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 DSC1 1823 broad.mit.edu 37 18 28725666 28725666 + Frame_Shift_Del DEL T T - TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr18:28725666delT ENST00000257198.5 - 7 1108 c.847delA c.(847-849)atcfs p.I283fs DSC1_ENST00000257197.3_Frame_Shift_Del_p.I283fs|RP11-408H20.2_ENST00000581836.1_RNA NM_024421.2 NP_077739.1 Q08554 DSC1_HUMAN desmocollin 1 53 OV - Ovarian serous cystadenocarcinoma(10;0.00778) TGTTGTAAGATTTTATATTTC 0.413000 0 SO:0001589 frameshift_variant ENST00000257198.5 1 0 hg19 CCDS11894.1 TCGA-HV-A7OL-01A-11D-A33T-08 DSC1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000254946.1 1 0 0 82 445 0 68 0 0 0 0 0 0 0 0 0 0 0 0 1 1.000000 105 440 1 68 25 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 1.678323 1 0.370000 1.920000 0.228745 0.680000 5.500000e-01 0.820000 0.680000 0.688349 0.680000 0 6.100000e-01 0.750000 SFXN4 119559 broad.mit.edu 37 10 120914629 120914629 + Missense_Mutation SNP G G A rs151157939 TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr10:120914629G>A ENST00000355697.2 - 11 696 c.677C>T c.(676-678)gCg>gTg p.A226V SFXN4_ENST00000461438.1_5'UTR|SFXN4_ENST00000330036.6_Missense_Mutation_p.A217V NM_213649.1 NP_998814.1 Q6P4A7 SFXN4_HUMAN sideroflexin 4 11 Lung NSC(174;0.094)|all_lung(145;0.123) GTCCATGACCGCAATCCCCTT 0.478000 0 SO:0001583 missense ENST00000355697.2 0 1 hg19 CCDS7610.1 . . . . . . . . . . G 9.568 1.120310 0.20877 2.27E-4 1.16E-4 ENSG00000183605 ENST00000355697;ENST00000330036;ENST00000392875;ENST00000369131 T;T;T 0.30714 1.52;1.52;1.52 4.77 2.38 0.29361 . 0.608708 0.17108 N 0.186736 T 0.19005 0.0456 L 0.36672 1.1 0.09310 N 1 P 0.47677 0.899 B 0.38755 0.281 T 0.08806 -1.0704 10 0.33940 T 0.23 -8.9942 5.8839 0.18870 0.0:0.0913:0.1753:0.7334 . 226 Q6P4A7 SFXN4_HUMAN V 226;217;109;110 ENSP00000347924:A226V;ENSP00000333200:A217V;ENSP00000358127:A110V ENSP00000333200:A217V A - 2 0 SFXN4 120904619 0.189000 0.23263 0.799000 0.32177 0.166000 0.22503 0.232000 0.17891 0.867000 0.35654 -0.281000 0.10026 GCG TCGA-HV-A7OL-01A-11D-A33T-08 SFXN4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050642.3 0 0 0 5 417 0 71 0 3.595399e-01 0 91 0 71 2 0 0 0 0 0 2 1 0.936716 5 414 0 71 2 0 0 0 0 71 2 -2.100855 0 1 121412 17 45 1 1 2 3 2.054153 0 0.370000 1.920000 0.374628 0.060000 2.000000e-02 1.000000 0.060000 0.103322 0.060000 0 4.000000e-02 0.110000 CUBN 8029 broad.mit.edu 37 10 16919089 16919089 + Silent SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr10:16919089G>A ENST00000377833.4 - 57 8978 c.8913C>T c.(8911-8913)tcC>tcT p.S2971S NM_001081.3 NP_001072.2 O60494 CUBN_HUMAN cubilin (intrinsic factor-cobalamin receptor) 241 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) CCGTCACAGCGGAACGAGCTG 0.453000 0 SO:0001819 synonymous_variant ENST00000377833.4 0 1 hg19 CCDS7113.1 TCGA-HV-A7OL-01A-11D-A33T-08 CUBN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047009.1 0 0 0 4 154 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 0.883673 4 149 0 27 2 0 0 0 0 28 2 -6.256320 1 1 121400 10 39 1 1 2 3 2.041138 0 0.370000 1.920000 0.372322 0.150000 4.000000e-02 0.360000 0.140000 0.175896 0.150000 0 9.000000e-02 0.240000 ARMC3 219681 broad.mit.edu 37 10 23250963 23250963 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr10:23250963G>A ENST00000298032.5 + 7 772 c.688G>A c.(688-690)Gac>Aac p.D230N ARMC3_ENST00000409983.3_Missense_Mutation_p.D230N|ARMC3_ENST00000376528.4_Intron|ARMC3_ENST00000409049.3_Missense_Mutation_p.D230N NM_173081.3 NP_775104.2 Q5W041 ARMC3_HUMAN armadillo repeat containing 3 47 AATGCTAAGAGACAATCAAGG 0.368000 0 SO:0001583 missense ENST00000298032.5 1 1 hg19 CCDS7142.1 . . . . . . . . . . G 17.80 3.478799 0.63849 . . ENSG00000165309 ENST00000298032;ENST00000409983;ENST00000376523;ENST00000409049 T;T;T 0.19105 2.17;2.17;2.17 5.67 5.67 0.87782 Armadillo-like helical (1);Armadillo-type fold (1); 0.258007 0.43747 D 0.000526 T 0.22322 0.0538 L 0.38531 1.155 0.80722 D 1 B;B 0.28713 0.07;0.22 B;B 0.28991 0.055;0.097 T 0.02026 -1.1227 10 0.48119 T 0.1 -1.008 19.746 0.96252 0.0:0.0:1.0:0.0 . 230;230 Q5W041-4;Q5W041 .;ARMC3_HUMAN N 230;230;166;230 ENSP00000298032:D230N;ENSP00000386943:D230N;ENSP00000387288:D230N ENSP00000298032:D230N D + 1 0 ARMC3 23290969 1.000000 0.71417 0.953000 0.39169 0.899000 0.52679 5.700000 0.68318 2.673000 0.90976 0.650000 0.86243 GAC TCGA-HV-A7OL-01A-11D-A33T-08 ARMC3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047197.2 1 0 1 35 128 0 24 0 0 0 0 24 2 0 0 0 0 0 2 1 1.000000 35 128 0 24 2 0 0 0 0 24 2 -20.000000 1 1 0 0 1 1 2 3 2.041138 0 0.370000 1.920000 0.372322 0.990000 8.400000e-01 1.000000 1.000000 0.987257 0.990000 1 9.900000e-01 1.000000 DUSP13 51207 broad.mit.edu 37 10 76855494 76855494 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr10:76855494G>A ENST00000472493.2 - 3 311 c.233C>T c.(232-234)gCc>gTc p.A78V DUSP13_ENST00000372702.3_3'UTR|DUSP13_ENST00000607009.1_5'Flank|DUSP13_ENST00000464872.1_Missense_Mutation_p.A78V|DUSP13_ENST00000607131.1_Missense_Mutation_p.A171V|DUSP13_ENST00000372700.3_Missense_Mutation_p.A128V|DUSP13_ENST00000478873.2_Missense_Mutation_p.A214V|DUSP13_ENST00000491677.2_Missense_Mutation_p.A207V|DUSP13_ENST00000605915.1_Missense_Mutation_p.A100V NM_016364.3 NP_057448.3 Q9UII6 DS13B_HUMAN dual specificity phosphatase 13 8 all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348) GCCTGCAGCGGCATTCACAAC 0.577000 NSCLC(174;1655 2059 12324 40663 42963) 0 SO:0001583 missense ENST00000472493.2 0 1 hg19 CCDS7346.1 . . . . . . . . . . G 8.989 0.977271 0.18812 . . ENSG00000079393 ENST00000308475;ENST00000472493;ENST00000491677;ENST00000372698;ENST00000464872;ENST00000372700 T;T;T;T;T 0.60548 0.42;0.42;0.42;0.18;0.42 5.11 -2.7 0.06004 Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2); 0.348638 0.33235 N 0.005130 T 0.30947 0.0781 N 0.13198 0.31 0.31631 N 0.648985 B;P;P 0.41265 0.342;0.678;0.744 B;B;B 0.36534 0.092;0.137;0.227 T 0.48198 -0.9056 10 0.14656 T 0.56 -2.9419 12.3709 0.55254 0.2733:0.0:0.7267:0.0 . 128;207;78 Q9UII6-4;F2Z2C4;Q9UII6 .;.;DUS13_HUMAN V 78;78;207;171;78;128 ENSP00000311051:A78V;ENSP00000444580:A78V;ENSP00000436312:A207V;ENSP00000434041:A78V;ENSP00000361785:A128V ENSP00000311051:A78V A - 2 0 DUSP13 76525500 0.981000 0.34729 0.126000 0.21872 0.401000 0.30781 2.524000 0.45589 -0.319000 0.08652 -0.150000 0.13652 GCC TCGA-HV-A7OL-01A-11D-A33T-08 DUSP13-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000048786.3 0 0 0 6 750 1 129 0 0 0 1 129 2 0 0 0 0 0 2 0 0.004092 6 744 1 127 20 0 0 0 1 129 2 -1.584131 0 1 0 0 1 1 2 3 2.054153 0 0.370000 1.920000 0.374628 0.040000 0 1.000000 0.040000 0.077478 0.040000 0 2.000000e-02 0.070000 NCAM1 4684 broad.mit.edu 37 11 113078690 113078690 + Silent SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr11:113078690C>T ENST00000533760.1 + 7 1127 c.528C>T c.(526-528)ggC>ggT p.G176G NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Silent_p.G293G|NCAM1_ENST00000316851.7_Silent_p.G284G NM_001242608.1 NP_001229537.1 P13591 NCAM1_HUMAN neural cell adhesion molecule 1 49 all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207) ACAAGGCTGGCGAGCAGGATG 0.532000 0 SO:0001819 synonymous_variant ENST00000533760.1 0 1 hg19 TCGA-HV-A7OL-01A-11D-A33T-08 NCAM1-003 NOVEL basic|appris_principal protein_coding protein_coding OTTHUMT00000394068.2 1 0 1 18 72 0 8 0 0 0 0 8 2 0 0 0 0 0 2 1 0.999990 18 71 0 8 2 0 0 0 0 8 2 -20.000000 1 1 0 0 1 1 2 3 2.043829 0 0.370000 1.920000 0.372322 0.990000 6.900000e-01 1.000000 1.000000 0.954463 0.990000 1 8.700000e-01 1.000000 CBL 867 broad.mit.edu 37 11 119148958 119148958 + Missense_Mutation SNP T T C TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr11:119148958T>C ENST00000264033.4 + 8 1554 c.1178T>C c.(1177-1179)aTt>aCt p.I393T NM_005188.3 NP_005179.2 P22681 CBL_HUMAN Cbl proto-oncogene, E3 ubiquitin protein ligase p.E366_Q409del(13)|p.E369_Q409del(1)|p.?(1)|p.E366_K477del(1) 251 Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112) GATGTAAAGATTGAGCCCTGT 0.368000 T, Mis S, O MLL AML, JMML, MDS Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies Dom, Rec yes 11 11q23.3 867 Cas-Br-M (murine) ecotropic retroviral transforming L 16 Deletion - In frame(15)|Unknown(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML ENST00000264033.4 0 1 hg19 CCDS8418.1 . . . . . . . . . . T 17.96 3.515433 0.64634 . . ENSG00000110395 ENST00000264033 D 0.96011 -3.88 5.52 5.52 0.82312 Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1); 0.000000 0.85682 D 0.000000 D 0.96116 0.8734 L 0.33485 1.01 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.97019 0.9742 10 0.87932 D 0 -15.1332 15.9527 0.79855 0.0:0.0:0.0:1.0 . 393 P22681 CBL_HUMAN T 393 ENSP00000264033:I393T ENSP00000264033:I393T I + 2 0 CBL 118654168 1.000000 0.71417 0.983000 0.44433 0.986000 0.74619 7.655000 0.83696 2.227000 0.72691 0.455000 0.32223 ATT TCGA-HV-A7OL-01A-11D-A33T-08 CBL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388219.4 0 0 0 6 462 0 62 0 0 0 1 0 62 2 0 0 0 0 0 2 1 0.965426 6 463 0 62 2 0 0 0 0 62 2 -6.046258 1 1 121412 1 30 1 1 2 3 2.043829 0 0.370000 1.920000 0.372322 0.070000 2.000000e-02 0.160000 0.070000 0.089532 0.070000 0 4.000000e-02 0.110000 USP2 9099 broad.mit.edu 37 11 119230302 119230302 + Missense_Mutation SNP C C A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr11:119230302C>A ENST00000260187.2 - 4 1188 c.894G>T c.(892-894)agG>agT p.R298S USP2_ENST00000455332.2_Missense_Mutation_p.R55S|USP2_ENST00000525735.1_Missense_Mutation_p.R89S NM_004205.4 NP_004196.4 O75604 UBP2_HUMAN ubiquitin specific peptidase 2 24 all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157) GCATGTAGAGCCTCTGGAGGC 0.582000 0 SO:0001583 missense ENST00000260187.2 0 1 hg19 CCDS8422.1 . . . . . . . . . . C 12.02 1.811636 0.32053 . . ENSG00000036672 ENST00000455332;ENST00000260187;ENST00000392808;ENST00000525735 T;T;T 0.29655 1.56;1.56;1.56 5.28 2.31 0.28768 Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2); 0.196121 0.52532 D 0.000067 T 0.17109 0.0411 N 0.25201 0.72 0.27590 N 0.949293 B;B;B 0.26483 0.15;0.048;0.0 B;B;B 0.28991 0.097;0.057;0.004 T 0.12760 -1.0535 10 0.34782 T 0.22 -7.6172 3.7498 0.08562 0.1619:0.4776:0.0:0.3605 . 55;298;89 E9PPM2;O75604;O75604-4 .;UBP2_HUMAN;. S 55;298;45;89 ENSP00000407842:R55S;ENSP00000260187:R298S;ENSP00000436952:R89S ENSP00000260187:R298S R - 3 2 USP2 118735512 0.993000 0.37304 0.995000 0.50966 0.905000 0.53344 1.262000 0.32992 0.339000 0.23719 -0.345000 0.07892 AGG TCGA-HV-A7OL-01A-11D-A33T-08 USP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388361.2 0 0 0 4 235 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.889142 4 233 0 35 2 0 0 0 0 36 2 -5.459253 1 1 0 0 1 1 2 3 2.043829 0 0.370000 1.920000 0.372322 0.100000 2.000000e-02 0.240000 0.090000 0.120459 0.100000 0 5.000000e-02 0.160000 TTC17 55761 broad.mit.edu 37 11 43471655 43471655 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr11:43471655C>T ENST00000039989.4 + 20 2824 c.2810C>T c.(2809-2811)gCc>gTc p.A937V NM_018259.5 NP_060729.2 Q96AE7 TTC17_HUMAN tetratricopeptide repeat domain 17 53 ATAGATTTTGCCACCCCTATA 0.473000 0 SO:0001583 missense ENST00000039989.4 0 1 hg19 CCDS31466.1 . . . . . . . . . . C 23.9 4.470025 0.84533 . . ENSG00000052841 ENST00000039989 T 0.34667 1.35 5.84 5.84 0.93424 . 0.000000 0.85682 D 0.000000 T 0.39145 0.1067 L 0.47716 1.5 0.80722 D 1 P 0.50443 0.935 B 0.43194 0.411 T 0.12116 -1.0560 10 0.42905 T 0.14 -13.769 20.1392 0.98050 0.0:1.0:0.0:0.0 . 937 Q96AE7 TTC17_HUMAN V 937 ENSP00000039989:A937V ENSP00000039989:A937V A + 2 0 TTC17 43428231 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 7.438000 0.80431 2.751000 0.94390 0.591000 0.81541 GCC TCGA-HV-A7OL-01A-11D-A33T-08 TTC17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389577.2 0 0 0 6 687 0 94 0 7.013803e-03 0 12 0 94 2 0 0 0 0 0 2 1 0.964124 6 681 0 94 2 0 0 0 0 94 2 -1.908540 0 1 0 0 1 1 2 3 2.042277 0 0.370000 1.920000 0.372322 0.040000 1.000000e-02 0.110000 0.050000 0.063782 0.040000 0 2.000000e-02 0.080000 ZDHHC5 25921 broad.mit.edu 37 11 57466302 57466302 + Missense_Mutation SNP A A G TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr11:57466302A>G ENST00000287169.3 + 11 2756 c.1394A>G c.(1393-1395)aAt>aGt p.N465S ZDHHC5_ENST00000527985.1_Missense_Mutation_p.N412S NM_015457.2 NP_056272.2 Q9C0B5 ZDHC5_HUMAN zinc finger, DHHC-type containing 5 18 CAGACACGCAATGGAAGCCTA 0.557000 0 SO:0001583 missense ENST00000287169.3 1 1 hg19 CCDS7965.1 . . . . . . . . . . A 19.93 3.918245 0.73098 0.0 1.16E-4 ENSG00000156599 ENST00000527985;ENST00000287169;ENST00000529447 T;T;D 0.85013 -0.09;0.89;-1.93 5.09 5.09 0.68999 . 0.269487 0.37219 N 0.002189 D 0.84224 0.5425 L 0.37561 1.115 0.80722 D 1 P 0.42827 0.791 P 0.48873 0.593 D 0.85335 0.1092 10 0.52906 T 0.07 -19.2371 14.709 0.69215 1.0:0.0:0.0:0.0 . 465 Q9C0B5 ZDHC5_HUMAN S 412;465;299 ENSP00000432202:N412S;ENSP00000287169:N465S;ENSP00000435722:N299S ENSP00000287169:N465S N + 2 0 ZDHHC5 57222878 1.000000 0.71417 0.991000 0.47740 0.979000 0.70002 8.502000 0.90505 2.146000 0.66826 0.460000 0.39030 AAT TCGA-HV-A7OL-01A-11D-A33T-08 ZDHHC5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393694.1 1 0 1 48 238 0 52 1 9.999622e-01 22 56 0 52 2 0 0 0 0 0 2 1 1.000000 47 236 0 52 2 0 0 0 0 52 2 -20.000000 1 1 121412 2 34 1 1 2 3 2.043824 0 0.370000 1.920000 0.372322 0.910000 6.900000e-01 1.000000 1.000000 0.900437 0.910000 1 7.900000e-01 1.000000 CTNND1 1500 broad.mit.edu 37 11 57559074 57559074 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr11:57559074G>A ENST00000399050.4 + 3 660 c.124G>A c.(124-126)Gaa>Aaa p.E42K CTNND1_ENST00000534579.1_5'UTR|CTNND1_ENST00000361332.4_Missense_Mutation_p.E42K|CTNND1_ENST00000529873.1_5'UTR|CTNND1_ENST00000426142.2_Intron|CTNND1_ENST00000526938.1_Missense_Mutation_p.E42K|CTNND1_ENST00000530748.1_5'UTR|CTNND1_ENST00000532245.1_Intron|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000532463.1_Intron|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000532787.1_Intron|CTNND1_ENST00000415361.2_Intron|CTNND1_ENST00000528621.1_5'UTR|CTNND1_ENST00000361796.4_Missense_Mutation_p.E42K|CTNND1_ENST00000428599.2_Missense_Mutation_p.E42K|CTNND1_ENST00000527467.1_Intron|CTNND1_ENST00000532844.1_5'UTR|CTNND1_ENST00000358694.6_Missense_Mutation_p.E42K|CTNND1_ENST00000530094.1_Intron|CTNND1_ENST00000529986.1_Intron|CTNND1_ENST00000361391.6_Missense_Mutation_p.E42K|CTNND1_ENST00000524630.1_Missense_Mutation_p.E42K|RP11-691N7.6_ENST00000531074.1_3'UTR|CTNND1_ENST00000360682.6_Missense_Mutation_p.E42K|CTNND1_ENST00000399039.4_Missense_Mutation_p.E42K|CTNND1_ENST00000529919.1_Missense_Mutation_p.E42K|CTNND1_ENST00000528232.1_Intron|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000531014.1_Intron|CTNND1_ENST00000526357.1_5'UTR|CTNND1_ENST00000529526.1_5'UTR|CTNND1_ENST00000532649.1_5'UTR NM_001085458.1 NP_001078927.1 O60716 CTND1_HUMAN catenin (cadherin-associated protein), delta 1 45 all_epithelial(135;0.155) GGCGCAGCTGGAACGCGTCCG 0.637000 0 SO:0001583 missense ENST00000399050.4 1 1 hg19 CCDS44604.1 . . . . . . . . . . G 23.4 4.405970 0.83230 . . ENSG00000198561 ENST00000524630;ENST00000529919;ENST00000399039;ENST00000360682;ENST00000361796;ENST00000399050;ENST00000361391;ENST00000361332;ENST00000358694;ENST00000428599;ENST00000526938 T;T;T;T;T;T;T;T;T;T;T 0.29917 1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55 5.62 5.62 0.85841 . 0.176390 0.50627 D 0.000116 T 0.35913 0.0948 L 0.59436 1.845 0.36574 D 0.873151 P;P;P;P;P;P 0.42248 0.774;0.774;0.665;0.774;0.762;0.665 B;B;B;B;B;B 0.39379 0.236;0.236;0.119;0.236;0.298;0.119 T 0.47484 -0.9114 10 0.72032 D 0.01 -9.2286 18.7943 0.91988 0.0:0.0:1.0:0.0 . 42;42;42;42;42;42 O60716-3;O60716-2;O60716;O60716-5;F8WA43;C9JZR2 .;.;CTND1_HUMAN;.;.;. K 42 ENSP00000436543:E42K;ENSP00000434808:E42K;ENSP00000381996:E42K;ENSP00000353902:E42K;ENSP00000354907:E42K;ENSP00000382004:E42K;ENSP00000354785:E42K;ENSP00000354823:E42K;ENSP00000351527:E42K;ENSP00000413586:E42K;ENSP00000432041:E42K ENSP00000351527:E42K E + 1 0 CTNND1 57315650 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 8.153000 0.89640 2.809000 0.96659 0.655000 0.94253 GAA TCGA-HV-A7OL-01A-11D-A33T-08 CTNND1-006 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000393944.1 1 0 1 37 198 0 41 0 0 0 1 0 41 2 0 0 0 0 0 2 1 1.000000 37 196 0 40 2 0 0 0 0 41 2 -20.000000 1 1 0 0 1 1 2 3 2.043824 0 0.370000 1.920000 0.372322 0.850000 6.200000e-01 1.000000 1.000000 0.854491 0.850000 1 7.300000e-01 1.000000 ATG2A 23130 broad.mit.edu 37 11 64666137 64666137 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr11:64666137G>A ENST00000377264.3 - 32 4754 c.4642C>T c.(4642-4644)Cgg>Tgg p.R1548W ATG2A_ENST00000421419.2_Missense_Mutation_p.R1550W NM_015104.2 NP_055919.2 Q2TAZ0 ATG2A_HUMAN autophagy related 2A 55 CGCGGCATCCGCTCACTCGTG 0.607000 0 SO:0001583 missense ENST00000377264.3 1 1 hg19 CCDS31602.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 22.9|22.9 4.352957|4.352957 0.82132|0.82132 .|. .|. ENSG00000110046|ENSG00000110046 ENST00000418259|ENST00000421419;ENST00000377264 .|T;T .|0.07444 .|3.19;3.19 4.27|4.27 3.28|3.28 0.37604|0.37604 .|. .|0.058658 .|0.64402 .|D .|0.000003 T|T 0.17408|0.17408 0.0418|0.0418 L|L 0.47716|0.47716 1.5|1.5 0.38104|0.38104 D|D 0.937356|0.937356 .|D;D .|0.76494 .|0.999;0.999 .|P;D .|0.66084 .|0.874;0.941 T|T 0.00875|0.00875 -1.1531|-1.1531 5|10 .|0.66056 .|D .|0.02 .|. 9.0664|9.0664 0.36467|0.36467 0.0:0.0:0.6774:0.3226|0.0:0.0:0.6774:0.3226 .|. .|1548;1550 .|Q2TAZ0;Q2TAZ0-3 .|ATG2A_HUMAN;. V|W 1351|1550;1548 .|ENSP00000410522:R1550W;ENSP00000366475:R1548W .|ENSP00000366475:R1548W A|R -|- 2|1 0|2 ATG2A|ATG2A 64422713|64422713 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.880000|0.880000 0.50808|0.50808 1.056000|1.056000 0.30480|0.30480 2.370000|2.370000 0.80446|0.80446 0.561000|0.561000 0.74099|0.74099 GCG|CGG TCGA-HV-A7OL-01A-11D-A33T-08 ATG2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000143224.1 1 0 1 70 278 0 53 1 8.813018e-01 7 10 0 53 2 0 0 0 0 0 2 1 1.000000 70 274 0 53 2 0 0 0 0 53 2 -3.482384 1 1 0 0 1 1 2 3 2.043829 0 0.370000 1.920000 0.372322 0.990000 8.700000e-01 1.000000 1.000000 0.987410 0.990000 1 9.700000e-01 1.000000 SYT12 91683 broad.mit.edu 37 11 66807334 66807334 + Missense_Mutation SNP G G A rs34985365 TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr11:66807334G>A ENST00000393946.2 + 7 1443 c.281G>A c.(280-282)cGc>cAc p.R94H SYT12_ENST00000527043.1_Missense_Mutation_p.R94H|SYT12_ENST00000525457.1_Missense_Mutation_p.R94H|SYT12_ENST00000526281.1_3'UTR Q8IV01 SYT12_HUMAN synaptotagmin XII 20 CCACCCAGCCGCAAAGGCAGT 0.637000 Ovarian(65;2862 3307) 0 SO:0001583 missense ENST00000393946.2 0 1 hg19 CCDS8154.1 . . . . . . . . . . G 19.51 3.840495 0.71488 . . ENSG00000173227 ENST00000393946;ENST00000525457;ENST00000527043;ENST00000533427 T;T;T 0.14391 2.51;2.51;2.51 5.1 5.1 0.69264 . 0.000000 0.85682 D 0.000000 T 0.24236 0.0587 L 0.27053 0.805 0.58432 D 0.999999 D 0.89917 1.0 D 0.78314 0.991 T 0.00787 -1.1566 10 0.52906 T 0.07 . 