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 IGHMBP2 3508 broad.mit.edu 37 11 68675791 68675791 + Frame_Shift_Del DEL C C - TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr11:68675791delC ENST00000255078.3 + 3 546 c.435delC c.(433-435)tacfs p.Y145fs IGHMBP2_ENST00000539224.1_Frame_Shift_Del_p.Y145fs NM_002180.2 NP_002171.2 P38935 SMBP2_HUMAN immunoglobulin mu binding protein 2 36 STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713) ATGTCACTTACAGGCGACTGA 0.458000 0 SO:0001589 frameshift_variant ENST00000255078.3 0 1 hg19 CCDS8187.1 TCGA-IB-A6UF-01A-23D-A33T-08 IGHMBP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396862.1 1 0 0 42 372 0 64 0 2.772671e-01 0 10 0 64 2 0 0 0 0 0 0 1 1 47 367 0 64 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.124139 0 0.580000 1.890000 0.586003 0.350000 2.500000e-01 1.000000 0.350000 0.385254 0.350000 0 0.300000 0.420000 ERC1 23085 broad.mit.edu 37 12 1292488 1292488 + Frame_Shift_Del DEL A A - TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr12:1292488delA ENST00000397203.2 + 11 2464 c.2058delA c.(2056-2058)gcafs p.A686fs ERC1_ENST00000546231.2_Frame_Shift_Del_p.A686fs|ERC1_ENST00000360905.4_Frame_Shift_Del_p.A686fs|ERC1_ENST00000536573.2_3'UTR|ERC1_ENST00000589028.1_Frame_Shift_Del_p.A686fs|ERC1_ENST00000543086.3_Frame_Shift_Del_p.A658fs|ERC1_ENST00000355446.5_Frame_Shift_Del_p.A686fs Q8IUD2 RB6I2_HUMAN ELKS/RAB6-interacting/CAST family member 1 38 all_epithelial(11;0.0698)|Ovarian(42;0.107) OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567) CTTCTCTGGCATCCTCAGGAC 0.368000 0 SO:0001589 frameshift_variant ENST00000397203.2 1 1 hg19 CCDS8508.1 TCGA-IB-A6UF-01A-23D-A33T-08 ERC1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398380.2 1 0 0 210 601 0 79 1 8.862921e-01 3 10 0 79 2 0 0 0 0 0 0 1 1 212 600 0 77 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.712258 1 0.580000 1.890000 0.674419 0.990000 9.900000e-01 1.000000 1.000000 0.999743 0.990000 1 0.990000 1.000000 PARP15 165631 broad.mit.edu 37 3 122345673 122345673 + Splice_Site DEL G G - TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr3:122345673delG ENST00000464300.2 + 9 1297 c.e9-1 PARP15_ENST00000310366.4_Splice_Site|PARP15_ENST00000465304.1_Splice_Site|PARP15_ENST00000493645.1_Intron|PARP15_ENST00000483793.1_Intron NM_001113523.1 NP_001106995.1 Q460N3 PAR15_HUMAN poly (ADP-ribose) polymerase family, member 15 24 TTTTTTTTCAGGAAATGCCGG 0.373000 0 SO:0001630 splice_region_variant ENST00000464300.2 1 1 hg19 CCDS46893.1 TCGA-IB-A6UF-01A-23D-A33T-08 PARP15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000355964.2 1 0 0 54 251 0 42 0 1.822986e-13 0 1 0 42 2 0 0 0 0 0 0 1 1 63 249 0 41 2 0 0 0 0 0 0 -3.156361 1 1 0 0 1 0 0 0 2.070095 0 0.580000 1.890000 0.580000 0.600000 4.600000e-01 0.760000 0.610000 0.616300 0.600000 0 0.530000 0.690000 PHF15 0 broad.mit.edu 37 5 133901907 133901907 + Frame_Shift_Del DEL C C - TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 C - C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:133901907delC ENST00000402835.1 + 9 1326 c.1071delC c.(1069-1071)ttcfs p.F357fs PHF15_ENST00000282605.4_Frame_Shift_Del_p.F357fs|PHF15_ENST00000361895.2_Frame_Shift_Del_p.F357fs|PHF15_ENST00000395003.1_Frame_Shift_Del_p.F357fs 22 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) AGGTCAAGTTCAAGTCATTCT 0.567000 0 SO:0001589 frameshift_variant ENST00000402835.1 1 1 hg19 TCGA-IB-A6UF-01A-23D-A33T-08 PHF15-007 PUTATIVE alternative_5_UTR|basic|exp_conf protein_coding protein_coding OTTHUMT00000318543.1 1 0 0 130 537 0 99 1 9.999950e-01 11 62 0 99 2 0 0 0 0 0 0 1 1 129 531 0 99 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.101368 0 0.580000 1.890000 0.582422 0.670000 5.700000e-01 0.800000 0.670000 0.681561 0.670000 0 0.620000 0.730000 GBF1 8729 broad.mit.edu 37 10 104117903 104117903 + Silent SNP G G T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr10:104117903G>T ENST00000369983.3 + 9 1007 c.747G>T c.(745-747)ctG>ctT p.L249L NM_001199378.1|NM_001199379.1|NM_004193.2 NP_001186307.1|NP_001186308.1|NP_004184.1 Q92538 GBF1_HUMAN golgi brefeldin A resistant guanine nucleotide exchange factor 1 71 Colorectal(252;0.0236) GTTCAGAGCTGCCCACTCCCA 0.507000 0 SO:0001819 synonymous_variant ENST00000369983.3 1 1 hg19 CCDS7533.1 TCGA-IB-A6UF-01A-23D-A33T-08 GBF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050051.1 1 0 1 241 781 0 179 1 9.997901e-01 19 23 0 179 2 0 0 0 0 0 2 1 1 238 776 0 178 2 0 0 0 0 179 2 -20.000000 1 1 0 0 1 1 2 3 2.146677 0 0.580000 1.890000 0.588356 0.820000 7.300000e-01 1.000000 0.830000 0.840325 0.820000 0 0.780000 0.890000 SORCS1 114815 broad.mit.edu 37 10 108412204 108412204 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr10:108412204G>A ENST00000263054.6 - 18 2418 c.2411C>T c.(2410-2412)aCg>aTg p.T804M SORCS1_ENST00000344440.6_Missense_Mutation_p.T804M|SORCS1_ENST00000369698.1_Missense_Mutation_p.T339M NM_001206570.1|NM_052918.4 NP_001193499.1|NP_443150.3 Q8WY21 SORC1_HUMAN sortilin-related VPS10 domain containing receptor 1 127 Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168) TCCATCAGCCGTGACTATCCG 0.532000 0 SO:0001583 missense ENST00000263054.6 1 1 hg19 CCDS7559.1 . . . . . . . . . . G 16.83 3.231893 0.58777 . . ENSG00000108018 ENST00000369698;ENST00000263054;ENST00000344440 T;T;T 0.69561 -0.41;-0.41;-0.41 5.74 5.74 0.90152 PKD/Chitinase domain (1);PKD domain (1); 0.000000 0.85682 D 0.000000 T 0.80924 0.4717 L 0.61218 1.895 0.54753 D 0.999989 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.87578 0.998;0.993;0.997;0.998;0.997 T 0.78580 -0.2149 9 . . . -17.2727 19.9145 0.97053 0.0:0.0:1.0:0.0 . 804;804;804;804;804 A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2 .;.;.;SORC1_HUMAN;. M 339;804;804 ENSP00000358712:T339M;ENSP00000263054:T804M;ENSP00000345964:T804M . T - 2 0 SORCS1 108402194 1.000000 0.71417 0.959000 0.39883 0.138000 0.21146 9.277000 0.95755 2.709000 0.92574 0.655000 0.94253 ACG TCGA-IB-A6UF-01A-23D-A33T-08 SORCS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050232.4 1 0 1 135 317 0 68 0 0 0 0 68 2 1 1 158 494 2 1110 5 1 1 135 309 0 68 2 0 0 0 0 68 2 -20.000000 1 1 121412 10 43 1 1 2 3 2.146677 0 0.580000 1.890000 0.588356 0.990000 9.000000e-01 1.000000 1.000000 0.989796 0.990000 1 0.970000 1.000000 GAD2 2572 broad.mit.edu 37 10 26589858 26589858 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr10:26589858G>A ENST00000376261.3 + 16 2229 c.1726G>A c.(1726-1728)Gaa>Aaa p.E576K GAD2_ENST00000259271.3_Missense_Mutation_p.E576K NM_001134366.1 NP_001127838.1 Q05329 DCE2_HUMAN glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa) 48 CTTCCTGATTGAAGAAATAGA 0.438000 0 SO:0001583 missense ENST00000376261.3 1 1 hg19 CCDS7149.1 . . . . . . . . . . G 17.34 3.366041 0.61513 . . ENSG00000136750 ENST00000376261;ENST00000259271 T;T 0.39592 1.07;1.07 5.71 5.71 0.89125 Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1); 0.173449 0.53938 D 0.000050 T 0.37865 0.1019 L 0.35542 1.07 0.80722 D 1 B 0.10296 0.003 B 0.09377 0.004 T 0.08269 -1.0730 10 0.46703 T 0.11 -27.4343 19.8579 0.96771 0.0:0.0:1.0:0.0 . 576 Q05329 DCE2_HUMAN K 576 ENSP00000365437:E576K;ENSP00000259271:E576K ENSP00000259271:E576K E + 1 0 GAD2 26629864 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.476000 0.97823 2.687000 0.91594 0.655000 0.94253 GAA TCGA-IB-A6UF-01A-23D-A33T-08 GAD2-001 KNOWN alternative_3_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047255.1 1 0 0 38 488 0 92 0 0 0 1 0 92 2 0 0 0 0 0 2 1 1 38 481 0 91 2 0 0 0 0 92 2 -9.272560 1 1 0 0 1 1 2 3 2.111627 0 0.580000 1.890000 0.584816 0.250000 1.700000e-01 1.000000 0.250000 0.278686 0.250000 0 0.210000 0.300000 PTCHD3 374308 broad.mit.edu 37 10 27702453 27702453 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr10:27702453G>A ENST00000438700.3 - 1 844 c.727C>T c.(727-729)Cgg>Tgg p.R243W NM_001034842.3 NP_001030014.2 Q3KNS1 PTHD3_HUMAN patched domain containing 3 55 CCCTTTTCCCGCGCCACGCGC 0.627000 0 SO:0001583 missense ENST00000438700.3 1 1 hg19 CCDS31173.1 . . . . . . . . . . G 11.05 1.524459 0.27299 . . ENSG00000182077 ENST00000438700 D 0.85702 -2.02 3.93 -0.963 0.10330 . 3.428320 0.00760 N 0.001132 T 0.75258 0.3825 N 0.08118 0 0.09310 N 1 B 0.20459 0.045 B 0.09377 0.004 T 0.63985 -0.6513 10 0.66056 D 0.02 -0.2446 14.3009 0.66352 0.0:0.7511:0.2489:0.0 . 243 Q3KNS1 PTHD3_HUMAN W 243 ENSP00000417658:R243W ENSP00000417658:R243W R - 1 2 PTCHD3 27742459 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.661000 0.05311 -0.023000 0.13963 -0.311000 0.09066 CGG TCGA-IB-A6UF-01A-23D-A33T-08 PTCHD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047325.3 1 0 1 78 225 0 51 0 0 0 0 51 2 0 0 0 0 0 2 1 1 78 225 0 49 2 0 0 0 0 51 2 -20.000000 1 1 121406 1 33 1 1 2 3 2.111627 0 0.580000 1.890000 0.584816 0.890000 7.300000e-01 1.000000 1.000000 0.898314 0.890000 1 0.810000 1.000000 RBP3 5949 broad.mit.edu 37 10 48388884 48388884 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr10:48388884C>T ENST00000224600.4 - 1 2107 c.1994G>A c.(1993-1995)cGg>cAg p.R665Q AL731561.2_ENST00000581861.1_RNA NM_002900.2 NP_002891.1 P10745 RET3_HUMAN retinol binding protein 3, interstitial 59 Vitamin A(DB00162) CAGCTTGGCCCGCAGGAGGGC 0.677000 0 SO:0001583 missense ENST00000224600.4 1 1 hg19 CCDS7218.1 . . . . . . . . . . C 0.005 -2.163647 0.00318 . . ENSG00000107618 ENST00000224600 T 0.61859 0.07 5.53 -2.86 0.05717 . 1.155020 0.06333 N 0.706523 T 0.31009 0.0783 N 0.03608 -0.345 0.09310 N 1 B 0.13594 0.008 B 0.04013 0.001 T 0.22871 -1.0204 10 0.13853 T 0.58 -0.4135 11.9866 0.53151 0.0:0.379:0.0:0.621 . 665 P10745 RET3_HUMAN Q 665 ENSP00000224600:R665Q ENSP00000224600:R665Q R - 2 0 RBP3 48008890 0.000000 0.05858 0.000000 0.03702 0.071000 0.16799 -1.070000 0.03440 -0.584000 0.05913 -0.254000 0.11334 CGG TCGA-IB-A6UF-01A-23D-A33T-08 RBP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047888.1 1 0 1 59 161 0 50 0 0 0 0 50 2 0 0 0 0 0 2 1 1 59 158 0 50 2 0 0 0 0 50 2 -5.215649 1 1 121232 1 31 1 1 2 3 2.126813 0 0.580000 1.890000 0.586003 0.940000 7.400000e-01 1.000000 1.000000 0.926020 0.940000 1 0.830000 1.000000 SLIT1 6585 broad.mit.edu 37 10 98764503 98764503 + Silent SNP G G C TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr10:98764503G>C ENST00000266058.4 - 33 3902 c.3657C>G c.(3655-3657)ggC>ggG p.G1219G ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Silent_p.G1219G NM_003061.2 NP_003052.2 O75093 SLIT1_HUMAN slit homolog 1 (Drosophila) 78 Colorectal(252;0.162) CACGCACATGGCCCTGGTACA 0.597000 0 SO:0001819 synonymous_variant ENST00000266058.4 1 1 hg19 CCDS7453.1 TCGA-IB-A6UF-01A-23D-A33T-08 SLIT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049636.1 1 0 1 86 197 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 1 85 194 0 57 2 0 0 0 0 58 2 -20.000000 1 1 0 0 1 1 2 3 2.146677 0 0.580000 1.890000 0.588356 0.990000 8.800000e-01 1.000000 1.000000 0.988343 0.990000 1 0.970000 1.000000 ELMOD1 55531 broad.mit.edu 37 11 107526732 107526732 + Missense_Mutation SNP A A T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr11:107526732A>T ENST00000265840.7 + 11 1037 c.772A>T c.(772-774)Acc>Tcc p.T258S ELMOD1_ENST00000531234.1_Missense_Mutation_p.T252S|ELMOD1_ENST00000443271.2_Missense_Mutation_p.T250S NM_018712.3 NP_061182.3 Q8N336 ELMD1_HUMAN ELMO/CED-12 domain containing 1 19 Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104) AGCTCTAAAAACCCATTTCTA 0.373000 0 SO:0001583 missense ENST00000265840.7 0 1 hg19 CCDS44723.1 . . . . . . . . . . A 15.53 2.861859 0.51482 . . ENSG00000110675 ENST00000531234;ENST00000265840;ENST00000443271 T;T;T 0.27720 1.65;1.65;1.65 6.16 6.16 0.99307 Engulfment/cell motility, ELMO (2); 0.141782 0.64402 D 0.000006 T 0.26340 0.0643 L 0.39147 1.195 0.80722 D 1 B;B 0.28470 0.213;0.178 B;B 0.30401 0.115;0.07 T 0.05699 -1.0869 10 0.06365 T 0.9 . 16.8061 0.85666 1.0:0.0:0.0:0.0 . 258;250 Q8N336;G5E9S5 ELMD1_HUMAN;. S 252;258;250 ENSP00000433232:T252S;ENSP00000265840:T258S;ENSP00000412257:T250S ENSP00000265840:T258S T + 1 0 ELMOD1 107031942 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 7.143000 0.77348 2.367000 0.80283 0.528000 0.53228 ACC TCGA-IB-A6UF-01A-23D-A33T-08 ELMOD1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000389406.1 0 0 0 13 17 0 8 0 0 0 0 8 2 0 0 0 0 0 2 1 9.998830e-01 13 17 0 8 2 0 0 0 0 8 2 -16.328000 1 1 119174 1 28 1 1 2 3 2.124139 0 0.580000 1.890000 0.586003 0.990000 9.300000e-01 1.000000 1.000000 0.995555 0.990000 1 0.990000 1.000000 ANO3 63982 broad.mit.edu 37 11 26463589 26463589 + Missense_Mutation SNP C C A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr11:26463589C>A ENST00000256737.3 + 2 1023 c.171C>A c.(169-171)ttC>ttA p.F57L ANO3_ENST00000537978.1_Missense_Mutation_p.F41L|ANO3_ENST00000525139.1_Missense_Mutation_p.F41L|ANO3_ENST00000531646.1_Missense_Mutation_p.F57L NM_031418.2 NP_113606.2 Q9BYT9 ANO3_HUMAN anoctamin 3 68 CTTCCCTCTTCCAGTCAACCG 0.468000 0 SO:0001583 missense ENST00000256737.3 1 1 hg19 CCDS31447.1 . . . . . . . . . . C 9.670 1.146527 0.21288 . . ENSG00000134343 ENST00000537978;ENST00000525139;ENST00000256737;ENST00000531646 T;T;T;T 0.62364 0.03;0.03;0.03;0.03 5.24 1.93 0.25924 . 0.141341 0.49916 D 0.000138 T 0.30230 0.0758 N 0.03608 -0.345 0.27524 N 0.951301 B 0.02656 0.0 B 0.01281 0.0 T 0.19063 -1.0317 10 0.10902 T 0.67 . 6.8171 0.23837 0.0:0.6403:0.0:0.3597 . 57 Q9BYT9 ANO3_HUMAN L 41;41;57;57 ENSP00000440737:F41L;ENSP00000432576:F41L;ENSP00000256737:F57L;ENSP00000435275:F57L ENSP00000256737:F57L F + 3 2 ANO3 26420165 0.978000 0.34361 1.000000 0.80357 0.958000 0.62258 -0.158000 0.10070 0.268000 0.21939 0.650000 0.86243 TTC TCGA-IB-A6UF-01A-23D-A33T-08 ANO3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000387806.1 1 0 1 239 595 0 135 0 0 0 0 135 2 0 0 0 0 0 2 1 1 239 584 0 134 2 0 0 0 0 135 2 -20.000000 1 1 0 0 1 1 2 3 2.084175 0 0.580000 1.890000 0.581214 0.980000 8.800000e-01 1.000000 1.000000 0.973933 0.980000 1 0.930000 1.000000 LPXN 9404 broad.mit.edu 37 11 58317463 58317463 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr11:58317463C>T ENST00000395074.2 - 6 731 c.643G>A c.(643-645)Gct>Act p.A215T LPXN_ENST00000528954.1_Missense_Mutation_p.A220T|LPXN_ENST00000528489.1_Missense_Mutation_p.A195T NM_004811.2 NP_004802.1 O60711 LPXN_HUMAN leupaxin 14 Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24) ATGGGAGCAGCGCAGTAAGCA 0.493000 0 SO:0001583 missense ENST00000395074.2 1 1 hg19 CCDS7969.1 . . . . . . . . . . C 16.69 3.194268 0.58017 . . ENSG00000110031 ENST00000528954;ENST00000395074 D;D 0.87029 -2.2;-2.2 5.95 5.95 0.96441 Zinc finger, LIM-type (5); 0.121122 0.64402 D 0.000017 D 0.84973 0.5591 N 0.21373 0.66 0.41615 D 0.988935 P;D;P 0.71674 0.845;0.998;0.853 B;P;B 0.58130 0.34;0.833;0.439 D 0.84694 0.0724 10 0.52906 T 0.07 . 8.061 0.30633 0.1594:0.7622:0.0:0.0784 . 195;220;215 B7Z5P7;B4DV71;O60711 .;.;LPXN_HUMAN T 220;215 ENSP00000431284:A220T;ENSP00000378512:A215T ENSP00000378512:A215T A - 1 0 LPXN 58074039 0.996000 0.38824 0.831000 0.32960 0.943000 0.58893 3.514000 0.53422 2.824000 0.97209 0.655000 0.94253 GCT TCGA-IB-A6UF-01A-23D-A33T-08 LPXN-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000394709.1 1 0 1 157 352 0 103 1 9.906770e-01 5 14 0 103 2 0 0 0 0 0 2 1 1 157 348 0 102 2 0 0 0 0 103 2 -11.755210 1 1 121412 2 33 1 1 2 3 2.093093 0 0.580000 1.890000 0.582422 0.990000 9.200000e-01 1.000000 1.000000 0.994293 0.990000 1 0.990000 1.000000 PLCB3 5331 broad.mit.edu 37 11 64031070 64031070 + Splice_Site SNP G G T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr11:64031070G>T ENST00000540288.1 + 20 2558 c.e20+1 PLCB3_ENST00000325234.5_Splice_Site|PLCB3_ENST00000279230.6_Splice_Site NM_000932.2 NP_000923.1 Q01970 PLCB3_HUMAN phospholipase C, beta 3 (phosphatidylinositol-specific) 33 ATCCGCTCCGGTGAGGCCTTG 0.647000 0 SO:0001630 splice_region_variant ENST00000540288.1 1 0 hg19 CCDS8064.1 . . . . . . . . . . G 21.8 4.205412 0.79127 . . ENSG00000149782 ENST00000279230;ENST00000540288;ENST00000325234 . . . 4.85 4.85 0.62838 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 17.0853 0.86610 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . PLCB3 63787646 1.000000 0.71417 1.000000 0.80357 0.843000 0.47879 9.400000 0.97290 2.404000 0.81709 0.561000 0.74099 . TCGA-IB-A6UF-01A-23D-A33T-08 PLCB3-002 KNOWN alternative_3_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396405.1 1 0 0 64 151 0 49 0 9.068617e-02 1 1 0 49 2 0 0 0 0 0 2 1 1 65 150 0 49 2 0 0 0 0 49 2 -20.000000 1 1 0 0 1 1 2 3 2.124139 0 0.580000 1.890000 0.586003 0.990000 8.300000e-01 1.000000 1.000000 0.976609 0.990000 1 0.930000 1.000000 POLR3B 55703 broad.mit.edu 37 12 106821038 106821038 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr12:106821038G>A ENST00000228347.4 + 13 1387 c.1165G>A c.(1165-1167)Gac>Aac p.D389N POLR3B_ENST00000549195.1_3'UTR|POLR3B_ENST00000539066.1_Missense_Mutation_p.D331N NM_018082.5 NP_060552.4 Q9NW08 RPC2_HUMAN polymerase (RNA) III (DNA directed) polypeptide B 57 AAAGATTGCCGACCAGGTGAT 0.353000 0 SO:0001583 missense ENST00000228347.4 0 1 hg19 CCDS9105.1 . . . . . . . . . . G 26.2 4.717076 0.89205 . . ENSG00000013503 ENST00000228347;ENST00000551370;ENST00000539066;ENST00000549569;ENST00000549195 T;T;T 0.76448 0.03;0.03;-1.02 5.75 5.75 0.90469 RNA polymerase, beta subunit, protrusion (1); 0.000000 0.85682 D 0.000000 T 0.81754 0.4889 M 0.72894 2.215 0.80722 D 1 P 0.35821 0.523 B 0.40940 0.344 T 0.81274 -0.1007 10 0.54805 T 0.06 -28.5091 20.3046 0.98621 0.0:0.0:1.0:0.0 . 