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 SPPL3 121665 broad.mit.edu 37 12 121221520 121221522 + In_Frame_Del DEL GGA GGA - TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 GGA - GGA GGA Valid Somatic Phase_I WXS RNA Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr12:121221520_121221522delGGA ENST00000353487.2 - 5 847_849 c.344_346delTCC c.(343-348)ctcccg>ccg p.L115del NM_139015.4 NP_620584.2 Q8TCT6 SPPL3_HUMAN signal peptide peptidase like 3 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) TGGCACATCGGGAGGAGAAGAAA 0.325000 0 SO:0001651 inframe_deletion ENST00000353487.2 1 1 hg19 CCDS9208.1 TCGA-YH-A8SY-01A-11D-A377-08 SPPL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402980.2 1 0 0 59 303 0 59 1 9.999943e-01 17 76 0 59 2 0 0 0 0 0 0 1 0.999972 79 310 2 61 28 0 0 0 0 0 0 -2.119162 0 0 0 0 1 0 3 3 1.842395 1 0.220000 3.360000 0.286694 0.990000 0.990000 1.000000 1.000000 0.999996 0.990000 1 0.990000 1.000000 CANX 821 broad.mit.edu 37 5 179151711 179151728 + In_Frame_Del DEL GAAGGAAGAGGAAGAAGA GAAGGAAGAGGAAGAAGA - TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 GAAGGAAGAGGAAGAAGA - GAAGGAAGAGGAAGAAGA GAAGGAAGAGGAAGAAGA Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr5:179151711_179151728delGAAGGAAGAGGAAGAAGA ENST00000247461.4 + 13 1772_1789 c.1572_1589delGAAGGAAGAGGAAGAAGA c.(1570-1590)gtgaaggaagaggaagaagag>gtg p.KEEEEE525del CANX_ENST00000415618.2_In_Frame_Del_p.KEEEEE560del|CANX_ENST00000452673.2_In_Frame_Del_p.KEEEEE525del|CANX_ENST00000504734.1_In_Frame_Del_p.KEEEEE525del|CANX_ENST00000512607.2_In_Frame_Del_p.KEEEEE417del NM_001746.3 NP_001737.1 P27824 CALX_HUMAN calnexin 22 all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218) all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) Antihemophilic Factor(DB00025)|Tenecteplase(DB00031) AACCGGATGTGAaggaagaggaagaagagaaggaagag 0.413000 0 SO:0001651 inframe_deletion ENST00000247461.4 1 1 hg19 CCDS4447.1 TCGA-YH-A8SY-01A-11D-A377-08 CANX-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253500.2 1 0 0 33 204 0 44 0 1 0 519 0 44 2 0 0 0 0 0 0 2 0.008683 110 281 11 56 85 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.949770 0 0.220000 3.360000 0.297297 0.990000 0.990000 1.000000 1.000000 0.998528 0.990000 1 0.990000 1.000000 VWA2 340706 broad.mit.edu 37 10 116046089 116046089 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr10:116046089C>T ENST00000392982.3 + 11 1639 c.1389C>T c.(1387-1389)ggC>ggT p.G463G VWA2_ENST00000603594.1_Silent_p.G463G Q5GFL6 VWA2_HUMAN von Willebrand factor A domain containing 2 26 AGGTTGCGGGCCCAGCGCGTC 0.657000 0 SO:0001819 synonymous_variant ENST00000392982.3 1 1 hg19 TCGA-YH-A8SY-01A-11D-A377-08 VWA2-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000050456.3 1 0 1 39 257 0 48 0 4.974722e-02 1 2 0 48 2 0 0 0 0 0 2 1 1.000000 39 254 0 48 2 0 0 0 0 48 2 -3.018321 1 1 0 0 1 2 2 4 2.114795 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 0.999551 0.990000 1 0.990000 1.000000 OGDHL 55753 broad.mit.edu 37 10 50966564 50966564 + Silent SNP C C T rs149391137 TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr10:50966564C>T ENST00000374103.4 - 2 160 c.75G>A c.(73-75)ccG>ccA p.P25P OGDHL_ENST00000432695.1_Intron|OGDHL_ENST00000419399.1_Silent_p.P25P NM_018245.2 NP_060715.2 Q9ULD0 OGDHL_HUMAN oxoglutarate dehydrogenase-like 61 AGCCAAACACCGGGACGTCAT 0.627000 0 SO:0001819 synonymous_variant ENST00000374103.4 1 1 hg19 CCDS7234.1 TCGA-YH-A8SY-01A-11D-A377-08 OGDHL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048007.1 1 0 1 43 199 0 29 0 0 0 0 29 2 0 0 0 0 0 2 1 1.000000 43 193 0 28 2 0 0 0 0 29 2 -3.323279 1 1 0 0 1 2 2 4 2.110973 1 0.220000 3.360000 0.359501 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ITIH2 3698 broad.mit.edu 37 10 7773950 7773950 + Silent SNP G G A rs150260189 TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr10:7773950G>A ENST00000358415.4 + 13 1804 c.1638G>A c.(1636-1638)acG>acA p.T546T ITIH2_ENST00000379587.4_Silent_p.T535T NM_002216.2 NP_002207.2 P19823 ITIH2_HUMAN inter-alpha-trypsin inhibitor heavy chain 2 64 GCGTTATCACGGCGACTTCGG 0.438000 0 SO:0001819 synonymous_variant ENST00000358415.4 0 1 hg19 CCDS31141.1 TCGA-YH-A8SY-01A-11D-A377-08 ITIH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046678.2 0 0 0 7 413 1 92 0 4.033478e-04 0 2 1 92 2 0 0 0 0 0 2 0 0.040124 7 406 1 91 16 0 0 0 1 92 2 -2.881760 1 1 121408 1 47 1 2 2 4 2.086287 0 0.220000 3.360000 0.351297 0.190000 0.080000 1.000000 0.190000 0.257374 0.190000 0 0.130000 0.300000 PVRL1 5818 broad.mit.edu 37 11 119535865 119535865 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr11:119535865C>T ENST00000264025.3 - 6 1676 c.1146G>A c.(1144-1146)cgG>cgA p.R382R PVRL1_ENST00000341398.2_Intron NM_002855.4 NP_002846.3 Q15223 PVRL1_HUMAN poliovirus receptor-related 1 (herpesvirus entry mediator C) p.R382R(1) 27 Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) TGAAGGTGTGCCGGCGCCGAC 0.657000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000264025.3 0 1 hg19 CCDS8426.1 TCGA-YH-A8SY-01A-11D-A377-08 PVRL1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388231.1 0 0 0 5 385 0 55 0 6.844956e-02 0 27 0 55 2 0 0 0 0 0 2 1 0.933587 5 376 0 54 2 0 0 0 0 55 2 -2.107250 0 1 121410 1 39 1 1 2 3 1.963246 0 0.220000 3.360000 0.297297 0.130000 0.040000 0.280000 0.120000 0.153515 0.130000 0 0.080000 0.210000 MUC5B 727897 broad.mit.edu 37 11 1272055 1272055 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr11:1272055G>A ENST00000529681.1 + 31 14003 c.13945G>A c.(13945-13947)Gcc>Acc p.A4649T MUC5B_ENST00000447027.1_Missense_Mutation_p.A4652T|RP11-532E4.2_ENST00000532061.2_RNA NM_002458.2 NP_002449.2 Q9HC84 MUC5B_HUMAN mucin 5B, oligomeric mucus/gel-forming p.A4649T(1)|p.A4604T(1) 137 all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) cacccacaccgccagagtgct 0.612000 2 Substitution - Missense(2) SO:0001583 missense ENST00000529681.1 1 1 hg19 CCDS44515.2 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. -|- 3.668|3.668 -0.068133|-0.068133 0.07228|0.07228 2.36E-4|2.36E-4 0.0|0.0 ENSG00000117983|ENSG00000117983 ENST00000529681;ENST00000447027;ENST00000349637|ENST00000535652 T;T|. 0.15834|. 2.39;2.57|. 0.976|0.976 -0.754|-0.754 0.11065|0.11065 .|. .|. .|. .|. .|. T|T 0.11623|0.11623 0.0283|0.0283 N|N 0.03608|0.03608 -0.345|-0.345 0.09310|0.09310 N|N 1|1 B|. 0.25235|. 0.121|. B|. 0.12156|. 0.007|. T|T 0.18366|0.18366 -1.0339|-1.0339 9|6 0.87932|0.45353 D|T 0|0.12 .|. 4.0397|4.0397 0.09745|0.09745 0.0:0.3403:0.4612:0.1985|0.0:0.3403:0.4612:0.1985 .|. 4652|. E9PBJ0|. .|. T|H 4649;4652;4593|423 ENSP00000436812:A4649T;ENSP00000415793:A4652T|. ENSP00000343037:A4593T|ENSP00000439776:R423H A|R +|+ 1|2 0|0 MUC5B|MUC5B 1228631|1228631 0.000000|0.000000 0.05858|0.05858 0.002000|0.002000 0.10522|0.10522 0.014000|0.014000 0.08584|0.08584 -5.897000|-5.897000 0.00092|0.00092 -1.423000|-1.423000 0.02002|0.02002 -1.123000|-1.123000 0.02005|0.02005 GCC|CGC TCGA-YH-A8SY-01A-11D-A377-08 MUC5B-002 NOVEL basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000390041.2 0 0 0 17 123 0 53 1 8.501358e-01 6 21 0 53 2 0 0 0 0 0 2 1 0.999954 10 120 0 52 2 0 0 0 0 53 2 -3.077458 1 1 120990 5 40 1 1 2 3 1.950487 0 0.220000 3.360000 0.297297 0.990000 0.760000 1.000000 1.000000 0.978461 0.990000 1 0.970000 1.000000 KCNC1 3746 broad.mit.edu 37 11 17758047 17758047 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr11:17758047C>T ENST00000379472.3 + 1 528 c.498C>T c.(496-498)ggC>ggT p.G166G KCNC1_ENST00000265969.6_Silent_p.G166G NM_004976.4 NP_004967.1 P48547 KCNC1_HUMAN potassium voltage-gated channel, Shaw-related subfamily, member 1 33 Dalfampridine(DB06637) GCCGGCCTGGCGGCTTTTGGC 0.687000 0 SO:0001819 synonymous_variant ENST00000379472.3 1 1 hg19 CCDS7827.1 TCGA-YH-A8SY-01A-11D-A377-08 KCNC1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000389389.1 1 0 0 21 72 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 0.999999 21 71 0 23 2 0 0 0 0 23 2 -20.000000 1 1 0 0 1 1 2 3 1.950487 0 0.220000 3.360000 0.297297 0.990000 0.990000 1.000000 1.000000 0.999990 0.990000 1 0.990000 1.000000 HIPK3 10114 broad.mit.edu 37 11 33373714 33373714 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr11:33373714G>A ENST00000303296.4 + 16 3379 c.3074G>A c.(3073-3075)cGa>cAa p.R1025Q HIPK3_ENST00000525975.1_Missense_Mutation_p.R1004Q|AL122015.1_ENST00000411202.1_RNA|HIPK3_ENST00000379016.3_Missense_Mutation_p.R1004Q|HIPK3_ENST00000456517.1_Missense_Mutation_p.R1004Q NM_005734.3 NP_005725.3 Q9H422 HIPK3_HUMAN homeodomain interacting protein kinase 3 39 ATAAAAGGACGATCTGCCCCT 0.378000 0 SO:0001583 missense ENST00000303296.4 0 1 hg19 CCDS7884.1 . . . . . . . . . . G 12.25 1.880365 0.33162 . . ENSG00000110422 ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517 T;T;T;T 0.50277 0.75;0.75;0.75;0.75 5.62 4.7 0.59300 . 0.145914 0.31872 N 0.006928 T 0.28267 0.0698 N 0.14661 0.345 0.49483 D 0.999795 B;B 0.14805 0.011;0.006 B;B 0.16289 0.015;0.006 T 0.08493 -1.0719 10 0.07325 T 0.83 . 13.6209 0.62136 0.0754:0.0:0.9246:0.0 . 1004;1025 Q9H422-2;Q9H422 .;HIPK3_HUMAN Q 1004;1025;1004;1004 ENSP00000431710:R1004Q;ENSP00000304226:R1025Q;ENSP00000368301:R1004Q;ENSP00000398241:R1004Q ENSP00000304226:R1025Q R + 2 0 HIPK3 33330290 1.000000 0.71417 0.617000 0.29091 0.818000 0.46254 4.652000 0.61454 1.359000 0.45940 0.655000 0.94253 CGA TCGA-YH-A8SY-01A-11D-A377-08 HIPK3-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000255358.1 0 0 0 9 743 0 170 0 6.254984e-02 0 30 0 170 2 0 0 0 0 0 2 1 0.993885 9 734 0 166 2 0 0 0 0 170 2 -2.665725 1 1 0 0 1 1 2 3 1.963246 0 0.220000 3.360000 0.297297 0.120000 0.050000 0.220000 0.120000 0.133401 0.120000 0 0.080000 0.170000 OR51E1 143503 broad.mit.edu 37 11 4674426 4674426 + Missense_Mutation SNP A A T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr11:4674426A>T ENST00000396952.5 + 2 1320 c.670A>T c.(670-672)Att>Ttt p.I224F OR51E1_ENST00000530215.1_Intron NM_152430.3 NP_689643.2 Q8TCB6 O51E1_HUMAN olfactory receptor, family 51, subfamily E, member 1 30 Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227) ATATCTGCTTATTCTTAAGAC 0.483000 0 SO:0001583 missense ENST00000396952.5 1 1 hg19 CCDS31358.2 . . . . . . . . . . A 22.6 4.309349 0.81247 . . ENSG00000180785 ENST00000396952 T 0.57436 0.4 4.68 4.68 0.58851 GPCR, rhodopsin-like superfamily (1); 0.000000 0.56097 D 0.000021 T 0.81870 0.4914 H 0.97829 4.085 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.88235 0.2906 10 0.87932 D 0 . 13.3903 0.60821 1.0:0.0:0.0:0.0 . 223 Q8TCB6 O51E1_HUMAN F 224 ENSP00000380155:I224F ENSP00000380155:I224F I + 1 0 OR51E1 4631002 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 8.711000 0.91396 2.105000 0.64084 0.533000 0.62120 ATT TCGA-YH-A8SY-01A-11D-A377-08 OR51E1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347136.2 1 0 0 30 300 0 79 0 0 0 0 79 2 0 0 0 0 0 2 1 1.000000 30 294 0 77 2 0 0 0 0 79 2 -20.000000 1 1 0 0 1 1 2 3 1.950487 0 0.220000 3.360000 0.297297 0.920000 0.630000 1.000000 1.000000 0.897681 0.920000 1 0.770000 1.000000 UTP20 27340 broad.mit.edu 37 12 101755761 101755761 + Missense_Mutation SNP G G A rs76643734 byFrequency TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr12:101755761G>A ENST00000261637.4 + 44 5887 c.5713G>A c.(5713-5715)Gtt>Att p.V1905I NM_014503.2 NP_055318.2 O75691 UTP20_HUMAN UTP20, small subunit (SSU) processome component, homolog (yeast) 88 GACTTTCACCGTTCACATGCT 0.413000 0 SO:0001583 missense ENST00000261637.4 1 0 hg19 CCDS9081.1 3 0.0013736263736263737 3 0.006097560975609756 0 0.0 0 0.0 0 0.0 G 13.14 2.148199 0.37923 0.004993 0.0 ENSG00000120800 ENST00000261637 T 0.40225 1.04 6.03 5.05 0.67936 Armadillo-type fold (1); 0.179437 0.48767 D 0.000171 T 0.24392 0.0591 L 0.39633 1.23 0.48185 D 0.999606 B 0.26935 0.164 B 0.19148 0.024 T 0.03981 -1.0987 10 0.17832 T 0.49 -22.9366 13.7726 0.63036 0.099:0.0:0.901:0.0 . 1905 O75691 UTP20_HUMAN I 1905 ENSP00000261637:V1905I ENSP00000261637:V1905I V + 1 0 UTP20 100279892 1.000000 0.71417 0.860000 0.33809 0.458000 0.32498 4.835000 0.62781 2.854000 0.98071 0.655000 0.94253 GTT TCGA-YH-A8SY-01A-11D-A377-08 UTP20-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408242.1 1 0 1 132 416 0 88 1 3.490724e-01 4 1 0 88 2 0 0 0 0 0 2 1 1.000000 131 410 0 87 2 0 0 0 0 88 2 -3.021590 1 1 121412 90 55 1 0 3 3 1.842395 1 0.220000 3.360000 0.286694 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PTPN11 5781 broad.mit.edu 37 12 112926259 112926259 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr12:112926259C>T ENST00000351677.2 + 12 1590 c.1392C>T c.(1390-1392)ggC>ggT p.G464G NM_002834.3 NP_002825.3 Q06124 PTN11_HUMAN protein tyrosine phosphatase, non-receptor type 11 451 CTGGAATTGGCCGGACAGGGA 0.443000 Mis JMML, AML, MDS Noonan Syndrome Noonan syndrome Dom yes 12 12q24.1 5781 protein tyrosine phosphatase, non-receptor type 11 yes L 0 SO:0001819 synonymous_variant Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome ENST00000351677.2 0 1 hg19 CCDS9163.1 TCGA-YH-A8SY-01A-11D-A377-08 PTPN11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000259496.2 0 0 0 5 363 1 53 0 5.544371e-03 0 20 1 53 3 0 0 0 0 0 2 0 0.000825 5 354 1 53 21 0 0 0 1 53 2 -1.960411 0 1 0 0 1 0 3 3 1.842395 1 0.220000 3.360000 0.286694 0.150000 0.050000 1.000000 0.140000 0.259874 0.150000 0 0.090000 0.280000 GPR133 283383 broad.mit.edu 37 12 131622750 131622750 + Silent SNP C C T rs34765022 TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr12:131622750C>T ENST00000261654.5 + 24 3064 c.2505C>T c.(2503-2505)aaC>aaT p.N835N GPR133_ENST00000535015.1_Silent_p.N867N|GPR133_ENST00000540207.1_3'UTR|GPR133_ENST00000376682.4_Silent_p.N521N|GPR133_ENST00000543617.1_Silent_p.N354N NM_198827.3 NP_942122.2 Q6QNK2 GP133_HUMAN G protein-coupled receptor 133 p.N835N(1) 67 all_neural(191;0.0982)|Medulloblastoma(191;0.163) GCACCTCCAACGCGAAGCCCT 0.612000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000261654.5 1 1 hg19 CCDS9272.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 C 3.018 -0.202417 0.06219 0.0 2.33E-4 ENSG00000111452 ENST00000335486 . . . 4.46 -0.207 0.13189 . . . . . T 0.31979 0.0814 . . . 0.09310 N 1 . . . . . . T 0.30090 -0.9990 4 . . . . 