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 ANKRD36BP2 0 broad.mit.edu 37 2 89086005 89086005 + RNA SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr2:89086005C>T ENST00000393525.3 + 0 830 CAGAAACAATCGGCCTGGAAG 0.303000 3 6 0 0 1 0 0 FRG1B 0 broad.mit.edu 37 20 29628243 29628243 + Missense_Mutation SNP T T C TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr20:29628243T>C ENST00000278882.3 + 6 625 c.245T>C c.(244-246)tTg>tCg p.L82S FRG1B_ENST00000439954.2_Missense_Mutation_p.L87S|FRG1B_ENST00000358464.4_Missense_Mutation_p.L82S p.L82S(2) endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9) 53 ATGGCTTTGTTGGCCTCAAAT 0.363000 4 190 0 0 1 0 0 KIF1A 547 broad.mit.edu 37 2 241725859 241725859 + Silent SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr2:241725859G>A ENST00000498729.2 - 6 747 c.501C>T c.(499-501)cgC>cgT p.R167R KIF1A_ENST00000320389.7_Silent_p.R167R NM_001244008.1 NP_001230937.1 Q12756 KIF1A_HUMAN kinesin family member 1A 167 Kinesin-motor. anterograde axon cargo transport cytoplasm|microtubule|nucleus ATP binding|microtubule motor activity NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1) 66 all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244) Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176) GCTCCCTCACGCGAAGGTTGC 0.602000 62 94 0 0 1 0 0 FRG1B 0 broad.mit.edu 37 20 29628245 29628245 + Missense_Mutation SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr20:29628245G>A ENST00000278882.3 + 6 627 c.247G>A c.(247-249)Gcc>Acc p.A83T FRG1B_ENST00000439954.2_Missense_Mutation_p.A88T|FRG1B_ENST00000358464.4_Missense_Mutation_p.A83T p.A83T(2) endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9) 53 GGCTTTGTTGGCCTCAAATAG 0.353000 4 188 0 0 1 0 0 RGPD3 653489 broad.mit.edu 37 2 107049631 107049631 + Silent SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr2:107049631C>T ENST00000409886.3 - 16 2403 c.2316G>A c.(2314-2316)gcG>gcA p.A772A RGPD3_ENST00000304514.7_Silent_p.A772A NM_001144013.1 NP_001137485.1 A6NKT7 RGPD3_HUMAN RANBP2-like and GRIP domain containing 3 772 intracellular transport binding p.A772A(4) breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2) 71 TTTCTGAATCCGCATTTCGCA 0.373000 5 311 0 0 1 0 0 OR9K2 441639 broad.mit.edu 37 12 55524135 55524135 + Missense_Mutation SNP G G A rs77545847 byFrequency TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr12:55524135G>A ENST00000305377.5 + 1 671 c.583G>A c.(583-585)Gct>Act p.A195T NM_001005243.1 NP_001005243.1 Q8NGE7 OR9K2_HUMAN olfactory receptor, family 9, subfamily K, member 2 195 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2) 31 ATCTTTTTGCGCTTCTCGGGC 0.418000 24 70 0 0 1 0 0 CCDC144A 9720 broad.mit.edu 37 17 16593777 16593777 + Silent SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr17:16593777C>T ENST00000443444.2 + 1 203 c.63C>T c.(61-63)taC>taT p.Y21Y CCDC144A_ENST00000436374.1_3'UTR|CCDC144A_ENST00000340621.5_Silent_p.Y21Y|RP11-219A15.1_ENST00000448331.3_Silent_p.Y21Y|CCDC144A_ENST00000360524.8_Silent_p.Y21Y|CCDC144A_ENST00000456009.1_Silent_p.Y21Y|CCDC144A_ENST00000399273.1_Silent_p.Y21Y A2RUR9 C144A_HUMAN coiled-coil domain containing 144A 21 CGGCAGTCTACGCCACGAGGA 0.667000 18 27 0 0 1 0 0 TRBC2 0 broad.mit.edu 37 7 142499092 142499092 + RNA SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr7:142499092C>T ENST00000466254.1 + 0 368 TCGTCAGCGCCGAGGCCTGGG 0.597000 28 184 0 0 1 0 0 ZSCAN30 100101467 broad.mit.edu 37 18 32843993 32843993 + Silent SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr18:32843993C>T ENST00000420878.3 - 3 779 c.324G>A c.