389 Q9NW08 RPC2_HUMAN N 389;389;331;147;52 ENSP00000228347:D389N;ENSP00000445721:D331N;ENSP00000448398:D147N ENSP00000228347:D389N D + 1 0 POLR3B 105345168 1.000000 0.71417 0.998000 0.56505 0.872000 0.50106 9.304000 0.96190 2.878000 0.98634 0.650000 0.86243 GAC TCGA-IB-A6UF-01A-23D-A33T-08 POLR3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407166.1 0 0 0 4 299 0 49 0 1.282031e-02 0 9 0 49 2 0 0 0 0 0 2 1 8.870701e-01 4 294 0 48 2 0 0 0 0 49 2 -2.874050 1 1 121404 2 33 1 1 2 3 2.092114 0 0.580000 1.890000 0.582422 0.040000 0 0.130000 0.040000 0.065805 0.040000 0 0.020000 0.080000 HIST4H4 121504 broad.mit.edu 37 12 14923783 14923783 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr12:14923783C>T ENST00000539745.1 - 1 282 c.236G>A c.(235-237)cGc>cAc p.R79H HIST4H4_ENST00000541592.1_5'Flank|RP11-174G6.5_ENST00000562691.2_RNA NM_175054.2 NP_778224.1 P62805 H4_HUMAN histone cluster 4, H4 6 GACGGTCTTGCGCTTGGCGTG 0.587000 OREG0021698 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000539745.1 0 1 hg19 CCDS8665.1 . . . . . . . . . . C 22.0 4.227488 0.79576 . . ENSG00000197837 ENST00000539745 T 0.77358 -1.09 3.99 3.09 0.35607 . 0.000000 0.50627 U 0.000116 T 0.81950 0.4931 . . . 0.53005 D 0.999961 . . . . . . T 0.82623 -0.0366 7 0.87932 D 0 . 9.6665 0.39988 0.0:0.8959:0.0:0.1041 . . . . H 79 ENSP00000443017:R79H ENSP00000350767:R79H R - 2 0 HIST4H4 14815050 1.000000 0.71417 0.991000 0.47740 0.588000 0.36517 5.280000 0.65603 1.035000 0.39972 0.585000 0.79938 CGC TCGA-IB-A6UF-01A-23D-A33T-08 HIST4H4-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400844.1 0 0 0 5 277 0 72 0 9.927413e-03 0 7 0 72 2 0 0 0 0 0 2 1 9.380859e-01 5 277 0 70 2 0 0 0 0 72 2 -2.784528 1 1 121412 1 30 1 0 1 1 1.502393 1 0.580000 1.890000 0.408451 0.040000 1.000000e-02 0.100000 0.040000 0.051452 0.040000 0 0.020000 0.070000 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 C G C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr12:25398285C>G ENST00000256078.4 - 2 97 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|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) CCTACGCCACCAGCTCCAACT 0.348000 G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE) 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 5144 Substitution - Missense(5142)|Insertion - In frame(2) GRCh37 CM076251 KRAS M rs121913530 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 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 28.6 4.930538 0.92389 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78246 -1.16;-1.16;-1.16;-1.16 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.84893 0.5573 M 0.84082 2.675 0.80722 D 1 P;P 0.43287 0.802;0.741 B;P 0.47941 0.36;0.562 D 0.86658 0.1902 10 0.66056 D 0.02 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN R 12 ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R ENSP00000256078:G12R G - 1 0 KRAS 25289552 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-IB-A6UF-01A-23D-A33T-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 67 112 0 21 1 9.999426e-01 17 12 0 21 2 1 1 248 277 0 634 2 1 1 67 112 0 21 2 1 1 4368 3647 0 21 2 -20.000000 1 1 0 0 1 1 4 5 3.331817 1 0.580000 1.890000 0.744494 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 SCN8A 6334 broad.mit.edu 37 12 52183167 52183167 + Missense_Mutation SNP G G T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr12:52183167G>T ENST00000354534.6 + 24 4562 c.4384G>T c.(4384-4386)Gtc>Ttc p.V1462F SCN8A_ENST00000545061.1_Missense_Mutation_p.V1421F NM_001177984.2|NM_014191.3 NP_001171455.1|NP_055006.1 Q9UQD0 SCN8A_HUMAN sodium channel, voltage gated, type VIII, alpha subunit 55 Valproic Acid(DB00313) GTTCATTGGTGTCATCATTGA 0.428000 0 SO:0001583 missense ENST00000354534.6 1 1 hg19 CCDS44891.1 . . . . . . . . . . G 27.6 4.844393 0.91197 . . ENSG00000196876 ENST00000354534;ENST00000545061;ENST00000355133 D;D;D 0.99080 -5.4;-5.4;-5.4 4.37 4.37 0.52481 Ion transport (1); 0.000000 0.85682 D 0.000000 D 0.99393 0.9786 M 0.89715 3.055 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.78314 0.991;0.989 D 0.98548 1.0635 10 0.87932 D 0 . 18.2498 0.89998 0.0:0.0:1.0:0.0 . 1421;1462 F8VWM7;Q9UQD0 .;SCN8A_HUMAN F 1462;1421;1421 ENSP00000346534:V1462F;ENSP00000440360:V1421F;ENSP00000347255:V1421F ENSP00000346534:V1462F V + 1 0 SCN8A 50469434 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 9.601000 0.98297 2.713000 0.92767 0.655000 0.94253 GTC TCGA-IB-A6UF-01A-23D-A33T-08 SCN8A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404372.3 1 0 1 130 273 0 83 0 0 0 0 83 2 0 0 0 0 0 2 1 1 130 272 0 82 2 0 0 0 0 83 2 -20.000000 1 1 0 0 1 1 2 3 2.092114 0 0.580000 1.890000 0.582422 0.990000 9.500000e-01 1.000000 1.000000 0.997775 0.990000 1 0.990000 1.000000 HOXC4 3221 broad.mit.edu 37 12 54448134 54448134 + Missense_Mutation SNP A A G TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr12:54448134A>G ENST00000430889.2 + 1 474 c.428A>G c.(427-429)cAc>cGc p.H143R HOXC4_ENST00000609810.1_Missense_Mutation_p.H143R|HOXC4_ENST00000303406.4_Missense_Mutation_p.H143R NM_153633.2 NP_705897.1 P09017 HXC4_HUMAN homeobox C4 13 AAAAAAATTCACGTTAGCACG 0.652000 0 SO:0001583 missense ENST00000430889.2 1 1 hg19 CCDS8873.1 . . . . . . . . . . A 15.83 2.949247 0.53186 . . ENSG00000198353 ENST00000303406;ENST00000430889 D;D 0.89681 -2.55;-2.55 4.26 4.26 0.50523 Homeodomain-like (1); 0.117106 0.56097 D 0.000028 D 0.95133 0.8423 M 0.92555 3.32 0.80722 D 1 D 0.89917 1.0 D 0.71184 0.972 D 0.95959 0.8960 10 0.87932 D 0 . 12.7918 0.57539 1.0:0.0:0.0:0.0 . 143 P09017 HXC4_HUMAN R 143 ENSP00000305973:H143R;ENSP00000399808:H143R ENSP00000305973:H143R H + 2 0 HOXC4 52734401 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 8.711000 0.91396 1.918000 0.55548 0.379000 0.24179 CAC TCGA-IB-A6UF-01A-23D-A33T-08 HOXC4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000358963.1 1 0 0 52 154 0 32 1 8.053945e-01 2 9 0 32 2 0 0 0 0 0 2 1 9.999951e-01 52 151 1 31 19 0 0 0 0 32 2 -20.000000 1 1 0 0 1 1 2 3 2.092114 0 0.580000 1.890000 0.582422 0.870000 6.700000e-01 1.000000 1.000000 0.874722 0.870000 1 0.770000 0.990000 ARHGAP9 64333 broad.mit.edu 37 12 57873000 57873000 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr12:57873000C>T ENST00000356411.2 - 2 328 c.190G>A c.(190-192)Gca>Aca p.A64T ARHGAP9_ENST00000550288.1_Missense_Mutation_p.A143T|ARHGAP9_ENST00000430041.2_5'Flank|ARHGAP9_ENST00000393791.3_Missense_Mutation_p.A64T|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000393797.2_Missense_Mutation_p.A135T|ARHGAP9_ENST00000424809.2_Missense_Mutation_p.A64T Q9BRR9 RHG09_HUMAN Rho GTPase activating protein 9 30 GBM - Glioblastoma multiforme(3;3.37e-34) AGGCGTCTTGCCAACCACCAG 0.537000 0 SO:0001583 missense ENST00000356411.2 0 1 hg19 . . . . . . . . . . C 25.0 4.587742 0.86851 . . ENSG00000123329 ENST00000393791;ENST00000356411;ENST00000424809;ENST00000393797;ENST00000340423 T;T;T;T 0.34275 1.37;1.37;1.37;1.37 4.97 4.97 0.65823 Src homology-3 domain (4); 0.079838 0.49916 D 0.000134 T 0.55210 0.1906 M 0.64997 1.995 0.33210 D 0.553344 D;D;P;D;D 0.65815 0.986;0.995;0.77;0.982;0.986 P;D;P;P;P 0.67231 0.894;0.95;0.478;0.78;0.86 T 0.67256 -0.5716 10 0.62326 D 0.03 . 14.0957 0.65019 0.0:1.0:0.0:0.0 . 64;143;64;64;64 B4E248;Q6ZN13;Q9BRR9;Q9BRR9-2;E9PDX9 .;.;RHG09_HUMAN;.;. T 64;64;64;135;113 ENSP00000377380:A64T;ENSP00000348782:A64T;ENSP00000394307:A64T;ENSP00000377386:A135T ENSP00000344852:A113T A - 1 0 ARHGAP9 56159267 1.000000 0.71417 1.000000 0.80357 0.975000 0.68041 4.695000 0.61767 2.460000 0.83146 0.655000 0.94253 GCA TCGA-IB-A6UF-01A-23D-A33T-08 ARHGAP9-201 KNOWN basic|appris_candidate protein_coding protein_coding 0 0 0 6 680 0 106 0 1.181355e-04 0 2 0 106 2 0 0 0 0 0 2 1 9.636218e-01 6 671 0 106 2 0 0 0 0 106 2 -2.287919 0 1 0 0 1 1 2 3 2.092114 0 0.580000 1.890000 0.582422 0.020000 0 0.070000 0.040000 0.043983 0.020000 0 0.010000 0.050000 C1R 715 broad.mit.edu 37 12 7187985 7187985 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr12:7187985C>T ENST00000542285.1 - 11 1962 c.1813G>A c.(1813-1815)Gtt>Att p.V605I P00736 C1R_HUMAN complement component 1, r subcomponent 16 Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072) ACTGCAAAAACGCCCCCACTA 0.572000 0 SO:0001583 missense ENST00000542285.1 1 1 hg19 . . . . . . . . . . C 16.64 3.178207 0.57692 . . ENSG00000159403 ENST00000290575;ENST00000542285 T 0.41758 0.99 5.7 5.7 0.88788 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 0.092388 0.46145 D 0.000303 T 0.51483 0.1677 . . . 0.30586 N 0.762027 P 0.34934 0.476 B 0.43445 0.42 T 0.56595 -0.7953 9 0.62326 D 0.03 . 19.8479 0.96722 0.0:1.0:0.0:0.0 . 657 P00736 C1R_HUMAN I 620;605 ENSP00000438615:V605I ENSP00000290575:V620I V - 1 0 C1R 7058240 0.988000 0.35896 0.993000 0.49108 0.102000 0.19082 2.342000 0.43992 2.681000 0.91329 0.655000 0.94253 GTT TCGA-IB-A6UF-01A-23D-A33T-08 C1R-201 KNOWN basic|appris_candidate_longest protein_coding protein_coding 0 0 1 95 114 0 46 1 1 152 1787 0 46 2 0 0 0 0 0 2 1 1 94 113 0 46 2 0 0 0 0 46 2 -20.000000 1 1 120996 9 39 1 0 1 1 1.518149 1 0.580000 1.890000 0.408451 0.960000 8.700000e-01 1.000000 0.990000 0.964953 0.960000 1 0.920000 1.000000 PPFIA2 8499 broad.mit.edu 37 12 81839441 81839441 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr12:81839441G>A ENST00000549396.1 - 6 624 c.464C>T c.(463-465)aCg>aTg p.T155M PPFIA2_ENST00000550359.2_Missense_Mutation_p.T2M|PPFIA2_ENST00000548586.1_Missense_Mutation_p.T155M|PPFIA2_ENST00000443686.3_Missense_Mutation_p.T81M|PPFIA2_ENST00000552948.1_Missense_Mutation_p.T155M|RP11-315E17.1_ENST00000550272.1_RNA|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000550584.2_Missense_Mutation_p.T155M|PPFIA2_ENST00000333447.7_Missense_Mutation_p.T137M|PPFIA2_ENST00000549325.1_Missense_Mutation_p.T137M|PPFIA2_ENST00000407050.4_Missense_Mutation_p.T81M NM_001220476.1|NM_001282536.1|NM_003625.3 NP_001207405.1|NP_001269465.1|NP_003616.2 O75334 LIPA2_HUMAN protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2 85 TTTTACCACCGTCATTCTTAG 0.423000 0 SO:0001583 missense ENST00000549396.1 1 1 hg19 CCDS55857.1 . . . . . . . . . . G 32 5.147230 0.94603 . . ENSG00000139220 ENST00000549396;ENST00000549325;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948;ENST00000551442 T;T;T;T;T;T;T;T 0.49720 0.77;0.77;0.77;0.77;0.77;0.77;0.77;0.77 5.83 5.83 0.93111 . 0.000000 0.85682 D 0.000000 T 0.61986 0.2391 L 0.32530 0.975 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.85130 0.997;0.99 T 0.63346 -0.6658 10 0.87932 D 0 -13.5925 20.115 0.97926 0.0:0.0:1.0:0.0 . 55;155 B7Z4H8;O75334 .;LIPA2_HUMAN M 155;137;81;166;137;155;81;155;137 ENSP00000450337:T155M;ENSP00000450298:T137M;ENSP00000385093:T81M;ENSP00000327416:T137M;ENSP00000449338:T155M;ENSP00000388373:T81M;ENSP00000447868:T155M;ENSP00000449469:T137M ENSP00000327416:T137M T - 2 0 PPFIA2 80363572 1.000000 0.71417 0.995000 0.50966 0.985000 0.73830 9.869000 0.99810 2.761000 0.94854 0.650000 0.86243 ACG TCGA-IB-A6UF-01A-23D-A33T-08 PPFIA2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000408030.1 1 0 1 54 130 0 53 0 0 0 1 0 53 2 0 0 0 0 0 2 1 1 54 128 0 53 2 0 0 0 0 53 2 -6.123750 1 1 120828 1 26 1 1 2 3 2.092114 0 0.580000 1.890000 0.582422 0.990000 7.900000e-01 1.000000 1.000000 0.964414 0.990000 1 0.900000 1.000000 TUBA3C 7278 broad.mit.edu 37 13 19751421 19751421 + Silent SNP G G A rs142245280 TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr13:19751421G>A ENST00000400113.3 - 4 806 c.702C>T c.(700-702)atC>atT p.I234I NM_006001.2 NP_005992.1 Q13748 TBA3C_HUMAN tubulin, alpha 3c 72 all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162) TGGAGGACACGATCTGCCCAA 0.567000 0 SO:0001819 synonymous_variant ENST00000400113.3 1 1 hg19 CCDS9284.1 TCGA-IB-A6UF-01A-23D-A33T-08 TUBA3C-002 KNOWN not_best_in_genome_evidence|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044007.2 1 0 0 250 563 0 126 0 0 0 0 126 2 0 0 0 0 0 2 1 1 244 548 0 128 2 0 0 0 0 126 2 -20.000000 1 0 121412 10 45 1 1 2 3 2.125837 0 0.580000 1.890000 0.586003 0.990000 9.600000e-01 1.000000 1.000000 0.997827 0.990000 1 0.990000 1.000000 MTUS2 23281 broad.mit.edu 37 13 30002979 30002979 + Translation_Start_Site SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr13:30002979G>A ENST00000542829.1 + 0 134 MTUS2_ENST00000380808.2_De_novo_Start_InFrame|MTUS2_ENST00000431530.3_Intron Q5JR59 MTUS2_HUMAN microtubule associated tumor suppressor candidate 2 20 AGCCTGCCGGGATGGGCCATT 0.607000 0 ENST00000542829.1 0 1 hg19 TCGA-IB-A6UF-01A-23D-A33T-08 MTUS2-201 KNOWN basic protein_coding protein_coding 0 0 0 66 229 0 49 0 0 0 0 49 2 0 0 0 0 0 2 1 1 66 224 0 49 2 0 0 0 0 49 2 -20.000000 1 1 0 0 1 0 1 1 2.057634 0 0.580000 1.890000 0.578778 0.760000 6.100000e-01 0.930000 0.770000 0.773584 0.760000 0 0.680000 0.850000 STXBP6 29091 broad.mit.edu 37 14 25325303 25325303 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr14:25325303G>A ENST00000323944.5 - 4 741 c.290C>T c.(289-291)tCg>tTg p.S97L STXBP6_ENST00000546511.1_Missense_Mutation_p.S97L|STXBP6_ENST00000550887.1_Missense_Mutation_p.S97L|STXBP6_ENST00000358326.2_Missense_Mutation_p.S97L|STXBP6_ENST00000548724.1_Missense_Mutation_p.S97L|STXBP6_ENST00000419632.2_Missense_Mutation_p.S97L|STXBP6_ENST00000396700.1_Missense_Mutation_p.S97L Q8NFX7 STXB6_HUMAN syntaxin binding protein 6 (amisyn) 7 AAACTCTGCCGAATCCTGGAA 0.388000 0 SO:0001583 missense ENST00000323944.5 0 1 hg19 CCDS9634.1 . . . . . . . . . . G 15.26 2.781990 0.49891 . . ENSG00000168952 ENST00000396700;ENST00000548724;ENST00000323944;ENST00000419632;ENST00000546511;ENST00000550887;ENST00000358326 . . . 5.15 5.15 0.70609 . 0.189920 0.47455 D 0.000223 T 0.33147 0.0853 N 0.14661 0.345 0.50171 D 0.999858 P 0.34587 0.458 B 0.14578 0.011 T 0.28299 -1.0048 9 0.48119 T 0.1 0.0641 16.1225 0.81369 0.0:0.0:1.0:0.0 . 97 Q8NFX7 STXB6_HUMAN L 97 . ENSP00000324302:S97L S - 2 0 STXBP6 24395143 1.000000 0.71417 1.000000 0.80357 0.910000 0.53928 5.030000 0.64128 2.405000 0.81733 0.563000 0.77884 TCG TCGA-IB-A6UF-01A-23D-A33T-08 STXBP6-006 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000409166.1 0 0 0 6 234 0 50 0 4.474082e-01 0 54 0 50 2 0 0 0 0 0 2 1 9.646186e-01 6 232 0 49 2 0 0 0 0 50 2 -2.322710 0 1 121374 1 28 1 1 2 3 2.075291 0 0.580000 1.890000 0.581214 0.090000 3.000000e-02 0.190000 0.080000 0.099740 0.090000 0 0.050000 0.140000 NPAS3 64067 broad.mit.edu 37 14 34269655 34269655 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr14:34269655G>A ENST00000356141.4 + 12 2142 c.2142G>A c.(2140-2142)tcG>tcA p.S714S NPAS3_ENST00000357798.5_Silent_p.S701S|NPAS3_ENST00000548645.1_Silent_p.S684S|NPAS3_ENST00000551492.1_Silent_p.S719S|NPAS3_ENST00000346562.2_Silent_p.S682S Q8IXF0 NPAS3_HUMAN neuronal PAS domain protein 3 40 Breast(36;0.0102)|Hepatocellular(127;0.133) LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968) TTCCCGACTCGGTCCTCAccc 0.781000 0 SO:0001819 synonymous_variant ENST00000356141.4 0 1 hg19 CCDS53891.1 TCGA-IB-A6UF-01A-23D-A33T-08 NPAS3-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000276645.1 0 0 0 5 66 0 15 0 0 0 0 15 2 0 0 0 0 0 2 1 9.351575e-01 5 64 0 14 2 0 0 0 0 15 2 -11.730440 1 1 0 0 1 1 2 3 2.075291 0 0.580000 1.890000 0.581214 0.260000 1.000000e-01 0.530000 0.240000 0.281397 0.260000 0 0.160000 0.390000 OCA2 4948 broad.mit.edu 37 15 28202828 28202828 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr15:28202828C>T ENST00000354638.3 - 16 1845 c.1690G>A c.(1690-1692)Gcc>Acc p.A564T OCA2_ENST00000382996.2_Missense_Mutation_p.A564T|OCA2_ENST00000353809.5_Missense_Mutation_p.A540T NM_000275.2 NP_000266.2 Q04671 P_HUMAN oculocutaneous albinism II 85 all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234) TCGCGGCTGGCCGGGCTGATG 0.637000 Oculocutaneous Albinism 0 SO:0001583 missense Familial Cancer Database ENST00000354638.3 0 1 hg19 CCDS10020.1 . . . . . . . . . . C 19.30 3.800578 0.70567 . . ENSG00000104044 ENST00000354638;ENST00000353809;ENST00000382996 D;D;D 0.90955 -2.76;-2.57;-2.74 5.8 5.8 0.92144 Divalent ion symporter (1); 0.000000 0.85682 D 0.000000 D 0.89825 0.6827 L 0.29908 0.895 0.53005 D 0.999962 P;P 0.50819 0.929;0.939 P;P 0.53549 0.729;0.673 D 0.87323 0.2319 10 0.23302 T 0.38 -14.3158 17.5483 0.87869 0.0:1.0:0.0:0.0 . 540;564 Q04671-2;Q04671 .;P_HUMAN T 564;540;564 ENSP00000346659:A564T;ENSP00000261276:A540T;ENSP00000372457:A564T ENSP00000261276:A540T A - 1 0 OCA2 25876423 1.000000 0.71417 0.994000 0.49952 0.464000 0.32679 6.883000 0.75595 2.746000 0.94184 0.591000 0.81541 GCC TCGA-IB-A6UF-01A-23D-A33T-08 OCA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250823.1 0 0 0 4 242 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 8.852180e-01 4 236 0 52 2 0 0 0 0 53 2 -3.761653 1 1 0 0 1 0 2 2 2.110430 1 0.580000 1.890000 0.580000 0.050000 1.000000e-02 0.140000 0.060000 0.069228 0.050000 0 0.030000 0.100000 IGDCC4 57722 broad.mit.edu 37 15 65681260 65681260 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr15:65681260G>A ENST00000352385.2 - 15 2802 c.2593C>T c.(2593-2595)Cgg>Tgg p.R865W NM_020962.1 NP_066013.1 Q8TDY8 IGDC4_HUMAN immunoglobulin superfamily, DCC subclass, member 4 44 CAGTGCAGCCGAACCGTGGAC 0.652000 0 SO:0001583 missense ENST00000352385.2 1 1 hg19 CCDS10206.1 . . . . . . . . . . G 18.81 3.703326 0.68501 . . ENSG00000103742 ENST00000352385;ENST00000356152 T 0.58210 0.35 4.97 4.04 0.47022 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.356482 0.27397 N 0.019557 T 0.73393 0.3581 M 0.83223 2.63 0.32760 N 0.505288 D 0.89917 1.0 D 0.72338 0.977 T 0.82617 -0.0369 10 0.66056 D 0.02 -15.3636 14.6226 0.68597 0.0:0.0:0.8533:0.1467 . 