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 ARCN1 372 broad.mit.edu 37 11 118451977 118452014 + Frame_Shift_Del DEL CGGTCTGCACAAAAGCAGGAAAGGCTATTGTTTCTCGA CGGTCTGCACAAAAGCAGGAAAGGCTATTGTTTCTCGA - rs142869705 by1000genomes TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 CGGTCTGCACAAAAGCAGGAAAGGCTATTGTTTCTCGA - CGGTCTGCACAAAAGCAGGAAAGGCTATTGTTTCTCGA CGGTCTGCACAAAAGCAGGAAAGGCTATTGTTTCTCGA Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr11:118451977_118452014delCGGTCTGCACAAAAGCAGGAAAGGCTATTGTTTCTCGA ENST00000264028.4 + 2 115_152 c.20_57delCGGTCTGCACAAAAGCAGGAAAGGCTATTGTTTCTCGA c.(19-57)gcggtctgcacaaaagcaggaaaggctattgtttctcgafs p.AVCTKAGKAIVSR7fs ARCN1_ENST00000359415.4_Frame_Shift_Del_p.AVCTKAGKAIVSR48fs|ARCN1_ENST00000534182.2_Frame_Shift_Del_p.AVCTKAGKAIVSR7fs|ARCN1_ENST00000392859.3_Intron NM_001655.4 NP_001646.2 P48444 COPD_HUMAN archain 1 p.A15T(1) 13 all_hematologic(175;0.0349) Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234) TTGGCAGCAGCGGTCTGCACAAAAGCAGGAAAGGCTATTGTTTCTCGACAGTTTGTGG 0.420000 1 Substitution - Missense(1) SO:0001589 frameshift_variant ENST00000264028.4 1 0 hg19 CCDS8400.1 TCGA-IB-7652-01A-11D-2154-08 ARCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389278.1 1 0 0 54 617 0 298 0 9.999996e-01 0 242 0 298 2 0 0 0 0 1 0.999990 104 664 5 302 24 -2.665581 1 1 0 0 1 1 2 3 2.285822 1 0.360000 1.990000 0.437016 0.520000 0.390000 1.000000 0.500000 0.599614 0.520000 0 0.450000 1.000000 E4F1 1877 broad.mit.edu 37 16 2284179 2284196 + In_Frame_Del DEL GCCGTTCGCCTGCGCGCA GCCGTTCGCCTGCGCGCA - rs137969975 TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr16:2284179_2284196delGCCGTTCGCCTGCGCGCA ENST00000301727.4 + 10 1431_1448 c.1383_1400delGCCGTTCGCCTGCGCGCA c.(1381-1401)aggccgttcgcctgcgcgcag>agg p.PFACAQ462del RP11-304L19.12_ENST00000564055.1_lincRNA|E4F1_ENST00000564139.1_In_Frame_Del_p.PFACAQ462del|DNASE1L2_ENST00000382437.4_5'Flank|DNASE1L2_ENST00000320700.5_5'Flank|E4F1_ENST00000565090.1_Intron|DNASE1L2_ENST00000567494.1_5'Flank|DNASE1L2_ENST00000564065.1_5'Flank NM_004424.3 NP_004415.2 Q66K89 E4F1_HUMAN E4F transcription factor 1 1 CAGGGCCGAGGCCGTTCGCCTGCGCGCAGTGTGGCAAG 0.693000 0 SO:0001651 inframe_deletion ENST00000301727.4 1 1 hg19 CCDS32370.1 TCGA-IB-7652-01A-11D-2154-08 E4F1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000435225.1 1 0 0 16 156 0 110 0 8.440212e-01 0 35 0 110 2 0 0 0 1 0 0 2 1 0.951935 24 165 2 119 10 -19.998440 1 1 0 0 1 1 2 3 2.029570 0 0.360000 1.990000 0.365709 0.530000 0.310000 1.000000 0.510000 0.559520 0.530000 0 0.410000 0.690000 RASSF2 9770 broad.mit.edu 37 20 4770321 4770339 + Frame_Shift_Del DEL TAGGCTGGTGTGAACACGG TAGGCTGGTGTGAACACGG - TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr20:4770321_4770339delTAGGCTGGTGTGAACACGG ENST00000379400.3 - 8 737_755 c.542_560delCCGTGTTCACACCAGCCTA c.(541-561)tccgtgttcacaccagcctatfs p.SVFTPAY181fs RASSF2_ENST00000478553.1_5'UTR|RASSF2_ENST00000379376.2_Frame_Shift_Del_p.SVFTPAY181fs NM_014737.2 NP_055552.1 P50749 RASF2_HUMAN Ras association (RalGDS/AF-6) domain family member 2 34 GACAGAGCCATAGGCTGGTGTGAACACGGATGTCTGTCA 0.539000 Melanoma(158;1891 3343 50738) 0 SO:0001589 frameshift_variant ENST00000379400.3 1 1 hg19 CCDS13083.1 TCGA-IB-7652-01A-11D-2154-08 RASSF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077828.1 1 0 0 17 228 0 131 0 8.708160e-01 0 51 0 131 2 0 0 0 0 1 0.999985 26 238 0 129 2 -19.970650 1 1 0 0 1 1 2 3 2.016887 0 0.360000 1.990000 0.362296 0.390000 0.230000 0.620000 0.390000 0.409252 0.390000 0 0.300000 0.500000 CACNA2D3 55799 broad.mit.edu 37 3 55021718 55021719 + Frame_Shift_Del DEL CT CT - TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr3:55021718_55021719delCT ENST00000474759.1 + 31 2676_2677 c.2628_2629delCT c.(2626-2631)gactttfs p.F878fs CACNA2D3_ENST00000490478.1_Frame_Shift_Del_p.F784fs|CACNA2D3_ENST00000415676.2_Frame_Shift_Del_p.F878fs|CACNA2D3_ENST00000288197.5_Frame_Shift_Del_p.F878fs|CACNA2D3_ENST00000478261.1_3'UTR NM_018398.2 NP_060868.2 Q8IZS8 CA2D3_HUMAN calcium channel, voltage-dependent, alpha 2/delta subunit 3 59 Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421) AGACTGGAGACTTTTTTGGTGA 0.436000 0 SO:0001589 frameshift_variant ENST00000474759.1 1 1 hg19 CCDS54598.1 TCGA-IB-7652-01A-11D-2154-08 CACNA2D3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351402.1 1 0 0 23 179 0 110 0 4.583729e-01 0 13 0 110 2 0 0 0 0 1 1.000000 25 176 0 111 2 -10.716640 1 0 0 0 1 0 0 0 1.994361 0 0.360000 1.990000 0.357688 0.630000 0.410000 0.880000 0.620000 0.645227 0.630000 0 0.510000 0.760000 PDZD2 23037 broad.mit.edu 37 5 32089602 32089631 + In_Frame_Del DEL CCCTAAATCTCCTAAGTGTAGAGCAGAGGG CCCTAAATCTCCTAAGTGTAGAGCAGAGGG - TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:32089602_32089631delCCCTAAATCTCCTAAGTGTAGAGCAGAGGG ENST00000438447.1 + 20 6436_6465 c.6048_6077delCCCTAAATCTCCTAAGTGTAGAGCAGAGGG c.(6046-6078)acccctaaatctcctaagtgtagagcagagggc>acc p.PKSPKCRAEG2017del PDZD2_ENST00000282493.3_In_Frame_Del_p.PKSPKCRAEG2017del O15018 PDZD2_HUMAN PDZ domain containing 2 p.C2022Y(1) 148 GCCCAACCACCCCTAAATCTCCTAAGTGTAGAGCAGAGGGCAGGGCGCCC 0.635000 1 Substitution - Missense(1) SO:0001651 inframe_deletion ENST00000438447.1 1 1 hg19 CCDS34137.1 TCGA-IB-7652-01A-11D-2154-08 PDZD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000366608.1 0 0 0 37 1259 0 784 0 2.582762e-03 0 3 0 784 2 0 0 0 0 1 0.903067 135 1349 10 784 32 -2.095622 0 1 0 0 1 0 0 0 1.992041 0 0.360000 1.990000 0.357688 0.150000 0.100000 0.210000 0.160000 0.161833 0.150000 0 0.120000 0.190000 DOCK11 139818 broad.mit.edu 37 X 117742086 117742096 + Frame_Shift_Del DEL TCTAAGATCAT TCTAAGATCAT - TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:117742086_117742096delTCTAAGATCAT ENST00000276202.7 + 25 2796_2806 c.2733_2743delTCTAAGATCAT c.(2731-2745)tatctaagatcattcfs p.LRSF912fs DOCK11_ENST00000276204.6_Frame_Shift_Del_p.LRSF912fs NM_144658.3 NP_653259.3 Q5JSL3 DOC11_HUMAN dedicator of cytokinesis 11 84 TGGATAGTTATCTAAGATCATTCATAAAGGT 0.313000 0 SO:0001589 frameshift_variant ENST00000276202.7 1 1 hg19 CCDS35373.1 TCGA-IB-7652-01A-11D-2154-08 DOCK11-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000356002.1 0 0 0 78 694 0 176 1 9.377920e-01 2 41 0 176 2 0 0 0 0 1 1.000000 125 740 3 178 29 -3.221883 1 1 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.550000 0.440000 0.680000 0.560000 0.565727 0.550000 0 0.490000 0.620000 KIAA1217 56243 broad.mit.edu 37 10 24762714 24762714 + Silent SNP C C A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr10:24762714C>A ENST00000376454.3 + 6 1434 c.1404C>A c.(1402-1404)tcC>tcA p.S468S KIAA1217_ENST00000307544.6_Silent_p.S186S|KIAA1217_ENST00000376462.1_Silent_p.S388S|KIAA1217_ENST00000396445.1_Silent_p.S186S|KIAA1217_ENST00000430453.2_Silent_p.S389S|KIAA1217_ENST00000376451.2_Silent_p.S186S|KIAA1217_ENST00000396446.1_Silent_p.S186S|KIAA1217_ENST00000458595.1_Silent_p.S468S|KIAA1217_ENST00000376452.3_Silent_p.S468S NM_019590.3 NP_062536.2 Q5T5P2 SKT_HUMAN KIAA1217 70 CACTGGGCTCCAAAACACCCC 0.507000 0 SO:0001819 synonymous_variant ENST00000376454.3 1 1 hg19 CCDS31165.1 TCGA-IB-7652-01A-11D-2154-08 KIAA1217-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047223.2 1 0 1 78 350 0 164 1 1 46 155 0 164 2 0 0 0 1 0 0 2 1 1.000000 78 346 0 161 2 -3.313313 1 1 0 0 1 1 2 3 2.003885 0 0.360000 1.990000 0.361150 0.990000 0.810000 1.000000 1.000000 0.967364 0.990000 1 0.910000 1.000000 ZEB1 6935 broad.mit.edu 37 10 31810814 31810814 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr10:31810814C>T ENST00000320985.10 + 7 2661 c.2551C>T c.(2551-2553)Cct>Tct p.P851S ZEB1_ENST00000446923.2_Missense_Mutation_p.P835S|ZEB1_ENST00000560721.2_Missense_Mutation_p.P831S|ZEB1_ENST00000361642.5_Missense_Mutation_p.P852S|ZEB1_ENST00000559858.1_3'UTR|ZEB1_ENST00000542815.3_Missense_Mutation_p.P784S P37275 ZEB1_HUMAN zinc finger E-box binding homeobox 1 77 Prostate(175;0.0156) TACGGTCAGCCCTGCAGTCCA 0.463000 Ovarian(40;423 959 14296 36701 49589) 0 SO:0001583 missense ENST00000320985.10 1 1 hg19 CCDS7169.1 . . . . . . . . . . C 12.87 2.067296 0.36470 . . ENSG00000148516 ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000543514;ENST00000446923 T;T;T;T;T 0.13778 2.86;2.57;2.59;2.56;2.6 5.68 4.78 0.61160 . 0.000000 0.56097 D 0.000028 T 0.28267 0.0698 L 0.47716 1.5 0.80722 D 1 B;D;D;P;D;B;D;P 0.89917 0.328;1.0;1.0;0.615;1.0;0.04;1.0;0.615 B;D;D;B;D;B;D;B 0.87578 0.076;0.998;0.996;0.158;0.996;0.034;0.996;0.158 T 0.03566 -1.1024 10 0.15499 T 0.54 -7.6384 15.0713 0.72040 0.0:0.9318:0.0:0.0682 . 784;851;835;851;851;831;852;851 F5H4I8;F5H1R1;E9PCM7;B2RBI8;A0JLS9;Q5VZ84;Q2KJ05;P37275 .;.;.;.;.;.;.;ZEB1_HUMAN S 633;851;852;846;784;851;831;742;835 ENSP00000444282:P633S;ENSP00000354487:P852S;ENSP00000444891:P784S;ENSP00000319248:P851S;ENSP00000391612:P835S ENSP00000319248:P851S P + 1 0 ZEB1 31850820 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 3.779000 0.55379 1.534000 0.49203 0.650000 0.86243 CCT TCGA-IB-7652-01A-11D-2154-08 ZEB1-018 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000419083.2 1 0 1 62 270 0 112 0 1 0 157 0 112 2 0 0 0 0 0 2 1 1.000000 62 266 0 109 2 -20.000000 1 1 0 0 1 1 2 3 2.003885 0 0.360000 1.990000 0.361150 0.990000 0.810000 1.000000 1.000000 0.972076 0.990000 1 0.920000 1.000000 MYOZ1 58529 broad.mit.edu 37 10 75399731 75399731 + Silent SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr10:75399731G>A ENST00000359322.4 - 2 409 c.45C>T c.(43-45)tcC>tcT p.S15S NM_021245.3 NP_067068.1 myozenin 1 12 Prostate(51;0.0112) TCAGCTTGCTGGATTTCCTCT 0.517000 0 SO:0001819 synonymous_variant ENST00000359322.4 1 1 hg19 CCDS7330.1 TCGA-IB-7652-01A-11D-2154-08 MYOZ1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048654.1 1 0 1 75 340 0 213 0 9.655258e-01 0 27 0 213 2 0 0 0 0 0 2 1 1.000000 73 338 0 213 2 -2.961924 1 1 0 0 1 1 2 3 2.023677 0 0.360000 1.990000 0.364575 0.990000 0.810000 1.000000 1.000000 0.966415 0.990000 1 0.900000 1.000000 NPAT 4863 broad.mit.edu 37 11 108032080 108032080 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr11:108032080C>T ENST00000278612.8 - 17 3838 c.3733G>A c.(3733-3735)Gaa>Aaa p.E1245K NM_002519.2 NP_002510.2 Q14207 NPAT_HUMAN nuclear protein, ataxia-telangiectasia locus 46 all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) TGTAACATTTCTGTGGTAATC 0.433000 0 SO:0001583 missense ENST00000278612.8 1 1 hg19 CCDS41710.1 . . . . . . . . . . C 18.41 3.616831 0.66672 . . ENSG00000149308 ENST00000278612 T 0.07567 3.18 5.24 5.24 0.73138 . 0.300838 0.34580 N 0.003851 T 0.23289 0.0563 M 0.69823 2.125 0.58432 D 0.999999 D 0.55385 0.971 P 0.53401 0.725 T 0.00164 -1.1968 10 0.66056 D 0.02 -12.4987 19.3787 0.94523 0.0:1.0:0.0:0.0 . 1245 Q14207 NPAT_HUMAN K 1245 ENSP00000278612:E1245K ENSP00000278612:E1245K E - 1 0 NPAT 107537290 1.000000 0.71417 0.909000 0.35828 0.109000 0.19521 6.781000 0.75068 2.890000 0.99128 0.650000 0.86243 GAA TCGA-IB-7652-01A-11D-2154-08 NPAT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389506.2 0 0 0 40 1398 0 423 0 7.800570e-01 1 101 0 423 2 0 0 0 0 0 2 1 1.000000 39 1387 0 419 2 -2.614862 1 1 120822 1 35 1 1 2 3 2.285822 1 0.360000 1.990000 0.437016 0.180000 0.120000 1.000000 0.170000 0.322576 0.180000 0 0.140000 1.000000 FDXACB1 91893 broad.mit.edu 37 11 111749420 111749420 + Silent SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr11:111749420G>A ENST00000260257.4 - 2 236 c.189C>T c.(187-189)ttC>ttT p.F63F C11orf1_ENST00000260276.3_5'Flank|C11orf1_ENST00000530214.1_5'Flank|C11orf1_ENST00000528125.1_5'Flank|ALG9_ENST00000527377.1_5'Flank|ALG9_ENST00000524880.1_Silent_p.F63F|FDXACB1_ENST00000542429.1_Intron|C11orf1_ENST00000529270.1_5'Flank NM_138378.2 NP_612387.1 Q9BRP7 FDXA1_HUMAN ferredoxin-fold anticodon binding domain containing 1 19 AGTCCACACCGAAACGTACAT 0.458000 OREG0021330 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001819 synonymous_variant ENST00000260257.4 0 1 hg19 CCDS44729.1 TCGA-IB-7652-01A-11D-2154-08 FDXACB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391497.1 0 0 0 3 73 0 45 0 2.905908e-01 0 21 0 45 2 0 0 0 0 0 2 1 0.812541 3 73 0 45 2 -6.198291 1 0 120856 1 22 1 1 2 3 2.285822 1 0.360000 1.990000 0.437016 0.330000 0.080000 1.000000 0.250000 0.437134 0.330000 0 0.170000 1.000000 OR9G1 390174 broad.mit.edu 37 11 56468064 56468064 + Silent SNP T T C TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr11:56468064T>C ENST00000312153.1 + 1 201 c.201T>C c.(199-201)ttT>ttC p.F67F NM_001005213.1 NP_001005213.1 Q8NH87 OR9G1_HUMAN olfactory receptor, family 9, subfamily G, member 1 31 ATCTGTCGTTTCTGGATCTCT 0.463000 0 SO:0001819 synonymous_variant ENST00000312153.1 1 1 hg19 CCDS31536.1 TCGA-IB-7652-01A-11D-2154-08 OR9G1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393253.1 0 0 0 72 489 0 145 0 0 0 0 145 2 0 0 0 0 0 2 1 1.000000 67 395 0 150 2 -20.000000 1 1 0 0 1 0 0 0 1.914842 0 0.360000 1.990000 0.328577 0.670000 0.530000 0.830000 0.680000 0.684137 0.670000 0 0.600000 0.760000 SLC22A11 55867 broad.mit.edu 37 11 64329841 64329841 + Missense_Mutation SNP T T A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr11:64329841T>A ENST00000301891.4 + 4 1129 c.755T>A c.(754-756)cTg>cAg p.L252Q SLC22A11_ENST00000377585.3_Missense_Mutation_p.L252Q|SLC22A11_ENST00000490834.1_3'UTR|SLC22A11_ENST00000377581.3_Missense_Mutation_p.L252Q NM_018484.2 NP_060954.1 Q9NSA0 S22AB_HUMAN solute carrier family 22 (organic anion/urate transporter), member 11 23 Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495) GCCTTTGCCCTGCGGGACTGG 0.627000 0 SO:0001583 missense ENST00000301891.4 0 1 hg19 CCDS8074.1 . . . . . . . . . . . 18.76 3.692873 0.68271 . . ENSG00000168065 ENST00000301891;ENST00000377585;ENST00000377581 T;T;T 0.68181 -0.31;-0.31;-0.31 3.58 3.58 0.41010 Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1); 0.173586 0.38326 U 0.001730 T 0.81772 0.4893 M 0.86502 2.82 0.38636 D 0.951485 D;D;D;D 0.89917 0.999;1.0;0.998;0.999 D;D;D;D 0.87578 0.969;0.998;0.98;0.98 D 0.85294 0.1069 10 0.87932 D 0 . 10.2369 0.43288 0.0:0.0:0.0:1.0 . 252;46;252;252 Q9NSA0-2;Q8NBZ3;A6NCG2;Q9NSA0 .;.;.;S22AB_HUMAN Q 252 ENSP00000301891:L252Q;ENSP00000366809:L252Q;ENSP00000366804:L252Q ENSP00000301891:L252Q L + 2 0 SLC22A11 64086417 0.996000 0.38824 1.000000 0.80357 0.752000 0.42762 6.548000 0.73896 1.512000 0.48834 0.454000 0.30748 CTG TCGA-IB-7652-01A-11D-2154-08 SLC22A11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000104886.4 0 0 0 11 662 0 271 0 1.008534e-03 0 3 0 271 2 0 0 0 0 0 2 1 0.998319 11 659 0 266 2 -8.621009 1 0 0 0 1 1 2 3 2.051876 0 0.360000 1.990000 0.369085 0.090000 0.040000 1.000000 0.090000 0.157837 0.090000 0 0.060000 0.140000 PC 5091 broad.mit.edu 37 11 66638642 66638642 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr11:66638642C>T ENST00000393958.2 - 6 607 c.514G>A c.(514-516)Gcc>Acc p.A172T PC_ENST00000393960.1_Missense_Mutation_p.A172T|PC_ENST00000393955.2_Missense_Mutation_p.A172T|PC_ENST00000355677.3_Missense_Mutation_p.A172T|PC_ENST00000524491.1_Missense_Mutation_p.A132T NM_000920.3 NP_000911.2 P11498 PYC_HUMAN pyruvate carboxylase 32 Melanoma(852;0.0525) Biotin(DB00121)|Pyruvic acid(DB00119) GTGATGGGGGCATCTGTGCCA 0.622000 0 SO:0001583 missense ENST00000393958.2 1 1 hg19 CCDS8152.1 . . . . . . . . . . C 14.69 2.611298 0.46631 . . ENSG00000173599 ENST00000393955;ENST00000393958;ENST00000393960;ENST00000524491;ENST00000355677 D;D;D;D;D 0.97772 -4.53;-4.53;-4.53;-4.53;-4.53 5.35 0.917 0.19380 ATP-grasp fold (1);ATP-grasp fold, subdomain 1 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1); 0.280748 0.33610 N 0.004721 D 0.91472 0.7308 N 0.13272 0.32 0.25049 N 0.991147 B 0.06786 0.001 B 0.11329 0.006 D 0.84620 0.0683 10 0.51188 T 0.08 -22.3962 3.8827 0.09085 0.407:0.3854:0.126:0.0816 . 172 P11498 PYC_HUMAN T 172;172;172;132;172 ENSP00000377527:A172T;ENSP00000377530:A172T;ENSP00000377532:A172T;ENSP00000434192:A132T;ENSP00000347900:A172T ENSP00000347900:A172T A - 1 0 PC 66395218 0.018000 0.18449 0.594000 0.28785 0.755000 0.42902 0.226000 0.17776 0.566000 0.29273 0.655000 0.94253 GCC TCGA-IB-7652-01A-11D-2154-08 PC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393115.1 1 0 1 48 269 0 146 0 8.045444e-01 1 18 0 146 2 0 0 0 0 0 2 1 1.000000 48 269 0 143 2 -19.999710 1 1 0 0 1 1 2 3 2.051876 0 0.360000 1.990000 0.369085 0.860000 0.640000 1.000000 1.000000 0.863497 0.860000 1 0.740000 1.000000 OR10A6 390093 broad.mit.edu 37 11 7949776 7949776 + Missense_Mutation SNP A A G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr11:7949776A>G ENST00000309838.2 - 1 433 c.434T>C c.(433-435)aTt>aCt p.I145T NM_001004461.1 NP_001004461.1 Q8NH74 O10A6_HUMAN olfactory receptor, family 10, subfamily A, member 6 22 TGAAAATATAATTAATTTCAT 0.338000 0 SO:0001583 missense ENST00000309838.2 1 1 hg19 CCDS31420.1 . . . . . . . . . . A 1.813 -0.474282 0.04414 . . ENSG00000175393 ENST00000309838 T 0.43688 0.94 4.41 4.41 0.53225 GPCR, rhodopsin-like superfamily (1); 0.614618 0.13200 N 0.406025 T 0.30039 0.0752 N 0.16862 0.45 0.09310 N 1 B 0.22080 0.064 B 0.23852 0.049 T 0.24225 -1.0166 10 0.62326 D 0.03 . 11.9092 0.52729 1.0:0.0:0.0:0.0 . 145 Q8NH74 O10A6_HUMAN T 145 ENSP00000312470:I145T ENSP00000312470:I145T I - 2 0 OR10A6 7906352 0.000000 0.05858 0.154000 0.22540 0.014000 0.08584 1.296000 0.33389 1.983000 0.57843 0.533000 0.62120 ATT TCGA-IB-7652-01A-11D-2154-08 OR10A6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385703.1 1 0 1 83 266 0 62 0 0 0 0 62 2 0 0 0 0 0 2 1 1.000000 82 265 0 62 2 -20.000000 1 1 121338 9 40 1 0 1 1 1.639578 1 0.360000 1.990000 0.219512 0.950000 0.820000 1.000000 0.990000 0.947551 0.950000 1 0.890000 0.990000 CCDC81 60494 broad.mit.edu 37 11 86131064 86131064 + Nonsense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr11:86131064C>T ENST00000445632.2 + 14 2058 c.1786C>T c.(1786-1788)Cag>Tag p.Q596* CCDC81_ENST00000354755.1_Nonsense_Mutation_p.Q506*|CCDC81_ENST00000278487.3_Nonsense_Mutation_p.Q331*|CCDC81_ENST00000528728.1_Nonsense_Mutation_p.Q331* NM_001156474.1 NP_001149946.1 Q6ZN84 CCD81_HUMAN coiled-coil domain containing 81 20 Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535) GATGAAGAAGCAGCGAGACCT 0.517000 0 SO:0001587 stop_gained ENST00000445632.2 0 1 hg19 CCDS53691.1 . . . . . . . . . . C 47 13.881331 0.99768 . . ENSG00000149201 ENST00000354755;ENST00000278487;ENST00000445632;ENST00000528728 . . . 5.69 5.69 0.88448 . 0.208392 0.41500 D 0.000867 . . . . . . 