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 BANK1 55024 broad.mit.edu 37 4 102981427 102981427 + Missense_Mutation SNP C C A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr4:102981427C>A ENST00000504592.1 + 16 2402 c.1984C>A c.(1984-1986)Cag>Aag p.Q662K BANK1_ENST00000322953.4_Missense_Mutation_p.Q677K|BANK1_ENST00000428908.1_Missense_Mutation_p.Q544K|BANK1_ENST00000508653.1_Missense_Mutation_p.Q544K|BANK1_ENST00000444316.2_Missense_Mutation_p.Q647K Q8NDB2 BANK1_HUMAN B-cell scaffold protein with ankyrin repeats 1 677 B cell activation NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1) 44 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;2.7e-07) AACTGATGGTCAGGAAGAACT 0.453000 40 61 5.71845e-15 6.74265e-15 1 1 0 CAMK2A 815 broad.mit.edu 37 5 149629830 149629830 + Missense_Mutation SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr5:149629830C>T ENST00000348628.6 - 11 1524 c.859G>A c.(859-861)Gtg>Atg p.V287M CAMK2A_ENST00000398376.3_Missense_Mutation_p.V287M NM_015981.3|NM_171825.2 NP_057065.2|NP_741960.1 Q9UQM7 KCC2A_HUMAN calcium/calmodulin-dependent protein kinase II alpha 287 interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1) 15 all_hematologic(541;0.224) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) AGGCAGTCCACGGTCTCCTGT 0.602000 23 41 0 0 1 0 0 DEF8 54849 broad.mit.edu 37 16 90028152 90028152 + Silent SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr16:90028152G>A ENST00000563594.1 + 8 1684 c.687G>A c.(685-687)gtG>gtA p.V229V DEF8_ENST00000563848.1_3'UTR|DEF8_ENST00000570182.1_Silent_p.V219V|DEF8_ENST00000569453.1_Silent_p.V229V|DEF8_ENST00000563795.1_Silent_p.V229V|DEF8_ENST00000567874.1_Silent_p.V169V|DEF8_ENST00000268676.7_Silent_p.V290V NM_001242818.1|NM_001242819.1 NP_001229747.1|NP_001229748.1 Q6ZN54 DEFI8_HUMAN differentially expressed in FDCP 8 homolog (mouse) 290 intracellular signal transduction zinc ion binding central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1) 12 all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194) BRCA - Breast invasive adenocarcinoma(80;0.0274) CAGGGGGTGTGCCCAGTGAGG 0.617000 26 32 0 0 1 0 0 FOXJ3 22887 broad.mit.edu 37 1 42660617 42660617 + Missense_Mutation SNP C C A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr1:42660617C>A ENST00000372572.1 - 10 1189 c.878G>T c.(877-879)aGt>aTt p.S293I FOXJ3_ENST00000545068.1_Missense_Mutation_p.S293I|FOXJ3_ENST00000372573.1_Missense_Mutation_p.S293I|FOXJ3_ENST00000361776.1_Missense_Mutation_p.S259I|FOXJ3_ENST00000361346.1_Missense_Mutation_p.S293I NM_001198851.1 NP_001185780.1 Q9UPW0 FOXJ3_HUMAN forkhead box J3 293 embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 18 Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0333) AAATGAGGCACTAAGATCTTC 0.348000 70 116 1.64915e-30 2.03567e-30 1 1 0 ANKS1A 23294 broad.mit.edu 37 6 34957002 34957002 + Splice_Site SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr6:34957002G>A ENST00000360359.3 + 9 1349 c.1209_splice c.e9-1 p.R404_splice ANKS1A_ENST00000535627.1_Intron NM_015245.2 NP_056060.2 Q92625 ANS1A_HUMAN ankyrin repeat and sterile alpha motif domain containing 1A 404 cytoplasm protein binding cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 31 CTTCTGCAGAGGGAACGTCCA 0.393000 52 85 0 0 1 0 0 MROH6 642475 broad.mit.edu 37 8 144650814 144650814 + Silent SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr8:144650814G>A ENST00000398882.3 - 10 1808 c.1552C>T c.(1552-1554)Ctg>Ttg p.L518L MROH6_ENST00000533679.1_5'UTR|MROH6_ENST00000524906.1_5'UTR|MROH6_ENST00000534459.1_5'UTR NM_001100878.1 NP_001094348.1 maestro heat-like repeat family member 6 cggagccccagccggagcccg 0.741000 4 1 0 0 1 0 0 SERPINC1 462 broad.mit.edu 37 1 173873136 173873136 + Missense_Mutation SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr1:173873136G>A ENST00000367698.3 - 7 1404 c.1286C>T c.(1285-1287)cCc>cTc p.P429L NM_000488.3 NP_000479.1 P01008 ANT3_HUMAN serpin peptidase inhibitor, clade C (antithrombin), member 1 429 blood coagulation|regulation of proteolysis extracellular space|plasma membrane heparin binding|protease binding|serine-type endopeptidase inhibitor activity NS(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(15)|ovary(1) 25 Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109) CACCCTGTTGGGGTTTAGCGA 0.458000 43 57 0 0 1 0 0 TTTY11 83866 broad.mit.edu 37 Y 8657050 8657050 + RNA SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chrY:8657050C>T ENST00000253470.4 - 0 414 NR_001548.2 CTTTAAAATCCGCTTTAGTCG 0.373000 18 0 0 0 1 0 0 ZNF598 90850 broad.mit.edu 37 16 2051046 2051046 + Missense_Mutation SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr16:2051046C>T ENST00000563630.1 - 7 1237 c.995G>A c.(994-996)cGt>cAt p.R332H ZNF598_ENST00000431526.1_Missense_Mutation_p.R387H|ZNF598_ENST00000562103.1_Missense_Mutation_p.R332H Q86UK7 ZN598_HUMAN zinc finger protein 598 387 intracellular zinc ion binding NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1) 16 CCGGGGGCCACGGGGATCCTC 0.692000 4 5 0 0 1 0 0 HIST3H2BB 128312 broad.mit.edu 37 1 228645862 228645862 + Missense_Mutation SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr1:228645862C>T ENST00000369160.2 + 1 55 c.32C>T c.