|RNA splicing spliceosomal complex NS(1)|kidney(3)|large_intestine(5)|lung(8)|prostate(1)|skin(1) 19 all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508) Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161) ACCAAGCCGGCGGTCTCCGGC 0.667000 4 49 0 0 0.150653 0 0 MCTP2 55784 broad.mit.edu 37 15 94858758 94858758 + Splice_Site SNP G G A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr15:94858758G>A ENST00000357742.4 + 3 529 c.528_splice c.e3-1 p.V177_splice MCTP2_ENST00000543482.1_Splice_Site_p.V177_splice|MCTP2_ENST00000451018.3_Splice_Site_p.V177_splice|MCTP2_ENST00000331706.4_5'UTR NM_018349.3 NP_060819.3 Q6DN12 MCTP2_HUMAN multiple C2 domains, transmembrane 2 177 calcium-mediated signaling integral to membrane|membrane fraction calcium ion binding autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2) 49 Lung NSC(78;0.0821)|all_lung(78;0.148) BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593) ATCTGTGCAGGTACCGGGGGA 0.512000 3 39 0 0 0.150653 0 0 KDM6B 23135 broad.mit.edu 37 17 7750709 7750709 + Missense_Mutation SNP G G C TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr17:7750709G>C ENST00000254846.5 + 10 1585 c.1196G>C c.(1195-1197)aGc>aCc p.S399T KDM6B_ENST00000448097.2_Missense_Mutation_p.S399T NM_001080424.1 NP_001073893.1 O15054 KDM6B_HUMAN lysine (K)-specific demethylase 6B 399 Pro-rich. inflammatory response nucleus metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen p.S399T(1) central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5) 37 ACCACCACcagcagcagcagt 0.672000 4 167 0 0 0.150653 0 0 TUBB8P7 0 broad.mit.edu 37 16 90162555 90162555 + RNA SNP C C T TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr16:90162555C>T ENST00000567960.1 + 0 1291 TUBB8P7_ENST00000564451.1_RNA ATGCCACGGCCGAGGAGGAGG 0.522000 4 192 0 0 0.217242 0 0 CELF2 10659 broad.mit.edu 37 10 11299727 11299727 + Missense_Mutation SNP G G A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr10:11299727G>A ENST00000379261.4 + 5 501 c.409G>A c.(409-411)Gga>Aga p.G137R CELF2_ENST00000537122.1_Missense_Mutation_p.G26R|CELF2_ENST00000354440.2_Missense_Mutation_p.G113R|CELF2_ENST00000427450.1_Missense_Mutation_p.G113R|CELF2_ENST00000450189.1_Missense_Mutation_p.G144R|CELF2_ENST00000354897.3_Missense_Mutation_p.G113R|CELF2_ENST00000416382.2_Missense_Mutation_p.G137R|CELF2_ENST00000399850.3_Missense_Mutation_p.G113R|CELF2_ENST00000315874.3_Missense_Mutation_p.G113R|CELF2_ENST00000542579.1_Missense_Mutation_p.G144R|CELF2_ENST00000417956.2_Missense_Mutation_p.G113R NM_001025077.2 NP_001020248.1 O95319 CELF2_HUMAN CUGBP, Elav-like family member 2 137 Necessary for RNA-binding, TNNT2 exon 5 and NMDA R1 exon 21 inclusion.|RRM 2. mRNA processing|regulation of heart contraction cytoplasm|nucleus nucleotide binding|protein binding|RNA binding breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|prostate(1)|skin(1) 16 ATTGTTCATAGGAATGGTATC 0.418000 10 72 0 0 0.387290 0 0 RAPGEF6 51735 broad.mit.edu 37 5 130825338 130825338 + Missense_Mutation SNP C C A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr5:130825338C>A ENST00000509018.1 - 15 1946 c.1741G>T c.