8.0838 0.30760 0.0:0.47:0.0:0.53 rs34765022 . . . M 189 . . T + 2 0 GPR133 130188703 0.201000 0.23410 0.000000 0.03702 0.034000 0.12701 0.158000 0.16422 0.022000 0.15160 -0.254000 0.11334 ACG TCGA-YH-A8SY-01A-11D-A377-08 GPR133-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399356.1 1 0 1 35 140 0 23 0 1.088827e-01 0 3 0 23 2 0 0 0 0 0 2 1 1.000000 33 138 0 23 2 0 0 0 0 23 2 -20.000000 1 1 121412 62 45 1 0 3 3 1.842395 1 0.220000 3.360000 0.286694 0.990000 0.990000 1.000000 1.000000 0.999998 0.990000 1 0.990000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 C A C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-YH-A8SY-01A-11D-A377-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 74 267 0 76 1 8.377904e-01 6 8 0 76 2 1 1 86 314 0 316 2 1 1.000000 74 266 0 75 2 1 1 2275 5743 0 76 2 -20.000000 1 1 0 0 1 3 5 8 2.589570 1 0.220000 3.360000 0.475947 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 C1RL 51279 broad.mit.edu 37 12 7254566 7254566 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr12:7254566G>A ENST00000266542.4 - 3 510 c.418C>T c.(418-420)Cgc>Tgc p.R140C C1RL_ENST00000545280.1_Intron|C1RL_ENST00000544702.1_Missense_Mutation_p.R140C|C1RL_ENST00000545337.1_Missense_Mutation_p.R140C NM_016546.2 NP_057630.2 Q9NZP8 C1RL_HUMAN complement component 1, r subcomponent-like 16 GGCTGTGTGCGGAAGGTCAGC 0.622000 0 SO:0001583 missense ENST00000266542.4 0 1 hg19 CCDS8573.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 5.842|5.842 0.339585|0.339585 0.11069|0.11069 .|. .|. ENSG00000139178|ENSG00000139178 ENST00000534950|ENST00000266542;ENST00000396661;ENST00000544702;ENST00000543933;ENST00000545337 .|T;T;T;T .|0.30448 .|1.53;1.53;1.53;1.53 3.76|3.76 -0.133|-0.133 0.13485|0.13485 .|CUB (5); .|1.399260 .|0.04433 .|N .|0.369511 T|T 0.35799|0.35799 0.0944|0.0944 M|M 0.88640|0.88640 2.97|2.97 0.24098|0.24098 N|N 0.995883|0.995883 .|B;B;B .|0.33919 .|0.432;0.038;0.285 .|B;B;B .|0.27887 .|0.051;0.007;0.084 T|T 0.30268|0.30268 -0.9984|-0.9984 5|10 .|0.45353 .|T .|0.12 .|. 3.3529|3.3529 0.07159|0.07159 0.2989:0.0:0.5228:0.1783|0.2989:0.0:0.5228:0.1783 .|. .|140;140;140 .|F5GWF3;F5H7C8;Q9NZP8 .|.;.;C1RL_HUMAN L|C 39|140 .|ENSP00000266542:R140C;ENSP00000441885:R140C;ENSP00000437398:R140C;ENSP00000442611:R140C .|ENSP00000266542:R140C P|R -|- 2|1 0|0 C1RL|C1RL 7145842|7145842 0.147000|0.147000 0.22687|0.22687 0.103000|0.103000 0.21229|0.21229 0.289000|0.289000 0.27227|0.27227 0.193000|0.193000 0.17116|0.17116 -0.034000|-0.034000 0.13713|0.13713 -1.529000|-1.529000 0.00923|0.00923 CCG|CGC TCGA-YH-A8SY-01A-11D-A377-08 C1RL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398367.1 0 0 0 7 793 0 96 0 1.220433e-01 0 59 0 96 2 0 0 0 0 0 2 1 0.979379 6 780 0 95 2 0 0 0 0 96 2 -2.133026 0 1 121412 1 35 1 3 5 8 2.599697 1 0.220000 3.360000 0.480554 0.140000 0.030000 1.000000 0.130000 0.286300 0.140000 0 0.080000 1.000000 NR2C1 7181 broad.mit.edu 37 12 95451597 95451597 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr12:95451597G>A ENST00000333003.5 - 6 932 c.602C>T c.(601-603)gCc>gTc p.A201V NR2C1_ENST00000330677.7_Missense_Mutation_p.A201V|NR2C1_ENST00000545833.1_5'UTR|NR2C1_ENST00000393101.3_Missense_Mutation_p.A201V NM_003297.3 NP_003288.2 P13056 NR2C1_HUMAN nuclear receptor subfamily 2, group C, member 1 13 TGTTGAAGCGGCACAGTTGGA 0.343000 0 SO:0001583 missense ENST00000333003.5 0 1 hg19 CCDS9051.1 . . . . . . . . . . G 28.6 4.934588 0.92458 . . ENSG00000120798 ENST00000333003;ENST00000393101;ENST00000330677 D;D;D 0.92149 -2.98;-2.7;-2.7 5.6 5.6 0.85130 Nuclear hormone receptor, ligand-binding (1); 0.000000 0.85682 D 0.000000 D 0.95921 0.8672 M 0.73962 2.25 0.80722 D 1 D;D;D;D 0.89917 0.998;0.998;1.0;0.997 D;D;D;D 0.80764 0.989;0.994;0.989;0.985 D 0.95074 0.8207 10 0.44086 T 0.13 . 19.6188 0.95647 0.0:0.0:1.0:0.0 . 201;201;201;201 B6ZGT7;P13056-3;P13056-2;P13056 .;.;.;NR2C1_HUMAN V 201 ENSP00000333275:A201V;ENSP00000376813:A201V;ENSP00000328843:A201V ENSP00000328843:A201V A - 2 0 NR2C1 93975728 1.000000 0.71417 0.966000 0.40874 0.889000 0.51656 9.385000 0.97223 2.646000 0.89796 0.655000 0.94253 GCC TCGA-YH-A8SY-01A-11D-A377-08 NR2C1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407565.2 0 0 0 5 594 1 116 0 3.835748e-03 0 28 1 116 3 0 0 0 0 0 2 0 0.004459 5 586 1 115 18 0 0 0 1 116 2 -2.031101 0 1 0 0 1 0 3 3 1.842395 1 0.220000 3.360000 0.286694 0.090000 0.020000 1.000000 0.090000 0.205853 0.090000 0 0.050000 0.180000 ELF1 1997 broad.mit.edu 37 13 41523989 41523989 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr13:41523989G>A ENST00000239882.3 - 5 796 c.482C>T c.(481-483)gCa>gTa p.A161V ELF1_ENST00000442101.1_Missense_Mutation_p.A137V|ELF1_ENST00000498824.1_5'UTR NM_172373.3 NP_758961.1 P32519 ELF1_HUMAN E74-like factor 1 (ets domain transcription factor) 37 Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367) CGGTGAGTCTGCATATTTTTC 0.473000 0 SO:0001583 missense ENST00000239882.3 0 1 hg19 CCDS9374.1 . . . . . . . . . . G 10.11 1.259936 0.23051 . . ENSG00000120690 ENST00000442101;ENST00000239882 T;T 0.20332 2.11;2.08 5.84 -2.05 0.07321 . 0.767917 0.12353 N 0.476371 T 0.07369 0.0186 N 0.08118 0 0.09310 N 1 B;B 0.14012 0.004;0.009 B;B 0.09377 0.003;0.004 T 0.27971 -1.0058 10 0.33940 T 0.23 . 1.3405 0.02153 0.2585:0.0968:0.3523:0.2924 . 137;161 E9PDQ9;P32519 .;ELF1_HUMAN V 137;161 ENSP00000405580:A137V;ENSP00000239882:A161V ENSP00000239882:A161V A - 2 0 ELF1 40421989 0.001000 0.12720 0.033000 0.17914 0.656000 0.38851 0.096000 0.15147 -0.099000 0.12263 -0.282000 0.10007 GCA TCGA-YH-A8SY-01A-11D-A377-08 ELF1-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044654.3 0 0 0 6 791 0 101 0 4.949738e-02 0 39 0 101 2 0 0 0 0 0 2 1 0.963223 7 778 0 100 2 0 0 0 0 101 2 -1.969131 0 1 0 0 1 2 2 4 2.119557 1 0.220000 3.360000 0.360656 0.080000 0.010000 0.180000 0.080000 0.096851 0.080000 0 0.050000 0.130000 PCDH8 5100 broad.mit.edu 37 13 53420520 53420520 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr13:53420520G>A ENST00000377942.3 - 1 2255 c.2052C>T c.(2050-2052)cgC>cgT p.R684R PCDH8_ENST00000338862.4_Silent_p.R684R NM_002590.3 NP_002581.2 O95206 PCDH8_HUMAN protocadherin 8 36 Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173) CCCTGAACACGCGACCGGGTG 0.706000 GBM(36;25 841 9273 49207) 0 SO:0001819 synonymous_variant ENST00000377942.3 1 1 hg19 CCDS9438.1 TCGA-YH-A8SY-01A-11D-A377-08 PCDH8-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000045108.2 1 0 0 26 91 0 18 0 0 0 0 18 2 0 0 0 0 0 2 1 1.000000 26 91 0 18 2 0 0 0 0 18 2 -20.000000 1 1 0 0 1 2 2 4 2.119557 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PCDH17 27253 broad.mit.edu 37 13 58208913 58208913 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr13:58208913G>A ENST00000377918.3 + 1 2259 c.2233G>A c.(2233-2235)Gcc>Acc p.A745T NM_001040429.2 NP_001035519.1 O14917 PCD17_HUMAN protocadherin 17 120 Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132) CTGCCGCATCGCCGAGTACAG 0.547000 Melanoma(72;952 1291 1619 12849 33676) 0 SO:0001583 missense ENST00000377918.3 1 1 hg19 CCDS31986.1 . . . . . . . . . . G 16.33 3.092421 0.55968 . . ENSG00000118946 ENST00000377918 T 0.56444 0.46 5.55 5.55 0.83447 . 0.097709 0.64402 D 0.000001 T 0.58680 0.2139 M 0.69823 2.125 0.53005 D 0.999961 P;P 0.47302 0.835;0.893 B;B 0.43331 0.416;0.285 T 0.60835 -0.7184 9 . . . . 19.5072 0.95124 0.0:0.0:1.0:0.0 . 745;745 O14917-2;O14917 .;PCD17_HUMAN T 745 ENSP00000367151:A745T . A + 1 0 PCDH17 57106914 1.000000 0.71417 0.992000 0.48379 0.917000 0.54804 7.968000 0.87980 2.607000 0.88179 0.591000 0.81541 GCC TCGA-YH-A8SY-01A-11D-A377-08 PCDH17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045139.1 1 0 1 26 170 0 53 0 5.199635e-02 0 3 0 53 2 0 0 0 0 0 2 1 1.000000 26 168 0 52 2 0 0 0 0 53 2 -13.396410 1 0 0 0 1 2 2 4 2.119557 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 0.998392 0.990000 1 0.990000 1.000000 RYR3 6263 broad.mit.edu 37 15 34040439 34040439 + Missense_Mutation SNP G G T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr15:34040439G>T ENST00000389232.4 + 54 8184 c.8114G>T c.(8113-8115)cGa>cTa p.R2705L RYR3_ENST00000415757.3_Missense_Mutation_p.R2705L NM_001036.3 NP_001027.3 Q15413 RYR3_HUMAN ryanodine receptor 3 p.R2705Q(2) 311 all_lung(180;7.18e-09) GAGAAGCTTCGAAGTGTGTCC 0.577000 2 Substitution - Missense(2) SO:0001583 missense ENST00000389232.4 1 1 hg19 CCDS45210.1 . . . . . . . . . . G 23.4 4.410408 0.83340 . . ENSG00000198838 ENST00000389232;ENST00000415757;ENST00000361728 D;D 0.96830 -4.14;-4.14 5.18 5.18 0.71444 . 0.071281 0.56097 D 0.000040 D 0.94155 0.8125 L 0.41492 1.28 0.58432 D 0.999992 B;B 0.32543 0.375;0.009 B;B 0.33392 0.163;0.018 D 0.93169 0.6564 10 0.49607 T 0.09 . 18.8778 0.92345 0.0:0.0:1.0:0.0 . 2705;2705 Q15413-2;Q15413 .;RYR3_HUMAN L 2705 ENSP00000373884:R2705L;ENSP00000399610:R2705L ENSP00000354735:R2705L R + 2 0 RYR3 31827731 1.000000 0.71417 0.991000 0.47740 0.897000 0.52465 7.158000 0.77470 2.679000 0.91253 0.655000 0.94253 CGA TCGA-YH-A8SY-01A-11D-A377-08 RYR3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000417514.1 1 0 0 15 135 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.999883 15 133 0 34 2 0 0 0 0 36 2 -8.165503 1 1 0 0 1 2 3 5 1.937316 0 0.220000 3.360000 0.300762 0.990000 0.630000 1.000000 1.000000 0.942475 0.990000 1 0.830000 1.000000 CHST14 113189 broad.mit.edu 37 15 40764233 40764233 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr15:40764233G>A ENST00000306243.5 + 1 1074 c.821G>A c.(820-822)cGc>cAc p.R274H CHST14_ENST00000559991.1_Missense_Mutation_p.R249H NM_130468.3 NP_569735.1 Q8NCH0 CHSTE_HUMAN carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 14 4 all_cancers(109;2.34e-14)|all_epithelial(112;1.08e-11)|Lung NSC(122;2.95e-09)|all_lung(180;6.03e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243) GACCCTGAGCGCATGAATGAG 0.587000 0 SO:0001583 missense ENST00000306243.5 0 1 hg19 CCDS10059.1 . . . . . . . . . . G 15.22 2.769808 0.49680 . . ENSG00000169105 ENST00000306243 T 0.75260 -0.92 4.92 3.02 0.34903 . 0.133960 0.44097 N 0.000487 T 0.61714 0.2369 L 0.40543 1.245 0.43403 D 0.995531 B 0.09022 0.002 B 0.08055 0.003 T 0.52859 -0.8519 10 0.28530 T 0.3 -11.2791 8.6952 0.34291 0.1901:0.0:0.8099:0.0 . 274 Q8NCH0 CHSTE_HUMAN H 274 ENSP00000307297:R274H ENSP00000307297:R274H R + 2 0 CHST14 38551525 0.991000 0.36638 0.986000 0.45419 0.982000 0.71751 1.809000 0.38922 0.650000 0.30769 0.655000 0.94253 CGC TCGA-YH-A8SY-01A-11D-A377-08 CHST14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252251.1 0 0 0 5 507 0 83 0 4.053859e-01 0 123 0 83 2 0 0 0 0 0 2 1 0.935871 5 501 0 83 2 0 0 0 0 83 2 -2.235578 0 1 0 0 1 2 3 5 1.937316 0 0.220000 3.360000 0.300762 0.120000 0.030000 1.000000 0.090000 0.311711 0.120000 0 0.070000 1.000000 CAPN3 825 broad.mit.edu 37 15 42695097 42695097 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr15:42695097C>T ENST00000397163.3 + 13 1861 c.1642C>T c.(1642-1644)Cgc>Tgc p.R548C CAPN3_ENST00000397204.4_5'Flank|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000569136.1_5'Flank|CAPN3_ENST00000356316.3_Missense_Mutation_p.R461C|CAPN3_ENST00000349748.3_Missense_Mutation_p.R500C|CAPN3_ENST00000337571.4_5'Flank|CAPN3_ENST00000561817.1_5'Flank|CAPN3_ENST00000397200.4_Missense_Mutation_p.R36C|CAPN3_ENST00000318023.7_Missense_Mutation_p.R548C|CAPN3_ENST00000357568.3_Missense_Mutation_p.R548C NM_000070.2 NP_000061.1 P20807 CAN3_HUMAN calpain 3, (p94) 47 all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152) CCAGCGCTTCCGCCTGCCTCC 0.592000 0 SO:0001583 missense ENST00000397163.3 1 1 hg19 CCDS45245.1 . . . . . . . . . . C 20.4 3.987438 0.74589 0.0 1.16E-4 ENSG00000092529 ENST00000356316;ENST00000337522;ENST00000397163;ENST00000357568;ENST00000349748;ENST00000318023;ENST00000397200 D;D;D;D;D;D 0.88046 -2.33;-2.33;-2.33;-2.33;-2.33;-2.33 4.87 4.87 0.63330 Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1); 0.000000 0.85682 U 0.000000 D 0.82481 0.5046 L 0.38649 1.16 0.80722 D 1 B;B;B;B;B;B 0.33857 0.102;0.208;0.083;0.206;0.429;0.053 B;B;B;B;B;B 0.31290 0.031;0.077;0.018;0.032;0.127;0.075 T 0.82752 -0.0302 10 0.49607 T 0.09 . 18.1939 0.89814 0.0:1.0:0.0:0.0 . 413;461;500;548;548;461 C6EVS4;C6EVS3;P20807-2;P20807-3;P20807;Q762C8 .;.;.;.;CAN3_HUMAN;. C 461;36;548;548;500;548;36 ENSP00000348667:R461C;ENSP00000380349:R548C;ENSP00000350181:R548C;ENSP00000183936:R500C;ENSP00000326281:R548C;ENSP00000380384:R36C ENSP00000326281:R548C R + 1 0 CAPN3 40482389 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 5.733000 0.68571 2.527000 0.85204 0.455000 0.32223 CGC TCGA-YH-A8SY-01A-11D-A377-08 CAPN3-009 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000421075.1 1 0 1 80 418 0 75 0 1.262146e-01 0 4 0 75 2 0 0 0 0 0 2 1 1.000000 78 415 0 75 2 0 0 0 0 75 2 -2.722726 1 1 121412 1 41 1 2 3 5 1.937316 0 0.220000 3.360000 0.300762 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 GLCE 26035 broad.mit.edu 37 15 69553616 69553616 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr15:69553616G>A ENST00000261858.2 + 4 1005 c.777G>A c.(775-777)gcG>gcA p.A259A GLCE_ENST00000559420.2_Silent_p.A195A|GLCE_ENST00000559500.1_3'UTR NM_015554.1 NP_056369.1 O94923 GLCE_HUMAN glucuronic acid epimerase 18 GCTTTATGGCGAATGTGGCTG 0.393000 0 SO:0001819 synonymous_variant ENST00000261858.2 0 1 hg19 CCDS32277.1 TCGA-YH-A8SY-01A-11D-A377-08 GLCE-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 5 555 0 117 0 1.327408e-04 0 2 0 117 2 0 0 0 0 0 2 1 0.933860 5 541 0 116 2 0 0 0 0 117 2 -2.510514 1 1 0 0 1 2 3 5 1.937316 0 0.220000 3.360000 0.300762 0.110000 0.030000 1.000000 0.090000 0.303882 0.110000 0 0.060000 1.000000 CASKIN1 57524 broad.mit.edu 37 16 2228602 2228602 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr16:2228602G>A ENST00000343516.6 - 20 4337 c.4245C>T c.(4243-4245)atC>atT p.I1415I NM_020764.3 NP_065815.1 Q8WXD9 CSKI1_HUMAN CASK interacting protein 1 28 ACATGCTGCCGATGTCGTCCA 0.741000 0 SO:0001819 synonymous_variant ENST00000343516.6 0 1 hg19 CCDS42103.1 TCGA-YH-A8SY-01A-11D-A377-08 CASKIN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000435055.1 1 0 0 12 153 0 14 0 0 0 0 14 2 0 0 0 0 0 2 1 0.999169 12 151 0 13 2 0 0 0 0 14 2 -3.319498 1 1 0 0 1 1 2 3 1.978101 0 0.220000 3.360000 0.297297 0.750000 0.410000 1.000000 1.000000 0.756480 0.750000 0 0.560000 0.970000 CREBBP 1387 broad.mit.edu 37 16 3823809 3823809 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr16:3823809G>A ENST00000262367.5 - 13 3215 c.2406C>T c.