(31-33)cCc>cTc p.P11L NM_175055.2 NP_778225.1 Q8N257 H2B3B_HUMAN histone cluster 3, H2bb 11 nucleosome assembly nucleosome|nucleus DNA binding skin(1) 1 Prostate(94;0.183) GCTCCTGCGCCCAAGAAGGGT 0.527000 46 69 0 0 1 0 0 PCDHGA11 56105 broad.mit.edu 37 5 140801542 140801542 + Missense_Mutation SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr5:140801542G>A ENST00000398587.2 + 1 781 c.748G>A c.(748-750)Gtg>Atg p.V250M PCDHGB1_ENST00000523390.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_Missense_Mutation_p.V250M|PCDHGB7_ENST00000398594.2_Intron|PCDHGA9_ENST00000573521.1_Intron NM_018914.2|NM_032092.1 NP_061737.1|NP_114481.1 breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1) 49 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CGTATATCGCGTGAGTGTTCC 0.498000 82 100 0 0 1 0 0 MDC1 9656 broad.mit.edu 37 6 30673819 30673819 + Silent SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr6:30673819G>A ENST00000376406.3 - 10 3788 c.3141C>T c.(3139-3141)gcC>gcT p.A1047A MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Silent_p.A783A NM_014641.2 NP_055456.2 Q14676 MDC1_HUMAN mediator of DNA-damage checkpoint 1 1047 Pro-rich. Missing (in Ref. 2; CAH18685). cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint focal adhesion|nucleoplasm FHA domain binding|protein C-terminus binding breast(2)|kidney(1)|ovary(1) 4 TTTGGGGTGGGGCTGGGGCTT 0.532000 Other conserved DNA damage response genes 63 79 0 0 1 0 0 WDR35 57539 broad.mit.edu 37 2 20137643 20137643 + Missense_Mutation SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr2:20137643G>A ENST00000345530.3 - 20 2276 c.2161C>T c.(2161-2163)Cgc>Tgc p.R721C WDR35_ENST00000416055.2_Missense_Mutation_p.R286C|WDR35_ENST00000281405.4_Missense_Mutation_p.R710C NM_001006657.1 NP_001006658.1 Q9P2L0 WDR35_HUMAN WD repeat domain 35 721 breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1) 43 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) TCTTTGCAGCGCACAAATGCT 0.428000 4 147 0 0 1 0 0 LRP5 4041 broad.mit.edu 37 11 68125186 68125186 + Missense_Mutation SNP G G A rs146895334 TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr11:68125186G>A ENST00000294304.7 + 3 663 c.557G>A c.(556-558)cGg>cAg p.R186Q NM_002335.2 NP_002326.2 O75197 LRP5_HUMAN low density lipoprotein receptor-related protein 5 186 Beta-propeller 1. adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex protein binding|receptor activity autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1) 63 GGCAGCACCCGGAAGATCATT 0.587000 3 39 0 0 1 0 0 TRGV2 6974 broad.mit.edu 37 7 38403051 38403051 + RNA SNP G G C rs4993385 by1000genomes TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr7:38403051G>C ENST00000426402.2 - 0 68 GTAGGAGGAGGTGGTCTTCCT 0.527000 3 10 0 0 1 0 0 KIAA0430 9665 broad.mit.edu 37 16 15694386 15694386 + Missense_Mutation SNP G G T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr16:15694386G>T ENST00000396368.3 - 25 4918 c.4712C>A c.(4711-4713)tCc>tAc p.S1571Y KIAA0430_ENST00000551742.1_Missense_Mutation_p.S1571Y|KIAA0430_ENST00000548025.1_Missense_Mutation_p.S1568Y|KIAA0430_ENST00000602337.1_Missense_Mutation_p.S1568Y|KIAA0430_ENST00000540441.2_Missense_Mutation_p.S1406Y|KIAA0430_ENST00000344181.3_Missense_Mutation_p.S1259Y NM_001184998.1|NM_001184999.1|NM_014647.3 NP_001171927.1|NP_001171928.1|NP_055462.2 Q9Y4F3 LKAP_HUMAN KIAA0430 1570 peroxisome nucleotide binding|RNA binding breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1) 40 ATTGGCAGGGGAGAGACTGAG 0.562000 20 95 4.35082e-09 4.77381e-09 1 1 0 SEMA3C 10512 broad.mit.edu 37 7 80430072 80430072 + Splice_Site SNP C C A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr7:80430072C>A ENST00000265361.3 - 10 1548 c.e10+1 SEMA3C_ENST00000544525.1_Splice_Site|SEMA3C_ENST00000419255.2_Splice_Site|SEMA3C_ENST00000536800.1_Splice_Site NM_006379.3 NP_006370.1 Q99985 SEM3C_HUMAN sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C immune response|response to drug membrane receptor activity NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1) 34 TGAATAATTACCTTGATGTTG 0.289000 23 36 7.92952e-12 9.21224e-12 1 1 0 CNGB3 54714 broad.mit.edu 37 8 87641258 87641258 + Missense_Mutation SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr8:87641258C>T ENST00000320005.5 - 12 1416 c.1369G>A c.(1369-1371)Gcc>Acc p.A457T NM_019098.4 NP_061971.3 Q9NQW8 CNGB3_HUMAN cyclic nucleotide gated channel beta 3 457 signal transduction|visual perception integral to membrane cGMP binding NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1) 80 TCCATGCAGGCGCGGAAGTAG 0.443000 65 202 0 0 1 0 0 PCDHGA4 56111 broad.mit.edu 37 5 140736453 140736453 + Silent SNP C C A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr5:140736453C>A ENST00000571252.1 + 1 1686 c.1686C>A c.(1684-1686)atC>atA p.I562I PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron NM_018917.2 NP_061740.1 endometrium(1)|kidney(1)|lung(3) 5 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TCCCTGAGATCCTGTACCCCA 0.582000 122 240 4.94232e-47 6.29747e-47 1 1 0 CSRNP3 80034 broad.mit.edu 37 2 166533063 166533063 + Missense_Mutation SNP G G T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr2:166533063G>T ENST00000314499.7 + 6 1026 c.650G>T c.