13.8906 0.63736 0.0:0.0:1.0:0.0 rs34985365 94 Q8IV01 SYT12_HUMAN H 94 ENSP00000377520:R94H;ENSP00000431400:R94H;ENSP00000435316:R94H ENSP00000377520:R94H R + 2 0 SYT12 66563910 1.000000 0.71417 1.000000 0.80357 0.062000 0.15995 9.228000 0.95250 2.655000 0.90218 0.462000 0.41574 CGC TCGA-HV-A7OL-01A-11D-A33T-08 SYT12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393129.1 0 0 0 6 782 0 122 0 0 0 0 122 2 0 0 0 0 0 2 1 0.963202 7 768 0 120 2 0 0 0 0 122 2 -1.977436 0 1 121408 22 47 1 1 2 3 2.043829 0 0.370000 1.920000 0.372322 0.040000 0 0.100000 0.040000 0.057232 0.040000 0 2.000000e-02 0.070000 ARAP1 116985 broad.mit.edu 37 11 72404390 72404390 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr11:72404390G>A ENST00000393609.3 - 29 4136 c.3934C>T c.(3934-3936)Cgg>Tgg p.R1312W ARAP1_ENST00000429686.1_Missense_Mutation_p.R1006W|ARAP1_ENST00000426523.1_Missense_Mutation_p.R1067W|ARAP1_ENST00000334211.8_Missense_Mutation_p.R1067W|ARAP1_ENST00000393605.3_Missense_Mutation_p.R1072W|ARAP1_ENST00000455638.2_Missense_Mutation_p.R1312W|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000359373.5_Missense_Mutation_p.R1312W|ARAP1-AS1_ENST00000542022.1_RNA NM_001040118.2 NP_001035207.1 Q96P48 ARAP1_HUMAN ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 27 TTGTAGAGCCGCAAGCAGCTG 0.612000 Ovarian(102;1198 1520 13195 17913 37529) 0 SO:0001583 missense ENST00000393609.3 0 1 hg19 CCDS41687.1 . . . . . . . . . . G 16.84 3.234264 0.58886 . . ENSG00000186635 ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000542596 T;T;T;T;T;T;T;T 0.75260 -0.92;-0.92;-0.92;-0.92;-0.92;-0.92;-0.92;-0.92 5.74 2.51 0.30379 Pleckstrin homology-type (1);Pleckstrin homology domain (3); 0.120365 0.53938 D 0.000046 T 0.77545 0.4146 L 0.38175 1.15 0.42463 D 0.99279 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.97110 0.985;1.0;0.994;0.978;0.975 T 0.77175 -0.2684 10 0.66056 D 0.02 . 9.5284 0.39178 0.0765:0.0:0.6605:0.263 . 1067;1006;1312;1312;1072 E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1 .;.;.;ARAP1_HUMAN;. W 1312;1312;1072;1067;1312;1067;1006;116 ENSP00000352332:R1312W;ENSP00000390461:R1312W;ENSP00000377230:R1072W;ENSP00000335506:R1067W;ENSP00000377233:R1312W;ENSP00000392264:R1067W;ENSP00000403127:R1006W;ENSP00000441741:R116W ENSP00000335506:R1067W R - 1 2 ARAP1 72082038 0.998000 0.40836 1.000000 0.80357 0.524000 0.34500 2.315000 0.43752 0.761000 0.33130 -0.266000 0.10368 CGG TCGA-HV-A7OL-01A-11D-A33T-08 ARAP1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000347428.1 0 0 0 5 434 0 80 0 4.552617e-01 0 118 0 80 2 0 0 0 0 0 2 1 0.934813 5 426 0 80 2 0 0 0 0 80 2 -2.456572 0 1 121412 2 34 1 1 2 3 2.043829 0 0.370000 1.920000 0.372322 0.060000 1.000000e-02 0.150000 0.060000 0.082601 0.060000 0 3.000000e-02 0.100000 CREBZF 58487 broad.mit.edu 37 11 85375165 85375165 + Missense_Mutation SNP T T C TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr11:85375165T>C ENST00000527447.1 - 1 981 c.755A>G c.(754-756)gAg>gGg p.E252G CREBZF_ENST00000398294.2_Missense_Mutation_p.E170G|CREBZF_ENST00000534224.1_Intron|CREBZF_ENST00000531515.1_Intron NM_001039618.2 NP_001034707.1 Q9NS37 ZHANG_HUMAN CREB/ATF bZIP transcription factor 9 Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033) TTTGCCCAGCTCCCGATTCTC 0.622000 OREG0021274 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NSCLC(172;674 2044 9050 18334 41735) 0 SO:0001583 missense ENST00000527447.1 1 1 hg19 CCDS41697.1 . . . . . . . . . . T 13.40 2.226321 0.39300 . . ENSG00000137504 ENST00000398294;ENST00000527447 T;T 0.56611 0.45;0.45 4.89 4.89 0.63831 Basic-leucine zipper (bZIP) transcription factor (1);bZIP transcription factor, bZIP-1 (1); 0.096735 0.41938 D 0.000795 T 0.37128 0.0992 L 0.34521 1.04 0.34338 D 0.688429 B 0.24651 0.108 B 0.22386 0.039 T 0.45659 -0.9246 9 . . . -7.8605 7.6471 0.28327 0.0:0.1284:0.0:0.8716 . 252 Q9NS37 ZHANG_HUMAN G 170;252 ENSP00000381342:E170G;ENSP00000433459:E252G . E - 2 0 CREBZF 85052813 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 3.330000 0.52068 2.058000 0.61347 0.533000 0.62120 GAG TCGA-HV-A7OL-01A-11D-A33T-08 CREBZF-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390191.2 1 0 1 245 1094 0 161 1 5.713735e-01 2 8 0 161 2 0 0 0 0 0 2 1 1.000000 243 1086 0 160 2 0 0 0 0 161 2 -20.000000 1 1 0 0 1 1 2 3 2.043829 0 0.370000 1.920000 0.372322 0.980000 8.700000e-01 1.000000 1.000000 0.974062 0.980000 1 9.300000e-01 1.000000 CUX2 23316 broad.mit.edu 37 12 111758041 111758041 + Missense_Mutation SNP C C A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr12:111758041C>A ENST00000261726.6 + 17 2382 c.2228C>A c.(2227-2229)gCc>gAc p.A743D NM_015267.3 NP_056082.2 O14529 CUX2_HUMAN cut-like homeobox 2 55 GGGGCCCCGGCCTTGGTGAAG 0.756000 0 SO:0001583 missense ENST00000261726.6 0 1 hg19 CCDS41837.1 . . . . . . . . . . C 10.32 1.316955 0.23908 . . ENSG00000111249 ENST00000261726 T 0.49432 0.78 4.22 4.22 0.49857 . 0.488256 0.23708 N 0.045351 T 0.34308 0.0893 L 0.36672 1.1 0.25926 N 0.983054 B 0.20052 0.041 B 0.16289 0.015 T 0.21109 -1.0255 10 0.52906 T 0.07 -3.2681 6.6322 0.22863 0.1789:0.7291:0.0:0.092 . 743 O14529 CUX2_HUMAN D 743 ENSP00000261726:A743D ENSP00000261726:A743D A + 2 0 CUX2 110242424 0.985000 0.35326 0.297000 0.24988 0.186000 0.23388 3.416000 0.52707 1.909000 0.55274 0.485000 0.47835 GCC TCGA-HV-A7OL-01A-11D-A33T-08 CUX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404765.1 1 0 0 12 60 0 8 0 0 0 0 8 2 0 0 0 0 0 2 1 0.999279 11 59 0 8 2 0 0 0 0 8 2 -20.000000 1 1 0 0 1 0 0 0 1.996170 0 0.370000 1.920000 0.358125 0.880000 5.000000e-01 1.000000 1.000000 0.854981 0.880000 1 6.700000e-01 1.000000 DDX47 51202 broad.mit.edu 37 12 12980302 12980302 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr12:12980302C>T ENST00000358007.3 + 11 1251 c.1229C>T c.(1228-1230)gCc>gTc p.A410V DDX47_ENST00000352940.4_Missense_Mutation_p.A361V NM_016355.3 NP_057439.2 Q9H0S4 DDX47_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 47 16 Prostate(47;0.0526) CAAAGGTTTGCCCGAATGGTA 0.428000 0 SO:0001583 missense ENST00000358007.3 0 1 hg19 CCDS8655.1 . . . . . . . . . . C 18.46 3.628472 0.67015 . . ENSG00000213782 ENST00000352940;ENST00000358007 T;T 0.28454 2.38;1.61 5.75 4.86 0.63082 . 0.055390 0.64402 D 0.000001 T 0.43299 0.1241 M 0.66378 2.025 0.80722 D 1 B;B 0.25850 0.115;0.136 B;B 0.41236 0.351;0.164 T 0.34378 -0.9831 10 0.35671 T 0.21 -11.3685 14.979 0.71299 0.0:0.9316:0.0:0.0684 . 361;410 G5E955;Q9H0S4 .;DDX47_HUMAN V 361;410 ENSP00000319578:A361V;ENSP00000350698:A410V ENSP00000319578:A361V A + 2 0 DDX47 12871569 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 7.531000 0.81973 1.435000 0.47434 0.655000 0.94253 GCC TCGA-HV-A7OL-01A-11D-A33T-08 DDX47-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400674.1 0 0 0 6 938 0 167 0 3.881578e-01 1 185 0 167 2 0 0 0 0 0 2 1 0.963723 6 927 0 167 2 0 0 0 0 167 2 -2.068352 0 1 0 0 1 0 0 0 2.015189 0 0.370000 1.920000 0.365303 0.030000 0 0.070000 0.040000 0.039324 0.030000 0 1.000000e-02 0.060000 GPR133 283383 broad.mit.edu 37 12 131487822 131487822 + Silent SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr12:131487822C>T ENST00000261654.5 + 10 1678 c.1119C>T c.(1117-1119)acC>acT p.T373T GPR133_ENST00000535015.1_Silent_p.T405T|GPR133_ENST00000376682.4_Silent_p.T59T NM_198827.3 NP_942122.2 Q6QNK2 GP133_HUMAN G protein-coupled receptor 133 67 all_neural(191;0.0982)|Medulloblastoma(191;0.163) CCCAGGTCACCGTGGAGGGCT 0.612000 0 SO:0001819 synonymous_variant ENST00000261654.5 1 1 hg19 CCDS9272.1 TCGA-HV-A7OL-01A-11D-A33T-08 GPR133-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399356.1 1 0 1 94 358 0 84 0 0 0 0 84 2 0 0 0 0 0 2 1 1.000000 92 354 0 83 2 0 0 0 0 84 2 -3.239418 1 1 121412 1 41 1 0 0 0 1.996170 0 0.370000 1.920000 0.358125 0.990000 9.000000e-01 1.000000 1.000000 0.992881 0.990000 1 9.900000e-01 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-HV-A7OL-01A-11D-A33T-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 27 84 0 15 1 6.841510e-01 4 5 0 15 2 1 1 90 515 0 482 2 1 1.000000 27 84 0 15 2 1 1 1593 6419 0 15 2 -19.927250 1 1 121404 2 44 1 0 0 0 2.015189 0 0.370000 1.920000 0.365303 0.990000 9.000000e-01 1.000000 1.000000 0.994640 0.990000 1 9.900000e-01 1.000000 PFKM 5213 broad.mit.edu 37 12 48536575 48536575 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr12:48536575G>A ENST00000312352.7 + 18 1703 c.1664G>A c.(1663-1665)cGc>cAc p.R555H PFKM_ENST00000340802.6_Missense_Mutation_p.R626H|PFKM_ENST00000359794.5_Missense_Mutation_p.R555H|PFKM_ENST00000547587.1_Missense_Mutation_p.R555H|PFKM_ENST00000395233.2_Missense_Mutation_p.R524H|PFKM_ENST00000551804.1_Missense_Mutation_p.R524H NM_001166687.1 NP_001160159.1 P08237 PFKAM_HUMAN phosphofructokinase, muscle 35 ACCTGTGACCGCATCAAGCAG 0.488000 0 SO:0001583 missense ENST00000312352.7 0 1 hg19 CCDS8760.1 . . . . . . . . . . G 27.0 4.795504 0.90453 . . ENSG00000152556 ENST00000340802;ENST00000359794;ENST00000395233;ENST00000551804;ENST00000547587;ENST00000312352;ENST00000546465 T;T;T;T;T;T;T 0.80994 -1.44;-1.44;-1.44;-1.44;-1.44;-1.44;-1.44 5.21 4.31 0.51392 Phosphofructokinase domain (2); 0.049858 0.85682 D 0.000000 D 0.91462 0.7305 M 0.92219 3.285 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.72982 0.979;0.953;0.933 D 0.93406 0.6764 10 0.62326 D 0.03 -12.3227 15.1275 0.72494 0.0:0.0:0.8573:0.1427 . 524;555;626 P08237-2;P08237;Q6ZTT1 .;K6PF_HUMAN;. H 626;555;524;524;555;555;170 ENSP00000345771:R626H;ENSP00000352842:R555H;ENSP00000378656:R524H;ENSP00000448177:R524H;ENSP00000449426:R555H;ENSP00000309438:R555H;ENSP00000446519:R170H ENSP00000309438:R555H R + 2 0 PFKM 46822842 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.758000 0.85224 1.541000 0.49316 0.655000 0.94253 CGC TCGA-HV-A7OL-01A-11D-A33T-08 PFKM-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406490.1 0 0 0 7 615 0 87 0 1.304132e-01 0 48 0 87 2 0 0 0 0 0 2 1 0.980241 7 611 0 87 2 0 0 0 0 87 2 -1.868052 0 1 121412 5 39 1 0 0 0 2.015189 0 0.370000 1.920000 0.365303 0.060000 2.000000e-02 0.120000 0.060000 0.068618 0.060000 0 3.000000e-02 0.090000 CCNT1 904 broad.mit.edu 37 12 49087735 49087735 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr12:49087735G>A ENST00000261900.3 - 9 1484 c.1262C>T c.(1261-1263)gCt>gTt p.A421V NM_001240.3 NP_001231.2 O60563 CCNT1_HUMAN cyclin T1 27 ATTCTGGGCAGCATATGCATA 0.463000 0 SO:0001583 missense ENST00000261900.3 0 1 hg19 CCDS8766.1 . . . . . . . . . . G 18.42 3.619480 0.66787 . . ENSG00000129315 ENST00000261900 T 0.20598 2.06 5.28 5.28 0.74379 . 0.000000 0.85682 D 0.000000 T 0.23133 0.0559 L 0.49126 1.545 0.58432 D 0.999998 P 0.41929 0.765 B 0.37198 0.243 T 0.03112 -1.1071 10 0.62326 D 0.03 -14.5086 18.0305 0.89282 0.0:0.0:1.0:0.0 . 421 O60563 CCNT1_HUMAN V 421 ENSP00000261900:A421V ENSP00000261900:A421V A - 2 0 CCNT1 47374002 1.000000 0.71417 1.000000 0.80357 0.959000 0.62525 6.377000 0.73145 2.634000 0.89283 0.561000 0.74099 GCT TCGA-HV-A7OL-01A-11D-A33T-08 CCNT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408853.1 0 0 0 6 801 0 130 0 0 0 0 130 2 0 0 0 0 0 2 1 0.964503 6 797 0 129 2 0 0 0 0 130 2 -2.545472 1 1 0 0 1 0 0 0 2.015189 0 0.370000 1.920000 0.365303 0.030000 0 0.090000 0.040000 0.046258 0.030000 0 2.000000e-02 0.060000 OSBPL8 114882 broad.mit.edu 37 12 76791663 76791663 + Silent SNP T T C rs35436760 byFrequency TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr12:76791663T>C ENST00000261183.3 - 8 962 c.483A>G c.(481-483)ctA>ctG p.L161L OSBPL8_ENST00000393249.2_Silent_p.L119L|OSBPL8_ENST00000393250.4_Silent_p.L119L NM_020841.4 NP_065892.1 Q9BZF1 OSBL8_HUMAN oxysterol binding protein-like 8 28 TCCAGCTCTTTAGAGTACCAC 0.363000 0 SO:0001819 synonymous_variant ENST00000261183.3 1 1 hg19 CCDS31862.1 TCGA-HV-A7OL-01A-11D-A33T-08 OSBPL8-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000406357.1 1 0 1 58 225 0 43 0 0 0 0 43 2 0 0 0 0 0 2 1 1.000000 58 223 0 42 2 0 0 0 0 43 2 -2.963092 1 1 121412 122 52 1 0 0 0 1.996170 0 0.370000 1.920000 0.358125 0.990000 8.400000e-01 1.000000 1.000000 0.983462 0.990000 1 9.500000e-01 1.000000 ANKS1B 56899 broad.mit.edu 37 12 99640630 99640630 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr12:99640630C>T ENST00000547776.2 - 13 1768 c.1769G>A c.(1768-1770)cGa>cAa p.R590Q ANKS1B_ENST00000329257.7_Missense_Mutation_p.R590Q|ANKS1B_ENST00000550833.1_5'UTR|ANKS1B_ENST00000547010.1_Missense_Mutation_p.R170Q NM_152788.4 NP_690001.3 Q7Z6G8 ANS1B_HUMAN ankyrin repeat and sterile alpha motif domain containing 1B 70 all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209) GTCATCCTGTCGGGAGAGGTC 0.468000 0 SO:0001583 missense ENST00000547776.2 1 1 hg19 CCDS55872.1 . . . . . . . . . . C 0.986 -0.695588 0.03279 0.0 1.22E-4 ENSG00000185046 ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702;ENST00000549866 T;T;T;T 0.58358 1.15;0.34;1.16;1.06 5.76 3.26 0.37387 . 0.838349 0.10666 N 0.648107 T 0.23289 0.0563 N 0.02539 -0.55 0.80722 D 1 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.01281 0.0;0.0;0.0 T 0.11966 -1.0566 9 . . . -5.1323 5.7192 0.17978 0.1489:0.0808:0.0:0.7703 . 556;170;590 F8VVQ4;Q7Z6G8-6;Q7Z6G8 .;.;ANS1B_HUMAN Q 590;170;590;169;556 ENSP00000449629:R590Q;ENSP00000448512:R170Q;ENSP00000331381:R590Q;ENSP00000449894:R556Q . R - 2 0 ANKS1B 98164761 0.847000 0.29606 0.995000 0.50966 0.026000 0.11368 0.765000 0.26546 1.124000 0.41980 -0.238000 0.12139 CGA TCGA-HV-A7OL-01A-11D-A33T-08 ANKS1B-003 KNOWN basic|appris_candidate_longest|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000408421.3 1 0 1 157 678 0 114 0 0 0 0 114 2 0 0 0 0 0 2 1 1.000000 156 673 0 114 2 0 0 0 0 114 2 -3.319627 1 1 120690 24 48 1 0 0 0 1.996170 0 0.370000 1.920000 0.358125 0.990000 8.500000e-01 1.000000 1.000000 0.970987 0.990000 1 9.200000e-01 1.000000 IRS2 8660 broad.mit.edu 37 13 110434482 110434482 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr13:110434482C>T ENST00000375856.3 - 1 4433 c.3919G>A c.(3919-3921)Ggg>Agg p.G1307R NM_003749.2 NP_003740.2 Q9Y4H2 IRS2_HUMAN insulin receptor substrate 2 19 all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155) Breast(118;0.159) all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147) CCCGGCCCCCCGCACCCGCCG 0.692000 Melanoma(100;613 2409 40847) 0 SO:0001583 missense ENST00000375856.3 0 1 hg19 CCDS9510.1 . . . . . . . . . . C 10.84 1.464796 0.26335 . . ENSG00000185950 ENST00000375856 T 0.59906 0.23 4.12 3.25 0.37280 . 0.226724 0.22451 U 0.059897 T 0.35128 0.0921 N 0.24115 0.695 0.09310 N 0.999996 P 0.42961 0.795 B 0.28709 0.093 T 0.19257 -1.0311 10 0.51188 T 0.08 -15.5233 10.7615 0.46268 0.1915:0.8085:0.0:0.0 . 1307 Q9Y4H2 IRS2_HUMAN R 1307 ENSP00000365016:G1307R ENSP00000365016:G1307R G - 1 0 IRS2 109232483 0.998000 0.40836 0.189000 0.23252 0.049000 0.14656 1.090000 0.30902 0.910000 0.36722 0.462000 0.41574 GGG TCGA-HV-A7OL-01A-11D-A33T-08 IRS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045755.1 1 0 0 25 109 0 10 0 0 0 0 10 2 0 0 0 0 0 2 1 1.000000 24 105 0 10 2 0 0 0 0 10 2 -3.527049 1 1 0 0 1 1 2 3 2.033455 0 0.370000 1.920000 0.371163 0.990000 6.800000e-01 1.000000 1.000000 0.939419 0.990000 1 8.300000e-01 1.000000 YLPM1 56252 broad.mit.edu 37 14 75230759 75230759 + Silent SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr14:75230759G>A ENST00000552421.1 + 1 691 c.567G>A c.(565-567)ccG>ccA p.P189P YLPM1_ENST00000238571.3_Silent_p.P189P|YLPM1_ENST00000325680.7_Silent_p.P189P P49750 YLPM1_HUMAN YLP motif containing 1 62 KIRC - Kidney renal clear cell carcinoma(43;0.238) CTGCTCAGCCGTCCCCTTCGC 0.597000 0 SO:0001819 synonymous_variant ENST00000552421.1 0 1 hg19 TCGA-HV-A7OL-01A-11D-A33T-08 YLPM1-008 NOVEL not_organism_supported|basic|exp_conf protein_coding protein_coding OTTHUMT00000404450.1 0 0 0 5 469 0 51 0 0 0 0 51 2 0 0 0 0 0 2 1 0.933172 5 456 0 50 2 0 0 0 0 51 2 -2.767071 1 1 0 0 1 0 1 1 2.024830 0 0.370000 1.920000 0.368832 0.050000 1.000000e-02 0.130000 0.060000 0.067752 0.050000 0 3.000000e-02 0.090000 STON2 85439 broad.mit.edu 37 14 81743580 81743580 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr14:81743580G>A ENST00000267540.2 - 4 2275 c.2075C>T c.(2074-2076)aCg>aTg p.T692M STON2_ENST00000555447.1_Missense_Mutation_p.T692M|STON2_ENST00000556280.1_5'Flank NM_033104.3 NP_149095.2 Q8WXE9 STON2_HUMAN stonin 2 34 ACTTGTGGCCGTCCTGAGTGT 0.557000 0 SO:0001583 missense ENST00000267540.2 0 1 hg19 CCDS9875.1 . . . . . . . . . . G 14.56 2.572943 0.45798 2.27E-4 0.0 ENSG00000140022 ENST00000555447;ENST00000546306;ENST00000267540 T;T 0.19105 2.17;2.17 6.06 6.06 0.98353 Clathrin adaptor, mu subunit, C-terminal (3); 0.000000 0.85682 D 0.000000 T 0.45054 0.1323 M 0.65498 2.005 0.58432 D 0.999992 D;D 0.89917 1.0;1.0 D;D 0.75020 0.985;0.985 T 0.27054 -1.0085 10 0.87932 D 0 -17.0297 14.7345 0.69406 0.0685:0.0:0.9315:0.0 . 692;692 Q8WXE9;G3V2T7 STON2_HUMAN;. M 692;704;692 ENSP00000450857:T692M;ENSP00000267540:T692M ENSP00000267540:T692M T - 2 0 STON2 80813333 1.000000 0.71417 0.972000 0.41901 0.371000 0.29859 8.029000 0.88807 2.879000 0.98667 0.650000 0.86243 ACG TCGA-HV-A7OL-01A-11D-A33T-08 STON2-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000413317.1 0 0 0 6 714 0 115 0 1.072785e-04 0 2 0 115 2 0 0 0 0 0 2 1 0.963681 6 705 0 115 2 0 0 0 0 115 2 -2.333984 0 1 121412 9 44 1 0 1 1 2.024830 0 0.370000 1.920000 0.368832 0.040000 0 0.090000 0.040000 0.052183 0.040000 0 2.000000e-02 0.070000 LGMN 5641 broad.mit.edu 37 14 93199026 93199026 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr14:93199026C>T ENST00000393218.2 - 3 443 c.106G>A c.(106-108)Ggt>Agt p.G36S LGMN_ENST00000557434.1_Missense_Mutation_p.G36S|LGMN_ENST00000555699.1_Missense_Mutation_p.G36S|LGMN_ENST00000334869.4_Missense_Mutation_p.G36S NM_001008530.2 NP_001008530.1 Q99538 LGMN_HUMAN legumain 18 all_cancers(154;0.0706) CCATTTGAACCTGCCACGATC 0.443000 0 SO:0001583 missense ENST00000393218.2 0 1 hg19 CCDS9904.1 . . . . . . . . . . C 19.46 3.832172 0.71258 . . ENSG00000100600 ENST00000555699;ENST00000334869;ENST00000557434;ENST00000334864;ENST00000262004;ENST00000393218;ENST00000539531;ENST00000535855;ENST00000553802;ENST00000554397;ENST00000554919;ENST00000554080;ENST00000553371 T;T;T;T;T;T;T;T;T 0.72942 0.48;0.4;0.52;0.4;0.51;0.38;0.38;-0.34;-0.7 4.56 4.56 0.56223 . 0.000000 0.85682 D 0.000000 D 0.87059 0.6083 M 0.90922 3.16 0.80722 D 1 D;D;D 0.89917 1.0;1.0;0.999 D;D;D 0.97110 1.0;0.999;0.996 D 0.90096 0.4181 10 0.62326 D 0.03 -23.6576 16.0812 0.81005 0.0:1.0:0.0:0.0 . 36;36;36 Q99538;Q86TV2;Q86TV3 LGMN_HUMAN;.;. S 36;36;36;36;36;36;13;36;36;36;36;36;36 ENSP00000451861:G36S;ENSP00000334052:G36S;ENSP00000452572:G36S;ENSP00000376911:G36S;ENSP00000450854:G36S;ENSP00000450677:G36S;ENSP00000451916:G36S;ENSP00000452268:G36S;ENSP00000451797:G36S ENSP00000262004:G36S G - 1 0 LGMN 92268779 1.000000 0.71417 0.146000 0.22360 0.387000 0.30353 6.348000 0.73009 2.086000 0.62901 0.313000 0.20887 GGT TCGA-HV-A7OL-01A-11D-A33T-08 LGMN-005 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412288.1 0 0 0 8 989 0 159 1 1.661851e-01 2 78 0 159 2 0 0 0 0 0 2 1 0.988211 8 964 0 153 2 0 0 0 0 159 2 -2.286640 0 1 0 0 1 0 1 1 2.024830 0 0.370000 1.920000 0.368832 0.040000 1.000000e-02 0.080000 0.040000 0.048678 0.040000 0 2.000000e-02 0.070000 GABRA5 2558 broad.mit.edu 37 15 27128316 27128316 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr15:27128316G>A ENST00000335625.5 + 5 1100 c.212G>A c.