(2404-2406)tcC>tcT p.S802S CREBBP_ENST00000382070.3_Silent_p.S764S NM_004380.2 NP_004371.2 Q92793 CBP_HUMAN CREB binding protein 295 Ovarian(90;0.0266) TCGCCCCGCTGGATGACGGGA 0.607000 T, N, F, Mis, O MLL, MORF, RUNXBP2 ALL, AML, DLBCL, B-NHL Rubinstein-Taybi syndrome Dom/Rec yes 16 16p13.3 1387 CREB binding protein (CBP) yes L 0 SO:0001819 synonymous_variant ENST00000262367.5 1 1 hg19 CCDS10509.1 TCGA-YH-A8SY-01A-11D-A377-08 CREBBP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251591.2 1 0 1 55 214 0 49 1 9.046553e-01 6 12 0 49 2 0 0 0 0 0 2 1 1.000000 55 209 0 48 2 0 0 0 0 49 2 -3.411199 1 1 121406 1 33 1 1 2 3 1.978101 0 0.220000 3.360000 0.297297 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 GPT2 84706 broad.mit.edu 37 16 46943627 46943627 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr16:46943627G>A ENST00000340124.4 + 6 720 c.608G>A c.(607-609)gGc>gAc p.G203D GPT2_ENST00000440783.2_Missense_Mutation_p.G103D NM_133443.2 NP_597700.1 Q8TD30 ALAT2_HUMAN glutamic pyruvate transaminase (alanine aminotransferase) 2 23 all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522) L-Alanine(DB00160)|Phenelzine(DB00780) TCCGGGGGCGGCAAGTCACGG 0.537000 0 SO:0001583 missense ENST00000340124.4 0 1 hg19 CCDS10725.1 . . . . . . . . . . G 11.78 1.740372 0.30865 . . ENSG00000166123 ENST00000340124;ENST00000440783 T;T 0.22134 1.97;2.87 5.12 5.12 0.69794 Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1); 0.052137 0.85682 D 0.000000 T 0.15565 0.0375 N 0.21448 0.665 0.80722 D 1 B 0.15141 0.012 B 0.20767 0.031 T 0.06770 -1.0808 10 0.07813 T 0.8 . 18.7502 0.91810 0.0:0.0:1.0:0.0 . 203 Q8TD30 ALAT2_HUMAN D 203;103 ENSP00000345282:G203D;ENSP00000413804:G103D ENSP00000345282:G203D G + 2 0 GPT2 45501128 1.000000 0.71417 0.998000 0.56505 0.298000 0.27526 6.049000 0.71053 2.664000 0.90586 0.655000 0.94253 GGC TCGA-YH-A8SY-01A-11D-A377-08 GPT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255741.2 0 0 0 4 275 0 53 0 7.272195e-03 0 7 0 53 2 0 0 0 0 0 2 1 0.887642 4 272 0 53 2 0 0 0 0 53 2 -2.670567 1 1 0 0 1 1 2 3 1.978101 0 0.220000 3.360000 0.297297 0.160000 0.040000 0.350000 0.150000 0.178021 0.160000 0 0.090000 0.250000 CIRH1A 84916 broad.mit.edu 37 16 69197063 69197063 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr16:69197063C>T ENST00000314423.7 + 14 1806 c.1629C>T c.(1627-1629)atC>atT p.I543I CIRH1A_ENST00000563094.1_Silent_p.I543I|CIRH1A_ENST00000352319.4_Silent_p.I428I Q969X6 CIR1A_HUMAN cirrhosis, autosomal recessive 1A (cirhin) 16 ACCTTGTCATCGCTCATTCGG 0.498000 Melanoma(69;1156 1278 4951 8715 52012) 0 SO:0001819 synonymous_variant ENST00000314423.7 1 1 hg19 CCDS10872.1 TCGA-YH-A8SY-01A-11D-A377-08 CIRH1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268950.2 1 0 0 57 551 0 126 1 9.998553e-01 25 100 0 126 2 0 0 0 0 0 2 1 1.000000 57 546 0 126 2 0 0 0 0 126 2 -16.039560 1 1 121412 12 47 1 1 2 3 1.980475 0 0.220000 3.360000 0.288126 0.950000 0.720000 1.000000 1.000000 0.926942 0.950000 1 0.820000 1.000000 MTSS1L 92154 broad.mit.edu 37 16 70713713 70713713 + Nonsense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr16:70713713G>A ENST00000338779.6 - 5 632 c.358C>T c.(358-360)Cag>Tag p.Q120* NM_138383.2 NP_612392.1 Q765P7 MTSSL_HUMAN metastasis suppressor 1-like 7 TTGTCCAGCTGGTTGGCCGCC 0.697000 0 SO:0001587 stop_gained ENST00000338779.6 0 1 hg19 CCDS32476.1 . . . . . . . . . . G 34 5.394476 0.96009 . . ENSG00000132613 ENST00000254951;ENST00000338779 . . . 4.84 4.84 0.62591 . 0.250943 0.41294 D 0.000908 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.07175 T 0.84 -5.8949 12.979 0.58554 0.0:0.0:0.8383:0.1617 . . . . X 120 . ENSP00000254951:Q120X Q - 1 0 MTSS1L 69271214 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 7.575000 0.82447 2.250000 0.74265 0.393000 0.25936 CAG TCGA-YH-A8SY-01A-11D-A377-08 MTSS1L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000434927.3 1 0 0 12 77 0 10 1 9.929075e-01 5 53 0 10 2 0 0 0 0 0 2 1 0.999185 12 74 0 10 2 0 0 0 0 10 2 -19.766950 1 1 0 0 1 1 2 3 1.980475 0 0.220000 3.360000 0.288126 0.990000 0.770000 1.000000 1.000000 0.983669 0.990000 1 0.990000 1.000000 ANKRD11 29123 broad.mit.edu 37 16 89347349 89347349 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr16:89347349G>A ENST00000301030.4 - 9 6061 c.5601C>T c.(5599-5601)tgC>tgT p.C1867C ANKRD11_ENST00000378330.2_Silent_p.C1867C NM_001256183.1|NM_013275.5 NP_001243112.1|NP_037407.4 Q6UB99 ANR11_HUMAN ankyrin repeat domain 11 83 all_hematologic(23;0.00824)|Colorectal(91;0.0475) CAGCCGGTGGGCAGTGCAAAG 0.622000 0 SO:0001819 synonymous_variant ENST00000301030.4 1 1 hg19 CCDS32513.1 TCGA-YH-A8SY-01A-11D-A377-08 ANKRD11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000430462.3 1 0 0 21 235 0 39 1 8.797368e-01 6 38 0 39 2 0 0 0 0 0 2 1 0.999998 20 235 0 39 2 0 0 0 0 39 2 -20.000000 1 1 121362 1 29 1 1 2 3 1.965588 0 0.220000 3.360000 0.297297 0.830000 0.530000 1.000000 1.000000 0.831076 0.830000 0 0.670000 1.000000 HOXB5 3215 broad.mit.edu 37 17 46670813 46670813 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr17:46670813C>T ENST00000239151.5 - 1 510 c.232G>A c.(232-234)Gcg>Acg p.A78T HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000460041.1_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000467155.2_RNA NM_002147.3 NP_002138.1 P09067 HXB5_HUMAN homeobox B5 3 TGGGCGGGCGCGGGGAAGGCG 0.687000 0 SO:0001583 missense ENST00000239151.5 0 1 hg19 CCDS11530.1 . . . . . . . . . . C 11.07 1.530435 0.27387 . . ENSG00000120075 ENST00000239151 D 0.92299 -3.01 5.44 0.916 0.19373 . 0.579461 0.18522 N 0.138741 D 0.82545 0.5060 N 0.21282 0.65 0.29926 N 0.822337 B 0.15930 0.015 B 0.06405 0.002 T 0.72811 -0.4180 10 0.32370 T 0.25 . 6.425 0.21764 0.2685:0.5605:0.0977:0.0732 . 78 P09067 HXB5_HUMAN T 78 ENSP00000239151:A78T ENSP00000239151:A78T A - 1 0 HOXB5 44025812 0.126000 0.22350 0.998000 0.56505 0.904000 0.53231 0.035000 0.13797 0.663000 0.31027 -0.300000 0.09419 GCG TCGA-YH-A8SY-01A-11D-A377-08 HOXB5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000358148.2 1 0 0 13 92 0 18 1 8.680183e-01 3 25 0 18 2 0 0 0 0 0 2 1 0.999547 13 88 0 18 2 0 0 0 0 18 2 -19.984010 1 1 0 0 1 3 3 6 2.173455 1 0.220000 3.360000 0.376399 0.990000 0.850000 1.000000 1.000000 0.991403 0.990000 1 0.990000 1.000000 TP53 7157 broad.mit.edu 37 17 7578406 7578406 + Missense_Mutation SNP C C T rs28934578 TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr17:7578406C>T ENST00000269305.4 - 5 713 c.524G>A c.(523-525)cGc>cAc p.R175H TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H 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.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GTGGGGGCAGCGCCTCACAAC 0.652000 R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY) 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 980 Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3) GRCh37 CM062017|CM951224 TP53 M rs28934578 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 . . . . . . . . . . C 31 5.079737 0.94050 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 D;D;D;D;D;D;D;D 0.99889 -7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55 5.41 5.41 0.78517 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.101149 0.64402 D 0.000008 D 0.99908 0.9956 M 0.92784 3.345 0.80722 A 1 D;P;D;D;P;B;D 0.89917 0.999;0.578;1.0;0.998;0.632;0.213;0.999 D;B;D;D;B;B;D 0.91635 0.985;0.26;0.999;0.921;0.378;0.144;0.939 D 0.96278 0.9204 9 0.87932 D 0 -11.8679 17.0767 0.86588 0.0:1.0:0.0:0.0 rs28934578 136;175;175;82;175;175;175 B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. H 175;175;175;175;175;175;164;82;43;82;43 ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H ENSP00000269305:R175H R - 2 0 TP53 7519131 1.000000 0.71417 0.989000 0.46669 0.795000 0.44927 6.042000 0.70996 2.702000 0.92279 0.655000 0.94253 CGC TCGA-YH-A8SY-01A-11D-A377-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 56 251 0 32 1 9.977413e-01 17 27 0 32 2 1 1 197 637 2 779 8 1 1.000000 56 249 0 31 2 0 0 0 0 32 2 -3.134589 1 1 121412 1 41 1 0 2 2 1.769858 1 0.220000 3.360000 0.220000 0.990000 0.990000 1.000000 1.000000 0.999997 0.990000 1 0.990000 1.000000 MALT1 10892 broad.mit.edu 37 18 56409220 56409220 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr18:56409220G>A ENST00000348428.3 + 14 1985 c.1727G>A c.(1726-1728)cGg>cAg p.R576Q MALT1_ENST00000345724.3_Missense_Mutation_p.R565Q|RP11-126O1.4_ENST00000588835.1_RNA NM_006785.2|NM_173844.1 NP_006776.1|NP_776216.1 Q9UDY8 MALT1_HUMAN mucosa associated lymphoid tissue lymphoma translocation gene 1 12 TCTCTTGTGCGGAATCTACAG 0.378000 T BIRC3 MALT Dom yes 18 18q21 10892 mucosa associated lymphoid tissue lymphoma translocation gene 1 L 0 SO:0001583 missense ENST00000348428.3 0 1 hg19 CCDS11967.1 . . . . . . . . . . G 25.0 4.587606 0.86851 . . ENSG00000172175 ENST00000348428;ENST00000345724 T;T 0.14144 2.54;2.53 5.53 5.53 0.82687 . 0.112546 0.64402 D 0.000012 T 0.35128 0.0921 L 0.59436 1.845 0.34914 D 0.747776 D;D 0.89917 1.0;0.999 D;P 0.67725 0.953;0.899 T 0.34551 -0.9824 10 0.62326 D 0.03 -17.4564 19.053 0.93053 0.0:0.0:1.0:0.0 . 565;576 Q9UDY8-2;Q9UDY8 .;MALT1_HUMAN Q 576;565 ENSP00000319279:R576Q;ENSP00000304161:R565Q ENSP00000304161:R565Q R + 2 0 MALT1 54560200 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 4.500000 0.60387 2.600000 0.87896 0.446000 0.29264 CGG TCGA-YH-A8SY-01A-11D-A377-08 MALT1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256132.2 0 0 0 4 273 0 83 0 4.992063e-02 0 19 0 83 2 0 0 0 0 0 2 1 0.888482 4 270 0 83 2 0 0 0 0 83 2 -2.516217 1 1 0 0 1 0 1 1 1.564562 1 0.220000 3.360000 0.130047 0.120000 0.040000 0.280000 0.120000 0.142560 0.120000 0 0.070000 0.200000 ATP1A3 478 broad.mit.edu 37 19 42471441 42471441 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr19:42471441G>A ENST00000302102.5 - 22 3123 c.2973C>T c.(2971-2973)taC>taT p.Y991Y ATP1A3_ENST00000602133.1_Silent_p.Y961Y|ATP1A3_ENST00000545399.1_Silent_p.Y1004Y|ATP1A3_ENST00000543770.1_Silent_p.Y1002Y NM_152296.4 NP_689509.1 P13637 AT1A3_HUMAN ATPase, Na+/K+ transporting, alpha 3 polypeptide 52 GGATTTCGTCGTAGACGAAGA 0.652000 0 SO:0001819 synonymous_variant ENST00000302102.5 1 1 hg19 CCDS12594.1 TCGA-YH-A8SY-01A-11D-A377-08 ATP1A3-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000268107.1 1 0 1 37 154 0 20 1 3.958122e-02 2 0 0 20 2 0 0 0 0 0 2 1 1.000000 37 152 0 20 2 0 0 0 0 20 2 -20.000000 1 1 121406 5 37 1 2 2 4 2.150199 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 WDR77 79084 broad.mit.edu 37 1 111991320 111991320 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:111991320G>A ENST00000235090.5 - 2 428 c.222C>T c.(220-222)tcC>tcT p.S74S ATP5F1_ENST00000483994.1_5'Flank|Y_RNA_ENST00000363020.1_RNA|ATP5F1_ENST00000369722.3_5'Flank|WDR77_ENST00000411751.2_Silent_p.S74S|WDR77_ENST00000497278.1_5'Flank NM_024102.2 NP_077007.1 Q9BQA1 MEP50_HUMAN WD repeat domain 77 10 all_cancers(81;0.000902)|all_epithelial(167;0.00056)|all_lung(203;0.00277)|Lung NSC(277;0.0043) GGACTCCGGCGGAGCAGAAGC 0.622000 0 SO:0001819 synonymous_variant ENST00000235090.5 0 1 hg19 CCDS835.1 . . . . . . . . . . G 12.25 1.880414 0.33255 . . ENSG00000116455 ENST00000449340 . . . 5.73 -1.3 0.09259 . . . . . T 0.22898 0.0553 . . . 0.80722 D 1 . . . . . . T 0.30679 -0.9970 4 . . . -18.7416 1.0705 0.01620 0.3009:0.1646:0.3524:0.1822 . . . . L 11 . . P - 2 0 WDR77 111792843 0.818000 0.29161 0.995000 0.50966 0.991000 0.79684 -0.097000 0.11042 0.077000 0.16863 0.561000 0.74099 CCG TCGA-YH-A8SY-01A-11D-A377-08 WDR77-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032465.1 0 0 0 4 174 0 33 0 2.260210e-01 0 32 0 33 2 0 0 0 0 0 2 1 0.875641 3 164 0 32 2 0 0 0 0 33 2 -5.907009 1 0 0 0 1 1 2 3 1.963322 0 0.220000 3.360000 0.295902 0.250000 0.080000 0.600000 0.230000 0.283117 0.250000 0 0.150000 0.400000 NGF 4803 broad.mit.edu 37 1 115829176 115829176 + Nonsense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:115829176G>A ENST00000369512.2 - 3 409 c.241C>T c.(241-243)Cga>Tga p.R81* RP4-663N10.1_ENST00000425449.1_RNA NM_002506.2 NP_002497.2 P01138 NGF_HUMAN nerve growth factor (beta polypeptide) 13 Lung SC(450;0.211) all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05) Clenbuterol(DB01407) GAACGGAGTCGCCGCTTTTTA 0.642000 0 SO:0001587 stop_gained ENST00000369512.2 0 1 hg19 CCDS882.1 . . . . . . . . . . G 25.5 4.640906 0.87859 . . ENSG00000134259 ENST00000369512 . . . 5.06 3.05 0.35203 . 0.058013 0.64402 D 0.000003 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -12.0674 11.9013 0.52685 0.0:0.0:0.5284:0.4716 . . . . X 81 . ENSP00000358525:R81X R - 1 2 NGF 115630699 0.998000 0.40836 0.836000 0.33094 0.748000 0.42578 3.935000 0.56560 0.536000 0.28733 0.467000 0.42956 CGA TCGA-YH-A8SY-01A-11D-A377-08 NGF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032832.1 1 0 1 23 144 0 30 0 2.088409e-02 1 1 0 30 2 0 0 0 0 0 2 1 1.000000 22 141 0 29 2 0 0 0 0 30 2 -3.328489 1 1 0 0 1 1 2 3 1.963322 0 0.220000 3.360000 0.295902 0.990000 0.920000 1.000000 1.000000 0.995616 0.990000 1 0.990000 1.000000 ADAM30 11085 broad.mit.edu 37 1 120436918 120436918 + Missense_Mutation SNP G G A rs115551394 byFrequency TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:120436918G>A ENST00000369400.1 - 1 2200 c.2042C>T c.(2041-2043)gCg>gTg p.A681V NM_021794.3 NP_068566.2 Q9UKF2 ADA30_HUMAN ADAM metallopeptidase domain 30 38 all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234) all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138) CGAGGGAATCGCCCCTCTGAG 0.473000 0 SO:0001583 missense ENST00000369400.1 1 0 hg19 CCDS907.1 4 0.0018315018315018315 1 0.0020325203252032522 3 0.008287292817679558 0 0.0 0 0.0 G 8.508 0.865747 0.17250 0.005447 9.3E-4 ENSG00000134249 ENST00000369400;ENST00000543066 T 0.01178 5.22 5.05 -5.85 0.02311 . 0.692560 0.11763 U 0.531905 T 0.00144 0.0004 N 0.03608 -0.345 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.41787 -0.9489 10 0.29301 T 0.29 . 