(649-651)cGa>cTa p.R217L CSRNP3_ENST00000409420.1_Missense_Mutation_p.R249L|CSRNP3_ENST00000342316.4_Missense_Mutation_p.R217L NM_001172173.1 NP_001165644.1 Q8WYN3 CSRN3_HUMAN cysteine-serine-rich nuclear protein 3 217 Cys-rich. apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter nucleus DNA binding|sequence-specific DNA binding transcription factor activity breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2) 33 TGTGACTGCCGAGTGTTCTGT 0.542000 35 16 5.8336e-16 7.09007e-16 1 1 0 OR13G1 441933 broad.mit.edu 37 1 247835701 247835701 + Missense_Mutation SNP A A T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr1:247835701A>T ENST00000359688.2 - 1 664 c.643T>A c.(643-645)Tat>Aat p.Y215N RP11-634B7.4_ENST00000449298.1_RNA NM_001005487.1 NP_001005487.1 Q8NGZ3 O13G1_HUMAN olfactory receptor, family 13, subfamily G, member 1 215 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2) 35 all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) OV - Ovarian serous cystadenocarcinoma(106;0.017) ATAAAACCATAGGAGATGCAG 0.458000 29 45 0 0 1 0 0 MFSD2A 84879 broad.mit.edu 37 1 40421045 40421045 + Silent SNP G G T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr1:40421045G>T ENST00000372809.5 + 1 224 c.81G>T c.(79-81)ccG>ccT p.P27P MFSD2A_ENST00000420632.2_5'UTR|MFSD2A_ENST00000372811.5_Silent_p.P27P NM_001136493.1 NP_001129965.1 Q8NA29 MFS2A_HUMAN major facilitator superfamily domain containing 2A 27 transmembrane transport endoplasmic reticulum membrane|integral to membrane breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2) 24 CTGAACGCCCGGCCCAGGTGA 0.731000 8 16 2.17888e-05 2.35796e-05 1 1 0 TAF1L 138474 broad.mit.edu 37 9 32631299 32631299 + Missense_Mutation SNP G G C TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr9:32631299G>C ENST00000242310.4 - 1 4368 c.4279C>G c.(4279-4281)Cca>Gca p.P1427A NM_153809.2 NP_722516.1 Q8IZX4 TAF1L_HUMAN TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like 1427 Bromo 1. male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent transcription factor TFIID complex DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding p.P1427T(1) breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1) 159 LUSC - Lung squamous cell carcinoma(29;0.0181) GBM - Glioblastoma multiforme(74;0.00301) GCATTGACTGGAGTGTGGAAA 0.478000 14 290 0 0 1 0 0 HDAC7 51564 broad.mit.edu 37 12 48189110 48189110 + Missense_Mutation SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr12:48189110C>T ENST00000080059.7 - 11 1140 c.1141G>A c.(1141-1143)Gag>Aag p.E381K HDAC7_ENST00000552960.1_Missense_Mutation_p.E364K|HDAC7_ENST00000380610.4_Missense_Mutation_p.E398K|HDAC7_ENST00000354334.3_Missense_Mutation_p.E344K|HDAC7_ENST00000427332.2_Missense_Mutation_p.E342K NM_015401.3 NP_056216.2 Q8WUI4 HDAC7_HUMAN histone deacetylase 7 342 Transcription repression 2 (By similarity). negative regulation of interleukin-2 production|negative regulation of osteoblast differentiation|positive regulation of cell migration involved in sprouting angiogenesis|transcription, DNA-dependent cytoplasm|histone deacetylase complex activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 25 GBM - Glioblastoma multiforme(48;0.137) GAGAGCCGCTCGGTGGTCATT 0.667000 12 22 0 0 1 0 0 CYP2D7 1564 broad.mit.edu 37 22 42538870 42538870 + RNA SNP A A C rs2982057 by1000genomes TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr22:42538870A>C ENST00000424775.1 - 0 440 CYP2D7P1_ENST00000433992.1_RNA|CYP2D7P1_ENST00000358097.4_RNA endometrium(1) 1 CCATAGCGCGACAGGAACACC 0.687000 5 45 0 0 1 0 0 CALCRL 10203 broad.mit.edu 37 2 188225462 188225462 + Missense_Mutation SNP G G C TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr2:188225462G>C ENST00000409998.1 - 11 1425 c.644C>G c.(643-645)tCc>tGc p.S215C CALCRL_ENST00000392370.3_Missense_Mutation_p.S215C|AC007319.1_ENST00000412276.1_RNA|AC007319.1_ENST00000453517.1_RNA|CALCRL_ENST00000410068.1_Missense_Mutation_p.S215C Q16602 CALRL_HUMAN calcitonin receptor-like 215 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) AATGAACTGGGACACTTTGCA 0.393000 28 28 0 0 1 0 0 KIAA0430 9665 broad.mit.edu 37 16 15694388 15694388 + Silent SNP G G T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr16:15694388G>T ENST00000396368.3 - 25 4916 c.4710C>A c.(4708-4710)ctC>ctA p.L1570L KIAA0430_ENST00000551742.1_Silent_p.L1570L|KIAA0430_ENST00000548025.1_Silent_p.L1567L|KIAA0430_ENST00000602337.1_Silent_p.L1567L|KIAA0430_ENST00000540441.2_Silent_p.L1405L|KIAA0430_ENST00000344181.3_Silent_p.L1258L NM_001184998.1|NM_001184999.1|NM_014647.3 NP_001171927.1|NP_001171928.1|NP_055462.2 Q9Y4F3 LKAP_HUMAN KIAA0430 1569 peroxisome nucleotide binding|RNA binding breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1) 40 TGGCAGGGGAGAGACTGAGTG 0.562000 19 95 2.4624e-09 2.73985e-09 1 1 0 KLHL34 257240 broad.mit.edu 37 X 21675273 21675273 + Missense_Mutation SNP G G T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chrX:21675273G>T ENST00000379499.2 - 1 1175 c.634C>A c.