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 KBTBD4 55709 broad.mit.edu 37 11 47595092 47595094 + In_Frame_Del DEL CGA CGA - TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr11:47595092_47595094delCGA ENST00000526005.1 - 4 1098_1100 c.945_947delTCG c.(943-948)cctcgg>ccg p.R316del RNU5E-10P_ENST00000363506.1_RNA|NDUFS3_ENST00000533507.1_Intron|KBTBD4_ENST00000430070.2_In_Frame_Del_p.R332del|KBTBD4_ENST00000395288.2_In_Frame_Del_p.R316del|KBTBD4_ENST00000533290.1_In_Frame_Del_p.R341del Q9NVX7 KBTB4_HUMAN kelch repeat and BTB (POZ) domain containing 4 24 GAGCCGGTCCCGAGGCAAAGGAG 0.571000 0 SO:0001651 inframe_deletion ENST00000526005.1 1 1 hg19 CCDS7940.1 TCGA-S4-A8RO-01A-12D-A377-08 KBTBD4-003 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000391763.1 1 0 0 53 250 0 60 1 9.589791e-01 6 21 0 60 2 0 0 0 0 0 0 1 1 60 253 0 59 2 0 0 0 0 0 0 -2.734738 1 1 0 0 1 1 2 3 2.034398 0 0.680000 2.080000 0.687439 0.530000 4.000000e-01 1.000000 0.520000 0.558403 0.530000 0 4.600000e-01 0.610000 KLF5 688 broad.mit.edu 37 13 73636195 73636195 + Frame_Shift_Del DEL C C - TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 C - C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr13:73636195delC ENST00000377687.4 + 2 994 c.458delC c.(457-459)tccfs p.S153fs KLF5_ENST00000477333.1_3'UTR|KLF5_ENST00000539231.1_Frame_Shift_Del_p.S62fs NM_001730.3 NP_001721.2 Q13887 KLF5_HUMAN Kruppel-like factor 5 (intestinal) 17 Prostate(6;0.00187)|Breast(118;0.0735) CTCTACAAATCCCAGAGACCG 0.532000 0 SO:0001589 frameshift_variant ENST00000377687.4 1 0 hg19 CCDS9448.1 TCGA-S4-A8RO-01A-12D-A377-08 KLF5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045263.1 1 0 0 126 413 0 101 1 1 38 205 0 101 2 0 0 0 0 0 0 1 1 141 408 2 100 25 0 0 0 0 0 0 -4.444923 1 1 0 0 1 0 0 0 1.894646 0 0.680000 2.080000 0.671053 0.660000 5.600000e-01 0.770000 0.670000 0.671050 0.660000 0 6.100000e-01 0.720000 GPR125 166647 broad.mit.edu 37 4 22436937 22436938 + Frame_Shift_Del DEL TT TT - TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr4:22436937_22436938delTT ENST00000334304.5 - 10 1708_1709 c.1439_1440delAA c.(1438-1440)aaafs p.K480fs GPR125_ENST00000502482.1_Frame_Shift_Del_p.K480fs|GPR125_ENST00000282943.5_5'UTR|GPR125_ENST00000508133.1_Frame_Shift_Del_p.K254fs NM_145290.3 NP_660333.2 Q8IWK6 GP125_HUMAN G protein-coupled receptor 125 56 Breast(46;0.198) GAAGTACCTCTTTTGATTTTTC 0.337000 0 SO:0001589 frameshift_variant ENST00000334304.5 1 0 hg19 CCDS33964.1 TCGA-S4-A8RO-01A-12D-A377-08 GPR125-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000362960.3 1 0 0 82 302 0 87 0 8.597445e-01 0 15 0 87 2 0 0 0 0 0 0 1 9.999993e-01 87 303 5 88 36 0 0 0 0 0 0 -3.586915 1 1 0 0 1 1 2 3 1.968126 0 0.680000 2.080000 0.681084 0.620000 5.100000e-01 0.760000 0.630000 0.633807 0.620000 0 5.600000e-01 0.700000 SORBS1 10580 broad.mit.edu 37 10 97096368 97096368 + Silent SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr10:97096368G>A ENST00000361941.3 - 28 3575 c.3549C>T c.(3547-3549)agC>agT p.S1183S SORBS1_ENST00000354106.3_Intron|SORBS1_ENST00000371247.2_Silent_p.S1183S|SORBS1_ENST00000393949.1_Intron|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000277982.5_Silent_p.S1042S|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000371227.4_Silent_p.S1137S|SORBS1_ENST00000371245.3_Intron|SORBS1_ENST00000371246.2_Silent_p.S1042S NM_001034954.1 NP_001030126 sorbin and SH3 domain containing 1 42 Colorectal(252;0.0429) CTGGAAAAGCGCTACCCAGGG 0.617000 0 SO:0001819 synonymous_variant ENST00000361941.3 1 1 hg19 CCDS31255.1 TCGA-S4-A8RO-01A-12D-A377-08 SORBS1-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000049517.1 1 0 1 179 144 0 81 0 0 0 0 81 2 0 0 0 0 0 2 1 1 178 142 0 81 2 0 0 0 0 81 2 -20.000000 1 1 0 0 1 0 1 1 1.472099 1 0.680000 2.080000 0.515152 0.970000 9.100000e-01 1.000000 0.990000 0.978554 0.970000 1 9.500000e-01 1.000000 ANGPTL5 253935 broad.mit.edu 37 11 101773403 101773403 + Silent SNP T T C TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr11:101773403T>C ENST00000334289.3 - 6 1084 c.489A>G c.(487-489)acA>acG p.T163T NM_178127.4 NP_835228.2 Q86XS5 ANGL5_HUMAN angiopoietin-like 5 29 Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.043) AACCACTCGGTGTTTTGGTGA 0.353000 0 SO:0001819 synonymous_variant ENST00000334289.3 1 1 hg19 CCDS8312.1 TCGA-S4-A8RO-01A-12D-A377-08 ANGPTL5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394138.1 1 0 1 112 228 0 64 0 0 0 0 64 2 0 0 0 0 0 2 1 1 109 225 0 64 2 0 0 0 0 64 2 -20.000000 1 1 0 0 1 1 2 3 2.033988 0 0.680000 2.080000 0.687439 0.990000 8.400000e-01 1.000000 1.000000 0.967906 0.990000 1 9.100000e-01 1.000000 PKNOX2 63876 broad.mit.edu 37 11 125299995 125299995 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr11:125299995G>A ENST00000298282.9 + 12 1421 c.1150G>A c.(1150-1152)Gtg>Atg p.V384M PKNOX2_ENST00000542175.1_Missense_Mutation_p.V320M|PKNOX2_ENST00000530517.1_3'UTR NM_022062.2 NP_071345.2 Q96KN3 PKNX2_HUMAN PBX/knotted 1 homeobox 2 29 Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116) CGCTGCGGGGGTGCTGCAGCA 0.622000 0 SO:0001583 missense ENST00000298282.9 0 1 hg19 CCDS41730.1 . . . . . . . . . . G 20.6 4.014071 0.75161 . . ENSG00000165495 ENST00000530517;ENST00000531116;ENST00000298282;ENST00000542175 D;D;D;D 0.85258 -1.95;-1.95;-1.96;-1.93 4.82 4.82 0.62117 . 0.000000 0.85682 D 0.000000 D 0.90328 0.6974 L 0.53249 1.67 0.80722 D 1 D;D;D 0.71674 0.998;0.989;0.978 D;P;P 0.70487 0.969;0.795;0.496 D 0.90201 0.4257 10 0.46703 T 0.11 -13.6476 18.252 0.90006 0.0:0.0:1.0:0.0 . 320;355;384 F5GZ15;B7Z3G7;Q96KN3 .;.;PKNX2_HUMAN M 355;355;384;320 ENSP00000434732:V355M;ENSP00000433971:V355M;ENSP00000298282:V384M;ENSP00000441470:V320M ENSP00000298282:V384M V + 1 0 PKNOX2 124805205 1.000000 0.71417 0.995000 0.50966 0.606000 0.37113 9.809000 0.99208 2.399000 0.81585 0.462000 0.41574 GTG TCGA-S4-A8RO-01A-12D-A377-08 PKNOX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000386866.3 0 0 0 5 328 0 52 0 3.731343e-04 0 2 0 52 2 0 0 0 0 0 2 1 9.339264e-01 5 320 0 50 2 0 0 0 0 52 2 -5.508372 1 1 0 0 1 0 2 2 1.994209 1 0.680000 2.080000 0.680000 0.040000 0 0.100000 0.040000 0.052475 0.040000 0 2.000000e-02 0.070000 OR51F2 119694 broad.mit.edu 37 11 4843156 4843156 + Missense_Mutation SNP T T C TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr11:4843156T>C ENST00000322110.5 + 1 606 c.541T>C c.(541-543)Tcc>Ccc p.S181P MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron NM_001004753.1 NP_001004753.1 Q8NH61 O51F2_HUMAN olfactory receptor, family 51, subfamily F, member 2 33 Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778) CAAGAGGTTGTCCTTCTGCAG 0.448000 0 SO:0001583 missense ENST00000322110.5 0 1 hg19 CCDS31361.1 . . . . . . . . . . T 2.880 -0.232112 0.05983 . . ENSG00000176925 ENST00000322110 T 0.00036 8.86 4.66 2.17 0.27698 GPCR, rhodopsin-like superfamily (1); 0.663319 0.12337 U 0.477833 T 0.00210 0.0006 L 0.35487 1.065 0.09310 N 1 D 0.69078 0.997 D 0.71656 0.974 T 0.32824 -0.9892 10 0.02654 T 1 . 5.3429 0.15994 0.4154:0.0:0.148:0.4366 . 181 Q8NH61 O51F2_HUMAN P 181 ENSP00000323952:S181P ENSP00000323952:S181P S + 1 0 OR51F2 4799732 0.000000 0.05858 0.977000 0.42913 0.614000 0.37383 -0.787000 0.04618 0.309000 0.22966 0.459000 0.35465 TCC TCGA-S4-A8RO-01A-12D-A377-08 OR51F2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000142181.1 0 0 0 9 528 0 201 0 0 0 0 201 2 0 0 0 0 0 2 1 9.942409e-01 9 527 0 199 2 0 0 0 0 201 2 -3.335725 1 1 0 0 1 0 1 1 1.316738 1 0.680000 2.080000 0.515152 0.020000 1.000000e-02 0.060000 0.030000 0.035941 0.020000 0 1.000000e-02 0.050000 OR51G1 79324 broad.mit.edu 37 11 4945382 4945382 + Missense_Mutation SNP T T A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr11:4945382T>A ENST00000321961.2 - 1 255 c.188A>T c.(187-189)tAt>tTt p.Y63F MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron NM_001005237.1 NP_001005237.1 Q8NGK1 O51G1_HUMAN olfactory receptor, family 51, subfamily G, member 1 25 Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086) GCCCAAGAAATAGTACATGGG 0.483000 0 SO:0001583 missense ENST00000321961.2 1 1 hg19 CCDS31366.1 . . . . . . . . . . T 14.38 2.517143 0.44763 . . ENSG00000176879 ENST00000321961 T 0.01685 4.69 4.2 4.2 0.49525 GPCR, rhodopsin-like superfamily (1); 0.000000 0.35739 U 0.003015 T 0.01592 0.0051 N 0.25060 0.705 0.27676 N 0.946609 B 0.15719 0.014 B 0.15484 0.013 T 0.37934 -0.9684 10 0.66056 D 0.02 . 6.9793 0.24694 0.3172:0.0:0.0:0.6828 . 63 Q8NGK1 O51G1_HUMAN F 63 ENSP00000322546:Y63F ENSP00000322546:Y63F Y - 2 0 OR51G1 4901958 0.901000 0.30685 1.000000 0.80357 0.963000 0.63663 1.508000 0.35769 1.760000 0.52011 0.455000 0.32223 TAT TCGA-S4-A8RO-01A-12D-A377-08 OR51G1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000142345.1 1 0 0 7 92 0 39 0 0 0 0 39 2 0 0 0 0 0 2 1 9.804965e-01 7 90 0 37 2 0 0 0 0 39 2 -11.939750 1 1 0 0 1 0 1 1 1.316738 1 0.680000 2.080000 0.515152 0.140000 6.000000e-02 0.260000 0.140000 0.152302 0.140000 0 9.000000e-02 0.200000 RPS6KB2 6199 broad.mit.edu 37 11 67200423 67200423 + Splice_Site SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr11:67200423G>A ENST00000312629.5 + 8 662 c.617G>A c.(616-618)gGc>gAc p.G206D RPS6KB2_ENST00000539188.1_3'UTR|AP003419.16_ENST00000535922.1_RNA|RPS6KB2_ENST00000524814.1_3'UTR NM_003952.2 NP_003943.2 Q9UBS0 KS6B2_HUMAN ribosomal protein S6 kinase, 70kDa, polypeptide 2 25 BRCA - Breast invasive adenocarcinoma(15;3.26e-06) CCTTCCTCAGGCCACATCAAA 0.612000 0 SO:0001630 splice_region_variant ENST00000312629.5 1 0 hg19 CCDS41677.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 15.69|15.69 2.909408|2.909408 0.52439|0.52439 .|. .|. ENSG00000175634|ENSG00000175634 ENST00000524814|ENST00000312629 .|T .|0.31510 .|1.49 4.76|4.76 4.76|4.76 0.60689|0.60689 .|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); .|0.000000 .|0.85682 .|D .|0.000000 T|T 0.58308|0.58308 0.2113|0.2113 M|M 0.80422|0.80422 2.495|2.495 0.80722|0.80722 D|D 1|1 .|D;D .|0.89917 .|1.0;1.0 .|D;D .|0.91635 .|0.999;0.999 T|T 0.61778|0.61778 -0.6993|-0.6993 5|9 .|. .|. .|. .|. 16.6904|16.6904 0.85320|0.85320 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|206;206 .|Q9BRS0;Q9UBS0 .|.;KS6B2_HUMAN T|D 157|206 .|ENSP00000308413:G206D .|. A|G +|+ 1|2 0|0 RPS6KB2|RPS6KB2 66956999|66956999 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.899000|0.899000 0.52679|0.52679 9.087000|9.087000 0.94110|0.94110 2.461000|2.461000 0.83175|0.83175 0.561000|0.561000 0.74099|0.74099 GCC|GGC TCGA-S4-A8RO-01A-12D-A377-08 RPS6KB2-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000395508.1 0 0 1 61 175 1 29 1 9.999898e-01 20 158 1 29 18 0 0 0 0 0 2 1 9.999987e-01 61 173 1 29 23 0 0 0 1 29 2 -20.000000 1 1 0 0 1 1 3 4 2.761429 1 0.680000 2.080000 0.768250 0.990000 8.400000e-01 1.000000 1.000000 0.982603 0.990000 1 9.500000e-01 1.000000 OR10A5 144124 broad.mit.edu 37 11 6867677 6867677 + Missense_Mutation SNP C C G TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr11:6867677C>G ENST00000299454.4 + 1 795 c.764C>G c.(763-765)tCt>tGt p.S255C OR10A5_ENST00000379831.2_Missense_Mutation_p.S259C Q9H207 O10A5_HUMAN olfactory receptor, family 10, subfamily A, member 5 21 Medulloblastoma(188;0.0523)|all_neural(188;0.236) TTCTATATATCTTCTAGCCTC 0.433000 Pancreas(44;21 1072 25662 28041 45559) 0 SO:0001583 missense ENST00000299454.4 0 1 hg19 CCDS7773.1 . . . . . . . . . . . 7.000 0.554679 0.13436 . . ENSG00000166363 ENST00000299454;ENST00000379831 T;T 0.00183 8.6;8.6 3.59 3.59 0.41128 GPCR, rhodopsin-like superfamily (1); 0.000000 0.64402 D 0.000018 T 0.00300 0.0009 L 0.29908 0.895 0.09310 N 1 D 0.71674 0.998 D 0.70016 0.967 T 0.68834 -0.5304 10 0.41790 T 0.15 . 13.509 0.61499 0.0:1.0:0.0:0.0 . 255 Q9H207 O10A5_HUMAN C 255;259 ENSP00000299454:S255C;ENSP00000369159:S259C ENSP00000299454:S255C S + 2 0 OR10A5 6824253 0.000000 0.05858 0.221000 0.23827 0.007000 0.05969 0.600000 0.24104 2.269000 0.75478 0.591000 0.81541 TCT TCGA-S4-A8RO-01A-12D-A377-08 OR10A5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385983.1 0 0 0 7 426 1 195 0 0 0 1 195 2 0 0 0 0 0 2 0 2.990150e-01 7 419 1 194 10 0 0 0 1 195 2 -2.713086 1 1 0 0 1 0 1 1 1.302272 1 0.680000 2.080000 0.515152 0.020000 0 0.060000 0.030000 0.035623 0.020000 0 1.000000e-02 0.050000 NOX4 50507 broad.mit.edu 37 11 89088203 89088203 + Nonsense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr11:89088203G>A ENST00000263317.4 - 13 1382 c.1144C>T c.(1144-1146)Cga>Tga p.R382* NOX4_ENST00000535633.1_Nonsense_Mutation_p.R358*|NOX4_ENST00000528341.1_Nonsense_Mutation_p.R357*|NOX4_ENST00000542487.1_Nonsense_Mutation_p.R358*|NOX4_ENST00000534731.1_Nonsense_Mutation_p.R382*|NOX4_ENST00000531342.1_Nonsense_Mutation_p.R75*|NOX4_ENST00000532825.1_Nonsense_Mutation_p.R358*|NOX4_ENST00000527626.1_Nonsense_Mutation_p.R216*|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000527956.1_Nonsense_Mutation_p.R358*|NOX4_ENST00000424319.1_Nonsense_Mutation_p.R358*|NOX4_ENST00000413594.2_Nonsense_Mutation_p.R403*|NOX4_ENST00000343727.5_Nonsense_Mutation_p.R358*|NOX4_ENST00000375979.3_Nonsense_Mutation_p.R75* Q9NPH5 NOX4_HUMAN NADPH oxidase 4 p.R382*(1) 44 Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011) AGTAAATCTCGAAATCGTTCT 0.328000 1 Substitution - Nonsense(1) SO:0001587 stop_gained ENST00000263317.4 0 1 hg19 CCDS8285.1 . . . . . . . . . . G 32 5.124446 0.94429 0.0 1.16E-4 ENSG00000086991 ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000527626;ENST00000528341;ENST00000413594;ENST00000531342;ENST00000375979 . . . 