(322-324)ctG>ctA p.L108L ZSCAN30_ENST00000333206.5_Silent_p.L108L|ZNF397_ENST00000589420.1_Intron|ZSCAN30_ENST00000601405.1_Intron|ZSCAN30_ENST00000592278.1_Silent_p.L108L|ZSCAN30_ENST00000383091.2_Silent_p.L108L|ZSCAN30_ENST00000589178.1_Silent_p.L108L NM_001166012.1 NP_001159484.1 Q86W11 ZSC30_HUMAN zinc finger and SCAN domain containing 30 108 SCAN box. viral reproduction nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding large_intestine(5)|lung(3)|urinary_tract(1) 9 GATGCTCTCGCAGCCAAGCTT 0.547000 5 96 0 0 1 0 0 AQP2 359 broad.mit.edu 37 12 50344881 50344881 + Missense_Mutation SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr12:50344881G>A ENST00000199280.3 + 1 353 c.268G>A c.(268-270)Gtg>Atg p.V90M NM_000486.5 NP_000477.1 P41181 AQP2_HUMAN aquaporin 2 (collecting duct) 90 cellular response to copper ion|cellular response to mercury ion|excretion apical plasma membrane|integral to membrane|transport vesicle membrane glycerol transmembrane transporter activity|water channel activity breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(4)|ovary(2) 10 CGCCTTCTACGTGGCTGCCCA 0.662000 13 37 0 0 1 0 0 PTPRA 0 broad.mit.edu 37 20 3017847 3017847 + Missense_Mutation SNP T T A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr20:3017847T>A ENST00000216877.6 + 22 2619 c.2219T>A c.(2218-2220)cTg>cAg p.L740Q PTPRA_ENST00000356147.3_Missense_Mutation_p.L740Q|PTPRA_ENST00000425918.2_Missense_Mutation_p.L760Q|PTPRA_ENST00000380393.3_Missense_Mutation_p.L749Q|PTPRA_ENST00000358719.4_Missense_Mutation_p.L605Q|PTPRA_ENST00000318266.5_Missense_Mutation_p.L740Q|PTPRA_ENST00000399903.2_Missense_Mutation_p.L749Q NM_080840.2 NP_543030.1 P18433 PTPRA_HUMAN protein tyrosine phosphatase, receptor type, A 749 Tyrosine-protein phosphatase 2. axon guidance|protein phosphorylation integral to plasma membrane transmembrane receptor protein tyrosine phosphatase activity NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 17 AGCACCGTCCTGGAGCGTGTG 0.592000 38 76 0 0 1 0 0 FAAH2 158584 broad.mit.edu 37 X 57458438 57458438 + Missense_Mutation SNP G G A rs138462668 byFrequency TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chrX:57458438G>A ENST00000374900.4 + 8 1204 c.1084G>A c.(1084-1086)Gca>Aca p.A362T FAAH2_ENST00000491179.1_3'UTR NM_174912.3 NP_777572.2 Q6GMR7 FAAH2_HUMAN fatty acid amide hydrolase 2 362 integral to membrane carbon-nitrogen ligase activity, with glutamine as amido-N-donor|hydrolase activity endometrium(2)|large_intestine(4)|lung(10)|ovary(3)|upper_aerodigestive_tract(3) 22 GTTGTGGATCGCAATGATGTC 0.348000 HNSCC(52;0.14) 31 4 0 0 1 0 0 TMC7 79905 broad.mit.edu 37 16 19041626 19041626 + Silent SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr16:19041626G>A ENST00000421369.3 + 6 1020 c.462G>A c.(460-462)ctG>ctA p.L154L TMC7_ENST00000304381.5_Silent_p.L264L|TMC7_ENST00000569532.1_Silent_p.L264L NM_001160364.1 NP_001153836.1 Q7Z402 TMC7_HUMAN transmembrane channel-like 7 264 integral to membrane breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1) 28 CCTATGATCTGCCCCTGGCGT 0.468000 36 63 0 0 1 0 0 CHRNA10 57053 broad.mit.edu 37 11 3691150 3691150 + Missense_Mutation SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr11:3691150C>T ENST00000250699.2 - 2 154 c.83G>A c.(82-84)cGg>cAg p.R28Q CHRNA10_ENST00000534359.1_Intron NM_020402.2 NP_065135.2 Q9GZZ6 ACH10_HUMAN cholinergic receptor, nicotinic, alpha 10 (neuronal) 28 elevation of cytosolic calcium ion concentration|regulation of cell proliferation|synaptic transmission, cholinergic cell junction|postsynaptic membrane calcium channel activity|receptor activity|receptor binding breast(1)|endometrium(2)|lung(3)|ovary(1) 7 Medulloblastoma(188;0.0075)|Breast(177;0.0164)|all_neural(188;0.0577) BRCA - Breast invasive adenocarcinoma(625;0.0344)|LUSC - Lung squamous cell carcinoma(625;0.192) Chloroprocaine(DB01161)|Methadone(DB00333)|Nicotine(DB00184)|Pentolinium(DB01090)|Procaine(DB00721)|Trimethaphan(DB01116) GAGAGCCAGCCGGCCCTCAGC 0.612000 31 62 0 0 1 0 0 DNAH17 8632 broad.mit.edu 37 17 76435207 76435207 + Missense_Mutation SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr17:76435207C>T ENST00000389840.5 - 73 11852 c.11728G>A c.