(1741-1743)Gta>Tta p.V581L RAPGEF6_ENST00000307984.5_Missense_Mutation_p.V581L|RAPGEF6_ENST00000512052.1_Missense_Mutation_p.V296L|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.V581L|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.V581L|FNIP1_ENST00000514667.1_Missense_Mutation_p.V631L|RAPGEF6_ENST00000510071.1_Missense_Mutation_p.V581L|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.V581L NM_001164386.1|NM_016340.5 NP_001157858.1|NP_057424.3 Q8TEU7 RPGF6_HUMAN Rap guanine nucleotide exchange factor (GEF) 6 581 PDZ. Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction cytoplasm|plasma membrane GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1) 31 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) Lung(113;0.0721) TGTCCATTTACTTCCATAATC 0.259000 3 34 0.115264 0.123123 0.115264 1 0 QPRT 23475 broad.mit.edu 37 16 29708392 29708392 + Missense_Mutation SNP G G A rs147793931 byFrequency TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr16:29708392G>A ENST00000395384.4 + 3 786 c.625G>A c.(625-627)Gtg>Atg p.V209M QPRT_ENST00000219771.7_3'UTR|QPRT_ENST00000562473.1_Missense_Mutation_p.V61M NM_014298.3 NP_055113.2 Q15274 NADC_HUMAN quinolinate phosphoribosyltransferase 209 protein oligomerization|quinolinate catabolic process|water-soluble vitamin metabolic process cytosol nicotinate-nucleotide diphosphorylase (carboxylating) activity|protein homodimerization activity breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5) 9 Niacin(DB00627) GCAGGAGGCCGTGCAGGCAGC 0.657000 3 31 0 0 0.150653 0 0 FRMPD4 9758 broad.mit.edu 37 X 12734288 12734288 + Missense_Mutation SNP A A G TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chrX:12734288A>G ENST00000380682.1 + 15 2216 c.1710A>G c.(1708-1710)atA>atG p.I570M NM_014728.3 NP_055543.2 Q14CM0 FRPD4_HUMAN FERM and PDZ domain containing 4 570 positive regulation of synapse structural plasticity cytoskeleton|dendritic spine phosphatidylinositol-4,5-bisphosphate binding|protein binding breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3) 22 AAGCCCAGATAACATACATAG 0.468000 10 201 0 0 0.361761 0 0 PNCK 139728 broad.mit.edu 37 X 152936612 152936612 + Silent SNP G G A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chrX:152936612G>A ENST00000393831.2 - 8 1151 c.717C>T c.(715-717)agC>agT p.S239S PNCK_ENST00000447676.2_Silent_p.S299S|PNCK_ENST00000370150.1_Silent_p.S216S|PNCK_ENST00000340888.3_Silent_p.S216S|PNCK_ENST00000370142.1_Silent_p.S239S|PNCK_ENST00000370145.4_Silent_p.S233S NM_001039582.3 NP_001034671.3 Q6P2M8 KCC1B_HUMAN pregnancy up-regulated nonubiquitous CaM kinase 216 Protein kinase. cytoplasm|nucleus ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity breast(2)|lung(3)|skin(1) 6 all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) GCTCAGGGTCGCTCTCGTCGT 0.602000 51 124 0 0 0.870114 0 0 DISC1 27185 broad.mit.edu 37 1 231885806 231885806 + Missense_Mutation SNP C C T TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr1:231885806C>T ENST00000439617.2 + 4 1305 c.1252C>T c.(1252-1254)Cgt>Tgt p.R418C DISC1_ENST00000539444.1_Missense_Mutation_p.R418C|DISC1_ENST00000602281.1_Missense_Mutation_p.R418C|TRAX_ENST00000602962.1_3'UTR|DISC1_ENST00000535983.1_Missense_Mutation_p.R418C|DISC1_ENST00000537876.1_Missense_Mutation_p.R418C|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000366633.3_Missense_Mutation_p.R418C|DISC1_ENST00000602873.1_Missense_Mutation_p.R68C|DISC1_ENST00000366636.4_Missense_Mutation_p.R418C NM_001164537.1|NM_001164540.1|NM_018662.2 NP_001158009.1|NP_001158012.1|NP_061132.2 Q9NRI5 