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 COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_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 ACHILLES_Lineage_Results_Top_Genes CGC_CancerGermlineMut CGC_CancerMolecularGenetics CGC_CancerSomaticMut CGC_CancerSyndrome CGC_Chr CGC_ChrBand CGC_GeneID CGC_Name CGC_OtherGermlineMut CGC_TissueType COSMIC_n_overlapping_mutations COSMIC_overlapping_mutation_descriptions ClinVar_ASSEMBLY ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_rs Ensembl_so_accession Ensembl_so_term Familial_Cancer_Genes_Reference Familial_Cancer_Genes_Synonym annotation_transcript bcgsc broad build ccds_id dbNSFP_1000Gp1_AC dbNSFP_1000Gp1_AF dbNSFP_1000Gp1_AFR_AC dbNSFP_1000Gp1_AFR_AF dbNSFP_1000Gp1_AMR_AC dbNSFP_1000Gp1_AMR_AF dbNSFP_1000Gp1_ASN_AC dbNSFP_1000Gp1_ASN_AF dbNSFP_1000Gp1_EUR_AC dbNSFP_1000Gp1_EUR_AF dbNSFP_Ancestral_allele dbNSFP_CADD_phred dbNSFP_CADD_raw dbNSFP_CADD_raw_rankscore dbNSFP_ESP6500_AA_AF dbNSFP_ESP6500_EA_AF dbNSFP_Ensembl_geneid dbNSFP_Ensembl_transcriptid dbNSFP_FATHMM_pred dbNSFP_FATHMM_rankscore dbNSFP_FATHMM_score dbNSFP_GERP_NR dbNSFP_GERP_RS dbNSFP_GERP_RS_rankscore dbNSFP_Interpro_domain dbNSFP_LRT_Omega dbNSFP_LRT_converted_rankscore dbNSFP_LRT_pred dbNSFP_LRT_score dbNSFP_LR_pred dbNSFP_LR_rankscore dbNSFP_LR_score dbNSFP_MutationAssessor_pred dbNSFP_MutationAssessor_rankscore dbNSFP_MutationAssessor_score dbNSFP_MutationTaster_converted_rankscore dbNSFP_MutationTaster_pred dbNSFP_MutationTaster_score dbNSFP_Polyphen2_HDIV_pred dbNSFP_Polyphen2_HDIV_rankscore dbNSFP_Polyphen2_HDIV_score dbNSFP_Polyphen2_HVAR_pred dbNSFP_Polyphen2_HVAR_rankscore dbNSFP_Polyphen2_HVAR_score dbNSFP_RadialSVM_pred dbNSFP_RadialSVM_rankscore dbNSFP_RadialSVM_score dbNSFP_Reliability_index dbNSFP_SIFT_converted_rankscore dbNSFP_SIFT_pred dbNSFP_SIFT_score dbNSFP_SLR_test_statistic dbNSFP_SiPhy_29way_logOdds dbNSFP_SiPhy_29way_logOdds_rankscore dbNSFP_SiPhy_29way_pi dbNSFP_UniSNP_ids dbNSFP_Uniprot_aapos dbNSFP_Uniprot_acc dbNSFP_Uniprot_id dbNSFP_aaalt dbNSFP_aapos dbNSFP_aapos_FATHMM dbNSFP_aapos_SIFT dbNSFP_aaref dbNSFP_cds_strand dbNSFP_codonpos dbNSFP_folddegenerate dbNSFP_genename dbNSFP_hg18_pos1coor dbNSFP_phastCons100way_vertebrate dbNSFP_phastCons100way_vertebrate_rankscore dbNSFP_phastCons46way_placental dbNSFP_phastCons46way_placental_rankscore dbNSFP_phastCons46way_primate dbNSFP_phastCons46way_primate_rankscore dbNSFP_phyloP100way_vertebrate dbNSFP_phyloP100way_vertebrate_rankscore dbNSFP_phyloP46way_placental dbNSFP_phyloP46way_placental_rankscore dbNSFP_phyloP46way_primate dbNSFP_phyloP46way_primate_rankscore dbNSFP_refcodon entrez_gene_id external_id_capture gencode_transcript_name gencode_transcript_status gencode_transcript_tags gencode_transcript_type gene_type havana_transcript hgsc igv_bad ucsc t_alt_count t_ref_count n_alt_count n_ref_count validation_judgement_rna validation_power_rna validation_tumor_alt_count_rna validation_tumor_ref_count_rna validation_normal_alt_count_rna validation_normal_ref_count_rna min_val_count_rna validation_judgement_targeted validation_power_targeted validation_tumor_alt_count_targeted validation_tumor_ref_count_targeted validation_normal_alt_count_targeted validation_normal_ref_count_targeted min_val_count_targeted validation_judgement_localAssembly validation_power_localAssembly t_alt_count_localAssembly t_ref_count_localAssembly n_alt_count_localAssembly n_ref_count_localAssembly min_val_count_localAssembly validation_judgement_KRAS validation_power_KRAS t_alt_count_KRAS t_ref_count_KRAS n_alt_count_KRAS n_ref_count_KRAS min_val_count_KRAS pon_loglike pon_pass_loglike localAssembly_detected ExAC_AN ExAC_AC ExAC_LQ passExAC SCNA_NA SCNA_NB SCNA_q_hat SCNA_tau IS_SCNA purity ploidy dna_fraction_in_tumor CCF_hat CCF_CI95_low CCF_CI95_high CCF_mode CCF_mean CCF_median clonal CCF_CI_low CCF_CI_high EVX2 344191 broad.mit.edu 37 2 176945342 176945368 + In_Frame_Del DEL AGCCGCGGCCGCCGCGCCTGAGGCTGC AGCCGCGGCCGCCGCGCCTGAGGCTGC - TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr2:176945342_176945368delAGCCGCGGCCGCCGCGCCTGAGGCTGC ENST00000308618.4 - 3 1034_1060 c.898_924delGCAGCCTCAGGCGCGGCGGCCGCGGCT c.(898-924)gcagcctcaggcgcggcggccgcggctdel p.AASGAAAAA300del NM_001080458.1 NP_001073927.1 Q03828 EVX2_HUMAN even-skipped homeobox 2 16 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) AGGGCGACGAAgccgcggccgccgcgcctgaggctgcagccgcggcc 0.731000 0 SO:0001651 inframe_deletion ENST00000308618.4 0 1 hg19 CCDS33333.1 TCGA-FB-AAQ6-01A-11D-A40W-08 EVX2-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359252.1 0 0 0 13 29 0 3 0 0 0 3 2 0.021576 41 61 6 9 51 -20.000000 1 0 0 0 1 0 0 0 2.048692 0 0.630000 1.870000 0.625279 0.960000 5.800000e-01 1.000000 1.000000 0.905359 0.960000 1 0.760000 1.000000 GOT1 2805 broad.mit.edu 37 10 101166530 101166530 + Missense_Mutation SNP C C A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr10:101166530C>A ENST00000370508.5 - 3 404 c.377G>T c.(376-378)gGa>gTa p.G126V GOT1_ENST00000543866.1_Missense_Mutation_p.G105V NM_002079.2 NP_002070.1 P17174 AATC_HUMAN glutamic-oxaloacetic transaminase 1, soluble 16 Ovarian(717;0.028)|Colorectal(252;0.234) L-Aspartic Acid(DB00128)|L-Cysteine(DB00151) GTTGTTTGTTCCATTGTACCA 0.468000 Melanoma(173;770 3544 21601) 0 SO:0001583 missense ENST00000370508.5 0 1 hg19 CCDS7479.1 . . . . . . . . . . C 25.0 4.596653 0.86953 . . ENSG00000120053 ENST00000370508;ENST00000535447;ENST00000543866 T;T 0.20738 2.05;2.05 5.92 5.92 0.95590 Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1); 0.000000 0.85682 D 0.000000 T 0.20047 0.0482 L 0.33137 0.985 0.80722 D 1 B 0.25772 0.134 B 0.27608 0.081 T 0.05733 -1.0867 10 0.17369 T 0.5 -3.717 19.9135 0.97033 0.0:1.0:0.0:0.0 . 126 P17174 AATC_HUMAN V 126;79;105 ENSP00000359539:G126V;ENSP00000445578:G105V ENSP00000359539:G126V G - 2 0 GOT1 101156520 1.000000 0.71417 0.972000 0.41901 0.891000 0.51852 7.379000 0.79691 2.807000 0.96579 0.549000 0.68633 GGA TCGA-FB-AAQ6-01A-11D-A40W-08 GOT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049794.1 0 0 0 52 100 0 49 1 1 22 37 0 49 2 1 1.000000 52 99 0 47 2 -20.000000 1 1 0 0 1 1 2 3 2.112726 0 0.630000 1.870000 0.632316 0.990000 8.500000e-01 1.000000 1.000000 0.985565 0.990000 1 0.960000 1.000000 ABCC2 1244 broad.mit.edu 37 10 101563916 101563916 + Silent SNP A A G TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr10:101563916A>G ENST00000370449.4 + 10 1463 c.1350A>G c.(1348-1350)ttA>ttG p.L450L NM_000392.3 NP_000383 Q92887 MRP2_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 2 67 Colorectal(252;0.234) Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541) AGATTGTCTTATCTATCTTCT 0.463000 0 SO:0001819 synonymous_variant ENST00000370449.4 0 1 hg19 CCDS7484.1 TCGA-FB-AAQ6-01A-11D-A40W-08 ABCC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049825.1 0 0 0 50 245 0 90 0 0 0 0 90 2 1 1.000000 49 243 0 90 2 -20.000000 1 1 0 0 1 1 2 3 2.112726 0 0.630000 1.870000 0.632316 0.540000 4.100000e-01 0.710000 0.540000 0.551923 0.540000 0 0.470000 0.620000 C10orf71 118461 broad.mit.edu 37 10 50532116 50532116 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr10:50532116G>A ENST00000374144.3 + 3 1814 c.1526G>A c.(1525-1527)cGt>cAt p.R509H C10orf71_ENST00000323868.4_Missense_Mutation_p.R509H Q711Q0 CJ071_HUMAN chromosome 10 open reading frame 71 1 GTGCGGAAGCGTGTTAAGAGC 0.493000 0 SO:0001583 missense ENST00000374144.3 0 1 hg19 CCDS44387.1 . . . . . . . . . . G 24.6 4.552873 0.86127 . . ENSG00000177354 ENST00000323868;ENST00000374144 T;T 0.20881 2.04;3.13 5.48 4.57 0.56435 . 0.401374 0.18493 N 0.139596 T 0.22244 0.0536 M 0.64997 1.995 0.42570 D 0.993178 P 0.46859 0.885 B 0.35688 0.208 T 0.10428 -1.0630 10 0.87932 D 0 . 14.0709 0.64858 0.0726:0.0:0.9274:0.0 . 509 Q711Q0-3 . H 509 ENSP00000318713:R509H;ENSP00000363259:R509H ENSP00000318713:R509H R + 2 0 C10orf71 50202122 0.918000 0.31147 0.862000 0.33874 0.940000 0.58332 3.531000 0.53546 1.320000 0.45209 0.586000 0.80456 CGT TCGA-FB-AAQ6-01A-11D-A40W-08 C10orf71-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047984.2 0 0 0 50 124 0 62 0 0 0 0 62 2 1 1.000000 49 121 0 61 2 -20.000000 1 1 121036 7 36 1 1 2 3 2.112726 0 0.630000 1.870000 0.632316 0.910000 7.100000e-01 1.000000 1.000000 0.907731 0.910000 1 0.800000 1.000000 CSTF2T 23283 broad.mit.edu 37 10 53458724 53458724 + Missense_Mutation SNP G G T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr10:53458724G>T ENST00000331173.4 - 1 631 c.586C>A c.(586-588)Cat>Aat p.H196N PRKG1_ENST00000373980.4_Intron|PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron NM_015235.2 NP_056050.1 Q9H0L4 CSTFT_HUMAN cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant 30 GGTGTGACATGTATCTTCCGA 0.512000 0 SO:0001583 missense ENST00000331173.4 0 1 hg19 CCDS7245.1 . . . . . . . . . . G 0.601 -0.829212 0.02734 . . ENSG00000177613 ENST00000331173 T 0.19669 2.13 5.1 4.13 0.48395 . 0.669626 0.15530 N 0.257547 T 0.05410 0.0143 N 0.00583 -1.355 0.25045 N 0.991177 B 0.09022 0.002 B 0.01281 0.0 T 0.29397 -1.0013 10 0.09590 T 0.72 -4.1716 10.3859 0.44140 0.0:0.0:0.8051:0.1949 . 196 Q9H0L4 CSTFT_HUMAN N 196 ENSP00000332444:H196N ENSP00000332444:H196N H - 1 0 CSTF2T 53128730 0.160000 0.22878 0.948000 0.38648 0.987000 0.75469 1.930000 0.40124 2.824000 0.97209 0.655000 0.94253 CAT TCGA-FB-AAQ6-01A-11D-A40W-08 CSTF2T-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048097.1 0 0 0 94 196 0 100 1 9.980352e-01 15 8 0 100 2 1 1.000000 94 193 0 99 2 -20.000000 1 1 0 0 1 1 2 3 2.112726 0 0.630000 1.870000 0.632316 0.990000 8.600000e-01 1.000000 1.000000 0.980943 0.990000 1 0.940000 1.000000 C11orf87 399947 broad.mit.edu 37 11 109294680 109294680 + Silent SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr11:109294680C>T ENST00000327419.6 + 2 724 c.321C>T c.(319-321)agC>agT p.S107S RP11-708B6.2_ENST00000532992.1_RNA|RP11-708B6.2_ENST00000532929.1_RNA NM_207645.3 NP_997528.2 Q6NUJ2 CK087_HUMAN chromosome 11 open reading frame 87 p.S107S(1) 17 ATCACTGCAGCGGCAGCCGCG 0.642000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000327419.6 0 1 hg19 CCDS31672.1 TCGA-FB-AAQ6-01A-11D-A40W-08 C11orf87-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390403.1 0 0 0 116 317 0 135 0 0 0 0 135 2 1 1.000000 93 277 0 118 2 -20.000000 1 1 121394 4 41 1 0 0 0 2.071234 0 0.630000 1.870000 0.627654 0.840000 7.100000e-01 0.970000 0.850000 0.846975 0.840000 0 0.770000 0.910000 PCSK7 9159 broad.mit.edu 37 11 117079612 117079612 + Splice_Site SNP C C T rs145370185 byFrequency TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr11:117079612C>T ENST00000320934.3 - 13 2322 c.e13+1 PCSK7_ENST00000529458.1_5'Flank|PCSK7_ENST00000540028.1_Splice_Site NM_004716.2 NP_004707.2 Q16549 PCSK7_HUMAN proprotein convertase subtilisin/kexin type 7 16 all_hematologic(175;0.0487) Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234) GGTGTACATACGAGTCCATGC 0.582000 T IGH@ MLCLS Dom yes 11 11q23.3 9159 proprotein convertase subtilisin/kexin type 7 L 0 SO:0001630 splice_region_variant ENST00000320934.3 0 1 hg19 CCDS8382.1 . . . . . . . . . . C 11.43 1.637607 0.29157 4.54E-4 0.001979 ENSG00000160613 ENST00000320934;ENST00000540028;ENST00000543900 . . . 4.56 4.56 0.56223 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 13.0225 0.58796 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . PCSK7 116584822 1.000000 0.71417 1.000000 0.80357 0.108000 0.19459 7.075000 0.76798 2.531000 0.85337 0.467000 0.42956 . TCGA-FB-AAQ6-01A-11D-A40W-08 PCSK7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385529.2 0 0 0 13 57 0 19 0 3.995434e-02 1 1 0 19 2 1 0.999710 13 57 0 19 2 -2.816350 1 1 121410 170 47 1 0 0 0 2.071234 0 0.630000 1.870000 0.627654 0.590000 3.400000e-01 0.890000 0.580000 0.607820 0.590000 0 0.450000 0.750000 B3GAT1 27087 broad.mit.edu 37 11 134253672 134253672 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr11:134253672G>A ENST00000524765.1 - 3 5067 c.523C>T c.(523-525)Cgc>Tgc p.R175C B3GAT1_ENST00000392580.1_Missense_Mutation_p.R175C|B3GAT1_ENST00000312527.4_Missense_Mutation_p.R175C|B3GAT1_ENST00000537389.1_Missense_Mutation_p.R188C|B3GAT1_ENST00000531510.1_5'Flank Q9P2W7 B3GA1_HUMAN beta-1,3-glucuronyltransferase 1 19 all_hematologic(175;0.127) all_cancers(12;1.39e-23)|all_epithelial(12;7.17e-17)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|Medulloblastoma(222;0.0125)|all_neural(223;0.0137)|Esophageal squamous(93;0.0559) CGCAGCCAGCGCAGGGCCAGG 0.682000 0 SO:0001583 missense ENST00000524765.1 0 1 hg19 CCDS8500.1 . . . . . . . . . . G 19.12 3.765228 0.69878 . . ENSG00000109956 ENST00000392580;ENST00000312527;ENST00000524765;ENST00000537389 T;T;T;T 0.66099 -0.19;-0.19;-0.19;-0.19 5.56 5.56 0.83823 . 0.000000 0.85682 D 0.000000 T 0.63117 0.2484 M 0.74647 2.275 0.80722 D 1 B;B 0.24576 0.106;0.055 B;B 0.19666 0.015;0.026 T 0.63545 -0.6613 10 0.59425 D 0.04 -29.3285 14.2768 0.66184 0.0:0.0:0.815:0.185 . 188;175 F5H0S0;Q9P2W7 .;B3GA1_HUMAN C 175;175;175;188 ENSP00000376359:R175C;ENSP00000307875:R175C;ENSP00000433847:R175C;ENSP00000445983:R188C ENSP00000307875:R175C R - 1 0 B3GAT1 133758882 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 3.114000 0.50383 2.623000 0.88846 0.561000 0.74099 CGC TCGA-FB-AAQ6-01A-11D-A40W-08 B3GAT1-002 KNOWN alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393639.1 0 0 0 8 38 0 10 0 0 0 0 10 2 1 0.987727 8 34 0 10 2 -16.214520 1 1 0 0 1 0 0 0 2.071234 0 0.630000 1.870000 0.627654 0.560000 2.700000e-01 0.930000 0.550000 0.582736 0.560000 0 0.400000 0.750000 IGSF22 283284 broad.mit.edu 37 11 18738333 18738333 + Silent SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr11:18738333G>A ENST00000513874.1 - 10 1327 c.1188C>T c.(1186-1188)agC>agT p.S396S RP11-1081L13.4_ENST00000527285.1_RNA NM_173588.3 NP_775859 Q8N9C0 IGS22_HUMAN immunoglobulin superfamily, member 22 56 AGAACTCGCCGCTGTCACTGA 0.542000 0 SO:0001819 synonymous_variant ENST00000513874.1 0 1 hg19 CCDS41625.2 TCGA-FB-AAQ6-01A-11D-A40W-08 IGSF22-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000360850.2 0 0 0 81 418 0 145 0 0 0 0 145 2 1 1.000000 79 411 0 143 2 -3.326447 1 1 120984 20 48 1 0 0 0 2.071234 0 0.630000 1.870000 0.627654 0.500000 4.100000e-01 0.610000 0.510000 0.515710 0.500000 0 0.450000 0.570000 MARK2 2011 broad.mit.edu 37 11 63665747 63665747 + Missense_Mutation SNP A A G TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr11:63665747A>G ENST00000509502.2 + 4 696 c.233A>G c.