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 FLVCR1 28982 broad.mit.edu 37 1 213061902 213061903 + Frame_Shift_Ins INS - - TACT TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr1:213061902_213061903insTACT ENST00000366971.4 + 7 1577_1578 c.1379_1380insTACT c.(1378-1383)ggtactfs p.-461fs FLVCR1_ENST00000483790.1_3'UTR NM_014053.3 NP_054772.1 Q9Y5Y0 FLVC1_HUMAN feline leukemia virus subgroup C cellular receptor 1 12 GAATCTGAAGGTACTTCATCTG 0.361000 Esophageal Squamous(199;2235 2952 19233 26256) 0 SO:0001589 frameshift_variant ENST00000366971.4 0 1 hg19 CCDS1510.1 TCGA-3A-A9IU-01A-11D-A397-08 FLVCR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000089678.2 1 0 0 63 509 0 64 0 4.713168e-01 0 14 0 64 2 0 0 0 0 1 1 75 506 0 64 2 0 0 0 0 0 0 -2.665581 1 1 0 0 1 1 2 3 2.627803 1 0.580000 1.910000 0.672948 0.480000 3.700000e-01 0.630000 0.480000 0.498290 0.480000 0 4.200000e-01 0.550000 ARHGAP21 57584 broad.mit.edu 37 10 24874291 24874291 + Missense_Mutation SNP C C T rs1143061 TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr10:24874291C>T ENST00000396432.2 - 26 5413 c.4927G>A c.(4927-4929)Gtg>Atg p.V1643M NM_020824.3 NP_065875.3 Q5T5U3 RHG21_HUMAN Rho GTPase activating protein 21 78 GTGGGGAACACGGGAAACTCG 0.532000 0 SO:0001583 missense ENST00000396432.2 0 1 hg19 CCDS7144.2 . . . . . . . . . . C 3.155 -0.173447 0.06421 . . ENSG00000107863 ENST00000396432;ENST00000447364 T 0.13901 2.55 5.19 -0.0832 0.13695 . 0.329273 0.31797 N 0.007043 T 0.07999 0.0200 L 0.55834 1.745 0.22754 N 0.998774 P 0.39352 0.669 B 0.27076 0.076 T 0.25117 -1.0141 10 0.46703 T 0.11 . 1.9574 0.03379 0.1301:0.4116:0.2524:0.206 rs1143061;rs3206462 1642 Q5T5U3 RHG21_HUMAN M 1643;1092 ENSP00000379709:V1643M ENSP00000379709:V1643M V - 1 0 ARHGAP21 24914297 0.810000 0.29049 0.000000 0.03702 0.007000 0.05969 1.633000 0.37113 -0.062000 0.13088 -0.974000 0.02594 GTG TCGA-3A-A9IU-01A-11D-A397-08 ARHGAP21-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047229.4 0 0 0 9 355 0 64 1 6.638481e-01 3 85 0 64 2 0 0 0 0 0 2 1 9.940669e-01 9 351 0 67 2 0 0 0 0 0 2 -3.200000 1 1 121412 1 30 1 0 1 1 1.504508 1 0.580000 1.910000 0.413244 0.050000 2.000000e-02 0.110000 0.060000 0.067177 0.050000 0 4.000000e-02 0.090000 PTPRJ 5795 broad.mit.edu 37 11 48186036 48186036 + Missense_Mutation SNP G G T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr11:48186036G>T ENST00000418331.2 + 24 4176 c.3824G>T c.(3823-3825)cGa>cTa p.R1275L NM_002843.3 NP_002834.3 Q12913 PTPRJ_HUMAN protein tyrosine phosphatase, receptor type, J 52 TATGACCTTCGAATGCATAGG 0.428000 0 SO:0001583 missense ENST00000418331.2 0 1 hg19 CCDS7945.1 . . . . . . . . . . G 29.1 4.976142 0.92982 . . ENSG00000149177 ENST00000418331 D 0.91521 -2.86 4.53 4.53 0.55603 Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1); . . . . D 0.97114 0.9057 H 0.98218 4.175 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.98523 1.0624 9 0.87932 D 0 . 15.133 0.72539 0.0:0.0:1.0:0.0 . 1275 Q12913 PTPRJ_HUMAN L 1275 ENSP00000400010:R1275L ENSP00000400010:R1275L R + 2 0 PTPRJ 48142612 1.000000 0.71417 0.885000 0.34714 0.992000 0.81027 9.735000 0.98825 2.237000 0.73441 0.650000 0.86243 CGA TCGA-3A-A9IU-01A-11D-A397-08 PTPRJ-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390525.1 0 0 0 4 259 0 33 0 1.351853e-01 0 33 0 33 2 0 0 0 0 0 2 1 8.777365e-01 4 245 0 32 2 0 0 0 0 0 2 -2.903911 1 1 0 0 1 1 2 3 2.062343 0 0.580000 1.910000 0.581214 0.050000 1.000000e-02 0.130000 0.060000 0.064980 0.050000 0 3.000000e-02 0.090000 ARAP1 116985 broad.mit.edu 37 11 72408662 72408662 + Missense_Mutation SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr11:72408662C>T ENST00000393609.3 - 20 2972 c.2770G>A c.(2770-2772)Gtg>Atg p.V924M ARAP1_ENST00000429686.1_Missense_Mutation_p.V618M|ARAP1_ENST00000426523.1_Missense_Mutation_p.V679M|ARAP1_ENST00000334211.8_Missense_Mutation_p.V679M|ARAP1_ENST00000393605.3_Missense_Mutation_p.V684M|ARAP1-AS2_ENST00000500163.2_RNA|ARAP1_ENST00000455638.2_Missense_Mutation_p.V924M|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000359373.5_Missense_Mutation_p.V924M NM_001040118.2 NP_001035207.1 Q96P48 ARAP1_HUMAN ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 27 TCCACCAGCACCAGCACCTGG 0.637000 Ovarian(102;1198 1520 13195 17913 37529) 0 SO:0001583 missense ENST00000393609.3 1 1 hg19 CCDS41687.1 . . . . . . . . . . C 26.0 4.694061 0.88735 . . ENSG00000186635 ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000427971;ENST00000452383 T;T;T;T;T;T;T;T;T 0.30448 1.53;1.53;1.53;1.53;1.53;1.53;1.53;1.53;1.53 4.93 4.93 0.64822 Pleckstrin homology domain (1); 0.133016 0.49916 D 0.000132 T 0.48926 0.1527 L 0.54323 1.7 0.41335 D 0.987265 P;D;P;P;P 0.69078 0.843;0.997;0.881;0.843;0.903 P;P;P;P;P 0.61533 0.779;0.845;0.746;0.677;0.89 T 0.52019 -0.8631 10 0.87932 D 0 . 17.0897 0.86618 0.0:1.0:0.0:0.0 . 679;618;924;924;684 E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1 .;.;.;ARAP1_HUMAN;. M 924;924;684;679;924;679;618;212;212 ENSP00000352332:V924M;ENSP00000390461:V924M;ENSP00000377230:V684M;ENSP00000335506:V679M;ENSP00000377233:V924M;ENSP00000392264:V679M;ENSP00000403127:V618M;ENSP00000411452:V212M;ENSP00000399118:V212M ENSP00000335506:V679M V - 1 0 ARAP1 72086310 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 2.823000 0.48081 2.435000 0.82474 0.563000 0.77884 GTG TCGA-3A-A9IU-01A-11D-A397-08 ARAP1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000347428.1 1 0 1 82 257 0 64 1 1 32 115 0 64 2 0 0 0 0 0 2 1 1 81 255 0 64 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.066243 0 0.580000 1.910000 0.581214 0.830000 6.800000e-01 1.000000 0.840000 0.839080 0.830000 0 7.500000e-01 0.920000 TYR 7299 broad.mit.edu 37 11 88924443 88924443 + Missense_Mutation SNP G G A rs148815276 by1000genomes TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr11:88924443G>A ENST00000263321.5 + 2 1395 c.893G>A c.(892-894)cGg>cAg p.R298Q TYR_ENST00000526139.1_3'UTR NM_000372.4 NP_000363.1 P14679 TYRO_HUMAN tyrosinase 48 Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033) Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600) GGACCTTTACGGCGTAATCCT 0.468000 0 SO:0001583 missense ENST00000263321.5 1 1 hg19 CCDS8284.1 . . . . . . . . . . G 7.767 0.706604 0.15239 2.27E-4 0.0 ENSG00000077498 ENST00000263321 D 0.97114 -4.25 5.59 0.524 0.17066 Tyrosinase (1);Uncharacterised domain, di-copper centre (2); 0.354131 0.29205 N 0.012826 D 0.91576 0.7339 L 0.39020 1.185 0.09310 N 1 P 0.40230 0.708 B 0.33750 0.169 D 0.84793 0.0780 9 . . . . 7.2211 0.25988 0.3203:0.0:0.2284:0.4513 . 298 P14679 TYRO_HUMAN Q 298 ENSP00000263321:R298Q . R + 2 0 TYR 88564091 0.004000 0.15560 0.033000 0.17914 0.384000 0.30261 1.222000 0.32515 -0.154000 0.11118 -2.213000 0.00299 CGG TCGA-3A-A9IU-01A-11D-A397-08 TYR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394045.2 1 0 1 150 358 0 37 0 0 0 0 37 2 0 0 0 0 0 2 1 1 148 348 0 36 2 0 0 0 0 0 2 -9.488467 1 1 121400 6 42 1 1 2 3 2.066243 0 0.580000 1.910000 0.581214 0.990000 8.800000e-01 1.000000 1.000000 0.981930 0.990000 1 9.400000e-01 1.000000 PRH2 5555 broad.mit.edu 37 12 11083320 11083320 + Missense_Mutation SNP C C G TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr12:11083320C>G ENST00000396400.3 + 3 198 c.160C>G c.