0.80722 D 1 . . . . . . . . . . . . . -12.0404 17.2949 0.87168 0.0:1.0:0.0:0.0 . . . . X 506;331;596;331 . . Q + 1 0 CCDC81 85808712 1.000000 0.71417 1.000000 0.80357 0.972000 0.66771 2.566000 0.45948 2.685000 0.91497 0.555000 0.69702 CAG TCGA-IB-7652-01A-11D-2154-08 CCDC81-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393756.1 1 0 1 63 271 0 147 0 3.214115e-01 0 6 0 147 2 0 0 0 0 0 2 1 1.000000 63 270 0 147 2 -20.000000 1 1 0 0 1 1 2 3 2.011981 0 0.360000 1.990000 0.361150 0.990000 0.820000 1.000000 1.000000 0.975612 0.990000 1 0.930000 1.000000 GPR83 10888 broad.mit.edu 37 11 94134167 94134167 + Missense_Mutation SNP C C A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr11:94134167C>A ENST00000243673.2 - 1 418 c.247G>T c.(247-249)Gtc>Ttc p.V83F GPR83_ENST00000539203.2_Missense_Mutation_p.V83F NM_016540.3 NP_057624.3 Q9NYM4 GPR83_HUMAN G protein-coupled receptor 83 19 Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123) AGTGAGAAGACAATGATGAAG 0.557000 0 SO:0001583 missense ENST00000243673.2 1 1 hg19 CCDS8297.1 . . . . . . . . . . C 14.24 2.475211 0.43942 . . ENSG00000123901 ENST00000243673;ENST00000539203 T;T 0.39997 1.05;1.05 4.84 -4.47 0.03525 . 0.508381 0.21011 N 0.081692 T 0.33673 0.0871 L 0.59436 1.845 0.44702 D 0.997697 B 0.19706 0.038 B 0.17433 0.018 T 0.02774 -1.1112 10 0.46703 T 0.11 . 11.5618 0.50780 0.0:0.4821:0.0:0.5179 . 83 Q9NYM4 GPR83_HUMAN F 83 ENSP00000243673:V83F;ENSP00000441550:V83F ENSP00000243673:V83F V - 1 0 GPR83 93773815 0.059000 0.20769 0.684000 0.30055 0.982000 0.71751 0.089000 0.15002 -1.110000 0.02992 0.455000 0.32223 GTC TCGA-IB-7652-01A-11D-2154-08 GPR83-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396232.1 1 0 1 38 135 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 1.000000 38 134 0 46 2 -20.000000 1 1 0 0 1 1 2 3 2.011981 0 0.360000 1.990000 0.361150 0.990000 0.900000 1.000000 1.000000 0.993773 0.990000 1 0.990000 1.000000 TAS2R42 353164 broad.mit.edu 37 12 11338898 11338898 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr12:11338898G>A ENST00000334266.1 - 1 645 c.646C>T c.(646-648)Ctc>Ttc p.L216F NM_181429.1 NP_852094.1 Q7RTR8 T2R42_HUMAN taste receptor, type 2, member 42 11 OV - Ovarian serous cystadenocarcinoma(49;0.0455) AAGGAACTGAGCTTCAAATTT 0.418000 Melanoma(15;352 722 10077 19546 48810) 0 SO:0001583 missense ENST00000334266.1 1 1 hg19 CCDS31747.1 . . . . . . . . . . G 6.563 0.472116 0.12461 . . ENSG00000186136 ENST00000334266 T 0.00832 5.64 3.46 1.58 0.23477 GPCR, rhodopsin-like superfamily (1); 0.571166 0.14537 N 0.313489 T 0.02304 0.0071 M 0.69248 2.105 0.09310 N 1 P 0.41475 0.751 P 0.50860 0.652 T 0.38650 -0.9651 10 0.49607 T 0.09 . 6.0575 0.19819 0.0:0.2103:0.5725:0.2171 . 216 Q7RTR8 T2R42_HUMAN F 216 ENSP00000334050:L216F ENSP00000334050:L216F L - 1 0 TAS2R42 11230165 0.000000 0.05858 0.250000 0.24296 0.001000 0.01503 0.335000 0.19806 0.302000 0.22762 -1.083000 0.02208 CTC TCGA-IB-7652-01A-11D-2154-08 TAS2R42-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400243.1 1 0 1 83 384 0 92 0 0 0 0 92 2 0 0 0 0 0 2 1 1.000000 82 383 0 91 2 -20.000000 1 1 0 0 1 2 2 4 2.241829 1 0.360000 1.990000 0.429793 0.990000 0.910000 1.000000 1.000000 0.993728 0.990000 1 0.990000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C G C C Valid Somatic Phase_I WXS targeted Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr12:25398285C>G ENST00000256078.4 - 2 97 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|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) CCTACGCCACCAGCTCCAACT 0.348000 G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE) 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 5144 Substitution - Missense(5142)|Insertion - In frame(2) GRCh37 CM076251 KRAS M rs121913530 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 28.6 4.930538 0.92389 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78246 -1.16;-1.16;-1.16;-1.16 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.84893 0.5573 M 0.84082 2.675 0.80722 D 1 P;P 0.43287 0.802;0.741 B;P 0.47941 0.36;0.562 D 0.86658 0.1902 10 0.66056 D 0.02 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN R 12 ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R ENSP00000256078:G12R G - 1 0 KRAS 25289552 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-IB-7652-01A-11D-2154-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 8 85 0 45 1 9.788113e-01 31 45 0 45 2 1 9.999997e-01 69 457 0 403 2 1 0.989988 8 84 0 45 2 -5.897826 1 1 0 0 1 2 2 4 2.241829 1 0.360000 1.990000 0.429793 0.620000 0.280000 1.000000 1.000000 0.671172 0.620000 0 0.420000 1.000000 NTF3 4908 broad.mit.edu 37 12 5603961 5603961 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr12:5603961G>A ENST00000331010.6 + 1 664 c.581G>A c.(580-582)cGa>cAa p.R194Q NTF3_ENST00000535299.1_Intron|NTF3_ENST00000423158.3_Missense_Mutation_p.R207Q NM_002527.4 NP_002518.1 P20783 NTF3_HUMAN neurotrophin 3 p.R194P(1) 22 TATGAAACGCGATGTAAGGAA 0.507000 GBM(194;1104 2182 8339 9578 18493) 1 Substitution - Missense(1) SO:0001583 missense ENST00000331010.6 1 1 hg19 CCDS8538.1 . . . . . . . . . . G 21.2 4.118561 0.77323 . . ENSG00000185652 ENST00000423158;ENST00000331010 T;T 0.68181 -0.31;-0.31 5.45 5.45 0.79879 Nerve growth factor-related (5); 0.049532 0.64402 D 0.000001 T 0.72203 0.3431 M 0.64997 1.995 0.46564 D 0.999104 D;D 0.76494 0.999;0.999 P;P 0.48815 0.591;0.591 T 0.76664 -0.2876 10 0.87932 D 0 -29.9681 18.2818 0.90101 0.0:0.0:1.0:0.0 . 194;207 P20783;B7Z1T5 NTF3_HUMAN;. Q 207;194 ENSP00000397297:R207Q;ENSP00000328738:R194Q ENSP00000328738:R194Q R + 2 0 NTF3 5474222 1.000000 0.71417 0.985000 0.45067 0.987000 0.75469 3.780000 0.55386 2.583000 0.87209 0.650000 0.86243 CGA TCGA-IB-7652-01A-11D-2154-08 NTF3-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000400486.1 1 0 1 47 254 0 114 0 3.072200e-01 0 7 0 114 2 0 0 0 0 0 2 1 1.000000 47 251 0 112 2 -19.999850 1 1 0 0 1 2 2 4 2.241829 1 0.360000 1.990000 0.429793 0.990000 0.740000 1.000000 1.000000 0.952284 0.990000 1 0.860000 1.000000 GDF11 10220 broad.mit.edu 37 12 56142711 56142711 + Missense_Mutation SNP G G C TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G C G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr12:56142711G>C ENST00000257868.5 + 2 824 c.787G>C c.(787-789)Gat>Cat p.D263H NM_005811.3 NP_005802.1 O95390 GDF11_HUMAN growth differentiation factor 11 12 CAACGCCTTTGATCCCAGTGG 0.622000 0 SO:0001583 missense ENST00000257868.5 1 1 hg19 CCDS8891.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 22.9|22.9 4.350476|4.350476 0.82132|0.82132 .|. .|. ENSG00000135414|ENSG00000135414 ENST00000257868|ENST00000546799 T|. 0.66280|. -0.2|. 4.39|4.39 4.39|4.39 0.52855|0.52855 Transforming growth factor-beta, N-terminal (1);|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.74786|0.74786 0.3762|0.3762 M|M 0.76838|0.76838 2.35|2.35 0.80722|0.80722 D|D 1|1 D|. 0.76494|. 0.999|. D|. 0.77004|. 0.989|. T|T 0.76107|0.76107 -0.3080|-0.3080 10|5 0.40728|. T|. 0.16|. -6.1484|-6.1484 14.8487|14.8487 0.70281|0.70281 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 263|. O95390|. GDF11_HUMAN|. H|F 263|235 ENSP00000257868:D263H|. ENSP00000257868:D263H|. D|L +|+ 1|3 0|2 GDF11|GDF11 54428978|54428978 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.998000|0.998000 0.95712|0.95712 9.657000|9.657000 0.98554|0.98554 2.450000|2.450000 0.82876|0.82876 0.555000|0.555000 0.69702|0.69702 GAT|TTG TCGA-IB-7652-01A-11D-2154-08 GDF11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407842.3 1 0 1 20 55 0 52 0 9.990535e-01 1 35 0 52 2 0 0 0 0 0 2 1 0.999999 20 55 0 52 2 -20.000000 1 1 0 0 1 0 2 2 1.857793 1 0.360000 1.990000 0.360000 0.990000 0.990000 1.000000 1.000000 0.997890 0.990000 1 0.990000 1.000000 PDS5B 23047 broad.mit.edu 37 13 33253063 33253063 + Missense_Mutation SNP A A T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr13:33253063A>T ENST00000315596.10 + 10 1240 c.1054A>T c.(1054-1056)Aca>Tca p.T352S NM_015032.3 NP_055847.1 Q9NTI5 PDS5B_HUMAN PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae) 62 Lung SC(185;0.0367) AAAAGACTTAACAGGTACTAT 0.368000 0 SO:0001583 missense ENST00000315596.10 1 1 hg19 CCDS41878.1 . . . . . . . . . . A 26.8 4.770135 0.90108 . . ENSG00000083642 ENST00000315596;ENST00000421084 T 0.67523 -0.27 5.49 5.49 0.81192 Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.71492 0.3346 L 0.54323 1.7 0.80722 D 1 P;B 0.45827 0.867;0.057 P;B 0.53062 0.717;0.058 T 0.67166 -0.5739 10 0.18276 T 0.48 -0.3507 15.5881 0.76502 1.0:0.0:0.0:0.0 . 352;352 Q9NTI5;Q9NTI5-3 PDS5B_HUMAN;. S 352 ENSP00000313851:T352S ENSP00000313851:T352S T + 1 0 PDS5B 32151063 1.000000 0.71417 1.000000 0.80357 0.948000 0.59901 9.191000 0.94940 2.090000 0.63153 0.459000 0.35465 ACA TCGA-IB-7652-01A-11D-2154-08 PDS5B-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044428.3 1 0 1 36 185 0 76 1 9.996982e-01 5 62 0 76 2 0 0 0 0 0 2 1 1.000000 36 184 0 76 2 -20.000000 1 1 0 0 1 1 2 3 2.096311 0 0.360000 1.990000 0.375732 0.940000 0.670000 1.000000 1.000000 0.917059 0.940000 1 0.800000 1.000000 PDS5B 23047 broad.mit.edu 37 13 33332728 33332728 + Silent SNP A A G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr13:33332728A>G ENST00000315596.10 + 28 3432 c.3246A>G c.(3244-3246)acA>acG p.T1082T NM_015032.3 NP_055847.1 Q9NTI5 PDS5B_HUMAN PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae) 62 Lung SC(185;0.0367) AGAGTACTACATACAGTTTGG 0.358000 0 SO:0001819 synonymous_variant ENST00000315596.10 1 1 hg19 CCDS41878.1 TCGA-IB-7652-01A-11D-2154-08 PDS5B-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044428.3 1 0 1 122 575 0 202 1 9.999859e-01 12 64 0 202 2 0 0 0 0 0 2 1 1.000000 122 568 0 198 2 -20.000000 1 1 120812 1 36 1 1 2 3 2.096311 0 0.360000 1.990000 0.375732 0.990000 0.840000 1.000000 1.000000 0.970807 0.990000 1 0.910000 1.000000 AKAP6 9472 broad.mit.edu 37 14 33291794 33291794 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr14:33291794G>A ENST00000280979.4 + 13 4945 c.4775G>A c.(4774-4776)cGa>cAa p.R1592Q AKAP6_ENST00000557272.1_Intron NM_004274.4 NP_004265.3 Q13023 AKAP6_HUMAN A kinase (PRKA) anchor protein 6 122 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) AGCCTCCAGCGAAGCACTTCT 0.433000 Melanoma(49;821 1200 7288 13647 42351) 0 SO:0001583 missense ENST00000280979.4 1 0 hg19 CCDS9644.1 . . . . . . . . . . G 22.9 4.344158 0.82022 . . ENSG00000151320 ENST00000280979 T 0.15834 2.39 5.98 5.98 0.97165 . 0.000000 0.85682 D 0.000000 T 0.45418 0.1341 M 0.71581 2.175 0.80722 D 1 D 0.89917 1.0 D 0.79108 0.992 T 0.25779 -1.0122 10 0.87932 D 0 -9.1931 20.4561 0.99145 0.0:0.0:1.0:0.0 . 1592 Q13023 AKAP6_HUMAN Q 1592 ENSP00000280979:R1592Q ENSP00000280979:R1592Q R + 2 0 AKAP6 32361545 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.335000 0.79234 2.843000 0.97960 0.650000 0.86243 CGA TCGA-IB-7652-01A-11D-2154-08 AKAP6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276617.2 0 0 1 126 536 2 196 0 3.681493e-02 0 2 2 196 2 0 0 0 0 0 2 1 1.000000 126 532 1 194 13 -20.000000 1 1 121406 5 38 1 1 2 3 2.005040 0 0.360000 1.990000 0.361150 0.990000 0.890000 1.000000 1.000000 0.988767 0.990000 1 0.970000 1.000000 ERO1L 30001 broad.mit.edu 37 14 53110325 53110325 + Nonsense_Mutation SNP A A T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr14:53110325A>T ENST00000395686.3 - 16 1593 c.1370T>A c.(1369-1371)tTa>tAa p.L457* RP11-841O20.2_ENST00000554055.1_RNA NM_014584.1 NP_055399.1 Q96HE7 ERO1A_HUMAN ERO1-like (S. cerevisiae) ERO1L/FERMT2(2) 12 Breast(41;0.226) GAAGTTTTCTAATTCTTTCAC 0.303000 0 SO:0001587 stop_gained ENST00000395686.3 0 1 hg19 CCDS9709.1 . . . . . . . . . . A 38 7.030927 0.98013 . . ENSG00000197930 ENST00000395686 . . . 5.54 5.54 0.83059 . 0.224298 0.37906 N 0.001898 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -11.329 15.1606 0.72782 1.0:0.0:0.0:0.0 . . . . X 457 . ENSP00000379042:L457X L - 2 0 ERO1L 52180075 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 8.104000 0.89551 2.230000 0.72887 0.528000 0.53228 TTA TCGA-IB-7652-01A-11D-2154-08 ERO1L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276892.1 0 0 1 4 43 0 22 1 9.999921e-01 201 435 0 22 2 0 0 0 0 0 2 1 0.893282 4 43 0 21 2 -9.338282 1 1 0 0 1 1 2 3 2.005040 0 0.360000 1.990000 0.361150 0.510000 0.180000 1.000000 1.000000 0.541594 0.510000 0 0.310000 0.770000 DAAM1 23002 broad.mit.edu 37 14 59789651 59789651 + Missense_Mutation SNP T T G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 T G T T Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr14:59789651T>G ENST00000395125.1 + 5 505 c.482T>G c.(481-483)aTc>aGc p.I161S DAAM1_ENST00000360909.3_Missense_Mutation_p.I161S|DAAM1_ENST00000351081.1_Missense_Mutation_p.I161S NM_014992.2 NP_055807.1 Q9Y4D1 DAAM1_HUMAN dishevelled associated activator of morphogenesis 1 37 CTATCATGTATCCTCAACTTT 0.418000 0 SO:0001583 missense ENST00000395125.1 1 1 hg19 CCDS9737.1 . . . . . . . . . . T 20.2 3.954100 0.73902 . . ENSG00000100592 ENST00000360909;ENST00000351081;ENST00000358498;ENST00000395125 D;D;D 0.89050 -2.46;-2.46;-2.46 6.16 6.16 0.99307 GTPase-binding/formin homology 3 (1);Armadillo-like helical (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1); 0.000000 0.85682 D 0.000000 D 0.90765 0.7101 L 0.44542 1.39 0.80722 D 1 D;D 0.54207 0.957;0.965 P;P 0.55749 0.677;0.783 D 0.91609 0.5301 10 0.87932 D 0 . 16.8061 0.85666 0.0:0.0:0.0:1.0 . 161;161 Q9Y4D1-2;Q9Y4D1 .;DAAM1_HUMAN S 161 ENSP00000354162:I161S;ENSP00000247170:I161S;ENSP00000378557:I161S ENSP00000247170:I161S I + 2 0 DAAM1 58859404 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 8.040000 0.89188 2.367000 0.80283 0.528000 0.53228 ATC TCGA-IB-7652-01A-11D-2154-08 DAAM1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000276942.2 0 0 1 99 505 0 189 1 9.997456e-01 21 42 0 189 2 0 0 0 0 0 2 1 1.000000 99 500 0 188 2 -20.000000 1 1 0 0 1 1 2 3 2.005040 0 0.360000 1.990000 0.361150 0.900000 0.750000 1.000000 1.000000 0.908312 0.900000 1 0.820000 1.000000 AK7 122481 broad.mit.edu 37 14 96864443 96864443 + Missense_Mutation SNP T T G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr14:96864443T>G ENST00000267584.4 + 2 181 c.137T>G c.(136-138)cTt>cGt p.L46R AK7_ENST00000555570.1_Missense_Mutation_p.L46R NM_152327.3 NP_689540.2 Q96M32 KAD7_HUMAN adenylate kinase 7 31 all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155) GGGGCTTCGCTTGAAGAAATT 0.418000 0 SO:0001583 missense ENST00000267584.4 1 1 hg19 CCDS9945.1 . . . . . . . . . . T 15.78 2.934844 0.52866 . . ENSG00000140057 ENST00000267584;ENST00000555570 T 0.59906 0.23 5.35 5.35 0.76521 . 0.410741 0.24182 N 0.040799 T 0.72771 0.3502 L 0.60455 1.87 0.54753 D 0.99998 B;D 0.89917 0.206;1.0 B;D 0.91635 0.043;0.999 T 0.75651 -0.3244 10 0.87932 D 0 -18.42 14.9864 0.71351 0.0:0.0:0.0:1.0 . 46;46 Q96M32;G3V365 KAD7_HUMAN;. R 46 ENSP00000267584:L46R ENSP00000267584:L46R L + 2 0 AK7 95934196 0.996000 0.38824 0.290000 0.24890 0.970000 0.65996 5.104000 0.64584 2.044000 0.60594 0.402000 0.26972 CTT TCGA-IB-7652-01A-11D-2154-08 AK7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000413340.1 1 0 1 78 487 0 178 1 9.655152e-01 13 23 0 178 2 0 0 0 0 0 2 1 1.000000 77 483 0 174 2 -20.000000 1 1 0 0 1 1 2 3 2.330571 1 0.360000 1.990000 0.454297 0.900000 0.720000 1.000000 1.000000 0.900107 0.900000 1 0.800000 1.000000 LRRK1 79705 broad.mit.edu 37 15 101529485 101529485 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr15:101529485G>A ENST00000388948.3 + 6 1003 c.644G>A c.(643-645)cGg>cAg p.R215Q LRRK1_ENST00000284395.5_Missense_Mutation_p.R212Q|LRRK1_ENST00000532029.2_Missense_Mutation_p.R215Q NM_024652.3 NP_078928.3 leucine-rich repeat kinase 1 72 Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094) OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23) TTCCTGCTTCGGCATGGGGCC 0.483000 0 SO:0001583 missense ENST00000388948.3 1 1 hg19 CCDS42086.1 . . . . . . . . . . G 13.31 2.200254 0.38905 2.5E-4 0.0 ENSG00000154237 ENST00000388948;ENST00000284395;ENST00000532029 T;T;T 0.70164 -0.46;-0.06;-0.46 5.27 4.36 0.52297 Ankyrin repeat-containing domain (3); 0.357809 0.27245 N 0.020253 T 0.43590 0.1254 N 0.11560 0.145 0.27090 N 0.962887 B;B 0.23891 0.0;0.093 B;B 0.17098 0.001;0.017 T 0.27468 -1.0073 10 0.26408 T 0.33 . 9.4521 0.38731 0.1609:0.0:0.8391:0.0 . 215;215 Q38SD2;Q38SD2-2 LRRK1_HUMAN;. Q 215;212;215 ENSP00000373600:R215Q;ENSP00000284395:R212Q;ENSP00000433268:R215Q ENSP00000284395:R212Q R + 2 0 LRRK1 99347008 0.896000 0.30565 0.239000 0.24122 0.988000 0.76386 3.161000 0.50747 1.362000 0.46000 0.650000 0.86243 CGG TCGA-IB-7652-01A-11D-2154-08 LRRK1-003 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000384567.2 1 0 1 98 554 0 248 1 9.931688e-01 7 38 0 248 2 0 0 0 0 0 2 1 1.000000 97 551 0 247 2 -2.774986 1 1 120936 1 37 1 1 2 3 2.394756 1 0.360000 1.990000 0.457627 0.980000 0.810000 1.000000 1.000000 0.958141 0.980000 1 0.890000 1.000000 HOMER2 9455 broad.mit.edu 37 15 83527855 83527855 + Missense_Mutation SNP C C A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr15:83527855C>A ENST00000304231.8 - 5 645 c.453G>T c.(451-453)aaG>aaT p.K151N HOMER2_ENST00000450735.2_Missense_Mutation_p.K140N|HOMER2_ENST00000399166.2_Missense_Mutation_p.K140N|HOMER2_ENST00000426485.1_Missense_Mutation_p.K151N NM_199330.2 NP_955362.1 Q9NSB8 HOME2_HUMAN homer homolog 2 (Drosophila) 9 CGTGAGAGGCCTTTTCATCGT 0.498000 0 SO:0001583 missense ENST00000304231.8 1 1 hg19 CCDS45334.1 . . . . . . . . . . c 19.00 3.741498 0.69304 . . ENSG00000103942 ENST00000304231;ENST00000450735;ENST00000426485;ENST00000399166 T;T;T;T 0.79454 2.15;-1.27;2.42;2.43 5.39 3.46 0.39613 . 0.094216 0.64402 D 0.000001 T 0.77883 0.4197 L 0.60455 1.87 0.39080 D 0.960886 B;D;D;P 0.57899 0.338;0.981;0.96;0.893 B;P;P;P 0.53360 0.187;0.724;0.711;0.486 T 0.75777 -0.3198 10 0.25106 T 0.35 . 9.2512 0.37555 0.0:0.7746:0.0:0.2254 . 140;151;140;151 F8W826;E9PAZ1;Q9NSB8-2;Q9NSB8 .;.;.;HOME2_HUMAN N 151;140;151;140 ENSP00000305632:K151N;ENSP00000407634:K140N;ENSP00000394293:K151N;ENSP00000382119:K140N ENSP00000305632:K151N K - 3 2 HOMER2 81324909 1.000000 0.71417 1.000000 0.80357 0.777000 0.43975 1.921000 0.40035 1.478000 0.48253 0.651000 0.88453 AAG TCGA-IB-7652-01A-11D-2154-08 HOMER2-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000418689.1 1 0 1 134 721 0 251 1 1 16 191 0 251 2 0 0 0 0 0 2 1 1.000000 133 711 0 247 2 -20.000000 1 1 0 0 1 1 2 3 2.394756 1 0.360000 1.990000 0.457627 0.990000 0.860000 1.000000 1.000000 0.980709 0.990000 1 0.940000 1.000000 AGBL1 123624 broad.mit.edu 37 15 86838550 86838550 + Missense_Mutation SNP T T C TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr15:86838550T>C ENST00000441037.2 + 16 2242 c.2147T>C c.