(232-234)aAc>aGc p.N78S MARK2_ENST00000413835.2_Missense_Mutation_p.N111S|MARK2_ENST00000513765.2_Missense_Mutation_p.N78S|MARK2_ENST00000425897.2_Missense_Mutation_p.N78S|MARK2_ENST00000502399.3_Missense_Mutation_p.N111S|MARK2_ENST00000408948.3_Missense_Mutation_p.N78S|MARK2_ENST00000350490.7_Missense_Mutation_p.N111S|MARK2_ENST00000361128.5_Missense_Mutation_p.N111S|MARK2_ENST00000377810.3_Missense_Mutation_p.N78S|MARK2_ENST00000402010.2_Missense_Mutation_p.N111S|MARK2_ENST00000508192.1_Missense_Mutation_p.N111S|MARK2_ENST00000377809.4_Missense_Mutation_p.N111S|MARK2_ENST00000315032.8_Missense_Mutation_p.N111S NM_017490.3 NP_059672.2 MAP/microtubule affinity-regulating kinase 2 33 AATCATCCCAACATAGGTGAG 0.478000 0 SO:0001583 missense ENST00000509502.2 0 1 hg19 CCDS41665.1 . . . . . . . . . . A 25.9 4.683613 0.88639 . . ENSG00000072518 ENST00000402010;ENST00000315032;ENST00000377809;ENST00000413835;ENST00000377810;ENST00000508192;ENST00000361128;ENST00000350490;ENST00000502399;ENST00000543220;ENST00000540169;ENST00000509502;ENST00000513765;ENST00000408948;ENST00000425897 T;T;T;T;T;T;T;T;T;T;T;T;T;T 0.35048 1.33;1.33;1.33;1.33;1.33;1.33;1.33;1.33;1.33;1.33;1.33;1.33;1.33;1.33 5.17 5.17 0.71159 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 T 0.62036 0.2395 M 0.80508 2.5 0.80722 D 1 D;D;P;D;D;D 0.89917 1.0;0.998;0.939;0.999;1.0;0.987 D;P;P;D;D;P 0.87578 0.996;0.796;0.448;0.982;0.998;0.719 T 0.67677 -0.5609 10 0.87932 D 0 . 14.1235 0.65205 1.0:0.0:0.0:0.0 . 78;78;111;111;111;111 E7ETY4;Q7KZI7-14;Q7KZI7-15;Q7KZI7-5;Q7KZI7;Q7KZI7-16 .;.;.;.;MARK2_HUMAN;. S 111;111;111;111;78;111;111;111;111;78;78;78;78;78;78 ENSP00000385751:N111S;ENSP00000326632:N111S;ENSP00000367040:N111S;ENSP00000389184:N111S;ENSP00000367041:N78S;ENSP00000425765:N111S;ENSP00000355091:N111S;ENSP00000294247:N111S;ENSP00000444956:N78S;ENSP00000437509:N78S;ENSP00000423974:N78S;ENSP00000421075:N78S;ENSP00000386128:N78S;ENSP00000415494:N78S ENSP00000326632:N111S N + 2 0 MARK2 63422323 1.000000 0.71417 1.000000 0.80357 0.937000 0.57800 9.117000 0.94347 2.171000 0.68590 0.460000 0.39030 AAC TCGA-FB-AAQ6-01A-11D-A40W-08 MARK2-003 NOVEL basic|appris_candidate_longest|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000360862.2 0 0 0 174 503 0 229 1 9.638870e-01 8 10 0 229 2 1 1.000000 171 498 0 228 2 -20.000000 1 1 0 0 1 0 0 0 2.071234 0 0.630000 1.870000 0.627654 0.800000 7.000000e-01 0.910000 0.810000 0.812325 0.800000 0 0.750000 0.860000 RNF169 254225 broad.mit.edu 37 11 74521280 74521280 + Nonsense_Mutation SNP A A T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr11:74521280A>T ENST00000299563.4 + 3 641 c.628A>T c.(628-630)Aag>Tag p.K210* NM_001098638.1 NP_001092108.1 Q8NCN4 RN169_HUMAN ring finger protein 169 15 TCAAATCCACAAGCTGTTACC 0.348000 0 SO:0001587 stop_gained ENST00000299563.4 0 1 hg19 CCDS41691.1 . . . . . . . . . . A 28.3 4.909386 0.92107 . . ENSG00000166439 ENST00000299563 . . . 5.89 5.89 0.94794 . 0.177649 0.48767 D 0.000167 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -10.116 12.7076 0.57070 1.0:0.0:0.0:0.0 . . . . X 210 . ENSP00000299563:K210X K + 1 0 RNF169 74198928 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 5.003000 0.63959 2.254000 0.74563 0.533000 0.62120 AAG TCGA-FB-AAQ6-01A-11D-A40W-08 RNF169-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000384741.1 0 0 0 5 419 0 206 0 3.279782e-03 0 6 0 206 2 1 0.935930 5 414 0 206 2 -3.144458 1 1 0 0 1 0 0 0 2.071234 0 0.630000 1.870000 0.627654 0.030000 0 0.080000 0.040000 0.044106 0.030000 0 0.010000 0.060000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 0 1 hg19 CCDS8703.1 . . . . . . . . . . C 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-FB-AAQ6-01A-11D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 0 0 0 48 170 0 100 1 8.133115e-01 8 5 0 100 2 1 1.000000 47 170 0 100 2 -20.000000 1 1 0 0 1 0 0 0 2.011783 0 0.630000 1.870000 0.615465 0.660000 5.100000e-01 0.840000 0.670000 0.678396 0.660000 0 0.580000 0.760000 KRT82 3888 broad.mit.edu 37 12 52793858 52793858 + Missense_Mutation SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr12:52793858C>T ENST00000257974.2 - 5 930 c.853G>A c.(853-855)Gtg>Atg p.V285M RP3-416H24.4_ENST00000547174.1_RNA NM_033033.3 NP_149022.3 Q9NSB4 KRT82_HUMAN keratin 82 p.V285M(1) 29 ATGCCGTCCACGTCCAGCTCC 0.612000 1 Substitution - Missense(1) SO:0001583 missense ENST00000257974.2 0 1 hg19 CCDS8826.1 . . . . . . . . . . C 0.082 -1.181497 0.01633 . . ENSG00000161850 ENST00000257974 D 0.88586 -2.4 5.18 1.04 0.20106 Filament (1); 0.532611 0.15770 N 0.245495 T 0.53916 0.1826 N 0.00186 -1.895 0.27603 N 0.948893 B 0.24533 0.105 B 0.21151 0.033 T 0.58393 -0.7644 10 0.10111 T 0.7 . 1.6566 0.02782 0.1103:0.3451:0.2299:0.3147 . 285 Q9NSB4 KRT82_HUMAN M 285 ENSP00000257974:V285M ENSP00000257974:V285M V - 1 0 KRT82 51080125 0.002000 0.14202 0.002000 0.10522 0.523000 0.34469 -0.851000 0.04313 0.300000 0.22699 0.561000 0.74099 GTG TCGA-FB-AAQ6-01A-11D-A40W-08 KRT82-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405189.1 0 0 0 6 267 0 74 0 0 0 0 74 2 1 0.962547 6 260 0 74 2 -3.866182 1 1 121412 9 41 1 0 0 0 2.011783 0 0.630000 1.870000 0.615465 0.060000 2.000000e-02 0.140000 0.070000 0.077596 0.060000 0 0.040000 0.110000 C12orf66 144577 broad.mit.edu 37 12 64609707 64609707 + Missense_Mutation SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr12:64609707C>T ENST00000398055.3 - 2 325 c.272G>A c.(271-273)cGc>cAc p.R91H C12orf66_ENST00000311915.8_Missense_Mutation_p.R91H|C12orf66_ENST00000544871.1_Missense_Mutation_p.R38H NM_152440.4 NP_689653 Q96MD2 CL066_HUMAN chromosome 12 open reading frame 66 p.R91H(1) 5 ATAGATGGTGCGGATGGAATC 0.507000 1 Substitution - Missense(1) SO:0001583 missense ENST00000398055.3 0 1 hg19 CCDS41803.1 . . . . . . . . . . C 25.1 4.605524 0.87157 . . ENSG00000174206 ENST00000311915;ENST00000544871;ENST00000398055 T;T;T 0.42131 0.98;0.98;0.98 5.73 4.84 0.62591 . 0.000000 0.85682 D 0.000000 T 0.57681 0.2070 L 0.59436 1.845 0.58432 D 0.999999 D;D 0.76494 0.98;0.999 P;D 0.64144 0.586;0.922 T 0.57631 -0.7778 9 . . . -9.8646 14.7258 0.69343 0.0:0.9305:0.0:0.0695 . 38;91 F5H2Q3;Q96MD2 .;CL066_HUMAN H 91;38;91 ENSP00000311486:R91H;ENSP00000445481:R38H;ENSP00000381132:R91H . R - 2 0 C12orf66 62895974 1.000000 0.71417 1.000000 0.80357 0.892000 0.51952 7.518000 0.81795 1.428000 0.47296 0.491000 0.48974 CGC TCGA-FB-AAQ6-01A-11D-A40W-08 C12orf66-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400921.1 0 0 0 28 97 0 35 0 5.351870e-02 0 2 0 35 2 1 1.000000 27 91 0 34 2 -20.000000 1 1 120926 1 25 1 0 0 0 2.011783 0 0.630000 1.870000 0.615465 0.680000 4.800000e-01 0.910000 0.680000 0.693802 0.680000 0 0.570000 0.800000 KCNC2 3747 broad.mit.edu 37 12 75601178 75601178 + Missense_Mutation SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr12:75601178C>T ENST00000549446.1 - 2 1266 c.586G>A c.(586-588)Gcg>Acg p.A196T KCNC2_ENST00000540018.1_Missense_Mutation_p.A196T|KCNC2_ENST00000548513.1_Missense_Mutation_p.A196T|KCNC2_ENST00000341669.3_Missense_Mutation_p.A196T|KCNC2_ENST00000298972.1_Missense_Mutation_p.A196T|KCNC2_ENST00000350228.2_Missense_Mutation_p.A196T|KCNC2_ENST00000393288.2_Missense_Mutation_p.A196T|KCNC2_ENST00000550433.1_Missense_Mutation_p.A196T NM_001260497.1|NM_139137.3 NP_001247426.1|NP_631875.1 Q96PR1 KCNC2_HUMAN potassium voltage-gated channel, Shaw-related subfamily, member 2 54 Dalfampridine(DB06637) CCGAGCCCCGCCGCGTCCTCG 0.716000 0 SO:0001583 missense ENST00000549446.1 0 1 hg19 CCDS9007.1 . . . . . . . . . . C 11.38 1.621045 0.28889 . . ENSG00000166006 ENST00000550433;ENST00000548513;ENST00000549446;ENST00000341669;ENST00000298972;ENST00000350228;ENST00000540018;ENST00000393288 D;D;D;D;D;D;D;D 0.97328 -4.33;-4.33;-4.32;-4.33;-4.33;-4.32;-4.32;-4.34 4.44 2.54 0.30619 . . . . . D 0.92264 0.7546 N 0.08118 0 0.39638 D 0.970289 B;P;B;P;B 0.40332 0.403;0.551;0.411;0.713;0.051 B;B;B;P;B 0.46299 0.04;0.356;0.08;0.511;0.062 D 0.87929 0.2709 9 0.21540 T 0.41 . 9.6841 0.40087 0.1599:0.6863:0.1538:0.0 . 196;196;196;196;196 F5H030;Q96PR1-2;Q96PR1;Q96PR1-4;Q96PR1-3 .;.;KCNC2_HUMAN;.;. T 196 ENSP00000448301:A196T;ENSP00000449941:A196T;ENSP00000449253:A196T;ENSP00000340121:A196T;ENSP00000298972:A196T;ENSP00000319877:A196T;ENSP00000438423:A196T;ENSP00000376966:A196T ENSP00000298972:A196T A - 1 0 KCNC2 73887445 0.222000 0.23652 0.681000 0.30009 0.804000 0.45430 1.796000 0.38794 0.557000 0.29117 -0.165000 0.13383 GCG TCGA-FB-AAQ6-01A-11D-A40W-08 KCNC2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000405581.2 0 0 0 13 35 0 8 0 0 0 0 8 2 1 0.999704 13 33 0 7 2 -20.000000 1 0 119846 2 36 1 0 0 0 2.011783 0 0.630000 1.870000 0.615465 0.820000 4.900000e-01 1.000000 1.000000 0.820462 0.820000 0 0.640000 1.000000 TRPM1 4308 broad.mit.edu 37 15 31334358 31334358 + Missense_Mutation SNP C C A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr15:31334358C>A ENST00000256552.6 - 17 2030 c.1883G>T c.(1882-1884)aGt>aTt p.S628I TRPM1_ENST00000397795.2_Missense_Mutation_p.S606I|TRPM1_ENST00000542188.1_Missense_Mutation_p.S645I|RP11-348B17.1_ENST00000561299.1_RNA NM_001252024.1 NP_001238953.1 transient receptor potential cation channel, subfamily M, member 1 99 all_lung(180;1.92e-11) CTGGAACCGACTCACGGCAGG 0.517000 0 SO:0001583 missense ENST00000256552.6 0 1 hg19 CCDS58346.1 . . . . . . . . . . C 22.1 4.240885 0.79912 . . ENSG00000134160 ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793 T;T;T 0.69926 -0.44;-0.44;-0.44 4.72 4.72 0.59763 . 0.042793 0.85682 D 0.000000 T 0.62196 0.2408 L 0.40543 1.245 0.80722 D 1 B;P 0.34934 0.137;0.476 B;B 0.36186 0.219;0.157 T 0.67995 -0.5526 10 0.87932 D 0 -20.8878 18.0463 0.89334 0.0:1.0:0.0:0.0 . 600;606 Q7Z4N2-3;Q7Z4N2 .;TRPM1_HUMAN I 606;645;628;606 ENSP00000380897:S606I;ENSP00000437849:S645I;ENSP00000256552:S628I ENSP00000256552:S628I S - 2 0 TRPM1 29121650 1.000000 0.71417 0.905000 0.35620 0.749000 0.42624 7.743000 0.85020 2.304000 0.77564 0.655000 0.94253 AGT TCGA-FB-AAQ6-01A-11D-A40W-08 TRPM1-004 PUTATIVE basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000417166.2 0 0 0 42 82 0 37 0 0 0 0 37 2 1 1.000000 40 80 0 37 2 -20.000000 1 1 0 0 1 0 0 0 2.074389 0 0.630000 1.870000 0.627654 0.990000 8.100000e-01 1.000000 1.000000 0.975902 0.990000 1 0.930000 1.000000 LCMT2 9836 broad.mit.edu 37 15 43621570 43621570 + Missense_Mutation SNP G G C TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr15:43621570G>C ENST00000305641.5 - 1 1233 c.1118C>G c.(1117-1119)gCa>gGa p.A373G LCMT2_ENST00000544735.1_5'UTR|LCMT2_ENST00000567039.1_3'UTR|ADAL_ENST00000428046.3_5'Flank|ADAL_ENST00000422466.2_5'Flank|ADAL_ENST00000389651.4_5'Flank NM_014793.4 NP_055608.2 O60294 TYW4_HUMAN leucine carboxyl methyltransferase 2 20 all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215) L-Leucine(DB00149) AAATCCTCCTGCACTGAGAAT 0.547000 0 SO:0001583 missense ENST00000305641.5 0 1 hg19 CCDS10094.1 . . . . . . . . . . G 12.64 1.998347 0.35226 . . ENSG00000168806 ENST00000305641 T 0.74526 -0.85 5.54 4.62 0.57501 . 0.176134 0.48767 D 0.000180 T 0.64821 0.2633 L 0.47716 1.5 0.31690 N 0.642009 B 0.28128 0.201 B 0.27608 0.081 T 0.65001 -0.6274 10 0.23302 T 0.38 -14.2982 10.1028 0.42515 0.0895:0.0:0.9105:0.0 . 373 O60294 LCMT2_HUMAN G 373 ENSP00000307214:A373G ENSP00000307214:A373G A - 2 0 LCMT2 41408862 0.163000 0.22920 0.377000 0.26055 0.889000 0.51656 2.230000 0.42999 1.573000 0.49748 0.655000 0.94253 GCA TCGA-FB-AAQ6-01A-11D-A40W-08 LCMT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253205.1 0 0 0 69 143 0 53 0 0 0 1 0 53 2 1 1.000000 68 142 0 52 2 -20.000000 1 1 0 0 1 0 0 0 2.091669 0 0.630000 1.870000 0.630000 0.990000 8.300000e-01 1.000000 1.000000 0.975003 0.990000 1 0.920000 1.000000 CHRNB4 1143 broad.mit.edu 37 15 78921685 78921685 + Missense_Mutation SNP T T G TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr15:78921685T>G ENST00000261751.3 - 5 1073 c.962A>C c.(961-963)cAc>cCc p.H321P RP11-335K5.2_ENST00000559120.1_RNA|CHRNB4_ENST00000560511.1_5'Flank|CHRNB4_ENST00000412074.2_Intron NM_000750.3 NP_000741.1 P30926 ACHB4_HUMAN cholinergic receptor, nicotinic, beta 4 (neuronal) 22 Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090) GGGCGAGCGGTGGTGCACATT 0.607000 0 SO:0001583 missense ENST00000261751.3 0 1 hg19 CCDS10306.1 . . . . . . . . . . T 23.0 4.366726 0.82463 . . ENSG00000117971 ENST00000261751 T 0.72282 -0.64 5.57 5.57 0.84162 Neurotransmitter-gated ion-channel transmembrane domain (2); 0.000000 0.85682 D 0.000000 D 0.90048 0.6892 H 0.98133 4.155 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.93552 0.6887 10 0.72032 D 0.01 . 15.3749 0.74596 0.0:0.0:0.0:1.0 . 321 P30926 ACHB4_HUMAN P 321 ENSP00000261751:H321P ENSP00000261751:H321P H - 2 0 CHRNB4 76708740 1.000000 0.71417 1.000000 0.80357 0.981000 0.71138 7.987000 0.88182 2.130000 0.65690 0.533000 0.62120 CAC TCGA-FB-AAQ6-01A-11D-A40W-08 CHRNB4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000290108.1 0 0 0 65 156 0 69 0 0 0 0 69 2 1 1.000000 62 156 0 68 2 -20.000000 1 1 0 0 1 0 0 0 2.091669 0 0.630000 1.870000 0.630000 0.920000 7.400000e-01 1.000000 1.000000 0.921619 0.920000 1 0.830000 1.000000 ALPK3 57538 broad.mit.edu 37 15 85384098 85384098 + Silent SNP C C A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr15:85384098C>A ENST00000258888.5 + 5 2361 c.2194C>A c.(2194-2196)Cgg>Agg p.R732R NM_020778.4 NP_065829.3 Q96L96 ALPK3_HUMAN alpha-kinase 3 81 BRCA - Breast invasive adenocarcinoma(143;0.0587) GCCCCCTGCCCGGCGGAGACA 0.647000 0 SO:0001819 synonymous_variant ENST00000258888.5 0 1 hg19 CCDS10333.1 TCGA-FB-AAQ6-01A-11D-A40W-08 ALPK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000308997.1 0 0 0 57 114 0 34 0 0 0 0 34 2 1 1.000000 58 111 0 33 2 -7.678165 1 1 0 0 1 0 0 0 2.091669 0 0.630000 1.870000 0.630000 0.990000 8.300000e-01 1.000000 1.000000 0.979104 0.990000 1 0.940000 1.000000 ATF7IP2 80063 broad.mit.edu 37 16 10524582 10524582 + Silent SNP T T C TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr16:10524582T>C ENST00000396560.2 + 3 332 c.105T>C c.(103-105)gtT>gtC p.V35V ATF7IP2_ENST00000356427.2_Silent_p.V35V|ATF7IP2_ENST00000324570.5_Silent_p.V35V|ATF7IP2_ENST00000396559.1_Silent_p.V35V|ATF7IP2_ENST00000543967.1_Intron NM_024997.3 NP_079273.2 Q5U623 MCAF2_HUMAN activating transcription factor 7 interacting protein 2 3 CAAGGAATGTTGAAGCGCTGA 0.413000 0 SO:0001819 synonymous_variant ENST00000396560.2 0 1 hg19 CCDS10540.1 TCGA-FB-AAQ6-01A-11D-A40W-08 ATF7IP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251961.1 0 0 0 89 199 0 98 0 0 0 1 0 98 2 1 1.000000 88 196 0 97 2 -20.000000 1 1 0 0 1 1 2 3 2.104910 0 0.630000 1.870000 0.631162 0.970000 8.100000e-01 1.000000 1.000000 0.958115 0.970000 1 0.890000 1.000000 MED1 5469 broad.mit.edu 37 17 37564572 37564572 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr17:37564572G>A ENST00000300651.6 - 17 4125 c.3902C>T c.(3901-3903)cCg>cTg p.P1301L CTB-131K11.1_ENST00000582842.1_RNA|MED1_ENST00000394287.3_Intron NM_004774.3 NP_004765.2 O95243 MBD4_HUMAN mediator complex subunit 1 59 Ovarian(249;1.78e-06)|Lung SC(565;0.0262) Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146) TGTCAAGGACGGCTTCTTGTT 0.522000 HNSCC(31;0.082) Pancreas(21;279 768 2492 4877 24026) 0 SO:0001583 missense ENST00000300651.6 0 1 hg19 CCDS11336.1 . . . . . . . . . . G 19.34 3.808847 0.70797 . . ENSG00000125686 ENST00000300651 T 0.56275 0.47 5.07 5.07 0.68467 . . . . . T 0.62146 0.2404 N 0.24115 0.695 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 T 0.66618 -0.5878 9 0.87932 D 0 -5.6283 19.0071 0.92856 0.0:0.0:1.0:0.0 . 