(634-636)Cgc>Agc p.R212S NM_153270.1 NP_695002.1 Q8N239 KLH34_HUMAN kelch-like family member 34 212 BACK. cervix(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1) 26 TGTGCCAGGCGCTCAGTTGTG 0.692000 18 7 1.02788e-11 1.17685e-11 1 1 0 ALG1L2 644974 broad.mit.edu 37 3 129817144 129817144 + RNA SNP G G T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr3:129817144G>T ENST00000507643.1 + 0 726 C9J202 AG1L2_HUMAN biosynthetic process transferase activity, transferring glycosyl groups TGCGGGAGTCGCAGCAGCTCT 0.527000 4 67 0.150653 0.150653 1 1 0 HEPACAM 220296 broad.mit.edu 37 11 124794758 124794758 + Missense_Mutation SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr11:124794758C>T ENST00000298251.4 - 2 698 c.293G>A c.(292-294)cGt>cAt p.R98H NM_152722.4 NP_689935.2 Q14CZ8 HECAM_HUMAN hepatic and glial cell adhesion molecule 98 Ig-like V-type. cell adhesion|cell cycle arrest|regulation of growth cytoplasm|integral to membrane p.R98H(1) breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 22 all_hematologic(175;0.215) Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308) GAGTCGGATACGGTCTCGATA 0.587000 56 82 0 0 1 0 0 GTF2IRD2P1 401375 broad.mit.edu 37 7 72664015 72664015 + RNA SNP C C G TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr7:72664015C>G ENST00000425256.1 - 0 885 NR_002164.1 ATACCACCCCCGGGGCATGCC 0.507000 3 21 0 0 1 0 0 FRG1BP 284802 broad.mit.edu 37 20 29628282 29628282 + Missense_Mutation SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr20:29628282G>A ENST00000278882.3 + 6 664 c.284G>A c.(283-285)gGg>gAg p.G95E FRG1B_ENST00000358464.4_Missense_Mutation_p.G95E|FRG1B_ENST00000439954.2_Missense_Mutation_p.G100E endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9) 53 AATGAAGCAGGGGACATAGAA 0.373000 4 171 0 0 1 0 0 CCDC106 29903 broad.mit.edu 37 19 56160925 56160925 + Silent SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr19:56160925C>T ENST00000586790.1 + 3 1192 c.288C>T c.(286-288)ttC>ttT p.F96F CCDC106_ENST00000308964.3_Silent_p.F96F|CCDC106_ENST00000591241.1_Silent_p.F61F|CCDC106_ENST00000588740.1_Silent_p.F96F|CCDC106_ENST00000591578.1_Silent_p.F96F Q9BWC9 CC106_HUMAN coiled-coil domain containing 106 96 nucleus endometrium(2)|large_intestine(3)|lung(5)|skin(1) 11 Colorectal(82;0.00403)|Ovarian(87;0.133) BRCA - Breast invasive adenocarcinoma(297;0.18) GBM - Glioblastoma multiforme(193;0.105) TGGACAAATTCATCTCTTCTG 0.607000 15 27 0 0 1 0 0 ZFYVE26 23503 broad.mit.edu 37 14 68228053 68228053 + Missense_Mutation SNP C C A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr14:68228053C>A ENST00000555452.1 - 35 6754 c.6618G>T c.(6616-6618)caG>caT p.Q2206H ZFYVE26_ENST00000557306.1_Intron|ZFYVE26_ENST00000347230.4_Intron Q68DK2 ZFY26_HUMAN zinc finger, FYVE domain containing 26 0 cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination centrosome|midbody metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4) 94 all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115) AAGGCAGGCACTGCCTTTTTG 0.552000 7 12 0.0293803 0.029757 1 1 0 TMTC4 84899 broad.mit.edu 37 13 101320926 101320926 + Silent SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr13:101320926C>T ENST00000342624.5 - 3 384 c.126G>A c.(124-126)aaG>aaA p.K42K TMTC4_ENST00000376234.3_Silent_p.K23K|TMTC4_ENST00000328767.5_Silent_p.K23K NM_032813.2 NP_116202.2 Q5T4D3 TMTC4_HUMAN transmembrane and tetratricopeptide repeat containing 4 23 integral to membrane binding breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 34 all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) CCACTACTAACTTAGCCCAGA 0.453000 18 34 0 0 1 0 0 ALG1L2 644974 broad.mit.edu 37 3 129817138 129817138 + RNA SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr3:129817138G>A ENST00000507643.1 + 0 720 C9J202 AG1L2_HUMAN biosynthetic process transferase activity, transferring glycosyl groups AGAACCTGCGGGAGTCGCAGC 0.522000 4 68 0 0 1 0 0 TMED6 146456 broad.mit.edu 37 16 69383522 69383522 + Missense_Mutation SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr16:69383522C>T ENST00000564737.1 - 2 222 c.223G>A c.(223-225)Gca>Aca p.A75T TMED6_ENST00000288025.3_Silent_p.R82R|RP11-343C2.9_ENST00000563634.1_Intron CAGCAACATGCCGGTCATGTG 0.532000 4 155 0 0 1 0 0 TRPM2 7226 broad.mit.edu 37 21 45861590 45861590 + Missense_Mutation SNP G G A rs145895219 TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr21:45861590G>A ENST00000397928.1 + 32 4847 c.4402G>A c.(4402-4404)Gac>Aac p.D1468N TRPM2_ENST00000397932.2_Missense_Mutation_p.D1518N|TRPM2_ENST00000300482.5_Missense_Mutation_p.D1468N|TRPM2_ENST00000300481.9_Missense_Mutation_p.D1414N|TRPM2_ENST00000498430.1_3'UTR NM_003307.3 NP_003298.1 O94759 TRPM2_HUMAN transient receptor potential cation channel, subfamily M, member 2 1468 Nudix hydrolase. integral to plasma membrane ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1) 76 GCACGCCTGCGACTCGGGGGC 0.662000 24 26 0 0 1 0 0 FOXP1 27086 broad.mit.edu 37 3 71247374 71247374 + Silent SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr3:71247374G>A ENST00000318789.4 - 6 684 c.159C>T c.