(160-162)Cag>Gag p.Q54E PRH2_ENST00000381847.3_Missense_Mutation_p.Q54E|PRR4_ENST00000536668.1_Intron NM_001110213.1 NP_001103683.1 P02810 PRPC_HUMAN proline-rich protein HaeIII subfamily 2 13 TTTGGGAGGACAGCAATCTCA 0.552000 0 SO:0001583 missense ENST00000396400.3 0 1 hg19 CCDS8636.1 . . . . . . . . . . C 0.588 -0.834193 0.02713 . . ENSG00000134551 ENST00000381847;ENST00000396400 T;T 0.16457 2.34;2.34 1.11 0.126 0.14722 . 5.544330 0.01935 N 0.041536 T 0.09905 0.0243 N 0.12182 0.205 0.09310 N 1 B 0.24426 0.103 B 0.17722 0.019 T 0.23476 -1.0187 10 0.44086 T 0.13 . 3.5402 0.07808 0.0:0.713:0.0:0.287 . 54 P02810 PRPC_HUMAN E 54 ENSP00000371271:Q54E;ENSP00000379682:Q54E ENSP00000371271:Q54E Q + 1 0 PRH2 10974587 0.000000 0.05858 0.000000 0.03702 0.051000 0.14879 -1.025000 0.03600 0.041000 0.15688 0.194000 0.17425 CAG TCGA-3A-A9IU-01A-11D-A397-08 PRH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400231.1 0 0 0 8 564 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 9.887433e-01 8 554 0 87 2 0 0 0 0 0 2 -2.925302 1 1 0 0 1 0 0 0 2.002191 0 0.580000 1.910000 0.570025 0.040000 1.000000e-02 0.090000 0.050000 0.052834 0.040000 0 2.000000e-02 0.070000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-3A-A9IU-01A-11D-A397-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 72 223 0 38 1 9.901401e-01 10 14 0 38 2 1 1 85 245 0 198 2 1 1 71 223 0 38 2 1 1 2786 5228 10 8009 19 -20.000000 1 1 121404 2 44 1 0 0 0 2.002191 0 0.580000 1.910000 0.570025 0.810000 6.600000e-01 0.980000 0.820000 0.825014 0.810000 0 7.300000e-01 0.910000 NELL2 4753 broad.mit.edu 37 12 45105106 45105106 + Silent SNP G G T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr12:45105106G>T ENST00000429094.2 - 11 1662 c.1158C>A c.(1156-1158)acC>acA p.T386T NELL2_ENST00000437801.2_Silent_p.T436T|NELL2_ENST00000549027.1_Silent_p.T385T|NELL2_ENST00000452445.2_Silent_p.T386T|NELL2_ENST00000395487.2_Silent_p.T385T|NELL2_ENST00000333837.4_Silent_p.T409T|NELL2_ENST00000551601.1_Silent_p.T385T NM_001145108.1 NP_001138580.1 Q99435 NELL2_HUMAN NEL-like 2 (chicken) 65 Lung SC(27;0.192) Lung NSC(34;0.144) TGTGAGACAAGGTTATCTGAT 0.398000 0 SO:0001819 synonymous_variant ENST00000429094.2 1 1 hg19 CCDS8746.1 . . . . . . . . . . G 8.433 0.849108 0.17034 . . ENSG00000184613 ENST00000550313 . . . 5.79 -1.97 0.07503 . . . . . T 0.39332 0.1074 . . . 0.58432 D 0.99999 . . . . . . T 0.31558 -0.9939 4 . . . -8.8524 1.4208 0.02311 0.3427:0.0865:0.3107:0.2601 . . . . H 130 . . P - 2 0 NELL2 43391373 0.938000 0.31826 0.982000 0.44146 0.983000 0.72400 -0.010000 0.12743 -0.109000 0.12044 -0.126000 0.14955 CCT TCGA-3A-A9IU-01A-11D-A397-08 NELL2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404180.1 1 0 1 65 224 0 30 0 5.168545e-02 0 2 0 30 2 0 0 0 0 0 2 1 1 64 224 0 30 2 0 0 0 0 0 2 -3.583185 1 1 0 0 1 0 0 0 2.002191 0 0.580000 1.910000 0.570025 0.750000 6.000000e-01 0.920000 0.760000 0.761861 0.750000 0 6.700000e-01 0.840000 IL26 55801 broad.mit.edu 37 12 68619408 68619408 + Silent SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr12:68619408G>A ENST00000229134.4 - 1 193 c.129C>T c.(127-129)gaC>gaT p.D43D IFNG-AS1_ENST00000536914.1_RNA NM_018402.1 NP_060872.1 Q9NPH9 IL26_HUMAN interleukin 26 12 Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018) TATAGAGAGCGTCAACAGCTT 0.438000 0 SO:0001819 synonymous_variant ENST00000229134.4 0 1 hg19 CCDS8981.1 TCGA-3A-A9IU-01A-11D-A397-08 IL26-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402302.1 0 0 0 6 741 0 96 0 0 0 0 96 2 0 0 0 0 0 2 1 9.638753e-01 6 733 0 96 2 0 0 0 0 0 2 -2.554088 1 1 121412 2 39 1 0 0 0 2.002191 0 0.580000 1.910000 0.570025 0.020000 0 0.060000 0.020000 0.030569 0.020000 0 1.000000e-02 0.040000 EML1 2009 broad.mit.edu 37 14 100405582 100405582 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr14:100405582G>A ENST00000262233.6 + 21 2379 c.2240G>A c.(2239-2241)cGg>cAg p.R747Q EML1_ENST00000327921.9_Missense_Mutation_p.R735Q|EML1_ENST00000334192.4_Missense_Mutation_p.R766Q NM_004434.2 NP_004425.2 O00423 EMAL1_HUMAN echinoderm microtubule associated protein like 1 p.R766Q(1) 42 Melanoma(154;0.0879)|all_epithelial(191;0.216) GCCGTCTGTCGGGCCCATGAG 0.552000 1 Substitution - Missense(1) SO:0001583 missense ENST00000262233.6 0 1 hg19 CCDS32155.1 . . . . . . . . . . G 21.2 4.117755 0.77323 . . ENSG00000066629 ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138 T;T;T 0.17854 2.25;2.25;2.25 4.56 4.56 0.56223 . 0.051684 0.64402 D 0.000001 T 0.47710 0.1460 M 0.90082 3.085 0.80722 D 1 P;D;D 0.71674 0.926;0.998;0.959 B;P;B 0.61397 0.388;0.888;0.293 T 0.62205 -0.6903 10 0.87932 D 0 -22.3911 17.6609 0.88193 0.0:0.0:1.0:0.0 . 735;747;766 F8W717;O00423;O00423-3 .;EMAL1_HUMAN;. Q 735;747;766;766 ENSP00000327384:R735Q;ENSP00000262233:R747Q;ENSP00000334314:R766Q ENSP00000262233:R747Q R + 2 0 EML1 99475335 1.000000 0.71417 0.997000 0.53966 0.556000 0.35491 7.627000 0.83176 2.240000 0.73641 0.561000 0.74099 CGG TCGA-3A-A9IU-01A-11D-A397-08 EML1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000413943.1 0 0 0 5 324 0 58 0 8.043302e-02 1 24 0 58 2 0 0 0 0 0 2 1 9.380017e-01 6 323 0 55 2 0 0 0 0 0 2 -2.900681 1 1 121412 3 36 1 0 0 0 2.059044 0 0.580000 1.910000 0.580000 0.050000 1.000000e-02 0.120000 0.060000 0.062318 0.050000 0 3.000000e-02 0.090000 FANCM 57697 broad.mit.edu 37 14 45665470 45665470 + Silent SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr14:45665470G>A ENST00000267430.5 + 21 5521 c.5436G>A c.(5434-5436)ccG>ccA p.P1812P FANCM_ENST00000542564.2_Silent_p.P1786P NM_020937.2 NP_065988.1 Q8IYD8 FANCM_HUMAN Fanconi anemia, complementation group M 85 TTAGACTTCCGCAGGAAGGAA 0.438000 Involved in tolerance or repair of DNA crosslinks Fanconi Anemia 0 SO:0001819 synonymous_variant Familial Cancer Database Pancytopenia Dysmelia, FA (several complementation groups) ENST00000267430.5 0 1 hg19 CCDS32070.1 . . . . . . . . . . G 6.510 0.462289 0.12342 2.27E-4 0.0 ENSG00000187790 ENST00000554809 . . . 5.27 -1.83 0.07833 . . . . . T 0.18800 0.0451 . . . 0.09310 N 1 . . . . . . T 0.25082 -1.0142 4 . . . . 1.3233 0.02121 0.293:0.1242:0.3414:0.2414 . . . . T 780 . . A + 1 0 FANCM 44735220 0.000000 0.05858 0.008000 0.14137 0.362000 0.29581 -0.041000 0.12084 -0.216000 0.10048 -0.414000 0.06135 GCA TCGA-3A-A9IU-01A-11D-A397-08 FANCM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000410474.1 0 0 0 6 589 0 78 0 1.522051e-03 0 5 0 78 2 0 0 0 0 0 2 1 9.649367e-01 7 587 0 78 2 0 0 0 0 0 2 -2.373405 0 1 121412 3 40 1 0 0 0 2.059044 0 0.580000 1.910000 0.580000 0.030000 0 0.070000 0.040000 0.040047 0.030000 0 1.000000e-02 0.060000 ATP10A 57194 broad.mit.edu 37 15 25953374 25953374 + Missense_Mutation SNP T T G TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr15:25953374T>G ENST00000356865.6 - 11 2529 c.2418A>C c.(2416-2418)gaA>gaC p.E806D NM_024490.3 NP_077816.1 O60312 AT10A_HUMAN ATPase, class V, type 10A 103 all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125) TGCGCAGGCCTTCCGCCGCAT 0.577000 0 SO:0001583 missense ENST00000356865.6 1 1 hg19 CCDS32178.1 . . . . . . . . . . T 7.022 0.558919 0.13436 . . ENSG00000206190 ENST00000356865 D 0.82433 -1.61 4.84 -4.91 0.03085 ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1); 0.093232 0.64402 N 0.000001 T 0.53578 0.1805 N 0.12920 0.275 0.46317 D 0.998986 B 0.06786 0.001 B 0.15484 0.013 T 0.51764 -0.8664 10 0.02654 T 1 -23.9456 2.2901 0.04136 0.283:0.4025:0.0988:0.2157 . 