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 CALCRL 10203 broad.mit.edu 37 2 188225389 188225389 + Silent SNP T T G TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr2:188225389T>G ENST00000409998.1 - 11 1498 c.717A>C c.(715-717)acA>acC p.T239T AC007319.1_ENST00000453517.1_RNA|CALCRL_ENST00000392370.3_Silent_p.T239T|CALCRL_ENST00000410068.1_Silent_p.T239T|AC007319.1_ENST00000412276.1_RNA Q16602 CALRL_HUMAN calcitonin receptor-like 239 integral to plasma membrane endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1) 32 OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227) CCACAATGAGTGTGTGTAGGT 0.403000 36 42 0 0 0.796494 0 0 RYR1 6261 broad.mit.edu 37 19 39070725 39070725 + Missense_Mutation SNP C C T rs148540135 TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr19:39070725C>T ENST00000355481.4 + 99 14584 c.14453C>T c.(14452-14454)aCg>aTg p.T4818M RYR1_ENST00000360985.3_Missense_Mutation_p.T4818M|RYR1_ENST00000359596.3_Missense_Mutation_p.T4823M NM_000540.2|NM_001042723.1 NP_000531.2|NP_001036188.1 P21817 RYR1_HUMAN ryanodine receptor 1 (skeletal) 4823 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) GGGGTCAAGACGCTGCGCACC 0.597000 43 52 0 0 0.859065 0 0 MT-ND5 4540 broad.mit.edu 37 MT 13133 13133 + Missense_Mutation SNP T T C TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chrM:13133T>C ENST00000361567.2 + 1 797 c.797T>C c.(796-798)cTa>cCa p.L266P P03915 NU5M_HUMAN mitochondrially encoded NADH dehydrogenase 5 266 mitochondrial electron transport, NADH to ubiquinone|transport integral to membrane|mitochondrial respiratory chain complex I NADH dehydrogenase (ubiquinone) activity breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7) 74 NADH(DB00157) CTTCCACCCCCTAGCAGAAAA 0.502000 7 186 0 0 0.248553 0 0 RTDR1 27156 broad.mit.edu 37 22 23404005 23404005 + Missense_Mutation SNP C C T TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr22:23404005C>T ENST00000216036.4 - 6 968 c.772G>A c.(772-774)Gcc>Acc p.A258T NM_014433.2 NP_055248.1 Q9UHP6 RTDR1_HUMAN rhabdoid tumor deletion region gene 1 258 binding breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1) 18 all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181) READ - Rectum adenocarcinoma(21;0.175) ATCACTGTGGCGAACATCAGG 0.587000 12 24 0 0 0.435327 0 0 SULF2 55959 broad.mit.edu 37 20 46291893 46291893 + Missense_Mutation SNP T T C rs145371797 TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr20:46291893T>C ENST00000359930.4 - 17 3142 c.2291A>G c.(2290-2292)aAt>aGt p.N764S SULF2_ENST00000467815.1_Missense_Mutation_p.N764S|SULF2_ENST00000361612.4_Missense_Mutation_p.N764S|SULF2_ENST00000484875.1_Missense_Mutation_p.N764S NM_018837.3 NP_061325.1 Q8IWU5 SULF2_HUMAN sulfatase 2 764 bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway cell surface|endoplasmic reticulum|extracellular space|Golgi stack arylsulfatase activity|calcium ion binding breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1) 54 GTGAGTCTCATTGATGGTCCT 0.517000 OREG0026005 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 5 102 0 0 0.184627 0 0 CDKN2A 1029 broad.mit.edu 37 9 21974684 21974684 + Missense_Mutation SNP G G C TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr9:21974684G>C ENST00000304494.5 - 1 413 c.143C>G c.(142-144)cCg>cGg p.P48R CDKN2A_ENST00000498124.1_Missense_Mutation_p.P48R|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000579755.1_Intron|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000579122.1_Missense_Mutation_p.P48R|CDKN2A_ENST00000498628.2_Intron|CDKN2A_ENST00000361570.3_Intron|CDKN2A_ENST00000446177.1_Missense_Mutation_p.P48R|CDKN2A_ENST00000494262.1_Intron NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A 48 P -> L (in CMM2 and a head and neck tumor; somatic mutation). cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence cytosol|nucleus cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein kinase binding p.0?(1315)|p.?(25)|p.P48L(8)|p.P48R(1)|p.0(1)|p.V28_V51del(1) NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2) 4199 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05) CACCTGGATCGGCCTCCGACC 0.677000 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 10 21 0 0 0.387290 0 0 TBC1D4 9882 broad.mit.edu 37 13 75873512 75873512 + Missense_Mutation SNP T T A TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr13:75873512T>A ENST00000377636.3 - 17 3456 c.3110A>T c.