(211-213)cGc>cAc p.R71H GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000400081.3_Missense_Mutation_p.R71H|GABRA5_ENST00000355395.5_Missense_Mutation_p.R71H|GABRA5_ENST00000557449.1_Intron NM_000810.3 NP_000801.1 P31644 GBRA5_HUMAN gamma-aminobutyric acid (GABA) A receptor, alpha 5 49 all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227) Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198) CTTTCAGAGCGCATCACTCAG 0.612000 0 SO:0001583 missense ENST00000335625.5 0 1 hg19 CCDS45194.1 . . . . . . . . . . G 23.5 4.426900 0.83667 . . ENSG00000186297 ENST00000335625;ENST00000355395;ENST00000555182;ENST00000400081;ENST00000554038;ENST00000554596;ENST00000554599;ENST00000554083 T;T;T;T;T;T;T;T 0.79352 -1.26;-1.26;-1.26;-1.26;-1.13;-1.26;-1.26;-1.26 5.39 4.47 0.54385 Neurotransmitter-gated ion-channel ligand-binding (3); 0.318671 0.37857 N 0.001907 T 0.81054 0.4743 L 0.55481 1.735 0.36586 D 0.873815 D 0.58268 0.982 P 0.54372 0.75 D 0.86010 0.1500 10 0.72032 D 0.01 . 13.2492 0.60041 0.0765:0.0:0.9235:0.0 . 71 P31644 GBRA5_HUMAN H 71;71;39;71;71;71;71;39 ENSP00000335592:R71H;ENSP00000347557:R71H;ENSP00000450653:R39H;ENSP00000382953:R71H;ENSP00000451527:R71H;ENSP00000450806:R71H;ENSP00000450717:R71H;ENSP00000450529:R39H ENSP00000335592:R71H R + 2 0 GABRA5 24679409 0.996000 0.38824 0.989000 0.46669 0.806000 0.45545 3.505000 0.53356 1.405000 0.46838 0.555000 0.69702 CGC TCGA-HV-A7OL-01A-11D-A33T-08 GABRA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000415234.1 0 0 0 4 226 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 0.884829 4 220 0 42 2 0 0 0 0 42 2 -3.806431 1 1 121152 4 35 1 1 2 3 2.051060 0 0.370000 1.920000 0.374628 0.100000 3.000000e-02 1.000000 0.100000 0.141932 0.100000 0 6.000000e-02 0.170000 RYR3 6263 broad.mit.edu 37 15 33954961 33954961 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr15:33954961C>T ENST00000389232.4 + 35 5300 c.5230C>T c.(5230-5232)Cgg>Tgg p.R1744W RYR3_ENST00000415757.3_Missense_Mutation_p.R1744W NM_001036.3 NP_001027.3 Q15413 RYR3_HUMAN ryanodine receptor 3 p.R1744R(1) 311 all_lung(180;7.18e-09) TGATGATGTTCGGCAGATCCT 0.552000 1 Substitution - coding silent(1) SO:0001583 missense ENST00000389232.4 1 1 hg19 CCDS45210.1 . . . . . . . . . . c 15.06 2.720660 0.48728 2.35E-4 0.0 ENSG00000198838 ENST00000389232;ENST00000415757;ENST00000361728 T;T 0.74421 -0.84;-0.84 5.41 3.54 0.40534 . 0.359807 0.23604 N 0.046403 T 0.74030 0.3663 L 0.38175 1.15 0.09310 N 0.999998 D;D 0.61697 0.988;0.99 P;P 0.57502 0.766;0.822 T 0.65030 -0.6267 10 0.87932 D 0 . 8.8635 0.35272 0.3151:0.6124:0.0:0.0724 . 1744;1744 Q15413-2;Q15413 .;RYR3_HUMAN W 1744 ENSP00000373884:R1744W;ENSP00000399610:R1744W ENSP00000354735:R1744W R + 1 2 RYR3 31742253 0.938000 0.31826 0.868000 0.34077 0.894000 0.52154 1.918000 0.40006 0.862000 0.35528 -0.119000 0.15052 CGG TCGA-HV-A7OL-01A-11D-A33T-08 RYR3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000417514.1 1 0 1 64 333 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 1.000000 64 329 0 70 2 0 0 0 0 71 2 -3.154547 1 1 121180 3 37 1 1 2 3 2.051060 0 0.370000 1.920000 0.374628 0.870000 6.900000e-01 1.000000 1.000000 0.880153 0.870000 1 7.800000e-01 0.990000 RYR3 6263 broad.mit.edu 37 15 34130099 34130099 + Missense_Mutation SNP T T C TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr15:34130099T>C ENST00000389232.4 + 89 11988 c.11918T>C c.(11917-11919)aTg>aCg p.M3973T RYR3_ENST00000415757.3_Missense_Mutation_p.M3968T NM_001036.3 NP_001027.3 Q15413 RYR3_HUMAN ryanodine receptor 3 311 all_lung(180;7.18e-09) GAGAATGACATGTTTAATTAC 0.428000 0 SO:0001583 missense ENST00000389232.4 1 1 hg19 CCDS45210.1 . . . . . . . . . . T 13.01 2.109599 0.37242 . . ENSG00000198838 ENST00000389232;ENST00000361728 D 0.81739 -1.53 5.4 5.4 0.78164 EF-hand-like domain (1); 0.000000 0.85682 D 0.000000 T 0.76011 0.3928 N 0.12831 0.26 0.53005 D 0.99996 P;B 0.52316 0.952;0.012 P;B 0.54499 0.754;0.014 T 0.76389 -0.2977 10 0.30854 T 0.27 . 15.5941 0.76566 0.0:0.0:0.0:1.0 . 3968;3973 Q15413-2;Q15413 .;RYR3_HUMAN T 3973;3969 ENSP00000373884:M3973T ENSP00000354735:M3969T M + 2 0 RYR3 31917391 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 5.871000 0.69628 2.272000 0.75746 0.450000 0.29827 ATG TCGA-HV-A7OL-01A-11D-A33T-08 RYR3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000417514.1 1 0 1 142 573 0 99 0 0 0 0 99 2 0 0 0 0 0 2 1 1.000000 142 570 0 98 2 0 0 0 0 99 2 -20.000000 1 1 0 0 1 1 2 3 2.051060 0 0.370000 1.920000 0.374628 0.990000 9.200000e-01 1.000000 1.000000 0.994102 0.990000 1 9.900000e-01 1.000000 MYO9A 4649 broad.mit.edu 37 15 72338352 72338352 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr15:72338352C>T ENST00000356056.5 - 2 1025 c.553G>A c.(553-555)Gtt>Att p.V185I MYO9A_ENST00000444904.1_Missense_Mutation_p.V185I|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000424560.1_Missense_Mutation_p.V185I|RNU2-65P_ENST00000410162.1_RNA|MYO9A_ENST00000564571.1_Missense_Mutation_p.V185I|MYO9A_ENST00000566885.1_Intron NM_006901.3 NP_008832.2 B2RTY4 MYO9A_HUMAN myosin IXA 88 GGGTTAATAACTATTAGAATA 0.328000 0 SO:0001583 missense ENST00000356056.5 1 1 hg19 CCDS10239.1 . . . . . . . . . . c 19.42 3.825008 0.71143 . . ENSG00000066933 ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864;ENST00000446448 D;D;D 0.88201 -2.35;-2.35;-2.35 5.8 5.8 0.92144 Myosin head, motor domain (3); . . . . D 0.89037 0.6601 L 0.52573 1.65 0.50171 D 0.999851 P;B;B 0.35139 0.486;0.38;0.268 B;B;B 0.39339 0.268;0.197;0.297 D 0.88674 0.3197 9 0.87932 D 0 . 20.1223 0.97967 0.0:1.0:0.0:0.0 . 185;185;185 B2RTY4-3;B7WP69;B2RTY4 .;.;MYO9A_HUMAN I 185 ENSP00000348349:V185I;ENSP00000399162:V185I;ENSP00000398250:V185I ENSP00000261864:V185I V - 1 0 MYO9A 70125406 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 6.017000 0.70805 2.749000 0.94314 0.650000 0.86243 GTT TCGA-HV-A7OL-01A-11D-A33T-08 MYO9A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257308.1 1 0 1 81 333 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 1.000000 81 331 0 53 2 0 0 0 0 53 2 -20.000000 1 1 0 0 1 1 2 3 2.051849 0 0.370000 1.920000 0.374628 0.990000 8.600000e-01 1.000000 1.000000 0.984628 0.990000 1 9.600000e-01 1.000000 TBL3 10607 broad.mit.edu 37 16 2024605 2024605 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr16:2024605C>T ENST00000568546.1 + 5 432 c.304C>T c.(304-306)Cgc>Tgc p.R102C NM_006453.2 NP_006444.2 Q12788 TBL3_HUMAN transducin (beta)-like 3 18 CAGCGTTACCCGCCTGTGGAA 0.672000 Melanoma(118;616 1651 35077 38081 48633) 0 SO:0001583 missense ENST00000568546.1 1 1 hg19 CCDS10453.1 . . . . . . . . . . C 11.56 1.674507 0.29693 . . ENSG00000183751 ENST00000332704 . . . 4.97 3.0 0.34707 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.237542 0.39146 N 0.001458 T 0.53642 0.1809 M 0.86651 2.83 0.80722 D 1 P 0.42757 0.789 B 0.25614 0.062 T 0.60949 -0.7161 9 0.72032 D 0.01 -15.7473 10.7503 0.46205 0.0:0.8435:0.0:0.1565 . 102 Q12788 TBL3_HUMAN C 102 . ENSP00000331815:R102C R + 1 0 TBL3 1964606 0.998000 0.40836 0.556000 0.28293 0.678000 0.39670 3.772000 0.55325 0.505000 0.28104 -0.291000 0.09656 CGC TCGA-HV-A7OL-01A-11D-A33T-08 TBL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250615.3 1 0 1 52 228 0 33 1 9.859876e-01 9 23 0 33 2 0 0 0 0 0 2 1 1.000000 49 194 0 30 2 0 0 0 0 33 2 -3.470092 1 1 121382 6 35 1 0 0 0 2.019029 0 0.370000 1.920000 0.367660 0.990000 7.600000e-01 1.000000 1.000000 0.953371 0.990000 1 8.700000e-01 1.000000 DNAH3 55567 broad.mit.edu 37 16 20976524 20976524 + Silent SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr16:20976524G>A ENST00000261383.3 - 53 8681 c.8682C>T c.(8680-8682)taC>taT p.Y2894Y DNAH3_ENST00000415178.1_3'UTR NM_017539.1 NP_060009.1 Q8TD57 DYH3_HUMAN dynein, axonemal, heavy chain 3 202 CCACGCGATCGTACACCTCCA 0.562000 0 SO:0001819 synonymous_variant ENST00000261383.3 1 1 hg19 CCDS10594.1 TCGA-HV-A7OL-01A-11D-A33T-08 DNAH3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207361.1 1 0 1 148 664 0 109 0 0 0 0 109 2 0 0 0 0 0 2 1 1.000000 146 649 0 106 2 0 0 0 0 109 2 -20.000000 1 1 0 0 1 0 0 0 2.010160 0 0.370000 1.920000 0.365303 0.970000 8.300000e-01 1.000000 1.000000 0.959708 0.970000 1 9.000000e-01 1.000000 ATP2A1 487 broad.mit.edu 37 16 28912189 28912189 + Missense_Mutation SNP G G C TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr16:28912189G>C ENST00000357084.3 + 15 2319 c.2052G>C c.(2050-2052)aaG>aaC p.K684N ATP2A1_ENST00000395503.4_Missense_Mutation_p.K684N|ATP2A1_ENST00000536376.1_Missense_Mutation_p.K559N NM_173201.3 NP_775293.1 O14983 AT2A1_HUMAN ATPase, Ca++ transporting, cardiac muscle, fast twitch 1 38 CCTCGCACAAGTCCAAGATTG 0.627000 0 SO:0001583 missense ENST00000357084.3 0 1 hg19 CCDS10643.1 . . . . . . . . . . G 22.5 4.296086 0.81025 . . ENSG00000196296 ENST00000357084;ENST00000395503;ENST00000395498;ENST00000536376 D;D;D 0.99769 -6.7;-6.7;-6.7 5.4 4.44 0.53790 Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, transmembrane domain (1); 0.000000 0.85682 D 0.000000 D 0.99896 0.9950 H 0.99783 4.775 0.54753 D 0.999987 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;1.0;1.0 D 0.96211 0.9153 10 0.87932 D 0 . 13.0151 0.58753 0.0797:0.0:0.9203:0.0 . 559;684;684 B3KY17;O14983;O14983-2 .;AT2A1_HUMAN;. N 684;684;721;559 ENSP00000349595:K684N;ENSP00000378879:K684N;ENSP00000443101:K559N ENSP00000349595:K684N K + 3 2 ATP2A1 28819690 1.000000 0.71417 1.000000 0.80357 0.740000 0.42216 4.048000 0.57390 1.278000 0.44430 0.555000 0.69702 AAG TCGA-HV-A7OL-01A-11D-A33T-08 ATP2A1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000254686.2 0 0 0 4 386 0 72 0 0 0 1 0 72 2 0 0 0 0 0 2 0 0.887876 0 385 0 71 2 0 0 0 0 72 2 -4.617620 1 0 0 0 1 0 0 0 2.010160 0 0.370000 1.920000 0.365303 0.050000 1.000000e-02 0.130000 0.060000 0.068062 0.050000 0 3.000000e-02 0.100000 CREBBP 1387 broad.mit.edu 37 16 3801767 3801767 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr16:3801767C>T ENST00000262367.5 - 20 4548 c.3739G>A c.(3739-3741)Gag>Aag p.E1247K CREBBP_ENST00000382070.3_Missense_Mutation_p.E1209K NM_004380.2 NP_004371.2 Q92793 CBP_HUMAN CREB binding protein 295 Ovarian(90;0.0266) GTCACATTCTCGCCCTGGATC 0.502000 T, N, F, Mis, O MLL, MORF, RUNXBP2 ALL, AML, DLBCL, B-NHL Rubinstein-Taybi syndrome Dom/Rec yes 16 16p13.3 1387 CREB binding protein (CBP) yes L 0 SO:0001583 missense ENST00000262367.5 1 1 hg19 CCDS10509.1 . . . . . . . . . . C 17.10 3.303906 0.60305 . . ENSG00000005339 ENST00000262367;ENST00000543883;ENST00000382070 D;D 0.83992 -1.79;-1.71 5.46 5.46 0.80206 . 0.000000 0.64402 D 0.000001 T 0.75539 0.3863 L 0.42487 1.325 0.53688 D 0.999978 P;P 0.44195 0.828;0.828 B;B 0.28991 0.097;0.097 T 0.78703 -0.2101 10 0.46703 T 0.11 -29.1663 19.3082 0.94173 0.0:1.0:0.0:0.0 . 1277;1247 Q4LE28;Q92793 .;CBP_HUMAN K 1247;1277;1209 ENSP00000262367:E1247K;ENSP00000371502:E1209K ENSP00000262367:E1247K E - 1 0 CREBBP 3741768 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 5.577000 0.67444 2.539000 0.85634 0.655000 0.94253 GAG TCGA-HV-A7OL-01A-11D-A33T-08 CREBBP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251591.2 1 0 1 51 202 0 29 0 4.221814e-02 0 2 0 29 2 0 0 0 0 0 2 1 1.000000 50 201 0 29 2 0 0 0 0 29 2 -3.188316 1 1 0 0 1 0 0 0 2.019029 0 0.370000 1.920000 0.367660 0.990000 8.300000e-01 1.000000 1.000000 0.980776 0.990000 1 9.500000e-01 1.000000 WDR90 197335 broad.mit.edu 37 16 703653 703653 + Silent SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr16:703653C>T ENST00000293879.4 + 12 1362 c.1362C>T c.(1360-1362)caC>caT p.H454H WDR90_ENST00000549091.1_Silent_p.H454H|LA16c-349E10.1_ENST00000573609.1_RNA Q96KV7 WDR90_HUMAN WD repeat domain 90 37 Hepatocellular(780;0.0218) GCCCAATGCACGTTGTCTGCT 0.637000 0 SO:0001819 synonymous_variant ENST00000293879.4 1 1 hg19 CCDS42092.1 TCGA-HV-A7OL-01A-11D-A33T-08 WDR90-002 NOVEL basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000404335.1 1 0 1 69 254 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 1.000000 69 252 0 58 2 0 0 0 0 58 2 -20.000000 1 1 120938 1 30 1 0 0 0 2.019029 0 0.370000 1.920000 0.367660 0.990000 9.100000e-01 1.000000 1.000000 0.994675 0.990000 1 9.900000e-01 1.000000 PRPF8 10594 broad.mit.edu 37 17 1576724 1576724 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr17:1576724C>T ENST00000572621.1 - 22 3849 c.3584G>A c.(3583-3585)cGc>cAc p.R1195H PRPF8_ENST00000304992.6_Missense_Mutation_p.R1195H Q6P2Q9 PRP8_HUMAN pre-mRNA processing factor 8 77 AGGCAGGATGCGGCACTCGAA 0.572000 0 SO:0001583 missense ENST00000572621.1 0 1 hg19 CCDS11010.1 . . . . . . . . . . C 35 5.548538 0.96488 . . ENSG00000174231 ENST00000304992 D 0.84873 -1.91 6.06 6.06 0.98353 . 0.000000 0.85682 D 0.000000 D 0.95290 0.8472 H 0.95043 3.615 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.95669 0.8722 10 0.87932 D 0 . 20.6244 0.99512 0.0:1.0:0.0:0.0 . 1195 Q6P2Q9 PRP8_HUMAN H 1195 ENSP00000304350:R1195H ENSP00000304350:R1195H R - 2 0 PRPF8 1523474 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 7.814000 0.86154 2.879000 0.98667 0.650000 0.86243 CGC TCGA-HV-A7OL-01A-11D-A33T-08 PRPF8-002 NOVEL alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438412.2 0 0 0 5 307 1 55 0 0 0 1 1 55 2 0 0 0 0 0 2 0 0.004233 5 304 1 55 18 0 0 0 1 55 2 -2.234427 0 1 0 0 1 0 1 1 1.640026 1 0.370000 1.920000 0.226994 0.070000 2.000000e-02 0.150000 0.070000 0.083256 0.070000 0 4.000000e-02 0.110000 GFAP 2670 broad.mit.edu 37 17 42990738 42990738 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr17:42990738C>T ENST00000253408.5 - 4 744 c.679G>A c.(679-681)Gcc>Acc p.A227T GFAP_ENST00000435360.2_Missense_Mutation_p.A227T|GFAP_ENST00000588735.1_Intron|GFAP_ENST00000591327.1_5'Flank|GFAP_ENST00000586793.1_Missense_Mutation_p.A227T NM_002055.4 NP_002046.1 P14136 GFAP_HUMAN glial fibrillary acidic protein 23 Prostate(33;0.0959) TCTGGCTTGGCCACGTCAAGC 0.607000 0 SO:0001583 missense ENST00000253408.5 0 1 hg19 CCDS11491.1 . . . . . . . . . . C 6.948 0.544765 0.13312 . . ENSG00000131095 ENST00000253408;ENST00000421021;ENST00000435360 D;D 0.95853 -3.83;-3.83 4.93 2.92 0.33932 Filament (1); 0.204172 0.43110 D 0.000602 D 0.88644 0.6492 N 0.17674 0.51 0.30072 N 0.809996 B;B 0.13594 0.008;0.001 B;B 0.16289 0.015;0.007 T 0.82680 -0.0337 10 0.66056 D 0.02 . 4.7956 0.13270 0.4228:0.4185:0.0:0.1588 . 227;227 E9PAX3;P14136 .;GFAP_HUMAN T 227;202;227 ENSP00000253408:A227T;ENSP00000403962:A227T ENSP00000253408:A227T A - 1 0 GFAP 40346264 0.009000 0.17119 0.653000 0.29593 0.053000 0.15095 0.375000 0.20518 0.788000 0.33755 -0.181000 0.13052 GCC TCGA-HV-A7OL-01A-11D-A33T-08 GFAP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000448701.1 0 0 0 5 406 0 60 0 0 0 0 60 2 0 0 0 0 0 2 1 0.936695 5 403 0 59 2 0 0 0 0 60 2 -2.521184 1 1 0 0 1 0 2 2 2.028987 1 0.370000 1.920000 0.370000 0.060000 2.000000e-02 0.150000 0.060000 0.078184 0.060000 0 4.000000e-02 0.110000 RNF43 54894 broad.mit.edu 37 17 56448270 56448270 + Splice_Site SNP A A G TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 A G A A Valid Somatic Phase_I WXS targeted Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr17:56448270A>G ENST00000584437.1 - 2 2331 c.e2+1 RNF43_ENST00000407977.2_Splice_Site|RNF43_ENST00000583753.1_Intron|RNF43_ENST00000500597.2_Intron|RNF43_ENST00000581868.1_Splice_Site|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Splice_Site|RNF43_ENST00000577625.1_Splice_Site Q68DV7 RNF43_HUMAN ring finger protein 43 60 Medulloblastoma(34;0.127)|all_neural(34;0.237) GTGTGAGTCTACCTTGCTAGC 0.582000 0 SO:0001630 splice_region_variant ENST00000584437.1 1 1 hg19 CCDS11607.1 . . . . . . . . . . A 23.2 4.384458 0.82792 . . ENSG00000108375 ENST00000407977 . . . 5.45 5.45 0.79879 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 14.6985 0.69139 1.0:0.0:0.0:0.0 . . . . . -1 . . . - . . RNF43 53803269 1.000000 0.71417 0.997000 0.53966 0.837000 0.47467 5.913000 0.69957 2.066000 0.61787 0.533000 0.62120 . TCGA-HV-A7OL-01A-11D-A33T-08 RNF43-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444713.1 1 0 1 116 247 0 54 1 9.635510e-01 14 0 0 54 2 1 1 180 307 1 355 7 1 1.000000 116 242 0 52 2 0 0 0 0 54 2 -10.801650 1 1 0 0 1 0 2 2 2.036083 1 0.370000 1.920000 0.370000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 TP53 7157 broad.mit.edu 37 17 7578538 7578538 + Missense_Mutation SNP T T A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 T A T T Valid Somatic Phase_I WXS targeted Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr17:7578538T>A ENST00000269305.4 - 5 581 c.392A>T c.(391-393)aAc>aTc p.N131I TP53_ENST00000445888.2_Missense_Mutation_p.N131I|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.N131I|TP53_ENST00000420246.2_Missense_Mutation_p.N131I|TP53_ENST00000359597.4_Missense_Mutation_p.N131I|TP53_ENST00000413465.2_Missense_Mutation_p.N131I 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.0?(8)|p.N131del(8)|p.N131I(7)|p.Y126_K132delYSPALNK(6)|p.Y126_N131delYSPALN(3)|p.N131S(3)|p.N131fs*27(2)|p.V73fs*9(1)|p.S127fs*36(1)|p.A129_K132delALNK(1)|p.Y126fs*11(1)|p.S127_Q136del10(1)|p.L130_M133delLNKM(1)|p.A129_N131delALN(1)|p.L130fs*16(1)|p.N131T(1)|p.N38I(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) AAACATCTTGTTGAGGGCAGG 0.557000 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 47 Deletion - In frame(21)|Substitution - Missense(12)|Whole gene deletion(8)|Deletion - Frameshift(6) 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 . . . . . . . . . . T 23.3 4.405466 0.83230 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793 D;D;D;D;D;D;D;D 0.99804 -6.83;-6.83;-6.83;-6.83;-6.83;-6.83;-6.83;-6.83 5.48 5.48 0.80851 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 0.99757 0.9902 M 0.87547 2.89 0.80722 D 1 D;D;D;D;D;D;D 0.89917 1.0;1.0;0.999;0.998;1.0;1.0;1.0 D;D;D;D;D;D;D 0.97110 0.992;0.998;0.992;0.974;0.999;1.0;1.0 D 0.97125 0.9814 10 0.87932 D 0 -30.8858 13.8301 0.63375 0.0:0.0:0.0:1.0 . 92;131;131;38;131;131;131 B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. I 131;131;131;131;131;131;120;38;38;131 ENSP00000410739:N131I;ENSP00000352610:N131I;ENSP00000269305:N131I;ENSP00000398846:N131I;ENSP00000391127:N131I;ENSP00000391478:N131I;ENSP00000423862:N38I;ENSP00000424104:N131I ENSP00000269305:N131I N - 2 0 TP53 7519263 1.000000 0.71417 0.998000 0.56505 0.771000 0.43674 7.993000 0.88291 2.206000 0.71126 0.533000 0.62120 AAC TCGA-HV-A7OL-01A-11D-A33T-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 47 123 0 25 1 8.073882e-01 7 3 0 25 2 1 1 446 1549 1 2101 6 1 1.000000 47 122 0 25 2 0 0 0 0 25 2 -20.000000 1 1 0 0 1 0 1 1 1.652064 1 0.370000 1.920000 0.226994 0.950000 8.000000e-01 1.000000 0.990000 0.944132 0.950000 1 8.800000e-01 0.990000 DHRS7C 201140 broad.mit.edu 37 17 9684814 9684814 + Silent SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr17:9684814C>T ENST00000330255.5 - 2 264 c.252G>A c.