(157-159)caC>caT p.H53H FOXP1_ENST00000468577.1_Silent_p.H53H|FOXP1_ENST00000475937.1_Silent_p.H53H|FOXP1_ENST00000493089.1_Silent_p.H53H|FOXP1_ENST00000484350.1_Silent_p.H53H|FOXP1_ENST00000318779.3_Silent_p.H53H|FOXP1_ENST00000498215.1_Silent_p.H53H NM_001244810.1|NM_001244813.1|NM_032682.5 NP_001231739.1|NP_001231742.1|NP_116071.2 Q9H334 FOXP1_HUMAN forkhead box P1 53 cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development cytoplasm|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 31 Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209) BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05) GCTGCTGGGCGTGGGCGAGGT 0.612000 T PAX5 ALL 4 164 0 0 1 0 0 VPS8 23355 broad.mit.edu 37 3 184588531 184588531 + Missense_Mutation SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr3:184588531G>A ENST00000437079.3 + 21 1843 c.1672G>A c.(1672-1674)Gat>Aat p.D558N VPS8_ENST00000446204.2_Missense_Mutation_p.D556N|VPS8_ENST00000436792.2_Missense_Mutation_p.D556N|VPS8_ENST00000287546.4_Missense_Mutation_p.D558N NM_001009921.2 NP_001009921.1 Q8N3P4 VPS8_HUMAN vacuolar protein sorting 8 homolog (S. cerevisiae) 558 zinc ion binding NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 54 all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247) Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22) CCATTATGCAGATCGAGCTCT 0.408000 11 14 0 0 1 0 0 TMEM132A 54972 broad.mit.edu 37 11 60698020 60698020 + Missense_Mutation SNP G G T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr11:60698020G>T ENST00000005286.4 + 5 1058 c.905G>T c.(904-906)cGc>cTc p.R302L TMEM132A_ENST00000453848.2_Missense_Mutation_p.R302L NM_017870.3|NM_178031.2 NP_060340.2|NP_821174.1 Q24JP5 T132A_HUMAN transmembrane protein 132A 302 endoplasmic reticulum membrane|Golgi membrane|integral to membrane breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3) 32 ACAGCCGCCCGCCCAGCCCAG 0.607000 110 152 5.10254e-61 6.6082e-61 1 1 0 FRG1 2483 broad.mit.edu 37 4 190864424 190864424 + Missense_Mutation SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr4:190864424G>A ENST00000226798.4 + 2 352 c.130G>A c.(130-132)Gtt>Att p.V44I FRG1_ENST00000514482.1_3'UTR NM_004477.2 NP_004468.1 Q14331 FRG1_HUMAN FSHD region gene 1 44 rRNA processing Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1) 32 all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147) all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161) GCTTGATATTGTTGGTGAGTC 0.313000 37 47 0 0 1 0 0 UBE2Q1 55585 broad.mit.edu 37 1 154527222 154527222 + Nonsense_Mutation SNP C C A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr1:154527222C>A ENST00000292211.4 - 4 656 c.577G>T c.(577-579)Gag>Tag p.E193* UBE2Q1_ENST00000497453.1_5'UTR|UBE2Q1-AS1_ENST00000441613.1_RNA NM_017582.6 NP_060052.3 Q7Z7E8 UB2Q1_HUMAN ubiquitin-conjugating enzyme E2Q family member 1 193 ATP binding|protein binding|ubiquitin-protein ligase activity endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1) 16 all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088) LUSC - Lung squamous cell carcinoma(543;0.185) TCAGGCATCTCCTCATCTTCA 0.527000 13 12 0.000151284 0.000159353 1 1 0 LRP1B 53353 broad.mit.edu 37 2 141093256 141093256 + Missense_Mutation SNP C C A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr2:141093256C>A ENST00000389484.3 - 78 13015 c.12044G>T c.(12043-12045)gGc>gTc p.G4015V NM_018557.2 NP_061027.2 Q9NZR2 LRP1B_HUMAN low density lipoprotein receptor-related protein 1B 4015 protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding p.G4015D(1) NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5) 606 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) GCAGTTGGGGCCATTCAGCTG 0.418000 TSP Lung(27;0.18) 45 55 1.00953e-15 1.20838e-15 1 1 0 NCF1 653361 broad.mit.edu 37 7 74193734 74193734 + Missense_Mutation SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr7:74193734C>T ENST00000289473.4 + 4 431 c.361C>T c.(361-363)Cgc>Tgc p.R121C NCF1_ENST00000443956.3_3'UTR NM_000265.4 NP_000256.3 P14598 NCF1_HUMAN neutrophil cytosolic factor 1 121 PX. cell communication|cellular defense response|innate immune response|protein targeting to membrane|respiratory burst|superoxide anion generation cytosol|NADPH oxidase complex|soluble fraction electron carrier activity|GTP binding|GTPase activity|phosphatidylinositol binding|SH3 domain binding|superoxide-generating NADPH oxidase activity p.R121C(1) breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(3) 10 CTTCAAGGTGCGCCCTGATGA 0.597000 9 52 0 0 1 0 0 ALPK2 115701 broad.mit.edu 37 18 56204900 56204900 + Missense_Mutation SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr18:56204900G>A ENST00000361673.3 - 5 2732 c.2519C>T c.(2518-2520)aCg>aTg p.T840M RP11-1151B14.4_ENST00000591360.1_RNA NM_052947.3 NP_443179.3 Q86TB3 ALPK2_HUMAN alpha-kinase 2 840 ATP binding|protein serine/threonine kinase activity NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2) 84 TGCCAGTTCCGTATCTACAGA 0.398000 22 48 0 0 1 0 0 RBPJL 11317 broad.mit.edu 37 20 43936862 43936862 + Silent SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr20:43936862C>T ENST00000343694.3 + 2 174 c.102C>T c.(100-102)gaC>gaT p.D34D MATN4_ENST00000342716.4_5'UTR|RBPJL_ENST00000372743.1_Silent_p.D34D|MATN4_ENST00000353917.5_5'UTR|MATN4_ENST00000360607.5_5'UTR|RBPJL_ENST00000372741.3_Silent_p.D34D|MATN4_ENST00000372751.4_5'UTR|MATN4_ENST00000537548.1_5'UTR NM_014276.2 NP_055091.2 Q9UBG7 RBPJL_HUMAN recombination signal binding protein for immunoglobulin kappa J region-like 34 signal transduction nucleus DNA binding|sequence-specific DNA binding transcription factor activity NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 19 Myeloproliferative disorder(115;0.0122) GCGAAGCCGACAGGCGGAGCC 0.647000 39 108 0 0 1 0 0 KNDC1 85442 broad.mit.edu 37 10 135015258 135015258 + Silent SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr10:135015258C>T ENST00000304613.3 + 17 3264 c.3243C>T c.