806 O60312 AT10A_HUMAN D 806 ENSP00000349325:E806D ENSP00000349325:E806D E - 3 2 ATP10A 23504467 1.000000 0.71417 0.792000 0.32020 0.854000 0.48673 1.151000 0.31651 -0.677000 0.05231 0.533000 0.62120 GAA TCGA-3A-A9IU-01A-11D-A397-08 ATP10A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414830.1 1 0 1 102 297 0 102 0 8.500320e-01 0 12 0 102 2 0 0 0 0 0 2 1 1 99 293 0 102 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.066352 0 0.580000 1.910000 0.581214 0.880000 7.300000e-01 1.000000 1.000000 0.884204 0.880000 1 8.000000e-01 0.960000 VPS33B 26276 broad.mit.edu 37 15 91557033 91557033 + Splice_Site SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr15:91557033C>T ENST00000333371.3 - 5 711 c.e5+1 VPS33B_ENST00000557358.1_Intron|VPS33B_ENST00000535906.1_Splice_Site|VPS33B_ENST00000535843.1_Splice_Site NM_018668.3 NP_061138.3 Q9H267 VP33B_HUMAN vacuolar protein sorting 33 homolog B (yeast) 16 Lung NSC(78;0.0987)|all_lung(78;0.175) TCCAAACTCACCTTTTGAGGG 0.522000 0 SO:0001630 splice_region_variant ENST00000333371.3 1 1 hg19 CCDS10369.1 . . . . . . . . . . C 25.1 4.600940 0.87055 . . ENSG00000184056 ENST00000333371;ENST00000535906;ENST00000535843;ENST00000537510 . . . 5.62 5.62 0.85841 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 19.2545 0.93940 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . VPS33B 89358037 1.000000 0.71417 1.000000 0.80357 0.949000 0.60115 5.902000 0.69869 2.647000 0.89833 0.650000 0.86243 . TCGA-3A-A9IU-01A-11D-A397-08 VPS33B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313496.1 1 0 1 110 330 0 68 0 6.349141e-02 1 1 0 68 2 0 0 0 0 0 2 1 1 109 327 0 67 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.064462 0 0.580000 1.910000 0.581214 0.860000 7.200000e-01 1.000000 0.860000 0.866016 0.860000 1 7.900000e-01 0.940000 SSTR5 6755 broad.mit.edu 37 16 1129924 1129924 + Silent SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr16:1129924C>T ENST00000293897.4 + 1 1144 c.1056C>T c.(1054-1056)cgC>cgT p.R352R SSTR5_ENST00000397547.2_Silent_p.R352R|SSTR5_ENST00000562758.1_Intron|SSTR5-AS1_ENST00000569832.1_RNA NM_001053.3 NP_001044.1 P35346 SSR5_HUMAN somatostatin receptor 5 9 Hepatocellular(780;0.00369) Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894) CCGCGCACCGCGCCGCAGCCA 0.711000 0 SO:0001819 synonymous_variant ENST00000293897.4 0 1 hg19 CCDS10429.1 TCGA-3A-A9IU-01A-11D-A397-08 SSTR5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000420836.1 0 0 0 9 39 0 14 0 0 0 0 14 2 0 0 0 0 0 2 1 9.952899e-01 9 38 0 13 2 0 0 0 0 0 2 -19.995970 1 1 119194 1 29 1 1 2 3 2.102201 0 0.580000 1.910000 0.584816 0.670000 3.400000e-01 1.000000 1.000000 0.690285 0.670000 0 4.900000e-01 0.900000 PKD1 5310 broad.mit.edu 37 16 2156826 2156826 + Missense_Mutation SNP T T C TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr16:2156826T>C ENST00000262304.4 - 17 7397 c.7189A>G c.(7189-7191)Agc>Ggc p.S2397G PKD1_ENST00000561991.1_5'Flank|PKD1_ENST00000423118.1_Missense_Mutation_p.S2397G NM_001009944.2 NP_001009944 P98161 PKD1_HUMAN polycystic kidney disease 1 (autosomal dominant) 72 GAGCCGCTGCTGCAATTGAGG 0.662000 0 SO:0001583 missense ENST00000262304.4 0 1 hg19 CCDS32369.1 . . . . . . . . . . t 2.685 -0.274485 0.05679 . . ENSG00000008710 ENST00000262304;ENST00000423118;ENST00000306101;ENST00000382481 T;T 0.69926 -0.44;-0.44 4.22 3.11 0.35812 Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);Polycystin cation channel (1); 0.607624 0.18369 N 0.143312 T 0.54679 0.1873 L 0.51422 1.61 0.22754 N 0.998778 B;B 0.18610 0.029;0.016 B;B 0.23852 0.049;0.026 T 0.38672 -0.9650 10 0.19590 T 0.45 . 5.6771 0.17755 0.0:0.1065:0.3359:0.5576 . 2397;2397 P98161-3;P98161 .;PKD1_HUMAN G 2397;2397;1748;676 ENSP00000262304:S2397G;ENSP00000399501:S2397G ENSP00000262304:S2397G S - 1 0 PKD1 2096827 1.000000 0.71417 0.960000 0.40013 0.494000 0.33585 2.464000 0.45067 0.782000 0.33613 0.445000 0.29226 AGC TCGA-3A-A9IU-01A-11D-A397-08 PKD1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000341688.1 0 0 0 7 72 0 14 0 1.174952e-01 1 5 0 14 2 0 0 0 0 0 2 1 7.484324e-01 5 24 0 19 2 0 0 0 0 0 2 -13.122090 1 1 0 0 1 1 2 3 2.102201 0 0.580000 1.910000 0.584816 0.320000 1.400000e-01 1.000000 0.310000 0.360419 0.320000 0 2.200000e-01 0.470000 ADCY9 115 broad.mit.edu 37 16 4016903 4016903 + Missense_Mutation SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr16:4016903C>T ENST00000294016.3 - 11 3473 c.2935G>A c.(2935-2937)Ggc>Agc p.G979S NM_001116.3 NP_001107.2 O60503 ADCY9_HUMAN adenylate cyclase 9 47 ACCTCCTGGCCGATGAGGCTG 0.582000 0 SO:0001583 missense ENST00000294016.3 1 1 hg19 CCDS32382.1 . . . . . . . . . . C 16.15 3.041963 0.55003 . . ENSG00000162104 ENST00000294016 D 0.83250 -1.7 5.48 5.48 0.80851 . 0.149249 0.64402 D 0.000011 D 0.82337 0.5015 N 0.22421 0.69 0.51767 D 0.999931 D 0.76494 0.999 P 0.59115 0.852 T 0.76348 -0.2992 10 0.08837 T 0.75 . 19.7084 0.96083 0.0:1.0:0.0:0.0 . 979 O60503 ADCY9_HUMAN S 979 ENSP00000294016:G979S ENSP00000294016:G979S G - 1 0 ADCY9 3956904 0.998000 0.40836 0.970000 0.41538 0.455000 0.32408 3.763000 0.55257 2.739000 0.93911 0.561000 0.74099 GGC TCGA-3A-A9IU-01A-11D-A397-08 ADCY9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438076.1 1 0 1 124 309 0 88 1 9.846138e-01 2 17 0 88 2 0 0 0 0 0 2 1 1 121 304 0 87 2 0 0 0 0 0 2 -7.874103 1 1 121400 2 38 1 1 2 3 2.102201 0 0.580000 1.910000 0.584816 0.990000 8.500000e-01 1.000000 1.000000 0.970957 0.990000 1 9.200000e-01 1.000000 HSDL1 83693 broad.mit.edu 37 16 84164829 84164829 + Missense_Mutation SNP G G A rs143907842 TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr16:84164829G>A ENST00000219439.4 - 3 274 c.98C>T c.(97-99)aCg>aTg p.T33M HSDL1_ENST00000434463.3_Missense_Mutation_p.T33M NM_001146051.1|NM_031463.4 NP_001139523.1|NP_113651.4 Q3SXM5 HSDL1_HUMAN hydroxysteroid dehydrogenase like 1 7 TTTTCTGGCCGTATACCAGGC 0.493000 0 SO:0001583 missense ENST00000219439.4 0 1 hg19 CCDS10942.1 . . . . . . . . . . G 15.61 2.883945 0.51908 0.0 5.81E-4 ENSG00000103160 ENST00000434463;ENST00000219439 T;D 0.83163 -1.11;-1.69 5.84 5.84 0.93424 . 0.185252 0.47852 D 0.000218 T 0.74581 0.3735 N 0.17082 0.46 0.42561 D 0.993148 D;P 0.64830 0.994;0.812 P;B 0.45449 0.481;0.137 T 0.77161 -0.2689 10 0.45353 T 0.12 -18.6731 14.306 0.66384 0.0706:0.0:0.9294:0.0 . 33;33 B4DSL2;Q3SXM5 .;HSDL1_HUMAN M 33 ENSP00000407437:T33M;ENSP00000219439:T33M ENSP00000219439:T33M T - 2 0 HSDL1 82722330 1.000000 0.71417 0.998000 0.56505 0.987000 0.75469 5.371000 0.66150 2.765000 0.95021 0.655000 0.94253 ACG TCGA-3A-A9IU-01A-11D-A397-08 HSDL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269076.3 0 0 0 6 654 0 122 0 2.889622e-02 0 24 0 122 2 0 0 0 0 0 2 1 9.652566e-01 6 655 0 122 2 0 0 0 0 0 2 -2.208772 0 1 121412 39 50 1 1 2 3 2.108988 0 0.580000 1.910000 0.586003 0.030000 0 1.000000 0.040000 0.072915 0.030000 0 1.000000e-02 0.060000 QRICH2 84074 broad.mit.edu 37 17 74288916 74288916 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr17:74288916G>A ENST00000262765.5 - 4 1573 c.1394C>T c.(1393-1395)gCc>gTc p.A465V NM_032134.1 NP_115510.1 Q9H0J4 QRIC2_HUMAN glutamine rich 2 62 accaggttgggccaaaccaga 0.557000 0 SO:0001583 missense ENST00000262765.5 0 1 hg19 CCDS32741.1 . . . . . . . . . . - 9.875 1.200097 0.22121 . . ENSG00000129646 ENST00000262765;ENST00000301613 T 0.08370 3.1 5.38 -5.83 0.02325 . . . . . T 0.01730 0.0055 N 0.00621 -1.32 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.43734 -0.9373 9 0.27082 T 0.32 -3.7961 2.3937 0.04385 0.3394:0.2868:0.2749:0.0989 . 