(250-252)gtG>gtA p.V84V DHRS7C_ENST00000571134.1_Silent_p.V84V NM_001105571.2|NM_001220493.1 NP_001099041.1|NP_001207422.1 A6NNS2 DRS7C_HUMAN dehydrogenase/reductase (SDR family) member 7C 15 TGGGGTCAGCCACGCTGATCA 0.552000 0 SO:0001819 synonymous_variant ENST00000330255.5 1 1 hg19 CCDS56020.1 TCGA-HV-A7OL-01A-11D-A33T-08 DHRS7C-001 KNOWN NAGNAG_splice_site|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000439863.1 1 0 1 47 168 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 1.000000 47 167 0 34 2 0 0 0 0 34 2 -20.000000 1 1 0 0 1 0 1 1 1.652064 1 0.370000 1.920000 0.226994 0.890000 7.000000e-01 1.000000 0.950000 0.889379 0.890000 1 8.000000e-01 0.970000 ARHGAP28 79822 broad.mit.edu 37 18 6859874 6859874 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr18:6859874C>T ENST00000383472.4 + 5 808 c.704C>T c.(703-705)gCg>gTg p.A235V ARHGAP28_ENST00000532996.1_Missense_Mutation_p.A58V|ARHGAP28_ENST00000419673.2_Missense_Mutation_p.A76V|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.A71V|ARHGAP28_ENST00000400091.2_Missense_Mutation_p.A235V|ARHGAP28_ENST00000262227.3_Missense_Mutation_p.A183V|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.A76V|ARHGAP28_ENST00000418986.1_Missense_Mutation_p.A76V Q9P2N2 RHG28_HUMAN Rho GTPase activating protein 28 37 Colorectal(10;0.168) GGGAGTTTTGCGGTTCCCAGG 0.433000 0 SO:0001583 missense ENST00000383472.4 0 1 hg19 3 0.0013736263736263737 0 0.0 0 0.0 3 0.005244755244755245 0 0.0 C 8.061 0.768218 0.15983 . . ENSG00000088756 ENST00000400091;ENST00000262227;ENST00000419673;ENST00000531294;ENST00000314319;ENST00000418986;ENST00000532996;ENST00000383472 T;T;T;T;T;T 0.08102 3.3;3.25;3.2;3.2;3.2;3.13 4.44 0.19 0.15125 . 1.318330 0.04466 N 0.375305 T 0.03136 0.0092 N 0.08118 0 0.09310 N 1 B;B;B;B 0.12630 0.001;0.003;0.006;0.004 B;B;B;B 0.08055 0.001;0.001;0.001;0.003 T 0.42015 -0.9476 10 0.25106 T 0.35 . 7.004 0.24826 0.0:0.5813:0.0:0.4187 . 235;67;76;183 Q9P2N2;E9PRP2;F6VKJ9;Q9P2N2-2 RHG28_HUMAN;.;.;. V 235;183;76;71;76;76;67;58 ENSP00000382963:A235V;ENSP00000262227:A183V;ENSP00000392660:A76V;ENSP00000437262:A71V;ENSP00000313506:A76V;ENSP00000406907:A76V ENSP00000262227:A183V A + 2 0 ARHGAP28 6849874 0.000000 0.05858 0.001000 0.08648 0.625000 0.37756 0.379000 0.20585 0.014000 0.14944 0.563000 0.77884 GCG TCGA-HV-A7OL-01A-11D-A33T-08 ARHGAP28-006 NOVEL basic|appris_principal protein_coding protein_coding OTTHUMT00000442123.3 0 0 0 6 450 1 86 0 0 0 1 86 2 0 0 0 0 0 2 0 0.010173 6 449 1 85 18 0 0 0 1 86 2 -1.522654 0 1 121412 24 48 1 0 1 1 1.645085 1 0.370000 1.920000 0.226994 0.050000 2.000000e-02 0.120000 0.060000 0.066822 0.050000 0 3.000000e-02 0.090000 ANKRD12 23253 broad.mit.edu 37 18 9255365 9255365 + Silent SNP T T C TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr18:9255365T>C ENST00000262126.4 + 9 2340 c.2100T>C c.(2098-2100)ttT>ttC p.F700F ANKRD12_ENST00000400020.3_Silent_p.F677F|ANKRD12_ENST00000383440.2_Silent_p.F677F NM_015208.4 NP_056023.3 Q6UB98 ANR12_HUMAN ankyrin repeat domain 12 65 aagagaatttttttaaaagtg 0.279000 0 SO:0001819 synonymous_variant ENST00000262126.4 0 1 hg19 CCDS11843.1 TCGA-HV-A7OL-01A-11D-A33T-08 ANKRD12-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000254478.2 0 0 0 4 208 0 34 0 0 0 1 0 34 2 0 0 0 0 0 2 1 0.886663 4 204 0 33 2 0 0 0 0 34 2 -7.556165 1 1 0 0 1 0 1 1 1.645085 1 0.370000 1.920000 0.226994 0.080000 2.000000e-02 0.200000 0.080000 0.101276 0.080000 0 5.000000e-02 0.140000 ILF3 3609 broad.mit.edu 37 19 10793838 10793838 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr19:10793838G>A ENST00000590261.1 + 13 1574 c.1574G>A c.(1573-1575)gGc>gAc p.G525D ILF3_ENST00000318511.3_Missense_Mutation_p.G525D|ILF3_ENST00000420083.1_Missense_Mutation_p.G525D|ILF3_ENST00000588657.1_Missense_Mutation_p.G529D|ILF3_ENST00000449870.1_Missense_Mutation_p.G529D|ILF3_ENST00000589998.1_Missense_Mutation_p.G525D|ILF3_ENST00000592763.1_Missense_Mutation_p.G529D|ILF3_ENST00000250241.8_Missense_Mutation_p.G525D|ILF3_ENST00000407004.3_Missense_Mutation_p.G529D Q12906 ILF3_HUMAN interleukin enhancer binding factor 3, 90kDa 31 Epithelial(33;6.86e-06)|all cancers(31;1.65e-05) ACAAAGCACGGCAAGAACCCA 0.557000 0 SO:0001583 missense ENST00000590261.1 0 1 hg19 CCDS12246.1 . . . . . . . . . . G 33 5.288199 0.95517 . . ENSG00000129351 ENST00000336059;ENST00000449870;ENST00000318511;ENST00000420083;ENST00000407004;ENST00000250241 T;T;T;T;T 0.18174 2.28;2.23;2.26;2.31;2.26 5.83 5.83 0.93111 Double-stranded RNA-binding (2);Double-stranded RNA-binding-like (1); 0.113792 0.64402 D 0.000011 T 0.39572 0.1083 L 0.49126 1.545 0.80722 D 1 D;D;D;D;B;D 0.89917 1.0;0.998;0.999;0.999;0.176;0.992 D;D;D;D;B;P 0.91635 0.999;0.943;0.941;0.968;0.191;0.906 T 0.04467 -1.0949 10 0.87932 D 0 . 18.8865 0.92379 0.0:0.0:1.0:0.0 . 529;529;525;529;525;525 Q12906-4;G5E9M5;Q12906;Q12906-6;Q12906-2;Q12906-5 .;.;ILF3_HUMAN;.;.;. D 525;529;525;525;529;525 ENSP00000404121:G529D;ENSP00000315205:G525D;ENSP00000405436:G525D;ENSP00000384660:G529D;ENSP00000250241:G525D ENSP00000250241:G525D G + 2 0 ILF3 10654838 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 9.771000 0.98977 2.761000 0.94854 0.650000 0.86243 GGC TCGA-HV-A7OL-01A-11D-A33T-08 ILF3-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452074.1 0 0 0 5 597 1 89 0 1.289190e-03 0 65 1 89 5 0 0 0 0 0 2 0 0.000614 5 592 1 88 22 0 0 0 1 89 2 -2.687305 1 1 0 0 1 0 0 0 1.986796 0 0.370000 1.920000 0.355696 0.040000 0 0.100000 0.040000 0.052293 0.040000 0 2.000000e-02 0.070000 UPF1 5976 broad.mit.edu 37 19 18960909 18960909 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr19:18960909G>A ENST00000599848.1 + 4 696 c.487G>A c.(487-489)Gca>Aca p.A163T UPF1_ENST00000262803.5_Missense_Mutation_p.A163T|UPF1_ENST00000600310.1_3'UTR Q92900 RENT1_HUMAN UPF1 regulator of nonsense transcripts homolog (yeast) p.A163T(1) 40 CCTTGTGAGGGCAAAATGCAA 0.517000 1 Substitution - Missense(1) SO:0001583 missense ENST00000599848.1 0 1 hg19 . . . . . . . . . . G 29.5 5.014153 0.93404 . . ENSG00000005007 ENST00000262803 D 0.91237 -2.81 4.51 4.51 0.55191 RNA helicase UPF1, UPF2-interacting domain (1); 0.000000 0.85682 D 0.000000 D 0.94142 0.8121 M 0.86805 2.84 0.80722 D 1 P;P 0.41159 0.74;0.695 P;B 0.49301 0.606;0.415 D 0.95400 0.8489 10 0.87932 D 0 -16.0301 16.5553 0.84483 0.0:0.0:1.0:0.0 . 163;163 Q92900;Q92900-2 RENT1_HUMAN;. T 163 ENSP00000262803:A163T ENSP00000262803:A163T A + 1 0 UPF1 18821909 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 9.374000 0.97172 2.221000 0.72209 0.591000 0.81541 GCA TCGA-HV-A7OL-01A-11D-A33T-08 UPF1-002 KNOWN basic protein_coding protein_coding OTTHUMT00000464684.1 0 0 0 6 545 0 96 0 2.625662e-03 0 6 0 96 2 0 0 0 0 0 2 1 0.964745 6 543 0 96 2 0 0 0 0 96 2 -2.228895 0 1 0 0 1 0 0 0 1.986796 0 0.370000 1.920000 0.355696 0.050000 1.000000e-02 0.120000 0.060000 0.066717 0.050000 0 3.000000e-02 0.090000 PEPD 5184 broad.mit.edu 37 19 33991872 33991872 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr19:33991872G>A ENST00000244137.7 - 4 398 c.365C>T c.(364-366)gCc>gTc p.A122V PEPD_ENST00000397032.4_Missense_Mutation_p.A122V|PEPD_ENST00000436370.3_Intron NM_000285.3 NP_000276.2 P12955 PEPD_HUMAN peptidase D p.A122V(1) 17 Esophageal squamous(110;0.137) GTCGTCCACGGCATACTTCTC 0.557000 1 Substitution - Missense(1) SO:0001583 missense ENST00000244137.7 0 1 hg19 CCDS42544.1 . . . . . . . . . . G 12.87 2.068639 0.36470 . . ENSG00000124299 ENST00000244137;ENST00000397032 T;T 0.77098 -1.07;-1.07 5.39 5.39 0.77823 Peptidase M24B, X-Pro dipeptidase/aminopeptidase P N-terminal (1); 0.148969 0.64402 D 0.000010 T 0.74427 0.3715 L 0.58925 1.835 0.80722 D 1 B;B 0.17038 0.02;0.017 B;B 0.19666 0.026;0.009 T 0.69450 -0.5142 10 0.32370 T 0.25 -26.8327 14.6656 0.68904 0.0:0.0:1.0:0.0 . 122;122 A8MX47;P12955 .;PEPD_HUMAN V 122 ENSP00000244137:A122V;ENSP00000380226:A122V ENSP00000244137:A122V A - 2 0 PEPD 38683712 1.000000 0.71417 0.503000 0.27626 0.454000 0.32378 5.746000 0.68681 2.510000 0.84645 0.462000 0.41574 GCC TCGA-HV-A7OL-01A-11D-A33T-08 PEPD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000451432.3 0 0 0 6 682 0 101 0 4.522464e-02 0 32 0 101 2 0 0 0 0 0 2 1 0.964765 7 679 0 99 2 0 0 0 0 101 2 -2.172608 0 1 0 0 1 1 2 3 2.336832 1 0.370000 1.920000 0.453860 0.060000 1.000000e-02 1.000000 0.060000 0.187122 0.060000 0 3.000000e-02 0.120000 MAP4K1 11184 broad.mit.edu 37 19 39100239 39100239 + Missense_Mutation SNP A A G TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 A G A A Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr19:39100239A>G ENST00000591517.1 - 13 1031 c.1003T>C c.(1003-1005)Tgt>Cgt p.C335R MAP4K1_ENST00000396857.2_Missense_Mutation_p.C335R|MAP4K1_ENST00000589130.1_Missense_Mutation_p.C331R|MAP4K1_ENST00000589002.1_5'UTR|MAP4K1_ENST00000586296.1_Splice_Site_p.C335R|MAP4K1_ENST00000423454.2_5'UTR NM_007181.4 NP_009112.1 Q92918 M4K1_HUMAN mitogen-activated protein kinase kinase kinase kinase 1 44 all_cancers(60;6.42e-06)|Ovarian(47;0.103) Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272) TACTCACGACAGCAGTCTGCA 0.582000 0 SO:0001583 missense ENST00000591517.1 1 1 hg19 CCDS59385.1 . . . . . . . . . . . 10.01 1.234740 0.22626 . . ENSG00000104814 ENST00000396857;ENST00000221409 T 0.71341 -0.56 4.25 0.715 0.18186 Protein kinase-like domain (1); 0.941218 0.09011 N 0.861554 T 0.50769 0.1635 L 0.29908 0.895 0.29651 N 0.843925 B;B 0.21905 0.062;0.057 B;B 0.17979 0.02;0.014 T 0.40251 -0.9573 10 0.11794 T 0.64 . 3.8459 0.08934 0.4194:0.2013:0.0:0.3793 . 335;335 Q92918-2;Q92918 .;M4K1_HUMAN R 335 ENSP00000380066:C335R ENSP00000221409:C335R C - 1 0 MAP4K1 43792079 0.569000 0.26643 0.816000 0.32577 0.990000 0.78478 0.529000 0.23019 0.176000 0.19873 0.459000 0.35465 TGT TCGA-HV-A7OL-01A-11D-A33T-08 MAP4K1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000453390.1 1 0 1 43 99 0 18 0 9.926880e-01 0 21 0 18 2 0 0 0 0 0 2 1 1.000000 42 97 0 18 2 0 0 0 0 18 2 -20.000000 1 1 0 0 1 1 2 3 2.335928 1 0.370000 1.920000 0.462480 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 CEACAM4 1089 broad.mit.edu 37 19 42132119 42132119 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr19:42132119C>T ENST00000221954.2 - 2 390 c.280G>A c.(280-282)Gca>Aca p.A94T CEACAM4_ENST00000600925.1_Missense_Mutation_p.A94T NM_001817.2 NP_001808.2 O75871 CEAM4_HUMAN carcinoembryonic antigen-related cell adhesion molecule 4 p.A94T(1) 16 CCACTGTATGCGGCCCCTGGG 0.488000 1 Substitution - Missense(1) SO:0001583 missense ENST00000221954.2 0 1 hg19 CCDS33033.1 . . . . . . . . . . C 14.79 2.639939 0.47153 . . ENSG00000105352 ENST00000221954 T 0.66280 -0.2 1.76 1.76 0.24704 Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); . . . . T 0.76278 0.3965 M 0.84219 2.685 0.09310 N 1 D;D 0.89917 0.997;1.0 D;D 0.73380 0.921;0.98 T 0.61207 -0.7109 9 0.66056 D 0.02 . 6.9535 0.24558 0.0:1.0:0.0:0.0 . 94;94 E7EMX3;O75871 .;CEAM4_HUMAN T 94 ENSP00000221954:A94T ENSP00000221954:A94T A - 1 0 CEACAM4 46823959 0.000000 0.05858 0.009000 0.14445 0.015000 0.08874 0.618000 0.24373 1.281000 0.44480 0.205000 0.17691 GCA TCGA-HV-A7OL-01A-11D-A33T-08 CEACAM4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321148.1 0 0 0 8 1053 0 139 0 0 0 0 139 2 0 0 0 0 0 2 1 0.989154 8 1048 0 137 2 0 0 0 0 139 2 -1.550212 0 1 121412 4 41 1 1 2 3 2.386725 1 0.370000 1.920000 0.466689 0.040000 0 0.110000 0.060000 0.062851 0.040000 0 2.000000e-02 0.080000 TRPM4 54795 broad.mit.edu 37 19 49671336 49671336 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr19:49671336C>T ENST00000252826.5 + 4 556 c.430C>T c.(430-432)Cgg>Tgg p.R144W TRPM4_ENST00000427978.2_Missense_Mutation_p.R144W|TRPM4_ENST00000355712.5_Intron NM_017636.3 NP_060106.2 Q8TD43 TRPM4_HUMAN transient receptor potential cation channel, subfamily M, member 4 49 all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15) TGGGCTGGTGCGGGCTGCCCA 0.731000 0 SO:0001583 missense ENST00000252826.5 0 1 hg19 CCDS33073.1 . . . . . . . . . . C 19.72 3.880335 0.72294 2.27E-4 0.0 ENSG00000130529 ENST00000252826;ENST00000427978 T;T 0.03301 3.98;3.98 4.33 1.96 0.26148 . 0.086004 0.46442 D 0.000284 T 0.12050 0.0293 L 0.58101 1.795 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.72625 0.978;0.952 T 0.01537 -1.1330 10 0.87932 D 0 -31.9032 10.4113 0.44294 0.5303:0.4697:0.0:0.0 . 144;144 Q8TD43-3;Q8TD43 .;TRPM4_HUMAN W 144 ENSP00000252826:R144W;ENSP00000407492:R144W ENSP00000252826:R144W R + 1 2 TRPM4 54363148 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 2.336000 0.43938 1.142000 0.42291 0.491000 0.48974 CGG TCGA-HV-A7OL-01A-11D-A33T-08 TRPM4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000465543.2 0 0 0 5 476 0 70 0 3.346890e-02 0 22 0 70 2 0 0 0 0 0 2 1 0.936465 5 472 0 67 2 0 0 0 0 70 2 -3.189999 1 1 0 0 1 1 2 3 2.387095 1 0.370000 1.920000 0.468354 0.070000 1.000000e-02 0.150000 0.060000 0.079213 0.070000 0 4.000000e-02 0.110000 KLK7 5650 broad.mit.edu 37 19 51480876 51480876 + Silent SNP G G A rs17855561 TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr19:51480876G>A ENST00000391807.1 - 6 779 c.678C>T c.(676-678)tgC>tgT p.C226C KLK7_ENST00000597707.1_Silent_p.C154C|CTB-147C22.9_ENST00000594512.1_RNA|KLK7_ENST00000336317.4_Silent_p.C113C|KLK7_ENST00000595820.1_Silent_p.C226C NM_139277.2 NP_644806.1 P49862 KLK7_HUMAN kallikrein-related peptidase 7 p.C226C(1) 19 all_neural(266;0.026) TGGGTTGGCCGCAAGGGAAAG 0.517000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000391807.1 0 1 hg19 CCDS12812.1 TCGA-HV-A7OL-01A-11D-A33T-08 KLK7-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464344.1 0 0 0 6 605 0 76 1 9.920532e-01 2 928 0 76 2 0 0 0 0 0 2 1 0.964393 7 600 0 75 2 0 0 0 0 76 2 -2.042599 0 1 121412 108 52 1 1 2 3 2.387095 1 0.370000 1.920000 0.468354 0.060000 1.000000e-02 0.130000 0.060000 0.072931 0.060000 0 3.000000e-02 0.100000 ZNF581 51545 broad.mit.edu 37 19 56156512 56156512 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr19:56156512C>T ENST00000587252.1 + 2 848 c.575C>T c.(574-576)aCg>aTg p.T192M ZNF581_ENST00000270451.5_Missense_Mutation_p.T192M|CCDC106_ENST00000586790.1_5'Flank|ZNF581_ENST00000588537.1_Missense_Mutation_p.T192M|CCDC106_ENST00000308964.3_5'Flank Q9P0T4 ZN581_HUMAN zinc finger protein 581 3 Ovarian(87;0.133) BRCA - Breast invasive adenocarcinoma(297;0.18) CAGAAACACACGCGGTGGAAG 0.632000 0 SO:0001583 missense ENST00000587252.1 0 1 hg19 CCDS12932.1 . . . . . . . . . . C 11.98 1.800114 0.31869 . . ENSG00000171425 ENST00000270451 T 0.09538 2.97 3.5 0.0648 0.14354 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.05547 0.0146 N 0.00760 -1.21 0.24781 N 0.992819 D 0.67145 0.996 P 0.53649 0.731 T 0.36432 -0.9748 9 0.87932 D 0 . 6.9073 0.24315 0.0:0.4032:0.0:0.5968 . 192 Q9P0T4 ZN581_HUMAN M 192 ENSP00000270451:T192M ENSP00000270451:T192M T + 2 0 ZNF581 60848324 0.000000 0.05858 0.014000 0.15608 0.453000 0.32348 -0.054000 0.11826 -0.004000 0.14419 0.407000 0.27541 ACG TCGA-HV-A7OL-01A-11D-A33T-08 ZNF581-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000453430.1 0 0 0 5 447 0 54 0 4.887685e-01 0 131 0 54 2 0 0 0 0 0 2 1 0.934131 5 438 0 54 2 0 0 0 0 54 2 -4.772330 1 1 117088 2 33 1 1 2 3 2.365756 1 0.370000 1.920000 0.464172 0.070000 1.000000e-02 1.000000 0.070000 0.118474 0.070000 0 4.000000e-02 0.130000 TRIM28 10155 broad.mit.edu 37 19 59061796 59061796 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr19:59061796G>A ENST00000253024.5 + 17 2673 c.2384G>A c.(2383-2385)cGc>cAc p.R795H TRIM28_ENST00000341753.6_Missense_Mutation_p.R713H NM_005762.2 NP_005753.1 Q13263 TIF1B_HUMAN tripartite motif containing 28 19 all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184) TTCGAGACGCGCATGAACGAG 0.602000 0 SO:0001583 missense ENST00000253024.5 0 1 hg19 CCDS12985.1 . . . . . . . . . . G 15.09 2.729403 0.48833 . . ENSG00000130726 ENST00000253024;ENST00000341753 T;T 0.43688 0.94;0.94 5.06 2.95 0.34219 Bromodomain (2); 0.154547 0.40469 N 0.001086 T 0.28532 0.0706 L 0.27053 0.805 0.34967 D 0.752756 B;B;B 0.31054 0.306;0.01;0.204 B;B;B 0.31337 0.128;0.025;0.086 T 0.36939 -0.9727 10 0.46703 T 0.11 -21.0615 9.4971 0.38995 0.1711:0.0:0.8289:0.0 . 713;795;795 Q13263-2;B2R8R5;Q13263 .;.;TIF1B_HUMAN H 795;713 ENSP00000253024:R795H;ENSP00000342232:R713H ENSP00000253024:R795H R + 2 0 TRIM28 63753608 0.633000 0.27181 0.989000 0.46669 0.989000 0.77384 1.837000 0.39201 0.857000 0.35407 0.462000 0.41574 CGC TCGA-HV-A7OL-01A-11D-A33T-08 TRIM28-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000467074.1 0 0 0 5 616 0 64 0 9.965438e-01 1 1476 0 64 2 0 0 0 0 0 2 1 0.936701 5 612 0 64 2 0 0 0 0 64 2 -2.354596 0 1 121410 1 33 1 1 2 3 2.365756 1 0.370000 1.920000 0.464172 0.050000 0 1.000000 0.060000 0.096193 0.050000 0 2.000000e-02 0.090000 ADAM30 11085 broad.mit.edu 37 1 120438703 120438703 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr1:120438703C>T ENST00000369400.1 - 1 415 c.257G>A c.(256-258)cGa>cAa p.R86Q NM_021794.3 NP_068566.2 Q9UKF2 ADA30_HUMAN ADAM metallopeptidase domain 30 38 all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234) all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138) GCGCAGATGTCGGGGCAACAG 0.527000 0 SO:0001583 missense ENST00000369400.1 0 1 hg19 CCDS907.1 . . . . . . . . . . C 18.29 3.590440 0.66219 . . ENSG00000134249 ENST00000369400;ENST00000543066 T 0.05996 3.36 4.56 1.5 0.22942 Peptidase M12B, propeptide (1); 0.000000 0.32655 U 0.005818 T 0.04227 0.0117 L 0.60957 1.885 0.09310 N 1 P 0.52842 0.956 P 0.53490 0.727 T 0.27262 -1.0079 10 0.56958 D 0.05 . 2.9046 0.05716 0.1851:0.5349:0.1794:0.1006 . 86 Q9UKF2 ADA30_HUMAN Q 86 ENSP00000358407:R86Q ENSP00000358407:R86Q R - 2 0 ADAM30 120240226 0.000000 0.05858 0.000000 0.03702 0.968000 0.65278 -1.640000 0.02009 0.132000 0.18615 0.462000 0.41574 CGA TCGA-HV-A7OL-01A-11D-A33T-08 ADAM30-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033678.1 0 0 0 5 372 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 0.935273 5 366 0 58 2 0 0 0 0 58 2 -2.607044 1 1 0 0 1 1 2 3 2.069750 0 0.370000 1.920000 0.376916 0.070000 2.000000e-02 1.000000 0.080000 0.129063 0.070000 0 4.000000e-02 0.130000 AADACL3 126767 broad.mit.edu 37 1 12779503 12779503 + Missense_Mutation SNP C C G TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr1:12779503C>G ENST00000359318.5 + 2 229 c.24C>G c.(22-24)atC>atG p.I8M AADACL3_ENST00000332530.3_Intron NM_001103170.1 NP_001096640.1 Q5VUY0 ADCL3_HUMAN arylacetamide deacetylase-like 3 15 Ovarian(185;0.249) Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255) AGCTCAGAATCTGTTCTATGC 0.478000 0 SO:0001583 missense ENST00000359318.5 1 1 hg19 CCDS41253.1 . . . . . . . . . . C 13.02 2.112902 0.37242 . . ENSG00000188984 ENST00000359318 T 0.07114 3.22 4.44 4.44 0.53790 . 0.459980 0.21394 N 0.075257 T 0.25158 0.0611 M 0.77313 2.365 0.28056 N 0.933172 D 0.67145 0.996 D 0.63877 0.919 T 0.03121 -1.1070 10 0.72032 D 0.01 -22.8393 10.4714 0.44640 0.0:0.8025:0.1975:0.0 . 