865 Q8TDY8 IGDC4_HUMAN W 865;594 ENSP00000319623:R865W ENSP00000319623:R865W R - 1 2 IGDCC4 63468313 1.000000 0.71417 0.796000 0.32109 0.754000 0.42855 4.717000 0.61923 1.074000 0.40909 0.561000 0.74099 CGG TCGA-IB-A6UF-01A-23D-A33T-08 IGDCC4-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000256825.2 1 0 1 72 92 0 39 0 0 0 1 0 39 2 0 0 0 0 0 2 1 1 69 91 0 39 2 0 0 0 0 39 2 -20.000000 1 1 0 0 1 0 1 1 1.514340 1 0.580000 1.890000 0.417960 0.980000 8.500000e-01 1.000000 1.000000 0.972118 0.980000 1 0.920000 1.000000 DIS3L 115752 broad.mit.edu 37 15 66607419 66607419 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr15:66607419G>A ENST00000319212.4 + 7 910 c.860G>A c.(859-861)cGc>cAc p.R287H RP11-352G18.2_ENST00000565993.1_RNA|DIS3L_ENST00000441424.2_Missense_Mutation_p.R153H|DIS3L_ENST00000319194.5_Missense_Mutation_p.R204H NM_001143688.1 NP_001137160.1 Q8TF46 DI3L1_HUMAN DIS3 like exosome 3'-5' exoribonuclease 33 GCTCGAAACCGCTCAATTCAT 0.478000 0 SO:0001583 missense ENST00000319212.4 0 1 hg19 CCDS45286.1 . . . . . . . . . . G 36 5.664037 0.96745 . . ENSG00000166938 ENST00000319194;ENST00000441424;ENST00000319212 T;T;T 0.36699 1.24;1.24;1.24 5.34 5.34 0.76211 . 0.156269 0.56097 D 0.000038 T 0.72566 0.3476 H 0.95260 3.645 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.994 T 0.81061 -0.1103 10 0.66056 D 0.02 -15.751 18.3807 0.90449 0.0:0.0:1.0:0.0 . 287;287 Q8TF46;Q8TF46-3 DI3L1_HUMAN;. H 204;153;287 ENSP00000321583:R204H;ENSP00000388980:R153H;ENSP00000321711:R287H ENSP00000321583:R204H R + 2 0 DIS3L 64394473 1.000000 0.71417 0.993000 0.49108 0.963000 0.63663 9.386000 0.97228 2.655000 0.90218 0.561000 0.74099 CGC TCGA-IB-A6UF-01A-23D-A33T-08 DIS3L-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000382792.2 0 0 0 6 342 1 68 0 4.306585e-02 0 16 1 68 2 0 0 0 0 0 2 0 1.455269e-02 5 339 1 67 17 0 0 0 1 68 2 -2.363023 0 1 0 0 1 0 1 1 1.514340 1 0.580000 1.890000 0.417960 0.040000 1.000000e-02 0.090000 0.040000 0.049567 0.040000 0 0.020000 0.070000 KIAA0556 23247 broad.mit.edu 37 16 27659970 27659970 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr16:27659970G>A ENST00000261588.4 + 6 473 c.454G>A c.(454-456)Gaa>Aaa p.E152K KIAA0556_ENST00000567894.1_3'UTR NM_015202.2 NP_056017.2 O60303 K0556_HUMAN KIAA0556 76 GCTCCACATCGAACCTCCTGT 0.493000 0 SO:0001583 missense ENST00000261588.4 1 1 hg19 CCDS32415.1 . . . . . . . . . . G 7.339 0.620581 0.14193 . . ENSG00000047578 ENST00000261588;ENST00000327217 T 0.50548 0.74 4.82 1.53 0.23141 . 0.621024 0.16295 N 0.220719 T 0.39989 0.1099 L 0.46157 1.445 0.28141 N 0.929802 D;B 0.55605 0.972;0.086 P;B 0.45099 0.469;0.01 T 0.35025 -0.9805 10 0.10111 T 0.7 -3.534 12.6071 0.56529 0.0:0.4961:0.5039:0.0 . 17;152 Q8N803;O60303 .;K0556_HUMAN K 152;16 ENSP00000261588:E152K ENSP00000261588:E152K E + 1 0 KIAA0556 27567471 0.034000 0.19679 0.958000 0.39756 0.186000 0.23388 0.800000 0.27042 0.134000 0.18681 -0.181000 0.13052 GAA TCGA-IB-A6UF-01A-23D-A33T-08 KIAA0556-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000433724.1 1 0 1 86 243 0 57 1 8.235598e-01 2 9 0 57 2 0 0 0 0 0 2 1 1 86 241 0 57 2 0 0 0 0 57 2 -20.000000 1 1 0 0 1 1 2 3 2.168314 0 0.580000 1.890000 0.590683 0.920000 7.600000e-01 1.000000 1.000000 0.924028 0.920000 1 0.840000 1.000000 MEFV 4210 broad.mit.edu 37 16 3293588 3293588 + Silent SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr16:3293588C>T ENST00000219596.1 - 10 1938 c.1899G>A c.(1897-1899)ccG>ccA p.P633P MEFV_ENST00000339854.4_Silent_p.P453P|MEFV_ENST00000541159.1_3'UTR|MEFV_ENST00000536379.1_Silent_p.P422P NM_000243.2 NP_000234.1 O15553 MEFV_HUMAN Mediterranean fever 50 CAAATCTTTGCGGGCCATCAG 0.517000 0 SO:0001819 synonymous_variant ENST00000219596.1 1 1 hg19 CCDS10498.1 TCGA-IB-A6UF-01A-23D-A33T-08 MEFV-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251464.1 1 0 1 352 818 1 196 0 0 0 1 1 196 2 0 0 0 0 0 2 1 1 347 808 1 196 20 0 0 0 1 196 2 -20.000000 1 1 121410 2 38 1 2 2 4 2.202141 0 0.580000 1.890000 0.607330 0.990000 9.900000e-01 1.000000 1.000000 0.999808 0.990000 1 0.990000 1.000000 DPEP2 64174 broad.mit.edu 37 16 68026461 68026461 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr16:68026461G>A ENST00000572888.1 - 2 992 c.342C>T c.(340-342)taC>taT p.Y114Y DPEP2_ENST00000393847.1_Silent_p.Y114Y|DPEP2_ENST00000412757.2_Silent_p.Y114Y Q9H4A9 DPEP2_HUMAN dipeptidase 2 17 Ovarian(137;0.192) TGGTCTGGCCGTAGCTGAAAT 0.602000 0 SO:0001819 synonymous_variant ENST00000572888.1 0 1 hg19 CCDS10857.1 TCGA-IB-A6UF-01A-23D-A33T-08 DPEP2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000437026.1 0 0 0 5 557 0 88 0 1.281202e-03 0 5 0 88 2 0 0 0 0 0 2 1 9.357163e-01 5 550 0 87 2 0 0 0 0 88 2 -2.503939 1 1 121412 2 34 1 1 2 3 2.128044 0 0.580000 1.890000 0.587183 0.030000 0 1.000000 0.040000 0.081876 0.030000 0 0.010000 0.060000 WFIKKN1 117166 broad.mit.edu 37 16 683104 683104 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr16:683104C>T ENST00000319070.2 + 2 1016 c.694C>T c.(694-696)Cgc>Tgc p.R232C NM_053284.2 NP_444514.1 Q96NZ8 WFKN1_HUMAN WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1 4 Hepatocellular(780;0.00335) CCTGATCATGCGCCCTGATCA 0.662000 0 SO:0001583 missense ENST00000319070.2 0 1 hg19 CCDS10414.1 . . . . . . . . . . c 15.20 2.763443 0.49574 . . ENSG00000127578 ENST00000319070 T 0.70631 -0.5 4.71 3.71 0.42584 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.057277 0.64402 D 0.000003 T 0.81163 0.4765 M 0.72624 2.21 0.58432 D 0.999993 D 0.89917 1.0 D 0.91635 0.999 T 0.82752 -0.0302 10 0.72032 D 0.01 . 11.0862 0.48089 0.3279:0.6721:0.0:0.0 . 232 Q96NZ8 WFKN1_HUMAN C 232 ENSP00000324763:R232C ENSP00000324763:R232C R + 1 0 WFIKKN1 623105 0.996000 0.38824 0.990000 0.47175 0.767000 0.43475 0.491000 0.22419 2.174000 0.68829 0.486000 0.48141 CGC TCGA-IB-A6UF-01A-23D-A33T-08 WFIKKN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206731.2 0 0 0 4 284 0 46 0 0 0 1 0 46 2 0 0 0 0 0 2 1 8.902209e-01 4 283 0 45 2 0 0 0 0 46 2 -4.086946 1 1 120734 1 26 1 1 2 3 2.156022 0 0.580000 1.890000 0.589523 0.050000 0 1.000000 0.050000 0.120980 0.050000 0 0.020000 0.100000 ZNF594 84622 broad.mit.edu 37 17 5085387 5085387 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr17:5085387G>A ENST00000399604.4 - 1 2305 c.2165C>T c.(2164-2166)gCt>gTt p.A722V ZNF594_ENST00000575779.1_Missense_Mutation_p.A722V Q96JF6 ZN594_HUMAN zinc finger protein 594 33 TTTGAGGAAAGCCGTGTGCCA 0.458000 0 SO:0001583 missense ENST00000399604.4 0 1 hg19 CCDS42241.1 . . . . . . . . . . g 1.376 -0.584769 0.03827 . . ENSG00000180626 ENST00000399604;ENST00000389222 T 0.28666 1.6 1.17 -2.35 0.06684 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.15003 0.0362 N 0.19112 0.55 0.09310 N 1 B 0.06786 0.001 B 0.01281 0.0 T 0.21245 -1.0251 9 0.28530 T 0.3 . 3.8079 0.08785 0.0:0.276:0.5078:0.2162 . 722 Q96JF6 ZN594_HUMAN V 722;289 ENSP00000382513:A722V ENSP00000373874:A289V A - 2 0 ZNF594 5026111 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -3.467000 0.00461 -1.230000 0.02561 -1.706000 0.00718 GCT TCGA-IB-A6UF-01A-23D-A33T-08 ZNF594-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438996.1 0 0 0 6 607 0 131 0 1.431008e-03 0 5 0 131 2 0 0 0 0 0 2 1 9.623361e-01 6 593 0 129 2 0 0 0 0 131 2 -2.836208 1 1 0 0 1 0 1 1 1.574888 1 0.580000 1.890000 0.417960 0.020000 0 0.050000 0.030000 0.028263 0.020000 0 0.010000 0.040000 USH1G 124590 broad.mit.edu 37 17 72915717 72915717 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr17:72915717G>A ENST00000319642.1 - 2 1396 c.1214C>T c.(1213-1215)gCc>gTc p.A405V NM_001282489.1|NM_173477.2 NP_001269418.1|NP_775748.2 Q495M9 USH1G_HUMAN Usher syndrome 1G (autosomal recessive) HN1/USH1G(2) 14 all_lung(278;0.172)|Lung NSC(278;0.207) CAGGAGGGCGGCAAAGTCCTC 0.627000 0 SO:0001583 missense ENST00000319642.1 0 1 hg19 CCDS32725.1 . . . . . . . . . . G 8.703 0.910112 0.17833 . . ENSG00000182040 ENST00000319642 T 0.49139 0.79 4.53 0.999 0.19862 Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1); 0.770174 0.12427 N 0.469921 T 0.18800 0.0451 N 0.02765 -0.5 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.16424 -1.0403 10 0.28530 T 0.3 -6.1315 3.7981 0.08747 0.2204:0.5:0.2796:0.0 . 405 Q495M9 USH1G_HUMAN V 405 ENSP00000320076:A405V ENSP00000320076:A405V A - 2 0 USH1G 70427312 0.662000 0.27439 0.015000 0.15790 0.947000 0.59692 3.769000 0.55303 0.479000 0.27511 0.555000 0.69702 GCC TCGA-IB-A6UF-01A-23D-A33T-08 USH1G-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000443676.1 0 0 0 5 296 1 78 0 0 0 1 78 2 0 0 0 0 0 2 0 2.593770e-02 5 290 1 78 14 0 0 0 1 78 2 -2.694812 1 1 0 0 1 0 1 1 1.629491 1 0.580000 1.890000 0.410857 0.040000 1.000000e-02 0.090000 0.040000 0.048453 0.040000 0 0.020000 0.070000 TP53 7157 broad.mit.edu 37 17 7577120 7577120 + Missense_Mutation SNP C C T rs28934576 by1000genomes TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr17:7577120C>T ENST00000269305.4 - 8 1007 c.818G>A c.(817-819)cGt>cAt p.R273H TP53_ENST00000445888.2_Missense_Mutation_p.R273H|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R273H|TP53_ENST00000420246.2_Missense_Mutation_p.R273H|TP53_ENST00000359597.4_Missense_Mutation_p.R273H|TP53_ENST00000413465.2_Intron 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.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GGCACAAACACGCACCTCAAA 0.542000 R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM) 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 669 Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1) GRCh37 CM004342|CM010472|CM920677 TP53 M rs28934576 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 1 1 hg19 CCDS11118.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 C 18.03 3.532510 0.64972 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D 0.99868 -7.32;-7.32;-7.32;-7.32;-7.32;-7.32 4.92 4.92 0.64577 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 0.99822 0.9921 M 0.79475 2.455 0.80722 A 1 P;D;P;P 0.89917 0.631;1.0;0.831;0.48 B;D;P;B 0.77004 0.274;0.989;0.516;0.242 D 0.96531 0.9393 9 0.72032 D 0.01 -11.9995 15.662 0.77193 0.0:1.0:0.0:0.0 rs28934576 273;273;273;273 P04637-2;P04637-3;P04637;Q1MSW8 .;.;P53_HUMAN;. H 273;273;273;273;273;262;141 ENSP00000352610:R273H;ENSP00000269305:R273H;ENSP00000398846:R273H;ENSP00000391127:R273H;ENSP00000391478:R273H;ENSP00000425104:R141H ENSP00000269305:R273H R - 2 0 TP53 7517845 1.000000 0.71417 0.068000 0.19968 0.665000 0.39181 7.587000 0.82613 2.556000 0.86216 0.462000 0.41574 CGT TCGA-IB-A6UF-01A-23D-A33T-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 54 68 0 34 1 1 25 27 0 34 2 1 1 254 448 0 1383 2 1 1 54 66 0 33 2 0 0 0 0 34 2 -20.000000 1 1 121412 3 34 1 0 1 1 1.575164 1 0.580000 1.890000 0.410857 0.950000 8.100000e-01 1.000000 1.000000 0.947607 0.950000 1 0.890000 1.000000 ZNF750 79755 broad.mit.edu 37 17 80788076 80788076 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr17:80788076G>A ENST00000269394.3 - 3 2947 c.2114C>T c.(2113-2115)gCg>gTg p.A705V TBCD_ENST00000539345.2_Intron|ZNF750_ENST00000572562.1_Missense_Mutation_p.A306V|TBCD_ENST00000355528.4_Intron|TBCD_ENST00000397466.2_Intron NM_024702.2 NP_078978.2 Q32MQ0 ZN750_HUMAN zinc finger protein 750 p.A705V(1) 31 Breast(20;0.000523)|all_neural(118;0.0779) all_cancers(8;0.0514)|all_epithelial(8;0.0748) OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149) CTGCAGCTTCGCCTTCTTAGC 0.567000 1 Substitution - Missense(1) SO:0001583 missense ENST00000269394.3 1 1 hg19 CCDS11819.1 . . . . . . . . . . G 2.983 -0.209835 0.06140 . . ENSG00000141579 ENST00000269394;ENST00000543850 T 0.11604 2.76 5.28 -0.647 0.11468 . 1.559540 0.03792 N 0.263027 T 0.06690 0.0171 L 0.27053 0.805 0.09310 N 1 B 0.24132 0.098 B 0.14578 0.011 T 0.33599 -0.9862 9 . . . 0.0083 1.0216 0.01519 0.3312:0.2658:0.2669:0.136 . 705 Q32MQ0 ZN750_HUMAN V 705;298 ENSP00000269394:A705V . A - 2 0 ZNF750 78381365 0.000000 0.05858 0.000000 0.03702 0.125000 0.20455 -0.130000 0.10498 -0.019000 0.14055 -0.339000 0.08088 GCG TCGA-IB-A6UF-01A-23D-A33T-08 ZNF750-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000439074.2 1 0 1 136 175 0 79 0 0 0 1 0 79 2 0 0 0 0 0 2 1 1 136 176 0 78 2 0 0 0 0 79 2 -19.999980 1 1 0 0 1 0 1 1 1.585809 1 0.580000 1.890000 0.420290 0.990000 9.100000e-01 1.000000 1.000000 0.989593 0.990000 1 0.960000 1.000000 GNAL 2774 broad.mit.edu 37 18 11752449 11752449 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr18:11752449G>A ENST00000423027.3 + 1 338 c.17G>A c.(16-18)gGc>gAc p.G6D GNAL_ENST00000334049.6_Intron|GNAL_ENST00000269162.5_Missense_Mutation_p.G6D|GNAL_ENST00000535121.1_Missense_Mutation_p.G6D P38405 GNAL_HUMAN guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type 12 TGTTTGGGCGGCAACAGCAAG 0.557000 0 SO:0001583 missense ENST00000423027.3 0 1 hg19 CCDS11852.1 . . . . . . . . . . G 25.1 4.599844 0.87055 . . ENSG00000141404 ENST00000535121;ENST00000269162;ENST00000423027 D;D;D 0.88975 -2.45;-2.45;-2.45 4.04 4.04 0.47022 . . . . . D 0.90783 0.7106 L 0.34521 1.04 0.34358 D 0.690637 D 0.57257 0.979 D 0.69654 0.965 D 0.93188 0.6580 9 0.59425 D 0.04 . 15.6287 0.76885 0.0:0.0:1.0:0.0 . 6 P38405 GNAL_HUMAN D 6 ENSP00000439023:G6D;ENSP00000269162:G6D;ENSP00000408489:G6D ENSP00000269162:G6D G + 2 0 GNAL 11742449 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 8.928000 0.92853 2.542000 0.85734 0.491000 0.48974 GGC TCGA-IB-A6UF-01A-23D-A33T-08 GNAL-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254561.2 0 0 0 5 474 0 107 0 0 0 0 107 2 0 6.879596e-02 0 33 0 83 2 1 9.375014e-01 5 473 0 105 2 0 0 0 0 107 2 -1.947327 0 1 0 0 1 0 1 1 1.489096 1 0.580000 1.890000 0.408451 0.020000 0 0.060000 0.030000 0.030418 0.020000 0 0.010000 0.040000 FHOD3 80206 broad.mit.edu 37 18 33952645 33952645 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr18:33952645G>A ENST00000359247.4 + 3 275 c.275G>A c.(274-276)cGg>cAg p.R92Q FHOD3_ENST00000590592.1_Missense_Mutation_p.R92Q|FHOD3_ENST00000445677.1_Missense_Mutation_p.R92Q|FHOD3_ENST00000257209.4_Missense_Mutation_p.R92Q NM_001281739.1 NP_001268668.1 Q2V2M9 FHOD3_HUMAN formin homology 2 domain containing 3 p.R92Q(1) 90 all_epithelial(2;0.0181)|Colorectal(2;0.0195) CTCGTTAGGCGGGGCAAGAAG 0.527000 1 Substitution - Missense(1) SO:0001583 missense ENST00000359247.4 1 1 hg19 . . . . . . . . . . G 23.9 4.469151 0.84533 . . ENSG00000134775 ENST00000257209;ENST00000359247;ENST00000445677 T;T;T 0.19250 2.16;2.16;2.16 5.07 5.07 0.68467 GTPase-binding/formin homology 3 (1); 0.059478 0.64402 D 0.000009 T 0.36635 0.0974 L 0.40543 1.245 0.28823 N 0.897568 D;D;P 0.71674 0.998;0.998;0.705 P;D;B 0.75484 0.74;0.986;0.016 T 0.09378 -1.0677 10 0.62326 D 0.03 . 13.8335 0.63395 0.0:0.0:1.0:0.0 . 92;92;92 Q2V2M9;Q2V2M9-3;E5F5Q0 FHOD3_HUMAN;.;. Q 92 ENSP00000257209:R92Q;ENSP00000352186:R92Q;ENSP00000411430:R92Q ENSP00000257209:R92Q R + 2 0 FHOD3 32206643 1.000000 0.71417 1.000000 0.80357 0.901000 0.52897 6.372000 0.73123 2.633000 0.89246 0.650000 0.86243 CGG TCGA-IB-A6UF-01A-23D-A33T-08 FHOD3-001 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460884.1 1 0 1 48 71 0 22 1 8.912068e-01 8 0 0 22 2 0 0 0 0 0 2 1 1 47 71 0 22 2 0 0 0 0 22 2 -9.849917 1 1 121410 3 31 1 0 1 1 1.487366 1 0.580000 1.890000 0.408451 0.910000 7.400000e-01 1.000000 0.980000 0.908998 0.910000 1 0.830000 0.980000 RFX1 5989 broad.mit.edu 37 19 14088833 14088833 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr19:14088833G>A ENST00000254325.4 - 8 1134 c.900C>T c.(898-900)ggC>ggT p.G300G NM_002918.4 NP_002909.4 P22670 RFX1_HUMAN regulatory factor X, 1 (influences HLA class II expression) 21 OV - Ovarian serous cystadenocarcinoma(19;6.67e-23) TGGCATCGCCGCCCTCCACAT 0.657000 0 SO:0001819 synonymous_variant ENST00000254325.4 0 1 hg19 CCDS12301.1 TCGA-IB-A6UF-01A-23D-A33T-08 RFX1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000458510.1 0 0 0 5 494 0 120 0 1.724434e-02 0 16 0 120 2 0 0 0 0 0 2 1 9.341090e-01 5 484 0 119 2 0 0 0 0 120 2 -2.293379 0 1 121406 1 34 1 0 1 1 1.628610 1 0.580000 1.890000 0.420290 0.020000 0 0.060000 0.030000 0.029799 0.020000 0 0.010000 0.040000 TSHZ3 57616 broad.mit.edu 37 19 31768582 31768582 + Missense_Mutation SNP G G A rs112525703 TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr19:31768582G>A ENST00000240587.4 - 2 2444 c.2117C>T c.(2116-2118)aCg>aTg p.T706M NM_020856.2 NP_065907.2 Q63HK5 TSH3_HUMAN teashirt zinc finger homeobox 3 123 Esophageal squamous(110;0.226) GATGATGGCCGTGCTGCCACT 0.627000 0 SO:0001583 missense ENST00000240587.4 1 1 hg19 CCDS12421.2 2 9.157509157509158E-4 2 0.0040650406504065045 0 0.0 0 0.0 0 0.0 G 17.95 3.514351 0.64522 . . ENSG00000121297 ENST00000240587 T 0.38722 1.12 5.4 5.4 0.78164 . 5.739330 0.00951 N 0.002966 T 0.67961 0.2949 L 0.51422 1.61 0.80722 D 1 D 0.89917 1.0 D 0.80764 0.994 T 0.49652 -0.8917 10 0.54805 T 0.06 -23.6274 19.176 0.93603 0.0:0.0:1.0:0.0 . 706 Q63HK5 TSH3_HUMAN M 706 ENSP00000240587:T706M ENSP00000240587:T706M T - 2 0 TSHZ3 36460422 1.000000 0.71417 0.990000 0.47175 0.987000 0.75469 9.441000 0.97557 2.520000 0.84964 0.650000 0.86243 ACG TCGA-IB-A6UF-01A-23D-A33T-08 TSHZ3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316743.2 1 0 1 116 272 0 83 0 6.684314e-01 0 7 0 83 2 0 0 0 0 0 2 1 1 116 269 0 81 2 0 0 0 0 83 2 -8.963517 1 1 119666 3 26 1 0 0 0 2.009038 0 0.580000 1.890000 0.567456 0.990000 8.400000e-01 1.000000 1.000000 0.970222 0.990000 1 0.910000 1.000000 MRPS12 6183 broad.mit.edu 37 19 39423173 39423173 + Missense_Mutation SNP C C T rs140018981 by1000genomes TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr19:39423173C>T ENST00000407800.2 + 2 591 c.250C>T c.