0.2119 0.00157 0.2303:0.2226:0.2471:0.3 . 681 Q9UKF2 ADA30_HUMAN V 681 ENSP00000358407:A681V ENSP00000358407:A681V A - 2 0 ADAM30 120238441 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.486000 0.06513 -1.165000 0.02786 -2.744000 0.00126 GCG TCGA-YH-A8SY-01A-11D-A377-08 ADAM30-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033678.1 1 0 1 60 246 0 103 0 0 0 0 103 2 0 0 0 0 0 2 1 1.000000 58 245 0 103 2 0 0 0 0 103 2 -2.865375 1 1 121412 189 55 1 1 2 3 1.963322 0 0.220000 3.360000 0.295902 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 KLHDC7A 127707 broad.mit.edu 37 1 18809344 18809344 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:18809344C>T ENST00000400664.1 + 1 1921 c.1869C>T c.(1867-1869)ttC>ttT p.F623F NM_152375.2 NP_689588.2 Q5VTJ3 KLD7A_HUMAN kelch domain containing 7A 22 Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255) GTGACACGTTCGCCCTGGCGC 0.667000 0 SO:0001819 synonymous_variant ENST00000400664.1 1 1 hg19 CCDS185.2 TCGA-YH-A8SY-01A-11D-A377-08 KLHDC7A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000006923.3 1 0 1 13 101 0 28 0 0 0 0 28 2 0 0 0 0 0 2 1 0.999452 11 96 0 24 2 0 0 0 0 28 2 -19.863460 1 1 0 0 1 1 2 3 1.984081 0 0.220000 3.360000 0.297297 0.990000 0.660000 1.000000 1.000000 0.958633 0.990000 1 0.890000 1.000000 SYT2 127833 broad.mit.edu 37 1 202568444 202568444 + Missense_Mutation SNP T T G TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:202568444T>G ENST00000367267.1 - 8 1147 c.955A>C c.(955-957)Aag>Cag p.K319Q SYT2_ENST00000367268.4_Missense_Mutation_p.K319Q NM_001136504.1 NP_001129976.1 Q8N9I0 SYT2_HUMAN synaptotagmin II 29 BRCA - Breast invasive adenocarcinoma(75;0.169) Botulinum Toxin Type B(DB00042) TTGAGCCTCTTGCCATTCTGC 0.532000 0 SO:0001583 missense ENST00000367267.1 1 1 hg19 CCDS1427.1 . . . . . . . . . . T 28.0 4.881455 0.91740 . . ENSG00000143858 ENST00000367268;ENST00000367267 T;T 0.72835 -0.69;-0.69 5.21 5.21 0.72293 C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1); 0.102327 0.64402 D 0.000003 T 0.72977 0.3528 N 0.25060 0.705 0.80722 D 1 D 0.60575 0.988 D 0.63192 0.912 T 0.76971 -0.2761 10 0.66056 D 0.02 . 14.7397 0.69445 0.0:0.0:0.0:1.0 . 319 Q8N9I0 SYT2_HUMAN Q 319 ENSP00000356237:K319Q;ENSP00000356236:K319Q ENSP00000356236:K319Q K - 1 0 SYT2 200835067 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 7.897000 0.87356 1.957000 0.56846 0.460000 0.39030 AAG TCGA-YH-A8SY-01A-11D-A377-08 SYT2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000099157.1 1 0 1 58 429 0 108 0 0 0 0 108 2 0 0 0 0 0 2 1 1.000000 58 425 0 107 2 0 0 0 0 108 2 -19.993890 1 1 0 0 1 3 3 6 2.322195 1 0.220000 3.360000 0.417389 0.990000 0.990000 1.000000 1.000000 0.999919 0.990000 1 0.990000 1.000000 USH2A 7399 broad.mit.edu 37 1 215987140 215987140 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:215987140C>T ENST00000307340.3 - 49 10063 c.9677G>A c.(9676-9678)cGa>cAa p.R3226Q USH2A_ENST00000366943.2_Missense_Mutation_p.R3226Q NM_206933.2 NP_996816 O75445 USH2A_HUMAN Usher syndrome 2A (autosomal recessive, mild) 527 CTCCTGTATTCGGCCACCACA 0.453000 HNSCC(13;0.011) 0 SO:0001583 missense ENST00000307340.3 1 1 hg19 CCDS31025.1 . . . . . . . . . . C 14.84 2.656431 0.47467 . . ENSG00000042781 ENST00000307340;ENST00000366943 T;T 0.12255 2.71;2.7 5.8 1.02 0.19986 Fibronectin, type III (2); 0.228496 0.22457 U 0.059807 T 0.04318 0.0119 N 0.21240 0.645 0.09310 N 1 P 0.48503 0.911 B 0.31946 0.138 T 0.30621 -0.9972 10 0.08599 T 0.76 . 2.9934 0.05990 0.3129:0.3248:0.0:0.3623 . 3226 O75445 USH2A_HUMAN Q 3226 ENSP00000305941:R3226Q;ENSP00000355910:R3226Q ENSP00000305941:R3226Q R - 2 0 USH2A 214053763 0.340000 0.24792 0.341000 0.25589 0.810000 0.45777 0.862000 0.27899 0.596000 0.29794 -0.282000 0.10007 CGA TCGA-YH-A8SY-01A-11D-A377-08 USH2A-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128138.1 1 0 1 105 374 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 1.000000 103 368 0 67 2 0 0 0 0 68 2 -3.997968 1 1 0 0 1 2 3 5 2.302493 1 0.220000 3.360000 0.412075 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MECR 51102 broad.mit.edu 37 1 29543100 29543100 + Splice_Site SNP C C A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:29543100C>A ENST00000263702.6 - 2 299 c.274G>T c.(274-276)Gga>Tga p.G92* MECR_ENST00000373791.3_Splice_Site_p.G16*|MECR_ENST00000489248.1_5'UTR Q9BV79 MECR_HUMAN mitochondrial trans-2-enoyl-CoA reductase 11 Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123) CCAAGGTTACCTTGGATCATA 0.458000 0 SO:0001630 splice_region_variant ENST00000263702.6 0 1 hg19 CCDS30659.1 . . . . . . . . . . C 38 7.283297 0.98186 . . ENSG00000116353 ENST00000373791;ENST00000263702;ENST00000373792 . . . 5.38 5.38 0.77491 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . . . . . 14.5119 0.67794 0.0:1.0:0.0:0.0 . . . . X 16;92;4 . . G - 1 0 MECR 29415687 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 6.673000 0.74482 2.802000 0.96397 0.655000 0.94253 GGA TCGA-YH-A8SY-01A-11D-A377-08 MECR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000130740.1 0 0 0 169 710 0 144 0 9.796430e-01 0 28 0 144 2 0 0 0 0 0 2 1 1.000000 166 704 0 144 2 0 0 0 0 144 2 -3.293877 1 1 0 0 1 1 2 3 1.963322 0 0.220000 3.360000 0.295902 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 STK40 83931 broad.mit.edu 37 1 36807372 36807372 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:36807372C>T ENST00000373129.3 - 12 1698 c.1292G>A c.(1291-1293)cGc>cAc p.R431H STK40_ENST00000373130.3_Missense_Mutation_p.R436H|STK40_ENST00000373132.3_Missense_Mutation_p.R431H|STK40_ENST00000359297.2_3'UTR NM_032017.1 NP_114406.1 Q8N2I9 STK40_HUMAN serine/threonine kinase 40 13 Myeloproliferative disorder(586;0.0393) CCGCAGGTAGCGCTGCGCCAG 0.672000 0 SO:0001583 missense ENST00000373129.3 1 1 hg19 CCDS407.1 . . . . . . . . . . C 17.60 3.431035 0.62844 0.0 1.16E-4 ENSG00000196182 ENST00000373129;ENST00000373130;ENST00000373132 T;T;T 0.68765 -0.34;-0.35;-0.34 5.18 4.26 0.50523 . 0.000000 0.85682 D 0.000000 T 0.70579 0.3240 L 0.27053 0.805 0.49051 D 0.999748 D;D 0.76494 0.999;0.998 D;D 0.74674 0.984;0.964 T 0.73895 -0.3838 10 0.87932 D 0 -21.1861 12.6841 0.56938 0.0:0.9199:0.0:0.0801 . 436;431 Q8N2I9-4;Q8N2I9 .;STK40_HUMAN H 431;436;431 ENSP00000362221:R431H;ENSP00000362222:R436H;ENSP00000362224:R431H ENSP00000362221:R431H R - 2 0 STK40 36579959 1.000000 0.71417 1.000000 0.80357 0.143000 0.21401 7.378000 0.79679 1.177000 0.42855 0.563000 0.77884 CGC TCGA-YH-A8SY-01A-11D-A377-08 STK40-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000022592.1 1 0 1 56 222 0 41 1 9.997914e-01 10 43 0 41 2 0 0 0 0 0 2 1 1.000000 54 218 0 40 2 0 0 0 0 41 2 -3.362224 1 1 121390 2 34 1 1 2 3 1.963322 0 0.220000 3.360000 0.295902 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PTCH2 8643 broad.mit.edu 37 1 45288266 45288266 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:45288266C>T ENST00000372192.3 - 22 3563 c.3433G>A c.(3433-3435)Gca>Aca p.A1145T PTCH2_ENST00000447098.2_Intron|RNU5E-6P_ENST00000365574.1_RNA NM_003738.4 NP_003729.3 Q9Y6C5 PTC2_HUMAN patched 2 50 Acute lymphoblastic leukemia(166;0.155) GAGGAGGATGCCCCCCACCTA 0.627000 Basal Cell Nevus syndrome 0 SO:0001583 missense Familial Cancer Database Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS ENST00000372192.3 0 1 hg19 CCDS516.1 . . . . . . . . . . c 9.847 1.192670 0.21954 . . ENSG00000117425 ENST00000372192 D 0.92299 -3.01 3.92 -7.85 0.01192 . 3.801910 0.00674 N 0.000646 T 0.76371 0.3978 N 0.08118 0 0.19945 N 0.999941 B 0.06786 0.001 B 0.08055 0.003 T 0.72782 -0.4189 10 0.13470 T 0.59 6.7686 0.1418 0.00084 0.2555:0.2463:0.2154:0.2828 . 1145 Q9Y6C5 PTC2_HUMAN T 1145 ENSP00000361266:A1145T ENSP00000361266:A1145T A - 1 0 PTCH2 45060853 0.000000 0.05858 0.000000 0.03702 0.355000 0.29361 -3.348000 0.00503 -2.059000 0.00894 -0.921000 0.02739 GCA TCGA-YH-A8SY-01A-11D-A377-08 PTCH2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000023428.4 0 0 0 5 450 1 67 0 5.949946e-04 0 3 1 67 2 0 0 0 0 0 2 0 0.000968 5 445 1 66 21 0 0 0 1 67 2 -1.947876 0 1 0 0 1 1 2 3 1.963322 0 0.220000 3.360000 0.295902 0.120000 0.030000 0.270000 0.120000 0.140044 0.120000 0 0.070000 0.190000 ELAVL4 1996 broad.mit.edu 37 1 50642759 50642759 + Splice_Site SNP A A G TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:50642759A>G ENST00000371823.4 + 3 474 c.e3-1 ELAVL4_ENST00000357083.4_Splice_Site|ELAVL4_ENST00000371821.1_Splice_Site|ELAVL4_ENST00000371824.1_Splice_Site|ELAVL4_ENST00000371819.1_Splice_Site|RP11-567C20.2_ENST00000442477.1_RNA|ELAVL4_ENST00000492299.1_Splice_Site|ELAVL4_ENST00000371827.1_Splice_Site|ELAVL4_ENST00000448907.2_Splice_Site NM_001144774.1|NM_021952.3 NP_001138246.1|NP_068771.2 P26378 ELAV4_HUMAN ELAV like neuron-specific RNA binding protein 4 32 ATATTTCCACAGGACAGAGTT 0.403000 0 SO:0001630 splice_region_variant ENST00000371823.4 1 1 hg19 CCDS553.1 . . . . . . . . . . A 17.24 3.339651 0.60963 . . ENSG00000162374 ENST00000448907;ENST00000371827;ENST00000357083;ENST00000371824;ENST00000371823;ENST00000371821;ENST00000371819 . . . 5.5 5.5 0.81552 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 15.7759 0.78214 1.0:0.0:0.0:0.0 . . . . . -1 . . . + . . ELAVL4 50415346 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 8.703000 0.91344 2.308000 0.77769 0.533000 0.62120 . TCGA-YH-A8SY-01A-11D-A377-08 ELAVL4-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000021712.1 1 0 1 20 178 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 0.999995 20 171 0 33 2 0 0 0 0 34 2 -9.262255 1 1 0 0 1 1 2 3 1.963322 0 0.220000 3.360000 0.295902 0.990000 0.650000 1.000000 1.000000 0.936548 0.990000 1 0.820000 1.000000 HFM1 164045 broad.mit.edu 37 1 91739306 91739306 + Silent SNP T T A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:91739306T>A ENST00000370425.3 - 34 3833 c.3735A>T c.(3733-3735)ggA>ggT p.G1245G HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_Silent_p.G477G|HFM1_ENST00000370424.3_Silent_p.G924G NM_001017975.3 NP_001017975.3 A2PYH4 HFM1_HUMAN HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae) 75 all_lung(203;0.00961)|Lung NSC(277;0.0351) GTCTAACTTTTCCATAGATTT 0.313000 0 SO:0001819 synonymous_variant ENST00000370425.3 1 1 hg19 CCDS30769.2 . . . . . . . . . . T 2.695 -0.272273 0.05716 . . ENSG00000162669 ENST00000430465 . . . 5.75 2.13 0.27403 . . . . . T 0.10680 0.0261 . . . 0.09310 N 1 . . . . . . T 0.33007 -0.9885 4 . . . . 4.7459 0.13036 0.0:0.1688:0.1611:0.6701 . . . . V 457 . . E - 2 0 HFM1 91511894 0.000000 0.05858 0.000000 0.03702 0.490000 0.33462 0.682000 0.25335 0.105000 0.17753 0.533000 0.62120 GAA TCGA-YH-A8SY-01A-11D-A377-08 HFM1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316716.2 1 0 0 55 587 0 129 0 0 0 0 129 2 0 0 0 0 0 2 1 1.000000 55 580 0 129 2 0 0 0 0 129 2 -14.863670 1 1 0 0 1 1 2 3 1.963322 0 0.220000 3.360000 0.295902 0.860000 0.660000 1.000000 1.000000 0.865749 0.860000 1 0.750000 0.990000 HFM1 164045 broad.mit.edu 37 1 91846537 91846537 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr1:91846537C>T ENST00000370425.3 - 7 903 c.805G>A c.(805-807)Gca>Aca p.A269T HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000370424.3_Intron NM_001017975.3 NP_001017975.3 A2PYH4 HFM1_HUMAN HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae) p.A269T(1) 75 all_lung(203;0.00961)|Lung NSC(277;0.0351) CTAAATTTTGCCGCTTACAAT 0.219000 1 Substitution - Missense(1) SO:0001583 missense ENST00000370425.3 0 1 hg19 CCDS30769.2 . . . . . . . . . . C 9.307 1.054465 0.19907 . . ENSG00000162669 ENST00000370425;ENST00000541820;ENST00000448819 T 0.58797 0.31 5.81 2.87 0.33458 . 0.000000 0.45606 U 0.000360 T 0.29093 0.0723 L 0.54323 1.7 0.80722 D 1 B;B 0.15719 0.014;0.002 B;B 0.08055 0.003;0.003 T 0.09100 -1.0690 10 0.23891 T 0.37 . 8.468 0.32969 0.0:0.5885:0.0:0.4115 . 269;269 B7ZM16;A2PYH4 .;HFM1_HUMAN T 269;302;128 ENSP00000359454:A269T ENSP00000359454:A269T A - 1 0 HFM1 91619125 0.079000 0.21365 0.903000 0.35520 0.987000 0.75469 0.529000 0.23019 0.339000 0.23719 -0.136000 0.14681 GCA TCGA-YH-A8SY-01A-11D-A377-08 HFM1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316716.2 0 0 0 5 410 0 102 0 0 0 0 102 2 0 0 0 0 0 2 1 0.936302 5 407 0 101 2 0 0 0 0 102 2 -1.974416 0 1 121328 2 31 1 1 2 3 1.963322 0 0.220000 3.360000 0.295902 0.130000 0.040000 0.300000 0.120000 0.152466 0.130000 0 0.080000 0.200000 NINL 22981 broad.mit.edu 37 20 25442226 25442226 + Nonsense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr20:25442226G>A ENST00000278886.6 - 21 3701 c.3628C>T c.(3628-3630)Cag>Tag p.Q1210* NINL_ENST00000464285.1_5'Flank|NINL_ENST00000422516.1_Nonsense_Mutation_p.Q861* NM_025176.4 NP_079452.3 Q9Y2I6 NINL_HUMAN ninein-like 57 TGATGTTCCTGATTCAGGCAT 0.468000 0 SO:0001587 stop_gained ENST00000278886.6 0 1 hg19 CCDS33452.1 . . . . . . . . . . G 25.0 4.593669 0.86953 . . ENSG00000101004 ENST00000278886;ENST00000422516 . . . 4.69 0.163 0.14986 . 0.257192 0.31673 N 0.007250 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.41790 T 0.15 -2.2951 7.9115 0.29793 0.0:0.2925:0.4189:0.2885 . . . . X 1210;861 . ENSP00000278886:Q1210X Q - 1 0 NINL 25390226 0.990000 0.36364 0.013000 0.15412 0.104000 0.19210 0.957000 0.29215 -0.084000 0.12595 0.555000 0.69702 CAG TCGA-YH-A8SY-01A-11D-A377-08 NINL-007 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000078445.3 1 0 1 63 267 0 57 0 5.985598e-01 0 10 0 57 2 0 0 0 0 0 2 1 1.000000 63 263 0 56 2 0 0 0 0 57 2 -3.512475 1 1 121412 2 38 1 2 2 4 2.126355 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MC3R 4159 broad.mit.edu 37 20 54824819 54824819 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr20:54824819G>A ENST00000243911.2 + 1 1032 c.920G>A c.(919-921)cGc>cAc p.R307H NM_019888.3 NP_063941.3 P41968 MC3R_HUMAN melanocortin 3 receptor 26 Colorectal(105;0.202) CTGGAATTGCGCAACACCTTT 0.517000 0 SO:0001583 missense ENST00000243911.2 0 1 hg19 CCDS13449.2 . . . . . . . . . . G 17.98 3.520625 0.64747 . . ENSG00000124089 ENST00000243911 T 0.58358 0.34 5.09 5.09 0.68999 . 0.000000 0.64402 D 0.000014 D 0.82917 0.5141 H 0.97440 4.005 0.51767 D 0.99993 D 0.89917 1.0 D 0.83275 0.996 D 0.89536 0.3789 10 0.87932 D 0 . 18.1096 0.89530 0.0:0.0:1.0:0.0 . 