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 SMAD4 4089 broad.mit.edu 37 18 48604761 48604764 + Frame_Shift_Del DEL ACTT ACTT - TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 ACTT - ACTT ACTT Valid Somatic Phase_I WXS targeted Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr18:48604761_48604764delACTT ENST00000342988.3 + 12 2121_2124 c.1583_1586delACTT c.(1582-1587)cacttafs p.HL528fs SMAD4_ENST00000588745.1_Frame_Shift_Del_p.HL432fs|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Frame_Shift_Del_p.HL528fs NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(2)|p.L529fs*7(1) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) ATTGAAATTCACTTACACCGGGCC 0.495000 39 Whole gene deletion(36)|Unknown(2)|Deletion - Frameshift(1) SO:0001589 frameshift_variant ENST00000342988.3 1 1 hg19 CCDS11950.1 TCGA-IB-A5SP-01A-11D-A32N-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 0 142 346 0 64 1 9.999932e-01 14 31 0 64 2 1 1 176 300 0 1119 2 1 1.000000 166 356 1 64 25 0 0 0 0 0 0 -9.475697 1 1 0 0 1 0 1 1 1.494535 1 0.740000 1.770000 0.587302 4.900000e-01 4.200000e-01 0.560000 0.490000 0.496197 4.900000e-01 0 4.500000e-01 0.530000 SCN7A 6332 broad.mit.edu 37 2 167313539 167313540 + Frame_Shift_Ins INS - - A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr2:167313539_167313540insA ENST00000409855.1 - 10 1256_1257 c.1130_1131insT c.(1129-1131)gtafs p.V377fs NM_002976.3 NP_002967.2 Q01118 SCN7A_HUMAN sodium channel, voltage-gated, type VII, alpha subunit 44 Valproic Acid(DB00313) ACAAAAAACTTACCACCACAAA 0.347000 0 SO:0001589 frameshift_variant ENST00000409855.1 0 1 hg19 CCDS46442.1 TCGA-IB-A5SP-01A-11D-A32N-08 SCN7A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000333745.1 1 0 0 38 143 0 16 0 4.632929e-02 0 2 0 16 2 0 0 0 0 1 1.000000 38 142 0 16 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.252328 0 0.740000 1.770000 0.743792 5.700000e-01 4.200000e-01 1.000000 0.570000 0.595394 5.700000e-01 0 4.900000e-01 0.680000 MECOM 2122 broad.mit.edu 37 3 168833756 168833762 + Frame_Shift_Del DEL TTATTAT TTATTAT - TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 TTATTAT - TTATTAT TTATTAT Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr3:168833756_168833762delTTATTAT ENST00000464456.1 - 7 2534_2540 c.1334_1340delATAATAA c.(1333-1341)aataataagfs p.NNK445fs MECOM_ENST00000472280.1_Frame_Shift_Del_p.NNK446fs|MECOM_ENST00000392736.3_Frame_Shift_Del_p.NNK445fs|MECOM_ENST00000460814.1_Frame_Shift_Del_p.NNK445fs|MECOM_ENST00000494292.1_Frame_Shift_Del_p.NNK633fs|MECOM_ENST00000433243.2_Frame_Shift_Del_p.NNK446fs|MECOM_ENST00000264674.3_Frame_Shift_Del_p.NNK510fs|MECOM_ENST00000468789.1_Frame_Shift_Del_p.NNK445fs NM_001164000.1 NP_001157472.1 Q13465 MDS1_HUMAN MDS1 and EVI1 complex locus 85 GTATTCTTTCTTATTATTTATTGAAGC 0.348000 0 SO:0001589 frameshift_variant ENST00000464456.1 1 1 hg19 CCDS54669.1 TCGA-IB-A5SP-01A-11D-A32N-08 MECOM-020 NOVEL basic|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000351519.1 1 0 0 87 289 0 54 0 9.999962e-01 1 62 0 54 2 0 0 0 0 1 1.000000 131 327 3 57 42 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 1.954591 1 0.740000 1.770000 0.700046 5.300000e-01 4.400000e-01 0.640000 0.540000 0.544772 5.300000e-01 0 4.800000e-01 0.590000 RREB1 6239 broad.mit.edu 37 6 7230570 7230570 + Frame_Shift_Del DEL C C - TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 C - C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr6:7230570delC ENST00000349384.6 + 10 2552 c.2238delC c.(2236-2238)gacfs p.D746fs RREB1_ENST00000379938.2_Frame_Shift_Del_p.D746fs|RREB1_ENST00000334984.6_Frame_Shift_Del_p.D746fs|RREB1_ENST00000379933.3_Frame_Shift_Del_p.D746fs NM_001003698.3 NP_001003698.1 Q92766 RREB1_HUMAN ras responsive element binding protein 1 58 Ovarian(93;0.0398) all_hematologic(90;0.0384)|Prostate(151;0.191) AGCTGGTGGACGCCTTCTGCG 0.662000 0 SO:0001589 frameshift_variant ENST00000349384.6 1 1 hg19 CCDS34336.1 TCGA-IB-A5SP-01A-11D-A32N-08 RREB1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000352985.1 1 0 0 123 259 0 110 1 9.902697e-01 8 10 0 110 2 0 0 0 0 1 1.000000 122 255 0 105 2 0 0 0 0 0 0 -11.307400 1 1 0 0 1 0 1 1 1.499983 1 0.740000 1.770000 0.592093 5.400000e-01 4.700000e-01 0.630000 0.550000 0.555287 5.400000e-01 0 5.000000e-01 0.590000 TACC2 10579 broad.mit.edu 37 10 123843041 123843041 + Silent SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr10:123843041G>A ENST00000369005.1 + 4 1366 c.1026G>A c.(1024-1026)ccG>ccA p.P342P TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515603.1_Silent_p.P342P|TACC2_ENST00000334433.3_Silent_p.P342P|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Silent_p.P342P|TACC2_ENST00000515273.1_Silent_p.P342P NM_206862.2 NP_996744.2 O95359 TACC2_HUMAN transforming, acidic coiled-coil containing protein 2 83 all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197) CATATCTGCCGCACGCAGAGC 0.632000 0 SO:0001819 synonymous_variant ENST00000369005.1 0 1 hg19 CCDS7626.1 TCGA-IB-A5SP-01A-11D-A32N-08 TACC2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000090004.1 0 0 0 5 491 0 108 0 4.439473e-03 0 8 0 108 2 0 0 0 1 0 0 2 1 0.936497 5 487 0 107 2 0 0 0 0 108 2 -3.107977 1 1 121382 6 39 1 2 2 4 2.343436 1 0.740000 1.770000 0.757914 2.000000e-02 0 1.000000 0.030000 0.112198 2.000000e-02 0 1.000000e-02 0.060000 PCDH15 65217 broad.mit.edu 37 10 55912915 55912915 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr10:55912915G>A ENST00000320301.6 - 14 2123 c.1729C>T c.(1729-1731)Cgg>Tgg p.R577W PCDH15_ENST00000395433.1_Missense_Mutation_p.R555W|PCDH15_ENST00000373965.2_Missense_Mutation_p.R584W|PCDH15_ENST00000395430.1_Missense_Mutation_p.R577W|PCDH15_ENST00000373957.3_Missense_Mutation_p.R555W|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395446.1_Missense_Mutation_p.R577W|PCDH15_ENST00000409834.1_Missense_Mutation_p.R188W|PCDH15_ENST00000395438.1_Missense_Mutation_p.R577W|PCDH15_ENST00000361849.3_Missense_Mutation_p.R577W|PCDH15_ENST00000437009.1_Missense_Mutation_p.R577W|PCDH15_ENST00000395445.1_Missense_Mutation_p.R584W|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.R540W|PCDH15_ENST00000373955.1_Missense_Mutation_p.R577W|PCDH15_ENST00000414778.1_Missense_Mutation_p.R582W NM_033056.3 NP_149045.3 Q96QU1 PCD15_HUMAN protocadherin-related 15 237 Melanoma(3;0.117)|Lung SC(717;0.238) GCGTAAGTCCGCCCGACTATC 0.483000 HNSCC(58;0.16) 0 SO:0001583 missense ENST00000320301.6 1 1 hg19 CCDS7248.1 . . . . . . . . . . G 12.460000 1.945863 0.343770 . . ENSG00000150275 ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955 T;T;T;T;T;T;T;T;T;T;T;T;T;T 0.61627 0.09;0.09;0.09;0.09;0.09;0.09;0.09;0.09;0.09;0.09;0.09;0.09;0.09;0.09 5.830000 2.870000 0.334580 Cadherin (4);Cadherin-like (1); . . . . T 0.76751 0.4031 M 0.88979 2.995 0.09310 N 1 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.89917 1.0;0.999;0.999;0.999;1.0;1.0;1.0;0.997;1.0;1.0;0.994;0.997;0.987;0.997;0.999 D;P;P;P;D;D;D;P;D;D;P;P;P;P;P 0.67725 0.932;0.901;0.901;0.849;0.932;0.932;0.932;0.883;0.953;0.953;0.832;0.832;0.742;0.893;0.901 T 0.66689 -0.5860 9 0.87932 D 0 . 10.5008 0.44804 0.0:0.1241:0.4926:0.3833 . 555;577;577;582;577;540;577;577;584;584;577;582;577;555;577 A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1 .;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN W 584;582;577;577;188;584;577;540;577;555;555;577;577;582;577;577 ENSP00000363076:R584W;ENSP00000410304:R582W;ENSP00000378826:R577W;ENSP00000386693:R188W;ENSP00000378832:R584W;ENSP00000378833:R577W;ENSP00000378820:R540W;ENSP00000354950:R577W;ENSP00000378821:R555W;ENSP00000363068:R555W;ENSP00000322604:R577W;ENSP00000378818:R577W;ENSP00000412628:R577W;ENSP00000363066:R577W ENSP00000322604:R577W R - 1 2 PCDH15 55582921 1.900000e-02 0.185530 6.000000e-03 0.133840 0.053000 0.150950 1.942000 0.402430 0.331000 0.235110 0.650000 0.862430 CGG TCGA-IB-A5SP-01A-11D-A32N-08 PCDH15-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000048121.2 1 0 1 149 227 0 39 0 0 0 0 39 2 0 0 0 0 0 2 1 1.000000 148 226 0 39 2 0 0 0 0 39 2 -19.870380 1 1 0 0 1 2 2 4 2.343436 1 0.740000 1.770000 0.757914 9.900000e-01 9.900000e-01 1.000000 1.000000 0.999562 9.900000e-01 1 9.900000e-01 1.000000 P4HA1 5033 broad.mit.edu 37 10 74828652 74828652 + Missense_Mutation SNP C C A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr10:74828652C>A ENST00000307116.2 - 5 531 c.415G>T c.(415-417)Gat>Tat p.D139Y P4HA1_ENST00000440381.1_Missense_Mutation_p.D139Y|RP11-344N10.2_ENST00000431293.2_RNA|P4HA1_ENST00000373008.2_Missense_Mutation_p.D139Y|P4HA1_ENST00000412021.2_Missense_Mutation_p.D139Y|P4HA1_ENST00000394890.2_Missense_Mutation_p.D139Y|P4HA1_ENST00000263556.3_Missense_Mutation_p.D139Y P13674 P4HA1_HUMAN prolyl 4-hydroxylase, alpha polypeptide I 15 Prostate(51;0.0198) Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126) TTGTAGGTATCCTGGAGACGT 0.398000 Colon(147;367 2405 2662 52127) 0 SO:0001583 missense ENST00000307116.2 1 1 hg19 . . . . . . . . . . C 27.900000 4.873543 0.916640 . . ENSG00000122884 ENST00000307116;ENST00000373008;ENST00000412021;ENST00000394890;ENST00000263556;ENST00000440381 T;T;T;T;T;T 0.52526 0.68;0.68;0.68;0.68;0.68;0.66 5.610000 5.610000 0.854770 Prolyl 4-hydroxylase alpha-subunit, N-terminal (1); 0.000000 0.85682 D 0.000000 T 0.79064 0.4383 H 0.94462 3.54 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;1.0;1.0 D 0.84676 0.0714 10 0.87932 D 0 -29.5049 19.6379 0.95744 0.0:1.0:0.0:0.0 . 139;139;139 C9JL12;Q5VSQ6;P13674 .;.;P4HA1_HUMAN Y 139 ENSP00000307318:D139Y;ENSP00000362099:D139Y;ENSP00000411688:D139Y;ENSP00000378353:D139Y;ENSP00000263556:D139Y;ENSP00000414464:D139Y ENSP00000263556:D139Y D - 1 0 P4HA1 74498658 1 0.714170 1 0.803570 0.991000 0.796840 7.374000 0.796330 2.657000 0.903040 0.655000 0.942530 GAT TCGA-IB-A5SP-01A-11D-A32N-08 P4HA1-001 KNOWN basic protein_coding protein_coding OTTHUMT00000048601.1 1 0 1 253 393 0 110 1 9.999999e-01 19 22 0 110 2 0 0 0 0 0 2 1 1.000000 246 388 0 109 2 0 0 0 0 110 2 -20.000000 1 1 0 0 1 2 2 4 2.343436 1 0.740000 1.770000 0.757914 9.900000e-01 9.900000e-01 1.000000 1.000000 0.999891 9.900000e-01 1 9.900000e-01 1.000000 GATA3 2625 broad.mit.edu 37 10 8100716 8100716 + Missense_Mutation SNP C C A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr10:8100716C>A ENST00000346208.3 + 3 1145 c.690C>A c.(688-690)agC>agA p.S230R GATA3_ENST00000379328.3_Missense_Mutation_p.S230R|GATA3_ENST00000461472.1_3'UTR P23771 GATA3_HUMAN GATA binding protein 3 87 CCGAGTACAGCTCCGGACTCT 0.697000 F, N, S breast HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE) Rec yes 10 10p15 2625 GATA binding protein 3 yes E 0 SO:0001583 missense ENST00000346208.3 1 1 hg19 CCDS7083.1 . . . . . . . . . . C 15.480000 2.846693 0.511640 . . ENSG00000107485 ENST00000379328;ENST00000346208 D;D 0.96459 -4.02;-4.0 5.550000 5.550000 0.834470 . 0.098818 0.64402 D 0.000001 D 0.94647 0.8274 L 0.50333 1.59 0.42485 D 0.99287 P;B 0.43826 0.818;0.317 B;B 0.39299 0.296;0.124 D 0.94291 0.7528 10 0.39692 T 0.17 -19.3456 19.5043 0.95108 0.0:1.0:0.0:0.0 . 230;230 P23771;P23771-2 GATA3_HUMAN;. R 230 ENSP00000368632:S230R;ENSP00000341619:S230R ENSP00000341619:S230R S + 3 2 GATA3 8140722 1 0.714170 1 0.803570 0.986000 0.746190 3.873000 0.560930 2.607000 0.881790 0.561000 0.740990 AGC TCGA-IB-A5SP-01A-11D-A32N-08 GATA3-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000046719.1 0 0 1 86 369 1 106 0 9.554913e-02 0 3 1 106 2 0 0 0 0 0 2 1 1.000000 85 361 2 105 21 0 0 0 1 106 2 -20.000000 1 0 0 0 1 2 2 4 2.306636 0 0.740000 1.770000 0.754532 5.400000e-01 4.400000e-01 1.000000 0.540000 0.573890 5.400000e-01 0 4.800000e-01 0.610000 MRGPRX2 117194 broad.mit.edu 37 11 19077764 19077764 + Silent SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr11:19077764G>A ENST00000329773.2 - 2 273 c.186C>T c.(184-186)aaC>aaT p.N62N NM_054030.2 NP_473371.1 Q96LB1 MRGX2_HUMAN MAS-related GPR, member X2 15 CAGAGAAGGCGTTCCTGCGCA 0.557000 GBM(198;1966 2199 4849 37227 49954) 0 SO:0001819 synonymous_variant ENST00000329773.2 1 1 hg19 CCDS7847.1 TCGA-IB-A5SP-01A-11D-A32N-08 MRGPRX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387819.1 1 0 1 89 570 0 93 0 0 0 0 93 2 0 0 0 0 0 2 1 1.000000 88 562 0 91 2 0 0 0 0 93 2 -20.000000 1 1 0 0 1 1 2 3 2.284513 0 0.740000 1.770000 0.745647 3.700000e-01 3.000000e-01 1.000000 0.370000 0.405274 3.700000e-01 0 3.300000e-01 0.420000 C11orf82 0 broad.mit.edu 37 11 82645017 82645017 + Silent SNP A A C TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr11:82645017A>C ENST00000533655.1 + 6 2849 c.2637A>C c.(2635-2637)ggA>ggC p.G879G C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000329143.3_Silent_p.G578G|C11orf82_ENST00000430323.2_Silent_p.G879G NM_145018.3 NP_659455.3 Q8IXT1 DDIAS_HUMAN 33 ATATGCTTGGATTCCAAGGCA 0.408000 0 SO:0001819 synonymous_variant ENST00000533655.1 1 1 hg19 CCDS8263.1 TCGA-IB-A5SP-01A-11D-A32N-08 C11orf82-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391936.1 1 0 1 40 298 0 63 0 1.485251e-02 0 2 0 63 2 0 0 0 0 0 2 1 1.000000 39 295 0 61 2 0 0 0 0 63 2 -20.000000 1 1 0 0 1 2 2 4 2.330246 0 0.740000 1.770000 0.756235 3.400000e-01 2.400000e-01 1.000000 0.340000 0.394753 3.400000e-01 0 2.900000e-01 0.420000 TRPV4 59341 broad.mit.edu 37 12 110236628 110236628 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr12:110236628G>A ENST00000418703.2 - 5 1037 c.943C>T c.(943-945)Cgg>Tgg p.R315W TRPV4_ENST00000544971.1_Missense_Mutation_p.R268W|TRPV4_ENST00000392719.2_Missense_Mutation_p.R268W|TRPV4_ENST00000541794.1_Missense_Mutation_p.R268W|TRPV4_ENST00000346520.2_Missense_Mutation_p.R315W|TRPV4_ENST00000536838.1_Missense_Mutation_p.R281W|TRPV4_ENST00000537083.1_Missense_Mutation_p.R315W|TRPV4_ENST00000261740.2_Missense_Mutation_p.R315W NM_001177431.1 NP_001170902.1 Q9HBA0 TRPV4_HUMAN transient receptor potential cation channel, subfamily V, member 4 35 TCCTGGCGCCGCATGTCCGCC 0.612000 0 SO:0001583 missense ENST00000418703.2 0 1 hg19 CCDS9134.1 . . . . . . . . . . G 19.050000 3.751278 0.695330 . . ENSG00000111199 ENST00000418703;ENST00000261740;ENST00000392719;ENST00000346520;ENST00000544971;ENST00000537083;ENST00000541794;ENST00000536838 T;T;T;T;T;T;T;T 0.71698 -0.59;-0.59;-0.59;-0.59;-0.59;-0.59;-0.59;-0.59 4.370000 2.430000 0.297440 Ankyrin repeat-containing domain (3); 0.055968 0.64402 D 0.000001 T 0.79370 0.4434 L 0.59967 1.855 0.33765 D 0.622362 D;D;D;D;D 0.89917 1.0;1.0;1.0;0.997;1.0 D;P;D;P;P 0.76575 0.988;0.899;0.985;0.827;0.863 D 0.84213 0.0457 10 0.66056 D 0.02 -17.2861 12.0415 0.53456 0.0:0.0:0.6756:0.3244 . 315;315;268;268;281 Q9HBA0-2;Q9HBA0;Q9HBA0-6;Q9HBA0-4;Q9HBA0-5 .;TRPV4_HUMAN;.;.;. W 315;315;268;315;268;315;268;281 ENSP00000406191:R315W;ENSP00000261740:R315W;ENSP00000376480:R268W;ENSP00000319003:R315W;ENSP00000443611:R268W;ENSP00000442738:R315W;ENSP00000442167:R268W;ENSP00000444336:R281W ENSP00000261740:R315W R - 1 2 TRPV4 108721011 1 0.714170 1 0.803570 0.817000 0.461930 4.154000 0.581250 0.525000 0.285220 0.655000 0.942530 CGG TCGA-IB-A5SP-01A-11D-A32N-08 TRPV4-006 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403270.1 0 0 0 5 444 0 135 0 1.019960e-02 0 11 0 135 2 0 0 0 0 0 2 1 0.936015 5 439 0 134 2 0 0 0 0 135 2 -2.394291 0 1 0 0 1 0 1 1 2.113057 1 0.740000 1.770000 0.723639 2.000000e-02 0 0.070000 0.030000 0.033265 2.000000e-02 0 1.000000e-02 0.050000 SDSL 113675 broad.mit.edu 37 12 113873183 113873183 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr12:113873183C>T ENST00000403593.4 + 6 755 c.493C>T c.(493-495)Cca>Tca p.P165S SDSL_ENST00000345635.4_Missense_Mutation_p.P165S Q96GA7 SDSL_HUMAN serine dehydratase-like 15 GCTGAGGACCCCACCAGGTGC 0.682000 0 SO:0001583 missense ENST00000403593.4 0 1 hg19 CCDS9170.1 . . . . . . . . . . C 10.620000 1.401157 0.252910 . . ENSG00000139410 ENST00000403593;ENST00000553248;ENST00000345635 D;D;D 0.96554 -4.05;-4.05;-4.05 4.490000 4.490000 0.547850 Pyridoxal phosphate-dependent enzyme, beta subunit (2); 0.187421 0.42682 D 0.000666 D 0.93255 0.7851 L 0.56280 1.765 0.31826 N 0.625354 B 0.17852 0.024 B 0.14023 0.01 D 0.88786 0.3274 10 0.12430 T 0.62 -12.8961 12.3743 0.55271 0.2143:0.7856:0.0:0.0 . 165 Q96GA7 SDSL_HUMAN S 165;107;165 ENSP00000385790:P165S;ENSP00000448868:P107S;ENSP00000341117:P165S ENSP00000341117:P165S P + 1 0 SDSL 112357566 9.930000e-01 0.373040 9.980000e-01 0.565050 0.402000 0.308110 3.344000 0.521740 2.209000 0.713650 0.462000 0.415740 CCA TCGA-IB-A5SP-01A-11D-A32N-08 SDSL-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404782.1 0 0 0 9 89 0 19 0 8.938730e-01 1 41 0 19 2 0 0 0 0 0 2 1 0.994945 9 89 0 19 2 0 0 0 0 19 2 -14.831980 1 1 0 0 1 0 1 1 2.113057 1 0.740000 1.770000 0.723639 2.400000e-01 1.100000e-01 0.410000 0.240000 0.253290 2.400000e-01 0 1.700000e-01 0.330000 PITPNM2 57605 broad.mit.edu 37 12 123472784 123472784 + Silent SNP C C A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr12:123472784C>A ENST00000542749.1 - 18 3057 c.2994G>T c.