5.31 5.31 0.75309 . 0.325791 0.27060 N 0.021133 . . . . . . 0.80722 A 1 . . . . . . . . . . . . . -6.9276 14.4891 0.67639 0.0:0.0:1.0:0.0 . . . . X 358;358;358;382;382;358;358;358;216;357;403;75;75 . . R - 1 2 NOX4 88727851 1.000000 0.71417 1.000000 0.80357 0.974000 0.67602 5.228000 0.65310 2.479000 0.83701 0.563000 0.77884 CGA TCGA-S4-A8RO-01A-12D-A377-08 NOX4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394054.1 1 0 1 126 85 0 27 0 9.952362e-01 0 9 0 27 2 0 0 0 0 0 2 1 1 117 78 0 28 2 0 0 0 0 27 2 -20.000000 1 1 121326 1 38 1 1 3 4 3.157427 1 0.680000 2.080000 0.803150 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 DNAH10 196385 broad.mit.edu 37 12 124317833 124317833 + Missense_Mutation SNP C C A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr12:124317833C>A ENST00000409039.3 + 26 4389 c.4364C>A c.(4363-4365)cCt>cAt p.P1455H NM_207437.3 NP_997320.2 Q8IVF4 DYH10_HUMAN dynein, axonemal, heavy chain 10 52 all_neural(191;0.101)|Medulloblastoma(191;0.163) TTTGTGGGGCCTTTTCTGCAA 0.433000 0 SO:0001583 missense ENST00000409039.3 1 1 hg19 CCDS9255.2 . . . . . . . . . . C 29.1 4.980145 0.92982 . . ENSG00000197653 ENST00000409039 T 0.62105 0.05 5.83 5.83 0.93111 Dynein heavy chain, domain-2 (1); 0.000000 0.64402 U 0.000001 T 0.80742 0.4681 M 0.79123 2.44 0.80722 D 1 D 0.89917 1.0 D 0.83275 0.996 T 0.78600 -0.2141 10 0.40728 T 0.16 . 20.1162 0.97934 0.0:1.0:0.0:0.0 . 1455 Q8IVF4 DYH10_HUMAN H 1455 ENSP00000386770:P1455H ENSP00000386770:P1455H P + 2 0 DNAH10 122883786 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.818000 0.86416 2.756000 0.94617 0.655000 0.94253 CCT TCGA-S4-A8RO-01A-12D-A377-08 DNAH10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335420.3 1 0 1 30 79 0 23 0 0 0 1 0 23 2 0 0 0 0 0 2 1 1 30 78 0 22 2 0 0 0 0 23 2 -20.000000 1 1 0 0 1 1 2 3 1.982775 0 0.680000 2.080000 0.682161 0.810000 5.800000e-01 1.000000 1.000000 0.820021 0.810000 0 6.900000e-01 0.950000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-S4-A8RO-01A-12D-A377-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 79 177 0 51 1 9.959214e-01 6 16 0 51 2 1 1 118 342 0 696 2 1 1 78 173 0 51 2 1 1 3068 4964 0 51 2 -20.000000 1 1 121404 2 44 1 1 2 3 2.002208 0 0.680000 2.080000 0.684294 0.910000 7.500000e-01 1.000000 1.000000 0.916249 0.910000 1 8.300000e-01 1.000000 SYT10 341359 broad.mit.edu 37 12 33538128 33538128 + Silent SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr12:33538128C>T ENST00000228567.3 - 4 1472 c.1176G>A c.(1174-1176)gcG>gcA p.A392A SYT10_ENST00000535526.1_Silent_p.A211A NM_198992.3 NP_945343.1 Q6XYQ8 SYT10_HUMAN synaptotagmin X 42 Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334) TAATATCCATCGCCTTCAGAT 0.413000 0 SO:0001819 synonymous_variant ENST00000228567.3 1 1 hg19 CCDS8732.1 TCGA-S4-A8RO-01A-12D-A377-08 SYT10-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403222.1 1 0 1 114 277 0 94 0 0 0 0 94 2 0 0 0 0 0 2 1 1 113 273 0 93 2 0 0 0 0 94 2 -8.396578 1 1 121412 1 38 1 1 2 3 1.982775 0 0.680000 2.080000 0.682161 0.860000 7.200000e-01 1.000000 0.860000 0.866062 0.860000 1 7.900000e-01 0.940000 PDZRN4 29951 broad.mit.edu 37 12 41966704 41966704 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr12:41966704G>A ENST00000402685.2 + 10 2131 c.2123G>A c.(2122-2124)cGg>cAg p.R708Q PDZRN4_ENST00000539469.2_Missense_Mutation_p.R450Q|PDZRN4_ENST00000298919.7_Missense_Mutation_p.R448Q NM_001164595.1 NP_001158067.1 Q6ZMN7 PZRN4_HUMAN PDZ domain containing ring finger 4 77 all_cancers(12;0.000673) Lung NSC(34;0.0205)|all_lung(34;0.0264) GGAGGATTCCGGAATTATAAC 0.443000 0 SO:0001583 missense ENST00000402685.2 1 1 hg19 CCDS53777.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 10.61 1.398179 0.25205 . . ENSG00000165966 ENST00000402685;ENST00000539469;ENST00000298919 T;T;T 0.72505 -0.66;3.83;3.83 4.32 3.42 0.39159 . 0.094359 0.43416 D 0.000561 T 0.65565 0.2703 M 0.76838 2.35 0.39920 D 0.974143 B;B;B 0.31503 0.114;0.326;0.043 B;B;B 0.24269 0.003;0.052;0.014 T 0.64892 -0.6300 10 0.34782 T 0.22 -7.5442 9.2356 0.37464 0.0828:0.1469:0.7702:0.0 . 708;448;450 Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2 PZRN4_HUMAN;.;. Q 708;450;448 ENSP00000384197:R708Q;ENSP00000439990:R450Q;ENSP00000298919:R448Q ENSP00000298919:R448Q R + 2 0 PDZRN4 40252971 1.000000 0.71417 0.981000 0.43875 0.762000 0.43233 2.333000 0.43912 1.124000 0.41980 0.650000 0.86243 CGG TCGA-S4-A8RO-01A-12D-A377-08 PDZRN4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403701.1 1 0 1 70 198 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 1 69 196 0 72 2 0 0 0 0 73 2 -5.095352 1 1 121412 3 38 1 1 2 3 1.982775 0 0.680000 2.080000 0.682161 0.770000 6.200000e-01 0.960000 0.770000 0.779414 0.770000 0 6.900000e-01 0.860000 KCNA5 3741 broad.mit.edu 37 12 5153999 5153999 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr12:5153999G>A ENST00000252321.3 + 1 915 c.686G>A c.(685-687)cGc>cAc p.R229H NM_002234.3 NP_002225.2 P22460 KCNA5_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 5 52 Dalfampridine(DB06637) CCCCTGCCCCGCAACGAGTTC 0.607000 0 SO:0001583 missense ENST00000252321.3 1 1 hg19 CCDS8536.1 . . . . . . . . . . G 12.70 2.016133 0.35606 . . ENSG00000130037 ENST00000252321 T 0.65549 -0.16 4.77 4.77 0.60923 . 1.183500 0.06286 U 0.698225 T 0.56906 0.2017 L 0.35644 1.08 0.29339 N 0.866187 B 0.13145 0.007 B 0.12837 0.008 T 0.46938 -0.9155 10 0.52906 T 0.07 . 12.4671 0.55764 0.0832:0.0:0.9168:0.0 . 229 P22460 KCNA5_HUMAN H 229 ENSP00000252321:R229H ENSP00000252321:R229H R + 2 0 KCNA5 5024260 0.000000 0.05858 0.996000 0.52242 0.991000 0.79684 -0.403000 0.07214 2.478000 0.83669 0.561000 0.74099 CGC TCGA-S4-A8RO-01A-12D-A377-08 KCNA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398925.2 1 0 1 136 201 0 76 0 0 0 1 0 76 2 0 0 0 0 0 2 1 1 136 200 0 76 2 0 0 0 0 76 2 -20.000000 1 1 121412 1 36 1 1 2 3 2.038143 0 0.680000 2.080000 0.687439 0.990000 9.900000e-01 1.000000 1.000000 0.999932 0.990000 1 9.900000e-01 1.000000 KRT1 3848 broad.mit.edu 37 12 53069133 53069133 + Silent SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr12:53069133G>A ENST00000252244.3 - 9 1837 c.1779C>T c.(1777-1779)ggC>ggT p.G593G NM_006121.3 NP_006112.3 P04264 K2C1_HUMAN keratin 1 p.G593G(1) 39 cgccgccgccgcctccagagc 0.721000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000252244.3 1 1 hg19 CCDS8836.1 TCGA-S4-A8RO-01A-12D-A377-08 KRT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405706.1 1 0 0 56 93 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 1 52 85 0 33 2 0 0 0 0 38 2 -9.192583 1 1 118658 1 30 1 1 2 3 1.982775 0 0.680000 2.080000 0.682161 0.990000 8.800000e-01 1.000000 1.000000 0.990479 0.990000 1 9.900000e-01 1.000000 ATP2B1 490 broad.mit.edu 37 12 90036041 90036041 + Missense_Mutation SNP T T A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr12:90036041T>A ENST00000428670.3 - 3 756 c.300A>T c.(298-300)caA>caT p.Q100H ATP2B1_ENST00000261173.2_Missense_Mutation_p.Q100H|ATP2B1_ENST00000348959.3_Missense_Mutation_p.Q100H|ATP2B1_ENST00000359142.3_Missense_Mutation_p.Q100H P20020 AT2B1_HUMAN ATPase, Ca++ transporting, plasma membrane 1 45 CCCATACTAATTGAAGAAAGG 0.343000 0 SO:0001583 missense ENST00000428670.3 1 1 hg19 CCDS9035.1 . . . . . . . . . . T 22.1 4.237947 0.79800 . . ENSG00000070961 ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.76 -5.69 0.02428 . 0.000000 0.85682 D 0.000000 D 0.83275 0.5219 M 0.79805 2.47 0.53005 D 0.99996 D;P 0.63880 0.993;0.5 P;P 0.60682 0.878;0.55 D 0.84356 0.0535 9 . . . -20.2557 15.3162 0.74081 0.0:0.6036:0.0:0.3964 . 100;100 P20020-3;P20020-2 .;. H 100 ENSP00000261173:Q100H;ENSP00000343599:Q100H;ENSP00000352054:Q100H;ENSP00000392043:Q100H . Q - 3 2 ATP2B1 88560172 0.015000 0.18098 0.906000 0.35671 0.986000 0.74619 -0.835000 0.04386 -0.979000 0.03529 0.379000 0.24179 CAA TCGA-S4-A8RO-01A-12D-A377-08 ATP2B1-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406653.1 1 0 1 449 823 0 322 1 9.411745e-01 2 9 0 322 2 0 0 0 0 0 2 1 1 443 816 0 322 2 0 0 0 0 322 2 -20.000000 1 1 0 0 1 1 2 3 1.982775 0 0.680000 2.080000 0.682161 0.990000 9.600000e-01 1.000000 1.000000 0.997460 0.990000 1 9.900000e-01 1.000000 TUBA3C 7278 broad.mit.edu 37 13 19751734 19751734 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr13:19751734G>A ENST00000400113.3 - 4 493 c.389C>T c.(388-390)aCg>aTg p.T130M NM_006001.2 NP_005992.1 Q13748 TBA3C_HUMAN tubulin, alpha 3c 72 all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162) CTGCAGTCCCGTGCACAGATC 0.582000 0 SO:0001583 missense ENST00000400113.3 1 1 hg19 CCDS9284.1 . . . . . . . . . . g 9.895 1.205228 0.22205 . . ENSG00000198033 ENST00000400113;ENST00000360801 T 0.68624 -0.34 1.19 1.19 0.21007 . 0.000000 0.48286 U 0.000184 T 0.70439 0.3224 . . . 0.40500 D 0.980633 . . . . . . T 0.72763 -0.4195 7 0.87932 D 0 . 8.3041 0.32032 0.0:0.0:1.0:0.0 . . . . M 130 ENSP00000382982:T130M ENSP00000354037:T130M T - 2 0 TUBA3C 18649734 1.000000 0.71417 0.920000 0.36463 0.408000 0.30992 4.910000 0.63321 0.966000 0.38159 0.162000 0.16502 ACG TCGA-S4-A8RO-01A-12D-A377-08 TUBA3C-002 KNOWN not_best_in_genome_evidence|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044007.2 1 0 1 61 104 0 47 0 0 0 0 47 2 0 0 0 0 0 2 1 1 58 102 0 48 2 0 0 0 0 47 2 -20.000000 1 1 0 0 1 0 0 0 1.894646 0 0.680000 2.080000 0.671053 0.990000 8.400000e-01 1.000000 1.000000 0.980914 0.990000 1 9.400000e-01 1.000000 PABPC3 5042 broad.mit.edu 37 13 25671262 25671262 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr13:25671262G>A ENST00000281589.3 + 1 963 c.926G>A c.(925-927)cGt>cAt p.R309H NM_030979.2 NP_112241.2 Q9H361 PABP3_HUMAN poly(A) binding protein, cytoplasmic 3 47 Lung SC(185;0.0225)|Breast(139;0.0602) GATGATGAACGTCTCCGGAAA 0.408000 0 SO:0001583 missense ENST00000281589.3 1 1 hg19 CCDS9311.1 . . . . . . . . . . G 8.903 0.956849 0.18507 . . ENSG00000151846 ENST00000281589 T 0.15952 2.38 0.875 -0.438 0.12268 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3); 0.135449 0.32473 N 0.006058 T 0.07007 0.0178 N 0.10685 0.025 0.50632 D 0.999884 P 0.43094 0.799 B 0.38985 0.287 T 0.30880 -0.9963 10 0.62326 D 0.03 . 6.1527 0.20320 0.0:0.3209:0.679:0.0 . 309 Q9H361 PABP3_HUMAN H 309 ENSP00000281589:R309H ENSP00000281589:R309H R + 2 0 PABPC3 24569262 1.000000 0.71417 0.851000 0.33527 0.226000 0.24999 3.068000 0.50018 -0.161000 0.10983 0.313000 0.20887 CGT TCGA-S4-A8RO-01A-12D-A377-08 PABPC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044220.2 1 0 1 378 755 0 310 0 0 0 1 0 310 2 0 0 0 0 0 2 1 1 376 733 0 309 2 0 0 0 0 310 2 -20.000000 1 0 121412 6 43 1 0 0 0 1.894646 0 0.680000 2.080000 0.671053 0.940000 8.700000e-01 1.000000 1.000000 0.952174 0.940000 1 9.000000e-01 0.990000 PPP2R5C 5527 broad.mit.edu 37 14 102360847 102360847 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr14:102360847G>A ENST00000334743.5 + 8 850 c.802G>A c.(802-804)Gca>Aca p.A268T PPP2R5C_ENST00000328724.5_Missense_Mutation_p.A323T|PPP2R5C_ENST00000557095.1_Missense_Mutation_p.A268T|PPP2R5C_ENST00000445439.3_Missense_Mutation_p.A268T|PPP2R5C_ENST00000422945.2_Missense_Mutation_p.A299T|PPP2R5C_ENST00000350249.3_Missense_Mutation_p.A268T NM_002719.3 NP_002710.2 Q13362 2A5G_HUMAN protein phosphatase 2, regulatory subunit B', gamma 20 TTTTTAGCTGGCATACTGTGT 0.403000 0 SO:0001583 missense ENST00000334743.5 0 1 hg19 CCDS9964.1 . . . . . . . . . . G 25.0 4.593023 0.86953 . . ENSG00000078304 ENST00000422945;ENST00000328724;ENST00000557268;ENST00000350249;ENST00000334756;ENST00000445439;ENST00000334743;ENST00000557095;ENST00000557716 T;T;T;T;T 0.49720 0.78;0.77;0.77;0.83;0.78 5.63 5.63 0.86233 Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.56615 0.1997 L 0.59436 1.845 0.80722 D 1 P;B;P;P;B;P 0.45531 0.831;0.083;0.765;0.86;0.148;0.567 B;B;B;P;B;B 0.48063 0.429;0.122;0.252;0.565;0.074;0.443 T 0.57487 -0.7803 10 0.54805 T 0.06 -6.5997 19.6959 0.96026 0.0:0.0:1.0:0.0 . 299;166;268;268;268;323 F5GWP3;E9PHN5;Q13362-3;Q13362;Q13362-2;Q6ZN33 .;.;.;2A5G_HUMAN;.;. T 299;323;297;268;166;268;268;268;64 ENSP00000412324:A299T;ENSP00000329009:A323T;ENSP00000450931:A297T;ENSP00000262239:A268T;ENSP00000333905:A268T ENSP00000329009:A323T A + 1 0 PPP2R5C 101430600 1.000000 0.71417 0.999000 0.59377 0.799000 0.45148 9.694000 0.98686 2.659000 0.90383 0.650000 0.86243 GCA TCGA-S4-A8RO-01A-12D-A377-08 PPP2R5C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414373.2 0 0 0 6 403 0 64 0 5.924434e-01 0 125 0 64 2 0 0 0 0 0 2 1 9.633321e-01 6 396 0 62 2 0 0 0 0 64 2 -2.802890 1 1 0 0 1 1 2 3 2.596884 1 0.680000 2.080000 0.761194 0.050000 1.000000e-02 0.120000 0.060000 0.066869 0.050000 0 3.000000e-02 0.090000 ACIN1 22985 broad.mit.edu 37 14 23531399 23531399 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr14:23531399G>A ENST00000262710.1 - 16 3578 c.3251C>T c.