344 P41968 MC3R_HUMAN H 307 ENSP00000243911:R307H ENSP00000243911:R307H R + 2 0 MC3R 54258226 1.000000 0.71417 0.990000 0.47175 0.182000 0.23217 9.731000 0.98807 2.362000 0.80069 0.555000 0.69702 CGC TCGA-YH-A8SY-01A-11D-A377-08 MC3R-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079786.2 0 0 0 5 671 0 93 0 0 0 0 93 2 0 0 0 0 0 2 1 0.934759 4 660 0 92 2 0 0 0 0 93 2 -1.750945 0 1 0 0 1 2 2 4 2.126355 1 0.220000 3.360000 0.360656 0.080000 0.010000 0.190000 0.080000 0.097547 0.080000 0 0.050000 0.140000 KRTAP8-1 337879 broad.mit.edu 37 21 32185365 32185365 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr21:32185365C>T ENST00000329621.4 - 1 205 c.174G>A c.(172-174)tcG>tcA p.S58S NM_175857.3 NP_787053.1 Q8IUC2 KRA81_HUMAN keratin associated protein 8-1 6 GAGCAAATGGCGAGTATCTCC 0.562000 0 SO:0001819 synonymous_variant ENST00000329621.4 1 1 hg19 CCDS13607.1 TCGA-YH-A8SY-01A-11D-A377-08 KRTAP8-1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128223.1 1 0 1 70 355 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 1.000000 69 347 0 74 2 0 0 0 0 74 2 -20.000000 1 1 121412 1 36 1 2 2 4 2.110881 1 0.220000 3.360000 0.359501 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 KRTAP11-1 337880 broad.mit.edu 37 21 32253572 32253572 + Missense_Mutation SNP C C A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr21:32253572C>A ENST00000332378.4 - 1 302 c.272G>T c.(271-273)tGt>tTt p.C91F NM_175858.2 NP_787054.1 Q8IUC1 KR111_HUMAN keratin associated protein 11-1 18 GTTGGAAATACAGGTAGTTTG 0.567000 0 SO:0001583 missense ENST00000332378.4 1 1 hg19 CCDS13608.1 . . . . . . . . . . C 14.59 2.579810 0.46006 . . ENSG00000182591 ENST00000332378 T 0.03065 4.06 5.17 4.27 0.50696 . 0.222920 0.39020 N 0.001497 T 0.16128 0.0388 M 0.79258 2.445 0.37098 D 0.899749 D 0.76494 0.999 D 0.74348 0.983 T 0.00907 -1.1519 10 0.49607 T 0.09 -6.145 12.4326 0.55583 0.0:0.9123:0.0:0.0877 . 91 Q8IUC1 KR111_HUMAN F 91 ENSP00000330720:C91F ENSP00000330720:C91F C - 2 0 KRTAP11-1 31175443 1.000000 0.71417 0.996000 0.52242 0.624000 0.37722 3.372000 0.52387 2.608000 0.88229 0.650000 0.86243 TGT TCGA-YH-A8SY-01A-11D-A377-08 KRTAP11-1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128225.1 1 0 1 37 215 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 1.000000 37 209 0 53 2 0 0 0 0 53 2 -20.000000 1 1 0 0 1 2 2 4 2.110881 1 0.220000 3.360000 0.359501 0.990000 0.990000 1.000000 1.000000 0.999918 0.990000 1 0.990000 1.000000 DOPEY2 9980 broad.mit.edu 37 21 37603002 37603002 + Missense_Mutation SNP G G T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr21:37603002G>T ENST00000399151.3 + 14 2005 c.1920G>T c.(1918-1920)aaG>aaT p.K640N NM_005128.2 NP_005119.2 Q9Y3R5 DOP2_HUMAN dopey family member 2 58 TTGCCAGCAAGAACATTTTTG 0.547000 0 SO:0001583 missense ENST00000399151.3 1 1 hg19 CCDS13643.1 . . . . . . . . . . G 15.93 2.977714 0.53720 . . ENSG00000142197 ENST00000399151 T 0.14144 2.53 5.43 4.55 0.56014 . 0.403370 0.29676 N 0.011497 T 0.24509 0.0594 M 0.63843 1.955 0.37959 D 0.932892 D;D 0.67145 0.996;0.992 D;P 0.65573 0.936;0.864 T 0.30679 -0.9970 10 0.09338 T 0.73 . 6.928 0.24426 0.296:0.0:0.704:0.0 . 640;640 Q9Y3R5-2;Q9Y3R5 .;DOP2_HUMAN N 640 ENSP00000382104:K640N ENSP00000382104:K640N K + 3 2 DOPEY2 36524872 1.000000 0.71417 1.000000 0.80357 0.926000 0.56050 2.513000 0.45494 1.436000 0.47453 0.491000 0.48974 AAG TCGA-YH-A8SY-01A-11D-A377-08 DOPEY2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000194636.1 1 0 1 60 270 0 80 1 4.467231e-01 4 4 0 80 2 0 0 0 0 0 2 1 1.000000 59 267 0 78 2 0 0 0 0 80 2 -20.000000 1 1 0 0 1 2 2 4 2.110881 1 0.220000 3.360000 0.359501 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 AFF3 3899 broad.mit.edu 37 2 100210257 100210257 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr2:100210257C>T ENST00000409236.2 - 13 1978 c.1866G>A c.(1864-1866)ccG>ccA p.P622P AFF3_ENST00000356421.2_Silent_p.P647P|AFF3_ENST00000409579.1_Silent_p.P647P|AFF3_ENST00000317233.4_Silent_p.P622P P51826 AFF3_HUMAN AF4/FMR2 family, member 3 86 TGGTGGGCTCCGGGGGGACCA 0.736000 0 SO:0001819 synonymous_variant ENST00000409236.2 1 1 hg19 CCDS42723.1 TCGA-YH-A8SY-01A-11D-A377-08 AFF3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000328982.3 1 0 0 9 167 0 31 0 0 0 0 31 2 0 0 0 0 0 2 1 0.994146 9 164 0 31 2 0 0 0 0 31 2 -2.939472 1 1 121154 1 20 1 2 2 4 2.140913 1 0.220000 3.360000 0.360656 0.590000 0.290000 1.000000 1.000000 0.613214 0.590000 0 0.420000 0.800000 STEAP3 55240 broad.mit.edu 37 2 120005557 120005557 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr2:120005557G>A ENST00000354888.5 + 4 1299 c.795G>A c.(793-795)gtG>gtA p.V265V STEAP3_ENST00000409811.1_Silent_p.V265V|STEAP3_ENST00000393106.2_Silent_p.V265V|STEAP3_ENST00000393107.2_Silent_p.V265V|STEAP3_ENST00000425223.2_Silent_p.V265V|STEAP3-AS1_ENST00000454260.1_RNA|STEAP3_ENST00000450943.2_Silent_p.V265V|STEAP3_ENST00000393110.2_Silent_p.V275V|STEAP3_ENST00000393108.2_Silent_p.V265V NM_182915.2 NP_878919.2 Q658P3 STEA3_HUMAN STEAP family member 3, metalloreductase 17 TGGCCTACGTGCTGCTGTCAC 0.647000 0 SO:0001819 synonymous_variant ENST00000354888.5 0 1 hg19 CCDS2125.1 TCGA-YH-A8SY-01A-11D-A377-08 STEAP3-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254193.1 0 0 0 8 385 0 59 0 6.593735e-02 1 17 0 59 2 0 0 0 0 0 2 1 0.988857 7 380 0 59 2 0 0 0 0 59 2 -7.693234 1 1 0 0 1 2 2 4 2.138506 1 0.220000 3.360000 0.360656 0.230000 0.100000 0.420000 0.240000 0.251572 0.230000 0 0.160000 0.330000 PXDN 7837 broad.mit.edu 37 2 1643096 1643096 + Missense_Mutation SNP T T A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 T A T T Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr2:1643096T>A ENST00000252804.4 - 20 4101 c.4051A>T c.(4051-4053)Aca>Tca p.T1351S NM_012293.1 NP_036425.1 Q92626 PXDN_HUMAN peroxidasin homolog (Drosophila) 112 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716) CGTGGTCTTGTTTTCTTGGTC 0.562000 0 SO:0001583 missense ENST00000252804.4 0 1 hg19 CCDS46221.1 . . . . . . . . . . T 6.749 0.507109 0.12883 . . ENSG00000130508 ENST00000252804 T 0.59772 0.24 5.49 -5.44 0.02624 . 2.195000 0.01825 N 0.034285 T 0.28764 0.0713 N 0.03608 -0.345 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.48636 -0.9018 10 0.02654 T 1 -4.7808 10.6794 0.45804 0.1126:0.5895:0.0:0.2979 . 1351 Q92626 PXDN_HUMAN S 1351 ENSP00000252804:T1351S ENSP00000252804:T1351S T - 1 0 PXDN 1622103 0.000000 0.05858 0.000000 0.03702 0.414000 0.31173 -1.513000 0.02256 -1.322000 0.02278 0.383000 0.25322 ACA TCGA-YH-A8SY-01A-11D-A377-08 PXDN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000322505.1 0 0 0 6 124 0 35 0 9.977962e-01 0 266 0 35 2 0 0 0 0 0 2 1 0.963555 5 122 0 34 2 0 0 0 0 35 2 -4.220467 1 1 0 0 1 0 2 2 1.757869 1 0.220000 3.360000 0.220000 0.440000 0.180000 0.820000 0.410000 0.468508 0.440000 0 0.290000 0.630000 DPYSL5 56896 broad.mit.edu 37 2 27150261 27150261 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr2:27150261C>T ENST00000288699.6 + 4 719 c.561C>T c.(559-561)atC>atT p.I187I DPYSL5_ENST00000401478.1_Silent_p.I187I NM_001253724.1|NM_020134.3 NP_001240653.1|NP_064519.2 Q9BPU6 DPYL5_HUMAN dihydropyrimidinase-like 5 27 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) TTGGGGCAATCGCCCGCGTCC 0.527000 0 SO:0001819 synonymous_variant ENST00000288699.6 1 1 hg19 CCDS1730.1 TCGA-YH-A8SY-01A-11D-A377-08 DPYSL5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214187.2 1 0 1 53 163 0 42 0 0 0 0 42 2 0 0 0 0 0 2 1 1.000000 53 162 0 41 2 0 0 0 0 42 2 -4.656197 1 1 121412 1 32 1 0 2 2 1.757869 1 0.220000 3.360000 0.220000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TLX2 3196 broad.mit.edu 37 2 74742813 74742813 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr2:74742813C>T ENST00000233638.7 + 2 777 c.454C>T c.(454-456)Cgg>Tgg p.R152W NM_016170.4 NP_057254.1 O43763 TLX2_HUMAN T-cell leukemia homeobox 2 2 CTACCAAAACCGGACCCCTCC 0.657000 Esophageal Squamous(7;240 533 18610 24312) 0 SO:0001583 missense ENST00000233638.7 1 1 hg19 CCDS1947.1 . . . . . . . . . . C 21.7 4.191186 0.78902 . . ENSG00000115297 ENST00000233638 D 0.95756 -3.8 4.29 3.41 0.39046 Homeodomain-related (1);Homeodomain-like (1); 0.000000 0.47093 D 0.000253 D 0.97204 0.9086 M 0.80982 2.52 0.54753 D 0.999983 D 0.89917 1.0 D 0.76575 0.988 D 0.97145 0.9827 10 0.87932 D 0 . 11.3327 0.49485 0.1828:0.8172:0.0:0.0 . 152 O43763 TLX2_HUMAN W 152 ENSP00000233638:R152W ENSP00000233638:R152W R + 1 2 TLX2 74596321 1.000000 0.71417 1.000000 0.80357 0.871000 0.50021 4.778000 0.62368 1.015000 0.39444 -0.152000 0.13540 CGG TCGA-YH-A8SY-01A-11D-A377-08 TLX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252224.3 1 0 1 55 303 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 1.000000 54 300 0 37 2 0 0 0 0 38 2 -20.000000 1 1 121408 1 29 1 2 2 4 2.134063 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 0.999998 0.990000 1 0.990000 1.000000 UPK1B 7348 broad.mit.edu 37 3 118913171 118913171 + Missense_Mutation SNP G G T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr3:118913171G>T ENST00000264234.3 + 6 723 c.574G>T c.(574-576)Gtt>Ttt p.V192F UPK1B_ENST00000497685.1_Missense_Mutation_p.V112F|UPK1B_ENST00000460625.1_Missense_Mutation_p.V184F NM_006952.3 NP_008883.2 O75841 UPK1B_HUMAN uroplakin 1B 14 TCAATGCTGTGTTATGAACAA 0.463000 0 SO:0001583 missense ENST00000264234.3 1 1 hg19 CCDS2985.1 . . . . . . . . . . G 23.2 4.391863 0.83011 . . ENSG00000114638 ENST00000497685;ENST00000264234;ENST00000460625 D;D;D 0.87179 -2.22;-2.22;-2.22 5.92 5.04 0.67666 Tetraspanin, EC2 domain (1); 0.270923 0.31847 N 0.006975 D 0.87676 0.6237 L 0.43152 1.355 0.41114 D 0.985767 P;P 0.50369 0.934;0.846 P;P 0.53593 0.73;0.452 D 0.86504 0.1805 10 0.39692 T 0.17 -20.5718 14.2934 0.66295 0.0733:0.0:0.9267:0.0 . 184;192 C9J9M7;O75841 .;UPK1B_HUMAN F 112;192;184 ENSP00000418972:V112F;ENSP00000264234:V192F;ENSP00000418116:V184F ENSP00000264234:V192F V + 1 0 UPK1B 120395861 1.000000 0.71417 1.000000 0.80357 0.964000 0.63967 4.124000 0.57924 2.809000 0.96659 0.467000 0.42956 GTT TCGA-YH-A8SY-01A-11D-A377-08 UPK1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354883.2 1 0 1 71 367 0 76 1 1 222 153 0 76 2 0 0 0 0 0 2 1 1.000000 71 363 0 74 2 0 0 0 0 76 2 -20.000000 1 1 0 0 1 2 2 4 2.127073 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 CLSTN2 64084 broad.mit.edu 37 3 140277663 140277663 + Missense_Mutation SNP G G A rs137889465 TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr3:140277663G>A ENST00000458420.3 + 12 2195 c.2005G>A c.(2005-2007)Gcc>Acc p.A669T NM_022131.2 NP_071414.2 Q9H4D0 CSTN2_HUMAN calsyntenin 2 p.A669T(1) 87 GAGCACCTTCGCCAAAACCGA 0.532000 HNSCC(16;0.037) GBM(45;858 913 3709 36904 37282) 1 Substitution - Missense(1) SO:0001583 missense ENST00000458420.3 1 1 hg19 CCDS3112.1 . . . . . . . . . . G 0.030 -1.341445 0.01277 4.54E-4 0.0 ENSG00000158258 ENST00000458420 T 0.29397 1.57 5.41 2.5 0.30297 . 0.215482 0.46442 N 0.000281 T 0.08802 0.0218 N 0.01219 -0.95 0.23376 N 0.9978 B 0.09022 0.002 B 0.04013 0.001 T 0.33163 -0.9879 9 . . . -0.0386 6.6275 0.22839 0.3845:0.0:0.6155:0.0 . 669 Q9H4D0 CSTN2_HUMAN T 669 ENSP00000402460:A669T . A + 1 0 CLSTN2 141760353 0.921000 0.31238 0.031000 0.17742 0.075000 0.17131 2.120000 0.41968 0.587000 0.29643 0.650000 0.86243 GCC TCGA-YH-A8SY-01A-11D-A377-08 CLSTN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359393.3 1 0 1 43 193 0 48 0 1.593831e-01 0 4 0 48 2 0 0 0 0 0 2 1 1.000000 42 192 0 48 2 0 0 0 0 48 2 -3.152367 1 1 121412 3 36 1 2 2 4 2.127073 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ATP11B 23200 broad.mit.edu 37 3 182591715 182591715 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr3:182591715C>T ENST00000323116.5 + 19 2424 c.2164C>T c.(2164-2166)Cat>Tat p.H722Y NM_014616.2 NP_055431.1 Q9Y2G3 AT11B_HUMAN ATPase, class VI, type 11B 41 all_cancers(143;9.04e-15)|Ovarian(172;0.0355) all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20) ATCATGTGGCCATTTTCATAG 0.398000 0 SO:0001583 missense ENST00000323116.5 1 1 hg19 CCDS33896.1 . . . . . . . . . . C 28.0 4.883120 0.91740 . . ENSG00000058063 ENST00000323116 T 0.62639 0.01 5.78 5.78 0.91487 HAD-like domain (2); 0.000000 0.85682 D 0.000000 D 0.84124 0.5403 M 0.89904 3.07 0.80722 D 1 D;D 0.76494 0.999;0.999 D;D 0.85130 0.997;0.985 D 0.86566 0.1844 10 0.87932 D 0 . 19.9991 0.97403 0.0:1.0:0.0:0.0 . 296;722 B3KSJ2;Q9Y2G3 .;AT11B_HUMAN Y 722 ENSP00000321195:H722Y ENSP00000321195:H722Y H + 1 0 ATP11B 184074409 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 7.440000 0.80464 2.724000 0.93272 0.655000 0.94253 CAT TCGA-YH-A8SY-01A-11D-A377-08 ATP11B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350598.1 1 0 1 54 283 0 72 1 9.412088e-01 4 23 0 72 2 0 0 0 0 0 2 1 1.000000 51 281 0 72 2 0 0 0 0 72 2 -20.000000 1 1 0 0 1 2 2 4 2.127073 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 0.990000 1.000000 SLC4A7 9497 broad.mit.edu 37 3 27431523 27431523 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr3:27431523G>A ENST00000295736.5 - 22 3302 c.3232C>T c.(3232-3234)Ccg>Tcg p.P1078S SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000428386.1_Missense_Mutation_p.P954S|SLC4A7_ENST00000437179.1_Missense_Mutation_p.P959S|SLC4A7_ENST00000445684.1_Missense_Mutation_p.P1074S|SLC4A7_ENST00000435667.2_Missense_Mutation_p.P963S|SLC4A7_ENST00000454389.1_Missense_Mutation_p.P1087S|SLC4A7_ENST00000440156.1_Missense_Mutation_p.P1074S|SLC4A7_ENST00000455077.1_Missense_Mutation_p.P959S|SLC4A7_ENST00000446700.1_Missense_Mutation_p.P1070S|SLC4A7_ENST00000388777.4_Missense_Mutation_p.P628S NM_003615.4 NP_003606.3 Q9Y6M7 S4A7_HUMAN solute carrier family 4, sodium bicarbonate cotransporter, member 7 38 Sodium bicarbonate(DB01390) TTCCAGAGCGGCACATAACGG 0.373000 0 SO:0001583 missense ENST00000295736.5 0 1 hg19 CCDS33721.1 . . . . . . . . . . G 27.0 4.790461 0.90367 . . ENSG00000033867 ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000428179 T;T;T;T;T;T;T;T;T;T;T;T 0.78816 -1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21 5.31 5.31 0.75309 Bicarbonate transporter, C-terminal (1); 0.000000 0.85682 D 0.000000 D 0.87892 0.6292 M 0.72624 2.21 0.80722 D 1 D;D;D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;0.998;1.0;1.0;1.0 D;D;D;D;D;D;D;D;D 0.97110 1.0;1.0;1.0;1.0;1.0;0.982;1.0;1.0;1.0 D 0.88424 0.3030 10 0.59425 D 0.04 . 