(2992-2994)ctG>ctT p.L998L PITPNM2_ENST00000280562.5_Silent_p.L992L|PITPNM2_ENST00000320201.4_Silent_p.L998L|PITPNM2_ENST00000392428.1_Silent_p.L719L Q9BZ72 PITM2_HUMAN phosphatidylinositol transfer protein, membrane-associated 2 39 all_neural(191;0.101)|Medulloblastoma(191;0.163) CCCTCACCCGCAGCTTCACGT 0.627000 0 SO:0001819 synonymous_variant ENST00000542749.1 0 1 hg19 CCDS9242.1 TCGA-IB-A5SP-01A-11D-A32N-08 PITPNM2-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401342.1 0 0 0 9 665 0 224 0 2.403573e-04 0 2 0 224 2 0 0 0 0 0 2 1 0.993895 9 656 0 225 2 0 0 0 0 224 2 -6.636570 1 1 0 0 1 0 1 1 2.113057 1 0.740000 1.770000 0.723639 3.000000e-02 0 0.070000 0.040000 0.037872 3.000000e-02 0 1.000000e-02 0.050000 CCDC92 80212 broad.mit.edu 37 12 124428832 124428832 + Silent SNP C C T rs148809811 TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr12:124428832C>T ENST00000238156.3 - 2 375 c.21G>A c.(19-21)tcG>tcA p.S7S CCDC92_ENST00000545891.1_Intron|CCDC92_ENST00000544798.1_5'UTR|CCDC92_ENST00000545135.1_5'UTR NM_025140.1 NP_079416.1 Q53HC0 CCD92_HUMAN coiled-coil domain containing 92 7 all_neural(191;0.101)|Medulloblastoma(191;0.163) CATCGTAACTCGAGAAATGTG 0.498000 0 SO:0001819 synonymous_variant ENST00000238156.3 1 1 hg19 CCDS9256.1 TCGA-IB-A5SP-01A-11D-A32N-08 CCDC92-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000400780.2 1 0 1 107 206 0 87 1 9.999879e-01 13 23 0 87 2 0 0 0 0 0 2 1 1.000000 106 203 0 87 2 0 0 0 0 87 2 -11.809940 1 1 121412 4 36 1 0 1 1 2.113057 1 0.740000 1.770000 0.723639 8.600000e-01 7.300000e-01 1.000000 0.870000 0.869868 8.600000e-01 1 7.900000e-01 0.940000 GOLGA3 2802 broad.mit.edu 37 12 133365860 133365860 + Missense_Mutation SNP T T G TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr12:133365860T>G ENST00000450791.2 - 12 2747 c.2564A>C c.(2563-2565)tAc>tCc p.Y855S GOLGA3_ENST00000545875.1_Missense_Mutation_p.Y855S|GOLGA3_ENST00000204726.3_Missense_Mutation_p.Y855S|GOLGA3_ENST00000456883.2_Missense_Mutation_p.Y855S|GOLGA3_ENST00000537452.1_Missense_Mutation_p.Y855S Q08378 GOGA3_HUMAN golgin A3 64 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0176)|Lung NSC(355;0.204) GTCGCGCCGGTAGGCCTCCAC 0.637000 0 SO:0001583 missense ENST00000450791.2 0 1 hg19 CCDS9281.1 . . . . . . . . . . T 25.400000 4.636969 0.877600 . . ENSG00000090615 ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875 T;T;T;T;T 0.37058 1.68;1.68;1.69;1.22;1.22 5.420000 5.420000 0.788660 . 0.000000 0.85682 D 0.000000 T 0.59473 0.2196 M 0.75264 2.295 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.91635 0.999;0.999;0.999 T 0.57957 -0.7721 10 0.29301 T 0.29 . 15.4572 0.75325 0.0:0.0:0.0:1.0 . 855;855;855 Q08378-4;Q08378-2;Q08378 .;.;GOGA3_HUMAN S 855 ENSP00000204726:Y855S;ENSP00000410378:Y855S;ENSP00000409303:Y855S;ENSP00000442143:Y855S;ENSP00000442603:Y855S ENSP00000204726:Y855S Y - 2 0 GOLGA3 131875933 1 0.714170 9.960000e-01 0.522420 0.734000 0.419520 7.959000 0.878850 2.064000 0.616790 0.460000 0.390300 TAC TCGA-IB-A5SP-01A-11D-A32N-08 GOLGA3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000397569.2 0 0 0 8 213 0 75 1 4.312760e-01 3 34 0 75 2 0 0 0 0 0 2 1 0.989161 8 210 0 73 2 0 0 0 0 75 2 -13.468770 1 1 0 0 1 0 1 1 2.113057 1 0.740000 1.770000 0.723639 9.000000e-02 4.000000e-02 0.170000 0.090000 0.102436 9.000000e-02 0 6.000000e-02 0.130000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.400000 4.409094 0.833400 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.680000 5.680000 0.881260 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1 0.714170 1 0.803570 0.998000 0.957120 7.743000 0.850200 2.668000 0.907890 0.563000 0.778840 GGT TCGA-IB-A5SP-01A-11D-A32N-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 49 35 0 18 1 9.989910e-01 11 1 0 18 2 1 1 105 109 0 1201 2 1 1.000000 49 34 0 18 2 1 1 5403 2618 0 18 2 -20.000000 1 1 121404 2 44 1 0 1 1 1.532613 1 0.740000 1.770000 0.592093 9.400000e-01 7.900000e-01 1.000000 1.000000 0.937091 9.400000e-01 1 8.700000e-01 1.000000 CACNA1C 775 broad.mit.edu 37 12 2716164 2716164 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr12:2716164C>T ENST00000347598.4 + 27 3284 c.3284C>T c.(3283-3285)aCg>aTg p.T1095M CACNA1C_ENST00000399637.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399644.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399603.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000480911.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000327702.7_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399641.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399655.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399597.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399617.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000402845.3_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399638.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399591.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399634.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399629.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399606.1_Missense_Mutation_p.T1095M|CACNA1C_ENST00000399621.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000335762.5_Missense_Mutation_p.T1100M|CACNA1C_ENST00000399649.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000344100.3_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399601.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000399595.1_Missense_Mutation_p.T1075M|CACNA1C_ENST00000406454.3_Missense_Mutation_p.T1075M|CACNA1C-AS3_ENST00000543559.1_RNA NM_001129827.1|NM_199460.2 NP_001123299.1|NP_955630.2 Q13936 CAC1C_HUMAN calcium channel, voltage-dependent, L type, alpha 1C subunit 132 OV - Ovarian serous cystadenocarcinoma(31;0.00256) Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661) AACTACATCACGTACAAAGAC 0.557000 0 SO:0001583 missense ENST00000347598.4 1 1 hg19 CCDS44788.1 . . . . . . . . . . c 13.730000 2.322899 0.410960 . . ENSG00000151067 ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.96685 -4.02;-4.01;-4.05;-4.01;-4.04;-4.01;-4.03;-3.92;-3.97;-4.01;-3.96;-3.94;-4.01;-4.09;-3.96;-3.86;-4.08;-4.02;-4.01;-4.05;-3.96;-4.04;-4.08 4.860000 4.860000 0.630820 Ion transport (1); 0.202841 0.52532 D 0.000071 D 0.97099 0.9052 L 0.42529 1.33 0.38378 D 0.945041 D;P;B;D;P;P;B;B;B;B;B;B;B;P;P;B;B;P;B;B;P;P;B;B;B 0.89917 1.0;0.466;0.265;1.0;0.719;0.466;0.212;0.224;0.024;0.33;0.239;0.123;0.212;0.469;0.636;0.414;0.4;0.525;0.119;0.239;0.525;0.525;0.286;0.013;0.286 D;B;B;D;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B 0.91635 0.999;0.071;0.041;0.999;0.148;0.071;0.091;0.024;0.024;0.071;0.023;0.04;0.091;0.04;0.284;0.034;0.058;0.049;0.04;0.034;0.071;0.049;0.024;0.011;0.047 D 0.97646 1.0151 10 0.46703 T 0.11 . 18.5389 0.91020 0.0:1.0:0.0:0.0 . 1075;1072;1095;1075;1075;1075;1075;1075;1075;1095;1075;1046;1095;1075;1075;1075;1075;1075;1075;1075;1075;1075;1075;1075;1075 Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;F5H638;Q13936-12 .;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;. M 1100;1075;1075;1075;1075;1075;1075;1075;1075;1075;1095;1095;1075;1075;1075;1075;1075;1075;1075;1075;1075;1075;1075;916 ENSP00000336982:T1100M;ENSP00000382563:T1075M;ENSP00000437936:T1075M;ENSP00000382552:T1075M;ENSP00000382547:T1075M;ENSP00000382506:T1075M;ENSP00000382530:T1075M;ENSP00000382546:T1075M;ENSP00000382500:T1075M;ENSP00000382549:T1075M;ENSP00000266376:T1095M;ENSP00000382515:T1095M;ENSP00000382510:T1075M;ENSP00000341092:T1075M;ENSP00000382537:T1075M;ENSP00000329877:T1075M;ENSP00000382557:T1075M;ENSP00000385724:T1075M;ENSP00000382512:T1075M;ENSP00000382542:T1075M;ENSP00000382526:T1075M;ENSP00000385896:T1075M;ENSP00000382504:T1075M ENSP00000323129:T916M T + 2 0 CACNA1C 2586425 1.390000e-01 0.225630 9.950000e-01 0.509660 0.979000 0.700020 1.089000 0.308900 2.687000 0.915940 0.651000 0.884530 ACG TCGA-IB-A5SP-01A-11D-A32N-08 CACNA1C-017 KNOWN non_canonical_conserved|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000317035.1 1 0 1 62 65 0 54 0 4.826940e-01 0 3 0 54 2 0 0 0 0 0 2 1 1.000000 62 63 0 53 2 0 0 0 0 54 2 -16.057770 1 1 121066 3 33 1 0 1 1 1.531743 1 0.740000 1.770000 0.592093 8.300000e-01 6.800000e-01 0.970000 0.840000 0.835235 8.300000e-01 0 7.500000e-01 0.910000 TMEM117 84216 broad.mit.edu 37 12 44782362 44782362 + Silent SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr12:44782362C>T ENST00000266534.3 + 8 1579 c.1452C>T c.(1450-1452)acC>acT p.T484T TMEM117_ENST00000536799.1_Silent_p.T380T|TMEM117_ENST00000546978.1_3'UTR|TMEM117_ENST00000551577.1_3'UTR NM_032256.1 NP_115632.1 Q9H0C3 TM117_HUMAN transmembrane protein 117 23 Lung SC(27;0.192) CCCACCTAACCTCGGAAAACT 0.453000 0 SO:0001819 synonymous_variant ENST00000266534.3 1 1 hg19 CCDS8745.1 TCGA-IB-A5SP-01A-11D-A32N-08 TMEM117-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403969.1 1 0 1 263 449 0 77 1 9.931152e-01 4 12 0 77 2 0 0 0 0 0 2 1 1.000000 260 436 0 75 2 0 0 0 0 77 2 -20.000000 1 1 121412 1 34 1 0 1 1 2.172560 0 0.740000 1.770000 0.736094 9.700000e-01 8.800000e-01 1.000000 1.000000 0.971541 9.700000e-01 1 9.300000e-01 1.000000 RASA3 22821 broad.mit.edu 37 13 114773065 114773065 + Silent SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr13:114773065C>T ENST00000334062.7 - 18 1807 c.1686G>A c.(1684-1686)tcG>tcA p.S562S RASA3_ENST00000389544.4_Silent_p.S530S NM_007368.2 NP_031394.2 Q14644 RASA3_HUMAN RAS p21 protein activator 3 47 Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188) BRCA - Breast invasive adenocarcinoma(86;0.128) TCCCCGAGGACGAAATCAGAT 0.552000 0 SO:0001819 synonymous_variant ENST00000334062.7 1 1 hg19 CCDS32016.1 TCGA-IB-A5SP-01A-11D-A32N-08 RASA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045957.2 1 0 1 84 137 0 70 1 1 34 30 0 70 2 0 0 0 0 0 2 1 1.000000 81 133 0 69 2 0 0 0 0 70 2 -20.000000 1 1 121346 2 31 1 0 0 0 2.145043 0 0.740000 1.770000 0.736094 9.900000e-01 8.400000e-01 1.000000 1.000000 0.971726 9.900000e-01 1 9.200000e-01 1.000000 GPC5 2262 broad.mit.edu 37 13 92380846 92380846 + Missense_Mutation SNP G G T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr13:92380846G>T ENST00000377067.3 + 4 1453 c.1081G>T c.(1081-1083)Gat>Tat p.D361Y GPC5_ENST00000483422.1_3'UTR NM_004466.4 NP_004457.1 P78333 GPC5_HUMAN glypican 5 69 all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163) Lung NSC(4;0.00454) TTGTTCTTTTGATCAGAGCAA 0.398000 0 SO:0001583 missense ENST00000377067.3 0 1 hg19 CCDS9468.1 . . . . . . . . . . G 18.710000 3.682939 0.681570 . . ENSG00000179399 ENST00000377067 T 0.55234 0.53 5.880000 5.040000 0.676660 . 0.478094 0.24502 N 0.037975 T 0.64091 0.2567 M 0.72894 2.215 0.37269 D 0.907309 P 0.44877 0.845 P 0.52514 0.701 T 0.72221 -0.4356 10 0.72032 D 0.01 2.7075 12.1984 0.54311 0.0779:0.0:0.9221:0.0 . 361 P78333 GPC5_HUMAN Y 361 ENSP00000366267:D361Y ENSP00000366267:D361Y D + 1 0 GPC5 91178847 1 0.714170 9.860000e-01 0.454190 0.989000 0.773840 3.232000 0.513020 1.499000 0.486170 0.557000 0.710580 GAT TCGA-IB-A5SP-01A-11D-A32N-08 GPC5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045454.1 0 0 0 5 509 0 78 0 0 0 0 78 2 0 0 0 0 0 2 1 0.936206 5 504 0 77 2 0 0 0 0 78 2 -2.834094 1 1 0 0 1 0 0 0 2.131965 0 0.740000 1.770000 0.736094 2.000000e-02 0 0.060000 0.020000 0.030160 2.000000e-02 0 1.000000e-02 0.040000 KIF26A 26153 broad.mit.edu 37 14 104642766 104642766 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr14:104642766C>T ENST00000423312.2 + 12 3641 c.3641C>T c.(3640-3642)cCg>cTg p.P1214L KIF26A_ENST00000315264.7_Missense_Mutation_p.P1075L NM_015656.1 NP_056471.1 Q9ULI4 KI26A_HUMAN kinesin family member 26A 21 all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767) Epithelial(46;0.152) CCCCGGAAACCGAGGACTGCC 0.721000 0 SO:0001583 missense ENST00000423312.2 1 1 hg19 CCDS45171.1 . . . . . . . . . . C 0.014000 -1.580981 0.008790 . . ENSG00000066735 ENST00000423312;ENST00000315264 T;T 0.76448 -1.02;-1.02 3.600000 0.264000 0.156070 . . . . . T 0.68146 0.2969 M 0.64404 1.975 0.09310 N 1 B 0.13145 0.007 B 0.06405 0.002 T 0.51601 -0.8685 9 0.21540 T 0.41 . 4.6768 0.12715 0.2952:0.5102:0.0:0.1946 . 1214 Q9ULI4 KI26A_HUMAN L 1214;1075 ENSP00000388241:P1214L;ENSP00000325452:P1075L ENSP00000325452:P1075L P + 2 0 KIF26A 103712519 2.000000e-03 0.142020 2.000000e-03 0.105220 0.106000 0.193360 0.517000 0.228320 0.199000 0.204270 -1.026000 0.024260 CCG TCGA-IB-A5SP-01A-11D-A32N-08 KIF26A-002 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414356.1 1 0 1 54 102 0 63 0 1.226017e-01 0 2 0 63 2 0 0 0 0 0 2 1 1.000000 54 100 0 63 2 0 0 0 0 63 2 -20.000000 1 1 119696 2 34 1 0 0 0 2.008487 0 0.740000 1.770000 0.716961 8.500000e-01 6.700000e-01 1.000000 1.000000 0.858834 8.500000e-01 1 7.600000e-01 0.950000 MAP3K9 4293 broad.mit.edu 37 14 71209085 71209085 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr14:71209085C>T ENST00000554752.2 - 6 1549 c.1550G>A c.(1549-1551)cGc>cAc p.R517H MAP3K9_ENST00000553414.1_Missense_Mutation_p.R211H|MAP3K9_ENST00000554146.1_Missense_Mutation_p.R254H|MAP3K9_ENST00000381250.4_Missense_Mutation_p.R517H|MAP3K9_ENST00000555993.2_Missense_Mutation_p.R517H NM_001284230.1 NP_001271159.1 P80192 M3K9_HUMAN mitogen-activated protein kinase kinase kinase 9 46 GAGGCTGATGCGGTTGCCATC 0.602000 GBM(114;411 1587 13539 28235 50070) 0 SO:0001583 missense ENST00000554752.2 0 1 hg19 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 C 12.470000 1.947067 0.343770 . . ENSG00000006432 ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284 T;T;T;T 0.11495 2.77;2.77;2.77;2.77 6.060000 5.170000 0.711590 Protein kinase-like domain (1); 0.211843 0.49305 D 0.000141 T 0.07413 0.0187 N 0.25245 0.725 0.50171 D 0.999854 B;B;B;B 0.20261 0.001;0.025;0.043;0.005 B;B;B;B 0.20577 0.005;0.009;0.03;0.013 T 0.28332 -1.0047 10 0.35671 T 0.21 . 7.1057 0.25362 0.1401:0.71:0.0:0.1499 . 254;517;517;211 G3V4P9;P80192;P80192-4;G3V347 .;M3K9_HUMAN;.;. H 517;517;211;517;254;245 ENSP00000451612:R517H;ENSP00000451038:R211H;ENSP00000370649:R517H;ENSP00000451921:R254H ENSP00000005198:R517H R - 2 0 MAP3K9 70278838 1 0.714170 1 0.803570 0.716000 0.411820 3.617000 0.541810 1.577000 0.498040 -0.150000 0.136520 CGC TCGA-IB-A5SP-01A-11D-A32N-08 MAP3K9-001 KNOWN basic protein_coding protein_coding OTTHUMT00000412550.2 0 0 0 5 651 1 147 0 2.882276e-04 0 3 1 147 2 0 0 0 0 0 2 0 0.010455 5 631 1 146 16 0 0 0 1 147 2 -2.163597 0 1 121412 8 42 1 0 0 0 2.008487 0 0.740000 1.770000 0.716961 1.000000e-02 0 0.050000 0.020000 0.022249 1.000000e-02 0 0 0.030000 PPIP5K1 9677 broad.mit.edu 37 15 43827457 43827457 + Silent SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr15:43827457G>A ENST00000396923.3 - 30 3838 c.3717C>T c.(3715-3717)tcC>tcT p.S1239S PPIP5K1_ENST00000360301.4_Silent_p.S1214S|PPIP5K1_ENST00000360135.4_Silent_p.S1212S|PPIP5K1_ENST00000381885.1_Silent_p.S1235S|PPIP5K1_ENST00000420765.1_Silent_p.S1239S|PPIP5K1_ENST00000348806.6_Silent_p.S1212S|PPIP5K1_ENST00000334933.4_Silent_p.S1214S|PPIP5K1_ENST00000381879.4_Silent_p.S1215S Q6PFW1 VIP1_HUMAN diphosphoinositol pentakisphosphate kinase 1 1 GCACCTGTGGGGACTGATTTG 0.562000 0 SO:0001819 synonymous_variant ENST00000396923.3 1 1 hg19 CCDS45252.1 TCGA-IB-A5SP-01A-11D-A32N-08 PPIP5K1-002 NOVEL basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000132907.1 1 0 1 240 390 0 152 1 9.999997e-01 16 23 0 152 2 0 0 0 0 0 2 1 1.000000 239 387 0 149 2 0 0 0 0 152 2 -20.000000 1 1 0 0 1 0 1 1 1.932441 1 0.740000 1.770000 0.692162 8.600000e-01 7.700000e-01 0.950000 0.870000 0.869822 8.600000e-01 1 8.200000e-01 0.910000 TLN2 83660 broad.mit.edu 37 15 63032911 63032911 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr15:63032911C>T ENST00000561311.1 + 31 4198 c.3968C>T c.(3967-3969)tCt>tTt p.S1323F TLN2_ENST00000306829.6_Missense_Mutation_p.S1323F Q9Y4G6 TLN2_HUMAN talin 2 p.S1323Y(1) 99 GCTGCCAAGTCTCTCTCTGTA 0.493000 1 Substitution - Missense(1) SO:0001583 missense ENST00000561311.1 1 1 hg19 CCDS32261.1 . . . . . . . . . . C 16.450000 3.126628 0.567210 . . ENSG00000171914 ENST00000306829 T 0.14893 2.47 5.870000 5.870000 0.943060 . 0.094038 0.85682 D 0.000000 T 0.20820 0.0501 L 0.49126 1.545 0.80722 D 1 B 0.11235 0.004 B 0.12837 0.008 T 0.04281 -1.0963 10 0.23302 T 0.38 -13.3132 20.5827 0.99408 0.0:1.0:0.0:0.0 . 