8 Q5VUY0 ADCL3_HUMAN M 8 ENSP00000352268:I8M ENSP00000352268:I8M I + 3 3 AADACL3 12702090 0.319000 0.24607 0.922000 0.36590 0.356000 0.29392 -0.363000 0.07593 2.307000 0.77673 0.491000 0.48974 ATC TCGA-HV-A7OL-01A-11D-A33T-08 AADACL3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000005324.2 1 0 1 181 861 0 144 0 0 0 0 144 2 0 0 0 0 0 2 1 1.000000 181 856 0 143 2 0 0 0 0 144 2 -20.000000 1 1 0 0 1 1 2 3 2.062195 0 0.370000 1.920000 0.375774 0.940000 8.200000e-01 1.000000 1.000000 0.943539 0.940000 1 8.800000e-01 1.000000 KPRP 448834 broad.mit.edu 37 1 152732580 152732580 + Silent SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr1:152732580C>T ENST00000606109.1 + 1 544 c.516C>T c.(514-516)tgC>tgT p.C172C KPRP_ENST00000368773.1_Silent_p.C172C Q5T749 KPRP_HUMAN keratinocyte proline-rich protein p.C172C(1) 60 Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.206) CTGCAGTGTGCCAGCCTCAGG 0.522000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000606109.1 0 1 hg19 CCDS30862.1 TCGA-HV-A7OL-01A-11D-A33T-08 KPRP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000034522.2 0 0 0 5 592 0 113 0 0 0 0 113 2 0 0 0 0 0 2 1 0.936111 5 587 0 110 2 0 0 0 0 113 2 -2.022659 0 1 0 0 1 1 2 3 2.054135 0 0.370000 1.920000 0.374628 0.040000 0 1.000000 0.040000 0.081509 0.040000 0 2.000000e-02 0.080000 C1orf110 339512 broad.mit.edu 37 1 162824686 162824686 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr1:162824686G>A ENST00000367910.1 - 4 898 c.778C>T c.(778-780)Cgg>Tgg p.R260W C1orf110_ENST00000367912.2_Intron|C1orf110_ENST00000524691.1_Intron|C1orf110_ENST00000367911.2_Intron NM_178550.4 NP_848645.3 Q86UF4 CA110_HUMAN chromosome 1 open reading frame 110 12 ACCCTGTGCCGGAGATAATGG 0.502000 0 SO:0001583 missense ENST00000367910.1 0 1 hg19 CCDS44269.1 . . . . . . . . . . G 14.23 2.474319 0.43942 . . ENSG00000185860 ENST00000367910 . . . 4.41 3.5 0.40072 . 0.000000 0.47455 D 0.000237 T 0.16599 0.0399 L 0.36672 1.1 0.34538 D 0.709987 P 0.46395 0.877 B 0.40901 0.343 T 0.04693 -1.0933 8 0.49607 T 0.09 -7.6072 8.1269 0.31003 0.1093:0.0:0.8907:0.0 . 260 Q86UF4 CA110_HUMAN W 260 . ENSP00000356886:R260W R - 1 2 C1orf110 161091310 1.000000 0.71417 0.991000 0.47740 0.269000 0.26545 1.845000 0.39279 1.051000 0.40369 0.655000 0.94253 CGG TCGA-HV-A7OL-01A-11D-A33T-08 C1orf110-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083211.2 0 0 0 4 354 0 64 0 0 0 1 0 64 2 0 0 0 0 0 2 1 0.888972 4 351 0 64 2 0 0 0 0 64 2 -2.885578 1 1 120816 6 41 1 1 2 3 2.060271 0 0.370000 1.920000 0.375774 0.060000 1.000000e-02 1.000000 0.060000 0.110471 0.060000 0 3.000000e-02 0.120000 MIA3 375056 broad.mit.edu 37 1 222802593 222802593 + Silent SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr1:222802593C>T ENST00000344922.5 + 4 2056 c.2031C>T c.(2029-2031)ctC>ctT p.L677L MIA3_ENST00000344507.1_Intron|MIA3_ENST00000344441.6_Silent_p.L677L|MIA3_ENST00000470521.1_3'UTR NM_198551.2 NP_940953.2 Q5JRA6 MIA3_HUMAN melanoma inhibitory activity family, member 3 p.L677L(1) 80 AGATAAGGCTCTCTGAGGGAG 0.488000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000344922.5 1 1 hg19 CCDS41470.1 . . . . . . . . . . C 2.388 -0.340457 0.05243 . . ENSG00000154305 ENST00000354906 T 0.19806 2.12 4.36 -6.82 0.01698 . . . . . T 0.06690 0.0171 . . . 0.09310 N 0.999999 . . . . . . T 0.34354 -0.9832 6 0.10111 T 0.7 . 3.8314 0.08876 0.0778:0.2549:0.3136:0.3537 . . . . F 260 ENSP00000355062:L260F ENSP00000355062:L260F L + 1 0 MIA3 220869216 0.000000 0.05858 0.000000 0.03702 0.020000 0.10135 -5.357000 0.00128 -2.045000 0.00910 -2.178000 0.00318 CTC TCGA-HV-A7OL-01A-11D-A33T-08 MIA3-001 NOVEL basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000091489.4 1 0 1 90 438 0 86 0 0 0 0 86 2 0 0 0 0 0 2 1 1.000000 90 435 0 86 2 0 0 0 0 86 2 -20.000000 1 1 0 0 1 1 2 3 2.055428 0 0.370000 1.920000 0.374628 0.920000 7.500000e-01 1.000000 1.000000 0.922388 0.920000 1 8.300000e-01 1.000000 OR11L1 391189 broad.mit.edu 37 1 248004586 248004586 + Missense_Mutation SNP C C A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr1:248004586C>A ENST00000355784.2 - 1 668 c.613G>T c.(613-615)Gcc>Tcc p.A205S NM_001001959.1 NP_001001959.1 Q8NGX0 O11L1_HUMAN olfactory receptor, family 11, subfamily L, member 1 p.A205S(1) 57 all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858) OV - Ovarian serous cystadenocarcinoma(106;0.0319) CACAGCACGGCAATTGACAGG 0.478000 1 Substitution - Missense(1) SO:0001583 missense ENST00000355784.2 1 1 hg19 CCDS31098.1 . . . . . . . . . . C 10.61 1.399533 0.25291 . . ENSG00000197591 ENST00000355784 T 0.37058 1.22 4.27 3.35 0.38373 GPCR, rhodopsin-like superfamily (1); 0.000000 0.34268 U 0.004118 T 0.25494 0.0620 N 0.17312 0.475 0.09310 N 1 P 0.42993 0.797 P 0.47346 0.544 T 0.04495 -1.0947 10 0.46703 T 0.11 . 5.0642 0.14574 0.0:0.5142:0.2962:0.1896 . 205 Q8NGX0 O11L1_HUMAN S 205 ENSP00000348033:A205S ENSP00000348033:A205S A - 1 0 OR11L1 246071209 0.000000 0.05858 0.013000 0.15412 0.246000 0.25737 -0.791000 0.04599 1.145000 0.42336 0.543000 0.68304 GCC TCGA-HV-A7OL-01A-11D-A33T-08 OR11L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096850.1 0 0 0 18 432 0 80 0 0 0 0 80 2 0 0 0 0 0 2 1 0.999981 19 425 0 79 2 0 0 0 0 80 2 -4.268643 1 1 0 0 1 1 2 3 2.045144 0 0.370000 1.920000 0.372322 0.210000 1.300000e-01 0.350000 0.220000 0.234777 0.210000 0 1.700000e-01 0.280000 CSF3R 1441 broad.mit.edu 37 1 36939177 36939177 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr1:36939177C>T ENST00000373106.1 - 6 1079 c.532G>A c.(532-534)Gtg>Atg p.V178M CSF3R_ENST00000361632.4_Missense_Mutation_p.V178M|CSF3R_ENST00000440588.2_Missense_Mutation_p.V178M|CSF3R_ENST00000418048.2_Missense_Mutation_p.V178M|CSF3R_ENST00000373103.1_Missense_Mutation_p.V178M|CSF3R_ENST00000331941.5_Missense_Mutation_p.V178M|CSF3R_ENST00000338937.5_Missense_Mutation_p.V178M|CSF3R_ENST00000373104.1_Missense_Mutation_p.V178M|CSF3R_ENST00000487540.2_5'Flank NM_000760.3 NP_000751.1 Q99062 CSF3R_HUMAN colony stimulating factor 3 receptor (granulocyte) 38 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) Filgrastim(DB00099)|Pegfilgrastim(DB00019) TCCTTGGGCACGCAGTCCAGG 0.607000 0 SO:0001583 missense ENST00000373106.1 1 1 hg19 CCDS413.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 C 7.097 0.573316 0.13623 . . ENSG00000119535 ENST00000373106;ENST00000373104;ENST00000373103;ENST00000361632;ENST00000331941;ENST00000418048;ENST00000338937;ENST00000440588 T;T;T;T;T;T;T;T 0.37058 1.22;1.22;1.22;1.22;1.22;1.22;1.22;1.22 5.22 -0.00103 0.14035 Fibronectin, type III (3);Immunoglobulin-like fold (1); 1.150820 0.06140 N 0.672141 T 0.21881 0.0527 L 0.31664 0.95 0.24342 N 0.99496 D;D;P;P 0.54047 0.964;0.958;0.929;0.723 B;B;B;B 0.36418 0.224;0.174;0.084;0.069 T 0.25606 -1.0127 10 0.34782 T 0.22 -5.3635 7.0679 0.25161 0.0:0.3842:0.0:0.6158 . 178;178;178;178 E1B6W6;Q99062-3;Q99062;Q99062-4 .;.;CSF3R_HUMAN;. M 178 ENSP00000362198:V178M;ENSP00000362196:V178M;ENSP00000362195:V178M;ENSP00000355406:V178M;ENSP00000332180:V178M;ENSP00000401588:V178M;ENSP00000345013:V178M;ENSP00000397568:V178M ENSP00000332180:V178M V - 1 0 CSF3R 36711764 0.188000 0.23250 0.026000 0.17262 0.003000 0.03518 0.000000 0.12993 0.159000 0.19401 -0.192000 0.12808 GTG TCGA-HV-A7OL-01A-11D-A33T-08 CSF3R-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000021997.2 1 0 1 61 254 0 54 0 1.750327e-01 0 4 0 54 2 0 0 0 0 0 2 1 1.000000 61 251 0 53 2 0 0 0 0 54 2 -20.000000 1 1 121412 7 37 1 1 2 3 2.069750 0 0.370000 1.920000 0.376916 0.990000 8.300000e-01 1.000000 1.000000 0.978602 0.990000 1 9.400000e-01 1.000000 ZC3H12A 80149 broad.mit.edu 37 1 37947303 37947303 + Missense_Mutation SNP A A G TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr1:37947303A>G ENST00000373087.6 + 4 801 c.685A>G c.(685-687)Att>Gtt p.I229V NM_025079.2 NP_079355.2 zinc finger CCCH-type containing 12A 21 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) CGACAGATTCATTGTGAAGCT 0.572000 0 SO:0001583 missense ENST00000373087.6 1 1 hg19 CCDS417.1 . . . . . . . . . . A 26.6 4.753618 0.89753 . . ENSG00000163874 ENST00000373087;ENST00000373082 T 0.56776 0.44 5.8 5.8 0.92144 Ribonuclease Zc3h12a-like (1); 0.000000 0.85682 D 0.000000 T 0.69833 0.3155 M 0.66939 2.045 0.80722 D 1 P 0.51351 0.944 D 0.64042 0.921 T 0.71258 -0.4646 10 0.54805 T 0.06 -24.1349 16.1549 0.81657 1.0:0.0:0.0:0.0 . 229 Q5D1E8 ZC12A_HUMAN V 229 ENSP00000362179:I229V ENSP00000362174:I229V I + 1 0 ZC3H12A 37719890 1.000000 0.71417 1.000000 0.80357 0.891000 0.51852 9.281000 0.95811 2.209000 0.71365 0.533000 0.62120 ATT TCGA-HV-A7OL-01A-11D-A33T-08 ZC3H12A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000012154.2 1 0 1 97 398 0 79 1 6.120596e-01 5 5 0 79 2 0 0 0 0 0 2 1 1.000000 97 395 0 79 2 0 0 0 0 79 2 -20.000000 1 1 0 0 1 1 2 3 2.069750 0 0.370000 1.920000 0.376916 0.990000 8.800000e-01 1.000000 1.000000 0.988538 0.990000 1 9.700000e-01 1.000000 ADA 100 broad.mit.edu 37 20 43257762 43257762 + Silent SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr20:43257762G>A ENST00000372874.4 - 3 278 c.144C>T c.(142-144)aaC>aaT p.N48N ADA_ENST00000537820.1_Silent_p.N48N|ADA_ENST00000464097.1_5'Flank NM_000022.2 NP_000013.2 P00813 ADA_HUMAN adenosine deaminase 18 all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122) COAD - Colon adenocarcinoma(18;0.00189) Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194) TGCCAATGACGTTCAGCAGCC 0.592000 Adenosine Deaminase Deficiency 0 SO:0001819 synonymous_variant Familial Cancer Database Severe Combined Immunodeficiency (SCID) due to ADA-deficiency ENST00000372874.4 0 1 hg19 CCDS13335.1 TCGA-HV-A7OL-01A-11D-A33T-08 ADA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080509.2 0 0 0 6 443 0 64 0 1.023690e-01 0 34 0 64 2 0 0 0 0 0 2 1 0.963727 5 439 0 64 2 0 0 0 0 64 2 -3.023610 1 1 121412 22 45 1 0 0 0 2.007960 0 0.370000 1.920000 0.365303 0.070000 2.000000e-02 0.150000 0.080000 0.082965 0.070000 0 4.000000e-02 0.110000 PABPC1L 80336 broad.mit.edu 37 20 43545506 43545506 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr20:43545506G>A ENST00000217073.2 + 3 497 c.497G>A c.(496-498)cGc>cAc p.R166H PABPC1L_ENST00000255136.3_Missense_Mutation_p.R166H|PABPC1L_ENST00000217074.4_Missense_Mutation_p.R166H|PABPC1L_ENST00000537323.1_Missense_Mutation_p.R166H Q4VXU2 PAP1L_HUMAN poly(A) binding protein, cytoplasmic 1-like p.R166H(1) 20 CTGAATGACCGCAAAGTGTGA 0.592000 1 Substitution - Missense(1) SO:0001583 missense ENST00000217073.2 0 1 hg19 CCDS42878.1 . . . . . . . . . . G 19.71 3.878785 0.72294 . . ENSG00000101104 ENST00000217074;ENST00000255136;ENST00000537323;ENST00000217073 D;D;D;D 0.92595 -3.07;-3.07;-3.07;-3.07 5.11 4.15 0.48705 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3); 0.000000 0.85682 D 0.000000 D 0.88618 0.6485 M 0.70787 2.145 0.58432 D 0.999999 P 0.43431 0.807 B 0.28638 0.092 D 0.90597 0.4541 10 0.66056 D 0.02 . 13.9611 0.64180 0.0751:0.0:0.9249:0.0 . 166 Q4VXU2 PAP1L_HUMAN H 166 ENSP00000217074:R166H;ENSP00000255136:R166H;ENSP00000445661:R166H;ENSP00000217073:R166H ENSP00000217073:R166H R + 2 0 PABPC1L 42978920 1.000000 0.71417 1.000000 0.80357 0.948000 0.59901 7.896000 0.87350 2.375000 0.81037 0.563000 0.77884 CGC TCGA-HV-A7OL-01A-11D-A33T-08 PABPC1L-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000127816.2 0 0 0 7 450 0 70 0 0 0 1 0 70 2 0 0 0 0 0 2 1 0.979840 7 444 0 68 2 0 0 0 0 70 2 -2.123705 0 1 0 0 1 0 0 0 2.007960 0 0.370000 1.920000 0.365303 0.080000 3.000000e-02 0.160000 0.080000 0.093162 0.080000 0 5.000000e-02 0.120000 RASSF2 9770 broad.mit.edu 37 20 4771183 4771183 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr20:4771183G>A ENST00000379400.3 - 7 646 c.451C>T c.(451-453)Cgc>Tgc p.R151C RASSF2_ENST00000478553.1_5'UTR|RASSF2_ENST00000379376.2_Missense_Mutation_p.R151C NM_014737.2 NP_055552.1 P50749 RASF2_HUMAN Ras association (RalGDS/AF-6) domain family member 2 34 TTGCCACGGCGACGCACCCCA 0.592000 Melanoma(158;1891 3343 50738) 0 SO:0001583 missense ENST00000379400.3 1 1 hg19 CCDS13083.1 . . . . . . . . . . G 21.1 4.097623 0.76870 . . ENSG00000101265 ENST00000379400;ENST00000379376 T;T 0.16897 2.31;2.31 5.2 5.2 0.72013 . 0.000000 0.85682 D 0.000000 T 0.44329 0.1288 M 0.85041 2.73 0.80722 D 1 D 0.89917 1.0 D 0.70716 0.97 T 0.45381 -0.9265 10 0.87932 D 0 . 12.5495 0.56218 0.0:0.0:0.8336:0.1664 . 151 P50749 RASF2_HUMAN C 151 ENSP00000368710:R151C;ENSP00000368684:R151C ENSP00000368684:R151C R - 1 0 RASSF2 4719183 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 4.709000 0.61867 2.706000 0.92434 0.563000 0.77884 CGC TCGA-HV-A7OL-01A-11D-A33T-08 RASSF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077828.1 1 0 1 54 154 0 25 0 6.885451e-02 0 2 0 25 2 0 0 0 0 0 2 1 1.000000 54 152 0 25 2 0 0 0 0 25 2 -20.000000 1 1 121410 12 38 1 0 0 0 2.007960 0 0.370000 1.920000 0.365303 0.990000 9.900000e-01 1.000000 1.000000 0.999802 0.990000 1 9.900000e-01 1.000000 ZNF217 7764 broad.mit.edu 37 20 52198591 52198591 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr20:52198591G>A ENST00000371471.2 - 2 1200 c.775C>T c.(775-777)Ccg>Tcg p.P259S ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Missense_Mutation_p.P259S O75362 ZN217_HUMAN zinc finger protein 217 50 all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398) BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198) CTCGAGGACGGCATTCCTCCT 0.512000 0 SO:0001583 missense ENST00000371471.2 0 1 hg19 CCDS13443.1 . . . . . . . . . . G 1.632 -0.518688 0.04171 . . ENSG00000171940 ENST00000371471;ENST00000302342 T;T 0.08634 3.07;3.07 5.46 -0.716 0.11212 . 0.952709 0.08770 N 0.896438 T 0.05686 0.0149 L 0.33485 1.01 0.09310 N 1 B 0.12630 0.006 B 0.15052 0.012 T 0.43734 -0.9373 10 0.33141 T 0.24 -5.7251 2.3642 0.04315 0.1675:0.1085:0.1954:0.5286 . 259 O75362 ZN217_HUMAN S 259 ENSP00000360526:P259S;ENSP00000304308:P259S ENSP00000304308:P259S P - 1 0 ZNF217 51631998 0.000000 0.05858 0.000000 0.03702 0.074000 0.17049 -0.254000 0.08781 0.235000 0.21160 0.591000 0.81541 CCG TCGA-HV-A7OL-01A-11D-A33T-08 ZNF217-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079757.2 0 0 0 6 735 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 0.963714 6 726 0 95 2 0 0 0 0 95 2 -2.016677 0 1 121412 1 41 1 0 0 0 2.007960 0 0.370000 1.920000 0.365303 0.040000 0 0.090000 0.040000 0.050421 0.040000 0 2.000000e-02 0.070000 ADRM1 11047 broad.mit.edu 37 20 60883799 60883799 + Missense_Mutation SNP G G T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr20:60883799G>T ENST00000253003.2 + 10 1252 c.1206G>T c.(1204-1206)gaG>gaT p.E402D RP11-157P1.4_ENST00000414042.1_RNA|LAMA5_ENST00000492698.1_Intron NM_007002.2|NM_175573.1 NP_008933.2|NP_783163.1 Q16186 ADRM1_HUMAN adhesion regulating molecule 1 5 Breast(26;7.76e-09) BRCA - Breast invasive adenocarcinoma(19;2.51e-06) ACGAAGAGGAGGACATGAGCC 0.557000 0 SO:0001583 missense ENST00000253003.2 1 1 hg19 CCDS13496.1 . . . . . . . . . . G 22.6 4.311241 0.81358 . . ENSG00000130706 ENST00000253003 . . . 5.74 -2.65 0.06095 . 0.000000 0.85682 D 0.000000 T 0.63988 0.2558 L 0.42581 1.335 0.80722 D 1 P 0.34699 0.464 P 0.53760 0.734 T 0.58847 -0.7564 9 0.31617 T 0.26 -32.0816 11.5512 0.50721 0.6719:0.0:0.3281:0.0 . 402 Q16186 ADRM1_HUMAN D 402 . ENSP00000253003:E402D E + 3 2 ADRM1 60317194 0.989000 0.36119 0.990000 0.47175 0.735000 0.41995 0.312000 0.19397 -0.272000 0.09259 0.561000 0.74099 GAG TCGA-HV-A7OL-01A-11D-A33T-08 ADRM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080007.1 1 0 1 32 168 0 28 1 1 296 637 0 28 2 0 0 0 0 0 2 1 1.000000 32 165 0 28 2 0 0 0 0 28 2 -3.357177 1 1 0 0 1 0 0 0 2.007960 0 0.370000 1.920000 0.365303 0.850000 6.100000e-01 1.000000 1.000000 0.854956 0.850000 1 7.200000e-01 1.000000 ADRM1 11047 broad.mit.edu 37 20 60883800 60883800 + Missense_Mutation SNP G G T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr20:60883800G>T ENST00000253003.2 + 10 1253 c.1207G>T c.(1207-1209)Gac>Tac p.D403Y RP11-157P1.4_ENST00000414042.1_RNA|LAMA5_ENST00000492698.1_Intron NM_007002.2|NM_175573.1 NP_008933.2|NP_783163.1 Q16186 ADRM1_HUMAN adhesion regulating molecule 1 5 Breast(26;7.76e-09) BRCA - Breast invasive adenocarcinoma(19;2.51e-06) CGAAGAGGAGGACATGAGCCT 0.562000 0 SO:0001583 missense ENST00000253003.2 1 1 hg19 CCDS13496.1 . . . . . . . . . . G 24.9 4.579440 0.86645 . . ENSG00000130706 ENST00000253003 . . . 5.74 4.78 0.61160 . 0.000000 0.85682 D 0.000000 T 0.76630 0.4014 M 0.73598 2.24 0.80722 D 1 D 0.61697 0.99 P 0.60415 0.874 T 0.80518 -0.1347 9 0.72032 D 0.01 -31.7805 16.5253 0.84329 0.0:0.131:0.869:0.0 . 403 Q16186 ADRM1_HUMAN Y 403 . ENSP00000253003:D403Y D + 1 0 ADRM1 60317195 1.000000 0.71417 0.999000 0.59377 0.745000 0.42441 9.313000 0.96297 1.414000 0.47017 0.561000 0.74099 GAC TCGA-HV-A7OL-01A-11D-A33T-08 ADRM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080007.1 1 0 1 32 160 0 28 1 1 295 642 0 28 2 0 0 0 0 0 2 1 1.000000 32 157 0 28 2 0 0 0 0 28 2 -18.388050 1 1 0 0 1 0 0 0 2.007960 0 0.370000 1.920000 0.365303 0.890000 6.300000e-01 1.000000 1.000000 0.881670 0.890000 1 7.500000e-01 1.000000 C20orf195 79025 broad.mit.edu 37 20 62187669 62187669 + Missense_Mutation SNP C C T rs117659219 byFrequency TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr20:62187669C>T ENST00000370098.3 + 2 745 c.653C>T c.(652-654)gCg>gTg p.A218V C20orf195_ENST00000370097.1_Missense_Mutation_p.A218V NM_024059.2 NP_076964.1 Q9BVV2 CT195_HUMAN chromosome 20 open reading frame 195 7 all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13) Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06) AAGGCGTCGGCGGCTCACCAG 0.622000 0 SO:0001583 missense ENST00000370098.3 1 1 hg19 CCDS13526.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 C 2.207 -0.381718 0.04966 0.0 6.98E-4 ENSG00000125531 ENST00000370098;ENST00000370097 . . . 5.47 3.22 0.36961 Fibronectin, type III (1);Immunoglobulin-like fold (1); 0.731967 0.11933 N 0.515501 T 0.13030 0.0316 N 0.02539 -0.55 0.24278 N 0.995215 B 0.02656 0.0 B 0.01281 0.0 T 0.28267 -1.0049 9 0.02654 T 1 -20.5053 9.1521 0.36969 0.0:0.1496:0.0:0.8504 . 218 Q9BVV2 CT195_HUMAN V 218 . ENSP00000359115:A218V A + 2 0 C20orf195 61658113 1.000000 0.71417 0.996000 0.52242 0.671000 0.39405 2.401000 0.44513 0.393000 0.25203 -0.302000 0.09304 GCG TCGA-HV-A7OL-01A-11D-A33T-08 C20orf195-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080155.1 1 0 1 187 915 0 200 1 3.399351e-01 4 3 0 200 2 0 0 0 0 0 2 1 1.000000 184 900 0 197 2 0 0 0 0 200 2 -5.567785 1 1 121380 22 50 1 0 0 0 2.007960 0 0.370000 1.920000 0.365303 0.900000 7.900000e-01 1.000000 1.000000 0.909969 0.900000 1 8.400000e-01 0.970000 UMODL1 89766 broad.mit.edu 37 21 43543258 43543258 + Missense_Mutation SNP A A C TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr21:43543258A>C ENST00000408910.2 + 17 3145 c.3145A>C c.