(250-252)Cgg>Tgg p.R84W MRPS12_ENST00000308018.4_Missense_Mutation_p.R84W|MRPS12_ENST00000402029.3_Missense_Mutation_p.R84W|SARS2_ENST00000600042.1_5'Flank|SARS2_ENST00000430193.3_5'Flank|SARS2_ENST00000448145.2_Intron|SARS2_ENST00000221431.6_5'Flank|CTC-360G5.8_ENST00000599996.1_Intron|CTC-360G5.9_ENST00000599320.1_lincRNA|SARS2_ENST00000594171.1_5'Flank NM_021107.1 NP_066930.1 O15235 RT12_HUMAN mitochondrial ribosomal protein S12 2 all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454) Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554) CTGTCGAGTGCGGCTCAGCAC 0.662000 0 SO:0001583 missense ENST00000407800.2 0 1 hg19 CCDS12525.1 2 9.157509157509158E-4 0 0.0 0 0.0 2 0.0034965034965034965 0 0.0 C 21.5 4.155882 0.78114 . . ENSG00000128626 ENST00000308018;ENST00000407800;ENST00000402029 T;T;T 0.56611 0.45;0.45;0.45 6.07 5.03 0.67393 Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1); 0.054650 0.85682 D 0.000000 D 0.82462 0.5042 H 0.97806 4.08 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.89042 0.3449 10 0.87932 D 0 -32.1337 14.5652 0.68171 0.1473:0.8527:0.0:0.0 . 84 O15235 RT12_HUMAN W 84 ENSP00000308845:R84W;ENSP00000384952:R84W;ENSP00000384579:R84W ENSP00000308845:R84W R + 1 2 MRPS12 44115013 1.000000 0.71417 0.997000 0.53966 0.411000 0.31082 3.906000 0.56340 1.559000 0.49555 0.655000 0.94253 CGG TCGA-IB-A6UF-01A-23D-A33T-08 MRPS12-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000463154.1 0 0 0 5 424 0 85 0 7.034281e-01 0 198 0 85 2 0 0 0 0 0 2 1 9.351500e-01 5 417 0 84 2 0 0 0 0 85 2 -2.875097 1 1 121398 5 35 1 0 0 0 2.009038 0 0.580000 1.890000 0.567456 0.030000 0 0.090000 0.040000 0.046371 0.030000 0 0.020000 0.070000 IRGQ 126298 broad.mit.edu 37 19 44096739 44096739 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr19:44096739G>A ENST00000602269.1 - 2 1496 c.1311C>T c.(1309-1311)ggC>ggT p.G437G IRGQ_ENST00000601520.1_Intron|IRGQ_ENST00000422989.1_Silent_p.G437G|L34079.2_ENST00000594374.1_Intron Q8WZA9 IRGQ_HUMAN immunity-related GTPase family, Q 18 Prostate(69;0.0199) CTGGGAGTCCGCCAGGCCGTA 0.721000 0 SO:0001819 synonymous_variant ENST00000602269.1 0 1 hg19 CCDS33040.1 TCGA-IB-A6UF-01A-23D-A33T-08 IRGQ-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000463205.1 0 0 0 5 400 0 75 0 2.431941e-03 0 5 0 75 2 0 0 0 0 0 2 1 9.358512e-01 5 395 0 73 2 0 0 0 0 75 2 -2.951012 1 1 0 0 1 2 2 4 2.278325 1 0.580000 1.890000 0.619703 0.050000 0 1.000000 0.050000 0.187137 0.050000 0 0.020000 0.110000 BCAM 4059 broad.mit.edu 37 19 45316707 45316707 + Missense_Mutation SNP C C A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr19:45316707C>A ENST00000270233.6 + 6 636 c.614C>A c.(613-615)aCc>aAc p.T205N BCAM_ENST00000589651.1_Missense_Mutation_p.T205N NM_001013257.2|NM_005581.4 NP_001013275.1|NP_005572.2 P50895 BCAM_HUMAN basal cell adhesion molecule (Lutheran blood group) 22 Lung NSC(12;0.000789)|all_lung(12;0.00218) Ovarian(192;0.0728)|all_neural(266;0.112) GGCTACATGACCAGCCGCACG 0.711000 0 SO:0001583 missense ENST00000270233.6 1 1 hg19 CCDS12644.1 . . . . . . . . . . . 9.602 1.128897 0.21041 . . ENSG00000187244 ENST00000270233;ENST00000391955 T;T 0.78126 -1.15;-1.15 4.15 2.85 0.33270 CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); . . . . T 0.76421 0.3985 M 0.74258 2.255 0.20196 N 0.999921 P 0.42556 0.783 B 0.44133 0.442 T 0.64989 -0.6277 9 0.27785 T 0.31 -14.6738 7.5419 0.27744 0.0:0.8263:0.0:0.1737 . 205 P50895 BCAM_HUMAN N 205 ENSP00000270233:T205N;ENSP00000375817:T205N ENSP00000270233:T205N T + 2 0 BCAM 50008547 0.118000 0.22208 0.873000 0.34254 0.413000 0.31143 0.707000 0.25704 2.026000 0.59711 0.462000 0.41574 ACC TCGA-IB-A6UF-01A-23D-A33T-08 BCAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000453220.1 0 0 1 105 286 0 71 1 1 33 198 0 71 2 0 0 0 0 0 2 1 1 104 283 0 70 2 0 0 0 0 71 2 -20.000000 1 1 0 0 1 2 2 4 2.278325 1 0.580000 1.890000 0.619703 0.990000 8.600000e-01 1.000000 1.000000 0.980470 0.990000 1 0.940000 1.000000 FTL 2512 broad.mit.edu 37 19 49468811 49468811 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr19:49468811C>T ENST00000331825.6 + 1 254 c.47C>T c.(46-48)gCc>gTc p.A16V CTD-2639E6.9_ENST00000599784.1_lincRNA NM_000146.3 NP_000137.2 P02792 FRIL_HUMAN ferritin, light polypeptide 9 all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261) Iron Dextran(DB00893) GTGGAGGCAGCCGTCAACAGC 0.567000 0 SO:0001583 missense ENST00000331825.6 0 1 hg19 CCDS33070.1 . . . . . . . . . . C 20.4 3.979521 0.74360 . . ENSG00000087086 ENST00000331825;ENST00000397259 T 0.66638 -0.22 5.14 1.49 0.22878 Ferritin/ribonucleotide reductase-like (1);Ferritin-related (1);Ferritin/DPS protein domain (1);Ferritin-like (1); 0.309717 0.34025 N 0.004328 T 0.68723 0.3032 M 0.88310 2.945 0.27691 N 0.946119 B;B 0.31730 0.236;0.337 B;B 0.32980 0.087;0.156 T 0.67309 -0.5703 10 0.72032 D 0.01 . 9.6464 0.39870 0.1386:0.5426:0.3188:0.0 . 16;16 P02792;F5H1X1 FRIL_HUMAN;. V 16 ENSP00000366525:A16V ENSP00000366525:A16V A + 2 0 FTL 54160623 0.985000 0.35326 1.000000 0.80357 0.998000 0.95712 1.633000 0.37113 0.787000 0.33731 0.655000 0.94253 GCC TCGA-IB-A6UF-01A-23D-A33T-08 FTL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466233.1 0 0 0 5 488 1 85 0 1.181639e-02 9 6999 1 85 185 0 0 0 0 0 2 0 2.690923e-03 5 482 1 84 19 0 0 0 1 85 2 -2.760313 1 1 0 0 1 2 2 4 2.313384 1 0.580000 1.890000 0.625602 0.040000 0 1.000000 0.050000 0.196499 0.040000 0 0.020000 0.120000 C3 718 broad.mit.edu 37 19 6678284 6678284 + Nonsense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr19:6678284G>A ENST00000245907.6 - 40 4821 c.4729C>T c.(4729-4731)Cag>Tag p.Q1577* C3_ENST00000599668.1_5'UTR NM_000064.2 NP_000055.2 P01024 CO3_HUMAN complement component 3 72 Intravenous Immunoglobulin(DB00028) TGTCCAACCTGCACCTCATCC 0.607000 0 SO:0001587 stop_gained ENST00000245907.6 0 1 hg19 CCDS32883.1 . . . . . . . . . . G 42 9.718089 0.99247 . . ENSG00000125730 ENST00000245907 . . . 5.24 5.24 0.73138 . 2.360010 0.02152 U 0.058110 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.05833 T 0.94 . 12.1339 0.53959 0.0:0.1729:0.8271:0.0 . . . . X 1577 . ENSP00000245907:Q1577X Q - 1 0 C3 6629284 0.738000 0.28186 0.992000 0.48379 0.134000 0.20937 1.336000 0.33850 2.463000 0.83235 0.454000 0.30748 CAG TCGA-IB-A6UF-01A-23D-A33T-08 C3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317636.2 0 0 0 5 211 0 55 1 1 4 6101 0 55 2 0 0 0 0 0 2 0 9.292954e-01 0 205 0 54 2 0 0 0 0 55 2 -6.691296 1 0 0 0 1 0 1 1 1.628610 1 0.580000 1.890000 0.420290 0.050000 1.000000e-02 0.130000 0.060000 0.068318 0.050000 0 0.030000 0.090000 RSBN1 54665 broad.mit.edu 37 1 114308998 114308998 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr1:114308998G>A ENST00000261441.5 - 7 2076 c.2013C>T c.(2011-2013)tgC>tgT p.C671C RSBN1_ENST00000369581.2_5'UTR NM_018364.3 NP_060834.2 Q5VWQ0 RSBN1_HUMAN round spermatid basic protein 1 29 Lung SC(450;0.184) all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05) TATCATTGTCGCAAAGCTGAA 0.418000 0 SO:0001819 synonymous_variant ENST00000261441.5 0 1 hg19 CCDS862.1 TCGA-IB-A6UF-01A-23D-A33T-08 RSBN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033022.2 0 0 0 6 531 0 87 0 2.733183e-02 0 19 0 87 2 0 0 0 0 0 2 1 9.645367e-01 6 528 0 85 2 0 0 0 0 87 2 -2.488091 0 1 121412 1 25 1 2 2 4 2.170352 0 0.580000 1.890000 0.600836 0.040000 0 1.000000 0.040000 0.116159 0.040000 0 0.020000 0.070000 COPA 1314 broad.mit.edu 37 1 160302256 160302256 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr1:160302256G>A ENST00000241704.7 - 6 707 c.478C>T c.(478-480)Cgc>Tgc p.R160C COPA_ENST00000368069.3_Missense_Mutation_p.R160C NM_001098398.1|NM_004371.3 NP_001091868.1|NP_004362.2 P53621 COPA_HUMAN coatomer protein complex, subunit alpha 46 all_cancers(52;8.15e-18)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.111) TCCCAAACGCGCACAGTCTGG 0.483000 0 SO:0001583 missense ENST00000241704.7 0 1 hg19 CCDS1202.1 . . . . . . . . . . G 22.7 4.326408 0.81690 . . ENSG00000122218 ENST00000368069;ENST00000241704 T;T 0.68025 -0.3;-0.3 5.05 4.13 0.48395 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1); 0.053904 0.64402 N 0.000001 T 0.79621 0.4477 M 0.88704 2.975 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.84076 0.0382 10 0.87932 D 0 -11.1798 12.468 0.55771 0.0814:0.0:0.9186:0.0 . 160;160 P53621;P53621-2 COPA_HUMAN;. C 160 ENSP00000357048:R160C;ENSP00000241704:R160C ENSP00000241704:R160C R - 1 0 COPA 158568880 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.381000 0.97205 1.351000 0.45789 0.561000 0.74099 CGC TCGA-IB-A6UF-01A-23D-A33T-08 COPA-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080638.1 0 0 0 6 506 0 63 0 6.921644e-01 0 192 0 63 2 0 0 0 0 0 2 1 9.645216e-01 6 503 0 63 2 0 0 0 0 63 2 -3.010007 1 1 0 0 1 1 2 3 2.671010 1 0.580000 1.890000 0.674419 0.050000 0 0.110000 0.060000 0.060039 0.050000 0 0.020000 0.080000 TOMM40L 84134 broad.mit.edu 37 1 161197719 161197719 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr1:161197719C>T ENST00000367988.3 + 6 693 c.424C>T c.(424-426)Cgg>Tgg p.R142W TOMM40L_ENST00000474486.1_3'UTR|TOMM40L_ENST00000367987.1_Missense_Mutation_p.R142W|NR1I3_ENST00000479324.1_5'Flank|TOMM40L_ENST00000545897.1_Missense_Mutation_p.R108W|MIR5187_ENST00000583479.1_RNA NM_032174.4 NP_115550.2 Q969M1 TM40L_HUMAN translocase of outer mitochondrial membrane 40 homolog (yeast)-like 10 all_cancers(52;1.86e-18)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.00376) TGGCGAGTATCGGGGAGATGA 0.517000 OREG0013943 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000367988.3 1 1 hg19 CCDS1227.1 . . . . . . . . . . C 18.12 3.552943 0.65425 . . ENSG00000158882 ENST00000367988;ENST00000545897;ENST00000542686;ENST00000367987 T;T;T 0.46819 0.86;0.86;0.86 5.91 4.99 0.66335 . 0.053759 0.64402 D 0.000001 T 0.34716 0.0907 M 0.74881 2.28 0.47214 D 0.999355 P;P;P 0.43431 0.807;0.807;0.807 B;B;B 0.40506 0.331;0.331;0.331 T 0.41716 -0.9493 9 0.42905 T 0.14 -26.3182 11.9964 0.53206 0.3146:0.6854:0.0:0.0 . 108;24;142 B7Z4U0;Q9H9G4;Q969M1 .;.;TM40L_HUMAN W 142;108;89;142 ENSP00000356967:R142W;ENSP00000443233:R108W;ENSP00000356966:R142W ENSP00000356966:R142W R + 1 2 TOMM40L 159464343 1.000000 0.71417 1.000000 0.80357 0.965000 0.64279 2.184000 0.42575 1.475000 0.48197 0.655000 0.94253 CGG TCGA-IB-A6UF-01A-23D-A33T-08 TOMM40L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083029.1 1 0 1 51 273 0 30 1 8.434478e-01 5 15 0 30 2 0 0 0 0 0 2 1 1 51 272 0 30 2 0 0 0 0 30 2 -3.234208 1 1 0 0 1 1 2 3 2.671010 1 0.580000 1.890000 0.674419 0.690000 5.300000e-01 0.880000 0.690000 0.708444 0.690000 0 0.610000 0.800000 RGS2 5997 broad.mit.edu 37 1 192779364 192779364 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr1:192779364C>T ENST00000235382.5 + 2 210 c.179C>T c.(178-180)aCc>aTc p.T60I RGS2_ENST00000483295.1_3'UTR NM_002923.3 NP_002914.1 P41220 RGS2_HUMAN regulator of G-protein signaling 2 5 AAGCCCAAAACCGGCAAAAAA 0.358000 Pancreas(71;51 2183 4981) 0 SO:0001583 missense ENST00000235382.5 1 1 hg19 CCDS1377.1 . . . . . . . . . . C 11.29 1.596210 0.28445 . . ENSG00000116741 ENST00000235382 T 0.70749 -0.51 5.9 4.97 0.65823 . 0.873372 0.10199 N 0.703678 T 0.53932 0.1827 N 0.14661 0.345 0.09310 N 0.99999 B 0.02656 0.0 B 0.01281 0.0 T 0.43410 -0.9393 10 0.41790 T 0.15 . 8.6472 0.34013 0.1532:0.7709:0.0:0.0759 . 60 P41220 RGS2_HUMAN I 60 ENSP00000235382:T60I ENSP00000235382:T60I T + 2 0 RGS2 191045987 0.003000 0.15002 0.641000 0.29422 0.958000 0.62258 0.491000 0.22419 1.469000 0.48083 0.655000 0.94253 ACC TCGA-IB-A6UF-01A-23D-A33T-08 RGS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086396.1 1 0 1 92 385 0 77 1 1 13 123 0 77 2 0 0 0 0 0 2 1 1 90 381 0 77 2 0 0 0 0 77 2 -20.000000 1 1 0 0 1 1 2 3 2.671010 1 0.580000 1.890000 0.674419 0.850000 7.000000e-01 1.000000 1.000000 0.860980 0.850000 1 0.770000 0.940000 LGR6 59352 broad.mit.edu 37 1 202287853 202287853 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr1:202287853G>A ENST00000367278.3 + 18 2511 c.2422G>A c.(2422-2424)Gtc>Atc p.V808I LGR6_ENST00000255432.7_Missense_Mutation_p.V756I|LGR6_ENST00000439764.2_Missense_Mutation_p.V669I NM_001017403.1 NP_001017403.1 Q9HBX8 LGR6_HUMAN leucine-rich repeat containing G protein-coupled receptor 6 36 GCCCGAGGCCGTCAAGTCTGT 0.647000 0 SO:0001583 missense ENST00000367278.3 0 1 hg19 CCDS30971.1 . . . . . . . . . . G 2.892 -0.229549 0.06022 . . ENSG00000133067 ENST00000367278;ENST00000255432;ENST00000439764 T;T;T 0.37058 1.22;1.22;1.22 4.6 1.6 0.23607 . 0.252924 0.32852 N 0.005573 T 0.12689 0.0308 N 0.04959 -0.14 0.22081 N 0.999379 B;B;B 0.25609 0.13;0.021;0.014 B;B;B 0.18561 0.022;0.004;0.007 T 0.19095 -1.0316 10 0.15952 T 0.53 . 3.813 0.08804 0.4036:0.1804:0.4161:0.0 . 669;756;808 Q9HBX8-1;Q9HBX8-2;Q9HBX8 .;.;LGR6_HUMAN I 808;756;669 ENSP00000356247:V808I;ENSP00000255432:V756I;ENSP00000387869:V669I ENSP00000255432:V756I V + 1 0 LGR6 200554476 0.967000 0.33354 0.995000 0.50966 0.988000 0.76386 1.184000 0.32053 0.260000 0.21731 0.485000 0.47835 GTC TCGA-IB-A6UF-01A-23D-A33T-08 LGR6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000099143.1 0 0 0 6 944 0 97 0 4.494163e-03 0 13 0 97 2 0 0 0 0 0 2 1 9.633681e-01 7 929 0 96 2 0 0 0 0 97 2 -2.111528 0 1 121412 1 39 1 1 3 4 2.724539 1 0.580000 1.890000 0.681577 0.030000 0 1.000000 0.030000 0.265663 0.030000 0 0.010000 1.000000 ELK4 2005 broad.mit.edu 37 1 205589560 205589560 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr1:205589560G>A ENST00000357992.4 - 3 953 c.614C>T c.(613-615)gCt>gTt p.A205V ELK4_ENST00000289703.4_Missense_Mutation_p.A205V|ELK4_ENST00000468523.1_5'Flank NM_001973.3 NP_001964.2 P28324 ELK4_HUMAN ELK4, ETS-domain protein (SRF accessory protein 1) SLC45A3/ELK4(18) 12 Breast(84;0.07) BRCA - Breast invasive adenocarcinoma(75;0.0908) AATGGTGGCAGCAACAGGTTC 0.478000 T SLC45A3 prostate Dom yes 1 1q32 2005 ELK4, ETS-domain protein (SRF accessory protein 1) E 0 SO:0001583 missense ENST00000357992.4 0 1 hg19 CCDS1456.1 . . . . . . . . . . G 0.006 -2.038791 0.00402 . . ENSG00000158711 ENST00000539916;ENST00000357992;ENST00000289703 T;T 0.29655 1.77;1.56 5.8 3.91 0.45181 . 0.648183 0.17214 N 0.182595 T 0.14700 0.0355 N 0.08118 0 0.09310 N 1 B;B 0.22683 0.073;0.006 B;B 0.21708 0.036;0.01 T 0.31223 -0.9951 10 0.10377 T 0.69 . 10.5205 0.44916 0.1355:0.1148:0.7496:0.0 . 205;205 P28324-2;P28324 .;ELK4_HUMAN V 295;205;205 ENSP00000350681:A205V;ENSP00000289703:A205V ENSP00000289703:A205V A - 2 0 ELK4 203856183 0.127000 0.22367 0.001000 0.08648 0.182000 0.23217 1.974000 0.40559 0.372000 0.24591 -0.813000 0.03139 GCT TCGA-IB-A6UF-01A-23D-A33T-08 ELK4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090615.1 0 0 0 5 566 0 89 0 2.458778e-02 0 22 0 89 2 0 0 0 0 0 2 1 9.360415e-01 5 560 0 89 2 0 0 0 0 89 2 -2.743540 1 1 0 0 1 1 3 4 2.724539 1 0.580000 1.890000 0.681577 0.040000 0 1.000000 0.030000 0.275181 0.040000 0 0.020000 1.000000 CTSE 1510 broad.mit.edu 37 1 206331027 206331027 + Missense_Mutation SNP G G A rs145069780 byFrequency TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr1:206331027G>A ENST00000358184.2 + 9 1151 c.1033G>A c.(1033-1035)Gtg>Atg p.V345M CTSE_ENST00000360218.2_Silent_p.S297S|CTSE_ENST00000432969.2_Silent_p.S222S|CTSE_ENST00000361052.3_Missense_Mutation_p.V350M NM_001910.3 NP_001901.1 P14091 CATE_HUMAN cathepsin E 16 BRCA - Breast invasive adenocarcinoma(75;0.0754) ACAGGACTTCGTGGATGGAAT 0.552000 0 SO:0001583 missense ENST00000358184.2 1 1 hg19 CCDS1462.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 g 9.329 1.060007 0.19987 2.27E-4 0.002558 ENSG00000196188 ENST00000358184;ENST00000361052 T;T 0.57752 0.38;0.38 4.98 4.05 0.47172 . 0.566694 0.16139 N 0.227824 T 0.33585 0.0868 N 0.25380 0.74 0.19775 N 0.99996 B 0.27498 0.18 B 0.19148 0.024 T 0.23476 -1.0187 10 0.62326 D 0.03 . 3.6214 0.08097 0.2362:0.0:0.5746:0.1892 . 345 P14091-1 . M 345;350 ENSP00000350911:V345M;ENSP00000354337:V350M ENSP00000350911:V345M V + 1 0 CTSE 204497650 0.000000 0.05858 0.282000 0.24776 0.431000 0.31685 0.742000 0.26216 1.421000 0.47157 0.551000 0.68910 GTG TCGA-IB-A6UF-01A-23D-A33T-08 CTSE-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000087998.1 1 0 1 304 976 0 184 1 1 172 386 0 184 2 0 0 0 0 0 2 1 1 301 969 0 183 2 0 0 0 0 184 2 -2.690609 1 1 121410 165 59 1 1 3 4 2.724539 1 0.580000 1.890000 0.681577 0.990000 9.700000e-01 1.000000 1.000000 0.998779 0.990000 1 0.990000 1.000000 FAM71A 149647 broad.mit.edu 37 1 212798637 212798637 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr1:212798637C>T ENST00000294829.3 + 1 849 c.418C>T c.(418-420)Cgc>Tgc p.R140C RP11-338C15.5_ENST00000427949.1_RNA NM_153606.3 NP_705834.2 Q8IYT1 FA71A_HUMAN family with sequence similarity 71, member A 36 ACAACAGCTGCGCCTGAAGTT 0.483000 0 SO:0001583 missense ENST00000294829.3 1 1 hg19 CCDS1507.1 . . . . . . . . . . C 18.54 3.645226 0.67358 . . ENSG00000162771 ENST00000294829 T 0.19250 2.16 4.29 4.29 0.51040 . 0.312745 0.22908 N 0.054176 T 0.45236 0.1332 M 0.74546 2.27 0.47698 D 0.999498 D 0.89917 1.0 D 0.83275 0.996 T 0.43589 -0.9382 10 0.72032 D 0.01 -20.9761 12.4812 0.55844 0.0:1.0:0.0:0.0 . 140 Q8IYT1 FA71A_HUMAN C 140 ENSP00000294829:R140C ENSP00000294829:R140C R + 1 0 FAM71A 210865260 0.385000 0.25172 1.000000 0.80357 0.701000 0.40568 0.230000 0.17852 2.405000 0.81733 0.557000 0.71058 CGC TCGA-IB-A6UF-01A-23D-A33T-08 FAM71A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000098529.1 1 0 0 396 453 0 109 0 0 0 0 109 2 0 0 0 0 0 2 1 1 394 450 0 109 2 0 0 0 0 109 2 -20.000000 1 1 0 0 1 1 2 3 2.682530 1 0.580000 1.890000 0.674419 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MTR 4548 broad.mit.edu 37 1 237057764 237057764 + Nonsense_Mutation SNP C C A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr1:237057764C>A ENST00000366577.5 + 30 3706 c.3312C>A c.