(3250-3252)gCt>gTt p.A1084V ACIN1_ENST00000357481.2_Missense_Mutation_p.A326V|ACIN1_ENST00000457657.1_Missense_Mutation_p.A1044V|ACIN1_ENST00000397341.3_Missense_Mutation_p.A326V|ACIN1_ENST00000557515.1_Missense_Mutation_p.A325V|ACIN1_ENST00000338631.6_Missense_Mutation_p.A357V|ACIN1_ENST00000555053.1_Missense_Mutation_p.A1071V|ACIN1_ENST00000605057.1_Missense_Mutation_p.A1026V NM_001164814.1|NM_014977.3 NP_001158286.1|NP_055792 Q9UKV3 ACINU_HUMAN apoptotic chromatin condensation inducer 1 37 all_cancers(95;1.36e-05) GGCATAGTCAGCACAAAGGAA 0.537000 0 SO:0001583 missense ENST00000262710.1 0 1 hg19 CCDS9587.1 . . . . . . . . . . G 9.790 1.177752 0.21787 . . ENSG00000100813 ENST00000557515;ENST00000338631;ENST00000357481;ENST00000262710;ENST00000457657;ENST00000397341;ENST00000555053 T;T;T;T;T;T;T 0.18502 2.21;2.21;2.21;2.21;2.21;2.21;2.21 5.19 5.19 0.71726 Nucleotide-binding, alpha-beta plait (1); 0.000000 0.38720 N 0.001589 T 0.04407 0.0121 N 0.00289 -1.7 0.44388 D 0.997291 B;B;B;B;B 0.27013 0.137;0.166;0.084;0.111;0.054 B;B;B;B;B 0.35859 0.135;0.212;0.064;0.016;0.011 T 0.41610 -0.9499 10 0.02654 T 1 -9.2231 11.4006 0.49868 0.0848:0.0:0.9152:0.0 . 1071;1084;1044;357;326 G3V3M7;Q9UKV3;E7EQT4;Q9UKV3-2;Q9UKV3-3 .;ACINU_HUMAN;.;.;. V 325;357;326;1084;1044;326;1071 ENSP00000451138:A325V;ENSP00000345541:A357V;ENSP00000350073:A326V;ENSP00000262710:A1084V;ENSP00000405677:A1044V;ENSP00000380502:A326V;ENSP00000451328:A1071V ENSP00000262710:A1084V A - 2 0 ACIN1 22601239 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 4.835000 0.62781 2.578000 0.87016 0.563000 0.77884 GCT TCGA-S4-A8RO-01A-12D-A377-08 ACIN1-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000071707.3 0 0 0 5 601 0 90 0 6.780961e-01 0 264 0 90 2 0 0 0 0 0 2 1 9.372288e-01 5 599 0 89 2 0 0 0 0 90 2 -2.446123 0 1 0 0 1 1 2 3 2.617345 1 0.680000 2.080000 0.760587 0.030000 0 0.080000 0.030000 0.037971 0.030000 0 1.000000e-02 0.060000 ZFYVE26 23503 broad.mit.edu 37 14 68238816 68238816 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr14:68238816G>A ENST00000347230.4 - 28 5570 c.5432C>T c.(5431-5433)cCg>cTg p.P1811L ZFYVE26_ENST00000555452.1_Missense_Mutation_p.P1811L NM_015346.3 NP_056161.2 Q68DK2 ZFY26_HUMAN zinc finger, FYVE domain containing 26 94 AGTCTCATCCGGTACCCACTG 0.562000 0 SO:0001583 missense ENST00000347230.4 0 1 hg19 CCDS9788.1 . . . . . . . . . . G 22.3 4.269444 0.80469 . . ENSG00000072121 ENST00000347230;ENST00000411699;ENST00000555452 T;T 0.49720 0.77;0.77 5.76 5.76 0.90799 Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE/PHD-type (1); 0.000000 0.85682 D 0.000000 T 0.77260 0.4104 M 0.90870 3.155 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.83275 0.994;0.996 T 0.81780 -0.0776 10 0.87932 D 0 -14.759 19.9574 0.97228 0.0:0.0:1.0:0.0 . 1811;1811 G3V2D8;Q68DK2 .;ZFY26_HUMAN L 1811;1790;1811 ENSP00000251119:P1811L;ENSP00000450603:P1811L ENSP00000251119:P1811L P - 2 0 ZFYVE26 67308569 1.000000 0.71417 0.432000 0.26747 0.625000 0.37756 7.804000 0.85993 2.715000 0.92844 0.561000 0.74099 CCG TCGA-S4-A8RO-01A-12D-A377-08 ZFYVE26-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412736.2 1 0 1 50 64 0 14 1 9.680347e-01 6 4 0 14 2 0 0 0 0 0 2 1 1 49 64 0 14 2 0 0 0 0 14 2 -20.000000 1 1 0 0 1 1 2 3 2.577519 1 0.680000 2.080000 0.757502 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 GALC 2581 broad.mit.edu 37 14 88411975 88411975 + Missense_Mutation SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr14:88411975C>T ENST00000261304.2 - 14 1698 c.1592G>A c.(1591-1593)cGc>cAc p.R531H GALC_ENST00000544807.2_Missense_Mutation_p.R475H|GALC_ENST00000393569.2_Missense_Mutation_p.R505H|GALC_ENST00000393568.4_Missense_Mutation_p.R508H NM_000153.3|NM_001201401.1 NP_000144.2|NP_001188330.1 P54803 GALC_HUMAN galactosylceramidase 21 GAGAACTTGGCGTAGCGTGAA 0.408000 0 GRCh37 CM990620 GALC M SO:0001583 missense ENST00000261304.2 1 1 hg19 CCDS9878.2 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 C 17.14 3.314547 0.60524 . . ENSG00000054983 ENST00000261304;ENST00000544807;ENST00000393569;ENST00000539620;ENST00000393568 D;D;D;D 0.95035 -3.59;-3.59;-3.59;-3.59 5.5 4.61 0.57282 . 0.048176 0.85682 D 0.000000 D 0.97745 0.9260 M 0.91140 3.18 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.997;0.999;0.997;0.999 D 0.98792 1.0736 10 0.87932 D 0 -13.106 15.9398 0.79745 0.1363:0.8637:0.0:0.0 . 475;508;505;531 P54803-5;E7EPA4;P54803-4;P54803 .;.;.;GALC_HUMAN H 531;475;505;320;508 ENSP00000261304:R531H;ENSP00000437513:R475H;ENSP00000377199:R505H;ENSP00000377198:R508H ENSP00000261304:R531H R - 2 0 GALC 87481728 1.000000 0.71417 0.840000 0.33206 0.012000 0.07955 7.637000 0.83313 1.441000 0.47550 0.585000 0.79938 CGC TCGA-S4-A8RO-01A-12D-A377-08 GALC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000071559.2 1 0 1 117 338 0 76 1 9.999999e-01 17 53 0 76 2 0 0 0 0 0 2 1 1 116 333 0 76 2 0 0 0 0 76 2 -6.177353 1 1 120816 7 43 1 1 2 3 2.596884 1 0.680000 2.080000 0.761194 0.990000 8.500000e-01 1.000000 1.000000 0.975393 0.990000 1 9.300000e-01 1.000000 IFT140 9742 broad.mit.edu 37 16 1612009 1612009 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr16:1612009G>A ENST00000426508.2 - 18 2539 c.2176C>T c.(2176-2178)Cct>Tct p.P726S IFT140_ENST00000439987.2_5'UTR NM_014714.3 NP_055529.2 Q96RY7 IF140_HUMAN intraflagellar transport 140 53 Hepatocellular(780;0.219) TAGTAATAAGGCACTTCCATC 0.557000 0 SO:0001583 missense ENST00000426508.2 1 1 hg19 CCDS10439.1 . . . . . . . . . . G 18.81 3.702254 0.68501 . . ENSG00000187535 ENST00000397417;ENST00000426508;ENST00000439987 T 0.68025 -0.3 5.12 5.12 0.69794 . 0.000000 0.85682 D 0.000000 D 0.84288 0.5439 M 0.84433 2.695 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.86852 0.2024 10 0.87932 D 0 . 18.9059 0.92460 0.0:0.0:1.0:0.0 . 726;451 Q96RY7;B4DR58 IF140_HUMAN;. S 726 ENSP00000406012:P726S ENSP00000380562:P726S P - 1 0 IFT140 1552010 1.000000 0.71417 0.797000 0.32132 0.084000 0.17831 9.225000 0.95219 2.535000 0.85469 0.563000 0.77884 CCT TCGA-S4-A8RO-01A-12D-A377-08 IFT140-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250438.2 1 0 1 93 86 0 52 1 9.833467e-01 6 3 0 52 2 0 0 0 0 0 2 1 1 92 85 0 50 2 0 0 0 0 52 2 -20.000000 1 1 0 0 1 0 1 1 1.413717 1 0.680000 2.080000 0.515152 0.950000 8.300000e-01 1.000000 0.990000 0.946414 0.950000 1 8.900000e-01 0.990000 NUDT21 11051 broad.mit.edu 37 16 56468701 56468701 + Missense_Mutation SNP T T C TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr16:56468701T>C ENST00000300291.5 - 5 684 c.512A>G c.(511-513)cAt>cGt p.H171R NM_007006.2 NP_008937.1 O43809 CPSF5_HUMAN nudix (nucleoside diphosphate linked moiety X)-type motif 21 7 CAACTTCTTATGTTCCTTAGG 0.303000 0 SO:0001583 missense ENST00000300291.5 1 1 hg19 CCDS10760.1 . . . . . . . . . . T 14.53 2.563365 0.45694 . . ENSG00000167005 ENST00000300291 . . . 5.34 5.34 0.76211 NUDIX hydrolase domain (1); 0.000000 0.85682 D 0.000000 T 0.62974 0.2472 L 0.42581 1.335 0.80722 D 1 D 0.63046 0.992 P 0.57152 0.814 T 0.58578 -0.7612 9 0.23302 T 0.38 . 15.602 0.76631 0.0:0.0:0.0:1.0 . 171 O43809 CPSF5_HUMAN R 171 . ENSP00000300291:H171R H - 2 0 NUDT21 55026202 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 7.582000 0.82546 2.145000 0.66743 0.477000 0.44152 CAT TCGA-S4-A8RO-01A-12D-A377-08 NUDT21-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256980.3 1 0 1 236 453 0 177 1 1 34 83 0 177 2 0 0 0 0 0 2 1 1 232 441 0 176 2 0 0 0 0 177 2 -20.000000 1 1 0 0 1 1 2 3 2.034749 0 0.680000 2.080000 0.687439 0.990000 9.200000e-01 1.000000 1.000000 0.991122 0.990000 1 9.700000e-01 1.000000 NRN1L 123904 broad.mit.edu 37 16 67920029 67920029 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr16:67920029G>A ENST00000339176.3 + 3 464 c.365G>A c.(364-366)cGg>cAg p.R122Q NRN1L_ENST00000576147.1_Missense_Mutation_p.G49R|CTC-479C5.10_ENST00000572067.1_lincRNA NM_198443.1 NP_940845.1 Q496H8 NRN1L_HUMAN neuritin 1-like 7 Ovarian(137;0.192) GTGCATGTTCGGGAGCGCGGC 0.667000 0 SO:0001583 missense ENST00000339176.3 1 1 hg19 CCDS10850.1 . . . . . . . . . . G 11.31 1.599853 0.28534 0.0 2.33E-4 ENSG00000188038 ENST00000339176 . . . 4.86 -3.54 0.04653 . 1.058750 0.07350 N 0.882262 T 0.10508 0.0257 N 0.01109 -1.01 0.09310 N 1 B 0.15719 0.014 B 0.06405 0.002 T 0.29822 -0.9999 9 0.19147 T 0.46 . 6.5616 0.22489 0.4412:0.2124:0.3464:0.0 . 122 Q496H8 NRN1L_HUMAN Q 122 . ENSP00000342411:R122Q R + 2 0 NRN1L 66477530 0.010000 0.17322 0.049000 0.19019 0.006000 0.05464 0.003000 0.13083 -0.579000 0.05952 -1.417000 0.01113 CGG TCGA-S4-A8RO-01A-12D-A377-08 NRN1L-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000268872.2 1 0 1 27 45 0 32 0 3.234139e-01 1 2 0 32 2 0 0 0 0 0 2 1 1 27 45 0 31 2 0 0 0 0 32 2 -6.860764 1 1 121372 13 39 1 1 2 3 2.034749 0 0.680000 2.080000 0.687439 0.990000 8.100000e-01 1.000000 1.000000 0.981270 0.990000 1 9.600000e-01 1.000000 GPR179 440435 broad.mit.edu 37 17 36485458 36485458 + Missense_Mutation SNP A A G TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr17:36485458A>G ENST00000342292.4 - 11 4014 c.3994T>C c.(3994-3996)Tcc>Ccc p.S1332P GPR179_ENST00000584976.1_5'Flank NM_001004334.2 NP_001004334.2 Q6PRD1 GP179_HUMAN G protein-coupled receptor 179 60 Breast(7;2.97e-12) Breast(25;0.0101)|Ovarian(249;0.15) GACCCAGGGGACAGACCTCCT 0.607000 0 SO:0001583 missense ENST00000342292.4 0 1 hg19 CCDS42308.1 . . . . . . . . . . A 2.564 -0.301204 0.05495 . . ENSG00000188888 ENST00000342292 T 0.53206 0.63 4.74 1.23 0.21249 . 0.407814 0.21212 N 0.078287 T 0.32912 0.0845 L 0.44542 1.39 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.14839 -1.0458 10 0.39692 T 0.17 -4.2878 4.6654 0.12662 0.6483:0.1668:0.185:0.0 . 1332 Q6PRD1 GP179_HUMAN P 1332 ENSP00000345060:S1332P ENSP00000345060:S1332P S - 1 0 GPR179 33738984 0.000000 0.05858 0.001000 0.08648 0.003000 0.03518 0.510000 0.22723 0.854000 0.35336 0.374000 0.22700 TCC TCGA-S4-A8RO-01A-12D-A377-08 GPR179-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255329.2 0 0 0 5 207 0 60 0 9.128450e-04 0 2 0 60 2 0 0 0 0 0 2 1 9.342993e-01 5 202 0 57 2 0 0 0 0 60 2 -6.856036 1 1 0 0 1 2 2 4 2.154984 1 0.680000 2.080000 0.711400 0.080000 2.000000e-02 1.000000 0.070000 0.205533 0.080000 0 5.000000e-02 0.170000 KRTAP4-3 85290 broad.mit.edu 37 17 39324213 39324213 + Missense_Mutation SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr17:39324213C>T ENST00000391356.2 - 1 211 c.212G>A c.(211-213)cGc>cAc p.R71H NM_033187.1 NP_149443.1 Q9BYR4 KRA43_HUMAN keratin associated protein 4-3 12 Breast(137;0.000496) STAD - Stomach adenocarcinoma(17;0.000449) gcagctggggcggcagcaggt 0.637000 0 SO:0001583 missense ENST00000391356.2 0 1 hg19 CCDS42331.1 . . . . . . . . . . . 14.27 2.484619 0.44147 . . ENSG00000196156 ENST00000391356 T 0.01495 4.83 4.46 1.32 0.21799 . . . . . T 0.01870 0.0059 L 0.54908 1.71 0.09310 N 1 P 0.38335 0.627 B 0.23018 0.043 T 0.44667 -0.9313 9 0.66056 D 0.02 . 8.1078 0.30896 0.0:0.721:0.0:0.279 . 71 Q9BYR4 KRA43_HUMAN H 71 ENSP00000375151:R71H ENSP00000375151:R71H R - 2 0 KRTAP4-3 36577739 0.000000 0.05858 0.174000 0.22961 0.413000 0.31143 -0.095000 0.11077 0.081000 0.16988 0.609000 0.83330 CGC TCGA-S4-A8RO-01A-12D-A377-08 KRTAP4-3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257784.1 1 0 0 12 25 0 9 0 0 0 0 9 2 0 0 0 0 0 2 0 0 0 0 0 2 0 0 0 0 9 2 -4.420187 1 0 0 0 1 2 2 4 2.154984 1 0.680000 2.080000 0.711400 0.990000 6.300000e-01 1.000000 1.000000 0.945630 0.990000 1 8.400000e-01 1.000000 KRT34 3885 broad.mit.edu 37 17 39537409 39537409 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr17:39537409G>A ENST00000394001.1 - 3 643 c.613C>T c.(613-615)Cgc>Tgc p.R205C NM_021013.3 NP_066293.2 O76011 KRT34_HUMAN keratin 34 25 Breast(137;0.000496) AGGATCCTGCGTATGCTGTTG 0.562000 0 SO:0001583 missense ENST00000394001.1 1 1 hg19 CCDS11390.1 . . . . . . . . . . g 17.97 3.519112 0.64634 2.27E-4 0.0 ENSG00000131737 ENST00000394001;ENST00000251648 . . . 5.52 5.52 0.82312 Filament (1); 0.000000 0.64402 D 0.000003 T 0.80019 0.4547 M 0.74881 2.28 0.48341 D 0.999631 D 0.89917 1.0 D 0.85130 0.997 T 0.81852 -0.0742 9 0.87932 D 0 . 18.419 0.90582 0.0:0.0:1.0:0.0 . 205 O76011 KRT34_HUMAN C 163;205 . ENSP00000251648:R205C R - 1 0 KRT34 36790935 0.995000 0.38212 1.000000 0.80357 0.497000 0.33675 2.210000 0.42816 2.606000 0.88127 0.655000 0.94253 CGC TCGA-S4-A8RO-01A-12D-A377-08 KRT34-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257304.3 1 0 1 112 166 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 1 110 165 0 65 2 0 0 0 0 66 2 -20.000000 1 1 121412 2 39 1 2 2 4 2.154984 1 0.680000 2.080000 0.711400 0.990000 9.900000e-01 1.000000 1.000000 0.999993 0.990000 1 9.900000e-01 1.000000 PTRF 284119 broad.mit.edu 37 17 40557353 40557353 + Silent SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr17:40557353C>T ENST00000357037.5 - 2 944 c.525G>A c.