1323 Q9Y4G6 TLN2_HUMAN F 1323 ENSP00000303476:S1323F ENSP00000303476:S1323F S + 2 0 TLN2 60820203 1 0.714170 1 0.803570 0.999000 0.989320 6.002000 0.706930 2.941000 0.997820 0.655000 0.942530 TCT TCGA-IB-A5SP-01A-11D-A32N-08 TLN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257878.2 1 0 1 67 215 0 43 1 5.264291e-01 2 5 0 43 2 0 0 0 0 0 2 1 1.000000 67 210 0 43 2 0 0 0 0 43 2 -20.000000 1 1 0 0 1 0 1 1 1.932441 1 0.740000 1.770000 0.692162 5.300000e-01 4.300000e-01 0.650000 0.540000 0.545703 5.300000e-01 0 4.800000e-01 0.600000 ERCC4 2072 broad.mit.edu 37 16 14014215 14014215 + Nonsense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr16:14014215C>T ENST00000311895.7 + 1 202 c.193C>T c.(193-195)Cag>Tag p.Q65* ERCC4_ENST00000575156.1_Nonsense_Mutation_p.Q65* NM_005236.2 NP_005227.1 Q92889 XPF_HUMAN excision repair cross-complementation group 4 38 GCTCAACACGCAGCCGGCCGA 0.697000 Mis, N, F skin basal cell, skin squamous cell, melanoma Nucleotide excision repair (NER) Xeroderma Pigmentosum yes Rec Xeroderma pigmentosum (F) 16 16p13.3-p13.13 2072 excision repair cross-complementing rodent repair deficiency, complementation group 4 E 0 SO:0001587 stop_gained Familial Cancer Database incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV ENST00000311895.7 0 1 hg19 CCDS32390.1 . . . . . . . . . . C 37.000000 6.363938 0.975070 . . ENSG00000175595 ENST00000311895;ENST00000439007;ENST00000389138 . . . 4.980000 4.980000 0.660770 . 0.436137 0.26696 N 0.022966 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.48119 T 0.1 -25.2254 11.0818 0.48064 0.2766:0.7234:0.0:0.0 . . . . X 65;54;54 . ENSP00000310520:Q65X Q + 1 0 ERCC4 13921716 9.760000e-01 0.341440 1 0.803570 0.937000 0.578000 3.363000 0.523210 2.741000 0.939830 0.655000 0.942530 CAG TCGA-IB-A5SP-01A-11D-A32N-08 ERCC4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109634.2 1 0 1 37 40 0 20 0 4.718823e-01 0 3 0 20 2 0 0 0 0 0 2 1 1.000000 37 39 0 20 2 0 0 0 0 20 2 -20.000000 1 1 0 0 1 1 2 3 2.232676 0 0.740000 1.770000 0.741910 9.900000e-01 9.900000e-01 1.000000 1.000000 0.998863 9.900000e-01 1 9.900000e-01 1.000000 IL21R 50615 broad.mit.edu 37 16 27448836 27448836 + Silent SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr16:27448836C>T ENST00000337929.3 + 4 653 c.180C>T c.(178-180)gaC>gaT p.D60D IL21R_ENST00000395755.1_Silent_p.D60D|IL21R_ENST00000564089.1_Silent_p.D60D|IL21R_ENST00000395754.4_Silent_p.D60D NM_181078.2 NP_851564.1 Q9HBE5 IL21R_HUMAN interleukin 21 receptor 8 AGCTGAAGGACGAGGCCACCT 0.597000 T BCL6 NHL Dom yes 16 16p11 50615 interleukin 21 receptor L 0 SO:0001819 synonymous_variant ENST00000337929.3 0 1 hg19 CCDS10630.1 TCGA-IB-A5SP-01A-11D-A32N-08 IL21R-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254578.2 0 0 0 9 394 0 103 0 1.967485e-03 0 3 0 103 2 0 0 0 0 0 2 1 0.994142 10 390 0 103 2 0 0 0 0 103 2 -8.496587 1 1 121412 4 37 1 1 2 3 2.232676 0 0.740000 1.770000 0.741910 6.000000e-02 2.000000e-02 0.120000 0.060000 0.076311 6.000000e-02 0 3.000000e-02 0.090000 NMRAL1 57407 broad.mit.edu 37 16 4516232 4516232 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr16:4516232G>A ENST00000574733.1 - 4 1180 c.451C>T c.(451-453)Cgg>Tgg p.R151W NMRAL1_ENST00000574425.1_Missense_Mutation_p.R151W|NMRAL1_ENST00000572391.1_5'UTR|NMRAL1_ENST00000404295.3_Missense_Mutation_p.R151W|NMRAL1_ENST00000283429.6_Missense_Mutation_p.R151W Q9HBL8 NMRL1_HUMAN NmrA-like family domain containing 1 15 CAGGGCAGCCGCACACTGGTC 0.572000 0 SO:0001583 missense ENST00000574733.1 0 1 hg19 CCDS10516.1 . . . . . . . . . . G 19.320000 3.804190 0.706820 . . ENSG00000153406 ENST00000283429;ENST00000404295 T;T 0.48836 0.8;0.8 5.840000 3.850000 0.443700 NAD(P)-binding domain (1);NmrA-like (1); 0.000000 0.64402 D 0.000005 T 0.64316 0.2587 M 0.68952 2.095 0.47862 D 0.999539 D 0.89917 1.0 D 0.97110 1.0 T 0.62034 -0.6939 10 0.35671 T 0.21 -32.0395 12.9284 0.58272 0.0:0.0:0.7042:0.2958 . 151 Q9HBL8 NMRL1_HUMAN W 151 ENSP00000283429:R151W;ENSP00000383962:R151W ENSP00000283429:R151W R - 1 2 NMRAL1 4456233 1 0.714170 1 0.803570 0.789000 0.446020 3.199000 0.510430 0.786000 0.337080 -0.309000 0.091370 CGG TCGA-IB-A5SP-01A-11D-A32N-08 NMRAL1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438579.1 0 0 0 5 387 0 74 0 6.939733e-01 0 177 0 74 2 0 0 0 0 0 2 1 0.936655 5 384 0 74 2 0 0 0 0 74 2 -2.906499 1 1 121412 2 33 1 1 2 3 2.232676 0 0.740000 1.770000 0.741910 3.000000e-02 0 0.090000 0.040000 0.050418 3.000000e-02 0 1.000000e-02 0.060000 RRAD 6236 broad.mit.edu 37 16 66956197 66956197 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr16:66956197G>A ENST00000299759.6 - 5 959 c.709C>T c.(709-711)Cac>Tac p.H237Y RRAD_ENST00000420652.1_Missense_Mutation_p.H237Y P55042 RAD_HUMAN Ras-related associated with diabetes 17 Ovarian(137;0.192) ACATTGTGGTGCAATGCCGCT 0.602000 0 SO:0001583 missense ENST00000299759.6 0 1 hg19 CCDS10824.1 . . . . . . . . . . G 21.400000 4.142870 0.778880 . . ENSG00000166592 ENST00000420652;ENST00000299759 T;T 0.79653 -1.29;-1.29 5.930000 5.930000 0.959200 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.88522 0.6459 M 0.69823 2.125 0.80722 D 1 D 0.62365 0.991 P 0.59546 0.859 D 0.88586 0.3140 10 0.72032 D 0.01 . 20.328 0.98708 0.0:0.0:1.0:0.0 . 237 P55042 RAD_HUMAN Y 237 ENSP00000388744:H237Y;ENSP00000299759:H237Y ENSP00000299759:H237Y H - 1 0 RRAD 65513698 1 0.714170 9.980000e-01 0.565050 0.449000 0.322280 9.471000 0.976960 2.802000 0.963970 0.561000 0.740990 CAC TCGA-IB-A5SP-01A-11D-A32N-08 RRAD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268830.1 0 0 0 5 412 0 108 0 9.666273e-03 0 10 0 108 2 0 0 0 0 0 2 1 0.935903 5 407 0 104 2 0 0 0 0 108 2 -4.749076 1 1 0 0 1 1 2 3 2.246134 0 0.740000 1.770000 0.743792 3.000000e-02 0 1.000000 0.040000 0.066394 3.000000e-02 0 1.000000e-02 0.060000 MYO15A 51168 broad.mit.edu 37 17 18023559 18023559 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr17:18023559G>A ENST00000205890.5 + 2 1783 c.1445G>A c.(1444-1446)cGa>cAa p.R482Q NM_016239.3 NP_057323.3 Q9UKN7 MYO15_HUMAN myosin XVA 99 all_neural(463;0.228) CTCTTCCCGCGACCCCAGGTG 0.632000 0 SO:0001583 missense ENST00000205890.5 1 1 hg19 CCDS42271.1 . . . . . . . . . . G 21.300000 4.131602 0.776620 . . ENSG00000091536 ENST00000205890 T 0.51325 0.71 5.100000 5.100000 0.692640 . . . . . T 0.59756 0.2217 L 0.32530 0.975 0.80722 D 1 D 0.89917 1.0 D 0.80764 0.994 T 0.61978 -0.6951 9 0.54805 T 0.06 . 18.1103 0.89533 0.0:0.0:1.0:0.0 . 482 Q9UKN7 MYO15_HUMAN Q 482 ENSP00000205890:R482Q ENSP00000205890:R482Q R + 2 0 MYO15A 17964284 1 0.714170 1 0.803570 0.976000 0.684990 7.973000 0.880320 2.374000 0.810150 0.561000 0.740990 CGA TCGA-IB-A5SP-01A-11D-A32N-08 MYO15A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000132048.1 1 0 1 31 190 1 89 0 0 0 1 89 2 0 0 0 0 0 2 1 0.999850 30 187 1 88 10 0 0 0 1 89 2 -20.000000 1 1 0 0 1 0 1 1 1.503745 1 0.740000 1.770000 0.589711 2.300000e-01 1.600000e-01 0.320000 0.240000 0.244999 2.300000e-01 0 1.900000e-01 0.280000 TP53 7157 broad.mit.edu 37 17 7577559 7577559 + Missense_Mutation SNP G G A rs28934573 TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr17:7577559G>A ENST00000269305.4 - 7 911 c.722C>T c.(721-723)tCc>tTc p.S241F TP53_ENST00000445888.2_Missense_Mutation_p.S241F|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.S241F|TP53_ENST00000420246.2_Missense_Mutation_p.S241F|TP53_ENST00000359597.4_Missense_Mutation_p.S241F|TP53_ENST00000413465.2_Missense_Mutation_p.S241F 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.S241F(85)|p.S241C(26)|p.0?(8)|p.S241Y(8)|p.C242fs*5(6)|p.?(5)|p.S241del(5)|p.S148F(4)|p.N239_C242delNSSC(3)|p.N239_C242>S(1)|p.C238fs*21(1)|p.S241fs*22(1)|p.N239_C242del(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.S148C(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GCCCATGCAGGAACTGTTACA 0.572000 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 160 Substitution - Missense(124)|Deletion - In frame(13)|Deletion - Frameshift(9)|Whole gene deletion(8)|Unknown(5)|Complex - deletion inframe(1) GRCh37 CM920673 TP53 M rs28934573 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . G 17.500000 3.404027 0.622880 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944 D;D;D;D;D;D;D;D 0.99857 -7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22 4.620000 3.640000 0.417300 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.120078 0.56097 D 0.000022 D 0.99871 0.9939 M 0.92784 3.345 0.53688 A 0.999973 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D 0.97110 1.0;1.0;1.0;1.0;1.0;1.0 D 0.96525 0.9388 9 0.87932 D 0 -35.4617 12.8645 0.57932 0.0:0.1651:0.8349:0.0 rs28934573 241;241;148;241;241;241 P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;P53_HUMAN;.;. F 241;241;241;241;241;241;230;148;109;148 ENSP00000410739:S241F;ENSP00000352610:S241F;ENSP00000269305:S241F;ENSP00000398846:S241F;ENSP00000391127:S241F;ENSP00000391478:S241F;ENSP00000425104:S109F;ENSP00000423862:S148F ENSP00000269305:S241F S - 2 0 TP53 7518284 1 0.714170 1 0.803570 0.995000 0.863560 2.346000 0.440270 1.295000 0.447240 0.462000 0.415740 TCC TCGA-IB-A5SP-01A-11D-A32N-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 107 110 0 91 1 1 79 14 0 91 2 1 1 286 243 2 2958 3 1 1.000000 105 109 0 91 2 0 0 0 0 91 2 -20.000000 1 1 0 0 1 0 1 1 1.503745 1 0.740000 1.770000 0.589711 8.300000e-01 7.200000e-01 0.950000 0.840000 0.841610 8.300000e-01 0 7.700000e-01 0.900000 ONECUT2 9480 broad.mit.edu 37 18 55103544 55103544 + Missense_Mutation SNP G G C TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr18:55103544G>C ENST00000491143.2 + 1 628 c.596G>C c.(595-597)cGc>cCc p.R199P AC090340.1_ENST00000581316.1_RNA NM_004852.2 NP_004843.2 O95948 ONEC2_HUMAN one cut homeobox 2 15 Colorectal(73;0.234) ACCCTCATGCGCGACGAGCGC 0.677000 0 SO:0001583 missense ENST00000491143.2 1 1 hg19 CCDS42440.1 . . . . . . . . . . G 19.280000 3.796477 0.705670 . . ENSG00000119547 ENST00000491143;ENST00000262095 . . . 4.370000 4.370000 0.524810 . 0.000000 0.64402 D 0.000001 T 0.78155 0.4239 M 0.76574 2.34 0.53688 D 0.999979 D 0.71674 0.998 D 0.79108 0.992 T 0.80984 -0.1138 9 0.56958 D 0.05 -18.0298 15.663 0.77203 0.0:0.0:1.0:0.0 . 199 O95948 ONEC2_HUMAN P 180;199 . ENSP00000262095:R199P R + 2 0 ONECUT2 53254542 1 0.714170 1 0.803570 0.754000 0.428550 9.544000 0.980920 1.990000 0.581190 0.455000 0.322230 CGC TCGA-IB-A5SP-01A-11D-A32N-08 ONECUT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357264.3 1 0 0 44 43 0 40 1 9.998059e-01 17 1 0 40 2 0 0 0 0 0 2 1 1.000000 44 43 0 40 2 0 0 0 0 40 2 -20.000000 1 1 0 0 1 0 1 1 1.494535 1 0.740000 1.770000 0.587302 8.400000e-01 6.700000e-01 0.980000 0.850000 0.844473 8.400000e-01 0 7.500000e-01 0.930000 ZNF441 126068 broad.mit.edu 37 19 11891903 11891903 + Missense_Mutation SNP A A G TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr19:11891903A>G ENST00000357901.4 + 4 1366 c.1264A>G c.(1264-1266)Aaa>Gaa p.K422E ZNF441_ENST00000454339.2_Missense_Mutation_p.K355E NM_152355.2 NP_689568.2 Q8N8Z8 ZN441_HUMAN zinc finger protein 441 19 ATATAAATGTAAACAATGTGG 0.368000 0 SO:0001583 missense ENST00000357901.4 1 1 hg19 CCDS12266.2 . . . . . . . . . . - 15.890000 2.966344 0.535070 . . ENSG00000197044 ENST00000409902;ENST00000357901;ENST00000454339 T;T 0.08370 3.1;3.1 1.220000 0.166000 0.149990 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.04048 0.0113 N 0.12611 0.24 0.09310 N 0.999999 B 0.28291 0.206 B 0.34418 0.182 T 0.44174 -0.9345 9 0.25751 T 0.34 . 0.0939 0.00042 0.3319:0.241:0.1882:0.239 . 422 Q8N8Z8 ZN441_HUMAN E 378;422;355 ENSP00000350576:K422E;ENSP00000403738:K355E ENSP00000350576:K422E K + 1 0 ZNF441 11752903 0 0.058580 1.220000e-01 0.217670 0.980000 0.705560 -4.770000 0.001880 -0.007000 0.143450 0.254000 0.183690 AAA TCGA-IB-A5SP-01A-11D-A32N-08 ZNF441-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335273.3 1 0 1 82 124 0 20 1 5.223269e-01 3 1 0 20 2 0 0 0 0 0 2 1 1.000000 82 122 0 20 2 0 0 0 0 20 2 -20.000000 1 1 0 0 1 0 0 0 2.149781 0 0.740000 1.770000 0.736094 9.900000e-01 8.800000e-01 1.000000 1.000000 0.986632 9.900000e-01 1 9.600000e-01 1.000000 MAN2B1 4125 broad.mit.edu 37 19 12763078 12763078 + Silent SNP G G A rs34853569 byFrequency TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr19:12763078G>A ENST00000456935.2 - 16 1975 c.1935C>T c.(1933-1935)aaC>aaT p.N645N MAN2B1_ENST00000221363.4_Silent_p.N644N NM_000528.3|NM_001173498.1 NP_000519.2|NP_001166969.1 O00754 MA2B1_HUMAN mannosidase, alpha, class 2B, member 1 33 CTATACTGGCGTTGTACCTGG 0.592000 0 SO:0001819 synonymous_variant ENST00000456935.2 1 0 hg19 CCDS32919.1 18 0.008241758241758242 16 0.032520325203252036 2 0.0055248618784530384 0 0.0 0 0.0 G 0.018000 -1.477523 0.010350 0.036768 1.16E-4 ENSG00000104774 ENST00000433513 . . . 5.600000 -11.200000 0.001270 . . . . . T 0.24431 0.0592 . . . 0.45439 D 0.998412 . . . . . . T 0.69343 -0.5170 4 . . . -8.3103 13.3469 0.60578 0.2157:0.0:0.6193:0.165 rs34853569 . . . C 181 . . R - 1 0 MAN2B1 12624078 2.000000e-03 0.142020 8.100000e-02 0.204880 0.002000 0.026280 -1.569000 0.021420 -3.131000 0.002360 -1.105000 0.021060 CGC TCGA-IB-A5SP-01A-11D-A32N-08 MAN2B1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000344062.1 0 0 1 166 277 0 104 1 1 23 69 0 104 2 0 0 0 0 0 2 1 1.000000 163 270 0 100 2 0 0 0 0 104 2 -2.204850 0 1 121412 427 59 1 0 0 0 2.149781 0 0.740000 1.770000 0.736094 9.900000e-01 8.700000e-01 1.000000 1.000000 0.974689 9.900000e-01 1 9.300000e-01 1.000000 MKNK2 2872 broad.mit.edu 37 19 2041073 2041073 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr19:2041073G>A ENST00000591601.1 - 11 1111 c.1076C>T c.(1075-1077)gCc>gTc p.A359V MKNK2_ENST00000541165.1_Missense_Mutation_p.A228V|MKNK2_ENST00000250896.3_Missense_Mutation_p.A359V|MKNK2_ENST00000591142.1_Missense_Mutation_p.A103V|MKNK2_ENST00000309340.7_Missense_Mutation_p.A359V|MKNK2_ENST00000588014.1_Missense_Mutation_p.A103V|MKNK2_ENST00000591588.1_Missense_Mutation_p.A103V Q9HBH9 MKNK2_HUMAN MAP kinase interacting serine/threonine kinase 2 p.A359V(2) 10 Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137) GACTTGGGCGGCACTCAGCCT 0.662000 2 Substitution - Missense(2) SO:0001583 missense ENST00000591601.1 0 1 hg19 CCDS12080.1 . . . . . . . . . . G 21.400000 4.140434 0.777750 . . ENSG00000099875 ENST00000309340;ENST00000250896;ENST00000541165;ENST00000545627 T;T;T 0.46063 0.88;0.88;0.88 3.940000 3.940000 0.455960 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.117336 0.56097 D 0.000022 T 0.52933 0.1765 L 0.38531 1.155 0.80722 D 1 D;D;P;P 0.71674 0.988;0.998;0.939;0.868 D;D;P;P 0.71414 0.951;0.973;0.779;0.859 T 0.55848 -0.8076 10 0.52906 T 0.07 -6.964 15.1499 0.72689 0.0:0.0:1.0:0.0 . 164;359;359;261 Q59GN5;Q9HBH9;Q9HBH9-2;Q9NT28 .;MKNK2_HUMAN;.;. V 359;359;228;299 ENSP00000309485:A359V;ENSP00000250896:A359V;ENSP00000438904:A228V ENSP00000250896:A359V A - 2 0 MKNK2 1992073 1 0.714170 5.400000e-01 0.280890 0.417000 0.312640 9.343000 0.970470 2.046000 0.607030 0.555000 0.697020 GCC TCGA-IB-A5SP-01A-11D-A32N-08 MKNK2-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000449312.1 0 0 0 5 535 1 169 0 4.522639e-02 0 387 1 169 10 0 0 0 0 0 2 0 0.043705 5 528 1 168 13 0 0 0 1 169 2 -2.739844 1 1 0 0 1 0 0 0 2.149781 0 0.740000 1.770000 0.736094 2.000000e-02 0 0.060000 0.020000 0.028665 2.000000e-02 0 0 0.040000 HIPK4 147746 broad.mit.edu 37 19 40886552 40886552 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr19:40886552G>A ENST00000291823.2 - 3 1630 c.1346C>T c.(1345-1347)gCg>gTg p.A449V NM_144685.3 NP_653286.2 Q8NE63 HIPK4_HUMAN homeodomain interacting protein kinase 4 20 Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292) GTCGGAGACCGCATTGGTGCA 0.632000 0 SO:0001583 missense ENST00000291823.2 0 1 hg19 CCDS12555.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 g 0.004000 -2.287071 0.002480 . . ENSG00000160396 ENST00000291823;ENST00000452139 T 0.66099 -0.19 4.840000 -4.350000 0.036560 . 1.367440 0.05006 N 0.470122 T 0.31136 0.0787 N 0.04508 -0.205 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.39683 -0.9602 10 0.02654 T 1 . 7.7812 0.29066 0.217:0.3469:0.4361:0.0 . 449 Q8NE63 HIPK4_HUMAN V 449;414 ENSP00000291823:A449V ENSP00000291823:A449V A - 2 0 HIPK4 45578392 0 0.058580 1.200000e-02 0.152000 0.008000 0.064300 -0.930000 0.039720 -0.596000 0.058210 -0.598000 0.041060 GCG TCGA-IB-A5SP-01A-11D-A32N-08 HIPK4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462593.1 0 0 0 6 839 1 236 0 0 0 1 236 2 0 0 0 0 0 2 0 0.051844 6 824 1 233 14 0 0 0 1 236 2 -2.123610 0 1 121410 1 37 1 1 2 3 2.221285 0 0.740000 1.770000 0.741910 1.000000e-02 0 0.050000 0.020000 0.031990 1.000000e-02 0 0 0.030000 SHANK1 50944 broad.mit.edu 37 19 51219616 51219616 + Silent SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr19:51219616G>A ENST00000293441.1 - 2 393 c.375C>T c.