465;465 B5MD94;Q9H0J4 .;QRIC2_HUMAN V 465 ENSP00000262765:A465V ENSP00000262765:A465V A - 2 0 QRICH2 71800511 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -1.107000 0.03316 -0.983000 0.03511 -0.272000 0.10252 GCC TCGA-3A-A9IU-01A-11D-A397-08 QRICH2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000395140.1 0 0 0 4 139 0 11 0 0 0 0 11 2 0 0 0 0 0 2 1 8.881317e-01 4 137 0 11 2 0 0 0 0 0 2 -3.328154 1 1 0 0 1 1 2 3 2.101218 0 0.580000 1.910000 0.584816 0.100000 3.000000e-02 1.000000 0.100000 0.145024 0.100000 0 6.000000e-02 0.180000 TP53 7157 broad.mit.edu 37 17 7579473 7579473 + Missense_Mutation SNP G G C TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 G C G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr17:7579473G>C ENST00000269305.4 - 4 403 c.214C>G c.(214-216)Ccc>Gcc p.P72A TP53_ENST00000445888.2_Missense_Mutation_p.P72A|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.P72A|TP53_ENST00000420246.2_Missense_Mutation_p.P72A|TP53_ENST00000359597.4_Missense_Mutation_p.P72A|TP53_ENST00000413465.2_Missense_Mutation_p.P72A 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.0?(8)|p.G59fs*23(3)|p.R72fs*51(2)|p.R72C(2)|p.E68fs*76(1)|p.D48fs*55(1)|p.P13fs*18(1)|p.R65fs*38(1)|p.D57_A76del20(1)|p.S33fs*23(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GGGGCCACGGGGGGAGCAGCC 0.602000 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 21 Whole gene deletion(8)|Deletion - Frameshift(8)|Substitution - Missense(2)|Complex - frameshift(2)|Deletion - In frame(1) 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 0 hg19 CCDS11118.1 . . . . . . . . . . G 2.042 -0.419843 0.04734 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591 D;D;D;D;D;D;D;D 0.99287 -5.17;-5.69;-5.4;-5.68;-5.68;-5.4;-4.05;-1.96 3.66 0.238 0.15480 . 2.010640 0.04441 U 0.370853 D 0.95500 0.8538 N 0.03608 -0.345 0.09310 N 1 B;B;B;B;B 0.10296 0.0;0.0;0.0;0.0;0.003 B;B;B;B;B 0.08055 0.0;0.001;0.001;0.0;0.003 D 0.93649 0.6971 10 0.26408 T 0.33 . 7.4166 0.27048 0.1022:0.4057:0.492:0.0 . 72;72;72;72;72 E7EMR6;P04637-2;P04637-3;P04637;E7EQX7 .;.;.;P53_HUMAN;. A 72 ENSP00000410739:P72A;ENSP00000352610:P72A;ENSP00000269305:P72A;ENSP00000398846:P72A;ENSP00000391127:P72A;ENSP00000391478:P72A;ENSP00000424104:P72A;ENSP00000426252:P72A ENSP00000269305:P72A P - 1 0 TP53 7520198 0.000000 0.05858 0.001000 0.08648 0.001000 0.01503 -0.284000 0.08422 0.102000 0.17638 -0.264000 0.10439 CCC TCGA-3A-A9IU-01A-11D-A397-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 194 315 0 135 0 9.998652e-01 0 25 0 135 2 1 1 78 171 0 192 2 1 1 222 291 1 132 14 0 0 0 0 0 2 -19.999790 1 0 121404 1 41 1 0 1 1 1.504503 1 0.580000 1.910000 0.408451 0.920000 8.200000e-01 1.000000 0.930000 0.922150 0.920000 1 8.700000e-01 0.970000 TP53 7157 broad.mit.edu 37 17 7579479 7579479 + Missense_Mutation SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr17:7579479C>T ENST00000269305.4 - 4 397 c.208G>A c.(208-210)Gct>Act p.A70T TP53_ENST00000445888.2_Missense_Mutation_p.A70T|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.A70T|TP53_ENST00000420246.2_Missense_Mutation_p.A70T|TP53_ENST00000359597.4_Missense_Mutation_p.A70T|TP53_ENST00000413465.2_Missense_Mutation_p.A70T 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.0?(8)|p.G59fs*23(3)|p.E68fs*76(1)|p.D48fs*55(1)|p.R65_P71delRMPEAAP(1)|p.A70T(1)|p.P13fs*18(1)|p.R65fs*38(1)|p.D57_A76del20(1)|p.S33fs*23(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) ACGGGGGGAGCAGCCTCTGGC 0.597000 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 19 Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(2)|Substitution - Missense(1)|Complex - frameshift(1) SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . C 9.093 1.002269 0.19121 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591 D;D;D;D;D;D;D;D 0.99376 -5.28;-5.79;-5.51;-5.79;-5.79;-5.51;-4.19;-2.14 3.66 -2.27 0.06846 . 4.481350 0.01345 N 0.011694 D 0.95092 0.8410 N 0.08118 0 0.09310 N 1 B;B;B;B;B;B;B 0.27971 0.079;0.049;0.196;0.013;0.031;0.025;0.0 B;B;B;B;B;B;B 0.29785 0.031;0.026;0.107;0.017;0.034;0.022;0.0 D 0.97004 0.9731 10 0.09843 T 0.71 . 1.4508 0.02374 0.1962:0.3205:0.3268:0.1566 . 31;70;70;70;70;70;70 B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. T 70 ENSP00000410739:A70T;ENSP00000352610:A70T;ENSP00000269305:A70T;ENSP00000398846:A70T;ENSP00000391127:A70T;ENSP00000391478:A70T;ENSP00000424104:A70T;ENSP00000426252:A70T ENSP00000269305:A70T A - 1 0 TP53 7520204 0.016000 0.18221 0.000000 0.03702 0.001000 0.01503 -0.099000 0.11007 -0.331000 0.08501 -1.242000 0.01536 GCT TCGA-3A-A9IU-01A-11D-A397-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 239 320 0 146 0 9.999616e-01 0 24 0 146 2 1 1 99 192 0 219 2 1 1 242 320 0 144 2 0 0 0 0 0 2 -20.000000 1 0 0 0 1 0 1 1 1.504503 1 0.580000 1.910000 0.408451 0.970000 9.100000e-01 1.000000 0.990000 0.975482 0.970000 1 9.400000e-01 1.000000 NPLOC4 55666 broad.mit.edu 37 17 79556050 79556050 + Silent SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr17:79556050G>A ENST00000331134.6 - 12 1416 c.1201C>T c.(1201-1203)Ctg>Ttg p.L401L NPLOC4_ENST00000374747.5_Silent_p.L401L|NPLOC4_ENST00000539314.1_Silent_p.L240L NM_017921.2 NP_060391.2 Q8TAT6 NPL4_HUMAN nuclear protein localization 4 homolog (S. cerevisiae) 11 all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246) BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739) TTGCATGGCAGCAAACACTCA 0.498000 0 SO:0001819 synonymous_variant ENST00000331134.6 0 1 hg19 CCDS45812.1 TCGA-3A-A9IU-01A-11D-A397-08 NPLOC4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000440140.1 0 0 0 5 325 0 54 0 4.603752e-01 0 90 0 54 2 0 0 0 0 0 2 1 9.354747e-01 5 321 0 54 2 0 0 0 0 0 2 -2.459651 0 1 0 0 1 1 2 3 2.101218 0 0.580000 1.910000 0.584816 0.050000 1.000000e-02 1.000000 0.060000 0.089843 0.050000 0 3.000000e-02 0.090000 CELF4 56853 broad.mit.edu 37 18 34901802 34901802 + Nonsense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr18:34901802G>A ENST00000591282.1 - 3 411 c.412C>T c.(412-414)Cga>Tga p.R138* CELF4_ENST00000601019.1_Nonsense_Mutation_p.R138*|CELF4_ENST00000420428.2_Nonsense_Mutation_p.R138*|CELF4_ENST00000334919.5_Nonsense_Mutation_p.R138*|CELF4_ENST00000603232.1_Nonsense_Mutation_p.R138*|CELF4_ENST00000588597.1_Nonsense_Mutation_p.R138*|CELF4_ENST00000361795.5_Nonsense_Mutation_p.R138*|CELF4_ENST00000591287.1_Nonsense_Mutation_p.R138*|CELF4_ENST00000412753.1_Nonsense_Mutation_p.R138* Q9BZC1 CELF4_HUMAN CUGBP, Elav-like family member 4 44 CTACCTCCTCGGCTCTCGCTG 0.647000 OREG0024927 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001587 stop_gained ENST00000591282.1 0 1 hg19 CCDS32818.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 41|41 8.838326|8.838326 0.98972|0.98972 .|. .|. ENSG00000101489|ENSG00000101489 ENST00000361683|ENST00000361795;ENST00000412753;ENST00000420428;ENST00000334919 .|. .|. .|. 5.19|5.19 5.19|5.19 0.71726|0.71726 .|. .|0.085967 .|0.47455 .|D .|0.000223 T|. 0.38214|. 0.1032|. .|. .|. .|. 0.80722|0.80722 A|A 1|1 .|. .|. .|. .|. .|. .|. T|. 0.31280|. -0.9949|. 4|. 0.51188|0.02654 T|T 0.08|1 -2.4113|-2.4113 16.1974|16.1974 0.82040|0.82040 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|. .|. .|. L|X 32|138 .