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 LRIG3 121227 broad.mit.edu 37 12 59277344 59277344 + Frame_Shift_Del DEL A A - TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 A - A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr12:59277344delA ENST00000320743.3 - 11 1560 c.1274delT c.(1273-1275)ttafs p.L425fs LRIG3_ENST00000379141.4_Frame_Shift_Del_p.L365fs NM_153377.4 NP_700356.2 Q6UXM1 LRIG3_HUMAN leucine-rich repeats and immunoglobulin-like domains 3 LRIG3/ROS1(2) 48 GBM - Glioblastoma multiforme(1;1.17e-18) ATTGCCTTGTAAAGACATGAT 0.383000 T ROS1 NSCLC Dom yes 12 12q14.1 121227 leucine-rich repeats and immunoglobulin-like domains 3 E 0 SO:0001589 frameshift_variant ENST00000320743.3 1 0 hg19 CCDS8960.1 TCGA-IB-A5SS-01A-11D-A32N-08 LRIG3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406623.1 1 0 0 36 199 0 58 1 9.983174e-01 6 51 0 58 2 0 0 0 0 1 0.959804 37 196 3 58 24 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.141350 0 0.460000 1.850000 0.469756 0.680000 4.900000e-01 1.000000 0.670000 0.707925 0.680000 0 0.580000 0.820000 SMAD4 4089 broad.mit.edu 37 18 48604697 48604698 + Frame_Shift_Del DEL AA AA - TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 AA - AA AA Valid Somatic Phase_I WXS targeted Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr18:48604697_48604698delAA ENST00000342988.3 + 12 2057_2058 c.1519_1520delAA c.(1519-1521)aaafs p.K507fs SMAD4_ENST00000588745.1_Frame_Shift_Del_p.K411fs|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Frame_Shift_Del_p.K507fs NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(2)|p.K507Q(2) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) GAGTTTTGTGAAAGGCTGGGGA 0.470000 40 Whole gene deletion(36)|Substitution - Missense(2)|Unknown(2) SO:0001589 frameshift_variant ENST00000342988.3 1 0 hg19 CCDS11950.1 TCGA-IB-A5SS-01A-11D-A32N-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 0 51 236 0 75 1 1 36 128 0 75 2 1 1 198 844 0 1078 2 1 1.000000 53 229 1 76 14 0 0 0 0 0 0 -3.407717 1 1 0 0 1 0 1 1 1.626997 1 0.460000 1.850000 0.298701 0.580000 4.500000e-01 0.740000 0.590000 0.597468 0.580000 0 0.510000 0.670000 PYROXD2 84795 broad.mit.edu 37 10 100155147 100155147 + Splice_Site SNP C C A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr10:100155147C>A ENST00000370575.4 - 7 736 c.e7+1 PYROXD2_ENST00000483923.1_Splice_Site|MIR1287_ENST00000408492.1_RNA NM_032709.2 NP_116098.2 Q8N2H3 PYRD2_HUMAN pyridine nucleotide-disulphide oxidoreductase domain 2 12 GAACCACTCACCTTGGTAATG 0.577000 0 SO:0001630 splice_region_variant ENST00000370575.4 0 1 hg19 CCDS7474.1 . . . . . . . . . . C 18.58 3.654104 0.67472 . . ENSG00000119943 ENST00000370575 . . . 5.14 5.14 0.70334 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 17.4032 0.87466 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . PYROXD2 100145137 1.000000 0.71417 0.993000 0.49108 0.817000 0.46193 3.922000 0.56462 2.386000 0.81285 0.655000 0.94253 . TCGA-IB-A5SS-01A-11D-A32N-08 PYROXD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049782.2 0 0 0 7 858 0 246 0 0 0 0 246 2 0 0 0 0 0 2 1 0.980057 7 851 0 241 2 0 0 0 0 246 2 -3.308682 1 1 0 0 1 1 2 3 2.587009 1 0.460000 1.850000 0.560976 0.040000 0 0.090000 0.040000 0.047916 0.040000 0 0.010000 0.070000 SLC39A12 221074 broad.mit.edu 37 10 18292111 18292111 + Missense_Mutation SNP G G A rs142064736 byFrequency TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr10:18292111G>A ENST00000377369.2 + 12 2044 c.1771G>A c.(1771-1773)Gtg>Atg p.V591M SLC39A12_ENST00000377374.4_Missense_Mutation_p.V554M|SLC39A12-AS1_ENST00000445287.1_RNA|SLC39A12_ENST00000539911.1_Missense_Mutation_p.V457M|SLC39A12-AS1_ENST00000439319.1_RNA|SLC39A12_ENST00000377371.3_Missense_Mutation_p.V590M NM_001145195.1|NM_001282733.1|NM_001282734.1 NP_001138667.1|NP_001269662.1|NP_001269663.1 Q504Y0 S39AC_HUMAN solute carrier family 39 (zinc transporter), member 12 60 AGACTTTGCCGTGCTCTTAAG 0.393000 0 SO:0001583 missense ENST00000377369.2 1 0 hg19 CCDS44362.1 9 0.004120879120879121 8 0.016260162601626018 1 0.0027624309392265192 0 0.0 0 0.0 G 24.0 4.485154 0.84854 0.008171 2.33E-4 ENSG00000148482 ENST00000377369;ENST00000377374;ENST00000377371;ENST00000539911;ENST00000425219 T;T;T;T 0.51071 0.72;0.72;0.72;0.72 5.48 5.48 0.80851 . 0.000000 0.85682 D 0.000000 T 0.52789 0.1756 M 0.64080 1.96 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;0.995;1.0 T 0.62378 -0.6867 10 0.52906 T 0.07 -15.6242 19.7024 0.96060 0.0:0.0:1.0:0.0 . 590;591;554 Q504Y0-4;Q504Y0;Q504Y0-3 .;S39AC_HUMAN;. M 591;554;590;457;511 ENSP00000366586:V591M;ENSP00000366591:V554M;ENSP00000366588:V590M;ENSP00000440445:V457M ENSP00000366586:V591M V + 1 0 SLC39A12 18332117 1.000000 0.71417 1.000000 0.80357 0.931000 0.56810 7.972000 0.88022 2.724000 0.93272 0.655000 0.94253 GTG TCGA-IB-A5SS-01A-11D-A32N-08 SLC39A12-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding 1 0 1 68 314 0 109 0 0 0 0 109 2 0 0 0 0 0 2 1 1.000000 68 313 0 109 2 0 0 0 0 109 2 -3.465666 1 1 121412 108 55 1 0 0 0 2.071590 0 0.460000 1.850000 0.460000 0.770000 6.100000e-01 0.940000 0.770000 0.778631 0.770000 0 0.680000 0.860000 APBB1IP 54518 broad.mit.edu 37 10 26785284 26785284 + Missense_Mutation SNP G G C TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr10:26785284G>C ENST00000376236.4 + 4 579 c.124G>C c.(124-126)Gaa>Caa p.E42Q APBB1IP_ENST00000356785.4_Missense_Mutation_p.E42Q NM_019043.3 NP_061916.3 Q7Z5R6 AB1IP_HUMAN amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein 45 ACCCAGAGCTGAATTTAACTA 0.348000 0 SO:0001583 missense ENST00000376236.4 0 1 hg19 CCDS31167.1 . . . . . . . . . . G 25.2 4.618637 0.87460 . . ENSG00000077420 ENST00000445780;ENST00000376236;ENST00000356785 T 0.35421 1.31 5.87 5.87 0.94306 . 0.086924 0.85682 D 0.000000 T 0.58438 0.2122 L 0.59436 1.845 0.52501 D 0.999951 P;D;D 0.89917 0.822;1.0;1.0 P;D;D 0.74023 0.651;0.946;0.982 T 0.55062 -0.8199 10 0.59425 D 0.04 . 18.7629 0.91860 0.0:0.0:1.0:0.0 . 42;42;42 B4E100;Q7Z5R6;Q8IYL7 .;AB1IP_HUMAN;. Q 42 ENSP00000365411:E42Q ENSP00000349237:E42Q E + 1 0 APBB1IP 26825290 1.000000 0.71417 0.993000 0.49108 0.986000 0.74619 6.107000 0.71517 2.941000 0.99782 0.655000 0.94253 GAA TCGA-IB-A5SS-01A-11D-A32N-08 APBB1IP-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047270.1 0 0 0 4 228 0 58 0 1.752873e-01 0 35 0 58 2 0 0 0 0 0 2 0 0.882774 0 226 0 57 2 0 0 0 0 58 2 -5.210345 1 0 0 0 1 0 0 0 2.071590 0 0.460000 1.850000 0.460000 0.080000 2.000000e-02 0.180000 0.080000 0.092395 0.080000 0 0.040000 0.130000 LRIT1 26103 broad.mit.edu 37 10 85991943 85991943 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr10:85991943C>T ENST00000372105.3 - 4 1633 c.1612G>A c.(1612-1614)Gtc>Atc p.V538I NM_015613.2 NP_056428.1 Q9P2V4 LRIT1_HUMAN leucine-rich repeat, immunoglobulin-like and transmembrane domains 1 p.V538I(1) 23 AGGGCAATGACGATGGCCACA 0.532000 1 Substitution - Missense(1) SO:0001583 missense ENST00000372105.3 1 1 hg19 CCDS7373.1 . . . . . . . . . . C 9.192 1.026386 0.19512 . . ENSG00000148602 ENST00000372105 T 0.42513 0.97 5.62 2.5 0.30297 . 0.565141 0.18543 N 0.138159 T 0.24044 0.0582 L 0.41632 1.29 0.42532 D 0.993043 P 0.36633 0.562 B 0.29862 0.108 T 0.07770 -1.0755 10 0.07030 T 0.85 . 7.4198 0.27065 0.0:0.6491:0.0:0.3509 . 538 Q9P2V4 LRIT1_HUMAN I 538 ENSP00000361177:V538I ENSP00000361177:V538I V - 1 0 LRIT1 85981923 0.981000 0.34729 0.410000 0.26471 0.092000 0.18411 2.499000 0.45372 0.580000 0.29522 0.563000 0.77884 GTC TCGA-IB-A5SS-01A-11D-A32N-08 LRIT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049109.1 1 0 1 30 163 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 30 160 0 44 2 0 0 0 0 44 2 -20.000000 1 1 121412 2 31 1 1 2 3 2.562086 1 0.460000 1.850000 0.560976 0.830000 5.800000e-01 1.000000 1.000000 0.835718 0.830000 0 0.700000 0.980000 SLIT1 6585 broad.mit.edu 37 10 98816094 98816094 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr10:98816094G>A ENST00000266058.4 - 13 1530 c.1285C>T c.(1285-1287)Cgg>Tgg p.R429W ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Missense_Mutation_p.R429W NM_003061.2 NP_003052.2 O75093 SLIT1_HUMAN slit homolog 1 (Drosophila) 78 Colorectal(252;0.162) TGGATGGCCCGCAGGGAGGTG 0.622000 0 SO:0001583 missense ENST00000266058.4 0 1 hg19 CCDS7453.1 . . . . . . . . . . G 20.8 4.056410 0.76074 . . ENSG00000187122 ENST00000266058;ENST00000371057;ENST00000371070;ENST00000314867 T;T;T 0.58210 1.8;1.8;0.35 4.91 1.86 0.25419 . 0.059286 0.64402 D 0.000002 T 0.65647 0.2711 L 0.54908 1.71 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.80764 0.994;0.922 T 0.66791 -0.5834 10 0.87932 D 0 . 13.5661 0.61819 0.0:0.0:0.593:0.407 . 439;429 E7EWQ8;O75093 .;SLIT1_HUMAN W 429;439;429;422 ENSP00000266058:R429W;ENSP00000360109:R429W;ENSP00000315005:R422W ENSP00000266058:R429W R - 1 2 SLIT1 98806084 1.000000 0.71417 0.998000 0.56505 0.979000 0.70002 5.433000 0.66520 0.194000 0.20326 0.561000 0.74099 CGG TCGA-IB-A5SS-01A-11D-A32N-08 SLIT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049636.1 0 0 0 6 362 0 98 0 1.197704e-03 0 3 0 98 2 0 0 0 0 0 2 1 0.964396 6 359 0 96 2 0 0 0 0 98 2 -2.637073 1 1 121410 2 34 1 1 2 3 2.587009 1 0.460000 1.850000 0.560976 0.090000 3.000000e-02 0.180000 0.090000 0.100985 0.090000 0 0.050000 0.140000 SORL1 6653 broad.mit.edu 37 11 121428026 121428026 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr11:121428026G>A ENST00000260197.7 + 19 2704 c.2575G>A c.(2575-2577)Gct>Act p.A859T NM_003105.5 NP_003096 Q92673 SORL_HUMAN sortilin-related receptor, L(DLR class) A repeats containing 91 Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113) TTGTCAGGTAGCTAATCCAGA 0.532000 0 SO:0001583 missense ENST00000260197.7 1 1 hg19 CCDS8436.1 . . . . . . . . . . G 15.99 2.994993 0.54041 . . ENSG00000137642 ENST00000260197 D 0.91124 -2.79 5.31 5.31 0.75309 Six-bladed beta-propeller, TolB-like (1); 0.334487 0.31519 N 0.007520 D 0.91597 0.7345 M 0.74258 2.255 0.80722 D 1 B 0.27910 0.193 B 0.34536 0.185 D 0.89616 0.3845 10 0.41790 T 0.15 . 18.9779 0.92745 0.0:0.0:1.0:0.0 . 859 Q92673 SORL_HUMAN T 859 ENSP00000260197:A859T ENSP00000260197:A859T A + 1 0 SORL1 120933236 0.998000 0.40836 0.999000 0.59377 0.998000 0.95712 3.282000 0.51693 2.487000 0.83934 0.655000 0.94253 GCT TCGA-IB-A5SS-01A-11D-A32N-08 SORL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387626.2 1 0 1 76 233 0 113 1 9.999614e-01 27 22 0 113 2 0 0 0 0 0 2 1 1.000000 76 229 0 110 2 0 0 0 0 113 2 -20.000000 1 1 0 0 1 1 2 3 2.087795 0 0.460000 1.850000 0.462473 0.990000 8.700000e-01 1.000000 1.000000 0.986102 0.990000 1 0.960000 1.000000 KCNC1 3746 broad.mit.edu 37 11 17757790 17757790 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr11:17757790G>A ENST00000379472.3 + 1 271 c.241G>A c.(241-243)Gac>Aac p.D81N KCNC1_ENST00000265969.6_Missense_Mutation_p.D81N NM_004976.4 NP_004967.1 P48547 KCNC1_HUMAN potassium voltage-gated channel, Shaw-related subfamily, member 1 33 Dalfampridine(DB06637) CTGCCCAGCCGACGTGTGCGG 0.662000 0 SO:0001583 missense ENST00000379472.3 0 1 hg19 CCDS7827.1 . . . . . . . . . . G 17.57 3.422598 0.62622 . . ENSG00000129159 ENST00000265969;ENST00000379472 T;T 0.76060 -0.99;-0.99 5.3 3.44 0.39384 BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1); 0.099935 0.64402 N 0.000002 T 0.57873 0.2083 L 0.27975 0.815 0.80722 D 1 B;P 0.42375 0.246;0.778 B;B 0.39503 0.052;0.301 T 0.50898 -0.8773 10 0.11794 T 0.64 . 11.4045 0.49889 0.1469:0.0:0.8531:0.0 . 81;81 Q3KNS8;P48547 .;KCNC1_HUMAN N 81 ENSP00000265969:D81N;ENSP00000368785:D81N ENSP00000265969:D81N D + 1 0 KCNC1 17714366 1.000000 0.71417 1.000000 0.80357 0.975000 0.68041 6.757000 0.74924 0.629000 0.30376 0.491000 0.48974 GAC TCGA-IB-A5SS-01A-11D-A32N-08 KCNC1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000389389.1 0 0 0 5 240 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 0.934743 2 238 0 61 2 0 0 0 0 61 2 -6.350677 1 0 0 0 1 1 2 3 2.076771 0 0.460000 1.850000 0.461239 0.090000 3.000000e-02 0.200000 0.090000 0.105360 0.090000 0 0.050000 0.150000 KIF18A 81930 broad.mit.edu 37 11 28080600 28080600 + Missense_Mutation SNP C C G TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr11:28080600C>G ENST00000263181.6 - 13 2111 c.1821G>C c.