(373-375)tcC>tcT p.S125S SHANK1_ENST00000391814.1_Silent_p.S125S|SHANK1_ENST00000359082.3_Silent_p.S125S NM_016148.2 NP_057232.2 Q9Y566 SHAN1_HUMAN SH3 and multiple ankyrin repeat domains 1 64 all_neural(266;0.057) CATCGCGGCCGGAGGTGGCCG 0.637000 0 SO:0001819 synonymous_variant ENST00000293441.1 0 1 hg19 CCDS12799.1 TCGA-IB-A5SP-01A-11D-A32N-08 SHANK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268071.1 0 0 0 5 478 0 108 0 0 0 1 0 108 2 0 0 0 0 0 2 1 0.936816 5 475 0 107 2 0 0 0 0 108 2 -4.433140 1 1 0 0 1 1 2 3 2.221285 0 0.740000 1.770000 0.741910 2.000000e-02 0 0.070000 0.030000 0.042377 2.000000e-02 0 1.000000e-02 0.050000 MUC16 94025 broad.mit.edu 37 19 9011412 9011412 + Missense_Mutation SNP C C T rs114676657 by1000genomes TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr19:9011412C>T ENST00000397910.4 - 36 39024 c.38821G>A c.(38821-38823)Gag>Aag p.E12941K NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 590 TACAGCTGCTCTCTGTTGAGT 0.572000 0 SO:0001583 missense ENST00000397910.4 1 0 hg19 CCDS54212.1 24 0.01098901098901099 3 0.006097560975609756 1 0.0027624309392265192 0 0.0 20 0.026385224274406333 . 12.850000 2.061979 0.363730 0.010194 0.026633 ENSG00000181143 ENST00000397910;ENST00000441155 T 0.63255 -0.03 2.760000 2.760000 0.324660 . . . . . T 0.54854 0.1884 M 0.79258 2.445 . . . D 0.71674 0.998 D 0.80764 0.994 T 0.76903 -0.2787 8 0.87932 D 0 -19.752 9.6026 0.39615 0.0:1.0:0.0:0.0 . 12941 B5ME49 . K 12941;94 ENSP00000381008:E12941K ENSP00000381008:E12941K E - 1 0 MUC16 8872412 1.000000e-03 0.127200 2.500000e-02 0.171560 0.022000 0.105750 0.101000 0.152510 1.474000 0.481780 0.305000 0.200340 GAG TCGA-IB-A5SP-01A-11D-A32N-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 0 0 1 337 670 0 207 0 0 0 0 207 2 0 0 0 0 0 2 1 1.000000 331 657 0 207 2 0 0 0 0 207 2 -1.349145 0 1 120900 2715 71 1 0 0 0 2.149781 0 0.740000 1.770000 0.736094 8.800000e-01 8.000000e-01 0.970000 0.890000 0.891598 8.800000e-01 1 8.400000e-01 0.930000 MUC16 94025 broad.mit.edu 37 19 9057140 9057140 + Missense_Mutation SNP C C A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr19:9057140C>A ENST00000397910.4 - 3 30509 c.30306G>T c.(30304-30306)atG>atT p.M10102I NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 590 TGGTCACTGCCATGCTTGAAG 0.468000 0 SO:0001583 missense ENST00000397910.4 1 1 hg19 CCDS54212.1 . . . . . . . . . . c 3.031000 -0.199690 0.062190 . . ENSG00000181143 ENST00000397910 T 0.20200 2.09 2.600000 -5.210000 0.028150 . . . . . T 0.07954 0.0199 N 0.08118 0 . . . B 0.02656 0.0 B 0.01281 0.0 T 0.29427 -1.0012 8 0.87932 D 0 . 1.7767 0.03023 0.1437:0.3395:0.3098:0.2071 . 10102 B5ME49 . I 10102 ENSP00000381008:M10102I ENSP00000381008:M10102I M - 3 0 MUC16 8918140 0 0.058580 0 0.037020 0.013000 0.082790 -3.069000 0.006190 -1.862000 0.011510 -1.436000 0.010780 ATG TCGA-IB-A5SP-01A-11D-A32N-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 1 0 1 127 268 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 1.000000 126 267 0 65 2 0 0 0 0 66 2 -11.413900 1 1 0 0 1 0 0 0 2.149781 0 0.740000 1.770000 0.736094 8.500000e-01 7.300000e-01 0.970000 0.860000 0.857421 8.500000e-01 1 7.800000e-01 0.920000 MUC16 94025 broad.mit.edu 37 19 9089947 9089947 + Missense_Mutation SNP G G T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr19:9089947G>T ENST00000397910.4 - 1 2071 c.1868C>A c.(1867-1869)aCa>aAa p.T623K NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 590 TAGGTGGGTTGTGCCCTGGCT 0.577000 0 SO:0001583 missense ENST00000397910.4 1 1 hg19 CCDS54212.1 . . . . . . . . . . g 3.239000 -0.155665 0.065440 . . ENSG00000181143 ENST00000397910 T 0.02472 4.28 1.680000 -0.919000 0.104780 . . . . . T 0.01489 0.0048 N 0.08118 0 . . . B 0.23540 0.087 B 0.15870 0.014 T 0.46247 -0.9205 8 0.87932 D 0 . 2.1688 0.03844 0.2075:0.0:0.4212:0.3713 . 623 B5ME49 . K 623 ENSP00000381008:T623K ENSP00000381008:T623K T - 2 0 MUC16 8950947 0 0.058580 0 0.037020 0.046000 0.143060 -0.135000 0.104200 -0.188000 0.104990 0.205000 0.176910 ACA TCGA-IB-A5SP-01A-11D-A32N-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 1 0 1 130 257 0 76 0 0 0 0 76 2 0 0 0 0 0 2 1 1.000000 128 254 0 76 2 0 0 0 0 76 2 -20.000000 1 1 121378 14 43 1 0 0 0 2.149781 0 0.740000 1.770000 0.736094 8.800000e-01 7.600000e-01 1.000000 1.000000 0.894340 8.800000e-01 1 8.200000e-01 0.960000 KCNA3 3738 broad.mit.edu 37 1 111216789 111216789 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr1:111216789C>T ENST00000369769.2 - 1 866 c.643G>A c.(643-645)Gac>Aac p.D215N NM_002232.3 NP_002223.3 P22001 KCNA3_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 3 38 all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398) Dalfampridine(DB06637) CGCTGGAAGTCGCGGCGGGGC 0.682000 0 SO:0001583 missense ENST00000369769.2 1 1 hg19 CCDS828.2 . . . . . . . . . . C 16.640000 3.180330 0.578000 . . ENSG00000177272 ENST00000369769 D 0.96830 -4.14 4.800000 3.870000 0.446320 . 0.844686 0.10366 U 0.683427 D 0.89332 0.6685 L 0.28192 0.835 0.41461 D 0.988045 P 0.34699 0.464 B 0.28849 0.095 D 0.85442 0.1155 10 0.87932 D 0 . 14.8698 0.70448 0.0:0.8552:0.1448:0.0 . 215 P22001 KCNA3_HUMAN N 215 ENSP00000358784:D215N ENSP00000358784:D215N D - 1 0 KCNA3 111018312 1 0.714170 9.970000e-01 0.539660 0.998000 0.957120 4.873000 0.630570 0.986000 0.386830 0.561000 0.740990 GAC TCGA-IB-A5SP-01A-11D-A32N-08 KCNA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083391.1 0 0 0 15 541 0 138 0 0 0 0 138 2 0 0 0 0 0 2 1 0.999676 14 475 0 112 2 0 0 0 0 138 2 -12.714770 1 1 0 0 1 0 1 1 2.013778 1 0.740000 1.770000 0.703839 6.000000e-02 3.000000e-02 0.100000 0.070000 0.068001 6.000000e-02 0 4.000000e-02 0.090000 PRDM2 7799 broad.mit.edu 37 1 14108213 14108213 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr1:14108213G>A ENST00000235372.7 + 8 4779 c.3923G>A c.(3922-3924)cGt>cAt p.R1308H PRDM2_ENST00000311066.5_Missense_Mutation_p.R1308H|PRDM2_ENST00000343137.4_Missense_Mutation_p.R1107H|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000413440.1_Missense_Mutation_p.R1107H NM_012231.4 NP_036363.2 Q13029 PRDM2_HUMAN PR domain containing 2, with ZNF domain 55 Ovarian(185;0.249) all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255) GBM - Glioblastoma multiforme(2;0.00182) TACCATCACCGTAACCCCATG 0.443000 0 SO:0001583 missense ENST00000235372.7 0 1 hg19 CCDS150.1 . . . . . . . . . . G 17.900000 3.502016 0.642980 . . ENSG00000116731 ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137 T;T;T;T 0.02050 4.59;4.48;4.48;4.48 6.170000 5.270000 0.740610 . 0.000000 0.85682 D 0.000000 T 0.06234 0.0161 L 0.29908 0.895 0.47037 D 0.999293 D;B;B 0.89917 1.0;0.167;0.257 D;B;B 0.74023 0.982;0.031;0.042 T 0.38672 -0.9650 10 0.87932 D 0 . 10.4416 0.44469 0.1477:0.0:0.8523:0.0 . 1166;1308;1308 Q5THJ0;Q13029;Q13029-2 .;PRDM2_HUMAN;. H 1308;1308;1308;1107;1107 ENSP00000235372:R1308H;ENSP00000312352:R1308H;ENSP00000411103:R1107H;ENSP00000341621:R1107H ENSP00000235372:R1308H R + 2 0 PRDM2 13980800 1 0.714170 9.990000e-01 0.593770 0.823000 0.465620 6.781000 0.750680 1.635000 0.505120 0.655000 0.942530 CGT TCGA-IB-A5SP-01A-11D-A32N-08 PRDM2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000021792.2 0 0 0 7 776 1 156 0 1.907308e-02 0 20 1 156 2 0 0 0 0 0 2 0 0.027969 6 764 1 156 17 0 0 0 1 156 2 -2.101181 0 1 121412 2 36 1 0 1 1 2.024600 1 0.740000 1.770000 0.708749 1.000000e-02 0 0.050000 0.020000 0.023370 1.000000e-02 0 0 0.030000 RGL1 23179 broad.mit.edu 37 1 183885789 183885789 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr1:183885789G>A ENST00000360851.3 + 16 2136 c.1958G>A c.(1957-1959)cGc>cAc p.R653H RGL1_ENST00000539189.1_Missense_Mutation_p.R624H|RGL1_ENST00000304685.4_Missense_Mutation_p.R688H|RGL1_ENST00000536277.1_Missense_Mutation_p.R651H Q9NZL6 RGL1_HUMAN ral guanine nucleotide dissociation stimulator-like 1 51 TGCATAATCCGCATCAGTGTG 0.498000 0 SO:0001583 missense ENST00000360851.3 0 1 hg19 . . . . . . . . . . G 35.000000 5.454279 0.962230 . . ENSG00000143344 ENST00000304685;ENST00000367531;ENST00000536277;ENST00000360851;ENST00000539189 T;T;T;T;T 0.25579 1.79;1.79;1.79;1.79;1.79 5.430000 5.430000 0.792020 Ras-association (3); 0.000000 0.85682 D 0.000000 T 0.58221 0.2107 M 0.85197 2.74 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.999;0.998;0.998;0.998 T 0.64567 -0.6377 10 0.87932 D 0 . 18.8583 0.92262 0.0:0.0:1.0:0.0 . 624;651;653;688 F5H6U6;B7Z2W5;Q9NZL6;Q5SXQ6 .;.;RGL1_HUMAN;. H 688;688;651;653;624 ENSP00000303192:R688H;ENSP00000356501:R688H;ENSP00000438662:R651H;ENSP00000354097:R653H;ENSP00000437355:R624H ENSP00000303192:R688H R + 2 0 RGL1 182152412 1 0.714170 1 0.803570 0.990000 0.784780 9.401000 0.972940 2.555000 0.861850 0.650000 0.862430 CGC TCGA-IB-A5SP-01A-11D-A32N-08 RGL1-002 KNOWN basic|appris_candidate protein_coding protein_coding OTTHUMT00000085742.1 0 0 0 5 383 0 85 0 1.335087e-02 0 11 0 85 2 0 0 0 0 0 2 1 0.934902 5 376 0 84 2 0 0 0 0 85 2 -2.406972 0 1 121412 3 37 1 0 1 1 2.004601 1 0.740000 1.770000 0.703839 2.000000e-02 0 0.070000 0.030000 0.036194 2.000000e-02 0 1.000000e-02 0.050000 HMCN1 83872 broad.mit.edu 37 1 185892601 185892601 + Missense_Mutation SNP C C G TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr1:185892601C>G ENST00000271588.4 + 8 1330 c.1101C>G c.(1099-1101)atC>atG p.I367M HMCN1_ENST00000367492.2_Missense_Mutation_p.I367M NM_031935.2 NP_114141.2 Q96RW7 HMCN1_HUMAN hemicentin 1 308 TTTTGAGTATCTCAGGAAGTT 0.353000 0 SO:0001583 missense ENST00000271588.4 1 1 hg19 CCDS30956.1 . . . . . . . . . . C 17.160000 3.318610 0.605240 . . ENSG00000143341 ENST00000271588;ENST00000367492 T;T 0.64438 -0.1;-0.1 5.400000 3.430000 0.392720 . 0.260319 0.43579 D 0.000544 T 0.53753 0.1816 L 0.47716 1.5 0.33535 D 0.594146 P 0.43169 0.8 B 0.42462 0.388 T 0.61850 -0.6978 10 0.34782 T 0.22 . 8.7355 0.34525 0.2826:0.6415:0.0:0.0759 . 367 Q96RW7 HMCN1_HUMAN M 367 ENSP00000271588:I367M;ENSP00000356462:I367M ENSP00000271588:I367M I + 3 3 HMCN1 184159224 1 0.714170 9.990000e-01 0.593770 0.997000 0.918780 3.005000 0.495210 0.558000 0.291350 0.655000 0.942530 ATC TCGA-IB-A5SP-01A-11D-A32N-08 HMCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131848.1 0 0 0 7 212 0 43 0 0 0 0 43 2 0 0 0 0 0 2 1 0.980795 7 212 0 42 2 0 0 0 0 43 2 -8.765153 1 1 0 0 1 0 1 1 2.004601 1 0.740000 1.770000 0.703839 7.000000e-02 3.000000e-02 0.150000 0.080000 0.085730 7.000000e-02 0 5.000000e-02 0.110000 KDM5B 10765 broad.mit.edu 37 1 202702804 202702804 + Missense_Mutation SNP C C A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr1:202702804C>A ENST00000367265.3 - 23 4798 c.3634G>T c.(3634-3636)Ggc>Tgc p.G1212C KDM5B_ENST00000367264.2_Missense_Mutation_p.G1248C NM_006618.3 NP_006609.3 Q9UGL1 KDM5B_HUMAN lysine (K)-specific demethylase 5B 6 ATTCGCAGGCCCTGTGAAATA 0.542000 0 SO:0001583 missense ENST00000367265.3 1 1 hg19 CCDS30974.1 . . . . . . . . . . C 17.450000 3.391676 0.620660 . . ENSG00000117139 ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790 D;D;D 0.88046 -2.33;-2.33;-2.33 6.090000 4.150000 0.487050 Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1); 0.449783 0.28871 N 0.013866 D 0.91036 0.7180 M 0.91140 3.18 0.33999 D 0.650031 P;P 0.49696 0.927;0.814 P;P 0.49276 0.605;0.563 D 0.93343 0.6711 10 0.56958 D 0.05 -5.713 9.9016 0.41351 0.0:0.8245:0.0:0.1755 . 1248;1212 Q9UGL1-2;Q9UGL1 .;KDM5B_HUMAN C 1212;1054;1248;1054 ENSP00000356234:G1212C;ENSP00000356233:G1248C;ENSP00000235790:G1054C ENSP00000235790:G1054C G - 1 0 KDM5B 200969427 4.320000e-01 0.255540 1.100000e-02 0.149720 0.797000 0.450370 0.847000 0.276960 0.798000 0.339940 0.643000 0.837060 GGC TCGA-IB-A5SP-01A-11D-A32N-08 KDM5B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000099184.2 1 0 1 135 143 0 52 1 1 18 21 0 52 2 0 0 0 0 0 2 1 1.000000 134 142 0 51 2 0 0 0 0 52 2 -20.000000 1 1 0 0 1 0 1 1 2.004601 1 0.740000 1.770000 0.703839 9.900000e-01 9.900000e-01 1.000000 1.000000 0.999589 9.900000e-01 1 9.900000e-01 1.000000 USH2A 7399 broad.mit.edu 37 1 215933091 215933091 + Silent SNP T T C TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr1:215933091T>C ENST00000307340.3 - 57 11528 c.11142A>G c.(11140-11142)caA>caG p.Q3714Q USH2A_ENST00000366943.2_Silent_p.Q3714Q NM_206933.2 NP_996816 O75445 USH2A_HUMAN Usher syndrome 2A (autosomal recessive, mild) 527 TCAATTGATATTGAGAAACGA 0.428000 HNSCC(13;0.011) 0 SO:0001819 synonymous_variant ENST00000307340.3 1 1 hg19 CCDS31025.1 TCGA-IB-A5SP-01A-11D-A32N-08 USH2A-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128138.1 1 0 1 112 314 0 79 0 0 0 0 79 2 0 0 0 0 0 2 1 1.000000 111 310 0 78 2 0 0 0 0 79 2 -20.000000 1 1 0 0 1 0 1 1 2.004601 1 0.740000 1.770000 0.703839 6.100000e-01 5.200000e-01 0.720000 0.620000 0.625822 6.100000e-01 0 5.600000e-01 0.670000 PLD5 200150 broad.mit.edu 37 1 242253380 242253380 + Missense_Mutation SNP G G C TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr1:242253380G>C ENST00000536534.2 - 10 1628 c.1387C>G c.(1387-1389)Cag>Gag p.Q463E PLD5_ENST00000427495.1_Missense_Mutation_p.Q401E|PLD5_ENST00000442594.2_Missense_Mutation_p.Q371E Q8N7P1 PLD5_HUMAN phospholipase D family, member 5 55 Melanoma(84;0.242) OV - Ovarian serous cystadenocarcinoma(106;0.0329) CCAGCATTCTGAGTGAAATCA 0.398000 0 SO:0001583 missense ENST00000536534.2 1 1 hg19 CCDS1621.2 . . . . . . . . . . G 0.017000 -1.505959 0.009920 . . ENSG00000180287 ENST00000427495;ENST00000442594;ENST00000536534 T;T;T 0.22134 1.97;1.97;1.97 5.770000 5.770000 0.911460 . 0.137275 0.53938 D 0.000055 T 0.16599 0.0399 L 0.49126 1.545 0.30380 N 0.782052 B;P;B 0.39250 0.372;0.665;0.372 B;B;B 0.32677 0.15;0.119;0.15 T 0.10870 -1.0611 10 0.08837 T 0.75 -7.7223 13.5982 0.62002 0.0:0.0:0.8451:0.1548 . 371;463;401 Q8N7P1-2;Q8N7P1;Q8N7P1-4 .;PLD5_HUMAN;. E 401;371;463 ENSP00000401285:Q401E;ENSP00000414188:Q371E;ENSP00000440896:Q463E ENSP00000401285:Q401E Q - 1 0 PLD5 240320003 1 0.714170 1 0.803570 0.064000 0.161820 3.937000 0.565750 2.723000 0.932090 0.655000 0.942530 CAG TCGA-IB-A5SP-01A-11D-A32N-08 PLD5-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397213.2 1 0 1 125 295 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 1.000000 125 292 0 86 2 0 0 0 0 87 2 -9.305342 1 1 0 0 1 0 1 1 1.963230 1 0.740000 1.770000 0.697463 6.800000e-01 5.800000e-01 0.790000 0.690000 0.692794 6.800000e-01 0 6.300000e-01 0.740000 SDCCAG8 10806 broad.mit.edu 37 1 243456473 243456473 + Silent SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr1:243456473C>T ENST00000366541.3 + 6 745 c.627C>T c.(625-627)gaC>gaT p.D209D SDCCAG8_ENST00000496361.1_3'UTR|SDCCAG8_ENST00000355875.4_Intron|SDCCAG8_ENST00000391846.1_Silent_p.D209D|SDCCAG8_ENST00000343783.6_Silent_p.D64D NM_006642.3 NP_006633.1 Q86SQ7 SDCG8_HUMAN serologically defined colon cancer antigen 8 29 all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218) all_cancers(173;0.00395) all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392) TTTCCCATGACAATGCAGATT 0.403000 0 SO:0001819 synonymous_variant ENST00000366541.3 0 1 hg19 CCDS31075.1 TCGA-IB-A5SP-01A-11D-A32N-08 SDCCAG8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096485.1 0 0 0 7 388 0 66 0 7.609216e-02 0 22 0 66 2 0 0 0 0 0 2 1 0.979552 7 381 0 66 2 0 0 0 0 66 2 -6.752073 1 1 0 0 1 0 1 1 1.963230 1 0.740000 1.770000 0.697463 4.000000e-02 1.000000e-02 0.080000 0.040000 0.046796 4.000000e-02 0 2.000000e-02 0.060000 MAP3K6 9064 broad.mit.edu 37 1 27687469 27687469 + Silent SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr1:27687469C>T ENST00000493901.1 - 15 2102 c.1863G>A c.(1861-1863)acG>acA p.T621T MAP3K6_ENST00000374040.3_Silent_p.T613T|MAP3K6_ENST00000357582.2_Silent_p.T621T NM_004672.3 NP_004663.3 O95382 M3K6_HUMAN mitogen-activated protein kinase kinase kinase 6 10 all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) AATCCGGGTTCGTCACCCAGG 0.716000 0 SO:0001819 synonymous_variant ENST00000493901.1 1 1 hg19 CCDS299.1 . . . . . . . . . . C 10.640000 1.407554 0.253780 . . ENSG00000142733 ENST00000472410 . . . 5.200000 -0.331000 0.126790 . . . . . T 0.20414 0.0491 . . . 0.09310 N 0.999998 . . . . . . T 0.23368 -1.0190 4 . . . . 1.4977 0.02470 0.1414:0.4258:0.1589:0.2739 . . . . Q 345 . . R - 2 0 MAP3K6 27560056 2.000000e-03 0.142020 9.550000e-01 0.393950 0.932000 0.569680 -1.018000 0.036260 0.198000 0.204070 0.655000 0.942530 CGA TCGA-IB-A5SP-01A-11D-A32N-08 MAP3K6-001 KNOWN alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000013469.2 1 0 1 19 85 0 29 1 9.955304e-01 3 40 0 29 2 0 0 0 0 0 2 1 0.999994 18 84 0 29 2 0 0 0 0 29 2 -20.000000 1 1 0 0 1 0 2 2 2.056041 1 0.740000 1.770000 0.740000 5.200000e-01 3.200000e-01 1.000000 0.490000 0.593906 5.200000e-01 0 4.100000e-01 1.000000 MATN1 4146 broad.mit.edu 37 1 31188936 31188936 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr1:31188936G>A ENST00000373765.4 - 5 1062 c.1027C>T c.