18.9786 0.92747 0.0:0.0:1.0:0.0 . 1074;959;1070;1074;1087;628;954;1078;959 E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53 .;.;.;.;.;.;.;S4A7_HUMAN;. S 629;1078;954;1087;1074;959;1070;959;1074;963;628;974 ENSP00000411031:P629S;ENSP00000295736:P1078S;ENSP00000416368:P954S;ENSP00000390394:P1087S;ENSP00000414797:P1074S;ENSP00000394252:P959S;ENSP00000406605:P1070S;ENSP00000407382:P959S;ENSP00000406804:P1074S;ENSP00000395336:P963S;ENSP00000373429:P628S;ENSP00000388703:P974S ENSP00000295736:P1078S P - 1 0 SLC4A7 27406527 1.000000 0.71417 0.995000 0.50966 0.770000 0.43624 9.869000 0.99810 2.479000 0.83701 0.650000 0.86243 CCG TCGA-YH-A8SY-01A-11D-A377-08 SLC4A7-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000341230.2 0 0 0 6 654 0 125 0 7.517827e-04 0 4 0 125 2 0 0 0 0 0 2 1 0.964087 6 648 0 124 2 0 0 0 0 125 2 -1.875789 0 1 0 0 1 0 2 2 1.759364 1 0.220000 3.360000 0.220000 0.080000 0.030000 0.170000 0.080000 0.095599 0.080000 0 0.050000 0.130000 FBXL2 25827 broad.mit.edu 37 3 33400492 33400492 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr3:33400492C>T ENST00000484457.1 + 3 190 c.99C>T c.(97-99)tgC>tgT p.C33C FBXL2_ENST00000507198.1_Silent_p.C33C|FBXL2_ENST00000538892.1_Silent_p.C33C|FBXL2_ENST00000542085.1_5'UTR|FBXL2_ENST00000538181.1_Intron|FBXL2_ENST00000446237.3_5'UTR|FBXL2_ENST00000283627.6_Intron NM_012157.3 NP_036289.3 F-box and leucine-rich repeat protein 2 p.C33C(2) 15 TAACTTTGTGCCGATGTGCAC 0.289000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000484457.1 0 1 hg19 CCDS2658.1 TCGA-YH-A8SY-01A-11D-A377-08 FBXL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253245.2 0 0 0 5 372 0 57 0 7.471398e-03 0 8 0 57 2 0 0 0 0 0 2 1 0.936624 5 370 0 57 2 0 0 0 0 57 2 -2.572614 1 1 121374 9 19 1 0 2 2 1.759364 1 0.220000 3.360000 0.220000 0.120000 0.040000 0.260000 0.120000 0.142553 0.120000 0 0.080000 0.200000 CACNA1D 776 broad.mit.edu 37 3 53810001 53810001 + Nonsense_Mutation SNP G G T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr3:53810001G>T ENST00000350061.5 + 35 4802 c.4291G>T c.(4291-4293)Gag>Tag p.E1431* CACNA1D_ENST00000288139.4_Nonsense_Mutation_p.E1451*|CACNA1D_ENST00000540742.1_Nonsense_Mutation_p.E323*|CACNA1D_ENST00000422281.2_Nonsense_Mutation_p.E1416* NM_001128840.1 NP_001122312.1 Q01668 CAC1D_HUMAN calcium channel, voltage-dependent, L type, alpha 1D subunit 90 Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661) CAACCCCGGGGAGGAGTATAC 0.507000 0 SO:0001587 stop_gained ENST00000350061.5 0 1 hg19 CCDS46848.1 . . . . . . . . . . G 45 11.508490 0.99570 . . ENSG00000157388 ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478;ENST00000540742 . . . 5.06 5.06 0.68205 . 0.136428 0.46758 D 0.000261 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.48119 T 0.1 . 18.6072 0.91271 0.0:0.0:1.0:0.0 . . . . X 1431;1451;1416;1124;323 . ENSP00000288139:E1451X E + 1 0 CACNA1D 53785041 1.000000 0.71417 1.000000 0.80357 0.919000 0.55068 9.657000 0.98554 2.624000 0.88883 0.650000 0.86243 GAG TCGA-YH-A8SY-01A-11D-A377-08 CACNA1D-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350557.1 0 0 0 23 559 0 123 0 0 0 0 123 2 0 0 0 0 0 2 1 0.999999 22 550 0 123 2 0 0 0 0 123 2 -3.442191 1 1 0 0 1 0 2 2 1.759364 1 0.220000 3.360000 0.220000 0.360000 0.230000 0.520000 0.360000 0.371314 0.360000 0 0.290000 0.440000 WNT5A 7474 broad.mit.edu 37 3 55504434 55504434 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr3:55504434G>A ENST00000474267.1 - 6 1350 c.829C>T c.(829-831)Cgg>Tgg p.R277W WNT5A_ENST00000264634.4_Missense_Mutation_p.R277W|WNT5A_ENST00000497027.1_Missense_Mutation_p.R262W|WNT5A_ENST00000493406.1_5'Flank P41221 WNT5A_HUMAN wingless-type MMTV integration site family, member 5A 13 CTGTTGAGCCGCATGGCCGCC 0.612000 0 SO:0001583 missense ENST00000474267.1 0 1 hg19 CCDS46850.1 . . . . . . . . . . G 19.24 3.789736 0.70337 . . ENSG00000114251 ENST00000474267;ENST00000264634;ENST00000536765;ENST00000497027 T;T;T 0.76709 -1.04;-1.04;-1.04 5.82 2.59 0.31030 . 0.138509 0.49916 D 0.000133 D 0.89121 0.6625 M 0.90542 3.125 0.49915 D 0.999835 D 0.65815 0.995 D 0.76575 0.988 D 0.90846 0.4727 10 0.87932 D 0 . 13.8804 0.63678 0.0:0.0:0.465:0.535 . 277 P41221 WNT5A_HUMAN W 277;277;188;262 ENSP00000417310:R277W;ENSP00000264634:R277W;ENSP00000420104:R262W ENSP00000264634:R277W R - 1 2 WNT5A 55479474 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 1.813000 0.38962 0.716000 0.32124 0.655000 0.94253 CGG TCGA-YH-A8SY-01A-11D-A377-08 WNT5A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350793.3 0 0 0 4 113 0 28 0 5.085514e-01 0 43 0 28 2 0 0 0 0 0 2 1 0.889632 4 112 0 25 2 0 0 0 0 28 2 -6.472079 1 1 0 0 1 0 2 2 1.759364 1 0.220000 3.360000 0.220000 0.340000 0.110000 0.710000 0.300000 0.370328 0.340000 0 0.200000 0.520000 TIGD4 201798 broad.mit.edu 37 4 153691293 153691293 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr4:153691293C>T ENST00000304337.2 - 2 1684 c.864G>A c.(862-864)gaG>gaA p.E288E NM_145720.3 NP_663772.1 Q8IY51 TIGD4_HUMAN tigger transposable element derived 4 26 all_hematologic(180;0.093) CTGGAAAAGACTCAACAAAAA 0.398000 0 SO:0001819 synonymous_variant ENST00000304337.2 1 1 hg19 CCDS34079.1 TCGA-YH-A8SY-01A-11D-A377-08 TIGD4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365028.1 1 0 0 92 472 0 128 0 0 0 0 128 2 0 0 0 0 0 2 1 1.000000 91 466 0 125 2 0 0 0 0 128 2 -20.000000 1 1 0 0 1 2 2 4 2.089236 0 0.220000 3.360000 0.352482 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 EPHA5 2044 broad.mit.edu 37 4 66230893 66230893 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr4:66230893C>T ENST00000273854.3 - 12 2678 c.2078G>A c.(2077-2079)cGt>cAt p.R693H EPHA5_ENST00000511294.1_Missense_Mutation_p.R694H|EPHA5_ENST00000354839.4_Missense_Mutation_p.R671H|EPHA5_ENST00000432638.2_Missense_Mutation_p.R530H NM_001281765.1|NM_004439.5 NP_001268694.1|NP_004430.4 P54756 EPHA5_HUMAN EPH receptor A5 p.R693H(2) 142 TAGTTTCAAACGTCCACTACA 0.358000 TSP Lung(17;0.13) 2 Substitution - Missense(2) SO:0001583 missense ENST00000273854.3 1 1 hg19 CCDS3513.1 . . . . . . . . . . C 26.3 4.722513 0.89298 . . ENSG00000145242 ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294 T;T;T;T 0.63744 -0.06;-0.06;-0.06;-0.06 5.97 5.97 0.96955 Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1); 0.000000 0.64402 D 0.000017 T 0.71609 0.3360 L 0.35341 1.055 0.53688 D 0.999971 D;B;D;D 0.89917 0.996;0.033;0.995;1.0 D;B;P;D 0.66497 0.942;0.047;0.903;0.944 T 0.70364 -0.4892 10 0.49607 T 0.09 . 20.4238 0.99064 0.0:1.0:0.0:0.0 . 672;694;671;693 B7ZKW7;B7ZKJ3;P54756-2;P54756 .;.;.;EPHA5_HUMAN H 693;530;671;694 ENSP00000273854:R693H;ENSP00000389208:R530H;ENSP00000346899:R671H;ENSP00000427638:R694H ENSP00000273854:R693H R - 2 0 EPHA5 65913488 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 3.308000 0.51896 2.834000 0.97654 0.650000 0.86243 CGT TCGA-YH-A8SY-01A-11D-A377-08 EPHA5-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000251388.2 1 0 1 57 347 0 88 0 0 0 0 88 2 0 0 0 0 0 2 1 1.000000 56 345 0 86 2 0 0 0 0 88 2 -19.999990 1 1 121406 2 36 1 2 2 4 2.089236 0 0.220000 3.360000 0.352482 0.990000 0.990000 1.000000 1.000000 0.999981 0.990000 1 0.990000 1.000000 THAP9 79725 broad.mit.edu 37 4 83827666 83827666 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr4:83827666G>A ENST00000302236.5 + 3 517 c.466G>A c.(466-468)Gta>Ata p.V156I NM_024672.4 NP_078948.3 Q9H5L6 THAP9_HUMAN THAP domain containing 9 33 Hepatocellular(203;0.114) ACTTATCTCCGTAAAGAACTA 0.388000 0 SO:0001583 missense ENST00000302236.5 0 1 hg19 CCDS3598.1 . . . . . . . . . . G 7.115 0.576724 0.13686 . . ENSG00000168152 ENST00000302236;ENST00000536314 T 0.35605 1.3 3.87 2.05 0.26809 . 1.248910 0.05868 N 0.624116 T 0.18841 0.0452 N 0.08118 0 0.09310 N 1 B 0.23806 0.091 B 0.17433 0.018 T 0.24584 -1.0156 10 0.21540 T 0.41 -1.8827 6.5895 0.22639 0.0:0.2004:0.5924:0.2072 . 156 Q9H5L6 THAP9_HUMAN I 156 ENSP00000305533:V156I ENSP00000305533:V156I V + 1 0 THAP9 84046690 0.002000 0.14202 0.015000 0.15790 0.903000 0.53119 0.939000 0.28978 0.556000 0.29098 0.591000 0.81541 GTA TCGA-YH-A8SY-01A-11D-A377-08 THAP9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252633.1 0 0 0 6 564 0 131 0 1.708588e-04 0 2 0 131 2 0 0 0 0 0 2 1 0.964163 6 559 0 131 2 0 0 0 0 131 2 -2.456386 0 1 121410 1 39 1 2 2 4 2.089236 0 0.220000 3.360000 0.352482 0.120000 0.040000 1.000000 0.120000 0.181925 0.120000 0 0.070000 0.200000 PCDHB3 56132 broad.mit.edu 37 5 140481563 140481563 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr5:140481563G>A ENST00000231130.2 + 1 1330 c.1330G>A c.(1330-1332)Gtc>Atc p.V444I AC005754.7_ENST00000607216.1_RNA NM_018937.2 NP_061760.1 Q9Y5E6 PCDB3_HUMAN protocadherin beta 3 72 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) GGTCTCCGACGTCAATGACAA 0.562000 0 SO:0001583 missense ENST00000231130.2 1 1 hg19 CCDS4245.1 . . . . . . . . . . G 8.241 0.806788 0.16467 . . ENSG00000113205 ENST00000231130 T 0.01258 5.09 4.39 1.49 0.22878 Cadherin (3);Cadherin conserved site (1);Cadherin-like (1); . . . . T 0.01061 0.0035 N 0.21324 0.655 0.26614 N 0.972776 B 0.20459 0.045 B 0.17098 0.017 T 0.45877 -0.9231 9 0.06625 T 0.88 . 7.9304 0.29899 0.1567:0.1339:0.7094:0.0 . 444 Q9Y5E6 PCDB3_HUMAN I 444 ENSP00000231130:V444I ENSP00000231130:V444I V + 1 0 PCDHB3 140461747 0.948000 0.32251 0.995000 0.50966 0.908000 0.53690 1.507000 0.35758 0.397000 0.25310 0.655000 0.94253 GTC TCGA-YH-A8SY-01A-11D-A377-08 PCDHB3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251817.2 1 0 0 34 467 0 112 0 6.094947e-02 0 6 0 112 2 0 0 0 0 0 2 1 1.000000 34 438 0 112 2 0 0 0 0 112 2 -8.119044 1 1 121412 1 37 1 1 2 3 1.953850 0 0.220000 3.360000 0.297297 0.680000 0.480000 0.920000 0.690000 0.698457 0.680000 0 0.570000 0.810000 PCDHGA1 56114 broad.mit.edu 37 5 140712177 140712177 + Silent SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr5:140712177C>T ENST00000517417.1 + 1 1926 c.1926C>T c.(1924-1926)ctC>ctT p.L642L PCDHGA1_ENST00000378105.3_Silent_p.L642L NM_018912.2 NP_061735.1 Q9Y5H4 PCDG1_HUMAN protocadherin gamma subfamily A, 1 78 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) AGCAGAGTCTCGTGGTGGCCG 0.701000 0 SO:0001819 synonymous_variant ENST00000517417.1 1 1 hg19 CCDS54922.1 TCGA-YH-A8SY-01A-11D-A377-08 PCDHGA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000374737.1 1 0 1 28 282 0 77 0 0 0 0 77 2 0 0 0 0 0 2 1 1.000000 19 256 0 79 2 0 0 0 0 77 2 -3.221884 1 1 0 0 1 1 2 3 1.953850 0 0.220000 3.360000 0.297297 0.910000 0.620000 1.000000 1.000000 0.892797 0.910000 1 0.760000 1.000000 MYOZ3 91977 broad.mit.edu 37 5 150050154 150050154 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr5:150050154G>A ENST00000297130.4 + 3 369 c.170G>A c.(169-171)cGc>cAc p.R57H CTC-345K18.2_ENST00000511626.2_RNA|MYOZ3_ENST00000517768.1_Missense_Mutation_p.R57H|MYOZ3_ENST00000520112.1_5'Flank NM_001122853.2|NM_133371.4 NP_001116325.1|NP_588612.2 myozenin 3 5 Medulloblastoma(196;0.134)|all_hematologic(541;0.224) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) AAGAGGCAGCGCCGTGTGCAG 0.582000 0 SO:0001583 missense ENST00000297130.4 0 1 hg19 CCDS4309.1 . . . . . . . . . . G 22.5 4.300097 0.81136 0.0 1.16E-4 ENSG00000164591 ENST00000517768;ENST00000297130 T;T 0.66099 -0.19;-0.19 4.89 4.0 0.46444 . 0.165666 0.29185 N 0.012897 T 0.74504 0.3725 M 0.76574 2.34 0.80722 D 1 D 0.89917 1.0 D 0.73380 0.98 T 0.76187 -0.3051 10 0.72032 D 0.01 -8.5437 8.1756 0.31281 0.1697:0.0:0.8303:0.0 . 57 Q8TDC0 MYOZ3_HUMAN H 57 ENSP00000428815:R57H;ENSP00000297130:R57H ENSP00000297130:R57H R + 2 0 MYOZ3 150030347 0.991000 0.36638 1.000000 0.80357 0.985000 0.73830 1.895000 0.39778 2.416000 0.81992 0.555000 0.69702 CGC TCGA-YH-A8SY-01A-11D-A377-08 MYOZ3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252369.1 1 0 1 11 72 0 12 0 0 0 0 12 2 0 0 0 0 0 2 1 0.998420 11 69 0 12 2 0 0 0 0 12 2 -19.033250 1 1 121406 1 28 1 1 2 3 1.949770 0 0.220000 3.360000 0.297297 0.990000 0.740000 1.000000 1.000000 0.979165 0.990000 1 0.990000 1.000000 ZNF622 90441 broad.mit.edu 37 5 16453182 16453182 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr5:16453182G>A ENST00000308683.2 - 5 1372 c.1246C>T c.(1246-1248)Cgg>Tgg p.R416W NM_033414.2 NP_219482.1 Q969S3 ZN622_HUMAN zinc finger protein 622 25 ACGGCCTTCCGATTTTTGGCA 0.498000 0 SO:0001583 missense ENST00000308683.2 0 1 hg19 CCDS3886.1 . . . . . . . . . . G 18.99 3.739888 0.69304 . . ENSG00000173545 ENST00000308683 . . . 5.7 3.8 0.43715 . 0.533295 0.20075 N 0.099768 T 0.41236 0.1150 M 0.63843 1.955 0.24481 N 0.994344 D 0.56968 0.978 B 0.40410 0.328 T 0.44329 -0.9335 9 0.72032 D 0.01 -6.7854 14.3331 0.66572 0.0:0.0:0.5622:0.4378 . 416 Q969S3 ZN622_HUMAN W 416 . ENSP00000310042:R416W R - 1 2 ZNF622 16506182 1.000000 0.71417 0.795000 0.32087 0.980000 0.70556 2.028000 0.41088 1.336000 0.45506 0.655000 0.94253 CGG TCGA-YH-A8SY-01A-11D-A377-08 ZNF622-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207105.1 0 0 0 9 510 0 92 0 7.071678e-01 1 137 0 92 2 0 0 0 0 0 2 1 0.993983 9 505 0 91 2 0 0 0 0 92 2 -2.780967 1 1 0 0 1 1 4 5 2.326018 1 0.220000 3.360000 0.413534 0.210000 0.090000 0.380000 0.200000 0.231388 0.210000 0 0.150000 0.300000 KCNMB1 3779 broad.mit.edu 37 5 169812420 169812420 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr5:169812420C>T ENST00000274629.4 - 2 474 c.32G>A c.(31-33)cGg>cAg p.R11Q KCNMB1_ENST00000521859.1_Missense_Mutation_p.R11Q|KCNIP1_ENST00000377360.4_Intron|KCNIP1_ENST00000518527.1_Intron NM_004137.3 NP_004128.1 Q16558 KCMB1_HUMAN potassium large conductance calcium-activated channel, subfamily M, beta member 1 11 Renal(175;0.000159)|Lung NSC(126;0.0165)|all_lung(126;0.026) Medulloblastoma(196;0.0109)|all_neural(177;0.0146) Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) Miconazole(DB01110)|Procaine(DB00721) TGTCTCTCCCCGCTTCTGGGC 0.537000 0 SO:0001583 missense ENST00000274629.4 1 1 hg19 CCDS4373.1 0 0.0 0 0.0 0 0.0 0 0.0 0 0.0 C 20.7 4.030060 0.75504 4.54E-4 0.001047 ENSG00000145936 ENST00000274629;ENST00000521859 T;T 0.09630 2.96;2.96 5.14 5.14 0.70334 . 