(3145-3147)Agc>Cgc p.S1049R UMODL1_ENST00000400427.1_Missense_Mutation_p.S1105R|UMODL1_ENST00000408989.2_Missense_Mutation_p.S1177R|UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000400424.2_Missense_Mutation_p.S977R NM_001004416.2 NP_001004416 Q5DID0 UROL1_HUMAN uromodulin-like 1 47 CCTCATGCAGAGCGTAAGACC 0.622000 Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435) 0 SO:0001583 missense ENST00000408910.2 1 1 hg19 CCDS42936.1 . . . . . . . . . . A 13.74 2.328296 0.41197 . . ENSG00000177398 ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910 T;T;T;T 0.80994 -1.44;-1.44;-1.44;-1.44 3.13 3.13 0.36017 Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3); 0.506608 0.16330 N 0.219167 D 0.84772 0.5546 L 0.52266 1.64 0.38979 D 0.958909 D;D 0.76494 0.999;0.999 D;D 0.73708 0.976;0.981 D 0.83927 0.0304 9 . . . -11.4154 10.9262 0.47191 1.0:0.0:0.0:0.0 . 1177;1049 Q5DID0-2;Q5DID0 .;UROL1_HUMAN R 1105;977;1177;1049 ENSP00000383279:S1105R;ENSP00000383276:S977R;ENSP00000386126:S1177R;ENSP00000386147:S1049R . S + 1 0 UMODL1 42416327 1.000000 0.71417 0.959000 0.39883 0.192000 0.23643 4.772000 0.62324 1.674000 0.50907 0.260000 0.18958 AGC TCGA-HV-A7OL-01A-11D-A33T-08 UMODL1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195292.2 1 0 1 30 166 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 1.000000 30 165 0 32 2 0 0 0 0 32 2 -20.000000 1 1 0 0 1 1 2 3 2.037550 0 0.370000 1.920000 0.371163 0.820000 5.800000e-01 1.000000 1.000000 0.830640 0.820000 0 6.900000e-01 0.980000 ODC1 4953 broad.mit.edu 37 2 10583672 10583672 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr2:10583672C>T ENST00000234111.4 - 7 1120 c.610G>A c.(610-612)Gat>Aat p.D204N ODC1_ENST00000446285.1_5'Flank|ODC1_ENST00000405333.1_Missense_Mutation_p.D204N NM_002539.1 NP_002530.1 P11926 DCOR_HUMAN ornithine decarboxylase 1 19 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Spermine(DB00127) GTCTCAGGATCGGTACAGCCG 0.478000 0 SO:0001583 missense ENST00000234111.4 1 1 hg19 CCDS1672.1 . . . . . . . . . . C 21.6 4.174909 0.78564 . . ENSG00000115758 ENST00000234111;ENST00000405333;ENST00000537630 T;T 0.52754 0.65;0.65 5.79 4.88 0.63580 Orn/DAP/Arg decarboxylase 2, N-terminal (1); 0.000000 0.85682 D 0.000000 T 0.48447 0.1500 L 0.61218 1.895 0.80722 D 1 B 0.06786 0.001 B 0.12837 0.008 T 0.46512 -0.9186 10 0.51188 T 0.08 . 16.9563 0.86260 0.0:0.873:0.127:0.0 . 204 P11926 DCOR_HUMAN N 204;204;75 ENSP00000234111:D204N;ENSP00000385333:D204N ENSP00000234111:D204N D - 1 0 ODC1 10501123 1.000000 0.71417 0.912000 0.35992 0.934000 0.57294 4.734000 0.62043 2.746000 0.94184 0.655000 0.94253 GAT TCGA-HV-A7OL-01A-11D-A33T-08 ODC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206896.2 0 0 1 83 469 1 94 1 9.934840e-01 13 67 1 94 5 0 0 0 0 0 2 1 1.000000 82 465 1 94 19 0 0 0 1 94 2 -3.222531 1 1 121412 9 43 1 1 2 3 2.038702 0 0.370000 1.920000 0.371163 0.810000 6.500000e-01 0.990000 0.810000 0.818004 0.810000 0 7.300000e-01 0.900000 FOXD4L1 200350 broad.mit.edu 37 2 114257073 114257073 + Silent SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr2:114257073C>T ENST00000306507.5 + 1 413 c.240C>T c.(238-240)agC>agT p.S80S NM_012184.4 NP_036316.1 Q9NU39 FX4L1_HUMAN forkhead box D4-like 1 26 GCGGCCCGAGCGACCCCTCAG 0.697000 0 SO:0001819 synonymous_variant ENST00000306507.5 0 1 hg19 CCDS2117.1 TCGA-HV-A7OL-01A-11D-A33T-08 FOXD4L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254148.1 0 0 0 6 433 1 77 0 0 0 1 77 2 0 0 0 0 0 2 0 0.017749 6 346 1 92 14 0 0 0 1 77 2 -1.988555 0 1 117044 20 31 1 1 2 3 2.038702 0 0.370000 1.920000 0.371163 0.070000 2.000000e-02 0.160000 0.080000 0.085640 0.070000 0 4.000000e-02 0.120000 GORASP2 26003 broad.mit.edu 37 2 171818252 171818252 + Silent SNP A A C TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr2:171818252A>C ENST00000234160.4 + 8 1718 c.903A>C c.(901-903)acA>acC p.T301T GORASP2_ENST00000493692.1_3'UTR|GORASP2_ENST00000452526.2_Silent_p.T313T NM_001201428.1|NM_015530.4 NP_001188357.1|NP_056345.3 Q9H8Y8 GORS2_HUMAN golgi reassembly stacking protein 2, 55kDa 14 CAGCTACTACATTACCAGGTA 0.393000 0 SO:0001819 synonymous_variant ENST00000234160.4 1 1 hg19 CCDS33325.1 TCGA-HV-A7OL-01A-11D-A33T-08 GORASP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000333719.2 1 0 1 107 470 0 96 1 9.999999e-01 34 65 0 96 2 0 0 0 0 0 2 1 1.000000 104 467 0 95 2 0 0 0 0 96 2 -20.000000 1 1 0 0 1 1 2 3 2.038702 0 0.370000 1.920000 0.371163 0.990000 8.300000e-01 1.000000 1.000000 0.968573 0.990000 1 9.100000e-01 1.000000 SPHKAP 80309 broad.mit.edu 37 2 228855826 228855826 + Missense_Mutation SNP G G T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr2:228855826G>T ENST00000392056.3 - 11 4895 c.4849C>A c.(4849-4851)Cca>Aca p.P1617T SPHKAP_ENST00000344657.5_Missense_Mutation_p.P1588T NM_001142644.1 NP_001136116.1 Q2M3C7 SPKAP_HUMAN SPHK1 interactor, AKAP domain containing 185 Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23) GGACACTCTGGCTCCAGGTCA 0.557000 0 SO:0001583 missense ENST00000392056.3 1 1 hg19 CCDS46537.1 . . . . . . . . . . G 20.8 4.053706 0.75960 . . ENSG00000153820 ENST00000392056;ENST00000344657 T;T 0.05996 3.36;3.36 6.17 6.17 0.99709 A-kinase anchor 110kDa, C-terminal (1); 0.167578 0.52532 D 0.000066 T 0.24353 0.0590 M 0.78049 2.395 0.48341 D 0.999631 D;D 0.76494 0.999;0.999 D;D 0.74674 0.961;0.984 T 0.00043 -1.2223 10 0.44086 T 0.13 . 13.0796 0.59107 0.0723:0.0:0.9277:0.0 . 1617;1588 Q2M3C7;Q2M3C7-2 SPKAP_HUMAN;. T 1617;1588 ENSP00000375909:P1617T;ENSP00000339886:P1588T ENSP00000339886:P1588T P - 1 0 SPHKAP 228564070 1.000000 0.71417 1.000000 0.80357 0.909000 0.53808 4.992000 0.63889 2.941000 0.99782 0.655000 0.94253 CCA TCGA-HV-A7OL-01A-11D-A33T-08 SPHKAP-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000331750.1 1 0 1 67 263 0 33 0 0 0 0 33 2 0 0 0 0 0 2 1 1.000000 66 261 0 33 2 0 0 0 0 33 2 -20.000000 1 1 121406 1 31 1 0 0 0 2.022532 0 0.370000 1.920000 0.367660 0.990000 8.600000e-01 1.000000 1.000000 0.987004 0.990000 1 9.700000e-01 1.000000 ATL2 64225 broad.mit.edu 37 2 38525479 38525479 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr2:38525479G>A ENST00000378954.4 - 12 1440 c.1439C>T c.(1438-1440)gCg>gTg p.A480V ATL2_ENST00000402054.1_Missense_Mutation_p.A309V|ATL2_ENST00000546051.1_Missense_Mutation_p.A309V|ATL2_ENST00000406122.1_Missense_Mutation_p.A309V|ATL2_ENST00000452935.2_Missense_Mutation_p.A462V|ATL2_ENST00000332337.4_Missense_Mutation_p.A462V|ATL2_ENST00000539122.1_Missense_Mutation_p.A309V|ATL2_ENST00000419554.2_Missense_Mutation_p.A480V NM_001135673.1|NM_022374.2 NP_001129145.1|NP_071769.2 Q8NHH9 ATLA2_HUMAN atlastin GTPase 2 22 AAACATGACCGCAAACAGTGT 0.408000 0 SO:0001583 missense ENST00000378954.4 0 1 hg19 CCDS46260.1 . . . . . . . . . . G 15.31 2.796474 0.50208 . . ENSG00000119787 ENST00000378954;ENST00000406122;ENST00000402054;ENST00000539122;ENST00000332337;ENST00000419554;ENST00000452935;ENST00000546051 D;D;D;D;D;D;D;D 0.97138 -4.26;-4.26;-4.26;-4.26;-4.26;-4.26;-4.26;-4.26 5.81 5.81 0.92471 . 0.000000 0.85682 D 0.000000 D 0.92430 0.7597 L 0.31065 0.9 0.80722 D 1 P;B;P;B;B 0.49635 0.926;0.397;0.531;0.183;0.216 B;B;B;B;B 0.31495 0.115;0.062;0.131;0.08;0.05 D 0.91673 0.5352 10 0.18710 T 0.47 -14.909 19.0794 0.93175 0.0:0.0:1.0:0.0 . 309;462;462;480;480 B5MCN0;B7Z7X8;Q8NHH9-4;Q8NHH9-2;Q8NHH9 .;.;.;.;ATLA2_HUMAN V 480;309;309;309;462;480;462;309 ENSP00000368237:A480V;ENSP00000385446:A309V;ENSP00000384062:A309V;ENSP00000446192:A309V;ENSP00000333393:A462V;ENSP00000415336:A480V;ENSP00000390743:A462V;ENSP00000438938:A309V ENSP00000333393:A462V A - 2 0 ATL2 38378983 1.000000 0.71417 0.996000 0.52242 0.995000 0.86356 6.583000 0.74053 2.746000 0.94184 0.591000 0.81541 GCG TCGA-HV-A7OL-01A-11D-A33T-08 ATL2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219886.2 0 0 0 6 414 0 79 0 4.238820e-02 0 19 0 79 2 0 0 0 0 0 2 1 0.962820 6 405 0 78 2 0 0 0 0 79 2 -2.398702 0 1 121412 1 37 1 1 2 3 2.038702 0 0.370000 1.920000 0.371163 0.080000 2.000000e-02 0.170000 0.080000 0.089478 0.080000 0 5.000000e-02 0.120000 PSME4 23198 broad.mit.edu 37 2 54120082 54120082 + Missense_Mutation SNP A A T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr2:54120082A>T ENST00000404125.1 - 36 4109 c.4054T>A c.(4054-4056)Ttt>Att p.F1352I PSME4_ENST00000421748.2_Missense_Mutation_p.F496I NM_014614.2 NP_055429.2 Q14997 PSME4_HUMAN proteasome (prosome, macropain) activator subunit 4 p.F1238V(1) 60 Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181) GCATCATCAAAATTCCTGAAT 0.363000 1 Substitution - Missense(1) SO:0001583 missense ENST00000404125.1 1 1 hg19 CCDS33197.2 . . . . . . . . . . A 23.4 4.417319 0.83449 . . ENSG00000068878 ENST00000421748;ENST00000404125 T;T 0.64438 -0.1;-0.1 5.51 5.51 0.81932 Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.73233 0.3561 M 0.72118 2.19 0.80722 D 1 D;D;P 0.59357 0.985;0.959;0.954 P;P;P 0.59357 0.856;0.647;0.721 T 0.70230 -0.4929 10 0.15952 T 0.53 . 15.6258 0.76855 1.0:0.0:0.0:0.0 . 727;496;1352 Q14997-2;Q14997-3;Q14997 .;.;PSME4_HUMAN I 496;1352 ENSP00000410830:F496I;ENSP00000384211:F1352I ENSP00000384211:F1352I F - 1 0 PSME4 53973586 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 9.339000 0.96797 2.105000 0.64084 0.454000 0.30748 TTT TCGA-HV-A7OL-01A-11D-A33T-08 PSME4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324163.1 1 0 1 54 237 0 44 1 2.373285e-01 3 2 0 44 2 0 0 0 0 0 2 1 1.000000 54 235 0 44 2 0 0 0 0 44 2 -20.000000 1 0 0 0 1 1 2 3 2.038702 0 0.370000 1.920000 0.371163 0.990000 7.700000e-01 1.000000 1.000000 0.956310 0.990000 1 8.800000e-01 1.000000 TEKT4 150483 broad.mit.edu 37 2 95542419 95542419 + Missense_Mutation SNP G G A rs75603622 TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr2:95542419G>A ENST00000295201.4 + 6 1350 c.1213G>A c.(1213-1215)Gcc>Acc p.A405T AC097374.2_ENST00000568768.1_RNA NM_144705.2 NP_653306.1 Q8WW24 TEKT4_HUMAN tektin 4 28 GAAGGACATTGCCGCCATGAC 0.587000 0 SO:0001583 missense ENST00000295201.4 0 0 hg19 CCDS2005.1 . . . . . . . . . . . 7.574 0.667319 0.14710 . . ENSG00000163060 ENST00000295201 T 0.02812 4.15 2.43 -2.21 0.06973 . 0.433987 0.24289 N 0.039834 T 0.04724 0.0128 M 0.89414 3.03 0.25870 N 0.983722 B 0.10296 0.003 B 0.15484 0.013 T 0.43360 -0.9396 10 0.17832 T 0.49 -6.8803 6.926 0.24416 0.1368:0.0:0.6998:0.1633 rs3209453 405 Q8WW24 TEKT4_HUMAN T 405 ENSP00000295201:A405T ENSP00000295201:A405T A + 1 0 TEKT4 94906146 0.004000 0.15560 0.111000 0.21465 0.365000 0.29674 0.130000 0.15850 -0.321000 0.08627 -0.923000 0.02734 GCC TCGA-HV-A7OL-01A-11D-A33T-08 TEKT4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252777.1 1 0 1 33 184 0 26 1 9.057854e-01 25 0 0 26 2 0 0 0 0 0 2 1 1.000000 10 181 0 25 2 0 0 0 0 26 2 -0.553865 0 0 121408 494 45 1 1 2 3 2.038702 0 0.370000 1.920000 0.371163 0.820000 5.800000e-01 1.000000 1.000000 0.826537 0.820000 0 6.900000e-01 0.960000 GPAT2 150763 broad.mit.edu 37 2 96690307 96690307 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr2:96690307G>A ENST00000434632.1 - 16 1996 c.1537C>T c.(1537-1539)Cgg>Tgg p.R513W GPAT2_ENST00000453542.1_Missense_Mutation_p.R442W|GPAT2_ENST00000359548.4_Missense_Mutation_p.R513W|FAHD2CP_ENST00000607780.1_RNA|GPAT2_ENST00000377137.3_Missense_Mutation_p.R513W Q6NUI2 GPAT2_HUMAN glycerol-3-phosphate acyltransferase 2, mitochondrial 16 ACGTGCGCCCGCAGCAGGCTC 0.642000 0 SO:0001583 missense ENST00000434632.1 0 1 hg19 CCDS42714.1 . . . . . . . . . . g 14.62 2.588560 0.46110 . . ENSG00000186281 ENST00000359548;ENST00000434632;ENST00000453542;ENST00000377137 T;T;T;T 0.77877 -1.12;-1.12;-0.13;-1.13 4.63 3.66 0.41972 . 0.754991 0.12365 N 0.475318 T 0.81730 0.4884 L 0.43152 1.355 0.32553 N 0.532168 D;D;D;D;D 0.89917 0.999;0.999;0.999;0.998;1.0 D;P;P;P;D 0.66084 0.913;0.809;0.847;0.721;0.941 T 0.81138 -0.1069 10 0.66056 D 0.02 -5.7184 9.2268 0.37412 0.0:0.0:0.6973:0.3027 . 442;513;519;513;442 E9PE95;Q6NUI2-3;Q6NUI2-4;Q6NUI2;B4DNZ9 .;.;.;GPAT2_HUMAN;. W 513;513;442;513 ENSP00000352547:R513W;ENSP00000389395:R513W;ENSP00000393770:R442W;ENSP00000366341:R513W ENSP00000352547:R513W R - 1 2 GPAT2 96054034 0.001000 0.12720 0.992000 0.48379 0.233000 0.25261 0.401000 0.20948 0.964000 0.38108 0.637000 0.83480 CGG TCGA-HV-A7OL-01A-11D-A33T-08 GPAT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000338786.1 0 0 0 5 441 0 73 0 2.014839e-03 0 5 0 73 2 0 0 0 0 0 2 1 0.935625 5 435 0 72 2 0 0 0 0 73 2 -2.913566 1 1 121098 7 40 1 1 2 3 2.038702 0 0.370000 1.920000 0.371163 0.060000 1.000000e-02 0.140000 0.060000 0.072248 0.060000 0 3.000000e-02 0.100000 CEP97 79598 broad.mit.edu 37 3 101446386 101446386 + Splice_Site SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr3:101446386G>A ENST00000341893.3 + 3 1097 c.e3+1 CEP97_ENST00000327230.4_Splice_Site|CEP97_ENST00000494050.1_Splice_Site Q8IW35 CEP97_HUMAN centrosomal protein 97kDa 29 TAATCTTAAGGTGAATGGTTT 0.343000 0 SO:0001630 splice_region_variant ENST00000341893.3 1 1 hg19 CCDS2944.1 . . . . . . . . . . G 23.5 4.419147 0.83559 . . ENSG00000182504 ENST00000341893;ENST00000327230;ENST00000494050 . . . 5.64 5.64 0.86602 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 19.7156 0.96119 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . CEP97 102929076 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 9.703000 0.98714 2.658000 0.90341 0.655000 0.94253 . TCGA-HV-A7OL-01A-11D-A33T-08 CEP97-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000353597.2 1 0 0 75 372 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 1.000000 74 369 0 48 2 0 0 0 0 48 2 -20.000000 1 1 121412 1 31 1 1 2 3 2.039940 0 0.370000 1.920000 0.372322 0.900000 7.300000e-01 1.000000 1.000000 0.905378 0.900000 1 8.100000e-01 1.000000 CPNE4 131034 broad.mit.edu 37 3 131442441 131442441 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr3:131442441C>T ENST00000512055.1 - 7 2335 c.209G>A c.(208-210)tGc>tAc p.C70Y CPNE4_ENST00000512332.1_Missense_Mutation_p.C88Y|CPNE4_ENST00000429747.1_Missense_Mutation_p.C70Y|CPNE4_ENST00000502818.1_Missense_Mutation_p.C88Y|CPNE4_ENST00000511604.1_Missense_Mutation_p.C70Y Q96A23 CPNE4_HUMAN copine IV 39 TGGGTTTATGCAGGTGCGAAT 0.418000 0 SO:0001583 missense ENST00000512055.1 0 1 hg19 CCDS3072.1 . . . . . . . . . . C 17.50 3.404858 0.62288 . . ENSG00000196353 ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818;ENST00000505881;ENST00000514999;ENST00000505957 T;T;T;T;T;T;T;T 0.39592 1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07 5.38 5.38 0.77491 C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1); 0.120680 0.85682 D 0.000000 T 0.58524 0.2128 M 0.77616 2.38 0.49299 D 0.999775 B;B 0.30482 0.147;0.281 B;B 0.42495 0.221;0.389 T 0.61973 -0.6952 10 0.72032 D 0.01 -7.8453 19.1819 0.93627 0.0:1.0:0.0:0.0 . 88;70 Q96A23-2;Q96A23 .;CPNE4_HUMAN Y 70;70;88;70;88;70;70;70 ENSP00000421705:C70Y;ENSP00000411904:C70Y;ENSP00000424853:C88Y;ENSP00000423811:C70Y;ENSP00000421646:C88Y;ENSP00000425506:C70Y;ENSP00000427561:C70Y;ENSP00000421394:C70Y ENSP00000411904:C70Y C - 2 0 CPNE4 132925131 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 3.896000 0.56266 2.542000 0.85734 0.555000 0.69702 TGC TCGA-HV-A7OL-01A-11D-A33T-08 CPNE4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356583.4 0 0 0 6 724 0 107 0 0 0 0 107 2 0 0 0 0 0 2 1 0.963854 6 716 0 106 2 0 0 0 0 107 2 -2.003323 0 1 0 0 1 1 2 3 2.039940 0 0.370000 1.920000 0.372322 0.040000 0 0.100000 0.040000 0.061040 0.040000 0 2.000000e-02 0.070000 ST6GAL1 6480 broad.mit.edu 37 3 186769122 186769122 + Silent SNP G G C TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr3:186769122G>C ENST00000169298.3 + 5 1367 c.693G>C c.(691-693)ctG>ctC p.L231L ST6GAL1_ENST00000457772.2_5'UTR|ST6GAL1_ENST00000448044.1_Silent_p.L231L NM_173216.2 NP_775323.1 P15907 SIAT1_HUMAN ST6 beta-galactosamide alpha-2,6-sialyltranferase 1 7 all_cancers(143;2.33e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;8.53e-19) CCATTCGCCTGATGAACTCTC 0.453000 0 SO:0001819 synonymous_variant ENST00000169298.3 0 1 hg19 CCDS3285.1 TCGA-HV-A7OL-01A-11D-A33T-08 ST6GAL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344399.1 0 0 0 26 270 0 46 0 2.381361e-02 0 3 0 46 2 0 0 0 0 0 2 1 1.000000 25 266 0 45 2 0 0 0 0 46 2 -9.658928 1 1 0 0 1 1 2 3 2.039940 0 0.370000 1.920000 0.372322 0.470000 3.200000e-01 0.700000 0.480000 0.493781 0.470000 0 3.900000e-01 0.580000 MUC4 4585 broad.mit.edu 37 3 195517556 195517556 + Missense_Mutation SNP T T A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr3:195517556T>A ENST00000463781.3 - 2 1354 c.895A>T c.(895-897)Aca>Tca p.T299S MUC4_ENST00000475231.1_Missense_Mutation_p.T299S|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron NM_018406.6 NP_060876.5 Q99102 MUC4_HUMAN mucin 4, cell surface associated 51 all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) GGATCAAATGTTACTAAGGCT 0.483000 0 SO:0001583 missense ENST00000463781.3 0 1 hg19 CCDS54700.1 . . . . . . . . . . - 6.636 0.485876 0.12641 . . ENSG00000145113 ENST00000463781;ENST00000475231;ENST00000392409 T;T 0.54071 0.59;0.62 3.57 -2.63 0.06133 . . . . . T 0.33030 0.0849 L 0.47190 1.495 0.09310 N 1 B;B 0.32781 0.259;0.384 B;B 0.25759 0.063;0.048 T 0.20140 -1.0284 9 0.15066 T 0.55 . 4.0135 0.09632 0.4013:0.1048:0.0:0.4939 . 299;304 E7ESK3;Q99102 .;MUC4_HUMAN S 299;299;273 ENSP00000417498:T299S;ENSP00000420243:T299S ENSP00000376209:T273S T - 1 0 MUC4 197001951 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.781000 0.04648 -0.425000 0.07371 -0.416000 0.06073 ACA TCGA-HV-A7OL-01A-11D-A33T-08 MUC4-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000324081.6 0 0 0 7 460 0 93 0 0 0 0 93 2 0 0 0 0 0 2 1 0.980318 7 457 0 93 2 0 0 0 0 93 2 -4.847725 1 1 0 0 1 0 1 1 2.023077 0 0.370000 1.920000 0.367660 0.080000 3.000000e-02 0.160000 0.080000 0.091528 0.080000 0 5.000000e-02 0.120000 CDCP1 64866 broad.mit.edu 37 3 45153640 45153640 + Missense_Mutation SNP T T C TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr3:45153640T>C ENST00000296129.1 - 3 724 c.590A>G c.(589-591)cAc>cGc p.H197R CDCP1_ENST00000425231.2_Missense_Mutation_p.H197R|CDCP1_ENST00000490471.1_5'Flank NM_022842.3 NP_073753.3 Q9H5V8 CDCP1_HUMAN CUB domain containing protein 1 29 CCATGGGAGGTGTAAGGCCAT 0.522000 0 SO:0001583 missense ENST00000296129.1 0 1 hg19 CCDS2727.1 . . . . . . . . . . T 14.05 2.419653 0.42918 . . ENSG00000163814 ENST00000296129;ENST00000425231 T;T 0.41065 1.92;1.01 5.42 4.25 0.50352 . 0.712205 0.14693 N 0.304050 T 0.41050 0.1142 L 0.54323 1.7 0.27687 N 0.946243 B;B 0.30439 0.279;0.279 B;B 0.31101 0.124;0.124 T 0.34950 -0.9808 10 0.59425 D 0.04 . 12.6997 0.57024 0.0:0.0:0.1375:0.8625 . 197;197 Q9H5V8-3;Q9H5V8 .;CDCP1_HUMAN R 197 ENSP00000296129:H197R;ENSP00000399342:H197R ENSP00000296129:H197R H - 2 0 CDCP1 45128644 0.981000 0.34729 0.994000 0.49952 0.773000 0.43773 2.658000 0.46733 0.872000 0.35775 0.460000 0.39030 CAC TCGA-HV-A7OL-01A-11D-A33T-08 CDCP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256748.3 0 0 0 8 493 0 82 0 1.765649e-01 0 42 0 82 2 0 0 0 0 0 2 1 0.989036 8 488 0 82 2 0 0 0 0 82 2 -3.025161 1 1 0 0 1 1 2 3 2.039940 0 0.370000 1.920000 0.372322 0.080000 3.000000e-02 0.180000 0.080000 0.105593 0.080000 0 5.000000e-02 0.130000 TLR9 54106 broad.mit.edu 37 3 52257640 52257640 + Missense_Mutation SNP C C T rs147300053 TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr3:52257640C>T ENST00000360658.2 - 2 1325 c.692G>A c.