DISC1_HUMAN disrupted in schizophrenia 1 418 Interaction with TRAF3IP1. microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway centrosome|microtubule protein binding breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1) 15 all_cancers(173;0.0208)|Prostate(94;0.0975) TGCCTTGCGCCGTGGGGCCAC 0.527000 5 94 0 0 0.217242 0 0 ITPR1 3708 broad.mit.edu 37 3 4824425 4824425 + Splice_Site SNP G G C TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr3:4824425G>C ENST00000354582.6 + 49 6815 c.6465_splice c.e49+1 p.Q2155_splice ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000456211.2_Splice_Site_p.Q2107_splice|ITPR1_ENST00000443694.2_Splice_Site_p.Q2155_splice|ITPR1_ENST00000423119.2_Splice_Site_p.Q2122_splice|ITPR1_ENST00000357086.4_Splice_Site_p.Q2122_splice|ITPR1_ENST00000302640.8_Splice_Site_p.Q2155_splice Q14643 ITPR1_HUMAN inositol 1,4,5-trisphosphate receptor, type 1 2170 activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2) 106 Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982) TAGCCCATCAGGTATGATCTC 0.527000 4 42 0 0 0.184627 0 0 GEMIN5 25929 broad.mit.edu 37 5 154315560 154315560 + Missense_Mutation SNP C C A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr5:154315560C>A ENST00000285873.7 - 3 425 c.350G>T c.(349-351)tGg>tTg p.W117L NM_001252156.1|NM_015465.4 NP_001239085.1|NP_056280.2 Q8TEQ6 GEMI5_HUMAN gem (nuclear organelle) associated protein 5 117 ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly Cajal body|cytosol|spliceosomal complex protein binding|snRNA binding breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1) 38 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.147) KIRC - Kidney renal clear cell carcinoma(527;0.00112) TCGAGGAGACCAATGTAATGT 0.328000 8 41 0.0581538 0.0650768 0.335167 1 0 OR4K5 79317 broad.mit.edu 37 14 20389468 20389468 + Missense_Mutation SNP A A C TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr14:20389468A>C ENST00000315915.4 + 1 728 c.703A>C c.(703-705)Aag>Cag p.K235Q NM_001005483.1 NP_001005483.1 Q8NGD3 OR4K5_HUMAN olfactory receptor, family 4, subfamily K, member 5 235 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1) 47 all_cancers(95;0.00108) Epithelial(56;9.96e-07)|all cancers(55;2.95e-06) GBM - Glioblastoma multiforme(265;0.00327) TGCAATGGCAAAGGCATTTTC 0.418000 21 541 0 0 0.608945 0 0 UBASH3B 84959 broad.mit.edu 37 11 122680513 122680513 + Silent SNP G G A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr11:122680513G>A ENST00000284273.5 + 14 2244 c.1869G>A c.(1867-1869)caG>caA p.Q623Q NM_032873.4 NP_116262.2 Q8TF42 UBS3B_HUMAN ubiquitin associated and SH3 domain containing B 623 Protein tyrosine phosphatase (By similarity). cytoplasm|nucleus protein tyrosine phosphatase activity breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2) 26 Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104) BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463) GAATATGGCAGCTGACAGATC 0.443000 3 110 0 0 0.150653 0 0 SLC12A4 6560 broad.mit.edu 37 16 67979074 67979074 + Missense_Mutation SNP C C A TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr16:67979074C>A ENST00000422611.2 - 22 3127 c.3088G>T c.