(1819-1821)ttG>ttC p.L607F MIR610_ENST00000385139.1_RNA NM_031217.3 NP_112494.3 Q8NI77 KI18A_HUMAN kinesin family member 18A 36 TCCTCTCTACCAAATGTTCGA 0.408000 0 SO:0001583 missense ENST00000263181.6 0 1 hg19 CCDS7867.1 . . . . . . . . . . C 14.40 2.524458 0.44969 . . ENSG00000121621 ENST00000263181 T 0.77098 -1.07 5.62 0.802 0.18686 . 0.070738 0.56097 D 0.000026 D 0.84215 0.5423 M 0.70275 2.135 0.46521 D 0.999083 D 0.89917 1.0 D 0.73380 0.98 T 0.81701 -0.0813 10 0.51188 T 0.08 . 10.6652 0.45726 0.0:0.2739:0.0:0.7261 . 607 Q8NI77 KI18A_HUMAN F 607 ENSP00000263181:L607F ENSP00000263181:L607F L - 3 2 KIF18A 28037176 0.986000 0.35501 0.989000 0.46669 0.381000 0.30169 0.007000 0.13174 -0.080000 0.12685 -0.229000 0.12294 TTG TCGA-IB-A5SS-01A-11D-A32N-08 KIF18A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388328.3 0 0 0 9 522 0 136 0 2.183688e-02 0 12 0 136 2 0 0 0 0 0 2 1 0.993828 9 513 0 135 2 0 0 0 0 136 2 -1.977695 0 1 0 0 1 1 2 3 2.076771 0 0.460000 1.850000 0.461239 0.070000 3.000000e-02 0.140000 0.080000 0.081580 0.070000 0 0.050000 0.110000 NOS1 4842 broad.mit.edu 37 12 117662845 117662845 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr12:117662845G>A ENST00000338101.4 - 25 3908 c.3904C>T c.(3904-3906)Cgg>Tgg p.R1302W NOS1_ENST00000317775.6_Missense_Mutation_p.R1268W|NOS1_ENST00000344089.3_3'UTR Q8WY41 NANO1_HUMAN nitric oxide synthase 1 (neuronal) 117 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) TCAAATTGCCGCTGTTGCCAG 0.612000 Esophageal Squamous(162;1748 2599 51982 52956) 0 SO:0001583 missense ENST00000338101.4 1 1 hg19 CCDS55890.1 . . . . . . . . . . G 19.69 3.874204 0.72180 . . ENSG00000089250 ENST00000397605;ENST00000317775;ENST00000338101 D;D 0.85258 -1.96;-1.96 4.93 4.0 0.46444 Oxidoreductase FAD/NAD(P)-binding (1);Flavoprotein pyridine nucleotide cytochrome reductase (1); 0.000000 0.85682 D 0.000000 D 0.93680 0.7981 M 0.93594 3.435 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.94520 0.7726 10 0.66056 D 0.02 -31.3949 13.4871 0.61373 0.0:0.0:0.731:0.269 . 1268 P29475 NOS1_HUMAN W 1163;1268;1302 ENSP00000320758:R1268W;ENSP00000337459:R1302W ENSP00000320758:R1268W R - 1 2 NOS1 116147228 1.000000 0.71417 1.000000 0.80357 0.911000 0.54048 2.995000 0.49441 2.555000 0.86185 0.561000 0.74099 CGG TCGA-IB-A5SS-01A-11D-A32N-08 NOS1-002 NOVEL basic|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000268053.1 1 0 1 189 383 0 295 0 0 0 0 295 2 0 0 0 0 0 2 1 1.000000 186 379 0 291 2 0 0 0 0 295 2 -20.000000 1 1 0 0 1 0 1 1 1.609290 1 0.460000 1.850000 0.298701 0.970000 9.100000e-01 1.000000 0.990000 0.976972 0.970000 1 0.940000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 0 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-IB-A5SS-01A-11D-A32N-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 11 61 0 12 1 9.785979e-01 23 17 0 12 2 1 1 71 291 0 353 2 1 0.998677 11 60 0 12 2 1 1 1532 6472 0 12 2 -9.068718 1 1 121404 2 44 1 1 2 3 2.141350 0 0.460000 1.850000 0.469756 0.700000 3.800000e-01 1.000000 1.000000 0.719443 0.700000 0 0.520000 0.950000 DHRS2 10202 broad.mit.edu 37 14 24114078 24114078 + Missense_Mutation SNP C C A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr14:24114078C>A ENST00000250383.6 + 8 1194 c.718C>A c.(718-720)Cat>Aat p.H240N DHRS2_ENST00000344777.7_Silent_p.I243I NM_005794.3 NP_005785.1 Q13268 DHRS2_HUMAN dehydrogenase/reductase (SDR family) member 2 14 CAAGGAACATCATCAGCTGCA 0.512000 0 SO:0001583 missense ENST00000250383.6 1 1 hg19 CCDS9604.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 8.123|8.123 0.781271|0.781271 0.16120|0.16120 .|. .|. ENSG00000100867|ENSG00000100867 ENST00000250383;ENST00000553600|ENST00000557535 D;T|. 0.87966|. -2.32;1.02|. 5.48|5.48 -5.45|-5.45 0.02616|0.02616 .|. .|. .|. .|. .|. T|. 0.18676|. 0.0448|. .|. .|. .|. 0.09310|0.09310 N|N 0.999999|0.999999 B|. 0.32010|. 0.351|. B|. 0.27380|. 0.079|. T|. 0.27400|. -1.0075|. 8|. 0.54805|. T|. 0.06|. .|. 3.8079|3.8079 0.08785|0.08785 0.1079:0.2756:0.1063:0.5103|0.1079:0.2756:0.1063:0.5103 .|. 240|. D3DS54|. .|. N|X 240;140|139 ENSP00000250383:H240N;ENSP00000451485:H140N|. ENSP00000250383:H240N|. H|S +|+ 1|2 0|0 DHRS2|DHRS2 23183918|23183918 0.000000|0.000000 0.05858|0.05858 0.000000|0.000000 0.03702|0.03702 0.000000|0.000000 0.00434|0.00434 -1.335000|-1.335000 0.02662|0.02662 -1.100000|-1.100000 0.03030|0.03030 -1.098000|-1.098000 0.02139|0.02139 CAT|TCA TCGA-IB-A5SS-01A-11D-A32N-08 DHRS2-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000071842.2 1 0 1 39 186 0 85 1 9.862541e-01 9 26 0 85 2 0 0 0 0 0 2 1 1.000000 39 184 0 84 2 0 0 0 0 85 2 -19.993090 1 1 0 0 1 0 1 1 2.065582 0 0.460000 1.850000 0.458755 0.740000 5.500000e-01 0.970000 0.750000 0.759511 0.740000 0 0.640000 0.860000 ADAMTS17 170691 broad.mit.edu 37 15 100636613 100636613 + Silent SNP G G A rs141443664 TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr15:100636613G>A ENST00000268070.4 - 15 2190 c.2085C>T c.(2083-2085)gaC>gaT p.D695D NM_139057.2 NP_620688.2 Q8TE56 ATS17_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 17 50 Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571) OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161) AGGTCTTGCCGTCCCCGCTGC 0.592000 0 SO:0001819 synonymous_variant ENST00000268070.4 0 1 hg19 CCDS10383.1 TCGA-IB-A5SS-01A-11D-A32N-08 ADAMTS17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313595.1 0 0 0 6 542 1 203 0 0 0 1 203 2 0 0 0 0 0 2 0 0.156723 7 534 1 201 11 0 0 0 1 203 2 -2.351779 0 1 121412 3 42 1 1 2 3 2.076387 0 0.460000 1.850000 0.461239 0.040000 1.000000e-02 0.110000 0.050000 0.055359 0.040000 0 0.020000 0.080000 NARG2 0 broad.mit.edu 37 15 60747571 60747571 + Missense_Mutation SNP A A G TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr15:60747571A>G ENST00000261520.4 - 7 971 c.737T>C c.(736-738)aTa>aCa p.I246T NARG2_ENST00000439632.1_Missense_Mutation_p.I109T|NARG2_ENST00000561114.1_Missense_Mutation_p.I246T NM_024611.4 NP_078887.2 32 AATGGTAGCTATATCGTCCTT 0.333000 0 SO:0001583 missense ENST00000261520.4 1 1 hg19 CCDS10176.1 . . . . . . . . . . A 1.299 -0.605421 0.03717 . . ENSG00000128915 ENST00000261520;ENST00000439632 . . . 4.68 -1.88 0.07713 . 0.620823 0.16985 N 0.191552 T 0.16599 0.0399 N 0.16478 0.41 0.09310 N 1 B;B 0.10296 0.0;0.003 B;B 0.09377 0.0;0.004 T 0.12016 -1.0564 9 0.32370 T 0.25 -0.2145 4.7993 0.13289 0.6043:0.0:0.211:0.1848 . 109;246 G3V0H6;Q659A1 .;NARG2_HUMAN T 246;109 . ENSP00000261520:I246T I - 2 0 NARG2 58534863 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 0.076000 0.14712 -0.078000 0.12730 -0.313000 0.08912 ATA TCGA-IB-A5SS-01A-11D-A32N-08 NARG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256136.1 1 0 1 81 247 0 99 1 9.928747e-01 6 20 0 99 2 0 0 0 0 0 2 1 1.000000 80 246 0 99 2 0 0 0 0 99 2 -20.000000 1 1 0 0 1 1 2 3 2.092296 0 0.460000 1.850000 0.462473 0.990000 8.800000e-01 1.000000 1.000000 0.987882 0.990000 1 0.970000 1.000000 TSC2 7249 broad.mit.edu 37 16 2136297 2136297 + Missense_Mutation SNP C C T rs137854039 TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr16:2136297C>T ENST00000219476.3 + 37 5396 c.4766C>T c.(4765-4767)cCg>cTg p.P1589L TSC2_ENST00000353929.4_Missense_Mutation_p.P1546L|TSC2_ENST00000439673.2_Missense_Mutation_p.P1486L|TSC2_ENST00000401874.2_Missense_Mutation_p.P1522L|TSC2_ENST00000350773.4_Missense_Mutation_p.P1566L|TSC2_ENST00000382538.6_Missense_Mutation_p.P1474L|TSC2_ENST00000568454.1_Missense_Mutation_p.P1533L NM_000548.3 NP_000539.2 P49815 TSC2_HUMAN tuberous sclerosis 2 56 Hepatocellular(780;0.0202) GACTGCCAGCCGGACAAGGTG 0.617000 D, Mis, N, F, S hamartoma, renal cell Tuberous Sclerosis yes Rec Tuberous sclerosis 2 16 16p13.3 7249 tuberous sclerosis 2 gene E, O 0 SO:0001583 missense Familial Cancer Database TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease ENST00000219476.3 1 1 hg19 CCDS10458.1 . . . . . . . . . . C 25.9 4.683119 0.88542 0.0 1.16E-4 ENSG00000103197 ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773 D;D;D;D;D 0.93811 -3.29;-3.29;-3.29;-3.29;-3.29 4.47 4.47 0.54385 Rap/ran-GAP (2); 0.062472 0.64402 D 0.000004 D 0.95114 0.8417 L 0.54323 1.7 0.80722 D 1 D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;0.995;1.0;1.0;1.0 D;D;D;P;D;D;D 0.91635 0.999;0.998;0.999;0.842;0.999;0.999;0.999 D 0.92958 0.6386 10 0.15499 T 0.54 -22.8344 17.3319 0.87267 0.0:1.0:0.0:0.0 . 1474;1486;1566;364;1545;1522;1589 B4DIL8;P49815-6;P49815-4;B3KSR9;P49815-3;P49815-5;P49815 .;.;.;.;.;.;TSC2_HUMAN L 1589;1523;1546;1486;1474;1566 ENSP00000219476:P1589L;ENSP00000248099:P1546L;ENSP00000399232:P1486L;ENSP00000371978:P1474L;ENSP00000344383:P1566L ENSP00000219476:P1589L P + 2 0 TSC2 2076298 1.000000 0.71417 0.952000 0.39060 0.768000 0.43524 7.588000 0.82629 2.319000 0.78375 0.561000 0.74099 CCG TCGA-IB-A5SS-01A-11D-A32N-08 TSC2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000250657.2 1 0 1 66 107 0 91 1 1 26 68 0 91 2 0 0 0 0 0 2 1 1.000000 66 105 0 91 2 0 0 0 0 91 2 -20.000000 1 1 121206 1 29 1 0 1 1 1.633385 1 0.460000 1.850000 0.298701 0.970000 8.600000e-01 1.000000 0.990000 0.965478 0.970000 1 0.920000 1.000000 SCNN1G 6340 broad.mit.edu 37 16 23226527 23226527 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr16:23226527C>T ENST00000300061.2 + 13 1830 c.1687C>T c.(1687-1689)Cgc>Tgc p.R563C CTC-391G2.1_ENST00000563471.1_RNA NM_001039.3 NP_001030.2 P51170 SCNNG_HUMAN sodium channel, non-voltage-gated 1, gamma subunit 34 Amiloride(DB00594)|Triamterene(DB00384) TATCATTGCCCGCCGCCAGTG 0.587000 0 SO:0001583 missense ENST00000300061.2 1 1 hg19 CCDS10608.1 . . . . . . . . . . C 15.33 2.801858 0.50315 . . ENSG00000166828 ENST00000300061 T 0.73258 -0.73 5.22 4.26 0.50523 . 0.000000 0.64402 D 0.000014 T 0.66790 0.2825 N 0.08118 0 0.51482 D 0.999928 D 0.89917 1.0 D 0.85130 0.997 T 0.67601 -0.5629 10 0.38643 T 0.18 -20.3075 9.9973 0.41907 0.1562:0.6932:0.1505:0.0 . 563 P51170 SCNNG_HUMAN C 563 ENSP00000300061:R563C ENSP00000300061:R563C R + 1 0 SCNN1G 23134028 1.000000 0.71417 0.466000 0.27168 0.654000 0.38779 2.845000 0.48254 1.154000 0.42482 0.561000 0.74099 CGC TCGA-IB-A5SS-01A-11D-A32N-08 SCNN1G-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254496.1 1 0 1 83 260 0 133 0 0 0 1 0 133 2 0 0 0 0 0 2 1 1.000000 83 260 0 130 2 0 0 0 0 133 2 -4.166446 1 1 0 0 1 0 1 1 2.066887 0 0.460000 1.850000 0.458755 0.990000 8.500000e-01 1.000000 1.000000 0.981389 0.990000 1 0.940000 1.000000 ATXN2L 11273 broad.mit.edu 37 16 28844418 28844418 + Silent SNP T T C TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr16:28844418T>C ENST00000336783.4 + 14 1865 c.1698T>C c.(1696-1698)ccT>ccC p.P566P ATXN2L_ENST00000325215.6_Silent_p.P566P|ATXN2L_ENST00000395547.2_Silent_p.P566P|ATXN2L_ENST00000382686.4_Silent_p.P566P|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000564304.1_Silent_p.P572P|ATXN2L_ENST00000570200.1_Silent_p.P566P|ATXN2L_ENST00000340394.8_Silent_p.P566P NM_007245.3 NP_009176.2 Q8WWM7 ATX2L_HUMAN ataxin 2-like 36 GCCTGGATCCTTTTCCTCCCC 0.532000 0 SO:0001819 synonymous_variant ENST00000336783.4 0 1 hg19 CCDS10641.1 TCGA-IB-A5SS-01A-11D-A32N-08 ATXN2L-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000214139.1 0 0 0 5 588 1 206 0 5.726435e-02 0 232 1 206 6 0 0 0 0 0 2 0 0.064273 5 576 1 204 12 0 0 0 1 206 2 -2.217963 0 1 0 0 1 0 0 0 2.072833 0 0.460000 1.850000 0.460000 0.030000 0 0.080000 0.040000 0.043431 0.030000 0 0.010000 0.060000 SEPHS2 22928 broad.mit.edu 37 16 30456111 30456111 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr16:30456111G>A ENST00000478753.2 - 1 1391 c.938C>T c.(937-939)gCg>gTg p.A313V SEPHS2_ENST00000500504.2_Missense_Mutation_p.A313V|SEPHS2_ENST00000542752.1_Missense_Mutation_p.A256V Q99611 SPS2_HUMAN selenophosphate synthetase 2 10 ATCTGTGGCCGCATGGGCATT 0.448000 Esophageal Squamous(81;1142 1261 11202 24614 35697) 0 SO:0001583 missense ENST00000478753.2 0 1 hg19 . . . . . . . . . . G 17.53 3.413384 0.62511 . . ENSG00000179918 ENST00000478753;ENST00000542752;ENST00000418751;ENST00000500504 T;T;T 0.64991 -0.13;-0.13;-0.13 5.28 5.28 0.74379 AIR synthase-related protein, C-terminal (2); 0.000000 0.85682 D 0.000000 T 0.76709 0.4025 H 0.94620 3.56 0.80722 D 1 P;P 0.49090 0.919;0.906 P;B 0.45343 0.477;0.2 D 0.84632 0.0690 10 0.87932 D 0 -10.0941 16.7892 0.85583 0.0:0.0:1.0:0.0 . 