(1027-1029)Cgg>Tgg p.R343W MATN1-AS1_ENST00000454613.1_RNA|MATN1-AS1_ENST00000414763.1_RNA|MATN1_ENST00000477320.1_5'UTR|MATN1-AS1_ENST00000414532.2_RNA NM_002379.3 NP_002370.1 P21941 MATN1_HUMAN matrilin 1, cartilage matrix protein 12 Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123) GACATATTCCGCACAGCCGCC 0.592000 0 SO:0001583 missense ENST00000373765.4 0 1 hg19 CCDS336.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 20.400000 3.990861 0.747030 . . ENSG00000162510 ENST00000373765 T 0.79554 -1.28 5.340000 0.615000 0.176080 von Willebrand factor, type A (3); . . . . D 0.88179 0.6367 M 0.78285 2.405 0.35079 D 0.763242 D;D 0.89917 0.999;1.0 D;D 0.68483 0.958;0.958 D 0.91112 0.4923 9 0.72032 D 0.01 -22.2694 14.8171 0.70041 0.0:0.0:0.2392:0.7608 . 327;343 A3KMG0;P21941 .;MATN1_HUMAN W 343 ENSP00000362870:R343W ENSP00000362870:R343W R - 1 2 MATN1 30961523 1 0.714170 9.980000e-01 0.565050 0.996000 0.888480 4.748000 0.621480 0.193000 0.203030 0.650000 0.862430 CGG TCGA-IB-A5SP-01A-11D-A32N-08 MATN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000010458.1 0 0 0 7 541 0 131 0 0 0 0 131 2 0 0 0 0 0 2 1 0.980210 8 536 0 130 2 0 0 0 0 131 2 -2.116668 0 1 121412 1 28 1 0 2 2 2.056041 1 0.740000 1.770000 0.740000 3.000000e-02 0 1.000000 0.040000 0.206485 3.000000e-02 0 1.000000e-02 1.000000 NINL 22981 broad.mit.edu 37 20 25462667 25462667 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr20:25462667G>A ENST00000278886.6 - 14 1820 c.1747C>T c.(1747-1749)Cgg>Tgg p.R583W NINL_ENST00000422516.1_Missense_Mutation_p.R583W NM_025176.4 NP_079452.3 Q9Y2I6 NINL_HUMAN ninein-like 57 GGGCTGTGCCGGTTCTTGGGC 0.692000 0 SO:0001583 missense ENST00000278886.6 0 1 hg19 CCDS33452.1 . . . . . . . . . . G 12.920000 2.083873 0.367580 . . ENSG00000101004 ENST00000278886;ENST00000422516 T;T 0.34859 1.58;1.34 4.730000 -5.110000 0.029010 . 2.414770 0.01809 N 0.033350 T 0.27765 0.0683 L 0.46741 1.465 0.09310 N 1 B;B 0.26147 0.143;0.001 B;B 0.15484 0.013;0.0 T 0.25433 -1.0132 10 0.51188 T 0.08 -6.8188 5.0826 0.14664 0.3951:0.0:0.3319:0.273 . 583;583 Q9Y2I6-2;Q9Y2I6 .;NINL_HUMAN W 583 ENSP00000278886:R583W;ENSP00000410431:R583W ENSP00000278886:R583W R - 1 2 NINL 25410667 0 0.058580 0 0.037020 0.001000 0.015030 -0.540000 0.061060 -0.682000 0.051970 0.555000 0.697020 CGG TCGA-IB-A5SP-01A-11D-A32N-08 NINL-007 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000078445.3 0 0 0 6 577 0 166 0 6.775956e-03 0 10 0 166 2 0 0 0 0 0 2 1 0.964371 6 573 0 166 2 0 0 0 0 166 2 -3.201131 1 1 121200 4 38 1 1 2 3 2.231308 0 0.740000 1.770000 0.741910 2.000000e-02 0 0.070000 0.030000 0.041081 2.000000e-02 0 1.000000e-02 0.050000 TOX2 84969 broad.mit.edu 37 20 42694515 42694515 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr20:42694515G>A ENST00000358131.5 + 6 1278 c.1070G>A c.(1069-1071)cGg>cAg p.R357Q TOX2_ENST00000372999.1_Missense_Mutation_p.R333Q|TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000341197.4_Missense_Mutation_p.R375Q|TOX2_ENST00000423191.2_Missense_Mutation_p.R333Q NM_001098798.1 NP_001092268.1 Q96NM4 TOX2_HUMAN TOX high mobility group box family member 2 26 Myeloproliferative disorder(115;0.00452) COAD - Colon adenocarcinoma(18;0.00189) AGCCTCGCCCGGACGCTGGGC 0.706000 0 SO:0001583 missense ENST00000358131.5 1 1 hg19 CCDS42875.1 . . . . . . . . . . G 14.440000 2.536841 0.451760 . . ENSG00000124191 ENST00000341197;ENST00000423191;ENST00000372999;ENST00000358131;ENST00000435864 T;T;T;T;T 0.14766 2.72;2.73;2.73;2.57;2.48 5.110000 4.160000 0.488620 . 0.000000 0.39687 N 0.001299 T 0.22003 0.0530 L 0.37850 1.14 0.45946 D 0.998777 D;D;D;D 0.76494 0.997;0.999;0.999;0.999 D;D;D;D 0.77557 0.968;0.99;0.978;0.978 T 0.03576 -1.1023 10 0.07325 T 0.83 . 12.5979 0.56481 0.0818:0.0:0.9182:0.0 . 253;375;357;333 B4DQV8;G3XAC7;Q96NM4;E1P5X0 .;.;TOX2_HUMAN;. Q 375;333;333;357;253 ENSP00000344724:R375Q;ENSP00000390278:R333Q;ENSP00000362090:R333Q;ENSP00000350849:R357Q;ENSP00000396777:R253Q ENSP00000344724:R375Q R + 2 0 TOX2 42127929 1 0.714170 9.980000e-01 0.565050 0.161000 0.222730 5.322000 0.658520 1.282000 0.444960 -0.136000 0.146810 CGG TCGA-IB-A5SP-01A-11D-A32N-08 TOX2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000079329.2 1 0 1 190 348 0 140 0 0 0 1 0 140 2 0 0 0 0 0 2 1 1.000000 188 342 0 136 2 0 0 0 0 140 2 -19.060080 1 1 121170 9 41 1 1 2 3 2.231308 0 0.740000 1.770000 0.741910 9.500000e-01 8.400000e-01 1.000000 1.000000 0.954210 9.500000e-01 1 9.000000e-01 1.000000 TSHZ2 128553 broad.mit.edu 37 20 51871857 51871857 + Silent SNP C C T rs143642849 TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr20:51871857C>T ENST00000371497.5 + 2 2747 c.1860C>T c.(1858-1860)caC>caT p.H620H TSHZ2_ENST00000603338.2_Silent_p.H617H|TSHZ2_ENST00000329613.6_Silent_p.H617H|RP4-678D15.1_ENST00000606932.1_RNA NM_001193421.1|NM_173485.5 NP_001180350.1|NP_775756.3 Q9NRE2 TSH2_HUMAN teashirt zinc finger homeobox 2 84 STAD - Stomach adenocarcinoma(23;0.1) AAAGTCCCCACGAAGAGGCCT 0.517000 0 SO:0001819 synonymous_variant ENST00000371497.5 1 1 hg19 CCDS33490.1 TCGA-IB-A5SP-01A-11D-A32N-08 TSHZ2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080398.6 1 0 0 189 375 0 95 1 9.858197e-01 5 11 0 95 2 0 0 0 0 0 2 1 1.000000 185 369 0 95 2 0 0 0 0 95 2 -20.000000 1 1 121412 2 37 1 1 2 3 2.231308 0 0.740000 1.770000 0.741910 9.000000e-01 8.000000e-01 1.000000 0.910000 0.912890 9.000000e-01 1 8.500000e-01 0.970000 COL20A1 57642 broad.mit.edu 37 20 61929336 61929336 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr20:61929336G>A ENST00000358894.6 + 3 257 c.157G>A c.(157-159)Ggc>Agc p.G53S COL20A1_ENST00000422202.1_Missense_Mutation_p.G53S|COL20A1_ENST00000435874.1_Missense_Mutation_p.G53S|COL20A1_ENST00000326996.6_Missense_Mutation_p.G53S NM_020882.2 NP_065933.2 Q9P218 COKA1_HUMAN collagen, type XX, alpha 1 36 all_cancers(38;1.39e-10) GGAGGGGAGCGGCCTCGGCTA 0.632000 0 SO:0001583 missense ENST00000358894.6 0 1 hg19 CCDS46628.1 . . . . . . . . . . G 2.312000 -0.357702 0.051380 . . ENSG00000101203 ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202 T;T;T;T 0.56611 0.45;0.45;0.45;0.45 3.950000 -1.670000 0.082380 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.543240 0.18383 N 0.142918 T 0.27933 0.0688 N 0.14661 0.345 0.09310 N 1 B 0.21309 0.054 B 0.15484 0.013 T 0.17137 -1.0379 10 0.21014 T 0.42 . 8.946 0.35758 0.8054:0.0:0.1946:0.0 . 53 Q9P218 COKA1_HUMAN S 53 ENSP00000351767:G53S;ENSP00000323077:G53S;ENSP00000408690:G53S;ENSP00000414753:G53S ENSP00000323077:G53S G + 1 0 COL20A1 61399781 0 0.058580 5.700000e-02 0.194520 0.005000 0.049000 0.036000 0.138190 -0.160000 0.110020 -0.229000 0.122940 GGC TCGA-IB-A5SP-01A-11D-A32N-08 COL20A1-006 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000144595.2 0 0 0 7 295 0 115 0 0 0 0 115 2 0 0 0 0 0 2 1 0.979507 6 290 0 113 2 0 0 0 0 115 2 -3.730716 1 1 120818 1 32 1 1 2 3 2.231308 0 0.740000 1.770000 0.741910 6.000000e-02 2.000000e-02 0.140000 0.060000 0.080684 6.000000e-02 0 4.000000e-02 0.100000 TPTE 7179 broad.mit.edu 37 21 10969096 10969096 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr21:10969096C>T ENST00000361285.4 - 7 481 c.152G>A c.(151-153)cGg>cAg p.R51Q TPTE_ENST00000298232.7_Intron|TPTE_ENST00000342420.5_Intron|TPTE_ENST00000415664.2_Intron NM_199261.2 NP_954870 P56180 TPTE_HUMAN transmembrane phosphatase with tensin homology 130 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) AGGTGACACCCGGGCTGCTCC 0.453000 0 SO:0001583 missense ENST00000361285.4 1 1 hg19 CCDS13560.2 . . . . . . . . . . A 4.078000 0.012302 0.079120 . . ENSG00000166157 ENST00000361285;ENST00000328758 D 0.94687 -3.49 0.558000 -1.120000 0.098080 . 0.602094 0.13783 U 0.363084 T 0.81880 0.4916 N 0.08118 0 0.09310 N 1 B 0.06786 0.001 B 0.01281 0.0 T 0.63484 -0.6627 9 0.21540 T 0.41 5.8346 . . . . 51 P56180 TPTE_HUMAN Q 51;33 ENSP00000355208:R51Q ENSP00000399471:R33Q R - 2 0 TPTE 9990967 0 0.058580 0 0.037020 0.001000 0.015030 -2.181000 0.012570 -2.672000 0.004130 -2.396000 0.002260 CGG TCGA-IB-A5SP-01A-11D-A32N-08 TPTE-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000157413.1 1 0 1 195 668 0 163 0 0 0 0 163 2 0 0 0 0 0 2 1 1.000000 186 551 0 163 2 0 0 0 0 163 2 -4.869643 1 1 121412 22 43 1 0 2 2 1.924057 0 0.740000 1.770000 0.740000 6.100000e-01 5.300000e-01 1.000000 0.610000 0.660918 6.100000e-01 0 5.700000e-01 0.680000 DYRK1A 1859 broad.mit.edu 37 21 38877757 38877757 + Missense_Mutation SNP T T A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr21:38877757T>A ENST00000398960.2 + 9 1486 c.1411T>A c.(1411-1413)Tat>Aat p.Y471N DYRK1A_ENST00000339659.4_Missense_Mutation_p.Y462N|DYRK1A_ENST00000398956.2_Missense_Mutation_p.Y471N|DYRK1A_ENST00000455387.2_Missense_Mutation_p.Y243N|DYRK1A_ENST00000338785.3_Missense_Mutation_p.Y471N|DYRK1A_ENST00000451934.1_Missense_Mutation_p.Y471N|DYRK1A_ENST00000321219.8_Missense_Mutation_p.Y471N NM_001396.3|NM_130438.2 NP_001387.2|NP_569122.1 Q13627 DYR1A_HUMAN dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A 42 AATTCAACCTTATTATGCTCT 0.438000 Melanoma(114;464 1602 31203 43785 45765) 0 SO:0001583 missense ENST00000398960.2 0 1 hg19 CCDS42925.1 . . . . . . . . . . T 16.090000 3.024460 0.546830 . . ENSG00000157540 ENST00000338785;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956;ENST00000455387 T;T;T;T;T;T;T 0.63744 -0.06;-0.06;-0.06;-0.06;-0.06;-0.06;-0.06 5.830000 5.830000 0.931110 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.120768 0.64402 D 0.000014 T 0.42899 0.1223 N 0.02685 -0.53 0.80722 D 1 B;B;B;B;B 0.26845 0.005;0.005;0.161;0.133;0.005 B;B;B;B;B 0.30179 0.035;0.035;0.112;0.068;0.035 T 0.49163 -0.8968 10 0.66056 D 0.02 . 16.1946 0.82018 0.0:0.0:0.0:1.0 . 471;471;471;462;471 Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5 .;.;DYR1A_HUMAN;.;. N 471;462;471;471;471;471;243 ENSP00000342690:Y471N;ENSP00000340373:Y462N;ENSP00000319032:Y471N;ENSP00000416089:Y471N;ENSP00000381932:Y471N;ENSP00000381929:Y471N;ENSP00000407854:Y243N ENSP00000319032:Y471N Y + 1 0 DYRK1A 37799627 1 0.714170 9.990000e-01 0.593770 0.983000 0.724000 7.977000 0.880810 2.228000 0.727670 0.528000 0.532280 TAT TCGA-IB-A5SP-01A-11D-A32N-08 DYRK1A-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000194804.1 0 0 0 5 417 0 110 0 2.084297e-02 0 15 0 110 2 0 0 0 0 0 2 1 0.937502 4 417 0 108 2 0 0 0 0 110 2 -5.377386 1 0 0 0 1 0 1 1 1.505428 1 0.740000 1.770000 0.592093 1.000000e-02 0 0.050000 0.020000 0.024238 1.000000e-02 0 0 0.030000 SLC19A1 6573 broad.mit.edu 37 21 46951654 46951654 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr21:46951654C>T ENST00000311124.4 - 3 750 c.598G>A c.(598-600)Gcc>Acc p.A200T SLC19A1_ENST00000567670.1_Missense_Mutation_p.A200T|SLC19A1_ENST00000485649.2_Missense_Mutation_p.A160T|SLC19A1_ENST00000380010.4_Missense_Mutation_p.A200T NM_194255.2 NP_919231.1 P41440 S19A1_HUMAN solute carrier family 19 (folate transporter), member 1 10 Methotrexate(DB00563)|Pralatrexate(DB06813) AGGAAGAGGGCGAGGACCACG 0.647000 0 SO:0001583 missense ENST00000311124.4 1 1 hg19 CCDS13725.1 . . . . . . . . . . C 14.350000 2.510194 0.446600 . . ENSG00000173638 ENST00000311124;ENST00000380010;ENST00000485649 T;T;T 0.81330 -1.48;-1.48;-1.48 4.620000 -5.280000 0.027550 Major facilitator superfamily domain, general substrate transporter (1); 0.404697 0.27544 N 0.018889 T 0.60830 0.2299 L 0.35288 1.05 0.25111 N 0.990718 P;P;B;P 0.35481 0.504;0.504;0.262;0.504 B;B;B;B 0.33960 0.173;0.058;0.019;0.032 T 0.55029 -0.8204 10 0.33940 T 0.23 -15.7351 5.7407 0.18092 0.2584:0.1321:0.0:0.6095 . 160;222;200;200 B7Z8C3;D3DSM6;E9PFY4;P41440 .;.;.;S19A1_HUMAN T 200;200;160 ENSP00000308895:A200T;ENSP00000369347:A200T;ENSP00000441772:A160T ENSP00000308895:A200T A - 1 0 SLC19A1 45776082 1.200000e-02 0.176700 1.720000e-01 0.229200 0.879000 0.507180 -0.237000 0.089900 -0.965000 0.035910 0.306000 0.203180 GCC TCGA-IB-A5SP-01A-11D-A32N-08 SLC19A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206796.1 1 0 0 54 44 0 47 1 8.628921e-01 4 1 0 47 2 0 0 0 0 0 2 1 1.000000 53 44 0 46 2 0 0 0 0 47 2 -20.000000 1 1 121298 2 23 1 0 1 1 1.452635 1 0.740000 1.770000 0.587302 9.000000e-01 7.500000e-01 1.000000 0.930000 0.901602 9.000000e-01 1 8.200000e-01 0.970000 HIRA 7290 broad.mit.edu 37 22 19365576 19365576 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr22:19365576C>T ENST00000263208.5 - 14 1685 c.1429G>A c.(1429-1431)Gca>Aca p.A477T HIRA_ENST00000340170.4_Missense_Mutation_p.A477T|HIRA_ENST00000541063.1_Missense_Mutation_p.A433T|HIRA_ENST00000546308.1_Missense_Mutation_p.A433T NM_003325.3 NP_003316.3 P54198 HIRA_HUMAN histone cell cycle regulator 37 Colorectal(54;0.0993) TTAAAGAATGCCGTGGAGAAG 0.488000 0 SO:0001583 missense ENST00000263208.5 0 1 hg19 CCDS13759.1 . . . . . . . . . . C 29.700000 5.030001 0.935750 . . ENSG00000100084 ENST00000340170;ENST00000263208;ENST00000541063;ENST00000546308 T;T;T;T 0.72282 -0.4;-0.64;-0.48;-0.46 5.280000 5.280000 0.743790 . 0.000000 0.85682 D 0.000000 T 0.75845 0.3905 L 0.29908 0.895 0.80722 D 1 D;D;P 0.67145 0.974;0.996;0.956 P;D;P 0.79784 0.647;0.993;0.549 T 0.69228 -0.5200 10 0.16896 T 0.51 -16.2298 19.1181 0.93350 0.0:1.0:0.0:0.0 . 433;477;477 F5H4M2;P54198-2;P54198 .;.;HIRA_HUMAN T 477;477;433;433 ENSP00000345350:A477T;ENSP00000263208:A477T;ENSP00000446073:A433T;ENSP00000441870:A433T ENSP00000263208:A477T A - 1 0 HIRA 17745576 1 0.714170 1 0.803570 0.999000 0.989320 6.297000 0.727570 2.756000 0.946170 0.655000 0.942530 GCA TCGA-IB-A5SP-01A-11D-A32N-08 HIRA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316488.2 0 0 0 5 330 0 115 0 1.890112e-01 0 44 0 115 2 0 0 0 0 0 2 1 0.936510 5 327 0 115 2 0 0 0 0 115 2 -2.013891 0 1 0 0 1 0 1 1 1.494306 1 0.740000 1.770000 0.589711 2.000000e-02 0 0.060000 0.030000 0.030412 2.000000e-02 0 1.000000e-02 0.040000 MED15 51586 broad.mit.edu 37 22 20929453 20929453 + Silent SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr22:20929453G>A ENST00000263205.7 + 9 1275 c.1206G>A c.(1204-1206)ccG>ccA p.P402P MED15_ENST00000382974.2_Intron|MED15_ENST00000542773.1_Intron|MED15_ENST00000406969.1_Intron|MED15_ENST00000292733.7_Intron|MED15_ENST00000478831.1_Intron|MED15_ENST00000425759.2_Intron|MED15_ENST00000541476.1_Intron NM_001003891.1 NP_001003891.1 Q96RN5 MED15_HUMAN mediator complex subunit 15 25 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) CCCGGTTCCCGCCTACCACCG 0.597000 0 SO:0001819 synonymous_variant ENST00000263205.7 0 1 hg19 CCDS33602.1 TCGA-IB-A5SP-01A-11D-A32N-08 MED15-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000320177.2 0 0 0 6 373 0 131 0 1.100247e-01 0 30 0 131 2 0 0 0 0 0 2 1 0.964991 6 372 0 131 2 0 0 0 0 131 2 -2.466742 0 1 0 0 1 0 1 1 1.494306 1 0.740000 1.770000 0.589711 2.000000e-02 0 0.060000 0.030000 0.031425 2.000000e-02 0 1.000000e-02 0.040000 MGAT5 4249 broad.mit.edu 37 2 135012053 135012053 + Missense_Mutation SNP A A G TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr2:135012053A>G ENST00000409645.1 + 2 331 c.79A>G c.(79-81)Atg>Gtg p.M27V MGAT5_ENST00000468758.1_3'UTR|MGAT5_ENST00000281923.2_Missense_Mutation_p.M27V Q09328 MGT5A_HUMAN mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase 36 CATTTGGGGTATGATGCTTCT 0.522000 0 SO:0001583 missense ENST00000409645.1 1 1 hg19 CCDS2171.1 . . . . . . . . . . A 17.620000 3.435716 0.629550 . . ENSG00000152127 ENST00000409645;ENST00000281923 . . . 4.880000 4.880000 0.635800 . 0.000000 0.85682 D 0.000000 T 0.63510 0.2517 L 0.38531 1.155 0.80722 D 1 P 0.43578 0.811 P 0.60789 0.879 T 0.56541 -0.7962 9 0.16420 T 0.52 -29.1494 14.9292 0.70903 1.0:0.0:0.0:0.0 . 27 Q09328 MGT5A_HUMAN V 27 . ENSP00000281923:M27V M + 1 0 MGAT5 134728523 1 0.714170 9.920000e-01 0.483790 0.996000 0.888480 9.087000 0.941100 2.162000 0.679170 0.528000 0.532280 ATG TCGA-IB-A5SP-01A-11D-A32N-08 MGAT5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254584.3 1 0 1 75 134 0 29 1 9.998141e-01 12 15 0 29 2 0 0 0 0 0 2 1 1.000000 74 134 0 29 2 0 0 0 0 29 2 -20.000000 1 1 0 0 1 1 2 3 2.252328 0 0.740000 1.770000 0.743792 9.800000e-01 8.000000e-01 1.000000 1.000000 0.957723 9.800000e-01 1 8.900000e-01 1.000000 SCN2A 6326 broad.mit.edu 37 2 166171996 166171996 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr2:166171996G>A ENST00000375437.2 + 11 1689 c.1399G>A c.(1399-1401)Gca>Aca p.A467T SCN2A_ENST00000357398.3_Missense_Mutation_p.A467T|SCN2A_ENST00000375427.2_Missense_Mutation_p.A467T|SCN2A_ENST00000283256.6_Missense_Mutation_p.A467T NM_001040142.1 NP_001035232.1 Q99250 SCN2A_HUMAN sodium channel, voltage-gated, type II, alpha subunit 118 Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909) AGCTGCAGCCGCATCTGCTGA 0.408000 0 SO:0001583 missense ENST00000375437.2 0 1 hg19 CCDS33314.1 . . . . . . . . . . G 11.480000 1.650394 0.293360 . . ENSG00000136531 ENST00000424833;ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427 D;D;D;D;D 0.96427 -4.01;-3.95;-3.95;-3.95;-3.95 5.900000 5.020000 0.671250 . 