(3088-3090)Gtc>Ttc p.V1030F SLC12A4_ENST00000572037.1_Missense_Mutation_p.V980F|SLC12A4_ENST00000338335.3_3'UTR|SLC12A4_ENST00000537830.2_Missense_Mutation_p.V1022F|SLC12A4_ENST00000541864.2_Missense_Mutation_p.V997F|SLC12A4_ENST00000576616.1_Missense_Mutation_p.V1028F|SLC12A4_ENST00000316341.3_Missense_Mutation_p.V1028F NM_001145962.1 NP_001139434.1 Q9UP95 S12A4_HUMAN solute carrier family 12 (potassium/chloride transporter), member 4 1028 cell volume homeostasis|potassium ion transport|sodium ion transport integral to plasma membrane|membrane fraction potassium:chloride symporter activity breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3) 29 Ovarian(137;0.192) OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121) Bumetanide(DB00887)|Potassium Chloride(DB00761) GTGACAATGACTTCATTGAGC 0.577000 4 146 0.00116845 0.00137292 0.217242 1 0 AC093642.5 0 broad.mit.edu 37 2 243056967 243056967 + RNA DEL T T - TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr2:243056967delT ENST00000456398.1 + 0 413 CAGTGCTATCTTATGAAATAA 0.299 4 8 --- --- --- --- MSH3 4437 broad.mit.edu 37 5 79950742 79950750 + In_Frame_Del DEL CCCCCAGCT CCCCCAGCT - rs3045983 TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr5:79950742_79950750delCCCCCAGCT ENST00000265081.6 + 1 276_284 c.196_204delCCCCCAGCT c.(196-204)del p.PPA66del DHFR_ENST00000439211.2_5'UTR NM_002439.4 NP_002430.3 P20585 MSH3_HUMAN mutS homolog 3 66 maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 29 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) gCCCCCAGCGCCCCCAGCTCCCGCCTTCC 0.732 Mismatch excision repair (MMR) 2 4 --- --- --- --- HLA-DRB6 0 broad.mit.edu 37 6 32523362 32523363 + RNA INS - - GATA rs142676080 by1000genomes TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr6:32523362_32523363insGATA ENST00000411500.1 - 0 458 NR_001298.1 AAAGCAATGTGGATAAAGGGAC 0.431 4 4 --- --- --- --- GIGYF1 64599 broad.mit.edu 37 7 100284335 100284337 + In_Frame_Del DEL CCT CCT - TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr7:100284335_100284337delCCT ENST00000275732.5 - 7 1838_1840 c.629_631delAGG c.(628-633)ggc>g p.EG210del GIGYF1_ENST00000471340.2_Intron NM_022574.4 NP_072096.2 O75420 PERQ1_HUMAN GRB10 interacting GYF protein 1 210 Poly-Glu. p.E210delE(1) central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 23 Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817) CTCCAGCTGCcctcctcctcctc 0.700 7 75 --- --- --- --- AL162419.1 0 broad.mit.edu 37 9 4378426 4378427 + RNA INS - - T TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr9:4378426_4378427insT ENST00000408803.1 - 0 67_68 GTTTGTTTATATTTTTTTCTTT 0.307 2 4 --- --- --- --- ZMIZ1 57178 broad.mit.edu 37 10 81072446 81072446 + Frame_Shift_Del DEL C C - TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr10:81072446delC ENST00000334512.5 + 25 3716 c.3144delC c.(3142-3144)gafs p.D1048fs ZMIZ1_ENST00000446377.2_Frame_Shift_Del_p.D114fs NM_020338.3 NP_065071.1 Q9ULJ6 ZMIZ1_HUMAN zinc finger, MIZ-type containing 1 1048 transcription, DNA-dependent cytoplasm|nuclear speck zinc ion binding breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1) 30 all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985) Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229) CTTATCTGGACCCCCCCGACC 0.557 7 541 --- --- --- --- DGKZ 8525 broad.mit.edu 37 11 46387931 46387933 + In_Frame_Del DEL CCT CCT - TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr11:46387931_46387933delCCT ENST00000454345.1 + 2 250_252 c.125_127delCCT c.