(3310-3312)tgC>tgA p.C1104* MTR_ENST00000470570.1_3'UTR|MTR_ENST00000535889.1_Nonsense_Mutation_p.C1053* NM_000254.2 NP_000245.2 Q99707 METH_HUMAN 5-methyltetrahydrofolate-homocysteine methyltransferase 67 Ovarian(103;0.0634)|Breast(184;0.221) all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117) OV - Ovarian serous cystadenocarcinoma(106;0.0106) Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116) CCGTTGCCTGCTTTGGGGTAG 0.582000 0 SO:0001587 stop_gained ENST00000366577.5 0 1 hg19 CCDS1614.1 . . . . . . . . . . C 39 7.595927 0.98381 . . ENSG00000116984 ENST00000417743;ENST00000366577;ENST00000535889;ENST00000366576 . . . 5.57 4.66 0.58398 . 0.270973 0.36591 N 0.002508 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.46703 T 0.11 -15.4112 10.8432 0.46728 0.0:0.8558:0.0:0.1442 . . . . X 958;1104;1053;658 . ENSP00000355535:C658X C + 3 2 MTR 235124387 0.998000 0.40836 1.000000 0.80357 0.998000 0.95712 0.490000 0.22403 1.495000 0.48549 0.655000 0.94253 TGC TCGA-IB-A6UF-01A-23D-A33T-08 MTR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096632.2 0 0 0 5 574 0 89 0 1.308971e-02 0 16 0 89 2 0 0 0 0 0 2 1 9.360644e-01 7 567 0 89 2 0 0 0 0 89 2 -4.291930 1 1 0 0 1 1 2 3 2.682530 1 0.580000 1.890000 0.674419 0.030000 0 0.090000 0.030000 0.044665 0.030000 0 0.010000 0.070000 ERMAP 114625 broad.mit.edu 37 1 43296629 43296629 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr1:43296629G>A ENST00000372517.2 + 4 520 c.276G>A c.(274-276)ccG>ccA p.P92P ERMAP_ENST00000328249.3_Silent_p.P2P|ERMAP_ENST00000487556.1_Intron|ERMAP_ENST00000372514.3_Silent_p.P92P NM_001017922.1 NP_001017922.1 Q96PL5 ERMAP_HUMAN erythroblast membrane-associated protein (Scianna blood group) 11 Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0333) ATCTGATGCCGGAATATAAGG 0.572000 0 SO:0001819 synonymous_variant ENST00000372517.2 0 1 hg19 CCDS475.1 TCGA-IB-A6UF-01A-23D-A33T-08 ERMAP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000020180.1 0 0 0 4 254 0 42 0 6.161030e-02 0 20 0 42 2 0 0 0 0 0 2 1 8.892517e-01 4 252 0 41 2 0 0 0 0 42 2 -3.019038 1 1 121412 2 31 1 2 2 4 2.170352 0 0.580000 1.890000 0.600836 0.060000 1.000000e-02 1.000000 0.060000 0.137153 0.060000 0 0.030000 0.110000 PTPRF 5792 broad.mit.edu 37 1 44054537 44054537 + Missense_Mutation SNP T T C TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr1:44054537T>C ENST00000359947.4 + 8 1155 c.815T>C c.(814-816)cTc>cCc p.L272P PTPRF_ENST00000438120.1_Missense_Mutation_p.L272P|PTPRF_ENST00000372414.3_Missense_Mutation_p.L272P|PTPRF_ENST00000372413.3_Missense_Mutation_p.L272P|PTPRF_ENST00000422171.2_5'Flank NM_002840.3 NP_002831.2 P10586 PTPRF_HUMAN protein tyrosine phosphatase, receptor type, F 72 all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0333) GCCGAGGAGCTCACCAAGGAG 0.622000 0 SO:0001583 missense ENST00000359947.4 1 1 hg19 CCDS489.2 . . . . . . . . . . T 21.6 4.180087 0.78564 . . ENSG00000142949 ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413 T;T;T;T 0.72725 -0.68;-0.68;-0.68;-0.68 5.62 5.62 0.85841 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.000000 0.30999 N 0.008451 D 0.86863 0.6035 M 0.90977 3.165 0.80722 D 1 D;D 0.89917 0.999;1.0 D;D 0.97110 0.996;1.0 D 0.87323 0.2319 10 0.33141 T 0.24 . 16.1281 0.81408 0.0:0.0:0.0:1.0 . 272;272 P10586-2;P10586 .;PTPRF_HUMAN P 272 ENSP00000353030:L272P;ENSP00000398822:L272P;ENSP00000361491:L272P;ENSP00000361490:L272P ENSP00000353030:L272P L + 2 0 PTPRF 43827124 1.000000 0.71417 1.000000 0.80357 0.566000 0.35808 8.036000 0.88901 2.268000 0.75426 0.533000 0.62120 CTC TCGA-IB-A6UF-01A-23D-A33T-08 PTPRF-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000019710.1 1 0 1 68 140 0 30 1 1 45 95 0 30 2 0 0 0 0 0 2 1 1 68 136 0 30 2 0 0 0 0 30 2 -20.000000 1 1 0 0 1 2 2 4 2.170352 0 0.580000 1.890000 0.600836 0.990000 9.600000e-01 1.000000 1.000000 0.997855 0.990000 1 0.990000 1.000000 ZFP64 55734 broad.mit.edu 37 20 50769918 50769918 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr20:50769918G>A ENST00000216923.4 - 6 1162 c.813C>T c.(811-813)agC>agT p.S271S ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000346617.4_Silent_p.S217S|ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000371515.4_Silent_p.S269S|ZFP64_ENST00000477786.1_Intron NM_018197.2|NM_199426.1 NP_060667.2|NP_955458.1 Q9NPA5 ZF64A_HUMAN ZFP64 zinc finger protein 33 TCAAGTCCGAGCTGATTTTGA 0.557000 0 SO:0001819 synonymous_variant ENST00000216923.4 1 1 hg19 CCDS13440.1 TCGA-IB-A6UF-01A-23D-A33T-08 ZFP64-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000079744.1 1 0 1 81 265 0 41 0 8.951666e-01 0 15 0 41 2 0 0 0 0 0 2 1 1 79 262 0 40 2 0 0 0 0 41 2 -20.000000 1 1 121412 1 26 1 1 2 3 2.663319 1 0.580000 1.890000 0.674419 0.990000 8.400000e-01 1.000000 1.000000 0.978973 0.990000 1 0.930000 1.000000 FERMT1 55612 broad.mit.edu 37 20 6090996 6090996 + Missense_Mutation SNP G G A rs147864238 TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr20:6090996G>A ENST00000217289.4 - 5 1483 c.695C>T c.(694-696)gCg>gTg p.A232V FERMT1_ENST00000536936.1_Intron NM_017671.4 NP_060141.3 Q9BQL6 FERM1_HUMAN fermitin family member 1 17 GTACATATCCGCAAGTGCTTC 0.532000 0 SO:0001583 missense ENST00000217289.4 0 1 hg19 CCDS13098.1 . . . . . . . . . . G 16.60 3.169656 0.57584 0.0 1.16E-4 ENSG00000101311 ENST00000217289;ENST00000339538 T 0.48201 0.82 5.81 4.85 0.62838 FERM, N-terminal (1);Band 4.1 domain (1); 0.047428 0.85682 D 0.000000 T 0.50837 0.1639 M 0.66506 2.035 0.80722 D 1 B;B 0.33044 0.326;0.395 B;B 0.35312 0.078;0.2 T 0.53450 -0.8437 10 0.49607 T 0.09 -4.3671 16.8229 0.85923 0.0:0.1287:0.8713:0.0 . 232;232 Q9BQL6-4;Q9BQL6 .;FERM1_HUMAN V 232 ENSP00000217289:A232V ENSP00000217289:A232V A - 2 0 FERMT1 6038996 1.000000 0.71417 0.595000 0.28798 0.348000 0.29142 6.593000 0.74100 1.427000 0.47276 0.655000 0.94253 GCG TCGA-IB-A6UF-01A-23D-A33T-08 FERMT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077908.2 0 0 0 4 221 0 57 0 1.478176e-01 0 30 0 57 2 0 0 0 0 0 2 1 8.890485e-01 4 219 0 56 2 0 0 0 0 57 2 -2.969779 1 1 121412 32 51 1 0 1 1 1.529228 1 0.580000 1.890000 0.408451 0.040000 1.000000e-02 0.100000 0.040000 0.053567 0.040000 0 0.020000 0.080000 PAK7 57144 broad.mit.edu 37 20 9546990 9546990 + Silent SNP C C G TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr20:9546990C>G ENST00000378429.3 - 6 1578 c.1032G>C c.(1030-1032)ctG>ctC p.L344L PAK7_ENST00000353224.5_Silent_p.L344L|PAK7_ENST00000378423.1_Silent_p.L344L NM_020341.3 NP_065074.1 Q9P286 PAK7_HUMAN p21 protein (Cdc42/Rac)-activated kinase 7 81 COAD - Colon adenocarcinoma(9;0.194) CAGACCCTGACAGTGGAGGGC 0.537000 0 SO:0001819 synonymous_variant ENST00000378429.3 1 1 hg19 CCDS13107.1 TCGA-IB-A6UF-01A-23D-A33T-08 PAK7-001 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077962.1 1 0 1 185 295 0 137 0 0 0 1 0 137 2 0 0 0 0 0 2 1 1 183 292 0 137 2 0 0 0 0 137 2 -20.000000 1 1 0 0 1 0 1 1 1.529228 1 0.580000 1.890000 0.408451 0.920000 8.200000e-01 1.000000 0.940000 0.928633 0.920000 1 0.870000 0.980000 TIAM1 7074 broad.mit.edu 37 21 32513695 32513695 + Missense_Mutation SNP C C A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr21:32513695C>A ENST00000286827.3 - 22 4074 c.3603G>T c.(3601-3603)agG>agT p.R1201S TIAM1_ENST00000541036.1_Missense_Mutation_p.R1141S NM_003253.2 NP_003244.2 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 115 CGAACAGCTCCCTGAGCAGAA 0.622000 0 SO:0001583 missense ENST00000286827.3 1 1 hg19 CCDS13609.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 16.53|16.53 3.149449|3.149449 0.57151|0.57151 .|. .|. ENSG00000156299|ENSG00000156299 ENST00000399841|ENST00000286827;ENST00000541036 .|T;T .|0.68181 .|-0.31;-0.31 5.54|5.54 4.6|4.6 0.57074|0.57074 .|Guanine-nucleotide dissociation stimulator, CDC24, conserved site (1);Dbl homology (DH) domain (5); .|0.286916 .|0.38663 .|N .|0.001620 .|T .|0.49779 .|0.1577 L|L 0.28740|0.28740 0.885|0.885 0.45580|0.45580 D|D 0.998526|0.998526 .|P;P;B .|0.38195 .|0.568;0.622;0.393 .|B;B;B .|0.35770 .|0.133;0.21;0.137 .|T .|0.53641 .|-0.8410 .|10 0.87932|0.54805 D|T 0|0.06 .|. 6.7797|6.7797 0.23638|0.23638 0.0:0.7003:0.1511:0.1486|0.0:0.7003:0.1511:0.1486 .|. .|1141;1141;1201 .|F5GZ53;B7ZLR6;Q13009 .|.;.;TIAM1_HUMAN X|S 1041|1201;1141 .|ENSP00000286827:R1201S;ENSP00000441570:R1141S ENSP00000382735:G1041X|ENSP00000286827:R1201S G|R -|- 1|3 0|2 TIAM1|TIAM1 31435566|31435566 0.996000|0.996000 0.38824|0.38824 1.000000|1.000000 0.80357|0.80357 0.903000|0.903000 0.53119|0.53119 1.201000|1.201000 0.32259|0.32259 2.590000|2.590000 0.87494|0.87494 0.563000|0.563000 0.77884|0.77884 GGA|AGG TCGA-IB-A6UF-01A-23D-A33T-08 TIAM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000192552.1 1 0 1 179 265 0 120 0 6.680394e-01 0 5 0 120 2 0 0 0 0 0 2 1 1 177 261 0 120 2 0 0 0 0 120 2 -20.000000 1 1 0 0 1 0 1 1 1.500265 1 0.580000 1.890000 0.408451 0.950000 8.500000e-01 1.000000 0.980000 0.951173 0.950000 1 0.900000 0.990000 PIWIL3 440822 broad.mit.edu 37 22 25124284 25124284 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr22:25124284G>A ENST00000332271.5 - 15 2208 c.1792C>T c.(1792-1794)Cta>Tta p.L598L PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000527701.1_Silent_p.L480L|PIWIL3_ENST00000533313.1_Silent_p.L480L NM_001008496.3|NM_001255975.1 NP_001008496.2|NP_001242904.1 Q7Z3Z3 PIWL3_HUMAN piwi-like RNA-mediated gene silencing 3 50 TTGGTACATAGGTATCTTTTT 0.418000 0 SO:0001819 synonymous_variant ENST00000332271.5 1 1 hg19 CCDS33623.1 TCGA-IB-A6UF-01A-23D-A33T-08 PIWIL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320084.2 0 0 1 193 289 0 132 0 0 0 0 132 2 0 0 0 0 0 2 1 1 192 288 0 131 2 0 0 0 0 132 2 -20.000000 1 1 0 0 1 0 1 1 1.577093 1 0.580000 1.890000 0.410857 0.950000 8.600000e-01 1.000000 1.000000 0.955915 0.950000 1 0.910000 1.000000 TBC1D22A 25771 broad.mit.edu 37 22 47189570 47189570 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr22:47189570G>A ENST00000337137.4 + 3 458 c.292G>A c.(292-294)Gcc>Acc p.A98T TBC1D22A_ENST00000406733.1_Missense_Mutation_p.A51T|TBC1D22A_ENST00000472791.1_3'UTR|TBC1D22A_ENST00000355704.3_Missense_Mutation_p.A79T|TBC1D22A_ENST00000407381.3_Missense_Mutation_p.A98T|TBC1D22A_ENST00000380995.1_Missense_Mutation_p.A51T NM_001284304.1|NM_001284305.1|NM_014346.2 NP_001271233.1|NP_001271234.1|NP_055161.1 Q8WUA7 TB22A_HUMAN TBC1 domain family, member 22A 22 all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236) CATGGAGACGGCCAACCGTGT 0.687000 0 SO:0001583 missense ENST00000337137.4 0 1 hg19 CCDS14078.1 . . . . . . . . . . G 33 5.260204 0.95368 . . ENSG00000054611 ENST00000337137;ENST00000380995;ENST00000407381;ENST00000355704;ENST00000406733 T;T;T;T;T 0.52295 1.71;0.67;1.27;0.99;1.71 4.8 4.8 0.61643 . 0.053327 0.85682 D 0.000000 T 0.68787 0.3039 M 0.79475 2.455 0.80722 D 1 P;D;D;P 0.76494 0.87;0.998;0.999;0.87 P;D;D;P 0.70935 0.542;0.969;0.971;0.542 T 0.71813 -0.4479 10 0.52906 T 0.07 -6.3978 16.6066 0.84831 0.0:0.0:1.0:0.0 . 98;79;98;98 B9A6M3;Q8WUA7-2;B0QYI1;Q8WUA7 .;.;.;TB22A_HUMAN T 98;51;98;79;51 ENSP00000336724:A98T;ENSP00000370383:A51T;ENSP00000384036:A98T;ENSP00000347932:A79T;ENSP00000385634:A51T ENSP00000336724:A98T A + 1 0 TBC1D22A 45568234 1.000000 0.71417 0.734000 0.30879 0.788000 0.44548 8.819000 0.91997 2.484000 0.83849 0.609000 0.83330 GCC TCGA-IB-A6UF-01A-23D-A33T-08 TBC1D22A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317600.3 0 0 0 5 216 0 42 0 3.788982e-01 0 50 0 42 2 0 0 0 0 0 2 1 9.328330e-01 5 209 0 42 2 0 0 0 0 42 2 -6.203835 1 1 0 0 1 0 1 1 1.577093 1 0.580000 1.890000 0.410857 0.050000 1.000000e-02 0.120000 0.060000 0.065718 0.050000 0 0.030000 0.090000 LYPD6B 130576 broad.mit.edu 37 2 150071135 150071135 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr2:150071135G>A ENST00000409029.1 + 7 665 c.463G>A c.(463-465)Gta>Ata p.V155I LYPD6B_ENST00000409876.1_Missense_Mutation_p.V155I|LYPD6B_ENST00000498249.1_3'UTR|LYPD6B_ENST00000280115.7_Missense_Mutation_p.V179I|LYPD6B_ENST00000409642.3_Missense_Mutation_p.V179I Q8NI32 LPD6B_HUMAN LY6/PLAUR domain containing 6B 11 AGTGTTTGCCGTAATGCACGC 0.483000 0 SO:0001583 missense ENST00000409029.1 0 1 hg19 . . . . . . . . . . G 10.06 1.245572 0.22796 0.0 1.19E-4 ENSG00000150556 ENST00000409642;ENST00000409876;ENST00000409029;ENST00000280115 T;T;T;T 0.16597 2.33;2.33;2.33;2.33 5.78 0.937 0.19494 . 0.357652 0.26983 N 0.021502 T 0.11922 0.0290 L 0.35723 1.085 0.09310 N 1 B;B 0.21821 0.035;0.061 B;B 0.16722 0.01;0.016 T 0.28586 -1.0039 9 . . . -22.7644 10.208 0.43124 0.3397:0.0:0.6603:0.0 . 155;179 Q8NI32;Q8NI32-2 LPD6B_HUMAN;. I 179;155;155;179 ENSP00000387077:V179I;ENSP00000386479:V155I;ENSP00000386650:V155I;ENSP00000280115:V179I . V + 1 0 LYPD6B 149779381 0.832000 0.29368 0.002000 0.10522 0.186000 0.23388 1.506000 0.35747 0.113000 0.18004 -1.871000 0.00553 GTA TCGA-IB-A6UF-01A-23D-A33T-08 LYPD6B-003 KNOWN alternative_5_UTR|basic protein_coding protein_coding OTTHUMT00000332299.2 0 0 0 6 727 0 150 0 4.984479e-02 0 35 0 150 2 0 0 0 0 0 2 1 9.633900e-01 5 717 0 150 2 0 0 0 0 150 2 -1.957102 0 1 121004 11 45 1 0 0 0 2.040573 0 0.580000 1.890000 0.575071 0.020000 0 0.060000 0.030000 0.031568 0.020000 0 0.010000 0.050000 LRP2 4036 broad.mit.edu 37 2 170044768 170044768 + Missense_Mutation SNP G G A rs142093111 byFrequency TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr2:170044768G>A ENST00000263816.3 - 49 9325 c.9040C>T c.(9040-9042)Cgg>Tgg p.R3014W NM_004525.2 NP_004516.2 P98164 LRP2_HUMAN low density lipoprotein receptor-related protein 2 315 """Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)" TCATTGTGCCGGTCACACCTG 0.468000 0 SO:0001583 missense ENST00000263816.3 0 1 hg19 CCDS2232.1 . . . . . . . . . . G 12.66 2.004957 0.35415 0.0 3.49E-4 ENSG00000081479 ENST00000263816 D 0.95588 -3.75 5.68 -1.28 0.09318 Low-density lipoprotein (LDL) receptor class A, conserved site (1); 0.158354 0.53938 N 0.000058 D 0.91331 0.7266 M 0.74881 2.28 0.80722 D 1 P 0.35307 0.494 B 0.27608 0.081 T 0.83269 -0.0044 10 0.44086 T 0.13 . 5.5847 0.17267 0.2891:0.0:0.3935:0.3174 . 3014 P98164 LRP2_HUMAN W 3014 ENSP00000263816:R3014W ENSP00000263816:R3014W R - 1 2 LRP2 169753014 1.000000 0.71417 0.145000 0.22337 0.574000 0.36063 1.361000 0.34136 -0.131000 0.11578 0.650000 0.86243 CGG TCGA-IB-A6UF-01A-23D-A33T-08 LRP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255231.2 0 0 0 5 343 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 9.370272e-01 5 341 0 61 2 0 0 0 0 61 2 -2.497065 0 1 121412 21 45 1 0 0 0 2.040573 0 0.580000 1.890000 0.575071 0.050000 1.000000e-02 0.110000 0.050000 0.058259 0.050000 0 0.020000 0.080000 HOXD10 3236 broad.mit.edu 37 2 176981813 176981813 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr2:176981813G>A ENST00000249501.4 + 1 507 c.252G>A c.(250-252)ccG>ccA p.P84P HOXD10_ENST00000490088.2_Intron NM_002148.3 NP_002139.2 P28358 HXD10_HUMAN homeobox D10 17 OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18) GGACAGATCCGAACAGATCTT 0.453000 0 SO:0001819 synonymous_variant ENST00000249501.4 1 1 hg19 CCDS2266.1 TCGA-IB-A6UF-01A-23D-A33T-08 HOXD10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255692.2 1 0 1 89 299 0 80 0 0 0 0 80 2 0 0 0 0 0 2 1 1 87 295 0 80 2 0 0 0 0 80 2 -4.225160 1 1 0 0 1 0 0 0 2.040573 0 0.580000 1.890000 0.575071 0.770000 6.400000e-01 0.920000 0.780000 0.784971 0.770000 0 0.700000 0.860000 CXCR2 3579 broad.mit.edu 37 2 219000390 219000390 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr2:219000390G>A ENST00000318507.2 + 3 1293 c.866G>A c.(865-867)cGc>cAc p.R289H NM_001557.3 NP_001548.1 P25025 CXCR2_HUMAN chemokine (C-X-C motif) receptor 2 22 TGTGAGCGCCGCAATCACATC 0.597000 0 SO:0001583 missense ENST00000318507.2 0 1 hg19 CCDS2408.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 13.03 2.114961 0.37339 . . ENSG00000180871 ENST00000318507 T 0.37411 1.2 5.36 4.47 0.54385 GPCR, rhodopsin-like superfamily (1); 0.057955 0.64402 D 0.000006 T 0.48502 0.1503 M 0.70108 2.13 0.09310 N 0.999998 P 0.38767 0.646 P 0.50231 0.635 T 0.40440 -0.9563 9 . . . . 9.7981 0.40748 0.1635:0.0:0.8365:0.0 . 289 P25025 CXCR2_HUMAN H 289 ENSP00000319635:R289H . R + 2 0 CXCR2 218708635 0.930000 0.31532 0.358000 0.25811 0.045000 0.14185 3.615000 0.54167 1.243000 0.43853 0.456000 0.33151 CGC TCGA-IB-A6UF-01A-23D-A33T-08 CXCR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256772.2 0 0 0 5 551 0 92 0 0 0 0 92 2 0 0 0 0 0 2 1 9.360015e-01 5 545 0 91 2 0 0 0 0 92 2 -2.383918 0 1 121412 6 40 1 0 0 0 2.040573 0 0.580000 1.890000 0.575071 0.020000 0 0.070000 0.040000 0.036049 0.020000 0 0.010000 0.050000 STK16 8576 broad.mit.edu 37 2 220113194 220113194 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr2:220113194G>A ENST00000409638.3 + 8 1003 c.831G>A c.(829-831)ccG>ccA p.P277P STK16_ENST00000409260.1_Silent_p.P322P|STK16_ENST00000396738.2_Silent_p.P277P|STK16_ENST00000409516.3_Silent_p.P159P|GLB1L_ENST00000295759.7_5'Flank|STK16_ENST00000409743.1_Silent_p.P245P|GLB1L_ENST00000392089.2_5'Flank|TUBA4A_ENST00000498660.1_5'Flank NM_001008910.2 NP_001008910.1 O75716 STK16_HUMAN serine/threonine kinase 16 1 Renal(207;0.0474) CCGTGGACCCGCATCAGCGTC 0.567000 Pancreas(34;887 922 17165 36961 39622) 0 SO:0001819 synonymous_variant ENST00000409638.3 0 1 hg19 CCDS42822.1 TCGA-IB-A6UF-01A-23D-A33T-08 STK16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335679.1 0 0 0 6 625 0 109 0 5.150588e-01 0 163 0 109 2 0 0 0 0 0 2 1 9.647575e-01 7 622 0 108 2 0 0 0 0 109 2 -1.930485 0 1 0 0 1 0 0 0 2.040573 0 0.580000 1.890000 0.575071 0.030000 0 0.070000 0.040000 0.037223 0.030000 0 0.010000 0.050000 SAG 6295 broad.mit.edu 37 2 234237147 234237147 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr2:234237147G>A ENST00000409110.1 + 8 766 c.536G>A c.