(523-525)tcG>tcA p.S175S NM_012232.5 NP_036364.2 polymerase I and transcript release factor p.S175S(1) 17 all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134) GCAGCGCCTCCGACTCTTTCA 0.647000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000357037.5 1 1 hg19 CCDS11425.1 TCGA-S4-A8RO-01A-12D-A377-08 PTRF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000449938.1 1 0 1 177 367 0 101 1 1 26 173 0 101 2 0 0 0 0 0 2 1 1 174 356 0 97 2 0 0 0 0 101 2 -14.659870 1 1 0 0 1 2 2 4 2.154984 1 0.680000 2.080000 0.711400 0.990000 9.300000e-01 1.000000 1.000000 0.994829 0.990000 1 9.900000e-01 1.000000 PLD2 5338 broad.mit.edu 37 17 4712837 4712837 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr17:4712837G>A ENST00000263088.6 + 7 736 c.605G>A c.(604-606)cGc>cAc p.R202H RP11-81A22.5_ENST00000571067.1_lincRNA|PLD2_ENST00000572940.1_Missense_Mutation_p.R202H NM_001243108.1|NM_002663.4 NP_001230037.1|NP_002654.3 O14939 PLD2_HUMAN phospholipase D2 31 Choline(DB00122) GACTTGGGCCGCAAAGGACTG 0.567000 0 SO:0001583 missense ENST00000263088.6 0 1 hg19 CCDS11057.1 . . . . . . . . . . G 12.45 1.940910 0.34283 . . ENSG00000129219 ENST00000263088 T 0.06449 3.3 5.1 0.825 0.18824 . 0.567307 0.19886 N 0.103853 T 0.02610 0.0079 N 0.04508 -0.205 0.19775 N 0.99996 B;B;B 0.21225 0.053;0.041;0.01 B;B;B 0.12156 0.001;0.007;0.002 T 0.48151 -0.9060 10 0.15499 T 0.54 -1.3847 9.5998 0.39596 0.0:0.495:0.426:0.079 . 59;202;202 B7Z905;O14939-2;O14939 .;.;PLD2_HUMAN H 202 ENSP00000263088:R202H ENSP00000263088:R202H R + 2 0 PLD2 4659801 0.761000 0.28439 0.852000 0.33557 0.645000 0.38454 1.825000 0.39081 0.056000 0.16144 -0.311000 0.09066 CGC TCGA-S4-A8RO-01A-12D-A377-08 PLD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207561.3 0 0 0 5 258 0 93 0 8.680755e-02 0 21 0 93 2 0 0 0 0 0 2 1 9.362356e-01 5 255 0 93 2 0 0 0 0 93 2 -2.064513 0 1 121412 1 36 1 0 1 1 1.467511 1 0.680000 2.080000 0.515152 0.030000 0 0.080000 0.040000 0.043786 0.030000 0 2.000000e-02 0.060000 TP53 7157 broad.mit.edu 37 17 7577094 7577094 + Missense_Mutation SNP G G A rs28934574 TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr17:7577094G>A ENST00000269305.4 - 8 1033 c.844C>T c.(844-846)Cgg>Tgg p.R282W TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000413465.2_Intron NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) TCTGTGCGCCGGTCTCTCCCA 0.557000 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 463 Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1) GRCh37 CM056413|CM920678 TP53 M rs28934574 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 20.8 4.057525 0.76074 0.0 2.33E-4 ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D 0.99869 -7.34;-7.34;-7.34;-7.34;-7.34;-7.34 4.75 1.49 0.22878 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99825 0.9922 M 0.89968 3.075 0.58432 A 0.999999 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 0.999;0.998;1.0;0.999 D 0.97713 1.0192 9 0.87932 D 0 -12.0909 8.7508 0.34613 0.0:0.1376:0.5833:0.2792 rs28934574 282;282;282;282 P04637-2;P04637-3;P04637;Q1MSW8 .;.;P53_HUMAN;. W 282;282;282;282;282;271;150 ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W ENSP00000269305:R282W R - 1 2 TP53 7517819 1.000000 0.71417 0.327000 0.25402 0.901000 0.52897 4.477000 0.60223 0.174000 0.19809 0.462000 0.41574 CGG TCGA-S4-A8RO-01A-12D-A377-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 50 35 0 28 1 1 61 16 0 28 2 1 1 524 485 0 1785 2 1 1 50 35 0 28 2 0 0 0 0 28 2 -17.795730 1 1 121412 2 36 1 0 1 1 1.467511 1 0.680000 2.080000 0.515152 0.960000 8.300000e-01 1.000000 0.990000 0.953847 0.960000 1 9.000000e-01 0.990000 DSC3 1825 broad.mit.edu 37 18 28610959 28610959 + Silent SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr18:28610959G>A ENST00000360428.4 - 3 414 c.334C>T c.(334-336)Ctg>Ttg p.L112L DSC3_ENST00000434452.1_Silent_p.L112L NM_001941.3 NP_001932.2 Q14574 DSC3_HUMAN desmocollin 3 56 OV - Ovarian serous cystadenocarcinoma(10;0.125) TGTTCTAGCAGCACAGTAACC 0.338000 0 SO:0001819 synonymous_variant ENST00000360428.4 1 1 hg19 CCDS32810.1 TCGA-S4-A8RO-01A-12D-A377-08 DSC3-001 KNOWN non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000447384.1 1 0 1 100 231 0 81 0 0 0 0 81 2 0 0 0 0 0 2 1 1 100 229 0 80 2 0 0 0 0 81 2 -20.000000 1 1 0 0 1 1 2 3 2.061145 0 0.680000 2.080000 0.689501 0.910000 7.600000e-01 1.000000 1.000000 0.918646 0.910000 1 8.400000e-01 1.000000 KEAP1 9817 broad.mit.edu 37 19 10610147 10610147 + Missense_Mutation SNP G G C TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr19:10610147G>C ENST00000171111.5 - 2 1110 c.563C>G c.(562-564)gCc>gGc p.A188G KEAP1_ENST00000393623.2_Missense_Mutation_p.A188G|KEAP1_ENST00000588024.1_5'UTR NM_203500.1 NP_987096.1 Q14145 KEAP1_HUMAN kelch-like ECH-associated protein 1 92 OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05) Dimethyl fumarate(DB08908) AGCGAAGTTGGCGATGCCGAT 0.597000 0 SO:0001583 missense ENST00000171111.5 1 1 hg19 CCDS12239.1 . . . . . . . . . . G 20.4 3.980801 0.74474 . . ENSG00000079999 ENST00000171111;ENST00000393623 T;T 0.69306 -0.39;-0.39 4.81 4.81 0.61882 BTB/Kelch-associated (2); 0.053770 0.64402 D 0.000001 T 0.76962 0.4061 L 0.53617 1.68 0.80722 D 1 D 0.67145 0.996 D 0.65573 0.936 T 0.79619 -0.1728 10 0.72032 D 0.01 . 15.3825 0.74669 0.0:0.0:1.0:0.0 . 188 Q14145 KEAP1_HUMAN G 188 ENSP00000171111:A188G;ENSP00000377245:A188G ENSP00000171111:A188G A - 2 0 KEAP1 10471147 1.000000 0.71417 1.000000 0.80357 0.928000 0.56348 4.017000 0.57167 2.232000 0.73038 0.561000 0.74099 GCC TCGA-S4-A8RO-01A-12D-A377-08 KEAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452000.1 1 0 0 38 82 0 33 1 1 41 66 0 33 2 0 0 0 0 0 2 1 1 38 81 0 32 2 0 0 0 0 33 2 -20.000000 1 1 0 0 1 2 2 4 2.177001 1 0.680000 2.080000 0.714897 0.990000 7.900000e-01 1.000000 1.000000 0.971735 0.990000 1 9.200000e-01 1.000000 UNC13A 23025 broad.mit.edu 37 19 17766751 17766751 + Silent SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr19:17766751G>A ENST00000519716.2 - 10 1223 c.1224C>T c.(1222-1224)ccC>ccT p.P408P UNC13A_ENST00000551649.1_Silent_p.P408P|UNC13A_ENST00000252773.7_Silent_p.P408P|UNC13A_ENST00000552293.1_Silent_p.P408P|UNC13A_ENST00000550896.1_Silent_p.P408P|UNC13A_ENST00000428389.2_Silent_p.P496P NM_001080421.2 NP_001073890.2 Q9UPW8 UN13A_HUMAN unc-13 homolog A (C. elegans) 61 GCACCTTGTCGGGCGTGGCTG 0.692000 0 SO:0001819 synonymous_variant ENST00000519716.2 1 1 hg19 CCDS46013.2 TCGA-S4-A8RO-01A-12D-A377-08 UNC13A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000376169.2 1 0 1 22 53 0 10 0 0 0 0 10 2 0 0 0 0 0 2 1 9.999995e-01 21 51 0 10 2 0 0 0 0 10 2 -4.735589 1 1 120118 10 36 1 1 2 3 2.034048 0 0.680000 2.080000 0.687439 0.890000 6.000000e-01 1.000000 1.000000 0.877317 0.890000 1 7.300000e-01 1.000000 FXYD3 5349 broad.mit.edu 37 19 35613737 35613737 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr19:35613737G>A ENST00000344013.6 + 6 362 c.166G>A c.(166-168)Gtc>Atc p.V56I FXYD3_ENST00000346446.5_Missense_Mutation_p.V56I|FXYD3_ENST00000604621.1_Missense_Mutation_p.V56I|FXYD3_ENST00000603524.1_Missense_Mutation_p.V85I|FXYD3_ENST00000604404.1_Missense_Mutation_p.V56I|FXYD3_ENST00000406242.3_Missense_Mutation_p.V56I|FXYD3_ENST00000406988.1_Missense_Mutation_p.V56I|LGI4_ENST00000493050.1_5'Flank|FXYD3_ENST00000535103.1_Missense_Mutation_p.V113I|FXYD3_ENST00000603181.1_Missense_Mutation_p.V56I|FXYD3_ENST00000604255.1_Missense_Mutation_p.V113I|FXYD3_ENST00000605677.1_Missense_Mutation_p.V56I|FXYD3_ENST00000604804.1_Missense_Mutation_p.V85I|FXYD3_ENST00000435734.2_Missense_Mutation_p.V56I|FXYD3_ENST00000605550.1_Missense_Mutation_p.V56I Q14802 FXYD3_HUMAN FXYD domain containing ion transport regulator 3 p.V56L(1) 4 all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162) Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849) CATCATCATCGTCATGAGTGA 0.637000 1 Substitution - Missense(1) SO:0001583 missense ENST00000344013.6 1 1 hg19 CCDS12442.1 . . . . . . . . . . G 7.337 0.620212 0.14193 . . ENSG00000089356 ENST00000406242;ENST00000435734;ENST00000346446;ENST00000344013;ENST00000406988;ENST00000535103 T;T;T;T;T 0.59083 0.29;0.29;0.29;0.29;0.29 4.97 2.77 0.32553 . 0.160135 0.41294 D 0.000906 T 0.24005 0.0581 N 0.02334 -0.595 0.20821 N 0.999848 B;B;B;B 0.33379 0.389;0.41;0.248;0.16 B;B;B;B 0.22386 0.039;0.036;0.024;0.027 T 0.23547 -1.0185 10 0.09084 T 0.74 -1.8921 11.7292 0.51726 0.0:0.6497:0.3503:0.0 . 113;56;56;56 F5H174;F8WB34;Q14802-2;Q14802 .;.;.;FXYD3_HUMAN I 56;113;56;56;56;113 ENSP00000385412:V56I;ENSP00000328259:V56I;ENSP00000339499:V56I;ENSP00000385200:V56I;ENSP00000443953:V113I ENSP00000339499:V56I V + 1 0 FXYD3 40305577 0.031000 0.19500 0.271000 0.24616 0.012000 0.07955 0.640000 0.24705 0.485000 0.27652 -0.153000 0.13522 GTC TCGA-S4-A8RO-01A-12D-A377-08 FXYD3-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000468985.1 1 0 1 108 204 0 45 1 1 1139 1443 0 45 2 0 0 0 0 0 2 1 1 109 202 0 43 2 0 0 0 0 45 2 -20.000000 1 1 0 0 1 1 2 3 2.034048 0 0.680000 2.080000 0.687439 0.990000 8.800000e-01 1.000000 1.000000 0.985950 0.990000 1 9.600000e-01 1.000000 HAUS5 23354 broad.mit.edu 37 19 36105981 36105981 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr19:36105981G>A ENST00000203166.5 + 5 282 c.257G>A c.(256-258)cGc>cAc p.R86H HAUS5_ENST00000379045.2_Missense_Mutation_p.R86H|AC002115.9_ENST00000589603.1_lincRNA NM_015302.1 NP_056117.1 O94927 HAUS5_HUMAN HAUS augmin-like complex, subunit 5 16 GCTGTGACCCGCCTGCGGGCA 0.607000 0 SO:0001583 missense ENST00000203166.5 0 1 hg19 CCDS42550.1 . . . . . . . . . . G 8.109 0.778332 0.16120 . . ENSG00000249115 ENST00000203166;ENST00000379045 T;T 0.35421 1.31;1.31 4.94 0.373 0.16178 . 0.501507 0.20263 N 0.095838 T 0.32224 0.0822 M 0.67953 2.075 0.09310 N 1 B 0.18013 0.025 B 0.12837 0.008 T 0.28870 -1.0030 10 0.59425 D 0.04 -19.0807 7.3956 0.26934 0.3627:0.0:0.6373:0.0 . 86 O94927 HAUS5_HUMAN H 86 ENSP00000439056:R86H;ENSP00000444373:R86H ENSP00000439056:R86H R + 2 0 HAUS5 40797821 0.859000 0.29813 0.931000 0.37212 0.070000 0.16714 0.651000 0.24873 -0.066000 0.12998 -0.234000 0.12200 CGC TCGA-S4-A8RO-01A-12D-A377-08 HAUS5-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459055.2 1 0 1 12 29 0 12 1 9.634036e-01 6 11 0 12 2 0 0 0 0 0 2 1 9.995117e-01 12 28 0 12 2 0 0 0 0 12 2 -20.000000 1 1 120806 2 26 1 1 2 3 2.034048 0 0.680000 2.080000 0.687439 0.900000 5.200000e-01 1.000000 1.000000 0.864858 0.900000 1 6.900000e-01 1.000000 PSG7 5676 broad.mit.edu 37 19 43433817 43433817 + RNA SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr19:43433817C>T ENST00000406070.2 - 0 582 PSG7_ENST00000446844.3_RNA NM_002783.2 NP_002774.2 Q13046 PSG7_HUMAN pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene) Prostate(69;0.00682) TCACAGCCTCCGTGGCCTCCC 0.532000 0 ENST00000406070.2 1 1 hg19 TCGA-S4-A8RO-01A-12D-A377-08 PSG7-001 KNOWN basic polymorphic_pseudogene polymorphic_pseudogene OTTHUMT00000321431.2 0 0 0 274 584 0 230 0 0 0 0 230 2 0 0 0 0 0 2 1 1 274 579 0 227 2 0 0 0 0 230 2 -18.962320 1 1 121340 1 33 1 1 2 3 2.047076 0 0.680000 2.080000 0.688474 0.960000 8.600000e-01 1.000000 1.000000 0.961279 0.960000 1 9.100000e-01 1.000000 HIF3A 64344 broad.mit.edu 37 19 46807230 46807230 + Silent SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr19:46807230G>A ENST00000377670.4 + 2 133 c.102G>A c.(100-102)ctG>ctA p.L34L HIF3A_ENST00000244303.6_Missense_Mutation_p.C14Y|HIF3A_ENST00000472815.1_Missense_Mutation_p.C14Y|HIF3A_ENST00000300862.3_Silent_p.L32L|RNU6-924P_ENST00000362926.1_RNA|HIF3A_ENST00000420102.2_Missense_Mutation_p.C32Y|HIF3A_ENST00000600383.1_Missense_Mutation_p.C14Y|HIF3A_ENST00000339613.2_5'UTR NM_152795.3 NP_690008.2 Q9Y2N7 HIF3A_HUMAN hypoxia inducible factor 3, alpha subunit 33 Ovarian(192;0.00965)|all_neural(266;0.0887) CCGAGGTGCTGTACCAGCTGG 0.672000 0 SO:0001819 synonymous_variant ENST00000377670.4 0 1 hg19 CCDS12681.2 . . . . . . . . . . G 18.94 3.729761 0.69074 . . ENSG00000124440 ENST00000457865;ENST00000244303;ENST00000533145;ENST00000457771;ENST00000420102 T;T 0.67171 -0.16;-0.25 4.97 2.85 0.33270 . . . . . T 0.53433 0.1796 . . . 0.80722 D 1 B;B;B 0.06786 0.001;0.001;0.001 B;B;B 0.08055 0.003;0.001;0.001 T 0.53287 -0.8460 8 0.87932 D 0 . 4.5387 0.12047 0.1824:0.0:0.6419:0.1757 . 32;14;32 F5H884;B4DNA2;B4DSD9 .;.;. Y 14;14;14;14;32 ENSP00000244303:C14Y;ENSP00000407771:C32Y ENSP00000244303:C14Y C + 2 0 HIF3A 51499070 0.834000 0.29399 1.000000 0.80357 0.998000 0.95712 -0.000000 0.12993 0.811000 0.34303 0.563000 0.77884 TGT TCGA-S4-A8RO-01A-12D-A377-08 HIF3A-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000280556.3 0 0 0 3 51 0 10 0 0 0 0 10 2 0 0 0 0 0 2 1 8.066311e-01 3 50 0 10 2 0 0 0 0 10 2 -7.466402 1 1 0 0 1 2 2 4 2.144197 1 0.680000 2.080000 0.709619 0.220000 6.000000e-02 1.000000 0.180000 0.321265 0.220000 0 1.200000e-01 0.440000 LILRA1 11024 broad.mit.edu 37 19 55107243 55107243 + Silent SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr19:55107243G>A ENST00000251372.3 + 6 983 c.801G>A c.