(3109-3111)gAc>gTc p.D1037V TBC1D4_ENST00000478591.1_5'UTR|TBC1D4_ENST00000377625.2_Missense_Mutation_p.D974V|TBC1D4_ENST00000425511.1_Missense_Mutation_p.D201V|TBC1D4_ENST00000431480.2_Missense_Mutation_p.D1029V NM_014832.2 NP_055647.2 O60343 TBCD4_HUMAN TBC1 domain family, member 4 1037 Rab-GAP TBC. cytoplasm Rab GTPase activator activity breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 50 Prostate(6;0.014)|Breast(118;0.0982) GBM - Glioblastoma multiforme(99;0.0116) GAAGCCGAGGTCATACATGAG 0.512000 3 43 0 0 0.150653 0 0 NBPF10 100132406 broad.mit.edu 37 1 145367739 145367739 + Silent SNP A A G rs146714035 by1000genomes TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr1:145367739A>G ENST00000342960.5 + 83 10370 c.10335A>G c.(10333-10335)aaA>aaG p.K3445K NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.2_Intron NM_001039703.4 NP_001034792.4 A6NDV3 A6NDV3_HUMAN neuroblastoma breakpoint family, member 10 3445 p.K3445K(4) NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2) 73 all_hematologic(923;0.032) Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258) ggaaggggaaaaaaagaaggg 0.413000 5 125 0 0 0.184627 0 0 GFPT2 9945 broad.mit.edu 37 5 179740844 179740844 + Missense_Mutation SNP A A T TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr5:179740844A>T ENST00000253778.8 - 14 1563 c.1394T>A c.(1393-1395)aTc>aAc p.I465N NM_005110.2 NP_005101.1 O94808 GFPT2_HUMAN glutamine-fructose-6-phosphate transaminase 2 465 SIS 1. dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process cytosol glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2) 34 all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137) Medulloblastoma(196;0.0392)|all_neural(177;0.0529) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) L-Glutamine(DB00130) CCCTGCGTTGATGTGGACGCC 0.701000 6 10 0 0 0.335167 0 0 NKAIN2 154215 broad.mit.edu 37 6 124979504 124979504 + Missense_Mutation SNP C C T TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr6:124979504C>T ENST00000368417.1 + 4 506 c.446C>T c.(445-447)gCt>gTt p.A149V NKAIN2_ENST00000545433.1_Missense_Mutation_p.A134V|NKAIN2_ENST00000368416.1_Missense_Mutation_p.A149V|NKAIN2_ENST00000546092.1_Intron NM_001040214.1 NP_001035304.1 Q5VXU1 NKAI2_HUMAN Na+/K+ transporting ATPase interacting 2 149 integral to membrane|plasma membrane cervix(1)|endometrium(1)|large_intestine(3)|lung(12)|skin(2) 19 GBM - Glioblastoma multiforme(226;0.104) ATAGAAGTGGCTCATAGTTCC 0.542000 38 50 0 0 0.819951 0 0 AC008103.5 0 broad.mit.edu 37 22 18842988 18842988 + RNA SNP G G T TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr22:18842988G>T ENST00000412938.1 + 0 2208 TCCCATCCATGCAAACCTAGG 0.602000 3 9 0.00024832 0.000265155 0.150653 1 0 ZNF761 388561 broad.mit.edu 37 19 53945909 53945909 + RNA SNP T T C rs28727441 by1000genomes TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr19:53945909T>C ENST00000454407.1 + 0 55 TPM3P9_ENST00000424846.3_RNA Q86XN6 ZN761_HUMAN zinc finger protein 761 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 30 GBM - Glioblastoma multiforme(134;0.00786) ACCCTGACTCTGCCTGAGGCC 0.562000 3 47 0 0 0.184627 0 0 SDHAP1 0 broad.mit.edu 37 3 195692347 195692347 + RNA SNP G G A rs62282794 by1000genomes TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr3:195692347G>A ENST00000427841.1 - 0 2155 NR_003264.2 TTCCTCCAGTGCTCCTCAAAG 0.572000 5 26 0 0 0.278610 0 0 EIF3B 8662 broad.mit.edu 37 7 2404028 2404028 + Missense_Mutation SNP C C T TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr7:2404028C>T ENST00000360876.4 + 6 1077 c.1021C>T c.(1021-1023)Cgt>Tgt p.R341C EIF3B_ENST00000397011.2_Missense_Mutation_p.R341C NM_001037283.1 NP_001032360.1 P55884 EIF3B_HUMAN eukaryotic translation initiation factor 3, subunit B 341 Sufficient for interaction with EIF3E. regulation of translational initiation cytosol|eukaryotic translation initiation factor 3 complex nucleotide binding|protein complex scaffold|translation initiation factor activity breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1) 24 Ovarian(82;0.0253) UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14) GACGTATGTGCGTTGGTCTCC 0.458000 88 107 0 0 0.870114 0 0 NUP214 8021 broad.mit.edu 37 9 134073213 134073213 + Silent SNP A A G TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr9:134073213A>G ENST00000359428.5 + 29 4476 c.4332A>G c.