(535-537)cGc>cAc p.R179H SAG_ENST00000449594.2_Missense_Mutation_p.R45H NM_000541.4 NP_000532.2 P10523 ARRS_HUMAN S-antigen; retina and pineal gland (arrestin) 9 Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054) TTACTGATCCGCAAAGTACAG 0.602000 0 SO:0001583 missense ENST00000409110.1 0 1 hg19 CCDS46545.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 20.3 3.967692 0.74131 0.0 1.2E-4 ENSG00000130561 ENST00000252857;ENST00000409110;ENST00000449594 T;T 0.26660 1.72;1.72 4.18 4.18 0.49190 Arrestin, N-terminal (1);Immunoglobulin E-set (1);Arrestin-like, N-terminal (1); 0.000000 0.85682 D 0.000000 T 0.58708 0.2141 M 0.91300 3.195 0.80722 D 1 D;D 0.89917 0.999;1.0 P;D 0.67900 0.731;0.954 T 0.71573 -0.4552 10 0.87932 D 0 -6.7464 17.0843 0.86606 0.0:0.0:1.0:0.0 . 45;179 B7Z7L5;P10523 .;ARRS_HUMAN H 179;179;45 ENSP00000386444:R179H;ENSP00000392889:R45H ENSP00000252857:R179H R + 2 0 SAG 233901886 1.000000 0.71417 0.962000 0.40283 0.213000 0.24496 9.551000 0.98112 2.337000 0.79520 0.650000 0.86243 CGC TCGA-IB-A6UF-01A-23D-A33T-08 SAG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000330126.1 0 0 0 6 639 0 122 0 0 0 0 122 2 0 0 0 0 0 2 1 9.642434e-01 6 634 0 122 2 0 0 0 0 122 2 -2.065670 0 1 120928 4 40 1 1 2 3 2.077192 0 0.580000 1.890000 0.581214 0.030000 0 0.070000 0.040000 0.036843 0.030000 0 0.010000 0.050000 TMEM214 54867 broad.mit.edu 37 2 27259437 27259437 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr2:27259437C>T ENST00000238788.9 + 6 865 c.803C>T c.(802-804)gCc>gTc p.A268V TMEM214_ENST00000404032.3_Missense_Mutation_p.A223V NM_017727.4 NP_060197.4 Q6NUQ4 TM214_HUMAN transmembrane protein 214 18 GCAGGTTTTGCCAACCTCACC 0.567000 0 SO:0001583 missense ENST00000238788.9 0 1 hg19 CCDS42664.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 9.596|9.596 1.127379|1.127379 0.20959|0.20959 .|. .|. ENSG00000119777|ENSG00000119777 ENST00000238788;ENST00000404032;ENST00000537397|ENST00000425720 T;T|. 0.42131|. 0.98;0.98|. 5.55|5.55 2.24|2.24 0.28232|0.28232 .|. 0.863457|. 0.10873|. N|. 0.624759|. T|T 0.23846|0.23846 0.0577|0.0577 N|N 0.16478|0.16478 0.41|0.41 0.09310|0.09310 N|N 0.999999|0.999999 B;B|. 0.11235|. 0.004;0.001|. B;B|. 0.12837|. 0.006;0.008|. T|T 0.23297|0.23297 -1.0192|-1.0192 10|5 0.22706|. T|. 0.39|. -0.0745|-0.0745 9.7642|9.7642 0.40550|0.40550 0.0:0.7292:0.1201:0.1507|0.0:0.7292:0.1201:0.1507 .|. 223;268|. Q6NUQ4-2;Q6NUQ4|. .;TM214_HUMAN|. V|S 268;223;10|27 ENSP00000238788:A268V;ENSP00000384417:A223V|. ENSP00000238788:A268V|. A|P +|+ 2|1 0|0 TMEM214|TMEM214 27112941|27112941 0.001000|0.001000 0.12720|0.12720 0.400000|0.400000 0.26346|0.26346 0.988000|0.988000 0.76386|0.76386 1.447000|1.447000 0.35101|0.35101 0.687000|0.687000 0.31509|0.31509 0.561000|0.561000 0.74099|0.74099 GCC|CCA TCGA-IB-A6UF-01A-23D-A33T-08 TMEM214-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324748.1 0 0 0 6 719 0 151 0 4.578474e-01 0 167 0 151 2 0 0 0 0 0 2 1 9.632171e-01 6 707 0 150 2 0 0 0 0 151 2 -2.180138 0 1 0 0 1 1 2 3 2.078345 0 0.580000 1.890000 0.581214 0.020000 0 0.070000 0.030000 0.032377 0.020000 0 0.010000 0.050000 SNRNP200 23020 broad.mit.edu 37 2 96967391 96967391 + Missense_Mutation SNP G G A rs150957097 TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr2:96967391G>A ENST00000323853.5 - 4 522 c.445C>T c.(445-447)Cgg>Tgg p.R149W SNRNP200_ENST00000349783.5_Missense_Mutation_p.R149W NM_014014.4 NP_054733.2 O75643 U520_HUMAN small nuclear ribonucleoprotein 200kDa (U5) 90 TCCTTGTCCCGCAGCTTTTCA 0.463000 0 SO:0001583 missense ENST00000323853.5 0 1 hg19 CCDS2020.1 . . . . . . . . . . G 20.5 3.994162 0.74703 . . ENSG00000144028 ENST00000323853;ENST00000349783 T;T 0.46819 0.86;0.86 5.58 5.58 0.84498 . 0.120859 0.53938 D 0.000047 T 0.59128 0.2171 M 0.62088 1.915 0.80722 D 1 D 0.69078 0.997 P 0.51657 0.676 T 0.63337 -0.6660 10 0.87932 D 0 -16.1737 18.3443 0.90315 0.0:0.0:1.0:0.0 . 149 O75643 U520_HUMAN W 149 ENSP00000317123:R149W;ENSP00000326937:R149W ENSP00000317123:R149W R - 1 2 SNRNP200 96331118 1.000000 0.71417 0.985000 0.45067 0.868000 0.49771 3.196000 0.51020 2.636000 0.89361 0.455000 0.32223 CGG TCGA-IB-A6UF-01A-23D-A33T-08 SNRNP200-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252846.2 0 0 0 7 670 0 114 0 1.298924e-01 0 52 0 114 2 0 0 0 0 0 2 1 9.802596e-01 7 666 0 113 2 0 0 0 0 114 2 -1.783854 0 1 121412 1 34 1 1 2 3 2.099429 0 0.580000 1.890000 0.582422 0.030000 0 0.080000 0.040000 0.050088 0.030000 0 0.010000 0.060000 OSBPL11 114885 broad.mit.edu 37 3 125298799 125298799 + Nonsense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr3:125298799G>A ENST00000296220.5 - 3 608 c.319C>T c.(319-321)Cag>Tag p.Q107* NM_022776.4 NP_073613.2 Q9BXB4 OSB11_HUMAN oxysterol binding protein-like 11 27 CCTGCAAGCTGCAAAGTTCCT 0.403000 0 SO:0001587 stop_gained ENST00000296220.5 0 1 hg19 CCDS3033.1 . . . . . . . . . . G 40 7.930052 0.98565 . . ENSG00000144909 ENST00000296220 . . . 5.07 5.07 0.68467 . 0.268957 0.38272 N 0.001758 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.16896 T 0.51 13.9553 18.6341 0.91371 0.0:0.0:1.0:0.0 . . . . X 107 . ENSP00000296220:Q107X Q - 1 0 OSBPL11 126781489 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.587000 0.98229 2.628000 0.89032 0.655000 0.94253 CAG TCGA-IB-A6UF-01A-23D-A33T-08 OSBPL11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356295.1 0 0 0 5 533 0 80 0 5.981737e-03 0 10 0 80 2 0 0 0 0 0 2 1 9.359506e-01 5 527 0 79 2 0 0 0 0 80 2 -2.461193 0 1 0 0 1 0 0 0 2.070095 0 0.580000 1.890000 0.580000 0.030000 0 0.070000 0.040000 0.037718 0.030000 0 0.010000 0.050000 C3orf22 152065 broad.mit.edu 37 3 126268739 126268739 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr3:126268739G>A ENST00000318225.2 - 4 776 c.398C>T c.(397-399)gCg>gTg p.A133V NM_152533.1 NP_689746.1 Q8N5N4 CC022_HUMAN chromosome 3 open reading frame 22 7 CAGCCCTGCCGCCTTGCTGGT 0.627000 0 SO:0001583 missense ENST00000318225.2 1 1 hg19 CCDS3040.1 . . . . . . . . . . G 13.41 2.228530 0.39399 0.0 1.16E-4 ENSG00000180697 ENST00000318225 . . . 1.92 -0.536 0.11876 . . . . . T 0.09818 0.0241 N 0.19112 0.55 0.09310 N 1 P 0.41188 0.741 B 0.25405 0.06 T 0.22730 -1.0208 8 0.02654 T 1 6.4871 4.5161 0.11935 0.4702:0.0:0.5298:0.0 . 133 Q8N5N4 CC022_HUMAN V 133 . ENSP00000316644:A133V A - 2 0 C3orf22 127751429 0.000000 0.05858 0.000000 0.03702 0.003000 0.03518 -0.292000 0.08332 -0.154000 0.11118 0.313000 0.20887 GCG TCGA-IB-A6UF-01A-23D-A33T-08 C3orf22-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000370231.2 1 0 1 83 174 0 43 0 0 0 0 43 2 0 0 0 0 0 2 1 1 82 174 0 43 2 0 0 0 0 43 2 -20.000000 1 1 121412 4 33 1 0 0 0 2.070095 0 0.580000 1.890000 0.580000 0.990000 9.100000e-01 1.000000 1.000000 0.994177 0.990000 1 0.990000 1.000000 MCM2 4171 broad.mit.edu 37 3 127337969 127337969 + Missense_Mutation SNP G G A rs147793264 TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr3:127337969G>A ENST00000265056.7 + 13 2357 c.2113G>A c.(2113-2115)Gcc>Acc p.A705T MCM2_ENST00000468414.1_3'UTR NM_004526.2 NP_004517.2 P49736 MCM2_HUMAN minichromosome maintenance complex component 2 6 TGCTGAGCCCGCCATGCCCAA 0.637000 0 SO:0001583 missense ENST00000265056.7 0 1 hg19 CCDS3043.1 . . . . . . . . . . G 1.635 -0.517936 0.04171 0.0 1.16E-4 ENSG00000073111 ENST00000265056;ENST00000539922;ENST00000543142 T 0.02421 4.3 5.61 0.559 0.17272 . 1.165010 0.06316 N 0.703534 T 0.01976 0.0062 N 0.05467 -0.045 0.19300 N 0.999978 B;B;B 0.14012 0.001;0.009;0.008 B;B;B 0.16289 0.002;0.015;0.009 T 0.50065 -0.8871 10 0.15066 T 0.55 -10.4948 10.4606 0.44577 0.4466:0.0:0.5534:0.0 . 755;575;705 F5H1E9;B4DSV5;P49736 .;.;MCM2_HUMAN T 705;609;755 ENSP00000265056:A705T ENSP00000265056:A705T A + 1 0 MCM2 128820659 0.111000 0.22076 0.014000 0.15608 0.049000 0.14656 0.425000 0.21346 -0.197000 0.10350 -0.964000 0.02622 GCC TCGA-IB-A6UF-01A-23D-A33T-08 MCM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356612.1 0 0 0 4 218 0 35 0 2.259680e-01 1 39 0 35 2 0 0 0 0 0 2 1 8.788610e-01 4 207 0 33 2 0 0 0 0 35 2 -5.364141 1 0 0 0 1 0 0 0 2.070095 0 0.580000 1.890000 0.580000 0.060000 1.000000e-02 0.150000 0.060000 0.076655 0.060000 0 0.030000 0.110000 ASTE1 28990 broad.mit.edu 37 3 130744081 130744081 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr3:130744081G>A ENST00000264992.3 - 3 511 c.70C>T c.(70-72)Cgg>Tgg p.R24W ASTE1_ENST00000514044.1_Missense_Mutation_p.R24W|NEK11_ENST00000510688.1_5'Flank|NEK11_ENST00000383366.4_5'Flank|NEK11_ENST00000507910.1_5'Flank|NEK11_ENST00000412440.2_5'Flank|NEK11_ENST00000511262.1_5'Flank|NEK11_ENST00000356918.4_5'Flank|NEK11_ENST00000510769.1_5'Flank|NEK11_ENST00000429253.2_5'Flank NM_014065.2 NP_054784.2 Q2TB18 ASTE1_HUMAN asteroid homolog 1 (Drosophila) p.R24W(1) 22 TTTGTGTCCCGCAACTTCAAA 0.403000 1 Substitution - Missense(1) SO:0001583 missense ENST00000264992.3 0 1 hg19 CCDS3068.1 . . . . . . . . . . G 18.16 3.562030 0.65538 . . ENSG00000034533 ENST00000514044;ENST00000264992;ENST00000446270;ENST00000505545;ENST00000504725 T;T;T;T 0.56611 0.45;0.45;0.45;0.45 5.44 2.22 0.28083 XPG N-terminal (1); 0.048280 0.85682 D 0.000000 T 0.70202 0.3197 M 0.74881 2.28 0.42751 D 0.993773 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 T 0.74682 -0.3583 10 0.87932 D 0 -23.8367 13.7698 0.63018 0.0:0.0:0.4438:0.5562 . 24;24 D6RG30;Q2TB18 .;ASTE1_HUMAN W 24 ENSP00000426421:R24W;ENSP00000264992:R24W;ENSP00000425683:R24W;ENSP00000422851:R24W ENSP00000264992:R24W R - 1 2 ASTE1 132226771 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 1.943000 0.40253 0.599000 0.29845 0.650000 0.86243 CGG TCGA-IB-A6UF-01A-23D-A33T-08 ASTE1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356659.1 0 0 0 6 722 0 136 0 2.115282e-03 0 7 0 136 2 0 0 0 0 0 2 1 9.643126e-01 6 717 0 136 2 0 0 0 0 136 2 -2.035640 0 1 0 0 1 0 0 0 2.070095 0 0.580000 1.890000 0.580000 0.020000 0 0.060000 0.030000 0.032122 0.020000 0 0.010000 0.050000 SCN11A 11280 broad.mit.edu 37 3 38938452 38938452 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr3:38938452G>A ENST00000302328.3 - 14 2485 c.2287C>T c.(2287-2289)Cgc>Tgc p.R763C SCN11A_ENST00000456224.3_Missense_Mutation_p.R763C|SCN11A_ENST00000450244.1_Missense_Mutation_p.R763C|SCN11A_ENST00000444237.2_Missense_Mutation_p.R763C NM_014139.2 NP_054858.2 Q9UI33 SCNBA_HUMAN sodium channel, voltage-gated, type XI, alpha subunit 119 Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909) CAGAGGATGCGGAATACCACT 0.473000 0 SO:0001583 missense ENST00000302328.3 1 1 hg19 CCDS33737.1 . . . . . . . . . . G 35 5.468244 0.96274 . . ENSG00000168356 ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237 D;D;D;D 0.97480 -4.4;-4.4;-4.4;-4.4 5.95 5.95 0.96441 Ion transport (1); 0.000000 0.85682 D 0.000000 D 0.99208 0.9725 H 0.97983 4.12 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.98760 1.0724 10 0.87932 D 0 . 20.4024 0.99000 0.0:0.0:1.0:0.0 . 763 Q9UI33 SCNBA_HUMAN C 763 ENSP00000307599:R763C;ENSP00000400945:R763C;ENSP00000416757:R763C;ENSP00000408028:R763C ENSP00000307599:R763C R - 1 0 SCN11A 38913456 1.000000 0.71417 1.000000 0.80357 0.896000 0.52359 7.812000 0.86109 2.827000 0.97445 0.650000 0.86243 CGC TCGA-IB-A6UF-01A-23D-A33T-08 SCN11A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109746.4 1 0 1 96 233 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 1 96 229 0 70 2 0 0 0 0 70 2 -7.485149 1 1 121412 5 38 1 1 2 3 2.093118 0 0.580000 1.890000 0.582422 0.990000 8.400000e-01 1.000000 1.000000 0.972358 0.990000 1 0.920000 1.000000 CCR2 729230 broad.mit.edu 37 3 46401296 46401296 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr3:46401296G>A ENST00000400888.2 + 2 1109 c.1070G>A c.(1069-1071)gGa>gAa p.G357E CCR2_ENST00000292301.4_Missense_Mutation_p.G357E P41597 CCR2_HUMAN chemokine (C-C motif) receptor 2 14 CGTGGAAAAGGAAAGTCAATT 0.493000 0 SO:0001583 missense ENST00000400888.2 0 1 hg19 CCDS43078.1 . . . . . . . . . . G 9.639 1.138456 0.21123 . . ENSG00000121807 ENST00000292301;ENST00000400888 T;T 0.68765 -0.35;-0.35 3.45 -1.8 0.07907 . 2.790660 0.01671 N 0.025619 T 0.43678 0.1258 N 0.08118 0 0.09310 N 1 B 0.25904 0.137 B 0.27887 0.084 T 0.19516 -1.0303 10 0.22109 T 0.4 . 4.2507 0.10693 0.3066:0.3232:0.3702:0.0 . 357 P41597 CCR2_HUMAN E 357 ENSP00000292301:G357E;ENSP00000383681:G357E ENSP00000292301:G357E G + 2 0 CCR2 46376300 0.000000 0.05858 0.000000 0.03702 0.004000 0.04260 -0.258000 0.08733 -0.422000 0.07405 -0.156000 0.13503 GGA TCGA-IB-A6UF-01A-23D-A33T-08 CCR2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000344292.1 0 0 0 6 439 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 9.639711e-01 6 435 0 63 2 0 0 0 0 63 2 -5.505612 1 1 0 0 1 1 2 3 2.093118 0 0.580000 1.890000 0.582422 0.040000 1.000000e-02 0.110000 0.040000 0.063499 0.040000 0 0.020000 0.080000 LHFPL4 375323 broad.mit.edu 37 3 9547694 9547694 + Silent SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr3:9547694C>T ENST00000287585.6 - 3 885 c.600G>A c.(598-600)cgG>cgA p.R200R NM_198560.2 NP_940962.1 Q86UP9 LHPL3_HUMAN lipoma HMGIC fusion partner-like 4 10 Medulloblastoma(99;0.227) GGTCTGTTTGCCGGTTGCCCA 0.657000 0 SO:0001819 synonymous_variant ENST00000287585.6 0 1 hg19 CCDS33691.1 TCGA-IB-A6UF-01A-23D-A33T-08 LHFPL4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000338298.1 0 0 0 6 748 1 108 0 0 0 1 108 2 0 0 0 0 0 2 0 1.564122e-05 6 745 2 107 31 0 0 0 1 108 2 -2.362691 0 1 0 0 1 1 2 3 2.093118 0 0.580000 1.890000 0.582422 0.020000 0 0.070000 0.020000 0.040568 0.020000 0 0.010000 0.050000 FSTL5 56884 broad.mit.edu 37 4 162841645 162841645 + Missense_Mutation SNP A A T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr4:162841645A>T ENST00000306100.5 - 4 756 c.320T>A c.(319-321)tTc>tAc p.F107Y FSTL5_ENST00000379164.4_Missense_Mutation_p.F106Y|FSTL5_ENST00000536695.1_Missense_Mutation_p.F106Y|FSTL5_ENST00000427802.2_Missense_Mutation_p.F106Y NM_001128427.2|NM_020116.4 NP_001121899.1|NP_064501.2 Q8N475 FSTL5_HUMAN follistatin-like 5 91 all_hematologic(180;0.24) GTTTTCATAGAATTCTCCGTC 0.433000 0 SO:0001583 missense ENST00000306100.5 1 1 hg19 CCDS3802.1 . . . . . . . . . . A 24.6 4.552502 0.86127 . . ENSG00000168843 ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695 T;T;T;T 0.04156 3.69;3.69;3.69;3.69 5.86 5.86 0.93980 Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1); 0.056975 0.64402 D 0.000001 T 0.08268 0.0206 L 0.33093 0.98 0.47994 D 0.999564 D;B;D 0.53619 0.961;0.134;0.961 P;B;P 0.48770 0.589;0.017;0.589 T 0.13176 -1.0519 10 0.51188 T 0.08 . 15.7408 0.77894 1.0:0.0:0.0:0.0 . 106;106;107 E9PCP6;F8VZ90;Q8N475 .;.;FSTL5_HUMAN Y 107;106;106;106 ENSP00000305334:F107Y;ENSP00000368462:F106Y;ENSP00000389270:F106Y;ENSP00000440409:F106Y ENSP00000305334:F107Y F - 2 0 FSTL5 163061095 1.000000 0.71417 0.993000 0.49108 0.993000 0.82548 8.910000 0.92685 2.367000 0.80283 0.528000 0.53228 TTC TCGA-IB-A6UF-01A-23D-A33T-08 FSTL5-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000364773.2 1 0 1 68 175 0 25 0 0 0 0 25 2 0 0 0 0 0 2 1 1 68 173 0 25 2 0 0 0 0 25 2 -20.000000 1 1 0 0 1 1 2 3 2.083006 0 0.580000 1.890000 0.581214 0.960000 7.700000e-01 1.000000 1.000000 0.944076 0.960000 1 0.860000 1.000000 CLCN3 1182 broad.mit.edu 37 4 170618575 170618575 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr4:170618575G>A ENST00000513761.1 + 9 1812 c.1253G>A c.(1252-1254)cGc>cAc p.R418H CLCN3_ENST00000360642.3_Missense_Mutation_p.R391H|CLCN3_ENST00000347613.4_Missense_Mutation_p.R418H|CLCN3_ENST00000504131.2_Missense_Mutation_p.R401H NM_001829.3 NP_001820.2 P51790 CLCN3_HUMAN chloride channel, voltage-sensitive 3 29 Prostate(90;0.00601)|Renal(120;0.0183) TGTCGTCGACGCAAGTCCACG 0.438000 0 SO:0001583 missense ENST00000513761.1 0 1 hg19 CCDS34101.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 27.9|27.9 4.870874|4.870874 0.91587|0.91587 .|. .|. ENSG00000109572|ENSG00000109572 ENST00000515420|ENST00000513761;ENST00000347613;ENST00000360642;ENST00000504131;ENST00000507875 .|D;D;D;D;D .|0.94650 .|-3.48;-3.48;-3.48;-3.48;-3.48 5.84|5.84 5.84|5.84 0.93424|0.93424 .|Chloride channel, core (2); .|0.046411 .|0.85682 .|D .|0.000000 D|D 0.98425|0.98425 0.9476|0.9476 H|H 0.96777|0.96777 3.88|3.88 0.80722|0.80722 D|D 1|1 .|D;D;D;D;D .|0.89917 .|0.999;1.0;0.999;0.999;1.0 .|D;D;D;D;D .|0.77557 .|0.984;0.99;0.984;0.984;0.972 D|D 0.99023|0.99023 1.0818|1.0818 5|10 .|0.87932 .|D .|0 -4.8294|-4.8294 20.1392|20.1392 0.98050|0.98050 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|391;401;391;418;418 .|B7Z932;B9EGJ9;E9PE15;P51790;P51790-2 .|.;.;.;CLCN3_HUMAN;. T|H 73|418;418;391;401;391 .|ENSP00000424603:R418H;ENSP00000261514:R418H;ENSP00000353857:R391H;ENSP00000424540:R401H;ENSP00000425323:R391H .|ENSP00000261514:R418H A|R +|+ 1|2 0|0 CLCN3|CLCN3 170855150|170855150 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.990000|0.990000 0.78478|0.78478 7.968000|7.968000 0.87980|0.87980 2.765000|2.765000 0.95021|0.95021 0.557000|0.557000 0.71058|0.71058 GCA|CGC TCGA-IB-A6UF-01A-23D-A33T-08 CLCN3-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000363210.2 0 0 0 6 617 0 117 0 8.874039e-02 0 43 0 117 2 0 0 0 0 0 2 1 9.638607e-01 5 611 0 115 2 0 0 0 0 117 2 -2.170206 0 1 0 0 1 1 2 3 2.083006 0 0.580000 1.890000 0.581214 0.030000 0 0.070000 0.040000 0.038253 0.030000 0 0.010000 0.050000 FRAS1 80144 broad.mit.edu 37 4 79462159 79462159 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr4:79462159C>T ENST00000264895.6 + 74 12360 c.11920C>T c.