0.539045 0.18025 N 0.154104 D 0.93360 0.7883 L 0.40543 1.245 0.49483 D 0.999793 B;B 0.21520 0.055;0.057 B;B 0.19666 0.026;0.013 D 0.90222 0.4272 10 0.21540 T 0.41 . 15.0639 0.71977 0.0677:0.0:0.9323:0.0 . 467;467 Q99250-2;Q99250 .;SCN2A_HUMAN T 467 ENSP00000406454:A467T;ENSP00000364586:A467T;ENSP00000349973:A467T;ENSP00000283256:A467T;ENSP00000364576:A467T ENSP00000283256:A467T A + 1 0 SCN2A 165880242 9.940000e-01 0.377170 7.460000e-01 0.310950 0.313000 0.280210 3.124000 0.504610 1.496000 0.485670 0.650000 0.862430 GCA TCGA-IB-A5SP-01A-11D-A32N-08 SCN2A-202 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000102659.2 0 0 0 11 422 1 45 0 0 0 1 45 2 0 0 0 0 0 2 0 0.005237 11 417 1 45 27 0 0 0 1 45 2 -2.871021 1 1 121412 4 39 1 1 2 3 2.252328 0 0.740000 1.770000 0.743792 6.000000e-02 2.000000e-02 1.000000 0.070000 0.102194 6.000000e-02 0 4.000000e-02 0.100000 TTN 7273 broad.mit.edu 37 2 179436286 179436286 + Missense_Mutation SNP A A T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr2:179436286A>T ENST00000591111.1 - 276 69874 c.69650T>A c.(69649-69651)aTt>aAt p.I23217N TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I22290N|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I15793N|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I24858N|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I15985N|TTN_ENST00000359218.5_Missense_Mutation_p.I15918N|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) AGCTGATACAATTTGCCAGGT 0.418000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . A 11.560000 1.674275 0.296930 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.55760 0.5;0.5;0.5;0.5 5.930000 5.930000 0.959200 Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.53786 0.1818 N 0.14661 0.345 0.51482 D 0.999922 D;D;D;D 0.58970 0.984;0.984;0.984;0.97 P;P;P;P 0.58331 0.837;0.837;0.837;0.828 T 0.61535 -0.7043 9 0.87932 D 0 . 16.3709 0.83357 1.0:0.0:0.0:0.0 . 15793;15918;15985;23217 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN N 22290;15793;15985;15918;15791 ENSP00000343764:I22290N;ENSP00000434586:I15793N;ENSP00000340554:I15985N;ENSP00000352154:I15918N ENSP00000340554:I15985N I - 2 0 TTN 179144532 1 0.714170 1 0.803570 0.978000 0.694770 7.251000 0.782970 2.261000 0.749720 0.528000 0.532280 ATT TCGA-IB-A5SP-01A-11D-A32N-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 1 54 114 0 19 0 0 0 0 19 2 0 0 0 0 0 2 1 1.000000 54 113 0 19 2 0 0 0 0 19 2 -20.000000 1 1 0 0 1 1 2 3 2.252328 0 0.740000 1.770000 0.743792 8.800000e-01 6.900000e-01 1.000000 1.000000 0.882675 8.800000e-01 1 7.800000e-01 0.990000 ASB18 401036 broad.mit.edu 37 2 237103689 237103689 + Silent SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr2:237103689C>T ENST00000409749.3 - 6 1226 c.1227G>A c.(1225-1227)ccG>ccA p.P409P ASB18_ENST00000330842.6_Silent_p.P380P|AC079135.1_ENST00000415226.1_RNA|AC079135.1_ENST00000483218.1_RNA NM_212556.2 NP_997721.2 Q6ZVZ8 ASB18_HUMAN ankyrin repeat and SOCS box containing 18 6 all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815) ACTGGTAGAACGGCTTGTGCA 0.542000 0 SO:0001819 synonymous_variant ENST00000409749.3 1 1 hg19 CCDS46548.1 TCGA-IB-A5SP-01A-11D-A32N-08 ASB18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000329436.1 1 0 1 56 100 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 1.000000 55 99 0 33 2 0 0 0 0 34 2 -20.000000 1 1 121092 1 38 1 1 2 3 2.221947 0 0.740000 1.770000 0.741910 9.700000e-01 7.700000e-01 1.000000 1.000000 0.948228 9.700000e-01 1 8.700000e-01 1.000000 POMC 5443 broad.mit.edu 37 2 25387630 25387630 + Silent SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr2:25387630C>T ENST00000405623.1 - 2 467 c.12G>A c.(10-12)tcG>tcA p.S4S POMC_ENST00000264708.3_Silent_p.S4S|POMC_ENST00000395826.2_Silent_p.S4S|POMC_ENST00000380794.1_Silent_p.S4S P01189 COLI_HUMAN proopiomelanocortin 12 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) Loperamide(DB00836) GGCTGCAGCACGATCTCGGCA 0.607000 Colon(110;1515 1566 8452 10082 43216) 0 SO:0001819 synonymous_variant ENST00000405623.1 0 1 hg19 CCDS1717.1 TCGA-IB-A5SP-01A-11D-A32N-08 POMC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000211573.3 0 0 0 6 367 0 73 0 0 0 1 0 73 2 0 0 0 0 0 2 1 0.964100 6 363 0 73 2 0 0 0 0 73 2 -6.192198 1 1 121412 1 30 1 1 2 3 2.261196 0 0.740000 1.770000 0.744723 4.000000e-02 0 1.000000 0.040000 0.087339 4.000000e-02 0 2.000000e-02 0.080000 DPYSL5 56896 broad.mit.edu 37 2 27121503 27121503 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr2:27121503G>A ENST00000288699.6 + 2 294 c.136G>A c.(136-138)Ggc>Agc p.G46S DPYSL5_ENST00000401478.1_Missense_Mutation_p.G46S 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) CATGATCCCTGGCGGGGCCAA 0.587000 0 SO:0001583 missense ENST00000288699.6 0 1 hg19 CCDS1730.1 . . . . . . . . . . G 26.300000 4.728087 0.893900 . . ENSG00000157851 ENST00000450961;ENST00000288699;ENST00000401478;ENST00000431402;ENST00000434719 T;D;D;T;T 0.85258 -1.06;-1.96;-1.96;-1.06;-1.06 4.850000 4.850000 0.628380 Metal-dependent hydrolase, composite domain (1); 0.000000 0.85682 D 0.000000 T 0.79003 0.4373 L 0.33485 1.01 0.58432 D 0.999992 B 0.30937 0.301 B 0.28139 0.086 T 0.77253 -0.2656 10 0.37606 T 0.19 -13.6077 17.1086 0.86669 0.0:0.0:1.0:0.0 . 46 Q9BPU6 DPYL5_HUMAN S 46 ENSP00000407174:G46S;ENSP00000288699:G46S;ENSP00000385549:G46S;ENSP00000399581:G46S;ENSP00000413075:G46S ENSP00000288699:G46S G + 1 0 DPYSL5 26975007 1 0.714170 5.040000e-01 0.276390 0.986000 0.746190 9.333000 0.964590 2.403000 0.816810 0.561000 0.740990 GGC TCGA-IB-A5SP-01A-11D-A32N-08 DPYSL5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214187.2 0 0 0 4 315 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 0.888013 4 311 0 62 2 0 0 0 0 63 2 -4.889804 1 1 0 0 1 1 2 3 2.261196 0 0.740000 1.770000 0.744723 3.000000e-02 0 1.000000 0.040000 0.078814 3.000000e-02 0 1.000000e-02 0.070000 MCF2L2 23101 broad.mit.edu 37 3 183027561 183027561 + Silent SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr3:183027561G>A ENST00000328913.3 - 10 1353 c.1056C>T c.(1054-1056)agC>agT p.S352S MCF2L2_ENST00000473233.1_Silent_p.S352S|MCF2L2_ENST00000414362.2_Silent_p.S352S|MCF2L2_ENST00000447025.2_Silent_p.S352S NM_015078.2 NP_055893 Q86YR7 MF2L2_HUMAN MCF.2 cell line derived transforming sequence-like 2 72 all_cancers(143;1.26e-12)|Ovarian(172;0.0355) all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21) CGTGCATCACGCTGTCTCCAA 0.448000 0 SO:0001819 synonymous_variant ENST00000328913.3 1 1 hg19 CCDS3243.1 TCGA-IB-A5SP-01A-11D-A32N-08 MCF2L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350868.1 0 0 0 11 402 0 84 0 2.650169e-03 0 3 0 84 2 0 0 0 0 0 2 1 0.998337 11 400 0 82 2 0 0 0 0 84 2 -2.872809 1 1 121412 3 36 1 0 1 1 1.954591 1 0.740000 1.770000 0.700046 6.000000e-02 2.000000e-02 0.110000 0.060000 0.067680 6.000000e-02 0 4.000000e-02 0.090000 PCYT1A 5130 broad.mit.edu 37 3 195965646 195965646 + Silent SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr3:195965646G>A ENST00000292823.2 - 10 1189 c.1017C>T c.(1015-1017)tcC>tcT p.S339S PCYT1A_ENST00000419333.1_Silent_p.S339S|PCYT1A_ENST00000431016.1_Silent_p.S339S NM_005017.2 NP_005008.2 P49585 PCY1A_HUMAN phosphate cytidylyltransferase 1, choline, alpha 18 all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206) Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06) Choline(DB00122)|Lamivudine(DB00709) AAGTCTTGCCGGAGAAGGGCC 0.607000 0 SO:0001819 synonymous_variant ENST00000292823.2 0 1 hg19 CCDS3315.1 TCGA-IB-A5SP-01A-11D-A32N-08 PCYT1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000341147.1 0 0 0 5 355 1 89 0 9.179977e-03 0 87 1 89 6 0 0 0 0 0 2 0 0.017052 6 347 1 86 15 0 0 0 1 89 2 -2.727133 1 1 121406 15 43 1 0 1 1 1.964826 1 0.740000 1.770000 0.701321 3.000000e-02 0 0.070000 0.030000 0.038766 3.000000e-02 0 1.000000e-02 0.050000 OSBPL10 114884 broad.mit.edu 37 3 31789494 31789494 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr3:31789494G>A ENST00000396556.2 - 5 970 c.848C>T c.(847-849)gCt>gTt p.A283V OSBPL10_ENST00000438237.2_Missense_Mutation_p.A219V|OSBPL10_ENST00000467647.1_5'UTR NM_017784.4 NP_060254.2 Q9BXB5 OSB10_HUMAN oxysterol binding protein-like 10 34 GAGGGTGGCAGCAGAGGTAGC 0.637000 0 SO:0001583 missense ENST00000396556.2 0 1 hg19 CCDS2651.1 . . . . . . . . . . G 20.500000 4.000746 0.748180 . . ENSG00000144645 ENST00000396556;ENST00000438237;ENST00000428241 T;T;T 0.45276 0.9;0.9;0.9 5.610000 4.740000 0.602240 . 0.047989 0.85682 D 0.000000 T 0.62962 0.2471 M 0.74881 2.28 0.50171 D 0.999853 D;P;P 0.89917 1.0;0.949;0.901 D;P;P 0.87578 0.998;0.642;0.49 T 0.62320 -0.6879 10 0.30078 T 0.28 -12.5971 14.4653 0.67480 0.0704:0.0:0.9296:0.0 . 219;283;51 B4E212;Q9BXB5;Q59ED9 .;OSB10_HUMAN;. V 283;219;91 ENSP00000379804:A283V;ENSP00000406124:A219V;ENSP00000399200:A91V ENSP00000379804:A283V A - 2 0 OSBPL10 31764498 1 0.714170 2.950000e-01 0.249600 0.993000 0.825480 9.459000 0.976380 1.367000 0.460950 0.549000 0.686330 GCT TCGA-IB-A5SP-01A-11D-A32N-08 OSBPL10-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000253165.2 0 0 0 5 509 0 122 0 4.021961e-02 0 26 0 122 2 0 0 0 0 0 2 0 0.018499 5 504 1 121 15 0 0 0 0 122 2 -2.680701 1 1 0 0 1 0 1 1 1.952909 1 0.740000 1.770000 0.697463 2.000000e-02 0 0.050000 0.020000 0.026381 2.000000e-02 0 0 0.040000 RNF123 63891 broad.mit.edu 37 3 49738081 49738081 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr3:49738081C>T ENST00000327697.6 + 15 1360 c.1216C>T c.(1216-1218)Cgg>Tgg p.R406W RNF123_ENST00000432042.1_Missense_Mutation_p.R260W NM_022064.3 NP_071347.2 Q5XPI4 RN123_HUMAN ring finger protein 123 38 CCATTACCTGCGGCTCACTAT 0.607000 0 SO:0001583 missense ENST00000327697.6 0 1 hg19 CCDS33758.1 . . . . . . . . . . C 23.100000 4.373157 0.825730 0.0 1.16E-4 ENSG00000164068 ENST00000327697;ENST00000389066;ENST00000432042 T;T 0.76060 -0.7;-0.99 5.260000 3.380000 0.387090 . 0.575264 0.18160 N 0.149820 T 0.68081 0.2962 N 0.19112 0.55 0.80722 D 1 D;D 0.65815 0.995;0.988 P;P 0.50231 0.635;0.513 T 0.68629 -0.5358 10 0.56958 D 0.05 -11.9117 13.28 0.60208 0.2744:0.7256:0.0:0.0 . 260;406 C9J266;Q5XPI4 .;RN123_HUMAN W 406;406;260 ENSP00000328287:R406W;ENSP00000392443:R260W ENSP00000328287:R406W R + 1 2 RNF123 49713085 1 0.714170 9.960000e-01 0.522420 0.974000 0.676020 3.753000 0.551800 0.541000 0.288270 0.561000 0.740990 CGG TCGA-IB-A5SP-01A-11D-A32N-08 RNF123-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346475.2 0 0 0 6 628 0 169 0 4.653204e-02 0 30 0 169 2 0 0 0 0 0 2 1 0.962973 6 616 0 165 2 0 0 0 0 169 2 -2.683539 1 1 121412 2 38 1 0 1 1 1.952909 1 0.740000 1.770000 0.697463 1.000000e-02 0 0.050000 0.020000 0.024732 1.000000e-02 0 0 0.040000 C4orf17 84103 broad.mit.edu 37 4 100460491 100460491 + Missense_Mutation SNP T T C TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr4:100460491T>C ENST00000326581.4 + 7 1162 c.800T>C c.(799-801)gTg>gCg p.V267A C4orf17_ENST00000514652.1_Missense_Mutation_p.V267A NM_032149.2 NP_115525.2 Q53FE4 CD017_HUMAN chromosome 4 open reading frame 17 18 AAATCAAAAGTGCTGACCAGA 0.458000 0 SO:0001583 missense ENST00000326581.4 1 1 hg19 CCDS3649.1 . . . . . . . . . . T 10.360000 1.329614 0.241670 . . ENSG00000138813 ENST00000326581;ENST00000514652 T;T 0.18810 2.21;2.19 5.030000 -0.460000 0.121750 . 0.437967 0.19567 N 0.111193 T 0.13841 0.0335 L 0.39898 1.24 0.09310 N 1 B 0.20052 0.041 B 0.19666 0.026 T 0.29731 -1.0002 10 0.20519 T 0.43 -0.8055 7.9028 0.29744 0.0:0.5021:0.0:0.4979 . 267 Q53FE4 CD017_HUMAN A 267 ENSP00000322582:V267A;ENSP00000427663:V267A ENSP00000322582:V267A V + 2 0 C4orf17 100679514 1.400000e-01 0.225790 6.800000e-02 0.199680 0.002000 0.026280 0.035000 0.137970 0.052000 0.160070 -0.290000 0.098290 GTG TCGA-IB-A5SP-01A-11D-A32N-08 C4orf17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253670.2 0 0 0 21 274 1 61 0 0 0 1 61 2 0 0 0 0 0 2 1 0.843303 21 274 1 61 16 0 0 0 1 61 2 -7.039774 1 1 0 0 1 0 1 1 1.671928 1 0.740000 1.770000 0.630682 1.300000e-01 8.000000e-02 0.200000 0.140000 0.140660 1.300000e-01 0 1.000000e-01 0.170000 GK2 2712 broad.mit.edu 37 4 80328648 80328648 + Missense_Mutation SNP G G C TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr4:80328648G>C ENST00000358842.3 - 1 724 c.707C>G c.(706-708)tCt>tGt p.S236C NM_033214.2 NP_149991.2 Q01415 GALK2_HUMAN glycerol kinase 2 39 GATCTCAGAAGAACTGAAGAC 0.413000 0 SO:0001583 missense ENST00000358842.3 1 1 hg19 CCDS3585.1 . . . . . . . . . . G 5.559000 0.287923 0.105130 . . ENSG00000196475 ENST00000358842 T 0.58060 0.36 4.570000 2.800000 0.328190 Carbohydrate kinase, FGGY, N-terminal (1); 0.115441 0.64402 N 0.000010 T 0.53206 0.1782 M 0.71581 2.175 0.58432 D 0.999998 B 0.31290 0.318 B 0.34093 0.175 T 0.57860 -0.7738 10 0.72032 D 0.01 -10.4064 13.132 0.59389 0.0:0.3081:0.6919:0.0 . 236 Q14410 GLPK2_HUMAN C 236 ENSP00000351706:S236C ENSP00000351706:S236C S - 2 0 GK2 80547672 1 0.714170 9.990000e-01 0.593770 0.136000 0.210420 3.061000 0.499630 0.612000 0.300710 -0.203000 0.127340 TCT TCGA-IB-A5SP-01A-11D-A32N-08 GK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252517.2 1 0 0 29 328 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 1.000000 26 326 0 73 2 0 0 0 0 73 2 -9.428238 1 1 0 0 1 0 1 1 1.671928 1 0.740000 1.770000 0.630682 1.500000e-01 1.000000e-01 0.210000 0.150000 0.158739 1.500000e-01 0 1.200000e-01 0.190000 ADAMTS19 171019 broad.mit.edu 37 5 128983486 128983486 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr5:128983486G>A ENST00000274487.4 + 12 2028 c.1883G>A c.(1882-1884)aGg>aAg p.R628K CTC-575N7.1_ENST00000503616.1_RNA NM_133638.3 NP_598377.3 Q8TE59 ATS19_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 19 91 all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) TGTACCAGCAGGACCTCAGCA 0.507000 0 SO:0001583 missense ENST00000274487.4 1 1 hg19 CCDS4146.1 . . . . . . . . . . G 12.100000 1.835992 0.324210 . . ENSG00000145808 ENST00000274487 T 0.62232 0.04 4.710000 3.840000 0.442390 . 0.133374 0.47852 N 0.000212 T 0.32645 0.0836 N 0.04245 -0.25 0.33562 D 0.59748 B 0.06786 0.001 B 0.04013 0.001 T 0.32348 -0.9910 9 . . . . 6.0807 0.19940 0.1582:0.0:0.6875:0.1543 . 628 Q8TE59 ATS19_HUMAN K 628 ENSP00000274487:R628K . R + 2 0 ADAMTS19 129011385 1 0.714170 1 0.803570 0.999000 0.989320 2.233000 0.430270 1.586000 0.499440 0.650000 0.862430 AGG TCGA-IB-A5SP-01A-11D-A32N-08 ADAMTS19-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250979.2 1 0 1 255 436 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 1.000000 255 433 0 70 2 0 0 0 0 70 2 -20.000000 1 1 0 0 1 2 2 4 2.296524 0 0.740000 1.770000 0.752805 9.900000e-01 9.400000e-01 1.000000 1.000000 0.995450 9.900000e-01 1 9.900000e-01 1.000000 PCDHA1 56147 broad.mit.edu 37 5 140166589 140166589 + Silent SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr5:140166589C>T ENST00000504120.2 + 1 714 c.714C>T c.(712-714)aaC>aaT p.N238N PCDHA1_ENST00000378133.3_Silent_p.N238N|PCDHA1_ENST00000394633.3_Silent_p.N238N NM_018900.2 NP_061723.1 Q9Y5I3 PCDA1_HUMAN protocadherin alpha 1 70 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TTAATGATAACGCCCCACTGT 0.488000 0 SO:0001819 synonymous_variant ENST00000504120.2 1 1 hg19 CCDS54913.1 TCGA-IB-A5SP-01A-11D-A32N-08 PCDHA1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000389127.1 1 0 1 173 282 0 101 0 0 0 1 0 101 2 0 0 0 0 0 2 1 1.000000 170 279 0 101 2 0 0 0 0 101 2 -20.000000 1 1 121412 1 30 1 2 2 4 2.296524 0 0.740000 1.770000 0.752805 9.900000e-01 9.500000e-01 1.000000 1.000000 0.997039 9.900000e-01 1 9.900000e-01 1.000000 ADAM19 8728 broad.mit.edu 37 5 156915309 156915309 + Silent SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr5:156915309C>T ENST00000517905.1 - 21 2558 c.2514G>A c.(2512-2514)cgG>cgA p.R838R ADAM19_ENST00000430702.2_Silent_p.R571R|ADAM19_ENST00000394020.1_Silent_p.R840R|ADAM19_ENST00000257527.4_Silent_p.R838R Q9H013 ADA19_HUMAN ADAM metallopeptidase domain 19 53 Renal(175;0.00488) Medulloblastoma(196;0.0359)|all_neural(177;0.14) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) GGGGAATTGGCCGGCTTGGAG 0.567000 0 SO:0001819 synonymous_variant ENST00000517905.1 0 1 hg19 . . . . . . . . . . C 4.950000 0.176471 0.094430 . . ENSG00000135074 ENST00000517374 . . . 5.690000 2.920000 0.339320 . . . . . T 0.59059 0.2166 . . . 0.80722 D 1 . . . . . . T 0.54077 -0.8347 4 . . . . 