1301 Q15648 MED1_HUMAN L 1301 ENSP00000300651:P1301L ENSP00000300651:P1301L P - 2 0 MED1 34818098 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.290000 0.96065 2.793000 0.96121 0.563000 0.77884 CCG TCGA-FB-AAQ6-01A-11D-A40W-08 MED1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256943.3 0 0 0 101 238 0 119 1 7.972502e-01 3 6 0 119 2 1 1.000000 101 233 0 116 2 -7.928147 1 1 121412 2 34 1 1 2 3 2.138624 0 0.630000 1.870000 0.634604 0.950000 8.000000e-01 1.000000 1.000000 0.945571 0.950000 1 0.870000 1.000000 PLD2 5338 broad.mit.edu 37 17 4712837 4712837 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr17:4712837G>A ENST00000263088.6 + 7 736 c.605G>A c.(604-606)cGc>cAc p.R202H RP11-81A22.5_ENST00000571067.1_lincRNA|PLD2_ENST00000572940.1_Missense_Mutation_p.R202H NM_001243108.1|NM_002663.4 NP_001230037.1|NP_002654.3 O14939 PLD2_HUMAN phospholipase D2 31 Choline(DB00122) GACTTGGGCCGCAAAGGACTG 0.567000 0 SO:0001583 missense ENST00000263088.6 0 1 hg19 CCDS11057.1 . . . . . . . . . . G 12.45 1.940910 0.34283 . . ENSG00000129219 ENST00000263088 T 0.06449 3.3 5.1 0.825 0.18824 . 0.567307 0.19886 N 0.103853 T 0.02610 0.0079 N 0.04508 -0.205 0.19775 N 0.99996 B;B;B 0.21225 0.053;0.041;0.01 B;B;B 0.12156 0.001;0.007;0.002 T 0.48151 -0.9060 10 0.15499 T 0.54 -1.3847 9.5998 0.39596 0.0:0.495:0.426:0.079 . 59;202;202 B7Z905;O14939-2;O14939 .;.;PLD2_HUMAN H 202 ENSP00000263088:R202H ENSP00000263088:R202H R + 2 0 PLD2 4659801 0.761000 0.28439 0.852000 0.33557 0.645000 0.38454 1.825000 0.39081 0.056000 0.16144 -0.311000 0.09066 CGC TCGA-FB-AAQ6-01A-11D-A40W-08 PLD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207561.3 0 0 0 5 290 0 144 0 9.115596e-03 0 7 0 144 2 1 0.935801 6 285 0 144 2 -2.032427 0 1 121412 1 36 1 0 1 1 1.473699 1 0.630000 1.870000 0.474357 0.030000 1.000000e-02 0.080000 0.040000 0.044969 0.030000 0 0.020000 0.060000 TP53 7157 broad.mit.edu 37 17 7577538 7577538 + Missense_Mutation SNP C C T rs11540652 TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr17:7577538C>T ENST00000269305.4 - 7 932 c.743G>A c.(742-744)cGg>cAg p.R248Q TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GATGGGCCTCCGGTTCATGCC 0.572000 R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE) 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 725 Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1) GRCh37 CM920675 TP53 M rs11540652 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 0 1 hg19 CCDS11118.1 . . . . . . . . . . C 27.3 4.822907 0.90873 0.0 1.16E-4 ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944 D;D;D;D;D;D;D;D 0.99864 -7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28 4.62 3.65 0.41850 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99840 0.9927 M 0.88640 2.97 0.58432 A 0.999994 D;D;D;D;D;D 0.89917 1.0;0.994;1.0;1.0;1.0;1.0 D;P;D;D;D;D 0.91635 0.996;0.882;0.999;0.995;0.996;0.995 D 0.96819 0.9602 9 0.72032 D 0.01 -9.5643 10.6687 0.45745 0.0:0.9059:0.0:0.0941 rs11540652;rs11540652 248;248;155;248;248;248 P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;P53_HUMAN;.;. Q 248;248;248;248;248;248;237;155;116;155 ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q ENSP00000269305:R248Q R - 2 0 TP53 7518263 1.000000 0.71417 1.000000 0.80357 0.887000 0.51463 5.884000 0.69729 1.305000 0.44909 0.462000 0.41574 CGG TCGA-FB-AAQ6-01A-11D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 0 0 0 34 138 0 79 1 9.753028e-01 11 16 0 79 2 1 1.000000 34 137 0 78 2 -2.879491 1 1 121412 7 38 1 0 1 1 1.466783 1 0.630000 1.870000 0.469610 0.430000 3.100000e-01 0.570000 0.440000 0.442560 0.430000 0 0.370000 0.510000 SMAD4 4089 broad.mit.edu 37 18 48591891 48591891 + Nonsense_Mutation SNP G G T rs121912581 TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr18:48591891G>T ENST00000342988.3 + 9 1592 c.1054G>T c.(1054-1056)Gga>Tga p.G352* SMAD4_ENST00000588745.1_Nonsense_Mutation_p.G256*|SMAD4_ENST00000398417.2_Nonsense_Mutation_p.G352* NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(2) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) TACTGTTGATGGATACGTGGA 0.443000 38 Whole gene deletion(36)|Unknown(2) GRCh37 CM024126 SMAD4 M rs121912581 SO:0001587 stop_gained ENST00000342988.3 0 1 hg19 CCDS11950.1 . . . . . . . . . . G 43 10.484127 0.99413 . . ENSG00000141646 ENST00000342988;ENST00000544926;ENST00000398417 . . . 5.86 5.86 0.93980 . 0.048668 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.87932 D 0 . 18.9646 0.92691 0.0:0.0:1.0:0.0 . . . . X 352 . ENSP00000341551:G352X G + 1 0 SMAD4 46845889 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.676000 0.98643 2.771000 0.95319 0.563000 0.77884 GGA TCGA-FB-AAQ6-01A-11D-A40W-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 0 0 0 112 184 0 165 1 9.077216e-01 2 7 0 165 2 1 1.000000 111 184 0 165 2 -14.850890 1 1 0 0 1 0 1 1 1.460212 1 0.630000 1.870000 0.459854 0.810000 6.900000e-01 0.930000 0.820000 0.820954 0.810000 0 0.750000 0.880000 SMAD4 4089 broad.mit.edu 37 18 48591892 48591892 + Missense_Mutation SNP G G T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr18:48591892G>T ENST00000342988.3 + 9 1593 c.1055G>T c.(1054-1056)gGa>gTa p.G352V SMAD4_ENST00000588745.1_Missense_Mutation_p.G256V|SMAD4_ENST00000398417.2_Missense_Mutation_p.G352V NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(2) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) ACTGTTGATGGATACGTGGAC 0.443000 38 Whole gene deletion(36)|Unknown(2) SO:0001583 missense ENST00000342988.3 0 1 hg19 CCDS11950.1 . . . . . . . . . . G 25.3 4.624653 0.87560 . . ENSG00000141646 ENST00000342988;ENST00000544926;ENST00000398417 D;D 0.98329 -4.87;-4.87 5.86 4.99 0.66335 SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3); 0.048668 0.85682 D 0.000000 D 0.99193 0.9720 H 0.94964 3.605 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.99056 1.0829 10 0.87932 D 0 . 13.6642 0.62384 0.075:0.0:0.925:0.0 . 352 Q13485 SMAD4_HUMAN V 352 ENSP00000341551:G352V;ENSP00000381452:G352V ENSP00000341551:G352V G + 2 0 SMAD4 46845890 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.828000 0.86729 1.474000 0.48178 0.563000 0.77884 GGA TCGA-FB-AAQ6-01A-11D-A40W-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 0 0 0 114 181 0 163 1 9.153421e-01 2 7 0 163 2 1 1.000000 113 181 0 163 2 -20.000000 1 1 0 0 1 0 1 1 1.460212 1 0.630000 1.870000 0.459854 0.830000 7.100000e-01 0.950000 0.840000 0.837827 0.830000 0 0.770000 0.900000 MYO9B 4650 broad.mit.edu 37 19 17295729 17295729 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr19:17295729G>A ENST00000594824.1 + 17 2576 c.2429G>A c.(2428-2430)cGc>cAc p.R810H MYO9B_ENST00000397274.2_Missense_Mutation_p.R810H|MYO9B_ENST00000595618.1_Missense_Mutation_p.R810H Q13459 MYO9B_HUMAN myosin IXB p.R810H(2) 39 CTGCACGACCGCACCACCAAG 0.582000 2 Substitution - Missense(2) SO:0001583 missense ENST00000594824.1 0 1 hg19 . . . . . . . . . . G 27.9 4.871098 0.91587 . . ENSG00000099331 ENST00000397274 T 0.72835 -0.69 5.12 5.12 0.69794 Myosin head, motor domain (2); 0.000000 0.53938 D 0.000056 D 0.84220 0.5424 M 0.77313 2.365 0.58432 D 0.999994 D;D;D 0.89917 0.999;0.999;1.0 D;D;D 0.97110 0.964;0.964;1.0 D 0.84405 0.0562 10 0.42905 T 0.14 . 17.579 0.87960 0.0:0.0:1.0:0.0 . 810;810;816 Q13459;B0I1T6;Q4LE74 MYO9B_HUMAN;.;. H 810 ENSP00000380444:R810H ENSP00000380444:R810H R + 2 0 MYO9B 17156729 1.000000 0.71417 0.985000 0.45067 0.788000 0.44548 9.674000 0.98633 2.395000 0.81488 0.561000 0.74099 CGC TCGA-FB-AAQ6-01A-11D-A40W-08 MYO9B-002 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000463236.1 0 0 0 5 427 0 121 0 2.796942e-02 0 18 0 121 2 1 0.935567 5 421 0 118 2 -2.375082 0 1 0 0 1 0 0 0 2.047941 0 0.630000 1.870000 0.625279 0.030000 0 0.080000 0.040000 0.042996 0.030000 0 0.010000 0.060000 GNA15 2769 broad.mit.edu 37 19 3162865 3162865 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr19:3162865G>A ENST00000262958.3 + 7 1231 c.973G>A c.(973-975)Gac>Aac p.D325N NM_002068.2 NP_002059.2 P30679 GNA15_HUMAN guanine nucleotide binding protein (G protein), alpha 15 (Gq class) 18 Hepatocellular(1079;0.137) CGGGTGCGTGGACGGCCCCGA 0.597000 OREG0025150 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000262958.3 0 1 hg19 CCDS12104.1 . . . . . . . . . . g 9.418 1.082262 0.20309 . . ENSG00000060558 ENST00000262958 D 0.88509 -2.39 3.67 2.6 0.31112 . 0.720175 0.11882 N 0.520430 T 0.80919 0.4716 N 0.14661 0.345 0.09310 N 1 B 0.30542 0.284 B 0.33568 0.166 T 0.71797 -0.4484 10 0.59425 D 0.04 . 10.6388 0.45582 0.0:0.1971:0.8029:0.0 . 325 P30679 GNA15_HUMAN N 325 ENSP00000262958:D325N ENSP00000262958:D325N D + 1 0 GNA15 3113865 0.109000 0.22037 0.004000 0.12327 0.002000 0.02628 3.225000 0.51246 0.722000 0.32252 0.561000 0.74099 GAC TCGA-FB-AAQ6-01A-11D-A40W-08 GNA15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452320.2 0 0 0 76 162 0 61 1 9.999994e-01 21 29 0 61 2 1 1.000000 75 156 0 61 2 -20.000000 1 1 0 0 1 0 0 0 2.047941 0 0.630000 1.870000 0.625279 0.990000 8.100000e-01 1.000000 1.000000 0.963938 0.990000 1 0.900000 1.000000 PRX 57716 broad.mit.edu 37 19 40901569 40901569 + Missense_Mutation SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr19:40901569C>T ENST00000324001.7 - 7 2960 c.2690G>A c.(2689-2691)cGa>cAa p.R897Q PRX_ENST00000291825.7_3'UTR NM_181882.2 NP_870998.2 Q9BXM0 PRAX_HUMAN periaxin 47 Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384) AGAGGGCACTCGGAAGCCCAC 0.612000 0 SO:0001583 missense ENST00000324001.7 0 1 hg19 CCDS33028.1 . . . . . . . . . . C 12.42 1.931525 0.34096 . . ENSG00000105227 ENST00000324001;ENST00000341562 T 0.01099 5.34 5.3 4.21 0.49690 . 0.354983 0.20353 N 0.094003 T 0.00724 0.0024 N 0.17082 0.46 0.37414 D 0.913344 B 0.33494 0.414 B 0.21360 0.034 T 0.64554 -0.6380 10 0.29301 T 0.29 -8.6739 4.1775 0.10358 0.0:0.6832:0.0:0.3168 . 897 Q9BXM0 PRAX_HUMAN Q 897 ENSP00000326018:R897Q ENSP00000326018:R897Q R - 2 0 PRX 45593409 0.000000 0.05858 0.928000 0.36995 0.979000 0.70002 0.904000 0.28491 2.496000 0.84212 0.650000 0.86243 CGA TCGA-FB-AAQ6-01A-11D-A40W-08 PRX-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000462582.1 0 0 0 99 296 0 108 0 6.392162e-02 0 2 0 108 2 1 1.000000 98 293 0 107 2 -5.000543 1 1 121410 6 39 1 0 0 0 2.047941 0 0.630000 1.870000 0.625279 0.780000 6.500000e-01 0.920000 0.790000 0.788343 0.780000 0 0.710000 0.850000 PGLYRP1 8993 broad.mit.edu 37 19 46522861 46522861 + Missense_Mutation SNP C C G TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr19:46522861C>G ENST00000008938.4 - 2 375 c.332G>C c.(331-333)tGg>tCg p.W111S CCDC61_ENST00000601763.1_Intron|MIR769_ENST00000390225.1_RNA NM_005091.2 NP_005082.1 O75594 PGRP1_HUMAN peptidoglycan recognition protein 1 10 all_neural(266;0.113)|Ovarian(192;0.127) CGTGAAGTTCCAGCCACGGCC 0.582000 0 SO:0001583 missense ENST00000008938.4 0 1 hg19 CCDS12680.1 . . . . . . . . . . C 13.11 2.139492 0.37728 . . ENSG00000008438 ENST00000008938 T 0.49720 0.77 5.01 5.01 0.66863 Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4); 0.000000 0.56097 D 0.000027 T 0.74921 0.3780 M 0.92268 3.29 0.58432 D 0.999999 D 0.89917 1.0 D 0.97110 1.0 T 0.81551 -0.0881 10 0.87932 D 0 -27.3543 13.8728 0.63629 0.0:1.0:0.0:0.0 . 111 O75594 PGRP1_HUMAN S 111 ENSP00000008938:W111S ENSP00000008938:W111S W - 2 0 PGLYRP1 51214701 1.000000 0.71417 0.996000 0.52242 0.011000 0.07611 3.970000 0.56824 2.335000 0.79485 0.650000 0.86243 TGG TCGA-FB-AAQ6-01A-11D-A40W-08 PGLYRP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461695.1 0 0 0 5 186 0 69 0 0 0 0 69 2 1 0.933934 5 181 0 68 2 -6.971575 1 1 0 0 1 0 0 0 2.047941 0 0.630000 1.870000 0.625279 0.080000 2.000000e-02 0.180000 0.080000 0.097147 0.080000 0 0.050000 0.130000 UHRF1 29128 broad.mit.edu 37 19 4910731 4910731 + RNA SNP C C A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr19:4910731C>A ENST00000592666.1 + 0 566 Q96T88 UHRF1_HUMAN ubiquitin-like with PHD and ring finger domains 1 16 GTGTCTGGTCCTGGCCAGGGT 0.502000 0 ENST00000592666.1 0 1 hg19 TCGA-FB-AAQ6-01A-11D-A40W-08 UHRF1-006 KNOWN sequence_error|basic processed_transcript processed_transcript OTTHUMT00000450444.1 0 0 0 17 27 0 10 0 0 0 0 10 2 1 0.999987 17 24 0 10 2 -20.000000 1 1 0 0 1 0 0 0 2.047941 0 0.630000 1.870000 0.625279 0.990000 7.800000e-01 1.000000 1.000000 0.981272 0.990000 1 0.980000 1.000000 XAB2 56949 broad.mit.edu 37 19 7686089 7686089 + Missense_Mutation SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr19:7686089C>T ENST00000358368.4 - 13 1749 c.1712G>A c.(1711-1713)cGc>cAc p.R571H XAB2_ENST00000534844.1_Missense_Mutation_p.R568H NM_020196.2 NP_064581.2 Q9HCS7 SYF1_HUMAN XPA binding protein 2 26 CTCCAGCTTGCGGCCCCCATA 0.627000 Direct reversal of damage;Nucleotide excision repair (NER) 0 SO:0001583 missense ENST00000358368.4 0 1 hg19 CCDS32892.1 . . . . . . . . . . C 16.68 3.190993 0.58017 4.54E-4 0.0 ENSG00000076924 ENST00000358368;ENST00000534844 T;T 0.03553 3.89;3.89 4.32 3.27 0.37495 Tetratricopeptide-like helical (1); 0.079176 0.49305 D 0.000157 T 0.03136 0.0092 L 0.29908 0.895 0.35535 D 0.802571 P 0.43701 0.815 B 0.40165 0.321 T 0.51655 -0.8678 10 0.51188 T 0.08 -22.9882 6.2129 0.20640 0.0:0.7055:0.0:0.2945 . 571 Q9HCS7 SYF1_HUMAN H 571;568 ENSP00000351137:R571H;ENSP00000438225:R568H ENSP00000351137:R571H R - 2 0 XAB2 7592089 1.000000 0.71417 0.999000 0.59377 0.992000 0.81027 1.857000 0.39399 1.021000 0.39600 0.467000 0.42956 CGC TCGA-FB-AAQ6-01A-11D-A40W-08 XAB2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000461021.1 0 0 0 6 181 0 48 0 6.000135e-01 0 58 0 48 2 1 0.963339 6 177 0 48 2 -3.319989 1 1 121374 5 34 1 0 0 0 2.047941 0 0.630000 1.870000 0.625279 0.100000 4.000000e-02 0.210000 0.100000 0.115729 0.100000 0 0.060000 0.160000 MUC16 94025 broad.mit.edu 37 19 9064926 9064926 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr19:9064926G>A ENST00000397910.4 - 3 22723 c.22520C>T c.(22519-22521)gCa>gTa p.A7507V NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 590 GGTACCCATTGCCGATGTGGC 0.463000 0 SO:0001583 missense ENST00000397910.4 0 1 hg19 CCDS54212.1 . . . . . . . . . . N 7.534 0.659360 0.14645 . . ENSG00000181143 ENST00000397910 T 0.21932 1.98 2.91 0.462 0.16695 . . . . . T 0.09730 0.0239 N 0.08118 0 . . . B 0.22146 0.065 B 0.19148 0.024 T 0.18241 -1.0343 8 0.87932 D 0 . 5.4895 0.16769 0.0:0.2195:0.5554:0.2251 . 7507 B5ME49 . V 7507 ENSP00000381008:A7507V ENSP00000381008:A7507V A - 2 0 MUC16 8925926 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 0.221000 0.17680 0.201000 0.20466 0.508000 0.49915 GCA TCGA-FB-AAQ6-01A-11D-A40W-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 0 0 0 107 262 0 117 0 0 0 0 117 2 1 1.000000 105 255 0 116 2 -20.000000 1 1 0 0 1 0 0 0 2.047941 0 0.630000 1.870000 0.625279 0.900000 7.600000e-01 1.000000 1.000000 0.906613 0.900000 1 0.830000 0.980000 ZNF317 57693 broad.mit.edu 37 19 9271674 9271674 + Silent SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr19:9271674C>T ENST00000247956.6 + 7 1658 c.1353C>T c.