(799-801)caG>caA p.Q267Q LILRA1_ENST00000453777.1_Intron|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000473156.1_3'UTR NM_006863.2 NP_006854.1 O75019 LIRA1_HUMAN leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1 p.L268I(1) 47 ACTTCCTCCAGCTCCCTGGCC 0.607000 1 Substitution - Missense(1) SO:0001819 synonymous_variant ENST00000251372.3 1 1 hg19 CCDS12901.1 TCGA-S4-A8RO-01A-12D-A377-08 LILRA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000140807.2 1 0 0 143 232 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 1 142 232 0 68 2 0 0 0 0 68 2 -20.000000 1 1 0 0 1 2 2 4 2.133410 1 0.680000 2.080000 0.707816 0.990000 9.900000e-01 1.000000 1.000000 0.999964 0.990000 1 9.900000e-01 1.000000 ANKRD34A 284615 broad.mit.edu 37 1 145474036 145474036 + Silent SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr1:145474036C>T ENST00000323397.4 + 4 2001 c.708C>T c.(706-708)cgC>cgT p.R236R RP11-315I20.1_ENST00000600340.1_RNA NM_001039888.2 NP_001034977.1 Q69YU3 AN34A_HUMAN ankyrin repeat domain 34A 20 all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786) AACCACCACGCCATCCCCCAA 0.622000 0 SO:0001819 synonymous_variant ENST00000323397.4 1 1 hg19 CCDS30829.1 TCGA-S4-A8RO-01A-12D-A377-08 ANKRD34A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000038512.1 1 0 1 164 672 0 124 0 3.364621e-01 1 5 0 124 2 0 0 0 0 0 2 1 1 161 644 0 120 2 0 0 0 0 124 2 -20.000000 1 1 0 0 1 1 3 4 2.762408 1 0.680000 2.080000 0.771624 0.820000 7.000000e-01 1.000000 0.800000 0.855398 0.820000 0 7.500000e-01 1.000000 ANKRD35 148741 broad.mit.edu 37 1 145558485 145558485 + Silent SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr1:145558485C>T ENST00000355594.4 + 6 513 c.426C>T c.(424-426)caC>caT p.H142H ANKRD35_ENST00000544626.1_Missense_Mutation_p.T123M NM_144698.3 NP_653299.4 Q8N283 ANR35_HUMAN ankyrin repeat domain 35 47 all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786) TGTGTGACCACGAAGCCTTCC 0.542000 Melanoma(9;127 754 22988 51047) 0 SO:0001819 synonymous_variant ENST00000355594.4 1 1 hg19 CCDS919.1 . . . . . . . . . . C 13.74 2.326612 0.41197 . . ENSG00000198483 ENST00000544626 T 0.15603 2.41 5.09 -7.84 0.01196 . . . . . T 0.11281 0.0275 . . . 0.19575 N 0.999965 . . . . . . T 0.14559 -1.0468 6 0.72032 D 0.01 -16.9738 16.3209 0.82951 0.0:0.2377:0.0:0.7623 . . . . M 123 ENSP00000442671:T123M ENSP00000442671:T123M T + 2 0 ANKRD35 144269842 0.000000 0.05858 0.525000 0.27900 0.977000 0.68977 -4.830000 0.00180 -1.784000 0.01272 -0.768000 0.03414 ACG TCGA-S4-A8RO-01A-12D-A377-08 ANKRD35-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000038515.1 0 0 1 91 290 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 1 91 283 0 66 2 0 0 0 0 68 2 -20.000000 1 1 0 0 1 1 3 4 2.762408 1 0.680000 2.080000 0.771624 0.990000 8.200000e-01 1.000000 1.000000 0.967891 0.990000 1 9.100000e-01 1.000000 C1orf105 92346 broad.mit.edu 37 1 172437641 172437641 + Silent SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr1:172437641C>T ENST00000367727.4 + 7 657 c.459C>T c.(457-459)caC>caT p.H153H C1orf105_ENST00000367726.1_3'UTR|C1orf105_ENST00000367725.4_Silent_p.H143H NM_139240.3 NP_640333.3 O95561 CA105_HUMAN chromosome 1 open reading frame 105 15 CTGTCTTCCACGGATTACTGA 0.478000 0 SO:0001819 synonymous_variant ENST00000367727.4 0 1 hg19 CCDS1301.1 TCGA-S4-A8RO-01A-12D-A377-08 C1orf105-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084062.2 0 0 0 23 1249 0 187 0 0 0 0 187 2 0 0 0 0 0 2 1 9.999992e-01 23 1229 0 186 2 0 0 0 0 187 2 -2.491726 0 1 121412 25 50 1 1 3 4 2.693787 1 0.680000 2.080000 0.765945 0.070000 3.000000e-02 1.000000 0.060000 0.297416 0.070000 0 5.000000e-02 1.000000 CRB1 23418 broad.mit.edu 37 1 197411423 197411423 + Splice_Site SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr1:197411423G>A ENST00000367400.3 + 11 4140 c.e11+1 RP11-75C23.1_ENST00000422250.1_RNA|CRB1_ENST00000367399.2_Splice_Site|CRB1_ENST00000544212.1_Splice_Site|CRB1_ENST00000535699.1_Splice_Site|CRB1_ENST00000538660.1_Splice_Site|CRB1_ENST00000367397.1_3'UTR NM_201253.2 NP_957705.1 P82279 CRUM1_HUMAN crumbs family member 1, photoreceptor morphogenesis associated 132 CGAGGTGGACGTAAGCAGCCT 0.478000 0 GRCh37 CS040833 CRB1 S SO:0001630 splice_region_variant ENST00000367400.3 0 1 hg19 CCDS1390.1 . . . . . . . . . . G 25.6 4.650712 0.87958 . . ENSG00000134376 ENST00000535699;ENST00000538660;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000448952 . . . 5.6 5.6 0.85130 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 19.6189 0.95647 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . CRB1 195678046 1.000000 0.71417 0.978000 0.43139 0.971000 0.66376 7.916000 0.87491 2.629000 0.89072 0.591000 0.81541 . TCGA-S4-A8RO-01A-12D-A377-08 CRB1-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086565.2 0 0 0 5 585 0 113 0 0 0 0 113 2 0 0 0 0 0 2 1 9.360915e-01 5 580 0 113 2 0 0 0 0 113 2 -2.219277 0 1 0 0 1 1 2 3 2.035892 0 0.680000 2.080000 0.687439 0.020000 0 1.000000 0.020000 0.083759 0.020000 0 1.000000e-02 0.050000 USH2A 7399 broad.mit.edu 37 1 216144042 216144042 + Silent SNP G G A rs147615382 TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr1:216144042G>A ENST00000307340.3 - 36 7268 c.6882C>T c.(6880-6882)taC>taT p.Y2294Y USH2A_ENST00000366943.2_Silent_p.Y2294Y NM_206933.2 NP_996816 O75445 USH2A_HUMAN Usher syndrome 2A (autosomal recessive, mild) 527 GAGCAAATCCGTAAGCACGAT 0.418000 HNSCC(13;0.011) 0 SO:0001819 synonymous_variant ENST00000307340.3 0 1 hg19 CCDS31025.1 TCGA-S4-A8RO-01A-12D-A377-08 USH2A-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128138.1 0 0 0 5 632 0 131 0 0 0 0 131 2 0 0 0 0 0 2 1 9.356635e-01 5 624 0 130 2 0 0 0 0 131 2 -2.620824 1 1 121398 11 44 1 1 2 3 2.041515 0 0.680000 2.080000 0.687439 0.020000 0 1.000000 0.020000 0.081753 0.020000 0 0 0.050000 FMN2 56776 broad.mit.edu 37 1 240256586 240256586 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr1:240256586G>A ENST00000319653.9 + 1 1407 c.1177G>A c.(1177-1179)Gcg>Acg p.A393T NM_020066.4 NP_064450.3 Q9NZ56 FMN2_HUMAN formin 2 p.A536T(1) 178 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) TGACGCCCCCGCGGCCGCTTC 0.726000 1 Substitution - Missense(1) SO:0001583 missense ENST00000319653.9 1 1 hg19 CCDS31069.2 . . . . . . . . . . G 3.560 -0.089766 0.07053 . . ENSG00000155816 ENST00000319653 T 0.28255 1.62 4.15 -0.182 0.13287 . 0.885835 0.09526 N 0.790278 T 0.15435 0.0372 N 0.12182 0.205 0.09310 N 0.999999 B 0.12630 0.006 B 0.06405 0.002 T 0.24476 -1.0159 10 0.46703 T 0.11 . 5.4466 0.16539 0.2993:0.1625:0.5382:0.0 . 393 Q9NZ56 FMN2_HUMAN T 393 ENSP00000318884:A393T ENSP00000318884:A393T A + 1 0 FMN2 238323209 0.000000 0.05858 0.001000 0.08648 0.023000 0.10783 -0.165000 0.09968 0.085000 0.17107 -0.379000 0.06801 GCG TCGA-S4-A8RO-01A-12D-A377-08 FMN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096217.2 1 0 0 38 62 0 16 0 0 0 1 0 16 2 0 0 0 0 0 2 1 1 37 62 0 16 2 0 0 0 0 16 2 -20.000000 1 1 0 0 1 1 2 3 2.041515 0 0.680000 2.080000 0.687439 0.990000 8.600000e-01 1.000000 1.000000 0.989597 0.990000 1 9.900000e-01 1.000000 PPP1R16B 26051 broad.mit.edu 37 20 37547257 37547257 + Missense_Mutation SNP C C G TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr20:37547257C>G ENST00000299824.1 + 11 1841 c.1652C>G c.(1651-1653)gCc>gGc p.A551G PPP1R16B_ENST00000373331.2_Missense_Mutation_p.A509G NM_015568.2 NP_056383.1 Q96T49 PP16B_HUMAN protein phosphatase 1, regulatory subunit 16B 49 Myeloproliferative disorder(115;0.00878) AAGTTCAAGGCCCCCATAGAG 0.572000 0 SO:0001583 missense ENST00000299824.1 1 1 hg19 CCDS13309.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 17.01|17.01 3.278924|3.278924 0.59758|0.59758 .|. .|. ENSG00000101445|ENSG00000101445 ENST00000299824;ENST00000373331|ENST00000438192 T;T|. 0.77229|. -0.81;-1.08|. 5.35|5.35 5.35|5.35 0.76521|0.76521 .|. 0.188207|. 0.48767|. D|. 0.000177|. T|T 0.64438|0.64438 0.2598|0.2598 M|M 0.61703|0.61703 1.905|1.905 0.32685|0.32685 N|N 0.514994|0.514994 D;D|. 0.61080|. 0.989;0.98|. P;P|. 0.57101|. 0.813;0.813|. T|T 0.70619|0.70619 -0.4822|-0.4822 10|5 0.59425|. D|. 0.04|. .|. 17.2316|17.2316 0.86985|0.86985 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 509;551|. E9PFS8;Q96T49|. .;PP16B_HUMAN|. G|A 551;509|452 ENSP00000299824:A551G;ENSP00000362428:A509G|. ENSP00000299824:A551G|. A|P +|+ 2|1 0|0 PPP1R16B|PPP1R16B 36980671|36980671 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.999000|0.999000 0.98932|0.98932 5.088000|5.088000 0.64486|0.64486 2.498000|2.498000 0.84270|0.84270 0.655000|0.655000 0.94253|0.94253 GCC|CCC TCGA-S4-A8RO-01A-12D-A377-08 PPP1R16B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079220.2 1 0 1 48 123 0 31 0 4.362384e-01 0 5 0 31 2 0 0 0 0 0 2 1 1 48 122 0 30 2 0 0 0 0 31 2 -20.000000 1 1 0 0 1 1 2 3 2.228471 1 0.680000 2.080000 0.718310 0.980000 7.300000e-01 1.000000 1.000000 0.939121 0.980000 1 8.400000e-01 1.000000 RIMS4 140730 broad.mit.edu 37 20 43386349 43386349 + Missense_Mutation SNP C C T rs141614672 byFrequency TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr20:43386349C>T ENST00000372851.3 - 4 479 c.413G>A c.(412-414)cGg>cAg p.R138Q RIMS4_ENST00000541604.2_Missense_Mutation_p.R139Q NM_001205317.1|NM_182970.3 NP_001192246.1|NP_892015.1 Q9H426 RIMS4_HUMAN regulating synaptic membrane exocytosis 4 p.R138Q(1) 29 Myeloproliferative disorder(115;0.0122) TGTCAGTCCCCGAGCCTGGAT 0.597000 1 Substitution - Missense(1) SO:0001583 missense ENST00000372851.3 1 1 hg19 CCDS13338.1 . . . . . . . . . . C 34 5.371169 0.95923 0.0 2.33E-4 ENSG00000101098 ENST00000372851;ENST00000541604 T;T 0.69806 -0.43;-0.43 5.76 4.82 0.62117 C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1); 0.000000 0.85682 D 0.000000 T 0.82240 0.4994 M 0.83774 2.66 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.70487 0.95;0.969 D 0.85425 0.1145 10 0.87932 D 0 . 14.8657 0.70412 0.0:0.9312:0.0:0.0688 . 139;138 E1P613;Q9H426 .;RIMS4_HUMAN Q 138;139 ENSP00000361942:R138Q;ENSP00000439287:R139Q ENSP00000361942:R138Q R - 2 0 RIMS4 42819763 1.000000 0.71417 0.813000 0.32504 0.910000 0.53928 6.089000 0.71384 1.457000 0.47850 0.655000 0.94253 CGG TCGA-S4-A8RO-01A-12D-A377-08 RIMS4-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000101027.2 1 0 1 109 263 0 57 0 0 0 0 57 2 0 0 0 0 0 2 1 1 107 258 0 55 2 0 0 0 0 57 2 -7.457733 1 1 121412 2 38 1 1 2 3 2.228471 1 0.680000 2.080000 0.718310 0.990000 8.300000e-01 1.000000 1.000000 0.968005 0.990000 1 9.100000e-01 1.000000 ZNF831 128611 broad.mit.edu 37 20 57769643 57769643 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr20:57769643G>A ENST00000371030.2 + 1 3569 c.3569G>A c.(3568-3570)cGc>cAc p.R1190H NM_178457.1 NP_848552.1 Q5JPB2 ZN831_HUMAN zinc finger protein 831 125 all_lung(29;0.0085) TGCCTGAGCCGCAGTGTCCCT 0.647000 0 SO:0001583 missense ENST00000371030.2 0 1 hg19 CCDS42894.1 . . . . . . . . . . G 18.84 3.708768 0.68615 . . ENSG00000124203 ENST00000371030 T 0.08896 3.04 5.05 5.05 0.67936 . 0.227351 0.29355 N 0.012399 T 0.21921 0.0528 L 0.52573 1.65 0.31710 N 0.639596 D 0.89917 1.0 D 0.71656 0.974 T 0.03112 -1.1071 10 0.87932 D 0 -16.6053 12.8728 0.57975 0.0814:0.0:0.9186:0.0 . 1190 Q5JPB2 ZN831_HUMAN H 1190 ENSP00000360069:R1190H ENSP00000360069:R1190H R + 2 0 ZNF831 57203038 0.988000 0.35896 1.000000 0.80357 0.678000 0.39670 3.840000 0.55843 2.352000 0.79861 0.609000 0.83330 CGC TCGA-S4-A8RO-01A-12D-A377-08 ZNF831-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000079916.2 0 0 0 5 239 0 50 0 0 0 0 50 2 0 0 0 0 0 2 1 9.318401e-01 5 230 0 49 2 0 0 0 0 50 2 -5.985948 1 1 121046 3 34 1 1 2 3 2.271971 1 0.680000 2.080000 0.721642 0.080000 2.000000e-02 1.000000 0.070000 0.301524 0.080000 0 4.000000e-02 1.000000 SLCO4A1 28231 broad.mit.edu 37 20 61300301 61300301 + Silent SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr20:61300301C>T ENST00000370507.1 + 10 1992 c.1896C>T c.(1894-1896)atC>atT p.I632I RP11-93B14.5_ENST00000433126.1_RNA|RP11-93B14.5_ENST00000411824.1_RNA|SLCO4A1_ENST00000470412.1_3'UTR|SLCO4A1_ENST00000217159.1_Silent_p.I632I|RP11-93B14.5_ENST00000451648.1_RNA Q96BD0 SO4A1_HUMAN solute carrier organic anion transporter family, member 4A1 21 Breast(26;3.65e-08) BRCA - Breast invasive adenocarcinoma(19;2.33e-06) Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583) CGGGGCCCATCGCCTTCGGCT 0.662000 OREG0026115 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) Pancreas(168;741 2006 10379 40139 45334) 0 SO:0001819 synonymous_variant ENST00000370507.1 1 1 hg19 CCDS13501.1 TCGA-S4-A8RO-01A-12D-A377-08 SLCO4A1-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080048.2 1 0 1 91 110 0 30 1 1 30 29 0 30 2 0 0 0 0 0 2 1 1 91 105 0 29 2 0 0 0 0 30 2 -20.000000 1 1 121276 1 34 1 1 2 3 2.271971 1 0.680000 2.080000 0.721642 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 TPTE 7179 broad.mit.edu 37 21 10942745 10942745 + Missense_Mutation SNP C C A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr21:10942745C>A ENST00000361285.4 - 13 1025 c.696G>T c.(694-696)agG>agT p.R232S TPTE_ENST00000298232.7_Missense_Mutation_p.R214S|TPTE_ENST00000342420.5_Missense_Mutation_p.R194S|TPTE_ENST00000415664.2_5'UTR 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) CAAATCCATCCCTTGTGTATC 0.308000 0 SO:0001583 missense ENST00000361285.4 1 1 hg19 CCDS13560.2 . . . . . . . . . . . 