9.7224 0.40311 0.0:0.7816:0.0:0.2184 . . . . D 409 . . G - 2 0 ADAM19 156847887 9.880000e-01 0.358960 9.980000e-01 0.565050 0.351000 0.292360 0.032000 0.137320 0.738000 0.326060 0.491000 0.489740 GGC TCGA-IB-A5SP-01A-11D-A32N-08 ADAM19-003 PUTATIVE basic protein_coding protein_coding OTTHUMT00000373918.1 0 0 0 7 1027 0 206 0 6.676050e-05 0 2 0 206 2 0 0 0 0 0 2 1 0.979986 7 1018 0 204 2 0 0 0 0 206 2 -1.850776 0 1 0 0 1 2 2 4 2.296524 0 0.740000 1.770000 0.752805 1.000000e-02 0 1.000000 0.020000 0.076948 1.000000e-02 0 0 0.030000 COL23A1 91522 broad.mit.edu 37 5 177688748 177688748 + Splice_Site SNP C C A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr5:177688748C>A ENST00000390654.3 - 11 1034 c.677G>T c.(676-678)gGc>gTc p.G226V COL23A1_ENST00000407622.1_Splice_Site_p.G190V NM_173465.3 NP_775736.2 Q86Y22 CONA1_HUMAN collagen, type XXIII, alpha 1 19 all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129) all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) TCCCTTTGGGCCCTGGAACAA 0.562000 0 SO:0001630 splice_region_variant ENST00000390654.3 1 0 hg19 CCDS4436.1 . . . . . . . . . . C 14.680000 2.606433 0.465270 . . ENSG00000050767 ENST00000390654;ENST00000407622 D;D 0.99637 -6.29;-6.29 5.290000 5.290000 0.746850 . 0.150367 0.42548 D 0.000684 D 0.99802 0.9915 H 0.98664 4.295 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.96894 0.9655 10 0.87932 D 0 -8.2243 14.438 0.67296 0.0:1.0:0.0:0.0 . 226 Q86Y22 CONA1_HUMAN V 226;190 ENSP00000375069:G226V;ENSP00000385092:G190V ENSP00000375069:G226V G - 2 0 COL23A1 177621354 1 0.714170 1 0.803570 0.222000 0.248450 3.891000 0.562270 2.469000 0.834160 0.491000 0.489740 GGC TCGA-IB-A5SP-01A-11D-A32N-08 COL23A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253475.1 1 0 1 146 230 0 85 0 3.364934e-01 0 3 0 85 2 0 0 0 0 0 2 1 1.000000 144 227 0 85 2 0 0 0 0 85 2 -19.621590 1 1 0 0 1 2 2 4 2.296524 0 0.740000 1.770000 0.752805 9.900000e-01 9.600000e-01 1.000000 1.000000 0.997942 9.900000e-01 1 9.900000e-01 1.000000 C5orf38 153571 broad.mit.edu 37 5 2752818 2752818 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr5:2752818G>A ENST00000334000.3 + 2 400 c.283G>A c.(283-285)Gag>Aag p.E95K C5orf38_ENST00000505778.1_Missense_Mutation_p.E95K|IRX2_ENST00000302057.5_5'Flank|C5orf38_ENST00000457752.2_Intron|IRX2_ENST00000382611.6_5'Flank|C5orf38_ENST00000397835.4_Missense_Mutation_p.E95K|IRX2_ENST00000502957.1_5'UTR|C5orf38_ENST00000515640.1_Missense_Mutation_p.E95K NM_178569.2 NP_848664.1 Q86SI9 CEI_HUMAN chromosome 5 open reading frame 38 4 CAGTCACGTCGAGAACGGGCA 0.602000 0 SO:0001583 missense ENST00000334000.3 0 1 hg19 CCDS34131.1 . . . . . . . . . . G 7.522000 0.656835 0.145800 . . ENSG00000186493 ENST00000397835;ENST00000334000;ENST00000505778;ENST00000515640 . . . 2.470000 -4.950000 0.030480 . . . . . T 0.14098 0.0341 N 0.08118 0 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.16837 -1.0389 8 0.87932 D 0 . 1.2249 0.01932 0.4102:0.2803:0.1664:0.143 . 95 Q86SI9 CEI_HUMAN K 95 . ENSP00000334267:E95K E + 1 0 C5orf38 2805818 0 0.058580 0 0.037020 0.015000 0.088740 -2.638000 0.008660 -1.913000 0.010790 0.313000 0.208870 GAG TCGA-IB-A5SP-01A-11D-A32N-08 C5orf38-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000365956.2 0 0 0 7 673 0 166 0 0 0 0 166 2 0 0 0 0 0 2 1 0.980049 7 667 0 163 2 0 0 0 0 166 2 -3.070793 1 1 121412 2 33 1 2 2 4 2.296524 0 0.740000 1.770000 0.752805 2.000000e-02 0 1.000000 0.030000 0.086038 2.000000e-02 0 1.000000e-02 0.050000 CEP72 55722 broad.mit.edu 37 5 633946 633946 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr5:633946C>T ENST00000264935.5 + 5 665 c.575C>T c.(574-576)gCg>gTg p.A192V CEP72_ENST00000444221.1_Intron NM_018140.3 NP_060610.2 Q9P209 CEP72_HUMAN centrosomal protein 72kDa 20 Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863) GTCATGGATGCGGATGACGAG 0.612000 0 SO:0001583 missense ENST00000264935.5 0 1 hg19 CCDS34126.1 . . . . . . . . . . C 8.455000 0.854063 0.171060 . . ENSG00000112877 ENST00000264935 T 0.09911 2.93 5.140000 2.140000 0.274770 . 0.406531 0.25458 N 0.030523 T 0.11410 0.0278 M 0.65975 2.015 0.29054 N 0.884302 B 0.15473 0.013 B 0.12837 0.008 T 0.09662 -1.0664 10 0.40728 T 0.16 -11.1821 6.2359 0.20762 0.4236:0.4884:0.0:0.088 . 192 Q9P209 CEP72_HUMAN V 192 ENSP00000264935:A192V ENSP00000264935:A192V A + 2 0 CEP72 686946 2.300000e-02 0.189210 2.100000e-02 0.166860 0.247000 0.257730 0.787000 0.268580 0.650000 0.307690 -0.355000 0.076370 GCG TCGA-IB-A5SP-01A-11D-A32N-08 CEP72-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000365967.3 0 0 0 7 1028 0 312 0 2.890763e-02 0 33 0 312 2 0 0 0 0 0 2 1 0.979492 7 1015 0 309 2 0 0 0 0 312 2 -1.810166 0 1 121412 2 39 1 2 2 4 2.296524 0 0.740000 1.770000 0.752805 1.000000e-02 0 1.000000 0.020000 0.076940 1.000000e-02 0 0 0.030000 GRM1 2911 broad.mit.edu 37 6 146755420 146755420 + Missense_Mutation SNP C C G TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr6:146755420C>G ENST00000282753.1 + 8 3308 c.3073C>G c.(3073-3075)Cca>Gca p.P1025A GRM1_ENST00000492807.2_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000361719.2_Missense_Mutation_p.P1025A|GRM1_ENST00000392299.2_3'UTR Q13255 GRM1_HUMAN glutamate receptor, metabotropic 1 126 Ovarian(120;0.0387) GCAACCCCCTCCACAGCAGAA 0.662000 0 SO:0001583 missense ENST00000282753.1 1 1 hg19 CCDS5209.1 . . . . . . . . . . C 5.758000 0.324185 0.109000 . . ENSG00000152822 ENST00000361719;ENST00000282753 D;D 0.87179 -2.22;-2.22 2.790000 0.452000 0.166340 . 1.033610 0.07658 N 0.933160 T 0.43211 0.1237 N 0.08118 0 0.09310 N 1 B 0.06786 0.001 B 0.06405 0.002 T 0.43861 -0.9365 10 0.05833 T 0.94 . 3.4837 0.07611 0.0:0.5533:0.2518:0.1949 . 1025 Q13255 GRM1_HUMAN A 1025 ENSP00000354896:P1025A;ENSP00000282753:P1025A ENSP00000282753:P1025A P + 1 0 GRM1 146797113 1.000000e-02 0.173220 5.200000e-02 0.191880 0.885000 0.512710 2.510000 0.454680 0.066000 0.165150 0.306000 0.203180 CCA TCGA-IB-A5SP-01A-11D-A32N-08 GRM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042574.1 1 0 1 114 333 0 148 0 0 0 0 148 2 0 0 0 0 0 2 1 1.000000 115 325 0 145 2 0 0 0 0 148 2 -5.752105 1 0 0 0 1 0 1 1 1.502892 1 0.740000 1.770000 0.589711 4.300000e-01 3.600000e-01 0.500000 0.440000 0.437982 4.300000e-01 0 3.900000e-01 0.470000 TIAM2 26230 broad.mit.edu 37 6 155458639 155458639 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr6:155458639G>A ENST00000461783.3 + 7 2796 c.1523G>A c.(1522-1524)cGg>cAg p.R508Q TIAM2_ENST00000360366.4_Missense_Mutation_p.R508Q|TIAM2_ENST00000367174.2_5'UTR|TIAM2_ENST00000318981.5_Missense_Mutation_p.R508Q|TIAM2_ENST00000456144.1_Missense_Mutation_p.R508Q|TIAM2_ENST00000529824.2_Missense_Mutation_p.R508Q Q8IVF5 TIAM2_HUMAN T-cell lymphoma invasion and metastasis 2 65 Ovarian(120;0.196) GGGGTGGTCCGGAAGGCCGGG 0.542000 0 SO:0001583 missense ENST00000461783.3 0 1 hg19 CCDS34558.1 . . . . . . . . . . G 36.000000 5.737056 0.968650 . . ENSG00000146426 ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000360366;ENST00000529824 T;T;T;T;T;T 0.79141 -1.24;-1.24;-1.24;-1.24;-1.24;-1.24 6.080000 6.080000 0.989890 Pleckstrin homology-type (1);Pleckstrin homology domain (3); 0.000000 0.85682 D 0.000000 D 0.85155 0.5632 L 0.55481 1.735 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.83275 0.994;0.996 D 0.84890 0.0836 10 0.87932 D 0 . 20.6634 0.99662 0.0:0.0:1.0:0.0 . 508;508 Q8IVF5-2;Q8IVF5 .;TIAM2_HUMAN Q 508;754;508;508;508;508;508 ENSP00000437188:R508Q;ENSP00000434901:R508Q;ENSP00000407746:R508Q;ENSP00000327315:R508Q;ENSP00000353528:R508Q;ENSP00000433348:R508Q ENSP00000327315:R508Q R + 2 0 TIAM2 155500331 1 0.714170 9.930000e-01 0.491080 0.972000 0.667710 9.476000 0.978230 2.894000 0.992530 0.655000 0.942530 CGG TCGA-IB-A5SP-01A-11D-A32N-08 TIAM2-005 KNOWN basic|appris_principal|readthrough_transcript|CCDS protein_coding protein_coding OTTHUMT00000387980.2 0 0 0 5 299 0 99 0 4.243622e-03 0 5 0 99 2 0 0 0 0 0 2 1 0.937504 5 298 0 99 2 0 0 0 0 99 2 -3.042169 1 1 121412 5 39 1 0 1 1 1.502892 1 0.740000 1.770000 0.589711 2.000000e-02 0 0.060000 0.030000 0.033500 2.000000e-02 0 1.000000e-02 0.050000 HIST1H2AC 8334 broad.mit.edu 37 6 26124800 26124800 + Missense_Mutation SNP G G T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr6:26124800G>T ENST00000602637.1 + 1 370 c.340G>T c.(340-342)Gcc>Tcc p.A114S HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2AC_ENST00000377791.2_Missense_Mutation_p.A114S Q93077 H2A1C_HUMAN histone cluster 1, H2ac 12 TAACATCCAGGCCGTGCTTCT 0.582000 0 SO:0001583 missense ENST00000602637.1 1 1 hg19 CCDS4585.1 . . . . . . . . . . . 13.940000 2.385900 0.423080 . . ENSG00000180573 ENST00000377791;ENST00000314088 T;T 0.40756 1.02;1.02 5.500000 5.500000 0.815520 Histone-fold (2);Histone H2A (2); 0.000000 0.44285 D 0.000478 T 0.20047 0.0482 L 0.31845 0.965 0.41553 D 0.988589 B 0.10296 0.003 B 0.12156 0.007 T 0.02728 -1.1118 10 0.37606 T 0.19 . 13.6874 0.62524 0.0:0.0:0.8458:0.1542 . 114 Q93077 H2A1C_HUMAN S 114 ENSP00000367022:A114S;ENSP00000321389:A114S ENSP00000321389:A114S A + 1 0 HIST1H2AC 26232779 1 0.714170 1 0.803570 0.559000 0.355860 7.712000 0.846840 2.750000 0.943510 0.467000 0.429560 GCC TCGA-IB-A5SP-01A-11D-A32N-08 HIST1H2AC-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000468023.1 1 0 0 28 257 0 89 1 9.996881e-01 14 103 0 89 2 0 0 0 0 0 2 1 1.000000 26 256 0 89 2 0 0 0 0 89 2 -20.000000 1 1 0 0 1 0 1 1 1.499983 1 0.740000 1.770000 0.592093 1.600000e-01 1.100000e-01 0.230000 0.170000 0.173650 1.600000e-01 0 1.300000e-01 0.200000 CUL9 23113 broad.mit.edu 37 6 43155033 43155033 + Silent SNP G G A rs148427416 TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr6:43155033G>A ENST00000252050.4 + 6 1521 c.1437G>A c.(1435-1437)ccG>ccA p.P479P CUL9_ENST00000354495.3_Intron|CUL9_ENST00000372647.2_Silent_p.P479P NM_015089.2 NP_055904.1 Q8IWT3 CUL9_HUMAN cullin 9 92 ACCCTTTGCCGTACCTCCAGC 0.532000 0 SO:0001819 synonymous_variant ENST00000252050.4 0 1 hg19 CCDS4890.1 TCGA-IB-A5SP-01A-11D-A32N-08 CUL9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040582.2 0 0 0 5 552 0 191 0 1.336898e-04 0 2 0 191 2 0 0 0 0 0 2 1 0.936007 6 545 0 188 2 0 0 0 0 191 2 -2.078869 0 1 121412 2 30 1 0 1 1 1.502892 1 0.740000 1.770000 0.589711 1.000000e-02 0 0.040000 0.020000 0.018051 1.000000e-02 0 0 0.030000 RCAN2 10231 broad.mit.edu 37 6 46214487 46214487 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr6:46214487G>A ENST00000330430.6 - 3 619 c.431C>T c.(430-432)cCa>cTa p.P144L RCAN2_ENST00000371374.1_Missense_Mutation_p.P190L|RCAN2_ENST00000405162.1_Missense_Mutation_p.P190L|RCAN2_ENST00000306764.7_Missense_Mutation_p.P190L NM_005822.3 NP_005813.2 Q14206 RCAN2_HUMAN regulator of calcineurin 2 8 AAGCTTACCTGGTCCTAGTTT 0.488000 0 SO:0001583 missense ENST00000330430.6 0 1 hg19 CCDS43469.1 . . . . . . . . . . G 31.000000 5.100723 0.942450 . . ENSG00000172348 ENST00000330430;ENST00000371374;ENST00000306764;ENST00000405162 . . . 5.700000 5.700000 0.887880 . 0.000000 0.85682 D 0.000000 T 0.72020 0.3409 M 0.73217 2.22 0.80722 D 1 P;P 0.50710 0.938;0.775 P;B 0.58130 0.833;0.396 T 0.74609 -0.3608 9 0.87932 D 0 -9.8695 18.8222 0.92102 0.0:0.0:1.0:0.0 . 190;144 Q14206-2;Q14206 .;RCAN2_HUMAN L 144;190;190;190 . ENSP00000305223:P190L P - 2 0 RCAN2 46322446 1 0.714170 1 0.803570 0.953000 0.610140 9.378000 0.971910 2.703000 0.923150 0.585000 0.799380 CCA TCGA-IB-A5SP-01A-11D-A32N-08 RCAN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040782.1 0 0 0 5 157 0 31 0 9.718456e-02 0 14 0 31 2 0 0 0 0 0 2 1 0.934359 5 153 0 31 2 0 0 0 0 31 2 -3.339483 1 1 0 0 1 0 1 1 1.502892 1 0.740000 1.770000 0.589711 5.000000e-02 1.000000e-02 0.110000 0.050000 0.062396 5.000000e-02 0 3.000000e-02 0.090000 NRF1 4899 broad.mit.edu 37 7 129349051 129349051 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr7:129349051G>A ENST00000393232.1 + 6 860 c.743G>A c.(742-744)cGc>cAc p.R248H NRF1_ENST00000393230.2_Missense_Mutation_p.R248H|NRF1_ENST00000353868.4_Missense_Mutation_p.R248H|NRF1_ENST00000393231.3_Missense_Mutation_p.R248H|NRF1_ENST00000311967.2_Missense_Mutation_p.R248H|NRF1_ENST00000223190.4_Missense_Mutation_p.R248H|NRF1_ENST00000539636.1_Missense_Mutation_p.R87H NM_005011.3 NP_005002.3 Q16656 NRF1_HUMAN nuclear respiratory factor 1 p.R248L(1) 24 AGTGATGTCCGCACAGAAGAG 0.493000 1 Substitution - Missense(1) SO:0001583 missense ENST00000393232.1 0 1 hg19 CCDS5813.2 . . . . . . . . . . G 35.000000 5.582880 0.965780 . . ENSG00000106459 ENST00000393232;ENST00000353868;ENST00000539636;ENST00000223190;ENST00000311967;ENST00000393230;ENST00000393231 D;D;D;D;D;D 0.89810 -2.57;-2.57;-2.57;-2.57;-2.57;-2.57 5.850000 5.850000 0.937110 Nuclear respiratory factor 1, NLS/DNA-binding, dimerisation domain (1); 0.000000 0.85682 D 0.000000 D 0.94804 0.8322 M 0.80616 2.505 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.94125 0.7383 9 . . . -9.5325 19.1648 0.93551 0.0:0.0:1.0:0.0 . 248;248 Q96AN2;Q16656 .;NRF1_HUMAN H 248;248;87;248;248;248;248 ENSP00000376924:R248H;ENSP00000440455:R87H;ENSP00000223190:R248H;ENSP00000309826:R248H;ENSP00000376922:R248H;ENSP00000376923:R248H . R + 2 0 NRF1 129136287 1 0.714170 1 0.803570 0.893000 0.520530 9.499000 0.979750 2.772000 0.953460 0.655000 0.942530 CGC TCGA-IB-A5SP-01A-11D-A32N-08 NRF1-203 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000289813.1 0 0 0 7 556 0 131 0 4.811622e-02 0 24 0 131 2 0 0 0 0 0 2 1 0.979702 5 551 0 129 2 0 0 0 0 131 2 -1.829393 0 1 0 0 1 0 1 1 2.009032 0 0.740000 1.770000 0.718096 2.000000e-02 0 0.060000 0.040000 0.035111 2.000000e-02 0 1.000000e-02 0.050000 HDAC9 9734 broad.mit.edu 37 7 18668998 18668998 + Silent SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr7:18668998G>A ENST00000432645.2 + 6 681 c.681G>A c.(679-681)cgG>cgA p.R227R HDAC9_ENST00000406072.1_Intron|HDAC9_ENST00000524023.1_Intron|HDAC9_ENST00000441542.2_Silent_p.R230R|HDAC9_ENST00000456174.2_Silent_p.R199R|HDAC9_ENST00000405010.3_Silent_p.R227R|HDAC9_ENST00000401921.1_Intron|HDAC9_ENST00000406451.4_Silent_p.R227R|HDAC9_ENST00000428307.2_Intron|HDAC9_ENST00000417496.2_Intron NM_058176.2 NP_478056.1 Q9UKV0 HDAC9_HUMAN histone deacetylase 9 82 all_lung(11;0.187) Valproic Acid(DB00313) TGAAGGTGCGGTCCAGGTTAA 0.408000 0 SO:0001819 synonymous_variant ENST00000432645.2 0 1 hg19 CCDS47555.1 TCGA-IB-A5SP-01A-11D-A32N-08 HDAC9-023 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000376176.1 1 0 0 33 66 0 8 0 5.423152e-01 0 5 0 8 2 0 0 0 0 0 2 1 1.000000 33 66 0 8 2 0 0 0 0 8 2 -20.000000 1 1 120746 1 30 1 2 2 4 2.366928 1 0.740000 1.770000 0.759571 9.800000e-01 7.200000e-01 1.000000 1.000000 0.940855 9.800000e-01 1 8.400000e-01 1.000000 ELN 2006 broad.mit.edu 37 7 73474290 73474290 + Missense_Mutation SNP T T G TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 T G T T Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr7:73474290T>G ENST00000252034.7 + 23 1888 c.1489T>G c.(1489-1491)Ttg>Gtg p.L497V CTB-51J22.1_ENST00000435932.1_RNA|ELN_ENST00000458204.1_Missense_Mutation_p.L487V|ELN_ENST00000380584.4_Missense_Mutation_p.L464V|ELN_ENST00000414324.1_Missense_Mutation_p.L473V|ELN_ENST00000445912.1_Missense_Mutation_p.L497V|ELN_ENST00000380576.5_Missense_Mutation_p.L478V|ELN_ENST00000380575.4_Missense_Mutation_p.L468V|ELN_ENST00000357036.5_Missense_Mutation_p.L502V|ELN_ENST00000380553.4_Missense_Mutation_p.L361V|ELN_ENST00000320399.6_Missense_Mutation_p.L497V|ELN_ENST00000429192.1_Missense_Mutation_p.L483V|ELN_ENST00000380562.4_Missense_Mutation_p.L503V|ELN_ENST00000320492.7_Missense_Mutation_p.L416V|ELN_ENST00000358929.4_Missense_Mutation_p.L532V NM_000501.2|NM_001278915.1 NP_000492.2|NP_001265844.1 P15502 ELN_HUMAN elastin 32 Lung NSC(55;0.159) TGGAGTTGGCTTGGCTCCTGG 0.607000 T PAX5 B-ALL Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome Dom yes 7 7q11.23 2006 elastin yes L 0 SO:0001583 missense ENST00000252034.7 1 0 hg19 CCDS5562.2 . . . . . . . . . . G 9.976000 1.226933 0.225420 . . ENSG00000049540 ENST00000445912;ENST00000252034;ENST00000358929;ENST00000320492;ENST00000414324;ENST00000380562;ENST00000380575;ENST00000380584;ENST00000458204;ENST00000357036;ENST00000429192;ENST00000380553;ENST00000380576;ENST00000320399 T;T;T;T;T;T;T;T;T;T;T;T;T;T 0.30981 1.55;1.56;1.53;1.52;1.52;1.51;1.55;1.56;1.54;1.54;1.53;1.55;1.55;1.54 3.570000 0.521000 0.170460 . . . . . T 0.11750 0.0286 . . . 0.09310 N 0.999999 B;B;B;B;B;B;B;B;B;B;B;B;B 0.02656 0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0 B;B;B;B;B;B;B;B;B;B;B;B;B 0.04013 0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.001;0.0;0.0;0.0 T 0.34378 -0.9831 8 0.08837 T 0.75 . 3.2149 0.06695 0.0914:0.1471:0.4594:0.3021 . 