(1351-1353)tgC>tgT p.C451C ZNF317_ENST00000360385.3_Silent_p.C419C NM_020933.4 NP_065984.3 Q96PQ6 ZN317_HUMAN zinc finger protein 317 27 GCGATCTCTGCGGGAAAGCTT 0.547000 0 SO:0001819 synonymous_variant ENST00000247956.6 0 1 hg19 CCDS12210.1 TCGA-FB-AAQ6-01A-11D-A40W-08 ZNF317-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000448995.1 0 0 0 41 124 0 62 1 7.478127e-01 3 7 0 62 2 1 1.000000 41 122 0 62 2 -20.000000 1 1 121412 5 38 1 0 0 0 2.047941 0 0.630000 1.870000 0.625279 0.770000 5.800000e-01 0.980000 0.780000 0.784413 0.770000 0 0.670000 0.890000 SLC6A17 388662 broad.mit.edu 37 1 110738217 110738217 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:110738217G>A ENST00000331565.4 + 10 1987 c.1502G>A c.(1501-1503)tGt>tAt p.C501Y NM_001010898.2 NP_001010898.1 Q9H1V8 S6A17_HUMAN solute carrier family 6 (neutral amino acid transporter), member 17 37 all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233) GTGGGCTGCTGTGTCTTTGCA 0.637000 0 SO:0001583 missense ENST00000331565.4 0 1 hg19 CCDS30799.1 . . . . . . . . . . G 29.2 4.983175 0.93044 . . ENSG00000197106 ENST00000331565;ENST00000450985 T 0.76186 -1.0 5.65 5.65 0.86999 . 0.000000 0.85682 D 0.000000 D 0.91808 0.7408 H 0.98629 4.285 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.94494 0.7704 10 0.87932 D 0 . 19.6998 0.96048 0.0:0.0:1.0:0.0 . 501 Q9H1V8 S6A17_HUMAN Y 501 ENSP00000330199:C501Y ENSP00000330199:C501Y C + 2 0 SLC6A17 110539740 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 9.734000 0.98822 2.657000 0.90304 0.655000 0.94253 TGT TCGA-FB-AAQ6-01A-11D-A40W-08 SLC6A17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032550.2 0 0 0 110 103 0 83 0 0 0 1 0 83 2 1 1.000000 108 101 0 82 2 -20.000000 1 1 0 0 1 0 1 1 1.628727 1 0.630000 1.870000 0.459854 0.970000 8.900000e-01 1.000000 0.990000 0.972366 0.970000 1 0.940000 1.000000 SNX27 81609 broad.mit.edu 37 1 151634647 151634647 + Silent SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:151634647C>T ENST00000458013.2 + 5 927 c.807C>T c.(805-807)taC>taT p.Y269Y SNX27_ENST00000368843.3_Silent_p.Y269Y|SNX27_ENST00000368838.1_Silent_p.Y176Y Q96L92 SNX27_HUMAN sorting nexin family member 27 5 Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185) LUSC - Lung squamous cell carcinoma(543;0.181) CCCAGAACTACAATGGTGTGT 0.418000 Colon(46;291 966 40145 41237 41888) 0 SO:0001819 synonymous_variant ENST00000458013.2 0 1 hg19 TCGA-FB-AAQ6-01A-11D-A40W-08 SNX27-003 NOVEL basic protein_coding protein_coding OTTHUMT00000036624.3 0 0 0 48 175 0 41 0 5.444518e-01 0 7 0 41 2 1 1.000000 46 173 0 41 2 -20.000000 1 1 0 0 1 2 4 6 2.868400 1 0.630000 1.870000 0.731495 0.980000 7.300000e-01 1.000000 1.000000 0.938581 0.980000 1 0.840000 1.000000 GBA 2629 broad.mit.edu 37 1 155205555 155205555 + Missense_Mutation SNP G G T rs80356768 TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:155205555G>T ENST00000327247.5 - 10 1537 c.1305C>A c.(1303-1305)aaC>aaA p.N435K GBA_ENST00000536770.1_Missense_Mutation_p.N322K|GBA_ENST00000427500.3_Missense_Mutation_p.N386K|GBA_ENST00000493842.1_5'Flank|GBA_ENST00000428024.3_Missense_Mutation_p.N348K|AL713999.1_ENST00000401290.1_RNA|GBA_ENST00000368373.3_Missense_Mutation_p.N435K NM_001005741.2|NM_001005742.2 NP_001005741.1|NP_001005742.1 P04062 GLCM_HUMAN glucosidase, beta, acid 26 all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088) Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) Velaglucerase alfa(DB06720) TGTCGACAAAGTTACGCACCC 0.547000 Gaucher disease type I 0 SO:0001583 missense Familial Cancer Database glucocerebrosidase insufficiency ENST00000327247.5 0 1 hg19 CCDS1102.1 . . . . . . . . . . . 14.55 2.569455 0.45798 . . ENSG00000177628 ENST00000427500;ENST00000428024;ENST00000368373;ENST00000327247;ENST00000536770;ENST00000536555;ENST00000402928 D;D;D;D;D 0.99329 -5.75;-5.75;-5.75;-5.75;-5.75 4.95 3.07 0.35406 Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1); 0.000000 0.64402 D 0.000001 D 0.99381 0.9782 M 0.93939 3.475 0.58432 D 0.999993 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.87578 0.998;0.99;0.994 D 0.99748 1.1017 10 0.87932 D 0 . 9.7187 0.40289 0.247:0.0:0.753:0.0 . 386;322;435 B7Z5G2;F5H241;P04062 .;.;GLCM_HUMAN K 386;348;435;435;322;392;420 ENSP00000402577:N386K;ENSP00000397986:N348K;ENSP00000357357:N435K;ENSP00000314508:N435K;ENSP00000445560:N322K ENSP00000314508:N435K N - 3 2 GBA 153472179 1.000000 0.71417 1.000000 0.80357 0.243000 0.25628 3.486000 0.53215 0.379000 0.24794 -0.797000 0.03246 AAC TCGA-FB-AAQ6-01A-11D-A40W-08 GBA-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087204.1 0 0 0 33 147 0 44 1 1 42 113 0 44 2 1 1.000000 33 142 0 44 2 -20.000000 1 0 0 0 1 2 4 6 2.868400 1 0.630000 1.870000 0.731495 0.840000 5.800000e-01 1.000000 1.000000 0.848835 0.840000 0 0.700000 1.000000 CCDC19 0 broad.mit.edu 37 1 159856380 159856380 + Nonsense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:159856380G>A ENST00000368099.4 - 6 752 c.688C>T c.(688-690)Cag>Tag p.Q230* CCDC19_ENST00000426543.2_Nonsense_Mutation_p.Q145*|CCDC19_ENST00000476696.1_5'UTR NM_012337.2 NP_036469.2 26 all_hematologic(112;0.0597) BRCA - Breast invasive adenocarcinoma(70;0.151) TCCATCATCTGATCCAACCGC 0.483000 0 SO:0001587 stop_gained ENST00000368099.4 0 1 hg19 CCDS30914.1 . . . . . . . . . . G 38 6.842086 0.97877 . . ENSG00000213085 ENST00000368099;ENST00000426543 . . . 5.51 4.57 0.56435 . 0.368018 0.31519 N 0.007516 . . . . . . 0.80722 A 1 . . . . . . . . . . . . . -18.3392 13.8298 0.63373 0.0:0.1546:0.8454:0.0 . . . . X 230;145 . . Q - 1 0 CCDC19 158123004 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 1.719000 0.38011 1.273000 0.44346 0.563000 0.77884 CAG TCGA-FB-AAQ6-01A-11D-A40W-08 CCDC19-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000085979.1 0 0 0 106 1200 0 297 0 8.069359e-02 0 6 0 297 2 1 1.000000 105 1188 0 296 2 -19.990180 1 1 0 0 1 2 4 6 2.868400 1 0.630000 1.870000 0.731495 0.360000 2.800000e-01 1.000000 0.350000 0.487559 0.360000 0 0.320000 1.000000 C1orf110 339512 broad.mit.edu 37 1 162824686 162824686 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:162824686G>A ENST00000367910.1 - 4 898 c.778C>T c.(778-780)Cgg>Tgg p.R260W C1orf110_ENST00000367912.2_Intron|C1orf110_ENST00000524691.1_Intron|C1orf110_ENST00000367911.2_Intron NM_178550.4 NP_848645.3 Q86UF4 CA110_HUMAN chromosome 1 open reading frame 110 12 ACCCTGTGCCGGAGATAATGG 0.502000 0 SO:0001583 missense ENST00000367910.1 0 1 hg19 CCDS44269.1 . . . . . . . . . . G 14.23 2.474319 0.43942 . . ENSG00000185860 ENST00000367910 . . . 4.41 3.5 0.40072 . 0.000000 0.47455 D 0.000237 T 0.16599 0.0399 L 0.36672 1.1 0.34538 D 0.709987 P 0.46395 0.877 B 0.40901 0.343 T 0.04693 -1.0933 8 0.49607 T 0.09 -7.6072 8.1269 0.31003 0.1093:0.0:0.8907:0.0 . 260 Q86UF4 CA110_HUMAN W 260 . ENSP00000356886:R260W R - 1 2 C1orf110 161091310 1.000000 0.71417 0.991000 0.47740 0.269000 0.26545 1.845000 0.39279 1.051000 0.40369 0.655000 0.94253 CGG TCGA-FB-AAQ6-01A-11D-A40W-08 C1orf110-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083211.2 0 0 0 5 370 0 100 0 0 0 0 100 2 1 0.936617 5 367 0 99 2 -2.907436 1 1 120816 6 41 1 2 4 6 2.868400 1 0.630000 1.870000 0.731495 0.070000 1.000000e-02 1.000000 0.060000 0.257198 0.070000 0 0.030000 1.000000 F5 2153 broad.mit.edu 37 1 169510549 169510549 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:169510549G>A ENST00000367797.3 - 13 3980 c.3779C>T c.(3778-3780)cCa>cTa p.P1260L F5_ENST00000367796.3_Missense_Mutation_p.P1265L NM_000130.4 NP_000121 P12259 FA5_HUMAN coagulation factor V (proaccelerin, labile factor) 128 all_hematologic(923;0.208) ART-123(DB05777)|Drotrecogin alfa(DB00055) ACTGAGTTCTGGAGAGAGGTT 0.512000 0 SO:0001583 missense ENST00000367797.3 0 1 hg19 CCDS1281.1 . . . . . . . . . . G 14.44 2.535336 0.45176 . . ENSG00000198734 ENST00000367797;ENST00000367796 T;T 0.38722 1.12;1.12 4.76 1.72 0.24424 . . . . . T 0.21590 0.0520 M 0.70595 2.14 0.22366 N 0.999165 B 0.14805 0.011 B 0.14023 0.01 T 0.06516 -1.0822 8 0.59425 D 0.04 -2.6912 7.0922 0.25289 0.0846:0.0:0.6134:0.302 . 1260 P12259 FA5_HUMAN L 1260;1265 ENSP00000356771:P1260L;ENSP00000356770:P1265L ENSP00000356770:P1265L P - 2 0 F5 167777173 0.003000 0.15002 0.001000 0.08648 0.010000 0.07245 1.214000 0.32419 0.143000 0.18926 0.650000 0.86243 CCA TCGA-FB-AAQ6-01A-11D-A40W-08 F5-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000083712.1 0 0 0 420 1142 0 390 1 9.985813e-01 8 21 0 390 2 1 1.000000 411 1107 0 384 2 -20.000000 1 1 0 0 1 2 4 6 2.868400 1 0.630000 1.870000 0.731495 0.990000 9.900000e-01 1.000000 1.000000 0.999999 0.990000 1 0.990000 1.000000 HMCN1 83872 broad.mit.edu 37 1 186017951 186017951 + Missense_Mutation SNP A A T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:186017951A>T ENST00000271588.4 + 42 6786 c.6557A>T c.(6556-6558)aAc>aTc p.N2186I HMCN1_ENST00000367492.2_Missense_Mutation_p.N2186I NM_031935.2 NP_114141.2 Q96RW7 HMCN1_HUMAN hemicentin 1 308 ACTGAAAAAAACTACAATGTC 0.358000 0 SO:0001583 missense ENST00000271588.4 0 1 hg19 CCDS30956.1 . . . . . . . . . . A 25.1 4.600104 0.87055 . . ENSG00000143341 ENST00000271588;ENST00000367492 T;T 0.67345 -0.26;-0.26 5.26 5.26 0.73747 Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.041576 0.85682 D 0.000000 T 0.71634 0.3363 N 0.25890 0.77 0.58432 D 0.999997 D 0.89917 1.0 D 0.91635 0.999 T 0.70795 -0.4775 10 0.33141 T 0.24 . 15.4776 0.75497 1.0:0.0:0.0:0.0 . 2186 Q96RW7 HMCN1_HUMAN I 2186 ENSP00000271588:N2186I;ENSP00000356462:N2186I ENSP00000271588:N2186I N + 2 0 HMCN1 184284574 1.000000 0.71417 1.000000 0.80357 0.739000 0.42172 8.910000 0.92685 2.106000 0.64143 0.455000 0.32223 AAC TCGA-FB-AAQ6-01A-11D-A40W-08 HMCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131848.1 0 0 0 34 407 1 140 0 0 0 1 140 2 1 0.999773 34 402 1 140 12 -20.000000 1 1 0 0 1 2 4 6 2.868400 1 0.630000 1.870000 0.731495 0.350000 2.300000e-01 1.000000 0.350000 0.477647 0.350000 0 0.290000 1.000000 ASPM 259266 broad.mit.edu 37 1 197072532 197072532 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:197072532G>A ENST00000367409.4 - 18 6105 c.5849C>T c.(5848-5850)gCg>gTg p.A1950V ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron NM_018136.4 NP_060606.3 Q8IZT6 ASPM_HUMAN asp (abnormal spindle) homolog, microcephaly associated (Drosophila) 165 CACCAGTACCGCATGACGGAG 0.393000 0 SO:0001583 missense ENST00000367409.4 0 1 hg19 CCDS1389.1 . . . . . . . . . . G 14.20 2.465838 0.43839 2.27E-4 1.16E-4 ENSG00000066279 ENST00000367409 T 0.72942 -0.7 5.62 5.62 0.85841 . 0.240301 0.35013 N 0.003508 T 0.73682 0.3618 M 0.88031 2.925 0.33688 D 0.61294 P 0.46512 0.879 B 0.40256 0.324 D 0.84790 0.0778 10 0.52906 T 0.07 . 11.2614 0.49085 0.0:0.2325:0.6416:0.1259 . 1950 Q8IZT6 ASPM_HUMAN V 1950 ENSP00000356379:A1950V ENSP00000356379:A1950V A - 2 0 ASPM 195339155 0.377000 0.25106 0.044000 0.18714 0.002000 0.02628 3.229000 0.51278 2.648000 0.89879 0.650000 0.86243 GCG TCGA-FB-AAQ6-01A-11D-A40W-08 ASPM-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000088256.1 0 0 0 10 1205 0 318 0 8.890434e-05 0 2 0 318 2 1 0.996752 10 1196 0 317 2 -1.810236 0 1 121412 3 41 1 2 4 6 2.892390 1 0.630000 1.870000 0.733928 0.030000 0 1.000000 0.030000 0.234822 0.030000 0 0.010000 1.000000 KLHL12 59349 broad.mit.edu 37 1 202864825 202864825 + Silent SNP A A T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:202864825A>T ENST00000367261.3 - 8 1178 c.960T>A c.(958-960)cgT>cgA p.R320R KLHL12_ENST00000367259.1_Silent_p.R53R|KLHL12_ENST00000435533.3_Silent_p.R358R NM_021633.2 NP_067646.1 Q53G59 KLH12_HUMAN kelch-like family member 12 14 BRCA - Breast invasive adenocarcinoma(75;0.166) AGGCCACATAACGTCTCTTAC 0.483000 0 SO:0001819 synonymous_variant ENST00000367261.3 0 1 hg19 CCDS1429.1 TCGA-FB-AAQ6-01A-11D-A40W-08 KLHL12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000099151.1 0 0 0 5 225 0 53 0 1.418647e-01 0 25 0 53 2 1 0.936051 5 222 0 53 2 -6.803067 1 1 0 0 1 2 4 6 2.892390 1 0.630000 1.870000 0.733928 0.110000 3.000000e-02 1.000000 0.100000 0.296530 0.110000 0 0.060000 1.000000 NFASC 23114 broad.mit.edu 37 1 204923462 204923462 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:204923462G>A ENST00000401399.1 + 5 561 c.362G>A c.(361-363)cGc>cAc p.R121H NFASC_ENST00000338586.6_Missense_Mutation_p.R121H|NFASC_ENST00000338515.6_Missense_Mutation_p.R121H|NFASC_ENST00000513543.1_Missense_Mutation_p.R115H|NFASC_ENST00000367172.4_Missense_Mutation_p.R121H|NFASC_ENST00000403080.1_Missense_Mutation_p.R121H|NFASC_ENST00000367170.4_Missense_Mutation_p.R121H|NFASC_ENST00000367171.4_Missense_Mutation_p.R121H|NFASC_ENST00000404076.1_Missense_Mutation_p.R115H|NFASC_ENST00000367169.4_Missense_Mutation_p.R121H|NFASC_ENST00000360049.4_Missense_Mutation_p.R115H|NFASC_ENST00000404907.1_Missense_Mutation_p.R115H|NFASC_ENST00000539706.1_Missense_Mutation_p.R115H|NFASC_ENST00000339876.6_Missense_Mutation_p.R121H O94856 NFASC_HUMAN neurofascin 81 all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19) KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158) TGCTTCGCCCGCAACAAATTT 0.607000 0 SO:0001583 missense ENST00000401399.1 0 1 hg19 CCDS53460.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 17.29|17.29 3.351348|3.351348 0.61183|0.61183 .|. .|. ENSG00000163531|ENSG00000163531 ENST00000367173|ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000446412;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000505079;ENST00000404907;ENST00000513543;ENST00000430393 .|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T .|0.67523 .|-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27 5.37|5.37 5.37|5.37 0.77165|0.77165 .|. .|0.000000 .|0.53938 .|D .|0.000050 T|T 0.74794|0.74794 0.3763|0.3763 M|M 0.72624|0.72624 2.21|2.21 0.40172|0.40172 D|D 0.977199|0.977199 .|P;P;B;P;P;D .|0.54601 .|0.711;0.64;0.206;0.838;0.752;0.967 .|B;B;B;B;B;P .|0.50270 .|0.1;0.083;0.162;0.144;0.083;0.636 T|T 0.77197|0.77197 -0.2676|-0.2676 5|10 .|0.46703 .|T .|0.11 .|. 18.6966|18.6966 0.91603|0.91603 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|115;115;217;121;115;121 .|O94856-11;O94856-8;B4DRH7;O94856-9;O94856-3;O94856-2 .|.;.;.;.;.;. T|H 91|121;121;121;121;121;121;115;115;115;121;121;121;115;121;121;115;115;91 .|ENSP00000356140:R121H;ENSP00000356139:R121H;ENSP00000356138:R121H;ENSP00000342128:R121H;ENSP00000344786:R121H;ENSP00000343509:R121H;ENSP00000438614:R115H;ENSP00000353154:R115H;ENSP00000356137:R121H;ENSP00000412161:R121H;ENSP00000384875:R121H;ENSP00000385676:R115H;ENSP00000385637:R121H;ENSP00000427586:R121H;ENSP00000384061:R115H;ENSP00000425908:R115H;ENSP00000415031:R91H .|ENSP00000295776:R115H A|R +|+ 1|2 0|0 NFASC|NFASC 203190085|203190085 0.782000|0.782000 0.28689|0.28689 1.000000|1.000000 0.80357|0.80357 0.994000|0.994000 0.84299|0.84299 2.659000|2.659000 0.46741|0.46741 2.516000|2.516000 0.84829|0.84829 0.655000|0.655000 0.94253|0.94253 GCA|CGC TCGA-FB-AAQ6-01A-11D-A40W-08 NFASC-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000131237.1 0 0 0 5 164 0 40 0 0 0 0 40 2 1 0.934493 5 160 0 40 2 -6.762718 1 0 121412 2 30 1 2 4 6 2.892390 1 0.630000 1.870000 0.733928 0.160000 5.000000e-02 1.000000 0.130000 0.328762 0.160000 0 0.090000 1.000000 PGBD5 79605 broad.mit.edu 37 1 230492737 230492737 + Missense_Mutation SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:230492737C>T ENST00000525115.1 - 2 478 c.455G>A c.