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 BTAF1 9044 broad.mit.edu 37 10 93786913 93786913 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr10:93786913G>T ENST00000265990.6 + 37 5570 c.5262G>T c.(5260-5262)ttG>ttT p.L1754F BTAF1_ENST00000544642.1_Missense_Mutation_p.L582F NM_003972.2 NP_003963.1 O14981 BTAF1_HUMAN BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa 59 Colorectal(252;0.0846) TATACCGATTGATAACCAGAG 0.378000 0 SO:0001583 missense ENST00000265990.6 1 1 hg19 CCDS7419.1 . . . . . . . . . . G 19.60 3.857996 0.71834 . . ENSG00000095564 ENST00000265990;ENST00000544642;ENST00000538688 T;T 0.79033 -1.23;-1.23 5.52 2.63 0.31362 Helicase, C-terminal (1); 0.000000 0.64402 D 0.000001 T 0.81754 0.4889 L 0.49350 1.555 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.80139 -0.1507 10 0.62326 D 0.03 -8.1932 7.3657 0.26772 0.2012:0.1222:0.6766:0.0 . 1754 O14981 BTAF1_HUMAN F 1754;582;604 ENSP00000265990:L1754F;ENSP00000439924:L582F ENSP00000265990:L1754F L + 3 2 BTAF1 93776893 1.000000 0.71417 0.997000 0.53966 0.914000 0.54420 2.707000 0.47143 0.814000 0.34374 0.561000 0.74099 TTG TCGA-XN-A8T3-01A-11D-A36O-08 BTAF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049380.4 1 0 1 68 373 0 91 1 9.894300e-01 12 29 0 91 2 0 0 0 0 0 2 1 1.000000 67 368 0 90 2 0 0 0 0 91 2 -20.000000 1 0 0 0 1 1 2 3 1.931020 0 0.190000 3.530000 0.260274 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MYOF 26509 broad.mit.edu 37 10 95121227 95121227 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr10:95121227G>T ENST00000359263.4 - 28 2955 c.2956C>A c.(2956-2958)Cga>Aga p.R986R MYOF_ENST00000371501.4_Silent_p.R986R|MYOF_ENST00000371502.4_Silent_p.R986R|MYOF_ENST00000358334.5_Silent_p.R973R NM_013451.3 NP_038479.1 Q9NZM1 MYOF_HUMAN myoferlin p.R986G(1) 67 TCCACCGCTCGATTTATGTCA 0.483000 1 Substitution - Missense(1) SO:0001819 synonymous_variant ENST00000359263.4 1 0 hg19 CCDS41551.1 TCGA-XN-A8T3-01A-11D-A36O-08 MYOF-005 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000049423.2 1 0 0 17 375 0 81 0 9.798764e-01 0 143 0 81 2 0 0 0 0 0 2 1 0.999961 17 367 0 78 2 0 0 0 0 81 2 -4.024528 1 1 0 0 1 1 2 3 1.931020 0 0.190000 3.530000 0.260274 0.500000 0.300000 0.760000 0.490000 0.522749 0.500000 0 0.390000 0.640000 TRIM29 23650 broad.mit.edu 37 11 119993732 119993732 + Silent SNP C C A rs137882673 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr11:119993732C>A ENST00000341846.5 - 5 1786 c.1365G>T c.(1363-1365)acG>acT p.T455T TRIM29_ENST00000528870.1_5'UTR|TRIM29_ENST00000524816.3_Silent_p.T21T|TRIM29_ENST00000541857.1_Silent_p.T188T|TRIM29_ENST00000529044.1_Silent_p.T194T|TRIM29_ENST00000525887.1_5'Flank NM_012101.3 NP_036233.2 Q14134 TRI29_HUMAN tripartite motif containing 29 30 Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) CGAAGCTGTTCGTGTAGTTGT 0.577000 0 SO:0001819 synonymous_variant ENST00000341846.5 1 0 hg19 CCDS8428.1 . . . . . . . . . . C 4.375 0.069135 0.08436 . . ENSG00000137699 ENST00000525327 . . . 4.12 -8.25 0.01025 . . . . . . . . . . . 0.18873 N 0.999985 . . . . . . . . . . . . . . 6.2926 0.21069 0.0942:0.2723:0.4906:0.1429 . . . . X 48 . . E - 1 0 TRIM29 119498942 0.000000 0.05858 0.001000 0.08648 0.690000 0.40134 -3.482000 0.00456 -4.073000 0.00076 -1.707000 0.00718 GAA TCGA-XN-A8T3-01A-11D-A36O-08 TRIM29-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000277108.2 1 0 0 21 478 1 109 0 2.357929e-01 0 21 1 109 2 0 0 0 0 0 2 1 0.999997 20 466 0 108 2 0 0 0 1 109 2 -2.777613 1 1 0 0 1 1 2 3 1.915771 0 0.190000 3.530000 0.260274 0.490000 0.310000 0.710000 0.480000 0.503266 0.490000 0 0.390000 0.600000 DCPS 28960 broad.mit.edu 37 11 126208220 126208220 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr11:126208220C>A ENST00000263579.4 + 4 891 c.562C>A c.(562-564)Cgg>Agg p.R188R DCPS_ENST00000530860.1_Intron NM_014026.3 NP_054745.1 Q96C86 DCPS_HUMAN decapping enzyme, scavenger 17 all_hematologic(175;0.145) Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604) TGAAGCGGACCGGATTGTTTT 0.502000 0 SO:0001819 synonymous_variant ENST00000263579.4 1 0 hg19 CCDS8473.1 TCGA-XN-A8T3-01A-11D-A36O-08 DCPS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000386455.1 1 0 0 13 298 0 53 0 7.123048e-01 0 58 0 53 2 0 0 0 0 0 2 1 0.999522 13 294 0 52 2 0 0 0 0 53 2 -2.619992 1 1 0 0 1 1 2 3 1.915771 0 0.190000 3.530000 0.260274 0.490000 0.270000 0.780000 0.480000 0.510782 0.490000 0 0.370000 0.640000 PIK3C2A 5286 broad.mit.edu 37 11 17190264 17190264 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr11:17190264C>A ENST00000265970.7 - 1 1024 c.1025G>T c.(1024-1026)cGa>cTa p.R342L PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Intron NM_002645.2 NP_002636.2 O00443 P3C2A_HUMAN phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha 58 CTGAGTTGTTCGAATATTTAA 0.373000 0 SO:0001583 missense ENST00000265970.7 1 0 hg19 CCDS7824.1 . . . . . . . . . . C 12.60 1.985990 0.35036 . . ENSG00000011405 ENST00000265970;ENST00000544896 T 0.64803 -0.12 5.39 2.39 0.29439 . 0.787528 0.11900 N 0.518665 T 0.47746 0.1462 L 0.32530 0.975 0.80722 D 1 P;B 0.40302 0.712;0.36 B;B 0.34536 0.185;0.09 T 0.38329 -0.9666 10 0.46703 T 0.11 -0.7378 10.8495 0.46761 0.0:0.6901:0.2424:0.0675 . 342;342 F5H5W9;O00443 .;P3C2A_HUMAN L 342 ENSP00000265970:R342L ENSP00000265970:R342L R - 2 0 PIK3C2A 17146840 1.000000 0.71417 1.000000 0.80357 0.965000 0.64279 3.430000 0.52807 0.633000 0.30452 -0.300000 0.09419 CGA TCGA-XN-A8T3-01A-11D-A36O-08 PIK3C2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387553.1 1 0 0 24 583 0 126 0 6.171081e-02 0 10 0 126 2 0 0 0 0 0 2 1 1.000000 25 574 0 126 2 0 0 0 0 126 2 -3.138803 1 1 0 0 1 1 2 3 1.918179 0 0.190000 3.530000 0.260274 0.450000 0.300000 0.650000 0.450000 0.470953 0.450000 0 0.370000 0.560000 TNNT3 7140 broad.mit.edu 37 11 1956113 1956113 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr11:1956113C>A ENST00000397301.1 + 15 686 c.678C>A c.(676-678)ttC>ttA p.F226L TNNT3_ENST00000381548.3_Missense_Mutation_p.F217L|TNNT3_ENST00000360603.3_Missense_Mutation_p.F209L|TNNT3_ENST00000397304.2_Missense_Mutation_p.F196L|TNNT3_ENST00000381561.4_Missense_Mutation_p.F218L|TNNT3_ENST00000446240.1_Missense_Mutation_p.F196L|TNNT3_ENST00000493234.1_3'UTR|TNNT3_ENST00000381589.3_Missense_Mutation_p.F213L|TNNT3_ENST00000381549.3_Missense_Mutation_p.F207L|TNNT3_ENST00000381579.3_Missense_Mutation_p.F207L|TNNT3_ENST00000381558.1_Missense_Mutation_p.F207L|TNNT3_ENST00000278317.6_Missense_Mutation_p.F215L P45378 TNNT3_HUMAN troponin T type 3 (skeletal, fast) 19 all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) TTGACAAGTTCGAGTTTGGGG 0.597000 0 SO:0001583 missense ENST00000397301.1 1 0 hg19 . . . . . . . . . . . 11.86 1.764327 0.31228 . . ENSG00000130595 ENST00000278317;ENST00000397309;ENST00000381561;ENST00000381548;ENST00000360603;ENST00000381549;ENST00000381589;ENST00000381579;ENST00000381557;ENST00000453458;ENST00000381563;ENST00000344578;ENST00000381558;ENST00000397301;ENST00000397304;ENST00000446240 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.91464 -2.85;-2.85;-2.85;-2.85;-2.85;-2.85;-2.85;-2.85;-2.85;-2.85;-2.85;-2.85;-2.85;-2.85;-2.85 4.28 -6.19 0.02078 . 0.210963 0.49916 D 0.000140 D 0.92648 0.7664 M 0.84219 2.685 0.50467 D 0.999874 D;P;D;D;P 0.53619 0.961;0.929;0.961;0.961;0.934 P;P;P;P;P 0.57152 0.814;0.748;0.748;0.745;0.656 D 0.91890 0.5523 10 0.54805 T 0.06 -1.9598 15.2622 0.73634 0.0:0.249:0.0:0.751 . 215;207;213;207;226 P45378-2;P45378-7;P45378-6;P45378-4;P45378 .;.;.;.;TNNT3_HUMAN L 215;227;218;217;209;207;213;207;201;196;218;202;207;226;196;196 ENSP00000278317:F215L;ENSP00000370973:F218L;ENSP00000370960:F217L;ENSP00000353815:F209L;ENSP00000370961:F207L;ENSP00000371001:F213L;ENSP00000370991:F207L;ENSP00000370969:F201L;ENSP00000415614:F196L;ENSP00000370975:F218L;ENSP00000344870:F202L;ENSP00000370970:F207L;ENSP00000380468:F226L;ENSP00000380471:F196L;ENSP00000413203:F196L ENSP00000278317:F215L F + 3 2 TNNT3 1912689 0.001000 0.12720 0.667000 0.29798 0.223000 0.24884 -2.010000 0.01454 -1.388000 0.02092 -0.657000 0.03884 TTC TCGA-XN-A8T3-01A-11D-A36O-08 TNNT3-010 KNOWN basic protein_coding protein_coding OTTHUMT00000142920.3 1 0 0 25 720 0 196 0 1.256362e-03 0 2 0 196 2 0 0 0 0 0 2 1 1.000000 25 709 0 194 2 0 0 0 0 196 2 -2.950824 1 1 0 0 1 1 2 3 1.918179 0 0.190000 3.530000 0.260274 0.380000 0.250000 0.550000 0.390000 0.399653 0.380000 0 0.310000 0.470000 PAX6 5080 broad.mit.edu 37 11 31815068 31815068 + Missense_Mutation SNP C C A rs75572362 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr11:31815068C>A ENST00000379132.3 - 10 1230 c.950G>T c.(949-951)cGa>cTa p.R317L PAX6_ENST00000419022.1_Missense_Mutation_p.R331L|PAX6_ENST00000379107.2_Missense_Mutation_p.R331L|PAX6_ENST00000379115.4_Missense_Mutation_p.R331L|PAX6_ENST00000241001.8_Missense_Mutation_p.R317L|PAX6_ENST00000379129.2_Missense_Mutation_p.R331L|PAX6_ENST00000379123.5_Missense_Mutation_p.R317L|PAX6_ENST00000379111.2_Missense_Mutation_p.R317L P26367 PAX6_HUMAN paired box 6 35 Lung SC(675;0.225) TGTGTCTGTTCGGCCCAACAT 0.532000 Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation 0 SO:0001583 missense Familial Cancer Database WAGR syndrome ENST00000379132.3 1 0 hg19 CCDS31451.1 . . . . . . . . . . C 24.1 4.497777 0.85069 . . ENSG00000007372 ENST00000419022;ENST00000379132;ENST00000379129;ENST00000531633;ENST00000379107;ENST00000464174;ENST00000241001;ENST00000379115;ENST00000379111;ENST00000379123;ENST00000494377;ENST00000470027;ENST00000379109;ENST00000533333;ENST00000530373 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.93859 -3.3;-3.3;-3.3;-2.95;-3.3;-2.92;-3.3;-3.3;-3.3;-3.3;-2.72;-2.72;-3.3;-3.04;-2.91 5.77 4.85 0.62838 . 0.209907 0.47093 D 0.000241 D 0.95918 0.8671 M 0.73962 2.25 0.58432 D 0.999999 D;D 0.89917 1.0;0.985 D;P 0.87578 0.998;0.78 D 0.94084 0.7347 10 0.23891 T 0.37 . 15.2159 0.73267 0.0:0.9313:0.0:0.0687 . 331;317 F1T0F8;P26367 .;PAX6_HUMAN L 331;317;331;146;331;116;317;331;317;317;181;181;317;272;116 ENSP00000404100:R331L;ENSP00000368427:R317L;ENSP00000368424:R331L;ENSP00000451885:R146L;ENSP00000368401:R331L;ENSP00000431961:R116L;ENSP00000241001:R317L;ENSP00000368410:R331L;ENSP00000368406:R317L;ENSP00000368418:R317L;ENSP00000451901:R181L;ENSP00000450775:R181L;ENSP00000368403:R317L;ENSP00000451372:R272L;ENSP00000452202:R116L ENSP00000241001:R317L R - 2 0 PAX6 31771644 1.000000 0.71417 0.999000 0.59377 0.995000 0.86356 5.740000 0.68629 2.698000 0.92095 0.643000 0.83706 CGA TCGA-XN-A8T3-01A-11D-A36O-08 PAX6-008 KNOWN not_organism_supported|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000099293.4 1 0 0 17 463 0 72 0 8.433578e-02 0 13 0 72 2 0 0 0 0 0 2 1 0.999962 17 456 0 70 2 0 0 0 0 72 2 -2.798772 1 1 0 0 1 1 2 3 1.918179 0 0.190000 3.530000 0.260274 0.410000 0.240000 0.620000 0.400000 0.427898 0.410000 0 0.320000 0.520000 ZFP91 80829 broad.mit.edu 37 11 58379764 58379764 + Nonsense_Mutation SNP C C T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr11:58379764C>T ENST00000316059.6 + 7 1042 c.871C>T c.(871-873)Cga>Tga p.R291* ZFP91-CNTF_ENST00000389919.4_Nonsense_Mutation_p.R291*|AP001350.1_ENST00000601906.1_5'Flank NM_001197051.1|NM_053023.4 NP_001183980.1|NP_444251.1 Q96JP5 ZFP91_HUMAN ZFP91 zinc finger protein 26 Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24) AGGAAGAAGACGAAAAGATGA 0.418000 0 SO:0001587 stop_gained ENST00000316059.6 0 1 hg19 CCDS31553.1 . . . . . . . . . . C 38 6.963557 0.97967 . . ENSG00000186660 ENST00000316059;ENST00000389918 . . . 5.69 4.75 0.60458 . . . . . . . . . . . 0.80722 A 1 . . . . . . . . . . 0.05620 T 0.96 -6.2665 11.456 0.50183 0.3271:0.6729:0.0:0.0 . . . . X 291 . ENSP00000374569:R291X R + 1 2 ZFP91 58136340 0.985000 0.35326 1.000000 0.80357 0.992000 0.81027 0.526000 0.22971 1.346000 0.45694 0.650000 0.86243 CGA TCGA-XN-A8T3-01A-11D-A36O-08 ZFP91-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268674.1 1 0 0 26 240 0 53 0 9.697699e-01 0 55 0 53 2 0 0 0 0 0 2 1 1.000000 26 237 0 51 2 0 0 0 0 53 2 -10.591580 1 1 0 0 1 1 2 3 1.915771 0 0.190000 3.530000 0.260274 0.990000 0.760000 1.000000 1.000000 0.973301 0.990000 1 0.930000 1.000000 OR52E8 390079 broad.mit.edu 37 11 5878138 5878138 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr11:5878138C>A ENST00000537935.1 - 1 826 c.795G>T c.(793-795)ttG>ttT p.L265F TRIM5_ENST00000380027.1_Intron NM_001005168.1 NP_001005168.1 Q6IFG1 O52E8_HUMAN olfactory receptor, family 52, subfamily E, member 8 20 Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114) AACGATGTGTCAAGAATGAAA 0.428000 0 SO:0001583 missense ENST00000537935.1 1 0 hg19 CCDS31400.1 . . . . . . . . . . C 2.139 -0.397187 0.04899 . . ENSG00000183269 ENST00000537935 T 0.41758 0.99 4.12 -0.562 0.11781 GPCR, rhodopsin-like superfamily (1); 0.000000 0.37095 N 0.002256 T 0.19446 0.0467 N 0.20401 0.57 0.09310 N 0.999992 B 0.14805 0.011 B 0.27170 0.077 T 0.08848 -1.0702 10 0.16896 T 0.51 . 0.7785 0.01036 0.1481:0.3064:0.2193:0.3262 . 265 Q6IFG1 O52E8_HUMAN F 265 ENSP00000444054:L265F ENSP00000444054:L265F L - 3 2 OR52E8 5834714 0.000000 0.05858 0.988000 0.46212 0.083000 0.17756 -3.965000 0.00324 0.104000 0.17725 -0.235000 0.12190 TTG TCGA-XN-A8T3-01A-11D-A36O-08 OR52E8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401145.1 1 0 0 31 839 0 216 0 0 0 0 216 2 0 0 0 0 0 2 1 1.000000 31 832 0 216 2 0 0 0 0 216 2 -3.122021 1 1 0 0 1 1 2 3 1.918179 0 0.190000 3.530000 0.260274 0.410000 0.280000 0.560000 0.420000 0.421602 0.410000 0 0.340000 0.490000 SLC22A12 116085 broad.mit.edu 37 11 64359303 64359303 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr11:64359303G>A ENST00000377574.1 + 1 1022 c.275G>A c.(274-276)cGc>cAc p.R92H SLC22A12_ENST00000377572.1_Missense_Mutation_p.R92H|SLC22A12_ENST00000473690.1_5'UTR|SLC22A12_ENST00000377567.2_Missense_Mutation_p.R92H|SLC22A12_ENST00000336464.7_Missense_Mutation_p.R92H NM_144585.2 NP_653186.2 Q96S37 S22AC_HUMAN solute carrier family 22 (organic anion/urate transporter), member 12 27 Losartan(DB00678)|Probenecid(DB01032) CGCCGCTTCCGCCAGCCACAG 0.677000 0 SO:0001583 missense ENST00000377574.1 1 0 hg19 CCDS8075.1 . . . . . . . . . . G 14.63 2.593237 0.46214 . . ENSG00000197891 ENST00000377567;ENST00000377574;ENST00000377572;ENST00000336464 T;T;T;T 0.15603 2.41;2.41;2.41;2.41 4.4 -0.511 0.11970 . 0.817974 0.10849 N 0.627391 T 0.40719 0.1128 M 0.88775 2.98 0.09310 N 1 D;D;D;D 0.89917 1.0;1.0;0.999;1.0 D;D;P;D 0.69479 0.964;0.964;0.898;0.964 T 0.15378 -1.0439 10 0.46703 T 0.11 . 6.9969 0.24786 0.0:0.2682:0.4327:0.2991 . 92;92;92;92 B5ME56;B3KV05;Q96S37-2;Q96S37 .;.;.;S22AC_HUMAN H 92 ENSP00000366790:R92H;ENSP00000366797:R92H;ENSP00000366795:R92H;ENSP00000336836:R92H ENSP00000336836:R92H R + 2 0 SLC22A12 64115879 0.000000 0.05858 0.977000 0.42913 0.296000 0.27459 -0.084000 0.11268 0.237000 0.21200 0.484000 0.47621 CGC TCGA-XN-A8T3-01A-11D-A36O-08 SLC22A12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000104966.2 1 0 1 35 152 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 1.000000 34 147 0 47 2 0 0 0 0 48 2 -1.133493 0 1 121256 9 31 1 1 2 3 1.915771 0 0.190000 3.530000 0.260274 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PPFIA1 8500 broad.mit.edu 37 11 70172768 70172768 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr11:70172768C>A ENST00000253925.7 + 7 989 c.774C>A c.(772-774)atC>atA p.I258I AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Silent_p.I258I|CTA-797E19.2_ENST00000526017.1_RNA NM_003626.3 NP_003617.1 Q13136 LIPA1_HUMAN protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 65 BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513) TCCAAGAAATCATAAGTAAGC 0.433000 0 SO:0001819 synonymous_variant ENST00000253925.7 0 1 hg19 CCDS31627.1 TCGA-XN-A8T3-01A-11D-A36O-08 PPFIA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000393905.1 0 0 0 28 1324 0 297 0 1.503440e-01 0 32 0 297 2 0 0 0 0 0 2 1 1.000000 25 1309 0 296 2 0 0 0 0 297 2 -2.675413 1 1 0 0 1 1 2 3 1.915771 0 0.190000 3.530000 0.260274 0.230000 0.150000 0.340000 0.240000 0.246347 0.230000 0 0.190000 0.290000 NADSYN1 55191 broad.mit.edu 37 11 71189504 71189504 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr11:71189504C>A ENST00000319023.2 + 10 1050 c.862C>A c.(862-864)Cga>Aga p.R288R NADSYN1_ENST00000530055.1_5'Flank|NADSYN1_ENST00000539574.1_Silent_p.R28R NM_018161.4 NP_060631.2 Q6IA69 NADE_HUMAN NAD synthetase 1 25 L-Glutamine(DB00130) GATTTCATCTCGAAACCTGGC 0.577000 Ovarian(79;763 1781 6490 50276) 0 SO:0001819 synonymous_variant ENST00000319023.2 0 1 hg19 CCDS8201.1 TCGA-XN-A8T3-01A-11D-A36O-08 NADSYN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394356.1 0 0 0 5 61 0 13 0 9.232580e-01 0 60 0 13 2 0 0 0 0 0 2 1 0.934978 5 59 0 13 2 0 0 0 0 13 2 -9.800195 1 0 121288 12 40 1 1 2 3 1.915771 0 0.190000 3.530000 0.260274 0.920000 0.360000 1.000000 1.000000 0.836876 0.920000 1 0.590000 1.000000 NUP37 79023 broad.mit.edu 37 12 102505967 102505967 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr12:102505967C>A ENST00000552283.1 - 3 339 c.200G>T c.(199-201)cGa>cTa p.R67L NUP37_ENST00000251074.1_Missense_Mutation_p.R67L|NUP37_ENST00000543021.1_5'UTR Q8NFH4 NUP37_HUMAN nucleoporin 37kDa p.R67L(1) 17 GTGAAATGTTCGAAGTGTTTT 0.368000 1 Substitution - Missense(1) SO:0001583 missense ENST00000552283.1 1 0 hg19 CCDS9089.1 . . . . . . . . . . C 17.27 3.347250 0.61183 . . ENSG00000075188 ENST00000552283;ENST00000251074;ENST00000551744 T;T;T 0.29397 1.57;1.57;2.86 5.43 3.61 0.41365 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.277784 0.35772 N 0.002997 T 0.30885 0.0779 M 0.71581 2.175 0.43965 D 0.996648 B;B 0.32203 0.36;0.36 B;B 0.31390 0.129;0.06 T 0.05550 -1.0878 10 0.34782 T 0.22 -2.6224 9.7045 0.40207 0.0:0.786:0.0:0.214 . 67;67 B4DKV8;Q8NFH4 .;NUP37_HUMAN L 67 ENSP00000448054:R67L;ENSP00000251074:R67L;ENSP00000448086:R67L ENSP00000251074:R67L R - 2 0 NUP37 101030097 1.000000 0.71417 0.871000 0.34182 0.884000 0.51177 2.501000 0.45389 0.775000 0.33450 0.585000 0.79938 CGA TCGA-XN-A8T3-01A-11D-A36O-08 NUP37-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000409330.1 1 0 0 20 394 0 67 0 6.773461e-01 0 47 0 67 2 0 0 0 0 0 2 1 0.539168 21 386 1 67 20 0 0 0 0 67 2 -4.624837 1 0 0 0 1 1 3 4 2.014333 1 0.190000 3.530000 0.306032 0.620000 0.380000 1.000000 0.600000 0.653585 0.620000 0 0.480000 0.820000 APPL2 55198 broad.mit.edu 37 12 105597519 105597519 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr12:105597519C>A ENST00000258530.3 - 9 891 c.666G>T c.(664-666)atG>atT p.M222I APPL2_ENST00000549573.1_5'UTR|APPL2_ENST00000551662.1_Missense_Mutation_p.M228I|APPL2_ENST00000539978.2_Missense_Mutation_p.M179I NM_001251904.1|NM_018171.3 NP_001238833.1|NP_060641.2 Q06481 APLP2_HUMAN adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2 33 AAAAGCTGTCCATACGTTTGG 0.418000 0 SO:0001583 missense ENST00000258530.3 0 1 hg19 CCDS9101.1 . . . . . . . . . . C 13.65 2.301684 0.40694 . . ENSG00000136044 ENST00000258530;ENST00000539978;ENST00000551662 T;T;T 0.03920 3.76;3.76;3.76 5.56 5.56 0.83823 . 0.037498 0.85682 D 0.000000 T 0.08714 0.0216 L 0.60455 1.87 0.58432 D 0.999999 B;B;B 0.31209 0.313;0.129;0.129 B;B;B 0.30251 0.113;0.053;0.048 T 0.04900 -1.0919 10 0.59425 D 0.04 -30.1684 17.7181 0.88343 0.0:1.0:0.0:0.0 . 228;179;222 F8W1P5;B7Z1Q8;Q8NEU8 .;.;DP13B_HUMAN I 222;179;228 ENSP00000258530:M222I;ENSP00000444472:M179I;ENSP00000446917:M228I ENSP00000258530:M222I M - 3 0 APPL2 104121649 1.000000 0.71417 1.000000 0.80357 0.525000 0.34531 5.448000 0.66612 2.620000 0.88729 0.655000 0.94253 ATG TCGA-XN-A8T3-01A-11D-A36O-08 APPL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406238.3 0 0 0 20 1022 0 212 0 2.444905e-01 0 47 0 212 2 0 0 0 0 0 2 1 0.999994 20 1005 0 211 2 0 0 0 0 212 2 -1.974054 0 1 0 0 1 1 3 4 2.014333 1 0.190000 3.530000 0.306032 0.240000 0.140000 1.000000 0.230000 0.319412 0.240000 0 0.180000 0.330000 GIT2 9815 broad.mit.edu 37 12 110421488 110421488 + Silent SNP C C A rs140917075 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr12:110421488C>A ENST00000355312.3 - 5 416 c.417G>T c.(415-417)tcG>tcT p.S139S GIT2_ENST00000551209.1_Silent_p.S139S|TCHP_ENST00000550780.1_3'UTR|GIT2_ENST00000356259.4_Silent_p.S139S|GIT2_ENST00000338373.5_Silent_p.S139S|GIT2_ENST00000360185.4_Silent_p.S139S|GIT2_ENST00000343646.5_Silent_p.S139S|GIT2_ENST00000354574.4_Silent_p.S139S|GIT2_ENST00000553118.1_Silent_p.S139S|GIT2_ENST00000547815.1_Silent_p.S139S|GIT2_ENST00000320063.9_Silent_p.S139S|GIT2_ENST00000361006.5_Silent_p.S139S|GIT2_ENST00000457474.2_Silent_p.S139S NM_057169.3 NP_476510.1 Q14161 GIT2_HUMAN G protein-coupled receptor kinase interacting ArfGAP 2 27 TTCTCACGCTCGAATGGAGTT 0.393000 0 SO:0001819 synonymous_variant ENST00000355312.3 1 0 hg19 CCDS9138.1 TCGA-XN-A8T3-01A-11D-A36O-08 GIT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403407.1 1 0 0 19 366 0 75 0 3.882651e-01 0 26 0 75 2 0 0 0 0 0 2 1 0.999990 19 359 0 74 2 0 0 0 0 75 2 -2.745973 1 1 0 0 1 1 3 4 2.014333 1 0.190000 3.530000 0.306032 0.630000 0.380000 1.000000 0.600000 0.666354 0.630000 0 0.490000 0.840000 TAS2R14 50840 broad.mit.edu 37 12 11091286 11091286 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr12:11091286C>A ENST00000537503.1 - 1 576 c.521G>T c.(520-522)cGa>cTa p.R174L TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron NM_023922.1 NP_076411.1 Q9NYV8 T2R14_HUMAN taste receptor, type 2, member 14 8 ACTGGAAAATCGTGTAAAGTT 0.348000 0 SO:0001583 missense ENST00000537503.1 1 0 hg19 CCDS8637.1 . . . . . . . . . . C 7.482 0.648867 0.14516 . . ENSG00000212127 ENST00000537503 T 0.34667 1.35 3.28 -3.63 0.04529 . 2.668170 0.02729 U 0.114892 T 0.08447 0.0210 N 0.00313 -1.665 0.09310 N 1 B 0.14805 0.011 B 0.24701 0.055 T 0.10941 -1.0608 10 0.14656 T 0.56 . 0.1052 0.00052 0.2579:0.2416:0.1753:0.3253 . 174 Q9NYV8 T2R14_HUMAN L 174 ENSP00000441949:R174L ENSP00000375094:R174L R - 2 0 TAS2R14 10982553 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.567000 0.05916 -0.650000 0.05423 -0.908000 0.02827 CGA TCGA-XN-A8T3-01A-11D-A36O-08 TAS2R14-001 KNOWN upstream_ATG|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000370194.4 1 0 0 15 404 0 67 0 1.530997e-03 0 2 0 67 2 0 0 0 0 0 2 1 0.999870 15 401 0 67 2 0 0 0 0 67 2 -3.052249 1 1 0 0 1 1 3 4 2.016404 1 0.190000 3.530000 0.312744 0.460000 0.260000 1.000000 0.430000 0.493964 0.460000 0 0.350000 0.610000 C12orf52 0 broad.mit.edu 37 12 113624632 113624632 + Silent SNP C C T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr12:113624632C>T ENST00000548278.1 + 3 773 c.81C>T c.(79-81)gtC>gtT p.V27V DDX54_ENST00000306014.5_5'Flank|DDX54_ENST00000314045.7_5'Flank|C12orf52_ENST00000552495.1_Silent_p.V51V|RP11-545P7.4_ENST00000552525.1_RNA|C12orf52_ENST00000549621.1_Silent_p.V27V NM_032848.1 NP_116237.1 Q96K30 RITA1_HUMAN 5 GCTACCGGGTCAAGGCCAGGA 0.652000 0 SO:0001819 synonymous_variant ENST00000548278.1 1 1 hg19 CCDS9166.1 TCGA-XN-A8T3-01A-11D-A36O-08 C12orf52-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405239.1 1 0 1 27 115 0 33 1 9.998859e-01 14 52 0 33 2 0 0 0 0 0 2 1 1.000000 26 111 0 33 2 0 0 0 0 33 2 -20.000000 1 1 0 0 1 1 3 4 2.014333 1 0.190000 3.530000 0.306032 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 0.990000 1.000000 PUS1 80324 broad.mit.edu 37 12 132426520 132426520 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr12:132426520G>A ENST00000376649.3 + 5 1728 c.1228G>A c.(1228-1230)Ggc>Agc p.G410S PUS1_ENST00000535067.1_Intron|PUS1_ENST00000443358.2_Missense_Mutation_p.G382S|PUS1_ENST00000542167.2_Missense_Mutation_p.G357S|PUS1_ENST00000440818.2_Missense_Mutation_p.G382S NM_025215.5 NP_079491.2 Q9Y606 TRUA_HUMAN pseudouridylate synthase 1 11 all_neural(191;0.0982)|Medulloblastoma(191;0.163) AGGTGGCACGGGCGCCAAGGT 0.612000 Esophageal Squamous(102;671 2009 17384 45666) 0 SO:0001583 missense ENST00000376649.3 0 1 hg19 CCDS9275.2 . . . . . . . . . . G 13.91 2.378889 0.42207 . . ENSG00000177192 ENST00000443358;ENST00000376649;ENST00000322060;ENST00000440818;ENST00000542167 T;T;T;T;T 0.54279 0.62;0.6;0.58;0.62;0.62 4.58 3.69 0.42338 . 0.639198 0.14819 N 0.296581 T 0.44265 0.1285 L 0.44542 1.39 0.09310 N 1 P;B 0.38078 0.617;0.005 B;B 0.37144 0.242;0.002 T 0.30416 -0.9979 10 0.49607 T 0.09 -10.2033 10.0242 0.42061 0.0981:0.0:0.9019:0.0 . 357;410 F5H1S9;Q9Y606 .;TRUA_HUMAN S 382;410;382;382;357 ENSP00000392451:G382S;ENSP00000365837:G410S;ENSP00000324726:G382S;ENSP00000400032:G382S;ENSP00000438948:G357S ENSP00000324726:G382S G + 1 0 PUS1 130992473 0.017000 0.18338 0.001000 0.08648 0.009000 0.06853 1.937000 0.40193 1.034000 0.39945 0.491000 0.48974 GGC TCGA-XN-A8T3-01A-11D-A36O-08 PUS1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000250313.2 1 0 0 10 91 0 22 1 9.877420e-01 4 69 0 22 2 0 0 0 0 0 2 1 0.995535 7 84 0 22 2 0 0 0 0 22 2 -16.927970 1 1 0 0 1 1 3 4 2.014333 1 0.190000 3.530000 0.306032 0.990000 0.660000 1.000000 1.000000 0.965953 0.990000 1 0.930000 1.000000 DCP1B 196513 broad.mit.edu 37 12 2062397 2062397 + Missense_Mutation SNP T T C TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr12:2062397T>C ENST00000280665.6 - 7 788 c.709A>G c.(709-711)Aaa>Gaa p.K237E DCP1B_ENST00000541700.1_5'UTR|DCP1B_ENST00000397173.4_Missense_Mutation_p.K135E|DCP1B_ENST00000540622.1_Missense_Mutation_p.K111E NM_152640.3 NP_689853.3 Q8IZD4 DCP1B_HUMAN decapping mRNA 1B 24 OV - Ovarian serous cystadenocarcinoma(31;0.00193) CATGTAGCTTTGTCCTGCTTC 0.488000 0 SO:0001583 missense ENST00000280665.6 1 1 hg19 CCDS31727.1 . . . . . . . . . . T 14.59 2.579542 0.46006 . . ENSG00000151065 ENST00000280665;ENST00000397173;ENST00000540622 T;T;T 0.19669 2.19;2.18;2.13 4.93 3.79 0.43588 . 