497;416;473;487;503;468;483;502;478;361;408;464;497 E7ENM0;G5E950;G3V0G6;E7EN65;P15502-1;P15502-7;P15502-12;P15502-5;P15502-13;P15502-11;B3KRT8;P15502-8;P15502-2 .;.;.;.;.;.;.;.;.;.;.;.;. V 497;497;532;416;473;503;468;464;487;502;483;361;478;497 ENSP00000389857:L497V;ENSP00000252034:L497V;ENSP00000351807:L532V;ENSP00000315607:L416V;ENSP00000392575:L473V;ENSP00000369936:L503V;ENSP00000369949:L468V;ENSP00000369958:L464V;ENSP00000403162:L487V;ENSP00000349540:L502V;ENSP00000391129:L483V;ENSP00000369926:L361V;ENSP00000369950:L478V;ENSP00000313565:L497V ENSP00000252034:L497V L + 1 2 ELN 73112226 4.690000e-01 0.258460 0 0.037020 0.028000 0.117280 0.540000 0.231910 -0.267000 0.093250 -0.126000 0.149550 TTG TCGA-IB-A5SP-01A-11D-A32N-08 ELN-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000316913.1 1 0 1 286 753 0 359 1 1 3 70 0 359 2 0 0 0 0 1 2 0 1.000000 0 654 0 303 2 0 0 0 0 359 2 -11.204800 1 0 0 0 1 0 0 0 2.012507 0 0.740000 1.770000 0.716961 6.700000e-01 6.100000e-01 0.750000 0.680000 0.684213 6.700000e-01 0 6.400000e-01 0.720000 CYP11B1 1584 broad.mit.edu 37 8 143958154 143958154 + Missense_Mutation SNP G G A rs34620645 by1000genomes TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr8:143958154G>A ENST00000292427.4 - 4 775 c.743C>T c.(742-744)aCc>aTc p.T248I CYP11B1_ENST00000377675.3_Missense_Mutation_p.T319I|CYP11B1_ENST00000517471.1_Missense_Mutation_p.T248I NM_000497.3 NP_000488.3 P15538 C11B1_HUMAN cytochrome P450, family 11, subfamily B, polypeptide 1 67 all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155) Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421) CTTGGGGCTGGTCCAGCGAGA 0.602000 Familial Hyperaldosteronism type I 0 SO:0001583 missense Familial Cancer Database Dexamethasone Sensitive Aldosteronism, FH-I ENST00000292427.4 0 1 hg19 CCDS6392.1 . . . . . . . . . . . 0.042000 -1.281373 0.013980 . . ENSG00000160882 ENST00000292427;ENST00000517471;ENST00000377675 T;T;T 0.66815 -0.23;-0.23;-0.23 3.640000 0.810000 0.187320 . 1.139050 0.06616 N 0.756477 T 0.44644 0.1303 N 0.17312 0.475 0.09310 N 1 B;B;B 0.09022 0.0;0.001;0.002 B;B;B 0.17979 0.006;0.013;0.02 T 0.28744 -1.0034 10 0.02654 T 1 . 7.2978 0.26403 0.3297:0.0:0.6703:0.0 rs34620645 319;248;248 Q4VAR0;Q4VAQ9;P15538 .;.;C11B1_HUMAN I 248;248;319 ENSP00000292427:T248I;ENSP00000428043:T248I;ENSP00000366903:T319I ENSP00000292427:T248I T - 2 0 CYP11B1 143955156 0 0.058580 3.200000e-01 0.253060 0.198000 0.238930 0.272000 0.186440 0.339000 0.237190 -0.226000 0.123460 ACC TCGA-IB-A5SP-01A-11D-A32N-08 CYP11B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000379475.2 0 0 0 8 162 0 38 0 0 0 0 38 2 0 0 0 0 0 2 0 0.089708 8 160 1 38 15 0 0 0 0 38 2 -1.842696 0 1 121410 128 41 1 1 2 3 2.250343 0 0.740000 1.770000 0.743792 1.300000e-01 6.000000e-02 1.000000 0.130000 0.167886 1.300000e-01 0 9.000000e-02 0.200000 RRS1 23212 broad.mit.edu 37 8 67341954 67341954 + Silent SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr8:67341954G>A ENST00000320270.2 + 1 692 c.588G>A c.(586-588)gcG>gcA p.A196A RP11-346I3.4_ENST00000499642.1_lincRNA|ADHFE1_ENST00000415254.1_5'Flank|ADHFE1_ENST00000379385.4_5'Flank|ADHFE1_ENST00000396623.3_5'Flank NM_015169.3 NP_055984.1 Q15050 RRS1_HUMAN RRS1 ribosome biogenesis regulator homolog (S. cerevisiae) 4 Lung NSC(129;0.197) Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226) TGGCCCGCGCGCACAAGATGC 0.652000 0 SO:0001819 synonymous_variant ENST00000320270.2 0 1 hg19 CCDS6189.1 TCGA-IB-A5SP-01A-11D-A32N-08 RRS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000380126.1 0 0 0 5 288 0 55 0 4.791068e-01 0 83 0 55 2 0 0 0 0 0 2 1 0.935789 5 284 0 54 2 0 0 0 0 55 2 -4.112707 1 1 0 0 1 1 2 3 2.250343 0 0.740000 1.770000 0.743792 4.000000e-02 0 1.000000 0.050000 0.082815 4.000000e-02 0 2.000000e-02 0.080000 ABCA1 19 broad.mit.edu 37 9 107556682 107556682 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr9:107556682G>A ENST00000374736.3 - 40 5886 c.5492C>T c.(5491-5493)gCc>gTc p.A1831V NM_005502.3 NP_005493.2 O95477 ABCA1_HUMAN ATP-binding cassette, sub-family A (ABC1), member 1 115 Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599) CCTTTCCAGGGCATCAGCCAT 0.468000 0 SO:0001583 missense ENST00000374736.3 0 1 hg19 CCDS6762.1 . . . . . . . . . . G 14.190000 2.460143 0.437360 . . ENSG00000165029 ENST00000374736 D 0.88664 -2.41 5.620000 5.620000 0.858410 . 0.000000 0.85682 D 0.000000 D 0.85256 0.5655 L 0.33189 0.99 0.80722 D 1 B 0.27450 0.179 B 0.33960 0.173 T 0.80339 -0.1424 10 0.12430 T 0.62 . 19.6523 0.95822 0.0:0.0:1.0:0.0 . 1831 O95477 ABCA1_HUMAN V 1831 ENSP00000363868:A1831V ENSP00000363868:A1831V A - 2 0 ABCA1 106596503 1 0.714170 1 0.803570 0.991000 0.796840 9.864000 0.995890 2.641000 0.895800 0.650000 0.862430 GCC TCGA-IB-A5SP-01A-11D-A32N-08 ABCA1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053491.1 0 0 0 6 664 0 104 0 1.205534e-03 0 5 0 104 2 0 0 0 0 0 2 1 0.963250 6 653 0 103 2 0 0 0 0 104 2 -2.345855 0 1 121412 15 46 1 1 2 3 2.224612 0 0.740000 1.770000 0.741910 2.000000e-02 0 0.060000 0.020000 0.036696 2.000000e-02 0 0 0.040000 PRPF4 9128 broad.mit.edu 37 9 116049072 116049072 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr9:116049072C>T ENST00000374198.4 + 9 1001 c.899C>T c.(898-900)gCg>gTg p.A300V PRPF4_ENST00000374199.4_Missense_Mutation_p.A299V NM_001244926.1|NM_004697.4 NP_001231855.1|NP_004688.2 O43172 PRP4_HUMAN pre-mRNA processing factor 4 23 GCCTCTTGTGCGGCTGATGGC 0.468000 0 SO:0001583 missense ENST00000374198.4 0 1 hg19 CCDS6791.1 . . . . . . . . . . C 32.000000 5.163644 0.947270 . . ENSG00000136875 ENST00000374199;ENST00000374198 T;T 0.61040 0.14;0.14 5.820000 5.820000 0.927950 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.155793 0.56097 D 0.000025 T 0.72244 0.3436 L 0.56340 1.77 0.80722 D 1 D;D 0.76494 0.999;0.992 D;P 0.65140 0.932;0.849 T 0.73040 -0.4108 10 0.72032 D 0.01 . 19.0872 0.93209 0.0:1.0:0.0:0.0 . 315;300 Q59EL4;O43172 .;PRP4_HUMAN V 299;300 ENSP00000363315:A299V;ENSP00000363313:A300V ENSP00000363313:A300V A + 2 0 PRPF4 115088893 1 0.714170 1 0.803570 0.956000 0.617450 7.378000 0.796790 2.752000 0.944350 0.655000 0.942530 GCG TCGA-IB-A5SP-01A-11D-A32N-08 PRPF4-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000053708.2 0 0 0 11 1795 0 418 0 7.429186e-02 0 66 0 418 2 0 0 0 0 0 2 1 0.998204 11 1775 0 413 2 0 0 0 0 418 2 -2.137060 0 1 121412 4 43 1 1 2 3 2.224612 0 0.740000 1.770000 0.741910 1.000000e-02 0 0.040000 0.020000 0.029858 1.000000e-02 0 0 0.030000 TNC 3371 broad.mit.edu 37 9 117791722 117791722 + Missense_Mutation SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr9:117791722C>T ENST00000350763.4 - 25 6497 c.6086G>A c.(6085-6087)cGc>cAc p.R2029H TNC_ENST00000535648.1_Missense_Mutation_p.R1574H|TNC_ENST00000346706.3_Missense_Mutation_p.R1483H|TNC_ENST00000345230.3_Missense_Mutation_p.R1392H|TNC_ENST00000423613.2_Missense_Mutation_p.R1756H|TNC_ENST00000340094.3_Missense_Mutation_p.R1665H|TNC_ENST00000341037.4_Missense_Mutation_p.R1847H|TNC_ENST00000542877.1_Missense_Mutation_p.R1666H|TNC_ENST00000537320.1_Missense_Mutation_p.R1392H NM_002160.3 NP_002151.2 P24821 TENA_HUMAN tenascin C 120 TCCGTTTTTGCGTCTCAGGAA 0.488000 0 SO:0001583 missense ENST00000350763.4 0 1 hg19 CCDS6811.1 . . . . . . . . . . C 33.000000 5.217894 0.951040 . . ENSG00000041982 ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877 D;D;D;D;D;D;D;D;D 0.86030 -2.06;-2.06;-2.06;-2.06;-2.06;-2.06;-2.06;-2.06;-2.06 5.480000 5.480000 0.808510 Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1); 0.000000 0.85682 D 0.000000 D 0.96068 0.8719 H 0.98936 4.375 0.44275 D 0.99713 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.97749 1.0213 10 0.87932 D 0 . 19.3449 0.94359 0.0:1.0:0.0:0.0 . 1756;2029 E9PC84;P24821 .;TENA_HUMAN H 1665;1574;1483;1392;2029;1847;1756;1392;1666 ENSP00000344400:R1665H;ENSP00000438152:R1574H;ENSP00000344555:R1483H;ENSP00000345861:R1392H;ENSP00000265131:R2029H;ENSP00000339553:R1847H;ENSP00000411406:R1756H;ENSP00000443478:R1392H;ENSP00000442242:R1666H ENSP00000344400:R1665H R - 2 0 TNC 116831543 1 0.714170 1 0.803570 0.868000 0.497710 7.363000 0.795160 2.587000 0.873810 0.655000 0.942530 CGC TCGA-IB-A5SP-01A-11D-A32N-08 TNC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055418.2 0 0 0 6 553 0 87 0 3.329349e-02 0 22 0 87 2 0 8.132015e-01 1 908 6 2260 7 1 0.962922 7 541 0 86 2 0 0 0 0 87 2 -1.887151 0 1 0 0 1 1 2 3 2.201964 0 0.740000 1.770000 0.740958 2.000000e-02 0 0.070000 0.030000 0.032992 2.000000e-02 0 1.000000e-02 0.050000 GCNT1 2650 broad.mit.edu 37 9 79118080 79118080 + Silent SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr9:79118080C>T ENST00000376730.4 + 4 1266 c.783C>T c.(781-783)gtC>gtT p.V261V GCNT1_ENST00000444201.2_Silent_p.V261V|GCNT1_ENST00000442371.1_Silent_p.V261V|GCNT1_ENST00000536223.1_Silent_p.V261V NM_001097636.1|NM_001490.4 NP_001091105.1|NP_001481.2 Q02742 GCNT1_HUMAN glucosaminyl (N-acetyl) transferase 1, core 2 30 GGTATGAGGTCGTTAATGGAA 0.463000 0 SO:0001819 synonymous_variant ENST00000376730.4 1 1 hg19 CCDS6653.1 TCGA-IB-A5SP-01A-11D-A32N-08 GCNT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052725.1 1 0 1 125 297 0 72 1 9.999925e-01 18 26 0 72 2 0 0 0 0 0 2 1 1.000000 124 296 0 71 2 0 0 0 0 72 2 -9.284615 1 1 0 0 1 1 2 3 2.224612 0 0.740000 1.770000 0.741910 8.000000e-01 6.800000e-01 0.940000 0.810000 0.810295 8.000000e-01 0 7.400000e-01 0.870000 PRUNE2 158471 broad.mit.edu 37 9 79323756 79323756 + Missense_Mutation SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chr9:79323756G>A ENST00000376718.3 - 8 3557 c.3434C>T c.(3433-3435)gCg>gTg p.A1145V PRUNE2_ENST00000428286.1_Missense_Mutation_p.A786V NM_015225.2 NP_056040.2 Q8WUY3 PRUN2_HUMAN prune homolog 2 (Drosophila) 16 GGGGATTGCCGCACCCCCACT 0.522000 0 SO:0001583 missense ENST00000376718.3 0 1 hg19 CCDS47982.1 . . . . . . . . . . A 2.851000 -0.238399 0.059440 . . ENSG00000106772 ENST00000376718;ENST00000428286;ENST00000422033 T;T 0.38401 1.15;1.14 6.080000 6.080000 0.989890 . 0.121361 0.37577 N 0.002034 T 0.12603 0.0306 N 0.01576 -0.805 0.80722 D 1 B 0.02656 0.0 B 0.01281 0.0 T 0.16748 -1.0392 10 0.02654 T 1 -10.7943 11.0795 0.48051 0.9304:0.0:0.0696:0.0 . 1145 Q8WUY3 PRUN2_HUMAN V 1145;786;1144 ENSP00000365908:A1145V;ENSP00000397425:A786V ENSP00000365908:A1145V A - 2 0 PRUNE2 78513576 2.180000e-01 0.236080 7.940000e-01 0.320650 0.308000 0.278560 0.910000 0.285710 1.126000 0.420160 -0.254000 0.113340 GCG TCGA-IB-A5SP-01A-11D-A32N-08 PRUNE2-003 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052730.2 0 0 0 6 545 1 112 0 5.424425e-04 0 3 1 112 2 0 0 0 0 0 2 0 0.015201 6 539 1 112 17 0 0 0 1 112 2 -1.924413 0 1 120486 4 37 1 1 2 3 2.224612 0 0.740000 1.770000 0.741910 2.000000e-02 0 0.070000 0.030000 0.043113 2.000000e-02 0 1.000000e-02 0.050000 WWC3 55841 broad.mit.edu 37 X 10090747 10090747 + Silent SNP C C T TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chrX:10090747C>T ENST00000380861.4 + 12 2110 c.1719C>T c.(1717-1719)agC>agT p.S573S WWC3_ENST00000454666.1_Silent_p.S573S NM_015691.3 NP_056506.2 Q9ULE0 WWC3_HUMAN WWC family member 3 52 CGCTAGCCAGCGACAGTGGGG 0.498000 0 SO:0001819 synonymous_variant ENST00000380861.4 0 1 hg19 CCDS14136.1 . . . . . . . . . . C 3.220000 -0.159648 0.065440 . . ENSG00000047644 ENST00000398613 . . . 4.720000 -3.990000 0.040690 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . -10.7804 15.226 0.73352 0.0:0.1046:0.0:0.8954 . . . . X 578 . . R + 1 2 WWC3 10050747 9.150000e-01 0.310590 2.000000e-03 0.105220 0.277000 0.268210 -0.063000 0.116550 -0.854000 0.041310 -0.198000 0.127610 CGA TCGA-IB-A5SP-01A-11D-A32N-08 WWC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055725.1 0 0 0 7 882 0 227 0 6.497841e-03 0 13 0 227 2 0 0 0 0 0 2 1 0.979906 8 872 0 226 2 0 0 0 0 227 2 -2.538101 1 1 121412 2 43 1 0 1 1 0.740000 1.770000 0.740000 0 0 0.020000 0.010000 0.011531 0 0 0 0.020000 ZMAT1 84460 broad.mit.edu 37 X 101138639 101138639 + Missense_Mutation SNP T T C TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chrX:101138639T>C ENST00000372782.3 - 7 1807 c.1760A>G c.(1759-1761)aAg>aGg p.K587R ZMAT1_ENST00000494068.1_5'UTR|ZMAT1_ENST00000540921.1_Missense_Mutation_p.K587R|ZMAT1_ENST00000458570.1_Missense_Mutation_p.K416R NM_001011657.3 NP_001011657 Q5H9K5 ZMAT1_HUMAN zinc finger, matrin-type 1 22 TGAACTGACCTTGACTCTATC 0.378000 0 SO:0001583 missense ENST00000372782.3 1 1 hg19 CCDS35348.1 . . . . . . . . . . T 0.008000 -1.914913 0.005030 . . ENSG00000166432 ENST00000372782;ENST00000540921;ENST00000458570 T;T;T 0.23552 2.48;2.48;1.9 3.750000 1.020000 0.199860 . 1.153020 0.06414 N 0.721174 T 0.06917 0.0176 N 0.00729 -1.24 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.32534 -0.9903 10 0.06099 T 0.92 2.4748 7.3368 0.26615 0.0:0.6725:0.0:0.3275 . 587 Q5H9K5 ZMAT1_HUMAN R 587;587;416 ENSP00000361868:K587R;ENSP00000437529:K587R;ENSP00000413044:K416R ENSP00000361868:K587R K - 2 0 ZMAT1 101025295 0 0.058580 0 0.037020 0.299000 0.275590 0.140000 0.160560 0.077000 0.168630 -0.296000 0.095430 AAG TCGA-IB-A5SP-01A-11D-A32N-08 ZMAT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057598.1 0 0 0 7 313 0 30 0 9.561274e-03 0 6 0 30 2 0 0 0 0 0 2 1 0.980471 7 311 0 29 2 0 0 0 0 30 2 -7.676197 1 1 0 0 1 0 1 1 0.740000 1.770000 0.740000 2.000000e-02 0 0.060000 0.030000 0.033543 2.000000e-02 0 1.000000e-02 0.050000 AFF2 2334 broad.mit.edu 37 X 147744171 147744171 + Nonsense_Mutation SNP C C A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chrX:147744171C>A ENST00000370460.2 + 3 1402 c.923C>A c.(922-924)tCa>tAa p.S308* AFF2_ENST00000370458.1_Nonsense_Mutation_p.S304*|AFF2_ENST00000370457.5_Nonsense_Mutation_p.S304*|AFF2_ENST00000342251.3_Nonsense_Mutation_p.S304* NM_001169123.1|NM_002025.3 NP_001162594.1|NP_002016.2 P51816 AFF2_HUMAN AF4/FMR2 family, member 2 109 Acute lymphoblastic leukemia(192;6.56e-05) CTGAAACCTTCAATTGAATTT 0.478000 0 SO:0001587 stop_gained ENST00000370460.2 0 1 hg19 CCDS14684.1 . . . . . . . . . . C 41.000000 8.941224 0.990100 . . ENSG00000155966 ENST00000370460;ENST00000370457;ENST00000342251;ENST00000370458 . . . 5.920000 4.890000 0.638310 . 0.113933 0.64402 D 0.000009 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 14.8604 0.70376 0.0:0.9173:0.0:0.0827 . . . . X 308;304;304;304 . ENSP00000345459:S304X S + 2 0 AFF2 147551863 9.990000e-01 0.422020 9.590000e-01 0.398830 0.949000 0.601150 4.247000 0.587500 2.492000 0.840950 0.600000 0.829820 TCA TCGA-IB-A5SP-01A-11D-A32N-08 AFF2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000058673.2 0 0 0 6 303 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 0.964668 6 301 0 51 2 0 0 0 0 52 2 -2.925983 1 1 0 0 1 0 1 1 0.740000 1.770000 0.740000 2.000000e-02 0 0.050000 0.030000 0.030384 2.000000e-02 0 1.000000e-02 0.040000 PTCHD1 139411 broad.mit.edu 37 X 23410819 23410819 + Missense_Mutation SNP A A G TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chrX:23410819A>G ENST00000379361.4 + 3 2044 c.1184A>G c.(1183-1185)aAc>aGc p.N395S NM_173495.2 NP_775766.2 Q96NR3 PTHD1_HUMAN patched domain containing 1 42 CCTTTCACGAACATTGAGGCA 0.483000 0 SO:0001583 missense ENST00000379361.4 0 1 hg19 CCDS35215.2 . . . . . . . . . . A 10.400000 1.340499 0.243390 . . ENSG00000165186 ENST00000379361 D 0.85088 -1.94 5.320000 5.320000 0.756190 Sterol-sensing domain (1); 0.000000 0.85682 D 0.000000 T 0.77605 0.4155 L 0.31752 0.955 0.50632 D 0.999886 B 0.11235 0.004 B 0.31290 0.127 T 0.68981 -0.5266 10 0.05436 T 0.98 . 14.5355 0.67958 1.0:0.0:0.0:0.0 . 395 Q96NR3 PTHD1_HUMAN S 395 ENSP00000368666:N395S ENSP00000368666:N395S N + 2 0 PTCHD1 23320740 1 0.714170 1 0.803570 0.970000 0.659960 8.910000 0.926850 1.881000 0.544920 0.486000 0.481410 AAC TCGA-IB-A5SP-01A-11D-A32N-08 PTCHD1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056047.2 0 0 0 5 264 0 35 0 0 0 0 35 2 0 0 0 0 0 2 1 0.935633 5 260 0 35 2 0 0 0 0 35 2 -3.306761 1 1 0 0 1 0 1 1 0.740000 1.770000 0.740000 2.000000e-02 0 0.060000 0.030000 0.029849 2.000000e-02 0 1.000000e-02 0.040000 FAM47A 158724 broad.mit.edu 37 X 34150174 34150174 + Silent SNP G G A TCGA-IB-A5SP-01A-11D-A32N-08 TCGA-IB-A5SP-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx cd4faec8-6fae-4ef2-95e0-7bbaea030219 c87e1799-db25-4e22-a193-f020949f79ac g.chrX:34150174G>A ENST00000346193.3 - 1 273 c.222C>T c.(220-222)gaC>gaT p.D74D NM_203408.3 NP_981953.2 Q5JRC9 FA47A_HUMAN family with sequence similarity 47, member A p.D74D(2) 97 GTAAAAACTCGTCACGGCGAC 0.532000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000346193.3 1 1 hg19 CCDS43926.1 TCGA-IB-A5SP-01A-11D-A32N-08 FAM47A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056205.1 1 0 1 248 107 0 78 0 0 0 0 78 2 0 0 0 0 0 2 1 1.000000 243 106 0 77 2 0 0 0 0 78 2 -20.000000 1 1 0 0 1 0 1 1 0.740000 1.770000 0.740000 9.300000e-01 8.700000e-01 0.990000 0.940000 0.939188 9.300000e-01 1 9.000000e-01 0.970000