313;256 Q99611;F5H8F9 SPS2_HUMAN;. V 313;256;264;313 ENSP00000418669:A313V;ENSP00000443601:A256V;ENSP00000426234:A313V ENSP00000390233:A264V A - 2 0 SEPHS2 30363612 1.000000 0.71417 0.991000 0.47740 0.267000 0.26476 9.772000 0.98984 2.652000 0.90054 0.655000 0.94253 GCG TCGA-IB-A5SS-01A-11D-A32N-08 SEPHS2-001 KNOWN basic|seleno protein_coding protein_coding OTTHUMT00000109640.11 0 0 0 5 358 0 132 0 7.514636e-01 0 188 0 132 2 0 5.147378e-01 0 633 3 586 10 1 0.936124 5 354 0 131 2 0 0 0 0 132 2 -2.199730 0 1 0 0 1 0 0 0 2.072833 0 0.460000 1.850000 0.460000 0.060000 1.000000e-02 0.130000 0.060000 0.071213 0.060000 0 0.030000 0.100000 NHLRC4 283948 broad.mit.edu 37 16 618370 618370 + Missense_Mutation SNP C C A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr16:618370C>A ENST00000424439.2 + 2 980 c.323C>A c.(322-324)gCc>gAc p.A108D PIGQ_ENST00000470411.2_5'Flank|PIGQ_ENST00000026218.5_5'Flank|PIGQ_ENST00000321878.5_5'Flank|NHLRC4_ENST00000540585.1_Missense_Mutation_p.A108D|PIGQ_ENST00000409527.2_Intron P0CG21 NHLC4_HUMAN NHL repeat containing 4 GTGGCTGATGCCAAGGACAAC 0.667000 0 SO:0001583 missense ENST00000424439.2 0 1 hg19 CCDS45366.1 . . . . . . . . . . C 5.854 0.341804 0.11069 . . ENSG00000257108 ENST00000424439;ENST00000540585 T;T 0.72282 -0.64;-0.64 4.16 1.95 0.26073 Six-bladed beta-propeller, TolB-like (1); 0.422812 0.16956 U 0.192698 T 0.65585 0.2705 L 0.46741 1.465 0.09310 N 1 P 0.51351 0.944 P 0.48524 0.58 T 0.55636 -0.8110 9 . . . . 8.147 0.31117 0.1711:0.7326:0.0:0.0963 . 108 P0CG21 NHLC4_HUMAN D 108 ENSP00000410858:A108D;ENSP00000442223:A108D . A + 2 0 NHLRC4 558371 0.001000 0.12720 0.030000 0.17652 0.024000 0.10985 1.330000 0.33781 1.906000 0.55180 0.585000 0.79938 GCC TCGA-IB-A5SS-01A-11D-A32N-08 NHLRC4-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397724.1 0 0 0 4 99 0 45 0 1.480101e-02 0 4 0 45 2 0 0 0 0 0 2 0 0.877122 0 97 0 44 2 0 0 0 0 45 2 -7.527087 1 0 0 0 1 0 1 1 1.633385 1 0.460000 1.850000 0.298701 0.140000 4.000000e-02 0.300000 0.130000 0.155814 0.140000 0 0.080000 0.220000 HAP1 9001 broad.mit.edu 37 17 39881075 39881075 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr17:39881075C>T ENST00000310778.5 - 12 1903 c.1894G>A c.(1894-1896)Gcc>Acc p.A632T JUP_ENST00000540235.1_Intron|HAP1_ENST00000393939.2_Missense_Mutation_p.A555T|HAP1_ENST00000347901.4_Missense_Mutation_p.A580T|HAP1_ENST00000341193.5_Missense_Mutation_p.A563T P54257 HAP1_HUMAN huntingtin-associated protein 1 21 Breast(137;0.000162) BRCA - Breast invasive adenocarcinoma(4;0.0677) TGCCAGTTGGCCAGCTGCTGG 0.627000 0 SO:0001583 missense ENST00000310778.5 0 1 hg19 . . . . . . . . . . C 13.04 2.117571 0.37339 . . ENSG00000173805 ENST00000458656;ENST00000442364;ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193 T;T;T;T;T;T 0.44881 1.32;0.91;3.15;3.41;3.27;3.16 4.14 2.06 0.26882 . 0.560677 0.15052 N 0.283242 T 0.36138 0.0956 L 0.27053 0.805 0.09310 N 0.99999 P;D;D;D 0.56968 0.872;0.965;0.974;0.978 P;P;P;P 0.54270 0.578;0.546;0.747;0.563 T 0.10064 -1.0646 10 0.32370 T 0.25 -11.1038 4.8636 0.13596 0.219:0.6683:0.0:0.1127 . 555;563;580;632 P54257-3;P54257-4;P54257-2;P54257 .;.;.;HAP1_HUMAN T 87;49;555;632;580;563 ENSP00000404640:A87T;ENSP00000388981:A49T;ENSP00000377513:A555T;ENSP00000309392:A632T;ENSP00000334002:A580T;ENSP00000343170:A563T ENSP00000309392:A632T A - 1 0 HAP1 37134601 0.215000 0.23574 0.948000 0.38648 0.014000 0.08584 -0.225000 0.09151 0.459000 0.27016 -0.350000 0.07774 GCC TCGA-IB-A5SS-01A-11D-A32N-08 HAP1-006 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000389619.1 0 0 0 7 636 0 243 0 5.130543e-04 0 3 0 243 2 0 0 0 0 0 2 1 0.979453 7 625 0 239 2 0 0 0 0 243 2 -1.981559 0 1 121412 1 31 1 1 2 3 2.123027 0 0.460000 1.850000 0.467351 0.040000 1.000000e-02 1.000000 0.050000 0.099051 0.040000 0 0.030000 0.080000 CCR10 2826 broad.mit.edu 37 17 40832279 40832279 + Silent SNP G G C TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr17:40832279G>C ENST00000332438.4 - 2 400 c.381C>G c.(379-381)ggC>ggG p.G127G CCR10_ENST00000591765.1_5'UTR|CTD-3193K9.3_ENST00000592440.1_RNA|CTD-3193K9.4_ENST00000593139.1_RNA|CNTNAP1_ENST00000264638.4_5'Flank NM_016602.2 NP_057686.2 P46092 CCR10_HUMAN chemokine (C-C motif) receptor 10 3 Breast(137;0.000153) GGAAGAGGAAGCCGGCGTGGA 0.706000 0 SO:0001819 synonymous_variant ENST00000332438.4 0 1 hg19 CCDS11435.1 TCGA-IB-A5SS-01A-11D-A32N-08 CCR10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255406.1 0 0 0 5 22 0 13 0 2.005006e-01 0 4 0 13 2 0 0 0 0 0 2 1 0.944039 5 22 0 13 2 0 0 0 0 13 2 -12.799970 1 1 0 0 1 1 2 3 2.123027 0 0.460000 1.850000 0.467351 0.860000 3.500000e-01 1.000000 1.000000 0.808826 0.860000 1 0.560000 1.000000 ARMC7 79637 broad.mit.edu 37 17 73125037 73125037 + Missense_Mutation SNP C C A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr17:73125037C>A ENST00000245543.1 + 3 803 c.501C>A c.(499-501)ttC>ttA p.F167L NT5C_ENST00000579082.1_5'Flank|ARMC7_ENST00000581078.1_3'UTR|ARMC7_ENST00000579096.1_3'UTR NM_024585.2 NP_078861.1 Q9H6L4 ARMC7_HUMAN armadillo repeat containing 7 p.F167F(1) 9 all_lung(278;0.14)|Lung NSC(278;0.168) LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235) TGGAGGACTTCTGCTCCCCCC 0.701000 1 Substitution - coding silent(1) SO:0001583 missense ENST00000245543.1 1 1 hg19 CCDS11714.1 . . . . . . . . . . C 12.54 1.969018 0.34754 . . ENSG00000125449 ENST00000245543 T 0.32272 1.46 5.18 4.22 0.49857 Armadillo-like helical (1);Armadillo-type fold (1); 0.478366 0.24633 N 0.036863 T 0.18923 0.0454 N 0.16478 0.41 0.80722 D 1 B 0.02656 0.0 B 0.01281 0.0 T 0.04017 -1.0984 10 0.35671 T 0.21 . 10.8273 0.46640 0.0:0.7987:0.0:0.2013 . 167 Q9H6L4 ARMC7_HUMAN L 167 ENSP00000245543:F167L ENSP00000245543:F167L F + 3 2 ARMC7 70636632 1.000000 0.71417 0.968000 0.41197 0.367000 0.29736 2.074000 0.41529 1.338000 0.45544 -0.137000 0.14449 TTC TCGA-IB-A5SS-01A-11D-A32N-08 ARMC7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445846.1 1 0 1 18 78 0 23 1 9.911319e-01 10 27 0 23 2 0 0 0 0 0 2 1 0.999988 18 75 0 23 2 0 0 0 0 23 2 -20.000000 1 1 0 0 1 1 2 3 2.123027 0 0.460000 1.850000 0.467351 0.840000 5.300000e-01 1.000000 1.000000 0.833307 0.840000 0 0.670000 1.000000 TP53 7157 broad.mit.edu 37 17 7577094 7577094 + Missense_Mutation SNP G G A rs28934574 TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr17:7577094G>A ENST00000269305.4 - 8 1033 c.844C>T c.(844-846)Cgg>Tgg p.R282W TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000413465.2_Intron NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) TCTGTGCGCCGGTCTCTCCCA 0.557000 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 463 Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1) GRCh37 CM056413|CM920678 TP53 M rs28934574 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . G 20.8 4.057525 0.76074 0.0 2.33E-4 ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D 0.99869 -7.34;-7.34;-7.34;-7.34;-7.34;-7.34 4.75 1.49 0.22878 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99825 0.9922 M 0.89968 3.075 0.58432 A 0.999999 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 0.999;0.998;1.0;0.999 D 0.97713 1.0192 9 0.87932 D 0 -12.0909 8.7508 0.34613 0.0:0.1376:0.5833:0.2792 rs28934574 282;282;282;282 P04637-2;P04637-3;P04637;Q1MSW8 .;.;P53_HUMAN;. W 282;282;282;282;282;271;150 ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W ENSP00000269305:R282W R - 1 2 TP53 7517819 1.000000 0.71417 0.327000 0.25402 0.901000 0.52897 4.477000 0.60223 0.174000 0.19809 0.462000 0.41574 CGG TCGA-IB-A5SS-01A-11D-A32N-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 44 84 0 55 1 1 47 64 0 55 2 1 1 227 625 0 1237 2 1 1.000000 44 82 0 53 2 0 0 0 0 55 2 -7.257383 1 1 121412 2 36 1 0 1 1 1.638444 1 0.460000 1.850000 0.298701 0.940000 7.900000e-01 1.000000 0.990000 0.936562 0.940000 1 0.870000 0.990000 KDM6B 23135 broad.mit.edu 37 17 7752044 7752044 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr17:7752044G>A ENST00000448097.2 + 11 2769 c.2438G>A c.(2437-2439)gGa>gAa p.G813E KDM6B_ENST00000254846.5_Missense_Mutation_p.G813E O15054 KDM6B_HUMAN lysine (K)-specific demethylase 6B 37 GTGCTGGAGGGACAAAAGTAC 0.647000 0 SO:0001583 missense ENST00000448097.2 1 1 hg19 . . . . . . . . . . G 12.51 1.958268 0.34565 . . ENSG00000132510 ENST00000254846;ENST00000448097 T;T 0.16897 2.31;2.31 4.54 4.54 0.55810 . 0.242138 0.31092 N 0.008272 T 0.22244 0.0536 N 0.19112 0.55 0.38701 D 0.952991 P;D 0.58268 0.816;0.982 B;P 0.55087 0.311;0.768 T 0.08229 -1.0732 10 0.87932 D 0 -5.6434 16.5716 0.84613 0.0:0.0:1.0:0.0 . 813;813 O15054;O15054-1 KDM6B_HUMAN;. E 813 ENSP00000254846:G813E;ENSP00000412513:G813E ENSP00000254846:G813E G + 2 0 KDM6B 7692769 1.000000 0.71417 1.000000 0.80357 0.958000 0.62258 4.418000 0.59828 2.526000 0.85167 0.462000 0.41574 GGA TCGA-IB-A5SS-01A-11D-A32N-08 KDM6B-002 KNOWN basic protein_coding protein_coding OTTHUMT00000440248.1 1 0 0 102 242 0 132 1 9.701730e-01 6 10 0 132 2 0 0 0 0 0 2 1 1.000000 101 239 0 132 2 0 0 0 0 132 2 -20.000000 1 1 0 0 1 0 1 1 1.638444 1 0.460000 1.850000 0.298701 0.930000 8.100000e-01 1.000000 0.990000 0.933991 0.930000 1 0.870000 0.980000 MC5R 4161 broad.mit.edu 37 18 13826098 13826098 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr18:13826098C>T ENST00000324750.3 + 1 556 c.334C>T c.(334-336)Cgc>Tgc p.R112C AP001525.1_ENST00000390194.2_RNA NM_005913.2 NP_005904.1 P33032 MC5R_HUMAN melanocortin 5 receptor 41 CGCCTTTGTGCGCCACATTGA 0.522000 0 SO:0001583 missense ENST00000324750.3 1 1 hg19 CCDS11868.1 . . . . . . . . . . C 15.00 2.704257 0.48412 . . ENSG00000176136 ENST00000324750 T 0.20738 2.05 4.9 3.1 0.35709 GPCR, rhodopsin-like superfamily (1); 0.103679 0.64402 D 0.000005 T 0.33789 0.0875 L 0.39898 1.24 0.58432 D 0.999999 D 0.89917 1.0 D 0.70716 0.97 T 0.02909 -1.1095 10 0.87932 D 0 . 10.9647 0.47406 0.1464:0.7129:0.1407:0.0 . 112 P33032 MC5R_HUMAN C 112 ENSP00000318077:R112C ENSP00000318077:R112C R + 1 0 MC5R 13816098 1.000000 0.71417 0.932000 0.37286 0.749000 0.42624 2.825000 0.48096 0.467000 0.27218 -0.384000 0.06662 CGC TCGA-IB-A5SS-01A-11D-A32N-08 MC5R-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254638.1 1 0 1 65 124 1 95 0 0 0 1 95 2 0 0 0 0 0 2 1 1.000000 65 123 1 94 9 0 0 0 1 95 2 -9.132377 1 1 121412 2 31 1 0 1 1 1.626997 1 0.460000 1.850000 0.298701 0.950000 8.300000e-01 1.000000 0.990000 0.952839 0.950000 1 0.900000 0.990000 LSR 51599 broad.mit.edu 37 19 35753550 35753550 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr19:35753550G>A ENST00000361790.3 + 5 1036 c.877G>A c.(877-879)Gtc>Atc p.V293I AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000347609.4_Missense_Mutation_p.V256I|LSR_ENST00000602122.1_Missense_Mutation_p.V274I|LSR_ENST00000597933.1_3'UTR|LSR_ENST00000427250.1_Intron|LSR_ENST00000354900.3_Missense_Mutation_p.V274I|LSR_ENST00000360798.3_Intron NM_205834.3 NP_991403.1 Q86X29 LSR_HUMAN lipolysis stimulated lipoprotein receptor 13 all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162) Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417) CTGCTGCTACGTCAGGTGCCC 0.627000 0 SO:0001583 missense ENST00000361790.3 1 1 hg19 CCDS12450.1 . . . . . . . . . . G 19.62 3.862120 0.71949 . . ENSG00000105699 ENST00000361790;ENST00000354900;ENST00000347609 T;T;T 0.57107 0.42;0.42;0.42 4.74 4.74 0.60224 LISCH7 (1); 0.065915 0.64402 D 0.000014 T 0.57286 0.2043 L 0.34521 1.04 0.80722 D 1 D;D;D;P 0.76494 0.999;0.977;0.982;0.84 P;P;P;B 0.61070 0.883;0.525;0.562;0.344 T 0.52155 -0.8613 10 0.27785 T 0.31 -37.3992 15.256 0.73585 0.0:0.0:1.0:0.0 . 