0.725582 0.14262 N 0.330731 T 0.29223 0.0727 M 0.67953 2.075 0.38015 D 0.934657 P;P 0.47762 0.884;0.9 P;B 0.46419 0.516;0.334 T 0.16041 -1.0416 10 0.62326 D 0.03 -2.4726 9.7109 0.40245 0.0:0.0816:0.0:0.9184 . 135;237 B4DRD1;Q8IZD4 .;DCP1B_HUMAN E 237;135;111 ENSP00000280665:K237E;ENSP00000380358:K135E;ENSP00000444374:K111E ENSP00000280665:K237E K - 1 0 DCP1B 1932658 0.998000 0.40836 0.662000 0.29724 0.161000 0.22273 2.946000 0.49050 0.912000 0.36772 0.528000 0.53228 AAA TCGA-XN-A8T3-01A-11D-A36O-08 DCP1B-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398244.1 1 0 1 27 204 0 49 1 8.218471e-01 5 21 0 49 2 0 0 0 0 0 2 1 1.000000 27 203 0 49 2 0 0 0 0 49 2 -20.000000 1 1 0 0 1 1 3 4 2.016404 1 0.190000 3.530000 0.312744 0.990000 0.990000 1.000000 1.000000 0.998291 0.990000 1 0.990000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 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-XN-A8T3-01A-11D-A36O-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 79 305 0 73 1 6.393962e-01 4 6 0 73 2 1 1 64 277 0 327 2 1 1.000000 77 299 0 73 2 1 1 2417 5606 0 73 2 -20.000000 1 1 121404 2 44 1 1 3 4 2.014333 1 0.190000 3.530000 0.306032 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 STK38L 23012 broad.mit.edu 37 12 27461299 27461299 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr12:27461299C>A ENST00000389032.3 + 4 383 c.214C>A c.(214-216)Cgc>Agc p.R72S STK38L_ENST00000539577.1_Intron NM_015000.3 NP_055815.1 serine/threonine kinase 38 like 12 Colorectal(261;0.0847) ACAACACGCTCGCAAAGAAAC 0.368000 0 SO:0001583 missense ENST00000389032.3 1 0 hg19 CCDS31761.1 . . . . . . . . . . C 17.50 3.405421 0.62288 . . ENSG00000211455 ENST00000541191;ENST00000389032;ENST00000540996;ENST00000543246;ENST00000544969 T;T;T;T;T 0.49720 0.99;0.77;0.99;0.99;0.99 4.54 4.54 0.55810 Protein kinase-like domain (1); 0.000000 0.85682 D 0.000000 T 0.46639 0.1403 L 0.56199 1.76 0.80722 D 1 B 0.10296 0.003 B 0.12837 0.008 T 0.46331 -0.9199 10 0.51188 T 0.08 . 17.29 0.87153 0.0:1.0:0.0:0.0 . 72 Q9Y2H1 ST38L_HUMAN S 72 ENSP00000437856:R72S;ENSP00000373684:R72S;ENSP00000443838:R72S;ENSP00000442253:R72S;ENSP00000440279:R72S ENSP00000373684:R72S R + 1 0 STK38L 27352566 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 4.515000 0.60489 2.257000 0.74773 0.460000 0.39030 CGC TCGA-XN-A8T3-01A-11D-A36O-08 STK38L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403297.1 1 0 0 37 680 0 159 0 8.402188e-01 0 63 0 159 2 0 0 0 0 0 2 1 1.000000 37 664 0 156 2 0 0 0 0 159 2 -2.489390 0 1 0 0 1 1 3 4 2.014333 1 0.190000 3.530000 0.306032 0.650000 0.450000 1.000000 0.640000 0.681334 0.650000 0 0.540000 0.800000 FGD4 121512 broad.mit.edu 37 12 32778699 32778699 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr12:32778699C>A ENST00000427716.2 + 14 2171 c.1747C>A c.(1747-1749)Cga>Aga p.R583R FGD4_ENST00000546442.1_Silent_p.R490R|FGD4_ENST00000531134.1_Silent_p.R668R|FGD4_ENST00000525053.1_Silent_p.R695R|FGD4_ENST00000534526.2_Silent_p.R720R|FGD4_ENST00000266482.3_Silent_p.R335R NM_139241.2 NP_640334.2 Q96M96 FGD4_HUMAN FYVE, RhoGEF and PH domain containing 4 27 Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204) GCATCATTGTCGAGCATGTGG 0.383000 0 SO:0001819 synonymous_variant ENST00000427716.2 0 1 hg19 CCDS8727.1 TCGA-XN-A8T3-01A-11D-A36O-08 FGD4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268017.1 0 0 0 19 731 0 123 0 1.171786e-01 0 22 0 123 2 0 0 0 0 0 2 1 0.999989 18 718 0 122 2 0 0 0 0 123 2 -2.547133 1 1 0 0 1 1 3 4 2.014333 1 0.190000 3.530000 0.306032 0.320000 0.190000 1.000000 0.300000 0.390956 0.320000 0 0.250000 0.440000 KRT74 121391 broad.mit.edu 37 12 52967109 52967109 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr12:52967109G>T ENST00000305620.2 - 1 500 c.453C>A c.(451-453)ttC>ttA p.F151L KRT74_ENST00000549343.1_Missense_Mutation_p.F151L NM_175053.3 NP_778223.2 Q7RTS7 K2C74_HUMAN keratin 74 p.F151F(1) 28 TGAAGGAGGCGAACTTGTCGT 0.592000 1 Substitution - coding silent(1) SO:0001583 missense ENST00000305620.2 1 0 hg19 CCDS8832.1 . . . . . . . . . . G 17.66 3.445032 0.63178 . . ENSG00000170484 ENST00000549343;ENST00000305620 D;D 0.84589 -1.87;-1.87 4.4 -8.37 0.00976 Filament (1); 0.000000 0.36002 N 0.002856 D 0.90679 0.7076 M 0.84846 2.72 0.37092 D 0.899483 D 0.76494 0.999 D 0.74348 0.983 D 0.92064 0.5659 10 0.87932 D 0 . 18.0861 0.89457 0.3591:0.0:0.6409:0.0 . 151 Q7RTS7 K2C74_HUMAN L 151 ENSP00000447447:F151L;ENSP00000307240:F151L ENSP00000307240:F151L F - 3 2 KRT74 51253376 0.000000 0.05858 0.806000 0.32338 0.804000 0.45430 -2.453000 0.01005 -1.528000 0.01756 -0.459000 0.05422 TTC TCGA-XN-A8T3-01A-11D-A36O-08 KRT74-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405324.1 1 0 0 20 419 0 104 0 0 0 0 104 2 0 0 0 0 0 2 1 0.999995 20 415 0 104 2 0 0 0 0 104 2 -3.010565 1 1 0 0 1 1 3 4 2.014333 1 0.190000 3.530000 0.306032 0.580000 0.360000 1.000000 0.560000 0.622349 0.580000 0 0.460000 0.770000 PROZ 8858 broad.mit.edu 37 13 113826319 113826319 + Missense_Mutation SNP C C T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr13:113826319C>T ENST00000375547.2 + 8 1110 c.1103C>T c.(1102-1104)aCg>aTg p.T368M PROZ_ENST00000342783.4_Missense_Mutation_p.T390M NM_003891.2 NP_003882.1 P22891 PROZ_HUMAN protein Z, vitamin K-dependent plasma glycoprotein 16 all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163) all_lung(25;0.216) all cancers(43;0.104) Menadione(DB00170) TGGTTTCTCACGGGGGTCCTG 0.562000 0 SO:0001583 missense ENST00000375547.2 1 1 hg19 CCDS9531.1 . . . . . . . . . . C 10.19 1.282979 0.23392 . . ENSG00000126231 ENST00000375547;ENST00000342783 D;D 0.89050 -2.46;-2.46 3.96 2.78 0.32641 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 0.303944 0.34986 N 0.003522 D 0.91720 0.7382 M 0.68593 2.085 0.39311 D 0.965077 D;D 0.89917 1.0;1.0 D;D 0.97110 0.998;1.0 D 0.91267 0.5041 10 0.87932 D 0 . 6.4669 0.21987 0.0:0.6801:0.1745:0.1454 . 390;368 P22891-2;P22891 .;PROZ_HUMAN M 368;390 ENSP00000364697:T368M;ENSP00000344458:T390M ENSP00000344458:T390M T + 2 0 PROZ 112874320 0.916000 0.31088 0.503000 0.27626 0.030000 0.12068 1.723000 0.38053 1.891000 0.54761 0.313000 0.20887 ACG TCGA-XN-A8T3-01A-11D-A36O-08 PROZ-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000045845.1 1 0 1 54 222 0 63 0 3.971017e-02 0 2 0 63 2 0 0 0 0 0 2 1 1.000000 53 216 0 59 2 0 0 0 0 63 2 -20.000000 1 1 121378 5 37 1 2 2 4 2.073623 0 0.190000 3.530000 0.319328 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 SGCG 6445 broad.mit.edu 37 13 23869565 23869565 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr13:23869565G>A ENST00000218867.3 + 6 641 c.517G>A c.(517-519)Gct>Act p.A173T SGCG_ENST00000537476.1_Missense_Mutation_p.A173T|SGCG_ENST00000545013.1_Missense_Mutation_p.A173T NM_000231.2 NP_000222 Q13326 SGCG_HUMAN sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein) 22 all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188) GCCTGAAGGGGCTCTTTTTGA 0.373000 0 SO:0001583 missense ENST00000218867.3 1 1 hg19 CCDS9299.1 . . . . . . . . . . G 16.65 3.182474 0.57800 . . ENSG00000102683 ENST00000218867;ENST00000537476;ENST00000545013 D;D;D 0.95307 -3.67;-3.67;-3.67 4.61 4.61 0.57282 . 0.000000 0.85682 D 0.000000 D 0.96386 0.8821 M 0.75447 2.3 0.54753 D 0.999985 D 0.89917 1.0 D 0.91635 0.999 D 0.94976 0.8121 10 0.23891 T 0.37 -20.3547 13.2912 0.60272 0.0:0.0:1.0:0.0 . 173 Q13326 SGCG_HUMAN T 173 ENSP00000218867:A173T;ENSP00000444100:A173T;ENSP00000442232:A173T ENSP00000218867:A173T A + 1 0 SGCG 22767565 1.000000 0.71417 0.998000 0.56505 0.580000 0.36256 4.816000 0.62642 2.264000 0.75181 0.563000 0.77884 GCT TCGA-XN-A8T3-01A-11D-A36O-08 SGCG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044151.1 1 0 1 173 809 0 164 0 0 0 0 164 2 0 0 0 0 0 2 1 1.000000 174 794 0 163 2 0 0 0 0 164 2 -20.000000 1 0 0 0 1 2 2 4 2.073623 0 0.190000 3.530000 0.319328 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ALOX5AP 241 broad.mit.edu 37 13 31330136 31330136 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr13:31330136C>A ENST00000380490.3 + 4 395 c.297C>A c.(295-297)gtC>gtA p.V99V NM_001204406.1|NM_001629.3 NP_001191335.1|NP_001620.2 P20292 AL5AP_HUMAN arachidonate 5-lipoxygenase-activating protein 4 Lung SC(185;0.0257)|Breast(139;0.203) AGTACTTTGTCGGTTACCTAG 0.448000 0 SO:0001819 synonymous_variant ENST00000380490.3 1 0 hg19 CCDS9337.1 TCGA-XN-A8T3-01A-11D-A36O-08 ALOX5AP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044372.1 1 0 0 15 381 0 78 0 9.971820e-01 0 247 0 78 2 0 0 0 0 0 2 1 0.999857 14 374 0 77 2 0 0 0 0 78 2 -2.778627 1 1 0 0 1 2 2 4 2.073623 0 0.190000 3.530000 0.319328 0.480000 0.280000 0.750000 0.480000 0.500852 0.480000 0 0.370000 0.620000 DGKH 160851 broad.mit.edu 37 13 42773954 42773954 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr13:42773954G>T ENST00000337343.4 + 20 2423 c.2402G>T c.(2401-2403)cGa>cTa p.R801L DGKH_ENST00000540693.1_Missense_Mutation_p.R801L|DGKH_ENST00000261491.5_Missense_Mutation_p.R801L|DGKH_ENST00000379274.2_Missense_Mutation_p.R665L|DGKH_ENST00000536612.1_Missense_Mutation_p.R665L|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_Missense_Mutation_p.R556L NM_178009.3 NP_821077.1 Q86XP1 DGKH_HUMAN diacylglycerol kinase, eta p.R801Q(1) 43 Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114) TTCAGGAGCCGAACTAAAAAC 0.348000 1 Substitution - Missense(1) SO:0001583 missense ENST00000337343.4 1 0 hg19 CCDS9381.1 . . . . . . . . . . G 19.67 3.871602 0.72065 . . ENSG00000102780 ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612;ENST00000538674 T;T;T;T;T;T 0.35789 1.29;1.29;1.29;1.29;1.29;1.29 5.79 5.79 0.91817 Diacylglycerol kinase, accessory domain (2); 0.073536 0.56097 D 0.000034 T 0.69033 0.3066 M 0.93678 3.445 0.80722 D 1 P;D;P;P 0.55172 0.844;0.97;0.5;0.951 P;P;B;P 0.59546 0.667;0.779;0.344;0.859 T 0.77189 -0.2679 10 0.87932 D 0 . 20.0367 0.97561 0.0:0.0:1.0:0.0 . 556;665;801;801 F5GYP2;Q86XP1-3;Q86XP1-2;Q86XP1 .;.;.;DGKH_HUMAN L 801;801;801;665;665;556 ENSP00000440823:R801L;ENSP00000337572:R801L;ENSP00000261491:R801L;ENSP00000368576:R665L;ENSP00000445114:R665L;ENSP00000441308:R556L ENSP00000261491:R801L R + 2 0 DGKH 41671954 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 7.956000 0.87863 2.727000 0.93392 0.591000 0.81541 CGA TCGA-XN-A8T3-01A-11D-A36O-08 DGKH-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044699.2 1 0 0 15 336 0 41 0 0 0 1 0 41 2 0 0 0 0 0 2 1 0.999869 14 333 0 41 2 0 0 0 0 41 2 -3.063285 1 1 0 0 1 2 2 4 2.073623 0 0.190000 3.530000 0.319328 0.540000 0.310000 0.840000 0.520000 0.564112 0.540000 0 0.420000 0.700000 HTR2A 3356 broad.mit.edu 37 13 47409499 47409499 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr13:47409499G>A ENST00000378688.4 - 3 1020 c.889C>T c.(889-891)Cgg>Tgg p.R297W HTR2A_ENST00000543956.1_Missense_Mutation_p.R213W|HTR2A_ENST00000542664.1_Missense_Mutation_p.R297W P28223 5HT2A_HUMAN 5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled 36 all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333) Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246) TGGATCGACCGCTGGAAGAGC 0.502000 0 SO:0001583 missense ENST00000378688.4 1 1 hg19 CCDS9405.1 . . . . . . . . . . G 16.64 3.180129 0.57800 2.27E-4 0.0 ENSG00000102468 ENST00000378688;ENST00000543956;ENST00000542664 T;T;T 0.63417 0.27;-0.04;0.27 5.78 0.475 0.16774 GPCR, rhodopsin-like superfamily (1); 0.124540 0.53938 D 0.000048 T 0.81536 0.4843 M 0.91872 3.25 0.45477 D 0.998448 D;D 0.89917 0.999;1.0 D;D 0.74348 0.94;0.983 D 0.84763 0.0763 10 0.62326 D 0.03 . 15.9291 0.79646 0.0:0.0:0.4023:0.5977 . 213;297 F5GWE8;P28223 .;5HT2A_HUMAN W 297;213;297 ENSP00000367959:R297W;ENSP00000441861:R213W;ENSP00000437737:R297W ENSP00000367959:R297W R - 1 2 HTR2A 46307500 1.000000 0.71417 0.984000 0.44739 0.974000 0.67602 3.113000 0.50376 -0.155000 0.11098 -0.293000 0.09583 CGG TCGA-XN-A8T3-01A-11D-A36O-08 HTR2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044835.3 1 0 1 35 183 0 35 0 0 0 0 35 2 0 0 0 0 0 2 1 1.000000 35 175 0 35 2 0 0 0 0 35 2 -3.353918 1 1 121398 2 35 1 2 2 4 2.073623 0 0.190000 3.530000 0.319328 0.990000 0.990000 1.000000 1.000000 0.999998 0.990000 1 0.990000 1.000000 ATP7B 540 broad.mit.edu 37 13 52548807 52548807 + Silent SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr13:52548807G>A ENST00000242839.4 - 2 705 c.549C>T c.(547-549)gcC>gcT p.A183A ATP7B_ENST00000542656.1_Silent_p.A151A|ATP7B_ENST00000448424.2_Silent_p.A183A|ATP7B_ENST00000418097.2_Silent_p.A183A|ATP7B_ENST00000400370.3_Silent_p.A183A|ATP7B_ENST00000400366.3_Silent_p.A183A|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000344297.5_Silent_p.A183A NM_000053.3 NP_000044.2 P35670 ATP7B_HUMAN ATPase, Cu++ transporting, beta polypeptide 55 Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19) Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526) AAGTGATGACGGCCTCTTGGT 0.512000 Wilson disease 0 SO:0001819 synonymous_variant Familial Cancer Database ENST00000242839.4 1 1 hg19 CCDS41892.1 TCGA-XN-A8T3-01A-11D-A36O-08 ATP7B-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045981.1 1 0 1 44 222 0 59 0 0 0 1 0 59 2 0 0 0 0 0 2 1 1.000000 43 219 0 59 2 0 0 0 0 59 2 -20.000000 1 1 121044 1 33 1 2 2 4 2.073623 0 0.190000 3.530000 0.319328 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TGDS 23483 broad.mit.edu 37 13 95246123 95246123 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr13:95246123G>T ENST00000261296.5 - 2 245 c.125C>A c.(124-126)cCa>cAa p.P42Q TGDS_ENST00000498294.1_5'UTR NM_014305.2 NP_055120.1 O95455 TGDS_HUMAN TDP-glucose 4,6-dehydratase 8 all_neural(89;0.0684)|Medulloblastoma(90;0.163) CATATAGTTTGGATAATCTTC 0.274000 0 SO:0001583 missense ENST00000261296.5 0 1 hg19 CCDS9471.1 . . . . . . . . . . G 21.8 4.204314 0.79127 . . ENSG00000088451 ENST00000261296 D 0.93019 -3.15 5.67 5.67 0.87782 NAD-dependent epimerase/dehydratase (1);NAD(P)-binding domain (1); 0.116101 0.64402 D 0.000014 D 0.96959 0.9007 M 0.88181 2.935 0.54753 D 0.999986 D 0.89917 1.0 D 0.91635 0.999 D 0.95736 0.8779 10 0.21014 T 0.42 . 17.5515 0.87878 0.0:0.0:1.0:0.0 . 42 O95455 TGDS_HUMAN Q 42 ENSP00000261296:P42Q ENSP00000261296:P42Q P - 2 0 TGDS 94044124 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 4.419000 0.59835 2.658000 0.90341 0.591000 0.81541 CCA TCGA-XN-A8T3-01A-11D-A36O-08 TGDS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000106904.2 0 0 0 22 1088 0 185 0 1.777944e-02 0 10 0 185 2 0 0 0 0 0 2 1 0.999999 22 1080 0 183 2 0 0 0 0 185 2 -2.151350 0 1 0 0 1 2 2 4 2.073623 0 0.190000 3.530000 0.319328 0.240000 0.150000 0.370000 0.240000 0.258596 0.240000 0 0.190000 0.310000 PPP1R13B 23368 broad.mit.edu 37 14 104209072 104209072 + Silent SNP C C A rs12891833 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr14:104209072C>A ENST00000202556.9 - 10 1521 c.1239G>T c.(1237-1239)ccG>ccT p.P413P PPP1R13B_ENST00000555391.1_5'UTR|PPP1R13B_ENST00000423488.2_5'UTR NM_015316.2 NP_056131.2 Q96KQ4 ASPP1_HUMAN protein phosphatase 1, regulatory subunit 13B 33 all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155) CCTCCACGCTCGGATCCTTCC 0.552000 0 SO:0001819 synonymous_variant ENST00000202556.9 1 0 hg19 CCDS41997.1 TCGA-XN-A8T3-01A-11D-A36O-08 PPP1R13B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414591.1 1 0 0 20 492 0 113 0 4.160658e-01 0 35 0 113 2 0 0 0 0 0 2 1 0.999995 20 487 0 109 2 0 0 0 0 113 2 -2.796323 1 1 0 0 1 2 2 4 2.088023 0 0.190000 3.530000 0.319328 0.490000 0.300000 0.730000 0.480000 0.509654 0.490000 0 0.390000 0.610000 EFS 10278 broad.mit.edu 37 14 23829013 23829013 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr14:23829013C>A ENST00000216733.3 - 4 1281 c.674G>T c.(673-675)cGa>cTa p.R225L EFS_ENST00000351354.3_Missense_Mutation_p.R132L|RP11-124D2.3_ENST00000554010.1_RNA|EFS_ENST00000429593.2_Intron NM_005864.2 NP_005855.1 O43281 EFS_HUMAN embryonal Fyn-associated substrate 16 all_cancers(95;7.12e-06) GGCTGACGCTCGTTTCAGGTT 0.622000 0 SO:0001583 missense ENST00000216733.3 1 0 hg19 CCDS9595.1 . . . . . . . . . . C 13.14 2.149251 0.37923 . . ENSG00000100842 ENST00000216733;ENST00000351354 T;T 0.59364 0.27;0.8 4.88 3.98 0.46160 . 0.541790 0.18247 N 0.147073 T 0.72495 0.3467 M 0.72894 2.215 0.80722 D 1 D;B 0.89917 1.0;0.023 D;B 0.87578 0.998;0.011 T 0.69446 -0.5143 10 0.25751 T 0.34 -15.8242 13.4706 0.61279 0.1582:0.8418:0.0:0.0 . 132;225 O43281-2;O43281 .;EFS_HUMAN L 225;132 ENSP00000216733:R225L;ENSP00000340607:R132L ENSP00000216733:R225L R - 2 0 EFS 22898853 0.998000 0.40836 0.958000 0.39756 0.003000 0.03518 2.042000 0.41222 1.271000 0.44313 -0.311000 0.09066 CGA TCGA-XN-A8T3-01A-11D-A36O-08 EFS-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000071770.2 1 0 0 25 467 0 97 0 3.209916e-01 0 22 0 97 2 0 0 0 0 0 2 1 1.000000 25 461 0 97 2 0 0 0 0 97 2 -2.876406 1 1 0 0 1 2 2 4 2.088023 0 0.190000 3.530000 0.319328 0.640000 0.420000 0.900000 0.640000 0.656039 0.640000 0 0.520000 0.780000 RABGGTA 5875 broad.mit.edu 37 14 24737795 24737795 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr14:24737795C>A ENST00000399409.3 - 9 1414 c.931G>T c.(931-933)Gac>Tac p.D311Y RABGGTA_ENST00000559586.1_5'Flank|RABGGTA_ENST00000216840.6_Missense_Mutation_p.D311Y|RABGGTA_ENST00000560777.1_Intron NM_004581.5 NP_004572.3 Q92696 PGTA_HUMAN Rab geranylgeranyltransferase, alpha subunit 12 GGCAACTGGTCGTTGAGGGAG 0.557000 0 SO:0001583 missense ENST00000399409.3 0 1 hg19 CCDS45088.1 . . . . . . . . . . C 13.55 2.269476 0.40095 . . ENSG00000100949 ENST00000216840;ENST00000399409;ENST00000543002 T;T 0.52057 0.68;0.68 5.11 4.22 0.49857 Rab geranylgeranyltransferase, alpha subunit, insert-domain (4); 0.000000 0.85682 D 0.000000 T 0.61489 0.2351 L 0.55481 1.735 0.80722 D 1 D 0.76494 0.999 D 0.69654 0.965 T 0.63804 -0.6554 10 0.59425 D 0.04 -24.6605 13.0558 0.58980 0.0:0.9196:0.0:0.0804 . 311 Q92696 PGTA_HUMAN Y 311;311;274 ENSP00000216840:D311Y;ENSP00000382341:D311Y ENSP00000216840:D311Y D - 1 0 RABGGTA 23807635 1.000000 0.71417 1.000000 0.80357 0.278000 0.26855 4.232000 0.58645 1.292000 0.44672 -0.448000 0.05591 GAC TCGA-XN-A8T3-01A-11D-A36O-08 RABGGTA-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000415308.5 0 0 0 12 478 0 90 0 5.093373e-01 0 66 0 90 2 0 0 0 0 0 2 1 0.999067 13 471 0 89 2 0 0 0 0 90 2 -3.222634 1 1 0 0 1 2 2 4 2.088023 0 0.190000 3.530000 0.319328 0.310000 0.160000 0.510000 0.320000 0.329550 0.310000 0 0.230000 0.420000 EML5 161436 broad.mit.edu 37 14 89124675 89124675 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr14:89124675G>T ENST00000380664.5 - 26 3732 c.3733C>A c.(3733-3735)Cgc>Agc p.R1245S EML5_ENST00000554922.1_Missense_Mutation_p.R1245S|EML5_ENST00000352093.5_Missense_Mutation_p.R1207S Q05BV3 EMAL5_HUMAN echinoderm microtubule associated protein like 5 50 TAAGTCCAGCGAACATTTGTG 0.398000 0 SO:0001583 missense ENST00000380664.5 1 0 hg19 CCDS45148.1 . . . . . . . . . . G 25.2 4.616462 0.87359 . . ENSG00000165521 ENST00000554922;ENST00000352093;ENST00000380664 T;T;T 0.37411 1.2;1.7;1.2 4.61 4.61 0.57282 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.000000 0.85682 D 0.000000 T 0.58991 0.2161 M 0.73217 2.22 0.58432 D 0.999999 D;D 0.76494 0.999;0.966 D;P 0.74348 0.983;0.727 T 0.56768 -0.7924 10 0.33940 T 0.23 -10.3411 17.9931 0.89175 0.0:0.0:1.0:0.0 . 1245;1245 Q05BV3-5;Q05BV3 .;EMAL5_HUMAN S 1245;1207;1245 ENSP00000451998:R1245S;ENSP00000298315:R1207S;ENSP00000370039:R1245S ENSP00000298315:R1207S R - 1 0 EML5 88194428 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.606000 0.82863 2.550000 0.86006 0.557000 0.71058 CGC TCGA-XN-A8T3-01A-11D-A36O-08 EML5-010 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000410491.1 1 0 0 28 603 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 1.000000 27 591 0 95 2 0 0 0 0 95 2 -3.100434 1 1 0 0 1 2 2 4 2.088023 0 0.190000 3.530000 0.319328 0.550000 0.370000 0.780000 0.560000 0.571941 0.550000 0 0.460000 0.670000 LRRK1 79705 broad.mit.edu 37 15 101550769 101550769 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr15:101550769C>A ENST00000388948.3 + 8 1463 c.1104C>A c.(1102-1104)ttC>ttA p.F368L LRRK1_ENST00000284395.5_Missense_Mutation_p.F365L NM_024652.3 NP_078928.3 leucine-rich repeat kinase 1 72 Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094) OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23) AAAAATTGTTCGAAGAAGAAA 0.343000 0 SO:0001583 missense ENST00000388948.3 1 0 hg19 CCDS42086.1 . . . . . . . . . . C 17.70 3.455231 0.63401 . . ENSG00000154237 ENST00000388948;ENST00000284395 T;T 0.18174 2.23;2.23 5.67 -3.74 0.04385 . 0.149661 0.47852 D 0.000204 T 0.15089 0.0364 N 0.05351 -0.065 0.42164 D 0.991611 D 0.69078 0.997 P 0.60345 0.873 T 0.00710 -1.1599 10 0.48119 T 0.1 . 13.9495 0.64106 0.0:0.5923:0.0:0.4077 . 368 Q38SD2 LRRK1_HUMAN L 368;365 ENSP00000373600:F368L;ENSP00000284395:F365L ENSP00000284395:F365L F + 3 2 LRRK1 99368292 0.255000 0.24002 0.915000 0.36163 0.867000 0.49689 -0.694000 0.05115 -0.668000 0.05296 -0.290000 0.09829 TTC TCGA-XN-A8T3-01A-11D-A36O-08 LRRK1-003 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000384567.2 1 0 0 18 370 0 74 0 7.172799e-03 0 3 0 74 2 0 0 0 0 0 2 1 0.999982 18 366 0 74 2 0 0 0 0 74 2 -3.126996 1 1 0 0 1 1 2 3 1.919646 0 0.190000 3.530000 0.260274 0.540000 0.330000 0.800000 0.540000 0.557365 0.540000 0 0.420000 0.680000 TMOD2 29767 broad.mit.edu 37 15 52069169 52069169 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr15:52069169C>A ENST00000249700.4 + 5 668 c.447C>A c.(445-447)ttC>ttA p.F149L TMOD2_ENST00000539962.2_Missense_Mutation_p.F105L|TMOD2_ENST00000435126.2_Missense_Mutation_p.F149L NM_001142885.1|NM_014548.3 NP_001136357.1|NP_055363.1 Q9NZR1 TMOD2_HUMAN tropomodulin 2 (neuronal) 16 ATCCAAAGTTCGATGAAGAAA 0.413000 0 SO:0001583 missense ENST00000249700.4 1 0 hg19 CCDS10144.1 . . . . . . . . . . c 13.54 2.269001 0.40095 . . ENSG00000128872 ENST00000435126;ENST00000249700;ENST00000539962 T;T;T 0.13538 2.58;2.59;2.59 5.64 -0.654 0.11443 . 0.281791 0.34700 N 0.003757 T 0.05640 0.0148 N 0.08118 0 0.30050 N 0.811855 B;B 0.14438 0.01;0.002 B;B 0.20955 0.032;0.009 T 0.26710 -1.0095 10 0.30078 T 0.28 -10.1337 6.8693 0.24111 0.1035:0.2248:0.0:0.6717 . 149;149 Q9NZR1-2;Q9NZR1 .;TMOD2_HUMAN L 149;149;105 ENSP00000404590:F149L;ENSP00000249700:F149L;ENSP00000437743:F105L ENSP00000249700:F149L F + 3 2 TMOD2 49856461 1.000000 0.71417 0.991000 0.47740 0.824000 0.46624 0.535000 0.23114 -0.247000 0.09597 -1.128000 0.01989 TTC TCGA-XN-A8T3-01A-11D-A36O-08 TMOD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254742.2 1 0 0 22 391 0 77 0 1.226083e-01 0 11 0 77 2 0 0 0 0 0 2 1 0.999999 21 388 0 77 2 0 0 0 0 77 2 -3.221195 1 1 0 0 1 1 2 3 1.919646 0 0.190000 3.530000 0.260274 0.610000 0.400000 0.890000 0.600000 0.634088 0.610000 0 0.500000 0.760000 KCTD13 253980 broad.mit.edu 37 16 29937241 29937241 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr16:29937241C>A ENST00000568000.1 - 1 1115 c.114G>T c.(112-114)ccG>ccT p.P38P KCTD13_ENST00000561540.1_Silent_p.P38P|CTD-2574D22.2_ENST00000450909.3_RNA|KCTD13_ENST00000568721.1_5'UTR NM_178863.3 NP_849194.1 Q8WZ19 BACD1_HUMAN potassium channel tetramerization domain containing 13 7 ATTTGCTGTTCGGGGTCAGCG 0.687000 0 SO:0001819 synonymous_variant ENST00000568000.1 1 0 hg19 CCDS10661.1 TCGA-XN-A8T3-01A-11D-A36O-08 KCTD13-001 PUTATIVE basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255162.2 1 0 0 11 290 0 57 0 1.338985e-01 0 16 0 57 2 0 0 0 0 0 2 1 0.998324 11 287 0 56 2 0 0 0 0 57 2 -11.947390 1 0 0 0 1 1 2 3 1.938267 0 0.190000 3.530000 0.260274 0.430000 0.220000 0.710000 0.420000 0.452170 0.430000 0 0.320000 0.570000 STX4 6810 broad.mit.edu 37 16 31045573 31045573 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr16:31045573C>A ENST00000313843.3 + 3 474 c.159C>A c.(157-159)gtC>gtA p.V53V STX4_ENST00000493902.1_3'UTR|STX4_ENST00000394998.1_Silent_p.V51V NM_004604.3 NP_004595.2 Q12846 STX4_HUMAN syntaxin 4 9 AGACTATTGTCAAACTGGGGA 0.592000 0 SO:0001819 synonymous_variant ENST00000313843.3 1 0 hg19 CCDS10700.1 TCGA-XN-A8T3-01A-11D-A36O-08 STX4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255538.3 1 0 0 30 704 0 148 0 9.797247e-01 0 147 0 148 2 0 0 0 0 0 2 1 1.000000 29 699 0 146 2 0 0 0 0 148 2 -4.124451 1 0 0 0 1 1 2 3 1.938267 0 0.190000 3.530000 0.260274 0.470000 0.320000 0.650000 0.480000 0.483606 0.470000 0 0.390000 0.570000 HYDIN 54768 broad.mit.edu 37 16 70843895 70843895 + Nonsense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr16:70843895C>A ENST00000393567.2 - 85 14824 c.14674G>T c.(14674-14676)Gaa>Taa p.E4892* NM_001270974.1 NP_001257903.1 Q4G0P3 HYDIN_HUMAN HYDIN, axonemal central pair apparatus protein 43 Ovarian(137;0.0654) GGCTGAAATTCAAATGAGAAC 0.483000 0 SO:0001587 stop_gained ENST00000393567.2 0 1 hg19 CCDS59269.1 . . . . . . . . . . C 56 26.157347 0.99968 . . ENSG00000157423 ENST00000393567;ENST00000316490 . . . 6.08 6.08 0.98989 . 0.000000 0.31797 U 0.007056 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.11794 T 0.64 . 20.2585 0.98435 0.0:1.0:0.0:0.0 . . . . X 4892;4891 . ENSP00000313052:E4891X E - 1 0 HYDIN 69401396 1.000000 0.71417 1.000000 0.80357 0.877000 0.50540 7.302000 0.78861 2.894000 0.99253 0.655000 0.94253 GAA TCGA-XN-A8T3-01A-11D-A36O-08 HYDIN-001 PUTATIVE not_organism_supported|basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000398624.3 0 0 0 29 814 0 237 0 7.401087e-03 0 4 0 237 2 0 0 0 0 0 2 1 1.000000 29 806 0 235 2 0 0 0 0 237 2 -3.035857 1 1 0 0 1 1 2 3 1.939292 0 0.190000 3.530000 0.260274 0.390000 0.260000 0.550000 0.390000 0.407838 0.390000 0 0.320000 0.480000 SLC5A10 125206 broad.mit.edu 37 17 18872442 18872442 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:18872442C>A ENST00000395645.3 + 6 549 c.531C>A c.