(3241-3243)ccC>ccT p.P1081P KNDC1_ENST00000368571.2_Silent_p.P1016P|KNDC1_ENST00000368572.2_Silent_p.P1083P Q76NI1 VKIND_HUMAN kinase non-catalytic C-lobe domain (KIND) containing 1 1081 regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1) 60 all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203) OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05) CCTTGTCCCCCGGCCCAGCCG 0.697000 13 16 0 0 1 0 0 SUSD4 55061 broad.mit.edu 37 1 223396790 223396790 + Silent SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr1:223396790G>A ENST00000343846.3 - 7 1878 c.1245C>T c.(1243-1245)ccC>ccT p.P415P SUSD4_ENST00000454695.2_Silent_p.P255P|SUSD4_ENST00000478605.1_5'UTR|SUSD4_ENST00000366878.4_Silent_p.P415P Q5VX71 SUSD4_HUMAN sushi domain containing 4 415 integral to membrane cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1) 17 GBM - Glioblastoma multiforme(131;0.0611) CCCCTGAGCCGGGGTATGCTG 0.637000 11 29 0 0 1 0 0 SSUH2 51066 broad.mit.edu 37 3 8671394 8671394 + Missense_Mutation SNP C C A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr3:8671394C>A ENST00000317371.4 - 14 1703 c.478G>T c.(478-480)Ggg>Tgg p.G160W SSUH2_ENST00000341795.3_Missense_Mutation_p.G160W|SSUH2_ENST00000415132.1_Missense_Mutation_p.G160W|SSUH2_ENST00000544814.1_Missense_Mutation_p.G182W ssu-2 homolog (C. elegans) CGCCCACGCCCATGGCATTTG 0.582000 63 52 5.80444e-35 7.27858e-35 1 1 0 KIAA0195 9772 broad.mit.edu 37 17 73481511 73481511 + Silent SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr17:73481511C>T ENST00000314256.7 + 3 421 c.27C>T c.(25-27)ggC>ggT p.G9G KIAA0195_ENST00000375248.5_Silent_p.G19G|KIAA0195_ENST00000579208.1_Intron NM_014738.4 NP_055553.3 Q12767 K0195_HUMAN KIAA0195 9 ATP biosynthetic process|cation transport integral to membrane ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1) 42 all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246) all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154) GCCTGCAGGGCGAGCCTCCCT 0.677000 4 109 0 0 1 0 0 PROSC 11212 broad.mit.edu 37 8 37623065 37623065 + Missense_Mutation SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr8:37623065C>T ENST00000328195.3 + 2 188 c.121C>T c.(121-123)Cgg>Tgg p.R41W NM_007198.3 NP_009129.1 O94903 PROSC_HUMAN proline synthetase co-transcribed homolog (bacterial) 41 pyridoxal phosphate binding central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1) 7 Lung NSC(58;0.174) BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10) L-Proline(DB00172)|Pyridoxal Phosphate(DB00114) CATCCAGCCCCGGCTAGTGGC 0.532000 6 473 0 0 1 0 0 FOXP2 93986 broad.mit.edu 37 7 114269973 114269973 + Silent SNP A A G rs149757187 TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr7:114269973A>G ENST00000393500.3 + 11 1105 c.285A>G c.(283-285)caA>caG p.Q95Q FOXP2_ENST00000378237.3_Silent_p.Q170Q|FOXP2_ENST00000350908.4_Silent_p.Q170Q|FOXP2_ENST00000390668.3_Silent_p.Q194Q|FOXP2_ENST00000360232.4_Silent_p.Q170Q|FOXP2_ENST00000393491.3_Silent_p.Q78Q|FOXP2_ENST00000393498.2_Silent_p.Q150Q|FOXP2_ENST00000393494.2_Silent_p.Q170Q|FOXP2_ENST00000408937.3_Silent_p.Q195Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393489.3_Silent_p.Q78Q|FOXP2_ENST00000403559.4_Silent_p.Q187Q O15409 FOXP2_HUMAN forkhead box P2 170 Gln-rich. camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning cytoplasm|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding p.Q195Q(1) breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 52 agcagcagcaacaacaacaac 0.502000 5 73 0 0 1 0 0 ROCK1 6093 broad.mit.edu 37 18 18547728 18547728 + Silent SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr18:18547728C>T ENST00000399799.1 - 26 4117 c.3177G>A c.(3175-3177)ctG>ctA p.L1059L NM_005406.2 NP_005397.1 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein kinase 1 1059 actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction centriole|cytosol|Golgi membrane ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2) 16 Melanoma(1;0.165) GCATGTCATTCAGTTCCTTCT 0.338000 81 174 0 0 1 0 0 HRH3 11255 broad.mit.edu 37 20 60791509 60791509 + Silent SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr20:60791509G>A ENST00000340177.5 - 3 1175 c.891C>T c.(889-891)ggC>ggT p.G297G HRH3_ENST00000317393.6_Silent_p.G297G NM_007232.2 NP_009163.2 Q9Y5N1 HRH3_HUMAN histamine receptor H3 297 Poly-Gly. G-protein signaling, coupled to cyclic nucleotide second messenger|neurotransmitter secretion integral to plasma membrane histamine receptor activity breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1) 9 Breast(26;7.76e-09) BRCA - Breast invasive adenocarcinoma(19;7.08e-07) Histamine Phosphate(DB00667) CCACGGAGCCGCCCCCACCGC 0.741000 8 1 0 0 1 0 0 SMC1A 8243 broad.mit.edu 37 X 53423264 53423264 + Silent SNP A A G TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chrX:53423264A>G ENST00000322213.4 - 18 2872 c.2745T>C c.