(691-693)cGc>cAc p.R231H TLR9_ENST00000494383.1_Silent_p.P384P|TLR9_ENST00000597542.1_Missense_Mutation_p.R255H NM_017442.3 NP_059138.1 Q9NR96 TLR9_HUMAN toll-like receptor 9 30 Chloroquine(DB00608)|Hydroxychloroquine(DB01611) TTTGACGATGCGGTTGTAGGA 0.617000 0 SO:0001583 missense ENST00000360658.2 0 1 hg19 CCDS2848.1 . . . . . . . . . . C 8.690 0.907217 0.17833 0.0 3.49E-4 ENSG00000239732 ENST00000360658 T 0.58210 0.35 5.38 -8.75 0.00834 . 0.955010 0.08543 N 0.930202 T 0.34337 0.0894 L 0.35288 1.05 0.09310 N 0.999997 B;B 0.11235 0.002;0.004 B;B 0.06405 0.002;0.002 T 0.22347 -1.0219 10 0.25106 T 0.35 . 12.031 0.53397 0.1005:0.6148:0.0:0.2847 . 328;231 B4E0A1;Q9NR96 .;TLR9_HUMAN H 231 ENSP00000353874:R231H ENSP00000353874:R231H R - 2 0 TLR9 52232680 0.003000 0.15002 0.245000 0.24217 0.163000 0.22366 -0.725000 0.04942 -1.469000 0.01890 -0.982000 0.02568 CGC TCGA-HV-A7OL-01A-11D-A33T-08 TLR9-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000350203.1 0 0 0 4 187 0 36 0 4.580858e-03 0 4 0 36 2 0 0 0 0 0 2 1 0.888765 4 185 0 35 2 0 0 0 0 36 2 -3.305162 1 1 121284 3 36 1 1 2 3 2.039940 0 0.370000 1.920000 0.372322 0.120000 3.000000e-02 0.300000 0.120000 0.147746 0.120000 0 7.000000e-02 0.200000 STAB1 23166 broad.mit.edu 37 3 52551596 52551596 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr3:52551596G>A ENST00000321725.6 + 44 4670 c.4594G>A c.(4594-4596)Ggg>Agg p.G1532R NM_015136.2 NP_055951.2 Q9NY15 STAB1_HUMAN stabilin 1 76 GGGTTACAGCGGGGATGGCAT 0.622000 0 SO:0001583 missense ENST00000321725.6 1 1 hg19 CCDS33768.1 . . . . . . . . . . G 20.3 3.965659 0.74131 . . ENSG00000010327 ENST00000321725 D 0.93953 -3.32 4.81 4.81 0.61882 EGF domain, merozoite surface protein 1-like (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1); 0.485095 0.20593 N 0.089304 D 0.96445 0.8840 M 0.81942 2.565 0.46336 D 0.998995 D 0.89917 1.0 D 0.72982 0.979 D 0.96640 0.9473 10 0.62326 D 0.03 . 14.9699 0.71226 0.0:0.0:1.0:0.0 . 1532 Q9NY15 STAB1_HUMAN R 1532 ENSP00000312946:G1532R ENSP00000312946:G1532R G + 1 0 STAB1 52526636 1.000000 0.71417 0.984000 0.44739 0.352000 0.29268 3.707000 0.54838 2.380000 0.81148 0.655000 0.94253 GGG TCGA-HV-A7OL-01A-11D-A33T-08 STAB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351380.2 1 0 1 59 271 0 53 0 2.246025e-01 0 5 0 53 2 0 0 0 0 0 2 1 1.000000 59 269 0 53 2 0 0 0 0 53 2 -3.052333 1 1 0 0 1 1 2 3 2.039940 0 0.370000 1.920000 0.372322 0.960000 7.500000e-01 1.000000 1.000000 0.941527 0.960000 1 8.500000e-01 1.000000 VGLL3 389136 broad.mit.edu 37 3 87017871 87017871 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr3:87017871G>A ENST00000398399.2 - 3 1169 c.806C>T c.(805-807)gCg>gTg p.A269V VGLL3_ENST00000383698.3_Missense_Mutation_p.A269V NM_016206.2 NP_057290.2 vestigial-like family member 3 19 all_cancers(8;0.109)|Lung SC(3;0.184) Lung NSC(201;0.0777) AATCCTGGCCGCATGCACTGA 0.572000 0 SO:0001583 missense ENST00000398399.2 0 1 hg19 CCDS43110.1 . . . . . . . . . . G 20.2 3.945134 0.73672 0.0 1.18E-4 ENSG00000206538 ENST00000398399;ENST00000383698 T;T 0.52754 0.82;0.65 5.71 5.71 0.89125 . 0.486738 0.20579 N 0.089580 T 0.44953 0.1318 L 0.54323 1.7 0.47949 D 0.99955 P 0.45428 0.858 B 0.35655 0.207 T 0.48917 -0.8992 10 0.45353 T 0.12 -0.046 19.446 0.94847 0.0:0.0:1.0:0.0 . 269 A8MV65 VGLL3_HUMAN V 269 ENSP00000381436:A269V;ENSP00000373199:A269V ENSP00000373199:A269V A - 2 0 VGLL3 87100561 0.956000 0.32656 0.475000 0.27278 0.820000 0.46376 6.223000 0.72257 2.709000 0.92574 0.561000 0.74099 GCG TCGA-HV-A7OL-01A-11D-A33T-08 VGLL3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000352805.1 0 0 0 4 216 0 40 0 0 0 0 40 2 0 0 0 0 0 2 1 0.887917 4 213 0 40 2 0 0 0 0 40 2 -2.918883 1 1 121192 13 41 1 1 2 3 2.039940 0 0.370000 1.920000 0.372322 0.100000 3.000000e-02 0.260000 0.100000 0.129861 0.100000 0 6.000000e-02 0.180000 ENAM 10117 broad.mit.edu 37 4 71508260 71508260 + Missense_Mutation SNP C C A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr4:71508260C>A ENST00000396073.3 + 9 1398 c.1117C>A c.(1117-1119)Cgt>Agt p.R373S ENAM_ENST00000472903.1_Intron NM_031889.2 NP_114095.2 Q9NRM1 ENAM_HUMAN enamelin 6 Lung(101;0.235) ACAAGTAGCTCGTCCAGGAAA 0.438000 0 SO:0001583 missense ENST00000396073.3 1 1 hg19 CCDS3544.2 . . . . . . . . . . C 9.070 0.996778 0.19043 . . ENSG00000132464 ENST00000396073 T 0.31510 1.49 5.93 1.05 0.20165 . 0.946121 0.08814 N 0.889824 T 0.37489 0.1005 M 0.69358 2.11 0.09310 N 1 P 0.43024 0.798 P 0.48488 0.579 T 0.24083 -1.0170 10 0.48119 T 0.1 0.5722 4.3221 0.11022 0.4017:0.3948:0.1299:0.0735 . 373 Q9NRM1 ENAM_HUMAN S 373 ENSP00000379383:R373S ENSP00000379383:R373S R + 1 0 ENAM 71727124 0.000000 0.05858 0.000000 0.03702 0.003000 0.03518 0.768000 0.26590 -0.116000 0.11893 -0.182000 0.12963 CGT TCGA-HV-A7OL-01A-11D-A33T-08 ENAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252166.3 1 0 1 168 632 0 99 0 0 0 0 99 2 0 0 0 0 0 2 1 1.000000 166 627 0 99 2 0 0 0 0 99 2 -3.713108 1 1 0 0 1 1 2 3 2.061157 0 0.370000 1.920000 0.375774 0.990000 9.900000e-01 1.000000 1.000000 0.999257 0.990000 1 9.900000e-01 1.000000 SLC12A7 10723 broad.mit.edu 37 5 1081769 1081769 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr5:1081769C>T ENST00000264930.5 - 9 1263 c.1220G>A c.(1219-1221)aGc>aAc p.S407N NM_006598.2 NP_006589.2 Q9Y666 S12A7_HUMAN solute carrier family 12 (potassium/chloride transporter), member 7 32 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09) Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165) Potassium Chloride(DB00761) GGGCAGTGCGCTGGCACGGCT 0.657000 0 SO:0001583 missense ENST00000264930.5 0 1 hg19 CCDS34129.1 . . . . . . . . . . C 4.580 0.107775 0.08780 . . ENSG00000113504 ENST00000264930 D 0.84442 -1.85 4.09 1.77 0.24775 . 1.016290 0.07831 N 0.961315 T 0.77765 0.4179 L 0.43152 1.355 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.58713 -0.7588 10 0.15066 T 0.55 . 8.0261 0.30438 0.0:0.5903:0.3043:0.1054 . 407 Q9Y666 S12A7_HUMAN N 407 ENSP00000264930:S407N ENSP00000264930:S407N S - 2 0 SLC12A7 1134769 0.000000 0.05858 0.000000 0.03702 0.002000 0.02628 0.155000 0.16362 0.686000 0.31488 0.491000 0.48974 AGC TCGA-HV-A7OL-01A-11D-A33T-08 SLC12A7-001 KNOWN non_canonical_TEC|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000366446.2 0 0 0 5 414 0 51 0 9.622736e-03 0 10 0 51 2 0 0 0 0 0 2 1 0.936310 5 410 0 51 2 0 0 0 0 51 2 -4.826088 1 1 121362 1 28 1 1 2 3 2.038376 0 0.370000 1.920000 0.371163 0.060000 2.000000e-02 0.150000 0.060000 0.076868 0.060000 0 4.000000e-02 0.110000 PCDHGA6 56109 broad.mit.edu 37 5 140755802 140755802 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr5:140755802C>T ENST00000517434.1 + 1 2152 c.2152C>T c.(2152-2154)Cgc>Tgc p.R718C PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron NM_018919.2|NM_032086.1 NP_061742.1|NP_114475.1 Q9Y5G7 PCDG6_HUMAN protocadherin gamma subfamily A, 6 2 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CAGACTGCAGCGCTGGCACAA 0.647000 0 SO:0001583 missense ENST00000517434.1 1 1 hg19 CCDS54926.1 . . . . . . . . . . . 11.42 1.632413 0.29068 . . ENSG00000253731 ENST00000517434 T 0.23147 1.92 5.15 3.22 0.36961 . 2.171190 0.04336 U 0.353247 T 0.40448 0.1117 M 0.86651 2.83 0.28148 N 0.929514 B;B 0.32010 0.351;0.047 B;B 0.29176 0.099;0.066 T 0.49679 -0.8914 10 0.72032 D 0.01 . 12.5336 0.56131 0.3755:0.6245:0.0:0.0 . 718;718 Q9Y5G7-2;Q9Y5G7 .;PCDG6_HUMAN C 718 ENSP00000429601:R718C ENSP00000429601:R718C R + 1 0 PCDHGA6 140735986 0.000000 0.05858 0.961000 0.40146 0.199000 0.23934 0.469000 0.22067 1.511000 0.48818 0.655000 0.94253 CGC TCGA-HV-A7OL-01A-11D-A33T-08 PCDHGA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374743.1 1 0 1 137 555 0 128 0 0 0 0 128 2 0 0 0 0 0 2 1 1.000000 135 550 0 127 2 0 0 0 0 128 2 -3.588126 1 1 0 0 1 1 2 3 2.030408 0 0.370000 1.920000 0.371163 0.990000 9.100000e-01 1.000000 1.000000 0.992188 0.990000 1 9.800000e-01 1.000000 CNOT6 57472 broad.mit.edu 37 5 179992902 179992902 + Silent SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr5:179992902G>A ENST00000393356.1 + 9 1066 c.642G>A c.(640-642)gcG>gcA p.A214A CNOT6_ENST00000261951.4_Silent_p.A214A Q9ULM6 CNOT6_HUMAN CCR4-NOT transcription complex, subunit 6 23 all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114) all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) CATCATGGGCGCTAAACTGGG 0.418000 0 SO:0001819 synonymous_variant ENST00000393356.1 0 1 hg19 CCDS4455.1 TCGA-HV-A7OL-01A-11D-A33T-08 CNOT6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253532.1 0 0 0 5 462 0 66 0 0 0 1 0 66 2 0 0 0 0 0 2 1 0.936073 5 457 0 66 2 0 0 0 0 66 2 -2.334326 0 1 121412 1 35 1 1 2 3 2.030408 0 0.370000 1.920000 0.371163 0.060000 1.000000e-02 0.140000 0.060000 0.069018 0.060000 0 3.000000e-02 0.100000 ERBB2IP 55914 broad.mit.edu 37 5 65288599 65288599 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr5:65288599G>A ENST00000284037.5 + 3 442 c.53G>A c.(52-54)cGa>cAa p.R18Q ERBB2IP_ENST00000416865.2_Missense_Mutation_p.R18Q|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.R18Q|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.R18Q|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.R18Q|ERBB2IP_ENST00000508515.1_Missense_Mutation_p.R18Q|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.R18Q|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.R18Q|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.R18Q|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.R18Q NM_001253697.1 NP_001240626.1 Q96RT1 LAP2_HUMAN erbb2 interacting protein 36 Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234) CGCTGTCTACGAGGGGAAGAG 0.363000 0 SO:0001583 missense ENST00000284037.5 1 1 hg19 CCDS58953.1 . . . . . . . . . . G 35 5.516152 0.96402 . . ENSG00000112851 ENST00000284037;ENST00000380943;ENST00000416865;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515 T;T;T;T;T;T;T;T;T;T 0.40476 1.23;1.23;1.39;1.23;1.42;1.03;1.3;1.22;1.26;1.03 5.15 5.15 0.70609 . 0.000000 0.85682 D 0.000000 T 0.62085 0.2399 L 0.54323 1.7 0.80722 D 1 D;D;D;D;D;D;D;D 0.89917 0.999;1.0;1.0;1.0;1.0;1.0;1.0;0.999 D;D;D;D;D;D;D;D 0.85130 0.922;0.997;0.934;0.996;0.99;0.992;0.983;0.994 T 0.64437 -0.6408 10 0.66056 D 0.02 . 18.6235 0.91330 0.0:0.0:1.0:0.0 . 18;18;18;18;18;18;18;18 B4DIP2;Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2 .;.;.;.;.;LAP2_HUMAN;.;. Q 18 ENSP00000284037:R18Q;ENSP00000370330:R18Q;ENSP00000397833:R18Q;ENSP00000370326:R18Q;ENSP00000370323:R18Q;ENSP00000370322:R18Q;ENSP00000370325:R18Q;ENSP00000422766:R18Q;ENSP00000426632:R18Q;ENSP00000422015:R18Q ENSP00000284037:R18Q R + 2 0 ERBB2IP 65324355 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 9.756000 0.98918 2.388000 0.81334 0.655000 0.94253 CGA TCGA-HV-A7OL-01A-11D-A33T-08 ERBB2IP-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000215070.1 1 0 1 87 406 0 81 0 0 0 0 81 2 0 0 0 0 0 2 1 1.000000 86 401 0 80 2 0 0 0 0 81 2 -2.966861 1 1 0 0 1 1 2 3 2.038376 0 0.370000 1.920000 0.371163 0.950000 7.700000e-01 1.000000 1.000000 0.938816 0.950000 1 8.600000e-01 1.000000 ARG1 383 broad.mit.edu 37 6 131894445 131894445 + Missense_Mutation SNP T T C rs149310631 TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr6:131894445T>C ENST00000368087.3 + 1 162 c.23T>C c.(22-24)aTa>aCa p.I8T ARG1_ENST00000498260.1_3'UTR|ARG1_ENST00000356962.2_Missense_Mutation_p.I8T P05089 ARGI1_HUMAN arginase 1 14 Breast(56;0.0753) L-Ornithine(DB00129) TCCAGAACCATAGGGATTATT 0.423000 0 SO:0001583 missense ENST00000368087.3 1 1 hg19 CCDS5145.1 . . . . . . . . . . T 8.586 0.883549 0.17467 . . ENSG00000118520 ENST00000368087;ENST00000356962;ENST00000476845 D;D;D 0.86366 -2.11;-2.11;-2.11 5.79 5.79 0.91817 Ureohydrolase domain (1); 0.325628 0.33290 N 0.005063 D 0.84325 0.5447 M 0.82323 2.585 0.09310 N 0.999999 B;B 0.30793 0.251;0.295 B;B 0.40410 0.318;0.328 T 0.80315 -0.1434 10 0.56958 D 0.05 -5.487 8.5965 0.33718 0.0:0.085:0.0:0.915 . 8;8 P05089-2;P05089 .;ARGI1_HUMAN T 8 ENSP00000357066:I8T;ENSP00000349446:I8T;ENSP00000417694:I8T ENSP00000349446:I8T I + 2 0 ARG1 131936138 0.030000 0.19436 0.132000 0.22025 0.004000 0.04260 2.543000 0.45752 2.213000 0.71641 0.533000 0.62120 ATA TCGA-HV-A7OL-01A-11D-A33T-08 ARG1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042223.1 1 0 1 68 205 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 1.000000 67 202 0 55 2 0 0 0 0 55 2 -20.000000 1 1 121412 1 35 1 0 1 1 1.667650 1 0.370000 1.920000 0.226994 0.940000 8.100000e-01 1.000000 0.990000 0.942874 0.940000 1 8.800000e-01 0.990000 ECT2L 345930 broad.mit.edu 37 6 139206663 139206663 + Silent SNP A A C TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr6:139206663A>C ENST00000423192.1 + 16 2210 c.2049A>C c.(2047-2049)gcA>gcC p.A683A ECT2L_ENST00000367682.2_Silent_p.A683A|ECT2L_ENST00000541398.1_Intron Q008S8 ECT2L_HUMAN epithelial cell transforming 2 like 30 TGATACCAGCATTCCGAACTT 0.443000 N, Splice, Mis ETP ALL Rec yes 6 6q24.1 345930 epithelial cell transforming sequence 2 oncogene-like L 0 SO:0001819 synonymous_variant ENST00000423192.1 0 1 hg19 CCDS43508.1 TCGA-HV-A7OL-01A-11D-A33T-08 ECT2L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042441.3 0 0 0 6 378 1 70 0 0 0 1 1 70 2 0 0 0 0 0 2 0 0.009128 6 372 1 70 18 0 0 0 1 70 2 -6.459637 1 0 0 0 1 0 1 1 1.667650 1 0.370000 1.920000 0.226994 0.070000 2.000000e-02 0.140000 0.070000 0.079176 0.070000 0 4.000000e-02 0.110000 FAM135A 57579 broad.mit.edu 37 6 71232278 71232278 + Silent SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr6:71232278C>T ENST00000418814.2 + 13 1706 c.1092C>T c.(1090-1092)taC>taT p.Y364Y FAM135A_ENST00000370479.3_Silent_p.Y347Y|FAM135A_ENST00000505769.1_Silent_p.Y364Y|FAM135A_ENST00000361499.3_Silent_p.Y364Y|FAM135A_ENST00000457062.2_Silent_p.Y347Y|FAM135A_ENST00000505868.1_Silent_p.Y364Y NM_001105531.2|NM_001162529.1 NP_001099001.1|NP_001156001.1 Q9P2D6 F135A_HUMAN family with sequence similarity 135, member A 38 CCATTGCATACCAGGAACTTC 0.333000 0 SO:0001819 synonymous_variant ENST00000418814.2 1 1 hg19 CCDS55028.1 TCGA-HV-A7OL-01A-11D-A33T-08 FAM135A-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000041137.2 1 0 0 108 345 0 97 0 0 0 0 97 2 0 0 0 0 0 2 1 1.000000 108 344 0 97 2 0 0 0 0 97 2 -20.000000 1 1 0 0 1 0 1 1 1.667650 1 0.370000 1.920000 0.226994 0.950000 8.400000e-01 1.000000 0.990000 0.949985 0.950000 1 9.000000e-01 0.990000 RRAGD 58528 broad.mit.edu 37 6 90097155 90097155 + Silent SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr6:90097155G>A ENST00000369415.4 - 2 579 c.303C>T c.(301-303)tgC>tgT p.C101C RRAGD_ENST00000492783.1_5'UTR|RRAGD_ENST00000359203.3_Intron NM_021244.4 NP_067067.1 Ras-related GTP binding D p.C101C(1) 15 all_cancers(76;7.01e-07)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00139) CATCTTCCCGGCATATCTTAT 0.428000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000369415.4 0 1 hg19 CCDS5022.1 TCGA-HV-A7OL-01A-11D-A33T-08 RRAGD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041484.1 0 0 0 8 993 0 172 0 1.809577e-03 0 7 0 172 2 0 0 0 0 0 2 1 0.988877 9 981 0 171 2 0 0 0 0 172 2 -1.953115 0 1 0 0 1 0 1 1 1.667650 1 0.370000 1.920000 0.226994 0.030000 1.000000e-02 0.070000 0.040000 0.039388 0.030000 0 2.000000e-02 0.050000 PCOLCE 5118 broad.mit.edu 37 7 100204241 100204241 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr7:100204241C>T ENST00000223061.5 + 6 1208 c.928C>T c.(928-930)Cct>Tct p.P310S PCOLCE-AS1_ENST00000446022.1_RNA|PCOLCE-AS1_ENST00000442166.2_RNA NM_002593.3 NP_002584.2 Q15113 PCOC1_HUMAN procollagen C-endopeptidase enhancer 23 Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439) AGAGGAATCTCCTTCAGCCCC 0.572000 0 SO:0001583 missense ENST00000223061.5 1 1 hg19 CCDS5700.1 . . . . . . . . . . C 10.72 1.429560 0.25726 . . ENSG00000106333 ENST00000223061 T 0.19938 2.11 4.69 3.78 0.43462 . 0.932278 0.09080 N 0.851413 T 0.11580 0.0282 N 0.08118 0 0.18873 N 0.999988 B 0.23937 0.094 B 0.16722 0.016 T 0.22800 -1.0206 10 0.48119 T 0.1 -3.7786 7.9145 0.29810 0.0:0.8816:0.0:0.1184 . 310 Q15113 PCOC1_HUMAN S 310 ENSP00000223061:P310S ENSP00000223061:P310S P + 1 0 PCOLCE 100042177 0.001000 0.12720 0.003000 0.11579 0.007000 0.05969 1.043000 0.30316 1.134000 0.42165 0.407000 0.27541 CCT TCGA-HV-A7OL-01A-11D-A33T-08 PCOLCE-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000345285.1 1 0 0 31 139 0 30 1 1 8 534 0 30 2 0 0 0 0 0 2 1 1.000000 30 137 0 29 2 0 0 0 0 30 2 -20.000000 1 1 0 0 1 0 0 0 2.019785 0 0.370000 1.920000 0.367660 0.970000 6.900000e-01 1.000000 1.000000 0.932832 0.970000 1 8.200000e-01 1.000000 ABCB8 11194 broad.mit.edu 37 7 150741223 150741223 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr7:150741223G>A ENST00000297504.6 + 16 2048 c.1982G>A c.(1981-1983)cGc>cAc p.R661H ABCB8_ENST00000542328.1_Missense_Mutation_p.R556H|ABCB8_ENST00000498578.1_Missense_Mutation_p.R644H|ABCB8_ENST00000358849.4_Missense_Mutation_p.R644H|ABCB8_ENST00000356058.4_3'UTR Q9NUT2 ABCB8_HUMAN ATP-binding cassette, sub-family B (MDR/TAP), member 8 26 OV - Ovarian serous cystadenocarcinoma(82;0.0121) Doxorubicin(DB00997) AGTGCAGGCCGCACGGTGCTG 0.642000 0 SO:0001583 missense ENST00000297504.6 0 1 hg19 . . . . . . . . . . G 33 5.237329 0.95240 . . ENSG00000197150 ENST00000358849;ENST00000360651;ENST00000297504;ENST00000542328;ENST00000498578 D;D;D;T 0.85088 -1.94;-1.94;-1.94;-0.67 4.79 4.79 0.61399 ATPase, AAA+ type, core (1);ABC transporter-like (1); 0.000000 0.85682 D 0.000000 D 0.90734 0.7092 M 0.65320 2 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.87578 0.998;0.996;0.996;0.998 D 0.90458 0.4444 10 0.49607 T 0.09 -2.0118 15.719 0.77694 0.0:0.0:1.0:0.0 . 556;644;661;644 G3XAP3;A5D8W3;Q9NUT2;Q9NUT2-2 .;.;ABCB8_HUMAN;. H 644;627;661;556;644 ENSP00000351717:R644H;ENSP00000297504:R661H;ENSP00000438776:R556H;ENSP00000418271:R644H ENSP00000297504:R661H R + 2 0 ABCB8 150372156 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 4.512000 0.60469 2.651000 0.90000 0.563000 0.77884 CGC TCGA-HV-A7OL-01A-11D-A33T-08 ABCB8-003 KNOWN basic protein_coding protein_coding OTTHUMT00000351733.2 0 0 0 5 349 0 49 0 6.280345e-01 0 137 0 49 2 0 0 0 0 0 2 1 0.936564 5 346 0 48 2 0 0 0 0 49 2 -4.472165 1 1 121406 2 34 1 1 2 3 2.033338 0 0.370000 1.920000 0.371163 0.080000 2.000000e-02 0.180000 0.080000 0.090840 0.080000 0 4.000000e-02 0.130000 POM121L12 285877 broad.mit.edu 37 7 53104235 53104235 + Missense_Mutation SNP G G T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr7:53104235G>T ENST00000408890.4 + 1 887 c.871G>T c.(871-873)Gct>Tct p.A291S NM_182595.3 NP_872401.3 Q8N7R1 P1L12_HUMAN POM121 transmembrane nucleoporin-like 12 61 CACCCAGTCTGCTGGCCCCTT 0.607000 0 SO:0001583 missense ENST00000408890.4 1 1 hg19 CCDS43584.1 . . . . . . . . . . G 9.797 1.179487 0.21787 . . ENSG00000221900 ENST00000408890 T 0.26810 1.71 1.78 0.86 0.19042 . . . . . T 0.24122 0.0584 N 0.08118 0 0.09310 N 1 D 0.76494 0.999 D 0.66602 0.945 T 0.12578 -1.0542 9 0.87932 D 0 . 6.0476 0.19768 0.0:0.3261:0.6739:0.0 . 