(529-531)ctC>ctA p.L177L SLC5A10_ENST00000395642.1_Silent_p.L121L|SLC5A10_ENST00000395643.2_Silent_p.L177L|FAM83G_ENST00000388995.6_3'UTR|SLC5A10_ENST00000317977.6_Silent_p.L121L|SLC5A10_ENST00000417251.2_Silent_p.L177L|SLC5A10_ENST00000395647.2_Silent_p.L177L NM_001042450.2 NP_001035915.1 A0PJK1 SC5AA_HUMAN solute carrier family 5 (sodium/sugar cotransporter), member 10 24 TCCTCACGCTCGGCATCACAG 0.622000 0 SO:0001819 synonymous_variant ENST00000395645.3 1 0 hg19 CCDS42275.1 TCGA-XN-A8T3-01A-11D-A36O-08 SLC5A10-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000132129.2 1 0 0 16 216 0 47 0 9.331962e-01 0 65 0 47 2 0 0 0 0 0 2 1 0.999938 16 214 0 46 2 0 0 0 0 47 2 -2.966721 1 1 0 0 1 0 2 2 1.782824 1 0.190000 3.530000 0.190000 0.730000 0.430000 1.000000 1.000000 0.742269 0.730000 0 0.570000 0.920000 FLOT2 2319 broad.mit.edu 37 17 27208342 27208342 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 G T G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:27208342G>T ENST00000394908.4 - 9 1070 c.966C>A c.(964-966)atC>atA p.I322I FLOT2_ENST00000394906.2_Silent_p.I377I|FLOT2_ENST00000577789.1_5'UTR|FLOT2_ENST00000585169.1_Silent_p.I322I NM_004475.2 NP_004466.2 Q14254 FLOT2_HUMAN flotillin 2 11 all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01) Epithelial(11;3.26e-06)|all cancers(11;1.76e-05)|BRCA - Breast invasive adenocarcinoma(11;0.00015)|OV - Ovarian serous cystadenocarcinoma(11;0.0602) CCGCCTCCCCGATTTTGCGGA 0.612000 0 SO:0001819 synonymous_variant ENST00000394908.4 1 0 hg19 CCDS11245.2 TCGA-XN-A8T3-01A-11D-A36O-08 FLOT2-003 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000255935.3 1 0 0 18 341 0 91 0 9.996707e-01 0 250 0 91 2 0 0 0 0 0 2 1 0.999981 18 336 0 90 2 0 0 0 0 91 2 -2.917909 1 1 0 0 1 1 2 3 1.946416 0 0.190000 3.530000 0.260274 0.580000 0.360000 0.870000 0.570000 0.601563 0.580000 0 0.460000 0.730000 CDC6 990 broad.mit.edu 37 17 38451686 38451686 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:38451686C>A ENST00000209728.4 + 8 1633 c.1162C>A c.(1162-1164)Cgc>Agc p.R388S NM_001254.3 NP_001245.1 Q99741 CDC6_HUMAN cell division cycle 6 21 AGGAGATGTTCGCAAAGCACT 0.393000 0 SO:0001583 missense ENST00000209728.4 1 0 hg19 CCDS11365.1 . . . . . . . . . . C 20.7 4.039774 0.75732 . . ENSG00000094804 ENST00000209728 T 0.64438 -0.1 5.97 5.97 0.96955 . 0.000000 0.85682 D 0.000000 D 0.87055 0.6082 H 0.96943 3.91 0.58432 D 0.999992 D 0.89917 1.0 D 0.97110 1.0 D 0.90538 0.4500 10 0.87932 D 0 -1.1769 19.185 0.93639 0.0:1.0:0.0:0.0 . 388 Q99741 CDC6_HUMAN S 388 ENSP00000209728:R388S ENSP00000209728:R388S R + 1 0 CDC6 35705212 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 3.941000 0.56607 2.835000 0.97688 0.591000 0.81541 CGC TCGA-XN-A8T3-01A-11D-A36O-08 CDC6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257129.1 1 0 0 25 628 0 128 0 1.059033e-01 0 14 0 128 2 0 0 0 0 0 2 1 1.000000 25 612 0 126 2 0 0 0 0 128 2 -2.885708 1 1 0 0 1 1 2 3 1.938332 0 0.190000 3.530000 0.260274 0.440000 0.290000 0.630000 0.450000 0.455544 0.440000 0 0.360000 0.540000 KRT27 342574 broad.mit.edu 37 17 38938439 38938439 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:38938439G>T ENST00000301656.3 - 1 347 c.307C>A c.(307-309)Cga>Aga p.R103R NM_181537.3 NP_853515.2 keratin 27 21 Breast(137;0.000812) TCTAGGGCTCGAACATTCTCC 0.542000 0 SO:0001819 synonymous_variant ENST00000301656.3 1 0 hg19 CCDS11375.1 TCGA-XN-A8T3-01A-11D-A36O-08 KRT27-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257216.1 1 0 0 23 530 0 155 0 0 0 0 155 2 0 0 0 0 0 2 1 0.999999 22 523 0 153 2 0 0 0 0 155 2 -3.034940 1 1 0 0 1 1 2 3 1.938332 0 0.190000 3.530000 0.260274 0.480000 0.310000 0.690000 0.480000 0.495877 0.480000 0 0.390000 0.590000 KRTAP9-9 81870 broad.mit.edu 37 17 39412064 39412064 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:39412064G>A ENST00000394008.1 + 1 429 c.427G>A c.(427-429)Gcc>Acc p.A143T NM_030975.2 NP_112237.2 Q9BYP9 KRA99_HUMAN keratin associated protein 9-9 6 Breast(137;0.000496) STAD - Stomach adenocarcinoma(17;0.000397) CTGCCGCCCCGCCTGCTGTGA 0.612000 0 SO:0001583 missense ENST00000394008.1 1 1 hg19 CCDS54127.1 . . . . . . . . . . . 14.35 2.507999 0.44558 0.0 1.16E-4 ENSG00000198083 ENST00000431129;ENST00000394008 T 0.01295 5.04 2.85 -2.54 0.06307 . . . . . T 0.00524 0.0017 N 0.00879 -1.12 0.09310 N 1 B 0.17268 0.021 B 0.08055 0.003 T 0.44982 -0.9292 9 0.37606 T 0.19 . 3.7095 0.08414 0.5122:0.0:0.3091:0.1786 . 128 Q9BYP9 KRA99_HUMAN T 149;143 ENSP00000377576:A143T ENSP00000377576:A143T A + 1 0 KRTAP9-9 36665590 0.000000 0.05858 0.000000 0.03702 0.448000 0.32197 -1.026000 0.03596 -0.748000 0.04753 0.205000 0.17691 GCC TCGA-XN-A8T3-01A-11D-A36O-08 KRTAP9-9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257710.1 0 0 0 62 676 1 232 0 0 0 1 232 2 0 0 0 0 0 2 1 1.000000 61 660 1 234 12 0 0 0 1 232 2 -14.632700 1 0 121412 9 46 1 1 2 3 1.938332 0 0.190000 3.530000 0.260274 0.960000 0.750000 1.000000 1.000000 0.940455 0.960000 1 0.850000 1.000000 MPP3 4356 broad.mit.edu 37 17 41886383 41886383 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:41886383G>T ENST00000398389.4 - 19 1687 c.1522C>A c.(1522-1524)Cag>Aag p.Q508K MPP3_ENST00000398393.1_Missense_Mutation_p.Q533K NM_001932.4 NP_001923.2 Q13368 MPP3_HUMAN membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3) 26 Breast(137;0.00394) CTTTTTTCCTGAATTGCAGGC 0.378000 0 SO:0001583 missense ENST00000398389.4 0 1 hg19 CCDS42344.1 . . . . . . . . . . G 8.912 0.959001 0.18507 . . ENSG00000161647 ENST00000398393;ENST00000398389 T;T 0.15603 2.41;2.41 5.36 5.36 0.76844 Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2); 0.278923 0.35291 N 0.003309 T 0.10937 0.0267 N 0.12471 0.22 0.29701 N 0.840156 B;B 0.18741 0.03;0.03 B;B 0.29440 0.071;0.102 T 0.13737 -1.0498 10 0.25751 T 0.34 . 11.4234 0.49996 0.0828:0.0:0.9172:0.0 . 508;533 Q13368;D3DX46 MPP3_HUMAN;. K 533;508 ENSP00000381430:Q533K;ENSP00000381425:Q508K ENSP00000381425:Q508K Q - 1 0 MPP3 39241909 0.999000 0.42202 0.988000 0.46212 0.988000 0.76386 3.512000 0.53407 2.782000 0.95742 0.655000 0.94253 CAG TCGA-XN-A8T3-01A-11D-A36O-08 MPP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000258371.1 0 0 0 15 624 0 125 0 9.014341e-02 0 20 0 125 2 0 0 0 0 0 2 1 0.999863 15 617 0 124 2 0 0 0 0 125 2 -2.812601 1 1 0 0 1 1 2 3 1.938332 0 0.190000 3.530000 0.260274 0.270000 0.150000 0.430000 0.270000 0.286426 0.270000 0 0.210000 0.350000 MSI2 124540 broad.mit.edu 37 17 55339540 55339540 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:55339540G>T ENST00000284073.2 + 5 508 c.299G>T c.(298-300)cGa>cTa p.R100L MSI2_ENST00000416426.2_Missense_Mutation_p.R78L|MSI2_ENST00000322684.3_Missense_Mutation_p.R96L NM_138962.2 NP_620412.1 Q96DH6 MSI2H_HUMAN musashi RNA-binding protein 2 p.R96Q(1) 7 Breast(9;1.78e-08) TTTCCTCGTCGAGCGCAACCC 0.363000 T HOXA9 CML Dom yes 17 17q23.2 124540 musashi homolog 2 (Drosophila) L 1 Substitution - Missense(1) SO:0001583 missense ENST00000284073.2 1 0 hg19 CCDS11596.1 . . . . . . . . . . G 16.99 3.275249 0.59649 . . ENSG00000153944 ENST00000416426;ENST00000284073;ENST00000322684 D;D;D 0.85702 -2.02;-2.02;-2.02 5.95 5.95 0.96441 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1); 0.178825 0.34725 N 0.003737 D 0.89983 0.6873 L 0.39514 1.22 0.80722 D 1 D;D;D 0.89917 0.995;1.0;1.0 D;D;D 0.91635 0.968;0.999;0.983 D 0.90033 0.4136 10 0.66056 D 0.02 . 19.3906 0.94581 0.0:0.0:1.0:0.0 . 78;96;100 B4DHE8;Q96DH6-2;Q96DH6 .;.;MSI2H_HUMAN L 78;100;96 ENSP00000414671:R78L;ENSP00000284073:R100L;ENSP00000313616:R96L ENSP00000284073:R100L R + 2 0 MSI2 52694539 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 8.454000 0.90352 2.827000 0.97445 0.650000 0.86243 CGA TCGA-XN-A8T3-01A-11D-A36O-08 MSI2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000441813.1 1 0 0 25 540 0 111 0 6.051497e-01 0 45 0 111 2 0 0 0 0 0 2 1 1.000000 22 524 0 109 2 0 0 0 0 111 2 -2.873120 1 1 0 0 1 1 2 3 1.941427 0 0.190000 3.530000 0.260274 0.510000 0.330000 0.720000 0.510000 0.525888 0.510000 0 0.410000 0.620000 HEATR6 63897 broad.mit.edu 37 17 58125680 58125680 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:58125680G>T ENST00000184956.6 - 17 2633 c.2617C>A c.(2617-2619)Cga>Aga p.R873R HEATR6_ENST00000585976.1_Silent_p.R761R NM_022070.4 NP_071353.4 Q6AI08 HEAT6_HUMAN HEAT repeat containing 6 p.R873*(1) 44 all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922) BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10) GCTTTGGCTCGAACATTCAGA 0.453000 1 Substitution - Nonsense(1) SO:0001819 synonymous_variant ENST00000184956.6 1 0 hg19 CCDS11623.1 TCGA-XN-A8T3-01A-11D-A36O-08 HEATR6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000449165.1 1 0 0 15 244 0 68 0 3.685742e-01 0 21 0 68 2 0 0 0 0 0 2 1 0.999859 15 237 0 67 2 0 0 0 0 68 2 -3.078274 1 1 0 0 1 1 2 3 1.941427 0 0.190000 3.530000 0.260274 0.670000 0.390000 1.000000 1.000000 0.694429 0.670000 0 0.520000 0.860000 HEATR6 63897 broad.mit.edu 37 17 58136792 58136792 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:58136792G>T ENST00000184956.6 - 11 1730 c.1714C>A c.(1714-1716)Cgc>Agc p.R572S HEATR6_ENST00000585976.1_Missense_Mutation_p.R572S NM_022070.4 NP_071353.4 Q6AI08 HEAT6_HUMAN HEAT repeat containing 6 44 all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922) BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10) CCTTTGTGGCGAATATAAGGC 0.348000 0 SO:0001583 missense ENST00000184956.6 1 0 hg19 CCDS11623.1 . . . . . . . . . . G 17.22 3.334590 0.60853 . . ENSG00000068097 ENST00000184956;ENST00000393017 T 0.62788 -0.0 5.62 4.65 0.58169 Armadillo-like helical (1);Armadillo-type fold (1); 0.149427 0.64402 D 0.000008 T 0.45597 0.1350 L 0.39020 1.185 0.45883 D 0.998739 B;B 0.34241 0.088;0.444 B;B 0.29176 0.099;0.097 T 0.34576 -0.9823 10 0.12430 T 0.62 -3.339 10.4854 0.44719 0.1647:0.0:0.8353:0.0 . 419;572 E7ESB9;Q6AI08 .;HEAT6_HUMAN S 572;419 ENSP00000184956:R572S ENSP00000184956:R572S R - 1 0 HEATR6 55491574 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 4.291000 0.59025 1.532000 0.49169 0.585000 0.79938 CGC TCGA-XN-A8T3-01A-11D-A36O-08 HEATR6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000449165.1 1 0 0 12 344 0 64 0 1.283188e-01 0 17 0 64 2 0 0 0 0 0 2 1 0.999124 12 342 0 64 2 0 0 0 0 64 2 -2.918380 1 1 0 0 1 1 2 3 1.941427 0 0.190000 3.530000 0.260274 0.390000 0.210000 0.640000 0.390000 0.415218 0.390000 0 0.290000 0.520000 ABCA9 10350 broad.mit.edu 37 17 67016572 67016572 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:67016572G>T ENST00000340001.4 - 19 2768 c.2557C>A c.(2557-2559)Cgc>Agc p.R853S ABCA9_ENST00000370732.2_Missense_Mutation_p.R853S|ABCA9_ENST00000453985.2_Missense_Mutation_p.R853S|ABCA9-AS1_ENST00000458677.1_RNA NM_080283.3 NP_525022.2 Q8IUA7 ABCA9_HUMAN ATP-binding cassette, sub-family A (ABC1), member 9 91 Breast(10;1.47e-12) TTTAGGAAGCGAACTTTTGCT 0.398000 0 SO:0001583 missense ENST00000340001.4 1 0 hg19 CCDS11681.1 . . . . . . . . . . G 25.8 4.673732 0.88445 . . ENSG00000154258 ENST00000340001;ENST00000453985;ENST00000370732;ENST00000453749 T;T 0.79653 -1.29;-1.29 5.08 5.08 0.68730 . 0.000000 0.46442 D 0.000283 D 0.90007 0.6880 M 0.80982 2.52 0.40094 D 0.97629 D;D 0.89917 1.0;0.999 D;D 0.80764 0.994;0.973 D 0.91683 0.5360 10 0.87932 D 0 . 17.3792 0.87400 0.0:0.0:1.0:0.0 . 853;853 Q8IUA7-3;Q8IUA7 .;ABCA9_HUMAN S 853;836;853;848 ENSP00000342216:R853S;ENSP00000359767:R853S ENSP00000342216:R853S R - 1 0 ABCA9 64528167 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 7.216000 0.77974 2.525000 0.85131 0.543000 0.68304 CGC TCGA-XN-A8T3-01A-11D-A36O-08 ABCA9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000277072.2 1 0 0 26 536 0 100 0 6.850329e-03 0 3 0 100 2 0 0 0 0 0 2 1 1.000000 26 530 0 99 2 0 0 0 0 100 2 -3.305096 1 1 0 0 1 1 2 3 1.941427 0 0.190000 3.530000 0.260274 0.530000 0.350000 0.750000 0.540000 0.549002 0.530000 0 0.440000 0.650000 ST6GALNAC1 55808 broad.mit.edu 37 17 74625340 74625340 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:74625340G>T ENST00000156626.7 - 2 784 c.585C>A c.(583-585)ctC>ctA p.L195L ST6GALNAC1_ENST00000590878.1_5'UTR NM_018414.3 NP_060884.1 Q9NSC7 SIA7A_HUMAN ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 22 TTTTGGGAATGAGCGTCTTGG 0.572000 0 SO:0001819 synonymous_variant ENST00000156626.7 1 0 hg19 CCDS11748.1 TCGA-XN-A8T3-01A-11D-A36O-08 ST6GALNAC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000450974.1 1 0 0 28 616 0 152 0 8.605182e-02 0 11 0 152 2 0 0 0 0 0 2 1 1.000000 28 609 0 151 2 0 0 0 0 152 2 -4.159221 1 0 0 0 1 1 2 3 1.941427 0 0.190000 3.530000 0.260274 0.500000 0.340000 0.700000 0.510000 0.515155 0.500000 0 0.410000 0.600000 TP53 7157 broad.mit.edu 37 17 7577121 7577121 + Missense_Mutation SNP G G A rs121913343 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr17:7577121G>A ENST00000269305.4 - 8 1006 c.817C>T c.(817-819)Cgt>Tgt p.R273C TP53_ENST00000445888.2_Missense_Mutation_p.R273C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R273C|TP53_ENST00000420246.2_Missense_Mutation_p.R273C|TP53_ENST00000359597.4_Missense_Mutation_p.R273C|TP53_ENST00000413465.2_Intron NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GCACAAACACGCACCTCAAAG 0.542000 R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID) 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 533 Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2) GRCh37 CM010471|CM010473|CM951233 TP53 M rs121913343 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 . . . . . . . . . . G 17.48 3.400216 0.62177 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D 0.99869 -7.34;-7.34;-7.34;-7.34;-7.34;-7.34 4.92 3.95 0.45737 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 0.99851 0.9931 M 0.90759 3.145 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.998;0.998;0.999;0.996 D 0.96877 0.9643 10 0.87932 D 0 -11.9995 11.2235 0.48869 0.0895:0.0:0.9105:0.0 . 273;273;273;273 P04637-2;P04637-3;P04637;Q1MSW8 .;.;P53_HUMAN;. C 273;273;273;273;273;262;141 ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C ENSP00000269305:R273C R - 1 0 TP53 7517846 1.000000 0.71417 0.066000 0.19879 0.723000 0.41478 4.540000 0.60664 1.299000 0.44798 0.462000 0.41574 CGT TCGA-XN-A8T3-01A-11D-A36O-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 18 94 0 24 1 9.983940e-01 13 46 0 24 2 1 1 142 668 0 930 2 1 0.999981 16 89 0 24 2 0 0 0 0 24 2 -20.000000 1 1 121412 1 37 1 0 2 2 1.764039 1 0.190000 3.530000 0.190000 0.990000 0.990000 1.000000 1.000000 0.998512 0.990000 1 0.990000 1.000000 CDH2 1000 broad.mit.edu 37 18 25570308 25570308 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr18:25570308C>A ENST00000269141.3 - 10 1774 c.1351G>T c.(1351-1353)Gac>Tac p.D451Y CDH2_ENST00000399380.3_Missense_Mutation_p.D420Y NM_001792.3 NP_001783.2 P19022 CADH2_HUMAN cadherin 2, type 1, N-cadherin (neuronal) 82 GTTTCAAAGTCGATTGGCTGG 0.393000 0 SO:0001583 missense ENST00000269141.3 1 0 hg19 CCDS11891.1 . . . . . . . . . . C 18.13 3.555450 0.65425 . . ENSG00000170558 ENST00000269141;ENST00000399380 T;T 0.65549 -0.16;-0.16 6.16 6.16 0.99307 Cadherin (5);Cadherin-like (1); 0.000000 0.85682 D 0.000000 T 0.80369 0.4610 H 0.98005 4.125 0.80722 D 1 P;P 0.42649 0.786;0.72 B;B 0.41332 0.354;0.185 D 0.86547 0.1832 10 0.87932 D 0 . 20.8598 0.99761 0.0:1.0:0.0:0.0 . 420;451 A8MWK3;P19022 .;CADH2_HUMAN Y 451;420 ENSP00000269141:D451Y;ENSP00000382312:D420Y ENSP00000269141:D451Y D - 1 0 CDH2 23824306 1.000000 0.71417 1.000000 0.80357 0.929000 0.56500 7.487000 0.81328 2.937000 0.99478 0.650000 0.86243 GAC TCGA-XN-A8T3-01A-11D-A36O-08 CDH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000133246.3 1 0 0 14 305 0 64 0 4.371911e-01 0 32 0 64 2 0 0 0 0 0 2 1 0.999732 13 299 0 63 2 0 0 0 0 64 2 -15.252200 1 1 0 0 1 2 2 4 1.864403 1 0.190000 3.530000 0.244544 0.550000 0.300000 1.000000 0.490000 0.631141 0.550000 0 0.400000 1.000000 ZNF442 79973 broad.mit.edu 37 19 12461420 12461420 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr19:12461420C>A ENST00000242804.4 - 6 1561 c.979G>T c.(979-981)Ggg>Tgg p.G327W CTD-3105H18.13_ENST00000563695.2_lincRNA|ZNF442_ENST00000438182.1_Missense_Mutation_p.G258W NM_030824.2 NP_110451.1 Q9H7R0 ZN442_HUMAN zinc finger protein 442 31 AATGCTTTCCCGCATTGCTTG 0.418000 0 SO:0001583 missense ENST00000242804.4 0 1 hg19 CCDS12271.1 . . . . . . . . . . C 13.91 2.379391 0.42207 . . ENSG00000198342 ENST00000242804;ENST00000438182 T;T 0.01051 5.4;5.4 0.832 -0.357 0.12579 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.08358 0.0208 H 0.96080 3.765 0.34524 D 0.708446 D 0.89917 1.0 D 0.97110 1.0 T 0.05131 -1.0904 9 0.87932 D 0 . 5.1771 0.15141 0.0:0.7619:0.0:0.2381 . 327 Q9H7R0 ZN442_HUMAN W 327;258 ENSP00000242804:G327W;ENSP00000388634:G258W ENSP00000242804:G327W G - 1 0 ZNF442 12322420 0.009000 0.17119 0.000000 0.03702 0.227000 0.25037 0.946000 0.29069 -0.077000 0.12752 0.313000 0.20887 GGG TCGA-XN-A8T3-01A-11D-A36O-08 ZNF442-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344109.1 0 0 0 11 1010 0 317 0 8.756327e-04 0 4 0 317 2 0 0 0 0 0 2 1 0.998185 11 996 0 317 2 0 0 0 0 317 2 -1.642139 0 1 0 0 1 1 2 3 1.790940 0 0.190000 3.530000 0.203618 0.120000 0.050000 1.000000 0.110000 0.246784 0.120000 0 0.080000 0.210000 ZNF14 7561 broad.mit.edu 37 19 19824904 19824904 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr19:19824904G>T ENST00000344099.3 - 3 325 c.187C>A c.(187-189)Cga>Aga p.R63R NM_021030.2 NP_066358.2 P17017 ZNF14_HUMAN zinc finger protein 14 p.R63*(1) 32 Renal(1328;0.0474) ACTCACCTTCGATTTTTCCCC 0.368000 1 Substitution - Nonsense(1) SO:0001819 synonymous_variant ENST00000344099.3 1 0 hg19 CCDS12409.1 TCGA-XN-A8T3-01A-11D-A36O-08 ZNF14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000460775.1 1 0 0 22 514 0 109 0 7.944101e-02 0 11 0 109 2 0 0 0 0 0 2 1 0.999999 20 509 0 106 2 0 0 0 0 109 2 -2.884132 1 1 0 0 1 1 2 3 1.790940 0 0.190000 3.530000 0.203618 0.460000 0.280000 1.000000 0.430000 0.530255 0.460000 0 0.360000 0.650000 ZNF461 92283 broad.mit.edu 37 19 37130742 37130742 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr19:37130742G>T ENST00000588268.1 - 6 732 c.505C>A c.(505-507)Cat>Aat p.H169N ZNF461_ENST00000540605.2_5'UTR|ZNF461_ENST00000360357.4_Missense_Mutation_p.H146N NM_153257.2 NP_694989.2 Q8TAF7 ZN461_HUMAN zinc finger protein 461 29 Esophageal squamous(110;0.198) COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065) ATGTTTTCATGGTTAATCATA 0.358000 0 SO:0001583 missense ENST00000588268.1 0 1 hg19 CCDS54257.1 . . . . . . . . . . G 0.120 -1.127098 0.01770 . . ENSG00000197808 ENST00000396893;ENST00000360357;ENST00000540605;ENST00000396892 T 0.05855 3.38 3.87 0.209 0.15226 . . . . . T 0.04679 0.0127 L 0.39898 1.24 0.09310 N 1 B;B;B 0.13145 0.004;0.007;0.007 B;B;B 0.08055 0.002;0.003;0.003 T 0.45056 -0.9287 9 0.19590 T 0.45 . 3.5785 0.07943 0.2434:0.2122:0.5444:0.0 . 146;91;169 B4DRP8;Q59G30;Q8TAF7 .;.;ZN461_HUMAN N 169;146;42;104 ENSP00000353515:H146N ENSP00000353515:H146N H - 1 0 ZNF461 41822582 0.004000 0.15560 0.001000 0.08648 0.041000 0.13682 0.721000 0.25911 0.399000 0.25367 -0.150000 0.13652 CAT TCGA-XN-A8T3-01A-11D-A36O-08 ZNF461-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000453202.1 0 0 0 14 976 0 183 0 2.436410e-04 0 2 0 183 2 0 0 0 0 0 2 1 0.999728 14 964 0 182 2 0 0 0 0 183 2 -1.891827 0 1 0 0 1 2 3 5 2.226927 1 0.190000 3.530000 0.364008 0.190000 0.100000 1.000000 0.200000 0.225330 0.190000 0 0.140000 0.260000 DLL3 10683 broad.mit.edu 37 19 39998549 39998549 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr19:39998549C>A ENST00000205143.4 + 8 1760 c.1753C>A c.(1753-1755)Cgg>Agg p.R585R DLL3_ENST00000356433.5_Silent_p.R585R NM_016941.3 NP_058637.1 Q9NYJ7 DLL3_HUMAN delta-like 3 (Drosophila) 19 all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159) Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657) CATCTACGCTCGGGAGGTAGC 0.562000 0 SO:0001819 synonymous_variant ENST00000205143.4 1 0 hg19 CCDS12538.1 TCGA-XN-A8T3-01A-11D-A36O-08 DLL3-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000464958.1 1 0 0 18 379 0 75 0 2.141656e-02 0 5 0 75 2 0 0 0 0 0 2 1 0.999980 16 374 0 74 2 0 0 0 0 75 2 -3.090621 1 1 0 0 1 2 3 5 2.226927 1 0.190000 3.530000 0.364008 0.620000 0.370000 1.000000 0.590000 0.645314 0.620000 0 0.490000 0.800000 PPFIA3 8541 broad.mit.edu 37 19 49651448 49651448 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr19:49651448C>A ENST00000334186.4 + 24 3293 c.2944C>A c.(2944-2946)Cga>Aga p.R982R PPFIA3_ENST00000602351.1_Silent_p.R973R NM_003660.2 NP_003651.1 O75145 LIPA3_HUMAN protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3 35 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) GGTGGACGCTCGAATGTTAGA 0.592000 0 SO:0001819 synonymous_variant ENST00000334186.4 1 0 hg19 CCDS12758.1 TCGA-XN-A8T3-01A-11D-A36O-08 PPFIA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465688.1 1 0 0 15 297 0 62 0 3.477715e-02 0 6 0 62 2 0 0 0 0 0 2 1 0.999869 15 294 0 61 2 0 0 0 0 62 2 -2.933436 1 1 0 0 1 3 4 7 2.294134 1 0.190000 3.530000 0.385549 0.740000 0.410000 1.000000 1.000000 0.762736 0.740000 0 0.550000 1.000000 MYADM 91663 broad.mit.edu 37 19 54377360 54377360 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 G T G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr19:54377360G>T ENST00000391769.2 + 3 857 c.577G>T c.(577-579)Gac>Tac p.D193Y MYADM_ENST00000336967.3_Missense_Mutation_p.D193Y|MYADM_ENST00000391771.1_Missense_Mutation_p.D193Y|MYADM_ENST00000391770.4_Missense_Mutation_p.D193Y|MYADM_ENST00000391768.2_Missense_Mutation_p.D193Y|AC008440.5_ENST00000413496.2_RNA NM_001020821.1 NP_001018657.1 Q96S97 MYADM_HUMAN myeloid-associated differentiation marker 12 Ovarian(34;0.19) GTTCATCAGCGACCCCAACCT 0.642000 0 SO:0001583 missense ENST00000391769.2 1 0 hg19 CCDS12866.1 . . . . . . . . . . G 3.909 -0.020465 0.07634 . . ENSG00000179820 ENST00000421337;ENST00000336967;ENST00000391770;ENST00000439000;ENST00000391771;ENST00000415619;ENST00000391769;ENST00000391768 T;T;T;T;T;T;T 0.25085 1.82;1.82;1.82;1.82;1.82;1.82;1.82 4.21 -5.25 0.02781 Marvel (1);MARVEL-like domain (1); 1.023760 0.07811 N 0.958108 T 0.27098 0.0664 L 0.41710 1.295 0.09310 N 1 P 0.42941 0.794 P 0.46076 0.503 T 0.41431 -0.9509 10 0.56958 D 0.05 -2.8128 14.9568 0.71120 0.1028:0.0:0.8972:0.0 . 193 Q96S97 MYADM_HUMAN Y 193;193;193;193;193;156;193;193 ENSP00000398269:D193Y;ENSP00000337222:D193Y;ENSP00000375650:D193Y;ENSP00000416919:D193Y;ENSP00000375651:D193Y;ENSP00000375649:D193Y;ENSP00000375648:D193Y ENSP00000337222:D193Y D + 1 0 MYADM 59069172 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 0.121000 0.15667 -1.181000 0.02730 -0.657000 0.03884 GAC TCGA-XN-A8T3-01A-11D-A36O-08 MYADM-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000134337.1 1 0 0 30 651 0 114 0 9.999941e-01 0 400 0 114 2 0 0 0 0 0 2 1 1.000000 30 644 0 114 2 0 0 0 0 114 2 -3.279883 1 1 0 0 1 3 4 7 2.294134 1 0.190000 3.530000 0.385549 0.650000 0.430000 1.000000 0.600000 0.707564 0.650000 0 0.520000 1.000000 C19orf18 147685 broad.mit.edu 37 19 58477954 58477954 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr19:58477954C>A ENST00000314391.3 - 4 416 c.315G>T c.(313-315)tcG>tcT p.S105S NM_152474.4 NP_689687.1 Q8NEA5 CS018_HUMAN chromosome 19 open reading frame 18 8 Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156) AGGCTACGCTCGAAATTAAAA 0.348000 0 SO:0001819 synonymous_variant ENST00000314391.3 1 0 hg19 CCDS12967.1 TCGA-XN-A8T3-01A-11D-A36O-08 C19orf18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466704.1 1 0 0 23 473 0 63 0 6.964828e-03 0 3 0 63 2 0 0 0 0 0 2 1 0.999999 23 467 0 60 2 0 0 0 0 63 2 -2.750138 1 1 0 0 1 3 3 6 2.304241 1 0.190000 3.530000 0.387755 0.670000 0.420000 1.000000 0.640000 0.707614 0.670000 0 0.540000 0.910000 INSR 3643 broad.mit.edu 37 19 7163065 7163065 + Missense_Mutation SNP G G T rs2962 byFrequency TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr19:7163065G>T ENST00000302850.5 - 9 2149 c.2007C>A c.(2005-2007)ttC>ttA p.F669L INSR_ENST00000341500.5_Missense_Mutation_p.F669L|AC010311.1_ENST00000581768.1_RNA NM_000208.2 NP_000199.2 P06213 INSR_HUMAN insulin receptor 66 """Insulin(DB00071)|""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)" AATCCAGCTCGAACAGCTCAC 0.537000 0 SO:0001583 missense ENST00000302850.5 1 0 hg19 CCDS12176.1 . . . . . . . . . . G 13.29 2.193146 0.38707 . . ENSG00000171105 ENST00000302850;ENST00000341500 T;T 0.71934 -0.61;-0.61 4.45 -4.7 0.03288 Fibronectin, type III (3); 0.184367 0.25804 U 0.028188 T 0.56001 0.1956 L 0.43152 1.355 0.33845 P 0.368139 B;B;B 0.09022 0.0;0.001;0.002 B;B;B 0.08055 0.003;0.002;0.003 T 0.45366 -0.9266 9 0.62326 D 0.03 . 11.1006 0.48172 0.7214:0.0:0.2786:0.0 . 660;669;669 Q86WY9;P06213-2;P06213 .;.;INSR_HUMAN L 669 ENSP00000303830:F669L;ENSP00000342838:F669L ENSP00000303830:F669L F - 3 2 INSR 7114065 0.967000 0.33354 0.091000 0.20842 0.524000 0.34500 0.178000 0.16820 -0.681000 0.05204 -0.140000 0.14226 TTC TCGA-XN-A8T3-01A-11D-A36O-08 INSR-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000458544.1 1 0 0 17 388 0 133 0 4.396495e-01 0 34 0 133 2 0 0 0 0 0 2 1 0.999963 17 382 0 133 2 0 0 0 0 133 2 -2.560141 1 1 0 0 1 1 2 3 1.790940 0 0.190000 3.530000 0.203618 0.470000 0.280000 1.000000 0.440000 0.542793 0.470000 0 0.360000 0.700000 S1PR1 1901 broad.mit.edu 37 1 101705326 101705326 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:101705326G>T ENST00000305352.6 + 2 1161 c.786G>T c.