|. ENSP00000355189:P32L|ENSP00000335631:R138X P|R -|- 2|1 0|2 CELF4|CELF4 33155800|33155800 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.998000|0.998000 0.95712|0.95712 3.015000|3.015000 0.49599|0.49599 2.413000|2.413000 0.81919|0.81919 0.484000|0.484000 0.47621|0.47621 CCG|CGA TCGA-3A-A9IU-01A-11D-A397-08 CELF4-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000440892.1 1 0 1 43 83 0 21 0 0 0 0 21 2 0 0 0 0 0 2 1 1 42 81 0 21 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.486081 1 0.580000 1.910000 0.410857 0.820000 6.300000e-01 0.980000 0.830000 0.825013 0.820000 0 7.200000e-01 0.920000 DSEL 92126 broad.mit.edu 37 18 65180274 65180274 + Missense_Mutation SNP C C A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr18:65180274C>A ENST00000310045.7 - 2 3075 c.1602G>T c.(1600-1602)caG>caT p.Q534H CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA NM_032160.2 NP_115536.1 Q8IZU8 DSEL_HUMAN dermatan sulfate epimerase-like 74 Esophageal squamous(42;0.129) ACTTAAGCCACTGCGCACATT 0.512000 0 SO:0001583 missense ENST00000310045.7 1 1 hg19 CCDS11995.1 . . . . . . . . . . C 18.07 3.541902 0.65198 . . ENSG00000171451 ENST00000310045;ENST00000397964 T 0.18810 2.19 5.67 2.89 0.33648 . 0.067597 0.64402 U 0.000016 T 0.32912 0.0845 L 0.51422 1.61 0.45704 D 0.998613 D 0.67145 0.996 P 0.59703 0.862 T 0.04454 -1.0950 10 0.72032 D 0.01 -9.1529 10.5565 0.45121 0.0:0.7858:0.0:0.2142 . 524 Q8IZU8 DSEL_HUMAN H 534;524 ENSP00000310565:Q534H ENSP00000310565:Q534H Q - 3 2 DSEL 63331254 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 3.112000 0.50368 0.735000 0.32537 0.563000 0.77884 CAG TCGA-3A-A9IU-01A-11D-A397-08 DSEL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256221.1 1 0 1 118 133 0 78 0 9.126792e-01 0 7 0 78 2 0 0 0 0 0 2 1 1 114 133 0 76 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.503831 1 0.580000 1.910000 0.410857 0.980000 9.100000e-01 1.000000 1.000000 0.981811 0.980000 1 9.500000e-01 1.000000 DSEL 92126 broad.mit.edu 37 18 65180275 65180275 + Missense_Mutation SNP T T A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr18:65180275T>A ENST00000310045.7 - 2 3074 c.1601A>T c.(1600-1602)cAg>cTg p.Q534L CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA NM_032160.2 NP_115536.1 Q8IZU8 DSEL_HUMAN dermatan sulfate epimerase-like 74 Esophageal squamous(42;0.129) CTTAAGCCACTGCGCACATTC 0.517000 0 SO:0001583 missense ENST00000310045.7 1 1 hg19 CCDS11995.1 . . . . . . . . . . T 20.2 3.954048 0.73902 . . ENSG00000171451 ENST00000310045;ENST00000397964 T 0.18657 2.2 5.67 5.67 0.87782 . 0.067597 0.64402 U 0.000016 T 0.24774 0.0601 L 0.51422 1.61 0.54753 D 0.999981 D 0.53151 0.958 B 0.42692 0.395 T 0.02526 -1.1146 10 0.87932 D 0 -9.1529 15.578 0.76408 0.0:0.0:0.0:1.0 . 524 Q8IZU8 DSEL_HUMAN L 534;524 ENSP00000310565:Q534L ENSP00000310565:Q534L Q - 2 0 DSEL 63331255 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 7.849000 0.86908 2.169000 0.68431 0.460000 0.39030 CAG TCGA-3A-A9IU-01A-11D-A397-08 DSEL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256221.1 1 0 1 119 134 0 75 0 9.128961e-01 0 7 0 75 2 0 0 0 0 0 2 1 1 115 134 0 73 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.503831 1 0.580000 1.910000 0.410857 0.980000 9.100000e-01 1.000000 1.000000 0.982048 0.980000 1 9.500000e-01 1.000000 PPP4R1 9989 broad.mit.edu 37 18 9583116 9583116 + Splice_Site SNP C C A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr18:9583116C>A ENST00000400556.3 - 9 990 c.917G>T c.(916-918)tGg>tTg p.W306L PPP4R1_ENST00000580583.1_Intron|PPP4R1_ENST00000400555.3_Splice_Site_p.W289L NM_001042388.2 NP_001035847.1 Q8TF05 PP4R1_HUMAN protein phosphatase 4, regulatory subunit 1 3 AAACCCTACCCAACGTGAAGG 0.328000 Melanoma(188;1232 2082 5061 11948 35994) 0 SO:0001630 splice_region_variant ENST00000400556.3 0 1 hg19 CCDS42412.1 . . . . . . . . . . C 27.7 4.856783 0.91433 . . ENSG00000154845 ENST00000400556;ENST00000400555;ENST00000285124 T;T 0.17854 2.25;2.25 5.65 5.65 0.86999 Armadillo-like helical (1);Armadillo-type fold (1); 0.309004 0.33040 N 0.005343 T 0.43743 0.1261 M 0.71206 2.165 0.80722 D 1 D;D 0.76494 0.999;0.999 D;D 0.76575 0.973;0.988 T 0.05305 -1.0893 9 . . . -13.8309 19.5069 0.95121 0.0:1.0:0.0:0.0 . 306;289 Q8TF05;Q8TF05-2 PP4R1_HUMAN;. L 306;289;217 ENSP00000383402:W306L;ENSP00000383401:W289L . W - 2 0 PPP4R1 9573116 1.000000 0.71417 1.000000 0.80357 0.903000 0.53119 7.294000 0.78760 2.941000 0.99782 0.655000 0.94253 TGG TCGA-3A-A9IU-01A-11D-A397-08 PPP4R1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000268571.1 0 0 0 4 223 0 32 0 3.986485e-01 0 65 0 32 2 0 0 0 0 0 2 1 8.890625e-01 4 221 0 32 2 0 0 0 0 0 2 -3.124691 1 1 0 0 1 0 0 0 2.028010 0 0.580000 1.910000 0.575071 0.060000 1.000000e-02 0.140000 0.060000 0.074128 0.060000 0 3.000000e-02 0.110000 ABHD8 79575 broad.mit.edu 37 19 17405196 17405196 + Silent SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr19:17405196G>A ENST00000247706.3 - 4 1289 c.1050C>T c.(1048-1050)ggC>ggT p.G350G CTD-2278I10.4_ENST00000594077.1_RNA|MRPL34_ENST00000600434.1_Intron|MRPL34_ENST00000595444.1_Intron NM_024527.4 NP_078803.4 Q96I13 ABHD8_HUMAN abhydrolase domain containing 8 p.G350G(1) 9 AGACCTCGTCGCCCTCGGGCC 0.612000 Ovarian(156;1368 2543 15275 41187) 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000247706.3 1 1 hg19 CCDS12355.1 TCGA-3A-A9IU-01A-11D-A397-08 ABHD8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462937.1 1 0 1 122 169 0 98 1 9.999997e-01 15 21 0 98 2 0 0 0 0 0 2 1 1 122 166 0 97 2 0 0 0 0 0 2 -19.854080 1 1 121412 1 27 1 0 1 1 1.500903 1 0.580000 1.910000 0.408451 0.950000 8.500000e-01 1.000000 0.990000 0.954827 0.950000 1 9.100000e-01 0.990000 RASIP1 54922 broad.mit.edu 37 19 49232704 49232704 + Silent SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr19:49232704G>A ENST00000222145.4 - 5 1527 c.1323C>T c.(1321-1323)cgC>cgT p.R441R RASIP1_ENST00000594232.1_5'Flank NM_017805.2 NP_060275.2 Q5U651 RAIN_HUMAN Ras interacting protein 1 21 all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261) CAGGGCCCGCGCGCACTGTGC 0.741000 0 SO:0001819 synonymous_variant ENST00000222145.4 0 1 hg19 CCDS12731.1 TCGA-3A-A9IU-01A-11D-A397-08 RASIP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466185.1 1 0 0 5 25 0 8 0 1.006016e-01 0 3 0 8 2 0 0 0 0 0 2 1 9.433425e-01 5 25 0 8 2 0 0 0 0 0 2 -14.364150 1 1 117836 2 33 1 1 2 3 2.708686 1 0.580000 1.910000 0.674419 0.780000 3.200000e-01 1.000000 1.000000 0.765730 0.780000 0 5.100000e-01 1.000000 A1BG 1 broad.mit.edu 37 19 58862886 58862886 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr19:58862886G>A ENST00000263100.3 - 5 842 c.781C>T c.(781-783)Cgc>Tgc p.R261C CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000599728.1_RNA|A1BG-AS1_ENST00000595302.1_RNA|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|A1BG-AS1_ENST00000593960.1_RNA NM_130786.3 NP_570602.2 P04217 A1BG_HUMAN alpha-1-B glycoprotein 15 all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157) AAGAAGATGCGATCTGGGCTG 0.637000 0 SO:0001583 missense ENST00000263100.3 1 1 hg19 CCDS12976.1 . . . . . . . . . . G 15.23 2.772683 0.49680 . . ENSG00000121410 ENST00000263100;ENST00000453054 T 0.13089 2.62 4.08 0.302 0.15786 Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 1.104360 0.07058 N 0.833228 T 0.37652 0.1011 M 0.77820 2.39 0.09310 N 1 D 0.89917 1.0 D 0.74023 0.982 T 0.28902 -1.0029 10 0.72032 D 0.01 . 11.1079 0.48214 0.0:0.0:0.5207:0.4793 . 261 P04217 A1BG_HUMAN C 261;139 ENSP00000263100:R261C ENSP00000263100:R261C R - 1 0 A1BG 63554698 0.000000 0.05858 0.000000 0.03702 0.042000 0.13812 0.465000 0.22004 0.042000 0.15717 0.462000 0.41574 CGC TCGA-3A-A9IU-01A-11D-A397-08 A1BG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466930.1 1 0 1 81 244 0 68 0 6.345566e-02 0 2 0 68 2 0 0 0 0 0 2 1 1 80 242 0 67 2 0 0 0 0 0 2 -20.000000 1 1 121410 1 35 1 1 2 3 2.696253 1 0.580000 1.910000 0.674419 0.990000 9.000000e-01 1.000000 1.000000 0.992676 0.990000 1 9.900000e-01 1.000000 C1orf43 25912 broad.mit.edu 37 1 154192337 154192337 + Missense_Mutation SNP A A T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr1:154192337A>T ENST00000368521.5 - 2 341 c.143T>A c.