(2146-2148)cTc>cCc p.L716P AGBL1_ENST00000421325.2_Missense_Mutation_p.L716P|AGBL1-AS1_ENST00000564487.1_RNA|AGBL1-AS1_ENST00000566878.1_RNA|AGBL1_ENST00000389298.3_Missense_Mutation_p.L447P NM_152336.2 NP_689549.2 Q96MI9 CBPC4_HUMAN ATP/GTP binding protein-like 1 62 CAAGATGTTCTCTGCCAGACG 0.483000 0 SO:0001583 missense ENST00000441037.2 0 1 hg19 CCDS58398.1 . . . . . . . . . . T 20.7 4.040625 0.75732 . . ENSG00000166748 ENST00000441037;ENST00000421325;ENST00000389298 T;T 0.13307 2.6;2.6 5.42 5.42 0.78866 Peptidase M14, carboxypeptidase A (1); 0.000000 0.64402 D 0.000003 T 0.50701 0.1631 H 0.96398 3.815 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 0.998;0.998;1.0 T 0.66500 -0.5908 10 0.87932 D 0 -23.9349 13.6996 0.62599 0.0:0.0:0.0:1.0 . 415;447;716 Q96MI9-2;Q96MI9-3;Q96MI9 .;.;CBPC4_HUMAN P 745;716;447 ENSP00000397173:L716P;ENSP00000373949:L447P ENSP00000373949:L447P L + 2 0 AGBL1 84639554 1.000000 0.71417 0.993000 0.49108 0.773000 0.43773 6.505000 0.73708 2.170000 0.68504 0.528000 0.53228 CTC TCGA-IB-7652-01A-11D-2154-08 AGBL1-001 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000314929.5 0 0 0 10 286 0 121 0 0 0 0 121 2 0 0 0 0 0 2 1 0.996909 10 284 0 120 2 -11.319690 1 1 0 0 1 1 2 3 2.394756 1 0.360000 1.990000 0.457627 0.220000 0.110000 0.390000 0.210000 0.241013 0.220000 0 0.160000 0.310000 CACNG3 10368 broad.mit.edu 37 16 24372859 24372859 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr16:24372859G>A ENST00000005284.3 + 4 1825 c.623G>A c.(622-624)cGa>cAa p.R208Q NM_006539.3 NP_006530.1 O60359 CCG3_HUMAN calcium channel, voltage-dependent, gamma subunit 3 40 CAGCAGTTACGAGCCAAATCC 0.488000 0 SO:0001583 missense ENST00000005284.3 1 1 hg19 CCDS10620.1 . . . . . . . . . . G 32 5.189450 0.94923 . . ENSG00000006116 ENST00000005284 T 0.81163 -1.46 4.96 4.96 0.65561 . 0.000000 0.85682 D 0.000000 D 0.89072 0.6611 M 0.75615 2.305 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 D 0.87820 0.2637 10 0.32370 T 0.25 -7.4112 17.8423 0.88718 0.0:0.0:1.0:0.0 . 208 O60359 CCG3_HUMAN Q 208 ENSP00000005284:R208Q ENSP00000005284:R208Q R + 2 0 CACNG3 24280360 1.000000 0.71417 0.991000 0.47740 0.995000 0.86356 9.476000 0.97823 2.274000 0.75844 0.655000 0.94253 CGA TCGA-IB-7652-01A-11D-2154-08 CACNG3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254548.1 1 0 1 69 610 0 201 0 0 0 0 201 2 0 0 0 0 0 2 1 1.000000 68 606 1 195 13 -3.017764 1 1 121412 1 37 1 1 2 3 2.050207 0 0.360000 1.990000 0.367964 0.570000 0.450000 1.000000 0.570000 0.600385 0.570000 0 0.500000 0.660000 TP53 7157 broad.mit.edu 37 17 7578406 7578406 + Missense_Mutation SNP C C T rs28934578 TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr17:7578406C>T ENST00000269305.4 - 5 713 c.524G>A c.(523-525)cGc>cAc p.R175H TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GTGGGGGCAGCGCCTCACAAC 0.652000 R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY) 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 980 Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3) GRCh37 CM062017|CM951224 TP53 M rs28934578 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . C 31 5.079737 0.94050 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 D;D;D;D;D;D;D;D 0.99889 -7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55 5.41 5.41 0.78517 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.101149 0.64402 D 0.000008 D 0.99908 0.9956 M 0.92784 3.345 0.80722 A 1 D;P;D;D;P;B;D 0.89917 0.999;0.578;1.0;0.998;0.632;0.213;0.999 D;B;D;D;B;B;D 0.91635 0.985;0.26;0.999;0.921;0.378;0.144;0.939 D 0.96278 0.9204 9 0.87932 D 0 -11.8679 17.0767 0.86588 0.0:1.0:0.0:0.0 rs28934578 136;175;175;82;175;175;175 B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. H 175;175;175;175;175;175;164;82;43;82;43 ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H ENSP00000269305:R175H R - 2 0 TP53 7519131 1.000000 0.71417 0.989000 0.46669 0.795000 0.44927 6.042000 0.70996 2.702000 0.92279 0.655000 0.94253 CGC TCGA-IB-7652-01A-11D-2154-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 51 164 1 117 1 1 87 81 1 117 7 1 1 219 657 0 906 2 1 1.000000 51 161 1 114 9 -4.108127 1 1 121412 1 41 1 0 1 1 1.717425 1 0.360000 1.990000 0.236277 0.990000 0.810000 1.000000 1.000000 0.968696 0.990000 1 0.910000 1.000000 DNAH17 8632 broad.mit.edu 37 17 76459132 76459132 + Missense_Mutation SNP A A G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr17:76459132A>G ENST00000585328.1 - 57 9077 c.8953T>C c.(8953-8955)Ttc>Ctc p.F2985L DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Missense_Mutation_p.F2976L NM_173628.3 NP_775899.3 Q9UFH2 DYH17_HUMAN dynein, axonemal, heavy chain 17 116 BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656) TAGGACATGAAGAAGCTGATG 0.542000 0 SO:0001583 missense ENST00000585328.1 1 1 hg19 . . . . . . . . . . A 25.9 4.688192 0.88639 . . ENSG00000187775 ENST00000300671;ENST00000389840 T 0.54071 0.59 4.91 4.91 0.64330 . . . . . T 0.64283 0.2584 M 0.64676 1.99 0.47862 D 0.999534 . . . . . . T 0.67917 -0.5546 7 0.66056 D 0.02 . 14.2019 0.65710 1.0:0.0:0.0:0.0 . . . . L 2985;2976 ENSP00000374490:F2976L ENSP00000300671:F2985L F - 1 0 DNAH17 73970727 1.000000 0.71417 0.940000 0.37924 0.747000 0.42532 8.838000 0.92115 1.847000 0.53656 0.454000 0.30748 TTC TCGA-IB-7652-01A-11D-2154-08 DNAH17-001 PUTATIVE not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000318962.2 1 0 1 46 133 0 64 0 0 0 1 0 64 2 0 0 0 0 0 2 1 1.000000 46 132 0 63 2 -20.000000 1 1 0 0 1 0 1 1 1.683774 1 0.360000 1.990000 0.222924 0.960000 0.800000 1.000000 1.000000 0.950506 0.960000 1 0.890000 1.000000 DNAH17 8632 broad.mit.edu 37 17 76571032 76571032 + Silent SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr17:76571032G>A ENST00000585328.1 - 2 232 c.108C>T c.(106-108)aaC>aaT p.N36N DNAH17_ENST00000389840.5_Silent_p.N36N NM_173628.3 NP_775899.3 Q9UFH2 DYH17_HUMAN dynein, axonemal, heavy chain 17 116 BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656) ACAGGGCCACGTTCTCCTCGG 0.587000 0 SO:0001819 synonymous_variant ENST00000585328.1 1 1 hg19 TCGA-IB-7652-01A-11D-2154-08 DNAH17-001 PUTATIVE not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000318962.2 1 0 0 10 138 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 0.996995 9 137 0 87 2 -3.078173 1 1 121024 17 43 1 0 1 1 1.683774 1 0.360000 1.990000 0.222924 0.310000 0.160000 0.520000 0.300000 0.327691 0.310000 0 0.220000 0.420000 ZNF521 25925 broad.mit.edu 37 18 22805592 22805592 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr18:22805592C>T ENST00000361524.3 - 4 2438 c.2290G>A c.(2290-2292)Gaa>Aaa p.E764K ZNF521_ENST00000538137.2_Missense_Mutation_p.E764K|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Missense_Mutation_p.E544K NM_015461.2 NP_056276.1 Q96K83 ZN521_HUMAN zinc finger protein 521 149 all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991) AAGTCAGTTTCGTTGCGGAAG 0.473000 T PAX5 ALL Dom yes 18 18q11.2 25925 zinc finger protein 521 L 0 SO:0001583 missense ENST00000361524.3 1 1 hg19 CCDS32806.1 . . . . . . . . . . C 10.38 1.334661 0.24253 . . ENSG00000198795 ENST00000361524;ENST00000538137;ENST00000399425 T;T 0.08370 3.1;3.13 6.17 6.17 0.99709 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2); 0.000000 0.85682 D 0.000000 T 0.12135 0.0295 N 0.04116 -0.275 0.53688 D 0.999972 D 0.89917 1.0 D 0.91635 0.999 T 0.41752 -0.9491 10 0.07482 T 0.82 -36.5484 20.8794 0.99867 0.0:1.0:0.0:0.0 . 764 Q96K83 ZN521_HUMAN K 764;798;764 ENSP00000354794:E764K;ENSP00000382352:E764K ENSP00000354794:E764K E - 1 0 ZNF521 21059590 1.000000 0.71417 0.973000 0.42090 0.406000 0.30931 7.487000 0.81328 2.941000 0.99782 0.655000 0.94253 GAA TCGA-IB-7652-01A-11D-2154-08 ZNF521-001 KNOWN overlapping_uORF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000446781.2 1 0 0 28 261 0 98 0 8.805710e-01 0 37 0 98 2 0 0 0 0 0 2 1 1.000000 27 260 0 97 2 -3.221884 1 1 0 0 1 0 1 1 1.639204 1 0.360000 1.990000 0.219512 0.430000 0.300000 0.600000 0.440000 0.448423 0.430000 0 0.360000 0.520000 GALR1 2587 broad.mit.edu 37 18 74962928 74962928 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr18:74962928C>T ENST00000299727.3 + 1 424 c.424C>T c.(424-426)Cgc>Tgc p.R142C NM_001480.3 NP_001471.2 P47211 GALR1_HUMAN galanin receptor 1 24 Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211) GCACTCGCGGCGCTCCTCCTC 0.657000 0 SO:0001583 missense ENST00000299727.3 1 1 hg19 CCDS12012.1 . . . . . . . . . . C 15.65 2.897440 0.52121 . . ENSG00000166573 ENST00000299727 T 0.43294 0.95 4.49 4.49 0.54785 GPCR, rhodopsin-like superfamily (1); 0.053378 0.64402 D 0.000001 T 0.60919 0.2306 M 0.79805 2.47 0.58432 D 0.999997 D 0.65815 0.995 P 0.60345 0.873 T 0.67213 -0.5727 10 0.87932 D 0 . 11.9672 0.53042 0.1737:0.8263:0.0:0.0 . 142 P47211 GALR1_HUMAN C 142 ENSP00000299727:R142C ENSP00000299727:R142C R + 1 0 GALR1 73091916 0.998000 0.40836 1.000000 0.80357 0.380000 0.30137 3.631000 0.54280 2.044000 0.60594 0.591000 0.81541 CGC TCGA-IB-7652-01A-11D-2154-08 GALR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256362.1 1 0 1 54 212 0 102 0 0 0 0 102 2 0 0 0 0 0 2 1 1.000000 54 211 0 100 2 -20.000000 1 1 0 0 1 0 0 0 1.961344 0 0.360000 1.990000 0.345871 0.990000 0.850000 1.000000 1.000000 0.985237 0.990000 1 0.960000 1.000000 COL5A3 50509 broad.mit.edu 37 19 10081324 10081324 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr19:10081324C>T ENST00000264828.3 - 54 3995 c.3910G>A c.(3910-3912)Ggc>Agc p.G1304S NM_015719.3 NP_056534.2 P25940 CO5A3_HUMAN collagen, type V, alpha 3 116 Epithelial(33;7.11e-05) ccgggggcgccgggcTCCCCA 0.607000 0 SO:0001583 missense ENST00000264828.3 0 1 hg19 CCDS12222.1 . . . . . . . . . . c 12.15 1.851005 0.32699 . . ENSG00000080573 ENST00000264828 D 0.99607 -6.27 3.28 3.28 0.37604 . 0.000000 0.64402 U 0.000001 D 0.99651 0.9871 H 0.94658 3.565 0.51482 D 0.999926 D 0.89917 1.0 D 0.85130 0.997 D 0.97697 1.0182 10 0.87932 D 0 . 10.3456 0.43903 0.0:1.0:0.0:0.0 . 1304 P25940 CO5A3_HUMAN S 1304 ENSP00000264828:G1304S ENSP00000264828:G1304S G - 1 0 COL5A3 9942324 0.354000 0.24912 0.334000 0.25495 0.015000 0.08874 2.226000 0.42963 2.126000 0.65437 0.486000 0.48141 GGC TCGA-IB-7652-01A-11D-2154-08 COL5A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000315788.1 1 0 0 5 26 0 20 0 7.303493e-01 0 15 0 20 2 0 0 0 0 0 2 1 0.937878 4 26 0 19 2 -11.583800 1 1 118176 4 26 1 1 2 3 2.079962 0 0.360000 1.990000 0.373532 0.980000 0.390000 1.000000 1.000000 0.861715 0.980000 1 0.640000 1.000000 CACNA1A 773 broad.mit.edu 37 19 13409765 13409765 + Missense_Mutation SNP C C A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr19:13409765C>A ENST00000360228.5 - 19 2681 c.2682G>T c.(2680-2682)gaG>gaT p.E894D CACNA1A_ENST00000573710.2_Missense_Mutation_p.E895D NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2 NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2 O00555 CAC1A_HUMAN calcium channel, voltage-dependent, P/Q type, alpha 1A subunit 42 OV - Ovarian serous cystadenocarcinoma(19;5.07e-21) Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661) CGTAGGGTCCCTCCCGGCTCA 0.771000 0 SO:0001583 missense ENST00000360228.5 1 1 hg19 CCDS45998.1 . . . . . . . . . . C 8.851 0.944677 0.18356 . . ENSG00000141837 ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084 D 0.95918 -3.85 4.22 1.84 0.25277 . 4.895700 0.00541 N 0.000225 D 0.94948 0.8366 L 0.34521 1.04 0.20703 N 0.999864 B;P;D 0.58268 0.0;0.729;0.982 B;B;D 0.67548 0.001;0.21;0.952 D 0.86068 0.1536 10 0.21540 T 0.41 . 2.0266 0.03520 0.2518:0.3677:0.0:0.3805 . 895;898;894 O00555;E9PD31;Q9NS88 CAC1A_HUMAN;.;. D 894;898;895;895 ENSP00000353362:E894D ENSP00000317661:E895D E - 3 2 CACNA1A 13270765 0.044000 0.20184 0.901000 0.35422 0.017000 0.09413 -0.312000 0.08113 0.768000 0.33290 -0.481000 0.04817 GAG TCGA-IB-7652-01A-11D-2154-08 CACNA1A-001 KNOWN non_canonical_U12|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000104062.2 1 0 0 13 48 0 38 0 0 0 1 0 38 2 0 0 0 0 0 2 1 0.999734 13 48 0 37 2 -19.999990 1 1 0 0 1 1 2 3 2.079962 0 0.360000 1.990000 0.373532 0.990000 0.710000 1.000000 1.000000 0.972150 0.990000 1 0.950000 1.000000 TIMM50 92609 broad.mit.edu 37 19 39980444 39980444 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr19:39980444G>A ENST00000607714.1 + 11 1068 c.1046G>A c.(1045-1047)cGc>cAc p.R349H TIMM50_ENST00000314349.4_Missense_Mutation_p.R452H|TIMM50_ENST00000544017.1_Missense_Mutation_p.R236H|TIMM50_ENST00000599794.1_Missense_Mutation_p.R153H Q3ZCQ8 TIM50_HUMAN translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae) p.R452H(1) 14 all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159) Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657) TTGTGGCCTCGCTCCAAACAG 0.617000 1 Substitution - Missense(1) SO:0001583 missense ENST00000607714.1 0 1 hg19 2 9.157509157509158E-4 0 0.0 0 0.0 0 0.0 2 0.002638522427440633 G 18.56 3.650107 0.67472 . . ENSG00000105197 ENST00000314349;ENST00000544017 . . . 5.61 4.58 0.56647 . 0.000000 0.85682 D 0.000000 T 0.66297 0.2775 L 0.47716 1.5 0.53688 D 0.999977 D;D 0.71674 0.996;0.998 P;D 0.63703 0.512;0.917 T 0.65138 -0.6241 8 . . . -17.7449 13.3117 0.60384 0.0775:0.0:0.9225:0.0 . 349;452 Q3ZCQ8;Q3ZCQ8-2 TIM50_HUMAN;. H 452;236 . . R + 2 0 TIMM50 44672284 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 6.227000 0.72282 1.360000 0.45960 0.655000 0.94253 CGC TCGA-IB-7652-01A-11D-2154-08 TIMM50-021 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000470728.1 1 0 0 3 43 0 21 0 9.939711e-01 0 189 0 21 2 0 0 0 0 0 2 1 0.812613 3 43 0 21 2 -4.600715 1 1 121346 30 37 1 1 2 3 2.079962 0 0.360000 1.990000 0.373532 0.440000 0.120000 1.000000 0.360000 0.506552 0.440000 0 0.250000 0.800000 SEMA6B 10501 broad.mit.edu 37 19 4555520 4555520 + Silent SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr19:4555520G>A ENST00000586582.1 - 7 838 c.528C>T c.(526-528)taC>taT p.Y176Y SEMA6B_ENST00000301293.3_Silent_p.Y176Y|SEMA6B_ENST00000586965.1_Silent_p.Y176Y NM_032108.3 NP_115484.2 Q9H3T3 SEM6B_HUMAN sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B 21 Hepatocellular(1079;0.137) GCTTGGGGTCGTACGGGCAGC 0.602000 0 SO:0001819 synonymous_variant ENST00000586582.1 1 1 hg19 CCDS12131.1 TCGA-IB-7652-01A-11D-2154-08 SEMA6B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000458656.2 1 0 1 39 178 0 123 0 9.999966e-01 0 92 0 123 2 0 0 0 0 0 2 1 1.000000 39 178 0 121 2 -20.000000 1 1 0 0 1 1 2 3 2.085608 0 0.360000 1.990000 0.373532 0.990000 0.750000 1.000000 1.000000 0.959431 0.990000 1 0.880000 1.000000 KCNA2 3737 broad.mit.edu 37 1 111147355 111147355 + Missense_Mutation SNP C C A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr1:111147355C>A ENST00000485317.1 - 3 723 c.50G>T c.(49-51)gGg>gTg p.G17V KCNA2_ENST00000440270.1_Missense_Mutation_p.G17V|KCNA2_ENST00000369770.3_Missense_Mutation_p.G17V|KCNA2_ENST00000525120.1_Intron|KCNA2_ENST00000316361.4_Missense_Mutation_p.G17V P16389 KCNA2_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 2 32 all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398) Dalfampridine(DB06637) CTGTGGGTGCCCAGGGAGGGC 0.597000 Pancreas(18;568 735 10587 23710 36357) 0 SO:0001583 missense ENST00000485317.1 1 1 hg19 CCDS827.1 . . . . . . . . . . C 18.50 3.638576 0.67130 . . ENSG00000177301 ENST00000369770;ENST00000485317;ENST00000440270;ENST00000316361 T;D;D;D 0.96334 -1.29;-3.98;-3.98;-3.98 5.76 5.76 0.90799 . 0.000000 0.85682 D 0.000000 D 0.95850 0.8649 L 0.56769 1.78 0.80722 D 1 B;P 0.45011 0.262;0.848 B;P 0.52823 0.101;0.71 D 0.94141 0.7397 10 0.17369 T 0.5 . 19.976 0.97309 0.0:1.0:0.0:0.0 . 17;17 Q86XG6;P16389 .;KCNA2_HUMAN V 17 ENSP00000358785:G17V;ENSP00000433109:G17V;ENSP00000415257:G17V;ENSP00000314520:G17V ENSP00000314520:G17V G - 2 0 KCNA2 110948878 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 7.770000 0.85390 2.713000 0.92767 0.655000 0.94253 GGG TCGA-IB-7652-01A-11D-2154-08 KCNA2-002 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128001.2 1 0 1 150 768 0 396 0 0 0 0 396 2 0 0 0 0 0 2 1 1.000000 147 757 0 386 2 -3.319885 1 1 0 0 1 1 2 3 2.036830 0 0.360000 1.990000 0.366838 0.910000 0.780000 1.000000 1.000000 0.919445 0.910000 1 0.840000 1.000000 VPS13D 55187 broad.mit.edu 37 1 12316444 12316444 + Missense_Mutation SNP G G C TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr1:12316444G>C ENST00000358136.3 + 8 854 c.724G>C c.(724-726)Gtg>Ctg p.V242L VPS13D_ENST00000356315.4_Missense_Mutation_p.V242L NM_015378.2 NP_056193.2 vacuolar protein sorting 13 homolog D (S. cerevisiae) 130 Ovarian(185;0.249) Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) CCTGGAGCCTGTGTTTGCATC 0.542000 0 SO:0001583 missense ENST00000358136.3 1 1 hg19 CCDS30588.1 . . . . . . . . . . G 19.03 3.748117 0.69533 . . ENSG00000048707 ENST00000356315;ENST00000358136 T;T 0.41400 1.0;1.0 5.94 5.03 0.67393 . 0.125158 0.53938 D 0.000060 T 0.37598 0.1009 L 0.50333 1.59 0.80722 D 1 B;B 0.28350 0.208;0.132 B;B 0.30572 0.117;0.055 T 0.26744 -1.0094 10 0.54805 T 0.06 . 9.8912 0.41292 0.1488:0.0:0.8512:0.0 . 242;242 Q5THJ4-2;Q5THJ4 .;VP13D_HUMAN L 242 ENSP00000348666:V242L;ENSP00000350854:V242L ENSP00000348666:V242L V + 1 0 VPS13D 12239031 1.000000 0.71417 0.972000 0.41901 0.972000 0.66771 5.297000 0.65704 2.820000 0.97059 0.650000 0.86243 GTG TCGA-IB-7652-01A-11D-2154-08 VPS13D-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000036897.2 1 0 1 295 671 0 270 1 9.997890e-01 10 21 0 270 2 0 0 0 0 0 2 1 1.000000 292 662 0 267 2 -20.000000 1 1 0 0 1 0 4 4 2.454452 1 0.360000 1.990000 0.504491 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 FLG 2312 broad.mit.edu 37 1 152284997 152284997 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr1:152284997G>A ENST00000368799.1 - 3 2400 c.2365C>T c.(2365-2367)Cgt>Tgt p.R789C FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA NM_002016.1 NP_002007.1 P20930 FILA_HUMAN filaggrin 424 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) GACCCTGAACGTCGAGACCTT 0.567000 Ichthyosis 0 SO:0001583 missense Familial Cancer Database X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris ENST00000368799.1 1 1 hg19 CCDS30860.1 . . . . . . . . . . - 5.373 0.254012 0.10185 . . ENSG00000143631 ENST00000368799 T 0.01725 4.67 2.52 -0.503 0.12000 . . . . . T 0.00906 0.0030 M 0.77820 2.39 0.09310 N 1 D 0.64830 0.994 B 0.40038 0.317 T 0.43245 -0.9403 9 0.62326 D 0.03 . 2.9569 0.05880 0.1583:0.0:0.4366:0.4051 . 