(784-786)ctG>ctT p.L262L NM_001400.4 NP_001391.2 P21453 S1PR1_HUMAN sphingosine-1-phosphate receptor 1 43 TTATCGTCCTGAGCGTCTTCA 0.592000 0 SO:0001819 synonymous_variant ENST00000305352.6 1 0 hg19 CCDS777.1 TCGA-XN-A8T3-01A-11D-A36O-08 S1PR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029908.1 1 0 0 31 670 0 171 0 5.547806e-01 0 41 0 171 2 0 0 0 0 0 2 1 1.000000 31 661 0 170 2 0 0 0 0 171 2 -2.803092 1 1 0 0 1 2 2 4 2.091950 0 0.190000 3.530000 0.319328 0.550000 0.380000 0.760000 0.560000 0.568464 0.550000 0 0.460000 0.660000 KCNA3 3738 broad.mit.edu 37 1 111215758 111215758 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:111215758C>A ENST00000369769.2 - 1 1897 c.1674G>T c.(1672-1674)acG>acT p.T558T NM_002232.3 NP_002223.3 P22001 KCNA3_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 3 38 all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398) Dalfampridine(DB06637) GATTATTGTTCGTGGTGCAGG 0.458000 0 SO:0001819 synonymous_variant ENST00000369769.2 1 0 hg19 CCDS828.2 TCGA-XN-A8T3-01A-11D-A36O-08 KCNA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083391.1 1 0 0 25 662 0 148 0 0 0 1 0 148 2 0 0 0 0 0 2 1 1.000000 25 647 0 144 2 0 0 0 0 148 2 -2.894383 1 1 0 0 1 2 2 4 2.091950 0 0.190000 3.530000 0.319328 0.450000 0.300000 0.650000 0.440000 0.471236 0.450000 0 0.370000 0.560000 ST7L 54879 broad.mit.edu 37 1 113098534 113098534 + Missense_Mutation SNP C C A rs6658555 byFrequency TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:113098534C>A ENST00000358039.4 - 12 1656 c.1352G>T c.(1351-1353)cGa>cTa p.R451L ST7L_ENST00000360743.4_Missense_Mutation_p.R451L|ST7L_ENST00000369669.1_Missense_Mutation_p.R268L|ST7L_ENST00000369666.1_Missense_Mutation_p.R434L|ST7L_ENST00000538187.1_Missense_Mutation_p.R395L|ST7L_ENST00000343210.7_Missense_Mutation_p.R451L|ST7L_ENST00000369668.2_Missense_Mutation_p.R451L|ST7L_ENST00000544629.1_Missense_Mutation_p.R386L|ST7L_ENST00000463235.1_5'UTR|ST7L_ENST00000543570.1_Intron|ST7L_ENST00000490067.1_Missense_Mutation_p.R434L NM_017744.4|NM_138727.3 NP_060214.2|NP_620055.1 Q8TDW4 ST7L_HUMAN suppression of tumorigenicity 7 like p.R451Q(1) 15 Lung SC(450;0.246) all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05) ACCTTCTATTCGTTTCCAGTG 0.363000 1 Substitution - Missense(1) SO:0001583 missense ENST00000358039.4 1 0 hg19 CCDS848.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 32|32 5.158765|5.158765 0.94686|0.94686 .|. .|. ENSG00000007341|ENSG00000007341 ENST00000418497|ENST00000358039;ENST00000360743;ENST00000369673;ENST00000544629;ENST00000369669;ENST00000490067;ENST00000369668;ENST00000343210;ENST00000369666;ENST00000538187 .|T;T;T;T;T;T;T;T;T .|0.22336 .|1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96 5.59|5.59 5.59|5.59 0.84812|0.84812 .|. .|0.000000 .|0.85682 .|D .|0.000000 .|T .|0.43942 .|0.1270 M|M 0.79475|0.79475 2.455|2.455 0.09310|0.09310 P|P 1.0|1.0 .|D;D;D;D;D;D;D;D .|0.89917 .|0.994;1.0;0.974;0.996;0.993;0.993;0.998;0.994 .|P;D;D;D;P;D;D;D .|0.91635 .|0.855;0.999;0.917;0.951;0.822;0.958;0.972;0.975 .|T .|0.42783 .|-0.9431 .|9 .|0.72032 .|D .|0.01 -6.2202|-6.2202 19.1881|19.1881 0.93653|0.93653 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|395;386;386;451;434;434;451;451 .|B7Z7D4;B7Z3J2;F5H2P3;Q8TDW4-5;Q8TDW4-6;Q8TDW4-3;Q8TDW4-2;Q8TDW4 .|.;.;.;.;.;.;.;ST7L_HUMAN X|L 226|451;451;232;386;268;434;451;451;434;395 .|ENSP00000350734:R451L;ENSP00000353972:R451L;ENSP00000445499:R386L;ENSP00000358683:R268L;ENSP00000417140:R434L;ENSP00000358682:R451L;ENSP00000345312:R451L;ENSP00000358680:R434L;ENSP00000444021:R395L .|ENSP00000345312:R451L E|R -|- 1|2 0|0 ST7L|ST7L 112900057|112900057 1.000000|1.000000 0.71417|0.71417 0.997000|0.997000 0.53966|0.53966 0.968000|0.968000 0.65278|0.65278 6.086000|6.086000 0.71352|0.71352 2.625000|2.625000 0.88918|0.88918 0.585000|0.585000 0.79938|0.79938 GAA|CGA TCGA-XN-A8T3-01A-11D-A36O-08 ST7L-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000032504.3 1 0 0 19 465 0 78 0 7.460477e-02 0 11 0 78 2 0 0 0 0 0 2 1 0.999990 20 459 0 78 2 0 0 0 0 78 2 -2.285200 0 1 0 0 1 2 2 4 2.091950 0 0.190000 3.530000 0.319328 0.490000 0.300000 0.740000 0.480000 0.513222 0.490000 0 0.390000 0.620000 LRIG2 9860 broad.mit.edu 37 1 113653034 113653034 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:113653034C>A ENST00000361127.5 + 13 1846 c.1648C>A c.(1648-1650)Cgt>Agt p.R550S LRIG2_ENST00000492207.1_3'UTR NM_014813.1 NP_055628.1 O94898 LRIG2_HUMAN leucine-rich repeats and immunoglobulin-like domains 2 31 Lung SC(450;0.246) all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986) GAATTTTGTTCGTTATTGGCA 0.418000 0 SO:0001583 missense ENST00000361127.5 1 0 hg19 CCDS30808.1 . . . . . . . . . . c 14.42 2.530545 0.45073 . . ENSG00000198799 ENST00000361127 T 0.37752 1.18 5.89 4.93 0.64822 Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.053044 0.64402 D 0.000001 T 0.18425 0.0442 L 0.43701 1.375 0.53005 D 0.999965 B 0.23540 0.087 B 0.30401 0.115 T 0.02844 -1.1103 10 0.14656 T 0.56 . 14.3328 0.66569 0.2175:0.7825:0.0:0.0 . 550 O94898 LRIG2_HUMAN S 550 ENSP00000355396:R550S ENSP00000355396:R550S R + 1 0 LRIG2 113454557 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 3.514000 0.53422 2.793000 0.96121 0.655000 0.94253 CGT TCGA-XN-A8T3-01A-11D-A36O-08 LRIG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033549.2 1 0 0 28 705 0 139 0 1.178861e-01 0 15 0 139 2 0 0 0 0 0 2 1 1.000000 27 695 0 139 2 0 0 0 0 139 2 -2.915294 1 1 0 0 1 2 2 4 2.091950 0 0.190000 3.530000 0.319328 0.480000 0.320000 0.670000 0.480000 0.492810 0.480000 0 0.390000 0.580000 MAGI3 260425 broad.mit.edu 37 1 114184571 114184571 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:114184571G>T ENST00000307546.9 + 10 1474 c.1399G>T c.(1399-1401)Ggt>Tgt p.G467C MAGI3_ENST00000369617.4_Missense_Mutation_p.G492C|MAGI3_ENST00000369615.1_Missense_Mutation_p.G467C|MAGI3_ENST00000369611.4_Missense_Mutation_p.G467C NM_001142782.1 NP_001136254.1 Q5TCQ9 MAGI3_HUMAN membrane associated guanylate kinase, WW and PDZ domain containing 3 41 Lung SC(450;0.184) all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05) CTGTGTCCTCGGTCACACTCA 0.358000 0 SO:0001583 missense ENST00000307546.9 0 1 hg19 CCDS44196.1 . . . . . . . . . . G 23.8 4.456418 0.84317 . . ENSG00000081026 ENST00000369617;ENST00000307546;ENST00000369615;ENST00000369611 T;T;T;T 0.55930 0.49;0.49;0.49;0.49 5.38 5.38 0.77491 . 0.000000 0.85682 D 0.000000 D 0.83317 0.5228 H 0.98918 4.37 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;1.0;1.0 D 0.89889 0.4036 10 0.87932 D 0 -28.5003 19.4992 0.95086 0.0:0.0:1.0:0.0 . 467;467;492 Q5TCQ9-4;Q5TCQ9-3;Q5TCQ9-2 .;.;. C 492;467;467;467 ENSP00000358630:G492C;ENSP00000304604:G467C;ENSP00000358628:G467C;ENSP00000358624:G467C ENSP00000304604:G467C G + 1 0 MAGI3 113986094 1.000000 0.71417 0.999000 0.59377 0.985000 0.73830 9.420000 0.97426 2.689000 0.91719 0.655000 0.94253 GGT TCGA-XN-A8T3-01A-11D-A36O-08 MAGI3-004 NOVEL basic|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000032429.1 0 0 0 11 594 0 107 0 8.195098e-03 0 7 0 107 2 0 0 0 0 0 2 1 0.998142 10 582 0 107 2 0 0 0 0 107 2 -2.560730 1 1 121412 1 31 1 2 2 4 2.091950 0 0.190000 3.530000 0.319328 0.230000 0.110000 0.390000 0.240000 0.246771 0.230000 0 0.170000 0.310000 PHTF1 10745 broad.mit.edu 37 1 114280825 114280825 + Silent SNP G G T rs78000844 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:114280825G>T ENST00000369604.1 - 5 721 c.238C>A c.(238-240)Cga>Aga p.R80R PHTF1_ENST00000393357.2_Silent_p.R80R|PHTF1_ENST00000447664.2_Silent_p.R80R|PHTF1_ENST00000369596.2_Intron|PHTF1_ENST00000357783.2_Silent_p.R80R|PHTF1_ENST00000369598.1_Silent_p.R80R|PHTF1_ENST00000369600.1_Intron Q9UMS5 PHTF1_HUMAN putative homeodomain transcription factor 1 27 Lung SC(450;0.184) all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05) AATACAACTCGAACAAGCCCC 0.358000 0 SO:0001819 synonymous_variant ENST00000369604.1 1 0 hg19 CCDS861.1 TCGA-XN-A8T3-01A-11D-A36O-08 PHTF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032666.1 1 0 0 17 347 0 64 0 3.651310e-01 0 26 0 64 2 0 0 0 0 0 2 1 0.999960 17 338 0 64 2 0 0 0 0 64 2 -4.614483 1 1 0 0 1 2 2 4 2.091950 0 0.190000 3.530000 0.319328 0.590000 0.350000 0.890000 0.590000 0.611940 0.590000 0 0.460000 0.750000 CRNN 49860 broad.mit.edu 37 1 152383339 152383339 + Silent SNP T T C TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:152383339T>C ENST00000271835.3 - 3 281 c.219A>G c.(217-219)gaA>gaG p.E73E RP1-91G5.3_ENST00000411804.1_RNA NM_016190.2 NP_057274.1 Q9UBG3 CRNN_HUMAN cornulin 35 Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.206) AGACCAGGAATTCCTTGAATT 0.537000 0 SO:0001819 synonymous_variant ENST00000271835.3 1 1 hg19 CCDS1010.1 TCGA-XN-A8T3-01A-11D-A36O-08 CRNN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000034503.1 1 0 0 26 439 0 110 0 0 0 0 110 2 0 0 0 0 0 2 1 1.000000 26 435 0 110 2 0 0 0 0 110 2 -20.000000 1 0 121404 1 32 1 2 2 4 2.085565 0 0.190000 3.530000 0.319328 0.700000 0.470000 0.980000 1.000000 0.719105 0.700000 0 0.580000 0.850000 GON4L 54856 broad.mit.edu 37 1 155736404 155736404 + Silent SNP G G T rs143360629 by1000genomes TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:155736404G>T ENST00000368331.1 - 21 2908 c.2860C>A c.(2860-2862)Cga>Aga p.R954R GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000437809.1_Silent_p.R954R|GON4L_ENST00000361040.5_Silent_p.R954R|GON4L_ENST00000271883.5_Silent_p.R954R NM_001282858.1|NM_001282860.1 NP_001269787.1|NP_001269789.1 Q3T8J9 GON4L_HUMAN gon-4-like (C. elegans) 45 Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195) TCTAGGCTTCGATCTGAGTTG 0.502000 0 SO:0001819 synonymous_variant ENST00000368331.1 1 0 hg19 TCGA-XN-A8T3-01A-11D-A36O-08 GON4L-201 KNOWN basic|appris_candidate_longest protein_coding protein_coding 1 0 0 18 431 0 90 0 3.447741e-01 0 29 0 90 2 0 0 0 0 0 2 1 0.999981 18 427 0 91 2 0 0 0 0 90 2 -3.744091 1 1 0 0 1 2 2 4 2.075565 0 0.190000 3.530000 0.319328 0.510000 0.310000 0.760000 0.510000 0.525205 0.510000 0 0.400000 0.640000 PYHIN1 149628 broad.mit.edu 37 1 158908227 158908227 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:158908227C>A ENST00000368140.1 + 3 551 c.306C>A c.(304-306)atC>atA p.I102I PYHIN1_ENST00000392254.2_Silent_p.I102I|PYHIN1_ENST00000392252.3_Silent_p.I93I|PYHIN1_ENST00000368138.3_Silent_p.I93I|PYHIN1_ENST00000368135.4_Silent_p.I102I NM_152501.4|NM_198928.4|NM_198929.4 NP_689714.2|NP_945146.1|NP_945147.1 Q6K0P9 IFIX_HUMAN pyrin and HIN domain family, member 1 60 all_hematologic(112;0.0378) AAGGAATAATCCCATCTAAAA 0.443000 0 SO:0001819 synonymous_variant ENST00000368140.1 0 1 hg19 CCDS1178.1 TCGA-XN-A8T3-01A-11D-A36O-08 PYHIN1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000090110.1 0 0 0 9 488 1 88 0 4.408818e-04 0 2 1 88 2 0 0 0 0 0 2 0 0.039016 8 485 1 87 19 0 0 0 1 88 2 -2.936063 1 1 0 0 1 2 2 4 2.075565 0 0.190000 3.530000 0.319328 0.230000 0.110000 0.410000 0.240000 0.249959 0.230000 0 0.160000 0.330000 SLAMF6 114836 broad.mit.edu 37 1 160458917 160458917 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:160458917C>A ENST00000368057.3 - 6 900 c.840G>T c.(838-840)acG>acT p.T280T SLAMF6_ENST00000368055.1_Silent_p.T169T|SLAMF6_ENST00000368059.3_Silent_p.T279T Q96DU3 SLAF6_HUMAN SLAM family member 6 22 all_cancers(52;1.05e-18)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.0923) CAGTGTTGTTCGTTGGAGACA 0.443000 0 SO:0001819 synonymous_variant ENST00000368057.3 1 0 hg19 CCDS53394.1 TCGA-XN-A8T3-01A-11D-A36O-08 SLAMF6-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000059010.1 1 0 0 19 512 0 102 0 1.358139e-02 0 5 0 102 2 0 0 0 0 0 2 1 0.999990 19 509 0 101 2 0 0 0 0 102 2 -2.848300 1 1 0 0 1 2 2 4 2.075565 0 0.190000 3.530000 0.319328 0.450000 0.280000 0.670000 0.440000 0.468156 0.450000 0 0.350000 0.570000 ARHGEF10L 55160 broad.mit.edu 37 1 17958842 17958842 + Silent SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:17958842G>A ENST00000361221.3 + 16 1770 c.1611G>A c.(1609-1611)ctG>ctA p.L537L ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000167825.4_Silent_p.L245L|ARHGEF10L_ENST00000375415.1_Silent_p.L498L|ARHGEF10L_ENST00000434513.1_Silent_p.L537L|ARHGEF10L_ENST00000375408.3_Silent_p.L315L|ARHGEF10L_ENST00000452522.1_Silent_p.L498L|ARHGEF10L_ENST00000375420.3_Silent_p.L295L NM_018125.3 NP_060595 Q9HCE6 ARGAL_HUMAN Rho guanine nucleotide exchange factor (GEF) 10-like 43 Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255) AGCGGCAGCTGCTCCTGTGTG 0.627000 0 SO:0001819 synonymous_variant ENST00000361221.3 1 1 hg19 CCDS182.1 TCGA-XN-A8T3-01A-11D-A36O-08 ARHGEF10L-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000007147.1 1 0 1 86 477 0 128 1 9.927308e-01 5 39 0 128 2 0 0 0 0 0 2 1 1.000000 84 470 0 125 2 0 0 0 0 128 2 -3.222839 1 1 0 0 1 2 2 4 2.117161 1 0.190000 3.530000 0.319328 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TPR 7175 broad.mit.edu 37 1 186304589 186304589 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:186304589G>T ENST00000367478.4 - 34 5088 c.4792C>A c.(4792-4794)Cgc>Agc p.R1598S NM_003292.2 NP_003283.2 P12270 TPR_HUMAN translocated promoter region, nuclear basket protein 123 Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157) GCAGTAATGCGAACATCCAAT 0.423000 T NTRK1 papillary thyroid Dom yes 1 1q25 7175 translocated promoter region E 0 SO:0001583 missense ENST00000367478.4 1 0 hg19 CCDS41446.1 . . . . . . . . . . G 29.2 4.989888 0.93106 . . ENSG00000047410 ENST00000367478 T 0.26518 1.73 5.14 5.14 0.70334 . 0.000000 0.85682 D 0.000000 T 0.54498 0.1862 M 0.79805 2.47 0.80722 D 1 D 0.89917 1.0 D 0.81914 0.995 T 0.53585 -0.8418 10 0.36615 T 0.2 . 18.9661 0.92697 0.0:0.0:1.0:0.0 . 1598 P12270 TPR_HUMAN S 1598 ENSP00000356448:R1598S ENSP00000356448:R1598S R - 1 0 TPR 184571212 1.000000 0.71417 1.000000 0.80357 0.958000 0.62258 9.065000 0.93941 2.545000 0.85829 0.650000 0.86243 CGC TCGA-XN-A8T3-01A-11D-A36O-08 TPR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086353.2 1 0 0 28 714 0 143 0 7.972226e-01 0 78 0 143 2 0 0 0 0 0 2 1 1.000000 28 708 0 142 2 0 0 0 0 143 2 -2.856187 1 1 0 0 1 2 2 4 2.082668 0 0.190000 3.530000 0.319328 0.470000 0.310000 0.660000 0.480000 0.486866 0.470000 0 0.390000 0.570000 ASPM 259266 broad.mit.edu 37 1 197102510 197102510 + Silent SNP G G T rs145489194 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:197102510G>T ENST00000367409.4 - 6 2645 c.2389C>A c.(2389-2391)Cga>Aga p.R797R ASPM_ENST00000294732.7_Silent_p.R797R|ASPM_ENST00000367408.1_Silent_p.R47R NM_018136.4 NP_060606.3 Q8IZT6 ASPM_HUMAN asp (abnormal spindle) homolog, microcephaly associated (Drosophila) 165 CTATCTTTTCGAACAATTAAC 0.348000 0 SO:0001819 synonymous_variant ENST00000367409.4 1 0 hg19 CCDS1389.1 TCGA-XN-A8T3-01A-11D-A36O-08 ASPM-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000088256.1 1 0 0 26 465 0 80 0 1.707018e-02 0 4 0 80 2 0 0 0 0 0 2 1 1.000000 26 461 0 79 2 0 0 0 0 80 2 -3.142371 1 1 0 0 1 2 2 4 2.082668 0 0.190000 3.530000 0.319328 0.660000 0.440000 0.930000 0.670000 0.682340 0.660000 0 0.540000 0.810000 USH2A 7399 broad.mit.edu 37 1 215844624 215844624 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:215844624C>A ENST00000307340.3 - 64 14209 c.13823G>T c.(13822-13824)cGa>cTa p.R4608L USH2A_ENST00000366943.2_Missense_Mutation_p.R4608L NM_206933.2 NP_996816 O75445 USH2A_HUMAN Usher syndrome 2A (autosomal recessive, mild) 527 CGCTTGAATTCGTATTTCATA 0.418000 HNSCC(13;0.011) 0 SO:0001583 missense ENST00000307340.3 1 0 hg19 CCDS31025.1 . . . . . . . . . . C 17.83 3.485952 0.63962 . . ENSG00000042781 ENST00000307340;ENST00000366943 T;T 0.60920 0.15;0.15 4.94 3.03 0.35002 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.214025 0.23633 N 0.046103 T 0.66157 0.2761 M 0.84326 2.69 0.37088 D 0.899288 P 0.52842 0.956 P 0.53912 0.737 T 0.71377 -0.4611 10 0.59425 D 0.04 . 5.2652 0.15595 0.0:0.5939:0.0:0.4061 . 4608 O75445 USH2A_HUMAN L 4608 ENSP00000305941:R4608L;ENSP00000355910:R4608L ENSP00000305941:R4608L R - 2 0 USH2A 213911247 0.982000 0.34865 0.193000 0.23327 0.855000 0.48748 2.517000 0.45529 1.202000 0.43218 0.650000 0.86243 CGA TCGA-XN-A8T3-01A-11D-A36O-08 USH2A-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128138.1 1 0 0 13 297 0 49 0 0 0 0 49 2 0 0 0 0 0 2 1 0.999533 13 294 0 49 2 0 0 0 0 49 2 -3.022593 1 1 0 0 1 2 2 4 2.082668 0 0.190000 3.530000 0.319328 0.530000 0.300000 0.850000 0.520000 0.557892 0.530000 0 0.400000 0.700000 RAB3GAP2 25782 broad.mit.edu 37 1 220356177 220356177 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:220356177G>T ENST00000358951.2 - 20 2211 c.2095C>A c.(2095-2097)Cga>Aga p.R699R NM_012414.3 NP_036546.2 Q9H2M9 RBGPR_HUMAN RAB3 GTPase activating protein subunit 2 (non-catalytic) 39 TCAGAAAATCGAACATTTGTC 0.348000 0 SO:0001819 synonymous_variant ENST00000358951.2 1 0 hg19 CCDS31028.1 TCGA-XN-A8T3-01A-11D-A36O-08 RAB3GAP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090205.2 1 0 0 21 463 0 82 0 6.119469e-02 0 9 0 82 2 0 0 0 0 0 2 1 0.999997 21 457 0 82 2 0 0 0 0 82 2 -3.126318 1 1 0 0 1 2 2 4 2.082668 0 0.190000 3.530000 0.319328 0.550000 0.340000 0.800000 0.550000 0.564511 0.550000 0 0.440000 0.680000 OBSCN 84033 broad.mit.edu 37 1 228432014 228432014 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:228432014G>T ENST00000422127.1 + 11 3267 c.3223G>T c.(3223-3225)Gca>Tca p.A1075S OBSCN_ENST00000284548.11_Missense_Mutation_p.A1075S|OBSCN_ENST00000570156.2_Missense_Mutation_p.A1167S|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR NM_001098623.2 NP_001092093.2 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF 223 Prostate(94;0.0405) GATGATGTTTGCAAAGGAGCA 0.572000 0 SO:0001583 missense ENST00000422127.1 1 1 hg19 CCDS58065.1 . . . . . . . . . . . 2.395 -0.338872 0.05243 . . ENSG00000154358 ENST00000284548;ENST00000422127 T;T 0.04551 3.6;3.6 3.69 2.78 0.32641 Immunoglobulin-like (1); 0.317255 0.27060 N 0.021125 T 0.04363 0.0120 L 0.39147 1.195 0.80722 D 1 P;B 0.37985 0.613;0.169 B;B 0.41466 0.358;0.049 T 0.40664 -0.9551 10 0.06891 T 0.86 . 6.4866 0.22093 0.3275:0.0:0.6725:0.0 . 1075;1075 Q5VST9;Q5VST9-3 OBSCN_HUMAN;. S 1075 ENSP00000284548:A1075S;ENSP00000409493:A1075S ENSP00000284548:A1075S A + 1 0 OBSCN 226498637 0.000000 0.05858 0.991000 0.47740 0.025000 0.11179 -0.621000 0.05559 0.757000 0.33036 0.455000 0.32223 GCA TCGA-XN-A8T3-01A-11D-A36O-08 OBSCN-204 KNOWN basic|CCDS protein_coding protein_coding 1 0 0 44 442 0 115 0 0 0 1 0 115 2 0 0 0 0 0 2 1 1.000000 33 392 0 99 2 0 0 0 0 115 2 -13.593880 1 1 0 0 1 2 2 4 2.082668 0 0.190000 3.530000 0.319328 0.990000 0.840000 1.000000 1.000000 0.985728 0.990000 1 0.980000 1.000000 EGLN1 54583 broad.mit.edu 37 1 231506425 231506425 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:231506425C>A ENST00000366641.3 - 3 4186 c.1031G>T c.(1030-1032)cGa>cTa p.R344L EGLN1_ENST00000476717.1_5'UTR NM_022051.2 NP_071334.1 egl-9 family hypoxia-inducible factor 1 p.R344Q(1) 16 Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244) TGGAAAAATTCGAAGTATACC 0.393000 1 Substitution - Missense(1) SO:0001583 missense ENST00000366641.3 1 0 hg19 CCDS1595.1 . . . . . . . . . . C 33 5.219054 0.95104 . . ENSG00000135766 ENST00000366641 T 0.59083 0.29 5.73 5.73 0.89815 Oxoglutarate/iron-dependent oxygenase (2);Prolyl 4-hydroxylase, alpha subunit (1); 0.000000 0.85682 D 0.000000 T 0.79441 0.4446 M 0.86178 2.8 0.80722 D 1 D 0.69078 0.997 D 0.69824 0.966 T 0.79688 -0.1699 10 0.46703 T 0.11 -4.6704 19.9155 0.97058 0.0:1.0:0.0:0.0 . 344 Q9GZT9 EGLN1_HUMAN L 344 ENSP00000355601:R344L ENSP00000355601:R344L R - 2 0 EGLN1 229573048 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 6.008000 0.70739 2.699000 0.92147 0.650000 0.86243 CGA TCGA-XN-A8T3-01A-11D-A36O-08 EGLN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000092879.1 1 0 0 17 373 0 82 0 8.488680e-01 0 77 0 82 2 0 0 0 0 0 2 1 0.999964 17 369 0 81 2 0 0 0 0 82 2 -3.128328 1 1 0 0 1 2 2 4 2.082668 0 0.190000 3.530000 0.319328 0.550000 0.330000 0.830000 0.550000 0.571900 0.550000 0 0.430000 0.700000 KMO 8564 broad.mit.edu 37 1 241714324 241714324 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:241714324C>A ENST00000366559.4 + 4 603 c.292C>A c.(292-294)Ccc>Acc p.P98T KMO_ENST00000484628.1_3'UTR|KMO_ENST00000366558.3_Missense_Mutation_p.P98T|KMO_ENST00000366557.4_Missense_Mutation_p.P98T NM_003679.4 NP_003670.2 kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) 33 Ovarian(103;0.103)|all_lung(81;0.23) OV - Ovarian serous cystadenocarcinoma(106;0.0176) GTCTGCAATTCCCTATGGGAC 0.413000 0 SO:0001583 missense ENST00000366559.4 0 1 hg19 CCDS1618.1 . . . . . . . . . . C 18.24 3.580937 0.65992 . . ENSG00000117009 ENST00000366559;ENST00000366558;ENST00000366557 T;T;T 0.49432 0.78;0.78;0.78 6.17 6.17 0.99709 Monooxygenase, FAD-binding (1); 0.000000 0.85682 D 0.000000 T 0.72391 0.3454 M 0.87456 2.885 0.80722 D 1 D;D;D 0.76494 0.999;0.999;0.999 D;D;D 0.73708 0.981;0.981;0.977 T 0.72312 -0.4331 10 0.40728 T 0.16 . 16.3795 0.83443 0.0:1.0:0.0:0.0 . 98;98;98 O15229;A8K693;O15229-2 KMO_HUMAN;.;. T 98 ENSP00000355517:P98T;ENSP00000355516:P98T;ENSP00000355515:P98T ENSP00000355515:P98T P + 1 0 KMO 239780947 1.000000 0.71417 1.000000 0.80357 0.447000 0.32167 2.444000 0.44890 2.941000 0.99782 0.655000 0.94253 CCC TCGA-XN-A8T3-01A-11D-A36O-08 KMO-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095612.1 0 0 0 11 676 0 146 0 0 0 1 0 146 2 0 0 0 0 0 2 1 0.998220 11 667 0 145 2 0 0 0 0 146 2 -2.927144 1 1 0 0 1 2 2 4 2.082668 0 0.190000 3.530000 0.319328 0.200000 0.100000 0.350000 0.200000 0.217494 0.200000 0 0.140000 0.280000 OR2M2 391194 broad.mit.edu 37 1 248344093 248344093 + Missense_Mutation SNP C C T rs149761766 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:248344093C>T ENST00000359682.2 + 1 806 c.806C>T c.(805-807)aCg>aTg p.T269M NM_001004688.1 NP_001004688.1 Q96R28 OR2M2_HUMAN olfactory receptor, family 2, subfamily M, member 2 70 all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0245) CACTCCCCAACGCAGGACAAG 0.502000 0 SO:0001583 missense ENST00000359682.2 1 1 hg19 CCDS31106.1 . . . . . . . . . . t 1.263 -0.615211 0.03663 0.0 1.16E-4 ENSG00000198601 ENST00000359682 T 0.00123 8.7 2.03 -4.06 0.03986 GPCR, rhodopsin-like superfamily (1); . . . . T 0.00178 0.0005 M 0.70275 2.135 0.09310 N 1 B 0.28439 0.212 B 0.29598 0.104 T 0.38178 -0.9673 9 0.51188 T 0.08 . 10.6476 0.45630 0.2235:0.6609:0.0:0.1157 . 269 Q96R28 OR2M2_HUMAN M 269 ENSP00000352710:T269M ENSP00000352710:T269M T + 2 0 OR2M2 246410716 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -7.426000 0.00036 -3.968000 0.00086 -3.185000 0.00055 ACG TCGA-XN-A8T3-01A-11D-A36O-08 OR2M2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097356.2 1 0 1 167 801 0 246 0 0 0 0 246 2 0 0 0 0 0 2 1 1.000000 165 786 0 249 2 0 0 0 0 246 2 -20.000000 1 1 121412 1 41 1 2 2 4 2.082668 0 0.190000 3.530000 0.319328 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 OR2T4 127074 broad.mit.edu 37 1 248524891 248524891 + Silent SNP C C T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:248524891C>T ENST00000366475.1 + 1 9 c.9C>T c.(7-9)aaC>aaT p.N3N NM_001004696.1 NP_001004696.1 Q8NH00 OR2T4_HUMAN olfactory receptor, family 2, subfamily T, member 4 56 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0265) TCATGGACAACATCACCTGGA 0.468000 0 SO:0001819 synonymous_variant ENST00000366475.1 1 1 hg19 CCDS31113.1 TCGA-XN-A8T3-01A-11D-A36O-08 OR2T4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097349.2 1 0 1 42 293 0 67 0 0 0 0 67 2 0 0 0 0 0 2 1 1.000000 41 283 0 60 2 0 0 0 0 67 2 -3.318880 1 1 0 0 1 2 2 4 2.082668 0 0.190000 3.530000 0.319328 0.990000 0.990000 1.000000 1.000000 0.999911 0.990000 1 0.990000 1.000000 ZMYM4 9202 broad.mit.edu 37 1 35859318 35859318 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:35859318C>A ENST00000314607.6 + 18 2969 c.2889C>A c.(2887-2889)acC>acA p.T963T ZMYM4_ENST00000373297.2_Silent_p.T874T NM_005095.2 NP_005086.2 Q5VZL5 ZMYM4_HUMAN zinc finger, MYM-type 4 54 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887) AACCACATACCCAAAACAAAG 0.393000 0 SO:0001819 synonymous_variant ENST00000314607.6 0 1 hg19 CCDS389.1 . . . . . . . . . . C 9.029 0.986755 0.18889 . . ENSG00000146463 ENST00000457946 . . . 5.18 -1.85 0.07784 . . . . . T 0.39989 0.1099 . . . 0.80722 D 1 . . . . . . T 0.32134 -0.9918 4 . . . -0.0487 1.9559 0.03376 0.4888:0.1835:0.1729:0.1547 . . . . T 623 . . P + 1 0 ZMYM4 35631905 0.666000 0.27475 0.994000 0.49952 0.990000 0.78478 -0.302000 0.08221 0.016000 0.14998 0.585000 0.79938 CCA TCGA-XN-A8T3-01A-11D-A36O-08 ZMYM4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000012207.3 0 0 0 11 665 0 98 1 2.611405e-01 2 54 0 98 2 0 0 0 0 0 2 1 0.998233 11 657 0 95 2 0 0 0 0 98 2 -2.619821 1 1 0 0 1 2 2 4 2.117161 1 0.190000 3.530000 0.319328 0.200000 0.100000 0.350000 0.200000 0.221011 0.200000 0 0.150000 0.280000 RLF 6018 broad.mit.edu 37 1 40668129 40668129 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:40668129G>T ENST00000372771.4 + 5 680 c.653G>T c.(652-654)cGa>cTa p.R218L NM_012421.3 NP_036553.2 Q13129 RLF_HUMAN rearranged L-myc fusion 68 Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461) CTGCAAATGCGAATAAAACAT 0.333000 0 SO:0001583 missense ENST00000372771.4 1 0 hg19 CCDS448.1 . . . . . . . . . . G 23.6 4.438077 0.83885 . . ENSG00000117000 ENST00000372771 T 0.52754 0.65 4.94 4.94 0.65067 . 