(2743-2745)atT>atC p.I915I NM_006306.2 NP_006297.2 Q14683 SMC1A_HUMAN structural maintenance of chromosomes 1A 915 cell cycle checkpoint|cell division|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic sister chromatid cohesion|mitotic spindle organization|negative regulation of DNA endoreduplication|nuclear mRNA splicing, via spliceosome|response to radiation|signal transduction in response to DNA damage cohesin core heterodimer|condensed chromosome kinetochore|condensed nuclear chromosome|cytoplasm|meiotic cohesin complex|nucleoplasm ATP binding|chromatin binding|microtubule motor activity|protein heterodimerization activity NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2) 49 GCTTGGTCTCAATGGCTGTCA 0.507000 67 6 0 0 1 0 0 ZFHX3 463 broad.mit.edu 37 16 72991587 72991587 + Missense_Mutation SNP G G A TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr16:72991587G>A ENST00000268489.5 - 2 3130 c.2458C>T c.(2458-2460)Cgc>Tgc p.R820C ZFHX3_ENST00000397992.5_Intron NM_006885.3 NP_008816.3 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 820 muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11) 153 Ovarian(137;0.13) ATGTGAATGCGGAGGTTCCTG 0.567000 79 118 0 0 1 0 0 ALG1L2 644974 broad.mit.edu 37 3 129817127 129817127 + RNA SNP A A C TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr3:129817127A>C ENST00000507643.1 + 0 709 C9J202 AG1L2_HUMAN biosynthetic process transferase activity, transferring glycosyl groups CCAGTTCCGGAAGAACCTGCG 0.522000 4 76 0 0 1 0 0 GRK5 2869 broad.mit.edu 37 10 121196183 121196183 + Silent SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr10:121196183C>T ENST00000392870.2 + 9 1088 c.759C>T c.(757-759)taC>taT p.Y253Y GRK5_ENST00000369108.3_Silent_p.Y148Y NM_005308.2 NP_005299.1 P34947 GRK5_HUMAN G protein-coupled receptor kinase 5 253 Protein kinase. G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway cytoplasm|plasma membrane|soluble fraction ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity endometrium(2)|large_intestine(5)|lung(15)|skin(3)|stomach(1)|urinary_tract(1) 27 Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249) all cancers(201;0.0227) CCTATGCCTACGAGACCAAGG 0.562000 5 48 0 0 1 0 0 USH2A 7399 broad.mit.edu 37 1 216258155 216258155 + Silent SNP C C T TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr1:216258155C>T ENST00000366943.2 - 25 5438 c.5052G>A c.(5050-5052)ccG>ccA p.P1684P RP11-22M7.2_ENST00000446411.1_RNA|USH2A_ENST00000307340.3_Silent_p.P1684P|RP11-22M7.2_ENST00000445619.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA O75445 USH2A_HUMAN Usher syndrome 2A (autosomal recessive, mild) 1684 Laminin G-like 1. maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound basement membrane|cytoplasm|integral to membrane|stereocilium membrane collagen binding NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3) 527 OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875) AAATAGCTGACGGATTGTAAT 0.393000 HNSCC(13;0.011) 15 77 0 0 1 0 0 CEP89 84902 broad.mit.edu 37 19 33444543 33444543 + Missense_Mutation SNP T T C TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr19:33444543T>C ENST00000305768.4 - 4 558 c.470A>G c.(469-471)tAc>tGc p.Y157C CEP89_ENST00000590597.1_Missense_Mutation_p.Y157C NM_032816.3 NP_116205.3 Q96ST8 CEP89_HUMAN centrosomal protein 89kDa 157 centrosome|spindle pole breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1) 35 TGGCACAGCGTACAGGTCATC 0.488000 13 693 0 0 1 0 0 ZNF98 148198 broad.mit.edu 37 19 22604998 22604998 + Splice_Site SNP A A G TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr19:22604998A>G ENST00000357774.5 - 1 150 c.30_splice c.e1+1 p.M10_splice ZNF98_ENST00000601553.1_Splice_Site_p.M10_splice NM_001098626.1 NP_001092096.1 A6NK75 ZNF98_HUMAN zinc finger protein 98 10 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2) 37 all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244) CACTCTCACCATTTCTAGGCT 0.607000 53 134 0 0 1 0 0 PLA2G4A 5321 broad.mit.edu 37 1 186823502 186823502 + Frame_Shift_Del DEL C C - TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr1:186823502delC ENST00000367466.3 + 2 168 c.16delC c.(16-18)ctfs p.P6fs PLA2G4A_ENST00000442353.2_Frame_Shift_Del_p.P6fs|PLA2G4A_ENST00000466600.1_3'UTR NM_024420.2 NP_077734.1 P47712 PA24A_HUMAN phospholipase A2, group IVA (cytosolic, calcium-dependent) 6 C2.|Phospholipid binding (Probable). phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation cytosol|endoplasmic reticulum membrane calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1) 53 Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103) ATTTATAGATCCTTACCAGCA 0.343 29 34 --- --- --- --- GFPT1 2673 broad.mit.edu 37 2 69614196 69614196 + Splice_Site DEL C C - TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr2:69614196delC ENST00000357308.4 - 1 186 c.e1+1 GFPT1_ENST00000494201.1_Splice_Site|GFPT1_ENST00000361060.4_Splice_Site NM_001244710.1 NP_001231639.1 Q06210 GFPT1_HUMAN glutamine--fructose-6-phosphate transaminase 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 endometrium(1)|large_intestine(3)|lung(5)|skin(3) 12 GGCCCCCTTACCACACATGAT 0.736 2 4 --- --- --- --- SYN2 6854 broad.mit.edu 37 3 12046124 12046126 + RNA DEL AGC AGC - rs76272937 TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr3:12046124_12046126delAGC ENST00000432424.2 + 0 245_247 Q86VA8 Q86VA8_HUMAN synapsin II neurotransmitter secretion synaptic vesicle ATP binding|ligase activity breast(5)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1) 18 AGCCCCAGCAAGCGCCGAcgccg 0.764 4 9 --- --- --- --- GRID2 2895 broad.mit.edu 37 4 94377041 94377041 + Frame_Shift_Del DEL C C - TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr4:94377041delC ENST00000282020.4 + 11 2032 c.1774delC c.