(11920-11922)Cgg>Tgg p.R3974W NM_025074.6 NP_079350.5 Q86XX4 FRAS1_HUMAN Fraser extracellular matrix complex subunit 1 103 CTGCACTGTGCGGAACGTCAA 0.473000 0 SO:0001583 missense ENST00000264895.6 0 1 hg19 CCDS54771.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 14.68|14.68 2.608257|2.608257 0.46527|0.46527 .|. .|. ENSG00000138759|ENSG00000138759 ENST00000512123|ENST00000264895 .|T .|0.51325 .|0.71 6.08|6.08 4.27|4.27 0.50696|0.50696 .|. .|0.056812 .|0.64402 .|D .|0.000004 T|T 0.62392|0.62392 0.2424|0.2424 L|L 0.51422|0.51422 1.61|1.61 0.80722|0.80722 D|D 1|1 .|D .|0.89917 .|1.0 .|D .|0.77004 .|0.989 T|T 0.66559|0.66559 -0.5893|-0.5893 5|10 .|0.87932 .|D .|0 .|. 14.4407|14.4407 0.67314|0.67314 0.4855:0.5145:0.0:0.0|0.4855:0.5145:0.0:0.0 .|. .|3974 .|E9PHH6 .|. V|W 2202|3974 .|ENSP00000264895:R3974W .|ENSP00000264895:R3974W A|R +|+ 2|1 0|2 FRAS1|FRAS1 79681183|79681183 1.000000|1.000000 0.71417|0.71417 0.997000|0.997000 0.53966|0.53966 0.071000|0.071000 0.16799|0.16799 2.329000|2.329000 0.43876|0.43876 1.543000|1.543000 0.49345|0.49345 0.591000|0.591000 0.81541|0.81541 GCG|CGG TCGA-IB-A6UF-01A-23D-A33T-08 FRAS1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 6 400 0 60 0 4.747088e-03 0 6 0 60 2 0 0 0 0 0 2 1 9.606618e-01 6 384 0 60 2 0 0 0 0 60 2 -2.927346 1 1 120856 1 31 1 1 2 3 2.151450 0 0.580000 1.890000 0.588356 0.050000 1.000000e-02 1.000000 0.060000 0.112669 0.050000 0 0.030000 0.090000 SEPT8 23176 broad.mit.edu 37 5 132098218 132098218 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:132098218G>A ENST00000378719.2 - 5 891 c.654C>T c.(652-654)ccC>ccT p.P218P SEPT8_ENST00000378706.1_Silent_p.P218P|SEPT8_ENST00000458488.2_Silent_p.P218P|SEPT8_ENST00000378721.4_Silent_p.P216P|SEPT8_ENST00000481030.1_5'Flank|SEPT8_ENST00000296873.7_Silent_p.P218P|SEPT8_ENST00000448933.1_Silent_p.P158P|SEPT8_ENST00000378699.2_Silent_p.P158P|SEPT8_ENST00000378701.1_Silent_p.P216P NM_001098811.1 NP_001092281.1 Q92599 SEPT8_HUMAN septin 8 SEPT8/AFF4(2) 11 all_cancers(142;0.0751)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) CATCATCCGTGGGGAACTGGT 0.582000 0 SO:0001819 synonymous_variant ENST00000378719.2 1 1 hg19 CCDS43358.1 TCGA-IB-A6UF-01A-23D-A33T-08 SEPT8-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000132827.2 1 0 1 127 272 0 58 1 1 10 63 0 58 2 0 0 0 0 0 2 1 1 124 271 0 58 2 0 0 0 0 58 2 -10.753750 1 1 0 0 1 1 2 3 2.101368 0 0.580000 1.890000 0.582422 0.990000 9.400000e-01 1.000000 1.000000 0.996589 0.990000 1 0.990000 1.000000 PPP2CA 5515 broad.mit.edu 37 5 133541798 133541798 + Missense_Mutation SNP A A G TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:133541798A>G ENST00000481195.1 - 2 407 c.127T>C c.(127-129)Tcc>Ccc p.S43P CDKL3_ENST00000609383.1_3'UTR|CDKL3_ENST00000609654.1_Missense_Mutation_p.S393P|PPP2CA_ENST00000231504.5_5'UTR|CTD-2410N18.5_ENST00000519718.1_Intron|CTD-2410N18.4_ENST00000518409.1_RNA NM_002715.2 NP_002706.1 P67775 PP2AA_HUMAN protein phosphatase 2, catalytic subunit, alpha isozyme 12 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) Vitamin E(DB00163) TGCACGTTGGATTCTTTTGTC 0.378000 0 SO:0001583 missense ENST00000481195.1 1 1 hg19 CCDS4173.1 . . . . . . . . . . A 19.20 3.782504 0.70222 . . ENSG00000113575 ENST00000481195;ENST00000523082 T;T 0.03745 3.82;3.82 5.35 5.35 0.76521 Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1); 0.107193 0.64402 D 0.000003 T 0.09423 0.0232 L 0.39245 1.2 0.80722 D 1 B;B 0.29571 0.249;0.001 P;B 0.46049 0.502;0.002 T 0.23013 -1.0200 10 0.62326 D 0.03 -5.6143 15.6174 0.76778 1.0:0.0:0.0:0.0 . 393;43 B7Z2C5;P67775 .;PP2AA_HUMAN P 43;30 ENSP00000418447:S43P;ENSP00000428816:S30P ENSP00000418447:S43P S - 1 0 PPP2CA 133569697 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 9.287000 0.95975 2.161000 0.67846 0.482000 0.46254 TCC TCGA-IB-A6UF-01A-23D-A33T-08 PPP2CA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251165.1 0 0 1 90 243 0 70 1 1 73 146 0 70 2 0 0 0 0 0 2 1 1 90 240 0 70 2 0 0 0 0 70 2 -20.000000 1 1 0 0 1 1 2 3 2.101368 0 0.580000 1.890000 0.582422 0.930000 7.700000e-01 1.000000 1.000000 0.928633 0.930000 1 0.850000 1.000000 PCDHB1 29930 broad.mit.edu 37 5 140431291 140431291 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:140431291G>A ENST00000306549.3 + 1 313 c.236G>A c.(235-237)cGc>cAc p.R79H NM_013340.2 NP_037472.2 Q9Y5F3 PCDB1_HUMAN protocadherin beta 1 p.R79L(1) 53 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) CGGCTCCACCGCAAGACGGGA 0.567000 1 Substitution - Missense(1) SO:0001583 missense ENST00000306549.3 0 1 hg19 CCDS4243.1 . . . . . . . . . . G 10.80 1.452174 0.26074 . . ENSG00000171815 ENST00000306549 T 0.38887 1.11 5.81 5.81 0.92471 Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1); 0.000000 0.48767 D 0.000178 T 0.38480 0.1042 L 0.46614 1.455 0.22719 N 0.998819 D 0.59357 0.985 P 0.48795 0.59 T 0.42749 -0.9433 10 0.30078 T 0.28 . 5.4729 0.16680 0.0748:0.1974:0.598:0.1299 . 79 Q9Y5F3 PCDB1_HUMAN H 79 ENSP00000307234:R79H ENSP00000307234:R79H R + 2 0 PCDHB1 140411475 0.000000 0.05858 1.000000 0.80357 0.929000 0.56500 0.076000 0.14712 2.756000 0.94617 0.655000 0.94253 CGC TCGA-IB-A6UF-01A-23D-A33T-08 PCDHB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251822.2 0 0 0 6 459 0 94 0 0 0 0 94 2 0 0 0 0 0 2 1 9.625183e-01 6 448 0 93 2 0 0 0 0 94 2 -2.618802 1 1 0 0 1 1 2 3 2.101368 0 0.580000 1.890000 0.582422 0.040000 0 0.110000 0.040000 0.061186 0.040000 0 0.020000 0.070000 PCDHGB1 56104 broad.mit.edu 37 5 140730509 140730509 + Nonsense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:140730509C>T ENST00000523390.1 + 1 682 c.682C>T c.(682-684)Cga>Tga p.R228* PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron NM_018922.2|NM_032095.1 NP_061745.1|NP_115266.1 Q9Y5G3 PCDGD_HUMAN protocadherin gamma subfamily B, 1 16 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TATCTGGATCCGAGTTACGGA 0.547000 0 SO:0001587 stop_gained ENST00000523390.1 0 1 hg19 CCDS54923.1 . . . . . . . . . . . 14.38 2.518092 0.44763 . . ENSG00000254221 ENST00000523390 . . . 5.36 1.88 0.25563 . . . . . . . . . . . 0.80722 A 1 . . . . . . . . . . 0.41790 T 0.15 . 7.6146 0.28150 0.6252:0.2816:0.0:0.0931 . . . . X 228 . ENSP00000429273:R228X R + 1 2 PCDHGB1 140710693 0.000000 0.05858 0.031000 0.17742 0.055000 0.15305 0.430000 0.21428 0.655000 0.30866 0.563000 0.77884 CGA TCGA-IB-A6UF-01A-23D-A33T-08 PCDHGB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374740.1 1 0 1 140 330 0 88 0 7.991053e-01 0 9 0 88 2 0 0 0 0 0 2 1 1 128 295 0 79 2 0 0 0 0 88 2 -9.525268 1 1 120854 1 29 1 1 2 3 2.101368 0 0.580000 1.890000 0.582422 0.990000 8.800000e-01 1.000000 1.000000 0.985139 0.990000 1 0.950000 1.000000 PCDH12 51294 broad.mit.edu 37 5 141335933 141335933 + Missense_Mutation SNP A A T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:141335933A>T ENST00000231484.3 - 1 2694 c.1484T>A c.(1483-1485)gTc>gAc p.V495D AC005740.6_ENST00000607378.1_RNA|PCDH12_ENST00000512221.1_5'Flank NM_016580.2 NP_057664.1 Q9NPG4 PCD12_HUMAN protocadherin 12 38 all_hematologic(541;0.0999) KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GCGGTATGAGACTTTTCCATT 0.473000 0 SO:0001583 missense ENST00000231484.3 1 1 hg19 CCDS4269.1 . . . . . . . . . . A 13.73 2.325820 0.41197 . . ENSG00000113555 ENST00000231484 T 0.55234 0.53 5.16 5.16 0.70880 Cadherin (4);Cadherin-like (1); 0.463335 0.22727 N 0.056374 T 0.77315 0.4112 H 0.94886 3.595 0.80722 D 1 D 0.67145 0.996 P 0.62089 0.898 D 0.83734 0.0200 10 0.87932 D 0 . 12.9983 0.58660 1.0:0.0:0.0:0.0 . 495 Q9NPG4 PCD12_HUMAN D 495 ENSP00000231484:V495D ENSP00000231484:V495D V - 2 0 PCDH12 141316117 1.000000 0.71417 0.835000 0.33067 0.159000 0.22180 9.139000 0.94554 2.169000 0.68431 0.533000 0.62120 GTC TCGA-IB-A6UF-01A-23D-A33T-08 PCDH12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251858.1 1 0 1 107 233 0 46 0 6.115445e-01 0 6 0 46 2 0 0 0 0 0 2 1 1 106 231 0 46 2 0 0 0 0 46 2 -20.000000 1 1 0 0 1 1 2 3 2.101368 0 0.580000 1.890000 0.582422 0.990000 9.200000e-01 1.000000 1.000000 0.993967 0.990000 1 0.990000 1.000000 FAT2 2196 broad.mit.edu 37 5 150930181 150930181 + Silent SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:150930181C>T ENST00000261800.5 - 7 4560 c.4548G>A c.(4546-4548)tcG>tcA p.S1516S 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) GGGAGGGCCCCGAGCCGAGGT 0.532000 0 SO:0001819 synonymous_variant ENST00000261800.5 0 1 hg19 CCDS4317.1 TCGA-IB-A6UF-01A-23D-A33T-08 FAT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252434.1 0 0 0 8 390 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 9.889771e-01 8 385 0 73 2 0 0 0 0 74 2 -2.046387 0 1 121412 2 35 1 1 2 3 2.101368 0 0.580000 1.890000 0.582422 0.070000 2.000000e-02 0.150000 0.070000 0.086931 0.070000 0 0.040000 0.110000 FAM71B 153745 broad.mit.edu 37 5 156593091 156593091 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:156593091C>T ENST00000302938.4 - 1 184 c.89G>A c.(88-90)cGa>cAa p.R30Q NM_130899.2 NP_570969.2 Q8TC56 FA71B_HUMAN family with sequence similarity 71, member B 68 Renal(175;0.00212) Medulloblastoma(196;0.0523)|all_neural(177;0.21) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) GTACAATTGTCGTTGCAGGTC 0.403000 0 SO:0001583 missense ENST00000302938.4 1 1 hg19 CCDS4335.1 . . . . . . . . . . C 6.047 0.377072 0.11466 . . ENSG00000170613 ENST00000302938 T 0.04970 3.52 4.67 2.9 0.33743 . 0.174270 0.35151 N 0.003414 T 0.02929 0.0087 N 0.12887 0.27 0.09310 N 1 P 0.35600 0.511 B 0.23419 0.046 T 0.44877 -0.9299 10 0.38643 T 0.18 -3.3554 8.0345 0.30484 0.0:0.8053:0.0:0.1947 . 30 Q8TC56 FA71B_HUMAN Q 30 ENSP00000305596:R30Q ENSP00000305596:R30Q R - 2 0 FAM71B 156525669 0.000000 0.05858 0.004000 0.12327 0.097000 0.18754 0.218000 0.17622 0.663000 0.31027 -0.143000 0.13931 CGA TCGA-IB-A6UF-01A-23D-A33T-08 FAM71B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252570.2 1 0 1 167 421 0 98 0 0 0 0 98 2 0 0 0 0 0 2 1 1 166 417 0 97 2 0 0 0 0 98 2 -20.000000 1 1 121412 1 33 1 1 2 3 2.101368 0 0.580000 1.890000 0.582422 0.980000 8.500000e-01 1.000000 1.000000 0.967033 0.980000 1 0.910000 1.000000 UNC5A 90249 broad.mit.edu 37 5 176301068 176301068 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:176301068G>A ENST00000329542.4 + 7 1260 c.986G>A c.(985-987)cGg>cAg p.R329Q UNC5A_ENST00000261961.3_Missense_Mutation_p.R289Q NM_133369.2 NP_588610.2 Q6ZN44 UNC5A_HUMAN unc-5 homolog A (C. elegans) 34 all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115) Medulloblastoma(196;0.00498)|all_neural(177;0.0138) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GTTTATTGCCGGAAGAAGGAG 0.622000 0 SO:0001583 missense ENST00000329542.4 0 1 hg19 CCDS34299.1 . . . . . . . . . . G 35 5.481357 0.96307 . . ENSG00000113763 ENST00000329542;ENST00000261961 T;T 0.51071 0.72;1.03 5.29 5.29 0.74685 . 0.000000 0.85682 D 0.000000 T 0.64746 0.2626 L 0.52126 1.63 0.58432 D 0.999997 D;D 0.89917 0.999;1.0 D;D 0.71414 0.973;0.973 T 0.66874 -0.5813 10 0.72032 D 0.01 -35.8421 18.9122 0.92490 0.0:0.0:1.0:0.0 . 289;329 Q6ZN44-3;Q6ZN44 .;UNC5A_HUMAN Q 329;289 ENSP00000332737:R329Q;ENSP00000261961:R289Q ENSP00000261961:R289Q R + 2 0 UNC5A 176233674 1.000000 0.71417 0.976000 0.42696 0.927000 0.56198 6.361000 0.73070 2.481000 0.83766 0.484000 0.47621 CGG TCGA-IB-A6UF-01A-23D-A33T-08 UNC5A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372166.1 0 0 0 4 301 1 58 0 0 0 1 58 2 0 0 0 0 0 2 0 1.719143e-03 4 299 1 57 18 0 0 0 1 58 2 -2.840249 1 1 0 0 1 1 2 3 2.101368 0 0.580000 1.890000 0.582422 0.040000 0 0.120000 0.040000 0.065436 0.040000 0 0.020000 0.080000 SQSTM1 8878 broad.mit.edu 37 5 179252186 179252186 + Missense_Mutation SNP G G C TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:179252186G>C ENST00000389805.4 + 5 892 c.714G>C c.(712-714)aaG>aaC p.K238N SQSTM1_ENST00000360718.5_Missense_Mutation_p.K154N|SQSTM1_ENST00000402874.3_Missense_Mutation_p.K154N|SQSTM1_ENST00000376929.3_Missense_Mutation_p.K154N|SQSTM1_ENST00000510187.1_Missense_Mutation_p.K238N NM_003900.4 NP_003891.1 Q13501 SQSTM_HUMAN sequestosome 1 SQSTM1/ALK(2) 13 all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243) all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) ATTTCCTGAAGAACGTTGGGG 0.468000 0 SO:0001583 missense ENST00000389805.4 1 1 hg19 CCDS34317.1 . . . . . . . . . . G 16.72 3.201297 0.58234 . . ENSG00000161011 ENST00000376929;ENST00000514093;ENST00000389805;ENST00000454378;ENST00000402874;ENST00000510187;ENST00000360718 D;T;D;D;T;D 0.83506 -1.73;1.84;-1.72;-1.73;2.33;-1.73 5.15 4.28 0.50868 . 0.267149 0.41097 N 0.000953 D 0.86590 0.5969 M 0.65498 2.005 0.58432 D 0.999996 P;D 0.63880 0.477;0.993 B;P 0.53954 0.106;0.738 D 0.87728 0.2577 10 0.72032 D 0.01 -32.8687 13.713 0.62680 0.0746:0.0:0.9254:0.0 . 238;238 Q13501;E7EMC7 SQSTM_HUMAN;. N 154;154;238;94;154;238;154 ENSP00000366128:K154N;ENSP00000427308:K154N;ENSP00000374455:K238N;ENSP00000385553:K154N;ENSP00000424477:K238N;ENSP00000353944:K154N ENSP00000353944:K154N K + 3 2 SQSTM1 179184792 1.000000 0.71417 0.995000 0.50966 0.124000 0.20399 3.988000 0.56951 1.167000 0.42706 0.561000 0.74099 AAG TCGA-IB-A6UF-01A-23D-A33T-08 SQSTM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319344.1 1 0 1 97 278 0 83 1 1 418 734 0 83 2 0 0 0 0 0 2 1 1 97 274 0 81 2 0 0 0 0 83 2 -20.000000 1 1 0 0 1 1 2 3 2.101368 0 0.580000 1.890000 0.582422 0.890000 7.400000e-01 1.000000 1.000000 0.896797 0.890000 1 0.810000 0.980000 IRX1 79192 broad.mit.edu 37 5 3599380 3599380 + Silent SNP C C T rs61743903 byFrequency TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:3599380C>T ENST00000302006.3 + 2 370 c.318C>T c.(316-318)ccC>ccT p.P106P CTD-2012M11.3_ENST00000559410.1_RNA NM_024337.3 NP_077313.3 P78414 IRX1_HUMAN iroquois homeobox 1 43 GGGTGCACCCCGCCACCTTCG 0.642000 0 SO:0001819 synonymous_variant ENST00000302006.3 1 0 hg19 CCDS34132.1 TCGA-IB-A6UF-01A-23D-A33T-08 IRX1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365546.1 0 0 1 85 226 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 1 84 223 0 46 2 0 0 0 0 46 2 -2.716909 1 1 121406 162 52 1 1 2 3 2.078617 0 0.580000 1.890000 0.581214 0.940000 7.700000e-01 1.000000 1.000000 0.932866 0.940000 1 0.850000 1.000000 ITGA2 3673 broad.mit.edu 37 5 52376439 52376439 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr5:52376439G>A ENST00000296585.5 + 25 3170 c.3027G>A c.(3025-3027)gtG>gtA p.V1009V NM_002203.3 NP_002194.2 P17301 ITA2_HUMAN integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) 47 Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181) TAACTGGGGTGCAAACAGACA 0.383000 0 SO:0001819 synonymous_variant ENST00000296585.5 0 1 hg19 CCDS3957.1 TCGA-IB-A6UF-01A-23D-A33T-08 ITGA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253857.2 0 0 0 5 366 0 54 0 3.847937e-01 0 84 0 54 2 0 0 0 0 0 2 1 9.366072e-01 5 363 0 53 2 0 0 0 0 54 2 -2.922330 1 1 0 0 1 1 2 3 2.078617 0 0.580000 1.890000 0.581214 0.040000 0 0.110000 0.040000 0.055443 0.040000 0 0.020000 0.080000 ASCC3 10973 broad.mit.edu 37 6 101248186 101248186 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr6:101248186G>A ENST00000369162.2 - 6 1461 c.1117C>T c.(1117-1119)Cgg>Tgg p.R373W ASCC3_ENST00000522650.1_Missense_Mutation_p.R373W NM_006828.2 NP_006819.2 Q8N3C0 ASCC3_HUMAN activating signal cointegrator 1 complex subunit 3 p.R373W(1) 92 all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13) CTTTGTATCCGCAATTCCTTA 0.348000 1 Substitution - Missense(1) SO:0001583 missense ENST00000369162.2 0 1 hg19 CCDS5046.1 . . . . . . . . . . G 16.15 3.041379 0.55003 2.27E-4 0.0 ENSG00000112249 ENST00000369162;ENST00000522650 T;T 0.61627 0.29;0.09 5.51 -2.59 0.06209 . 0.066271 0.64402 D 0.000020 T 0.64170 0.2574 M 0.69823 2.125 0.80722 D 1 D;D 0.89917 0.999;1.0 D;D 0.71414 0.973;0.958 T 0.73075 -0.4097 10 0.49607 T 0.09 . 18.3564 0.90358 0.0:0.0:0.3701:0.6299 . 373;373 E7EW23;Q8N3C0 .;HELC1_HUMAN W 373 ENSP00000358159:R373W;ENSP00000430769:R373W ENSP00000358159:R373W R - 1 2 ASCC3 101354907 0.988000 0.35896 0.515000 0.27774 0.665000 0.39181 0.223000 0.17719 -0.294000 0.08973 -0.310000 0.09108 CGG TCGA-IB-A6UF-01A-23D-A33T-08 ASCC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041632.2 0 0 0 4 253 0 62 0 8.556404e-03 0 7 0 62 2 0 0 0 0 0 2 1 8.873700e-01 4 249 0 62 2 0 0 0 0 62 2 -2.132978 0 1 121406 15 42 1 0 1 1 1.475687 1 0.580000 1.890000 0.408451 0.030000 0 0.090000 0.040000 0.046980 0.030000 0 0.020000 0.070000 VARS 7407 broad.mit.edu 37 6 31760017 31760017 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr6:31760017G>A ENST00000375663.3 - 6 1288 c.848C>T c.(847-849)cCa>cTa p.P283L VARS_ENST00000444930.2_5'UTR NM_006295.2 NP_006286.1 P26640 SYVC_HUMAN valyl-tRNA synthetase 30 L-Valine(DB00161) GGGTGGGGTTGGGAGGTCATA 0.537000 0 SO:0001583 missense ENST00000375663.3 0 1 hg19 CCDS34412.1 . . . . . . . . . . G 16.09 3.025223 0.54683 . . ENSG00000204394 ENST00000375663 T 0.04234 3.67 5.25 4.36 0.52297 . 0.058877 0.64402 D 0.000002 T 0.03095 0.0091 M 0.61703 1.905 0.80722 D 1 B 0.20671 0.047 B 0.14578 0.011 T 0.16660 -1.0395 10 0.54805 T 0.06 -15.574 12.7975 0.57567 0.0:0.0:0.835:0.165 . 283 P26640 SYVC_HUMAN L 283 ENSP00000364815:P283L ENSP00000364815:P283L P - 2 0 VARS 31867996 1.000000 0.71417 0.997000 0.53966 0.970000 0.65996 5.919000 0.70005 1.166000 0.42689 0.313000 0.20887 CCA TCGA-IB-A6UF-01A-23D-A33T-08 VARS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076619.2 0 0 0 13 464 0 87 1 6.400332e-01 4 72 0 87 2 0 0 0 0 0 2 1 9.994839e-01 13 455 0 87 2 0 0 0 0 87 2 -2.232479 0 1 0 0 1 0 2 2 2.179468 1 0.580000 1.890000 0.580000 0.090000 4.000000e-02 0.160000 0.100000 0.100615 0.090000 0 0.060000 0.130000 BTNL2 56244 broad.mit.edu 37 6 32362627 32362627 + Silent SNP G G A rs144584698 TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr6:32362627G>A ENST00000374993.1 - 6 1253 c.1254C>T c.