10.06 1.246943 0.22796 . . ENSG00000166157 ENST00000298232;ENST00000361285;ENST00000342420 T;T;T 0.29142 1.58;1.58;1.58 2.07 0.162 0.14981 Phosphatase tensin type (1); 0.162065 0.52532 U 0.000067 T 0.24890 0.0604 L 0.46157 1.445 0.26087 N 0.981001 B;B;B 0.33345 0.409;0.409;0.012 B;B;B 0.37422 0.196;0.249;0.008 T 0.16188 -1.0411 10 0.66056 D 0.02 -10.1256 6.055 0.19807 0.0:0.6974:0.0:0.3026 . 194;214;232 P56180-3;P56180-2;P56180 .;.;TPTE_HUMAN S 214;232;194 ENSP00000298232:R214S;ENSP00000355208:R232S;ENSP00000344441:R194S ENSP00000298232:R214S R - 3 2 TPTE 9964616 0.996000 0.38824 0.396000 0.26296 0.598000 0.36846 0.311000 0.19380 0.028000 0.15324 0.194000 0.17425 AGG TCGA-S4-A8RO-01A-12D-A377-08 TPTE-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000157413.1 0 0 0 144 740 1 282 0 0 0 1 282 2 0 0 0 0 0 2 1 1 142 727 0 281 2 0 0 0 1 282 2 -3.319936 1 1 121412 1 31 1 0 2 2 1.636674 1 0.680000 2.080000 0.680000 0.470000 4.000000e-01 0.550000 0.480000 0.481077 0.470000 0 4.300000e-01 0.520000 LRP1B 53353 broad.mit.edu 37 2 141264372 141264372 + Silent SNP C C T rs139084384 byFrequency TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr2:141264372C>T ENST00000389484.3 - 53 9485 c.8514G>A c.(8512-8514)ccG>ccA p.P2838P NM_018557.2 NP_061027.2 Q9NZR2 LRP1B_HUMAN low density lipoprotein receptor-related protein 1B 606 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) TACCACACTGCGGTGACTCAT 0.383000 TSP Lung(27;0.18) Colon(99;50 2074 2507 20106) 0 SO:0001819 synonymous_variant ENST00000389484.3 1 0 hg19 CCDS2182.1 TCGA-S4-A8RO-01A-12D-A377-08 LRP1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254736.2 1 0 1 184 517 0 176 0 0 0 0 176 2 0 0 0 0 0 2 1 1 180 510 0 176 2 0 0 0 0 176 2 -2.598642 1 1 121412 152 56 1 1 2 3 2.024125 0 0.680000 2.080000 0.686397 0.780000 6.800000e-01 1.000000 0.790000 0.799164 0.780000 0 7.300000e-01 0.850000 MYT1L 23040 broad.mit.edu 37 2 1983497 1983497 + Missense_Mutation SNP C C A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr2:1983497C>A ENST00000399161.2 - 6 800 c.53G>T c.(52-54)cGa>cTa p.R18L MYT1L_ENST00000428368.2_Missense_Mutation_p.R18L NM_015025.2 NP_055840.2 Q9UL68 MYT1L_HUMAN myelin transcription factor 1-like 97 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.037)|all_epithelial(98;0.241) GGACATACCTCGAACCCCTTT 0.582000 0 SO:0001583 missense ENST00000399161.2 1 1 hg19 . . . . . . . . . . C 22.7 4.324853 0.81580 . . ENSG00000186487 ENST00000399161;ENST00000295067;ENST00000428368 T;T 0.56444 0.46;0.46 5.1 5.1 0.69264 . 0.000000 0.47852 D 0.000207 T 0.69251 0.3090 L 0.54323 1.7 0.58432 D 0.999995 D;D 0.63046 0.987;0.992 D;D 0.70487 0.931;0.969 T 0.71656 -0.4527 10 0.72032 D 0.01 -19.3941 18.8902 0.92397 0.0:1.0:0.0:0.0 . 18;18 Q9UL68;Q9UL68-4 MYT1L_HUMAN;. L 18 ENSP00000382114:R18L;ENSP00000396103:R18L ENSP00000295067:R18L R - 2 0 MYT1L 1962504 1.000000 0.71417 1.000000 0.80357 0.976000 0.68499 6.591000 0.74090 2.539000 0.85634 0.591000 0.81541 CGA TCGA-S4-A8RO-01A-12D-A377-08 MYT1L-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000322493.1 1 0 1 37 115 0 26 0 0 0 1 0 26 2 0 0 0 0 0 2 1 1 37 114 0 26 2 0 0 0 0 26 2 -20.000000 1 1 0 0 1 1 2 3 2.047543 0 0.680000 2.080000 0.688474 0.740000 5.400000e-01 1.000000 0.740000 0.759420 0.740000 0 6.300000e-01 0.880000 WNT6 7475 broad.mit.edu 37 2 219735855 219735855 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr2:219735855G>A ENST00000233948.3 + 2 404 c.187G>A c.(187-189)Gca>Aca p.A63T WNT6_ENST00000486233.1_Intron NM_006522.3 NP_006513.1 Q9Y6F9 WNT6_HUMAN wingless-type MMTV integration site family, member 6 4 Renal(207;0.0474) GGAAGTGGTGGCAGAGCTAGC 0.682000 0 SO:0001583 missense ENST00000233948.3 1 1 hg19 CCDS2425.1 . . . . . . . . . . g 12.69 2.013700 0.35511 . . ENSG00000115596 ENST00000233948 T 0.76448 -1.02 5.17 5.17 0.71159 . 0.451424 0.24781 N 0.035645 T 0.63581 0.2523 L 0.31926 0.97 0.24988 N 0.991557 B 0.16396 0.017 B 0.19391 0.025 T 0.46386 -0.9195 10 0.14252 T 0.57 . 7.7483 0.28881 0.0881:0.1792:0.7326:0.0 . 63 Q9Y6F9 WNT6_HUMAN T 63 ENSP00000233948:A63T ENSP00000233948:A63T A + 1 0 WNT6 219444099 0.948000 0.32251 0.996000 0.52242 0.887000 0.51463 1.737000 0.38197 2.407000 0.81776 0.586000 0.80456 GCA TCGA-S4-A8RO-01A-12D-A377-08 WNT6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256727.2 1 0 1 302 298 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 1 300 294 0 62 2 0 0 0 0 66 2 -20.000000 1 1 0 0 1 1 2 3 2.532077 1 0.680000 2.080000 0.750429 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 AGXT 189 broad.mit.edu 37 2 241817502 241817502 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr2:241817502G>A ENST00000307503.3 + 10 1393 c.1006G>A c.(1006-1008)Gtc>Atc p.V336I NM_000030.2 NP_000021.1 P21549 SPYA_HUMAN alanine-glyoxylate aminotransferase p.V336I(1) 18 all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244) Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133) GAGAGACATCGTCAGCTACGT 0.617000 1 Substitution - Missense(1) SO:0001583 missense ENST00000307503.3 1 1 hg19 CCDS2543.1 . . . . . . . . . . G 3.824 -0.037151 0.07497 . . ENSG00000172482 ENST00000307503 D 0.93547 -3.24 4.02 1.11 0.20524 Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1); 0.923809 0.09133 N 0.844131 D 0.86460 0.5938 L 0.41573 1.285 0.09310 N 1 B;B 0.32338 0.365;0.109 B;B 0.22386 0.039;0.018 T 0.72487 -0.4278 10 0.19147 T 0.46 -28.2281 6.537 0.22359 0.4922:0.0:0.5077:0.0 . 214;336 Q9UJX1;P21549 .;SPYA_HUMAN I 336 ENSP00000302620:V336I ENSP00000302620:V336I V + 1 0 AGXT 241466175 0.000000 0.05858 0.445000 0.26908 0.097000 0.18754 0.572000 0.23684 0.294000 0.22547 0.563000 0.77884 GTC TCGA-S4-A8RO-01A-12D-A377-08 AGXT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257186.1 1 0 1 53 48 0 23 0 0 1 0 0 23 2 0 0 0 0 0 2 1 1 52 47 0 23 2 0 0 0 0 23 2 -20.000000 1 1 121410 3 36 1 0 1 1 1.295188 1 0.680000 2.080000 0.515152 0.930000 7.900000e-01 1.000000 0.990000 0.930125 0.930000 1 8.600000e-01 0.990000 CRIM1 51232 broad.mit.edu 37 2 36704145 36704145 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr2:36704145G>A ENST00000280527.2 + 6 1472 c.1105G>A c.(1105-1107)Gcc>Acc p.A369T NM_016441.2 NP_057525.1 Q9NZV1 CRIM1_HUMAN cysteine rich transmembrane BMP regulator 1 (chordin-like) 45 all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154) CTGCTTCACCGCCCAGTGTGG 0.483000 0 SO:0001583 missense ENST00000280527.2 0 1 hg19 CCDS1783.1 . . . . . . . . . . G 32 5.175054 0.94807 . . ENSG00000150938 ENST00000280527 T 0.71579 -0.58 5.93 5.93 0.95920 von Willebrand factor, type C (4); 0.000000 0.85682 D 0.000000 T 0.72558 0.3475 N 0.14661 0.345 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.67169 -0.5738 10 0.14656 T 0.56 -18.4323 19.3421 0.94347 0.0:0.0:1.0:0.0 . 369 Q9NZV1 CRIM1_HUMAN T 369 ENSP00000280527:A369T ENSP00000280527:A369T A + 1 0 CRIM1 36557649 1.000000 0.71417 0.982000 0.44146 0.988000 0.76386 9.714000 0.98744 2.826000 0.97356 0.655000 0.94253 GCC TCGA-S4-A8RO-01A-12D-A377-08 CRIM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000216878.2 0 0 0 5 338 0 81 0 5.081038e-02 0 20 0 81 2 0 0 0 0 0 2 1 9.350545e-01 6 331 0 79 2 0 0 0 0 81 2 -2.829005 1 1 121412 1 28 1 1 2 3 2.047543 0 0.680000 2.080000 0.688474 0.040000 0 1.000000 0.040000 0.113295 0.040000 0 2.000000e-02 0.080000 GFPT1 2673 broad.mit.edu 37 2 69556893 69556893 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr2:69556893G>A ENST00000357308.4 - 16 1698 c.1520C>T c.(1519-1521)gCc>gTc p.A507V GFPT1_ENST00000361060.5_Missense_Mutation_p.A489V NM_001244710.1 NP_001231639.1 Q06210 GFPT1_HUMAN glutamine--fructose-6-phosphate transaminase 1 12 CATCATAAGGGCAAACATCAC 0.408000 0 SO:0001583 missense ENST00000357308.4 0 1 hg19 CCDS58713.1 . . . . . . . . . . G 27.9 4.875075 0.91664 . . ENSG00000198380 ENST00000357308;ENST00000361060 T;T 0.62941 -0.01;-0.01 5.28 5.28 0.74379 . 0.000000 0.85682 D 0.000000 T 0.79673 0.4486 M 0.86268 2.805 0.80722 D 1 D 0.65815 0.995 P 0.59761 0.863 T 0.82959 -0.0198 10 0.87932 D 0 -11.8633 18.081 0.89441 0.0:0.0:1.0:0.0 . 489 Q06210-2 . V 507;489 ENSP00000349860:A507V;ENSP00000354347:A489V ENSP00000349860:A507V A - 2 0 GFPT1 69410397 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 4.388000 0.59633 2.758000 0.94735 0.563000 0.77884 GCC TCGA-S4-A8RO-01A-12D-A377-08 GFPT1-201 KNOWN basic|CCDS protein_coding protein_coding 0 0 0 4 186 0 43 0 3.043414e-01 0 43 0 43 2 0 0 0 0 0 2 1 8.887550e-01 4 184 0 42 2 0 0 0 0 43 2 -2.831103 1 1 0 0 1 0 1 1 1.369433 1 0.680000 2.080000 0.515152 0.040000 1.000000e-02 0.100000 0.040000 0.050286 0.040000 0 2.000000e-02 0.070000 MED12L 116931 broad.mit.edu 37 3 151075109 151075109 + Missense_Mutation SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr3:151075109C>T ENST00000474524.1 + 18 2703 c.2665C>T c.(2665-2667)Cgc>Tgc p.R889C MED12L_ENST00000273432.4_Missense_Mutation_p.R749C|P2RY12_ENST00000302632.3_Intron NM_053002.4 NP_443728.3 Q86YW9 MD12L_HUMAN mediator complex subunit 12-like 128 LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517) TGTTCTCAGGCGCTATCACAG 0.453000 0 SO:0001583 missense ENST00000474524.1 1 1 hg19 CCDS33876.1 . . . . . . . . . . C 20.2 3.953030 0.73902 2.27E-4 0.0 ENSG00000144893 ENST00000474524;ENST00000273432 T;T 0.79454 -1.27;-1.27 5.3 4.42 0.53409 . 0.000000 0.85682 D 0.000000 D 0.85418 0.5692 L 0.60455 1.87 0.80722 D 1 D;D;D 0.89917 1.0;0.997;0.995 D;P;P 0.72982 0.979;0.616;0.635 D 0.86975 0.2100 10 0.72032 D 0.01 -26.0088 15.3411 0.74296 0.141:0.859:0.0:0.0 . 749;889;889 F8WAE6;Q86YW9-4;Q86YW9 .;.;MD12L_HUMAN C 889;749 ENSP00000417235:R889C;ENSP00000273432:R749C ENSP00000273432:R749C R + 1 0 MED12L 152557799 1.000000 0.71417 0.866000 0.34008 0.957000 0.61999 2.622000 0.46427 1.336000 0.45506 -0.169000 0.13324 CGC TCGA-S4-A8RO-01A-12D-A377-08 MED12L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357707.2 1 0 1 145 308 0 88 0 0 0 0 88 2 0 0 0 0 0 2 1 1 145 303 0 88 2 0 0 0 0 88 2 -20.000000 1 1 121412 1 36 1 1 2 3 1.966254 0 0.680000 2.080000 0.681084 0.940000 8.100000e-01 1.000000 1.000000 0.938448 0.940000 1 8.700000e-01 1.000000 PROS1 5627 broad.mit.edu 37 3 93611912 93611912 + Nonsense_Mutation SNP G G C TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr3:93611912G>C ENST00000394236.3 - 10 1336 c.1020C>G c.(1018-1020)taC>taG p.Y340* PROS1_ENST00000407433.1_Nonsense_Mutation_p.Y209* NM_000313.3 NP_000304.2 P07225 PROS_HUMAN protein S (alpha) 46 Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464) TAGATTCTGCGTACAGTATCA 0.393000 0 SO:0001587 stop_gained ENST00000394236.3 0 1 hg19 CCDS2923.1 . . . . . . . . . . G 36 5.885622 0.97068 . . ENSG00000184500 ENST00000394236;ENST00000407433 . . . 4.47 2.05 0.26809 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 7.4211 0.27073 0.7526:0.0:0.2474:0.0 . . . . X 340;209 . ENSP00000377783:Y340X Y - 3 2 PROS1 95094602 1.000000 0.71417 0.997000 0.53966 0.557000 0.35523 0.858000 0.27845 0.263000 0.21812 -0.324000 0.08512 TAC TCGA-S4-A8RO-01A-12D-A377-08 PROS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317762.1 1 0 1 60 113 0 46 1 9.999993e-01 2 44 0 46 2 0 0 0 0 0 2 1 1 59 110 0 46 2 0 0 0 0 46 2 -20.000000 1 1 0 0 1 1 2 3 1.966254 0 0.680000 2.080000 0.681084 0.990000 8.100000e-01 1.000000 1.000000 0.969547 0.990000 1 9.100000e-01 1.000000 OR5H1 26341 broad.mit.edu 37 3 97852022 97852022 + Nonsense_Mutation SNP G G T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr3:97852022G>T ENST00000354565.2 + 1 481 c.481G>T c.(481-483)Gga>Tga p.G161* RP11-343D2.11_ENST00000508964.1_RNA NM_001005338.1 NP_001005338.1 A6NKK0 OR5H1_HUMAN olfactory receptor, family 5, subfamily H, member 1 34 AATCCATGAAGGATTTTTATT 0.358000 0 SO:0001587 stop_gained ENST00000354565.2 0 1 hg19 CCDS33797.1 . . . . . . . . . . G 7.459 0.644345 0.14451 . . ENSG00000231192 ENST00000354565 . . . 3.57 2.68 0.31781 . 0.626401 0.13894 N 0.355411 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.34782 T 0.22 . 8.4928 0.33110 0.121:0.0:0.879:0.0 . . . . X 161 . ENSP00000346575:G161X G + 1 0 OR5H1 99334712 0.000000 0.05858 0.005000 0.12908 0.014000 0.08584 -0.384000 0.07389 0.683000 0.31428 0.195000 0.17529 GGA TCGA-S4-A8RO-01A-12D-A377-08 OR5H1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359100.2 0 0 0 39 385 0 177 0 0 0 0 177 2 0 0 0 0 0 2 1 1 30 332 0 227 2 0 0 0 0 177 2 -3.318794 1 1 0 0 1 1 2 3 1.966254 0 0.680000 2.080000 0.681084 0.270000 1.900000e-01 0.360000 0.270000 0.276802 0.270000 0 2.200000e-01 0.320000 OR5H14 403273 broad.mit.edu 37 3 97868710 97868710 + Nonsense_Mutation SNP G G T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr3:97868710G>T ENST00000437310.1 + 1 541 c.481G>T c.(481-483)Gga>Tga p.G161* RP11-343D2.11_ENST00000508964.1_RNA NM_001005514.1 NP_001005514.1 A6NHG9 O5H14_HUMAN olfactory receptor, family 5, subfamily H, member 14 31 AATCCATGAAGGATTTTTATT 0.353000 0 SO:0001587 stop_gained ENST00000437310.1 0 1 hg19 CCDS33798.1 . . . . . . . . . . g 10.51 1.369165 0.24771 . . ENSG00000236032 ENST00000437310 . . . 2.49 -4.97 0.03029 . 0.899723 0.09201 N 0.834639 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.31617 T 0.26 . 