(454-456)cGc>cAc p.R152H PGBD5_ENST00000391860.1_Missense_Mutation_p.R106H|PGBD5_ENST00000321327.2_Missense_Mutation_p.R251H Q8N414 PGBD5_HUMAN piggyBac transposable element derived 5 33 Breast(184;0.0397) Prostate(94;0.167) CTGGCTGGAGCGGAAGGCCAC 0.617000 0 SO:0001583 missense ENST00000525115.1 0 1 hg19 . . . . . . . . . . C 35 5.549386 0.96501 . . ENSG00000177614 ENST00000391860;ENST00000321327;ENST00000525115 T;T;T 0.18016 2.24;2.24;2.24 6.03 6.03 0.97812 . 0.000000 0.85682 D 0.000000 T 0.32971 0.0847 L 0.27053 0.805 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.01512 -1.1336 10 0.48119 T 0.1 -48.7684 20.5568 0.99304 0.0:1.0:0.0:0.0 . 152 Q8N414 PGBD5_HUMAN H 106;251;152 ENSP00000375733:R106H;ENSP00000322530:R251H;ENSP00000431404:R152H ENSP00000322530:R251H R - 2 0 PGBD5 228559360 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.802000 0.85969 2.861000 0.98227 0.655000 0.94253 CGC TCGA-FB-AAQ6-01A-11D-A40W-08 PGBD5-002 PUTATIVE basic|exp_conf protein_coding protein_coding OTTHUMT00000382617.1 0 0 0 66 284 1 51 0 9.520442e-02 0 3 1 51 2 1 1.000000 64 278 1 51 21 -3.130525 1 1 0 0 1 2 4 6 2.909323 1 0.630000 1.870000 0.736317 0.870000 6.700000e-01 1.000000 1.000000 0.877165 0.870000 1 0.760000 1.000000 RCAN3 11123 broad.mit.edu 37 1 24859625 24859625 + Missense_Mutation SNP C C G TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr1:24859625C>G ENST00000374395.4 + 4 735 c.422C>G c.(421-423)cCt>cGt p.P141R RCAN3_ENST00000374393.2_Intron|RCAN3_ENST00000412742.2_Intron|RCAN3_ENST00000436717.2_Missense_Mutation_p.P131R|RCAN3_ENST00000538532.1_Missense_Mutation_p.P83R NM_001251978.1|NM_001251979.1|NM_001251984.1 NP_001238907.1|NP_001238908.1|NP_001238913.1 Q9UKA8 RCAN3_HUMAN RCAN family member 3 7 Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19) CCGCCCCAGCCTGTCAAGCAG 0.567000 0 SO:0001583 missense ENST00000374395.4 0 1 hg19 CCDS254.1 . . . . . . . . . . C 22.1 4.242107 0.79912 . . ENSG00000117602 ENST00000374395;ENST00000436717;ENST00000538532 T;T;T 0.50548 0.76;0.75;0.74 5.08 5.08 0.68730 . 0.000000 0.85682 D 0.000000 T 0.75700 0.3885 M 0.90650 3.135 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 0.999;1.0;1.0 T 0.80487 -0.1361 10 0.72032 D 0.01 -28.9874 19.094 0.93242 0.0:1.0:0.0:0.0 . 83;131;141 A4GU14;Q9UKA8-2;Q9UKA8 .;.;RCAN3_HUMAN R 141;131;83 ENSP00000363516:P141R;ENSP00000414447:P131R;ENSP00000445401:P83R ENSP00000363516:P141R P + 2 0 RCAN3 24732212 1.000000 0.71417 0.967000 0.41034 0.498000 0.33706 7.278000 0.78587 2.822000 0.97130 0.558000 0.71614 CCT TCGA-FB-AAQ6-01A-11D-A40W-08 RCAN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000009176.2 0 0 0 92 68 0 68 1 9.854147e-01 7 1 0 68 2 1 1.000000 89 66 0 68 2 -20.000000 1 1 0 0 1 0 1 1 1.716275 1 0.630000 1.870000 0.464777 0.990000 9.200000e-01 1.000000 1.000000 0.990003 0.990000 1 0.970000 1.000000 BTBD3 22903 broad.mit.edu 37 20 11899817 11899817 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr20:11899817G>A ENST00000405977.1 + 3 1035 c.410G>A c.(409-411)gGa>gAa p.G137E BTBD3_ENST00000399006.2_Missense_Mutation_p.G76E|RP4-742J24.2_ENST00000439529.1_RNA|BTBD3_ENST00000378226.2_Missense_Mutation_p.G137E|BTBD3_ENST00000254977.3_Missense_Mutation_p.G76E NM_001282550.1|NM_001282552.1|NM_001282554.1 NP_001269479.1|NP_001269481.1|NP_001269483.1 Q9Y2F9 BTBD3_HUMAN BTB (POZ) domain containing 3 34 CGGTTGCCAGGACACAAAGTA 0.473000 0 SO:0001583 missense ENST00000405977.1 0 1 hg19 CCDS13113.1 . . . . . . . . . . G 17.82 3.482599 0.63962 . . ENSG00000132640 ENST00000254977;ENST00000399006;ENST00000405977;ENST00000422390;ENST00000378226;ENST00000455911;ENST00000430557 T;T;T;T;T;T;T 0.22134 1.97;1.97;1.97;1.97;1.97;1.97;1.97 5.93 5.93 0.95920 BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2); 0.000000 0.85682 D 0.000000 T 0.39306 0.1073 M 0.72894 2.215 0.80722 D 1 P 0.41188 0.741 P 0.48141 0.568 T 0.09684 -1.0663 10 0.87932 D 0 . 19.3421 0.94347 0.0:0.0:1.0:0.0 . 137 Q9Y2F9 BTBD3_HUMAN E 76;76;137;76;137;26;26 ENSP00000254977:G76E;ENSP00000381971:G76E;ENSP00000384545:G137E;ENSP00000397809:G76E;ENSP00000367471:G137E;ENSP00000408817:G26E;ENSP00000404582:G26E ENSP00000254977:G76E G + 2 0 BTBD3 11847817 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.904000 0.87408 2.826000 0.97356 0.655000 0.94253 GGA TCGA-FB-AAQ6-01A-11D-A40W-08 BTBD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078021.3 0 0 0 37 104 0 54 1 9.279847e-01 5 10 0 54 2 1 1.000000 35 103 0 52 2 -20.000000 1 1 0 0 1 1 2 3 2.284427 1 0.630000 1.870000 0.659989 0.940000 6.800000e-01 1.000000 1.000000 0.915215 0.940000 1 0.800000 1.000000 RBM12 10137 broad.mit.edu 37 20 34241168 34241168 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr20:34241168G>A ENST00000374114.3 - 3 2340 c.2077C>T c.(2077-2079)Ccc>Tcc p.P693S CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000317677.5_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.P693S|RBM12_ENST00000359646.1_Missense_Mutation_p.P693S|CPNE1_ENST00000397445.1_Intron NM_001198838.1|NM_001198840.1|NM_006047.5 NP_001185767.1|NP_001185769.1|NP_006038.2 Q9NTZ6 RBM12_HUMAN RNA binding motif protein 12 36 Lung NSC(9;0.00608)|all_lung(11;0.00918) BRCA - Breast invasive adenocarcinoma(18;0.00953) CCTGCACTGGGCATTCCCGCA 0.557000 0 SO:0001583 missense ENST00000374114.3 0 1 hg19 CCDS13261.1 . . . . . . . . . . G 36 5.653504 0.96724 . . ENSG00000244462 ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942 T;T;T 0.22336 1.96;1.96;1.96 4.03 4.03 0.46877 . 0.000000 0.64402 D 0.000018 T 0.27663 0.0680 N 0.19112 0.55 0.80722 D 1 D 0.63880 0.993 D 0.70227 0.968 T 0.02365 -1.1170 10 0.19590 T 0.45 -3.377 14.4866 0.67622 0.0:0.0:1.0:0.0 . 693 Q9NTZ6 RBM12_HUMAN S 693;693;693;492 ENSP00000363228:P693S;ENSP00000352668:P693S;ENSP00000363217:P693S ENSP00000339879:P492S P - 1 0 RBM12 33704582 0.002000 0.14202 0.997000 0.53966 0.903000 0.53119 -0.160000 0.10041 2.528000 0.85240 0.563000 0.77884 CCC TCGA-FB-AAQ6-01A-11D-A40W-08 RBM12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078894.1 0 0 0 6 511 1 196 0 5.487445e-02 0 27 1 196 2 0 0.156180 6 504 1 193 11 -2.180157 0 1 0 0 1 1 2 3 2.284427 1 0.630000 1.870000 0.659989 0.040000 0 1.000000 0.050000 0.230889 0.040000 0 0.020000 1.000000 EDN3 1908 broad.mit.edu 37 20 57899466 57899466 + Silent SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr20:57899466C>T ENST00000337938.2 + 5 1055 c.669C>T c.(667-669)ctC>ctT p.L223L EDN3_ENST00000371028.2_Silent_p.L223L|EDN3_ENST00000311585.7_3'UTR|EDN3_ENST00000371025.3_3'UTR|EDN3_ENST00000395654.3_Silent_p.L209L NM_207034.1 NP_996917.1 P14138 EDN3_HUMAN endothelin 3 19 all_lung(29;0.0115) GACTCGCCCTCGCTCCATCTA 0.592000 0 SO:0001819 synonymous_variant ENST00000337938.2 0 1 hg19 CCDS13477.1 TCGA-FB-AAQ6-01A-11D-A40W-08 EDN3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000079919.2 0 0 0 8 697 0 153 0 2.843676e-02 0 20 0 153 2 1 0.988777 8 687 0 151 2 -2.429460 0 1 121412 5 40 1 1 2 3 2.304725 1 0.630000 1.870000 0.662916 0.040000 0 1.000000 0.050000 0.241188 0.040000 0 0.020000 1.000000 KRTAP11-1 337880 broad.mit.edu 37 21 32253686 32253686 + Missense_Mutation SNP A A G TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr21:32253686A>G ENST00000332378.4 - 1 188 c.158T>C c.(157-159)cTg>cCg p.L53P NM_175858.2 NP_787054.1 Q8IUC1 KR111_HUMAN keratin associated protein 11-1 18 ACAGTGGTCCAGGAGCCAAGA 0.567000 0 SO:0001583 missense ENST00000332378.4 0 1 hg19 CCDS13608.1 . . . . . . . . . . A 16.34 3.095059 0.56075 . . ENSG00000182591 ENST00000332378 T 0.03689 3.84 5.4 5.4 0.78164 . 0.167269 0.38272 N 0.001753 T 0.15305 0.0369 M 0.84948 2.725 0.58432 D 0.999998 D 0.61080 0.989 D 0.63113 0.911 T 0.00817 -1.1554 10 0.35671 T 0.21 -7.1524 8.316 0.32100 0.9117:0.0:0.0883:0.0 . 53 Q8IUC1 KR111_HUMAN P 53 ENSP00000330720:L53P ENSP00000330720:L53P L - 2 0 KRTAP11-1 31175557 1.000000 0.71417 1.000000 0.80357 0.948000 0.59901 4.106000 0.57804 2.197000 0.70478 0.529000 0.55759 CTG TCGA-FB-AAQ6-01A-11D-A40W-08 KRTAP11-1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128225.1 0 0 0 48 182 0 97 0 0 0 0 97 2 1 1.000000 46 181 0 97 2 -20.000000 1 1 0 0 1 0 0 0 2.079131 0 0.630000 1.870000 0.630000 0.660000 5.000000e-01 0.830000 0.660000 0.668782 0.660000 0 0.570000 0.750000 CRYZL1 9946 broad.mit.edu 37 21 34969588 34969588 + Nonsense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr21:34969588G>A ENST00000381554.3 - 10 881 c.796C>T c.(796-798)Cag>Tag p.Q266* CRYZL1_ENST00000480893.1_5'UTR|AP000304.12_ENST00000429238.1_Intron|CRYZL1_ENST00000445393.1_Intron|CRYZL1_ENST00000381540.3_Nonsense_Mutation_p.Q266*|CRYZL1_ENST00000361534.2_Nonsense_Mutation_p.Q290*|CRYZL1_ENST00000290244.5_Nonsense_Mutation_p.Q251* NM_145858.2 NP_665857.2 O95825 QORL1_HUMAN crystallin, zeta (quinone reductase)-like 1 3 GATAGTACCTGAAGGTTTTCT 0.373000 0 SO:0001587 stop_gained ENST00000381554.3 0 1 hg19 CCDS13633.2 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 25.8|25.8 4.674981|4.674981 0.88445|0.88445 .|. .|. ENSG00000205758|ENSG00000205758 ENST00000381554;ENST00000290244;ENST00000381540;ENST00000361534|ENST00000441940;ENST00000440526 .|. .|. .|. 5.25|5.25 5.25|5.25 0.73442|0.73442 .|. 0.000000|. 0.85682|. D|. 0.000000|. .|T .|0.74854 .|0.3771 .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|. .|. .|. .|. .|. .|. .|T .|0.73461 .|-0.3975 .|4 0.42905|. T|. 0.14|. -16.5157|-16.5157 18.807|18.807 0.92041|0.92041 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|. .|. .|. X|L 266;251;266;290|41;209 .|. ENSP00000290244:Q251X|. Q|S -|- 1|2 0|0 CRYZL1|CRYZL1 33891458|33891458 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.958000|0.958000 0.62258|0.62258 7.661000|7.661000 0.83786|0.83786 2.591000|2.591000 0.87537|0.87537 0.650000|0.650000 0.86243|0.86243 CAG|TCA TCGA-FB-AAQ6-01A-11D-A40W-08 CRYZL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000141282.2 0 0 0 120 254 0 185 0 8.784994e-01 0 10 0 185 2 1 1.000000 120 249 0 185 2 -11.135130 1 1 0 0 1 0 0 0 2.079131 0 0.630000 1.870000 0.630000 0.990000 8.600000e-01 1.000000 1.000000 0.978486 0.990000 1 0.930000 1.000000 DSCAM 1826 broad.mit.edu 37 21 41741051 41741051 + Missense_Mutation SNP G G T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr21:41741051G>T ENST00000400454.1 - 4 1107 c.630C>A c.(628-630)agC>agA p.S210R NM_001271534.1|NM_001389.3 NP_001258463.1|NP_001380.2 O60469 DSCAM_HUMAN Down syndrome cell adhesion molecule 142 all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103) TGGCGCTGTTGCTCTGCCTCG 0.438000 Melanoma(134;970 1778 1785 21664 32388) 0 SO:0001583 missense ENST00000400454.1 0 1 hg19 CCDS42929.1 . . . . . . . . . . G 21.4 4.137474 0.77775 . . ENSG00000171587 ENST00000400454 T 0.19394 2.15 6.07 -3.03 0.05429 Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 T 0.43831 0.1265 M 0.83603 2.65 0.41002 D 0.98493 D 0.76494 0.999 D 0.83275 0.996 T 0.39542 -0.9609 10 0.66056 D 0.02 . 12.8167 0.57669 0.6272:0.0:0.3728:0.0 . 210 O60469 DSCAM_HUMAN R 210 ENSP00000383303:S210R ENSP00000383303:S210R S - 3 2 DSCAM 40662921 1.000000 0.71417 0.853000 0.33588 0.951000 0.60555 0.640000 0.24705 -1.031000 0.03308 0.655000 0.94253 AGC TCGA-FB-AAQ6-01A-11D-A40W-08 DSCAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195029.1 0 0 0 9 326 0 110 0 0 0 0 110 2 1 0.994302 9 325 0 110 2 -9.104522 1 1 0 0 1 0 0 0 2.079131 0 0.630000 1.870000 0.630000 0.080000 3.000000e-02 0.150000 0.080000 0.094017 0.080000 0 0.050000 0.120000 TRPM2 7226 broad.mit.edu 37 21 45833885 45833885 + Missense_Mutation SNP C C T rs138586774 TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr21:45833885C>T ENST00000397928.1 + 20 3519 c.3074C>T c.(3073-3075)aCg>aTg p.T1025M TRPM2_ENST00000397932.2_Missense_Mutation_p.T1025M|AP001065.2_ENST00000456880.1_RNA|AP001065.2_ENST00000423310.1_RNA|TRPM2_ENST00000300482.5_Missense_Mutation_p.T1025M|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000300481.9_Missense_Mutation_p.T1005M NM_003307.3 NP_003298 O94759 TRPM2_HUMAN transient receptor potential cation channel, subfamily M, member 2 76 GAGTGGCTGACGGTCCTCCTA 0.637000 0 SO:0001583 missense ENST00000397928.1 0 1 hg19 CCDS13710.1 . . . . . . . . . . C 22.9 4.347791 0.82022 2.27E-4 0.0 ENSG00000142185 ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932 D;D;D;D 0.98437 -4.93;-4.93;-4.93;-4.93 4.74 4.74 0.60224 Ion transport (1); 0.000000 0.85682 D 0.000000 D 0.99086 0.9686 M 0.88906 2.99 0.58432 D 0.999997 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;1.0;1.0 D 0.99616 1.0982 10 0.87932 D 0 -22.3961 18.1214 0.89572 0.0:1.0:0.0:0.0 . 1025;811;1025 E9PGK7;Q5KTC1;O94759 .;.;TRPM2_HUMAN M 1025;1025;1005;1025 ENSP00000300482:T1025M;ENSP00000381023:T1025M;ENSP00000300481:T1005M;ENSP00000381026:T1025M ENSP00000300481:T1005M T + 2 0 TRPM2 44658313 1.000000 0.71417 0.902000 0.35471 0.965000 0.64279 5.679000 0.68160 2.352000 0.79861 0.591000 0.81541 ACG TCGA-FB-AAQ6-01A-11D-A40W-08 TRPM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000098086.1 0 0 0 38 1262 0 387 0 0 0 1 0 387 2 1 1.000000 37 1240 0 386 2 -2.677007 1 1 121412 38 52 1 0 0 0 2.079131 0 0.630000 1.870000 0.630000 0.080000 5.000000e-02 0.130000 0.100000 0.095017 0.080000 0 0.070000 0.110000 CHEK2 11200 broad.mit.edu 37 22 29130542 29130542 + Missense_Mutation SNP G G C TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr22:29130542G>C ENST00000405598.1 - 3 359 c.168C>G c.(166-168)agC>agG p.S56R CHEK2_ENST00000403642.1_Missense_Mutation_p.S56R|CHEK2_ENST00000382565.1_Missense_Mutation_p.S56R|CHEK2_ENST00000402731.1_Missense_Mutation_p.S56R|CHEK2_ENST00000382580.2_Missense_Mutation_p.S56R|CHEK2_ENST00000348295.3_Missense_Mutation_p.S56R|CHEK2_ENST00000382578.1_Missense_Mutation_p.S56R|CHEK2_ENST00000382566.1_Missense_Mutation_p.S56R|CHEK2_ENST00000328354.6_Missense_Mutation_p.S56R|CHEK2_ENST00000404276.1_Missense_Mutation_p.S56R|CHEK2_ENST00000544772.1_5'UTR O96017 CHK2_HUMAN checkpoint kinase 2 50 GTGTCCCAGAGCTGGAGTGAG 0.562000 F breast Direct reversal of damage;Other conserved DNA damage response genes yes Rec familial breast cancer 22 22q12.1 11200 CHK2 checkpoint homolog (S. pombe) E 0 SO:0001583 missense ENST00000405598.1 0 1 hg19 CCDS13843.1 . . . . . . . . . . G 19.25 3.791600 0.70452 . . ENSG00000183765 ENST00000348295;ENST00000382578;ENST00000382565;ENST00000382563;ENST00000382566;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731;ENST00000447421;ENST00000439200;ENST00000398017 T;T;T;D;T;T;T;T;T;T;T;T;D 0.95103 0.58;-0.25;-0.67;-3.61;-0.38;-0.38;-0.38;2.13;-0.25;0.58;0.03;2.13;-2.79 5.42 2.08 0.27032 . 0.125544 0.85682 D 0.000000 D 0.95446 0.8521 L 0.56769 1.78 0.41295 D 0.987004 D;D;D;D;D;D 0.89917 1.0;0.999;0.998;0.999;0.998;0.999 D;D;D;D;D;D 0.85130 0.997;0.996;0.991;0.996;0.991;0.996 D 0.93676 0.6994 10 0.41790 T 0.15 -2.6501 9.8378 0.40980 0.2972:0.0:0.7028:0.0 . 