(11728-11730)Gtg>Atg p.V3910M DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000585328.1_Missense_Mutation_p.V3919M dynein, axonemal, heavy chain 17 NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3) 116 BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656) TCTGCAGCCACGTCCAGGGCG 0.562000 4 37 0 0 1 0 0 RPA4 29935 broad.mit.edu 37 X 96140039 96140039 + Missense_Mutation SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chrX:96140039G>A ENST00000373040.3 + 1 1133 c.730G>A c.(730-732)Gtt>Att p.V244I DIAPH2_ENST00000373049.4_Intron|DIAPH2_ENST00000373054.4_Intron|DIAPH2_ENST00000355827.4_Intron|DIAPH2_ENST00000324765.8_Intron|DIAPH2_ENST00000373061.3_Intron NM_013347.4 NP_037479.1 Q13156 RFA4_HUMAN replication protein A4, 30kDa 244 DNA damage checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair DNA replication factor A complex|nucleoplasm single-stranded DNA binding endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1) 13 TTATCTGACCGTTGAGGGCCA 0.507000 Other identified genes with known or suspected DNA repair function 3 39 0 0 1 0 0 TMC6 11322 broad.mit.edu 37 17 76117241 76117241 + Missense_Mutation SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr17:76117241G>A ENST00000590602.1 - 12 1547 c.1388C>T c.(1387-1389)cCa>cTa p.P463L TMC6_ENST00000306591.7_Intron|TMC6_ENST00000392467.3_Missense_Mutation_p.P463L|TMC6_ENST00000592076.1_Intron|TMC6_ENST00000589553.1_Missense_Mutation_p.P236L|TMC6_ENST00000591436.1_Missense_Mutation_p.P102L|TMC6_ENST00000322933.4_Missense_Mutation_p.P102L|TMC6_ENST00000322914.3_Missense_Mutation_p.P463L Q7Z403 TMC6_HUMAN transmembrane channel-like 6 463 endoplasmic reticulum membrane|integral to membrane NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1) 14 BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973) AGCAGCCTCTGGACTCTGCAG 0.697000 6 15 0 0 1 0 0 AKNA 80709 broad.mit.edu 37 9 117104291 117104291 + Missense_Mutation SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr9:117104291G>A ENST00000307564.4 - 20 4033 c.3872C>T c.(3871-3873)tCt>tTt p.S1291F AKNA_ENST00000374079.4_Missense_Mutation_p.S236F|AKNA_ENST00000223791.3_Missense_Mutation_p.S751F|AKNA_ENST00000374075.5_Missense_Mutation_p.S1210F|AKNA_ENST00000374088.3_Missense_Mutation_p.S1291F|AKNA_ENST00000492875.1_5'UTR NM_030767.4 NP_110394.3 Q7Z591 AKNA_HUMAN AT-hook transcription factor 1291 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2) 51 GTCCCTACCAGAGGTGGCTGA 0.567000 33 71 0 0 1 0 0 CD27 939 broad.mit.edu 37 12 6554692 6554692 + Missense_Mutation SNP A A G TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr12:6554692A>G ENST00000266557.3 + 2 468 c.239A>G c.(238-240)cAc>cGc p.H80R CD27_ENST00000541233.1_3'UTR|CD27-AS1_ENST00000399492.2_RNA|CD27-AS1_ENST00000545339.1_RNA NM_001242.4 NP_001233.1 P26842 CD27_HUMAN CD27 molecule 80 anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway|immunoglobulin mediated immune response|induction of apoptosis|positive regulation of B cell differentiation|positive regulation of JNK cascade|release of cytoplasmic sequestered NF-kappaB extracellular region|integral to plasma membrane caspase inhibitor activity|protein binding|transmembrane receptor activity kidney(1)|large_intestine(5)|lung(1)|urinary_tract(3) 10 ACCCGGCCCCACTGTGAGAGC 0.587000 21 45 0 0 1 0 0 HCN4 10021 broad.mit.edu 37 15 73622050 73622050 + Missense_Mutation SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr15:73622050G>A ENST00000261917.3 - 4 2447 c.1454C>T c.