(4330-4332)caA>caG p.Q1444Q NUP214_ENST00000465486.2_3'UTR|NUP214_ENST00000451030.1_Silent_p.Q1445Q|NUP214_ENST00000411637.2_Silent_p.Q1434Q|NUP214_ENST00000483497.2_Silent_p.Q270Q P35658 NU214_HUMAN nucleoporin 214kDa 1444 11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich. carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear pore|nucleoplasm protein binding NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 86 all_hematologic(7;0.0028) Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256) TTGGAAGCCAACAGACCAATA 0.522000 T """DEK, SET, ABL1""" """AML, T-ALL""" 20 98 0 0 0.592651 0 0 PCDH11Y 83259 broad.mit.edu 37 Y 5369105 5369105 + Missense_Mutation SNP G G T TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chrY:5369105G>T ENST00000215473.6 + 3 3137 c.3137G>T c.(3136-3138)cGg>cTg p.R1046L Q9BZA8 PC11Y_HUMAN protocadherin 11 Y-linked 1046 homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding autonomic_ganglia(1)|kidney(2)|large_intestine(7)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 27 CAGTCCCAGCGGCGTGTCACA 0.473000 3 59 0.00909568 0.00955046 0.150653 1 0 PKD1L1 168507 broad.mit.edu 37 7 47876598 47876598 + Missense_Mutation SNP G G A TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr7:47876598G>A ENST00000289672.2 - 37 5914 c.5864C>T c.(5863-5865)cCg>cTg p.P1955L NM_138295.3 NP_612152.1 Q8TDX9 PK1L1_HUMAN polycystic kidney disease 1 like 1 1955 cell-cell adhesion integral to membrane BBS9/PKD1L1(2) NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5) 142 GGTGAGGCGCGGCGTGTGCAG 0.582000 3 41 0 0 0.150653 0 0 DDX5 1655 broad.mit.edu 37 17 62498302 62498302 + Missense_Mutation SNP T T G TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr17:62498302T>G ENST00000225792.5 - 10 1535 c.1134A>C c.(1132-1134)caA>caC p.Q378H DDX5_ENST00000578804.1_Missense_Mutation_p.Q378H|DDX5_ENST00000450599.2_Missense_Mutation_p.Q299H NM_004396.3 NP_004387.1 P17844 DDX5_HUMAN DEAD (Asp-Glu-Ala-Asp) box helicase 5 378 Helicase C-terminal. cell growth|regulation of alternative nuclear mRNA splicing, via spliceosome catalytic step 2 spliceosome|nucleolus ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA helicase activity|transcription cofactor activity breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2) 19 Breast(5;2.15e-14) BRCA - Breast invasive adenocarcinoma(8;8.6e-12) AGTCACGCTCTTGTTGACTCT 0.378000 T ETV4 prostate 10 51 0 0 0.435327 0 0 GBP1 2633 broad.mit.edu 37 1 89520410 89520410 + Silent SNP G G C TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr1:89520410G>C ENST00000370473.4 - 10 1839 c.1620C>G c.(1618-1620)gtC>gtG p.V540V GBP1_ENST00000484970.1_5'UTR NM_002053.2 NP_002044.2 P32455 GBP1_HUMAN guanylate binding protein 1, interferon-inducible 540 interferon-gamma-mediated signaling pathway plasma membrane GTP binding|GTPase activity endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1) 30 Lung NSC(277;0.123) all cancers(265;0.0156)|Epithelial(280;0.0291) TCAGCAACTGGACCCTGTCGT 0.433000 86 281 0 0 0.870114 0 0 IDH1 3417 broad.mit.edu 37 2 209113112 209113112 + Missense_Mutation SNP C C T rs121913500 TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr2:209113112C>T ENST00000415913.1 - 4 776 c.395G>A c.(394-396)cGt>cAt p.R132H IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H O75874 IDHC_HUMAN isocitrate dehydrogenase 1 (NADP+), soluble 132 R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). 2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle cytosol|peroxisomal matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1) NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1) 4887 Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136) ATAAGCATGACGACCTATGAT 0.393000 Mis gliobastoma 41 48 0 0 0.840704 0 0 SIRPA 140885 broad.mit.edu 37 20 1902301 1902301 + Missense_Mutation SNP G G A TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr20:1902301G>A ENST00000358771.4 + 3 849 c.697G>A c.