0.000000 0.85682 D 0.000000 T 0.70675 0.3251 M 0.79258 2.445 0.53688 D 0.999978 D 0.76494 0.999 D 0.81914 0.995 T 0.75328 -0.3356 10 0.87932 D 0 -7.763 18.5314 0.90993 0.0:0.0:1.0:0.0 . 218 Q13129 RLF_HUMAN L 218 ENSP00000361857:R218L ENSP00000361857:R218L R + 2 0 RLF 40440716 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 7.076000 0.76806 2.462000 0.83206 0.313000 0.20887 CGA TCGA-XN-A8T3-01A-11D-A36O-08 RLF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000015767.1 1 0 0 22 481 0 57 0 1.179004e-01 0 13 0 57 2 0 0 0 0 0 2 1 0.999999 20 477 0 55 2 0 0 0 0 57 2 -4.197773 1 1 0 0 1 2 2 4 2.117161 1 0.190000 3.530000 0.319328 0.550000 0.350000 0.800000 0.560000 0.568066 0.550000 0 0.440000 0.680000 CCDC30 728621 broad.mit.edu 37 1 43047064 43047064 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:43047064C>A ENST00000340612.4 + 7 1099 c.1099C>A c.(1099-1101)Cat>Aat p.H367N CCDC30_ENST00000342022.4_Missense_Mutation_p.H367N|CCDC30_ENST00000507855.1_Missense_Mutation_p.H156N|CCDC30_ENST00000390640.4_Missense_Mutation_p.H156N|CCDC30_ENST00000428554.2_Missense_Mutation_p.H367N Q5VVM6 CCD30_HUMAN coiled-coil domain containing 30 30 AGAACATGCTCATAAAGTCTG 0.348000 0 SO:0001583 missense ENST00000340612.4 0 1 hg19 CCDS30690.1 . . . . . . . . . . C 11.65 1.701346 0.30142 . . ENSG00000186409 ENST00000428554;ENST00000507855;ENST00000340612;ENST00000342022;ENST00000390640 T;T;T;T;T 0.50548 0.74;0.74;0.74;0.74;0.74 5.65 1.32 0.21799 . 0.550040 0.19977 N 0.101853 T 0.32194 0.0821 L 0.38838 1.175 0.09310 N 1 B;B;B 0.22003 0.002;0.0;0.063 B;B;B 0.15870 0.001;0.001;0.014 T 0.16070 -1.0415 10 0.24483 T 0.36 . 8.5805 0.33626 0.3756:0.5512:0.0:0.0732 . 367;151;156 Q5VVM6;Q6N081;Q5VVM6-2 CCD30_HUMAN;.;. N 367;156;367;367;156 ENSP00000397035:H367N;ENSP00000426711:H156N;ENSP00000340378:H367N;ENSP00000339280:H367N;ENSP00000375051:H156N ENSP00000340378:H367N H + 1 0 CCDC30 42819651 0.497000 0.26067 0.064000 0.19789 0.955000 0.61496 0.970000 0.29383 0.377000 0.24735 0.650000 0.86243 CAT TCGA-XN-A8T3-01A-11D-A36O-08 CCDC30-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000019524.3 0 0 0 14 684 0 121 0 9.473108e-03 0 7 0 121 2 0 0 0 0 0 2 1 0.999734 15 675 0 121 2 0 0 0 0 121 2 -2.527275 1 1 0 0 1 2 2 4 2.117161 1 0.190000 3.530000 0.319328 0.250000 0.140000 0.410000 0.240000 0.267608 0.250000 0 0.190000 0.330000 LRRC7 57554 broad.mit.edu 37 1 70446077 70446077 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:70446077C>A ENST00000035383.5 + 7 643 c.613C>A c.(613-615)Caa>Aaa p.Q205K LRRC7_ENST00000310961.5_Missense_Mutation_p.Q210K|LRRC7_ENST00000415775.2_5'UTR NM_020794.2 NP_065845.1 Q96NW7 LRRC7_HUMAN leucine rich repeat containing 7 p.Q205K(1) 162 AGTTCTGGATCAAATACAAAA 0.328000 1 Substitution - Missense(1) SO:0001583 missense ENST00000035383.5 0 1 hg19 CCDS645.1 . . . . . . . . . . C 18.70 3.679363 0.68042 . . ENSG00000033122 ENST00000310961;ENST00000035383;ENST00000370957 T;T 0.23950 1.88;1.9 5.25 5.25 0.73442 . 0.059688 0.64402 D 0.000002 T 0.11153 0.0272 N 0.13168 0.305 0.80722 D 1 P 0.40197 0.706 B 0.43623 0.425 T 0.11299 -1.0593 10 0.25751 T 0.34 . 16.3726 0.83370 0.0:1.0:0.0:0.0 . 205 Q96NW7 LRRC7_HUMAN K 210;205;28 ENSP00000309245:Q210K;ENSP00000035383:Q205K ENSP00000035383:Q205K Q + 1 0 LRRC7 70218665 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.238000 0.78173 2.608000 0.88229 0.650000 0.86243 CAA TCGA-XN-A8T3-01A-11D-A36O-08 LRRC7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131261.1 0 0 0 22 939 0 138 0 0 0 0 138 2 0 0 0 0 0 2 1 0.999998 23 921 0 137 2 0 0 0 0 138 2 -2.693470 1 1 0 0 1 2 2 4 2.117161 1 0.190000 3.530000 0.319328 0.280000 0.170000 0.420000 0.280000 0.298518 0.280000 0 0.230000 0.360000 ZZZ3 26009 broad.mit.edu 37 1 78047706 78047706 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:78047706G>T ENST00000370801.3 - 7 2225 c.1750C>A c.(1750-1752)Cgt>Agt p.R584S ZZZ3_ENST00000476275.1_5'UTR|ZZZ3_ENST00000370798.1_Missense_Mutation_p.R90S NM_015534.4 NP_056349.1 Q8IYH5 ZZZ3_HUMAN zinc finger, ZZ-type containing 3 39 TGTCTTTTACGATTTTTAAAT 0.323000 0 SO:0001583 missense ENST00000370801.3 1 0 hg19 CCDS677.1 . . . . . . . . . . G 15.62 2.886661 0.51908 . . ENSG00000036549 ENST00000370801;ENST00000370798 . . . 5.33 4.41 0.53225 . 0.132552 0.51477 D 0.000085 T 0.32734 0.0839 L 0.40543 1.245 0.48901 D 0.999723 B;P;P 0.44877 0.369;0.845;0.841 B;B;B 0.44108 0.197;0.256;0.441 T 0.08126 -1.0737 9 0.25106 T 0.35 . 14.2206 0.65823 0.0726:0.0:0.9274:0.0 . 90;584;584 Q8IYH5-3;Q8IYH5;Q8IYH5-2 .;ZZZ3_HUMAN;. S 584;90 . ENSP00000359834:R90S R - 1 0 ZZZ3 77820294 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 5.551000 0.67274 1.373000 0.46208 0.655000 0.94253 CGT TCGA-XN-A8T3-01A-11D-A36O-08 ZZZ3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000026615.1 1 0 0 24 531 0 92 0 3.241572e-01 0 26 0 92 2 0 0 0 0 0 2 1 1.000000 24 522 0 92 2 0 0 0 0 92 2 -2.768866 1 1 0 0 1 2 2 4 2.117161 1 0.190000 3.530000 0.319328 0.540000 0.350000 0.780000 0.530000 0.560062 0.540000 0 0.440000 0.670000 VAMP3 9341 broad.mit.edu 37 1 7837333 7837333 + Silent SNP G G T rs114336504 by1000genomes TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:7837333G>T ENST00000054666.6 + 3 301 c.186G>T c.(184-186)acG>acT p.T62T VAMP3_ENST00000470357.1_Silent_p.T34T|RP3-467L1.6_ENST00000602406.1_RNA NM_004781.3 NP_004772.1 Q15836 VAMP3_HUMAN vesicle-associated membrane protein 3 6 Ovarian(185;0.0634)|all_lung(157;0.178) all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255) AATTTGAAACGAGCGCAGCCA 0.463000 0 SO:0001819 synonymous_variant ENST00000054666.6 1 0 hg19 CCDS88.1 TCGA-XN-A8T3-01A-11D-A36O-08 VAMP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000003625.1 1 0 0 14 401 0 90 0 9.171974e-01 1 125 0 90 2 0 0 0 0 0 2 1 0.999752 14 398 0 90 2 0 0 0 0 90 2 -3.455922 1 1 0 0 1 3 3 6 2.138687 1 0.190000 3.530000 0.340391 0.490000 0.260000 1.000000 0.440000 0.587646 0.490000 0 0.350000 1.000000 WDR63 126820 broad.mit.edu 37 1 85595745 85595745 + Missense_Mutation SNP C C A rs143304188 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:85595745C>A ENST00000294664.6 + 22 2662 c.2482C>A c.(2482-2484)Cgt>Agt p.R828S WDR63_ENST00000326813.8_Missense_Mutation_p.R789S|WDR63_ENST00000370596.1_Missense_Mutation_p.R789S NM_145172.3 NP_660155.2 Q8IWG1 WDR63_HUMAN WD repeat domain 63 36 CAAAAAAATTCGTGAGCAAGA 0.368000 0 SO:0001583 missense ENST00000294664.6 1 0 hg19 CCDS702.1 . . . . . . . . . . C 13.69 2.313546 0.40996 . . ENSG00000162643 ENST00000370596;ENST00000326813;ENST00000294664;ENST00000484007 T;T;T;T 0.42131 0.98;0.98;0.98;0.98 5.43 4.48 0.54585 . 0.207201 0.42053 D 0.000774 T 0.59169 0.2174 M 0.85041 2.73 0.39974 D 0.974832 D;D 0.76494 0.999;0.999 D;D 0.72338 0.977;0.954 T 0.62129 -0.6919 10 0.44086 T 0.13 -16.1661 13.8453 0.63463 0.2776:0.7224:0.0:0.0 . 789;828 Q8IWG1-2;Q8IWG1 .;WDR63_HUMAN S 789;789;828;110 ENSP00000359628:R789S;ENSP00000317463:R789S;ENSP00000294664:R828S;ENSP00000435544:R110S ENSP00000294664:R828S R + 1 0 WDR63 85368333 0.974000 0.33945 0.995000 0.50966 0.030000 0.12068 1.142000 0.31540 2.546000 0.85860 0.655000 0.94253 CGT TCGA-XN-A8T3-01A-11D-A36O-08 WDR63-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000027565.2 1 0 0 26 582 0 122 0 2.015162e-03 0 2 0 122 2 0 0 0 0 0 2 1 1.000000 26 578 0 122 2 0 0 0 0 122 2 -3.760306 1 1 121412 1 38 1 2 2 4 2.091950 0 0.190000 3.530000 0.319328 0.540000 0.350000 0.760000 0.520000 0.552507 0.540000 0 0.440000 0.650000 ABCA4 24 broad.mit.edu 37 1 94466426 94466426 + Nonsense_Mutation SNP G G A rs140142529 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr1:94466426G>A ENST00000370225.3 - 47 6531 c.6445C>T c.(6445-6447)Cga>Tga p.R2149* ABCA4_ENST00000535881.1_Nonsense_Mutation_p.R268*|ABCA4_ENST00000465352.1_5'Flank|ABCA4_ENST00000536513.1_Nonsense_Mutation_p.R419* NM_000350.2 NP_000341.2 P78363 ABCA4_HUMAN ATP-binding cassette, sub-family A (ABC1), member 4 147 all_lung(203;0.000757)|Lung NSC(277;0.00335) CCCATACATCGAAAGGCGCCC 0.562000 0 GRCh37 CM990078 ABCA4 M rs140142529 SO:0001587 stop_gained ENST00000370225.3 0 1 hg19 CCDS747.1 . . . . . . . . . . G 38 6.739809 0.97801 0.0 1.16E-4 ENSG00000198691 ENST00000546054;ENST00000370225;ENST00000536513;ENST00000535881 . . . 5.84 5.84 0.93424 . 0.166997 0.50627 D 0.000112 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 13.0922 0.59172 0.0:0.0:0.7351:0.2649 rs61750654 . . . X 941;2149;419;268 . ENSP00000359245:R2149X R - 1 2 ABCA4 94239014 1.000000 0.71417 1.000000 0.80357 0.948000 0.59901 5.696000 0.68287 2.779000 0.95612 0.655000 0.94253 CGA TCGA-XN-A8T3-01A-11D-A36O-08 ABCA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029320.1 1 0 1 48 326 0 72 1 8.518733e-02 2 2 0 72 2 0 0 0 0 0 2 1 1.000000 47 324 0 72 2 0 0 0 0 72 2 -19.610750 1 1 121412 2 37 1 2 2 4 2.091950 0 0.190000 3.530000 0.319328 0.990000 0.990000 1.000000 1.000000 0.999975 0.990000 1 0.990000 1.000000 SALL4 57167 broad.mit.edu 37 20 50401200 50401200 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr20:50401200C>A ENST00000217086.4 - 4 2877 c.2766G>T c.(2764-2766)gcG>gcT p.A922A SALL4_ENST00000395997.3_Silent_p.A485A|SALL4_ENST00000371539.3_Silent_p.A145A NM_020436.3 NP_065169.1 Q9UJQ4 SALL4_HUMAN spalt-like transcription factor 4 63 AGTTATTGTTCGCCCCGTGTG 0.473000 0 SO:0001819 synonymous_variant ENST00000217086.4 1 0 hg19 CCDS13438.1 TCGA-XN-A8T3-01A-11D-A36O-08 SALL4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079738.3 1 0 0 16 369 0 87 0 1.402038e-01 0 14 0 87 2 0 0 0 0 0 2 1 0.999925 16 362 0 86 2 0 0 0 0 87 2 -2.930996 1 1 0 0 1 1 2 3 1.915087 0 0.190000 3.530000 0.260274 0.480000 0.280000 0.740000 0.480000 0.502579 0.480000 0 0.370000 0.620000 DSCAM 1826 broad.mit.edu 37 21 41423897 41423897 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr21:41423897G>T ENST00000400454.1 - 30 5650 c.5173C>A c.(5173-5175)Cgg>Agg p.R1725R NM_001271534.1|NM_001389.3 NP_001258463.1|NP_001380.2 O60469 DSCAM_HUMAN Down syndrome cell adhesion molecule 142 all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103) GTTCCCGGCCGAGCGTCTGAA 0.483000 Melanoma(134;970 1778 1785 21664 32388) 0 SO:0001819 synonymous_variant ENST00000400454.1 1 0 hg19 CCDS42929.1 TCGA-XN-A8T3-01A-11D-A36O-08 DSCAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195029.1 1 0 0 20 487 0 133 0 0 0 0 133 2 0 0 0 0 0 2 1 0.999995 19 480 0 133 2 0 0 0 0 133 2 -2.737967 1 1 0 0 1 0 2 2 1.761989 1 0.190000 3.530000 0.190000 0.410000 0.260000 0.610000 0.410000 0.430632 0.410000 0 0.330000 0.520000 TUBA8 51807 broad.mit.edu 37 22 18606952 18606952 + Missense_Mutation SNP C C T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr22:18606952C>T ENST00000330423.3 + 3 329 c.256C>T c.(256-258)Ctc>Ttc p.L86F TUBA8_ENST00000316027.6_Missense_Mutation_p.L20F NM_018943.2 NP_061816.1 Q9NY65 TBA8_HUMAN tubulin, alpha 8 14 CTACCGCCAGCTCTTCCATCC 0.582000 0 SO:0001583 missense ENST00000330423.3 1 1 hg19 CCDS13751.1 . . . . . . . . . . C 18.17 3.565399 0.65651 . . ENSG00000183785 ENST00000426208;ENST00000316027;ENST00000330423;ENST00000416740 T;T;T;T 0.71341 -0.56;-0.56;-0.56;-0.56 5.11 5.11 0.69529 Tubulin/FtsZ, GTPase domain (4); 0.065611 0.64402 N 0.000012 D 0.88599 0.6480 H 0.95224 3.64 0.54753 D 0.999981 P;D;P 0.76494 0.767;0.999;0.767 B;D;B 0.67103 0.356;0.949;0.36 D 0.91998 0.5608 10 0.87932 D 0 . 17.8832 0.88846 0.0:1.0:0.0:0.0 . 110;86;85 C9J2C0;Q9NY65;Q7Z3M3 .;TBA8_HUMAN;. F 20;20;86;110 ENSP00000407624:L20F;ENSP00000318575:L20F;ENSP00000333326:L86F;ENSP00000412646:L110F ENSP00000318575:L20F L + 1 0 TUBA8 16986952 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 7.818000 0.86416 2.554000 0.86153 0.462000 0.41574 CTC TCGA-XN-A8T3-01A-11D-A36O-08 TUBA8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316232.3 1 0 0 15 161 0 45 1 3.601247e-01 2 12 0 45 2 0 0 0 0 0 2 1 0.999875 15 156 0 45 2 0 0 0 0 45 2 -3.318846 1 1 0 0 1 1 2 3 1.942683 0 0.190000 3.530000 0.260274 0.990000 0.590000 1.000000 1.000000 0.913576 0.990000 1 0.770000 1.000000 SNAP29 9342 broad.mit.edu 37 22 21242113 21242113 + Silent SNP C C A rs148156702 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr22:21242113C>A ENST00000215730.7 + 5 894 c.766C>A c.(766-768)Cga>Aga p.R256R AC007308.7_ENST00000608856.1_RNA NM_004782.3 NP_004773.1 O95721 SNP29_HUMAN synaptosomal-associated protein, 29kDa p.R256*(2) 9 all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117) AAGAAAAGTTCGACAACTCTG 0.353000 2 Substitution - Nonsense(2) SO:0001819 synonymous_variant ENST00000215730.7 1 0 hg19 CCDS13784.1 TCGA-XN-A8T3-01A-11D-A36O-08 SNAP29-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320000.4 1 0 0 16 316 0 56 0 9.185550e-01 0 88 0 56 2 0 0 0 0 0 2 1 0.999928 16 310 0 56 2 0 0 0 0 56 2 -3.139115 1 1 0 0 1 1 2 3 1.942683 0 0.190000 3.530000 0.260274 0.560000 0.330000 0.850000 0.540000 0.581392 0.560000 0 0.430000 0.710000 CCDC157 550631 broad.mit.edu 37 22 30766541 30766541 + Missense_Mutation SNP C C T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr22:30766541C>T ENST00000405659.1 + 5 1356 c.647C>T c.(646-648)aCg>aTg p.T216M CCDC157_ENST00000338306.3_Missense_Mutation_p.T216M Q569K6 CC157_HUMAN coiled-coil domain containing 157 15 ACCATTGAGACGGCCCTGGTG 0.622000 0 SO:0001583 missense ENST00000405659.1 1 1 hg19 CCDS33632.2 . . . . . . . . . . C 28.9 4.961385 0.92791 . . ENSG00000187860 ENST00000405659;ENST00000338306 T;T 0.32515 1.45;1.45 5.54 5.54 0.83059 . 0.129526 0.53938 D 0.000060 T 0.55273 0.1910 M 0.61703 1.905 0.80722 D 1 D 0.89917 1.0 D 0.74023 0.982 T 0.54490 -0.8286 10 0.87932 D 0 -22.7807 19.2866 0.94077 0.0:1.0:0.0:0.0 . 216 Q569K6 CC157_HUMAN M 216 ENSP00000385357:T216M;ENSP00000343087:T216M ENSP00000343087:T216M T + 2 0 CCDC157 29096541 1.000000 0.71417 0.959000 0.39883 0.856000 0.48823 7.005000 0.76323 2.884000 0.98904 0.655000 0.94253 ACG TCGA-XN-A8T3-01A-11D-A36O-08 CCDC157-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000320936.1 1 0 0 27 245 0 72 0 0 0 1 0 72 2 0 0 0 0 0 2 1 0.987529 27 242 1 70 14 0 0 0 0 72 2 -8.628704 1 1 121412 6 40 1 1 2 3 1.942683 0 0.190000 3.530000 0.260274 0.990000 0.780000 1.000000 1.000000 0.977408 0.990000 1 0.950000 1.000000 CSF2RB 1439 broad.mit.edu 37 22 37333569 37333569 + Silent SNP G G A rs140662059 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr22:37333569G>A ENST00000403662.3 + 14 1941 c.1719G>A c.(1717-1719)ccG>ccA p.P573P CSF2RB_ENST00000262825.5_Silent_p.P579P|CSF2RB_ENST00000536485.1_Silent_p.P520P|CSF2RB_ENST00000406230.1_Silent_p.P579P P32927 IL3RB_HUMAN colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage) 42 Sargramostim(DB00020) AGCCAGGCCCGCCTGCCGCCT 0.647000 0 SO:0001819 synonymous_variant ENST00000403662.3 1 1 hg19 CCDS13936.1 TCGA-XN-A8T3-01A-11D-A36O-08 CSF2RB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318854.1 0 0 1 16 100 0 34 0 5.847458e-02 0 3 0 34 2 0 0 0 0 0 2 1 0.999920 16 92 0 28 2 0 0 0 0 34 2 -20.000000 1 1 121378 4 33 1 1 2 3 1.942683 0 0.190000 3.530000 0.260274 0.990000 0.970000 1.000000 1.000000 0.997053 0.990000 1 0.990000 1.000000 CYB5R3 1727 broad.mit.edu 37 22 43026970 43026970 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr22:43026970C>A ENST00000352397.5 - 4 503 c.251G>T c.(250-252)cGa>cTa p.R84L CYB5R3_ENST00000407623.3_Missense_Mutation_p.R61L|CYB5R3_ENST00000361740.4_Missense_Mutation_p.R117L|CYB5R3_ENST00000402438.1_Missense_Mutation_p.R61L|CYB5R3_ENST00000396303.3_Missense_Mutation_p.R61L|CYB5R3_ENST00000407332.1_Missense_Mutation_p.R61L NM_000398.6 NP_000389.1 P00387 NB5R3_HUMAN cytochrome b5 reductase 3 6 Flavin adenine dinucleotide(DB03147) TCCATCAATTCGAGCCGAGAG 0.587000 0 SO:0001583 missense ENST00000352397.5 1 0 hg19 CCDS33658.1 . . . . . . . . . . C 12.04 1.818274 0.32145 . . ENSG00000100243 ENST00000361740;ENST00000396303;ENST00000352397;ENST00000407623;ENST00000407332;ENST00000402438;ENST00000438270 D;D;D;D;D;D;D 0.85171 -1.95;-1.95;-1.95;-1.95;-1.95;-1.95;-1.95 3.73 0.507 0.16967 Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);Oxidoreductase, FAD-binding domain (1); 0.257317 0.35495 N 0.003177 T 0.81508 0.4837 M 0.73962 2.25 0.09310 N 0.999999 P;B 0.35493 0.505;0.013 B;B 0.34138 0.176;0.01 T 0.73553 -0.3946 10 0.62326 D 0.03 -6.1245 8.6969 0.34301 0.0:0.7335:0.0:0.2665 . 117;84 B7Z7L3;P00387 .;NB5R3_HUMAN L 117;61;84;61;61;61;61 ENSP00000354468:R117L;ENSP00000379597:R61L;ENSP00000338461:R84L;ENSP00000384834:R61L;ENSP00000384457:R61L;ENSP00000385679:R61L;ENSP00000403439:R61L ENSP00000338461:R84L R - 2 0 CYB5R3 41356914 0.739000 0.28196 0.001000 0.08648 0.613000 0.37349 2.646000 0.46630 0.202000 0.20498 -0.362000 0.07510 CGA TCGA-XN-A8T3-01A-11D-A36O-08 CYB5R3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320439.1 1 0 0 12 245 0 63 0 9.999998e-01 0 759 0 63 2 0 0 0 0 0 2 1 0.999074 12 240 0 62 2 0 0 0 0 63 2 -2.933916 1 1 0 0 1 1 2 3 1.942683 0 0.190000 3.530000 0.260274 0.550000 0.300000 0.880000 0.540000 0.571528 0.550000 0 0.410000 0.720000 WNT7B 7477 broad.mit.edu 37 22 46327040 46327040 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr22:46327040G>T ENST00000339464.4 - 3 882 c.508C>A c.(508-510)Cgg>Agg p.R170R WNT7B_ENST00000410089.1_Silent_p.R154R|WNT7B_ENST00000410058.1_Silent_p.R170R|WNT7B_ENST00000409496.3_Silent_p.R174R NM_058238.2 NP_478679.1 P56706 WNT7B_HUMAN wingless-type MMTV integration site family, member 7B 19 Ovarian(80;0.00965)|all_neural(38;0.0416) TTGATCTCCCGAGCGTCCACG 0.657000 0 SO:0001819 synonymous_variant ENST00000339464.4 1 0 hg19 CCDS33667.1 TCGA-XN-A8T3-01A-11D-A36O-08 WNT7B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336418.1 1 0 0 20 234 0 57 0 3.777756e-01 0 16 0 57 2 0 0 0 0 0 2 1 0.999996 20 232 0 55 2 0 0 0 0 57 2 -2.966627 1 1 121324 2 34 1 1 2 3 1.942683 0 0.190000 3.530000 0.260274 0.910000 0.580000 1.000000 1.000000 0.883986 0.910000 1 0.730000 1.000000 SPOPL 339745 broad.mit.edu 37 2 139326586 139326586 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr2:139326586G>T ENST00000280098.4 + 11 1494 c.1115G>T c.(1114-1116)cGa>cTa p.R372L AC092620.2_ENST00000458007.2_RNA NM_001001664.2 NP_001001664.1 Q6IQ16 SPOPL_HUMAN speckle-type POZ protein-like 21 GAAGCCTTTCGAGCACTAGCA 0.423000 0 SO:0001583 missense ENST00000280098.4 0 1 hg19 CCDS33298.1 . . . . . . . . . . G 28.6 4.933375 0.92458 . . ENSG00000144228 ENST00000280098 T 0.71461 -0.57 5.97 5.97 0.96955 . 0.058159 0.64402 D 0.000001 T 0.79953 0.4535 L 0.58810 1.83 0.80722 D 1 D 0.58268 0.982 P 0.57057 0.812 T 0.76812 -0.2821 9 . . . -11.9914 20.428 0.99075 0.0:0.0:1.0:0.0 . 372 Q6IQ16 SPOPL_HUMAN L 372 ENSP00000280098:R372L . R + 2 0 SPOPL 139043056 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.869000 0.99810 2.837000 0.97791 0.655000 0.94253 CGA TCGA-XN-A8T3-01A-11D-A36O-08 SPOPL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000331897.1 0 0 0 28 1379 0 273 0 8.744944e-02 0 24 0 273 2 0 0 0 0 0 2 1 1.000000 28 1360 0 269 2 0 0 0 0 273 2 -1.876711 0 1 0 0 1 2 2 4 2.042778 0 0.190000 3.530000 0.310521 0.250000 0.160000 1.000000 0.240000 0.302109 0.250000 0 0.200000 0.320000 MYCN 4613 broad.mit.edu 37 2 16086208 16086208 + Silent SNP C C A rs144531796 by1000genomes TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr2:16086208C>A ENST00000281043.3 + 3 1681 c.1384C>A c.(1384-1386)Cgg>Agg p.R462R NM_005378.4 NP_005369.2 P04198 MYCN_HUMAN v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog 31 all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197) GBM - Glioblastoma multiforme(3;0.000332) TGAACACGCTCGGACTTGCTA 0.428000 A neuroblastoma Dom yes 2 2p24.1 4613 v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) O 0 SO:0001819 synonymous_variant ENST00000281043.3 1 0 hg19 CCDS1687.1 TCGA-XN-A8T3-01A-11D-A36O-08 MYCN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095469.2 1 0 0 30 471 0 109 0 1.118422e-02 0 3 0 109 2 0 0 0 0 0 2 1 1.000000 29 463 0 109 2 0 0 0 0 109 2 -2.522905 1 1 121406 6 42 1 2 2 4 2.081774 0 0.190000 3.530000 0.319328 0.750000 0.520000 1.000000 1.000000 0.765249 0.750000 0 0.620000 0.900000 TTN 7273 broad.mit.edu 37 2 179583118 179583118 + Missense_Mutation SNP C C T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr2:179583118C>T ENST00000591111.1 - 83 23988 c.23764G>A c.(23764-23766)Gca>Aca p.A7922T TTN_ENST00000342992.6_Missense_Mutation_p.A6995T|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.A8239T|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CTGTACTGTGCATAATCCTCT 0.398000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . C 14.74 2.626923 0.46840 . . ENSG00000155657 ENST00000342992 T 0.45276 0.9 6.16 6.16 0.99307 Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.55433 0.1920 M 0.79926 2.475 0.80722 D 1 B 0.31459 0.324 B 0.36418 0.224 T 0.56823 -0.7915 9 0.87932 D 0 . 20.8598 0.99761 0.0:1.0:0.0:0.0 . 7922 Q8WZ42 TITIN_HUMAN T 6995 ENSP00000343764:A6995T ENSP00000343764:A6995T A - 1 0 TTN 179291363 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 4.607000 0.61133 2.937000 0.99478 0.650000 0.86243 GCA TCGA-XN-A8T3-01A-11D-A36O-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 0 45 273 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 45 270 0 43 2 0 0 0 0 44 2 -19.921240 1 1 0 0 1 2 2 4 2.042778 0 0.190000 3.530000 0.310521 0.990000 0.990000 1.000000 1.000000 0.999995 0.990000 1 0.990000 1.000000 STAT1 6772 broad.mit.edu 37 2 191847210 191847210 + Missense_Mutation SNP C C T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr2:191847210C>T ENST00000361099.3 - 18 1868 c.1481G>A c.(1480-1482)cGa>cAa p.R494Q STAT1_ENST00000392322.3_Missense_Mutation_p.R494Q|STAT1_ENST00000409465.1_Missense_Mutation_p.R494Q|STAT1_ENST00000540176.1_3'UTR|STAT1_ENST00000392323.2_Missense_Mutation_p.R496Q NM_007315.3 NP_009330.1 P42224 STAT1_HUMAN signal transducer and activator of transcription 1, 91kDa 39 OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141) CTGAGCCCATCGTGCACATGG 0.463000 0 SO:0001583 missense ENST00000361099.3 1 1 hg19 CCDS2309.1 . . . . . . . . . . C 13.02 2.112096 0.37242 . . ENSG00000115415 ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323 T;T;T;T 0.76448 -1.02;-1.02;-1.02;-1.02 5.31 3.15 0.36227 STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);EF-hand-like domain (1); 0.310219 0.34932 N 0.003580 T 0.61986 0.2391 L 0.31664 0.95 0.18873 N 0.999986 B;B 0.20780 0.048;0.005 B;B 0.17098 0.016;0.017 T 0.41945 -0.9480 10 0.12766 T 0.61 -3.6255 10.1437 0.42751 0.0:0.7608:0.0:0.2392 . 494;494 P42224-2;P42224 .;STAT1_HUMAN Q 494;494;494;496 ENSP00000354394:R494Q;ENSP00000386244:R494Q;ENSP00000376136:R494Q;ENSP00000376137:R496Q ENSP00000354394:R494Q R - 2 0 STAT1 191555455 0.002000 0.14202 0.932000 0.37286 0.981000 0.71138 0.290000 0.18975 1.304000 0.44892 0.655000 0.94253 CGA TCGA-XN-A8T3-01A-11D-A36O-08 STAT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255997.3 1 0 0 44 465 0 92 1 9.999954e-01 9 183 0 92 2 0 0 0 0 0 2 1 1.000000 44 459 0 92 2 0 0 0 0 92 2 -12.316120 1 1 0 0 1 2 2 4 2.042778 0 0.190000 3.530000 0.310521 0.990000 0.790000 1.000000 1.000000 0.974466 0.990000 1 0.930000 1.000000 ALS2CR11 151254 broad.mit.edu 37 2 202466489 202466489 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr2:202466489G>T ENST00000286195.3 - 4 533 c.489C>A c.(487-489)ttC>ttA p.F163L ALS2CR11_ENST00000450242.1_Missense_Mutation_p.F163L|ALS2CR11_ENST00000439140.1_Missense_Mutation_p.F163L|ALS2CR11_ENST00000439802.1_Missense_Mutation_p.F163L NM_152525.5 NP_689738.3 Q53TS8 AL2SA_HUMAN amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11 p.F163F(2) 33 TCACTTCATCGAACTTAATTA 0.313000 2 Substitution - coding silent(2) SO:0001583 missense ENST00000286195.3 1 0 hg19 CCDS2349.1 . . . . . . . . . . G 16.32 3.090430 0.55968 . . ENSG00000155754 ENST00000286195;ENST00000439802;ENST00000439140;ENST00000450242 D;D;D;D 0.97066 -4.23;-4.23;-4.23;-4.23 5.02 2.58 0.30949 . 0.263401 0.27406 N 0.019510 D 0.96981 0.9014 L 0.55481 1.735 0.29814 N 0.831439 D;B;P 0.89917 1.0;0.389;0.818 D;B;B 0.87578 0.998;0.081;0.186 D 0.92906 0.6343 10 0.42905 T 0.14 . 6.5355 0.22350 0.8033:0.0:0.1967:0.0 . 163;163;163 Q53TS8-2;E9PGG4;Q53TS8 .;.;AL2SA_HUMAN L 163 ENSP00000286195:F163L;ENSP00000400672:F163L;ENSP00000409937:F163L;ENSP00000399016:F163L ENSP00000286195:F163L F - 3 2 ALS2CR11 202174734 0.997000 0.39634 0.927000 0.36925 0.768000 0.43524 1.854000 0.39368 0.374000 0.24650 -0.474000 0.04947 TTC TCGA-XN-A8T3-01A-11D-A36O-08 ALS2CR11-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000256296.2 1 0 0 16 333 0 54 0 0 0 0 54 2 0 0 0 0 0 2 1 0.999925 16 325 0 54 2 0 0 0 0 54 2 -4.747922 1 1 0 0 1 2 2 4 2.042778 0 0.190000 3.530000 0.310521 0.590000 0.340000 1.000000 0.570000 0.620800 0.590000 0 0.450000 0.780000 MPP4 58538 broad.mit.edu 37 2 202512489 202512489 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr2:202512489C>A ENST00000409474.3 - 21 1851 c.1644G>T c.(1642-1644)tcG>tcT p.S548S MPP4_ENST00000359962.5_Silent_p.S548S|MPP4_ENST00000315506.7_Silent_p.S504S|MPP4_ENST00000428900.2_Silent_p.S524S|RNU6-651P_ENST00000411040.1_RNA|MPP4_ENST00000447335.2_Silent_p.S541S|MPP4_ENST00000409143.1_Silent_p.S490S|MPP4_ENST00000396886.3_Silent_p.S473S NM_033066.2 NP_149055 Q96JB8 MPP4_HUMAN membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4) 12 ACCTCATATTCGATGGCTTTA 0.348000 0 SO:0001819 synonymous_variant ENST00000409474.3 1 0 hg19 CCDS46491.1 TCGA-XN-A8T3-01A-11D-A36O-08 MPP4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000335748.2 1 0 0 12 224 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 0.999097 12 220 0 41 2 0 0 0 0 41 2 -3.283854 1 1 0 0 1 2 2 4 2.042778 0 0.190000 3.530000 0.310521 0.660000 0.350000 1.000000 1.000000 0.686171 0.660000 0 0.490000 0.910000 CYP20A1 57404 broad.mit.edu 37 2 204154519 204154519 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr2:204154519C>A ENST00000356079.4 + 10 1126 c.1003C>A c.