0.193157 0.46145 D 0.000307 T 0.28665 0.0710 L 0.57536 1.79 0.35602 D 0.807915 D;D 0.89917 1.0;1.0 D;D 0.87578 0.997;0.998 T 0.11991 -1.0565 9 . . . . 14.4764 0.67548 0.0:1.0:0.0:0.0 . 11;11 Q16558-2;Q16558 .;KCMB1_HUMAN Q 11 ENSP00000274629:R11Q;ENSP00000427940:R11Q . R - 2 0 KCNMB1 169744998 1.000000 0.71417 0.998000 0.56505 0.652000 0.38707 2.535000 0.45685 2.545000 0.85829 0.655000 0.94253 CGG TCGA-YH-A8SY-01A-11D-A377-08 KCNMB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252830.3 1 0 1 67 293 0 61 0 5.817372e-01 0 10 0 61 2 0 0 0 0 0 2 1 1.000000 66 288 0 60 2 0 0 0 0 61 2 -2.525824 1 1 121412 80 50 1 1 2 3 1.949770 0 0.220000 3.360000 0.297297 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 HK3 3101 broad.mit.edu 37 5 176308805 176308805 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr5:176308805G>A ENST00000292432.5 - 17 2372 c.2281C>T c.(2281-2283)Cgc>Tgc p.R761C NM_002115.2 NP_002106.2 P52790 HXK3_HUMAN hexokinase 3 (white cell) 47 all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115) Medulloblastoma(196;0.00498)|all_neural(177;0.0138) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) AGGATGTGGCGGACGATCTCC 0.562000 0 SO:0001583 missense ENST00000292432.5 1 1 hg19 CCDS4407.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 17.39 3.377756 0.61735 . . ENSG00000160883 ENST00000292432 D 0.98987 -5.3 4.82 3.95 0.45737 Hexokinase, C-terminal (1); 0.000000 0.53938 D 0.000048 D 0.99597 0.9854 H 0.99090 4.425 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.97583 1.0112 10 0.87932 D 0 . 13.13 0.59375 0.0786:0.0:0.9214:0.0 . 761 P52790 HXK3_HUMAN C 761 ENSP00000292432:R761C ENSP00000292432:R761C R - 1 0 HK3 176241411 1.000000 0.71417 0.996000 0.52242 0.628000 0.37860 2.855000 0.48333 1.389000 0.46526 0.561000 0.74099 CGC TCGA-YH-A8SY-01A-11D-A377-08 HK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253428.1 1 0 1 46 374 0 79 0 5.054404e-01 0 15 0 79 2 0 0 0 0 0 2 1 1.000000 45 370 0 77 2 0 0 0 0 79 2 -3.142702 1 1 121412 3 36 1 1 2 3 1.949770 0 0.220000 3.360000 0.297297 0.990000 0.820000 1.000000 1.000000 0.981769 0.990000 1 0.950000 1.000000 GFPT2 9945 broad.mit.edu 37 5 179763567 179763567 + Missense_Mutation SNP G G C TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 G C G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr5:179763567G>C ENST00000253778.8 - 3 295 c.126C>G c.(124-126)atC>atG p.I42M NM_005110.2 NP_005101.1 O94808 GFPT2_HUMAN glutamine-fructose-6-phosphate transaminase 2 34 all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137) Medulloblastoma(196;0.0392)|all_neural(177;0.0529) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) L-Glutamine(DB00130) TATTCCCATCGATCGCCACAC 0.473000 0 SO:0001583 missense ENST00000253778.8 1 1 hg19 CCDS43411.1 . . . . . . . . . . G 12.34 1.910022 0.33721 . . ENSG00000131459 ENST00000253778 T 0.77489 -1.1 6.17 -5.21 0.02815 Glutamine amidotransferase, type II (1);Glutamine amidotransferase, class-II (1); 0.051024 0.85682 D 0.000000 D 0.83147 0.5191 M 0.79011 2.435 0.40542 D 0.981037 P 0.51449 0.945 P 0.57324 0.818 D 0.83771 0.0220 9 . . . -28.7535 18.0332 0.89291 0.7778:0.0:0.2222:0.0 . 42 O94808 GFPT2_HUMAN M 42 ENSP00000253778:I42M . I - 3 3 GFPT2 179696173 0.002000 0.14202 0.243000 0.24186 0.061000 0.15899 -1.368000 0.02580 -1.095000 0.03050 -0.150000 0.13652 ATC TCGA-YH-A8SY-01A-11D-A377-08 GFPT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000373444.4 1 0 1 180 758 0 201 0 9.986316e-01 0 43 0 201 2 0 0 0 0 0 2 1 1.000000 179 751 0 200 2 0 0 0 0 201 2 -3.459961 1 1 0 0 1 1 2 3 1.949770 0 0.220000 3.360000 0.297297 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 HTR1A 3350 broad.mit.edu 37 5 63257304 63257304 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr5:63257304G>A ENST00000323865.3 - 1 476 c.243C>T c.(241-243)acC>acT p.T81T RP11-158J3.2_ENST00000502882.1_RNA NM_000524.3 NP_000515.2 P08908 5HT1A_HUMAN 5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled 56 Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234) Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315) CCATGAGGTCGGTGACCGCCA 0.612000 0 SO:0001819 synonymous_variant ENST00000323865.3 1 1 hg19 CCDS34168.1 TCGA-YH-A8SY-01A-11D-A377-08 HTR1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000368397.1 1 0 1 26 87 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 1.000000 26 84 0 33 2 0 0 0 0 34 2 -20.000000 1 1 121408 1 29 1 1 2 3 1.953850 0 0.220000 3.360000 0.297297 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 0.990000 1.000000 RASA1 5921 broad.mit.edu 37 5 86672813 86672813 + Nonsense_Mutation SNP C C A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr5:86672813C>A ENST00000274376.6 + 17 2864 c.2300C>A c.(2299-2301)tCg>tAg p.S767* RASA1_ENST00000512763.1_Nonsense_Mutation_p.S600*|RASA1_ENST00000456692.2_Nonsense_Mutation_p.S590*|RASA1_ENST00000506290.1_Nonsense_Mutation_p.S601*|CTC-428H11.2_ENST00000607486.1_RNA NM_002890.2 NP_002881.1 P20936 RASA1_HUMAN RAS p21 protein activator (GTPase activating protein) 1 48 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) AAGCTTGAATCGTTGTTGTTA 0.383000 0 SO:0001587 stop_gained ENST00000274376.6 0 1 hg19 CCDS34200.1 . . . . . . . . . . C 39 7.861260 0.98531 . . ENSG00000145715 ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290 . . . 5.52 5.52 0.82312 . 0.056401 0.64402 D 0.000001 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.05525 T 0.97 . 19.8119 0.96549 0.0:1.0:0.0:0.0 . . . . X 767;800;590;600;601 . ENSP00000274376:S767X S + 2 0 RASA1 86708569 1.000000 0.71417 1.000000 0.80357 0.946000 0.59487 6.050000 0.71063 2.756000 0.94617 0.563000 0.77884 TCG TCGA-YH-A8SY-01A-11D-A377-08 RASA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000369729.1 1 0 1 61 360 0 103 1 9.250679e-01 5 23 0 103 2 0 0 0 0 0 2 1 1.000000 61 352 0 102 2 0 0 0 0 103 2 -3.143560 1 1 0 0 1 1 2 3 1.953850 0 0.220000 3.360000 0.297297 0.990000 0.990000 1.000000 1.000000 0.999946 0.990000 1 0.990000 1.000000 COL11A2 1302 broad.mit.edu 37 6 33143391 33143391 + Missense_Mutation SNP G G A rs150877886 byFrequency TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr6:33143391G>A ENST00000374708.4 - 28 2336 c.2078C>T c.(2077-2079)cCg>cTg p.P693L COL11A2_ENST00000341947.2_Missense_Mutation_p.P779L|COL11A2_ENST00000374712.1_Missense_Mutation_p.P698L|COL11A2_ENST00000374714.1_Missense_Mutation_p.P753L|COL11A2_ENST00000395197.1_Missense_Mutation_p.P719L|COL11A2_ENST00000361917.1_Missense_Mutation_p.P672L|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374713.1_Missense_Mutation_p.P732L|COL11A2_ENST00000357486.1_Missense_Mutation_p.P758L NM_080681.2 NP_542412.2 P13942 COBA2_HUMAN collagen, type XI, alpha 2 68 GTCTCCAGTCGGTCCAGTGCG 0.647000 Melanoma(1;90 116 3946 5341 17093) 0 SO:0001583 missense ENST00000374708.4 1 0 hg19 CCDS43452.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 14.05 2.418368 0.42918 6.62E-4 0.001846 ENSG00000204248 ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917 D;D;D;D;D;D;D;D 0.93426 -3.22;-3.22;-3.22;-3.22;-3.22;-3.22;-3.22;-3.22 4.3 3.44 0.39384 . 0.067235 0.64402 D 0.000012 D 0.83936 0.5362 L 0.37466 1.105 0.80722 D 1 P;P;P 0.50443 0.87;0.758;0.935 B;B;B 0.43867 0.434;0.307;0.334 T 0.81760 -0.0785 10 0.26408 T 0.33 . 10.4953 0.44775 0.0961:0.0:0.9039:0.0 . 672;693;779 P13942-8;P13942-6;P13942 .;.;COBA2_HUMAN L 693;779;758;753;732;719;698;672 ENSP00000363840:P693L;ENSP00000339915:P779L;ENSP00000350079:P758L;ENSP00000363846:P753L;ENSP00000363845:P732L;ENSP00000378623:P719L;ENSP00000363844:P698L;ENSP00000355123:P672L ENSP00000339915:P779L P - 2 0 COL11A2 33251369 0.999000 0.42202 0.992000 0.48379 0.889000 0.51656 3.017000 0.49615 1.201000 0.43203 -0.350000 0.07774 CCG TCGA-YH-A8SY-01A-11D-A377-08 COL11A2-001 KNOWN not_organism_supported|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000076032.2 1 0 1 50 164 0 25 0 5.657962e-02 0 2 0 25 2 0 0 0 0 0 2 1 1.000000 50 161 0 25 2 0 0 0 0 25 2 -2.441409 0 1 118344 359 58 1 1 2 3 1.971587 0 0.220000 3.360000 0.297297 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ACHE 43 broad.mit.edu 37 7 100491685 100491685 + Missense_Mutation SNP C C T rs17234982 byFrequency TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr7:100491685C>T ENST00000412389.1 - 1 324 c.169G>A c.(169-171)Ggg>Agg p.G57R ACHE_ENST00000497647.1_5'Flank|ACHE_ENST00000241069.5_Missense_Mutation_p.G57R|ACHE_ENST00000411582.1_Missense_Mutation_p.G57R|ACHE_ENST00000428317.1_Missense_Mutation_p.G57R|ACHE_ENST00000302913.4_Missense_Mutation_p.G57R|ACHE_ENST00000419336.2_Missense_Mutation_p.G57R P22303 ACES_HUMAN acetylcholinesterase (Yt blood group) 16 Lung NSC(181;0.041)|all_lung(186;0.0581) Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199) ACAGGGCCCCCGGGGGTCTTC 0.701000 0 SO:0001583 missense ENST00000412389.1 1 1 hg19 CCDS5709.1 3 0.0013736263736263737 2 0.0040650406504065045 0 0.0 1 0.0017482517482517483 0 0.0 c 9.302 1.053449 0.19907 0.0 2.33E-4 ENSG00000087085 ENST00000419336;ENST00000241069;ENST00000428317;ENST00000302913;ENST00000412389;ENST00000426415;ENST00000430554;ENST00000411582;ENST00000422451;ENST00000441605 T;T;T;T;T;T;T;T;T 0.67865 1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;-0.29 4.85 3.97 0.46021 Carboxylesterase, type B (1); 0.245457 0.40222 N 0.001147 T 0.57902 0.2085 M 0.63169 1.94 0.34490 D 0.704821 B;B;B;B 0.28552 0.02;0.215;0.028;0.002 B;B;B;B 0.17433 0.004;0.018;0.004;0.003 T 0.66400 -0.5933 10 0.66056 D 0.02 . 6.5296 0.22320 0.1779:0.7276:0.0:0.0944 rs17234982 57;57;57;57 B7WPI6;P22303-3;P22303-2;P22303 .;.;.;ACES_HUMAN R 57 ENSP00000403474:G57R;ENSP00000241069:G57R;ENSP00000414858:G57R;ENSP00000303211:G57R;ENSP00000394976:G57R;ENSP00000397143:G57R;ENSP00000399725:G57R;ENSP00000404865:G57R;ENSP00000396360:G57R ENSP00000241069:G57R G - 1 0 ACHE 100329621 0.005000 0.15991 0.042000 0.18584 0.166000 0.22503 0.103000 0.15292 1.162000 0.42619 0.556000 0.70494 GGG TCGA-YH-A8SY-01A-11D-A377-08 ACHE-013 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347201.1 1 0 1 19 79 0 22 1 2.606560e-01 2 3 0 22 2 0 0 0 0 0 2 1 0.999994 18 77 0 22 2 0 0 0 0 22 2 -3.080742 1 1 120996 239 48 1 2 2 4 2.136248 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 0.999957 0.990000 1 0.990000 1.000000 WEE2 494551 broad.mit.edu 37 7 141418884 141418884 + Nonsense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr7:141418884C>T ENST00000397541.2 + 4 1004 c.598C>T c.(598-600)Cga>Tga p.R200* WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000484172.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000488785.1_RNA NM_001105558.1 NP_001099028.1 P0C1S8 WEE2_HUMAN WEE1 homolog 2 (S. pombe) 31 Melanoma(164;0.0171) ATGTGTTTTACGAGAAACCAA 0.343000 0 SO:0001587 stop_gained ENST00000397541.2 0 1 hg19 CCDS43660.1 . . . . . . . . . . C 40 8.074404 0.98640 . . ENSG00000214102 ENST00000397541 . . . 5.52 4.53E-4 0.14042 . 0.719074 0.11076 U 0.602382 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 12.8902 0.58068 0.3292:0.5127:0.1582:0.0 . . . . X 200 . ENSP00000380675:R200X R + 1 2 WEE2 141065353 0.837000 0.29446 0.491000 0.27477 0.937000 0.57800 0.581000 0.23819 0.007000 0.14760 -1.367000 0.01198 CGA TCGA-YH-A8SY-01A-11D-A377-08 WEE2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000349091.1 1 0 1 116 529 0 132 0 0 0 0 132 2 0 0 0 0 0 2 1 1.000000 115 524 0 131 2 0 0 0 0 132 2 -20.000000 1 1 120776 3 37 1 2 2 4 2.136248 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 GARS 2617 broad.mit.edu 37 7 30656770 30656770 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr7:30656770G>A ENST00000389266.3 + 10 1476 c.1235G>A c.(1234-1236)cGc>cAc p.R412H NM_002047.2 NP_002038.2 P41250 SYG_HUMAN glycyl-tRNA synthetase p.R412H(1) 24 Glycine(DB00145) TTCATTGGCCGCATCTACCTC 0.433000 1 Substitution - Missense(1) SO:0001583 missense ENST00000389266.3 0 1 hg19 CCDS43564.1 . . . . . . . . . . G 34 5.303525 0.95601 . . ENSG00000106105 ENST00000389266 T 0.79247 -1.25 5.22 5.22 0.72569 Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1); 0.000000 0.85682 D 0.000000 D 0.89525 0.6740 M 0.87180 2.865 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.91138 0.4943 10 0.87932 D 0 -10.2399 16.6573 0.85232 0.0:0.0:1.0:0.0 . 412 P41250 SYG_HUMAN H 412 ENSP00000373918:R412H ENSP00000373918:R412H R + 2 0 GARS 30623295 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.827000 0.99397 2.603000 0.88011 0.557000 0.71058 CGC TCGA-YH-A8SY-01A-11D-A377-08 GARS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000327735.1 0 0 0 6 568 0 109 0 4.950395e-01 0 143 0 109 2 0 0 0 0 0 2 1 0.964168 5 564 0 108 2 0 0 0 0 109 2 -1.956203 0 1 0 0 1 2 2 4 2.129864 1 0.220000 3.360000 0.360656 0.120000 0.040000 0.240000 0.120000 0.134416 0.120000 0 0.070000 0.180000 COL28A1 340267 broad.mit.edu 37 7 7570984 7570984 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr7:7570984G>A ENST00000399429.3 - 3 816 c.676C>T c.(676-678)Cgt>Tgt p.R226C NM_001037763.2 NP_001032852.2 Q2UY09 COSA1_HUMAN collagen, type XXVIII, alpha 1 42 Ovarian(82;0.0789) CCTACCAGACGATCTTGAATT 0.373000 0 SO:0001583 missense ENST00000399429.3 1 1 hg19 CCDS43553.1 . . . . . . . . . . G 10.03 1.239447 0.22711 . . ENSG00000215018 ENST00000399429;ENST00000399419;ENST00000448652 T 0.55760 0.5 3.88 3.88 0.44766 von Willebrand factor, type A (2); 0.303428 0.24176 U 0.040860 T 0.43366 0.1244 N 0.08118 0 0.18873 N 0.999983 D 0.64830 0.994 P 0.54965 0.765 T 0.30592 -0.9973 10 0.59425 D 0.04 -0.8455 10.5423 0.45039 0.0:0.0:0.8065:0.1935 . 226 Q2UY09 COSA1_HUMAN C 226 ENSP00000382356:R226C ENSP00000382347:R226C R - 1 0 COL28A1 7537509 0.326000 0.24669 0.825000 0.32803 0.038000 0.13279 0.862000 0.27899 2.183000 0.69458 0.655000 0.94253 CGT TCGA-YH-A8SY-01A-11D-A377-08 COL28A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000315899.1 1 0 1 41 217 0 56 0 0 0 0 56 2 0 0 0 0 0 2 1 1.000000 41 213 0 56 2 0 0 0 0 56 2 -20.000000 1 1 120684 2 28 1 2 2 4 2.129864 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 0.999992 0.990000 1 0.990000 1.000000 SEMA3E 9723 broad.mit.edu 37 7 83029563 83029563 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr7:83029563C>T ENST00000307792.3 - 11 1614 c.1147G>A c.