(1774-1776)ccfs p.P593fs GRID2_ENST00000510992.1_Frame_Shift_Del_p.P498fs NM_001510.2 NP_001501.2 O43424 GRID2_HUMAN glutamate receptor, ionotropic, delta 2 593 glutamate signaling pathway cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1) 100 Hepatocellular(203;0.114)|all_hematologic(202;0.177) OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191) L-Glutamic Acid(DB00142) CTGGCTTAATCCCCCACGATT 0.453 40 73 --- --- --- --- CLINT1 9685 broad.mit.edu 37 5 157216481 157216485 + Frame_Shift_Del DEL GGCAA GGCAA - TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr5:157216481_157216485delGGCAA ENST00000523094.1 - 11 1622_1626 c.1417_1421delTTGCC c.(1417-1422)cfs p.LP473fs CLINT1_ENST00000411809.2_Frame_Shift_Del_p.LP473fs|CLINT1_ENST00000296951.5_Frame_Shift_Del_p.LP473fs|CLINT1_ENST00000530742.1_Frame_Shift_Del_p.LP473fs|CLINT1_ENST00000523908.1_Frame_Shift_Del_p.LP491fs NM_001195555.1|NM_001195556.1 NP_001182484.1|NP_001182485.1 Q14677 EPN4_HUMAN clathrin interactor 1 473 endocytosis|post-Golgi vesicle-mediated transport clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm clathrin binding|lipid binding breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1) 21 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.138) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) CCAAGTAGAGGGCAAGGTTTTGCTG 0.439 52 105 --- --- --- --- GTF2IRD1P1 729156 broad.mit.edu 37 7 66304731 66304731 + RNA DEL T T - TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr7:66304731delT ENST00000457166.1 - 0 189 NR_003934.1 TTTCTTTCCCttttttttttt 0.512 4 8 --- --- --- --- UBXN8 7993 broad.mit.edu 37 8 30612473 30612474 + RNA INS - - T rs34741520 TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr8:30612473_30612474insT ENST00000519246.1 + 0 604 O00124 UBXN8_HUMAN UBX domain protein 8 single fertilization central_nervous_system(1)|lung(2) 3 GGGGTTGGTCGttttttttttt 0.391 2 4 --- --- --- --- C8orf37-AS1 100616530 broad.mit.edu 37 8 96415908 96415918 + RNA DEL TTTTTTTTTTT TTTTTTTTTTT - rs59279759 TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr8:96415908_96415918delTTTTTTTTTTT ENST00000521905.1 + 0 126 aataaaAGACttttttttttttttttttttt 0.322 3 6 --- --- --- --- NLRP6 171389 broad.mit.edu 37 11 281553 281555 + In_Frame_Del DEL GAG GAG - TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr11:281553_281555delGAG ENST00000534750.1 + 4 2024_2026 c.1819_1821delGAG c.(1819-1821)del p.E611del NLRP6_ENST00000312165.5_In_Frame_Del_p.E611del NM_001276700.1 NP_001263629.1 P59044 NALP6_HUMAN NLR family, pyrin domain containing 6 611 Poly-Glu. cytoplasm ATP binding breast(1)|skin(1)|upper_aerodigestive_tract(2) 4 all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122) CGAAGAGCCAGAGGAGGAGGAGG 0.670 7 173 --- --- --- --- RP11-160C18.2 0 broad.mit.edu 37 15 79023175 79023175 + RNA DEL C C - TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr15:79023175delC ENST00000568337.1 + 0 31 GGTGCAGTGACCCTGCAGGCC 0.537 2 4 --- --- --- --- CCNF 899 broad.mit.edu 37 16 2481177 2481177 + Frame_Shift_Del DEL A A - TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr16:2481177delA ENST00000397066.4 + 2 151 c.63delA c.(61-63)cgfs p.R22fs NM_001761.2 NP_001752.2 P41002 CCNF_HUMAN cyclin F 22 cell division|mitosis|negative regulation of centrosome duplication|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process centriole|nucleus|SCF ubiquitin ligase complex protein binding breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(2)|lung(5)|prostate(4)|skin(1) 20 Ovarian(90;0.17) CTACAAAGCGAAGAATAAGGA 0.443 46 80 --- --- --- --- LYPD3 27076 broad.mit.edu 37 19 43969653 43969655 + In_Frame_Del DEL AGC AGC - rs141441894 byFrequency TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chr19:43969653_43969655delAGC ENST00000244333.3 - 1 157_159 c.69_71delGCT c.(67-72)ctt>ct p.LL23del NM_014400.2 NP_055215.2 O95274 LYPD3_HUMAN LY6/PLAUR domain containing 3 23 anchored to plasma membrane cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2) 11 Prostate(69;0.0153) ACCTCCGCGAAGCAGCAGCAGCA 0.675 7 235 --- --- --- --- USP9X 8239 broad.mit.edu 37 X 41060380 41060380 + Frame_Shift_Del DEL G G - TCGA-HD-A634-01A-11D-A28R-08 TCGA-HD-A634-10A-01D-A28U-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86 cb781355-b159-46e4-9f27-c4a3e5113845 g.chrX:41060380delG ENST00000324545.7 + 31 5304 c.4671delG c.(4669-4671)gtfs p.V1557fs USP9X_ENST00000378308.2_Frame_Shift_Del_p.V1557fs NM_001039590.2|NM_001039591.2 NP_001034679.2|NP_001034680.2 Q93008 USP9X_HUMAN ubiquitin specific peptidase 9, X-linked 1557 BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process cytoplasm co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 87 AAGGATTCGTGGGGCTGAAAA 0.463 51 10 --- --- --- ---