1.2356 0.01952 0.3199:0.1452:0.3874:0.1475 . . . . X 161 . ENSP00000401706:G161X G + 1 0 OR5H14 99351400 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -2.434000 0.01021 -1.909000 0.01085 -1.051000 0.02340 GGA TCGA-S4-A8RO-01A-12D-A377-08 OR5H14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359112.1 0 0 0 9 814 0 260 0 0 0 0 260 2 0 0 0 0 0 2 1 9.937334e-01 9 799 0 260 2 0 0 0 0 260 2 -2.213149 0 1 0 0 1 1 2 3 1.966254 0 0.680000 2.080000 0.681084 0.030000 0 0.070000 0.040000 0.035617 0.030000 0 1.000000e-02 0.050000 KCTD8 386617 broad.mit.edu 37 4 44177058 44177058 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr4:44177058G>A ENST00000360029.3 - 2 1454 c.1171C>T c.(1171-1173)Cgc>Tgc p.R391C NM_198353.2 NP_938167.1 Q6ZWB6 KCTD8_HUMAN potassium channel tetramerization domain containing 8 41 TTAGAGGGGCGATCCAATGTT 0.507000 HNSCC(17;0.042) 0 SO:0001583 missense ENST00000360029.3 0 1 hg19 CCDS3467.1 . . . . . . . . . . G 11.87 1.768485 0.31320 . . ENSG00000183783 ENST00000360029 T 0.44083 0.93 4.56 3.68 0.42216 . 0.000000 0.46758 D 0.000275 T 0.50939 0.1645 L 0.36672 1.1 0.49582 D 0.999805 D 0.89917 1.0 D 0.64595 0.927 T 0.54655 -0.8261 10 0.87932 D 0 . 12.9862 0.58594 0.0:0.0:0.8317:0.1682 . 391 Q6ZWB6 KCTD8_HUMAN C 391 ENSP00000353129:R391C ENSP00000353129:R391C R - 1 0 KCTD8 43871815 1.000000 0.71417 0.995000 0.50966 0.196000 0.23810 3.014000 0.49590 1.202000 0.43218 0.650000 0.86243 CGC TCGA-S4-A8RO-01A-12D-A377-08 KCTD8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000216868.1 0 0 0 6 515 0 162 0 0 0 0 162 2 0 0 0 0 0 2 1 9.632236e-01 6 506 0 159 2 0 0 0 0 162 2 -2.390467 0 1 121412 4 40 1 1 2 3 1.968126 0 0.680000 2.080000 0.681084 0.030000 0 0.080000 0.040000 0.039083 0.030000 0 1.000000e-02 0.060000 PCDHB7 56129 broad.mit.edu 37 5 140553979 140553979 + Silent SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr5:140553979C>T ENST00000231137.3 + 1 1737 c.1563C>T c.(1561-1563)taC>taT p.Y521Y NM_018940.2 NP_061763.1 Q9Y5E2 PCDB7_HUMAN protocadherin beta 7 119 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) CCCTGGACTACGAGGCCCTGC 0.711000 0 SO:0001819 synonymous_variant ENST00000231137.3 1 1 hg19 CCDS4249.1 TCGA-S4-A8RO-01A-12D-A377-08 PCDHB7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251803.2 1 0 1 47 388 0 91 0 1.346715e-01 0 6 0 91 2 0 0 0 0 0 2 1 1 44 373 0 90 2 0 0 0 0 91 2 -16.516610 1 1 121412 1 34 1 1 2 3 1.999080 0 0.680000 2.080000 0.684294 0.320000 2.300000e-01 1.000000 0.320000 0.346475 0.320000 0 2.700000e-01 0.380000 PCDH1 5097 broad.mit.edu 37 5 141248263 141248263 + Silent SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr5:141248263G>A ENST00000394536.3 - 2 913 c.774C>T c.(772-774)ccC>ccT p.P258P PCDH1_ENST00000503492.1_Silent_p.P258P|PCDH1_ENST00000511044.1_5'Flank|PCDH1_ENST00000456271.1_Silent_p.P246P|PCDH1_ENST00000287008.3_Silent_p.P258P|PCDH1_ENST00000536585.1_Silent_p.P236P NM_001278613.1|NM_001278615.1 NP_001265542.1|NP_001265544.1 Q08174 PCDH1_HUMAN protocadherin 1 51 Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238) KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGGCGCGTGGGGGGCTGCCGC 0.607000 Ovarian(132;1609 1739 4190 14731 45037) 0 SO:0001819 synonymous_variant ENST00000394536.3 1 1 hg19 CCDS43375.1 TCGA-S4-A8RO-01A-12D-A377-08 PCDH1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000251862.1 1 0 1 46 101 0 41 1 9.999999e-01 24 37 0 41 2 0 0 0 0 0 2 1 1 45 100 0 40 2 0 0 0 0 41 2 -6.450983 1 1 0 0 1 1 2 3 1.999080 0 0.680000 2.080000 0.684294 0.930000 7.100000e-01 1.000000 1.000000 0.918823 0.930000 1 8.200000e-01 1.000000 IRX2 153572 broad.mit.edu 37 5 2749835 2749835 + Missense_Mutation SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr5:2749835C>T ENST00000382611.6 - 2 564 c.316G>A c.(316-318)Gcg>Acg p.A106T C5orf38_ENST00000505778.1_5'Flank|C5orf38_ENST00000334000.3_5'Flank|IRX2_ENST00000302057.5_Missense_Mutation_p.A106T|C5orf38_ENST00000457752.2_5'Flank|C5orf38_ENST00000397835.4_5'Flank|IRX2_ENST00000502957.1_5'UTR|C5orf38_ENST00000515640.1_5'Flank NM_001134222.1 NP_001127694.1 Q9BZI1 IRX2_HUMAN iroquois homeobox 2 26 GGGTAGGCCGCGCTGCCGTAC 0.662000 0 SO:0001583 missense ENST00000382611.6 1 1 hg19 CCDS3868.1 . . . . . . . . . . C 17.75 3.467539 0.63625 . . ENSG00000170561 ENST00000382611;ENST00000302057;ENST00000502957 T;T;T 0.66280 -0.2;-0.2;-0.15 4.85 3.96 0.45880 Homeodomain-like (1); 0.108027 0.64402 D 0.000004 T 0.40448 0.1117 N 0.17474 0.49 0.42845 D 0.994069 B 0.32382 0.368 B 0.20184 0.028 T 0.35968 -0.9767 10 0.21540 T 0.41 -22.7679 13.2911 0.60272 0.0:0.7288:0.2712:0.0 . 106 Q9BZI1 IRX2_HUMAN T 106;106;13 ENSP00000372056:A106T;ENSP00000307006:A106T;ENSP00000426151:A13T ENSP00000307006:A106T A - 1 0 IRX2 2802835 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 4.500000 0.60387 2.239000 0.73571 0.655000 0.94253 GCG TCGA-S4-A8RO-01A-12D-A377-08 IRX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206749.2 1 0 1 85 160 0 52 0 2.800953e-01 0 3 0 52 2 0 0 0 0 0 2 1 1 83 159 0 52 2 0 0 0 0 52 2 -20.000000 1 1 0 0 1 1 2 3 1.969744 0 0.680000 2.080000 0.681084 0.990000 8.400000e-01 1.000000 1.000000 0.975774 0.990000 1 9.300000e-01 1.000000 AP3B1 8546 broad.mit.edu 37 5 77436974 77436974 + Missense_Mutation SNP G G C TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr5:77436974G>C ENST00000255194.6 - 15 1818 c.1643C>G c.(1642-1644)tCc>tGc p.S548C AP3B1_ENST00000519295.1_Missense_Mutation_p.S499C NM_001271769.1 NP_001258698.1 O00203 AP3B1_HUMAN adaptor-related protein complex 3, beta 1 subunit 39 all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215) CACCTGTTTGGAGTTGGTTAA 0.408000 Hermansky-Pudlak syndrome 0 SO:0001583 missense Familial Cancer Database HPS, HPS1-8 ENST00000255194.6 1 1 hg19 CCDS4041.1 . . . . . . . . . . G 25.9 4.686301 0.88639 . . ENSG00000132842 ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667 T;T 0.14266 2.52;2.52 5.63 5.63 0.86233 Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.41926 0.1180 M 0.79258 2.445 0.80722 D 1 D 0.76494 0.999 D 0.74023 0.982 T 0.29579 -1.0007 10 0.87932 D 0 -8.1557 19.6633 0.95882 0.0:0.0:1.0:0.0 . 548 O00203 AP3B1_HUMAN C 548;499;548;452 ENSP00000255194:S548C;ENSP00000430597:S499C ENSP00000255194:S548C S - 2 0 AP3B1 77472730 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 9.864000 0.99589 2.638000 0.89438 0.655000 0.94253 TCC TCGA-S4-A8RO-01A-12D-A377-08 AP3B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000225548.2 1 0 1 89 235 0 93 1 9.997728e-01 15 21 0 93 2 0 0 0 0 0 2 1 1 89 232 0 91 2 0 0 0 0 93 2 -6.497701 1 1 121410 1 35 1 1 2 3 1.969744 0 0.680000 2.080000 0.681084 0.800000 6.600000e-01 0.960000 0.810000 0.813388 0.800000 0 7.300000e-01 0.890000 SYCP2L 221711 broad.mit.edu 37 6 10894138 10894138 + Silent SNP A A T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr6:10894138A>T ENST00000283141.6 + 3 413 c.117A>T c.(115-117)ggA>ggT p.G39G SYCP2L_ENST00000543878.1_5'UTR|RP11-637O19.3_ENST00000480294.1_3'UTR NM_001040274.2 NP_001035364.2 Q5T4T6 SYC2L_HUMAN synaptonemal complex protein 2-like 36 Breast(50;0.0838)|Ovarian(93;0.107) all_hematologic(90;0.135) Epithelial(50;0.239) ATGATAAAGGATTTCAGAAAA 0.299000 0 SO:0001819 synonymous_variant ENST00000283141.6 1 1 hg19 CCDS43423.1 TCGA-S4-A8RO-01A-12D-A377-08 SYCP2L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039845.3 1 0 1 47 73 0 56 0 0 0 0 56 2 0 0 0 0 0 2 1 1 47 72 0 54 2 0 0 0 0 56 2 -20.000000 1 1 0 0 1 1 2 3 2.028779 0 0.680000 2.080000 0.686397 0.990000 9.200000e-01 1.000000 1.000000 0.995110 0.990000 1 9.900000e-01 1.000000 IGF2R 3482 broad.mit.edu 37 6 160465585 160465585 + Missense_Mutation SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr6:160465585C>T ENST00000356956.1 + 13 1809 c.1661C>T c.(1660-1662)tCt>tTt p.S554F NM_000876.2 NP_000867 P11717 MPRI_HUMAN insulin-like growth factor 2 receptor 95 Breast(66;0.000777)|Ovarian(120;0.0305) Mecasermin(DB01277) TTTATTTCCTCTCCCATGAAA 0.348000 0 SO:0001583 missense ENST00000356956.1 0 1 hg19 CCDS5273.1 . . . . . . . . . . C 18.83 3.706258 0.68615 . . ENSG00000197081 ENST00000356956 T 0.02656 4.21 5.91 5.91 0.95273 Mannose-6-phosphate receptor, binding (1); 0.210963 0.51477 D 0.000082 T 0.12008 0.0292 M 0.82517 2.595 0.53688 D 0.999974 D 0.58620 0.983 P 0.62649 0.905 T 0.00583 -1.1659 10 0.66056 D 0.02 -9.3461 20.2985 0.98592 0.0:1.0:0.0:0.0 . 554 P11717 MPRI_HUMAN F 554 ENSP00000349437:S554F ENSP00000349437:S554F S + 2 0 IGF2R 160385575 1.000000 0.71417 0.927000 0.36925 0.330000 0.28571 5.766000 0.68843 2.793000 0.96121 0.655000 0.94253 TCT TCGA-S4-A8RO-01A-12D-A377-08 IGF2R-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042931.1 0 0 0 6 209 0 61 0 1.624572e-01 1 21 0 61 2 0 0 0 0 0 2 1 9.645928e-01 6 207 0 59 2 0 0 0 0 61 2 -3.645305 1 1 0 0 1 1 2 3 1.997743 0 0.680000 2.080000 0.684294 0.080000 3.000000e-02 1.000000 0.080000 0.121988 0.080000 0 5.000000e-02 0.140000 C6orf118 168090 broad.mit.edu 37 6 165715133 165715133 + Silent SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr6:165715133G>A ENST00000230301.8 - 2 698 c.678C>T c.(676-678)ctC>ctT p.L226L C6orf118_ENST00000543069.1_Silent_p.L122L NM_144980.3 NP_659417.2 Q5T5N4 CF118_HUMAN chromosome 6 open reading frame 118 40 Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157) CTTGCTTGGCGAGCACTTCCT 0.622000 0 SO:0001819 synonymous_variant ENST00000230301.8 1 1 hg19 CCDS5288.1 TCGA-S4-A8RO-01A-12D-A377-08 C6orf118-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000043026.1 1 0 1 73 191 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 1 73 190 0 53 2 0 0 0 0 53 2 -6.139397 1 1 0 0 1 1 2 3 1.997743 0 0.680000 2.080000 0.684294 0.820000 6.600000e-01 1.000000 0.820000 0.832202 0.820000 0 7.400000e-01 0.920000 RBM24 221662 broad.mit.edu 37 6 17283114 17283114 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr6:17283114G>A ENST00000379052.5 + 2 483 c.247G>A c.(247-249)Gtg>Atg p.V83M RBM24_ENST00000318204.5_Missense_Mutation_p.V38M|RBM24_ENST00000425446.2_Missense_Mutation_p.V25M NM_001143942.1 NP_001137414.1 Q9BX46 RBM24_HUMAN RNA binding motif protein 24 13 Breast(50;0.0615)|Ovarian(93;0.0733) all_hematologic(90;0.062) all cancers(50;0.131)|Epithelial(50;0.15) AAAGGCCAACGTGAACCTGGC 0.537000 0 SO:0001583 missense ENST00000379052.5 0 1 hg19 CCDS47378.1 . . . . . . . . . . G 28.1 4.889107 0.91814 . . ENSG00000112183 ENST00000379052;ENST00000509686;ENST00000425446;ENST00000318204 T;D;T;T 0.84298 2.72;-1.83;1.47;2.72 4.8 4.8 0.61643 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2); 0.135582 0.48767 D 0.000169 D 0.93936 0.8059 H 0.95437 3.67 0.80722 D 1 D;P;P 0.65815 0.995;0.652;0.652 D;P;P 0.66084 0.941;0.459;0.459 D 0.95757 0.8797 10 0.87932 D 0 -12.3307 17.9074 0.88923 0.0:0.0:1.0:0.0 . 38;83;83 Q9BX46-2;Q9BX46;A8KAI7 .;RBM24_HUMAN;. M 83;42;25;38 ENSP00000368341:V83M;ENSP00000426222:V42M;ENSP00000396898:V25M;ENSP00000319551:V38M ENSP00000319551:V38M V + 1 0 RBM24 17391093 1.000000 0.71417 0.997000 0.53966 0.998000 0.95712 9.547000 0.98100 2.222000 0.72286 0.650000 0.86243 GTG TCGA-S4-A8RO-01A-12D-A377-08 RBM24-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039946.2 1 0 1 19 152 0 25 0 0 0 0 25 2 0 0 0 0 0 2 1 9.999935e-01 19 152 0 25 2 0 0 0 0 25 2 -20.000000 1 1 0 0 1 1 2 3 2.028779 0 0.680000 2.080000 0.686397 0.340000 2.100000e-01 1.000000 0.330000 0.376748 0.340000 0 2.700000e-01 0.430000 RGL2 5863 broad.mit.edu 37 6 33263940 33263940 + Silent SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr6:33263940G>A ENST00000497454.1 - 6 1128 c.633C>T c.(631-633)ctC>ctT p.L211L RGL2_ENST00000437840.2_5'UTR|PFDN6_ENST00000463584.1_Intron|RGL2_ENST00000444031.2_Silent_p.L129L NM_001243738.1|NM_004761.4 NP_001230667.1|NP_004752.1 O15211 RGL2_HUMAN ral guanine nucleotide dissociation stimulator-like 2 34 CCCGGGACCGGAGATTGCGGA 0.662000 0 SO:0001819 synonymous_variant ENST00000497454.1 0 1 hg19 CCDS4774.1 TCGA-S4-A8RO-01A-12D-A377-08 RGL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076098.2 0 0 0 6 646 0 113 0 1.088041e-01 0 51 0 113 2 0 0 0 0 0 2 1 9.628481e-01 6 633 0 112 2 0 0 0 0 113 2 -2.576665 1 1 0 0 1 1 2 3 2.028779 0 0.680000 2.080000 0.686397 0.020000 0 1.000000 0.020000 0.076529 0.020000 0 1.000000e-02 0.050000 DAAM2 23500 broad.mit.edu 37 6 39845988 39845988 + Silent SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr6:39845988C>T ENST00000398904.2 + 12 1493 c.1311C>T c.(1309-1311)aaC>aaT p.N437N DAAM2_ENST00000274867.4_Silent_p.N437N|DAAM2_ENST00000538976.1_Silent_p.N437N Q86T65 DAAM2_HUMAN dishevelled associated activator of morphogenesis 2 49 Ovarian(28;0.0355)|Colorectal(47;0.196) GGCTCATCAACGAGAATGAAG 0.547000 0 SO:0001819 synonymous_variant ENST00000398904.2 1 1 hg19 CCDS56426.1 TCGA-S4-A8RO-01A-12D-A377-08 DAAM2-003 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000280648.1 1 0 1 52 123 0 32 0 7.960949e-01 0 9 0 32 2 0 0 0 0 0 2 1 1 52 122 0 32 2 0 0 0 0 32 2 -20.000000 1 1 121022 1 34 1 1 2 3 1.997743 0 0.680000 2.080000 0.684294 0.880000 6.900000e-01 1.000000 1.000000 0.885767 0.880000 1 7.800000e-01 1.000000 GTPBP2 54676 broad.mit.edu 37 6 43593543 43593543 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr6:43593543G>A ENST00000307126.5 - 4 456 c.457C>T c.