(697-699)Gtc>Atc p.V233I SIRPA_ENST00000356025.3_Missense_Mutation_p.V233I|SIRPA_ENST00000400068.3_Missense_Mutation_p.V233I NM_001040023.1 NP_001035112.1 P78324 SHPS1_HUMAN signal-regulatory protein alpha 233 Ig-like C1-type 1. blood coagulation|cell adhesion|cell junction assembly|leukocyte migration integral to membrane|plasma membrane SH3 domain binding p.V233I(1) cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1) 21 Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556) GGTGGCCCACGTCACCTTGCA 0.617000 5 120 0 0 0.184627 0 0 AQPEP 0 broad.mit.edu 37 5 115351039 115351039 + Silent SNP T T C TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr5:115351039T>C ENST00000357872.4 + 17 2665 c.2541T>C c.(2539-2541)acT>acC p.T847T AQPEP_ENST00000515454.1_3'UTR NM_173800.4 NP_776161.3 Q6Q4G3 AMPQ_HUMAN 847 proteolysis integral to membrane metallopeptidase activity|zinc ion binding ATACTTACACTAATACAACAA 0.348000 6 86 0 0 0.217242 0 0 PLCG2 5336 broad.mit.edu 37 16 81969947 81969947 + Missense_Mutation SNP G G A TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr16:81969947G>A ENST00000359376.3 + 27 3230 c.3016G>A c.(3016-3018)Ggt>Agt p.G1006S NM_002661.3 NP_002652.2 P16885 PLCG2_HUMAN phospholipase C, gamma 2 (phosphatidylinositol-specific) 1006 PI-PLC Y-box. intracellular signal transduction|phospholipid catabolic process|platelet activation plasma membrane phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1) 58 CTGGCTGTGCGGTTCTCAGAT 0.572000 51 55 0 0 0.870114 0 0 RSBN1 54665 broad.mit.edu 37 1 114310931 114310931 + Missense_Mutation SNP C C G TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr1:114310931C>G ENST00000261441.5 - 5 1802 c.1739G>C c.(1738-1740)aGa>aCa p.R580T NM_018364.3 NP_060834.2 Q5VWQ0 RSBN1_HUMAN round spermatid basic protein 1 580 nucleus breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2) 29 Lung SC(450;0.184) all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133) AGCATGAGCTCTAGTCCTATC 0.433000 45 67 0 0 0.859065 0 0 TP53 7157 broad.mit.edu 37 17 7578190 7578190 + Missense_Mutation SNP T T C rs121912666 TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr17:7578190T>C ENST00000420246.2 - 6 791 c.659A>G c.(658-660)tAt>tGt p.Y220C TP53_ENST00000269305.4_Missense_Mutation_p.Y220C|TP53_ENST00000359597.4_Missense_Mutation_p.Y220C|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.Y220C|TP53_ENST00000445888.2_Missense_Mutation_p.Y220C|TP53_ENST00000455263.2_Missense_Mutation_p.Y220C NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 220 Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Required for interaction with FBXO42. Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.Y220C(278)|p.Y127C(24)|p.Y220S(12)|p.?(11)|p.0?(8)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y127S(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(1) NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) AGGCGGCTCATAGGGCACCAC 0.557000 111 """Mis, N, F""" """breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types""" """breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types""" Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) 45 8 0 0 0.870114 0 0 ALS2 57679 broad.mit.edu 37 2 202609063 202609063 + Silent SNP G G A TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr2:202609063G>A ENST00000264276.6 - 10 2460 c.2088C>T c.(2086-2088)caC>caT p.H696H ALS2_ENST00000457679.2_Silent_p.H8H NM_020919.3 NP_065970.2 Q96Q42 ALS2_HUMAN amyotrophic lateral sclerosis 2 (juvenile) 696 DH. cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1) 72 TAGCTAACTCGTGGAGACTGG 0.398000 31 35 0 0 0.740014 0 0 CP 1356 broad.mit.edu 37 3 148930358 148930358 + Missense_Mutation SNP A A G TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr3:148930358A>G ENST00000264613.6 - 2 536 c.274T>C c.(274-276)Ttt>Ctt p.F92L NM_000096.3 NP_000087.1 P00450 CERU_HUMAN ceruloplasmin (ferroxidase) 92 F5/8 type A 1.|Plastocyanin-like 1. cellular iron ion homeostasis|copper ion transport|transmembrane transport extracellular space chaperone binding|ferroxidase activity breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 44 Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152) LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607) Drotrecogin alfa(DB00055) GGGCCTAAAAACCCAAGCCAG 0.398000 6 88 0 0 0.217242 0 0 MCM2 4171 broad.mit.edu 37 3 127337890 127337890 + Silent SNP C C T TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr3:127337890C>T ENST00000265056.7 + 13 2278 c.2034C>T c.