(1453-1455)gCg>gTg p.A485V NM_005477.2 NP_005468.1 Q9Y3Q4 HCN4_HUMAN hyperpolarization activated cyclic nucleotide-gated potassium channel 4 485 blood circulation|muscle contraction integral to membrane cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1) 55 COAD - Colon adenocarcinoma(1;0.142) GCCCACGGGCGCCTGCCGCCC 0.622000 39 62 0 0 1 0 0 TPTE2P6 0 broad.mit.edu 37 13 25161397 25161397 + RNA SNP C C G rs3874227 by1000genomes TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr13:25161397C>G ENST00000453498.1 + 0 921 TGAAACATCTCTACAACTGGA 0.343000 4 45 0 0 1 0 0 SBF1 6305 broad.mit.edu 37 22 50900484 50900484 + Missense_Mutation SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr22:50900484C>T ENST00000380817.2 - 20 2644 c.2461G>A c.(2461-2463)Gac>Aac p.D821N SBF1_ENST00000390679.3_Missense_Mutation_p.D821N|SBF1_ENST00000348911.6_Missense_Mutation_p.D822N NM_002972.2 NP_002963.2 O95248 MTMR5_HUMAN SET binding factor 1 821 protein dephosphorylation integral to membrane|nucleus protein tyrosine/serine/threonine phosphatase activity breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1) 43 all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247) CCAGCTACGTCGCAGGTCTCT 0.617000 63 158 0 0 1 0 0 SOGA3 387104 broad.mit.edu 37 6 127796912 127796912 + Silent SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr6:127796912G>A ENST00000556132.1 - 6 3123 c.2259C>T c.(2257-2259)gcC>gcT p.A753A SOGA3_ENST00000481848.2_Silent_p.A753A|SOGA3_ENST00000525778.1_Silent_p.A753A|SOGA3_ENST00000465909.2_Silent_p.A753A|SOGA3_ENST00000368268.2_Silent_p.A753A NM_001012279.2 NP_001012279.1 Q5TF21 CF174_HUMAN SOGA family member 3 753 integral to membrane CGTCGCTCTCGGCGTCGCTGT 0.697000 7 132 0 0 1 0 0 DNAH1 25981 broad.mit.edu 37 3 52383437 52383437 + Splice_Site SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr3:52383437G>A ENST00000420323.2 + 14 2787 c.e14+1 NM_015512.4 NP_056327.4 Q9P2D7 DYH1_HUMAN dynein, axonemal, heavy chain 1 ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus axonemal dynein complex|cilium axoneme|cytoplasm|microtubule ATP binding|ATPase activity|microtubule motor activity cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1) 62 BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245) GGTGGATAGCGTAAGTGCCCA 0.582000 3 35 0 0 1 0 0 CDC20B 166979 broad.mit.edu 37 5 54410070 54410070 + Silent SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr5:54410070C>T ENST00000296733.1 - 12 1698 c.1524G>A c.(1522-1524)acG>acA p.T508T CDC20B_ENST00000322374.6_Silent_p.T470T|CDC20B_ENST00000334206.5_3'UTR|CDC20B_ENST00000381375.2_Silent_p.T512T NM_001170402.1|NM_152623.2 NP_001163873.1|NP_689836.2 Q86Y33 CD20B_HUMAN cell division cycle 20B 512 kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1) 19 Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194) LUSC - Lung squamous cell carcinoma(15;0.225) atacagaggccgtcccatcag 0.527000 26 57 0 0 1 0 0 CYFIP2 26999 broad.mit.edu 37 5 156786061 156786061 + Missense_Mutation SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr5:156786061G>A ENST00000347377.6 + 24 3153 c.2722G>A c.(2722-2724)Gtg>Atg p.V908M CYFIP2_ENST00000541131.1_Missense_Mutation_p.V833M|CYFIP2_ENST00000435847.2_Missense_Mutation_p.V607M|CYFIP2_ENST00000318218.6_Missense_Mutation_p.V933M|CYFIP2_ENST00000377576.3_Missense_Mutation_p.V908M|CYFIP2_ENST00000522463.1_Missense_Mutation_p.V712M|CYFIP2_ENST00000442283.2_Missense_Mutation_p.R192H|CYFIP2_ENST00000521420.1_Missense_Mutation_p.V882M NM_001037332.2 NP_001032409.2 Q96F07 CYFP2_HUMAN cytoplasmic FMR1 interacting protein 2 933 apoptosis|cell-cell adhesion cell junction|perinuclear region of cytoplasm|synapse|synaptosome protein binding breast(1)|endometrium(12)|kidney(2)|lung(23) 38 Renal(175;0.00212) Medulloblastoma(196;0.0306)|all_neural(177;0.0897) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) CAGGAATTTCGTGGGGCCACC 0.488000 6 280 0 0 1 0 0 TMEM246 84302 broad.mit.edu 37 9 104238562 104238562 + Missense_Mutation SNP C C A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr9:104238562C>A ENST00000374851.1 - 4 1960 c.813G>T c.