56;56;56;56;56;56 O96017-7;O96017-4;A8JZZ5;O96017-12;O96017;O96017-9 .;.;.;.;CHK2_HUMAN;. R 56;56;56;56;56;56;56;56;56;56;56;56;56;66 ENSP00000329012:S56R;ENSP00000372021:S56R;ENSP00000372006:S56R;ENSP00000372007:S56R;ENSP00000329178:S56R;ENSP00000385747:S56R;ENSP00000386087:S56R;ENSP00000372023:S56R;ENSP00000384919:S56R;ENSP00000384835:S56R;ENSP00000397478:S56R;ENSP00000408065:S56R;ENSP00000381099:S66R ENSP00000329178:S56R S - 3 2 CHEK2 27460542 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 0.539000 0.23175 0.749000 0.32854 0.655000 0.94253 AGC TCGA-FB-AAQ6-01A-11D-A40W-08 CHEK2-005 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000321150.1 0 0 0 110 302 0 108 1 5.958219e-01 2 5 0 108 2 1 1.000000 107 289 0 108 2 -20.000000 1 1 0 0 1 1 2 3 2.151451 0 0.630000 1.870000 0.635737 0.860000 7.200000e-01 1.000000 0.860000 0.867749 0.860000 1 0.780000 0.940000 NCF4 4689 broad.mit.edu 37 22 37273798 37273798 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr22:37273798G>A ENST00000248899.6 + 10 1137 c.953G>A c.(952-954)cGc>cAc p.R318H NCF4_ENST00000397147.4_3'UTR NM_000631.4 NP_000622.2 Q15080 NCF4_HUMAN neutrophil cytosolic factor 4, 40kDa 16 Dextromethorphan(DB00514) TCCCAGAAGCGCCTCTTCCCC 0.617000 0 SO:0001583 missense ENST00000248899.6 0 1 hg19 CCDS13934.1 . . . . . . . . . . G 12.87 2.067255 0.36470 2.27E-4 0.0 ENSG00000100365 ENST00000248899 T 0.23552 1.9 5.31 0.851 0.18989 Phox/Bem1p (2); . . . . T 0.13157 0.0319 N 0.16233 0.39 0.58432 D 0.999999 B 0.11235 0.004 B 0.08055 0.003 T 0.10245 -1.0638 9 0.30854 T 0.27 . 6.9148 0.24354 0.4921:0.0:0.5079:0.0 . 318 Q15080 NCF4_HUMAN H 318 ENSP00000248899:R318H ENSP00000248899:R318H R + 2 0 NCF4 35603744 0.735000 0.28153 0.982000 0.44146 0.789000 0.44602 0.840000 0.27600 0.240000 0.21263 0.557000 0.71058 CGC TCGA-FB-AAQ6-01A-11D-A40W-08 NCF4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318863.1 0 0 0 42 88 0 25 1 9.999533e-01 8 29 0 25 2 1 1.000000 41 85 0 25 2 -20.000000 1 1 121412 3 36 1 1 2 3 2.151451 0 0.630000 1.870000 0.635737 0.990000 7.900000e-01 1.000000 1.000000 0.969158 0.990000 1 0.910000 1.000000 EP300 2033 broad.mit.edu 37 22 41573306 41573306 + Missense_Mutation SNP C C G TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr22:41573306C>G ENST00000263253.7 + 31 6810 c.5591C>G c.(5590-5592)aCc>aGc p.T1864S RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA NM_001429.3 NP_001420.2 Q09472 EP300_HUMAN E1A binding protein p300 171 CAACAGCCAACCACCCCGCAG 0.642000 T, N, F, Mis, O MLL, RUNXBP2 colorectal, breast, pancreatic, AML, ALL, DLBCL Rubinstein-Taybi syndrome Rec yes 22 22q13 2033 300 kd E1A-Binding protein gene L, E 0 SO:0001583 missense Familial Cancer Database Broad Thumb-Hallux syndrome ENST00000263253.7 0 1 hg19 CCDS14010.1 . . . . . . . . . . C 4.675 0.125490 0.08931 . . ENSG00000100393 ENST00000263253 D 0.82081 -1.57 5.47 4.42 0.53409 . 0.509983 0.15738 N 0.247047 T 0.64283 0.2584 N 0.04508 -0.205 0.27890 N 0.939351 B 0.02656 0.0 B 0.04013 0.001 T 0.37220 -0.9715 10 0.05721 T 0.95 -0.4911 16.0157 0.80439 0.0:0.8652:0.1348:0.0 . 1864 Q09472 EP300_HUMAN S 1864 ENSP00000263253:T1864S ENSP00000263253:T1864S T + 2 0 EP300 39903252 0.042000 0.20092 0.813000 0.32504 0.206000 0.24218 3.270000 0.51600 1.251000 0.43983 0.561000 0.74099 ACC TCGA-FB-AAQ6-01A-11D-A40W-08 EP300-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320600.1 0 0 0 77 236 0 86 1 9.985262e-01 9 24 0 86 2 1 1.000000 75 217 0 80 2 -20.000000 1 1 0 0 1 1 2 3 2.173353 0 0.630000 1.870000 0.637982 0.800000 6.400000e-01 1.000000 0.790000 0.812796 0.800000 0 0.720000 0.900000 LPIN1 23175 broad.mit.edu 37 2 11935562 11935562 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr2:11935562G>A ENST00000256720.2 + 13 1820 c.1727G>A c.(1726-1728)gGc>gAc p.G576D LPIN1_ENST00000396097.1_Missense_Mutation_p.G306D|LPIN1_ENST00000396099.1_Missense_Mutation_p.G618D|LPIN1_ENST00000425416.2_Missense_Mutation_p.G582D|LPIN1_ENST00000449576.2_Missense_Mutation_p.G661D|LPIN1_ENST00000404113.2_Missense_Mutation_p.G77D NM_145693.2 NP_663731.1 Q14693 LPIN1_HUMAN lipin 1 45 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) TGCTTGGCTGGCAAGGCCCAT 0.557000 0 SO:0001583 missense ENST00000256720.2 0 1 hg19 CCDS1682.1 . . . . . . . . . . G 9.785 1.176287 0.21704 . . ENSG00000134324 ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113;ENST00000454151 T;T;T;T;T;T;T 0.80738 -1.41;-1.4;-1.38;-1.38;-1.24;-0.39;0.52 4.62 3.72 0.42706 . 0.160285 0.56097 D 0.000028 T 0.77164 0.4090 M 0.65975 2.015 0.38288 D 0.942626 B;B;B 0.14805 0.0;0.011;0.008 B;B;B 0.15870 0.002;0.014;0.007 T 0.73297 -0.4027 10 0.30854 T 0.27 -16.8688 12.3844 0.55325 0.0:0.1712:0.8288:0.0 . 77;661;576 B4DET9;F5GY24;Q14693 .;.;LPIN1_HUMAN D 661;618;582;576;306;77;103 ENSP00000397908:G661D;ENSP00000379406:G618D;ENSP00000401522:G582D;ENSP00000256720:G576D;ENSP00000379404:G306D;ENSP00000386120:G77D;ENSP00000413714:G103D ENSP00000256720:G576D G + 2 0 LPIN1 11853013 0.713000 0.27926 0.024000 0.17045 0.016000 0.09150 2.551000 0.45820 0.923000 0.37045 0.655000 0.94253 GGC TCGA-FB-AAQ6-01A-11D-A40W-08 LPIN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000239296.3 0 0 0 5 365 0 137 0 7.781872e-03 0 8 0 137 2 1 0.935692 5 360 0 137 2 -2.649287 1 1 0 0 1 0 1 1 2.074801 0 0.630000 1.870000 0.628831 0.040000 0 0.100000 0.040000 0.050834 0.040000 0 0.020000 0.070000 OSBPL6 114880 broad.mit.edu 37 2 179253838 179253838 + Silent SNP T T C TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr2:179253838T>C ENST00000190611.4 + 21 2635 c.2259T>C c.(2257-2259)aaT>aaC p.N753N OSBPL6_ENST00000315022.2_Silent_p.N757N|OSBPL6_ENST00000409631.1_Silent_p.N717N|OSBPL6_ENST00000392505.2_Silent_p.N778N|OSBPL6_ENST00000409045.3_Silent_p.N722N|OSBPL6_ENST00000359685.3_Silent_p.N717N NM_032523.3 NP_115912.1 Q9BZF3 OSBL6_HUMAN oxysterol binding protein-like 6 46 OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335) CCATCAGAAATACCAAAAGCA 0.348000 0 SO:0001819 synonymous_variant ENST00000190611.4 0 1 hg19 CCDS2277.1 TCGA-FB-AAQ6-01A-11D-A40W-08 OSBPL6-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000334393.2 0 0 0 73 157 0 62 0 0 0 1 0 62 2 1 1.000000 73 157 0 61 2 -20.000000 1 1 121412 1 17 1 0 0 0 2.048692 0 0.630000 1.870000 0.625279 0.980000 8.000000e-01 1.000000 1.000000 0.960366 0.980000 1 0.890000 1.000000 BARD1 580 broad.mit.edu 37 2 215645418 215645418 + Missense_Mutation SNP T T C TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr2:215645418T>C ENST00000260947.4 - 4 1314 c.1180A>G c.(1180-1182)Aca>Gca p.T394A BARD1_ENST00000471787.1_5'Flank|BARD1_ENST00000449967.2_Missense_Mutation_p.T250A NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1 NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1 Q99728 BARD1_HUMAN BRCA1 associated RING domain 1 35 Renal(323;0.0243) GAAGGTGGTGTACCTGGTGAA 0.418000 Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome 0 SO:0001583 missense Familial Cancer Database Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease ENST00000260947.4 0 1 hg19 CCDS2397.1 . . . . . . . . . . T 13.22 2.172231 0.38315 . . ENSG00000138376 ENST00000260947;ENST00000449967 T;T 0.74421 -0.84;-0.23 5.24 4.05 0.47172 . 0.507037 0.19811 N 0.105540 T 0.70806 0.3266 M 0.71581 2.175 0.26675 N 0.971643 B;B 0.30406 0.278;0.172 B;B 0.24974 0.057;0.039 T 0.64415 -0.6413 10 0.56958 D 0.05 -0.3721 11.0331 0.47785 0.0:0.0:0.2982:0.7018 . 250;394 E7EUI3;Q99728 .;BARD1_HUMAN A 394;250 ENSP00000260947:T394A;ENSP00000406752:T250A ENSP00000260947:T394A T - 1 0 BARD1 215353663 0.001000 0.12720 0.030000 0.17652 0.101000 0.19017 0.916000 0.28651 0.796000 0.33947 0.379000 0.24179 ACA TCGA-FB-AAQ6-01A-11D-A40W-08 BARD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256602.1 0 0 0 47 295 0 125 1 1.981800e-02 2 0 0 125 2 1 1.000000 47 293 0 125 2 -20.000000 1 1 0 0 1 0 0 0 2.048692 0 0.630000 1.870000 0.625279 0.420000 3.200000e-01 0.550000 0.430000 0.436622 0.420000 0 0.370000 0.490000 ALPP 250 broad.mit.edu 37 2 233244230 233244230 + Missense_Mutation SNP A A G rs1130341 TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr2:233244230A>G ENST00000392027.2 + 4 586 c.317A>G c.(316-318)aAt>aGt p.N106S AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA NM_001632.3 NP_001623.3 P05187 PPB1_HUMAN alkaline phosphatase, placental 22 all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132) CAGACATACAATGTAGACAAA 0.577000 0 SO:0001583 missense ENST00000392027.2 0 1 hg19 CCDS2490.1 . . . . . . . . . . . 2.668 -0.278125 0.05679 2.27E-4 0.0 ENSG00000163283 ENST00000392027 D 0.95103 -3.61 2.31 -0.39 0.12450 Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1); 0.295720 0.40818 N 0.001001 D 0.83487 0.5265 N 0.12831 0.26 0.29049 N 0.884612 B 0.30889 0.299 B 0.25405 0.06 T 0.75230 -0.3391 10 0.30854 T 0.27 . 6.227 0.20714 0.7126:0.1707:0.1167:0.0 rs1130341;rs3189051;rs17412756 106 P05187 PPB1_HUMAN S 106 ENSP00000375881:N106S ENSP00000375881:N106S N + 2 0 ALPP 232952474 0.992000 0.36948 0.984000 0.44739 0.510000 0.34073 0.843000 0.27640 -0.220000 0.09988 -0.817000 0.03123 AAT TCGA-FB-AAQ6-01A-11D-A40W-08 ALPP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257032.3 0 0 0 8 116 0 42 0 1.590621e-02 0 3 0 42 2 1 0.988713 6 114 0 42 2 -12.536750 1 0 121408 6 30 1 0 0 0 2.048692 0 0.630000 1.870000 0.625279 0.210000 9.000000e-02 0.370000 0.200000 0.222827 0.210000 0 0.140000 0.290000 ALPP 250 broad.mit.edu 37 2 233244240 233244240 + Silent SNP A A G rs1130342 byFrequency TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr2:233244240A>G ENST00000392027.2 + 4 596 c.327A>G c.(325-327)aaA>aaG p.K109K AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA NM_001632.3 NP_001623.3 P05187 PPB1_HUMAN alkaline phosphatase, placental 22 all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132) ATGTAGACAAACATGTGCCAG 0.567000 0 SO:0001819 synonymous_variant ENST00000392027.2 0 1 hg19 CCDS2490.1 TCGA-FB-AAQ6-01A-11D-A40W-08 ALPP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257032.3 0 0 0 9 118 0 46 0 6.559332e-03 0 2 0 46 2 1 0.993930 7 116 0 46 2 -13.892200 1 0 121408 7 34 1 0 0 0 2.048692 0 0.630000 1.870000 0.625279 0.220000 1.100000e-01 0.390000 0.220000 0.241855 0.220000 0 0.160000 0.310000 ELMOD3 84173 broad.mit.edu 37 2 85617280 85617280 + Missense_Mutation SNP A A C TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr2:85617280A>C ENST00000409890.2 + 13 1502 c.835A>C c.(835-837)Aag>Cag p.K279Q ELMOD3_ENST00000393852.4_Missense_Mutation_p.K279Q|ELMOD3_ENST00000315658.7_Missense_Mutation_p.K279Q|ELMOD3_ENST00000490508.1_3'UTR|ELMOD3_ENST00000409344.3_Missense_Mutation_p.K279Q|ELMOD3_ENST00000409013.3_Missense_Mutation_p.K279Q Q96FG2 ELMD3_HUMAN ELMO/CED-12 domain containing 3 12 TCGGCAGCAGAAGGTCATCCC 0.567000 0 SO:0001583 missense ENST00000409890.2 0 1 hg19 CCDS46352.1 . . . . . . . . . . A 7.253 0.603569 0.14002 . . ENSG00000115459 ENST00000409013;ENST00000409890;ENST00000409344;ENST00000393852;ENST00000315658 T;T;T;T;T 0.29917 1.55;1.55;1.55;1.55;1.55 4.98 2.38 0.29361 Engulfment/cell motility, ELMO (2); 0.194639 0.44483 D 0.000460 T 0.08758 0.0217 N 0.01081 -1.03 0.80722 D 1 B;B 0.23937 0.094;0.01 B;B 0.19946 0.027;0.006 T 0.16867 -1.0388 10 0.09084 T 0.74 -18.2695 10.0611 0.42275 0.51:0.49:0.0:0.0 . 279;279 Q96FG2-6;Q96FG2 .;ELMD3_HUMAN Q 279 ENSP00000387139:K279Q;ENSP00000386304:K279Q;ENSP00000386248:K279Q;ENSP00000377434:K279Q;ENSP00000318264:K279Q ENSP00000318264:K279Q K + 1 0 ELMOD3 85470791 1.000000 0.71417 0.946000 0.38457 0.990000 0.78478 2.853000 0.48317 0.730000 0.32425 0.460000 0.39030 AAG TCGA-FB-AAQ6-01A-11D-A40W-08 ELMOD3-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000329124.1 0 0 0 9 327 0 113 0 4.280553e-02 0 11 0 113 2 0 0.311566 9 321 1 109 12 -9.480012 1 1 0 0 1 0 1 1 2.074801 0 0.630000 1.870000 0.628831 0.080000 3.000000e-02 0.150000 0.080000 0.093464 0.080000 0 0.050000 0.120000 DNAJC13 23317 broad.mit.edu 37 3 132207849 132207849 + Missense_Mutation SNP C C G TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr3:132207849C>G ENST00000260818.6 + 31 3700 c.3452C>G c.(3451-3453)gCt>gGt p.A1151G NM_015268.3 NP_056083.3 O75165 DJC13_HUMAN DnaJ (Hsp40) homolog, subfamily C, member 13 34 ACCAAACAGGCTTTCAAGTCA 0.333000 0 SO:0001583 missense ENST00000260818.6 0 1 hg19 CCDS33857.1 . . . . . . . . . . C 18.89 3.718859 0.68844 . . ENSG00000138246 ENST00000260818 T 0.21031 2.03 5.57 5.57 0.84162 Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.32133 0.0819 M 0.69463 2.115 0.80722 D 1 D 0.58268 0.982 P 0.46144 0.505 T 0.02567 -1.1140 10 0.34782 T 0.22 . 19.5228 0.95192 0.0:1.0:0.0:0.0 . 1151 O75165 DJC13_HUMAN G 1151 ENSP00000260818:A1151G ENSP00000260818:A1151G A + 2 0 DNAJC13 133690539 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 4.950000 0.63603 2.770000 0.95276 0.650000 0.86243 GCT TCGA-FB-AAQ6-01A-11D-A40W-08 DNAJC13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356807.2 0 0 0 72 186 0 117 1 6.254414e-01 4 3 0 117 2 1 1.000000 72 184 0 116 2 -20.000000 1 1 121406 1 26 1 0 0 0 2.072118 0 0.630000 1.870000 0.627654 0.870000 7.100000e-01 1.000000 1.000000 0.879516 0.870000 1 0.790000 0.970000 TGFBR2 7048 broad.mit.edu 37 3 30732996 30732996 + Missense_Mutation SNP C C T rs104893809 TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr3:30732996C>T ENST00000295754.5 + 7 1991 c.1609C>T c.(1609-1611)Cgc>Tgc p.R537C TGFBR2_ENST00000359013.4_Missense_Mutation_p.R562C NM_003242.5 NP_003233.4 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II (70/80kDa) p.R537C(1) 53 TGTGGCAGAACGCTTCAGTGA 0.577000 1 Substitution - Missense(1) GRCh37 CM042122|CM064325 TGFBR2 M rs104893809 SO:0001583 missense ENST00000295754.5 0 1 hg19 CCDS2648.1 . . . . . . . . . . C 27.9 4.869682 0.91587 . . ENSG00000163513 ENST00000295754;ENST00000359013;ENST00000439925 D;D 0.93604 -3.25;-3.25 5.91 5.91 0.95273 Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 D 0.96972 0.9011 M 0.87038 2.855 0.80722 A 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.97216 0.9874 9 0.87932 D 0 . 15.0515 0.71877 0.142:0.858:0.0:0.0 rs28934869 537;562 P37173;D2JYI1 TGFR2_HUMAN;. C 537;562;367 ENSP00000295754:R537C;ENSP00000351905:R562C ENSP00000295754:R537C R + 1 0 TGFBR2 30708000 1.000000 0.71417 0.994000 0.49952 0.992000 0.81027 5.930000 0.70104 2.803000 0.96430 0.650000 0.86243 CGC TCGA-FB-AAQ6-01A-11D-A40W-08 TGFBR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252994.2 0 0 0 120 132 0 115 1 1 25 20 0 115 2 1 1.000000 118 127 0 115 2 -20.000000 1 1 0 0 1 0 1 1 1.443903 1 0.630000 1.870000 0.459854 0.960000 8.600000e-01 1.000000 0.990000 0.959017 0.960000 1 0.910000 0.990000 PLXNB1 5364 broad.mit.edu 37 3 48462686 48462686 + Missense_Mutation SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr3:48462686C>T ENST00000358536.4 - 8 2030 c.1761G>A c.(1759-1761)atG>atA p.M587I PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000456774.1_Missense_Mutation_p.M587I|PLXNB1_ENST00000358459.4_Missense_Mutation_p.M587I|PLXNB1_ENST00000296440.6_Missense_Mutation_p.M587I NM_002673.4 NP_002664.2 O43157 PLXB1_HUMAN plexin B1 47 GGGAGGGGCACATCACACCAG 0.642000 0 SO:0001583 missense ENST00000358536.4 0 1 hg19 CCDS2765.1 . . . . . . . . . . C 6.217 0.408216 0.11754 . . ENSG00000164050 ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774 T;T;T;T 0.02974 4.09;4.09;4.09;4.09 5.02 5.02 0.67125 . 