(2032-2034)ttC>ttT p.F678F MCM2_ENST00000468414.1_3'UTR NM_004526.2 NP_004517.2 P49736 MCM2_HUMAN minichromosome maintenance complex component 2 678 MCM. cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle chromatin|MCM complex ATP binding|helicase activity|metal ion binding ovary(3)|skin(2)|stomach(1) 6 TGGCCCGCTTCGTGGTGGGCA 0.632000 5 24 0 0 0.217242 0 0 XPA 7507 broad.mit.edu 37 9 100459509 100459509 + Silent SNP G G A TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr9:100459509G>A ENST00000375128.4 - 1 130 c.66C>T c.(64-66)gcC>gcT p.A22A NM_000380.3 NP_000371.1 P23025 XPA_HUMAN xeroderma pigmentosum, complementation group A 22 Interaction with CEP164 and required for UV resistance. nucleotide-excision repair, DNA damage removal nucleoplasm damaged DNA binding|metal ion binding|nucleotide binding|protein domain specific binding|protein homodimerization activity breast(1)|endometrium(4)|large_intestine(1)|lung(4)|prostate(1) 11 Acute lymphoblastic leukemia(62;0.158) CCCGCACCGAGGCAGGCAGCT 0.736000 """Mis, N, F, S""" """skin basal cell, skin squamous cell, melanoma""" Nucleotide excision repair (NER) Xeroderma Pigmentosum 4 12 0 0 0.184627 0 0 RP11-909M7.3 0 broad.mit.edu 37 14 101438447 101438447 + RNA SNP A A G TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr14:101438447A>G ENST00000554693.2 + 0 299 SNORD114-14_ENST00000362723.1_RNA TCCTGGACCAATGATGACAAC 0.373000 15 26 0 0 0.500413 0 0 WNK2 65268 broad.mit.edu 37 9 96080327 96080327 + Missense_Mutation SNP G G A TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr9:96080327G>A ENST00000427277.2 + 29 6646 c.5482G>A c.(5482-5484)Gcc>Acc p.A1828T WNK2_ENST00000395475.2_Intron|WNK2_ENST00000297954.4_3'UTR|WNK2_ENST00000395477.2_Intron|WNK2_ENST00000471076.1_Intron|WNK2_ENST00000356055.3_Intron|WNK2_ENST00000349097.3_Intron Q9Y3S1 WNK2_HUMAN WNK lysine deficient protein kinase 2 118 intracellular protein kinase cascade ATP binding|protein binding|protein serine/threonine kinase activity breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2) 54 TGGTCCACGCGCCGTCTCCAC 0.582000 7 104 0 0 0.387290 0 0 ROS1 6098 broad.mit.edu 37 6 117609712 117609712 + Silent SNP A A G TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr6:117609712A>G ENST00000368508.3 - 43 7185 c.6987T>C c.(6985-6987)ccT>ccC p.P2329P ROS1_ENST00000368507.3_Silent_p.P2323P NM_002944.2 NP_002935.2 P08922 ROS_HUMAN c-ros oncogene 1 , receptor tyrosine kinase 2329 transmembrane receptor protein tyrosine kinase signaling pathway membrane fraction|sodium:potassium-exchanging ATPase complex ATP binding|transmembrane receptor protein tyrosine kinase activity TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7) NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3) 162 all_cancers(87;0.00846)|all_epithelial(87;0.0242) GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137) TCAGGCCTTCAGGCTTGCCAG 0.438000 T """GOPC, SDC4, SLC34A2, EZR, LRIG3""" """glioblastoma, NSCLC""" 43 69 0 0 0.853193 0 0 TP53 7157 broad.mit.edu 37 17 7577548 7577548 + Missense_Mutation SNP C C T rs28934575 TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr17:7577548C>T ENST00000420246.2 - 7 865 c.733G>A c.(733-735)Ggc>Agc p.G245S TP53_ENST00000269305.4_Missense_Mutation_p.G245S|TP53_ENST00000359597.4_Missense_Mutation_p.G245S|TP53_ENST00000413465.2_Missense_Mutation_p.G245S|TP53_ENST00000445888.2_Missense_Mutation_p.G245S|TP53_ENST00000455263.2_Missense_Mutation_p.G245S NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 245 Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain. G -> A (in sporadic cancers; somatic mutation).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|G -> D (in LFS; germline mutation and in sporadic cancers; somatic mutation).|G -> E (in a sporadic cancer; somatic mutation).|G -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> L (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934575).|G -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.G245S(304)|p.G245C(59)|p.G245R(10)|p.G152S(8)|p.0?(8)|p.?