256;274;274;293 Q86X29-2;Q86X29-3;E9PHD4;Q86X29 .;.;.;LSR_HUMAN I 293;274;256 ENSP00000354575:V293I;ENSP00000346976:V274I;ENSP00000262627:V256I ENSP00000262627:V256I V + 1 0 LSR 40445390 1.000000 0.71417 0.946000 0.38457 0.967000 0.64934 4.937000 0.63513 2.448000 0.82819 0.591000 0.81541 GTC TCGA-IB-A5SS-01A-11D-A32N-08 LSR-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465513.2 1 0 1 75 345 0 106 1 1 195 446 0 106 2 0 0 0 0 0 2 1 1.000000 73 342 0 105 2 0 0 0 0 106 2 -20.000000 1 1 121412 4 41 1 1 2 3 2.485102 1 0.460000 1.850000 0.560976 0.950000 7.600000e-01 1.000000 1.000000 0.937296 0.950000 1 0.850000 1.000000 ZNF585A 199704 broad.mit.edu 37 19 37643142 37643142 + Silent SNP G G A rs113590010 byFrequency TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr19:37643142G>A ENST00000356958.4 - 5 1917 c.1659C>T c.(1657-1659)caC>caT p.H553H ZNF585A_ENST00000355533.2_Intron|ZNF585A_ENST00000292841.5_Silent_p.H498H|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000392157.2_Silent_p.H498H Q6P3V2 Z585A_HUMAN zinc finger protein 585A 42 COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177) TCCCACATTCGTGGCATTCAT 0.403000 0 SO:0001819 synonymous_variant ENST00000356958.4 1 0 hg19 TCGA-IB-A5SS-01A-11D-A32N-08 ZNF585A-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000457980.2 1 0 0 63 233 0 64 0 0 0 0 64 2 0 0 0 0 0 2 1 1.000000 63 227 0 117 2 0 0 0 0 64 2 -20.000000 1 1 121412 21 47 1 1 2 3 2.485102 1 0.460000 1.850000 0.560976 0.990000 9.000000e-01 1.000000 1.000000 0.992826 0.990000 1 0.990000 1.000000 LTBP4 8425 broad.mit.edu 37 19 41123123 41123123 + Missense_Mutation SNP C C G TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr19:41123123C>G ENST00000308370.7 + 25 3261 c.3261C>G c.(3259-3261)caC>caG p.H1087Q LTBP4_ENST00000545697.1_Intron|LTBP4_ENST00000204005.9_Missense_Mutation_p.H1050Q|LTBP4_ENST00000396819.3_Missense_Mutation_p.H1020Q|LTBP4_ENST00000243562.9_Missense_Mutation_p.H141Q|LTBP4_ENST00000602240.1_3'UTR NM_001042544.1 NP_001036009.1 Q8N2S1 LTBP4_HUMAN latent transforming growth factor beta binding protein 4 1 Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384) ATGGGCGTCACTGCGTGGGTA 0.622000 0 SO:0001583 missense ENST00000308370.7 1 1 hg19 . . . . . . . . . . C 16.00 2.999789 0.54147 . . ENSG00000090006 ENST00000204005;ENST00000308370;ENST00000396819;ENST00000243562 D;D;D;D 0.91631 -2.19;-2.88;-2.19;-2.88 4.19 4.19 0.49359 EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1); 0.000000 0.42420 D 0.000715 D 0.94138 0.8120 . . . 0.80722 D 1 D;D;D 0.89917 0.995;1.0;1.0 D;D;D 0.87578 0.993;0.998;0.998 D 0.91644 0.5329 9 0.13470 T 0.59 . 15.8101 0.78552 0.0:1.0:0.0:0.0 . 1020;1088;1050 E7EUU1;Q8N2S1;E7ENG9 .;LTBP4_HUMAN;. Q 1050;1087;1020;141 ENSP00000204005:H1050Q;ENSP00000311905:H1087Q;ENSP00000380031:H1020Q;ENSP00000243562:H141Q ENSP00000204005:H1050Q H + 3 2 LTBP4 45814963 0.611000 0.26992 1.000000 0.80357 0.994000 0.84299 -0.142000 0.10311 2.330000 0.79161 0.563000 0.77884 CAC TCGA-IB-A5SS-01A-11D-A32N-08 LTBP4-203 KNOWN basic|appris_candidate_longest protein_coding protein_coding 0 0 1 22 159 0 43 1 1 22 267 0 43 2 0 0 0 0 0 2 1 0.999999 22 159 0 43 2 0 0 0 0 43 2 -20.000000 1 1 0 0 1 1 4 5 3.505587 1 0.460000 1.850000 0.680473 0.900000 5.900000e-01 1.000000 1.000000 0.880398 0.900000 1 0.730000 1.000000 CCDC9 26093 broad.mit.edu 37 19 47774764 47774764 + Missense_Mutation SNP G G T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr19:47774764G>T ENST00000221922.6 + 12 1647 c.1425G>T c.(1423-1425)gaG>gaT p.E475D NM_015603.2 NP_056418.1 Q9Y3X0 CCDC9_HUMAN coiled-coil domain containing 9 12 all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114) GTCCGGAGGAGCCCCTGCTGG 0.677000 0 SO:0001583 missense ENST00000221922.6 0 1 hg19 CCDS12698.1 . . . . . . . . . . . 15.91 2.971115 0.53614 . . ENSG00000105321 ENST00000221922;ENST00000504556 T 0.25749 1.78 4.25 0.667 0.17907 . 0.951510 0.08620 N 0.918598 T 0.17577 0.0422 L 0.33485 1.01 0.31583 N 0.654852 B 0.06786 0.001 B 0.08055 0.003 T 0.28744 -1.0034 10 0.36615 T 0.2 -8.8316 5.4815 0.16727 0.1917:0.1632:0.6451:0.0 . 475 Q9Y3X0 CCDC9_HUMAN D 475;457 ENSP00000221922:E475D ENSP00000221922:E475D E + 3 2 CCDC9 52466604 0.998000 0.40836 0.009000 0.14445 0.138000 0.21146 2.748000 0.47483 0.445000 0.26639 0.281000 0.19383 GAG TCGA-IB-A5SS-01A-11D-A32N-08 CCDC9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466917.1 0 0 0 5 357 0 152 0 3.643418e-01 0 79 0 152 2 0 0 0 0 0 2 1 0.937045 5 355 0 151 2 0 0 0 0 152 2 -5.302741 1 0 0 0 1 0 1 1 1.646124 1 0.460000 1.850000 0.298701 0.040000 1.000000e-02 0.100000 0.050000 0.054819 0.040000 0 0.020000 0.080000 NUP62 23636 broad.mit.edu 37 19 50412865 50412865 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr19:50412865G>A ENST00000596217.1 - 2 2087 c.200C>T c.(199-201)cCg>cTg p.P67L NUP62_ENST00000597723.1_Missense_Mutation_p.P67L|IL4I1_ENST00000341114.3_Intron|CTC-326K19.6_ENST00000451973.1_3'UTR|NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000413454.1_Missense_Mutation_p.P67L|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000352066.3_Missense_Mutation_p.P67L|NUP62_ENST00000597029.1_Missense_Mutation_p.P67L|NUP62_ENST00000422090.2_Missense_Mutation_p.P67L P37198 NUP62_HUMAN nucleoporin 62kDa 19 all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481) CTGTGTGGCCGGAGTCTGGGT 0.552000 0 SO:0001583 missense ENST00000596217.1 0 1 hg19 CCDS12788.1 . . . . . . . . . . G 11.83 1.755489 0.31046 . . ENSG00000213024 ENST00000319225;ENST00000352066;ENST00000422090;ENST00000413454 T;T;T 0.38722 1.12;1.12;1.12 4.16 3.12 0.35913 Nucleoporin, NSP1-like, C-terminal (1); 0.403038 0.21678 U 0.070777 T 0.29716 0.0742 L 0.38531 1.155 0.42109 D 0.991379 P;P 0.47545 0.89;0.897 B;B 0.39419 0.299;0.157 T 0.13683 -1.0500 10 0.72032 D 0.01 -4.6212 7.9938 0.30256 0.1097:0.0:0.8903:0.0 . 67;67 Q8WYU3;P37198 .;NUP62_HUMAN L 67 ENSP00000305503:P67L;ENSP00000407331:P67L;ENSP00000387991:P67L ENSP00000321866:P67L P - 2 0 NUP62 55104677 0.914000 0.31030 0.018000 0.16275 0.019000 0.09904 6.760000 0.74939 1.339000 0.45563 0.655000 0.94253 CCG TCGA-IB-A5SS-01A-11D-A32N-08 NUP62-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464991.1 0 0 0 6 613 0 259 0 3.634614e-01 0 115 0 259 2 0 0 0 0 0 2 0 0.212976 6 601 1 258 10 0 0 0 0 259 2 -1.734053 0 1 0 0 1 0 1 1 1.646124 1 0.460000 1.850000 0.298701 0.030000 0 0.070000 0.030000 0.037593 0.030000 0 0.010000 0.050000 KLK13 26085 broad.mit.edu 37 19 51561826 51561826 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr19:51561826C>T ENST00000595793.1 - 4 656 c.614G>A c.(613-615)gGc>gAc p.G205D KLK13_ENST00000595547.1_Missense_Mutation_p.G132D|KLK13_ENST00000335422.3_Missense_Mutation_p.G53D NM_015596.1 NP_056411.1 Q9UKR3 KLK13_HUMAN kallikrein-related peptidase 13 16 all_neural(266;0.026) CTCTTTTGTGCCGGCACACAA 0.527000 0 SO:0001583 missense ENST00000595793.1 0 1 hg19 CCDS12822.1 . . . . . . . . . . C 16.46 3.130091 0.56721 . . ENSG00000167759 ENST00000156476;ENST00000335422 D 0.90133 -2.62 4.67 4.67 0.58626 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 0.136174 0.33732 N 0.004605 D 0.95971 0.8688 M 0.90595 3.13 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.91635 0.983;0.999;0.999 D 0.96571 0.9423 10 0.87932 D 0 . 15.4416 0.75187 0.0:1.0:0.0:0.0 . 53;132;205 Q86VI8;Q86VI7;Q9UKR3 .;.;KLK13_HUMAN D 205;53 ENSP00000334079:G53D ENSP00000156476:G205D G - 2 0 KLK13 56253638 0.998000 0.40836 0.858000 0.33744 0.171000 0.22731 6.159000 0.71856 2.588000 0.87417 0.561000 0.74099 GGC TCGA-IB-A5SS-01A-11D-A32N-08 KLK13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464298.2 0 0 0 6 491 0 221 0 0 0 1 0 221 2 0 0 0 0 0 2 1 0.964288 6 487 0 218 2 0 0 0 0 221 2 -1.719904 0 1 0 0 1 0 1 1 1.646124 1 0.460000 1.850000 0.298701 0.030000 1.000000e-02 0.080000 0.040000 0.046736 0.030000 0 0.020000 0.060000 KIR3DL1 3811 broad.mit.edu 37 19 55333120 55333120 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr19:55333120G>A ENST00000391728.4 + 5 789 c.756G>A c.(754-756)atG>atA p.M252I KIR3DL1_ENST00000541392.1_Missense_Mutation_p.M252I|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.M252I|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.M252I|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.M252I|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.M157I NM_013289.2 NP_037421.2 P43629 KI3L1_HUMAN killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1 11 CCTATGACATGTACCATCTAT 0.587000 0 SO:0001583 missense ENST00000391728.4 0 1 hg19 CCDS42621.1 . . . . . . . . . . - 0.425 -0.906123 0.02453 . . ENSG00000167633 ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178 T;T;T;T;T;T 0.19532 2.14;2.14;2.14;2.14;2.14;2.14 1.47 -2.94 0.05581 Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1); 3.298930 0.01900 N 0.039137 T 0.12390 0.0301 N 0.17594 0.5 0.09310 N 1 B;B;B;B 0.02656 0.0;0.0;0.0;0.0 B;B;B;B 0.13407 0.009;0.004;0.001;0.009 T 0.25572 -1.0128 10 0.19147 T 0.46 . 5.1298 0.14903 0.0:0.1775:0.4406:0.3819 . 252;157;252;252 Q15702;Q14946;F6QF33;P43629 .;.;.;KI3L1_HUMAN I 252;252;252;230;252;252;157 ENSP00000384528:M252I;ENSP00000443350:M252I;ENSP00000442355:M252I;ENSP00000375608:M252I;ENSP00000326868:M252I;ENSP00000350901:M157I ENSP00000326868:M252I M + 3 0 KIR3DL1 60024932 0.001000 0.12720 0.000000 0.03702 0.001000 0.01503 0.385000 0.20685 -3.201000 0.00217 -3.594000 0.00028 ATG TCGA-IB-A5SS-01A-11D-A32N-08 KIR3DL1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000141238.1 0 0 0 55 102 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 1.000000 29 63 0 122 2 0 0 0 0 71 2 -20.000000 1 1 0 0 1 0 1 1 2.044852 0 0.460000 1.850000 0.451164 0.990000 9.900000e-01 1.000000 1.000000 0.999982 0.990000 1 0.990000 1.000000 OR2Z1 284383 broad.mit.edu 37 19 8841649 8841649 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr19:8841649C>T ENST00000324060.2 + 1 334 c.259C>T c.(259-261)Cgg>Tgg p.R87W NM_001004699.1 NP_001004699.1 Q8NG97 OR2Z1_HUMAN olfactory receptor, family 2, subfamily Z, member 1 18 AGACTTTCTGCGGGGAGAAGG 0.552000 0 SO:0001583 missense ENST00000324060.2 0 1 hg19 CCDS32895.1 1 4.578754578754579E-4 0 0.0 1 0.0027624309392265192 0 0.0 0 0.0 C 2.412 -0.335123 0.05278 2.27E-4 0.0 ENSG00000181733 ENST00000324060 T 0.00406 7.55 4.33 3.05 0.35203 GPCR, rhodopsin-like superfamily (1); 2.610920 0.01162 N 0.006663 T 0.00384 0.0012 L 0.39514 1.22 0.09310 N 1 B 0.09022 0.002 B 0.04013 0.001 T 0.49606 -0.8922 10 0.38643 T 0.18 . 7.9281 0.29887 0.0:0.8369:0.0:0.1631 . 87 Q8NG97 OR2Z1_HUMAN W 87 ENSP00000316284:R87W ENSP00000316284:R87W R + 1 2 OR2Z1 8702649 0.000000 0.05858 0.009000 0.14445 0.011000 0.07611 -0.537000 0.06128 2.182000 0.69389 0.543000 0.68304 CGG TCGA-IB-A5SS-01A-11D-A32N-08 OR2Z1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459954.1 0 0 0 5 539 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 0.936893 5 536 0 95 2 0 0 0 0 95 2 -2.330848 0 1 121412 2 37 1 1 4 5 3.572793 1 0.460000 1.850000 0.680473 0.060000 1.000000e-02 0.160000 0.050000 0.078659 0.060000 0 0.030000 0.120000 ATP13A2 23400 broad.mit.edu 37 1 17322564 17322564 + Silent SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr1:17322564G>A ENST00000326735.8 - 15 1482 c.1449C>T c.(1447-1449)taC>taT p.Y483Y ATP13A2_ENST00000502860.1_5'UTR|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Silent_p.Y478Y|ATP13A2_ENST00000452699.1_Silent_p.Y478Y Q9NQ11 AT132_HUMAN ATPase type 13A2 32 Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646) GGCTCTGGGCGTAGAGCGTGC 0.622000 0 SO:0001819 synonymous_variant ENST00000326735.8 0 1 hg19 CCDS175.1 TCGA-IB-A5SS-01A-11D-A32N-08 ATP13A2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000006617.1 0 0 0 5 512 0 197 0 4.554295e-01 0 139 0 197 2 0 0 0 0 0 2 1 0.936213 5 507 0 197 2 0 0 0 0 197 2 -2.360717 0 1 121412 14 46 1 1 2 3 2.142064 0 0.460000 1.850000 0.469756 0.040000 0 1.000000 0.040000 0.111962 0.040000 0 0.020000 0.080000 ASTN1 460 broad.mit.edu 37 1 176926840 176926840 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr1:176926840G>A ENST00000367654.3 - 11 2096 c.1885C>T c.(1885-1887)Cgc>Tgc p.R629C ASTN1_ENST00000367657.3_Missense_Mutation_p.R621C|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000361833.2_Missense_Mutation_p.R621C|ASTN1_ENST00000424564.2_Missense_Mutation_p.R621C NM_004319.1 NP_004310.1 O14525 ASTN1_HUMAN astrotactin 1 153 TCCAGCTTGCGATCTGAAATA 0.537000 0 SO:0001583 missense ENST00000367654.3 1 1 hg19 . . . . . . . . . . G 32 5.191818 0.94923 . . ENSG00000152092 ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808 D;D;T;D 0.87571 -2.27;-2.27;2.64;-2.27 5.58 5.58 0.84498 Epidermal growth factor-like (1); 0.000000 0.85682 D 0.000000 D 0.90363 0.6984 L 0.29908 0.895 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.85130 0.997;0.992;0.992 D 0.91468 0.5194 10 0.87932 D 0 -28.5238 19.1684 0.93567 0.0:0.0:1.0:0.0 . 