(142-144)gTc>gAc p.V48D C1orf43_ENST00000350592.3_Intron|UBAP2L_ENST00000271877.7_5'Flank|UBAP2L_ENST00000343815.6_5'Flank|C1orf43_ENST00000362076.4_Intron|UBAP2L_ENST00000428931.1_5'Flank|C1orf43_ENST00000368516.1_Intron|C1orf43_ENST00000368519.1_Missense_Mutation_p.V48D|C1orf43_ENST00000368518.1_Missense_Mutation_p.V48D NM_001098616.1 NP_001092086.1 Q9BWL3 CA043_HUMAN chromosome 1 open reading frame 43 10 all_lung(78;1.98e-30)|Lung NSC(65;2.87e-28)|Hepatocellular(266;0.0877) TCCCACAGGGACATGAGGTCC 0.428000 0 SO:0001583 missense ENST00000368521.5 1 1 hg19 CCDS41404.1 . . . . . . . . . . A 26.4 4.736629 0.89482 . . ENSG00000143612 ENST00000368521;ENST00000368519;ENST00000368518 . . . 6.17 6.17 0.99709 . 0.054326 0.64402 D 0.000001 T 0.72479 0.3465 M 0.75615 2.305 0.80722 D 1 D;D 0.62365 0.982;0.991 P;P 0.62184 0.682;0.899 T 0.76515 -0.2931 9 0.72032 D 0.01 -18.2699 16.0034 0.80327 1.0:0.0:0.0:0.0 . 48;48 Q9BWL3-5;Q9BWL3 .;CA043_HUMAN D 48 . ENSP00000357504:V48D V - 2 0 C1orf43 152458961 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 5.842000 0.69417 2.371000 0.80710 0.533000 0.62120 GTC TCGA-3A-A9IU-01A-11D-A397-08 C1orf43-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087664.2 1 0 1 82 311 0 65 1 1 121 262 0 65 2 0 0 0 0 0 2 1 1 82 311 0 65 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.611330 1 0.580000 1.910000 0.670717 0.920000 7.400000e-01 1.000000 1.000000 0.915880 0.920000 1 8.300000e-01 1.000000 TMEM79 84283 broad.mit.edu 37 1 156256255 156256255 + Missense_Mutation SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr1:156256255C>T ENST00000405535.2 + 3 1133 c.962C>T c.(961-963)gCc>gTc p.A321V TMEM79_ENST00000495881.1_3'UTR|TMEM79_ENST00000295694.5_Missense_Mutation_p.A321V|TMEM79_ENST00000357501.2_Silent_p.C82C NM_032323.2 NP_115699.1 Q9BSE2 TMM79_HUMAN transmembrane protein 79 21 Hepatocellular(266;0.158) GGTCTCTTTGCCGTCTCCCGG 0.562000 0 SO:0001583 missense ENST00000405535.2 0 1 hg19 CCDS1138.1 . . . . . . . . . . C 18.62 3.663832 0.67700 . . ENSG00000163472 ENST00000295694;ENST00000405535 T;T 0.50277 0.75;0.75 5.62 5.62 0.85841 . 0.169075 0.52532 D 0.000061 T 0.29684 0.0741 N 0.11427 0.14 0.58432 D 0.999999 P 0.51537 0.946 P 0.52646 0.705 T 0.10989 -1.0606 10 0.30854 T 0.27 -1.5462 16.3903 0.83532 0.0:1.0:0.0:0.0 . 321 Q9BSE2 TMM79_HUMAN V 321 ENSP00000295694:A321V;ENSP00000384748:A321V ENSP00000295694:A321V A + 2 0 TMEM79 154522879 1.000000 0.71417 0.996000 0.52242 0.971000 0.66376 4.836000 0.62789 2.645000 0.89757 0.462000 0.41574 GCC TCGA-3A-A9IU-01A-11D-A397-08 TMEM79-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052101.1 0 0 0 6 616 0 73 0 7.890499e-02 0 40 0 73 2 0 0 0 0 0 2 1 9.644004e-01 6 612 0 72 2 0 0 0 0 0 2 -2.140398 0 1 0 0 1 1 2 3 2.611330 1 0.580000 1.910000 0.670717 0.040000 0 1.000000 0.040000 0.084190 0.040000 0 2.000000e-02 0.070000 KCNJ9 3765 broad.mit.edu 37 1 160054516 160054516 + Silent SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr1:160054516C>T ENST00000368088.3 + 2 938 c.696C>T c.(694-696)ttC>ttT p.F232F NM_004983.2 NP_004974.2 Q92806 KCNJ9_HUMAN potassium inwardly-rectifying channel, subfamily J, member 9 16 all_cancers(52;5.86e-16)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.111) GCGTGGGCTTCGACACGGGAG 0.682000 0 SO:0001819 synonymous_variant ENST00000368088.3 0 1 hg19 CCDS1194.1 TCGA-3A-A9IU-01A-11D-A397-08 KCNJ9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060628.1 0 0 0 3 52 0 10 0 0 0 0 10 2 0 0 0 0 0 2 1 8.125789e-01 3 52 0 10 2 0 0 0 0 0 2 -7.238686 1 1 0 0 1 1 2 3 2.611330 1 0.580000 1.910000 0.670717 0.280000 8.000000e-02 1.000000 0.230000 0.332260 0.280000 0 1.600000e-01 0.480000 DNMT3B 1789 broad.mit.edu 37 20 31388677 31388677 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr20:31388677G>A ENST00000328111.2 + 18 2263 c.1942G>A c.(1942-1944)Gga>Aga p.G648R DNMT3B_ENST00000348286.2_Missense_Mutation_p.G628R|DNMT3B_ENST00000353855.2_Missense_Mutation_p.G628R|DNMT3B_ENST00000375623.4_3'UTR|DNMT3B_ENST00000344505.4_Missense_Mutation_p.G628R|DNMT3B_ENST00000456297.2_Missense_Mutation_p.G552R|DNMT3B_ENST00000443239.3_Missense_Mutation_p.G586R|DNMT3B_ENST00000201963.3_Missense_Mutation_p.G640R NM_006892.3 NP_008823.1 Q9UBC3 DNM3B_HUMAN DNA (cytosine-5-)-methyltransferase 3 beta 39 GGTGATTGGCGGAAGCCCATG 0.522000 0 SO:0001583 missense ENST00000328111.2 0 1 hg19 CCDS13205.1 . . . . . . . . . . G 36 5.691842 0.96793 . . ENSG00000088305 ENST00000328111;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000201963 D;D;D;D;D;D;D 0.93547 -3.24;-3.24;-3.24;-3.24;-3.24;-3.24;-3.24 6.07 6.07 0.98685 . 0.000000 0.85682 D 0.000000 D 0.98172 0.9396 H 0.97635 4.045 0.80722 D 1 D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;0.997;1.0;1.0 D;D;D;D;D;D;D 0.97110 0.998;0.996;0.988;1.0;0.997;1.0;1.0 D 0.98850 1.0758 10 0.87932 D 0 -22.4387 19.2231 0.93806 0.0:0.0:1.0:0.0 . 552;586;347;640;628;628;648 E9PBF2;E7EN63;B3KM53;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3 .;.;.;.;.;.;DNM3B_HUMAN R 648;628;628;586;552;628;640 ENSP00000328547:G648R;ENSP00000313397:G628R;ENSP00000337764:G628R;ENSP00000403169:G586R;ENSP00000412305:G552R;ENSP00000345105:G628R;ENSP00000201963:G640R ENSP00000201963:G640R G + 1 0 DNMT3B 30852338 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 9.779000 0.99018 2.885000 0.99019 0.655000 0.94253 GGA TCGA-3A-A9IU-01A-11D-A397-08 DNMT3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078643.2 0 0 0 5 804 1 147 0 6.362132e-05 0 2 1 147 2 0 0 0 0 0 2 0 2.948121e-03 5 799 1 146 19 0 0 0 0 0 2 -1.781598 0 1 0 0 1 0 1 1 2.044812 0 0.580000 1.910000 0.578778 0.010000 0 0.050000 0.020000 0.024952 0.010000 0 0 0.040000 OGFR 11054 broad.mit.edu 37 20 61444872 61444872 + Silent SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr20:61444872C>T ENST00000290291.6 + 7 1930 c.1905C>T c.(1903-1905)gcC>gcT p.A635A OGFR_ENST00000370461.1_Silent_p.A583A NM_007346.2 NP_031372.2 Q9NZT2 OGFR_HUMAN opioid growth factor receptor 17 Breast(26;3.65e-08) ACGAGCCAGCCGAGAGCCCAT 0.736000 0 SO:0001819 synonymous_variant ENST00000290291.6 0 1 hg19 CCDS13504.1 TCGA-3A-A9IU-01A-11D-A397-08 OGFR-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000080067.1 0 0 0 4 308 0 60 0 1.213840e-02 0 10 0 60 2 0 0 0 0 0 2 0 0 0 0 0 2 0 0 0 0 0 2 -5.006299 1 0 0 0 1 0 1 1 2.044812 0 0.580000 1.910000 0.578778 0.040000 0 0.110000 0.040000 0.054451 0.040000 0 2.000000e-02 0.080000 GMEB2 26205 broad.mit.edu 37 20 62250746 62250746 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr20:62250746G>A ENST00000266068.1 - 1 483 c.5C>T c.(4-6)gCg>gTg p.A2V GMEB2_ENST00000370077.1_Missense_Mutation_p.A2V Q9UKD1 GMEB2_HUMAN glucocorticoid modulatory element binding protein 2 18 all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13) Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114) GTCGGGAGTCGCCATGGCTCA 0.632000 0 SO:0001583 missense ENST00000266068.1 0 1 hg19 CCDS13528.1 . . . . . . . . . . G 17.93 3.509854 0.64522 . . ENSG00000101216 ENST00000370077;ENST00000266068 T;T 0.67345 -0.26;-0.26 4.57 4.57 0.56435 . 