(5)|p.G152C(4)|p.G244_M246>V(3)|p.G245N(2)|p.G245fs*2(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.G245fs*22(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.M243fs*18(1)|p.G151_M153>V(1)|p.G245del(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*16(1) NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) CGGTTCATGCCGCCCATGCAG 0.577000 G245S(LS1034_LARGE_INTESTINE)|G245S(NUGC2_STOMACH)|G245S(PANC0403_PANCREAS)|G245S(SKLMS1_SOFT_TISSUE)|G245S(SKMEL2_SKIN) 111 """Mis, N, F""" """breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types""" """breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types""" Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) 4 90 0 0 0.150653 0 0 ROCK2 9475 broad.mit.edu 37 2 11355517 11355517 + Missense_Mutation SNP A A T TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr2:11355517A>T ENST00000315872.6 - 15 2067 c.1619T>A c.(1618-1620)cTt>cAt p.L540H ROCK2_ENST00000401753.1_Missense_Mutation_p.L297H NM_004850.3 NP_004841.2 O75116 ROCK2_HUMAN Rho-associated, coiled-coil containing protein kinase 2 540 Interaction with PPP1R12A. axon guidance|cytokinesis|intracellular signal transduction cytosol|plasma membrane ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2) 43 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162) CAAATCTTCAAGTTGATCTTT 0.308000 33 40 0 0 0.740014 0 0 LINC00854 0 broad.mit.edu 37 17 41381938 41381938 + RNA SNP C C G rs4986161 TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr17:41381938C>G ENST00000433702.2 - 0 14 NR_047479.1 aagagctgatcttatgcaggg 0.552000 4 17 0 0 0.184627 0 0 ATRX 546 broad.mit.edu 37 X 76829760 76829760 + Nonsense_Mutation SNP G G C TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chrX:76829760G>C ENST00000373344.5 - 28 6495 c.6281C>G c.(6280-6282)tCa>tGa p.S2094* ATRX_ENST00000395603.3_Nonsense_Mutation_p.S2056*|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 2094 Helicase C-terminal. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding p.?(1) bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 145 Phosphatidylserine(DB00144) CTTCTTCCTTGACTGTGCAGT 0.313000 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 69 12 0 0 0.870114 0 0 MT-ND5 4540 broad.mit.edu 37 MT 13143 13143 + Silent SNP T T C TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chrM:13143T>C ENST00000361567.2 + 1 807 c.807T>C c.(805-807)aaT>aaC p.N269N P03915 NU5M_HUMAN mitochondrially encoded NADH dehydrogenase 5 269 mitochondrial electron transport, NADH to ubiquinone|transport integral to membrane|mitochondrial respiratory chain complex I NADH dehydrogenase (ubiquinone) activity breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7) 74 NADH(DB00157) CTAGCAGAAAATAGCCCACTA 0.483000 113 85 0 0 0.870114 0 0 KCNH8 131096 broad.mit.edu 37 3 19575087 19575087 + Silent SNP C C T rs151258565 by1000genomes TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr3:19575087C>T ENST00000328405.2 + 16 3086 c.2820C>T c.(2818-2820)ggC>ggT p.G940G NM_144633.2 NP_653234.2 Q96L42 KCNH8_HUMAN potassium voltage-gated channel, subfamily H (eag-related), member 8 940 integral to membrane two-component sensor activity NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2) 77 TGCAAACAGGCGGGGCTGCTT 0.542000 50 76 0 0 0.870114 0 0 RYR1 6261 broad.mit.edu 37 19 39071043 39071043 + Missense_Mutation SNP G G T rs118192168 TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr19:39071043G>T ENST00000355481.4 + 100 14661 c.14530G>T c.(14530-14532)Gtc>Ttc p.V4844F RYR1_ENST00000360985.3_Missense_Mutation_p.V4844F|RYR1_ENST00000359596.3_Missense_Mutation_p.V4849F NM_000540.2|NM_001042723.1 NP_000531.2|NP_001036188.1 P21817 RYR1_HUMAN ryanodine receptor 1 (skeletal) 4849 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) GGCGGTGGTCGTCTACCTGTA 0.602000 22 25 6.44725e-10 7.00305e-10 0.624587 1 0 CDC45 8318 broad.mit.edu 37 22 19470284 19470284 + Silent SNP C C T TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr22:19470284C>T ENST00000407835.1 + 5 532 c.276C>T c.(274-276)gaC>gaT p.D92D CDC45_ENST00000404724.3_Intron|CDC45_ENST00000483431.1_3'UTR|CDC45_ENST00000437685.2_Silent_p.D92D|CDC45_ENST00000263201.1_Silent_p.D92D O75419 CDC45_HUMAN cell division cycle 45 92 DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle centrosome|nucleoplasm protein binding breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1) 19 CTGATGAAGACACTATATTCT 0.363000 6 288 0 0 0.248553 0 0 USP25 29761 broad.mit.edu 37 21 17238647 17238647 + Missense_Mutation SNP A A G TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr21:17238647A>G ENST00000285681.2 + 21 3044 c.2675A>G c.