789 P20930 FILA_HUMAN C 789 ENSP00000357789:R789C ENSP00000357789:R789C R - 1 0 FLG 150551621 0.000000 0.05858 0.000000 0.03702 0.011000 0.07611 -0.133000 0.10451 -0.248000 0.09583 0.479000 0.44913 CGT TCGA-IB-7652-01A-11D-2154-08 FLG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033742.1 0 0 0 40 1793 0 691 0 0 0 1 0 691 2 0 0 0 0 0 2 1 1.000000 40 1776 0 680 2 -2.753389 1 1 121410 3 39 1 1 2 3 2.070548 0 0.360000 1.990000 0.371316 0.120000 0.080000 1.000000 0.130000 0.196933 0.120000 0 0.100000 0.160000 FMO1 2326 broad.mit.edu 37 1 171254564 171254564 + Nonsense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr1:171254564C>T ENST00000354841.4 + 8 1611 c.1480C>T c.(1480-1482)Cga>Tga p.R494* FMO1_ENST00000402921.2_Nonsense_Mutation_p.R431*|FMO1_ENST00000469112.1_3'UTR|FMO1_ENST00000367750.3_Nonsense_Mutation_p.R494* NM_001282692.1 NP_001269621.1 Q01740 FMO1_HUMAN flavin containing monooxygenase 1 27 all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181) Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582) CCAGTGGGACCGAACATTCAA 0.478000 0 SO:0001587 stop_gained ENST00000354841.4 0 1 hg19 CCDS1294.1 . . . . . . . . . . C 37 6.316156 0.97467 . . ENSG00000010932 ENST00000367750;ENST00000402921;ENST00000354841 . . . 5.61 4.7 0.59300 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -7.1246 9.8702 0.41168 0.139:0.7877:0.0:0.0732 . . . . X 494;431;494 . ENSP00000346901:R494X R + 1 2 FMO1 169521188 0.653000 0.27358 0.971000 0.41717 0.929000 0.56500 1.341000 0.33907 1.372000 0.46190 -0.259000 0.10710 CGA TCGA-IB-7652-01A-11D-2154-08 FMO1-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086212.1 1 0 1 78 339 0 92 0 9.989949e-01 0 47 0 92 2 0 0 0 0 0 2 1 1.000000 78 338 0 92 2 -2.852775 1 1 0 0 1 1 2 3 2.029486 0 0.360000 1.990000 0.365709 0.990000 0.840000 1.000000 1.000000 0.979895 0.990000 1 0.940000 1.000000 ASPM 259266 broad.mit.edu 37 1 197071382 197071382 + Silent SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr1:197071382C>T ENST00000367409.4 - 18 7255 c.6999G>A c.(6997-6999)gaG>gaA p.E2333E ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron NM_018136.4 NP_060606.3 Q8IZT6 ASPM_HUMAN asp (abnormal spindle) homolog, microcephaly associated (Drosophila) 165 CCCTGTGCATCTCTCGCATCC 0.408000 0 SO:0001819 synonymous_variant ENST00000367409.4 1 1 hg19 CCDS1389.1 TCGA-IB-7652-01A-11D-2154-08 ASPM-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000088256.1 0 0 0 116 561 0 195 1 4.743704e-01 2 7 0 195 2 0 0 0 0 0 2 1 1.000000 116 559 0 192 2 -20.000000 1 1 0 0 1 1 2 3 2.011309 0 0.360000 1.990000 0.361150 0.940000 0.790000 1.000000 1.000000 0.941168 0.940000 1 0.870000 1.000000 PCNXL2 80003 broad.mit.edu 37 1 233394271 233394271 + Missense_Mutation SNP G G C TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr1:233394271G>C ENST00000258229.9 - 5 1571 c.1337C>G c.(1336-1338)cCc>cGc p.P446R PCNXL2_ENST00000430153.1_5'UTR NM_014801.3 NP_055616.3 A6NKB5 PCX2_HUMAN pecanex-like 2 (Drosophila) 86 all_cancers(173;0.0347)|Prostate(94;0.137) ATTGCCTTCGGGACAGGGAAC 0.572000 0 SO:0001583 missense ENST00000258229.9 1 1 hg19 CCDS44335.1 . . . . . . . . . . G 10.75 1.439400 0.25900 . . ENSG00000135749 ENST00000258229 T 0.08458 3.09 4.82 4.82 0.62117 . . . . . T 0.06462 0.0166 N 0.19112 0.55 0.23293 N 0.997962 B 0.28713 0.22 B 0.24006 0.05 T 0.33292 -0.9874 9 0.23891 T 0.37 . 13.897 0.63778 0.0:0.0:0.8472:0.1528 . 446 A6NKB5 PCX2_HUMAN R 446 ENSP00000258229:P446R ENSP00000258229:P446R P - 2 0 PCNXL2 231460894 0.205000 0.23458 0.018000 0.16275 0.005000 0.04900 2.254000 0.43214 2.484000 0.83849 0.655000 0.94253 CCC TCGA-IB-7652-01A-11D-2154-08 PCNXL2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000092480.3 1 0 1 106 376 0 211 1 9.985190e-01 11 26 0 211 2 0 0 0 0 0 2 1 1.000000 106 371 0 209 2 -3.658720 1 1 0 0 1 0 0 0 1.987797 0 0.360000 1.990000 0.355359 0.990000 0.990000 1.000000 1.000000 0.999471 0.990000 1 0.990000 1.000000 CSMD2 114784 broad.mit.edu 37 1 34068023 34068023 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr1:34068023C>T ENST00000373380.1 - 22 3495 c.3275G>A c.(3274-3276)cGc>cAc p.R1092H CSMD2_ENST00000373377.1_Missense_Mutation_p.R318H|CSMD2_ENST00000373388.2_Missense_Mutation_p.R318H|CSMD2_ENST00000373381.4_Missense_Mutation_p.R2219H|CSMD2_ENST00000489419.1_5'UTR Q7Z408 CSMD2_HUMAN CUB and Sushi multiple domains 2 246 Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249) GAGGTTGAGGCGGACGCCATG 0.577000 0 SO:0001583 missense ENST00000373380.1 1 1 hg19 . . . . . . . . . . C 11.50 1.657455 0.29425 0.0 1.16E-4 ENSG00000121904 ENST00000373381;ENST00000373380;ENST00000373377;ENST00000373388 T;T;T;T 0.18174 2.23;2.23;2.23;2.23 5.28 -3.3 0.05003 CUB (5); 0.777035 0.12272 N 0.483686 T 0.07773 0.0195 N 0.16478 0.41 0.26223 N 0.979134 B;B;B 0.06786 0.001;0.001;0.001 B;B;B 0.04013 0.001;0.001;0.001 T 0.39375 -0.9617 10 0.18710 T 0.47 . 7.3106 0.26473 0.1403:0.1536:0.0:0.7061 . 1092;2221;2219 Q7Z408-2;Q7Z408;E7EUA6 .;CSMD2_HUMAN;. H 2219;1092;318;318 ENSP00000362479:R2219H;ENSP00000362478:R1092H;ENSP00000362475:R318H;ENSP00000362486:R318H ENSP00000241312:R2221H R - 2 0 CSMD2 33840610 0.246000 0.23909 0.678000 0.29963 0.858000 0.48976 0.231000 0.17872 -0.459000 0.07013 -0.143000 0.13931 CGC TCGA-IB-7652-01A-11D-2154-08 CSMD2-002 KNOWN basic protein_coding protein_coding OTTHUMT00000030635.4 1 0 1 39 177 0 183 0 0 0 1 0 183 2 0 0 0 0 0 2 1 1.000000 38 174 0 182 2 -19.998740 1 1 121412 40 46 1 0 1 1 1.703950 1 0.360000 1.990000 0.219512 0.800000 0.590000 0.980000 0.810000 0.804804 0.800000 0 0.690000 0.910000 ZFYVE9 9372 broad.mit.edu 37 1 52740258 52740258 + Splice_Site SNP T T C TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr1:52740258T>C ENST00000371591.1 + 7 2877 c.e7+2 ZFYVE9_ENST00000287727.3_Splice_Site|ZFYVE9_ENST00000357206.2_Splice_Site NM_004799.2|NM_007324.2 NP_004790.2|NP_015563.2 O95405 ZFYV9_HUMAN zinc finger, FYVE domain containing 9 53 TAAAAGGAGGTAAGTGGACTA 0.398000 0 SO:0001630 splice_region_variant ENST00000371591.1 1 1 hg19 CCDS563.1 . . . . . . . . . . T 14.65 2.598319 0.46318 . . ENSG00000157077 ENST00000357206;ENST00000287727;ENST00000371591 . . . 5.27 4.13 0.48395 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 12.3915 0.55360 0.0:0.0:0.1407:0.8593 . . . . . -1 . . . + . . ZFYVE9 52512846 1.000000 0.71417 0.998000 0.56505 0.451000 0.32288 7.744000 0.85034 0.832000 0.34804 -0.313000 0.08912 . TCGA-IB-7652-01A-11D-2154-08 ZFYVE9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000022083.1 1 0 1 84 400 0 140 0 0 0 0 140 2 0 0 0 0 0 2 1 1.000000 82 399 0 137 2 -20.000000 1 1 0 0 1 1 2 3 2.087080 0 0.360000 1.990000 0.410898 0.990000 0.860000 1.000000 1.000000 0.984885 0.990000 1 0.960000 1.000000 HCK 3055 broad.mit.edu 37 20 30662501 30662501 + Silent SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr20:30662501C>T ENST00000520553.1 + 5 588 c.342C>T c.(340-342)cgC>cgT p.R114R HCK_ENST00000375862.2_Silent_p.R134R|HCK_ENST00000534862.1_Silent_p.R115R|HCK_ENST00000375852.2_Silent_p.R135R|HCK_ENST00000518730.1_Silent_p.R113R|HCK_ENST00000538448.1_Silent_p.R114R NM_001172129.1|NM_001172130.1|NM_001172131.1|NM_002110.3 NP_001165600.1|NP_001165601.1|NP_001165602.1|NP_002101.2 P08631 HCK_HUMAN HCK proto-oncogene, Src family tyrosine kinase 36 UCEC - Uterine corpus endometrioid carcinoma (5;0.0241) Bosutinib(DB06616) ATGTCGCCCGCGTTGACTCTC 0.552000 0 SO:0001819 synonymous_variant ENST00000520553.1 1 1 hg19 CCDS54455.1 TCGA-IB-7652-01A-11D-2154-08 HCK-006 KNOWN NAGNAG_splice_site|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000375751.1 1 0 0 98 489 0 252 0 1 1 134 0 252 2 0 0 0 0 0 2 1 1.000000 98 483 0 249 2 -20.000000 1 1 0 0 1 1 2 3 2.016887 0 0.360000 1.990000 0.362296 0.920000 0.760000 1.000000 1.000000 0.923653 0.920000 1 0.840000 1.000000 CCT8L2 150160 broad.mit.edu 37 22 17073061 17073061 + Missense_Mutation SNP A A T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr22:17073061A>T ENST00000359963.3 - 1 639 c.380T>A c.(379-381)cTg>cAg p.L127Q NM_014406.4 NP_055221.1 Q96SF2 TCPQM_HUMAN chaperonin containing TCP1, subunit 8 (theta)-like 2 67 all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977) all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175) CGGGCGAGGCAGGCCAGCCTT 0.642000 0 SO:0001583 missense ENST00000359963.3 1 1 hg19 CCDS13738.1 . . . . . . . . . . a 11.60 1.688445 0.29962 . . ENSG00000198445 ENST00000359963 T 0.80909 -1.43 2.0 2.0 0.26442 . 0.000000 0.29073 U 0.013223 D 0.86969 0.6061 M 0.80982 2.52 0.34168 D 0.669424 D 0.89917 1.0 D 0.83275 0.996 D 0.87908 0.2695 10 0.87932 D 0 -12.4381 5.9541 0.19263 1.0:0.0:0.0:0.0 . 127 Q96SF2 TCPQM_HUMAN Q 127 ENSP00000353048:L127Q ENSP00000353048:L127Q L - 2 0 CCT8L2 15453061 1.000000 0.71417 0.739000 0.30968 0.152000 0.21847 3.227000 0.51262 0.930000 0.37217 0.324000 0.21423 CTG TCGA-IB-7652-01A-11D-2154-08 CCT8L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000280580.1 1 0 1 39 161 0 103 0 0 0 0 103 2 0 0 0 0 0 2 1 1.000000 38 158 0 100 2 -20.000000 1 1 0 0 1 1 2 3 2.060051 0 0.360000 1.990000 0.370203 0.990000 0.810000 1.000000 1.000000 0.980160 0.990000 1 0.950000 1.000000 CECR2 27443 broad.mit.edu 37 22 18003349 18003349 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr22:18003349G>A ENST00000262608.8 + 8 1037 c.1037G>A c.(1036-1038)cGt>cAt p.R346H CECR2_ENST00000400585.2_Intron|CECR2_ENST00000400573.5_Intron|CECR2_ENST00000342247.5_Missense_Mutation_p.R317H NM_031413.3 NP_113601.2 Q9BXF3 CECR2_HUMAN cat eye syndrome chromosome region, candidate 2 59 all_epithelial(15;0.139) TCGACCAGCCGTCCTGTAGCC 0.448000 0 SO:0001583 missense ENST00000262608.8 1 1 hg19 . . . . . . . . . . G 4.349 0.064200 0.08388 . . ENSG00000099954 ENST00000342247;ENST00000262608 T;T 0.25414 2.08;1.8 3.24 -6.48 0.01896 . . . . . T 0.08403 0.0209 N 0.08118 0 0.09310 N 0.999995 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.26643 -1.0097 8 . . . . 2.4034 0.04407 0.5132:0.1197:0.1998:0.1673 . 387;359 Q9BXF3;Q9BXF3-2 CECR2_HUMAN;. H 317;346 ENSP00000341219:R317H;ENSP00000262608:R346H . R + 2 0 CECR2 16383349 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -3.710000 0.00387 -2.277000 0.00677 -2.302000 0.00260 CGT TCGA-IB-7652-01A-11D-2154-08 CECR2-201 KNOWN basic protein_coding protein_coding 0 0 1 7 42 0 27 0 0 0 0 27 2 0 0 0 0 0 2 1 0.983355 7 42 0 26 2 -6.863299 1 1 120998 4 26 1 1 2 3 2.060051 0 0.360000 1.990000 0.370203 0.850000 0.390000 1.000000 1.000000 0.814269 0.850000 1 0.590000 1.000000 APOL5 80831 broad.mit.edu 37 22 36124922 36124922 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr22:36124922G>A ENST00000249044.2 + 4 1279 c.1279G>A c.(1279-1281)Gcc>Acc p.A427T NM_030642.1 NP_085145.1 Q9BWW9 APOL5_HUMAN apolipoprotein L, 5 19 GGGGAGACAGGCCCCGGGAAG 0.612000 0 SO:0001583 missense ENST00000249044.2 0 1 hg19 CCDS13920.1 . . . . . . . . . . G 18.13 3.555711 0.65425 . . ENSG00000128313 ENST00000249044 T 0.05139 3.49 2.28 1.18 0.20946 . . . . . T 0.03011 0.0089 N 0.08118 0 0.09310 N 1 B 0.20671 0.047 B 0.08055 0.003 T 0.42155 -0.9468 9 0.87932 D 0 . 2.8292 0.05495 0.5743:0.0:0.4257:0.0 . 427 Q9BWW9 APOL5_HUMAN T 427 ENSP00000249044:A427T ENSP00000249044:A427T A + 1 0 APOL5 34454868 0.002000 0.14202 0.057000 0.19452 0.873000 0.50193 1.096000 0.30976 0.380000 0.24823 0.430000 0.28490 GCC TCGA-IB-7652-01A-11D-2154-08 APOL5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318979.1 0 0 0 7 293 0 102 0 0 0 0 102 2 0 0 0 0 0 2 1 0.979500 7 287 0 98 2 -7.534923 1 0 0 0 1 1 2 3 2.060051 0 0.360000 1.990000 0.370203 0.140000 0.050000 1.000000 0.130000 0.210612 0.140000 0 0.090000 0.220000 LRP1B 53353 broad.mit.edu 37 2 141641448 141641448 + Missense_Mutation SNP T T A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr2:141641448T>A ENST00000389484.3 - 25 5078 c.4107A>T c.(4105-4107)agA>agT p.R1369S 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) TTAGTGTAGTTCTTAGGGAGC 0.458000 TSP Lung(27;0.18) Colon(99;50 2074 2507 20106) 0 SO:0001583 missense ENST00000389484.3 1 1 hg19 CCDS2182.1 . . . . . . . . . . T 15.27 2.782993 0.49891 . . ENSG00000168702 ENST00000389484;ENST00000544579;ENST00000434794 D;D 0.97598 -4.45;-4.45 5.64 1.83 0.25207 Six-bladed beta-propeller, TolB-like (1); 0.000000 0.85682 D 0.000000 D 0.98292 0.9434 M 0.92691 3.335 0.46725 D 0.999171 P;D 0.89917 0.771;1.0 P;D 0.87578 0.531;0.998 D 0.96886 0.9649 10 0.66056 D 0.02 . 6.582 0.22600 0.0:0.249:0.119:0.632 . 552;1369 Q96NT6;Q9NZR2 .;LRP1B_HUMAN S 1369;1307;514 ENSP00000374135:R1369S;ENSP00000413239:R514S ENSP00000374135:R1369S R - 3 2 LRP1B 141357918 0.999000 0.42202 0.982000 0.44146 0.896000 0.52359 0.411000 0.21115 0.125000 0.18397 0.533000 0.62120 AGA TCGA-IB-7652-01A-11D-2154-08 LRP1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254736.2 1 0 1 113 548 0 202 0 0 0 1 0 202 2 0 0 0 0 0 2 1 1.000000 113 546 0 200 2 -20.000000 1 1 0 0 1 1 2 3 2.356307 1 0.360000 1.990000 0.457627 0.990000 0.930000 1.000000 1.000000 0.996057 0.990000 1 0.990000 1.000000 SCN1A 6323 broad.mit.edu 37 2 166848439 166848439 + Silent SNP G G A rs121918763 TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr2:166848439G>A ENST00000303395.4 - 26 5345 c.5346C>T c.(5344-5346)atC>atT p.I1782I AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Silent_p.I1771I|SCN1A_ENST00000409050.1_Silent_p.I1754I|SCN1A_ENST00000423058.2_Silent_p.I1782I P35498 SCN1A_HUMAN sodium channel, voltage-gated, type I, alpha subunit 200 Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909) GGATGACCGCGATGTACATGT 0.443000 0 SO:0001819 synonymous_variant ENST00000303395.4 1 1 hg19 CCDS54413.1 TCGA-IB-7652-01A-11D-2154-08 SCN1A-001 KNOWN non_canonical_U12|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000102661.1 0 0 1 190 915 0 279 0 0 0 0 279 2 0 0 0 0 0 2 1 1.000000 174 843 0 337 2 -3.322969 1 1 121412 2 36 1 1 2 3 2.356307 1 0.360000 1.990000 0.457627 0.990000 0.980000 1.000000 1.000000 0.998902 0.990000 1 0.990000 1.000000 MYO3B 140469 broad.mit.edu 37 2 171375968 171375968 + Missense_Mutation SNP C C T rs56052422 by1000genomes TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr2:171375968C>T ENST00000408978.4 + 30 3636 c.3493C>T c.(3493-3495)Cgt>Tgt p.R1165C MYO3B_ENST00000334231.6_Missense_Mutation_p.R1174C|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.R1138C NM_138995.4 NP_620482.3 Q8WXR4 MYO3B_HUMAN myosin IIIB 59 CTCTGTACATCGTAGGAGCCA 0.468000 0 SO:0001583 missense ENST00000408978.4 1 0 hg19 CCDS42773.1 32 0.014652014652014652 14 0.028455284552845527 3 0.008287292817679558 9 0.015734265734265736 6 0.0079155672823219 C 12.17 1.856140 0.32791 0.029718 0.004725 ENSG00000071909 ENST00000409044;ENST00000408978;ENST00000317915;ENST00000334231 T;T;T 0.78707 -1.2;-1.16;-1.16 3.82 3.82 0.43975 . 1.065760 0.07515 U 0.909616 T 0.37433 0.1003 N 0.08118 0 0.09310 N 1 P;P;P 0.49358 0.923;0.825;0.733 B;B;B 0.40101 0.319;0.121;0.083 T 0.49597 -0.8923 10 0.66056 D 0.02 . 11.3838 0.49773 0.0:1.0:0.0:0.0 rs56052422 1165;1138;1165 Q8WXR4-5;Q8WXR4-4;Q8WXR4 .;.;MYO3B_HUMAN C 1138;1165;1164;1174 ENSP00000386497:R1138C;ENSP00000386213:R1165C;ENSP00000335100:R1174C ENSP00000314213:R1164C R + 1 0 MYO3B 171084214 0.000000 0.05858 0.003000 0.11579 0.006000 0.05464 0.016000 0.13377 2.120000 0.65058 0.446000 0.29264 CGT TCGA-IB-7652-01A-11D-2154-08 MYO3B-004 NOVEL basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000333410.1 0 0 1 25 235 0 82 0 1.011061e-02 0 2 0 82 2 0 0 0 0 0 2 1 1.000000 25 233 0 81 2 -3.017737 1 1 120846 1766 62 1 1 2 3 2.356307 1 0.360000 1.990000 0.457627 0.630000 0.420000 0.880000 0.630000 0.647377 0.630000 0 0.520000 0.760000 HECW2 57520 broad.mit.edu 37 2 197208385 197208385 + Missense_Mutation SNP C C G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr2:197208385C>G ENST00000260983.3 - 3 578 c.396G>C c.(394-396)atG>atC p.M132I HECW2_ENST00000409111.1_5'UTR NM_020760.1 NP_065811.1 Q9P2P5 HECW2_HUMAN HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 113 ACTTACGTTCCATGAAATAGG 0.358000 0 SO:0001583 missense ENST00000260983.3 1 1 hg19 CCDS33354.1 . . . . . . . . . . C 15.84 2.953035 0.53293 . . ENSG00000138411 ENST00000260983;ENST00000452031 T 0.31247 1.5 6.06 6.06 0.98353 . 0.046101 0.85682 D 0.000000 T 0.31358 0.0794 L 0.54323 1.7 0.50171 D 0.99985 B 0.12013 0.005 B 0.15484 0.013 T 0.02533 -1.1145 10 0.37606 T 0.19 . 14.2555 0.66048 0.1491:0.8509:0.0:0.0 . 132 Q9P2P5 HECW2_HUMAN I 132 ENSP00000260983:M132I ENSP00000260983:M132I M - 3 0 HECW2 196916630 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 4.483000 0.60264 2.882000 0.98803 0.655000 0.94253 ATG TCGA-IB-7652-01A-11D-2154-08 HECW2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335199.3 1 0 0 80 1028 0 346 0 2.714016e-01 0 14 0 346 2 0 0 0 0 0 2 1 1.000000 78 1020 0 340 2 -14.217010 1 1 0 0 1 0 0 0 1.973393 0 0.360000 1.990000 0.348269 0.390000 0.310000 0.480000 0.400000 0.397439 0.390000 0 0.340000 0.440000 ASB1 51665 broad.mit.edu 37 2 239342283 239342283 + Nonsense_Mutation SNP C C G rs140110697 TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr2:239342283C>G ENST00000264607.4 + 2 385 c.138C>G c.(136-138)taC>taG p.Y46* ASB1_ENST00000409297.1_Nonsense_Mutation_p.Y46*|ASB1_ENST00000469885.1_3'UTR NM_001040445.1 NP_001035535.1 Q9Y576 ASB1_HUMAN ankyrin repeat and SOCS box containing 1 8 all_epithelial(40;2.65e-14)|Breast(86;7.61e-05)|Renal(207;0.00183)|all_lung(227;0.0283)|Ovarian(221;0.0365)|Lung NSC(271;0.0941)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244) ATGCAGCTTACGTCGGGGACC 0.597000 0 SO:0001587 stop_gained ENST00000264607.4 0 1 hg19 CCDS33416.1 . . . . . . . . . . C 35 5.436599 0.96168 . . ENSG00000065802 ENST00000264607;ENST00000409297 . . . 5.49 0.519 0.17035 . 0.253973 0.41823 D 0.000807 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 9.4737 0.38858 0.0:0.574:0.0:0.426 . . . . X 46 . ENSP00000264607:Y46X Y + 3 2 ASB1 239007022 0.656000 0.27385 0.998000 0.56505 0.974000 0.67602 -0.326000 0.07965 0.037000 0.15575 -0.258000 0.10820 TAC TCGA-IB-7652-01A-11D-2154-08 ASB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000328294.1 0 0 0 6 227 0 85 0 3.184728e-01 0 39 0 85 2 0 0 0 0 0 2 1 0.963155 6 222 0 84 2 -7.381409 1 1 0 0 1 1 2 3 2.316627 1 0.360000 1.990000 0.455967 0.180000 0.070000 0.380000 0.170000 0.201584 0.180000 0 0.110000 0.270000 KIAA1524 57650 broad.mit.edu 37 3 108270112 108270112 + Missense_Mutation SNP C C G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr3:108270112C>G ENST00000295746.8 - 21 2678 c.2602G>C c.(2602-2604)Gag>Cag p.E868Q KIAA1524_ENST00000491772.1_Missense_Mutation_p.E709Q NM_020890.2 NP_065941.2 Q8TCG1 CIP2A_HUMAN KIAA1524 38 ACCAAGGACTCTTTCTCTTCC 0.418000 0 SO:0001583 missense ENST00000295746.8 1 1 hg19 CCDS33812.1 . . . . . . . . . . C 29.5 5.013192 0.93346 . . ENSG00000163507 ENST00000491772;ENST00000295746 T;T 0.55052 0.54;0.54 5.53 5.53 0.82687 . 