0.150819 0.43260 D 0.000590 T 0.74007 0.3660 L 0.32530 0.975 0.43137 D 0.994882 D 0.76494 0.999 D 0.70716 0.97 T 0.78448 -0.2200 10 0.87932 D 0 -3.3315 17.3087 0.87202 0.0:0.0:1.0:0.0 . 2 Q9UKD1 GMEB2_HUMAN V 2 ENSP00000359094:A2V;ENSP00000266068:A2V ENSP00000266068:A2V A - 2 0 GMEB2 61721190 1.000000 0.71417 0.970000 0.41538 0.153000 0.21895 6.679000 0.74513 2.239000 0.73571 0.462000 0.41574 GCG TCGA-3A-A9IU-01A-11D-A397-08 GMEB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080166.1 0 0 0 5 202 0 46 0 2.890168e-02 0 9 0 46 2 0 0 0 0 0 2 1 9.367036e-01 5 200 0 45 2 0 0 0 0 0 2 -3.710251 1 1 121412 1 29 1 0 1 1 2.044812 0 0.580000 1.910000 0.578778 0.080000 2.000000e-02 0.180000 0.080000 0.098365 0.080000 0 5.000000e-02 0.140000 ZBED4 9889 broad.mit.edu 37 22 50279783 50279783 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr22:50279783G>A ENST00000216268.5 + 2 2950 c.2473G>A c.(2473-2475)Gtg>Atg p.V825M NM_014838.2 NP_055653.2 O75132 ZBED4_HUMAN zinc finger, BED-type containing 4 44 all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164) GCACTCGAGCGTGCAGTGCTT 0.627000 0 SO:0001583 missense ENST00000216268.5 1 1 hg19 CCDS33677.1 . . . . . . . . . . G 14.69 2.611814 0.46631 . . ENSG00000100426 ENST00000216268 T 0.28069 1.63 5.57 4.56 0.56223 Ribonuclease H-like (1); 0.118290 0.53938 D 0.000043 T 0.27866 0.0686 L 0.38175 1.15 0.48087 D 0.999586 D 0.57257 0.979 P 0.44518 0.452 T 0.02144 -1.1206 10 0.31617 T 0.26 -40.5602 14.3766 0.66881 0.071:0.0:0.929:0.0 . 825 O75132 ZBED4_HUMAN M 825 ENSP00000216268:V825M ENSP00000216268:V825M V + 1 0 ZBED4 48665787 1.000000 0.71417 0.995000 0.50966 0.809000 0.45718 2.802000 0.47916 1.345000 0.45676 0.655000 0.94253 GTG TCGA-3A-A9IU-01A-11D-A397-08 ZBED4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317408.2 1 0 1 36 55 0 24 1 9.914573e-01 6 9 0 24 2 0 0 0 0 0 2 1 1 36 53 0 24 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.534266 1 0.580000 1.910000 0.410857 0.900000 7.000000e-01 1.000000 1.000000 0.895051 0.900000 1 8.000000e-01 0.980000 NMS 129521 broad.mit.edu 37 2 101089991 101089991 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr2:101089991G>A ENST00000376865.1 + 3 180 c.173G>A c.(172-174)cGc>cAc p.R58H NM_001011717.1 NP_001011717.1 Q5H8A3 NMS_HUMAN neuromedin S 14 CCTCTTTCTCGCCAACCTAAG 0.343000 0 SO:0001583 missense ENST00000376865.1 1 1 hg19 CCDS33259.1 1 4.578754578754579E-4 0 0.0 1 0.0027624309392265192 0 0.0 0 0.0 G 3.177 -0.168837 0.06461 . . ENSG00000204640 ENST00000376865 T 0.23754 1.89 3.81 -3.39 0.04868 . 1.207740 0.05936 N 0.636093 T 0.16428 0.0395 L 0.44542 1.39 0.09310 N 1 P 0.46220 0.874 B 0.35971 0.215 T 0.25222 -1.0138 10 0.45353 T 0.12 3.2782 4.8169 0.13371 0.5921:0.0:0.2415:0.1664 . 58 Q5H8A3 NMS_HUMAN H 58 ENSP00000366061:R58H ENSP00000366061:R58H R + 2 0 NMS 100456423 0.000000 0.05858 0.000000 0.03702 0.022000 0.10575 -0.190000 0.09615 -0.676000 0.05238 0.650000 0.86243 CGC TCGA-3A-A9IU-01A-11D-A397-08 NMS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000329737.1 1 0 1 39 121 0 15 0 0 0 0 15 2 0 0 0 0 0 2 1 1 39 120 0 15 2 0 0 0 0 0 2 -4.184800 1 1 121220 20 39 1 0 1 1 2.043824 0 0.580000 1.910000 0.578778 0.830000 6.200000e-01 1.000000 1.000000 0.839517 0.830000 0 7.200000e-01 0.960000 ROCK2 9475 broad.mit.edu 37 2 11337396 11337396 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr2:11337396G>A ENST00000315872.6 - 27 3806 c.3358C>T c.(3358-3360)Cgg>Tgg p.R1120W ROCK2_ENST00000401753.1_Missense_Mutation_p.R877W NM_004850.3 NP_004841.2 O75116 ROCK2_HUMAN Rho-associated, coiled-coil containing protein kinase 2 43 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) AGTTGTGACCGCAGCTGCTCA 0.438000 0 SO:0001583 missense ENST00000315872.6 0 1 hg19 CCDS42654.1 . . . . . . . . . . G 22.5 4.302523 0.81136 . . ENSG00000134318 ENST00000315872;ENST00000401753;ENST00000399089 T;T 0.64803 -0.12;0.93 5.72 4.85 0.62838 . 0.000000 0.85682 D 0.000000 T 0.77322 0.4113 M 0.71581 2.175 0.58432 D 0.999994 D 0.89917 1.0 D 0.71414 0.973 T 0.80453 -0.1376 10 0.87932 D 0 . 14.8283 0.70130 0.0692:0.0:0.9308:0.0 . 1120 O75116 ROCK2_HUMAN W 1120;877;478 ENSP00000317985:R1120W;ENSP00000385509:R877W ENSP00000317985:R1120W R - 1 2 ROCK2 11254847 1.000000 0.71417 0.987000 0.45799 0.990000 0.78478 3.726000 0.54977 1.418000 0.47098 0.563000 0.77884 CGG TCGA-3A-A9IU-01A-11D-A397-08 ROCK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313886.3 0 0 0 6 438 0 59 0 9.475727e-02 0 32 0 59 2 0 0 0 0 0 2 1 9.639671e-01 5 434 0 58 2 0 0 0 0 0 2 -2.392674 0 1 0 0 1 0 0 0 2.053432 0 0.580000 1.910000 0.580000 0.040000 1.000000e-02 0.100000 0.040000 0.054021 0.040000 0 2.000000e-02 0.070000 SMPD4 55627 broad.mit.edu 37 2 130910653 130910653 + Missense_Mutation SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr2:130910653C>T ENST00000409031.1 - 19 3382 c.2234G>A c.(2233-2235)cGc>cAc p.R745H SMPD4_ENST00000339679.7_Missense_Mutation_p.R603H|SMPD4_ENST00000443958.2_Missense_Mutation_p.R409H|SMPD4_ENST00000453750.1_Missense_Mutation_p.R494H|SMPD4_ENST00000351288.6_Missense_Mutation_p.R716H|SMPD4_ENST00000426662.2_Missense_Mutation_p.R381H|SMPD4_ENST00000452225.2_Missense_Mutation_p.R486H|SMPD4_ENST00000431183.2_Missense_Mutation_p.R643H|SMPD4_ENST00000473720.1_5'Flank NM_017951.4 NP_060421.2 Q9NXE4 NSMA3_HUMAN sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3) 29 Colorectal(110;0.1) Phosphatidylserine(DB00144) AAAGAGTGTGCGGACCAAGCT 0.582000 0 SO:0001583 missense ENST00000409031.1 0 1 hg19 CCDS42751.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. 18.14|18.14 3.557063|3.557063 0.65425|0.65425 2.27E-4|2.27E-4 0.0|0.0 ENSG00000136699|ENSG00000136699 ENST00000439886|ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750;ENST00000443958;ENST00000339679;ENST00000452225;ENST00000426662 .|. .|. .|. 4.09|4.09 4.09|4.09 0.47781|0.47781 .|. .|0.000000 .|0.85682 .|D .|0.000000 T|T 0.79604|0.79604 0.4474|0.4474 M|M 0.82323|0.82323 2.585|2.585 0.54753|0.54753 D|D 0.99998|0.99998 .|D;D;D;D;D;D;D;D;D;D .|0.89917 .|1.0;1.0;1.0;1.0;1.0;0.997;1.0;1.0;1.0;1.0 .|D;D;D;D;D;D;D;D;D;D .|0.85130 .|0.984;0.987;0.995;0.989;0.997;0.937;0.959;0.997;0.993;0.984 T|T 0.83285|0.83285 -0.0036|-0.0036 5|9 .|0.72032 .|D .|0.01 .|. 13.8586|13.8586 0.63545|0.63545 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|381;486;643;603;494;677;706;745;752;277 .|B4E0L6;B4DQ31;E7ESA2;B4E0T5;B4DM23;Q9NXE4-2;Q9NXE4;B1PBA3;Q9NXE4-4;Q9NXE4-5 .|.;.;.;.;.;.;NSMA3_HUMAN;.;.;. T|H 620|716;745;643;494;409;603;486;381 .|. .|ENSP00000339721:R603H A|R -|- 1|2 0|0 SMPD4|SMPD4 130627123|130627123 1.000000|1.000000 0.71417|0.71417 0.871000|0.871000 0.34182|0.34182 0.066000|0.066000 0.16364|0.16364 7.434000|7.434000 0.80377|0.80377 1.820000|1.820000 0.53075|0.53075 0.549000|0.549000 0.68633|0.68633 GCA|CGC TCGA-3A-A9IU-01A-11D-A397-08 SMPD4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254516.3 0 0 0 5 431 0 109 0 6.516198e-01 0 179 0 109 2 0 0 0 0 0 2 1 9.371228e-01 5 429 0 108 2 0 0 0 0 0 2 -1.770476 0 1 121412 2 36 1 0 1 1 2.043824 0 0.580000 1.910000 0.578778 0.030000 0 0.090000 0.040000 0.046817 0.030000 0 2.000000e-02 0.070000 ITGA6 3655 broad.mit.edu 37 2 173333951 173333951 + Missense_Mutation SNP G G T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr2:173333951G>T ENST00000264106.6 + 4 689 c.486G>T c.