(2674-2676)aAc>aGc p.N892S USP25_ENST00000285679.6_Missense_Mutation_p.N860S|USP25_ENST00000400183.2_Missense_Mutation_p.N930S|USP25_ENST00000351097.5_Intron Q9UHP3 UBP25_HUMAN ubiquitin specific peptidase 25 860 protein modification process|ubiquitin-dependent protein catabolic process cytoplasm|nucleus ubiquitin thiolesterase activity|ubiquitin-specific protease activity breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2) 52 Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889) GAAGAAGTAAACTTGGAGGAA 0.358000 16 51 0 0 0.539581 0 0 FBXO7 25793 broad.mit.edu 37 22 32879927 32879927 + Missense_Mutation SNP A A G TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr22:32879927A>G ENST00000266087.7 + 3 788 c.461A>G c.(460-462)aAt>aGt p.N154S FBXO7_ENST00000382058.3_Missense_Mutation_p.N75S|FBXO7_ENST00000397426.1_Missense_Mutation_p.N40S NM_012179.3 NP_036311.3 Q9Y3I1 FBX7_HUMAN F-box protein 7 154 cell death|regulation of protein stability|ubiquitin-dependent protein catabolic process ubiquitin ligase complex protein binding|ubiquitin-protein ligase activity breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 19 ATTCAAGATAATGCGCATATG 0.383000 26 47 0 0 0.681144 0 0 HOXC13 3229 broad.mit.edu 37 12 54338833 54338833 + Silent SNP G G A TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr12:54338833G>A ENST00000243056.3 + 2 942 c.786G>A c.(784-786)aaG>aaA p.K262K NM_017410.2 NP_059106.2 P31276 HXC13_HUMAN homeobox C13 262 nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity breast(1)|large_intestine(1)|skin(1) 3 GCGGGCGCAAGAAACGCGTGC 0.612000 T NUP98 AML 86 144 0 0 0.870114 0 0 C2CD3 26005 broad.mit.edu 37 11 73829328 73829328 + Missense_Mutation SNP C C G TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr11:73829328C>G ENST00000334126.7 - 9 1691 c.1465G>C c.(1465-1467)Gtt>Ctt p.V489L C2CD3_ENST00000313663.7_Missense_Mutation_p.V489L Q4AC94 C2CD3_HUMAN C2 calcium-dependent domain containing 3 489 centrosome NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3) 64 Breast(11;4.16e-06) GACTCCAGAACCTTAGATGAT 0.413000 50 75 0 0 0.870114 0 0 ST14 6768 broad.mit.edu 37 11 130069892 130069892 + Silent SNP C C T TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr11:130069892C>T ENST00000278742.5 + 16 2272 c.1854C>T c.(1852-1854)ggC>ggT p.G618G NM_021978.3 NP_068813.1 Q9Y5Y6 ST14_HUMAN suppression of tumorigenicity 14 (colon carcinoma) 618 Peptidase S1. proteolysis integral to plasma membrane serine-type endopeptidase activity central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3) 32 all_hematologic(175;0.0429) Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837) OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228) Urokinase(DB00013) TTGTTGGGGGCACGGATGCGG 0.617000 6 119 0 0 0.248553 0 0 GLYAT 10249 broad.mit.edu 37 11 58477535 58477535 + Missense_Mutation SNP G G A rs138125182 TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr11:58477535G>A ENST00000344743.3 - 6 736 c.595C>T c.(595-597)Cgc>Tgc p.R199C GLYAT_ENST00000529732.1_Missense_Mutation_p.R199C NM_201648.2 NP_964011.2 Q6IB77 GLYAT_HUMAN glycine-N-acyltransferase 199 acyl-CoA metabolic process|response to toxin|xenobiotic metabolic process mitochondrial matrix glycine N-acyltransferase activity|glycine N-benzoyltransferase activity NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1) 16 Breast(21;0.0044)|all_epithelial(135;0.0157) Glycine(DB00145) TGAATGCAGCGCTCAATGAAT 0.502000 62 78 0 0 0.870114 0 0 CDRT1 374286 broad.mit.edu 37 17 15496762 15496762 + Missense_Mutation SNP C C T TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr17:15496762C>T ENST00000395906.3 - 11 1894 c.1895G>A c.(1894-1896)tGt>tAt p.C632Y CDRT1_ENST00000583965.1_Intron|RP11-385D13.1_ENST00000455584.2_Intron|CDRT1_ENST00000354433.3_Missense_Mutation_p.C132Y NM_006382.3 NP_006373.2 O95170 CDRT1_HUMAN CMT1A duplicated region transcript 1 632 endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1) 10 UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541) GCCATCTGCACAGGCGCTGAT 0.498000 15 308 0 0 0.500413 0 0 LIMS2 55679 broad.mit.edu 37 2 128399630 128399630 + Silent SNP G G A TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr2:128399630G>A ENST00000409455.1 - 6 1274 c.639C>T c.