629;621;621 O14525;O14525-2;B1AJS1 ASTN1_HUMAN;.;. C 621;621;629;621;621 ENSP00000356629:R621C;ENSP00000354536:R621C;ENSP00000356626:R629C;ENSP00000395041:R621C ENSP00000354536:R621C R - 1 0 ASTN1 175193463 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.296000 0.96104 2.618000 0.88619 0.563000 0.77884 CGC TCGA-IB-A5SS-01A-11D-A32N-08 ASTN1-201 KNOWN basic protein_coding protein_coding 1 0 1 68 172 0 82 0 0 0 0 82 2 0 0 0 0 0 2 1 1.000000 66 171 0 80 2 0 0 0 0 82 2 -6.215812 1 1 121412 3 36 1 1 2 3 2.095873 0 0.460000 1.850000 0.462473 0.990000 9.900000e-01 1.000000 1.000000 0.998943 0.990000 1 0.990000 1.000000 HLX 3142 broad.mit.edu 37 1 221057751 221057751 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr1:221057751C>T ENST00000366903.6 + 4 2673 c.1172C>T c.(1171-1173)aCg>aTg p.T391M HLX_ENST00000549319.1_Missense_Mutation_p.T177M NM_021958.3 NP_068777.1 Q14774 HLX_HUMAN H2.0-like homeobox 32 CCCAGCGACACGGAGCGGACT 0.642000 0 SO:0001583 missense ENST00000366903.6 1 1 hg19 CCDS1527.1 . . . . . . . . . . C 15.84 2.952214 0.53293 . . ENSG00000136630 ENST00000366903;ENST00000427693;ENST00000549319 D;T;T 0.90385 -2.66;0.51;3.29 5.03 4.09 0.47781 . 0.247697 0.27811 N 0.017749 D 0.84174 0.5414 N 0.24115 0.695 0.09310 N 1 P 0.48640 0.913 B 0.43809 0.432 T 0.77587 -0.2532 10 0.66056 D 0.02 -14.4125 9.6566 0.39930 0.1598:0.6859:0.1543:0.0 . 391 Q14774 HLX_HUMAN M 391;124;177 ENSP00000355870:T391M;ENSP00000408248:T124M;ENSP00000449882:T177M ENSP00000355870:T391M T + 2 0 HLX 219124374 0.977000 0.34250 0.038000 0.18304 0.737000 0.42083 2.102000 0.41796 1.207000 0.43291 0.561000 0.74099 ACG TCGA-IB-A5SS-01A-11D-A32N-08 HLX-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090902.3 1 0 1 59 166 0 58 0 1 0 114 0 58 2 0 0 0 0 0 2 1 1.000000 59 160 0 56 2 0 0 0 0 58 2 -20.000000 1 1 0 0 1 1 2 3 2.095873 0 0.460000 1.850000 0.462473 0.990000 9.000000e-01 1.000000 1.000000 0.993210 0.990000 1 0.990000 1.000000 OR2G6 391211 broad.mit.edu 37 1 248685733 248685733 + Silent SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr1:248685733G>A ENST00000343414.4 + 1 818 c.786G>A c.(784-786)ccG>ccA p.P262P NM_001013355.1 NP_001013373.1 Q5TZ20 OR2G6_HUMAN olfactory receptor, family 2, subfamily G, member 6 61 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) all_cancers(173;0.0156) OV - Ovarian serous cystadenocarcinoma(106;0.0265) ACCTTCAACCGGCCAATAGGA 0.448000 0 SO:0001819 synonymous_variant ENST00000343414.4 0 1 hg19 CCDS31119.1 TCGA-IB-A5SS-01A-11D-A32N-08 OR2G6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097358.1 0 0 0 5 283 0 88 0 0 0 0 88 2 0 0 0 0 0 2 1 0.936928 5 281 0 88 2 0 0 0 0 88 2 -2.694931 1 1 121412 5 44 1 1 2 3 2.095873 0 0.460000 1.850000 0.462473 0.080000 2.000000e-02 0.190000 0.080000 0.098920 0.080000 0 0.040000 0.130000 LPAR3 23566 broad.mit.edu 37 1 85279562 85279562 + Missense_Mutation SNP G G C TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr1:85279562G>C ENST00000440886.1 - 2 1067 c.1029C>G c.(1027-1029)agC>agG p.S343R LPAR3_ENST00000370611.3_Missense_Mutation_p.S343R|LPAR3_ENST00000491034.1_5'Flank Q9UBY5 LPAR3_HUMAN lysophosphatidic acid receptor 3 24 CTGCACCTTGGCTAATACTAT 0.532000 0 SO:0001583 missense ENST00000440886.1 0 1 hg19 CCDS700.1 . . . . . . . . . . G 10.85 1.465648 0.26335 . . ENSG00000171517 ENST00000440886;ENST00000370611 T;T 0.74421 -0.84;-0.84 5.85 3.99 0.46301 . 0.513877 0.21711 N 0.070278 T 0.35422 0.0931 N 0.14661 0.345 0.36935 D 0.892083 B 0.19583 0.037 B 0.14023 0.01 T 0.10451 -1.0629 10 0.21540 T 0.41 . 9.1901 0.37193 0.2425:0.0:0.7575:0.0 . 343 Q9UBY5 LPAR3_HUMAN R 343 ENSP00000395389:S343R;ENSP00000359643:S343R ENSP00000359643:S343R S - 3 2 LPAR3 85052150 1.000000 0.71417 0.087000 0.20705 0.257000 0.26127 1.974000 0.40559 0.824000 0.34613 0.650000 0.86243 AGC TCGA-IB-A5SS-01A-11D-A32N-08 LPAR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000027467.1 0 0 0 4 122 0 65 0 0 0 1 0 65 2 0 0 0 0 0 2 0 0.883847 0 122 0 64 2 0 0 0 0 65 2 -6.755027 1 0 0 0 1 0 1 1 1.642911 1 0.460000 1.850000 0.298701 0.110000 3.000000e-02 0.250000 0.100000 0.128349 0.110000 0 0.060000 0.180000 PTPRT 11122 broad.mit.edu 37 20 40827934 40827934 + Missense_Mutation SNP C C T rs61749502 by1000genomes TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr20:40827934C>T ENST00000373187.1 - 16 2436 c.2437G>A c.(2437-2439)Gcc>Acc p.A813T PTPRT_ENST00000373198.4_Missense_Mutation_p.A832T|PTPRT_ENST00000356100.2_Missense_Mutation_p.A822T|PTPRT_ENST00000373184.1_Missense_Mutation_p.A803T|PTPRT_ENST00000373201.1_Missense_Mutation_p.A803T|PTPRT_ENST00000373190.1_Missense_Mutation_p.A813T|PTPRT_ENST00000373193.3_Missense_Mutation_p.A816T O14522 PTPRT_HUMAN protein tyrosine phosphatase, receptor type, T 176 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) TTGCGGCTGGCGCTGAGCTTG 0.577000 0 SO:0001583 missense ENST00000373187.1 1 0 hg19 CCDS42874.1 51 0.023351648351648352 46 0.09349593495934959 5 0.013812154696132596 0 0.0 0 0.0 C 5.956 0.360303 0.11296 0.075499 1.19E-4 ENSG00000196090 ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201 T;T;T;T;T;T;T 0.32988 1.46;1.46;1.46;1.46;1.45;1.44;1.43 6.03 -12.1 0.00011 . 0.964896 0.08646 N 0.914735 T 0.00300 0.0009 N 0.02225 -0.63 0.09310 N 1 B;B 0.09022 0.002;0.001 B;B 0.06405 0.002;0.001 T 0.22661 -1.0210 10 0.02654 T 1 . 12.1518 0.54053 0.2949:0.6078:0.0:0.0973 . 835;813 O14522-1;O14522 .;PTPRT_HUMAN T 813;813;816;822;835;803;803 ENSP00000362286:A813T;ENSP00000362283:A813T;ENSP00000362289:A816T;ENSP00000348408:A822T;ENSP00000362294:A835T;ENSP00000362280:A803T;ENSP00000362297:A803T ENSP00000348408:A822T A - 1 0 PTPRT 40261348 0.920000 0.31207 0.000000 0.03702 0.902000 0.53008 -0.011000 0.12721 -2.596000 0.00453 -0.140000 0.14226 GCC TCGA-IB-A5SS-01A-11D-A32N-08 PTPRT-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000080315.1 0 0 1 177 604 0 308 0 0 0 0 308 2 0 0 0 0 0 2 1 1.000000 175 591 0 305 2 0 0 0 0 308 2 -1.843438 0 1 120968 899 66 1 0 0 0 2.047877 0 0.460000 1.850000 0.454986 0.970000 8.400000e-01 1.000000 1.000000 0.961421 0.970000 1 0.900000 1.000000 CDH26 60437 broad.mit.edu 37 20 58574705 58574705 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr20:58574705C>T ENST00000244047.5 + 14 2395 c.2084C>T c.(2083-2085)aCg>aTg p.T695M CDH26_ENST00000244049.3_Missense_Mutation_p.T28M|CDH26_ENST00000348616.4_Missense_Mutation_p.T695M|CDH26_ENST00000350849.6_Missense_Mutation_p.T28M|CDH26_ENST00000497614.1_3'UTR Q8IXH8 CAD26_HUMAN cadherin 26 44 all_lung(29;0.00963) BRCA - Breast invasive adenocarcinoma(7;5.58e-09) GCAGGACCCACGCAGGGAGTT 0.522000 0 SO:0001583 missense ENST00000244047.5 1 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 2.687|2.687 -0.274118|-0.274118 0.05679|0.05679 4.54E-4|4.54E-4 1.16E-4|1.16E-4 ENSG00000124215|ENSG00000124215 ENST00000370991|ENST00000244047;ENST00000348616;ENST00000244049;ENST00000350849;ENST00000456106 .|T;T;T .|0.59638 .|0.25;0.54;0.54 2.88|2.88 -5.76|-5.76 0.02376|0.02376 .|. .|. .|. .|. .|. T|T 0.22704|0.22704 0.0548|0.0548 N|N 0.08118|0.08118 0|0 0.09310|0.09310 N|N 1|1 .|P;P;P;B .|0.43024 .|0.798;0.798;0.474;0.434 .|B;B;B;B .|0.32465 .|0.094;0.146;0.032;0.07 T|T 0.20940|0.20940 -1.0260|-1.0260 5|9 .|0.34782 .|T .|0.22 .|. 2.0821|2.0821 0.03637|0.03637 0.2073:0.422:0.0986:0.2721|0.2073:0.422:0.0986:0.2721 .|. .|28;28;695;695 .|Q8IXH8-5;Q8IXH8-2;Q8IXH8;Q8IXH8-4 .|.;.;CAD26_HUMAN;. C|M 287|695;695;28;28;28 .|ENSP00000244047:T695M;ENSP00000339390:T695M;ENSP00000310845:T28M .|ENSP00000244047:T695M R|T +|+ 1|2 0|0 CDH26|CDH26 58008100|58008100 0.000000|0.000000 0.05858|0.05858 0.000000|0.000000 0.03702|0.03702 0.000000|0.000000 0.00434|0.00434 -2.002000|-2.002000 0.01464|0.01464 -1.744000|-1.744000 0.01338|0.01338 -3.845000|-3.845000 0.00018|0.00018 CGC|ACG TCGA-IB-A5SS-01A-11D-A32N-08 CDH26-201 KNOWN basic protein_coding protein_coding 1 0 1 51 229 0 84 0 6.726205e-01 1 11 0 84 2 0 0 0 0 0 2 1 1.000000 48 228 0 84 2 0 0 0 0 84 2 -20.000000 1 1 121412 8 40 1 0 0 0 2.047877 0 0.460000 1.850000 0.454986 0.780000 6.000000e-01 0.980000 0.780000 0.790043 0.780000 0 0.680000 0.890000 RFPL1 5988 broad.mit.edu 37 22 29835118 29835118 + Missense_Mutation SNP T T A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr22:29835118T>A ENST00000354373.2 + 1 547 c.338T>A c.(337-339)aTt>aAt p.I113N RFPL1S_ENST00000461286.3_RNA|RFPL1S_ENST00000539579.1_RNA NM_021026.2 NP_066306.2 O75677 RFPL1_HUMAN ret finger protein-like 1 16 CTGAAGAAGATTCTGCAGATG 0.512000 0 SO:0001583 missense ENST00000354373.2 0 1 hg19 CCDS13857.2 . . . . . . . . . . - 12.72 2.023419 0.35701 . . ENSG00000128250 ENST00000354373 T 0.30448 1.53 1.66 -1.88 0.07713 RDM domain, Ret finger protein-like (1);B30.2/SPRY domain (1); . . . . T 0.37705 0.1013 L 0.52573 1.65 0.09310 N 1 D 0.59767 0.986 D 0.69307 0.963 T 0.24333 -1.0163 9 0.37606 T 0.19 . 2.2276 0.03988 0.0:0.235:0.315:0.45 . 113 O75677 RFPL1_HUMAN N 113 ENSP00000346342:I113N ENSP00000346342:I113N I + 2 0 RFPL1 28165118 0.004000 0.15560 0.004000 0.12327 0.209000 0.24338 -0.522000 0.06237 -0.097000 0.12307 0.342000 0.21767 ATT TCGA-IB-A5SS-01A-11D-A32N-08 RFPL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318719.1 0 0 0 6 441 0 131 0 0 0 1 0 131 2 0 0 0 0 0 2 1 0.963464 6 434 0 132 2 0 0 0 0 131 2 -6.096757 1 1 0 0 1 1 2 3 2.134110 0 0.460000 1.850000 0.468556 0.060000 2.000000e-02 1.000000 0.060000 0.120641 0.060000 0 0.030000 0.100000 CACNA1I 8911 broad.mit.edu 37 22 40042649 40042649 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr22:40042649C>T ENST00000402142.3 + 8 1225 c.1225C>T c.(1225-1227)Cac>Tac p.H409Y CACNA1I_ENST00000400164.3_Missense_Mutation_p.H409Y|CACNA1I_ENST00000404898.1_Missense_Mutation_p.H409Y|CACNA1I_ENST00000401624.1_Missense_Mutation_p.H409Y|CACNA1I_ENST00000336649.4_Missense_Mutation_p.H409Y|CACNA1I_ENST00000407673.1_Missense_Mutation_p.H409Y NM_021096.3 NP_066919.2 Q9P0X4 CAC1I_HUMAN calcium channel, voltage-dependent, T type, alpha 1I subunit 60 Melanoma(58;0.0749) Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909) GCAACGGGAGCACCGGCTGAT 0.607000 0 SO:0001583 missense ENST00000402142.3 0 1 hg19 CCDS46710.1 . . . . . . . . . . C 13.13 2.144395 0.37825 . . ENSG00000100346 ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164 D;D;D;D;D;D 0.96885 -4.14;-4.09;-4.13;-4.09;-4.16;-4.06 3.49 3.49 0.39957 . 0.300797 0.30151 U 0.010282 D 0.96725 0.8931 M 0.63843 1.955 0.50813 D 0.999896 P;D;P;D 0.63880 0.919;0.969;0.919;0.993 B;P;B;D 0.72982 0.441;0.792;0.441;0.979 D 0.95148 0.8270 10 0.02654 T 1 . 15.8737 0.79145 0.0:1.0:0.0:0.0 . 409;409;409;409 Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4 .;.;.;CAC1I_HUMAN Y 409 ENSP00000385019:H409Y;ENSP00000384093:H409Y;ENSP00000383887:H409Y;ENSP00000385680:H409Y;ENSP00000337829:H409Y;ENSP00000383028:H409Y ENSP00000337829:H409Y H + 1 0 CACNA1I 38372595 1.000000 0.71417 1.000000 0.80357 0.937000 0.57800 1.658000 0.37376 1.899000 0.54978 0.305000 0.20034 CAC TCGA-IB-A5SS-01A-11D-A32N-08 CACNA1I-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000321290.1 1 0 1 6 22 0 10 0 0 0 0 10 2 0 0 0 0 0 2 1 0.970955 6 22 0 10 2 0 0 0 0 10 2 -14.565670 1 1 0 0 1 1 2 3 2.134110 0 0.460000 1.850000 0.468556 0.980000 4.300000e-01 1.000000 1.000000 0.873955 0.980000 1 0.670000 1.000000 SBF1 6305 broad.mit.edu 37 22 50900742 50900742 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr22:50900742C>T ENST00000390679.3 - 19 2472 c.2288G>A c.(2287-2289)cGc>cAc p.R763H SBF1_ENST00000348911.6_Missense_Mutation_p.R764H|SBF1_ENST00000380817.3_Missense_Mutation_p.R763H O95248 MTMR5_HUMAN SET binding factor 1 43 all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) GTAGCTCATGCGGTTGGCATA 0.647000 0 SO:0001583 missense ENST00000390679.3 0 1 hg19 . . . . . . . . . . C 24.2 4.503927 0.85176 0.0 1.18E-4 ENSG00000100241 ENST00000380817;ENST00000348911;ENST00000356279;ENST00000337034;ENST00000390679 T;T;T 0.49432 0.78;0.78;0.78 4.52 4.52 0.55395 . 