(1003-1005)Cga>Aga p.R335R CYP20A1_ENST00000461371.1_3'UTR|CYP20A1_ENST00000429815.2_Silent_p.R343R NM_177538.2 NP_803882.1 Q6UW02 CP20A_HUMAN cytochrome P450, family 20, subfamily A, polypeptide 1 11 TGAAACTGTTCGAACTGCCAA 0.323000 0 SO:0001819 synonymous_variant ENST00000356079.4 1 0 hg19 CCDS2357.1 TCGA-XN-A8T3-01A-11D-A36O-08 CYP20A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256328.3 1 0 0 21 509 0 62 0 3.663424e-01 0 31 0 62 2 0 0 0 0 0 2 1 0.999997 21 498 0 61 2 0 0 0 0 62 2 -2.847844 1 1 0 0 1 2 2 4 2.042778 0 0.190000 3.530000 0.310521 0.500000 0.310000 1.000000 0.500000 0.540820 0.500000 0 0.400000 0.650000 SENP7 57337 broad.mit.edu 37 3 101044840 101044840 + Silent SNP G G T rs144603399 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:101044840G>T ENST00000394095.2 - 24 3153 c.3100C>A c.(3100-3102)Cga>Aga p.R1034R SENP7_ENST00000348610.3_Silent_p.R1001R|SENP7_ENST00000358203.3_Silent_p.R870R|SENP7_ENST00000314261.7_Silent_p.R968R|SENP7_ENST00000394094.2_Silent_p.R969R|SENP7_ENST00000394091.1_Silent_p.R870R|SENP7_ENST00000394085.3_Silent_p.R222R NM_001282802.1|NM_020654.3 NP_001269731.1|NP_065705.3 Q9BQF6 SENP7_HUMAN SUMO1/sentrin specific peptidase 7 44 ATGAGCTCTCGAATATCTTCC 0.373000 0 SO:0001819 synonymous_variant ENST00000394095.2 1 0 hg19 CCDS2941.2 TCGA-XN-A8T3-01A-11D-A36O-08 SENP7-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000313957.2 1 0 0 18 476 0 93 0 3.324091e-01 0 31 0 93 2 0 0 0 0 0 2 1 0.999979 18 466 0 93 2 0 0 0 0 93 2 -3.193771 1 1 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.460000 0.280000 0.690000 0.440000 0.477780 0.460000 0 0.360000 0.580000 MRPL3 11222 broad.mit.edu 37 3 131219286 131219286 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:131219286G>T ENST00000264995.3 - 3 504 c.357C>A c.(355-357)gtC>gtA p.V119V MRPL3_ENST00000506946.1_5'UTR|MRPL3_ENST00000425847.2_Silent_p.V146V NM_007208.3 NP_009139.1 P09001 RM03_HUMAN mitochondrial ribosomal protein L3 10 GAAGTAATGTGACCACATGCT 0.398000 0 SO:0001819 synonymous_variant ENST00000264995.3 0 1 hg19 CCDS3071.1 . . . . . . . . . . G 3.702 -0.061285 0.07317 . . ENSG00000114686 ENST00000511168 . . . 5.62 4.73 0.59995 . . . . . T 0.71099 0.3300 . . . 0.80722 D 1 . . . . . . T 0.70498 -0.4855 4 . . . -2.7541 15.3528 0.74402 0.0:0.1405:0.8595:0.0 . . . . N 134 . . H - 1 0 MRPL3 132701976 1.000000 0.71417 0.999000 0.59377 0.354000 0.29330 4.626000 0.61269 1.340000 0.45581 0.555000 0.69702 CAC TCGA-XN-A8T3-01A-11D-A36O-08 MRPL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356471.3 0 0 0 21 918 0 166 0 6.651004e-01 0 100 0 166 2 0 0 0 0 0 2 1 0.999997 20 910 0 165 2 0 0 0 0 166 2 -3.186564 1 1 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.280000 0.170000 0.420000 0.280000 0.292199 0.280000 0 0.220000 0.350000 EPHB1 2047 broad.mit.edu 37 3 134873104 134873104 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:134873104C>A ENST00000398015.3 + 6 1778 c.1408C>A c.(1408-1410)Cgg>Agg p.R470R EPHB1_ENST00000493838.1_Silent_p.R31R NM_004441.4 NP_004432.1 P54762 EPHB1_HUMAN EPH receptor B1 130 CTATGAGATCCGGTACTATGA 0.542000 0 SO:0001819 synonymous_variant ENST00000398015.3 0 1 hg19 CCDS46921.1 TCGA-XN-A8T3-01A-11D-A36O-08 EPHB1-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357671.1 0 0 0 9 377 0 83 0 0 0 0 83 2 0 0 0 0 0 2 1 0.993853 8 371 0 80 2 0 0 0 0 83 2 -2.980051 1 1 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.300000 0.140000 0.530000 0.280000 0.321071 0.300000 0 0.210000 0.420000 PAQR9 344838 broad.mit.edu 37 3 142681266 142681266 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:142681266C>A ENST00000340634.3 - 1 912 c.913G>T c.(913-915)Gac>Tac p.D305Y RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA NM_198504.2 NP_940906.1 Q6ZVX9 PAQR9_HUMAN progestin and adipoQ receptor family member IX 22 CCGATAATGTCGAAAAGACCC 0.577000 0 SO:0001583 missense ENST00000340634.3 1 0 hg19 CCDS3128.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 18.51|18.51 3.639348|3.639348 0.67244|0.67244 .|. .|. ENSG00000188582|ENSG00000188582 ENST00000340634|ENST00000492509 T|. 0.38887|. 1.11|. 5.62|5.62 3.73|3.73 0.42828|0.42828 .|. 0.060822|. 0.64402|. D|. 0.000005|. T|T 0.73241|0.73241 0.3562|0.3562 M|M 0.81239|0.81239 2.535|2.535 0.51012|0.51012 D|D 0.999907|0.999907 D|. 0.89917|. 1.0|. D|. 0.91635|. 0.999|. T|T 0.74654|0.74654 -0.3593|-0.3593 10|5 0.87932|. D|. 0|. -44.4143|-44.4143 11.0086|11.0086 0.47649|0.47649 0.0:0.8011:0.1293:0.0696|0.0:0.8011:0.1293:0.0696 .|. 305|. Q6ZVX9|. PAQR9_HUMAN|. Y|L 305|45 ENSP00000341564:D305Y|. ENSP00000341564:D305Y|. D|R -|- 1|2 0|0 PAQR9|PAQR9 144163956|144163956 1.000000|1.000000 0.71417|0.71417 0.996000|0.996000 0.52242|0.52242 0.979000|0.979000 0.70002|0.70002 3.966000|3.966000 0.56795|0.56795 1.381000|1.381000 0.46364|0.46364 0.650000|0.650000 0.86243|0.86243 GAC|CGA TCGA-XN-A8T3-01A-11D-A36O-08 PAQR9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354538.1 1 0 0 16 313 0 72 0 0 0 0 72 2 0 0 0 0 0 2 1 0.999927 14 308 0 71 2 0 0 0 0 72 2 -4.858763 1 1 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.620000 0.360000 0.940000 0.600000 0.637980 0.620000 0 0.480000 0.780000 SPATA16 83893 broad.mit.edu 37 3 172634107 172634107 + Splice_Site SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:172634107C>A ENST00000351008.3 - 9 1686 c.1503G>T c.(1501-1503)ttG>ttT p.L501F NM_031955.5 NP_114161.3 Q9BXB7 SPT16_HUMAN spermatogenesis associated 16 43 Ovarian(172;0.00319)|Breast(254;0.197) LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14) AAATACTTACCAATTCTGCCT 0.408000 0 SO:0001630 splice_region_variant ENST00000351008.3 0 1 hg19 CCDS3221.1 . . . . . . . . . . C 17.85 3.491014 0.64074 . . ENSG00000144962 ENST00000351008 T 0.26660 1.72 6.16 6.16 0.99307 . 0.109181 0.40908 D 0.000983 T 0.40546 0.1121 L 0.32530 0.975 0.44871 D 0.997886 D 0.63046 0.992 P 0.62298 0.9 T 0.01130 -1.1442 9 . . . -5.1947 20.8598 0.99761 0.0:1.0:0.0:0.0 . 501 Q9BXB7 SPT16_HUMAN F 501 ENSP00000341765:L501F . L - 3 2 SPATA16 174116801 1.000000 0.71417 0.998000 0.56505 0.184000 0.23303 3.061000 0.49963 2.937000 0.99478 0.650000 0.86243 TTG TCGA-XN-A8T3-01A-11D-A36O-08 SPATA16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346322.1 0 0 0 14 899 0 168 0 0 0 0 168 2 0 0 0 0 0 2 1 0.999718 12 885 0 166 2 0 0 0 0 168 2 -1.905127 0 1 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.190000 0.100000 0.310000 0.200000 0.204875 0.190000 0 0.140000 0.260000 NLGN1 22871 broad.mit.edu 37 3 173998609 173998609 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:173998609G>A ENST00000457714.1 + 7 2417 c.1988G>A c.(1987-1989)aGt>aAt p.S663N NLGN1_ENST00000401917.3_Missense_Mutation_p.S703N|NLGN1_ENST00000545397.1_Missense_Mutation_p.S663N|NLGN1_ENST00000361589.4_Missense_Mutation_p.S663N NM_014932.2 NP_055747.1 Q8N2Q7 NLGN1_HUMAN neuroligin 1 83 Ovarian(172;0.0025) LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13) CAACAACCAAGTCCATTTTCA 0.468000 0 SO:0001583 missense ENST00000457714.1 1 1 hg19 CCDS3222.1 . . . . . . . . . . G 9.582 1.123955 0.20959 . . ENSG00000169760 ENST00000457714;ENST00000361589;ENST00000545397;ENST00000401917 T;T;T;T 0.66280 -0.2;-0.2;-0.2;-0.2 5.59 5.59 0.84812 . 0.000000 0.85682 D 0.000000 T 0.50803 0.1637 N 0.24115 0.695 0.44694 D 0.997688 B 0.06786 0.001 B 0.06405 0.002 T 0.39482 -0.9612 10 0.21014 T 0.42 . 19.9651 0.97262 0.0:0.0:1.0:0.0 . 663 Q8N2Q7-2 . N 663;663;663;703 ENSP00000392500:S663N;ENSP00000354541:S663N;ENSP00000441108:S663N;ENSP00000385750:S703N ENSP00000354541:S663N S + 2 0 NLGN1 175481303 1.000000 0.71417 1.000000 0.80357 0.981000 0.71138 5.166000 0.64965 2.793000 0.96121 0.655000 0.94253 AGT TCGA-XN-A8T3-01A-11D-A36O-08 NLGN1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000347054.3 1 0 0 31 418 0 86 0 5.180229e-03 1 1 0 86 2 0 0 0 0 0 2 1 1.000000 31 413 0 85 2 0 0 0 0 86 2 -20.000000 1 1 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.860000 0.600000 1.000000 1.000000 0.863504 0.860000 1 0.720000 1.000000 MCF2L2 23101 broad.mit.edu 37 3 182925517 182925517 + Missense_Mutation SNP C C A rs143903251 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:182925517C>A ENST00000328913.3 - 23 2888 c.2591G>T c.(2590-2592)cGa>cTa p.R864L MCF2L2_ENST00000468976.1_5'Flank|MCF2L2_ENST00000473233.1_Missense_Mutation_p.R864L NM_015078.2 NP_055893 Q86YR7 MF2L2_HUMAN MCF.2 cell line derived transforming sequence-like 2 p.R864L(1)|p.R864Q(1) 72 all_cancers(143;1.26e-12)|Ovarian(172;0.0355) all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21) GGGTTTAAATCGAATCAAATC 0.438000 2 Substitution - Missense(2) SO:0001583 missense ENST00000328913.3 1 0 hg19 CCDS3243.1 . . . . . . . . . . C 25.7 4.669066 0.88348 0.0 1.16E-4 ENSG00000053524 ENST00000328913;ENST00000473233 T;T 0.02525 4.26;4.26 4.8 4.8 0.61643 Pleckstrin homology-type (1);Pleckstrin homology domain (2); 0.000000 0.64402 D 0.000001 T 0.11665 0.0284 L 0.58583 1.82 0.80722 D 1 D 0.76494 0.999 D 0.81914 0.995 T 0.00585 -1.1658 10 0.54805 T 0.06 . 13.7009 0.62608 0.0:1.0:0.0:0.0 . 864 Q86YR7 MF2L2_HUMAN L 864 ENSP00000328118:R864L;ENSP00000420070:R864L ENSP00000328118:R864L R - 2 0 MCF2L2 184408211 0.985000 0.35326 0.987000 0.45799 0.991000 0.79684 5.629000 0.67798 2.370000 0.80446 0.491000 0.48974 CGA TCGA-XN-A8T3-01A-11D-A36O-08 MCF2L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350868.1 1 0 0 18 397 0 101 0 0 0 0 101 2 0 0 0 0 0 2 1 0.999981 17 393 0 101 2 0 0 0 0 101 2 -4.155578 1 0 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.550000 0.330000 0.820000 0.550000 0.567721 0.550000 0 0.430000 0.690000 EIF4A2 1974 broad.mit.edu 37 3 186503747 186503747 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:186503747C>A ENST00000323963.5 + 5 488 c.424C>A c.(424-426)Cga>Aga p.R142R SNORA4_ENST00000584302.1_RNA|SNORA63_ENST00000363450.1_RNA|EIF4A2_ENST00000440191.2_Silent_p.R143R|SNORD2_ENST00000459163.1_RNA|EIF4A2_ENST00000356531.5_Silent_p.R47R|SNORA81_ENST00000408493.2_RNA|SNORA63_ENST00000363548.1_RNA|RP11-573D15.9_ENST00000577781.1_RNA Q14240 IF4A2_HUMAN eukaryotic translation initiation factor 4A2 28 all_cancers(143;2.68e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;1.07e-20) AACAAATGTTCGAAATGAAAT 0.398000 T BCL6 NHL Dom yes 3 3q27.3 1974 eukaryotic translation initiation factor 4A, isoform 2 L 0 SO:0001819 synonymous_variant ENST00000323963.5 1 0 hg19 CCDS3282.1 TCGA-XN-A8T3-01A-11D-A36O-08 EIF4A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344609.1 1 0 0 34 570 0 112 0 1 1 506 0 112 2 0 0 0 0 0 2 1 1.000000 33 557 0 111 2 0 0 0 0 112 2 -6.421663 1 1 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.700000 0.490000 0.950000 0.710000 0.720121 0.700000 0 0.590000 0.830000 IQCG 84223 broad.mit.edu 37 3 197665429 197665429 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:197665429G>T ENST00000265239.6 - 5 929 c.505C>A c.(505-507)Cag>Aag p.Q169K IQCG_ENST00000480302.1_5'Flank|IQCG_ENST00000455191.1_Missense_Mutation_p.Q169K|IQCG_ENST00000453254.1_Missense_Mutation_p.Q169K NM_032263.3 NP_115639.1 Q9H095 IQCG_HUMAN IQ motif containing G 21 all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976) Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07) CTATCAATCTGAATTTTCTTC 0.453000 0 SO:0001583 missense ENST00000265239.6 0 1 hg19 CCDS3331.1 . . . . . . . . . . G 22.2 4.251946 0.80135 . . ENSG00000114473 ENST00000265239;ENST00000455191;ENST00000453254;ENST00000416896 T;T;T;T 0.57107 0.66;0.66;0.96;0.42 5.5 5.5 0.81552 . 0.000000 0.85682 D 0.000000 T 0.73560 0.3602 M 0.81341 2.54 0.46927 D 0.999252 P;D 0.89917 0.911;1.0 P;D 0.71656 0.558;0.974 T 0.75764 -0.3203 10 0.59425 D 0.04 -21.4276 16.5383 0.84377 0.0:0.0:1.0:0.0 . 169;169 C9JKX8;Q9H095 .;IQCG_HUMAN K 169;169;169;150 ENSP00000265239:Q169K;ENSP00000407736:Q169K;ENSP00000389897:Q169K;ENSP00000406411:Q150K ENSP00000265239:Q169K Q - 1 0 IQCG 199149826 1.000000 0.71417 1.000000 0.80357 0.835000 0.47333 3.181000 0.50903 2.759000 0.94783 0.558000 0.71614 CAG TCGA-XN-A8T3-01A-11D-A36O-08 IQCG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000339730.1 0 0 0 16 803 0 193 0 7.145390e-02 0 21 0 193 2 0 0 0 0 0 2 1 0.999925 16 793 0 193 2 0 0 0 0 193 2 -2.492374 0 1 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.240000 0.140000 0.390000 0.240000 0.258707 0.240000 0 0.190000 0.320000 DNAH1 25981 broad.mit.edu 37 3 52398935 52398935 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:52398935C>A ENST00000420323.2 + 34 5679 c.5418C>A c.(5416-5418)tcC>tcA p.S1806S NM_015512.4 NP_056327 Q9P2D7 DYH1_HUMAN dynein, axonemal, heavy chain 1 62 GCATCGTGTCCGACCTGTTTC 0.607000 0 SO:0001819 synonymous_variant ENST00000420323.2 1 1 hg19 CCDS46842.1 TCGA-XN-A8T3-01A-11D-A36O-08 DNAH1-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350816.1 0 0 0 11 365 0 86 0 3.153512e-03 0 3 0 86 2 0 0 0 0 0 2 1 0.998292 10 363 0 84 2 0 0 0 0 86 2 -2.623419 1 1 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.370000 0.190000 0.620000 0.360000 0.395419 0.370000 0 0.270000 0.500000 PROK2 60675 broad.mit.edu 37 3 71821900 71821900 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:71821900C>A ENST00000295619.3 - 4 373 c.365G>T c.(364-366)cGa>cTa p.R122L PROK2_ENST00000353065.3_Missense_Mutation_p.R101L NM_001126128.1 NP_001119600.1 Q9HC23 PROK2_HUMAN prokineticin 2 p.R101Q(1) 6 Prostate(10;0.00899) ACAAATAAATCGGTTAAATGA 0.408000 1 Substitution - Missense(1) SO:0001583 missense ENST00000295619.3 1 0 hg19 CCDS46868.1 . . . . . . . . . . C 17.04 3.286476 0.59867 . . ENSG00000163421 ENST00000353065;ENST00000295619 T;T 0.66638 -0.22;-0.22 5.67 3.88 0.44766 Prokineticin domain (2); 0.167345 0.36519 N 0.002560 T 0.57095 0.2030 L 0.55481 1.735 0.35060 D 0.761469 B;P 0.39665 0.449;0.682 B;B 0.36922 0.202;0.236 T 0.68727 -0.5332 10 0.66056 D 0.02 -16.0798 6.6965 0.23201 0.0:0.7429:0.0:0.2571 . 122;101 Q9HC23;Q6ISR0 PROK2_HUMAN;. L 101;122 ENSP00000295618:R101L;ENSP00000295619:R122L ENSP00000295619:R122L R - 2 0 PROK2 71904590 0.998000 0.40836 0.948000 0.38648 0.980000 0.70556 0.952000 0.29149 1.404000 0.46819 0.655000 0.94253 CGA TCGA-XN-A8T3-01A-11D-A36O-08 PROK2-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000352302.1 1 0 0 22 476 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 0.999999 21 474 0 73 2 0 0 0 0 73 2 -3.041735 1 1 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.550000 0.350000 0.800000 0.560000 0.573713 0.550000 0 0.450000 0.690000 PDZRN3 23024 broad.mit.edu 37 3 73432928 73432928 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:73432928G>A ENST00000263666.4 - 10 2903 c.2789C>T c.(2788-2790)aCg>aTg p.T930M PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000535920.1_Missense_Mutation_p.T652M|PDZRN3_ENST00000466780.1_Missense_Mutation_p.T587M|PDZRN3_ENST00000479530.1_Missense_Mutation_p.T647M|PDZRN3_ENST00000462146.2_Missense_Mutation_p.T587M NM_015009.1 NP_055824.1 Q9UPQ7 PZRN3_HUMAN PDZ domain containing ring finger 3 69 Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236) GATGTAGCGCGTCCCGTCGCT 0.672000 0 SO:0001583 missense ENST00000263666.4 1 1 hg19 CCDS33789.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 21.5|21.5 4.162279|4.162279 0.78226|0.78226 .|. .|. ENSG00000121440|ENSG00000121440 ENST00000494559|ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530 .|T;T;T;T;T .|0.45276 .|0.9;0.9;0.9;0.9;0.9 5.4|5.4 5.4|5.4 0.78164|0.78164 .|. .|0.150407 .|0.64402 .|D .|0.000015 T|T 0.68274|0.68274 0.2983|0.2983 M|M 0.80982|0.80982 2.52|2.52 0.80722|0.80722 D|D 1|1 .|D;D;D;D .|0.89917 .|1.0;1.0;1.0;1.0 .|D;P;D;D .|0.75484 .|0.986;0.874;0.957;0.911 T|T 0.72717|0.72717 -0.4209|-0.4209 5|10 .|0.87932 .|D .|0 .|. 18.7949|18.7949 0.91990|0.91990 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|652;647;647;930 .|F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7 .|.;.;.;PZRN3_HUMAN C|M 246|930;652;587;587;647 .|ENSP00000263666:T930M;ENSP00000442026:T652M;ENSP00000418168:T587M;ENSP00000418484:T587M;ENSP00000418624:T647M .|ENSP00000263666:T930M R|T -|- 1|2 0|0 PDZRN3|PDZRN3 73515618|73515618 1.000000|1.000000 0.71417|0.71417 0.964000|0.964000 0.40570|0.40570 0.915000|0.915000 0.54546|0.54546 7.532000|7.532000 0.81985|0.81985 2.522000|2.522000 0.85027|0.85027 0.655000|0.655000 0.94253|0.94253 CGC|ACG TCGA-XN-A8T3-01A-11D-A36O-08 PDZRN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352460.1 1 0 1 31 213 0 64 0 7.659549e-01 0 21 0 64 2 0 0 0 0 0 2 1 1.000000 31 208 0 63 2 0 0 0 0 64 2 -20.000000 1 1 121400 1 23 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.990000 0.990000 1.000000 1.000000 0.999704 0.990000 1 0.990000 1.000000 THUMPD3 25917 broad.mit.edu 37 3 9416208 9416208 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr3:9416208G>T ENST00000345094.3 + 5 1150 c.816G>T c.(814-816)ttG>ttT p.L272F THUMPD3_ENST00000515662.2_Missense_Mutation_p.L272F|SETD5-AS1_ENST00000468186.1_RNA|THUMPD3_ENST00000452837.2_Missense_Mutation_p.L272F NM_001114092.1|NM_015453.2 NP_001107564.1|NP_056268.2 Q9BV44 THUM3_HUMAN THUMP domain containing 3 19 Medulloblastoma(99;0.227) AGGTTCTTTTGAACATCCATG 0.393000 0 SO:0001583 missense ENST00000345094.3 1 1 hg19 CCDS2573.1 .|.|. .|.|. .|.|. .|.|. .|.|. .|.|. .|.|. .|.|. .|.|. .|.|. G|G|G 16.68|16.68|16.68 3.190198|3.190198|3.190198 0.58017|0.58017|0.58017 .|.|. .|.|. ENSG00000134077|ENSG00000134077|ENSG00000134077 ENST00000416603|ENST00000452837;ENST00000345094;ENST00000515662|ENST00000441127 .|T;T;T|. .|0.52526|. .|0.66;0.66;0.66|. 5.57|5.57|5.57 4.7|4.7|4.7 0.59300|0.59300|0.59300 .|THUMP (3);|. .|0.000000|. .|0.85682|. .|D|. .|0.000000|. .|T|. .|0.77624|. .|0.4158|. M|M|M 0.88570|0.88570|0.88570 2.965|2.965|2.965 0.58432|0.58432|0.58432 D|D|D 0.999997|0.999997|0.999997 .|D|. .|0.76494|. .|0.999|. .|D|. .|0.83275|. .|0.996|. .|T|. .|0.80111|. .|-0.1519|. .|10|. .|0.40728|. .|T|. .|0.16|. -16.9958|-16.9958|-16.9958 10.3831|10.3831|10.3831 0.44123|0.44123|0.44123 0.0738:0.1354:0.7908:0.0|0.0738:0.1354:0.7908:0.0|0.0738:0.1354:0.7908:0.0 .|.|. .|272|. .|Q9BV44|. .|THUM3_HUMAN|. X|F|L 105|272|129 .|ENSP00000395893:L272F;ENSP00000339532:L272F;ENSP00000424064:L272F|. .|ENSP00000339532:L272F|. E|L|X +|+|+ 1|3|2 0|2|2 THUMPD3|THUMPD3|THUMPD3 9391208|9391208|9391208 1.000000|1.000000|1.000000 0.71417|0.71417|0.71417 1.000000|1.000000|1.000000 0.80357|0.80357|0.80357 0.698000|0.698000|0.698000 0.40448|0.40448|0.40448 1.299000|1.299000|1.299000 0.33424|0.33424|0.33424 1.347000|1.347000|1.347000 0.45714|0.45714|0.45714 0.585000|0.585000|0.585000 0.79938|0.79938|0.79938 GAA|TTG|TGA TCGA-XN-A8T3-01A-11D-A36O-08 THUMPD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214127.1 0 0 0 24 671 0 151 0 2.923036e-01 0 30 0 151 2 0 0 0 0 0 2 1 1.000000 22 663 0 148 2 0 0 0 0 151 2 -3.282933 1 1 0 0 1 2 2 4 2.085353 0 0.190000 3.530000 0.319328 0.430000 0.280000 0.620000 0.440000 0.447927 0.430000 0 0.350000 0.530000 DNAJB14 79982 broad.mit.edu 37 4 100830014 100830014 + Missense_Mutation SNP T T C TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr4:100830014T>C ENST00000442697.2 - 4 645 c.491A>G c.(490-492)aAg>aGg p.K164R NM_001031723.2|NM_001278310.1 NP_001026893.1|NP_001265239.1 Q8TBM8 DJB14_HUMAN DnaJ (Hsp40) homolog, subfamily B, member 14 5 CTGTTTTCGCTTTTCTGGATT 0.353000 0 SO:0001583 missense ENST00000442697.2 1 1 hg19 CCDS34035.1 . . . . . . . . . . T 31 5.079506 0.94050 . . ENSG00000164031 ENST00000442697 T 0.35973 1.28 5.8 5.8 0.92144 Heat shock protein DnaJ, N-terminal (5);Heat shock protein DnaJ, conserved site (1); 0.000000 0.85682 D 0.000000 T 0.46483 0.1395 N 0.20685 0.6 0.80722 D 1 D;D 0.71674 0.994;0.998 D;D 0.78314 0.954;0.991 T 0.50608 -0.8808 10 0.62326 D 0.03 . 16.1549 0.81657 0.0:0.0:0.0:1.0 . 164;79 Q8TBM8;Q8TBM8-2 DJB14_HUMAN;. R 164 ENSP00000404381:K164R ENSP00000404381:K164R K - 2 0 DNAJB14 101049037 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.490000 0.81461 2.209000 0.71365 0.533000 0.62120 AAG TCGA-XN-A8T3-01A-11D-A36O-08 DNAJB14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253696.2 1 0 0 37 382 0 76 1 4.589017e-01 2 15 0 76 2 0 0 0 0 0 2 1 1.000000 36 375 0 79 2 0 0 0 0 76 2 -11.297400 1 0 0 0 1 2 2 4 2.088030 0 0.190000 3.530000 0.319328 0.990000 0.800000 1.000000 1.000000 0.977599 0.990000 1 0.940000 1.000000 PRDM5 11107 broad.mit.edu 37 4 121739540 121739540 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr4:121739540C>A ENST00000264808.3 - 5 858 c.618G>T c.(616-618)aaG>aaT p.K206N PRDM5_ENST00000428209.2_Missense_Mutation_p.K206N|PRDM5_ENST00000515109.1_Missense_Mutation_p.K206N NM_018699.2 NP_061169.2 Q9NQX1 PRDM5_HUMAN PR domain containing 5 34 CTGGGAATTTCTTCCCACAGT 0.373000 0 SO:0001583 missense ENST00000264808.3 1 1 hg19 CCDS3716.1 . . . . . . . . . . C 23.0 4.358729 0.82243 . . ENSG00000138738 ENST00000264808;ENST00000515109;ENST00000428209 T;T;T 0.61158 0.13;0.13;0.13 5.32 5.32 0.75619 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.85682 D 0.000000 T 0.79257 0.4415 M 0.84219 2.685 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.87578 0.998;0.997;0.998 T 0.82165 -0.0592 10 0.72032 D 0.01 -32.109 19.0126 0.92879 0.0:1.0:0.0:0.0 . 206;206;206 Q0VAI9;Q9NQX1-2;Q9NQX1 .;.;PRDM5_HUMAN N 206 ENSP00000264808:K206N;ENSP00000422309:K206N;ENSP00000404832:K206N ENSP00000264808:K206N K - 3 2 PRDM5 121958990 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 4.395000 0.59678 2.498000 0.84270 0.555000 0.69702 AAG TCGA-XN-A8T3-01A-11D-A36O-08 PRDM5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256528.2 1 0 1 69 479 0 87 0 4.492156e-02 0 3 0 87 2 0 0 0 0 0 2 1 1.000000 66 472 0 87 2 0 0 0 0 87 2 -20.000000 1 1 0 0 1 2 2 4 2.088030 0 0.190000 3.530000 0.319328 0.990000 0.990000 1.000000 1.000000 0.999997 0.990000 1 0.990000 1.000000 FAT4 79633 broad.mit.edu 37 4 126370128 126370128 + Nonsense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr4:126370128G>T ENST00000394329.3 + 9 7970 c.7957G>T c.(7957-7959)Gag>Tag p.E2653* FAT4_ENST00000335110.5_Nonsense_Mutation_p.E951* NM_024582.4 NP_078858.4 Q6V0I7 FAT4_HUMAN FAT atypical cadherin 4 355 ctCCTCTTACGAGAAACTTGA 0.373000 0 SO:0001587 stop_gained ENST00000394329.3 0 1 hg19 CCDS3732.3 . . . . . . . . . . G 49 15.050129 0.99820 . . ENSG00000196159 ENST00000394329;ENST00000335110 . . . 5.71 5.71 0.89125 . 0.214766 0.22554 U 0.058541 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.27082 T 0.32 . 13.5378 0.61655 0.0799:0.0:0.9201:0.0 . . . . X 2653;951 . ENSP00000335169:E951X E + 1 0 FAT4 126589578 1.000000 0.71417 1.000000 0.80357 0.900000 0.52787 5.431000 0.66507 2.686000 0.91538 0.650000 0.86243 GAG TCGA-XN-A8T3-01A-11D-A36O-08 FAT4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256765.2 0 0 0 10 351 0 107 0 0 0 0 107 2 0 0 0 0 0 2 1 0.996894 10 349 0 105 2 0 0 0 0 107 2 -2.943021 1 1 0 0 1 2 2 4 2.088030 0 0.190000 3.530000 0.319328 0.360000 0.180000 0.610000 0.360000 0.377357 0.360000 0 0.260000 0.480000 DDX60 55601 broad.mit.edu 37 4 169227778 169227778 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr4:169227778G>T ENST00000393743.3 - 5 649 c.358C>A c.(358-360)Cga>Aga p.R120R NM_017631.5 NP_060101.3 Q8IY21 DDX60_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 60 63 Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132) AATGTTGTTCGAACATCAATG 0.408000 0 SO:0001819 synonymous_variant ENST00000393743.3 1 0 hg19 CCDS34097.1 TCGA-XN-A8T3-01A-11D-A36O-08 DDX60-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000364622.1 1 0 0 26 476 0 90 0 1.334524e-01 0 12 0 90 2 0 0 0 0 0 2 1 1.000000 26 472 0 89 2 0 0 0 0 90 2 -5.316327 1 0 0 0 1 2 2 4 2.088030 0 0.190000 3.530000 0.319328 0.650000 0.430000 0.910000 0.640000 0.667736 0.650000 0 0.530000 0.790000 GALNT7 51809 broad.mit.edu 37 4 174213298 174213298 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr4:174213298G>T ENST00000265000.4 + 3 710 c.627G>T c.(625-627)tcG>tcT p.S209S GALNT7_ENST00000502407.1_3'UTR|GALNT7_ENST00000512285.1_Silent_p.S209S NM_017423.2 NP_059119.2 Q86SF2 GALT7_HUMAN polypeptide N-acetylgalactosaminyltransferase 7 19 Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122) TGCTCACTTCGAGCGTTGTCA 0.368000 0 SO:0001819 synonymous_variant ENST00000265000.4 1 0 hg19 CCDS3815.1 . . . . . . . . . . G 0.308 -0.969448 0.02232 . . ENSG00000109586 ENST00000505308 . . . 5.76 1.61 0.23674 . . . . . T 0.60792 0.2296 . . . 0.80722 D 1 . . . . . . T 0.54768 -0.8244 4 . . . . 11.4461 0.50125 0.1701:0.6473:0.1826:0.0 . . . . L 6 . . R + 2 0 GALNT7 174449873 0.998000 0.40836 0.901000 0.35422 0.029000 0.11900 0.733000 0.26087 0.063000 0.16370 -2.258000 0.00281 CGA TCGA-XN-A8T3-01A-11D-A36O-08 GALNT7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000362456.2 1 0 0 20 524 0 103 0 3.343032e-01 0 31 0 103 2 0 0 0 0 0 2 1 0.999995 20 520 0 103 2 0 0 0 0 103 2 -2.660457 1 1 0 0 1 2 2 4 2.088030 0 0.190000 3.530000 0.319328 0.460000 0.290000 0.680000 0.450000 0.479906 0.460000 0 0.370000 0.580000 GPR125 166647 broad.mit.edu 37 4 22389706 22389706 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr4:22389706C>A ENST00000334304.5 - 19 3857 c.3588G>T c.