(637-639)caC>caT p.H213H LIMS2_ENST00000409754.1_Silent_p.H66H|LIMS2_ENST00000409286.1_Silent_p.H66H|LIMS2_ENST00000410011.1_Silent_p.H213H|LIMS2_ENST00000409808.2_Silent_p.H213H|LIMS2_ENST00000410038.1_Silent_p.H66H|LIMS2_ENST00000355119.4_Silent_p.H218H|LIMS2_ENST00000545738.2_Silent_p.H240H|LIMS2_ENST00000409254.1_Silent_p.H66H|LIMS2_ENST00000324938.5_Silent_p.H242H Q7Z4I7 LIMS2_HUMAN LIM and senescent cell antigen-like domains 2 218 LIM zinc-binding 4. cell junction assembly cytosol|focal adhesion|nucleus zinc ion binding p.H242H(1) endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 15 Colorectal(110;0.1) BRCA - Breast invasive adenocarcinoma(221;0.0681) TCACCTCCACGTGCCACTGCT 0.677000 15 26 0 0 0.539581 0 0 MT-CO1 4512 broad.mit.edu 37 MT 6762 6762 + Missense_Mutation SNP G G A TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chrM:6762G>A ENST00000361624.2 + 1 859 c.859G>A c.(859-861)Gtg>Atg p.287_287insM mitochondrially encoded cytochrome c oxidase I breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3) 54 TAGGGTTTATCGTGTGAGCAC 0.418000 19 37 0 0 0.750413 0 0 DOC2A 8448 broad.mit.edu 37 16 30018527 30018529 + In_Frame_Del DEL CTT CTT - rs139431507 byFrequency TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr16:30018527_30018529delCTT ENST00000350119.4 - 6 809_811 c.619_621delAAG c.(619-621)del p.K207del DOC2A_ENST00000564979.1_In_Frame_Del_p.K207del|DOC2A_ENST00000564944.1_In_Frame_Del_p.K207del NM_003586.2 NP_003577.2 Q14183 DOC2A_HUMAN double C2-like domains, alpha 207 nervous system development|regulation of calcium ion-dependent exocytosis cell junction|lysosome|synaptic vesicle membrane|synaptosome calcium-dependent phospholipid binding|protein binding|transporter activity central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2) 9 TGTTAAAATGCTTCTTCTGCGAA 0.635 45 75 --- --- --- --- RP11-697E22.2 0 broad.mit.edu 37 17 36003613 36003614 + RNA INS - - T rs10543338 TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr17:36003613_36003614insT ENST00000586163.1 + 0 590 RP11-697E22.2_ENST00000586950.1_RNA CATTAtttatcttttttttttt 0.510 4 8 --- --- --- --- CDC27 996 broad.mit.edu 37 17 45219612 45219612 + Frame_Shift_Del DEL A A - TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr17:45219612delA ENST00000066544.3 - 11 1454 c.1361delT c.(1360-1362)cafs p.L454fs CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs|CDC27_ENST00000527547.1_Frame_Shift_Del_p.L454fs|CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs NM_001114091.1|NM_001256.3 NP_001107563.1|NP_001247.3 P30260 CDC27_HUMAN cell division cycle 27 454 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule protein phosphatase binding NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2) 90 TGCTTTTTGTAGATTAAAGGC 0.308 8 52 --- --- --- --- RP4-684O24.5 0 broad.mit.edu 37 20 1933766 1933773 + RNA DEL AAGGAAGG AAGGAAGG - rs147387918 by1000genomes TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr20:1933766_1933773delAAGGAAGG ENST00000446562.1 + 0 476 ggaggaaggaaaggaaggaaggaaggaa 0.519 3 5 --- --- --- --- RP5-1043L13.1 0 broad.mit.edu 37 20 58889651 58889662 + RNA DEL CATTCTCCCATT CATTCTCCCATT - rs117834183 by1000genomes TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chr20:58889651_58889662delCATTCTCCCATT ENST00000432910.1 + 0 332 NR_046099.1 tccatccatccattctcccattcatccatcct 0.538 11 14 --- --- --- --- ATRX 546 broad.mit.edu 37 X 76938044 76938044 + Frame_Shift_Del DEL T T - TCGA-CS-4943-01A-01D-1468-08 TCGA-CS-4943-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 14627ffd-642c-42b5-9d95-ad436c9b1d35 0d4a92bf-0624-4dfa-9d95-8f91a693ea3f g.chrX:76938044delT ENST00000373344.5 - 9 2918 c.2704delA c.(2704-2706)tgfs p.M902fs ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.M864fs NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 902 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding p.?(1) bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 145 Phosphatidylserine(DB00144) CTTAATTCCATGATGGTCGTG 0.428 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 7 207 --- --- --- ---