0.933584 0.09027 N 0.859341 T 0.69593 0.3128 M 0.72118 2.19 0.58432 D 0.999999 D;D;D 0.89917 0.998;1.0;1.0 D;D;D 0.66716 0.946;0.938;0.938 T 0.66516 -0.5904 10 0.59425 D 0.04 . 17.0388 0.86483 0.0:1.0:0.0:0.0 . 763;764;763 O95248;G5E933;O95248-4 MTMR5_HUMAN;.;. H 763;764;774;773;763 ENSP00000370196:R763H;ENSP00000252027:R764H;ENSP00000375097:R763H ENSP00000336522:R773H R - 2 0 SBF1 49247608 0.984000 0.35163 1.000000 0.80357 0.965000 0.64279 1.018000 0.30002 2.366000 0.80165 0.655000 0.94253 CGC TCGA-IB-A5SS-01A-11D-A32N-08 SBF1-201 KNOWN basic protein_coding protein_coding 0 0 0 5 358 0 158 0 4.975705e-01 0 107 0 158 2 0 0 0 0 0 2 1 0.936587 5 355 0 157 2 0 0 0 0 158 2 -2.844892 1 1 121210 29 46 1 1 2 3 2.129916 0 0.460000 1.850000 0.468556 0.060000 1.000000e-02 1.000000 0.060000 0.124098 0.060000 0 0.030000 0.110000 CXCR2 3579 broad.mit.edu 37 2 219000390 219000390 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr2:219000390G>A ENST00000318507.2 + 3 1293 c.866G>A c.(865-867)cGc>cAc p.R289H NM_001557.3 NP_001548.1 P25025 CXCR2_HUMAN chemokine (C-X-C motif) receptor 2 22 TGTGAGCGCCGCAATCACATC 0.597000 0 SO:0001583 missense ENST00000318507.2 0 1 hg19 CCDS2408.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 13.03 2.114961 0.37339 . . ENSG00000180871 ENST00000318507 T 0.37411 1.2 5.36 4.47 0.54385 GPCR, rhodopsin-like superfamily (1); 0.057955 0.64402 D 0.000006 T 0.48502 0.1503 M 0.70108 2.13 0.09310 N 0.999998 P 0.38767 0.646 P 0.50231 0.635 T 0.40440 -0.9563 9 . . . . 9.7981 0.40748 0.1635:0.0:0.8365:0.0 . 289 P25025 CXCR2_HUMAN H 289 ENSP00000319635:R289H . R + 2 0 CXCR2 218708635 0.930000 0.31532 0.358000 0.25811 0.045000 0.14185 3.615000 0.54167 1.243000 0.43853 0.456000 0.33151 CGC TCGA-IB-A5SS-01A-11D-A32N-08 CXCR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256772.2 0 0 0 5 303 0 108 0 0 0 0 108 2 0 0 0 0 0 2 1 0.936422 5 300 0 108 2 0 0 0 0 108 2 -2.437072 0 1 121412 6 40 1 0 0 0 2.054531 0 0.460000 1.850000 0.457505 0.070000 2.000000e-02 0.150000 0.070000 0.083445 0.070000 0 0.040000 0.120000 VWA3B 200403 broad.mit.edu 37 2 98914394 98914394 + Missense_Mutation SNP G G A rs146321928 by1000genomes TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr2:98914394G>A ENST00000477737.1 + 24 3386 c.3182G>A c.(3181-3183)cGc>cAc p.R1061H AC092675.1_ENST00000401293.1_RNA|VWA3B_ENST00000490947.2_3'UTR NM_144992.4 NP_659429.4 Q502W6 VWA3B_HUMAN von Willebrand factor A domain containing 3B 70 TGTGTGAGCCGCACCCAAGCA 0.532000 0 SO:0001583 missense ENST00000477737.1 0 1 hg19 CCDS42718.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 7.890 0.732062 0.15507 . . ENSG00000168658 ENST00000477737;ENST00000358269 T 0.23147 1.92 4.93 -0.398 0.12418 . 750.824000 0.00166 N 0.000000 T 0.15782 0.0380 N 0.08118 0 0.09310 N 1 B;B 0.09022 0.001;0.002 B;B 0.06405 0.001;0.002 T 0.32455 -0.9906 10 0.56958 D 0.05 . 8.6816 0.34212 0.2741:0.4468:0.279:0.0 . 453;1061 Q502W6-5;Q502W6 .;VWA3B_HUMAN H 1061;183 ENSP00000417955:R1061H ENSP00000351009:R183H R + 2 0 VWA3B 98280826 0.000000 0.05858 0.093000 0.20910 0.314000 0.28054 0.066000 0.14489 0.036000 0.15547 -0.151000 0.13558 CGC TCGA-IB-A5SS-01A-11D-A32N-08 VWA3B-020 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353469.2 0 0 0 5 237 0 85 0 7.025761e-04 0 2 0 85 2 0 0 0 0 0 2 1 0.935420 5 233 0 84 2 0 0 0 0 85 2 -2.576463 1 1 120908 8 41 1 0 0 0 2.054531 0 0.460000 1.850000 0.457505 0.090000 3.000000e-02 0.200000 0.090000 0.105905 0.090000 0 0.050000 0.150000 SLC6A1 6529 broad.mit.edu 37 3 11059035 11059035 + Silent SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr3:11059035G>A ENST00000287766.4 + 3 559 c.138G>A c.(136-138)acG>acA p.T46T SLC6A1_ENST00000536032.1_Intron|SLC6A1-AS1_ENST00000414969.2_RNA|SLC6A1_ENST00000462473.1_Intron NM_003042.3 NP_003033.3 P30531 SC6A1_HUMAN solute carrier family 6 (neurotransmitter transporter), member 1 26 Ovarian(110;0.0392) Clobazam(DB00349)|Tiagabine(DB00906) ACCGGGACACGTGGAAGGGCC 0.617000 0 SO:0001819 synonymous_variant ENST00000287766.4 1 0 hg19 CCDS2603.1 TCGA-IB-A5SS-01A-11D-A32N-08 SLC6A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000102767.2 0 0 1 80 263 0 114 0 5.564212e-02 0 2 0 114 2 0 0 0 0 0 2 1 1.000000 80 259 0 112 2 0 0 0 0 114 2 -2.496433 0 1 121412 780 62 1 0 0 0 2.058891 0 0.460000 1.850000 0.457505 0.990000 8.200000e-01 1.000000 1.000000 0.966777 0.990000 1 0.900000 1.000000 CPNE4 131034 broad.mit.edu 37 3 131261421 131261421 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr3:131261421G>A ENST00000512055.1 - 19 3645 c.1519C>T c.(1519-1521)Ccc>Tcc p.P507S CPNE4_ENST00000512332.1_Missense_Mutation_p.P525S|CPNE4_ENST00000429747.1_Missense_Mutation_p.P507S|CPNE4_ENST00000502818.1_Missense_Mutation_p.P525S|CPNE4_ENST00000511604.1_Missense_Mutation_p.P507S Q96A23 CPNE4_HUMAN copine IV 39 TTCCTGAAGGGCACGAACTGG 0.502000 0 SO:0001583 missense ENST00000512055.1 0 1 hg19 CCDS3072.1 . . . . . . . . . . G 24.1 4.496921 0.85069 . . ENSG00000196353 ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818 T;T;T;T;T 0.56103 0.49;0.49;0.48;0.49;0.48 5.48 5.48 0.80851 von Willebrand factor, type A (1); 0.000000 0.85682 D 0.000000 T 0.76779 0.4035 M 0.84433 2.695 0.80722 D 1 D;D 0.89917 0.999;1.0 D;D 0.79108 0.991;0.992 T 0.79342 -0.1843 10 0.56958 D 0.05 -17.478 19.3471 0.94367 0.0:0.0:1.0:0.0 . 525;507 Q96A23-2;Q96A23 .;CPNE4_HUMAN S 507;507;525;507;525 ENSP00000421705:P507S;ENSP00000411904:P507S;ENSP00000424853:P525S;ENSP00000423811:P507S;ENSP00000421646:P525S ENSP00000411904:P507S P - 1 0 CPNE4 132744111 1.000000 0.71417 1.000000 0.80357 0.749000 0.42624 9.624000 0.98398 2.566000 0.86566 0.655000 0.94253 CCC TCGA-IB-A5SS-01A-11D-A32N-08 CPNE4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356583.4 0 0 0 5 223 0 69 0 4.811178e-02 0 13 0 69 2 0 0 0 0 0 2 1 0.937506 5 222 0 69 2 0 0 0 0 69 2 -3.255014 1 1 0 0 1 0 0 0 2.072413 0 0.460000 1.850000 0.460000 0.100000 3.000000e-02 0.210000 0.100000 0.112824 0.100000 0 0.060000 0.160000 PIK3CB 5291 broad.mit.edu 37 3 138382857 138382857 + Missense_Mutation SNP C C T rs142933486 by1000genomes TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr3:138382857C>T ENST00000477593.1 - 20 2760 c.2687G>A c.(2686-2688)cGa>cAa p.R896Q PIK3CB_ENST00000289153.2_Missense_Mutation_p.R896Q|PIK3CB_ENST00000544716.1_Missense_Mutation_p.R347Q P42338 PK3CB_HUMAN phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta 41 Caffeine(DB00201) CTCAATGGCTCGGTCCAGGTC 0.448000 0 SO:0001583 missense ENST00000477593.1 1 1 hg19 CCDS3104.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 17.04|17.04 3.286996|3.286996 0.59867|0.59867 .|. .|. ENSG00000051382|ENSG00000051382 ENST00000493568|ENST00000477593;ENST00000544716;ENST00000289153 .|T;T;T .|0.76060 .|-0.99;-0.99;-0.99 5.63|5.63 5.63|5.63 0.86233|0.86233 .|Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4); .|0.000000 .|0.85682 .|D .|0.000000 T|T 0.63640|0.63640 0.2528|0.2528 L|L 0.31207|0.31207 0.915|0.915 0.58432|0.58432 D|D 0.999998|0.999998 .|B;B;B .|0.33379 .|0.269;0.178;0.41 .|B;B;B .|0.24541 .|0.041;0.044;0.054 T|T 0.60662|0.60662 -0.7219|-0.7219 5|10 .|0.28530 .|T .|0.3 -11.8261|-11.8261 20.0442|20.0442 0.97604|0.97604 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|896;483;347 .|P42338;B4DZI3;Q68DL0 .|PK3CB_HUMAN;.;. K|Q 528|896;347;896 .|ENSP00000418143:R896Q;ENSP00000438259:R347Q;ENSP00000289153:R896Q .|ENSP00000289153:R896Q E|R -|- 1|2 0|0 PIK3CB|PIK3CB 139865547|139865547 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.999000|0.999000 0.98932|0.98932 3.138000|3.138000 0.50570|0.50570 2.814000|2.814000 0.96858|0.96858 0.655000|0.655000 0.94253|0.94253 GAG|CGA TCGA-IB-A5SS-01A-11D-A32N-08 PIK3CB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000358019.1 1 0 1 28 99 0 35 1 9.999955e-01 33 44 0 35 2 0 0 0 0 0 2 1 1.000000 27 99 0 35 2 0 0 0 0 35 2 -3.470118 1 0 0 0 1 0 0 0 2.072413 0 0.460000 1.850000 0.460000 0.950000 6.700000e-01 1.000000 1.000000 0.919559 0.950000 1 0.800000 1.000000 DVL3 1857 broad.mit.edu 37 3 183884692 183884692 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr3:183884692G>A ENST00000313143.3 + 11 1375 c.1127G>A c.(1126-1128)gGc>gAc p.G376D DVL3_ENST00000431765.1_Missense_Mutation_p.G359D|EIF2B5_ENST00000444495.1_Intron NM_004423.3 NP_004414.3 Q92997 DVL3_HUMAN dishevelled segment polarity protein 3 35 all_cancers(143;1.12e-10)|Ovarian(172;0.0339) Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22) CCTGCATACGGCATGAGCCCC 0.647000 0 SO:0001583 missense ENST00000313143.3 0 1 hg19 CCDS3253.1 . . . . . . . . . . G 23.3 4.398229 0.83120 . . ENSG00000161202 ENST00000313143;ENST00000415612;ENST00000431765 T;T 0.04156 3.71;3.69 5.97 5.97 0.96955 . 0.000000 0.85682 D 0.000000 T 0.16557 0.0398 M 0.68593 2.085 0.80722 D 1 P;P;B;D 0.57257 0.94;0.94;0.232;0.979 P;P;B;P 0.55222 0.694;0.76;0.113;0.771 T 0.00172 -1.1958 10 0.33141 T 0.24 -34.8595 20.4387 0.99107 0.0:0.0:1.0:0.0 . 359;208;376;376 B4E3E5;Q9UG07;F5GWR8;Q92997 .;.;.;DVL3_HUMAN D 376;376;359 ENSP00000316054:G376D;ENSP00000405885:G359D ENSP00000316054:G376D G + 2 0 DVL3 185367386 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 8.008000 0.88588 2.836000 0.97738 0.655000 0.94253 GGC TCGA-IB-A5SS-01A-11D-A32N-08 DVL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346184.1 0 0 0 6 462 0 171 0 7.584087e-01 0 207 0 171 2 0 0 0 0 0 2 1 0.963527 5 456 0 169 2 0 0 0 0 171 2 -2.154265 0 1 0 0 1 0 0 0 2.072413 0 0.460000 1.850000 0.460000 0.050000 1.000000e-02 0.120000 0.060000 0.064597 0.050000 0 0.030000 0.090000 GADL1 339896 broad.mit.edu 37 3 30875345 30875345 + Splice_Site SNP A A T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr3:30875345A>T ENST00000282538.5 - 11 1200 c.1050T>A c.(1048-1050)tcT>tcA p.S350S GADL1_ENST00000454381.3_Splice_Site_p.S350S NM_207359.2 NP_997242.2 Q6ZQY3 GADL1_HUMAN glutamate decarboxylase-like 1 25 GAAAACTTACAGATTTGTCTT 0.502000 0 SO:0001630 splice_region_variant ENST00000282538.5 1 0 hg19 CCDS2649.2 TCGA-IB-A5SS-01A-11D-A32N-08 GADL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253106.2 1 0 1 32 125 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 1.000000 32 124 0 58 2 0 0 0 0 58 2 -20.000000 1 1 0 0 1 0 0 0 2.072413 0 0.460000 1.850000 0.460000 0.880000 6.300000e-01 1.000000 1.000000 0.876483 0.880000 1 0.750000 1.000000 CNTN3 5067 broad.mit.edu 37 3 74351867 74351867 + Nonsense_Mutation SNP G G T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr3:74351867G>T ENST00000263665.6 - 13 1787 c.1760C>A c.(1759-1761)tCa>tAa p.S587* NM_020872.1 NP_065923.1 Q9P232 CNTN3_HUMAN contactin 3 (plasmacytoma associated) 83 Lung NSC(201;0.138)|Lung SC(41;0.21) AGCAGCAGATGAAACACTGTC 0.418000 0 SO:0001587 stop_gained ENST00000263665.6 0 1 hg19 CCDS33790.1 . . . . . . . . . . G 38 6.834241 0.97873 . . ENSG00000113805 ENST00000263665 . . . 5.08 5.08 0.68730 . 0.136971 0.51477 D 0.000086 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 16.9949 0.86365 0.0:0.0:1.0:0.0 . . . . X 587 . ENSP00000263665:S587X S - 2 0 CNTN3 74434557 1.000000 0.71417 0.403000 0.26384 0.815000 0.46073 6.862000 0.75484 2.523000 0.85059 0.585000 0.79938 TCA TCGA-IB-A5SS-01A-11D-A32N-08 CNTN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352306.1 1 0 1 26 80 0 36 0 0 1 0 0 36 2 0 0 0 0 0 2 1 1.000000 26 79 0 37 2 0 0 0 0 36 2 -4.274286 1 1 0 0 1 0 0 0 2.072413 0 0.460000 1.850000 0.460000 0.990000 7.300000e-01 1.000000 1.000000 0.961195 0.990000 1 0.890000 1.000000 CNTN3 5067 broad.mit.edu 37 3 74351868 74351868 + Missense_Mutation SNP A A T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr3:74351868A>T ENST00000263665.6 - 13 1786 c.1759T>A c.(1759-1761)Tca>Aca p.S587T NM_020872.1 NP_065923.1 Q9P232 CNTN3_HUMAN contactin 3 (plasmacytoma associated) 83 Lung NSC(201;0.138)|Lung SC(41;0.21) GCAGCAGATGAAACACTGTCC 0.418000 0 SO:0001583 missense ENST00000263665.6 1 1 hg19 CCDS33790.1 . . . . . . . . . . A 17.58 3.425150 0.62733 . . ENSG00000113805 ENST00000263665 T 0.64991 -0.13 5.08 5.08 0.68730 Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.136971 0.51477 D 0.000086 T 0.60702 0.2289 L 0.53249 1.67 0.46749 D 0.999185 P 0.35192 0.489 B 0.41691 0.364 T 0.60806 -0.7190 10 0.38643 T 0.18 . 