(811-813)ttG>ttT p.L271F TMEM246_ENST00000374848.3_Missense_Mutation_p.L271F|RP11-490D19.6_ENST00000450109.1_RNA|RP11-490D19.6_ENST00000431507.1_RNA|RP11-490D19.6_ENST00000425734.1_RNA|RP11-490D19.6_ENST00000424154.1_RNA|TMEM246_ENST00000374847.1_Missense_Mutation_p.L271F Q9BRR3 CI125_HUMAN transmembrane protein 246 271 integral to membrane AGGGCCCCAGCAACATGCCTA 0.537000 70 129 4.37588e-27 4.74054e-27 1 1 0 ABCG2 9429 broad.mit.edu 37 4 89013441 89013441 + Missense_Mutation SNP A A G TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr4:89013441A>G ENST00000237612.3 - 16 2458 c.1913T>C c.(1912-1914)gTt>gCt p.V638A ABCG2_ENST00000515655.1_3'UTR NM_004827.2 NP_004818.2 Q9UNQ0 ABCG2_HUMAN ATP-binding cassette, sub-family G (WHITE), member 2 638 ABC transmembrane type-2. cellular iron ion homeostasis|urate metabolic process integral to membrane|plasma membrane ATP binding|heme transporter activity|protein homodimerization activity|xenobiotic-transporting ATPase activity breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 42 Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;7.02e-05) Imatinib(DB00619)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nitrendipine(DB01054)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Topotecan(DB01030) GAGGAAAATAACAATCATACA 0.363000 22 45 0 0 1 0 0 HSD17B7P2 0 broad.mit.edu 37 10 38654432 38654432 + RNA SNP A A G rs2257765 TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr10:38654432A>G ENST00000494540.1 + 0 599 NR_003086.1 TCATCTCGCAATGCAAGGAAA 0.453000 5 60 0 0 1 0 0 C1QTNF9 338872 broad.mit.edu 37 13 24895797 24895797 + Missense_Mutation SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr13:24895797G>A ENST00000382071.2 + 4 978 c.893G>A c.(892-894)gGg>gAg p.G298E C1QTNF9_ENST00000332018.4_Missense_Mutation_p.G298E P0C862 C1T9A_HUMAN C1q and tumor necrosis factor related protein 9 298 C1q. collagen hormone activity endometrium(1)|kidney(2)|lung(6) 9 all_cancers(29;3.55e-20)|all_epithelial(30;4.25e-17)|all_lung(29;1.04e-16)|Lung SC(185;0.0225)|Breast(139;0.052) all cancers(112;0.00565)|Epithelial(112;0.027)|OV - Ovarian serous cystadenocarcinoma(117;0.115)|Lung(94;0.159) CTGAAGCTCGGGGATGAGGTG 0.507000 4 121 0 0 1 0 0 DPY19L4 286148 broad.mit.edu 37 8 95795914 95795914 + Missense_Mutation SNP G G T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr8:95795914G>T ENST00000414645.2 + 17 1831 c.1732G>T c.(1732-1734)Gca>Tca p.A578S NM_181787.2 NP_861452.2 Q7Z388 D19L4_HUMAN dpy-19-like 4 (C. elegans) 578 integral to membrane p.A578T(1) breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2) 21 Breast(36;3.85e-06) AGCTCCAGTTGCAGCTGTGTT 0.403000 15 24 5.01169e-05 5.31853e-05 1 1 0 RP1L1 94137 broad.mit.edu 37 8 10464989 10464989 + Missense_Mutation SNP G G T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr8:10464989G>T ENST00000382483.3 - 4 6842 c.6619C>A c.(6619-6621)Cca>Aca p.P2207T NM_178857.5 NP_849188.4 A6NKC6 A6NKC6_HUMAN retinitis pigmentosa 1-like 1 2207 intracellular signal transduction breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3) 148 COAD - Colon adenocarcinoma(149;0.0811) TCTAACTCTGGTTGGGCCTCC 0.632000 26 429 0.000117367 0.000122062 1 1 0 CRISPLD1 83690 broad.mit.edu 37 8 75929559 75929559 + Missense_Mutation SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr8:75929559C>T ENST00000262207.4 + 10 1469 c.1001C>T c.(1000-1002)tCc>tTc p.S334F CRISPLD1_ENST00000523524.1_Missense_Mutation_p.S146F|CRISPLD1_ENST00000517786.1_Missense_Mutation_p.S148F NM_031461.5 NP_113649.1 Q9H336 CRLD1_HUMAN cysteine-rich secretory protein LCCL domain containing 1 334 LCCL 1. extracellular region biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 43 Breast(64;0.0799) Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161) TCCAAGCAATCCAGCATCTGT 0.338000 5 84 0 0 1 0 0 SLC10A2 6555 broad.mit.edu 37 13 103718522 103718522 + Missense_Mutation SNP G G T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr13:103718522G>T ENST00000245312.3 - 1 674 c.78C>A c.