(1252-1254)caC>caT p.H418H BTNL2_ENST00000540315.1_Silent_p.H208H|BTNL2_ENST00000414363.1_Silent_p.H208H|BTNL2_ENST00000454136.3_Silent_p.H418H|BTNL2_ENST00000429232.2_3'UTR|BTNL2_ENST00000544175.1_Silent_p.H141H|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000374995.3_Silent_p.H324H NM_019602.1 NP_062548.1 Q9UIR0 BTNL2_HUMAN butyrophilin-like 2 (MHC class II associated) p.H418H(1) 19 ATGTCTGCACGTGGAACAGCC 0.547000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000374993.1 0 1 hg19 TCGA-IB-A6UF-01A-23D-A33T-08 BTNL2-201 KNOWN basic|appris_principal protein_coding protein_coding 0 0 0 10 571 0 127 0 0 0 0 127 2 0 0 0 0 0 2 1 9.966688e-01 10 562 0 126 2 0 0 0 0 127 2 -3.092293 1 1 121412 42 49 1 0 1 1 1.554870 1 0.580000 1.890000 0.408451 0.030000 1.000000e-02 0.070000 0.040000 0.046069 0.030000 0 0.020000 0.060000 ZAN 7455 broad.mit.edu 37 7 100383688 100383688 + RNA SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr7:100383688G>A ENST00000348028.3 + 0 7068 ZAN_ENST00000546292.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000538115.1_RNA Q9Y493 ZAN_HUMAN zonadhesin (gene/pseudogene) 139 Lung NSC(181;0.041)|all_lung(186;0.0581) STAD - Stomach adenocarcinoma(171;0.19) CATTCAGTGCGGGGACTTCCG 0.582000 0 ENST00000348028.3 0 1 hg19 . . . . . . . . . . G 12.39 1.924391 0.34002 . . ENSG00000146839 ENST00000546292;ENST00000538115;ENST00000542585;ENST00000546213 T;T;T;T 0.04119 3.7;3.7;3.7;3.7 4.77 -3.44 0.04796 von Willebrand factor, type C (1); 1.461850 0.04593 N 0.397035 T 0.02193 0.0068 . . . 0.09310 N 1 B;B;B 0.06786 0.001;0.001;0.001 B;B;B 0.04013 0.001;0.001;0.001 T 0.43988 -0.9357 9 0.15066 T 0.55 . 1.2273 0.01936 0.3587:0.2435:0.2418:0.1559 . 775;2301;2302 F5GX59;F5H0T8;Q9Y493 .;.;ZAN_HUMAN R 2301;2301;2301;775 ENSP00000445943:G2301R;ENSP00000445091:G2301R;ENSP00000444427:G2301R;ENSP00000441117:G775R ENSP00000445091:G2301R G + 1 0 ZAN 100221624 0.000000 0.05858 0.000000 0.03702 0.633000 0.38033 -1.866000 0.01647 -0.883000 0.03982 -0.823000 0.03104 GGG TCGA-IB-A6UF-01A-23D-A33T-08 ZAN-006 KNOWN basic polymorphic_pseudogene polymorphic_pseudogene OTTHUMT00000347214.1 0 0 0 156 363 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 1 154 361 0 72 2 0 0 0 0 75 2 -10.081640 1 1 0 0 1 1 2 3 2.105735 0 0.580000 1.890000 0.584816 0.990000 9.100000e-01 1.000000 1.000000 0.990528 0.990000 1 0.970000 1.000000 DGKI 9162 broad.mit.edu 37 7 137269964 137269964 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr7:137269964G>A ENST00000288490.5 - 14 1554 c.1554C>T c.(1552-1554)ggC>ggT p.G518G DGKI_ENST00000424189.2_Silent_p.G518G|DGKI_ENST00000446122.1_Silent_p.G518G|DGKI_ENST00000453654.2_Silent_p.G218G NM_004717.2 NP_004708.1 O75912 DGKI_HUMAN diacylglycerol kinase, iota 84 CCTTACATACGCCATCTTCAA 0.483000 0 SO:0001819 synonymous_variant ENST00000288490.5 1 1 hg19 CCDS5845.1 TCGA-IB-A6UF-01A-23D-A33T-08 DGKI-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000341286.3 1 0 0 144 448 1 84 0 0 0 1 84 2 0 0 0 0 0 2 1 1 144 447 1 84 22 0 0 0 1 84 2 -20.000000 1 1 121412 10 42 1 1 2 3 2.105735 0 0.580000 1.890000 0.584816 0.840000 7.200000e-01 1.000000 0.850000 0.854595 0.840000 0 0.780000 0.920000 PDAP1 11333 broad.mit.edu 37 7 98997952 98997952 + Silent SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr7:98997952C>T ENST00000350498.3 - 4 589 c.309G>A c.(307-309)ggG>ggA p.G103G PDAP1_ENST00000496335.1_5'Flank NM_014891.6 NP_055706.1 Q13442 HAP28_HUMAN PDGFA associated protein 1 9 all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166) STAD - Stomach adenocarcinoma(171;0.215) GCTCCTTTGGCCCGTCCAGAT 0.562000 0 SO:0001819 synonymous_variant ENST00000350498.3 0 1 hg19 CCDS5662.1 TCGA-IB-A6UF-01A-23D-A33T-08 PDAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336388.2 0 0 0 5 325 0 46 0 9.935721e-01 1 670 0 46 2 0 0 0 0 0 2 1 9.370029e-01 5 323 0 46 2 0 0 0 0 46 2 -2.564360 1 1 0 0 1 1 2 3 2.105735 0 0.580000 1.890000 0.584816 0.050000 1.000000e-02 1.000000 0.060000 0.089843 0.050000 0 0.030000 0.090000 SNTB1 6641 broad.mit.edu 37 8 121644818 121644818 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr8:121644818C>T ENST00000395601.3 - 4 1276 c.862G>A c.(862-864)Gca>Aca p.A288T SNTB1_ENST00000519177.1_5'UTR|SNTB1_ENST00000517992.1_Missense_Mutation_p.A288T NM_021021.3 NP_066301.1 Q13884 SNTB1_HUMAN syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1) 24 Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997) STAD - Stomach adenocarcinoma(47;0.00503) CTGAACCATGCCTGGGCCGTG 0.552000 0 SO:0001583 missense ENST00000395601.3 0 1 hg19 CCDS6334.1 . . . . . . . . . . C 16.98 3.270243 0.59540 . . ENSG00000172164 ENST00000395601;ENST00000517992 T;T 0.54675 0.56;0.56 6.03 6.03 0.97812 Pleckstrin homology domain (2); 0.098404 0.64402 D 0.000001 T 0.50171 0.1600 L 0.45581 1.43 0.54753 D 0.999987 B;B 0.28350 0.017;0.208 B;B 0.26310 0.013;0.068 T 0.36286 -0.9754 10 0.30854 T 0.27 . 20.5596 0.99324 0.0:1.0:0.0:0.0 . 288;288 Q13884;Q13884-2 SNTB1_HUMAN;. T 288 ENSP00000378965:A288T;ENSP00000431124:A288T ENSP00000378965:A288T A - 1 0 SNTB1 121713999 1.000000 0.71417 1.000000 0.80357 0.867000 0.49689 2.745000 0.47459 2.868000 0.98415 0.555000 0.69702 GCA TCGA-IB-A6UF-01A-23D-A33T-08 SNTB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381535.1 0 0 0 5 380 0 37 0 1.596156e-01 0 45 0 37 2 0 0 0 0 0 2 1 9.330520e-01 4 370 0 37 2 0 0 0 0 37 2 -5.088515 1 0 0 0 1 1 2 3 2.557942 1 0.580000 1.890000 0.668456 0.060000 1.000000e-02 1.000000 0.060000 0.127310 0.060000 0 0.030000 0.110000 ADRA1A 148 broad.mit.edu 37 8 26722237 26722237 + Missense_Mutation SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr8:26722237C>T ENST00000519229.1 - 1 256 c.250G>A c.(250-252)Gcc>Acc p.A84T ADRA1A_ENST00000380572.3_Missense_Mutation_p.A84T|ADRA1A_ENST00000380581.2_Missense_Mutation_p.A84T|ADRA1A_ENST00000380573.3_Missense_Mutation_p.A84T|ADRA1A_ENST00000380582.3_Missense_Mutation_p.A84T|ADRA1A_ENST00000354550.4_Missense_Mutation_p.A84T|ADRA1A_ENST00000380587.1_Missense_Mutation_p.A84T|ADRA1A_ENST00000380586.1_Missense_Mutation_p.A84T|ADRA1A_ENST00000358857.5_Missense_Mutation_p.A84T|ADRA1A_ENST00000276393.4_Missense_Mutation_p.A84T P25100 ADA1D_HUMAN adrenoceptor alpha 1A 36 all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118) Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694) TCGAAGATGGCGGAGAAGGGC 0.627000 0 SO:0001583 missense ENST00000519229.1 0 1 hg19 . . . . . . . . . . C 27.5 4.836309 0.91117 . . ENSG00000120907 ENST00000380586;ENST00000380587;ENST00000380582;ENST00000380581;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573;ENST00000380572;ENST00000358857 T;T;T;T;T;T;T;T;T;T 0.37915 1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17;1.17 4.83 4.83 0.62350 GPCR, rhodopsin-like superfamily (1); 0.057498 0.64402 D 0.000001 T 0.57504 0.2058 L 0.61387 1.9 0.80722 D 1 D;D;D;D;P;D 0.89917 0.992;0.992;0.997;0.998;0.944;1.0 P;P;D;D;B;D 0.67900 0.875;0.875;0.918;0.923;0.284;0.954 T 0.61337 -0.7083 10 0.66056 D 0.02 . 17.898 0.88895 0.0:1.0:0.0:0.0 . 84;84;84;84;84;84 P35348-9;P35348-8;P35348;P35348-4;P35348-3;B0ZBD3 .;.;ADA1A_HUMAN;.;.;. T 84 ENSP00000369960:A84T;ENSP00000369961:A84T;ENSP00000369956:A84T;ENSP00000369955:A84T;ENSP00000430793:A84T;ENSP00000346557:A84T;ENSP00000276393:A84T;ENSP00000369947:A84T;ENSP00000369946:A84T;ENSP00000351725:A84T ENSP00000276393:A84T A - 1 0 ADRA1A 26778154 1.000000 0.71417 0.941000 0.38009 0.992000 0.81027 7.776000 0.85560 2.365000 0.80145 0.563000 0.77884 GCC TCGA-IB-A6UF-01A-23D-A33T-08 ADRA1A-009 PUTATIVE not_organism_supported|basic|exp_conf protein_coding protein_coding OTTHUMT00000376207.1 0 0 0 6 557 0 188 0 0 0 0 188 2 0 0 0 0 0 2 1 9.637538e-01 6 550 0 187 2 0 0 0 0 188 2 -2.195804 0 1 121412 1 41 1 0 1 1 1.557174 1 0.580000 1.890000 0.408451 0.020000 0 0.050000 0.030000 0.030257 0.020000 0 0.010000 0.040000 SNTG1 54212 broad.mit.edu 37 8 51664572 51664572 + Missense_Mutation SNP G G C TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr8:51664572G>C ENST00000522124.1 + 18 1957 c.1296G>C c.(1294-1296)tgG>tgC p.W432C SNTG1_ENST00000276467.5_Intron|SNTG1_ENST00000517473.1_Intron|SNTG1_ENST00000518864.1_Missense_Mutation_p.W432C NM_018967.2 NP_061840.1 Q9NSN8 SNTG1_HUMAN syntrophin, gamma 1 66 all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22) CTGTCCTTTGGAGGTATAAAT 0.333000 0 SO:0001583 missense ENST00000522124.1 1 1 hg19 CCDS6147.1 . . . . . . . . . . G 18.15 3.560557 0.65538 . . ENSG00000147481 ENST00000518864;ENST00000522124 T;T 0.78816 -1.21;-1.21 5.07 5.07 0.68467 . 0.000000 0.85682 D 0.000000 D 0.87783 0.6264 M 0.74467 2.265 0.80722 D 1 D 0.69078 0.997 D 0.75020 0.985 D 0.89183 0.3545 10 0.87932 D 0 -14.0967 17.8066 0.88602 0.0:0.0:1.0:0.0 . 432 Q9NSN8 SNTG1_HUMAN C 432 ENSP00000429276:W432C;ENSP00000429842:W432C ENSP00000429276:W432C W + 3 0 SNTG1 51827125 1.000000 0.71417 1.000000 0.80357 0.772000 0.43724 9.157000 0.94714 2.501000 0.84356 0.637000 0.83480 TGG TCGA-IB-A6UF-01A-23D-A33T-08 SNTG1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000377964.1 1 0 1 110 411 0 92 0 0 0 1 0 92 2 0 0 0 0 0 2 1 1 110 409 0 92 2 0 0 0 0 92 2 -3.522370 1 1 0 0 1 1 2 3 2.557942 1 0.580000 1.890000 0.668456 0.920000 7.700000e-01 1.000000 1.000000 0.923702 0.920000 1 0.840000 1.000000 OPRK1 4986 broad.mit.edu 37 8 54163405 54163405 + Missense_Mutation SNP C C G TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr8:54163405C>G ENST00000265572.3 - 2 490 c.193G>C c.(193-195)Gtc>Ctc p.V65L OPRK1_ENST00000520287.1_Missense_Mutation_p.V65L NM_000912.3 NP_000903.2 P41145 OPRK_HUMAN opioid receptor, kappa 1 43 all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136) Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193) ACGGAGTAGACCGCCGTGATG 0.701000 0 SO:0001583 missense ENST00000265572.3 1 1 hg19 CCDS6152.1 . . . . . . . . . . C 26.9 4.781523 0.90282 . . ENSG00000082556 ENST00000265572;ENST00000520287;ENST00000396798 T;T 0.35421 1.31;1.31 4.93 4.93 0.64822 . 0.124940 0.56097 D 0.000033 T 0.28830 0.0715 L 0.42245 1.32 0.80722 D 1 B 0.13594 0.008 B 0.16722 0.016 T 0.10520 -1.0626 10 0.02654 T 1 . 16.1573 0.81676 0.0:1.0:0.0:0.0 . 65 P41145 OPRK_HUMAN L 65;65;51 ENSP00000265572:V65L;ENSP00000429706:V65L ENSP00000265572:V65L V - 1 0 OPRK1 54325958 0.999000 0.42202 0.962000 0.40283 0.954000 0.61252 4.205000 0.58466 2.586000 0.87340 0.456000 0.33151 GTC TCGA-IB-A6UF-01A-23D-A33T-08 OPRK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378048.1 1 0 0 135 195 0 27 0 0 0 0 27 2 0 0 0 0 0 2 1 1 132 193 0 26 2 0 0 0 0 27 2 -20.000000 1 1 0 0 1 1 2 3 2.557942 1 0.580000 1.890000 0.668456 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MOS 4342 broad.mit.edu 37 8 57025772 57025772 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr8:57025772G>A ENST00000311923.1 - 1 769 c.770C>T c.(769-771)aCg>aTg p.T257M NM_005372.1 NP_005363.1 P00540 MOS_HUMAN v-mos Moloney murine sarcoma viral oncogene homolog 22 Epithelial(17;0.00117)|all cancers(17;0.00879) GGCTTTAGGCGTCACGCCCTC 0.572000 Esophageal Squamous(124;373 2870 4778) 0 SO:0001583 missense ENST00000311923.1 1 1 hg19 CCDS6164.1 . . . . . . . . . . G 14.73 2.623610 0.46840 . . ENSG00000172680 ENST00000311923 D 0.94613 -3.47 5.8 4.93 0.64822 Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.063339 0.64402 D 0.000005 D 0.97770 0.9268 M 0.92412 3.305 0.49582 D 0.999808 D 0.89917 1.0 D 0.79784 0.993 D 0.98669 1.0687 10 0.87932 D 0 . 14.8663 0.70419 0.0686:0.0:0.9314:0.0 . 257 P00540 MOS_HUMAN M 257 ENSP00000310722:T257M ENSP00000310722:T257M T - 2 0 MOS 57188326 1.000000 0.71417 0.031000 0.17742 0.125000 0.20455 9.281000 0.95811 1.470000 0.48102 0.561000 0.74099 ACG TCGA-IB-A6UF-01A-23D-A33T-08 MOS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378174.1 1 0 1 104 386 0 65 0 0 0 0 65 2 0 0 0 0 0 2 1 1 101 381 0 65 2 0 0 0 0 65 2 -20.000000 1 1 0 0 1 1 2 3 2.557942 1 0.580000 1.890000 0.668456 0.930000 7.700000e-01 1.000000 1.000000 0.926916 0.930000 1 0.840000 1.000000 CDH17 1015 broad.mit.edu 37 8 95142932 95142932 + Missense_Mutation SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr8:95142932G>A ENST00000027335.3 - 17 2444 c.2320C>T c.(2320-2322)Cgg>Tgg p.R774W CDH17_ENST00000441892.2_Intron|CDH17_ENST00000450165.2_Missense_Mutation_p.R774W NM_004063.3 NP_004054.3 Q12864 CAD17_HUMAN cadherin 17, LI cadherin (liver-intestine) p.R774W(1) 52 Breast(36;4.65e-06) BRCA - Breast invasive adenocarcinoma(8;0.00691) CCTGCTGGCCGGAAACAACTT 0.448000 1 Substitution - Missense(1) SO:0001583 missense ENST00000027335.3 0 1 hg19 CCDS6260.1 . . . . . . . . . . G 10.68 1.417426 0.25552 . . ENSG00000079112 ENST00000027335;ENST00000450165 T;T 0.58358 0.34;0.34 5.84 2.83 0.33086 Cadherin (1); 0.561125 0.16175 N 0.226091 T 0.46014 0.1371 L 0.56769 1.78 0.27273 N 0.95831 D 0.63046 0.992 B 0.40534 0.332 T 0.37549 -0.9701 10 0.37606 T 0.19 -0.1227 11.2752 0.49163 0.0:0.0:0.5163:0.4836 . 774 Q12864 CAD17_HUMAN W 774 ENSP00000027335:R774W;ENSP00000401468:R774W ENSP00000027335:R774W R - 1 2 CDH17 95212108 0.965000 0.33210 0.969000 0.41365 0.045000 0.14185 1.376000 0.34306 0.760000 0.33108 -0.282000 0.10007 CGG TCGA-IB-A6UF-01A-23D-A33T-08 CDH17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378560.1 0 0 0 5 287 0 36 0 1.888756e-02 0 10 0 36 2 0 0 0 0 0 2 1 9.380657e-01 5 287 0 36 2 0 0 0 0 36 2 -2.840292 1 1 121390 1 26 1 1 2 3 2.557942 1 0.580000 1.890000 0.668456 0.080000 2.000000e-02 1.000000 0.080000 0.147558 0.080000 0 0.040000 0.140000 GARNL3 84253 broad.mit.edu 37 9 130145778 130145778 + Silent SNP T T G TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr9:130145778T>G ENST00000373387.4 + 23 2575 c.2223T>G c.(2221-2223)tcT>tcG p.S741S GARNL3_ENST00000496711.1_3'UTR|GARNL3_ENST00000314904.5_Silent_p.S741S|GARNL3_ENST00000435213.2_Silent_p.S719S NM_032293.4 NP_115669.3 Q5VVW2 GARL3_HUMAN GTPase activating Rap/RanGAP domain-like 3 41 TTCAACCTTCTGCGTCAGATT 0.388000 0 SO:0001819 synonymous_variant ENST00000373387.4 1 1 hg19 CCDS6869.2 TCGA-IB-A6UF-01A-23D-A33T-08 GARNL3-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054151.3 1 0 0 15 286 0 45 0 8.510238e-03 0 3 0 45 2 0 0 0 0 0 2 1 9.998663e-01 15 281 0 45 2 0 0 0 0 45 2 -4.890839 1 1 0 0 1 1 2 3 2.116127 0 0.580000 1.890000 0.586003 0.170000 1.000000e-01 1.000000 0.170000 0.215270 0.170000 0 0.130000 0.240000 EHMT1 79813 broad.mit.edu 37 9 140671243 140671243 + Silent SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr9:140671243C>T ENST00000460843.1 + 12 1992 c.1965C>T c.(1963-1965)ccC>ccT p.P655P EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000462484.1_Silent_p.P655P|EHMT1_ENST00000334856.6_Silent_p.P624P NM_024757.4 NP_079033.4 Q9H9B1 EHMT1_HUMAN euchromatic histone-lysine N-methyltransferase 1 41 all_cancers(76;0.164) CACCAGTCCCCGGGCAGGAGA 0.627000 0 SO:0001819 synonymous_variant ENST00000460843.1 1 1 hg19 CCDS7050.2 TCGA-IB-A6UF-01A-23D-A33T-08 EHMT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055371.2 1 0 1 81 230 0 60 1 9.999974e-01 15 42 0 60 2 0 0 0 0 0 2 1 1 78 226 0 59 2 0 0 0 0 60 2 -4.905162 1 1 121412 10 42 1 1 2 3 2.116127 0 0.580000 1.890000 0.586003 0.910000 7.400000e-01 1.000000 1.000000 0.910080 0.910000 1 0.820000 1.000000 FRMPD1 22844 broad.mit.edu 37 9 37708409 37708409 + Silent SNP C C T TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chr9:37708409C>T ENST00000539465.1 + 4 866 c.273C>T c.(271-273)caC>caT p.H91H FRMPD1_ENST00000377765.3_Silent_p.H91H|RP11-613M10.9_ENST00000540557.1_Intron Q5SYB0 FRPD1_HUMAN FERM and PDZ domain containing 1 93 GCTCTGCTCACGGCAAGCTTT 0.493000 0 SO:0001819 synonymous_variant ENST00000539465.1 1 1 hg19 CCDS6612.1 TCGA-IB-A6UF-01A-23D-A33T-08 FRMPD1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402969.1 1 0 1 149 369 0 83 0 0 0 0 83 2 0 0 0 0 0 2 1 1 149 366 0 83 2 0 0 0 0 83 2 -9.314138 1 1 121412 4 39 1 0 0 0 2.054757 0 0.580000 1.890000 0.577550 0.980000 8.500000e-01 1.000000 1.000000 0.965970 0.980000 1 0.910000 1.000000 KIAA2022 340533 broad.mit.edu 37 X 73960072 73960072 + Silent SNP G G A TCGA-IB-A6UF-01A-23D-A33T-08 TCGA-IB-A6UF-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4d6b923f-0fd7-4174-b1e8-5dd4ffaa618c b6896b2e-5d98-49fd-a3e7-f3e75306d1ee g.chrX:73960072G>A ENST00000055682.6 - 3 4931 c.4320C>T c.(4318-4320)aaC>aaT p.N1440N NM_001008537.2 NP_001008537.1 Q5QGS0 K2022_HUMAN KIAA2022 109 GTGTCGGTCCGTTATTGCCTA 0.453000 0 SO:0001819 synonymous_variant ENST00000055682.6 1 1 hg19 CCDS35337.1 . . . . . . . . . . G 3.844 -0.033191 0.07543 . . ENSG00000050030 ENST00000424929 . . . 5.36 -7.06 0.01568 . . . . . T 0.59878 0.2226 . . . 0.80722 D 1 . . . . . . T 0.64232 -0.6456 4 . . . -17.3921 13.7648 0.62988 0.309:0.0916:0.5995:0.0 . . . . W 42 . . R - 1 2 KIAA2022 73876797 0.008000 0.16893 0.938000 0.37757 0.996000 0.88848 -0.935000 0.03950 -1.139000 0.02881 0.544000 0.68410 CGG TCGA-IB-A6UF-01A-23D-A33T-08 KIAA2022-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057270.2 1 0 1 183 135 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 1 183 135 0 44 2 0 0 0 0 45 2 -20.000000 1 1 121410 8 41 1 0 1 1 0.580000 1.890000 0.580000 0.960000 8.800000e-01 1.000000 0.990000 0.960084 0.960000 1 0.920000 0.990000