291 Q8N7R1 P1L12_HUMAN S 291 ENSP00000386133:A291S ENSP00000386133:A291S A + 1 0 POM121L12 53071729 0.000000 0.05858 0.018000 0.16275 0.002000 0.02628 -0.523000 0.06230 0.316000 0.23135 -0.304000 0.09214 GCT TCGA-HV-A7OL-01A-11D-A33T-08 POM121L12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342656.1 1 0 1 56 330 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 1.000000 55 327 0 61 2 0 0 0 0 61 2 -20.000000 1 1 0 0 1 0 0 0 2.019785 0 0.370000 1.920000 0.367660 0.770000 6.000000e-01 0.970000 0.770000 0.786903 0.770000 0 6.800000e-01 0.880000 COL1A2 1278 broad.mit.edu 37 7 94052353 94052353 + Nonsense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr7:94052353C>T ENST00000297268.6 + 40 2959 c.2488C>T c.(2488-2490)Cga>Tga p.R830* NM_000089.3 NP_000080.2 P08123 CO1A2_HUMAN collagen, type I, alpha 2 COL1A2/PLAG1(3) 115 all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08) STAD - Stomach adenocarcinoma(171;0.0031) Collagenase(DB00048) TCCAGTTGGCCGAACTGGAGA 0.567000 HNSCC(75;0.22) 0 SO:0001587 stop_gained ENST00000297268.6 0 1 hg19 CCDS34682.1 . . . . . . . . . . C 44 11.258435 0.99538 . . ENSG00000164692 ENST00000297268;ENST00000545487 . . . 5.23 4.34 0.51931 . 0.146062 0.46758 D 0.000268 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 15.5039 0.75722 0.1397:0.8603:0.0:0.0 . . . . X 830;831 . ENSP00000297268:R830X R + 1 2 COL1A2 93890289 0.998000 0.40836 1.000000 0.80357 0.991000 0.79684 1.529000 0.35996 1.335000 0.45486 0.563000 0.77884 CGA TCGA-HV-A7OL-01A-11D-A33T-08 COL1A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000309045.2 1 0 1 108 427 0 80 0 1 1 1188 0 80 2 0 0 0 0 0 2 1 1.000000 105 421 0 80 2 0 0 0 0 80 2 -3.235997 1 1 0 0 1 0 0 0 2.019785 0 0.370000 1.920000 0.367660 0.990000 9.000000e-01 1.000000 1.000000 0.992100 0.990000 1 9.900000e-01 1.000000 LZTS1 11178 broad.mit.edu 37 8 20112535 20112535 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr8:20112535C>T ENST00000381569.1 - 2 515 c.158G>A c.(157-159)gGc>gAc p.G53D LZTS1_ENST00000265801.6_Missense_Mutation_p.G53D|LZTS1_ENST00000522290.1_Missense_Mutation_p.G53D Q9Y250 LZTS1_HUMAN leucine zipper, putative tumor suppressor 1 29 GCTGGACTTGCCGTGACCGGA 0.577000 0 SO:0001583 missense ENST00000381569.1 0 1 hg19 CCDS6015.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 15.43|15.43 2.830957|2.830957 0.50845|0.50845 .|. .|. ENSG00000061337|ENSG00000061337 ENST00000334294|ENST00000381569;ENST00000265801;ENST00000522290;ENST00000360248 .|T;T;T .|0.24151 .|2.2;2.2;1.87 5.98|5.98 5.98|5.98 0.97165|0.97165 .|. .|0.457888 .|0.25601 .|N .|0.029548 .|T .|0.17577 .|0.0422 N|N 0.14661|0.14661 0.345|0.345 0.42195|0.42195 D|D 0.991743|0.991743 .|P;P .|0.41366 .|0.589;0.747 .|B;B .|0.39258 .|0.295;0.255 .|T .|0.02844 .|-1.1103 .|10 .|0.62326 .|D .|0.03 .|-41.4352 13.5254|13.5254 0.61593|0.61593 0.0:0.8439:0.1561:0.0|0.0:0.8439:0.1561:0.0 .|. .|53;53 .|Q9Y250-4;Q9Y250 .|.;LZTS1_HUMAN .|D -1|53 .|ENSP00000370981:G53D;ENSP00000265801:G53D;ENSP00000429263:G53D .|ENSP00000265801:G53D .|G -|- .|2 .|0 LZTS1|LZTS1 20156815|20156815 1.000000|1.000000 0.71417|0.71417 0.997000|0.997000 0.53966|0.53966 0.993000|0.993000 0.82548|0.82548 2.376000|2.376000 0.44292|0.44292 2.835000|2.835000 0.97688|0.97688 0.650000|0.650000 0.86243|0.86243 .|GGC TCGA-HV-A7OL-01A-11D-A33T-08 LZTS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214122.1 0 0 0 5 527 0 72 0 0 0 0 72 2 0 0 0 0 0 2 1 0.936566 5 523 0 72 2 0 0 0 0 72 2 -2.374609 0 1 0 0 1 1 2 3 2.035597 0 0.370000 1.920000 0.371163 0.050000 1.000000e-02 0.120000 0.050000 0.060613 0.050000 0 3.000000e-02 0.090000 MYOM2 9172 broad.mit.edu 37 8 2041801 2041801 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr8:2041801G>A ENST00000262113.4 + 17 2149 c.2008G>A c.(2008-2010)Gtg>Atg p.V670M MYOM2_ENST00000523438.1_Missense_Mutation_p.V95M NM_003970.2 NP_003961.2 P54296 MYOM2_HUMAN myomesin 2 104 Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217) TCTCAGGTTCGTGGTGCACGG 0.498000 0 SO:0001583 missense ENST00000262113.4 1 1 hg19 CCDS5957.1 . . . . . . . . . . G 21.1 4.095427 0.76870 . . ENSG00000036448 ENST00000262113;ENST00000523438 T;T 0.57595 0.39;0.39 5.44 4.57 0.56435 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.065948 0.64402 D 0.000013 T 0.70307 0.3209 M 0.76328 2.33 0.41362 D 0.987435 D 0.76494 0.999 D 0.65443 0.935 T 0.75238 -0.3388 10 0.72032 D 0.01 . 14.5057 0.67750 0.071:0.0:0.929:0.0 . 670 P54296 MYOM2_HUMAN M 670;95 ENSP00000262113:V670M;ENSP00000428396:V95M ENSP00000262113:V670M V + 1 0 MYOM2 2029208 1.000000 0.71417 0.913000 0.36048 0.847000 0.48162 6.115000 0.71566 1.298000 0.44778 0.655000 0.94253 GTG TCGA-HV-A7OL-01A-11D-A33T-08 MYOM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251249.1 1 0 1 67 324 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 1.000000 67 319 0 69 2 0 0 0 0 69 2 -20.000000 1 1 121412 2 37 1 1 2 3 2.035597 0 0.370000 1.920000 0.371163 0.920000 7.300000e-01 1.000000 1.000000 0.916391 0.920000 1 8.200000e-01 1.000000 FBXW2 26190 broad.mit.edu 37 9 123527025 123527025 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr9:123527025G>A ENST00000608872.1 - 8 1364 c.1177C>T c.(1177-1179)Cgg>Tgg p.R393W FBXW2_ENST00000493559.1_Intron|FBXW2_ENST00000340778.5_Missense_Mutation_p.R328W NM_012164.3 NP_036296.2 Q9UKT8 FBXW2_HUMAN F-box and WD repeat domain containing 2 4 CTCTCTGTCCGCAAGTCCATG 0.517000 0 SO:0001583 missense ENST00000608872.1 0 1 hg19 CCDS43872.1 . . . . . . . . . . G 12.55 1.972103 0.34754 . . ENSG00000119402 ENST00000373926;ENST00000340778;ENST00000444833 T;T 0.19250 2.16;2.16 4.95 0.397 0.16314 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.000000 0.85682 D 0.000000 T 0.35422 0.0931 L 0.47716 1.5 0.58432 D 0.999996 B;D;D 0.89917 0.107;1.0;0.999 B;D;D 0.75020 0.009;0.985;0.985 T 0.09443 -1.0674 10 0.72032 D 0.01 -9.1372 13.1259 0.59354 0.0:0.0:0.4582:0.5418 . 328;393;393 Q9UKT8-2;B2RAW3;Q9UKT8 .;.;FBXW2_HUMAN W 393;328;393 ENSP00000363036:R393W;ENSP00000341161:R328W ENSP00000341161:R328W R - 1 2 FBXW2 122566846 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.010000 0.40913 0.155000 0.19261 0.563000 0.77884 CGG TCGA-HV-A7OL-01A-11D-A33T-08 FBXW2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053834.2 0 0 0 7 573 0 90 0 5.114182e-01 1 129 0 90 2 0 0 0 0 0 2 1 0.980224 7 569 0 90 2 0 0 0 0 90 2 -1.804728 0 1 0 0 1 1 2 3 2.030095 0 0.370000 1.920000 0.371163 0.060000 2.000000e-02 0.130000 0.060000 0.074241 0.060000 0 4.000000e-02 0.100000 ANGPTL2 23452 broad.mit.edu 37 9 129854112 129854112 + Silent SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr9:129854112G>A ENST00000373425.3 - 4 1736 c.1119C>T c.(1117-1119)tcC>tcT p.S373S RALGPS1_ENST00000259351.5_Intron|RALGPS1_ENST00000394022.3_Intron|RALGPS1_ENST00000424082.2_Intron|RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000373436.1_Intron|ANGPTL2_ENST00000373417.1_Silent_p.S71S NM_012098.2 NP_036230.1 Q9UKU9 ANGL2_HUMAN angiopoietin-like 2 p.S373S(1) 18 CTTTGCGGCCGGACCAGTCCT 0.552000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000373425.3 0 1 hg19 CCDS6868.1 TCGA-HV-A7OL-01A-11D-A33T-08 ANGPTL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054129.1 0 0 0 8 1458 0 224 0 1.385979e-02 0 28 0 224 2 0 0 0 0 0 2 1 0.988781 9 1440 0 220 2 0 0 0 0 224 2 -1.705499 0 1 0 0 1 1 2 3 2.030095 0 0.370000 1.920000 0.371163 0.020000 0 0.060000 0.030000 0.032339 0.020000 0 1.000000e-02 0.050000 PRRX2 51450 broad.mit.edu 37 9 132481624 132481624 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr9:132481624G>A ENST00000372469.4 + 2 601 c.374G>A c.(373-375)cGc>cAc p.R125H RP11-483H20.6_ENST00000440413.1_RNA NM_016307.3 NP_057391.1 Q99811 PRRX2_HUMAN paired related homeobox 2 3 Ovarian(14;0.00556) GTGTTCGAGCGCACGCACTAC 0.701000 0 SO:0001583 missense ENST00000372469.4 0 1 hg19 CCDS6926.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 34|34 5.387915|5.387915 0.95988|0.95988 .|. .|. ENSG00000167157|ENSG00000167157 ENST00000557730|ENST00000372469 .|D .|0.96334 .|-3.98 4.18|4.18 4.18|4.18 0.49190|0.49190 .|Homeodomain-related (1);Homeobox (3);Homeodomain-like (1); .|0.000000 .|0.85682 .|D .|0.000000 D|D 0.97340|0.97340 0.9130|0.9130 L|L 0.58925|0.58925 1.835|1.835 0.80722|0.80722 D|D 1|1 .|D .|0.89917 .|1.0 .|D .|0.80764 .|0.994 D|D 0.98098|0.98098 1.0413|1.0413 5|10 .|0.87932 .|D .|0 .|. 15.6697|15.6697 0.77264|0.77264 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|125 .|Q99811 .|PRRX2_HUMAN T|H 40|125 .|ENSP00000361547:R125H .|ENSP00000361547:R125H A|R +|+ 1|2 0|0 PRRX2|PRRX2 131521445|131521445 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.993000|0.993000 0.82548|0.82548 5.471000|5.471000 0.66762|0.66762 2.187000|2.187000 0.69744|0.69744 0.462000|0.462000 0.41574|0.41574 GCA|CGC TCGA-HV-A7OL-01A-11D-A33T-08 PRRX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054598.2 0 0 0 4 57 0 11 0 6.561796e-01 0 31 0 11 2 0 0 0 0 0 2 1 0.892642 4 57 0 11 2 0 0 0 0 11 2 -8.845400 1 1 0 0 1 1 2 3 2.030095 0 0.370000 1.920000 0.371163 0.380000 1.300000e-01 0.830000 0.340000 0.417604 0.380000 0 2.300000e-01 0.590000 FIBCD1 84929 broad.mit.edu 37 9 133779512 133779512 + Missense_Mutation SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr9:133779512C>T ENST00000372338.4 - 7 1567 c.1325G>A c.(1324-1326)gGc>gAc p.G442D FIBCD1_ENST00000253018.4_Intron|FIBCD1_ENST00000448616.1_Missense_Mutation_p.G442D|FIBCD1_ENST00000372337.2_Missense_Mutation_p.G284D NM_032843.4 NP_116232.3 Q8N539 FBCD1_HUMAN fibrinogen C domain containing 1 12 all_hematologic(7;0.0028) GTACTGCCAGCCGGTCCAGGA 0.637000 0 SO:0001583 missense ENST00000372338.4 0 1 hg19 CCDS6937.1 . . . . . . . . . . C 26.1 4.702186 0.88924 . . ENSG00000130720 ENST00000448616;ENST00000372338;ENST00000372337 D;D;D 0.82619 -1.63;-1.63;-1.63 4.66 4.66 0.58398 Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1); 0.000000 0.85682 D 0.000000 D 0.91116 0.7203 M 0.80028 2.48 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.92390 0.5920 10 0.66056 D 0.02 . 16.1061 0.81223 0.0:1.0:0.0:0.0 . 442 Q8N539 FBCD1_HUMAN D 442;442;284 ENSP00000414501:G442D;ENSP00000361413:G442D;ENSP00000361412:G284D ENSP00000361412:G284D G - 2 0 FIBCD1 132769333 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 5.967000 0.70403 2.138000 0.66242 0.455000 0.32223 GGC TCGA-HV-A7OL-01A-11D-A33T-08 FIBCD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054687.2 0 0 0 5 414 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 0.935907 5 409 0 86 2 0 0 0 0 87 2 -2.916400 1 1 0 0 1 1 2 3 2.030095 0 0.370000 1.920000 0.371163 0.060000 2.000000e-02 0.150000 0.060000 0.076868 0.060000 0 4.000000e-02 0.110000 COL5A1 1289 broad.mit.edu 37 9 137593148 137593148 + Missense_Mutation SNP G G A TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr9:137593148G>A ENST00000371817.3 + 4 1037 c.623G>A c.(622-624)gGc>gAc p.G208D COL5A1_ENST00000464187.1_3'UTR NM_000093.3|NM_001278074.1 NP_000084.3|NP_001265003.1 P20908 CO5A1_HUMAN collagen, type V, alpha 1 115 Myeloproliferative disorder(178;0.0341) ATCGTGTTTGGCACCCGGATC 0.552000 0 SO:0001583 missense ENST00000371817.3 1 1 hg19 CCDS6982.1 . . . . . . . . . . G 16.27 3.075833 0.55646 . . ENSG00000130635 ENST00000371817 D 0.95918 -3.85 4.93 4.04 0.47022 Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);Laminin G, subdomain 2 (1); 0.000000 0.64402 U 0.000001 D 0.97870 0.9300 H 0.95260 3.645 0.58432 D 0.999994 P 0.52692 0.955 P 0.57204 0.815 D 0.98523 1.0624 10 0.87932 D 0 . 13.5115 0.61515 0.0763:0.0:0.9237:0.0 . 208 P20908 CO5A1_HUMAN D 208 ENSP00000360882:G208D ENSP00000360882:G208D G + 2 0 COL5A1 136732969 1.000000 0.71417 0.742000 0.31022 0.439000 0.31926 9.489000 0.97949 1.196000 0.43129 0.491000 0.48974 GGC TCGA-HV-A7OL-01A-11D-A33T-08 COL5A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054954.2 1 0 0 8 143 0 27 0 2.436969e-01 0 16 0 27 2 0 0 0 0 0 2 1 0.989415 8 141 0 27 2 0 0 0 0 27 2 -11.499900 1 1 0 0 1 1 2 3 2.030095 0 0.370000 1.920000 0.371163 0.290000 1.400000e-01 0.540000 0.280000 0.315003 0.290000 0 2.000000e-01 0.410000 CDKN2A 1029 broad.mit.edu 37 9 21971120 21971120 + Nonsense_Mutation SNP G G A rs121913388 TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr9:21971120G>A ENST00000304494.5 - 2 508 c.238C>T c.(238-240)Cga>Tga p.R80* CDKN2A_ENST00000530628.2_Missense_Mutation_p.P94L|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P94L|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P135L|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R80*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.R29* NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.R80*(100)|p.?(44)|p.P135L(7)|p.L65fs*38(1)|p.T79fs*37(1)|p.0(1)|p.A76fs*64(1)|p.T79fs*65(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.R80fs*34(1) 4199 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) TGCACGGGTCGGGTGAGAGTG 0.726000 R80*(HSC4_UPPER_AERODIGESTIVE_TRACT)|R80*(MEWO_SKIN) 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1474 Whole gene deletion(1316)|Substitution - Nonsense(100)|Unknown(44)|Substitution - Missense(7)|Deletion - Frameshift(6)|Deletion - In frame(1) GRCh37 CM014695 CDKN2A M rs121913388 SO:0001587 stop_gained ENST00000304494.5 0 1 hg19 CCDS6510.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 39|39 7.328457|7.328457 0.98214|0.98214 .|. .|. ENSG00000147889|ENSG00000147889 ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177 D;D|. 0.86497|. -2.13;-2.02|. 5.93|5.93 5.01|5.01 0.66863|0.66863 .|. 0.000000|. 0.37136|. N|. 0.002233|. T|. 0.44561|. 0.1299|. L|L 0.36672|0.36672 1.1|1.1 0.47511|0.47511 D|D 0.999443|0.999443 D|. 0.59357|. 0.985|. B|. 0.40602|. 0.334|. T|. 0.34825|. -0.9813|. 10|. 0.13108|0.02654 T|T 0.6|1 -2.989|-2.989 8.7197|8.7197 0.34434|0.34434 0.0759:0.0:0.7715:0.1526|0.0759:0.0:0.7715:0.1526 .|. 135|. Q8N726|. CD2A2_HUMAN|. L|X 135;94|80 ENSP00000355153:P135L;ENSP00000432664:P94L|. ENSP00000355153:P135L|ENSP00000307101:R80X P|R -|- 2|1 0|2 CDKN2A|CDKN2A 21961120|21961120 0.995000|0.995000 0.38212|0.38212 1.000000|1.000000 0.80357|0.80357 0.899000|0.899000 0.52679|0.52679 2.363000|2.363000 0.44178|0.44178 1.464000|1.464000 0.47987|0.47987 0.650000|0.650000 0.86243|0.86243 CCG|CGA TCGA-HV-A7OL-01A-11D-A33T-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 28 90 0 16 1 9.999910e-01 56 10 0 16 2 1 1 33 115 0 155 2 1 1.000000 21 75 0 11 2 0 0 0 0 16 2 -3.594689 1 1 0 0 1 0 1 1 1.677653 1 0.370000 1.920000 0.226994 0.890000 6.700000e-01 1.000000 0.990000 0.887197 0.890000 1 7.900000e-01 0.970000 PRUNE2 158471 broad.mit.edu 37 9 79438590 79438590 + Silent SNP T T C TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chr9:79438590T>C ENST00000376718.3 - 6 837 c.714A>G c.(712-714)ggA>ggG p.G238G PRUNE2_ENST00000376713.3_Silent_p.G238G|PRUNE2_ENST00000428286.1_5'UTR NM_015225.2 NP_056040.2 Q8WUY3 PRUN2_HUMAN prune homolog 2 (Drosophila) 16 CTTTTATTTCTCCATCTGACA 0.373000 0 SO:0001819 synonymous_variant ENST00000376718.3 1 1 hg19 CCDS47982.1 TCGA-HV-A7OL-01A-11D-A33T-08 PRUNE2-003 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052730.2 1 0 1 90 486 0 76 0 0 0 0 76 2 0 0 0 0 0 2 1 1.000000 90 485 0 76 2 0 0 0 0 76 2 -20.000000 1 1 0 0 1 1 2 3 2.030095 0 0.370000 1.920000 0.371163 0.840000 6.900000e-01 1.000000 0.840000 0.848710 0.840000 0 7.600000e-01 0.930000 SCML1 6322 broad.mit.edu 37 X 17770059 17770059 + Silent SNP C C T TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chrX:17770059C>T ENST00000380041.3 + 7 1156 c.828C>T c.(826-828)tgC>tgT p.C276C SCML1_ENST00000380043.3_Silent_p.C249C|SCML1_ENST00000398080.1_Silent_p.C155C|SCML1_ENST00000380045.3_Silent_p.C155C NM_001037540.1 NP_001032629.1 Q9UN30 SCML1_HUMAN sex comb on midleg-like 1 (Drosophila) 10 Hepatocellular(33;0.183) TTGCATTATGCCCTCTTGTCG 0.448000 0 SO:0001819 synonymous_variant ENST00000380041.3 0 1 hg19 CCDS35210.1 TCGA-HV-A7OL-01A-11D-A33T-08 SCML1-006 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000060495.5 0 0 0 7 962 0 152 0 0 0 1 0 152 2 0 0 0 0 0 2 1 0.979802 7 951 0 152 2 0 0 0 0 152 2 -1.737522 0 1 0 0 1 0 1 1 0.370000 1.920000 0.370000 0.010000 0 0.040000 0.020000 0.022227 0.010000 0 0 0.030000 PCDH11X 27328 broad.mit.edu 37 X 91090548 91090548 + Silent SNP A A G TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chrX:91090548A>G ENST00000373094.1 + 1 890 c.45A>G c.(43-45)gcA>gcG p.A15A PCDH11X_ENST00000298274.8_Silent_p.A15A|PCDH11X_ENST00000361724.1_Silent_p.A15A|PCDH11X_ENST00000373088.1_Silent_p.A15A|PCDH11X_ENST00000395337.2_Silent_p.A15A|PCDH11X_ENST00000504220.2_Silent_p.A15A|PCDH11X_ENST00000361655.2_Silent_p.A15A|PCDH11X_ENST00000406881.1_Silent_p.A15A|PCDH11X_ENST00000373097.1_Silent_p.A15A NM_032968.3 NP_116750.1 Q9BZA7 PC11X_HUMAN protocadherin 11 X-linked 159 TCCTGCTAGCATGCGTGGTGT 0.478000 NSCLC(38;925 1092 2571 38200 45895) 0 SO:0001819 synonymous_variant ENST00000373094.1 0 1 hg19 CCDS14461.1 TCGA-HV-A7OL-01A-11D-A33T-08 PCDH11X-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000057436.1 0 0 0 6 208 1 36 0 0 0 1 36 2 0 0 0 0 0 2 0 0.008958 6 207 1 36 18 0 0 0 1 36 2 -8.192649 1 0 0 0 1 0 1 1 0.370000 1.920000 0.370000 0.070000 2.000000e-02 0.150000 0.080000 0.086886 0.070000 0 5.000000e-02 0.120000 DIAPH2 1730 broad.mit.edu 37 X 96185760 96185760 + Missense_Mutation SNP T T G TCGA-HV-A7OL-01A-11D-A33T-08 TCGA-HV-A7OL-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0760de9f-10f1-43db-a96a-7c82c37d4cf3 306b21fa-27e2-44ab-8b5b-583be65a9182 g.chrX:96185760T>G ENST00000324765.8 + 10 1354 c.1007T>G c.(1006-1008)cTt>cGt p.L336R DIAPH2_ENST00000355827.4_Missense_Mutation_p.L336R|DIAPH2_ENST00000373061.3_Missense_Mutation_p.L336R|DIAPH2_ENST00000373054.4_Missense_Mutation_p.L332R|DIAPH2_ENST00000373049.4_Missense_Mutation_p.L336R O60879 DIAP2_HUMAN diaphanous-related formin 2 51 ATAAATGCCCTTGTCACTTCT 0.303000 0 SO:0001583 missense ENST00000324765.8 1 1 hg19 CCDS14467.1 . . . . . . . . . . T 16.84 3.234447 0.58886 . . ENSG00000147202 ENST00000373061;ENST00000373054;ENST00000355827;ENST00000373049;ENST00000324765;ENST00000537885 D;D;D;D;D 0.91740 -2.9;-2.9;-2.9;-2.9;-2.9 4.93 4.93 0.64822 GTPase-binding/formin homology 3 (1);Diaphanous FH3 (1);Armadillo-type fold (1); 0.000000 0.64402 D 0.000011 D 0.96411 0.8829 M 0.89095 3.005 0.58432 D 0.999991 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;0.999;1.0 D 0.97111 0.9804 10 0.87932 D 0 . 13.9748 0.64265 0.0:0.0:0.0:1.0 . 336;336;343 O60879;O60879-2;B7ZLJ0 DIAP2_HUMAN;.;. R 336;332;336;336;336;343 ENSP00000362152:L336R;ENSP00000362145:L332R;ENSP00000348082:L336R;ENSP00000362140:L336R;ENSP00000321348:L336R ENSP00000321348:L336R L + 2 0 DIAPH2 96072416 1.000000 0.71417 0.998000 0.56505 0.992000 0.81027 7.424000 0.80242 1.745000 0.51790 0.481000 0.45027 CTT TCGA-HV-A7OL-01A-11D-A33T-08 DIAPH2-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000058871.2 1 0 1 65 125 0 28 1 2.743426e-01 3 0 0 28 2 0 0 0 0 0 2 1 1.000000 64 124 0 28 2 0 0 0 0 28 2 -20.000000 1 1 0 0 1 0 1 1 0.370000 1.920000 0.370000 0.890000 7.300000e-01 1.000000 0.920000 0.890351 0.890000 1 8.100000e-01 0.960000