(124-129)gcc>g p.AS42del DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000525434.1_3'UTR|DGKZ_ENST00000343674.6_Intron|DGKZ_ENST00000456247.2_Intron|DGKZ_ENST00000528615.1_Intron|DGKZ_ENST00000318201.8_Intron|DGKZ_ENST00000421244.2_Intron|DGKZ_ENST00000527911.1_Intron|DGKZ_ENST00000395574.3_Intron|DGKZ_ENST00000532868.2_Intron NM_001105540.1 NP_001099010.1 Q13574 DGKZ_HUMAN diacylglycerol kinase, zeta 42 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell migration|intracellular signal transduction|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of mitotic cell cycle|platelet activation cytoplasm|lamellipodium|nucleus|plasma membrane ATP binding|diacylglycerol kinase activity|lipid kinase activity|metal ion binding|protein binding|protein C-terminus binding central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1) 25 GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141) GCTGGGCAGGCCTCCTCCTCACT 0.759 6 3 --- --- --- --- RAB40C 57799 broad.mit.edu 37 16 677579 677580 + Frame_Shift_Ins INS - - C TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr16:677579_677580insC ENST00000535977.1 + 7 1025_1026 c.803_804insC c.(802-804)accfs p.T268fs RAB40C_ENST00000248139.3_Frame_Shift_Ins_p.T268fs|RAB40C_ENST00000539661.1_Frame_Shift_Ins_p.T268fs|RAB40C_ENST00000538492.1_Frame_Shift_Ins_p.T268fs NM_001172663.1 NP_001166134.1 Q96S21 RB40C_HUMAN RAB40C, member RAS oncogene family 268 protein transport|small GTPase mediated signal transduction plasma membrane GTP binding p.Q271fs*7(1) NS(1)|endometrium(2)|large_intestine(1)|lung(1)|prostate(1) 6 Hepatocellular(780;0.0218) CCACCCCAGAGCCCCCCCCAGA 0.678 7 135 --- --- --- --- CTD-2547E10.2 0 broad.mit.edu 37 16 21469994 21469994 + RNA DEL A A - TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr16:21469994delA ENST00000520823.2 - 0 749 ACTGTACATTAAAAAAAAAAA 0.294 3 4 --- --- --- --- AFG3L1P 0 broad.mit.edu 37 16 90053824 90053824 + RNA DEL G G - TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr16:90053824delG ENST00000437774.1 + 0 731 NR_003226.1 aggtggaggaggtggaggagg 0.622 2 4 --- --- --- --- HOXB7 3217 broad.mit.edu 37 17 46685277 46685277 + Frame_Shift_Del DEL T T - TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chr17:46685277delT ENST00000239165.7 - 2 679 c.581delA c.(580-582)agfs p.K194fs HOXB7_ENST00000567101.1_5'UTR NM_004502.3 NP_004493.3 P09629 HXB7_HUMAN homeobox B7 194 K -> N (in Ref. 7; AAB19469). nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1) 8 CTTGTTCTCCTTTTTCCACTT 0.592 8 497 --- --- --- --- HS6ST2 90161 broad.mit.edu 37 X 131762582 131762582 + Frame_Shift_Del DEL A A - TCGA-BJ-A3PT-01A-12D-A21Z-08 TCGA-BJ-A3PT-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx 08d1b350-92cd-4a94-91f6-68734dd228f7 ca1e236e-e01e-44f2-931b-0840aa54a37f g.chrX:131762582delA ENST00000370836.2 - 4 1902 c.1487delT c.(1486-1488)tgfs p.L496fs HS6ST2_ENST00000370837.1_Frame_Shift_Del_p.L350fs|HS6ST2_ENST00000406696.3_Frame_Shift_Del_p.L222fs|HS6ST2_ENST00000521489.1_Frame_Shift_Del_p.L536fs|HS6ST2_ENST00000370833.2_Frame_Shift_Del_p.L390fs NM_147175.3 NP_671704.3 Q96MM7 H6ST2_HUMAN heparan sulfate 6-O-sulfotransferase 2 496 integral to membrane sulfotransferase activity central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2) 9 Acute lymphoblastic leukemia(192;0.000127) ATACCTCTGCAAAAAAAGGTC 0.453 16 433 --- --- --- ---