10.7556 0.46234 0.8287:0.1713:0.0:0.0 . 587 Q9P232 CNTN3_HUMAN T 587 ENSP00000263665:S587T ENSP00000263665:S587T S - 1 0 CNTN3 74434558 1.000000 0.71417 0.433000 0.26760 0.861000 0.49209 4.988000 0.63863 2.039000 0.60335 0.477000 0.44152 TCA TCGA-IB-A5SS-01A-11D-A32N-08 CNTN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352306.1 1 0 1 26 81 0 37 0 0 1 0 0 37 2 0 0 0 0 0 2 1 1.000000 26 80 0 37 2 0 0 0 0 37 2 -19.583500 1 1 0 0 1 0 0 0 2.072413 0 0.460000 1.850000 0.460000 0.990000 7.300000e-01 1.000000 1.000000 0.958196 0.990000 1 0.880000 1.000000 TBC1D1 23216 broad.mit.edu 37 4 38022213 38022213 + Splice_Site SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr4:38022213G>A ENST00000261439.4 + 5 1329 c.974G>A c.(973-975)gGc>gAc p.G325D TBC1D1_ENST00000508802.1_Splice_Site_p.G325D NM_001253914.1|NM_001253915.1|NM_015173.3 NP_001240843.1|NP_001240844.1|NP_055988.2 Q86TI0 TBCD1_HUMAN TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1 36 CTTTGGCAGGGCATCAGACAC 0.458000 0 SO:0001630 splice_region_variant ENST00000261439.4 0 1 hg19 CCDS33972.1 . . . . . . . . . . G 28.3 4.905016 0.92035 . . ENSG00000065882 ENST00000508802;ENST00000261439;ENST00000446803 T;T;T 0.14266 2.52;2.52;2.52 5.48 5.48 0.80851 Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1); 0.000000 0.51477 D 0.000095 T 0.36054 0.0953 L 0.54908 1.71 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;1.0;1.0 T 0.03555 -1.1025 10 0.87932 D 0 -20.7573 19.3503 0.94381 0.0:0.0:1.0:0.0 . 325;325;325 B9A6J6;E9PGH8;Q86TI0 .;.;TBCD1_HUMAN D 325;325;196 ENSP00000423651:G325D;ENSP00000261439:G325D;ENSP00000396877:G196D ENSP00000261439:G325D G + 2 0 TBC1D1 37698608 1.000000 0.71417 1.000000 0.80357 0.651000 0.38670 9.730000 0.98797 2.576000 0.86940 0.467000 0.42956 GGC TCGA-IB-A5SS-01A-11D-A32N-08 TBC1D1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317443.2 0 0 0 6 700 0 258 0 2.153403e-01 0 87 0 258 2 0 0 0 0 0 2 1 0.963657 6 691 0 258 2 0 0 0 0 258 2 -1.704822 0 1 0 0 1 1 2 3 2.095274 0 0.460000 1.850000 0.462473 0.030000 0 0.090000 0.040000 0.052283 0.030000 0 0.010000 0.060000 PCDHA4 56144 broad.mit.edu 37 5 140188813 140188813 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr5:140188813C>T ENST00000530339.1 + 1 2041 c.2041C>T c.(2041-2043)Cgg>Tgg p.R681W PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.R681W|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.R681W|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) GGCCTCCTCACGGGCGTTGGT 0.632000 0 SO:0001583 missense ENST00000530339.1 1 1 hg19 CCDS54916.1 . . . . . . . . . . c 11.80 1.746491 0.30955 . . ENSG00000204967 ENST00000512229;ENST00000356878;ENST00000530339 T;T;T 0.54071 0.63;0.59;0.6 3.93 -0.744 0.11101 . 0.210729 0.23351 U 0.049123 T 0.51466 0.1676 M 0.89601 3.045 0.09310 N 1 B;B;B 0.32717 0.381;0.082;0.137 B;B;B 0.32289 0.143;0.022;0.022 T 0.52366 -0.8585 10 0.66056 D 0.02 . 4.0101 0.09619 0.4068:0.383:0.1322:0.078 . 681;681;681 Q9UN74-2;Q9UN74;D6RA20 .;PCDA4_HUMAN;. W 681 ENSP00000423470:R681W;ENSP00000349344:R681W;ENSP00000435300:R681W ENSP00000349344:R681W R + 1 2 PCDHA4 140168997 0.171000 0.23029 0.001000 0.08648 0.014000 0.08584 0.000000 0.12993 -0.051000 0.13334 -0.516000 0.04426 CGG TCGA-IB-A5SS-01A-11D-A32N-08 PCDHA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372864.2 1 0 1 59 227 0 93 0 0 0 1 0 93 2 0 0 0 0 0 2 1 1.000000 59 224 0 93 2 0 0 0 0 93 2 -20.000000 1 1 0 0 1 1 2 3 2.084628 0 0.460000 1.850000 0.461239 0.890000 7.000000e-01 1.000000 1.000000 0.893490 0.890000 1 0.790000 1.000000 PCDHGA12 26025 broad.mit.edu 37 5 140810888 140810888 + Missense_Mutation SNP G G A rs112186927 byFrequency TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr5:140810888G>A ENST00000252085.3 + 1 704 c.562G>A c.(562-564)Ggt>Agt p.G188S PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000518882.1_Intron NM_003735.2|NM_032094.1 NP_003726.1|NP_115265.1 O60330 PCDGC_HUMAN protocadherin gamma subfamily A, 12 58 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGGAGCCGACGGTAGTAAGTA 0.607000 0 SO:0001583 missense ENST00000252085.3 1 0 hg19 CCDS4260.1 . . . . . . . . . . g 15.60 2.882516 0.51908 . . ENSG00000253159 ENST00000252085 T 0.20332 2.08 5.8 5.8 0.92144 Cadherin (4);Cadherin-like (1); . . . . T 0.57080 0.2029 M 0.93375 3.41 0.30472 N 0.773188 D;D 0.65815 0.993;0.995 P;P 0.60473 0.766;0.875 T 0.65899 -0.6056 9 0.59425 D 0.04 . 19.6649 0.95889 0.0:0.0:1.0:0.0 . 188;188 O60330-2;O60330 .;PCDGC_HUMAN S 188 ENSP00000252085:G188S ENSP00000252085:G188S G + 1 0 PCDHGA12 140791072 1.000000 0.71417 0.311000 0.25182 0.004000 0.04260 2.963000 0.49184 2.748000 0.94277 0.655000 0.94253 GGT TCGA-IB-A5SS-01A-11D-A32N-08 PCDHGA12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251806.2 1 0 1 108 442 0 161 0 5.545100e-01 0 9 0 161 2 0 0 0 0 0 2 1 1.000000 107 437 0 159 2 0 0 0 0 161 2 -2.793535 1 1 0 0 1 1 2 3 2.084628 0 0.460000 1.850000 0.461239 0.850000 7.100000e-01 1.000000 0.850000 0.857698 0.850000 1 0.780000 0.930000 PCDH1 5097 broad.mit.edu 37 5 141243880 141243880 + Silent SNP G G A rs149691852 by1000genomes TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr5:141243880G>A ENST00000394536.3 - 3 2155 c.2016C>T c.(2014-2016)agC>agT p.S672S PCDH1_ENST00000503492.1_Intron|PCDH1_ENST00000511044.1_5'UTR|PCDH1_ENST00000456271.1_Silent_p.S660S|PCDH1_ENST00000287008.3_Silent_p.S672S|PCDH1_ENST00000536585.1_Silent_p.S650S NM_001278613.1|NM_001278615.1 NP_001265542.1|NP_001265544.1 Q08174 PCDH1_HUMAN protocadherin 1 51 Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238) KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CTCGATCAAAGCTCAGGCTGG 0.552000 Ovarian(132;1609 1739 4190 14731 45037) 0 SO:0001819 synonymous_variant ENST00000394536.3 1 1 hg19 CCDS43375.1 TCGA-IB-A5SS-01A-11D-A32N-08 PCDH1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000251862.1 1 0 1 70 222 0 96 1 1 246 279 0 96 2 0 0 0 0 0 2 1 1.000000 70 219 0 96 2 0 0 0 0 96 2 -20.000000 1 1 121412 2 35 1 1 2 3 2.084628 0 0.460000 1.850000 0.461239 0.990000 8.300000e-01 1.000000 1.000000 0.977066 0.990000 1 0.930000 1.000000 RASGEF1C 255426 broad.mit.edu 37 5 179538479 179538479 + Silent SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr5:179538479G>A ENST00000393371.2 - 11 1577 c.1281C>T c.(1279-1281)acC>acT p.T427T RASGEF1C_ENST00000522500.1_Silent_p.T276T|RASGEF1C_ENST00000361132.4_Silent_p.T427T Q8N431 RGF1C_HUMAN RasGEF domain family, member 1C 12 all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137) all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) AGATGGGGGCGGTGTACAGGT 0.592000 0 SO:0001819 synonymous_variant ENST00000393371.2 1 1 hg19 CCDS4452.1 TCGA-IB-A5SS-01A-11D-A32N-08 RASGEF1C-001 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253506.2 1 0 1 44 150 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 1.000000 44 150 0 73 2 0 0 0 0 73 2 -4.108868 1 1 121412 2 34 1 1 2 3 2.084628 0 0.460000 1.850000 0.461239 0.980000 7.400000e-01 1.000000 1.000000 0.945306 0.980000 1 0.860000 1.000000 SLC45A2 51151 broad.mit.edu 37 5 33984521 33984521 + Silent SNP C C G TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr5:33984521C>G ENST00000296589.4 - 1 314 c.168G>C c.(166-168)gtG>gtC p.V56V SLC45A2_ENST00000509381.1_Silent_p.V56V|SLC45A2_ENST00000342059.3_Silent_p.V56V|SLC45A2_ENST00000345083.5_Silent_p.V56V|SLC45A2_ENST00000382102.3_Silent_p.V56V NM_016180.3 NP_057264 Q9UMX9 S45A2_HUMAN solute carrier family 45, member 2 48 GGACTGGGGTCACATACGCTG 0.592000 Ovarian(31;380 859 8490 22203 49048) 0 SO:0001819 synonymous_variant ENST00000296589.4 1 1 hg19 CCDS3901.1 TCGA-IB-A5SS-01A-11D-A32N-08 SLC45A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207443.2 1 0 1 16 52 0 29 0 0 0 0 29 2 0 0 0 0 0 2 1 0.999970 16 52 0 29 2 0 0 0 0 29 2 -20.000000 1 1 0 0 1 1 2 3 2.084628 0 0.460000 1.850000 0.461239 0.990000 6.400000e-01 1.000000 1.000000 0.932565 0.990000 1 0.810000 1.000000 TMEM161B 153396 broad.mit.edu 37 5 87502295 87502295 + Missense_Mutation SNP C C A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr5:87502295C>A ENST00000296595.6 - 7 744 c.620G>T c.(619-621)aGt>aTt p.S207I TMEM161B_ENST00000512429.1_Missense_Mutation_p.S196I|TMEM161B_ENST00000514135.1_Missense_Mutation_p.S207I|TMEM161B_ENST00000506536.1_Missense_Mutation_p.S25I|TMEM161B_ENST00000511218.1_Missense_Mutation_p.S25I|TMEM161B_ENST00000509387.1_Missense_Mutation_p.S80I NM_153354.3 NP_699185.1 Q8NDZ6 T161B_HUMAN transmembrane protein 161B 20 all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1) CTGCATCGCACTGTCTGAAAA 0.279000 0 SO:0001583 missense ENST00000296595.6 0 1 hg19 CCDS4065.1 . . . . . . . . . . C 15.63 2.891151 0.52014 . . ENSG00000164180 ENST00000514135;ENST00000296595;ENST00000506536;ENST00000511218;ENST00000512429;ENST00000443393;ENST00000509387 . . . 5.51 3.71 0.42584 . 0.186558 0.64402 D 0.000002 T 0.67382 0.2887 M 0.67397 2.05 0.80722 D 1 B;B 0.33044 0.083;0.395 P;B 0.44860 0.462;0.164 T 0.70550 -0.4841 9 0.72032 D 0.01 -7.8376 10.9255 0.47189 0.0:0.7979:0.1312:0.0709 . 25;207 B7Z6A5;Q8NDZ6 .;T161B_HUMAN I 207;207;25;25;196;207;80 . ENSP00000296595:S207I S - 2 0 TMEM161B 87538051 1.000000 0.71417 1.000000 0.80357 0.974000 0.67602 4.025000 0.57225 1.304000 0.44892 0.467000 0.42956 AGT TCGA-IB-A5SS-01A-11D-A32N-08 TMEM161B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254094.1 1 0 1 7 50 0 13 1 7.526785e-01 7 14 0 13 2 0 0 0 0 0 2 1 0.982949 7 50 0 13 2 0 0 0 0 13 2 -13.623610 1 1 0 0 1 1 2 3 2.084628 0 0.460000 1.850000 0.461239 0.550000 2.500000e-01 0.990000 1.000000 0.576708 0.550000 0 0.380000 0.770000 DNAH11 8701 broad.mit.edu 37 7 21657266 21657266 + Silent SNP C C A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr7:21657266C>A ENST00000409508.3 + 23 4156 c.4125C>A c.(4123-4125)cgC>cgA p.R1375R DNAH11_ENST00000328843.6_Silent_p.R1380R NM_001277115.1 NP_001264044.1 Q96DT5 DYH11_HUMAN dynein, axonemal, heavy chain 11 230 AGGAAGTCCGCGTCTGGGATG 0.483000 Kartagener syndrome 0 SO:0001819 synonymous_variant Familial Cancer Database Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome ENST00000409508.3 1 1 hg19 TCGA-IB-A5SS-01A-11D-A32N-08 DNAH11-001 KNOWN basic|appris_candidate protein_coding protein_coding OTTHUMT00000326582.6 0 0 1 23 90 0 28 0 0 0 1 0 28 2 0 0 0 0 0 2 1 1.000000 23 89 0 27 2 0 0 0 0 28 2 -20.000000 1 1 0 0 1 1 2 3 2.085237 0 0.460000 1.850000 0.461239 0.880000 5.900000e-01 1.000000 1.000000 0.871895 0.880000 1 0.730000 1.000000 NEUROD6 63974 broad.mit.edu 37 7 31377972 31377972 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr7:31377972G>A ENST00000297142.3 - 2 1233 c.911C>T c.(910-912)gCc>gTc p.A304V NM_022728.2 NP_073565.2 Q96NK8 NDF6_HUMAN neuronal differentiation 6 32 CCTGAACATGGCACCCTGCCC 0.468000 0 SO:0001583 missense ENST00000297142.3 0 1 hg19 CCDS5434.1 . . . . . . . . . . G 14.75 2.629527 0.46944 . . ENSG00000164600 ENST00000297142 D 0.95238 -3.65 5.13 5.13 0.70059 . 0.108251 0.64402 D 0.000004 D 0.89181 0.6642 L 0.27053 0.805 0.50813 D 0.999898 B 0.16396 0.017 B 0.18263 0.021 D 0.84308 0.0509 10 0.02654 T 1 -19.6987 18.5931 0.91222 0.0:0.0:1.0:0.0 . 304 Q96NK8 NDF6_HUMAN V 304 ENSP00000297142:A304V ENSP00000297142:A304V A - 2 0 NEUROD6 31344497 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 9.414000 0.97362 2.386000 0.81285 0.650000 0.86243 GCC TCGA-IB-A5SS-01A-11D-A32N-08 NEUROD6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000215050.1 0 0 0 5 235 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 0.936113 5 232 0 67 2 0 0 0 0 68 2 -2.802347 1 1 0 0 1 1 2 3 2.085237 0 0.460000 1.850000 0.461239 0.090000 3.000000e-02 0.210000 0.090000 0.107526 0.090000 0 0.050000 0.150000 ASL 435 broad.mit.edu 37 7 65557066 65557066 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr7:65557066G>A ENST00000304874.9 + 15 1238 c.1136G>A c.