0.169599 0.52532 D 0.000070 T 0.02533 0.0077 N 0.13352 0.335 0.80722 D 1 B;B 0.06786 0.001;0.0 B;B 0.09377 0.001;0.004 T 0.58239 -0.7671 10 0.21014 T 0.42 . 16.9108 0.86139 0.0:1.0:0.0:0.0 . 587;587 O43157;O43157-2 PLXB1_HUMAN;. I 587 ENSP00000296440:M587I;ENSP00000351242:M587I;ENSP00000351338:M587I;ENSP00000414199:M587I ENSP00000296440:M587I M - 3 0 PLXNB1 48437690 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 1.851000 0.39338 2.350000 0.79820 0.561000 0.74099 ATG TCGA-FB-AAQ6-01A-11D-A40W-08 PLXNB1-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344454.1 0 0 0 151 179 0 95 1 9.994035e-01 15 2 0 95 2 1 1.000000 149 176 0 91 2 -20.000000 1 1 0 0 1 0 1 1 1.443903 1 0.630000 1.870000 0.459854 0.950000 8.500000e-01 1.000000 0.990000 0.952241 0.950000 1 0.900000 0.990000 PDLIM3 27295 broad.mit.edu 37 4 186423581 186423581 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr4:186423581G>A ENST00000284770.5 - 8 1035 c.962C>T c.(961-963)gCc>gTc p.A321V PDLIM3_ENST00000284767.5_3'UTR|PDLIM3_ENST00000284771.6_Missense_Mutation_p.A273V NM_014476.5 NP_055291.2 Q53GG5 PDLI3_HUMAN PDZ and LIM domain 3 17 all_lung(41;1.03e-13)|Lung NSC(41;2.49e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.00996)|Colorectal(36;0.0161)|all_hematologic(60;0.0592)|all_neural(102;0.243) GTTGCAGTCGGCACACACGAA 0.557000 0 SO:0001583 missense ENST00000284770.5 0 1 hg19 CCDS3844.1 . . . . . . . . . . G 20.8 4.047505 0.75846 . . ENSG00000154553 ENST00000284770;ENST00000284771 D;D 0.88277 -2.36;-2.36 5.5 5.5 0.81552 Zinc finger, LIM-type (5); 0.104803 0.64402 D 0.000002 D 0.87293 0.6141 L 0.28649 0.875 0.80722 D 1 B;B 0.32302 0.363;0.24 B;B 0.39935 0.209;0.314 D 0.86544 0.1830 10 0.72032 D 0.01 -24.6852 19.757 0.96298 0.0:0.0:1.0:0.0 . 273;321 Q53GG5-2;Q53GG5 .;PDLI3_HUMAN V 321;273 ENSP00000284770:A321V;ENSP00000284771:A273V ENSP00000284770:A321V A - 2 0 PDLIM3 186660575 1.000000 0.71417 0.748000 0.31131 0.843000 0.47879 7.823000 0.86660 2.758000 0.94735 0.561000 0.74099 GCC TCGA-FB-AAQ6-01A-11D-A40W-08 PDLIM3-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000360499.2 0 0 0 7 578 0 189 0 6.672765e-02 0 30 0 189 2 1 0.979855 6 572 0 187 2 -2.108969 0 1 0 0 1 1 2 3 2.098859 0 0.630000 1.870000 0.631162 0.030000 0 0.080000 0.040000 0.043347 0.030000 0 0.020000 0.060000 PCDHGB7 56099 broad.mit.edu 37 5 140799542 140799542 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr5:140799542G>A ENST00000398594.2 + 1 2116 c.2116G>A c.(2116-2118)Gcg>Acg p.A706T PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA5_ENST00000518069.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank NM_018927.3 NP_061750.1 Q9Y5F8 PCDGJ_HUMAN protocadherin gamma subfamily B, 7 56 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CTTTCTCCTCGCGGTGATTCT 0.557000 0 SO:0001583 missense ENST00000398594.2 0 1 hg19 CCDS47293.1 . . . . . . . . . . g 0.012 -1.656858 0.00779 0.0 2.35E-4 ENSG00000254122 ENST00000398594 T 0.14640 2.49 5.77 1.43 0.22495 . 0.277852 0.18696 U 0.133734 T 0.07279 0.0184 L 0.31578 0.945 0.09310 N 1 B;B 0.28470 0.213;0.141 B;B 0.25884 0.021;0.064 T 0.37430 -0.9706 10 0.13853 T 0.58 . 4.5122 0.11917 0.3841:0.0:0.4673:0.1486 . 706;706 Q9Y5F8;Q9Y5F8-2 PCDGJ_HUMAN;. T 706 ENSP00000381594:A706T ENSP00000381594:A706T A + 1 0 PCDHGB7 140779726 0.000000 0.05858 0.002000 0.10522 0.026000 0.11368 1.191000 0.32138 0.352000 0.24053 0.561000 0.74099 GCG TCGA-FB-AAQ6-01A-11D-A40W-08 PCDHGB7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376973.1 0 0 0 114 214 0 152 0 0 0 1 0 152 2 1 1.000000 112 212 0 151 2 -20.000000 1 1 121178 6 42 1 1 2 3 2.093621 0 0.630000 1.870000 0.631162 0.990000 9.400000e-01 1.000000 1.000000 0.996336 0.990000 1 0.990000 1.000000 FAT2 2196 broad.mit.edu 37 5 150891812 150891812 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr5:150891812G>A ENST00000261800.5 - 20 11831 c.11819C>T c.(11818-11820)gCc>gTc p.A3940V CTC-251D13.1_ENST00000606930.1_RNA NM_001447.2 NP_001438.1 Q9NYQ8 FAT2_HUMAN FAT atypical cadherin 2 196 Medulloblastoma(196;0.0912)|all_hematologic(541;0.104) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) CTGGGTGAGGGCTTGTGTCTC 0.607000 0 SO:0001583 missense ENST00000261800.5 0 1 hg19 CCDS4317.1 . . . . . . . . . . G 2.261 -0.369196 0.05069 . . ENSG00000086570 ENST00000261800 T 0.69561 -0.41 5.16 3.33 0.38152 Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1); 0.459686 0.18025 N 0.154102 T 0.59293 0.2183 L 0.51422 1.61 0.09310 N 1 B;B 0.32245 0.361;0.136 B;B 0.35470 0.203;0.042 T 0.47484 -0.9114 10 0.29301 T 0.29 . 9.7829 0.40660 0.0:0.3639:0.503:0.1331 . 3940;1045 Q9NYQ8;E9PDJ8 FAT2_HUMAN;. V 3940 ENSP00000261800:A3940V ENSP00000261800:A3940V A - 2 0 FAT2 150872005 0.971000 0.33674 0.132000 0.22025 0.017000 0.09413 1.409000 0.34680 0.638000 0.30545 -0.121000 0.15023 GCC TCGA-FB-AAQ6-01A-11D-A40W-08 FAT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252434.1 0 0 0 47 158 0 62 0 0 0 0 62 2 1 1.000000 47 157 0 60 2 -20.000000 1 1 0 0 1 1 2 3 2.093621 0 0.630000 1.870000 0.631162 0.720000 5.500000e-01 0.930000 0.720000 0.736237 0.720000 0 0.630000 0.830000 GRM6 2916 broad.mit.edu 37 5 178413297 178413297 + Missense_Mutation SNP C C T rs62638622 TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr5:178413297C>T ENST00000517717.1 - 9 1996 c.1958G>A c.(1957-1959)cGc>cAc p.R653H RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Missense_Mutation_p.R653H O15303 GRM6_HUMAN glutamate receptor, metabotropic 6 55 all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351) all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GAAGAGCCTGCGGGCGGCACA 0.642000 0 SO:0001583 missense ENST00000517717.1 0 1 hg19 CCDS4442.1 . . . . . . . . . . C 17.77 3.471230 0.63625 0.0 2.33E-4 ENSG00000113262 ENST00000319065;ENST00000231188;ENST00000517717 D;D 0.90676 -2.71;-2.71 5.02 5.02 0.67125 GPCR, family 3, C-terminal (2); . . . . D 0.96087 0.8725 M 0.90425 3.115 0.58432 D 0.999997 D;D 0.89917 1.0;0.979 D;P 0.87578 0.998;0.581 D 0.96814 0.9599 9 0.87932 D 0 . 16.2011 0.82078 0.0:1.0:0.0:0.0 rs62638622 809;653 E7EX65;O15303 .;GRM6_HUMAN H 809;653;653 ENSP00000231188:R653H;ENSP00000430767:R653H ENSP00000231188:R653H R - 2 0 GRM6 178345903 1.000000 0.71417 0.091000 0.20842 0.116000 0.19942 7.658000 0.83755 2.495000 0.84180 0.462000 0.41574 CGC TCGA-FB-AAQ6-01A-11D-A40W-08 GRM6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253474.2 0 0 0 4 99 0 27 0 0 0 0 27 2 1 0.882257 4 95 0 26 2 -6.898672 1 1 121358 30 43 1 1 2 3 2.093621 0 0.630000 1.870000 0.631162 0.130000 4.000000e-02 0.300000 0.120000 0.150794 0.130000 0 0.080000 0.210000 C5orf42 65250 broad.mit.edu 37 5 37125474 37125474 + Missense_Mutation SNP C C G TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr5:37125474C>G ENST00000508244.1 - 45 8761 c.8668G>C c.(8668-8670)Gac>Cac p.D2890H C5orf42_ENST00000512288.1_Intron|C5orf42_ENST00000274258.7_Missense_Mutation_p.D1788H|C5orf42_ENST00000425232.2_Missense_Mutation_p.D2890H Q9H799 CE042_HUMAN chromosome 5 open reading frame 42 79 all_lung(31;0.000616) COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202) CTTTCCTTGTCAGTTCTTTGT 0.348000 0 SO:0001583 missense ENST00000508244.1 0 1 hg19 CCDS34146.2 . . . . . . . . . . C 25.4 4.633422 0.87660 . . ENSG00000197603 ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429 T;T;T;T 0.47869 0.83;0.83;0.83;0.83 5.97 5.97 0.96955 . 0.392756 0.27792 N 0.017821 T 0.43055 0.1230 L 0.29908 0.895 0.31060 N 0.714288 P;P 0.46220 0.547;0.874 B;B 0.44224 0.444;0.444 T 0.52859 -0.8519 10 0.66056 D 0.02 . 15.924 0.79597 0.0:1.0:0.0:0.0 . 2890;1788 E9PH94;Q9H799 .;CE042_HUMAN H 2890;2890;1788;1956 ENSP00000421690:D2890H;ENSP00000389014:D2890H;ENSP00000274258:D1788H;ENSP00000424223:D1956H ENSP00000274258:D1788H D - 1 0 C5orf42 37161231 1.000000 0.71417 0.997000 0.53966 0.989000 0.77384 3.754000 0.55189 2.828000 0.97474 0.655000 0.94253 GAC TCGA-FB-AAQ6-01A-11D-A40W-08 C5orf42-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000360806.1 0 0 0 13 412 0 157 0 1.061092e-02 0 5 0 157 2 1 0.999504 12 408 0 157 2 -3.316190 1 1 121412 4 42 1 0 0 0 2.091204 0 0.630000 1.870000 0.630000 0.090000 4.000000e-02 0.160000 0.100000 0.103924 0.090000 0 0.070000 0.130000 NOL7 51406 broad.mit.edu 37 6 13620462 13620462 + Missense_Mutation SNP G G A rs143778341 TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr6:13620462G>A ENST00000451315.2 + 6 555 c.523G>A c.(523-525)Gta>Ata p.V175I NOL7_ENST00000474485.1_3'UTR|RANBP9_ENST00000469916.1_5'Flank|AL441883.1_ENST00000600057.1_Missense_Mutation_p.T105M NM_016167.3 NP_057251.2 Q9UMY1 NOL7_HUMAN nucleolar protein 7, 27kDa 5 Breast(50;0.00669)|Ovarian(93;0.0634) all_hematologic(90;0.135) Epithelial(50;0.176) CTACTTGGCCGTAAGGCTAAA 0.383000 0 SO:0001583 missense ENST00000451315.2 0 1 hg19 CCDS4528.1 . . . . . . . . . . G 10.07 1.249688 0.22880 2.27E-4 0.0 ENSG00000225921 ENST00000451315 . . . 5.8 -11.6 0.00059 . 1.503030 0.04455 N 0.373256 T 0.16214 0.0390 N 0.24115 0.695 0.09310 N 1 B 0.32128 0.357 B 0.24394 0.053 T 0.20107 -1.0285 9 0.52906 T 0.07 -6.5213 23.1364 0.99980 0.0:0.6737:0.2507:0.0756 . 175 Q9UMY1 NOL7_HUMAN I 175 . ENSP00000405674:V175I V + 1 0 NOL7 13728441 0.000000 0.05858 0.000000 0.03702 0.215000 0.24574 -1.036000 0.03560 -1.984000 0.00985 -0.211000 0.12701 GTA TCGA-FB-AAQ6-01A-11D-A40W-08 NOL7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039904.1 0 0 0 5 309 0 135 0 7.067690e-01 0 146 0 135 2 1 0.935905 5 305 0 135 2 -2.688085 1 1 0 0 1 0 1 1 2.077905 0 0.630000 1.870000 0.628831 0.050000 1.000000e-02 0.110000 0.050000 0.059935 0.050000 0 0.030000 0.080000 PACRG 135138 broad.mit.edu 37 6 163510311 163510311 + Nonsense_Mutation SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr6:163510311C>T ENST00000337019.3 + 5 708 c.484C>T c.(484-486)Cga>Tga p.R162* PACRG_ENST00000366888.2_Nonsense_Mutation_p.R162*|PACRG_ENST00000366889.2_Nonsense_Mutation_p.R162* NM_152410.2 NP_689623.2 Q96M98 PACRG_HUMAN PARK2 co-regulated p.R162*(1) 20 Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203) CCTCCGAAACCGACAGGTCAT 0.453000 1 Substitution - Nonsense(1) SO:0001587 stop_gained ENST00000337019.3 0 1 hg19 CCDS5284.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 27.2|27.2 4.811865|4.811865 0.90707|0.90707 0.0|0.0 1.16E-4|1.16E-4 ENSG00000112530|ENSG00000112530 ENST00000534958|ENST00000337019;ENST00000366889;ENST00000366888 .|. .|. .|. 5.63|5.63 3.76|3.76 0.43208|0.43208 .|. .|0.126644 .|0.53938 .|D .|0.000055 T|. 0.23688|. 0.0573|. .|. .|. .|. 0.80722|0.80722 A|A 1|1 .|. .|. .|. .|. .|. .|. T|. 0.08953|. -1.0697|. 3|. .|0.08381 .|T .|0.77 -12.2326|-12.2326 14.4441|14.4441 0.67338|0.67338 0.2765:0.7235:0.0:0.0|0.2765:0.7235:0.0:0.0 .|. .|. .|. .|. L|X 77|162 .|. .|ENSP00000337946:R162X P|R +|+ 2|1 0|2 PACRG|PACRG 163430301|163430301 1.000000|1.000000 0.71417|0.71417 0.993000|0.993000 0.49108|0.49108 0.928000|0.928000 0.56348|0.56348 1.974000|1.974000 0.40559|0.40559 0.656000|0.656000 0.30886|0.30886 0.591000|0.591000 0.81541|0.81541 CCG|CGA TCGA-FB-AAQ6-01A-11D-A40W-08 PACRG-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000400424.1 0 0 0 128 165 0 177 0 0 0 1 0 177 2 1 1.000000 127 164 0 176 2 -19.998010 1 1 121412 3 40 1 0 1 1 1.467522 1 0.630000 1.870000 0.459854 0.920000 8.100000e-01 1.000000 0.950000 0.926608 0.920000 1 0.870000 0.980000 NKAPL 222698 broad.mit.edu 37 6 28227596 28227596 + Silent SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr6:28227596C>T ENST00000343684.3 + 1 499 c.447C>T c.(445-447)gaC>gaT p.D149D ZKSCAN4_ENST00000423974.2_5'Flank NM_001007531.1 NP_001007532.1 Q5M9Q1 NKAPL_HUMAN NFKB activating protein-like 31 TAGATTCTGACGAACATACCC 0.512000 0 SO:0001819 synonymous_variant ENST00000343684.3 0 1 hg19 CCDS34353.1 TCGA-FB-AAQ6-01A-11D-A40W-08 NKAPL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040185.1 0 0 0 182 487 0 205 0 0 0 0 205 2 1 1.000000 180 483 0 202 2 -20.000000 1 1 0 0 1 0 1 1 2.077905 0 0.630000 1.870000 0.628831 0.850000 7.500000e-01 0.960000 0.860000 0.862176 0.850000 1 0.800000 0.920000 PHF3 23469 broad.mit.edu 37 6 64412409 64412409 + Missense_Mutation SNP G G T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr6:64412409G>T ENST00000262043.3 + 10 3451 c.3111G>T c.(3109-3111)atG>atT p.M1037I PHF3_ENST00000393387.1_Missense_Mutation_p.M1037I Q92576 PHF3_HUMAN PHD finger protein 3 75 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) CCATAGAAATGATTGAGAAAG 0.308000 GBM(135;136 1820 29512 34071 46235) 0 SO:0001583 missense ENST00000262043.3 0 1 hg19 CCDS4966.1 . . . . . . . . . . G 20.3 3.971366 0.74246 . . ENSG00000118482 ENST00000506783;ENST00000515594;ENST00000262043;ENST00000393387 T;T;T;T 0.46819 2.09;0.86;2.13;2.13 5.49 5.49 0.81192 Transcription elongation factor S-II, central domain (2); 0.000000 0.48286 D 0.000195 T 0.41696 0.1170 L 0.39147 1.195 0.80722 D 1 P 0.52842 0.956 P 0.48982 0.597 T 0.33189 -0.9878 10 0.52906 T 0.07 -16.5771 19.3501 0.94379 0.0:0.0:1.0:0.0 . 1037 Q92576 PHF3_HUMAN I 851;306;1037;1037 ENSP00000424694:M851I;ENSP00000425338:M306I;ENSP00000262043:M1037I;ENSP00000377048:M1037I ENSP00000262043:M1037I M + 3 0 PHF3 64470368 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 9.773000 0.98989 2.576000 0.86940 0.591000 0.81541 ATG TCGA-FB-AAQ6-01A-11D-A40W-08 PHF3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041086.2 0 0 0 38 209 0 59 0 8.844976e-01 0 23 0 59 2 1 1.000000 38 207 0 59 2 -20.000000 1 1 0 0 1 0 1 1 2.077905 0 0.630000 1.870000 0.628831 0.480000 3.500000e-01 0.630000 0.480000 0.494481 0.480000 0 0.410000 0.560000 PHF3 23469 broad.mit.edu 37 6 64413463 64413463 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr6:64413463G>A ENST00000262043.3 + 11 3609 c.3269G>A c.(3268-3270)gGa>gAa p.G1090E PHF3_ENST00000393387.1_Missense_Mutation_p.G1090E Q92576 PHF3_HUMAN PHD finger protein 3 75 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) AAGCCAGAAGGATCTGAAAAA 0.368000 GBM(135;136 1820 29512 34071 46235) 0 SO:0001583 missense ENST00000262043.3 0 1 hg19 CCDS4966.1 . . . . . . . . . . G 11.58 1.681306 0.29872 . . ENSG00000118482 ENST00000506783;ENST00000515594;ENST00000262043;ENST00000393387 T;T;T;T 0.41758 2.35;0.99;2.37;2.37 5.54 1.03 0.20045 . 0.238263 0.21734 N 0.069931 T 0.02727 0.0082 N 0.02539 -0.55 0.25439 N 0.988114 B 0.02656 0.0 B 0.01281 0.0 T 0.36504 -0.9745 10 0.02654 T 1 -7.4536 0.8723 0.01217 0.2381:0.1955:0.3717:0.1947 . 1090 Q92576 PHF3_HUMAN E 904;359;1090;1090 ENSP00000424694:G904E;ENSP00000425338:G359E;ENSP00000262043:G1090E;ENSP00000377048:G1090E ENSP00000262043:G1090E G + 2 0 PHF3 64471422 0.998000 0.40836 0.995000 0.50966 0.968000 0.65278 2.108000 0.41854 0.222000 0.20900 0.591000 0.81541 GGA TCGA-FB-AAQ6-01A-11D-A40W-08 PHF3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041086.2 0 0 0 35 263 0 124 0 3.411968e-01 0 10 0 124 2 1 1.000000 35 261 0 124 2 -14.817710 1 0 121412 2 29 1 0 1 1 2.077905 0 0.630000 1.870000 0.628831 0.370000 2.600000e-01 0.490000 0.370000 0.379003 0.370000 0 0.310000 0.440000 PHF3 23469 broad.mit.edu 37 6 64413504 64413504 + Missense_Mutation SNP G G C TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr6:64413504G>C ENST00000262043.3 + 11 3650 c.3310G>C c.