0.000000 0.85682 D 0.000000 T 0.73055 0.3538 M 0.69823 2.125 0.80722 D 1 D 0.89917 1.0 D 0.74674 0.984 T 0.74910 -0.3503 10 0.66056 D 0.02 -12.9123 19.4773 0.94994 0.0:1.0:0.0:0.0 . 868 Q8TCG1 CIP2A_HUMAN Q 709;868 ENSP00000419487:E709Q;ENSP00000295746:E868Q ENSP00000295746:E868Q E - 1 0 KIAA1524 109752802 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.308000 0.65768 2.593000 0.87608 0.655000 0.94253 GAG TCGA-IB-7652-01A-11D-2154-08 KIAA1524-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353975.2 1 0 1 45 143 0 81 1 9.770954e-01 6 16 0 81 2 0 0 0 0 0 2 1 1.000000 45 142 0 79 2 -4.399536 1 1 0 0 1 0 0 0 1.994361 0 0.360000 1.990000 0.357688 0.990000 0.990000 1.000000 1.000000 0.998848 0.990000 1 0.990000 1.000000 DNAJC13 23317 broad.mit.edu 37 3 132209833 132209833 + Missense_Mutation SNP G G T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr3:132209833G>T ENST00000260818.6 + 32 3809 c.3561G>T c.(3559-3561)aaG>aaT p.K1187N NM_015268.3 NP_056083.3 O75165 DJC13_HUMAN DnaJ (Hsp40) homolog, subfamily C, member 13 34 AACCTGAAAAGTTTTCTGAGA 0.323000 0 SO:0001583 missense ENST00000260818.6 1 1 hg19 CCDS33857.1 . . . . . . . . . . G 17.35 3.367442 0.61513 . . ENSG00000138246 ENST00000260818 T 0.19669 2.13 5.13 3.06 0.35304 Armadillo-type fold (1); 0.072208 0.56097 D 0.000039 T 0.27832 0.0685 M 0.72576 2.205 0.50467 D 0.999872 P 0.52577 0.954 P 0.47981 0.563 T 0.03829 -1.1000 10 0.46703 T 0.11 . 8.6112 0.33804 0.2823:0.0:0.7177:0.0 . 1187 O75165 DJC13_HUMAN N 1187 ENSP00000260818:K1187N ENSP00000260818:K1187N K + 3 2 DNAJC13 133692523 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 1.013000 0.29937 1.166000 0.42689 0.591000 0.81541 AAG TCGA-IB-7652-01A-11D-2154-08 DNAJC13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356807.2 1 0 1 15 200 0 91 1 8.936727e-01 9 46 0 91 2 0 0 0 0 0 2 1 0.999881 15 199 0 90 2 -19.503150 1 1 0 0 1 1 2 3 2.033691 0 0.360000 1.990000 0.365709 0.400000 0.230000 1.000000 0.390000 0.432400 0.400000 0 0.300000 0.520000 A4GNT 51146 broad.mit.edu 37 3 137849964 137849964 + Silent SNP G G C TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr3:137849964G>C ENST00000236709.3 - 2 336 c.135C>G c.(133-135)ctC>ctG p.L45L NM_016161.2 NP_057245.1 Q9UNA3 A4GCT_HUMAN alpha-1,4-N-acetylglucosaminyltransferase 16 TGTGGCTCAGGAGGGCTTCCA 0.537000 0 SO:0001819 synonymous_variant ENST00000236709.3 1 1 hg19 CCDS3097.1 TCGA-IB-7652-01A-11D-2154-08 A4GNT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357557.1 1 0 1 68 348 0 120 0 7.299940e-01 0 15 0 120 2 0 0 0 0 0 2 1 1.000000 68 345 0 118 2 -20.000000 1 1 121412 1 34 1 1 2 3 2.033691 0 0.360000 1.990000 0.365709 0.910000 0.720000 1.000000 1.000000 0.911537 0.910000 1 0.810000 1.000000 MUC4 4585 broad.mit.edu 37 3 195517059 195517059 + Silent SNP C C A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr3:195517059C>A ENST00000463781.3 - 2 1851 c.1392G>T c.(1390-1392)cgG>cgT p.R464R MUC4_ENST00000475231.1_Silent_p.R464R|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron NM_018406.6 NP_060876.5 Q99102 MUC4_HUMAN mucin 4, cell surface associated 51 all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) TCTCATGAGGCCGTCCTGTGG 0.493000 0 SO:0001819 synonymous_variant ENST00000463781.3 0 1 hg19 CCDS54700.1 TCGA-IB-7652-01A-11D-2154-08 MUC4-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000324081.6 0 0 0 15 757 0 360 0 0 0 0 360 2 0 0 0 0 0 2 1 0.999863 15 751 0 357 2 -2.560979 1 1 0 0 1 0 1 1 1.665638 1 0.360000 1.990000 0.219512 0.080000 0.040000 0.140000 0.090000 0.093730 0.080000 0 0.060000 0.120000 FLNB 2317 broad.mit.edu 37 3 58107201 58107201 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr3:58107201G>A ENST00000295956.4 + 20 3262 c.3097G>A c.(3097-3099)Gag>Aag p.E1033K FLNB_ENST00000493452.1_Missense_Mutation_p.E864K|FLNB_ENST00000357272.4_Missense_Mutation_p.E1033K|FLNB_ENST00000429972.2_Missense_Mutation_p.E1033K|FLNB_ENST00000490882.1_Missense_Mutation_p.E1033K|FLNB_ENST00000358537.3_Missense_Mutation_p.E1033K|FLNB_ENST00000419752.2_Missense_Mutation_p.E864K|FLNB_ENST00000348383.5_Missense_Mutation_p.E1033K NM_001457.3 NP_001448.2 O75369 FLNB_HUMAN filamin B, beta 120 CTACACAGTGGAGGCCTCGCT 0.567000 0 SO:0001583 missense ENST00000295956.4 1 1 hg19 CCDS2885.1 . . . . . . . . . . G 27.7 4.855482 0.91355 . . ENSG00000136068 ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752 T;T;T;T;T;T;T;T 0.39592 1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07 5.87 5.87 0.94306 Immunoglobulin E-set (2);Immunoglobulin-like fold (1); 0.136651 0.64402 D 0.000004 T 0.49660 0.1570 L 0.35723 1.085 0.80722 D 1 P;P;B;B;P;P 0.48640 0.913;0.893;0.415;0.121;0.774;0.774 P;P;B;B;B;B 0.52217 0.693;0.493;0.299;0.246;0.345;0.345 T 0.36480 -0.9746 10 0.46703 T 0.11 . 20.2191 0.98319 0.0:0.0:1.0:0.0 . 1033;1033;864;864;1033;1033 O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369 .;.;.;.;.;FLNB_HUMAN K 1033;1033;1033;1033;1033;1033;864;864 ENSP00000295956:E1033K;ENSP00000420213:E1033K;ENSP00000351339:E1033K;ENSP00000415599:E1033K;ENSP00000232447:E1033K;ENSP00000349819:E1033K;ENSP00000418510:E864K;ENSP00000414532:E864K ENSP00000295956:E1033K E + 1 0 FLNB 58082241 1.000000 0.71417 0.999000 0.59377 0.903000 0.53119 7.890000 0.87313 2.780000 0.95670 0.655000 0.94253 GAG TCGA-IB-7652-01A-11D-2154-08 FLNB-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000353569.1 1 0 1 120 537 0 302 1 1 207 239 0 302 2 0 0 0 0 0 2 1 1.000000 118 535 0 294 2 -20.000000 1 1 0 0 1 0 0 0 1.994361 0 0.360000 1.990000 0.357688 0.990000 0.840000 1.000000 1.000000 0.973170 0.990000 1 0.920000 1.000000 FLNB 2317 broad.mit.edu 37 3 58134060 58134060 + Nonsense_Mutation SNP T T A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr3:58134060T>A ENST00000295956.4 + 35 6021 c.5856T>A c.(5854-5856)tgT>tgA p.C1952* FLNB_ENST00000493452.1_Nonsense_Mutation_p.C1759*|FLNB_ENST00000357272.4_Nonsense_Mutation_p.C1952*|FLNB_ENST00000429972.2_Nonsense_Mutation_p.C1941*|FLNB_ENST00000490882.1_Nonsense_Mutation_p.C1983*|FLNB_ENST00000358537.3_Nonsense_Mutation_p.C1928*|FLNB_ENST00000419752.2_Nonsense_Mutation_p.C1772*|FLNB_ENST00000348383.5_Nonsense_Mutation_p.C1952* NM_001457.3 NP_001448.2 O75369 FLNB_HUMAN filamin B, beta 120 ACGAGCCCTGTCTCCTGAAGA 0.602000 0 SO:0001587 stop_gained ENST00000295956.4 0 1 hg19 CCDS2885.1 . . . . . . . . . . T 46 12.749215 0.99693 . . ENSG00000136068 ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752 . . . 6.17 -0.893 0.10567 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 12.3262 0.55011 0.0:0.4478:0.0:0.5522 . . . . X 1952;1983;1928;1941;1952;1952;1759;1772 . ENSP00000295956:C1952X C + 3 2 FLNB 58109100 0.944000 0.32072 0.994000 0.49952 0.995000 0.86356 0.021000 0.13489 -0.232000 0.09811 0.533000 0.62120 TGT TCGA-IB-7652-01A-11D-2154-08 FLNB-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000353569.1 1 0 0 11 123 0 51 1 9.999999e-01 19 447 0 51 2 0 0 0 0 0 2 1 0.998501 11 122 0 51 2 -16.723850 1 1 0 0 1 0 0 0 1.994361 0 0.360000 1.990000 0.357688 0.460000 0.240000 0.750000 0.450000 0.481896 0.460000 0 0.340000 0.610000 FAT4 79633 broad.mit.edu 37 4 126371342 126371342 + Missense_Mutation SNP C C G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr4:126371342C>G ENST00000394329.3 + 9 9184 c.9171C>G c.(9169-9171)atC>atG p.I3057M FAT4_ENST00000335110.5_Missense_Mutation_p.I1355M NM_024582.4 NP_078858.4 Q6V0I7 FAT4_HUMAN FAT atypical cadherin 4 355 ACTTTTTTATCACAGTCACTG 0.398000 0 SO:0001583 missense ENST00000394329.3 0 1 hg19 CCDS3732.3 . . . . . . . . . . C 2.000 -0.429562 0.04701 . . ENSG00000196159 ENST00000394329;ENST00000335110 T;T 0.55760 0.5;1.95 5.53 3.77 0.43336 Cadherin (4);Cadherin-like (1); 0.250386 0.20094 U 0.099377 T 0.36082 0.0954 L 0.34521 1.04 0.31081 N 0.711959 B;B;B 0.20459 0.006;0.045;0.016 B;B;B 0.23716 0.005;0.048;0.019 T 0.41251 -0.9519 10 0.72032 D 0.01 . 1.0954 0.01672 0.1406:0.3872:0.2043:0.2679 . 1355;3057;3057 Q6V0I7-2;Q6V0I7;Q6V0I7-3 .;FAT4_HUMAN;. M 3057;1355 ENSP00000377862:I3057M;ENSP00000335169:I1355M ENSP00000335169:I1355M I + 3 3 FAT4 126590792 0.985000 0.35326 0.990000 0.47175 0.286000 0.27126 0.286000 0.18902 1.340000 0.45581 0.655000 0.94253 ATC TCGA-IB-7652-01A-11D-2154-08 FAT4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256765.2 0 0 0 8 397 0 127 0 5.662453e-02 0 17 0 127 2 0 0 0 0 0 2 1 0.989422 8 396 0 127 2 -3.997423 1 1 0 0 1 1 2 3 2.006995 0 0.360000 1.990000 0.361150 0.110000 0.040000 0.210000 0.110000 0.122536 0.110000 0 0.070000 0.160000 PCDH10 57575 broad.mit.edu 37 4 134072871 134072871 + Missense_Mutation SNP T T G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr4:134072871T>G ENST00000264360.5 + 1 2402 c.1576T>G c.(1576-1578)Tac>Gac p.Y526D RP11-9G1.3_ENST00000505289.1_lincRNA NM_032961.1 NP_116586.1 Q9P2E7 PCD10_HUMAN protocadherin 10 136 CGGCTACTTGTACGCCCTGCG 0.597000 0 SO:0001583 missense ENST00000264360.5 1 1 hg19 CCDS34063.1 . . . . . . . . . . T 17.59 3.427385 0.62733 . . ENSG00000138650 ENST00000264360;ENST00000394248 T 0.51574 0.7 4.51 4.51 0.55191 Cadherin (5);Cadherin-like (1); 0.000000 0.39146 N 0.001442 T 0.68026 0.2956 M 0.76838 2.35 0.80722 D 1 D;D 0.89917 1.0;0.996 D;D 0.91635 0.999;0.985 T 0.73020 -0.4114 10 0.87932 D 0 . 12.9618 0.58462 0.0:0.0:0.0:1.0 . 526;526 Q9P2E7;Q96SF0 PCD10_HUMAN;. D 526 ENSP00000264360:Y526D ENSP00000264360:Y526D Y + 1 0 PCDH10 134292321 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.836000 0.86788 1.889000 0.54706 0.533000 0.62120 TAC TCGA-IB-7652-01A-11D-2154-08 PCDH10-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000364457.2 1 0 1 80 407 0 176 0 7.378839e-02 0 3 0 176 2 0 0 0 0 0 2 1 1.000000 79 404 0 172 2 -20.000000 1 1 0 0 1 1 2 3 2.006995 0 0.360000 1.990000 0.361150 0.910000 0.730000 1.000000 1.000000 0.908113 0.910000 1 0.820000 1.000000 GRSF1 2926 broad.mit.edu 37 4 71691088 71691088 + Missense_Mutation SNP T T C TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr4:71691088T>C ENST00000254799.6 - 8 1435 c.1318A>G c.(1318-1320)Act>Gct p.T440A GRSF1_ENST00000508091.1_Intron|GRSF1_ENST00000439371.1_Missense_Mutation_p.T278A|GRSF1_ENST00000545193.1_Missense_Mutation_p.T322A|GRSF1_ENST00000502323.1_Missense_Mutation_p.T278A NM_002092.3 NP_002083 Q12849 GRSF1_HUMAN G-rich RNA sequence binding factor 1 17 all_hematologic(202;0.21) Lung(101;0.235) GCTTCTCCAGTGGCCTTCCCA 0.488000 0 SO:0001583 missense ENST00000254799.6 1 1 hg19 CCDS47069.1 . . . . . . . . . . T 25.7 4.665232 0.88251 . . ENSG00000132463 ENST00000254799;ENST00000439371;ENST00000540657;ENST00000499044;ENST00000502323;ENST00000545193 T;T;T;T;T 0.09073 3.02;3.02;3.02;3.02;3.02 6.07 4.88 0.63580 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2); 0.044997 0.85682 D 0.000000 T 0.26159 0.0638 M 0.72576 2.205 0.53005 D 0.999964 D;P 0.60160 0.987;0.581 D;P 0.70016 0.967;0.702 T 0.00660 -1.1622 10 0.62326 D 0.03 -9.2706 12.0784 0.53657 0.0:0.0668:0.0:0.9332 . 353;440 B7Z5F9;Q12849 .;GRSF1_HUMAN A 440;278;372;413;278;322 ENSP00000254799:T440A;ENSP00000389219:T278A;ENSP00000427354:T413A;ENSP00000425430:T278A;ENSP00000443380:T322A ENSP00000254799:T440A T - 1 0 GRSF1 71909952 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 5.967000 0.70403 1.114000 0.41781 0.533000 0.62120 ACT TCGA-IB-7652-01A-11D-2154-08 GRSF1-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000362642.1 0 0 1 23 108 1 51 1 9.999837e-01 97 359 1 51 26 0 0 0 0 0 2 1 0.995220 23 107 1 50 10 -15.100990 1 1 0 0 1 1 2 3 2.006995 0 0.360000 1.990000 0.361150 0.970000 0.650000 1.000000 1.000000 0.922508 0.970000 1 0.800000 1.000000 PTPN13 5783 broad.mit.edu 37 4 87684337 87684337 + Silent SNP A A T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 A T A A Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr4:87684337A>T ENST00000411767.2 + 24 4074 c.4011A>T c.(4009-4011)ccA>ccT p.P1337P PTPN13_ENST00000316707.6_Silent_p.P1146P|PTPN13_ENST00000511467.1_Silent_p.P1337P|PTPN13_ENST00000436978.1_Silent_p.P1337P|PTPN13_ENST00000427191.2_Silent_p.P1318P Q12923 PTN13_HUMAN protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase) 93 Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242) ATCAAACACCAAAACAGGCAT 0.363000 0 SO:0001819 synonymous_variant ENST00000411767.2 1 1 hg19 CCDS47094.1 TCGA-IB-7652-01A-11D-2154-08 PTPN13-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000363191.1 1 0 1 94 465 0 221 0 9.950115e-01 0 42 0 221 2 0 0 0 0 0 2 1 1.000000 94 463 0 220 2 -20.000000 1 1 0 0 1 1 2 3 2.006995 0 0.360000 1.990000 0.361150 0.930000 0.760000 1.000000 1.000000 0.926182 0.930000 1 0.840000 1.000000 SLCO6A1 133482 broad.mit.edu 37 5 101748803 101748803 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:101748803C>T ENST00000506729.1 - 9 1688 c.1517G>A c.(1516-1518)tGt>tAt p.C506Y SLCO6A1_ENST00000379807.3_Missense_Mutation_p.C506Y|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.C253Y|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.C253Y|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.C444Y Q86UG4 SO6A1_HUMAN solute carrier organic anion transporter family, member 6A1 p.C506S(1) 60 all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323) TGAGCATCTACATTTTTCATT 0.333000 1 Substitution - Missense(1) SO:0001583 missense ENST00000506729.1 1 1 hg19 CCDS34206.1 . . . . . . . . . . C 16.28 3.077737 0.55753 . . ENSG00000205359 ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810 T;T;T;T;T 0.65364 -0.15;-0.15;-0.15;-0.15;-0.15 5.25 5.25 0.73442 Major facilitator superfamily domain, general substrate transporter (1); 0.000000 0.64402 D 0.000001 D 0.86264 0.5891 H 0.97440 4.005 0.50313 D 0.999866 P;D;D 0.89917 0.933;1.0;0.957 P;D;P 0.87578 0.479;0.998;0.688 D 0.90071 0.4163 10 0.56958 D 0.05 . 15.8626 0.79038 0.0:1.0:0.0:0.0 . 444;253;506 Q86UG4-2;C9J020;Q86UG4 .;.;SO6A1_HUMAN Y 506;506;444;253;253 ENSP00000421339:C506Y;ENSP00000369135:C506Y;ENSP00000373671:C444Y;ENSP00000421990:C253Y;ENSP00000369138:C253Y ENSP00000369135:C506Y C - 2 0 SLCO6A1 101776702 0.999000 0.42202 0.564000 0.28396 0.046000 0.14306 4.586000 0.60984 2.720000 0.93068 0.655000 0.94253 TGT TCGA-IB-7652-01A-11D-2154-08 SLCO6A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000370335.1 1 0 1 32 159 0 90 0 0 0 0 90 2 0 0 0 0 0 2 1 0.999975 32 159 1 89 9 -18.282950 1 1 0 0 1 0 1 1 1.626977 1 0.360000 1.990000 0.219512 0.740000 0.530000 0.960000 0.750000 0.755245 0.740000 0 0.630000 0.870000 TERT 7015 broad.mit.edu 37 5 1253880 1253880 + Missense_Mutation SNP G G T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G T G G Valid Somatic Phase_I WXS targeted Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:1253880G>T ENST00000310581.5 - 16 3419 c.3362C>A c.(3361-3363)cCg>cAg p.P1121Q TERT_ENST00000296820.5_3'UTR|TERT_ENST00000334602.6_Missense_Mutation_p.P1058Q NM_001193376.1|NM_198253.2 NP_001180305.1|NP_937983.2 O14746 TERT_HUMAN telomerase reverse transcriptase 41 all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10) Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185) Zidovudine(DB00495) GGGCAGTGCCGGGTTGGCTGC 0.662000 TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis 0 SO:0001583 missense Familial Cancer Database ;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita ENST00000310581.5 1 1 hg19 CCDS3861.2 . . . . . . . . . . g 16.53 3.147750 0.57151 . . ENSG00000164362 ENST00000310581;ENST00000334602 D;D 0.97870 -4.58;-4.31 3.83 3.83 0.44106 . 0.000000 0.85682 D 0.000000 D 0.98381 0.9462 M 0.80183 2.485 0.58432 D 0.999999 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.995 D 0.98501 1.0614 10 0.66056 D 0.02 -17.5136 11.4366 0.50072 0.0:0.0:1.0:0.0 . 1058;1121 O14746-3;O14746 .;TERT_HUMAN Q 1121;1058 ENSP00000309572:P1121Q;ENSP00000334346:P1058Q ENSP00000309572:P1121Q P - 2 0 TERT 1306880 0.987000 0.35691 0.320000 0.25306 0.012000 0.07955 2.740000 0.47418 2.134000 0.65973 0.561000 0.74099 CCG TCGA-IB-7652-01A-11D-2154-08 TERT-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000206729.2 1 0 1 17 69 0 40 0 0 0 0 40 2 1 1 222 1124 1 1002 7 1 0.999982 17 69 0 39 2 -3.126970 1 1 0 0 1 0 0 0 1.992041 0 0.360000 1.990000 0.357688 0.990000 0.680000 1.000000 1.000000 0.954283 0.990000 1 0.870000 1.000000 FSTL4 23105 broad.mit.edu 37 5 132535363 132535363 + Silent SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:132535363G>A ENST00000265342.7 - 16 2202 c.1953C>T c.(1951-1953)caC>caT p.H651H CTB-49A3.2_ENST00000509051.1_RNA NM_015082.1 NP_055897.1 Q6MZW2 FSTL4_HUMAN follistatin-like 4 23 all_cancers(142;0.244) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) AGCCGCCCAGGTGGGTGTGTG 0.622000 0 SO:0001819 synonymous_variant ENST00000265342.7 1 1 hg19 CCDS34238.1 TCGA-IB-7652-01A-11D-2154-08 FSTL4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000370212.1 1 0 0 38 151 0 83 0 3.547850e-01 1 5 0 83 2 0 0 0 0 0 2 1 1.000000 38 146 0 81 2 -20.000000 1 1 0 0 1 1 2 3 2.393020 1 0.360000 1.990000 0.457627 0.990000 0.970000 1.000000 1.000000 0.997877 0.990000 1 0.990000 1.000000 EGR1 1958 broad.mit.edu 37 5 137803753 137803753 + Missense_Mutation SNP A A G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:137803753A>G ENST00000239938.4 + 2 1887 c.1615A>G c.(1615-1617)Aca>Gca p.T539A NM_001964.2 NP_001955.1 P18146 EGR1_HUMAN early growth response 1 6 KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592) TTCTCCCAGGACAATTGAAAT 0.502000 0 SO:0001583 missense ENST00000239938.4 1 1 hg19 CCDS4206.1 . . . . . . . . . . A 14.19 2.461456 0.43736 . . ENSG00000120738 ENST00000411801;ENST00000239938 T 0.10960 2.82 4.24 4.24 0.50183 . 0.000000 0.85682 D 0.000000 T 0.27169 0.0666 L 0.58101 1.795 0.58432 D 0.999997 D 0.58970 0.984 D 0.68192 0.956 T 0.01375 -1.1371 10 0.87932 D 0 -6.6955 12.7025 0.57041 1.0:0.0:0.0:0.0 . 539 P18146 EGR1_HUMAN A 196;539 ENSP00000239938:T539A ENSP00000239938:T539A T + 1 0 EGR1 137831652 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 8.536000 0.90627 1.781000 0.52344 0.533000 0.62120 ACA TCGA-IB-7652-01A-11D-2154-08 EGR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251274.1 1 0 1 80 510 0 183 1 1 430 1842 0 183 2 0 0 0 0 0 2 1 1.000000 80 501 0 182 2 -20.000000 1 1 0 0 1 1 2 3 2.393020 1 0.360000 1.990000 0.457627 0.880000 0.710000 1.000000 1.000000 0.888497 0.880000 1 0.790000 0.980000 PCDHA4 56144 broad.mit.edu 37 5 140188280 140188280 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:140188280C>T ENST00000530339.1 + 1 1508 c.1508C>T c.