(1135-1137)cGc>cAc p.R379H ASL_ENST00000395332.3_Missense_Mutation_p.R379H|ASL_ENST00000380839.4_Missense_Mutation_p.R353H|AC068533.7_ENST00000450043.1_Silent_p.P147P|ASL_ENST00000464970.1_3'UTR|ASL_ENST00000395331.3_Missense_Mutation_p.R359H NM_000048.3 NP_000039.2 P04424 ARLY_HUMAN argininosuccinate lyase p.R379L(1) 18 L-Arginine(DB00125) TACCTGGTCCGCAAAGGGGTA 0.637000 1 Substitution - Missense(1) SO:0001583 missense ENST00000304874.9 0 1 hg19 CCDS5531.1 . . . . . . . . . . g 27.0 4.786704 0.90367 . . ENSG00000126522 ENST00000304874;ENST00000380839;ENST00000395332;ENST00000395331 D;D;D;D 0.91464 -2.85;-2.85;-2.85;-2.85 5.5 4.63 0.57726 L-Aspartase-like (1); 0.000000 0.85682 D 0.000000 D 0.92909 0.7744 M 0.89601 3.045 0.58432 D 0.999999 P;P;B 0.42871 0.792;0.6;0.445 B;B;B 0.43838 0.433;0.077;0.102 D 0.93527 0.6866 10 0.87932 D 0 . 13.5557 0.61757 0.0753:0.0:0.9247:0.0 . 353;359;379 E9PE48;E7EMI0;P04424 .;.;ARLY_HUMAN H 379;353;379;359 ENSP00000307188:R379H;ENSP00000370219:R353H;ENSP00000378741:R379H;ENSP00000378740:R359H ENSP00000307188:R379H R + 2 0 ASL 65194501 1.000000 0.71417 1.000000 0.80357 0.960000 0.62799 4.997000 0.63921 1.327000 0.45338 0.491000 0.48974 CGC TCGA-IB-A5SS-01A-11D-A32N-08 ASL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251695.2 0 0 0 5 473 1 162 0 6.574152e-02 0 241 1 162 7 0 0 0 0 0 2 0 0.064224 5 464 1 161 12 0 0 0 1 162 2 -1.793686 0 1 121412 3 37 1 1 2 3 2.085237 0 0.460000 1.850000 0.461239 0.040000 0 0.110000 0.040000 0.054248 0.040000 0 0.020000 0.080000 SGCZ 137868 broad.mit.edu 37 8 13947958 13947958 + Nonsense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr8:13947958C>T ENST00000382080.1 - 8 1648 c.933G>A c.(931-933)tgG>tgA p.W311* SGCZ_ENST00000421524.2_Nonsense_Mutation_p.W264* NM_139167.2 NP_631906.2 Q96LD1 SGCZ_HUMAN sarcoglycan, zeta 47 CACTTCAGCTCCACAGGCAGA 0.498000 0 SO:0001587 stop_gained ENST00000382080.1 0 1 hg19 CCDS5992.2 . . . . . . . . . . C 41 8.963007 0.99018 . . ENSG00000185053 ENST00000382080;ENST00000421524 . . . 5.5 5.5 0.81552 . 0.000000 0.85682 D 0.000000 . . . . . . 0.39948 D 0.974498 . . . . . . . . . . 0.02654 T 1 . 18.7556 0.91832 0.0:1.0:0.0:0.0 . . . . X 311;264 . ENSP00000371512:W311X W - 3 0 SGCZ 13992329 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.487000 0.81328 2.760000 0.94817 0.655000 0.94253 TGG TCGA-IB-A5SS-01A-11D-A32N-08 SGCZ-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207636.2 1 0 0 76 314 0 136 0 0 0 0 136 2 0 0 0 0 0 2 1 1.000000 76 312 0 133 2 0 0 0 0 136 2 -3.555108 1 1 0 0 1 0 0 0 2.074056 0 0.460000 1.850000 0.460000 0.840000 6.800000e-01 1.000000 1.000000 0.849543 0.840000 0 0.750000 0.940000 HSPA5 3309 broad.mit.edu 37 9 128000914 128000914 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr9:128000914C>T ENST00000324460.6 - 6 1392 c.1189G>A c.(1189-1191)Ggt>Agt p.G397S NM_005347.4 NP_005338.1 P11021 GRP78_HUMAN heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) 23 Acetylsalicylic acid(DB00945)|Antihemophilic Factor(DB00025) ACAGCAGCACCATACGCTACA 0.478000 Prostate(1;0.17) 0 SO:0001583 missense ENST00000324460.6 1 1 hg19 CCDS6863.1 . . . . . . . . . . C 33 5.269740 0.95429 . . ENSG00000044574 ENST00000324460 T 0.74526 -0.85 4.61 4.61 0.57282 . 0.000000 0.85682 D 0.000000 D 0.93167 0.7824 H 0.99937 4.99 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.96722 0.9533 10 0.87932 D 0 -2.7014 16.4549 0.84009 0.0:1.0:0.0:0.0 . 397 P11021 GRP78_HUMAN S 397 ENSP00000324173:G397S ENSP00000324173:G397S G - 1 0 HSPA5 127040735 1.000000 0.71417 1.000000 0.80357 0.956000 0.61745 7.818000 0.86416 2.097000 0.63578 0.563000 0.77884 GGT TCGA-IB-A5SS-01A-11D-A32N-08 HSPA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054062.1 1 0 1 58 188 0 86 1 1 819 2245 0 86 2 0 0 0 0 0 2 1 1.000000 58 183 0 86 2 0 0 0 0 86 2 -3.784387 1 1 0 0 1 0 1 1 2.067028 0 0.460000 1.850000 0.458755 0.990000 8.000000e-01 1.000000 1.000000 0.966002 0.990000 1 0.900000 1.000000 C9orf106 414318 broad.mit.edu 37 9 132084600 132084600 + RNA SNP C C A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr9:132084600C>A ENST00000316786.1 + 0 561 Q8NAJ2 CI106_HUMAN chromosome 9 open reading frame 106 4 Ovarian(14;0.00556)|Medulloblastoma(224;0.235) TGGCTCTGCCCTCAGAGCACT 0.612000 0 ENST00000316786.1 1 1 hg19 TCGA-IB-A5SS-01A-11D-A32N-08 C9orf106-001 KNOWN basic processed_transcript processed_transcript OTTHUMT00000054576.2 0 0 0 45 144 0 69 0 0 0 1 0 69 2 0 0 0 0 0 2 1 1.000000 46 142 0 69 2 0 0 0 0 69 2 -4.126252 1 1 0 0 1 0 1 1 2.067028 0 0.460000 1.850000 0.458755 0.990000 7.800000e-01 1.000000 1.000000 0.964240 0.990000 1 0.890000 1.000000 LCN9 392399 broad.mit.edu 37 9 138557549 138557549 + Silent SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr9:138557549C>T ENST00000277526.3 + 5 426 c.426C>T c.(424-426)tgC>tgT p.C142C LCN9_ENST00000430290.2_3'UTR NM_001001676.1 NP_001001676.1 Q8WX39 LCN9_HUMAN lipocalin 9 6 Myeloproliferative disorder(178;0.0821) AAGAAACCTGCGAAAAGTACG 0.572000 0 SO:0001819 synonymous_variant ENST00000277526.3 1 1 hg19 CCDS56593.1 TCGA-IB-A5SS-01A-11D-A32N-08 LCN9-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000410711.1 1 0 1 16 61 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 0.999962 15 61 0 34 2 0 0 0 0 34 2 -20.000000 1 1 120860 1 30 1 0 1 1 2.067028 0 0.460000 1.850000 0.458755 0.900000 5.600000e-01 1.000000 1.000000 0.873432 0.900000 1 0.710000 1.000000 SNAPC4 6621 broad.mit.edu 37 9 139272186 139272186 + Missense_Mutation SNP G G A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr9:139272186G>A ENST00000298532.2 - 21 4461 c.4093C>T c.(4093-4095)Cgg>Tgg p.R1365W NM_003086.2 NP_003077.2 small nuclear RNA activating complex, polypeptide 4, 190kDa 33 Myeloproliferative disorder(178;0.0511) AACCGCGCCCGCAACAGGAGG 0.726000 0 SO:0001583 missense ENST00000298532.2 0 1 hg19 CCDS6998.1 . . . . . . . . . . g 11.34 1.610741 0.28712 0.0 2.33E-4 ENSG00000165684 ENST00000298532 T 0.24908 1.83 4.06 1.66 0.24008 . 0.196559 0.34507 N 0.003920 T 0.19167 0.0460 L 0.40543 1.245 0.09310 N 1 B 0.26081 0.141 B 0.14023 0.01 T 0.15694 -1.0428 10 0.87932 D 0 -13.5129 10.0768 0.42366 0.0:0.0:0.3652:0.6348 . 1365 Q5SXM2 SNPC4_HUMAN W 1365 ENSP00000298532:R1365W ENSP00000298532:R1365W R - 1 2 SNAPC4 138392007 0.983000 0.35010 0.012000 0.15200 0.005000 0.04900 1.417000 0.34770 0.044000 0.15775 -0.408000 0.06270 CGG TCGA-IB-A5SS-01A-11D-A32N-08 SNAPC4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055071.1 0 0 0 4 123 0 50 0 3.064773e-01 0 29 0 50 2 0 0 0 0 0 2 1 0.889710 4 122 0 50 2 0 0 0 0 50 2 -6.565011 1 1 120812 3 32 1 0 1 1 2.067028 0 0.460000 1.850000 0.458755 0.150000 4.000000e-02 0.320000 0.140000 0.166582 0.150000 0 0.090000 0.230000 CDKN2A 1029 broad.mit.edu 37 9 21971186 21971186 + Nonsense_Mutation SNP G G A rs121913387 TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr9:21971186G>A ENST00000304494.5 - 2 442 c.172C>T c.(172-174)Cga>Tga p.R58* CDKN2A_ENST00000530628.2_Missense_Mutation_p.P72L|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R58*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P72L|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R58*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P113L|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R58*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.R7* NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.R58*(78)|p.?(45)|p.M53_R58del(3)|p.P113L(3)|p.R58fs*59(2)|p.M54fs*61(2)|p.R58fs*88(2)|p.0(1)|p.V28_V51del(1)|p.A57_R58>V*(1)|p.P113fs*>61(1)|p.R58fs*62(1)|p.R58fs*61(1)|p.G55fs*86(1)|p.R58R(1)|p.A57fs*85(1) 4199 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) TCCGCCACTCGGGCGCTGCCC 0.677000 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1459 Whole gene deletion(1316)|Substitution - Nonsense(78)|Unknown(45)|Deletion - Frameshift(10)|Deletion - In frame(4)|Substitution - Missense(3)|Insertion - Frameshift(1)|Substitution - coding silent(1)|Complex - compound substitution(1) GRCh37 CM940227 CDKN2A M rs121913387 SO:0001587 stop_gained ENST00000304494.5 0 1 hg19 CCDS6510.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 28.1|28.1 4.893482|4.893482 0.91889|0.91889 .|. .|. ENSG00000147889|ENSG00000147889 ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177 T;T|. 0.75367|. -0.93;-0.89|. 5.79|5.79 2.71|2.71 0.32032|0.32032 .|. 0.409080|. 0.18162|. N|. 0.149742|. T|. 0.29288|. 0.0729|. L|L 0.27053|0.27053 0.805|0.805 0.09310|0.09310 N|N 1|1 P|. 0.44006|. 0.824|. B|. 0.33121|. 0.158|. T|. 0.21381|. -1.0247|. 10|. 0.72032|0.13470 D|T 0.01|0.59 -3.0019|-3.0019 9.6681|9.6681 0.39996|0.39996 0.0:0.1288:0.474:0.3972|0.0:0.1288:0.474:0.3972 .|. 113|. Q8N726|. CD2A2_HUMAN|. L|X 113;72|58 ENSP00000355153:P113L;ENSP00000432664:P72L|. ENSP00000355153:P113L|ENSP00000307101:R58X P|R -|- 2|1 0|2 CDKN2A|CDKN2A 21961186|21961186 0.000000|0.000000 0.05858|0.05858 0.002000|0.002000 0.10522|0.10522 0.277000|0.277000 0.26821|0.26821 0.096000|0.096000 0.15147|0.15147 0.738000|0.738000 0.32606|0.32606 0.555000|0.555000 0.69702|0.69702 CCG|CGA TCGA-IB-A5SS-01A-11D-A32N-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 18 59 0 28 1 9.999927e-01 68 9 0 28 2 1 9.987984e-01 10 31 0 31 2 1 0.999991 18 57 0 28 2 0 0 0 0 28 2 -3.658803 1 1 0 0 1 0 1 1 2.067028 0 0.460000 1.850000 0.458755 0.990000 6.500000e-01 1.000000 1.000000 0.932111 0.990000 1 0.810000 1.000000 RUSC2 9853 broad.mit.edu 37 9 35555589 35555589 + Missense_Mutation SNP T T A TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr9:35555589T>A ENST00000455600.1 + 3 3116 c.2547T>A c.(2545-2547)caT>caA p.H849Q NM_001135999.1 NP_001129471 Q8N2Y8 RUSC2_HUMAN RUN and SH3 domain containing 2 32 Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194) ACCGGCTCCATGGAACAGGAA 0.647000 0 SO:0001583 missense ENST00000455600.1 1 1 hg19 CCDS35008.1 . . . . . . . . . . T 17.20 3.328553 0.60743 . . ENSG00000198853 ENST00000361226;ENST00000455600;ENST00000543478 T;T 0.23348 1.91;1.91 4.15 4.15 0.48705 . 0.295723 0.38272 N 0.001756 T 0.25306 0.0615 L 0.29908 0.895 0.39729 D 0.971581 D 0.61697 0.99 P 0.50537 0.643 T 0.02901 -1.1096 10 0.37606 T 0.19 -8.6196 11.4069 0.49902 0.0:0.0:0.0:1.0 . 849 Q8N2Y8 RUSC2_HUMAN Q 849 ENSP00000355177:H849Q;ENSP00000393922:H849Q ENSP00000355177:H849Q H + 3 2 RUSC2 35545589 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.372000 0.44257 1.863000 0.54032 0.533000 0.62120 CAT TCGA-IB-A5SS-01A-11D-A32N-08 RUSC2-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052309.1 1 0 1 82 243 0 107 1 9.999999e-01 18 58 0 107 2 0 0 0 0 0 2 1 1.000000 82 242 0 106 2 0 0 0 0 107 2 -20.000000 1 1 0 0 1 0 1 1 2.067028 0 0.460000 1.850000 0.458755 0.990000 8.900000e-01 1.000000 1.000000 0.990686 0.990000 1 0.980000 1.000000 ZCCHC7 84186 broad.mit.edu 37 9 37349387 37349387 + Missense_Mutation SNP C C T TCGA-IB-A5SS-01A-11D-A32N-08 TCGA-IB-A5SS-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf 735bd846-c248-4ee8-a1bb-08a3f8738776 g.chr9:37349387C>T ENST00000336755.5 + 7 1127 c.1021C>T c.(1021-1023)Cct>Tct p.P341S ZCCHC7_ENST00000461038.1_3'UTR|ZCCHC7_ENST00000534928.1_Missense_Mutation_p.P51S NM_032226.2 NP_115602.2 Q8N3Z6 ZCHC7_HUMAN zinc finger, CCHC domain containing 7 30 GCCGAAGACCCCTTCAAGACC 0.418000 0 SO:0001583 missense ENST00000336755.5 1 1 hg19 CCDS6608.2 . . . . . . . . . . C 9.590 1.125878 0.20959 . . ENSG00000147905 ENST00000336755;ENST00000534928 T;T 0.75938 -0.98;-0.98 5.7 3.63 0.41609 Zinc finger, CCHC retroviral-type (1); 0.593530 0.19292 N 0.117876 T 0.57344 0.2047 L 0.40543 1.245 0.32348 N 0.558818 B 0.20052 0.041 B 0.20767 0.031 T 0.51865 -0.8651 10 0.07813 T 0.8 -13.1561 4.7253 0.12938 0.188:0.6049:0.0:0.2071 . 341 Q8N3Z6 ZCHC7_HUMAN S 341;51 ENSP00000337839:P341S;ENSP00000443113:P51S ENSP00000337839:P341S P + 1 0 ZCCHC7 37339387 0.952000 0.32445 1.000000 0.80357 0.896000 0.52359 1.796000 0.38794 1.413000 0.46997 -0.289000 0.09944 CCT TCGA-IB-A5SS-01A-11D-A32N-08 ZCCHC7-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052453.2 1 0 1 53 187 0 84 1 9.998260e-01 16 33 0 84 2 0 0 0 0 0 2 1 1.000000 53 184 0 82 2 0 0 0 0 84 2 -3.307612 1 1 121412 2 33 1 0 1 1 2.067028 0 0.460000 1.850000 0.458755 0.950000 7.400000e-01 1.000000 1.000000 0.932823 0.950000 1 0.840000 1.000000