(457-459)Ccc>Tcc p.P153S GTPBP2_ENST00000476510.1_5'UTR|GTPBP2_ENST00000307114.7_Missense_Mutation_p.P65S NM_019096.3 NP_061969.3 GTP binding protein 2 18 all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004) all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167) ATCTTCCGGGGCATGTCGCTA 0.552000 GBM(116;405 1620 28302 32150 44768) 0 SO:0001583 missense ENST00000307126.5 0 1 hg19 CCDS4903.1 . . . . . . . . . . G 10.62 1.400940 0.25291 . . ENSG00000172432 ENST00000307126;ENST00000307114;ENST00000452781 T;T;T 0.42513 1.56;1.59;0.97 4.78 4.78 0.61160 . 0.114076 0.64402 D 0.000013 T 0.11965 0.0291 N 0.05574 -0.02 0.50467 D 0.999875 B;B 0.09022 0.002;0.0 B;B 0.09377 0.004;0.001 T 0.09164 -1.0687 10 0.12766 T 0.61 -15.4253 17.9977 0.89189 0.0:0.0:1.0:0.0 . 145;153 Q9BX10-4;Q9BX10 .;GTPB2_HUMAN S 153;65;145 ENSP00000303997:P153S;ENSP00000304893:P65S;ENSP00000410676:P145S ENSP00000304893:P65S P - 1 0 GTPBP2 43701521 1.000000 0.71417 0.980000 0.43619 0.797000 0.45037 4.912000 0.63335 2.480000 0.83734 0.561000 0.74099 CCC TCGA-S4-A8RO-01A-12D-A377-08 GTPBP2-011 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040679.1 0 0 0 5 355 0 72 0 2.620823e-01 0 60 0 72 2 0 0 0 0 0 2 1 9.365796e-01 5 352 0 71 2 0 0 0 0 72 2 -2.179393 0 1 121412 1 31 1 1 2 3 1.997743 0 0.680000 2.080000 0.684294 0.040000 0 1.000000 0.040000 0.076536 0.040000 0 2.000000e-02 0.070000 RAMP3 10268 broad.mit.edu 37 7 45222846 45222846 + Silent SNP C C T rs138821752 TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr7:45222846C>T ENST00000242249.4 + 3 320 c.282C>T c.(280-282)acC>acT p.T94T RAMP3_ENST00000481345.1_Silent_p.T94T|RAMP3_ENST00000496212.1_Silent_p.T94T NM_005856.2 NP_005847.1 O60896 RAMP3_HUMAN receptor (G protein-coupled) activity modifying protein 3 11 Pramlintide(DB01278) GCTTCATCACCGGCATCCACA 0.592000 0 SO:0001819 synonymous_variant ENST00000242249.4 1 1 hg19 CCDS5503.1 TCGA-S4-A8RO-01A-12D-A377-08 RAMP3-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000251343.1 1 0 1 116 229 0 85 0 1 0 80 0 85 2 0 0 0 0 0 2 1 1 115 225 0 85 2 0 0 0 0 85 2 -11.636590 1 1 121412 36 48 1 1 2 3 2.042212 0 0.680000 2.080000 0.687439 0.990000 8.600000e-01 1.000000 1.000000 0.977301 0.990000 1 9.300000e-01 1.000000 SQLE 6713 broad.mit.edu 37 8 126030321 126030321 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr8:126030321G>A ENST00000265896.5 + 8 2123 c.1225G>A c.(1225-1227)Gca>Aca p.A409T SQLE_ENST00000523430.1_Missense_Mutation_p.A314T NM_003129.3 NP_003120.2 Q14534 ERG1_HUMAN squalene epoxidase 14 Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108) STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205) Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857) TTTGGGAGACGCATATAATAT 0.353000 0 SO:0001583 missense ENST00000265896.5 0 1 hg19 CCDS47918.1 . . . . . . . . . . G 20.7 4.039032 0.75617 . . ENSG00000104549 ENST00000523430;ENST00000265896;ENST00000541193;ENST00000518931 T;T;T 0.75050 -0.9;-0.9;-0.9 5.48 5.48 0.80851 Aromatic-ring hydroxylase-like (1);Squalene epoxidase (1); 0.000000 0.85682 D 0.000000 D 0.89639 0.6773 M 0.91872 3.25 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.91448 0.5179 10 0.72032 D 0.01 -14.8692 19.3542 0.94404 0.0:0.0:1.0:0.0 . 409 Q14534 ERG1_HUMAN T 314;409;214;61 ENSP00000430331:A314T;ENSP00000265896:A409T;ENSP00000429916:A61T ENSP00000265896:A409T A + 1 0 SQLE 126099503 1.000000 0.71417 0.950000 0.38849 0.012000 0.07955 9.609000 0.98334 2.575000 0.86900 0.655000 0.94253 GCA TCGA-S4-A8RO-01A-12D-A377-08 SQLE-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381362.1 0 0 0 5 436 0 73 0 7.877531e-01 0 251 0 73 2 0 0 0 0 0 2 1 9.363703e-01 5 432 0 73 2 0 0 0 0 73 2 -2.534913 1 1 120800 3 34 1 2 2 4 3.161472 1 0.680000 2.080000 0.803150 0.050000 0 1.000000 0.050000 0.123574 0.050000 0 2.000000e-02 0.100000 LOXL2 4017 broad.mit.edu 37 8 23155589 23155589 + Silent SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr8:23155589G>A ENST00000389131.3 - 14 2661 c.2292C>T c.(2290-2292)agC>agT p.S764S NM_002318.2 NP_002309.1 Q9Y4K0 LOXL2_HUMAN lysyl oxidase-like 2 35 Prostate(55;0.0453)|Breast(100;0.143) TTAAGAGCCCGCTGAAGTGCT 0.532000 0 SO:0001819 synonymous_variant ENST00000389131.3 1 1 hg19 CCDS34864.1 TCGA-S4-A8RO-01A-12D-A377-08 LOXL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000375603.1 1 0 1 61 120 0 23 0 1 1 140 0 23 2 0 0 0 0 0 2 1 1 61 118 0 23 2 0 0 0 0 23 2 -20.000000 1 1 121412 1 35 1 1 3 4 2.732590 1 0.680000 2.080000 0.768250 0.990000 9.900000e-01 1.000000 1.000000 0.999917 0.990000 1 9.900000e-01 1.000000 OR13C3 138803 broad.mit.edu 37 9 107298219 107298219 + Silent SNP C C T rs145221004 TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chr9:107298219C>T ENST00000374781.2 - 1 918 c.876G>A c.(874-876)ccG>ccA p.P292P NM_001001961.1 NP_001001961.1 Q8NGS6 O13C3_HUMAN olfactory receptor, family 13, subfamily C, member 3 19 CTTGAGACTTCGGTTTCGCAT 0.438000 GBM(86;1248 1274 14222 15028 46219) 0 SO:0001819 synonymous_variant ENST00000374781.2 1 1 hg19 CCDS35089.1 TCGA-S4-A8RO-01A-12D-A377-08 OR13C3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053477.2 1 0 1 162 279 0 126 0 0 0 0 126 2 0 0 0 0 0 2 1 1 161 277 0 125 2 0 0 0 0 126 2 -18.816990 1 1 121412 114 53 1 1 2 3 1.980807 0 0.680000 2.080000 0.682161 0.990000 9.500000e-01 1.000000 1.000000 0.997045 0.990000 1 9.900000e-01 1.000000 COL4A5 1287 broad.mit.edu 37 X 107909779 107909779 + Missense_Mutation SNP G G A rs104886237 TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chrX:107909779G>A ENST00000361603.2 + 39 3752 c.3508G>A c.(3508-3510)Ggt>Agt p.G1170S COL4A5_ENST00000328300.6_Missense_Mutation_p.G1170S NM_000495.4 NP_000486.1 P29400 CO4A5_HUMAN collagen, type IV, alpha 5 99 AGGCAAACCCGGTCAAGATGG 0.443000 Alport syndrome with Diffuse Leiomyomatosis 0 GRCh37 CM993122 COL4A5 M rs104886237 SO:0001583 missense Familial Cancer Database ENST00000361603.2 1 0 hg19 CCDS14543.1 . . . . . . . . . . G 21.4 4.146532 0.77888 . . ENSG00000188153 ENST00000328300;ENST00000361603;ENST00000508186 D;D 0.99329 -5.75;-5.75 5.49 5.49 0.81192 . 0.000000 0.85682 D 0.000000 D 0.99729 0.9894 H 0.98965 4.385 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 D 0.96983 0.9716 10 0.87932 D 0 . 18.4199 0.90587 0.0:0.0:1.0:0.0 . 1170;1170 E7EVY4;P29400 .;CO4A5_HUMAN S 1170 ENSP00000331902:G1170S;ENSP00000354505:G1170S ENSP00000331902:G1170S G + 1 0 COL4A5 107796435 1.000000 0.71417 0.969000 0.41365 0.927000 0.56198 8.265000 0.89869 2.290000 0.77057 0.600000 0.82982 GGT TCGA-S4-A8RO-01A-12D-A377-08 COL4A5-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000057880.2 1 0 1 46 58 0 18 0 9.248327e-01 0 8 0 18 2 0 0 0 0 0 2 1 1 44 58 0 18 2 0 0 0 0 18 2 -11.387680 1 0 121274 1 31 1 0 1 1 0.680000 2.080000 0.680000 0.990000 9.900000e-01 1.000000 1.000000 0.999274 0.990000 1 9.900000e-01 1.000000 DCX 1641 broad.mit.edu 37 X 110644391 110644391 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chrX:110644391G>A ENST00000338081.3 - 3 946 c.775C>T c.(775-777)Cgc>Tgc p.R259C DCX_ENST00000488120.1_Missense_Mutation_p.R178C|DCX_ENST00000371993.2_Missense_Mutation_p.R178C|DCX_ENST00000356915.2_Missense_Mutation_p.R178C|DCX_ENST00000496551.1_5'UTR|DCX_ENST00000356220.3_Missense_Mutation_p.R178C NM_000555.3 NP_000546.2 O43602 DCX_HUMAN doublecortin p.R178C(1)|p.R259C(1) 41 AGCTTGGGGCGCACAAAGTCC 0.537000 2 Substitution - Missense(2) GRCh37 CM023910 DCX M SO:0001583 missense ENST00000338081.3 0 1 hg19 CCDS14556.1 . . . . . . . . . . G 25.8 4.679772 0.88542 . . ENSG00000077279 ENST00000356915;ENST00000371993;ENST00000338081;ENST00000356220;ENST00000488120 D;D;D;D;D 0.93953 -3.32;-3.32;-3.32;-3.32;-3.32 4.74 4.74 0.60224 Doublecortin domain (3); 0.131721 0.50627 D 0.000104 D 0.95592 0.8567 L 0.59436 1.845 0.80722 D 1 D;D 0.76494 0.999;0.999 D;D 0.66351 0.943;0.917 D 0.96124 0.9087 10 0.72032 D 0.01 . 17.6068 0.88040 0.0:0.0:1.0:0.0 . 247;259 B4DM53;O43602 .;DCX_HUMAN C 178;178;259;178;178 ENSP00000349385:R178C;ENSP00000361061:R178C;ENSP00000337697:R259C;ENSP00000348553:R178C;ENSP00000419861:R178C ENSP00000337697:R259C R - 1 0 DCX 110531047 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 6.624000 0.74243 2.283000 0.76528 0.600000 0.82982 CGC TCGA-S4-A8RO-01A-12D-A377-08 DCX-006 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000357058.1 0 0 0 5 442 1 95 0 0 0 1 95 2 0 0 0 0 0 2 0 7.473249e-03 5 440 1 94 17 0 0 0 1 95 2 -2.153610 0 1 0 0 1 0 1 1 0.680000 2.080000 0.680000 0.030000 0 0.070000 0.040000 0.038764 0.030000 0 1.000000e-02 0.060000 BCORL1 63035 broad.mit.edu 37 X 129190051 129190051 + Silent SNP C C T TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chrX:129190051C>T ENST00000218147.7 + 13 5273 c.5076C>T c.(5074-5076)taC>taT p.Y1692Y BCORL1_ENST00000359304.2_Silent_p.Y1562Y|BCORL1_ENST00000303743.5_Silent_p.Y1766Y|BCORL1_ENST00000540052.1_Silent_p.Y1692Y Q5H9F3 BCORL_HUMAN BCL6 corepressor-like 1 75 TGGTGCGGTACGAGCCAGACC 0.607000 0 SO:0001819 synonymous_variant ENST00000218147.7 1 1 hg19 CCDS14616.1 TCGA-S4-A8RO-01A-12D-A377-08 BCORL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058223.1 1 0 0 95 195 0 73 0 9.996660e-01 0 27 0 73 2 1 1 303 896 0 1064 2 1 1 92 185 0 71 2 0 0 0 0 73 2 -20.000000 1 1 121394 6 38 1 0 1 1 0.680000 2.080000 0.680000 0.950000 8.000000e-01 1.000000 1.000000 0.947312 0.950000 1 8.700000e-01 1.000000 GDI1 2664 broad.mit.edu 37 X 153670920 153670920 + Silent SNP C C T rs76578139 TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chrX:153670920C>T ENST00000447750.2 + 11 1580 c.1245C>T c.(1243-1245)aaC>aaT p.N415N FAM50A_ENST00000393600.3_5'Flank|GDI1_ENST00000465640.1_3'UTR NM_001493.2 NP_001484.1 P31150 GDIA_HUMAN GDP dissociation inhibitor 1 16 all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176) CAACCTGCAACGACATCAAAG 0.522000 0 SO:0001819 synonymous_variant ENST00000447750.2 1 1 hg19 CCDS35452.1 TCGA-S4-A8RO-01A-12D-A377-08 GDI1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000081649.2 1 0 0 304 259 0 98 0 1 0 332 0 98 2 0 0 0 0 0 2 1 1 300 257 0 98 2 0 0 0 0 98 2 -20.000000 1 1 121410 4 40 1 0 1 1 0.680000 2.080000 0.680000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 NAP1L2 4674 broad.mit.edu 37 X 72434324 72434324 + Missense_Mutation SNP G G A TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chrX:72434324G>A ENST00000373517.3 - 1 360 c.5C>T c.(4-6)gCc>gTc p.A2V NAP1L2_ENST00000536638.1_Intron NM_021963.3 NP_068798.1 Q9ULW6 NP1L2_HUMAN nucleosome assembly protein 1-like 2 29 Renal(35;0.156) CTCTGACTCGGCCATTTTTCA 0.532000 0 SO:0001583 missense ENST00000373517.3 0 1 hg19 CCDS14423.1 . . . . . . . . . . g 16.18 3.049801 0.55218 . . ENSG00000186462 ENST00000373517 T 0.37584 1.19 3.03 2.16 0.27623 . 0.517494 0.18149 U 0.150154 T 0.20740 0.0499 N 0.19112 0.55 0.80722 D 1 B 0.19445 0.036 B 0.12837 0.008 T 0.06881 -1.0802 10 0.87932 D 0 -3.1541 5.4474 0.16544 0.1624:0.0:0.8376:0.0 . 2 Q9ULW6 NP1L2_HUMAN V 2 ENSP00000362616:A2V ENSP00000362616:A2V A - 2 0 NAP1L2 72351049 1.000000 0.71417 1.000000 0.80357 0.756000 0.42949 2.935000 0.48963 0.660000 0.30964 -0.208000 0.12717 GCC TCGA-S4-A8RO-01A-12D-A377-08 NAP1L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057225.1 0 0 0 6 352 0 54 0 4.099149e-03 0 5 0 54 2 0 0 0 0 0 2 1 9.627839e-01 5 345 0 53 2 0 0 0 0 54 2 -2.669227 1 1 0 0 1 0 1 1 0.680000 2.080000 0.680000 0.040000 1.000000e-02 0.100000 0.050000 0.057114 0.040000 0 2.000000e-02 0.080000 FAM133A 286499 broad.mit.edu 37 X 92964906 92964906 + Nonsense_Mutation SNP C C G TCGA-S4-A8RO-01A-12D-A377-08 TCGA-S4-A8RO-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5e046033-4c1a-4a72-9345-ffaf332048d3 0e737350-f1ee-4cf6-a7d4-b0a2d9c88b0a g.chrX:92964906C>G ENST00000355813.5 + 4 1014 c.488C>G c.(487-489)tCa>tGa p.S163* FAM133A_ENST00000538690.1_Nonsense_Mutation_p.S163*|FAM133A_ENST00000322139.4_Nonsense_Mutation_p.S163*|FAM133A_ENST00000332647.4_Nonsense_Mutation_p.S163* NM_001171109.1|NM_173698.2 NP_001164580.1|NP_775969.1 Q8N9E0 F133A_HUMAN family with sequence similarity 133, member A 20 AAAAAGAAGTCAAAGGATGAA 0.363000 0 SO:0001587 stop_gained ENST00000355813.5 0 1 hg19 CCDS14466.1 . . . . . . . . . . c 38 6.748977 0.97809 . . ENSG00000179083 ENST00000538690;ENST00000355813;ENST00000322139;ENST00000332647 . . . 3.0 2.13 0.27403 . 0.239763 0.36409 U 0.002607 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.51188 T 0.08 -0.0917 5.3653 0.16111 0.0:0.8372:0.0:0.1628 . . . . X 163 . ENSP00000318974:S163X S + 2 0 FAM133A 92851562 1.000000 0.71417 1.000000 0.80357 0.961000 0.63080 0.909000 0.28558 0.668000 0.31126 0.597000 0.82753 TCA TCGA-S4-A8RO-01A-12D-A377-08 FAM133A-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057452.1 1 0 1 25 96 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 9.999999e-01 25 95 0 47 2 0 0 0 0 48 2 -20.000000 1 1 0 0 1 0 1 1 0.680000 2.080000 0.680000 0.600000 4.100000e-01 0.820000 0.600000 0.619281 0.600000 0 5.000000e-01 0.720000