(1507-1509)gCg>gTg p.A503V PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.A503V|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.A503V|PCDHA1_ENST00000394633.3_Intron NM_018907.2 NP_061730.1 Q9UN74 PCDA4_HUMAN protocadherin alpha 4 78 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GGGGAGCGCGCGCTGTCGAGC 0.662000 0 SO:0001583 missense ENST00000530339.1 1 1 hg19 CCDS54916.1 . . . . . . . . . . c 13.82 2.350279 0.41599 . . ENSG00000204967 ENST00000512229;ENST00000356878;ENST00000530339 T;T;T 0.54071 0.65;0.59;0.62 4.18 1.28 0.21552 Cadherin (4);Cadherin-like (1); 0.515141 0.14366 U 0.324099 T 0.47097 0.1427 L 0.28344 0.845 0.19300 N 0.999977 P;P;D 0.54047 0.902;0.937;0.964 P;P;P 0.56398 0.559;0.797;0.596 T 0.32771 -0.9894 10 0.72032 D 0.01 . 3.1704 0.06550 0.1412:0.561:0.1371:0.1606 . 503;503;503 Q9UN74-2;Q9UN74;D6RA20 .;PCDA4_HUMAN;. V 503 ENSP00000423470:A503V;ENSP00000349344:A503V;ENSP00000435300:A503V ENSP00000349344:A503V A + 2 0 PCDHA4 140168464 0.000000 0.05858 0.562000 0.28370 0.709000 0.40893 -0.289000 0.08365 0.030000 0.15379 0.580000 0.79431 GCG TCGA-IB-7652-01A-11D-2154-08 PCDHA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372864.2 1 0 1 60 367 0 193 0 3.180636e-01 0 8 0 193 2 0 0 0 0 0 2 1 1.000000 59 360 0 190 2 -20.000000 1 1 0 0 1 1 2 3 2.393020 1 0.360000 1.990000 0.457627 0.910000 0.710000 1.000000 1.000000 0.911249 0.910000 1 0.810000 1.000000 PCDHA7 56141 broad.mit.edu 37 5 140215334 140215334 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:140215334G>A ENST00000525929.1 + 1 1366 c.1366G>A c.(1366-1368)Gcg>Acg p.A456T PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.A456T|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron NM_018910.2 NP_061733.1 Q9UN72 PCDA7_HUMAN protocadherin alpha 7 63 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CCCGGCGTTCGCGCAGCCCGA 0.677000 NSCLC(160;258 2013 5070 22440 28951) 0 SO:0001583 missense ENST00000525929.1 1 1 hg19 CCDS54918.1 . . . . . . . . . . G 1.229 -0.624705 0.03636 . . ENSG00000204963 ENST00000525929;ENST00000378125 T;T 0.01359 4.98;4.98 4.0 -1.5 0.08691 Cadherin (3);Cadherin-like (1); 0.287183 0.17581 U 0.169114 T 0.00815 0.0027 N 0.05534 -0.03 0.09310 N 1 B;B 0.25105 0.118;0.091 B;B 0.30495 0.069;0.116 T 0.45775 -0.9238 10 0.44086 T 0.13 . 1.4843 0.02444 0.2051:0.1061:0.364:0.3248 . 456;456 Q9UN72-2;Q9UN72 .;PCDA7_HUMAN T 456 ENSP00000436426:A456T;ENSP00000367365:A456T ENSP00000367365:A456T A + 1 0 PCDHA7 140195518 0.000000 0.05858 0.006000 0.13384 0.002000 0.02628 -0.809000 0.04510 -0.802000 0.04421 -2.305000 0.00258 GCG TCGA-IB-7652-01A-11D-2154-08 PCDHA7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372887.2 1 0 1 85 490 0 220 0 6.028650e-02 0 3 0 220 2 0 0 0 0 0 2 1 1.000000 85 483 0 217 2 -20.000000 1 1 0 0 1 1 2 3 2.393020 1 0.360000 1.990000 0.457627 0.960000 0.780000 1.000000 1.000000 0.947086 0.960000 1 0.870000 1.000000 ARHGEF37 389337 broad.mit.edu 37 5 149001460 149001460 + Silent SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:149001460C>T ENST00000333677.6 + 9 1333 c.1170C>T c.(1168-1170)gcC>gcT p.A390A NM_001001669.2 NP_001001669.2 A1IGU5 ARH37_HUMAN Rho guanine nucleotide exchange factor (GEF) 37 17 AGGAGGAGGCCGCCCGGCACA 0.577000 0 SO:0001819 synonymous_variant ENST00000333677.6 1 1 hg19 CCDS43385.1 TCGA-IB-7652-01A-11D-2154-08 ARHGEF37-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000373763.1 0 0 0 36 412 0 158 1 9.687245e-01 3 63 0 158 2 0 0 0 0 0 2 1 1.000000 36 408 0 157 2 -20.000000 1 1 121088 3 39 1 1 2 3 2.393020 1 0.360000 1.990000 0.457627 0.520000 0.370000 0.700000 0.520000 0.537590 0.520000 0 0.440000 0.620000 FAT2 2196 broad.mit.edu 37 5 150923942 150923942 + Missense_Mutation SNP G G T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:150923942G>T ENST00000261800.5 - 9 6758 c.6746C>A c.(6745-6747)gCt>gAt p.A2249D NM_001447.2 NP_001438.1 Q9NYQ8 FAT2_HUMAN FAT atypical cadherin 2 196 Medulloblastoma(196;0.0912)|all_hematologic(541;0.104) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) TGACCCCAGAGCTGTATCCGT 0.473000 0 SO:0001583 missense ENST00000261800.5 1 1 hg19 CCDS4317.1 . . . . . . . . . . G 16.94 3.261414 0.59431 . . ENSG00000086570 ENST00000261800 T 0.60171 0.21 5.68 5.68 0.88126 Cadherin (4);Cadherin-like (1); 0.000000 0.64402 D 0.000003 T 0.65080 0.2657 L 0.42008 1.315 0.47245 D 0.999369 D 0.89917 1.0 D 0.77557 0.99 T 0.57365 -0.7824 10 0.12103 T 0.63 . 13.0521 0.58960 0.0733:0.0:0.9267:0.0 . 2249 Q9NYQ8 FAT2_HUMAN D 2249 ENSP00000261800:A2249D ENSP00000261800:A2249D A - 2 0 FAT2 150904135 1.000000 0.71417 1.000000 0.80357 0.944000 0.59088 6.043000 0.71004 2.683000 0.91414 0.561000 0.74099 GCT TCGA-IB-7652-01A-11D-2154-08 FAT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252434.1 1 0 1 104 554 0 138 0 0 0 0 138 2 0 0 0 0 0 2 1 1.000000 104 548 0 137 2 -20.000000 1 1 0 0 1 1 2 3 2.393020 1 0.360000 1.990000 0.457627 0.990000 0.850000 1.000000 1.000000 0.979927 0.990000 1 0.940000 1.000000 SPARC 6678 broad.mit.edu 37 5 151049237 151049237 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:151049237C>T ENST00000231061.4 - 6 752 c.439G>A c.(439-441)Ggg>Agg p.G147R SPARC_ENST00000537849.1_5'Flank NM_003118.3 NP_003109.1 P09486 SPRC_HUMAN secreted protein, acidic, cysteine-rich (osteonectin) 15 Medulloblastoma(196;0.109)|all_hematologic(541;0.122) Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785) TTGCAAGGCCCGATGTAGTCC 0.572000 0 SO:0001583 missense ENST00000231061.4 1 1 hg19 CCDS4318.1 . . . . . . . . . . C 31 5.075918 0.94000 . . ENSG00000113140 ENST00000231061;ENST00000538026;ENST00000521569 D;D;D 0.87650 -2.28;-2.28;-2.28 5.7 5.7 0.88788 Proteinase inhibitor I1, Kazal (2); 0.093699 0.85682 D 0.000000 D 0.95252 0.8460 M 0.91090 3.175 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.95663 0.8717 10 0.87932 D 0 -29.1188 19.8471 0.96713 0.0:1.0:0.0:0.0 . 147 P09486 SPRC_HUMAN R 147;56;56 ENSP00000231061:G147R;ENSP00000440127:G56R;ENSP00000428119:G56R ENSP00000231061:G147R G - 1 0 SPARC 151029430 1.000000 0.71417 0.992000 0.48379 0.990000 0.78478 7.311000 0.78958 2.688000 0.91661 0.655000 0.94253 GGG TCGA-IB-7652-01A-11D-2154-08 SPARC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252430.1 1 0 0 27 246 0 108 0 1 0 7346 0 108 2 0 0 0 0 0 2 1 1.000000 26 243 0 106 2 -2.841674 1 1 121412 2 31 1 1 2 3 2.393020 1 0.360000 1.990000 0.457627 0.650000 0.440000 0.900000 0.640000 0.664316 0.650000 0 0.540000 0.780000 ITK 3702 broad.mit.edu 37 5 156608099 156608099 + Silent SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:156608099C>T ENST00000422843.3 + 1 263 c.111C>T c.(109-111)agC>agT p.S37S NM_005546.3 NP_005537.3 Q08881 ITK_HUMAN IL2-inducible T-cell kinase 70 Renal(175;0.00212) Medulloblastoma(196;0.0354)|all_neural(177;0.1) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) Pazopanib(DB06589) CCAAAGCCAGCCTGGCATACT 0.398000 T SYK peripheral T-cell lymphoma Esophageal Squamous(70;1378 1469 8785 19883) Dom yes 5 5q31-q32 3702 IL2-inducible T-cell kinase L 0 SO:0001819 synonymous_variant ENST00000422843.3 1 1 hg19 CCDS4336.1 TCGA-IB-7652-01A-11D-2154-08 ITK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252569.2 1 0 1 121 638 0 284 0 2.587768e-02 0 2 0 284 2 0 0 0 0 0 2 1 1.000000 121 635 0 276 2 -20.000000 1 1 0 0 1 1 2 3 2.393020 1 0.360000 1.990000 0.457627 0.990000 0.870000 1.000000 1.000000 0.984625 0.990000 1 0.950000 1.000000 FLT4 2324 broad.mit.edu 37 5 180057054 180057054 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr5:180057054G>A ENST00000261937.6 - 5 643 c.565C>T c.(565-567)Cgg>Tgg p.R189W FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Missense_Mutation_p.R189W|FLT4_ENST00000393347.3_Missense_Mutation_p.R189W NM_182925.4 NP_891555.2 P35916 VGFR3_HUMAN fms-related tyrosine kinase 4 71 all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114) all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268) AGCATGCCCCGCCGGTCATCC 0.647000 Colon(97;1075 1466 27033 27547 35871) 0 SO:0001583 missense ENST00000261937.6 1 1 hg19 CCDS4457.1 . . . . . . . . . . G 18.38 3.611614 0.66558 . . ENSG00000037280 ENST00000261937;ENST00000393347;ENST00000502649 T;T;T 0.05258 3.47;3.47;3.47 5.16 3.02 0.34903 Tyrosine-protein kinase, vascular endothelial growth factor receptor (VEGFR), N-terminal (1);Immunoglobulin-like fold (1); . . . . T 0.17152 0.0412 M 0.65975 2.015 0.38025 D 0.934989 D;D;D;D 0.89917 0.999;1.0;0.989;0.989 P;D;P;P 0.65010 0.855;0.931;0.677;0.582 T 0.02138 -1.1207 9 0.56958 D 0.05 . 7.5225 0.27637 0.0:0.1296:0.4182:0.4522 . 189;189;189;189 B5A927;P35916-3;E9PD35;P35916 .;.;.;VGFR3_HUMAN W 189 ENSP00000261937:R189W;ENSP00000377016:R189W;ENSP00000426057:R189W ENSP00000261937:R189W R - 1 2 FLT4 179989660 0.824000 0.29247 1.000000 0.80357 0.821000 0.46438 0.873000 0.28052 1.262000 0.44165 0.561000 0.74099 CGG TCGA-IB-7652-01A-11D-2154-08 FLT4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253527.4 1 0 1 39 314 0 185 0 7.796675e-01 0 25 0 185 2 0 0 0 0 0 2 1 1.000000 39 300 0 173 2 -3.017765 1 1 0 0 1 1 2 3 2.381313 1 0.360000 1.990000 0.457627 0.720000 0.520000 0.950000 0.720000 0.735591 0.720000 0 0.620000 0.840000 FOXO3 2309 broad.mit.edu 37 6 108985160 108985160 + Missense_Mutation SNP C C G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr6:108985160C>G ENST00000343882.6 + 3 1428 c.1124C>G c.(1123-1125)aCc>aGc p.T375S FOXO3_ENST00000406360.1_Missense_Mutation_p.T375S|FOXO3_ENST00000540898.1_Missense_Mutation_p.T155S NM_201559.2 NP_963853.1 O43524 FOXO3_HUMAN forkhead box O3 26 all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152) ATGGCAGGCACCATGAATCTG 0.582000 0 SO:0001583 missense ENST00000343882.6 0 1 hg19 CCDS5068.1 . . . . . . . . . . C 10.93 1.488937 0.26686 . . ENSG00000118689 ENST00000343882;ENST00000406360;ENST00000540258;ENST00000540898 D;D 0.89681 -2.55;-2.55 5.52 5.52 0.82312 . 0.000000 0.85682 D 0.000000 T 0.78660 0.4318 L 0.43923 1.385 0.80722 D 1 P 0.40660 0.726 B 0.39617 0.305 T 0.80350 -0.1419 10 0.07325 T 0.83 -33.6779 19.4179 0.94709 0.0:1.0:0.0:0.0 . 375 O43524 FOXO3_HUMAN S 375;375;155;155 ENSP00000339527:T375S;ENSP00000385824:T375S ENSP00000339527:T375S T + 2 0 FOXO3 109091853 1.000000 0.71417 1.000000 0.80357 0.624000 0.37722 7.412000 0.80091 2.595000 0.87683 0.462000 0.41574 ACC TCGA-IB-7652-01A-11D-2154-08 FOXO3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041722.2 0 0 0 6 232 0 103 0 8.784722e-01 0 148 0 103 2 0 0 0 0 0 2 1 0.962194 6 225 0 99 2 -7.589620 1 1 121412 1 26 1 0 0 0 1.993689 0 0.360000 1.990000 0.357688 0.140000 0.050000 0.280000 0.140000 0.160241 0.140000 0 0.090000 0.220000 PARK2 5071 broad.mit.edu 37 6 162864492 162864492 + Missense_Mutation SNP G G T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr6:162864492G>T ENST00000366898.1 - 2 123 c.21C>A c.(19-21)ttC>ttA p.F7L PARK2_ENST00000366894.1_5'UTR|PARK2_ENST00000338468.3_5'UTR|PARK2_ENST00000366892.1_Missense_Mutation_p.F7L|PARK2_ENST00000366896.1_Missense_Mutation_p.F7L|PARK2_ENST00000366897.1_Missense_Mutation_p.F7L NM_004562.2 NP_004553.2 O60260 PRKN2_HUMAN parkin RBR E3 ubiquitin protein ligase 39 all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102) GGCTGGAGTTGAACCTGACAA 0.498000 0 SO:0001583 missense ENST00000366898.1 1 1 hg19 CCDS5281.1 . . . . . . . . . . G 18.71 3.682026 0.68042 . . ENSG00000185345 ENST00000366898;ENST00000366897;ENST00000366896;ENST00000366892;ENST00000542682 D;D;D;D 0.95885 -3.84;-3.84;-3.84;-3.84 5.63 5.63 0.86233 Ubiquitin supergroup (1);Ubiquitin (1); 0.058575 0.64402 D 0.000002 D 0.96371 0.8816 M 0.61703 1.905 0.33160 D 0.546906 D;P;D;D 0.76494 0.999;0.88;0.997;0.995 D;D;D;D 0.80764 0.994;0.946;0.958;0.958 D 0.95618 0.8678 10 0.44086 T 0.13 . 14.8348 0.70175 0.0:0.0:0.8561:0.1438 . 7;7;7;7 O60260-5;Q5VVX3;Q5VVX4;O60260 .;.;.;PRKN2_HUMAN L 7;7;7;7;6 ENSP00000355865:F7L;ENSP00000355863:F7L;ENSP00000355862:F7L;ENSP00000355858:F7L ENSP00000355858:F7L F - 3 2 PARK2 162784482 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 3.700000 0.54786 2.805000 0.96524 0.655000 0.94253 TTC TCGA-IB-7652-01A-11D-2154-08 PARK2-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042995.1 0 0 0 19 294 0 203 0 0 0 1 0 203 2 0 0 0 0 0 2 1 0.999991 18 293 0 203 2 -5.902384 1 1 0 0 1 0 0 0 1.950015 0 0.360000 1.990000 0.341021 0.320000 0.200000 0.490000 0.330000 0.340469 0.320000 0 0.260000 0.410000 TBP 6908 broad.mit.edu 37 6 170871100 170871100 + Silent SNP G G A rs139333134 byFrequency TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr6:170871100G>A ENST00000392092.2 + 3 555 c.276G>A c.(274-276)caG>caA p.Q92Q TBP_ENST00000230354.6_Silent_p.Q92Q|TBP_ENST00000540980.1_Silent_p.Q72Q NM_003194.4 NP_003185.1 P20226 TBP_HUMAN TATA box binding protein 26 Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246) agcagcagcagcagcaacagg 0.612000 0 SO:0001819 synonymous_variant ENST00000392092.2 1 0 hg19 CCDS5315.1 TCGA-IB-7652-01A-11D-2154-08 TBP-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000043271.2 0 0 1 90 284 2 108 1 9.473800e-01 5 19 2 108 3 0 0 0 0 0 2 1 1.000000 27 263 0 87 2 -2.884778 1 0 0 0 1 0 0 0 1.950015 0 0.360000 1.990000 0.341021 0.990000 0.990000 1.000000 1.000000 0.999874 0.990000 1 0.990000 1.000000 E2F3 1871 broad.mit.edu 37 6 20490617 20490617 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr6:20490617G>A ENST00000346618.3 + 7 1420 c.1354G>A c.(1354-1356)Gat>Aat p.D452N E2F3_ENST00000535432.1_Missense_Mutation_p.D321N NM_001949.4 NP_001940.1 O00716 E2F3_HUMAN E2F transcription factor 3 7 all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148) OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562) CGATGCTTACGATTTGGAAAA 0.468000 0 SO:0001583 missense ENST00000346618.3 1 1 hg19 CCDS4545.1 . . . . . . . . . . . 23.9 4.470974 0.84533 . . ENSG00000112242 ENST00000378646;ENST00000346618;ENST00000535432 T;T 0.10288 2.89;3.01 5.79 5.79 0.91817 . 0.046857 0.85682 D 0.000000 T 0.21841 0.0526 M 0.67397 2.05 0.80722 D 1 D 0.89917 1.0 P 0.57911 0.829 T 0.00379 -1.1777 10 0.66056 D 0.02 . 20.0407 0.97588 0.0:0.0:1.0:0.0 . 452 O00716 E2F3_HUMAN N 115;452;321 ENSP00000262904:D452N;ENSP00000443418:D321N ENSP00000262904:D452N D + 1 0 E2F3 20598596 1.000000 0.71417 0.941000 0.38009 0.685000 0.39939 9.476000 0.97823 2.746000 0.94184 0.561000 0.74099 GAT TCGA-IB-7652-01A-11D-2154-08 E2F3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000043828.1 1 0 1 155 732 0 278 1 9.974819e-01 16 28 0 278 2 0 0 0 0 0 2 1 1.000000 155 725 0 275 2 -20.000000 1 1 0 0 1 1 2 3 2.050700 0 0.360000 1.990000 0.367964 0.980000 0.840000 1.000000 1.000000 0.965245 0.980000 1 0.910000 1.000000 OR12D2 26529 broad.mit.edu 37 6 29365221 29365221 + Missense_Mutation SNP C C A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr6:29365221C>A ENST00000383555.2 + 1 806 c.745C>A c.(745-747)Ctt>Att p.L249I OR5V1_ENST00000377154.1_Intron NM_013936.3 NP_039224.2 P58182 O12D2_HUMAN olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene) p.L249V(1) 31 GGTAGTTATTCTTTTCTATGC 0.443000 1 Substitution - Missense(1) SO:0001583 missense ENST00000383555.2 1 1 hg19 CCDS4659.1 . . . . . . . . . . C 10.28 1.306945 0.23821 . . ENSG00000168787 ENST00000383555 T 0.00256 8.42 3.94 1.01 0.19927 GPCR, rhodopsin-like superfamily (1); 0.000000 0.47852 D 0.000216 T 0.00073 0.0002 L 0.37630 1.12 0.09310 N 1 B 0.33755 0.424 B 0.43916 0.436 T 0.07693 -1.0759 10 0.22109 T 0.4 . 6.48 0.22057 0.0:0.5558:0.275:0.1692 . 249 P58182 O12D2_HUMAN I 249 ENSP00000373047:L249I ENSP00000373047:L249I L + 1 0 OR12D2 29473200 0.000000 0.05858 0.002000 0.10522 0.350000 0.29205 -0.686000 0.05161 0.314000 0.23086 0.205000 0.17691 CTT TCGA-IB-7652-01A-11D-2154-08 OR12D2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076054.2 1 0 1 160 757 0 321 0 0 0 1 0 321 2 0 0 0 0 0 2 1 1.000000 159 755 0 318 2 -20.000000 1 1 0 0 1 1 2 3 2.050700 0 0.360000 1.990000 0.367964 0.980000 0.840000 1.000000 1.000000 0.964822 0.980000 1 0.910000 1.000000 PRSS35 167681 broad.mit.edu 37 6 84233558 84233558 + Missense_Mutation SNP T T C TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr6:84233558T>C ENST00000369700.3 + 2 575 c.398T>C c.(397-399)aTc>aCc p.I133T PRSS35_ENST00000536636.1_Missense_Mutation_p.I133T NM_153362.2 NP_699193.2 Q8N3Z0 PRS35_HUMAN protease, serine, 35 32 all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575) AGGTTCAGCATCTTGGACAAA 0.458000 0 SO:0001583 missense ENST00000369700.3 1 1 hg19 CCDS4999.1 . . . . . . . . . . T 21.0 4.078192 0.76528 . . ENSG00000146250 ENST00000536636;ENST00000369700 T;T 0.50277 0.75;0.75 5.78 5.78 0.91487 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1); 0.000000 0.85682 D 0.000000 T 0.66416 0.2787 M 0.83118 2.625 0.80722 D 1 D 0.76494 0.999 D 0.85130 0.997 T 0.72944 -0.4138 10 0.87932 D 0 -14.2535 16.0993 0.81158 0.0:0.0:0.0:1.0 . 133 Q8N3Z0 PRS35_HUMAN T 133 ENSP00000440870:I133T;ENSP00000358714:I133T ENSP00000358714:I133T I + 2 0 PRSS35 84290277 1.000000 0.71417 1.000000 0.80357 0.903000 0.53119 7.698000 0.84413 2.207000 0.71202 0.459000 0.35465 ATC TCGA-IB-7652-01A-11D-2154-08 PRSS35-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041352.1 1 0 1 105 422 0 184 0 2.638746e-01 0 5 0 184 2 0 0 0 0 0 2 1 1.000000 105 419 0 180 2 -20.000000 1 1 121412 1 32 1 0 0 0 1.993689 0 0.360000 1.990000 0.357688 0.990000 0.910000 1.000000 1.000000 0.993863 0.990000 1 0.990000 1.000000 FLNC 2318 broad.mit.edu 37 7 128478769 128478769 + Missense_Mutation SNP A A T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr7:128478769A>T ENST00000325888.8 + 8 1584 c.1323A>T c.(1321-1323)agA>agT p.R441S FLNC_ENST00000346177.6_Missense_Mutation_p.R441S NM_001458.4 NP_001449.3 Q14315 FLNC_HUMAN filamin C, gamma 128 GCACATACAGACCTGCCATGG 0.637000 0 SO:0001583 missense ENST00000325888.8 1 1 hg19 CCDS43644.1 . . . . . . . . . . A 14.39 2.522233 0.44866 . . ENSG00000128591 ENST00000325888;ENST00000346177 T;T 0.63096 -0.02;-0.02 4.9 4.01 0.46588 Immunoglobulin E-set (1);Immunoglobulin-like fold (1); 0.483889 0.21640 N 0.071355 T 0.51924 0.1703 L 0.48642 1.525 0.43164 D 0.994953 B;B 0.21225 0.053;0.039 B;B 0.29440 0.038;0.102 T 0.52578 -0.8557 10 0.48119 T 0.1 . 4.0045 0.09595 0.1951:0.0:0.6163:0.1886 . 