(76-78)ttC>ttA p.F26L NM_000452.2 NP_000443.1 Q12908 NTCP2_HUMAN solute carrier family 10 (sodium/bile acid cotransporter), member 2 26 bile acid metabolic process|organic anion transport integral to plasma membrane bile acid:sodium symporter activity breast(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 34 all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211) GGATGTTATTGAAATTGCTCT 0.478000 7 133 0.000157383 0.000160469 1 1 0 ZFYVE27 118813 broad.mit.edu 37 10 99502873 99502873 + Missense_Mutation SNP T T G TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr10:99502873T>G ENST00000393677.4 + 3 424 c.220T>G c.(220-222)Ttg>Gtg p.L74V ZFYVE27_ENST00000357540.4_Intron|ZFYVE27_ENST00000356257.4_Missense_Mutation_p.L74V|ZFYVE27_ENST00000359980.3_Missense_Mutation_p.L74V|ZFYVE27_ENST00000453958.2_Missense_Mutation_p.L74V|ZFYVE27_ENST00000337540.7_Intron|ZFYVE27_ENST00000370610.3_Intron|ZFYVE27_ENST00000370613.3_Intron NM_144588.6 NP_653189.3 Q5T4F4 ZFY27_HUMAN zinc finger, FYVE domain containing 27 74 cell death|nerve growth factor receptor signaling pathway|neuron projection development|protein localization in plasma membrane axon|dendrite|endoplasmic reticulum membrane|growth cone membrane|integral to membrane|recycling endosome membrane metal ion binding|protein binding endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1) 8 Colorectal(252;0.0846) Epithelial(162;7.08e-10)|all cancers(201;5.18e-08) TTTGTGTTCCTTGCTGACCTG 0.547000 41 87 0 0 1 0 0 NUP98 4928 broad.mit.edu 37 11 3797159 3797159 + Missense_Mutation SNP G G T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr11:3797159G>T ENST00000324932.7 - 5 868 c.448C>A c.(448-450)Cca>Aca p.P150T NUP98_ENST00000397004.4_Missense_Mutation_p.P150T|NUP98_ENST00000397007.4_Missense_Mutation_p.P150T|NUP98_ENST00000359171.4_Missense_Mutation_p.P150T|NUP98_ENST00000355260.3_Missense_Mutation_p.P150T NM_016320.4|NM_139132.3 NP_057404.2|NP_624358.2 P52948 NUP98_HUMAN nucleoporin 98kDa 150 Gly/Thr-rich. carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex protein binding|structural constituent of nuclear pore|transporter activity NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 66 Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227) BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199) AAACTACTTGGCCCAAAGAGG 0.398000 T """HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11""" AML 4 131 1 1 1 1 0 ACAN 176 broad.mit.edu 37 15 89398710 89398710 + Missense_Mutation SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr15:89398710C>T ENST00000439576.2 + 12 3268 c.2894C>T c.(2893-2895)aCc>aTc p.T965I ACAN_ENST00000561243.1_Missense_Mutation_p.T965I|ACAN_ENST00000559004.1_Missense_Mutation_p.T965I|ACAN_ENST00000352105.7_Missense_Mutation_p.T965I NM_013227.3 NP_037359.3 E7EX88 E7EX88_HUMAN aggrecan 965 cell adhesion hyaluronic acid binding|sugar binding NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2) 93 Lung NSC(78;0.0392)|all_lung(78;0.077) BRCA - Breast invasive adenocarcinoma(143;0.146) GTTCTAGAGACCTCTGCCTCT 0.562000 5 226 0 0 1 0 0 GLI2 2736 broad.mit.edu 37 2 121746844 121746844 + Silent SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr2:121746844C>T ENST00000452319.1 + 14 3414 c.3354C>T c.(3352-3354)ggC>ggT p.G1118G GLI2_ENST00000361492.4_Silent_p.G1118G|GLI2_ENST00000314490.11_Silent_p.G790G P10070 GLI2_HUMAN GLI family zinc finger 2 1118 axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1) 64 Renal(3;0.0496) Prostate(154;0.0623) CCAACGTGGGCCCCTCCGCCC 0.622000 33 62 0 0 1 0 0 NDUFS3 4722 broad.mit.edu 37 11 47605984 47605984 + Missense_Mutation SNP C C T rs9600 TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr11:47605984C>T ENST00000263774.4 + 7 828 c.746C>T c.