(3586-3588)acG>acT p.T1196T GPR125_ENST00000282943.5_5'UTR NM_145290.3 NP_660333.2 Q8IWK6 GP125_HUMAN G protein-coupled receptor 125 56 Breast(46;0.198) CTTCCACGCTCGTTGGGACAT 0.517000 0 SO:0001819 synonymous_variant ENST00000334304.5 1 0 hg19 CCDS33964.1 TCGA-XN-A8T3-01A-11D-A36O-08 GPR125-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000362960.3 1 0 0 41 666 0 129 0 9.985448e-01 0 158 0 129 2 0 0 0 0 0 2 1 1.000000 41 655 0 128 2 0 0 0 0 129 2 -2.774725 1 1 0 0 1 2 2 4 2.088030 0 0.190000 3.530000 0.319328 0.720000 0.530000 0.950000 0.720000 0.739078 0.720000 0 0.620000 0.850000 HSD17B11 51170 broad.mit.edu 37 4 88258508 88258508 + Nonsense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr4:88258508C>A ENST00000358290.4 - 7 1138 c.823G>T c.(823-825)Gag>Tag p.E275* HSD17B11_ENST00000507286.1_Nonsense_Mutation_p.E231*|RP11-529H2.2_ENST00000508163.1_RNA|HSD17B11_ENST00000507518.1_5'UTR NM_016245.3 NP_057329.2 Q8NBQ5 DHB11_HUMAN hydroxysteroid (17-beta) dehydrogenase 11 11 Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242) AGGAAACGCTCAGGAAGGATC 0.294000 0 SO:0001587 stop_gained ENST00000358290.4 0 1 hg19 CCDS3619.1 . . . . . . . . . . C 13.36 2.214804 0.39102 . . ENSG00000198189 ENST00000358290;ENST00000507286 . . . 5.49 4.64 0.57946 . 0.079681 0.51477 D 0.000087 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.22706 T 0.39 . 13.4986 0.61440 0.0:0.8429:0.1571:0.0 . . . . X 275;231 . ENSP00000351035:E275X E - 1 0 HSD17B11 88477532 1.000000 0.71417 1.000000 0.80357 0.045000 0.14185 3.940000 0.56599 1.307000 0.44944 0.563000 0.77884 GAG TCGA-XN-A8T3-01A-11D-A36O-08 HSD17B11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253041.1 0 0 0 21 622 0 102 0 9.940142e-01 1 240 0 102 2 0 0 0 0 0 2 1 0.999997 21 607 0 102 2 0 0 0 0 102 2 -2.821360 1 1 0 0 1 2 2 4 2.088030 0 0.190000 3.530000 0.319328 0.410000 0.250000 0.600000 0.400000 0.425849 0.410000 0 0.330000 0.510000 HERC5 51191 broad.mit.edu 37 4 89400623 89400623 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr4:89400623C>A ENST00000264350.3 + 13 1855 c.1702C>A c.(1702-1704)Caa>Aaa p.Q568K HERC5_ENST00000508159.1_Missense_Mutation_p.Q206K NM_016323.3 NP_057407.2 Q9UII4 HERC5_HUMAN HECT and RLD domain containing E3 ubiquitin protein ligase 5 53 Hepatocellular(203;0.114) TGGTAATGTTCAAGCTCTCCT 0.418000 Esophageal Squamous(39;887 1012 34045 50514) 0 SO:0001583 missense ENST00000264350.3 1 0 hg19 CCDS3630.1 . . . . . . . . . . C 0.159 -1.083120 0.01888 . . ENSG00000138646 ENST00000264350;ENST00000508159 T;T 0.34859 1.34;1.41 4.59 -1.37 0.09056 . 0.494741 0.17118 N 0.186342 T 0.07999 0.0200 N 0.00926 -1.1 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.33727 -0.9857 10 0.02654 T 1 . 5.0553 0.14529 0.3925:0.4185:0.189:0.0 . 568 Q9UII4 HERC5_HUMAN K 568;206 ENSP00000264350:Q568K;ENSP00000424129:Q206K ENSP00000264350:Q568K Q + 1 0 HERC5 89619646 0.005000 0.15991 0.001000 0.08648 0.243000 0.25628 0.216000 0.17585 -0.352000 0.08237 -0.484000 0.04775 CAA TCGA-XN-A8T3-01A-11D-A36O-08 HERC5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253554.2 1 0 0 20 421 0 73 0 4.148375e-02 0 7 0 73 2 0 0 0 0 0 2 1 0.999994 20 411 0 72 2 0 0 0 0 73 2 -4.697256 1 1 0 0 1 2 2 4 2.088030 0 0.190000 3.530000 0.319328 0.570000 0.360000 0.840000 0.560000 0.590805 0.570000 0 0.450000 0.710000 HSD17B4 3295 broad.mit.edu 37 5 118844936 118844936 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr5:118844936C>A ENST00000256216.6 + 16 1567 c.1434C>A c.(1432-1434)gtC>gtA p.V478V HSD17B4_ENST00000510025.1_Silent_p.V454V|HSD17B4_ENST00000515320.1_Silent_p.V460V|HSD17B4_ENST00000513628.1_Silent_p.V341V|HSD17B4_ENST00000414835.2_Silent_p.V338V|HSD17B4_ENST00000509514.1_Silent_p.V216V|HSD17B4_ENST00000522415.1_3'UTR|HSD17B4_ENST00000504811.1_Silent_p.V503V NM_000414.3 NP_000405.1 P51659 DHB4_HUMAN hydroxysteroid (17-beta) dehydrogenase 4 25 all_cancers(142;0.0206)|Prostate(80;0.0322) CAGACAAAGTCAAGGTAAGCC 0.393000 Colon(35;490 801 34689 41394 43344) 0 SO:0001819 synonymous_variant ENST00000256216.6 1 0 hg19 CCDS4126.1 TCGA-XN-A8T3-01A-11D-A36O-08 HSD17B4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250863.3 1 0 0 21 493 0 107 0 9.839130e-01 0 157 0 107 2 0 0 0 0 0 2 1 0.999997 21 484 0 107 2 0 0 0 0 107 2 -3.146762 1 1 0 0 1 1 2 3 1.926416 0 0.190000 3.530000 0.260274 0.470000 0.300000 0.690000 0.480000 0.488719 0.470000 0 0.380000 0.590000 SLC12A2 6558 broad.mit.edu 37 5 127487009 127487009 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr5:127487009C>A ENST00000262461.2 + 14 2373 c.2184C>A c.(2182-2184)ttC>ttA p.F728L SLC12A2_ENST00000343225.4_Missense_Mutation_p.F728L NM_001046.2 NP_001037.1 P55011 S12A2_HUMAN solute carrier family 12 (sodium/potassium/chloride transporter), member 2 48 all_cancers(142;0.0972)|Prostate(80;0.151) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325) TAGTAATGTTCGTCATTAACT 0.358000 0 SO:0001583 missense ENST00000262461.2 1 0 hg19 CCDS4144.1 . . . . . . . . . . C 16.04 3.010041 0.54361 . . ENSG00000064651 ENST00000262461;ENST00000343225 D;D 0.98747 -5.11;-5.11 4.7 -0.669 0.11388 Amino acid permease domain (1); 0.115149 0.64402 D 0.000013 D 0.97470 0.9172 M 0.70903 2.155 0.80722 D 1 P;P 0.49635 0.909;0.926 B;P 0.47251 0.407;0.542 D 0.94969 0.8115 10 0.87932 D 0 . 9.3862 0.38345 0.0:0.2836:0.0:0.7164 . 728;728 P55011-3;P55011 .;S12A2_HUMAN L 728 ENSP00000262461:F728L;ENSP00000340878:F728L ENSP00000262461:F728L F + 3 2 SLC12A2 127514908 0.988000 0.35896 0.997000 0.53966 0.988000 0.76386 0.178000 0.16820 -0.167000 0.10871 -0.294000 0.09567 TTC TCGA-XN-A8T3-01A-11D-A36O-08 SLC12A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250972.1 1 0 0 20 491 0 102 0 3.178234e-01 0 28 0 102 2 0 0 0 0 0 2 1 0.999995 17 485 0 102 2 0 0 0 0 102 2 -3.083980 1 1 0 0 1 1 2 3 1.926416 0 0.190000 3.530000 0.260274 0.450000 0.280000 0.670000 0.450000 0.469217 0.450000 0 0.360000 0.570000 DDX46 9879 broad.mit.edu 37 5 134109505 134109505 + Silent SNP C C A rs140064519 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr5:134109505C>A ENST00000354283.4 + 5 702 c.567C>A c.(565-567)atC>atA p.I189I DDX46_ENST00000452510.2_Silent_p.I189I Q7L014 DDX46_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 46 30 KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233) AAAAGGAAATCGAAGAGATGA 0.353000 Colon(13;391 453 4901 21675 24897) 0 SO:0001819 synonymous_variant ENST00000354283.4 1 0 hg19 CCDS34240.1 TCGA-XN-A8T3-01A-11D-A36O-08 DDX46-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000371584.1 1 0 0 17 312 0 37 0 6.439212e-01 0 41 0 37 2 0 0 0 0 0 2 1 0.999966 17 309 0 37 2 0 0 0 0 37 2 -3.139300 1 1 0 0 1 1 2 3 1.926416 0 0.190000 3.530000 0.260274 0.600000 0.360000 0.900000 0.600000 0.620783 0.600000 0 0.470000 0.760000 PCDHA11 56138 broad.mit.edu 37 5 140250312 140250312 + Missense_Mutation SNP C C T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr5:140250312C>T ENST00000398640.2 + 1 1624 c.1624C>T c.(1624-1626)Ccg>Tcg p.P542S PCDHA6_ENST00000529310.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron NM_018902.3 NP_061725.1 Q9Y5I1 PCDAB_HUMAN protocadherin alpha 11 2 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGCGGGCGTGCCGCCTCTGAG 0.692000 0 SO:0001583 missense ENST00000398640.2 0 1 hg19 CCDS47284.1 . . . . . . . . . . C 19.23 3.788483 0.70337 . . ENSG00000249158 ENST00000398640 T 0.56776 0.44 5.15 5.15 0.70609 Cadherin (4);Cadherin-like (1); . . . . T 0.78698 0.4324 M 0.92026 3.265 0.35643 D 0.811176 D;D 0.89917 1.0;1.0 D;D 0.71414 0.969;0.973 D 0.87476 0.2417 9 0.87932 D 0 . 18.2779 0.90089 0.0:1.0:0.0:0.0 . 542;542 Q9Y5I1-2;Q9Y5I1 .;PCDAB_HUMAN S 542 ENSP00000381636:P542S ENSP00000381636:P542S P + 1 0 PCDHA11 140230496 0.999000 0.42202 0.994000 0.49952 0.949000 0.60115 5.585000 0.67497 2.398000 0.81561 0.556000 0.70494 CCG TCGA-XN-A8T3-01A-11D-A36O-08 PCDHA11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372885.2 0 0 0 7 732 1 227 0 0 0 1 1 227 2 0 0 0 0 0 2 0 0.119184 8 716 1 224 13 0 0 0 1 227 2 -2.017182 0 1 0 0 1 1 2 3 1.926416 0 0.190000 3.530000 0.260274 0.110000 0.040000 0.220000 0.120000 0.123967 0.110000 0 0.070000 0.170000 GLRA1 2741 broad.mit.edu 37 5 151208531 151208531 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr5:151208531C>A ENST00000455880.2 - 8 1296 c.1010G>T c.(1009-1011)cGg>cTg p.R337L GLRA1_ENST00000545569.1_Missense_Mutation_p.R254L|GLRA1_ENST00000274576.4_Missense_Mutation_p.R337L P23415 GLRA1_HUMAN glycine receptor, alpha 1 23 all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912) Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785) Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236) CTTATGTTGCCGAGACACAAA 0.478000 0 SO:0001583 missense ENST00000455880.2 0 1 hg19 CCDS54942.1 . . . . . . . . . . C 23.1 4.369025 0.82463 . . ENSG00000145888 ENST00000274576;ENST00000455880;ENST00000545569 D;D;D 0.85411 -1.98;-1.98;-1.98 5.07 5.07 0.68467 Neurotransmitter-gated ion-channel transmembrane domain (2); 0.000000 0.85682 D 0.000000 D 0.90428 0.7003 M 0.79693 2.465 0.80722 D 1 P;P;P 0.36789 0.57;0.493;0.514 P;P;B 0.47376 0.545;0.545;0.313 D 0.91347 0.5101 10 0.72032 D 0.01 . 18.826 0.92119 0.0:1.0:0.0:0.0 . 337;254;337 P23415;Q14C71;P23415-2 GLRA1_HUMAN;.;. L 337;337;254 ENSP00000274576:R337L;ENSP00000411593:R337L;ENSP00000445913:R254L ENSP00000274576:R337L R - 2 0 GLRA1 151188724 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 7.557000 0.82243 2.524000 0.85096 0.650000 0.86243 CGG TCGA-XN-A8T3-01A-11D-A36O-08 GLRA1-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000373959.1 0 0 0 11 745 0 167 0 0 0 0 167 2 0 0 0 0 0 2 1 0.998227 11 736 0 166 2 0 0 0 0 167 2 -1.949272 0 1 0 0 1 1 2 3 1.926416 0 0.190000 3.530000 0.260274 0.170000 0.080000 0.290000 0.180000 0.181783 0.170000 0 0.120000 0.230000 ITK 3702 broad.mit.edu 37 5 156608060 156608060 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr5:156608060G>T ENST00000422843.3 + 1 224 c.72G>T c.(70-72)tcG>tcT p.S24S NM_005546.3 NP_005537.3 Q08881 ITK_HUMAN IL2-inducible T-cell kinase p.S24S(1) 70 Renal(175;0.00212) Medulloblastoma(196;0.0354)|all_neural(177;0.1) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) Pazopanib(DB06589) CTTCTCCCTCGAACTTTAAAG 0.423000 T SYK peripheral T-cell lymphoma Esophageal Squamous(70;1378 1469 8785 19883) Dom yes 5 5q31-q32 3702 IL2-inducible T-cell kinase L 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000422843.3 1 0 hg19 CCDS4336.1 TCGA-XN-A8T3-01A-11D-A36O-08 ITK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252569.2 1 0 0 23 576 0 107 0 1.658366e-03 0 2 0 107 2 0 0 0 0 0 2 1 0.999999 24 564 0 107 2 0 0 0 0 107 2 -3.374308 1 1 0 0 1 1 2 3 1.926416 0 0.190000 3.530000 0.260274 0.440000 0.280000 0.640000 0.450000 0.458104 0.440000 0 0.360000 0.550000 RUFY1 80230 broad.mit.edu 37 5 179016622 179016622 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr5:179016622C>A ENST00000319449.4 + 9 1114 c.1102C>A c.(1102-1104)Cga>Aga p.R368R RUFY1_ENST00000393438.2_Silent_p.R260R|RUFY1_ENST00000377001.2_3'UTR|RUFY1_ENST00000437570.2_Silent_p.R260R NM_025158.4 NP_079434.3 Q96T51 RUFY1_HUMAN RUN and FYVE domain containing 1 26 all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195) all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) TGAATTAATTCGAGAAAGAAG 0.388000 HNSCC(44;0.11) 0 SO:0001819 synonymous_variant ENST00000319449.4 1 0 hg19 CCDS4445.2 . . . . . . . . . . C 10.33 1.321386 0.23994 . . ENSG00000176783 ENST00000508609 . . . 5.47 5.47 0.80525 . . . . . T 0.75384 0.3842 . . . 0.80722 D 1 . . . . . . T 0.73597 -0.3932 4 . . . -12.448 19.3849 0.94553 0.0:1.0:0.0:0.0 . . . . L 156 . . F + 3 2 RUFY1 178949228 1.000000 0.71417 0.960000 0.40013 0.990000 0.78478 4.156000 0.58138 2.581000 0.87130 0.549000 0.68633 TTC TCGA-XN-A8T3-01A-11D-A36O-08 RUFY1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000253505.2 1 0 0 24 494 0 109 0 8.437151e-01 0 71 0 109 2 0 0 0 0 0 2 1 1.000000 24 489 0 108 2 0 0 0 0 109 2 -2.868109 1 1 0 0 1 1 2 3 1.926416 0 0.190000 3.530000 0.260274 0.530000 0.350000 0.760000 0.540000 0.551106 0.530000 0 0.430000 0.650000 CENPH 64946 broad.mit.edu 37 5 68490517 68490517 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr5:68490517C>A ENST00000283006.2 + 3 321 c.234C>A c.(232-234)atC>atA p.I78I CENPH_ENST00000515001.1_Silent_p.I78I NM_022909.3 NP_075060.1 centromere protein H p.I78I(1) 20 Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198) AAAAGCAAATCGAAGCGTATG 0.279000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000283006.2 1 0 hg19 CCDS3998.1 TCGA-XN-A8T3-01A-11D-A36O-08 CENPH-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000215083.1 1 0 0 15 298 0 58 0 4.472482e-01 0 30 0 58 2 0 0 0 0 0 2 1 0.999869 15 294 0 57 2 0 0 0 0 58 2 -16.599580 1 1 0 0 1 1 2 3 1.924566 0 0.190000 3.530000 0.260274 0.560000 0.320000 0.860000 0.540000 0.579827 0.560000 0 0.430000 0.710000 CMYA5 202333 broad.mit.edu 37 5 79025398 79025398 + Silent SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr5:79025398G>A ENST00000446378.2 + 2 841 c.810G>A c.(808-810)gaG>gaA p.E270E NM_153610.3 NP_705838.3 Q8N3K9 CMYA5_HUMAN cardiomyopathy associated 5 128 Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262) TTAGTCTAGAGCCAGATTTGG 0.353000 0 SO:0001819 synonymous_variant ENST00000446378.2 1 1 hg19 CCDS47238.1 TCGA-XN-A8T3-01A-11D-A36O-08 CMYA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000369497.1 1 0 0 20 265 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 0.999996 20 263 0 53 2 0 0 0 0 53 2 -19.999970 1 0 0 0 1 1 2 3 1.926416 0 0.190000 3.530000 0.260274 0.810000 0.510000 1.000000 1.000000 0.816180 0.810000 0 0.650000 1.000000 MCM9 254394 broad.mit.edu 37 6 119238766 119238766 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr6:119238766G>T ENST00000316316.6 - 5 1150 c.864C>A c.(862-864)ttC>ttA p.F288L MCM9_ENST00000316068.3_Missense_Mutation_p.F288L NM_017696.2 NP_060166.2 Q9NXL9 MCM9_HUMAN minichromosome maintenance complex component 9 18 all_cancers(87;0.122)|all_epithelial(87;0.179) AAAAATCTTCGAATTCCTTTT 0.378000 0 SO:0001583 missense ENST00000316316.6 1 0 hg19 CCDS56447.1 . . . . . . . . . . G 23.8 4.454336 0.84209 . . ENSG00000111877 ENST00000316316;ENST00000316068 T;T 0.06142 3.73;3.34 5.81 4.65 0.58169 . . . . . T 0.16085 0.0387 M 0.87682 2.9 0.52099 D 0.999949 D 0.89917 1.0 D 0.70016 0.967 T 0.02098 -1.1214 9 0.36615 T 0.2 . 11.7956 0.52098 0.9314:0.0:0.0686:0.0 . 288 Q9NXL9-2 . L 288 ENSP00000314505:F288L;ENSP00000312870:F288L ENSP00000312870:F288L F - 3 2 MCM9 119280465 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 4.102000 0.57776 1.044000 0.40200 -0.251000 0.11542 TTC TCGA-XN-A8T3-01A-11D-A36O-08 MCM9-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042005.4 1 0 0 26 648 0 130 0 3.896453e-02 0 8 0 130 2 0 0 0 0 0 2 1 1.000000 24 638 0 128 2 0 0 0 0 130 2 -3.493684 1 1 0 0 1 0 2 2 1.748141 1 0.190000 3.530000 0.190000 0.400000 0.270000 0.570000 0.400000 0.417763 0.400000 0 0.330000 0.490000 ENPP3 5169 broad.mit.edu 37 6 131979467 131979467 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr6:131979467G>T ENST00000414305.1 + 7 797 c.469G>T c.(469-471)Gac>Tac p.D157Y ENPP3_ENST00000543135.1_Missense_Mutation_p.D123Y|ENPP3_ENST00000470930.1_3'UTR|ENPP3_ENST00000427148.2_Missense_Mutation_p.D123Y|ENPP3_ENST00000357639.3_Missense_Mutation_p.D157Y|ENPP3_ENST00000358229.5_Missense_Mutation_p.D157Y O14638 ENPP3_HUMAN ectonucleotide pyrophosphatase/phosphodiesterase 3 53 Breast(56;0.0753) TTTCAGGTTTGACCTGCCACC 0.328000 0 SO:0001583 missense ENST00000414305.1 0 1 hg19 CCDS5148.1 . . . . . . . . . . G 17.61 3.432322 0.62844 . . ENSG00000154269 ENST00000414305;ENST00000357639;ENST00000543135;ENST00000427148;ENST00000358229 T;T;T;T;T 0.74842 -0.88;-0.88;-0.88;-0.88;-0.88 5.46 5.46 0.80206 Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1); 0.726895 0.12959 N 0.425153 T 0.77032 0.4071 M 0.73962 2.25 0.38009 D 0.934463 P 0.47545 0.897 P 0.49561 0.615 T 0.79536 -0.1763 10 0.66056 D 0.02 -12.1846 16.5792 0.84710 0.0:0.0:1.0:0.0 . 157 O14638 ENPP3_HUMAN Y 157;157;123;123;157 ENSP00000406261:D157Y;ENSP00000350265:D157Y;ENSP00000440810:D123Y;ENSP00000399269:D123Y;ENSP00000350964:D157Y ENSP00000350265:D157Y D + 1 0 ENPP3 132021160 1.000000 0.71417 0.998000 0.56505 0.671000 0.39405 2.644000 0.46613 2.722000 0.93159 0.650000 0.86243 GAC TCGA-XN-A8T3-01A-11D-A36O-08 ENPP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043627.2 0 0 0 8 283 0 62 0 0 0 0 62 2 0 0 0 0 0 2 1 0.989634 8 283 0 61 2 0 0 0 0 62 2 -3.607918 1 1 0 0 1 0 2 2 1.748141 1 0.190000 3.530000 0.190000 0.300000 0.140000 0.530000 0.280000 0.318600 0.300000 0 0.210000 0.420000 HBS1L 10767 broad.mit.edu 37 6 135318671 135318671 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr6:135318671C>A ENST00000367837.5 - 6 869 c.663G>T c.(661-663)acG>acT p.T221T HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367826.2_Silent_p.T179T|HBS1L_ENST00000527578.1_Silent_p.T57T|HBS1L_ENST00000415177.2_Silent_p.T156T|HBS1L_ENST00000367824.4_Silent_p.T57T NM_001145158.1|NM_006620.3 NP_001138630.1|NP_006611.1 Q9Y450 HBS1L_HUMAN HBS1-like translational GTPase 20 Colorectal(23;0.221) ATGCTTGAATCGTGTGGGGTG 0.493000 0 SO:0001819 synonymous_variant ENST00000367837.5 1 0 hg19 CCDS5173.1 TCGA-XN-A8T3-01A-11D-A36O-08 HBS1L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042339.2 1 0 0 19 403 0 115 0 5.029439e-01 0 36 0 115 2 0 0 0 0 0 2 1 0.999989 18 396 0 112 2 0 0 0 0 115 2 -4.045674 1 1 0 0 1 0 2 2 1.748141 1 0.190000 3.530000 0.190000 0.470000 0.290000 0.700000 0.470000 0.491507 0.470000 0 0.370000 0.590000 TRIM38 10475 broad.mit.edu 37 6 25972146 25972146 + Missense_Mutation SNP T T G TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr6:25972146T>G ENST00000357085.3 + 5 1033 c.557T>G c.(556-558)cTc>cGc p.L186R TRIM38_ENST00000349458.3_Missense_Mutation_p.L186R NM_006355.3 NP_006346.1 O00635 TRI38_HUMAN tripartite motif containing 38 23 TTTAAGAATCTCCAGTGTTTC 0.438000 0 SO:0001583 missense ENST00000357085.3 1 1 hg19 CCDS4568.1 . . . . . . . . . . t 8.516 0.867585 0.17250 . . ENSG00000112343 ENST00000540262;ENST00000349458;ENST00000357085 T;T;T 0.07216 3.21;3.21;3.21 4.55 3.37 0.38596 . 0.000000 0.39985 N 0.001212 T 0.07999 0.0200 M 0.80746 2.51 0.09310 N 0.999999 P 0.52316 0.952 P 0.52267 0.694 T 0.16188 -1.0411 10 0.27082 T 0.32 . 7.6274 0.28220 0.1881:0.0:0.0:0.8119 . 186 O00635 TRI38_HUMAN R 186 ENSP00000443976:L186R;ENSP00000230099:L186R;ENSP00000349596:L186R ENSP00000230099:L186R L + 2 0 TRIM38 26080125 0.041000 0.20044 0.012000 0.15200 0.001000 0.01503 2.090000 0.41682 1.047000 0.40274 -0.327000 0.08410 CTC TCGA-XN-A8T3-01A-11D-A36O-08 TRIM38-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040076.2 1 0 1 22 223 0 57 1 8.179919e-01 5 29 0 57 2 0 0 0 0 0 2 1 0.899604 22 217 1 56 15 0 0 0 0 57 2 -9.032588 1 1 0 0 1 0 2 2 1.736554 1 0.190000 3.530000 0.190000 0.940000 0.610000 1.000000 1.000000 0.903557 0.940000 1 0.760000 1.000000 TNXB 7148 broad.mit.edu 37 6 32049954 32049954 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr6:32049954G>A ENST00000375244.3 - 9 3796 c.3595C>T c.(3595-3597)Cgg>Tgg p.R1199W TNXB_ENST00000375247.2_Missense_Mutation_p.R1199W P22105 TENX_HUMAN tenascin XB 8 ACCTGGGGCCGTCCATCCCTG 0.562000 0 SO:0001583 missense ENST00000375244.3 1 1 hg19 . . . . . . . . . . G 17.01 3.278036 0.59758 . . ENSG00000168477 ENST00000375244;ENST00000375247 T;T 0.57273 0.41;0.41 4.74 4.74 0.60224 . 0.905187 0.09249 N 0.828076 T 0.53867 0.1823 M 0.61703 1.905 0.09310 N 1 D 0.64830 0.994 P 0.61397 0.888 T 0.41698 -0.9494 10 0.39692 T 0.17 . 10.3406 0.43875 0.0:0.0:0.804:0.196 . 1199 P22105-3 . W 1199 ENSP00000364393:R1199W;ENSP00000364396:R1199W ENSP00000364393:R1199W R - 1 2 TNXB 32157932 0.003000 0.15002 0.035000 0.18076 0.930000 0.56654 1.320000 0.33666 2.461000 0.83175 0.407000 0.27541 CGG TCGA-XN-A8T3-01A-11D-A36O-08 TNXB-001 PUTATIVE not_organism_supported|basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000268927.2 1 0 1 44 130 0 20 0 0 0 1 0 20 2 0 0 0 0 0 2 1 1.000000 43 129 0 20 2 0 0 0 0 20 2 -20.000000 1 1 0 0 1 2 10 12 3.031716 1 0.190000 3.530000 0.537275 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 EFHC1 114327 broad.mit.edu 37 6 52357122 52357122 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr6:52357122C>A ENST00000371068.5 + 11 2009 c.1906C>A c.(1906-1908)Cgt>Agt p.R636S EFHC1_ENST00000538167.1_Missense_Mutation_p.R617S|EFHC1_ENST00000433625.2_Intron NM_018100.3 NP_060570.2 Q5JVL4 EFHC1_HUMAN EF-hand domain (C-terminal) containing 1 27 Lung NSC(77;0.109) TAACTTTGTTCGTGCTTTCTC 0.393000 0 SO:0001583 missense ENST00000371068.5 1 0 hg19 CCDS4942.1 . . . . . . . . . . C 20.4 3.992193 0.74703 . . ENSG00000096093 ENST00000371068;ENST00000538167 T;T 0.42131 0.98;0.98 4.72 3.78 0.43462 EF-hand-like domain (1); 0.235946 0.38381 N 0.001710 T 0.33000 0.0848 L 0.59436 1.845 0.80722 D 1 D;P 0.54964 0.969;0.947 P;P 0.54460 0.753;0.571 T 0.08617 -1.0713 10 0.11794 T 0.64 -7.7181 9.6159 0.39692 0.2083:0.7917:0.0:0.0 . 617;636 F5GZD8;Q5JVL4 .;EFHC1_HUMAN S 636;617 ENSP00000360107:R636S;ENSP00000444521:R617S ENSP00000360107:R636S R + 1 0 EFHC1 52465081 0.627000 0.27129 0.946000 0.38457 0.995000 0.86356 1.315000 0.33608 2.612000 0.88384 0.591000 0.81541 CGT TCGA-XN-A8T3-01A-11D-A36O-08 EFHC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040905.2 1 0 0 34 819 0 147 0 7.143613e-01 0 61 0 147 2 0 0 0 0 0 2 1 1.000000 35 814 0 146 2 0 0 0 0 147 2 -4.691567 1 1 0 0 1 2 4 6 2.398453 1 0.190000 3.530000 0.409793 0.580000 0.400000 0.820000 0.590000 0.594379 0.580000 0 0.480000 0.690000 GFRAL 389400 broad.mit.edu 37 6 55216353 55216353 + Missense_Mutation SNP C C T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr6:55216353C>T ENST00000340465.2 + 5 759 c.673C>T c.(673-675)Cgc>Tgc p.R225C NM_207410.2 NP_997293.2 Q6UXV0 GFRAL_HUMAN GDNF family receptor alpha like 48 Lung NSC(77;0.0875)|Renal(3;0.122) LUSC - Lung squamous cell carcinoma(124;0.23) CAGTGTAATTCGCAGCTGCCA 0.428000 0 SO:0001583 missense ENST00000340465.2 1 1 hg19 CCDS4957.1 . . . . . . . . . . C 25.0 4.588449 0.86851 . . ENSG00000187871 ENST00000340465 T 0.64991 -0.13 6.05 6.05 0.98169 GDNF/GAS1 (2); 0.376195 0.29424 N 0.012190 T 0.62551 0.2437 L 0.34521 1.04 0.43014 D 0.994552 D 0.67145 0.996 P 0.56788 0.806 T 0.64084 -0.6490 10 0.62326 D 0.03 -2.3631 20.6087 0.99469 0.0:1.0:0.0:0.0 . 225 Q6UXV0 GFRAL_HUMAN C 225 ENSP00000343636:R225C ENSP00000343636:R225C R + 1 0 GFRAL 55324312 1.000000 0.71417 0.999000 0.59377 0.985000 0.73830 3.954000 0.56708 2.866000 0.98385 0.650000 0.86243 CGC TCGA-XN-A8T3-01A-11D-A36O-08 GFRAL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040995.2 1 0 0 17 243 0 47 0 0 0 0 47 2 0 0 0 0 0 2 1 0.999966 16 240 0 44 2 0 0 0 0 47 2 -19.885110 1 0 0 0 1 2 4 6 2.398453 1 0.190000 3.530000 0.409793 0.960000 0.580000 1.000000 1.000000 0.904320 0.960000 1 0.760000 1.000000 FASTK 10922 broad.mit.edu 37 7 150775665 150775665 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr7:150775665G>A ENST00000297532.6 - 4 886 c.809C>T c.(808-810)aCg>aTg p.T270M RP11-148K1.12_ENST00000485974.1_RNA|FASTK_ENST00000482571.1_Missense_Mutation_p.T243M|FASTK_ENST00000540185.1_Intron|FASTK_ENST00000353841.2_Missense_Mutation_p.T129M|FASTK_ENST00000489884.1_5'UTR NM_006712.4 NP_006703.1 Q14296 FASTK_HUMAN Fas-activated serine/threonine kinase 6 OV - Ovarian serous cystadenocarcinoma(82;0.00989) GCTGAGTTGCGTTTCCTGAAC 0.642000 0 SO:0001583 missense ENST00000297532.6 1 1 hg19 CCDS5918.1 . . . . . . . . . . G 11.50 1.657389 0.29425 0.0 1.16E-4 ENSG00000164896 ENST00000483105;ENST00000297530;ENST00000353841;ENST00000297532;ENST00000482571 T;T;T 0.30448 1.94;1.94;1.53 4.75 0.664 0.17890 . 0.729997 0.12332 N 0.478305 T 0.11793 0.0287 N 0.08118 0 0.80722 D 1 P;B;B 0.47545 0.897;0.002;0.0 B;B;B 0.37091 0.241;0.001;0.0 T 0.10660 -1.0620 10 0.56958 D 0.05 6.7165 3.399 0.07316 0.0809:0.2673:0.3781:0.2737 . 243;129;270 F8VTW9;Q8IVA0;Q14296 .;.;FASTK_HUMAN M 270;270;129;270;243 ENSP00000324817:T129M;ENSP00000297532:T270M;ENSP00000418516:T243M ENSP00000297530:T270M T - 2 0 FASTK 150406598 1.000000 0.71417 0.964000 0.40570 0.859000 0.49053 1.929000 0.40114 0.003000 0.14656 -0.152000 0.13540 ACG TCGA-XN-A8T3-01A-11D-A36O-08 FASTK-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351832.2 1 0 1 40 138 0 48 1 1 60 82 0 48 2 0 0 0 0 0 2 1 1.000000 39 136 0 47 2 0 0 0 0 48 2 -20.000000 1 0 121402 3 35 1 0 3 3 1.935171 1 0.190000 3.530000 0.260274 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 CROT 54677 broad.mit.edu 37 7 86978419 86978419 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr7:86978419G>T ENST00000331536.3 + 3 220 c.35G>T c.(34-36)cGa>cTa p.R12L CROT_ENST00000419147.2_Missense_Mutation_p.R12L|CROT_ENST00000412227.2_Missense_Mutation_p.R12L|CROT_ENST00000442291.1_Missense_Mutation_p.R12L NM_021151.3 NP_066974.2 Q9UKG9 OCTC_HUMAN carnitine O-octanoyltransferase 37 Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203) L-Carnitine(DB00583) ACTGAAGAACGAACATTTCAG 0.338000 0 SO:0001583 missense ENST00000331536.3 1 0 hg19 CCDS5604.1 . . . . . . . . . . G 23.1 4.371237 0.82573 . . ENSG00000005469 ENST00000419147;ENST00000412227;ENST00000331536;ENST00000442291 D;D;D;D 0.88975 -2.45;-2.45;-2.45;-2.45 5.85 5.85 0.93711 . 0.303544 0.31167 N 0.008131 D 0.91185 0.7223 L 0.41961 1.31 0.58432 D 0.999997 D;D;P 0.64830 0.994;0.991;0.953 P;P;P 0.59487 0.858;0.618;0.748 D 0.88293 0.2944 10 0.25106 T 0.35 -13.5987 19.7758 0.96391 0.0:0.0:1.0:0.0 . 