441;441 Q14315-2;Q14315 .;FLNC_HUMAN S 441 ENSP00000327145:R441S;ENSP00000344002:R441S ENSP00000327145:R441S R + 3 2 FLNC 128266005 0.385000 0.25172 0.997000 0.53966 0.975000 0.68041 -0.139000 0.10358 1.257000 0.44085 -0.366000 0.07423 AGA TCGA-IB-7652-01A-11D-2154-08 FLNC-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000059948.3 0 0 1 106 607 1 354 0 5.043645e-01 0 11 1 354 2 0 0 0 0 0 2 1 1.000000 104 602 1 343 9 -2.920951 1 1 0 0 1 2 2 4 2.116647 1 0.360000 1.990000 0.394856 0.880000 0.720000 1.000000 1.000000 0.890745 0.880000 1 0.800000 1.000000 NOBOX 135935 broad.mit.edu 37 7 144097345 144097345 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr7:144097345C>T ENST00000467773.1 - 5 904 c.905G>A c.(904-906)cGc>cAc p.R302H NOBOX_ENST00000483238.1_Missense_Mutation_p.R302H|NOBOX_ENST00000223140.5_Missense_Mutation_p.R217H NM_001080413.3 NP_001073882.3 O60393 NOBOX_HUMAN NOBOX oogenesis homeobox 26 Melanoma(164;0.14) AATCTCTCGGCGTTTATCACT 0.557000 0 SO:0001583 missense ENST00000467773.1 1 1 hg19 . . . . . . . . . . C 19.76 3.888183 0.72524 . . ENSG00000106410 ENST00000483238;ENST00000467773;ENST00000223140;ENST00000555556 D;D;D 0.97505 -4.41;-4.41;-4.41 5.79 4.91 0.64330 Homeodomain-related (1);Homeobox (3);Homeodomain-like (1); 0.139728 0.38778 N 0.001576 D 0.99010 0.9662 H 0.98111 4.15 0.36943 D 0.892459 D 0.89917 1.0 D 0.97110 1.0 D 0.99947 1.1488 10 0.87932 D 0 -29.743 12.7537 0.57321 0.0:0.9207:0.0:0.0793 . 302 O60393 NOBOX_HUMAN H 302;302;217;91 ENSP00000419565:R302H;ENSP00000419457:R302H;ENSP00000223140:R217H ENSP00000223140:R217H R - 2 0 NOBOX 143728278 1.000000 0.71417 0.745000 0.31077 0.663000 0.39108 5.277000 0.65586 1.450000 0.47717 0.650000 0.86243 CGC TCGA-IB-7652-01A-11D-2154-08 NOBOX-002 KNOWN basic protein_coding protein_coding OTTHUMT00000350095.1 1 0 1 69 292 0 158 0 0 0 0 158 2 0 0 0 0 0 2 1 1.000000 68 289 0 155 2 -20.000000 1 1 0 0 1 2 2 4 2.116647 1 0.360000 1.990000 0.394856 0.990000 0.900000 1.000000 1.000000 0.992807 0.990000 1 0.990000 1.000000 GTF2IRD2B 389524 broad.mit.edu 37 7 74563983 74563983 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr7:74563983C>T ENST00000312575.7 + 16 1905 c.1730C>T c.(1729-1731)tCc>tTc p.S577F GTF2IRD2B_ENST00000418185.2_Missense_Mutation_p.S124F NM_001003795.2 NP_001003795.1 Q6EKJ0 GTD2B_HUMAN GTF2I repeat domain containing 2B 4 ttcgatgtgtccgaagaactt 0.443000 0 SO:0001583 missense ENST00000312575.7 1 0 hg19 CCDS34659.1 . . . . . . . . . . C 4.259 0.047024 0.08243 . . ENSG00000174428 ENST00000312575;ENST00000418185 T;T 0.22539 1.95;1.95 1.53 1.53 0.23141 Ribonuclease H-like (1); . . . . T 0.18045 0.0433 L 0.43923 1.385 0.33876 D 0.635526 B;P 0.48911 0.021;0.917 B;P 0.46049 0.009;0.502 T 0.27191 -1.0081 9 0.22706 T 0.39 -4.1018 6.5351 0.22348 0.0:1.0:0.0:0.0 . 72;577 Q86Y00;Q6EKJ0 .;GTD2B_HUMAN F 577;124 ENSP00000308080:S577F;ENSP00000411454:S124F ENSP00000308080:S577F S + 2 0 GTF2IRD2B 74201919 0.018000 0.18449 0.895000 0.35142 0.475000 0.33008 1.774000 0.38573 1.164000 0.42652 0.430000 0.28490 TCC TCGA-IB-7652-01A-11D-2154-08 GTF2IRD2B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342728.1 1 0 0 32 158 0 60 1 7.459707e-01 3 12 0 60 2 0 0 0 0 0 2 1 1.000000 30 148 0 145 2 -18.427890 1 1 0 0 1 2 2 4 2.116647 1 0.360000 1.990000 0.394856 0.990000 0.710000 1.000000 1.000000 0.945569 0.990000 1 0.850000 1.000000 DLGAP2 9228 broad.mit.edu 37 8 1497384 1497384 + Silent SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr8:1497384C>T ENST00000421627.2 + 2 659 c.525C>T c.(523-525)aaC>aaT p.N175N NM_004745.3 NP_004736.2 Q9P1A6 DLGP2_HUMAN discs, large (Drosophila) homolog-associated protein 2 41 Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846) GCAACGCCAACGGCACCAAGG 0.672000 0 SO:0001819 synonymous_variant ENST00000421627.2 1 1 hg19 CCDS47760.1 . . . . . . . . . . C 1.430 -0.570388 0.03910 0.001382 1.17E-4 ENSG00000198010 ENST00000520901 . . . 5.57 -4.39 0.03611 . . . . . T 0.63616 0.2526 . . . 0.80722 D 1 . . . . . . T 0.63377 -0.6651 4 . . . -13.2071 15.0453 0.71822 0.0:0.285:0.0:0.715 . . . . M 192 . . T + 2 0 DLGAP2 1484791 0.085000 0.21516 0.019000 0.16419 0.196000 0.23810 -0.644000 0.05415 -0.909000 0.03852 -0.783000 0.03347 ACG TCGA-IB-7652-01A-11D-2154-08 DLGAP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374478.1 1 0 1 18 53 0 16 0 0 0 0 16 2 0 0 0 0 0 2 1 0.999993 18 53 0 16 2 -20.000000 1 1 120940 13 38 1 0 1 1 1.681487 1 0.360000 1.990000 0.219512 0.890000 0.640000 1.000000 0.990000 0.879063 0.890000 1 0.770000 0.970000 PXDNL 137902 broad.mit.edu 37 8 52384855 52384855 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr8:52384855C>T ENST00000356297.4 - 8 804 c.704G>A c.(703-705)cGa>cAa p.R235Q PXDNL_ENST00000543296.1_Missense_Mutation_p.R235Q NM_144651.4 NP_653252 A1KZ92 PXDNL_HUMAN peroxidasin homolog (Drosophila)-like 48 all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015) AAAAGTAATTCGGGGGCTCTC 0.413000 0 SO:0001583 missense ENST00000356297.4 1 1 hg19 CCDS47855.1 . . . . . . . . . . C 8.831 0.940018 0.18281 . . ENSG00000147485 ENST00000356297;ENST00000543296 T;T 0.66815 -0.23;-0.23 3.84 2.96 0.34315 Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); . . . . T 0.51975 0.1706 N 0.25332 0.735 0.24906 N 0.992072 P 0.47350 0.894 B 0.42495 0.389 T 0.30909 -0.9962 9 0.27785 T 0.31 . 9.0746 0.36513 0.0:0.8869:0.0:0.1131 . 235 A1KZ92 PXDNL_HUMAN Q 235 ENSP00000348645:R235Q;ENSP00000444865:R235Q ENSP00000348645:R235Q R - 2 0 PXDNL 52547408 0.542000 0.26426 0.060000 0.19600 0.164000 0.22412 3.613000 0.54152 0.627000 0.30340 -0.350000 0.07774 CGA TCGA-IB-7652-01A-11D-2154-08 PXDNL-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000377905.1 1 0 0 17 367 0 161 0 6.632273e-03 0 3 0 161 2 0 0 0 0 0 2 1 0.999964 17 363 0 158 2 -3.157053 1 1 0 0 1 0 0 0 1.982820 0 0.360000 1.990000 0.355359 0.240000 0.140000 0.370000 0.240000 0.255990 0.240000 0 0.190000 0.310000 OR13F1 138805 broad.mit.edu 37 9 107267140 107267140 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr9:107267140G>A ENST00000334726.2 + 1 686 c.597G>A c.(595-597)atG>atA p.M199I NM_001004485.1 NP_001004485.1 Q8NGS4 O13F1_HUMAN olfactory receptor, family 13, subfamily F, member 1 31 AGTTAATCATGCTGGTGATCA 0.433000 0 SO:0001583 missense ENST00000334726.2 1 1 hg19 CCDS35087.1 . . . . . . . . . . G 8.738 0.918213 0.17982 . . ENSG00000186881 ENST00000334726 T 0.00048 8.82 4.29 2.16 0.27623 GPCR, rhodopsin-like superfamily (1); 0.091249 0.47093 N 0.000241 T 0.00073 0.0002 N 0.05608 -0.01 0.09310 N 1 B 0.17038 0.02 B 0.20384 0.029 T 0.06391 -1.0829 10 0.30078 T 0.28 . 5.7443 0.18112 0.3867:0.0:0.6133:0.0 . 199 Q8NGS4 O13F1_HUMAN I 199 ENSP00000334452:M199I ENSP00000334452:M199I M + 3 0 OR13F1 106306961 0.006000 0.16342 0.148000 0.22405 0.993000 0.82548 0.163000 0.16520 0.572000 0.29383 0.650000 0.86243 ATG TCGA-IB-7652-01A-11D-2154-08 OR13F1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053475.1 0 0 0 80 1122 0 365 0 0 0 0 365 2 0 0 0 0 0 2 1 1.000000 80 1118 0 364 2 -12.923450 1 1 0 0 1 0 1 1 2.002675 0 0.360000 1.990000 0.358846 0.360000 0.290000 0.450000 0.370000 0.372527 0.360000 0 0.320000 0.410000 SVEP1 79987 broad.mit.edu 37 9 113169147 113169147 + Missense_Mutation SNP C C G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr9:113169147C>G ENST00000401783.2 - 38 9069 c.8733G>C c.(8731-8733)aaG>aaC p.K2911N SVEP1_ENST00000374469.1_Missense_Mutation_p.K2888N|SVEP1_ENST00000297826.5_Missense_Mutation_p.K837N NM_153366.3 NP_699197.3 Q4LDE5 SVEP1_HUMAN sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 147 ATGTTACTTCCTTCATGAAGC 0.552000 0 SO:0001583 missense ENST00000401783.2 1 1 hg19 CCDS48004.1 . . . . . . . . . . C 12.40 1.927013 0.34002 . . ENSG00000165124 ENST00000401783;ENST00000374469;ENST00000297826 T;T;T 0.64085 -0.08;-0.08;-0.08 5.51 3.64 0.41730 Complement control module (2);Sushi/SCR/CCP (3); 0.285646 0.43919 D 0.000511 T 0.44808 0.1311 L 0.31526 0.94 0.80722 D 1 P 0.40578 0.722 B 0.39617 0.305 T 0.29912 -0.9996 10 0.30854 T 0.27 . 5.6066 0.17383 0.0:0.6236:0.0:0.3764 . 2911 Q4LDE5 SVEP1_HUMAN N 2911;2888;837 ENSP00000384917:K2911N;ENSP00000363593:K2888N;ENSP00000297826:K837N ENSP00000297826:K837N K - 3 2 SVEP1 112208968 0.920000 0.31207 1.000000 0.80357 0.876000 0.50452 -0.039000 0.12124 1.303000 0.44873 0.591000 0.81541 AAG TCGA-IB-7652-01A-11D-2154-08 SVEP1-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 1 0 1 92 654 0 216 0 9.874727e-01 0 50 0 216 2 0 0 0 0 0 2 1 1.000000 91 647 0 214 2 -2.966611 1 1 0 0 1 1 2 3 2.368430 1 0.360000 1.990000 0.457627 0.800000 0.650000 0.960000 0.810000 0.813369 0.800000 0 0.720000 0.890000 DAB2IP 153090 broad.mit.edu 37 9 124535711 124535711 + Missense_Mutation SNP G G T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr9:124535711G>T ENST00000408936.3 + 12 3086 c.2904G>T c.(2902-2904)agG>agT p.R968S DAB2IP_ENST00000309989.1_Missense_Mutation_p.R844S|DAB2IP_ENST00000259371.2_Missense_Mutation_p.R940S Q5VWQ8 DAB2P_HUMAN DAB2 interacting protein 27 CCCGCCTGAGGCAGCAGTCCT 0.652000 0 SO:0001583 missense ENST00000408936.3 1 1 hg19 . . . . . . . . . . G 10.61 1.397162 0.25205 . . ENSG00000136848 ENST00000259371;ENST00000408936;ENST00000373782;ENST00000309989 T;T;T;T 0.13657 2.57;2.57;2.57;2.57 4.7 3.73 0.42828 . 0.237534 0.39759 N 0.001274 T 0.17534 0.0421 L 0.53561 1.675 0.46954 D 0.999269 B;P 0.35033 0.271;0.481 B;B 0.42738 0.079;0.396 T 0.03852 -1.0998 10 0.13108 T 0.6 . 13.3473 0.60582 0.0:0.1591:0.8409:0.0 . 968;940 Q5VWQ8;G3XA90 DAB2P_HUMAN;. S 940;968;877;844 ENSP00000259371:R940S;ENSP00000386183:R968S;ENSP00000362887:R877S;ENSP00000310827:R844S ENSP00000259371:R940S R + 3 2 DAB2IP 123575532 1.000000 0.71417 1.000000 0.80357 0.702000 0.40608 1.058000 0.30504 2.169000 0.68431 0.313000 0.20887 AGG TCGA-IB-7652-01A-11D-2154-08 DAB2IP-009 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000317857.1 1 0 0 10 61 0 38 1 9.999612e-01 32 106 0 38 2 0 0 0 0 0 2 1 0.997189 10 59 0 38 2 -18.550380 1 1 0 0 1 1 2 3 2.409872 1 0.360000 1.990000 0.457627 0.940000 0.500000 1.000000 1.000000 0.877559 0.940000 1 0.690000 1.000000 PTGS1 5742 broad.mit.edu 37 9 125140773 125140773 + Silent SNP G G T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G T G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr9:125140773G>T ENST00000362012.2 + 4 278 c.273G>T c.(271-273)ctG>ctT p.L91L PTGS1_ENST00000223423.4_Silent_p.L91L|PTGS1_ENST00000540753.1_Silent_p.L66L|PTGS1_ENST00000373698.5_5'UTR NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2 NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1 P23219 PGH1_HUMAN prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase) 8 Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bortezomib(DB00188)|Bromfenac(DB00963)|Candesartan(DB00796)|Carprofen(DB00821)|Carvedilol(DB01136)|Chlorpropamide(DB00672)|Dapsone(DB00250)|Desmopressin(DB00035)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Diphenhydramine(DB01075)|Dronabinol(DB00470)|Eletriptan(DB00216)|Eszopiclone(DB00402)|Etodolac(DB00749)|Etoposide(DB00773)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Hexobarbital(DB01355)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Icosapent(DB00159)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indomethacin(DB00328)|Irbesartan(DB01029)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Minoxidil(DB00350)|Montelukast(DB00471)|Nabumetone(DB00461)|Naproxen(DB00788)|Nateglinide(DB00731)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nortriptyline(DB00540)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Rosiglitazone(DB00412)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfamethoxazole(DB01015)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Torasemide(DB00214)|Trabectedin(DB05109)|Triflusal(DB08814)|Trisalicylate-choline(DB01401)|Valproic Acid(DB00313)|Voriconazole(DB00582)|Zafirlukast(DB00549)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198) CCCACTTCCTGCTCACTCACG 0.622000 0 SO:0001819 synonymous_variant ENST00000362012.2 1 1 hg19 CCDS6842.1 TCGA-IB-7652-01A-11D-2154-08 PTGS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053933.1 1 0 0 117 584 0 324 0 9.999994e-01 1 100 0 324 2 0 0 0 0 0 2 1 1.000000 117 577 0 314 2 -20.000000 1 1 0 0 1 1 2 3 2.409872 1 0.360000 1.990000 0.457627 0.990000 0.910000 1.000000 1.000000 0.993602 0.990000 1 0.990000 1.000000 OR1K1 392392 broad.mit.edu 37 9 125563309 125563309 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr9:125563309G>A ENST00000277309.2 + 1 940 c.908G>A c.(907-909)cGa>cAa p.R303Q NM_080859.1 NP_543135.1 Q8NGR3 OR1K1_HUMAN olfactory receptor, family 1, subfamily K, member 1 17 GGGGCACTCCGAGCCCTTCTC 0.582000 0 SO:0001583 missense ENST00000277309.2 1 1 hg19 CCDS35132.1 . . . . . . . . . . G 5.138 0.211147 0.09757 . . ENSG00000165204 ENST00000277309 T 0.39406 1.08 4.49 1.68 0.24146 . 0.252216 0.20517 N 0.090769 T 0.24547 0.0595 N 0.22421 0.69 0.09310 N 0.999999 B 0.15719 0.014 B 0.09377 0.004 T 0.16867 -1.0388 10 0.23891 T 0.37 . 8.1058 0.30885 0.2689:0.0:0.7311:0.0 . 303 Q8NGR3 OR1K1_HUMAN Q 303 ENSP00000277309:R303Q ENSP00000277309:R303Q R + 2 0 OR1K1 124603130 0.000000 0.05858 0.004000 0.12327 0.009000 0.06853 0.119000 0.15626 0.171000 0.19730 -0.244000 0.11960 CGA TCGA-IB-7652-01A-11D-2154-08 OR1K1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053958.1 1 0 0 110 227 0 148 0 0 0 0 148 2 0 0 0 0 0 2 1 1.000000 108 223 0 144 2 -20.000000 1 1 121382 2 33 1 1 2 3 2.409872 1 0.360000 1.990000 0.457627 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PRDM12 59335 broad.mit.edu 37 9 133540159 133540159 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr9:133540159G>A ENST00000253008.2 + 1 179 c.119G>A c.(118-120)cGc>cAc p.R40H NM_021619.2 NP_067632.2 Q9H4Q4 PRD12_HUMAN PR domain containing 12 11 all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534) CTGTACGGCCGCTGGCGCAAC 0.677000 0 SO:0001583 missense ENST00000253008.2 0 1 hg19 CCDS6934.1 . . . . . . . . . . G 15.68 2.905725 0.52333 . . ENSG00000130711 ENST00000253008 T 0.09723 2.95 4.48 3.51 0.40186 . 0.054397 0.64402 D 0.000002 T 0.06645 0.0170 L 0.29908 0.895 0.44079 D 0.996835 P 0.48640 0.913 B 0.36766 0.232 T 0.44190 -0.9344 10 0.16420 T 0.52 -16.2368 11.8827 0.52583 0.0:0.0:0.8247:0.1752 . 40 Q9H4Q4 PRD12_HUMAN H 40 ENSP00000253008:R40H ENSP00000253008:R40H R + 2 0 PRDM12 132529980 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 6.872000 0.75536 2.026000 0.59711 0.462000 0.41574 CGC TCGA-IB-7652-01A-11D-2154-08 PRDM12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054664.1 0 0 0 3 62 0 31 0 0 0 0 31 2 0 0 0 1 0 0 2 1 0.802560 2 61 0 31 2 -6.927076 1 0 0 0 1 1 2 3 2.414666 1 0.360000 1.990000 0.457627 0.340000 0.100000 0.780000 0.300000 0.383772 0.340000 0 0.190000 0.560000 DDX31 64794 broad.mit.edu 37 9 135487492 135487492 + Missense_Mutation SNP C C G TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr9:135487492C>G ENST00000372159.3 - 19 2442 c.2291G>C c.(2290-2292)aGg>aCg p.R764T DDX31_ENST00000438527.3_Missense_Mutation_p.R635T|DDX31_ENST00000372153.1_Missense_Mutation_p.R691T NM_022779.7 NP_073616.6 Q9H8H2 DDX31_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 31 27 GTGTGCTTTCCTCTTCTTTCT 0.532000 0 SO:0001583 missense ENST00000372159.3 1 1 hg19 CCDS6951.1 . . . . . . . . . . C 11.71 1.719394 0.30503 . . ENSG00000125485 ENST00000372159;ENST00000372153;ENST00000438527 T;T;T 0.03717 4.33;3.83;4.29 5.84 -2.42 0.06542 . 0.976044 0.08418 N 0.948855 T 0.03434 0.0099 L 0.38175 1.15 0.80722 D 1 B;B 0.20671 0.047;0.04 B;B 0.15484 0.013;0.008 T 0.34601 -0.9822 10 0.34782 T 0.22 -5.4579 8.5087 0.33204 0.0:0.2988:0.1156:0.5855 . 691;764 Q9H8H2-2;Q9H8H2 .;DDX31_HUMAN T 764;691;635 ENSP00000361232:R764T;ENSP00000361226:R691T;ENSP00000387730:R635T ENSP00000361226:R691T R - 2 0 DDX31 134477313 0.449000 0.25689 0.028000 0.17463 0.076000 0.17211 -0.315000 0.08081 -0.512000 0.06505 -0.768000 0.03414 AGG TCGA-IB-7652-01A-11D-2154-08 DDX31-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000054794.1 1 0 1 126 612 0 199 1 9.989779e-01 13 38 0 199 2 0 0 0 0 0 2 1 1.000000 126 608 0 198 2 -2.931160 1 1 0 0 1 1 2 3 2.414666 1 0.360000 1.990000 0.457627 0.990000 0.940000 1.000000 1.000000 0.996668 0.990000 1 0.990000 1.000000 ADAMTSL2 9719 broad.mit.edu 37 9 136402618 136402618 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr9:136402618G>A ENST00000354484.4 + 3 739 c.182G>A c.(181-183)cGc>cAc p.R61H ADAMTSL2_ENST00000393061.3_Missense_Mutation_p.R170H|ADAMTSL2_ENST00000393060.1_Missense_Mutation_p.R61H NM_001145320.1 NP_001138792.1 Q86TH1 ATL2_HUMAN ADAMTS-like 2 14 GCGTGTTCCCGCAGTTGCGGG 0.672000 0 SO:0001583 missense ENST00000354484.4 1 1 hg19 CCDS6976.1 . . . . . . . . . . G 32 5.156452 0.94686 . . ENSG00000197859 ENST00000354484;ENST00000393061;ENST00000393060 T;T;T 0.52983 0.64;0.64;0.64 4.84 4.84 0.62591 . 0.000000 0.56097 U 0.000031 T 0.74496 0.3724 M 0.88704 2.975 0.54753 D 0.999981 D 0.89917 1.0 D 0.97110 1.0 T 0.81093 -0.1089 10 0.87932 D 0 . 17.9259 0.88983 0.0:0.0:1.0:0.0 . 61 Q86TH1 ATL2_HUMAN H 61;170;61 ENSP00000346478:R61H;ENSP00000376781:R170H;ENSP00000376780:R61H ENSP00000346478:R61H R + 2 0 ADAMTSL2 135392439 1.000000 0.71417 1.000000 0.80357 0.790000 0.44656 9.401000 0.97294 2.229000 0.72834 0.491000 0.48974 CGC TCGA-IB-7652-01A-11D-2154-08 ADAMTSL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254619.1 1 0 1 51 245 0 143 0 9.997805e-01 1 62 0 143 2 0 0 0 0 0 2 1 1.000000 48 242 0 138 2 -20.000000 1 1 0 0 1 1 2 3 2.338965 1 0.360000 1.990000 0.457627 0.990000 0.860000 1.000000 1.000000 0.988490 0.990000 1 0.990000 1.000000 KCNT1 57582 broad.mit.edu 37 9 138675926 138675926 + Silent SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chr9:138675926C>T ENST00000263604.3 + 25 2841 c.2841C>T c.(2839-2841)gcC>gcT p.A947A KCNT1_ENST00000486577.2_Silent_p.A925A|KCNT1_ENST00000488444.2_Silent_p.A947A|KCNT1_ENST00000298480.5_Silent_p.A966A|KCNT1_ENST00000371757.2_Silent_p.A966A|KCNT1_ENST00000491806.2_Silent_p.A933A|KCNT1_ENST00000487664.1_Silent_p.A921A|KCNT1_ENST00000490355.2_Silent_p.A945A Q5JUK3 KCNT1_HUMAN potassium channel, subfamily T, member 1 50 Myeloproliferative disorder(178;0.0821) CGTTCGCCGCCGGCCGCGTCT 0.667000 0 SO:0001819 synonymous_variant ENST00000263604.3 1 1 hg19 TCGA-IB-7652-01A-11D-2154-08 KCNT1-201 KNOWN basic|appris_candidate protein_coding protein_coding 0 0 1 41 353 0 222 0 0 0 0 222 2 0 0 0 0 0 2 1 1.000000 39 342 0 203 2 -2.879461 1 1 121396 11 40 1 1 2 3 2.338965 1 0.360000 1.990000 0.457627 0.680000 0.500000 0.890000 0.690000 0.693090 0.680000 0 0.580000 0.790000 TCEAL5 340543 broad.mit.edu 37 X 102529240 102529240 + Silent SNP T T A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:102529240T>A ENST00000372680.1 - 3 546 c.252A>T c.