(745-747)cCg>cTg p.P249L NDUFS3_ENST00000533507.1_3'UTR NM_004551.2 NP_004542.1 O75489 NDUS3_HUMAN NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase) 249 P -> Q (in dbSNP:rs9600). induction of apoptosis|mitochondrial electron transport, NADH to ubiquinone|negative regulation of cell growth|reactive oxygen species metabolic process|transport mitochondrial respiratory chain complex I electron carrier activity|NADH dehydrogenase (ubiquinone) activity|protein binding breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2) 9 NADH(DB00157) CGCCAACCCCCGGAGAGTCTC 0.567000 61 190 0 0 1 0 0 NCOA6 23054 broad.mit.edu 37 20 33345744 33345744 + Silent SNP C C T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr20:33345744C>T ENST00000374796.2 - 8 3377 c.807G>A c.(805-807)caG>caA p.Q269Q NCOA6_ENST00000359003.2_Silent_p.Q269Q Q14686 NCOA6_HUMAN nuclear receptor coactivator 6 269 CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region. brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter transcription factor complex chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding p.Q269Q(15) NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1) 107 gctgctgctgctgttgttgtt 0.537000 4 58 0 0 1 0 0 FAT4 79633 broad.mit.edu 37 4 126328050 126328050 + Missense_Mutation SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr4:126328050G>A ENST00000394329.3 + 3 5336 c.5323G>A c.(5323-5325)Gtc>Atc p.V1775I FAT4_ENST00000335110.5_Missense_Mutation_p.V73I NM_024582.4 NP_078858.4 Q6V0I7 FAT4_HUMAN FAT atypical cadherin 4 1775 Cadherin 17. homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6) 355 AAATGCTCTCGTCACATACAC 0.433000 17 127 0 0 1 0 0 NDRG4 65009 broad.mit.edu 37 16 58545390 58545390 + Silent SNP G G A TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr16:58545390G>A ENST00000394282.4 + 16 1493 c.1086G>A c.(1084-1086)tcG>tcA p.S362S NDRG4_ENST00000569923.1_Silent_p.S255S|NDRG4_ENST00000568640.1_Silent_p.S328S|NDRG4_ENST00000356752.4_Silent_p.S340S|NDRG4_ENST00000562999.1_Silent_p.S298S|NDRG4_ENST00000566192.1_Silent_p.S310S|NDRG4_ENST00000563799.1_Silent_p.S328S|NDRG4_ENST00000570248.1_Silent_p.S323S|NDRG4_ENST00000394279.2_Silent_p.S342S|NDRG4_ENST00000258187.5_Silent_p.S342S NM_001130487.1 NP_001123959.1 Q9ULP0 NDRG4_HUMAN NDRG family member 4 323 cell differentiation|cell growth|multicellular organismal development|response to stress cytoplasm breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1) 11 GTGCCAGCTCGGTGGATGGCA 0.657000 4 136 0 0 1 0 0 CERKL 0 broad.mit.edu 37 2 182468750 182468751 + Frame_Shift_Del DEL AT AT - TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr2:182468750_182468751delAT ENST00000410087.3 - 2 394_395 c.294_295delAT c.(292-297)attcfs p.IF98fs CERKL_ENST00000479558.1_5'UTR|CERKL_ENST00000409440.3_Frame_Shift_Del_p.IF98fs|CERKL_ENST00000374969.2_Frame_Shift_Del_p.IF98fs|CERKL_ENST00000374970.2_Frame_Shift_Del_p.IF98fs|CERKL_ENST00000339098.5_Frame_Shift_Del_p.IF98fs NM_001030311.2|NM_201548.4 NP_001025482.1|NP_963842.1 Q49MI3 CERKL_HUMAN ceramide kinase-like 98 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis endoplasmic reticulum|Golgi apparatus|nucleolus diacylglycerol kinase activity NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3) 32 OV - Ovarian serous cystadenocarcinoma(117;0.088) TTCACAGAGAATATGTCTTTGA 0.307 19 34 --- --- --- --- ABCA12 26154 broad.mit.edu 37 2 215843155 215843156 + Frame_Shift_Ins INS - - T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr2:215843155_215843156insT ENST00000272895.7 - 33 5231_5232 c.5012_5013insA c.