(3310-3312)Gat>Cat p.D1104H PHF3_ENST00000393387.1_Missense_Mutation_p.D1104H Q92576 PHF3_HUMAN PHD finger protein 3 75 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) TATGTCTAAAGATACCACTAG 0.363000 GBM(135;136 1820 29512 34071 46235) 0 SO:0001583 missense ENST00000262043.3 0 1 hg19 CCDS4966.1 . . . . . . . . . . G 16.47 3.133046 0.56828 . . ENSG00000118482 ENST00000506783;ENST00000515594;ENST00000262043;ENST00000393387 T;T;T;T 0.59906 1.23;0.23;1.63;1.63 5.78 5.78 0.91487 . 0.000000 0.37348 N 0.002136 T 0.71247 0.3317 M 0.82193 2.58 0.58432 D 0.999999 D 0.89917 1.0 D 0.70716 0.97 T 0.75249 -0.3384 10 0.66056 D 0.02 -23.8579 12.4924 0.55907 0.0767:0.0:0.9233:0.0 . 1104 Q92576 PHF3_HUMAN H 918;373;1104;1104 ENSP00000424694:D918H;ENSP00000425338:D373H;ENSP00000262043:D1104H;ENSP00000377048:D1104H ENSP00000262043:D1104H D + 1 0 PHF3 64471463 1.000000 0.71417 1.000000 0.80357 0.962000 0.63368 7.246000 0.78247 2.716000 0.92895 0.591000 0.81541 GAT TCGA-FB-AAQ6-01A-11D-A40W-08 PHF3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041086.2 0 0 0 31 333 0 148 0 3.161037e-01 0 13 0 148 2 1 1.000000 31 331 0 148 2 -20.000000 1 0 0 0 1 0 1 1 2.077905 0 0.630000 1.870000 0.628831 0.260000 1.800000e-01 0.370000 0.270000 0.276241 0.260000 0 0.220000 0.320000 RREB1 6239 broad.mit.edu 37 6 7229470 7229470 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr6:7229470G>A ENST00000349384.6 + 10 1452 c.1138G>A c.(1138-1140)Gcc>Acc p.A380T RREB1_ENST00000379938.2_Missense_Mutation_p.A380T|RREB1_ENST00000334984.6_Missense_Mutation_p.A380T|RREB1_ENST00000379933.3_Missense_Mutation_p.A380T NM_001003698.3 NP_001003698.1 Q92766 RREB1_HUMAN ras responsive element binding protein 1 58 Ovarian(93;0.0398) all_hematologic(90;0.0384)|Prostate(151;0.191) GCCTGCCCCCGCCGAGGAGCC 0.652000 0 SO:0001583 missense ENST00000349384.6 0 1 hg19 CCDS34336.1 . . . . . . . . . . G 2.187 -0.386212 0.04966 . . ENSG00000124782 ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984;ENST00000483150 T;T;T;T;T 0.09723 3.07;3.05;3.07;2.95;3.1 5.71 -3.44 0.04796 . 0.637364 0.13362 N 0.393588 T 0.01905 0.0060 N 0.20685 0.6 0.09310 N 1 B;B;B 0.15473 0.009;0.013;0.002 B;B;B 0.09377 0.004;0.004;0.002 T 0.45687 -0.9244 10 0.56958 D 0.05 -3.7986 8.2984 0.31999 0.433:0.2:0.3669:0.0 . 380;380;380 Q92766-3;Q92766;Q92766-2 .;RREB1_HUMAN;. T 380 ENSP00000369265:A380T;ENSP00000369270:A380T;ENSP00000305560:A380T;ENSP00000335574:A380T;ENSP00000419511:A380T ENSP00000335574:A380T A + 1 0 RREB1 7174469 0.000000 0.05858 0.000000 0.03702 0.790000 0.44656 -0.498000 0.06420 -0.332000 0.08489 -0.672000 0.03802 GCC TCGA-FB-AAQ6-01A-11D-A40W-08 RREB1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000352985.1 0 0 0 35 151 0 50 0 9.746707e-02 0 3 0 50 2 1 1.000000 35 145 0 49 2 -20.000000 1 1 121412 3 35 1 0 1 1 2.077905 0 0.630000 1.870000 0.628831 0.590000 4.300000e-01 0.780000 0.590000 0.604073 0.590000 0 0.500000 0.690000 DGKI 9162 broad.mit.edu 37 7 137092622 137092622 + Splice_Site SNP G G A rs79823365 TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr7:137092622G>A ENST00000288490.5 - 31 2943 c.2943C>T c.(2941-2943)caC>caT p.H981H DGKI_ENST00000494390.1_5'UTR|DGKI_ENST00000424189.2_Splice_Site_p.H994H|DGKI_ENST00000446122.1_Splice_Site_p.H963H|DGKI_ENST00000453654.2_Splice_Site_p.H650H NM_004717.2 NP_004708.1 O75912 DGKI_HUMAN diacylglycerol kinase, iota 84 CCTACTTACCGTGGTCAAGGA 0.443000 0 SO:0001630 splice_region_variant ENST00000288490.5 0 1 hg19 CCDS5845.1 TCGA-FB-AAQ6-01A-11D-A40W-08 DGKI-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000341286.3 0 0 0 142 366 0 203 0 0 0 0 203 2 1 1.000000 141 364 0 202 2 -20.000000 1 1 121412 1 31 1 0 0 0 2.086534 0 0.630000 1.870000 0.630000 0.880000 7.600000e-01 1.000000 0.880000 0.887939 0.880000 1 0.820000 0.950000 TAS2R4 50832 broad.mit.edu 37 7 141478409 141478409 + Missense_Mutation SNP A A G TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr7:141478409A>G ENST00000247881.2 + 1 168 c.121A>G c.(121-123)Atc>Gtc p.I41V SSBP1_ENST00000465582.1_Intron NM_016944.1 NP_058640.1 Q9NYW5 TA2R4_HUMAN taste receptor, type 2, member 4 7 Melanoma(164;0.0171) AAGCCATAGAATCTCCTCTTC 0.383000 0 SO:0001583 missense ENST00000247881.2 0 1 hg19 CCDS5868.1 . . . . . . . . . . A 8.257 0.810241 0.16537 . . ENSG00000127364 ENST00000247881 T 0.00873 5.59 5.57 2.23 0.28157 . 0.805187 0.11220 N 0.586826 T 0.01189 0.0039 L 0.49126 1.545 0.09310 N 1 B 0.19200 0.034 B 0.17098 0.017 T 0.46992 -0.9151 10 0.30078 T 0.28 . 5.7936 0.18373 0.3662:0.4428:0.191:0.0 . 41 Q9NYW5 TA2R4_HUMAN V 41 ENSP00000247881:I41V ENSP00000247881:I41V I + 1 0 TAS2R4 141124878 0.000000 0.05858 0.136000 0.22124 0.939000 0.58152 -0.260000 0.08708 0.214000 0.20742 0.528000 0.53228 ATC TCGA-FB-AAQ6-01A-11D-A40W-08 TAS2R4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000349285.1 0 0 0 156 422 0 227 0 0 0 0 227 2 1 1.000000 152 412 0 226 2 -20.000000 1 1 0 0 1 1 2 3 2.102894 0 0.630000 1.870000 0.631162 0.850000 7.400000e-01 0.980000 0.860000 0.860932 0.850000 1 0.790000 0.920000 STAG3L4 64940 broad.mit.edu 37 7 66785098 66785098 + RNA SNP A A C TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr7:66785098A>C ENST00000416602.2 + 0 728 NR_040586.1 Q8TBR4 ST3L4_HUMAN stromal antigen 3-like 4 (pseudogene) 7 Lung NSC(55;0.0839)|all_lung(88;0.181) AGCTGCATTAATACTACATTG 0.368000 0 ENST00000416602.2 0 1 hg19 . . . . . . . . . . a 4.956 0.177539 0.09443 . . ENSG00000106610 ENST00000416602;ENST00000437742 . . . 2.19 2.19 0.27852 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6.3172 0.21196 1.0:0.0:0.0:0.0 . . . . Y 151 . . X + 3 2 STAG3L4 66422533 1.000000 0.71417 0.992000 0.48379 0.373000 0.29922 1.725000 0.38074 1.031000 0.39867 0.076000 0.15429 TAA TCGA-FB-AAQ6-01A-11D-A40W-08 STAG3L4-001 KNOWN basic processed_transcript pseudogene OTTHUMT00000346611.1 0 0 0 41 234 0 111 0 7.138993e-01 1 15 0 111 2 1 1.000000 40 230 0 116 2 -20.000000 1 1 0 0 1 1 2 3 2.108476 0 0.630000 1.870000 0.631162 0.470000 3.400000e-01 0.620000 0.470000 0.481842 0.470000 0 0.400000 0.550000 ENPP2 5168 broad.mit.edu 37 8 120633644 120633644 + Silent SNP C C T TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr8:120633644C>T ENST00000075322.6 - 4 466 c.408G>A c.(406-408)gtG>gtA p.V136V ENPP2_ENST00000522826.1_Silent_p.V136V|ENPP2_ENST00000427067.2_Silent_p.V132V|ENPP2_ENST00000259486.6_Silent_p.V136V NM_001040092.2 NP_001035181.1 Q13822 ENPP2_HUMAN ectonucleotide pyrophosphatase/phosphodiesterase 2 69 Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161) STAD - Stomach adenocarcinoma(47;0.00185) CTTTGCAAACCACTTGGTAAT 0.463000 Melanoma(20;305 879 2501 4818 31020) 0 SO:0001819 synonymous_variant ENST00000075322.6 0 1 hg19 CCDS34936.1 TCGA-FB-AAQ6-01A-11D-A40W-08 ENPP2-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000381390.1 0 0 0 86 203 0 101 0 9.999485e-01 0 38 0 101 2 1 1.000000 84 200 0 99 2 -7.495295 1 1 0 0 1 0 0 0 2.050546 0 0.630000 1.870000 0.625279 0.920000 7.600000e-01 1.000000 1.000000 0.924234 0.920000 1 0.840000 1.000000 FAM135B 51059 broad.mit.edu 37 8 139268947 139268947 + Missense_Mutation SNP G G A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr8:139268947G>A ENST00000395297.1 - 5 523 c.353C>T c.(352-354)aCg>aTg p.T118M NM_015912.3 NP_056996.2 Q49AJ0 F135B_HUMAN family with sequence similarity 135, member B 238 all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.0805) TTCACTGTCCGTAAAGTGCAG 0.458000 HNSCC(54;0.14) 0 SO:0001583 missense ENST00000395297.1 0 1 hg19 CCDS6375.2 . . . . . . . . . . G 24.8 4.569217 0.86439 . . ENSG00000147724 ENST00000395297;ENST00000160713 T 0.15834 2.39 5.35 5.35 0.76521 . 0.000000 0.85682 D 0.000000 T 0.45357 0.1338 M 0.79475 2.455 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.31613 -0.9937 10 0.46703 T 0.11 -10.4338 18.4074 0.90541 0.0:0.0:1.0:0.0 . 118 Q49AJ0 F135B_HUMAN M 118 ENSP00000378710:T118M ENSP00000160713:T118M T - 2 0 FAM135B 139338129 1.000000 0.71417 0.580000 0.28601 0.904000 0.53231 9.597000 0.98273 2.663000 0.90544 0.655000 0.94253 ACG TCGA-FB-AAQ6-01A-11D-A40W-08 FAM135B-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313590.3 0 0 0 14 194 0 51 0 0 0 0 51 2 1 0.999786 14 194 0 51 2 -3.220807 1 1 120916 1 32 1 1 2 3 2.671199 1 0.630000 1.870000 0.709588 0.280000 1.500000e-01 1.000000 0.270000 0.362512 0.280000 0 0.210000 0.410000 RAB11FIP1 80223 broad.mit.edu 37 8 37728914 37728914 + Missense_Mutation SNP C C A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr8:37728914C>A ENST00000330843.4 - 4 3418 c.3406G>T c.(3406-3408)Gct>Tct p.A1136S RAB11FIP1_ENST00000523182.1_5'UTR|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000287263.4_Intron NM_001002814.2 NP_001002814.2 Q6WKZ4 RFIP1_HUMAN RAB11 family interacting protein 1 (class I) p.A1136T(1) 49 Lung NSC(58;0.118)|all_lung(54;0.195) LUSC - Lung squamous cell carcinoma(8;3.62e-11) ACTCTACCAGCGGAGCCCTCT 0.542000 OREG0018713 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 1 Substitution - Missense(1) SO:0001583 missense ENST00000330843.4 0 1 hg19 CCDS34882.1 . . . . . . . . . . C 12.35 1.911299 0.33721 . . ENSG00000156675 ENST00000330843 T 0.44881 0.91 5.29 0.0514 0.14297 . 0.867765 0.09895 N 0.741866 T 0.16938 0.0407 N 0.19112 0.55 0.20926 N 0.999823 P;B 0.43826 0.818;0.239 B;B 0.36378 0.223;0.054 T 0.08576 -1.0715 10 0.07030 T 0.85 -1.0042 1.2767 0.02032 0.2411:0.4183:0.1345:0.2061 . 465;1136 Q67C35;Q6WKZ4 .;RFIP1_HUMAN S 1136 ENSP00000331342:A1136S ENSP00000331342:A1136S A - 1 0 RAB11FIP1 37848072 0.003000 0.15002 0.106000 0.21319 0.878000 0.50629 0.172000 0.16704 -0.054000 0.13266 0.555000 0.69702 GCT TCGA-FB-AAQ6-01A-11D-A40W-08 RAB11FIP1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000376816.1 0 0 0 153 447 0 211 0 7.655763e-01 0 10 0 211 2 1 1.000000 152 425 0 208 2 -3.319003 1 1 0 0 1 0 0 0 2.050546 0 0.630000 1.870000 0.625279 0.790000 6.800000e-01 0.910000 0.800000 0.801069 0.790000 0 0.730000 0.860000 RP1 6101 broad.mit.edu 37 8 55533850 55533850 + Silent SNP C C T rs141074157 TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr8:55533850C>T ENST00000220676.1 + 2 472 c.324C>T c.(322-324)caC>caT p.H108H NM_006269.1 NP_006260.1 P56715 RP1_HUMAN retinitis pigmentosa 1 (autosomal dominant) 169 all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123) OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285) TATGTTCCCACGGCAGGAAGG 0.682000 Colon(91;1014 1389 7634 14542 40420) 0 SO:0001819 synonymous_variant ENST00000220676.1 0 1 hg19 CCDS6160.1 TCGA-FB-AAQ6-01A-11D-A40W-08 RP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378532.2 0 0 0 143 276 0 126 0 1.169709e-01 0 2 0 126 2 1 1.000000 137 268 0 124 2 -14.558440 1 1 121412 11 41 1 0 0 0 2.050546 0 0.630000 1.870000 0.625279 0.990000 9.200000e-01 1.000000 1.000000 0.993809 0.990000 1 0.990000 1.000000 CRISPLD1 83690 broad.mit.edu 37 8 75928804 75928804 + Silent SNP G G C TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr8:75928804G>C ENST00000262207.4 + 7 1200 c.732G>C c.(730-732)ggG>ggC p.G244G CRISPLD1_ENST00000523524.1_Silent_p.G56G|CRISPLD1_ENST00000517786.1_Silent_p.G58G NM_031461.5 NP_113649.1 Q9H336 CRLD1_HUMAN cysteine-rich secretory protein LCCL domain containing 1 43 Breast(64;0.0799) Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161) TAACAGAAGGGTCAGACAGGT 0.353000 0 SO:0001819 synonymous_variant ENST00000262207.4 0 1 hg19 CCDS6219.1 TCGA-FB-AAQ6-01A-11D-A40W-08 CRISPLD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000379117.1 0 0 0 62 422 0 146 0 2.277480e-01 0 7 0 146 2 1 1.000000 60 416 0 146 2 -20.000000 1 1 0 0 1 0 0 0 2.050546 0 0.630000 1.870000 0.625279 0.390000 3.100000e-01 0.500000 0.400000 0.405835 0.390000 0 0.350000 0.450000 JAK2 3717 broad.mit.edu 37 9 5064981 5064981 + Silent SNP A A G TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chr9:5064981A>G ENST00000381652.3 + 9 1649 c.1155A>G c.(1153-1155)aaA>aaG p.K385K JAK2_ENST00000544510.1_Silent_p.K236K|JAK2_ENST00000539801.1_Silent_p.K385K NM_004972.3 NP_004963.1 O60674 JAK2_HUMAN Janus kinase 2 BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18) 32998 all_hematologic(13;0.137) Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147) Ruxolitinib(DB08877)|Tofacitinib(DB08895) ACCTCTGTAAAGAAGTAGCAC 0.348000 1 T, Mis, O ETV6, PCM1, BCR ALL, AML, MPD, CML Polycythemia Vera, Familial Dom yes 9 9p24 3717 Janus kinase 2 L 0 SO:0001819 synonymous_variant Familial Cancer Database ENST00000381652.3 0 1 hg19 CCDS6457.1 TCGA-FB-AAQ6-01A-11D-A40W-08 JAK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051609.1 0 0 0 69 79 0 75 1 8.512072e-01 6 0 0 75 2 1 1.000000 67 77 0 75 2 -20.000000 1 1 0 0 1 0 1 1 1.418992 1 0.630000 1.870000 0.459854 0.940000 8.000000e-01 1.000000 0.990000 0.935313 0.940000 1 0.870000 0.990000 AIFM1 9131 broad.mit.edu 37 X 129265770 129265770 + Missense_Mutation SNP C C A TCGA-FB-AAQ6-01A-11D-A40W-08 TCGA-FB-AAQ6-11A-11D-A40W-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d1327445-448e-492d-98c6-09a511e3b54b a05a5cde-bbd2-4c57-b5b9-b57586d42274 g.chrX:129265770C>A ENST00000287295.3 - 14 1683 c.1453G>T c.(1453-1455)Gat>Tat p.D485Y AIFM1_ENST00000535724.1_3'UTR|AIFM1_ENST00000440263.1_Missense_Mutation_p.D133Y|AIFM1_ENST00000346424.2_Missense_Mutation_p.D198Y|AIFM1_ENST00000319908.3_Missense_Mutation_p.D481Y|AIFM1_ENST00000460436.2_Missense_Mutation_p.D146Y NM_001130847.3|NM_004208.3 NP_001124319.1|NP_004199.1 O95831 AIFM1_HUMAN apoptosis-inducing factor, mitochondrion-associated, 1 30 Flavin adenine dinucleotide(DB03147) GGGCCCAAATCACTCCTAAGA 0.443000 0 SO:0001583 missense ENST00000287295.3 0 1 hg19 CCDS14618.1 . . . . . . . . . . C 27.3 4.819926 0.90873 . . ENSG00000156709 ENST00000460436;ENST00000346424;ENST00000319908;ENST00000440263;ENST00000287295 T;T;D;T;T 0.85258 0.59;0.57;-1.96;0.6;-0.96 5.8 5.8 0.92144 FAD/NAD-linked reductase, dimerisation (1);Pyridine nucleotide-disulphide oxidoreductase, dimerisation (1); 0.000000 0.85682 D 0.000000 D 0.94528 0.8238 M 0.92555 3.32 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;1.0;0.999 D 0.95449 0.8532 10 0.87932 D 0 -18.3899 19.0045 0.92844 0.0:1.0:0.0:0.0 . 198;481;485 O95831-2;O95831-3;O95831 .;.;AIFM1_HUMAN Y 146;198;481;133;485 ENSP00000431222:D146Y;ENSP00000316320:D198Y;ENSP00000315122:D481Y;ENSP00000405879:D133Y;ENSP00000287295:D485Y ENSP00000287295:D485Y D - 1 0 AIFM1 129093451 1.000000 0.71417 0.999000 0.59377 0.969000 0.65631 7.487000 0.81328 2.436000 0.82500 0.600000 0.82982 GAT TCGA-FB-AAQ6-01A-11D-A40W-08 AIFM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058247.2 0 0 0 186 122 0 111 1 1 52 9 0 111 2 1 1.000000 183 118 0 110 2 -20.000000 1 1 0 0 1 0 1 1 0.630000 1.870000 0.630000 0.940000 8.600000e-01 1.000000 0.960000 0.944458 0.940000 1 0.900000 0.980000