(250-252)ccA>ccT p.P84P NM_001012979.2 NP_001012997.1 Q5H9L2 TCAL5_HUMAN transcription elongation factor A (SII)-like 5 11 CCTCACTTTGTGGCTTGTCCT 0.587000 0 SO:0001819 synonymous_variant ENST00000372680.1 1 1 hg19 CCDS35356.1 TCGA-IB-7652-01A-11D-2154-08 TCEAL5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057696.1 1 0 1 148 796 0 332 0 4.253071e-01 0 9 0 332 2 0 0 0 0 0 2 1 1.000000 142 654 0 259 2 -20.000000 1 1 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.860000 0.740000 1.000000 0.870000 0.872519 0.860000 1 0.800000 0.940000 IGSF1 3547 broad.mit.edu 37 X 130409231 130409231 + Missense_Mutation SNP G G C TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:130409231G>C ENST00000361420.3 - 17 3293 c.3214C>G c.(3214-3216)Cag>Gag p.Q1072E IGSF1_ENST00000370903.3_Missense_Mutation_p.Q1077E|IGSF1_ENST00000370904.1_Missense_Mutation_p.Q1063E|IGSF1_ENST00000467244.1_5'Flank|IGSF1_ENST00000370910.1_Missense_Mutation_p.Q1063E Q8N6C5 IGSF1_HUMAN immunoglobulin superfamily, member 1 p.Q1072*(1) 78 GGACCAGGCTGGGCTAATAGG 0.542000 1 Substitution - Nonsense(1) SO:0001583 missense ENST00000361420.3 1 1 hg19 CCDS14629.1 . . . . . . . . . . G 10.88 1.474766 0.26511 . . ENSG00000147255 ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903 T;T;T;T 0.02974 4.09;4.09;4.09;4.09 4.83 4.83 0.62350 Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.751183 0.12360 N 0.475750 T 0.03651 0.0104 L 0.38953 1.18 0.28842 N 0.89655 B;B;B 0.23650 0.082;0.089;0.079 B;B;B 0.25614 0.036;0.062;0.039 T 0.25293 -1.0136 10 0.29301 T 0.29 . 12.231 0.54488 0.0:0.0:1.0:0.0 . 1063;516;1072 Q8N6C5-2;C9JP68;Q8N6C5 .;.;IGSF1_HUMAN E 1063;1072;1063;1077 ENSP00000359947:Q1063E;ENSP00000355010:Q1072E;ENSP00000359941:Q1063E;ENSP00000359940:Q1077E ENSP00000355010:Q1072E Q - 1 0 IGSF1 130236912 1.000000 0.71417 0.998000 0.56505 0.863000 0.49368 1.912000 0.39946 2.376000 0.81061 0.594000 0.82650 CAG TCGA-IB-7652-01A-11D-2154-08 IGSF1-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000058288.1 1 0 1 163 949 0 326 0 2.754233e-01 0 7 0 326 2 0 0 0 0 0 2 1 1.000000 162 940 0 322 2 -3.221884 1 1 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.800000 0.690000 0.930000 0.820000 0.816533 0.800000 0 0.750000 0.870000 IDS 3423 broad.mit.edu 37 X 148579704 148579704 + Silent SNP C C A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C A C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:148579704C>A ENST00000340855.6 - 5 851 c.642G>T c.(640-642)acG>acT p.T214T IDS_ENST00000370443.4_Silent_p.T214T|IDS_ENST00000541269.1_Silent_p.T3T|IDS_ENST00000370441.4_Silent_p.T214T|IDS_ENST00000490775.1_5'UTR|IDS_ENST00000422081.2_Silent_p.T3T NM_000202.5|NM_001166550.1 NP_000193.1|NP_001160022.1 P22304 IDS_HUMAN iduronate 2-sulfatase 20 Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662) GACTGGCTGACGTTTTCATCT 0.532000 0 SO:0001819 synonymous_variant ENST00000340855.6 1 1 hg19 CCDS14685.1 TCGA-IB-7652-01A-11D-2154-08 IDS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058677.3 0 0 0 24 651 0 209 0 1 0 835 0 209 2 0 0 0 0 0 2 1 1.000000 23 640 0 198 2 -3.193399 1 1 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.190000 0.120000 0.280000 0.200000 0.204598 0.190000 0 0.150000 0.240000 MTM1 4534 broad.mit.edu 37 X 149826497 149826497 + Silent SNP A A C TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:149826497A>C ENST00000370396.2 + 11 1311 c.1257A>C c.(1255-1257)gcA>gcC p.A419A MTM1_ENST00000306167.7_3'UTR|MTM1_ENST00000543350.1_Silent_p.A304A|MTM1_ENST00000413012.2_Silent_p.A382A|MTM1_ENST00000542741.1_Silent_p.A324A NM_000252.2 NP_000243.1 Q13496 MTM1_HUMAN myotubularin 1 26 Acute lymphoblastic leukemia(192;6.56e-05) ATAAATTTGCATCTGTGAGTA 0.318000 0 SO:0001819 synonymous_variant ENST00000370396.2 1 1 hg19 CCDS14694.1 TCGA-IB-7652-01A-11D-2154-08 MTM1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060847.3 1 0 1 50 270 0 76 1 9.999199e-01 27 51 0 76 2 0 0 0 0 0 2 1 1.000000 50 270 0 74 2 -20.000000 1 1 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.860000 0.660000 1.000000 1.000000 0.866615 0.860000 1 0.750000 0.980000 ASB9 140462 broad.mit.edu 37 X 15266898 15266898 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:15266898C>T ENST00000380488.4 - 6 1001 c.728G>A c.(727-729)aGc>aAc p.S243N ASB9_ENST00000546332.1_Missense_Mutation_p.S243N|ASB9_ENST00000473862.1_5'UTR|ASB9_ENST00000380485.3_Missense_Mutation_p.S243N|ASB9_ENST00000380483.3_Missense_Mutation_p.S233N NM_001031739.2 NP_001026909.1 Q96DX5 ASB9_HUMAN ankyrin repeat and SOCS box containing 9 15 Hepatocellular(33;0.183) GGCCAAGGGGCTCTCTGGAGG 0.557000 0 SO:0001583 missense ENST00000380488.4 1 1 hg19 CCDS35208.1 . . . . . . . . . . C 6.967 0.548435 0.13312 . . ENSG00000102048 ENST00000380483;ENST00000380485;ENST00000380488;ENST00000546332 T;T;T;T 0.65732 0.99;-0.17;-0.12;-0.17 5.78 1.15 0.20763 . 0.332697 0.42682 N 0.000673 T 0.47967 0.1474 L 0.39467 1.215 0.09310 N 1 B;B;B;B 0.24576 0.035;0.003;0.051;0.106 B;B;B;B 0.28139 0.019;0.005;0.086;0.063 T 0.35649 -0.9780 10 0.40728 T 0.16 -4.9969 6.2251 0.20703 0.0:0.6104:0.1283:0.2613 . 214;233;243;243 Q7Z4A2;Q9BVF5;Q96DX5;Q96DX5-2 .;.;ASB9_HUMAN;. N 233;243;243;243 ENSP00000369850:S233N;ENSP00000369852:S243N;ENSP00000369855:S243N;ENSP00000438943:S243N ENSP00000369850:S233N S - 2 0 ASB9 15176819 0.002000 0.14202 0.000000 0.03702 0.003000 0.03518 0.883000 0.28200 -0.105000 0.12132 -0.191000 0.12829 AGC TCGA-IB-7652-01A-11D-2154-08 ASB9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055844.1 1 0 1 80 421 0 163 0 9.980183e-01 1 50 0 163 2 0 0 0 0 0 2 1 1.000000 79 419 0 159 2 -20.000000 1 0 121412 6 35 1 0 1 1 0.360000 1.990000 0.360000 0.880000 0.710000 1.000000 1.000000 0.885739 0.880000 1 0.790000 0.980000 ASB9 140462 broad.mit.edu 37 X 15266926 15266926 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:15266926G>A ENST00000380488.4 - 6 973 c.700C>T c.(700-702)Cgt>Tgt p.R234C ASB9_ENST00000546332.1_Missense_Mutation_p.R234C|ASB9_ENST00000473862.1_5'UTR|ASB9_ENST00000380485.3_Missense_Mutation_p.R234C|ASB9_ENST00000380483.3_Missense_Mutation_p.R224C NM_001031739.2 NP_001026909.1 Q96DX5 ASB9_HUMAN ankyrin repeat and SOCS box containing 9 15 Hepatocellular(33;0.183) TCCACAGGACGTTTGCCTTCA 0.557000 0 SO:0001583 missense ENST00000380488.4 1 1 hg19 CCDS35208.1 . . . . . . . . . . G 11.24 1.580533 0.28180 . . ENSG00000102048 ENST00000380483;ENST00000380485;ENST00000380488;ENST00000546332 T;T;T;T 0.53640 0.61;0.61;0.61;0.61 5.92 4.17 0.49024 Ankyrin repeat-containing domain (3); 0.273432 0.42420 N 0.000717 T 0.41328 0.1154 L 0.54965 1.715 0.49483 D 0.999798 B;B;B;B 0.29188 0.236;0.05;0.03;0.157 B;B;B;B 0.29598 0.104;0.019;0.012;0.026 T 0.29941 -0.9995 10 0.62326 D 0.03 -10.1573 7.8005 0.29172 0.1464:0.0:0.7222:0.1313 . 205;224;234;234 Q7Z4A2;Q9BVF5;Q96DX5;Q96DX5-2 .;.;ASB9_HUMAN;. C 224;234;234;234 ENSP00000369850:R224C;ENSP00000369852:R234C;ENSP00000369855:R234C;ENSP00000438943:R234C ENSP00000369850:R224C R - 1 0 ASB9 15176847 0.993000 0.37304 0.143000 0.22291 0.565000 0.35776 1.270000 0.33086 0.638000 0.30545 -0.208000 0.12717 CGT TCGA-IB-7652-01A-11D-2154-08 ASB9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055844.1 1 0 1 78 395 0 168 1 9.991435e-01 4 51 0 168 2 0 0 0 0 0 2 1 1.000000 73 393 0 164 2 -20.000000 1 0 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.910000 0.730000 1.000000 1.000000 0.909305 0.910000 1 0.820000 1.000000 FLNA 2316 broad.mit.edu 37 X 153577233 153577233 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:153577233C>T ENST00000369850.3 - 48 8164 c.7928G>A c.(7927-7929)cGc>cAc p.R2643H FLNA_ENST00000369856.3_Missense_Mutation_p.R776H|FLNA_ENST00000422373.1_Missense_Mutation_p.R2635H|FLNA_ENST00000344736.4_Missense_Mutation_p.R2603H|FLNA_ENST00000360319.4_Missense_Mutation_p.R2635H|FLNA_ENST00000498491.1_5'Flank NM_001110556.1 NP_001104026.1 P21333 FLNA_HUMAN filamin A, alpha 6 all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176) CACCACAACGCGGTAGGGGCT 0.687000 0 SO:0001583 missense ENST00000369850.3 1 1 hg19 CCDS48194.1 . . . . . . . . . . C 11.21 1.570226 0.28003 . . ENSG00000196924 ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000369856;ENST00000344736 D;D;D;D;D 0.84589 -1.87;-1.87;-1.87;-1.87;-1.87 5.74 3.7 0.42460 Immunoglobulin E-set (1);Immunoglobulin-like fold (1); 0.062457 0.64402 D 0.000011 T 0.61022 0.2314 N 0.03948 -0.315 0.35918 D 0.831602 B;B;B;B 0.09022 0.002;0.0;0.001;0.001 B;B;B;B 0.15484 0.001;0.001;0.013;0.013 T 0.53809 -0.8386 10 0.17832 T 0.49 . 2.1844 0.03882 0.0:0.3694:0.3076:0.323 . 776;2635;2643;2643 E9PHF0;P21333-2;P21333;E9KL45 .;.;FLNA_HUMAN;. H 2635;2311;2635;2643;776;2603 ENSP00000353467:R2635H;ENSP00000416926:R2635H;ENSP00000358866:R2643H;ENSP00000358872:R776H;ENSP00000358863:R2603H ENSP00000358863:R2603H R - 2 0 FLNA 153230427 0.644000 0.27277 0.766000 0.31476 0.858000 0.48976 1.084000 0.30828 1.172000 0.42781 0.529000 0.55759 CGC TCGA-IB-7652-01A-11D-2154-08 FLNA-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000058942.3 0 0 0 12 388 0 218 0 9.999954e-01 1 822 0 218 2 0 0 0 0 0 2 1 0.999064 12 382 0 216 2 -3.386818 1 1 120942 3 31 1 0 1 1 0.360000 1.990000 0.360000 0.160000 0.080000 0.280000 0.160000 0.178844 0.160000 0 0.120000 0.230000 PPEF1 5475 broad.mit.edu 37 X 18845404 18845404 + Silent SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:18845404C>T ENST00000361511.4 + 19 2255 c.1761C>T c.(1759-1761)tcC>tcT p.S587S PPEF1_ENST00000349874.5_Silent_p.S525S|PPEF1_ENST00000544635.1_Silent_p.S522S|PPEF1_ENST00000543630.1_3'UTR|PPEF1_ENST00000359763.6_Silent_p.S534S NM_006240.2|NM_152224.1 NP_006231.2|NP_689410.1 O14829 PPE1_HUMAN protein phosphatase, EF-hand calcium binding domain 1 43 Hepatocellular(33;0.183) GCCTGATCTCCGTGGAAGAAT 0.418000 0 SO:0001819 synonymous_variant ENST00000361511.4 1 1 hg19 CCDS14188.1 TCGA-IB-7652-01A-11D-2154-08 PPEF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055953.3 1 0 1 108 442 0 184 0 3.913671e-02 0 2 0 184 2 0 0 0 0 0 2 1 1.000000 109 437 0 184 2 -2.887929 1 1 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.990000 0.900000 1.000000 1.000000 0.992583 0.990000 1 0.990000 1.000000 CXorf21 80231 broad.mit.edu 37 X 30578132 30578132 + Missense_Mutation SNP G G T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:30578132G>T ENST00000378962.3 - 3 663 c.341C>A c.(340-342)cCa>cAa p.P114Q NM_025159.2 NP_079435.1 Q9HAI6 CX021_HUMAN chromosome X open reading frame 21 20 GCAAGAAGATGGAACCAAGTA 0.443000 0 SO:0001583 missense ENST00000378962.3 1 1 hg19 CCDS14224.1 . . . . . . . . . . G 17.96 3.515532 0.64634 . . ENSG00000120280 ENST00000378962 . . . 4.94 4.05 0.47172 . 0.000000 0.64402 D 0.000005 T 0.75221 0.3820 M 0.66939 2.045 0.52501 D 0.999955 D 0.89917 1.0 D 0.81914 0.995 T 0.76934 -0.2775 9 0.54805 T 0.06 -14.154 12.9145 0.58199 0.0824:0.0:0.9176:0.0 . 114 Q9HAI6 CX021_HUMAN Q 114 . ENSP00000368245:P114Q P - 2 0 CXorf21 30488053 1.000000 0.71417 1.000000 0.80357 0.965000 0.64279 7.264000 0.78432 2.279000 0.76181 0.422000 0.28245 CCA TCGA-IB-7652-01A-11D-2154-08 CXorf21-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056164.1 1 0 1 155 714 0 291 0 9.511243e-01 0 25 0 291 2 0 0 0 0 0 2 1 1.000000 155 710 0 288 2 -2.691029 1 1 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.980000 0.840000 1.000000 1.000000 0.967438 0.980000 1 0.910000 1.000000 DMD 1756 broad.mit.edu 37 X 31198512 31198512 + Missense_Mutation SNP T T A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:31198512T>A ENST00000357033.4 - 69 10267 c.10061A>T c.(10060-10062)tAt>tTt p.Y3354F DMD_ENST00000378723.3_Missense_Mutation_p.Y286F|DMD_ENST00000343523.2_Missense_Mutation_p.Y894F|DMD_ENST00000474231.1_Missense_Mutation_p.Y894F|DMD_ENST00000378702.4_Missense_Mutation_p.Y286F|DMD_ENST00000378707.3_Missense_Mutation_p.Y894F|DMD_ENST00000359836.1_Missense_Mutation_p.Y894F|DMD_ENST00000378680.2_Missense_Mutation_p.Y286F|DMD_ENST00000541735.1_Missense_Mutation_p.Y894F|DMD_ENST00000361471.4_Missense_Mutation_p.Y286F|DMD_ENST00000378677.2_Missense_Mutation_p.Y3350F NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2 NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1 P11532 DMD_HUMAN dystrophin 77 all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203) CACCATGGGATAGTGCATTTT 0.418000 0 SO:0001583 missense ENST00000357033.4 1 1 hg19 CCDS14233.1 . . . . . . . . . . T 23.4 4.417414 0.83449 . . ENSG00000198947 ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378723;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000378702;ENST00000474231;ENST00000361471;ENST00000378680;ENST00000378705 D;D;D;D;D;D;D;D;D;D;D;D;D 0.87334 -2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24 5.03 3.8 0.43715 Zinc finger, ZZ-type (1); 0.000000 0.32372 U 0.006187 D 0.92590 0.7646 M 0.83953 2.67 0.58432 D 0.999999 B;D;D;B;D;D;D;D;D;D;D;D;D;D;P;D 0.89917 0.002;0.957;0.997;0.06;0.997;0.997;0.995;0.996;0.996;0.999;0.999;1.0;0.974;0.985;0.743;0.997 B;P;D;B;D;D;D;D;D;D;D;D;D;P;P;D 0.80764 0.003;0.754;0.97;0.018;0.97;0.97;0.962;0.917;0.917;0.986;0.994;0.986;0.969;0.871;0.493;0.97 D 0.92983 0.6408 10 0.87932 D 0 . 10.1983 0.43067 0.1502:0.0:0.0:0.8498 . 286;3346;3354;3350;2013;2010;894;894;894;894;894;3231;286;286;286;286 B4DSV7;P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3;P11532-5;Q8N754;Q6NSJ9;E9PDN1 .;.;DMD_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;. F 3346;2013;2010;286;1050;3350;3354;894;894;3354;3231;894;894;286;894;286;286;144 ENSP00000367997:Y286F;ENSP00000350765:Y1050F;ENSP00000367948:Y3350F;ENSP00000354923:Y3354F;ENSP00000352894:Y894F;ENSP00000340057:Y894F;ENSP00000367979:Y894F;ENSP00000444119:Y894F;ENSP00000367974:Y286F;ENSP00000417123:Y894F;ENSP00000354464:Y286F;ENSP00000367951:Y286F;ENSP00000367977:Y144F ENSP00000340057:Y894F Y - 2 0 DMD 31108433 1.000000 0.71417 0.995000 0.50966 0.998000 0.95712 7.825000 0.86693 1.868000 0.54150 0.441000 0.28932 TAT TCGA-IB-7652-01A-11D-2154-08 DMD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056182.2 0 0 0 16 410 0 119 0 5.798785e-01 0 50 0 119 2 0 0 0 0 0 2 1 0.999930 16 406 0 117 2 -16.057510 1 1 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.210000 0.120000 0.320000 0.210000 0.219730 0.210000 0 0.160000 0.270000 CXorf22 170063 broad.mit.edu 37 X 35989882 35989882 + Missense_Mutation SNP G G A TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:35989882G>A ENST00000297866.5 + 12 2216 c.2150G>A c.(2149-2151)aGa>aAa p.R717K NM_152632.3 NP_689845.2 Q6ZTR5 CX022_HUMAN chromosome X open reading frame 22 44 GAGTCTGTGAGAAGAAAGGCA 0.368000 0 SO:0001583 missense ENST00000297866.5 1 1 hg19 CCDS14237.2 . . . . . . . . . . G 0.010 -1.793016 0.00623 . . ENSG00000165164 ENST00000297866 T 0.13307 2.6 5.6 -7.87 0.01183 . 1.479880 0.03603 N 0.233690 T 0.05547 0.0146 N 0.05124 -0.11 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.43081 -0.9413 10 0.06365 T 0.9 -14.1458 12.5433 0.56184 0.7855:0.1024:0.1122:0.0 . 717 Q6ZTR5 CX022_HUMAN K 717 ENSP00000297866:R717K ENSP00000297866:R717K R + 2 0 CXorf22 35899803 0.000000 0.05858 0.000000 0.03702 0.012000 0.07955 -1.217000 0.02979 -1.390000 0.02087 -0.190000 0.12839 AGA TCGA-IB-7652-01A-11D-2154-08 CXorf22-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056216.2 0 0 1 70 332 0 139 0 0 0 0 139 2 0 0 0 0 0 2 1 1.000000 69 330 0 139 2 -20.000000 1 1 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.960000 0.760000 1.000000 1.000000 0.942435 0.960000 1 0.860000 1.000000 HEPH 9843 broad.mit.edu 37 X 65409671 65409671 + Silent SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:65409671C>T ENST00000343002.2 + 5 1618 c.954C>T c.(952-954)caC>caT p.H318H HEPH_ENST00000336279.5_Silent_p.H51H|HEPH_ENST00000419594.1_Silent_p.H321H|HEPH_ENST00000441993.2_Silent_p.H321H|HEPH_ENST00000519389.1_Silent_p.H372H|HEPH_ENST00000374727.3_Silent_p.H321H Q9BQS7 HEPH_HUMAN hephaestin 89 CCCGTGGACACCACACTGATG 0.507000 0 SO:0001819 synonymous_variant ENST00000343002.2 0 1 hg19 TCGA-IB-7652-01A-11D-2154-08 HEPH-002 KNOWN alternative_5_UTR|basic|appris_candidate protein_coding protein_coding OTTHUMT00000056995.1 0 0 0 45 189 0 56 1 9.996183e-01 4 49 0 56 2 0 0 0 0 0 2 1 1.000000 45 185 0 56 2 -20.000000 1 1 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.990000 0.800000 1.000000 1.000000 0.973951 0.990000 1 0.920000 1.000000 PCDH11X 27328 broad.mit.edu 37 X 91090988 91090988 + Missense_Mutation SNP C C T TCGA-IB-7652-01A-11D-2154-08 TCGA-IB-7652-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx ecd22f1b-a14d-4374-a187-e549cce31df3 ac6e1f37-95f0-4fc5-b7be-72c734fc19c9 g.chrX:91090988C>T ENST00000373094.1 + 1 1330 c.485C>T c.(484-486)gCg>gTg p.A162V PCDH11X_ENST00000298274.8_Missense_Mutation_p.A162V|PCDH11X_ENST00000361724.1_Missense_Mutation_p.A162V|PCDH11X_ENST00000373088.1_Missense_Mutation_p.A162V|PCDH11X_ENST00000395337.2_Missense_Mutation_p.A162V|PCDH11X_ENST00000504220.2_Missense_Mutation_p.A162V|PCDH11X_ENST00000361655.2_Missense_Mutation_p.A162V|PCDH11X_ENST00000406881.1_Missense_Mutation_p.A162V|PCDH11X_ENST00000373097.1_Missense_Mutation_p.A162V NM_032968.3 NP_116750.1 Q9BZA7 PC11X_HUMAN protocadherin 11 X-linked 159 ACTCTCCCAGCGGCTGTTGAT 0.343000 NSCLC(38;925 1092 2571 38200 45895) 0 SO:0001583 missense ENST00000373094.1 1 1 hg19 CCDS14461.1 . . . . . . . . . . C 11.22 1.575181 0.28092 . . ENSG00000102290 ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274 T;T;T;T;T;T;T;T;T 0.53857 0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6 4.44 3.54 0.40534 Cadherin (4);Cadherin-like (1); 0.138116 0.49916 D 0.000122 T 0.29190 0.0726 N 0.11651 0.15 0.35926 D 0.832189 B;B;P;P;P;P;B;B 0.37101 0.083;0.191;0.526;0.526;0.526;0.582;0.047;0.047 B;B;B;B;B;B;B;B 0.31442 0.018;0.036;0.08;0.08;0.08;0.13;0.019;0.019 T 0.31503 -0.9941 10 0.25106 T 0.35 . 12.5927 0.56451 0.0:0.836:0.164:0.0 . 162;162;162;162;162;162;162;162 Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2 .;.;.;.;.;PC11X_HUMAN;.;. V 162 ENSP00000378746:A162V;ENSP00000362186:A162V;ENSP00000362189:A162V;ENSP00000355040:A162V;ENSP00000362180:A162V;ENSP00000423762:A162V;ENSP00000355105:A162V;ENSP00000384758:A162V;ENSP00000298274:A162V ENSP00000298274:A162V A + 2 0 PCDH11X 90977644 0.999000 0.42202 0.953000 0.39169 0.537000 0.34900 4.217000 0.58547 0.938000 0.37419 0.506000 0.49869 GCG TCGA-IB-7652-01A-11D-2154-08 PCDH11X-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000057436.1 1 0 1 68 423 0 132 0 0 0 0 132 2 0 0 0 0 0 2 1 1.000000 65 402 0 144 2 -20.000000 1 1 0 0 1 0 1 1 0.360000 1.990000 0.360000 0.760000 0.600000 0.940000 0.760000 0.774502 0.760000 0 0.680000 0.860000