(5011-5013)aagfs p.K1671fs ABCA12_ENST00000389661.4_Frame_Shift_Ins_p.K1353fs NM_173076.2 NP_775099.2 Q86UK0 ABCAC_HUMAN ATP-binding cassette, sub-family A (ABC1), member 12 1671 cellular homeostasis|lipid transport integral to membrane ATP binding|ATPase activity NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1) 139 Renal(323;0.127) Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011) TCATAGCACTATTTTTTTGTGA 0.376 7 23 --- --- --- --- RP11-553L6.2 0 broad.mit.edu 37 3 113951738 113951739 + RNA INS - - CC rs60004852 by1000genomes TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr3:113951738_113951739insCC ENST00000493033.1 + 0 160 RP11-553L6.2_ENST00000481773.1_RNA ACTGCCCCCTGCCCCCCCCCCA 0.653 4 3 --- --- --- --- SAMD3 154075 broad.mit.edu 37 6 130535491 130535491 + Frame_Shift_Del DEL G G - TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr6:130535491delG ENST00000532763.1 - 3 389 c.260delC c.(259-261)gafs p.A88fs SAMD3_ENST00000437477.2_Frame_Shift_Del_p.A88fs|SAMD3_ENST00000368134.2_Frame_Shift_Del_p.A88fs|SAMD3_ENST00000324172.6_Frame_Shift_Del_p.A88fs|SAMD3_ENST00000533296.1_5'UTR|SAMD3_ENST00000439090.2_Frame_Shift_Del_p.A88fs|SAMD3_ENST00000457563.2_Frame_Shift_Del_p.A112fs Q8N6K7 SAMD3_HUMAN sterile alpha motif domain containing 3 88 breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(15)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2) 29 GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128) CTCTCGAGCTGCTTCTGTTTG 0.428 12 197 --- --- --- --- FJX1 24147 broad.mit.edu 37 11 35640220 35640220 + Frame_Shift_Del DEL G G - TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr11:35640220delG ENST00000317811.4 + 1 486 c.36delG c.(34-36)gcfs p.A12fs NM_014344.3 NP_055159.2 Q86VR8 FJX1_HUMAN four jointed box 1 (Drosophila) 12 extracellular space lung(1)|urinary_tract(1) 2 all_cancers(35;0.177)|all_lung(20;0.0238)|Lung NSC(22;0.0494)|all_epithelial(35;0.0739) all_hematologic(20;0.107) CCGCCACCGCGGGGCTCTGGC 0.801 2 4 --- --- --- --- MLH3 27030 broad.mit.edu 37 14 75514337 75514338 + Frame_Shift_Ins INS - - T TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr14:75514337_75514338insT ENST00000355774.2 - 2 2236_2237 c.2021_2022insA c.(2020-2022)atgfs p.M674fs MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000238662.7_Frame_Shift_Ins_p.M674fs|MLH3_ENST00000556740.1_Frame_Shift_Ins_p.M674fs|MLH3_ENST00000556257.1_Frame_Shift_Ins_p.M674fs NM_001040108.1 NP_001035197.1 Q9UHC1 MLH3_HUMAN mutL homolog 3 674 mismatch repair|reciprocal meiotic recombination chiasma|MutLbeta complex|synaptonemal complex ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 44 BRCA - Breast invasive adenocarcinoma(234;0.00688) TCGTTCTGCAATTTTTTTTGTT 0.347 Mismatch excision repair (MMR) 26 48 --- --- --- --- DNM1P47 0 broad.mit.edu 37 15 102293062 102293064 + RNA DEL CTC CTC - rs4965539 TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr15:102293062_102293064delCTC ENST00000561463.1 + 0 1108_1110 AGTTCATCTTCTCAGAGCTGCTG 0.576 3 3 --- --- --- --- CACNA1H 8912 broad.mit.edu 37 16 1259227 1259227 + Frame_Shift_Del DEL G G - TCGA-H9-A6BY-01A-11D-A30E-08 TCGA-H9-A6BY-10A-01D-A30H-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4e25c1b9-c691-44c5-bc32-85ddca3e1196 57d5137e-6a41-4e03-a279-e4ee1cf06472 g.chr16:1259227delG ENST00000348261.5 + 17 3807 c.3559delG c.(3559-3561)ggfs p.G1187fs CACNA1H_ENST00000358590.4_Frame_Shift_Del_p.G1187fs|CACNA1H_ENST00000565831.1_Frame_Shift_Del_p.G1187fs NM_021098.2 NP_066921.2 O95180 CAC1H_HUMAN calcium channel, voltage-dependent, T type, alpha 1H subunit 1187 aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction voltage-gated calcium channel complex low voltage-gated calcium channel activity breast(4)|endometrium(5)|kidney(2)|lung(23) 34 Hepatocellular(780;0.00369) Flunarizine(DB04841)|Mibefradil(DB01388) GGCCGCGCCCGGGCCCCGTGC 0.761 2 4 --- --- --- ---