12;12;12 E7EQF2;Q9UKG9;Q86V17 .;OCTC_HUMAN;. L 12 ENSP00000413575:R12L;ENSP00000404867:R12L;ENSP00000331981:R12L;ENSP00000411983:R12L ENSP00000331981:R12L R + 2 0 CROT 86816355 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.489000 0.81451 2.782000 0.95742 0.655000 0.94253 CGA TCGA-XN-A8T3-01A-11D-A36O-08 CROT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253485.1 1 0 0 26 556 0 107 0 6.323854e-02 0 9 0 107 2 0 0 0 0 0 2 1 1.000000 26 547 0 106 2 0 0 0 0 107 2 -2.942352 1 1 0 0 1 0 3 3 1.919343 1 0.190000 3.530000 0.260274 0.510000 0.340000 0.730000 0.510000 0.530296 0.510000 0 0.420000 0.630000 GTPBP10 85865 broad.mit.edu 37 7 90006865 90006865 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr7:90006865G>T ENST00000222511.6 + 7 702 c.636G>T c.(634-636)atG>atT p.M212I GTPBP10_ENST00000257659.8_Missense_Mutation_p.M133I NM_033107.3 NP_149098.2 A4D1E9 GTPBA_HUMAN GTP-binding protein 10 (putative) 10 GAGCACATATGAACAAAGGAA 0.318000 0 SO:0001583 missense ENST00000222511.6 1 0 hg19 CCDS5617.1 . . . . . . . . . . G 12.73 2.025864 0.35701 . . ENSG00000105793 ENST00000426366;ENST00000450619;ENST00000257659;ENST00000222511;ENST00000417207 T;T;T;T;T 0.16743 2.32;2.32;2.32;2.32;2.32 5.89 5.89 0.94794 GTP1/OBG (1);GTP-binding domain, HSR1-related (1); 0.624103 0.18956 N 0.126524 T 0.18882 0.0453 L 0.58583 1.82 0.39265 D 0.964286 B;B;B;B 0.20988 0.05;0.015;0.04;0.034 B;B;B;B 0.23852 0.013;0.049;0.048;0.026 T 0.04281 -1.0963 9 . . . -9.5889 10.8413 0.46718 0.0697:0.1307:0.7995:0.0 . 133;212;203;229 A4D1E9-2;A4D1E9;C9J8R7;C9JNI1 .;GTPBA_HUMAN;.;. I 203;229;133;212;139 ENSP00000405697:M203I;ENSP00000389510:M229I;ENSP00000257659:M133I;ENSP00000222511:M212I;ENSP00000416596:M139I . M + 3 0 GTPBP10 89844801 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.153000 0.42282 2.787000 0.95880 0.650000 0.86243 ATG TCGA-XN-A8T3-01A-11D-A36O-08 GTPBP10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059976.3 1 0 0 41 1039 0 205 0 4.193923e-01 0 37 0 205 2 0 0 0 0 0 2 1 1.000000 41 1016 0 203 2 0 0 0 0 205 2 -3.685974 1 1 0 0 1 0 3 3 1.919343 1 0.190000 3.530000 0.260274 0.430000 0.310000 0.580000 0.430000 0.446240 0.430000 0 0.370000 0.510000 RIMS2 9699 broad.mit.edu 37 8 105257203 105257203 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr8:105257203G>A ENST00000436393.2 + 24 3689 c.3448G>A c.(3448-3450)Gtg>Atg p.V1150M RIMS2_ENST00000507740.1_Missense_Mutation_p.V946M|RIMS2_ENST00000406091.3_Missense_Mutation_p.V1132M|RIMS2_ENST00000339750.2_Missense_Mutation_p.V68M|RIMS2_ENST00000262231.10_Missense_Mutation_p.V971M Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 144 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) AGGCCTGGCCGTGGAAATGAG 0.463000 HNSCC(12;0.0054) 0 SO:0001583 missense ENST00000436393.2 1 1 hg19 . . . . . . . . . . G 16.59 3.166677 0.57476 0.0 1.2E-4 ENSG00000176406 ENST00000329869;ENST00000406091;ENST00000402998;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393;ENST00000523362;ENST00000339750 T;T;T;T;T;T;T 0.21361 2.58;2.28;2.27;2.03;2.48;2.02;2.01 5.05 5.05 0.67936 . . . . . T 0.28797 0.0714 L 0.43152 1.355 0.58432 D 0.999996 D;P;D;B;B 0.56035 0.974;0.669;0.966;0.161;0.161 P;B;P;B;B 0.49047 0.499;0.032;0.599;0.024;0.024 T 0.01051 -1.1468 9 0.44086 T 0.13 . 18.5918 0.91215 0.0:0.0:1.0:0.0 . 1194;1150;971;946;1132 Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47 RIMS2_HUMAN;.;.;.;. M 1169;1132;1194;971;946;1139;1150;68;68 ENSP00000384892:V1132M;ENSP00000262231:V971M;ENSP00000423559:V946M;ENSP00000386228:V1139M;ENSP00000390665:V1150M;ENSP00000428478:V68M;ENSP00000342051:V68M ENSP00000262231:V971M V + 1 0 RIMS2 105326379 1.000000 0.71417 1.000000 0.80357 0.981000 0.71138 7.807000 0.86032 2.623000 0.88846 0.650000 0.86243 GTG TCGA-XN-A8T3-01A-11D-A36O-08 RIMS2-007 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000367217.1 1 0 1 109 616 0 132 0 0 0 1 0 132 2 0 0 0 0 0 2 1 1.000000 108 613 0 131 2 0 0 0 0 132 2 -20.000000 1 1 120954 2 39 1 2 3 5 2.222887 1 0.190000 3.530000 0.366841 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 CSMD3 114788 broad.mit.edu 37 8 113599442 113599442 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr8:113599442C>A ENST00000297405.5 - 23 3982 c.3738G>T c.(3736-3738)acG>acT p.T1246T CSMD3_ENST00000352409.3_Silent_p.T1246T|CSMD3_ENST00000455883.2_Silent_p.T1142T|CSMD3_ENST00000343508.3_Silent_p.T1206T NM_198123.1 NP_937756.1 Q7Z407 CSMD3_HUMAN CUB and Sushi multiple domains 3 646 CTTCATTATTCGTTGCAGATG 0.353000 HNSCC(6;0.00088)|TCGA Ovarian(7;0.080) 0 SO:0001819 synonymous_variant ENST00000297405.5 1 0 hg19 CCDS6315.1 TCGA-XN-A8T3-01A-11D-A36O-08 CSMD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347141.1 1 0 0 20 593 0 78 0 0 0 0 78 2 0 0 0 0 0 2 1 0.999995 20 584 0 78 2 0 0 0 0 78 2 -2.866560 1 1 0 0 1 2 3 5 2.222887 1 0.190000 3.530000 0.366841 0.440000 0.270000 0.700000 0.440000 0.463835 0.440000 0 0.350000 0.560000 FER1L6 654463 broad.mit.edu 37 8 124989741 124989741 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr8:124989741C>A ENST00000522917.1 + 10 1161 c.955C>A c.(955-957)Cgg>Agg p.R319R FER1L6_ENST00000399018.1_Silent_p.R319R NM_001039112.2 NP_001034201.2 Q2WGJ9 FR1L6_HUMAN fer-1-like family member 6 118 Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741) STAD - Stomach adenocarcinoma(47;0.00186) TCCCTTGTGTCGGAGGGTGAA 0.502000 0 SO:0001819 synonymous_variant ENST00000522917.1 1 0 hg19 CCDS43767.1 TCGA-XN-A8T3-01A-11D-A36O-08 FER1L6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381400.1 1 0 0 20 528 0 77 0 0 0 1 0 77 2 0 0 0 0 0 2 1 0.999995 20 526 0 76 2 0 0 0 0 77 2 -3.471697 1 1 0 0 1 2 3 5 2.222887 1 0.190000 3.530000 0.366841 0.500000 0.310000 0.780000 0.490000 0.517319 0.500000 0 0.390000 0.630000 PCM1 5108 broad.mit.edu 37 8 17814853 17814853 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr8:17814853G>T ENST00000519253.1 + 12 1978 c.1727G>T c.(1726-1728)cGa>cTa p.R576L PCM1_ENST00000325083.8_Missense_Mutation_p.R576L|PCM1_ENST00000524226.1_Missense_Mutation_p.R576L Q15154 PCM1_HUMAN pericentriolar material 1 PCM1/JAK2(30) 48 AGAGATGGGCGAACAGTTAAT 0.363000 T RET, JAK2 papillary thyroid, CML, MPD Dom yes 8 8p22-p21.3 5108 pericentriolar material 1 (PTC4) E, L 0 SO:0001583 missense ENST00000519253.1 1 0 hg19 . . . . . . . . . . G 22.1 4.247804 0.80024 . . ENSG00000078674 ENST00000325083;ENST00000517730;ENST00000519253;ENST00000524226 T;T;T;T 0.44083 0.93;0.93;0.93;0.93 5.15 5.15 0.70609 . 0.000000 0.85682 D 0.000000 T 0.63768 0.2539 M 0.64997 1.995 0.80722 D 1 D;D;D;D 0.76494 0.997;0.998;0.999;0.997 D;D;D;D 0.77557 0.986;0.99;0.923;0.986 T 0.63047 -0.6724 10 0.52906 T 0.07 -16.4836 19.5116 0.95144 0.0:0.0:1.0:0.0 . 576;615;576;576 E7ETA6;E7EV93;E7EV56;Q15154 .;.;.;PCM1_HUMAN L 576;615;576;576 ENSP00000327077:R576L;ENSP00000428131:R615L;ENSP00000431099:R576L;ENSP00000430521:R576L ENSP00000327077:R576L R + 2 0 PCM1 17859133 1.000000 0.71417 0.561000 0.28357 0.360000 0.29518 8.857000 0.92250 2.787000 0.95880 0.585000 0.79938 CGA TCGA-XN-A8T3-01A-11D-A36O-08 PCM1-003 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000374800.1 1 0 0 21 512 0 84 0 2.891131e-01 0 26 0 84 2 0 0 0 0 0 2 1 0.999997 21 506 0 84 2 0 0 0 0 84 2 -2.849753 1 1 0 0 1 0 3 3 1.948911 1 0.190000 3.530000 0.260274 0.450000 0.290000 0.670000 0.450000 0.471456 0.450000 0 0.360000 0.570000 RB1CC1 9821 broad.mit.edu 37 8 53558288 53558288 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr8:53558288G>T ENST00000025008.5 - 16 4484 c.3961C>A c.(3961-3963)Cga>Aga p.R1321R RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Silent_p.R1321R|RB1CC1_ENST00000435644.2_Silent_p.R1321R NM_014781.4 NP_055596.3 Q8TDY2 RBCC1_HUMAN RB1-inducible coiled-coil 1 60 all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023) AAAGATGTTCGAACATTTTGC 0.313000 GBM(180;1701 2102 13475 42023 52570) 0 SO:0001819 synonymous_variant ENST00000025008.5 1 0 hg19 CCDS34892.1 TCGA-XN-A8T3-01A-11D-A36O-08 RB1CC1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000378011.1 1 0 0 23 397 0 63 0 8.377993e-01 0 59 0 63 2 0 0 0 0 0 2 1 0.999999 23 395 0 63 2 0 0 0 0 63 2 -5.842960 1 0 0 0 1 2 3 5 2.222887 1 0.190000 3.530000 0.366841 0.750000 0.480000 1.000000 1.000000 0.759499 0.750000 0 0.600000 0.920000 C8orf34 116328 broad.mit.edu 37 8 69552683 69552683 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr8:69552683G>A ENST00000539993.1 + 8 1469 c.920G>A c.(919-921)cGt>cAt p.R307H C8orf34_ENST00000337103.4_Missense_Mutation_p.R282H|C8orf34_ENST00000518698.1_Missense_Mutation_p.R393H|C8orf34_ENST00000325233.3_Missense_Mutation_p.R51H Q49A92 CH034_HUMAN chromosome 8 open reading frame 34 36 Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502) AACCAAGGCCGTCCTACTTAC 0.413000 0 SO:0001583 missense ENST00000539993.1 1 1 hg19 . . . . . . . . . . G 26.0 4.691944 0.88735 . . ENSG00000165084 ENST00000518698;ENST00000539993;ENST00000337103;ENST00000325233 T;T;T;T 0.63913 0.66;0.71;0.7;-0.07 5.46 5.46 0.80206 . 0.000000 0.85682 D 0.000000 T 0.77157 0.4089 L 0.56769 1.78 0.52099 D 0.999942 D 0.89917 1.0 D 0.83275 0.996 T 0.75158 -0.3416 9 . . . -10.9267 19.3134 0.94202 0.0:0.0:1.0:0.0 . 307 Q49A92 CH034_HUMAN H 393;307;282;51 ENSP00000427820:R393H;ENSP00000438159:R307H;ENSP00000337174:R282H;ENSP00000319532:R51H . R + 2 0 C8orf34 69715237 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.376000 0.97181 2.567000 0.86603 0.585000 0.79938 CGT TCGA-XN-A8T3-01A-11D-A36O-08 C8orf34-201 KNOWN basic|appris_candidate protein_coding protein_coding 1 0 0 39 462 0 83 0 0 0 0 83 2 0 0 0 0 0 2 1 1.000000 38 460 0 82 2 0 0 0 0 83 2 -3.318793 1 1 121404 5 38 1 2 3 5 2.222887 1 0.190000 3.530000 0.366841 0.990000 0.760000 1.000000 1.000000 0.964698 0.990000 1 0.900000 1.000000 OR2K2 26248 broad.mit.edu 37 9 114090194 114090194 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr9:114090194C>A ENST00000374428.1 - 1 606 c.607G>T c.(607-609)Gat>Tat p.D203Y OR2K2_ENST00000302681.1_Missense_Mutation_p.D174Y Q8NGT1 OR2K2_HUMAN olfactory receptor, family 2, subfamily K, member 2 20 GTGAAGTGATCGATGAGATTC 0.537000 0 SO:0001583 missense ENST00000374428.1 1 0 hg19 . . . . . . . . . . C 10.85 1.467826 0.26335 . . ENSG00000171133 ENST00000302681;ENST00000374428 T;T 0.00193 8.58;8.58 4.92 2.01 0.26516 GPCR, rhodopsin-like superfamily (1); 0.361129 0.19488 U 0.113053 T 0.00412 0.0013 M 0.71920 2.185 0.09310 N 1 D 0.71674 0.998 D 0.67900 0.954 T 0.47100 -0.9143 10 0.72032 D 0.01 . 7.2851 0.26333 0.0:0.6995:0.1395:0.161 . 203 Q8NGT1 OR2K2_HUMAN Y 174;203 ENSP00000305055:D174Y;ENSP00000363550:D203Y ENSP00000305055:D174Y D - 1 0 OR2K2 113130015 0.000000 0.05858 0.082000 0.20525 0.386000 0.30323 -0.200000 0.09478 0.350000 0.24002 0.591000 0.81541 GAT TCGA-XN-A8T3-01A-11D-A36O-08 OR2K2-201 KNOWN basic protein_coding protein_coding 1 0 0 13 351 0 82 0 4.505699e-03 0 3 0 82 2 0 0 0 0 0 2 1 0.999503 13 345 0 81 2 0 0 0 0 82 2 -3.235573 1 1 0 0 1 3 4 7 2.239264 1 0.190000 3.530000 0.369650 0.550000 0.280000 1.000000 0.500000 0.627595 0.550000 0 0.390000 1.000000 RABGAP1 23637 broad.mit.edu 37 9 125861826 125861826 + Silent SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr9:125861826C>A ENST00000373647.4 + 24 3021 c.2887C>A c.(2887-2889)Cgg>Agg p.R963R RABGAP1_ENST00000373643.5_Silent_p.R302R NM_012197.3 NP_036329.3 Q9Y3P9 RBGP1_HUMAN RAB GTPase activating protein 1 p.R963W(1)|p.R891W(1) 41 TGAGAAAATTCGGGTAAGACT 0.353000 2 Substitution - Missense(2) SO:0001819 synonymous_variant ENST00000373647.4 1 0 hg19 CCDS6848.2 TCGA-XN-A8T3-01A-11D-A36O-08 RABGAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053976.3 1 0 0 15 327 0 60 0 9.602939e-01 0 120 0 60 2 0 0 0 0 0 2 1 0.999883 15 328 0 60 2 0 0 0 0 60 2 -3.082850 1 1 0 0 1 3 3 6 2.263265 1 0.190000 3.530000 0.377019 0.650000 0.360000 1.000000 0.610000 0.690100 0.650000 0 0.490000 1.000000 DENND1A 57706 broad.mit.edu 37 9 126146178 126146178 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr9:126146178C>A ENST00000373624.2 - 21 1793 c.1592G>T c.(1591-1593)cGg>cTg p.R531L DENND1A_ENST00000542603.1_Missense_Mutation_p.R316L|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394219.3_Missense_Mutation_p.R542L NM_020946.1 NP_065997.1 Q8TEH3 DEN1A_HUMAN DENN/MADD domain containing 1A 43 CCTGAGTGTCCGATACGGCTG 0.662000 0 SO:0001583 missense ENST00000373624.2 0 1 hg19 CCDS35133.1 . . . . . . . . . . C 13.62 2.290799 0.40494 . . ENSG00000119522 ENST00000373624;ENST00000542603;ENST00000394219 T;T;T 0.30714 3.13;1.52;2.83 4.89 4.89 0.63831 . 0.188343 0.45361 D 0.000366 T 0.51822 0.1697 M 0.72118 2.19 0.80722 D 1 P;P;P;D 0.65815 0.738;0.612;0.478;0.995 B;B;B;P 0.59357 0.38;0.253;0.129;0.856 T 0.52373 -0.8584 10 0.41790 T 0.15 -6.3349 18.1242 0.89581 0.0:1.0:0.0:0.0 . 542;532;531;394 Q8TEH3-6;Q8TEH3-7;Q8TEH3;Q9HCG4 .;.;DEN1A_HUMAN;. L 531;316;542 ENSP00000362727:R531L;ENSP00000437457:R316L;ENSP00000377766:R542L ENSP00000362727:R531L R - 2 0 DENND1A 125185999 1.000000 0.71417 0.972000 0.41901 0.158000 0.22134 1.211000 0.32382 2.265000 0.75225 0.555000 0.69702 CGG TCGA-XN-A8T3-01A-11D-A36O-08 DENND1A-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000053997.1 0 0 0 8 508 0 107 0 7.808229e-02 0 26 0 107 2 0 0 0 0 0 2 1 0.984078 8 457 0 93 2 0 0 0 0 107 2 -2.643874 1 1 0 0 1 3 3 6 2.263265 1 0.190000 3.530000 0.377019 0.240000 0.100000 1.000000 0.210000 0.357247 0.240000 0 0.160000 0.510000 LCN8 138307 broad.mit.edu 37 9 139650984 139650984 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr9:139650984G>T ENST00000371688.3 - 3 511 c.216C>A c.(214-216)ttC>ttA p.F72L LCN8_ENST00000482893.1_5'UTR NM_178469.3 NP_848564.2 Q6JVE9 LCN8_HUMAN lipocalin 8 10 all_cancers(76;0.0882)|all_epithelial(76;0.228) Myeloproliferative disorder(178;0.0821) CAGGAAAAGCGAATTTTCCCG 0.517000 0 SO:0001583 missense ENST00000371688.3 1 0 hg19 CCDS35183.1 . . . . . . . . . . G 13.59 2.281328 0.40394 . . ENSG00000204001 ENST00000371688 T 0.14391 2.51 3.55 -7.1 0.01547 Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1); . . . . T 0.29423 0.0733 M 0.62723 1.935 0.09310 N 1 D;D 0.89917 1.0;0.998 D;D 0.87578 0.998;0.992 T 0.32188 -0.9916 9 0.72032 D 0.01 . 13.594 0.61978 0.2986:0.0:0.7014:0.0 . 95;72 Q6JVE9;Q6JVE9-2 LCN8_HUMAN;. L 72 ENSP00000360753:F72L ENSP00000360753:F72L F - 3 2 LCN8 138770805 0.000000 0.05858 0.000000 0.03702 0.044000 0.14063 -0.446000 0.06837 -1.525000 0.01762 -1.564000 0.00881 TTC TCGA-XN-A8T3-01A-11D-A36O-08 LCN8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055109.1 1 0 0 22 503 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 0.999999 22 496 0 87 2 0 0 0 0 87 2 -3.674093 1 1 0 0 1 2 3 5 2.276796 1 0.190000 3.530000 0.369650 0.570000 0.360000 0.830000 0.550000 0.588294 0.570000 0 0.460000 0.700000 RNF38 152006 broad.mit.edu 37 9 36339793 36339793 + Missense_Mutation SNP T T C TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr9:36339793T>C ENST00000259605.6 - 12 1611 c.1504A>G c.(1504-1506)Att>Gtt p.I502V RNF38_ENST00000377885.2_Missense_Mutation_p.I419V|RNF38_ENST00000350199.4_Missense_Mutation_p.I419V|RNF38_ENST00000353739.4_Missense_Mutation_p.I452V|RNF38_ENST00000357058.3_Missense_Mutation_p.I419V|RNF38_ENST00000377877.4_Missense_Mutation_p.I426V NM_022781.4 NP_073618.3 Q9H0F5 RNF38_HUMAN ring finger protein 38 11 STAD - Stomach adenocarcinoma(86;0.228) GCTCGGCAAATTGGGCAAGTA 0.378000 0 SO:0001583 missense ENST00000259605.6 1 1 hg19 CCDS6603.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 T 14.75 2.629377 0.46944 . . ENSG00000137075 ENST00000259605;ENST00000353739;ENST00000377885;ENST00000357058;ENST00000350199;ENST00000377876;ENST00000377870;ENST00000377877 T;T;T;T;T;T 0.39997 1.05;1.05;1.05;1.05;1.05;1.05 5.55 5.55 0.83447 Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1); 0.000000 0.85682 D 0.000000 T 0.39545 0.1082 N 0.03948 -0.315 0.80722 D 1 P;B;P 0.48911 0.917;0.124;0.904 D;B;D 0.64321 0.924;0.344;0.924 T 0.52275 -0.8597 10 0.48119 T 0.1 -7.5111 13.6403 0.62246 0.0:0.0:0.0:1.0 . 426;452;502 B1AM81;Q9H0F5-2;Q9H0F5 .;.;RNF38_HUMAN V 502;452;419;419;419;319;426;426 ENSP00000259605:I502V;ENSP00000335239:I452V;ENSP00000367117:I419V;ENSP00000349566:I419V;ENSP00000343947:I419V;ENSP00000367109:I426V ENSP00000259605:I502V I - 1 0 RNF38 36329793 1.000000 0.71417 1.000000 0.80357 0.913000 0.54294 7.381000 0.79718 2.096000 0.63516 0.533000 0.62120 ATT TCGA-XN-A8T3-01A-11D-A36O-08 RNF38-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000052422.3 1 0 1 47 214 0 36 1 9.504272e-01 4 21 0 36 2 0 0 0 0 0 2 1 1.000000 47 212 0 36 2 0 0 0 0 36 2 -20.000000 1 1 121408 3 33 1 3 4 7 2.239264 1 0.190000 3.530000 0.369650 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MAMDC2 256691 broad.mit.edu 37 9 72785470 72785470 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr9:72785470G>A ENST00000377182.4 + 11 2191 c.1574G>A c.(1573-1575)cGg>cAg p.R525Q MAMDC2-AS1_ENST00000535188.1_RNA|MAMDC2-AS1_ENST00000420573.1_RNA|MAMDC2-AS1_ENST00000448377.3_RNA|MAMDC2_ENST00000460688.1_3'UTR|MAMDC2-AS1_ENST00000377178.3_RNA|MAMDC2-AS1_ENST00000591368.1_RNA NM_153267.4 NP_694999.3 Q7Z304 MAMC2_HUMAN MAM domain containing 2 14 AAAAGAAACCGGAGCAGCTGG 0.498000 0 SO:0001583 missense ENST00000377182.4 0 1 hg19 CCDS6631.1 . . . . . . . . . . G 20.5 3.995045 0.74703 . . ENSG00000165072 ENST00000377182 T 0.01963 4.53 5.25 4.33 0.51752 Concanavalin A-like lectin/glucanase (1);MAM domain (4); 0.500904 0.21233 N 0.077953 T 0.02767 0.0083 N 0.16478 0.41 0.43118 D 0.994837 P 0.40602 0.723 B 0.44315 0.446 T 0.67799 -0.5577 10 0.25106 T 0.35 -12.7011 15.9892 0.80188 0.0:0.1352:0.8648:0.0 . 525 Q7Z304 MAMC2_HUMAN Q 525 ENSP00000366387:R525Q ENSP00000366387:R525Q R + 2 0 MAMDC2 71975290 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 5.458000 0.66679 1.297000 0.44761 0.491000 0.48974 CGG TCGA-XN-A8T3-01A-11D-A36O-08 MAMDC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052600.1 0 0 0 6 384 0 66 0 1.442244e-02 0 10 0 66 2 0 0 0 0 0 2 1 0.963260 6 378 0 65 2 0 0 0 0 66 2 -3.249916 1 1 0 0 1 3 4 7 2.239264 1 0.190000 3.530000 0.369650 0.260000 0.090000 1.000000 0.200000 0.416974 0.260000 0 0.150000 1.000000 OSTF1 26578 broad.mit.edu 37 9 77761608 77761608 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 G T G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chr9:77761608G>T ENST00000346234.6 + 10 746 c.596G>T c.(595-597)cGa>cTa p.R199L NM_012383.4 NP_036515.4 Q92882 OSTF1_HUMAN osteoclast stimulating factor 1 2 GATGCAGTTCGAACATTAAGC 0.343000 0 SO:0001583 missense ENST00000346234.6 1 0 hg19 CCDS6651.1 . . . . . . . . . . G 21.8 4.208427 0.79240 . . ENSG00000134996 ENST00000346234 T 0.46063 0.88 5.84 5.84 0.93424 . 0.000000 0.85682 D 0.000000 T 0.62454 0.2429 M 0.63428 1.95 0.80722 D 1 B;D 0.60160 0.234;0.987 B;D 0.65010 0.039;0.931 T 0.61292 -0.7092 10 0.56958 D 0.05 -12.0759 18.9168 0.92508 0.0:0.0:1.0:0.0 . 199;199 A8K646;Q92882 .;OSTF1_HUMAN L 199 ENSP00000340836:R199L ENSP00000340836:R199L R + 2 0 OSTF1 76951428 1.000000 0.71417 1.000000 0.80357 0.872000 0.50106 6.005000 0.70716 2.748000 0.94277 0.650000 0.86243 CGA TCGA-XN-A8T3-01A-11D-A36O-08 OSTF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052704.1 1 0 0 26 536 0 91 0 9.998741e-01 0 287 0 91 2 0 0 0 0 0 2 1 1.000000 26 527 0 90 2 0 0 0 0 91 2 -2.918079 1 1 121412 1 34 1 3 4 7 2.239264 1 0.190000 3.530000 0.369650 0.680000 0.430000 1.000000 0.610000 0.727714 0.680000 0 0.530000 1.000000 LUZP4 51213 broad.mit.edu 37 X 114540856 114540856 + Silent SNP G G A rs148942179 TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chrX:114540856G>A ENST00000371920.3 + 4 436 c.429G>A c.(427-429)ccG>ccA p.P143P LUZP4_ENST00000451986.2_Silent_p.P61P NM_016383.3 NP_057467.1 Q9P127 LUZP4_HUMAN leucine zipper protein 4 14 AAGGAAATCCGGACAAATCAG 0.473000 0 SO:0001819 synonymous_variant ENST00000371920.3 1 1 hg19 CCDS14567.1 TCGA-XN-A8T3-01A-11D-A36O-08 LUZP4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000057972.1 1 0 1 37 166 0 35 0 0 0 0 35 2 0 0 0 0 0 2 1 1.000000 37 162 0 35 2 0 0 0 0 35 2 -2.987853 1 1 121410 5 39 1 0 1 1 0.190000 3.530000 0.190000 0.880000 0.670000 1.000000 0.940000 0.874520 0.880000 1 0.770000 0.970000 SLITRK4 139065 broad.mit.edu 37 X 142716900 142716900 + Silent SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chrX:142716900G>T ENST00000381779.4 - 2 2250 c.2025C>A c.(2023-2025)acC>acA p.T675T SLITRK4_ENST00000356928.1_Silent_p.T675T|SLITRK4_ENST00000338017.4_Silent_p.T675T NM_001184749.2|NM_001184750.1|NM_173078.4 NP_001171678.1|NP_001171679.1|NP_775101.1 Q8IW52 SLIK4_HUMAN SLIT and NTRK-like family, member 4 60 Acute lymphoblastic leukemia(192;6.56e-05) CTTTTTTATTGGTTTTGTGGT 0.483000 0 SO:0001819 synonymous_variant ENST00000381779.4 0 1 hg19 CCDS14679.1 TCGA-XN-A8T3-01A-11D-A36O-08 SLITRK4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058617.1 0 0 0 9 410 0 102 0 8.569361e-03 0 6 0 102 2 0 0 0 0 0 2 1 0.993945 9 405 0 100 2 0 0 0 0 102 2 -2.414136 0 1 0 0 1 0 1 1 0.190000 3.530000 0.190000 0.110000 0.050000 0.200000 0.110000 0.123739 0.110000 0 0.080000 0.160000 SCML1 6322 broad.mit.edu 37 X 17767568 17767568 + Missense_Mutation SNP C C A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chrX:17767568C>A ENST00000380041.3 + 5 575 c.247C>A c.(247-249)Cgt>Agt p.R83S SCML1_ENST00000380043.3_Missense_Mutation_p.R56S|SCML1_ENST00000398080.1_5'UTR|SCML1_ENST00000380045.3_5'UTR NM_001037540.1 NP_001032629.1 Q9UN30 SCML1_HUMAN sex comb on midleg-like 1 (Drosophila) 10 Hepatocellular(33;0.183) TGATGTGATTCGTAGAAAGGT 0.303000 0 SO:0001583 missense ENST00000380041.3 1 0 hg19 CCDS35210.1 . . . . . . . . . . C 12.48 1.949167 0.34377 . . ENSG00000047634 ENST00000380041;ENST00000380043;ENST00000419185 . . . 4.96 -1.83 0.07833 . 1.225180 0.05738 N 0.600913 T 0.15825 0.0381 N 0.03608 -0.345 0.09310 N 0.999998 B;B 0.06786 0.001;0.001 B;B 0.08055 0.002;0.003 T 0.25745 -1.0123 9 0.18710 T 0.47 -9.9658 8.3928 0.32540 0.4512:0.3997:0.1491:0.0 . 56;83 Q9UN30-2;Q9UN30 .;SCML1_HUMAN S 83;56;56 . ENSP00000369380:R83S R + 1 0 SCML1 17677489 0.001000 0.12720 0.000000 0.03702 0.000000 0.00434 -0.395000 0.07287 -0.672000 0.05266 -1.059000 0.02297 CGT TCGA-XN-A8T3-01A-11D-A36O-08 SCML1-006 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000060495.5 1 0 0 12 193 0 41 0 2.666017e-01 0 16 0 41 2 0 0 0 0 0 2 1 0.999127 11 191 0 40 2 0 0 0 0 41 2 -3.138427 1 1 0 0 1 0 1 1 0.190000 3.530000 0.190000 0.310000 0.170000 0.500000 0.300000 0.323693 0.310000 0 0.230000 0.410000 STS 412 broad.mit.edu 37 X 7268006 7268006 + Missense_Mutation SNP G G A TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chrX:7268006G>A ENST00000217961.4 + 10 1676 c.1456G>A c.(1456-1458)Gtg>Atg p.V486M NM_000351.4 NP_000342.2 P08842 STS_HUMAN steroid sulfatase (microsomal), isozyme S 27 Colorectal(8;0.0136)|Medulloblastoma(8;0.184) Norelgestromin(DB06713) TGCCACACACGTGTGCTTCTG 0.488000 Ichthyosis 0 SO:0001583 missense Familial Cancer Database X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris ENST00000217961.4 1 1 hg19 CCDS14127.1 . . . . . . . . . . G 12.41 1.928468 0.34002 . . ENSG00000101846 ENST00000217961 D 0.91068 -2.78 4.22 4.22 0.49857 Sulfatase (1);Alkaline-phosphatase-like, core domain (1); 0.186047 0.33023 N 0.005369 D 0.91432 0.7296 M 0.85630 2.765 0.35164 D 0.770921 P 0.51147 0.942 B 0.43301 0.415 D 0.94820 0.7986 10 0.49607 T 0.09 . 14.6151 0.68541 0.0:0.0:1.0:0.0 . 486 P08842 STS_HUMAN M 486 ENSP00000217961:V486M ENSP00000217961:V486M V + 1 0 STS 7278006 0.997000 0.39634 0.494000 0.27515 0.029000 0.11900 2.447000 0.44917 1.720000 0.51447 0.600000 0.82982 GTG TCGA-XN-A8T3-01A-11D-A36O-08 STS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055686.1 1 0 1 50 263 0 61 0 8.288955e-01 1 18 0 61 2 0 0 0 0 0 2 1 1.000000 48 261 0 61 2 0 0 0 0 61 2 -20.000000 1 1 0 0 1 0 1 1 0.190000 3.530000 0.190000 0.820000 0.630000 0.980000 0.830000 0.823812 0.820000 0 0.720000 0.920000 DIAPH2 1730 broad.mit.edu 37 X 96013193 96013193 + Missense_Mutation SNP G G T TCGA-XN-A8T3-01A-11D-A36O-08 TCGA-XN-A8T3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5cf08adf-ece6-4625-8279-2994b8acb873 165d0321-64d0-4625-be7b-5c3403120bd9 g.chrX:96013193G>T ENST00000324765.8 + 4 730 c.383G>T c.(382-384)cGa>cTa p.R128L DIAPH2_ENST00000355827.4_Missense_Mutation_p.R128L|DIAPH2_ENST00000373061.3_Missense_Mutation_p.R128L|DIAPH2_ENST00000373054.4_Missense_Mutation_p.R117L|DIAPH2_ENST00000373049.4_Missense_Mutation_p.R128L O60879 DIAP2_HUMAN diaphanous-related formin 2 51 GCTCCTTTACGAAACAAAGAC 0.383000 0 SO:0001583 missense ENST00000324765.8 1 0 hg19 CCDS14467.1 . . . . . . . . . . G 19.09 3.760417 0.69763 . . ENSG00000147202 ENST00000373061;ENST00000373054;ENST00000355827;ENST00000373049;ENST00000324765;ENST00000537885 D;D;D;D;D 0.86627 -2.15;-2.15;-2.15;-2.15;-2.15 5.73 4.87 0.63330 GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1); 0.000000 0.49305 D 0.000141 D 0.89546 0.6746 L 0.55103 1.725 0.46927 D 0.999257 D;P;D 0.89917 1.0;0.951;0.999 D;B;D 0.91635 0.999;0.438;0.997 D 0.86292 0.1674 10 0.02654 T 1 . 13.361 0.60657 0.0783:0.0:0.9217:0.0 . 128;128;128 O60879;O60879-2;B7ZLJ0 DIAP2_HUMAN;.;. L 128;117;128;128;128;128 ENSP00000362152:R128L;ENSP00000362145:R117L;ENSP00000348082:R128L;ENSP00000362140:R128L;ENSP00000321348:R128L ENSP00000321348:R128L R + 2 0 DIAPH2 95899849 1.000000 0.71417 0.999000 0.59377 0.991000 0.79684 9.239000 0.95389 1.175000 0.42826 0.600000 0.82982 CGA TCGA-XN-A8T3-01A-11D-A36O-08 DIAPH2-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000058871.2 1 0 0 20 241 0 40 0 1.880924e-01 0 10 0 40 2 0 0 0 0 0 2 1 0.999995 19 238 0 39 2 0 0 0 0 40 2 -3.318788 1 1 0 0 1 0 1 1 0.190000 3.530000 0.190000 0.400000 0.250000 0.580000 0.400000 0.413412 0.400000 0 0.320000 0.500000