(1147-1149)Gcc>Acc p.A383T SEMA3E_ENST00000427262.1_Missense_Mutation_p.A323T NM_012431.2 NP_036563.1 O15041 SEM3E_HUMAN sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E 51 Medulloblastoma(109;0.109) ACTTTGCTGGCACACTGAAAA 0.373000 0 SO:0001583 missense ENST00000307792.3 1 1 hg19 CCDS34674.1 . . . . . . . . . . C 20.7 4.038932 0.75617 . . ENSG00000170381 ENST00000307792;ENST00000427262;ENST00000541514 T;T 0.22945 1.93;1.93 5.52 4.62 0.57501 WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4); 0.000000 0.85682 D 0.000000 T 0.42899 0.1223 L 0.58354 1.805 0.58432 D 0.999999 P 0.50617 0.937 P 0.56865 0.808 T 0.32693 -0.9897 10 0.49607 T 0.09 . 16.1726 0.81828 0.0:0.8664:0.1336:0.0 . 383 O15041 SEM3E_HUMAN T 383;323;383 ENSP00000303212:A383T;ENSP00000405052:A323T ENSP00000303212:A383T A - 1 0 SEMA3E 82867499 1.000000 0.71417 1.000000 0.80357 0.767000 0.43475 2.836000 0.48183 1.282000 0.44496 0.585000 0.79938 GCC TCGA-YH-A8SY-01A-11D-A377-08 SEMA3E-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336606.1 1 0 0 54 300 0 115 0 0 0 0 115 2 0 0 0 0 0 2 1 1.000000 54 298 0 114 2 0 0 0 0 115 2 -20.000000 1 1 0 0 1 2 2 4 2.129864 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 0.999997 0.990000 1 0.990000 1.000000 PLEC 5339 broad.mit.edu 37 8 144994097 144994097 + Missense_Mutation SNP G G T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr8:144994097G>T ENST00000322810.4 - 32 10472 c.10303C>A c.(10303-10305)Ctg>Atg p.L3435M PLEC_ENST00000436759.2_Missense_Mutation_p.L3325M|PLEC_ENST00000354589.3_Missense_Mutation_p.L3298M|PLEC_ENST00000527096.1_Missense_Mutation_p.L3321M|PLEC_ENST00000357649.2_Missense_Mutation_p.L3302M|PLEC_ENST00000354958.2_Missense_Mutation_p.L3276M|PLEC_ENST00000345136.3_Missense_Mutation_p.L3298M|PLEC_ENST00000356346.3_Missense_Mutation_p.L3284M|PLEC_ENST00000398774.2_Missense_Mutation_p.L3266M NM_201380.2 NP_958782.1 Q15149 PLEC_HUMAN plectin 137 TCCTGCCGCAGGGTCTCCACC 0.637000 0 SO:0001583 missense ENST00000322810.4 1 1 hg19 CCDS43772.1 . . . . . . . . . . G 8.254 0.809766 0.16537 . . ENSG00000178209 ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096 T;T;T;T;T;T;T;T;T 0.76968 -1.02;-1.02;-1.06;-1.05;-1.04;-1.02;-1.02;-1.02;-1.02 4.81 -4.87 0.03123 . 1.138360 0.06912 U 0.807848 T 0.57636 0.2067 N 0.08118 0 0.09310 N 1 B;B;B;B;B;B;B;B 0.23591 0.088;0.088;0.088;0.053;0.088;0.088;0.088;0.088 B;B;B;B;B;B;B;B 0.29598 0.086;0.104;0.104;0.039;0.104;0.086;0.086;0.086 T 0.52200 -0.8607 10 0.52906 T 0.07 . 8.9149 0.35576 0.0:0.121:0.2943:0.5847 . 3325;3284;3276;3435;3266;3298;3302;3298 Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4 .;.;.;PLEC_HUMAN;.;.;.;. M 3298;3302;3298;3266;3435;3276;3284;3325;3321 ENSP00000344848:L3298M;ENSP00000350277:L3302M;ENSP00000346602:L3298M;ENSP00000381756:L3266M;ENSP00000323856:L3435M;ENSP00000347044:L3276M;ENSP00000348702:L3284M;ENSP00000388180:L3325M;ENSP00000434583:L3321M ENSP00000323856:L3435M L - 1 2 PLEC 145066085 0.000000 0.05858 0.000000 0.03702 0.944000 0.59088 0.834000 0.27518 -0.457000 0.07033 0.448000 0.29417 CTG TCGA-YH-A8SY-01A-11D-A377-08 PLEC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383281.1 1 0 1 78 320 0 64 1 1 98 242 0 64 2 0 0 0 0 0 2 1 1.000000 77 317 0 64 2 0 0 0 0 64 2 -3.394676 1 1 0 0 1 2 2 4 2.169004 1 0.220000 3.360000 0.360656 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ZFHX4 79776 broad.mit.edu 37 8 77617904 77617904 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr8:77617904G>A ENST00000521891.2 + 2 2029 c.1581G>A c.(1579-1581)gcG>gcA p.A527A ZFHX4_ENST00000518282.1_Silent_p.A527A|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000050961.6_Silent_p.A527A|ZFHX4_ENST00000455469.2_Silent_p.A527A NM_024721.4 NP_078997.4 Q86UP3 ZFHX4_HUMAN zinc finger homeobox 4 432 BRCA - Breast invasive adenocarcinoma(89;0.0895) CCTCCTCGGCGACTGTTTCTG 0.433000 HNSCC(33;0.089) 0 SO:0001819 synonymous_variant ENST00000521891.2 1 1 hg19 CCDS47878.2 TCGA-YH-A8SY-01A-11D-A377-08 ZFHX4-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000379197.2 1 0 1 27 225 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 1.000000 27 222 0 45 2 0 0 0 0 45 2 -3.142725 1 1 0 0 1 2 2 4 2.150082 1 0.220000 3.360000 0.360656 0.990000 0.810000 1.000000 1.000000 0.984429 0.990000 1 0.990000 1.000000 PHF19 26147 broad.mit.edu 37 9 123636876 123636876 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr9:123636876G>A ENST00000373896.3 - 2 396 c.144C>T c.(142-144)tgC>tgT p.C48C PHF19_ENST00000312189.6_Silent_p.C48C NM_015651.1 NP_056466.1 Q5T6S3 PHF19_HUMAN PHD finger protein 19 19 CTGTCCACCGGCACAGCACAT 0.557000 0 SO:0001819 synonymous_variant ENST00000373896.3 0 1 hg19 CCDS35116.1 TCGA-YH-A8SY-01A-11D-A377-08 PHF19-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053838.3 0 0 0 5 362 0 79 0 1.768193e-01 0 46 0 79 2 0 0 0 0 0 2 1 0.934742 5 355 0 76 2 0 0 0 0 79 2 -2.550046 1 1 0 0 1 0 2 2 1.772823 1 0.220000 3.360000 0.220000 0.130000 0.040000 0.270000 0.120000 0.146379 0.130000 0 0.080000 0.200000 CD72 971 broad.mit.edu 37 9 35616044 35616044 + Missense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chr9:35616044G>A ENST00000396757.1 - 6 748 c.584C>T c.(583-585)aCg>aTg p.T195M CD72_ENST00000259633.4_Missense_Mutation_p.T195M|CD72_ENST00000490239.1_5'UTR P21854 CD72_HUMAN CD72 molecule 12 Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194) GGTCTCCTTCGTCTTCTGTCT 0.577000 0 SO:0001583 missense ENST00000396757.1 0 1 hg19 CCDS6581.1 . . . . . . . . . . G 15.02 2.709706 0.48517 . . ENSG00000137101 ENST00000396757;ENST00000396759;ENST00000259633 T;T 0.61627 0.09;0.09 5.14 2.28 0.28536 . 0.467428 0.19886 N 0.103850 T 0.68357 0.2992 M 0.69823 2.125 0.09310 N 1 D;D 0.89917 1.0;1.0 D;D 0.68765 0.96;0.96 T 0.56511 -0.7967 10 0.59425 D 0.04 -5.2731 6.2975 0.21095 0.3715:0.0:0.6285:0.0 . 195;195 Q5TLG3;P21854 .;CD72_HUMAN M 195 ENSP00000379980:T195M;ENSP00000259633:T195M ENSP00000259633:T195M T - 2 0 CD72 35606044 0.001000 0.12720 0.056000 0.19401 0.029000 0.11900 0.385000 0.20685 0.569000 0.29329 0.491000 0.48974 ACG TCGA-YH-A8SY-01A-11D-A377-08 CD72-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052336.1 0 0 0 5 487 0 96 0 1.662923e-03 0 5 0 96 2 0 0 0 0 0 2 1 0.935803 5 481 0 94 2 0 0 0 0 96 2 -2.799745 1 1 121412 3 40 1 0 2 2 1.772823 1 0.220000 3.360000 0.220000 0.090000 0.030000 0.200000 0.100000 0.109606 0.090000 0 0.060000 0.150000 AMOT 154796 broad.mit.edu 37 X 112048243 112048243 + Nonsense_Mutation SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chrX:112048243G>A ENST00000524145.1 - 6 1782 c.1708C>T c.(1708-1710)Cga>Tga p.R570* AMOT_ENST00000304758.1_Nonsense_Mutation_p.R161*|AMOT_ENST00000371962.1_Nonsense_Mutation_p.R338*|AMOT_ENST00000371959.3_Nonsense_Mutation_p.R570*|AMOT_ENST00000371958.1_Nonsense_Mutation_p.R338* Q4VCS5 AMOT_HUMAN angiomotin 43 TCGATGTGTCGTCTTTGGTCC 0.512000 0 SO:0001587 stop_gained ENST00000524145.1 0 1 hg19 CCDS48154.1 . . . . . . . . . . g 39 7.434134 0.98282 . . ENSG00000126016 ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145;ENST00000371958 . . . 5.96 4.17 0.49024 . 0.054811 0.64402 D 0.000001 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -11.5027 12.9983 0.58660 0.0:0.0:0.4395:0.5605 . . . . X 161;570;338;570;338 . ENSP00000305557:R161X R - 1 2 AMOT 111934899 0.999000 0.42202 0.985000 0.45067 0.996000 0.88848 2.872000 0.48467 0.623000 0.30267 0.597000 0.82753 CGA TCGA-YH-A8SY-01A-11D-A377-08 AMOT-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000378570.1 1 0 0 167 881 0 150 0 1.229260e-01 0 4 0 150 2 0 0 0 0 0 2 1 1.000000 165 870 0 148 2 0 0 0 0 150 2 -20.000000 1 1 0 0 1 0 1 1 0.220000 3.360000 0.220000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 NKRF 55922 broad.mit.edu 37 X 118725258 118725258 + Nonsense_Mutation SNP T T A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chrX:118725258T>A ENST00000371527.1 - 2 782 c.130A>T c.(130-132)Aaa>Taa p.K44* NKRF_ENST00000542113.1_Nonsense_Mutation_p.K59*|NKRF_ENST00000487600.1_5'UTR|NKRF_ENST00000304449.5_Nonsense_Mutation_p.K44* NM_001173488.1 NP_001166959.1 O15226 NKRF_HUMAN NFKB repressing factor 30 GCTTGCTTTTTAGGAGGATTT 0.353000 0 SO:0001587 stop_gained ENST00000371527.1 0 1 hg19 CCDS35375.1 . . . . . . . . . . T 38 6.702982 0.97776 . . ENSG00000186416 ENST00000371527;ENST00000304449;ENST00000542113 . . . 5.41 5.41 0.78517 . 0.288673 0.39020 N 0.001490 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -17.1562 12.1414 0.54000 0.0:0.0:0.0:1.0 . . . . X 44;44;59 . ENSP00000304803:K44X K - 1 0 NKRF 118609286 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.298000 0.59067 1.800000 0.52685 0.486000 0.48141 AAA TCGA-YH-A8SY-01A-11D-A377-08 NKRF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058044.1 1 0 1 100 497 0 133 0 6.673818e-01 0 13 0 133 2 0 0 0 0 0 2 1 1.000000 98 489 0 129 2 0 0 0 0 133 2 -20.000000 1 1 0 0 1 0 1 1 0.220000 3.360000 0.220000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 FRMPD4 9758 broad.mit.edu 37 X 12516909 12516909 + Missense_Mutation SNP T T C TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chrX:12516909T>C ENST00000380682.1 + 2 658 c.152T>C c.(151-153)tTc>tCc p.F51S NM_014728.3 NP_055543.2 Q14CM0 FRPD4_HUMAN FERM and PDZ domain containing 4 22 CGAGACTACTTCATCAAGTAG 0.488000 0 SO:0001583 missense ENST00000380682.1 1 1 hg19 CCDS35201.1 . . . . . . . . . . T 15.94 2.981669 0.53827 . . ENSG00000169933 ENST00000380682;ENST00000429478;ENST00000304087 T 0.13657 2.57 5.13 5.13 0.70059 WW/Rsp5/WWP (2);PDZ/DHR/GLGF (1); 0.281292 0.34200 N 0.004165 T 0.25865 0.0630 M 0.89287 3.02 0.42617 D 0.993335 B;B 0.18013 0.025;0.025 B;B 0.18561 0.022;0.022 T 0.10451 -1.0629 10 0.87932 D 0 . 14.3389 0.66611 0.0:0.0:0.0:1.0 . 43;51 B7ZLE1;Q14CM0 .;FRPD4_HUMAN S 51;42;40 ENSP00000370057:F51S ENSP00000304583:F40S F + 2 0 FRMPD4 12426830 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 3.718000 0.54919 1.834000 0.53371 0.486000 0.48141 TTC TCGA-YH-A8SY-01A-11D-A377-08 FRMPD4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055771.1 1 0 1 42 249 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 1.000000 42 247 0 30 2 0 0 0 0 30 2 -20.000000 1 1 0 0 1 0 1 1 0.220000 3.360000 0.220000 0.990000 0.970000 1.000000 1.000000 0.997869 0.990000 1 0.990000 1.000000 TFDP3 51270 broad.mit.edu 37 X 132351883 132351883 + Silent SNP G G A TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chrX:132351883G>A ENST00000310125.4 - 1 493 c.405C>T c.(403-405)ggC>ggT p.G135G NM_016521.2 NP_057605.3 Q5H9I0 TFDP3_HUMAN transcription factor Dp family, member 3 p.G135G(1)|p.G75G(1) 19 Acute lymphoblastic leukemia(192;0.000127) CGACCAGCTCGCCCACCACTT 0.552000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000310125.4 1 1 hg19 CCDS14636.2 TCGA-YH-A8SY-01A-11D-A377-08 TFDP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058337.1 1 0 1 75 354 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 1.000000 74 336 0 68 2 0 0 0 0 70 2 -20.000000 1 1 121394 2 36 1 0 1 1 0.220000 3.360000 0.220000 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 0.990000 1.000000 DUSP9 1852 broad.mit.edu 37 X 152915638 152915638 + Missense_Mutation SNP C C T TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chrX:152915638C>T ENST00000342782.3 + 4 1298 c.1033C>T c.(1033-1035)Cgg>Tgg p.R345W DUSP9_ENST00000370167.4_Missense_Mutation_p.R345W Q99956 DUS9_HUMAN dual specificity phosphatase 9 16 all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) GCGCAGCTTGCGGCTGGAGGA 0.612000 0 SO:0001583 missense ENST00000342782.3 0 1 hg19 CCDS14724.1 . . . . . . . . . . c 13.51 2.258205 0.39896 . . ENSG00000130829 ENST00000370167;ENST00000342782 T;T 0.61274 0.12;0.12 4.53 2.62 0.31277 Dual specificity phosphatase, subgroup, catalytic domain (1); 1.080270 0.07212 N 0.859447 T 0.55705 0.1937 M 0.73319 2.225 0.40260 D 0.978167 D 0.58268 0.982 B 0.41412 0.356 T 0.55192 -0.8179 10 0.66056 D 0.02 . 5.9303 0.19134 0.4195:0.3277:0.2528:0.0 . 345 Q99956 DUS9_HUMAN W 345 ENSP00000359186:R345W;ENSP00000345853:R345W ENSP00000345853:R345W R + 1 2 DUSP9 152568832 1.000000 0.71417 0.272000 0.24630 0.422000 0.31414 2.428000 0.44749 0.422000 0.26005 -0.263000 0.10527 CGG TCGA-YH-A8SY-01A-11D-A377-08 DUSP9-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000061022.3 0 0 0 7 892 0 136 0 2.373203e-03 0 8 0 136 2 0 0 0 0 0 2 1 0.979502 7 878 0 131 2 0 0 0 0 136 2 -2.041577 0 1 0 0 1 0 1 1 0.220000 3.360000 0.220000 0.070000 0.020000 0.140000 0.070000 0.080391 0.070000 0 0.040000 0.110000 FLNA 2316 broad.mit.edu 37 X 153593084 153593084 + Missense_Mutation SNP A A G TCGA-YH-A8SY-01A-11D-A377-08 TCGA-YH-A8SY-10A-01D-A37A-08 A G A A Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 3dc82cb2-1730-46ca-b5e1-4dbb57bd5f75 20866917-ab2f-4c68-9874-ea8be01bd72b g.chrX:153593084A>G ENST00000369850.3 - 13 2068 c.1832T>C c.(1831-1833)tTc>tCc p.F611S FLNA_ENST00000422373.1_Missense_Mutation_p.F611S|FLNA_ENST00000344736.4_Missense_Mutation_p.F611S|FLNA_ENST00000360319.4_Missense_Mutation_p.F611S NM_001110556.1 NP_001104026.1 P21333 FLNA_HUMAN filamin A, alpha 6 all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176) TTCCACCGAGAAGCCTGACAA 0.642000 0 SO:0001583 missense ENST00000369850.3 1 1 hg19 CCDS48194.1 . . . . . . . . . . A 19.04 3.750803 0.69533 . . ENSG00000196924 ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736 D;D;D;D 0.91843 -1.86;-1.86;-2.92;-2.92 4.86 4.86 0.63082 Immunoglobulin E-set (1);Immunoglobulin-like fold (1); 0.000000 0.85682 U 0.000000 D 0.96519 0.8864 M 0.90252 3.1 0.80722 D 1 D;D 0.89917 1.0;0.991 D;D 0.97110 1.0;0.955 D 0.97193 0.9859 10 0.87932 D 0 . 13.6752 0.62449 1.0:0.0:0.0:0.0 . 611;611 P21333-2;P21333 .;FLNA_HUMAN S 611;584;611;611;611 ENSP00000353467:F611S;ENSP00000416926:F611S;ENSP00000358866:F611S;ENSP00000358863:F611S ENSP00000358863:F611S F - 2 0 FLNA 153246278 1.000000 0.71417 1.000000 0.80357 0.611000 0.37282 9.336000 0.96533 1.602000 0.50124 0.427000 0.28365 TTC TCGA-YH-A8SY-01A-11D-A377-08 FLNA-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000058942.3 1 0 1 65 379 0 100 0 1 0 323 0 100 2 0 0 0 0 0 2 1 1.000000 65 372 0 98 2 0 0 0 0 100 2 -20.000000 1 1 0 0 1 0 1 1 0.220000 3.360000 0.220000 0.990000 0.990000 1.000000 1.000000 0.999610 0.990000 1 0.990000 1.000000