(484-486)agG>agT p.R162S ITGA6_ENST00000409532.1_Missense_Mutation_p.R48S|ITGA6_ENST00000264107.7_Missense_Mutation_p.R162S|ITGA6_ENST00000409080.1_Missense_Mutation_p.R162S|ITGA6_ENST00000375221.2_Missense_Mutation_p.R162S|ITGA6_ENST00000343713.4_Missense_Mutation_p.R162S P23229 ITA6_HUMAN integrin, alpha 6 44 OV - Ovarian serous cystadenocarcinoma(117;0.0979) AGAATCTCAGGATTGAAGACG 0.473000 0 SO:0001583 missense ENST00000264106.6 0 1 hg19 . . . . . . . . . . G 11.49 1.653589 0.29425 . . ENSG00000091409 ENST00000412899;ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358 T;T;T;T;T;T;T;T;T 0.69926 -0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44;-0.44 6.17 -0.233 0.13078 . 0.138320 0.64402 D 0.000003 T 0.23370 0.0565 N 0.01152 -0.98 0.36788 D 0.884674 B;B;B 0.06786 0.001;0.001;0.0 B;B;B 0.09377 0.004;0.004;0.004 T 0.18555 -1.0333 10 0.06365 T 0.9 . 0.6097 0.00759 0.3751:0.2013:0.241:0.1826 . 162;162;162 P23229-4;G5E9H1;P23229-2 .;.;. S 48;48;162;162;162;162;162;162;162 ENSP00000413470:R48S;ENSP00000386614:R48S;ENSP00000264107:R162S;ENSP00000264106:R162S;ENSP00000364369:R162S;ENSP00000341078:R162S;ENSP00000386896:R162S;ENSP00000406694:R162S;ENSP00000394169:R162S ENSP00000264106:R162S R + 3 2 ITGA6 173042197 0.334000 0.24739 1.000000 0.80357 0.995000 0.86356 0.224000 0.17738 0.471000 0.27319 0.655000 0.94253 AGG TCGA-3A-A9IU-01A-11D-A397-08 ITGA6-201 KNOWN basic protein_coding protein_coding 0 0 0 10 638 0 96 0 4.999536e-01 0 102 0 96 2 0 0 0 0 0 2 1 9.968389e-01 10 635 0 96 2 0 0 0 0 0 2 -2.885254 1 1 0 0 1 0 1 1 2.043824 0 0.580000 1.910000 0.578778 0.050000 2.000000e-02 0.100000 0.060000 0.058132 0.050000 0 3.000000e-02 0.080000 CHRNA1 1134 broad.mit.edu 37 2 175612881 175612881 + Nonsense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr2:175612881G>A ENST00000261007.5 - 10 1486 c.1420C>T c.(1420-1422)Cga>Tga p.R474* CHRNA1_ENST00000409542.1_Nonsense_Mutation_p.R367*|CHRNA1_ENST00000409219.1_Nonsense_Mutation_p.R369*|AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000348749.5_Nonsense_Mutation_p.R449* NM_001039523.2 NP_001034612.1 P02708 ACHA_HUMAN cholinergic receptor, nicotinic, alpha 1 (muscle) 37 Galantamine(DB00674) TCAATGAGTCGACCTGCAAAC 0.502000 0 SO:0001587 stop_gained ENST00000261007.5 0 1 hg19 CCDS33331.1 . . . . . . . . . . G 36 5.913560 0.97099 . . ENSG00000138435 ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219 . . . 5.24 5.24 0.73138 . 0.159217 0.56097 D 0.000024 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.33141 T 0.24 . 19.1987 0.93701 0.0:0.0:1.0:0.0 . . . . X 449;474;367;369 . ENSP00000261007:R474X R - 1 2 CHRNA1 175321127 1.000000 0.71417 0.998000 0.56505 0.989000 0.77384 6.397000 0.73239 2.607000 0.88179 0.655000 0.94253 CGA TCGA-3A-A9IU-01A-11D-A397-08 CHRNA1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000334116.1 0 0 0 4 245 0 25 0 6.607742e-03 0 6 0 25 2 0 0 0 0 0 2 1 8.892017e-01 4 243 0 25 2 0 0 0 0 0 2 -5.306639 1 1 0 0 1 0 1 1 2.043824 0 0.580000 1.910000 0.578778 0.050000 1.000000e-02 0.130000 0.060000 0.068220 0.050000 0 3.000000e-02 0.100000 FOSL2 2355 broad.mit.edu 37 2 28635275 28635275 + Missense_Mutation SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr2:28635275C>T ENST00000264716.4 + 4 1804 c.941C>T c.(940-942)tCa>tTa p.S314L FOSL2_ENST00000379619.1_Missense_Mutation_p.S306L|FOSL2_ENST00000545753.1_Missense_Mutation_p.S275L NM_005253.3 NP_005244.1 P15408 FOSL2_HUMAN FOS-like antigen 2 14 Acute lymphoblastic leukemia(172;0.155) GGGGACCAATCATCAGACTCC 0.622000 0 SO:0001583 missense ENST00000264716.4 1 1 hg19 CCDS1766.1 . . . . . . . . . . C 33 5.217527 0.95104 . . ENSG00000075426 ENST00000379619;ENST00000264716;ENST00000545753 D;T;D 0.86497 -2.06;-1.13;-2.13 5.71 5.71 0.89125 . 0.000000 0.85682 D 0.000000 D 0.88518 0.6458 M 0.77616 2.38 0.80722 D 1 P 0.47762 0.9 B 0.40602 0.334 D 0.90308 0.4335 10 0.87932 D 0 -0.9556 19.8481 0.96728 0.0:1.0:0.0:0.0 . 314 P15408 FOSL2_HUMAN L 306;314;275 ENSP00000368939:S306L;ENSP00000264716:S314L;ENSP00000439303:S275L ENSP00000264716:S314L S + 2 0 FOSL2 28488779 1.000000 0.71417 0.986000 0.45419 0.994000 0.84299 4.804000 0.62554 2.693000 0.91896 0.655000 0.94253 TCA TCGA-3A-A9IU-01A-11D-A397-08 FOSL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000215116.2 1 0 1 54 147 0 41 1 1 42 191 0 41 2 0 0 0 0 0 2 1 1 54 146 0 41 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.053432 0 0.580000 1.910000 0.580000 0.920000 7.200000e-01 1.000000 1.000000 0.913582 0.920000 1 8.100000e-01 1.000000 TTC27 55622 broad.mit.edu 37 2 33003024 33003024 + Missense_Mutation SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr2:33003024C>T ENST00000317907.4 + 14 1987 c.1756C>T c.(1756-1758)Cgc>Tgc p.R586C NM_001193509.1|NM_017735.4 NP_001180438.1|NP_060205.3 Q6P3X3 TTC27_HUMAN tetratricopeptide repeat domain 27 38 GGCATTTCAGCGCTGTGTGAC 0.438000 0 SO:0001583 missense ENST00000317907.4 0 1 hg19 CCDS33176.1 . . . . . . . . . . C 18.14 3.557601 0.65425 . . ENSG00000018699 ENST00000317907 T 0.61859 0.07 5.32 5.32 0.75619 Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1); 0.049606 0.64402 D 0.000001 D 0.85230 0.5649 H 0.97758 4.07 0.80722 D 1 D 0.89917 1.0 D 0.81914 0.995 D 0.90675 0.4601 10 0.87932 D 0 -9.9189 19.0041 0.92843 0.0:1.0:0.0:0.0 . 586 Q6P3X3 TTC27_HUMAN C 586 ENSP00000313953:R586C ENSP00000313953:R586C R + 1 0 TTC27 32856528 1.000000 0.71417 1.000000 0.80357 0.532000 0.34746 4.480000 0.60243 2.465000 0.83290 0.557000 0.71058 CGC TCGA-3A-A9IU-01A-11D-A397-08 TTC27-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000325395.1 0 0 0 4 247 0 42 0 2.125085e-01 0 43 0 42 2 0 0 0 0 0 2 1 8.872906e-01 4 243 0 42 2 0 0 0 0 0 2 -2.975077 1 1 121412 2 36 1 0 0 0 2.053432 0 0.580000 1.910000 0.580000 0.050000 1.000000e-02 0.130000 0.060000 0.067856 0.050000 0 3.000000e-02 0.100000 LMAN2L 81562 broad.mit.edu 37 2 97400208 97400208 + Missense_Mutation SNP C C G TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr2:97400208C>G ENST00000264963.4 - 3 384 c.362G>C c.(361-363)gGa>gCa p.G121A LMAN2L_ENST00000426463.2_Missense_Mutation_p.E4Q|LMAN2L_ENST00000537039.1_5'UTR|LMAN2L_ENST00000534882.1_Missense_Mutation_p.E4Q|LMAN2L_ENST00000377079.4_Missense_Mutation_p.G121A NM_030805.3 NP_110432.1 Q9H0V9 LMA2L_HUMAN lectin, mannose-binding 2-like 7 ATTCTTCTTTCCTTGTCCATG 0.468000 0 SO:0001583 missense ENST00000264963.4 1 1 hg19 CCDS2023.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 20.6|20.6 4.011148|4.011148 0.75046|0.75046 .|. .|. ENSG00000114988|ENSG00000114988 ENST00000426463;ENST00000534882|ENST00000264963;ENST00000377079 T;T|T;T 0.78924|0.63255 -1.22;-1.16|-0.03;-0.03 5.95|5.95 5.95|5.95 0.96441|0.96441 .|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1); .|0.000000 .|0.85682 .|D .|0.000000 T|T 0.81828|0.81828 0.4905|0.4905 M|M 0.83223|0.83223 2.63|2.63 0.80722|0.80722 D|D 1|1 B;B|D;D 0.20550|0.89917 0.046;0.046|0.986;1.0 B;B|P;D 0.22386|0.91635 0.039;0.039|0.768;0.999 T|T 0.82348|0.82348 -0.0502|-0.0502 9|10 0.39692|0.56958 T|D 0.17|0.05 .|. 19.1527|19.1527 0.93495|0.93495 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 4;4|121;121 B4DVH1;B4DSH3|Q9H0V9-2;Q9H0V9 .;.|.;LMA2L_HUMAN Q|A 4|121 ENSP00000396391:E4Q;ENSP00000438501:E4Q|ENSP00000264963:G121A;ENSP00000366280:G121A ENSP00000396391:E4Q|ENSP00000264963:G121A E|G -|- 1|2 0|0 LMAN2L|LMAN2L 96763935|96763935 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.967000|0.967000 0.64934|0.64934 7.468000|7.468000 0.80943|0.80943 2.821000|2.821000 0.97095|0.97095 0.650000|0.650000 0.86243|0.86243 GAA|GGA TCGA-3A-A9IU-01A-11D-A397-08 LMAN2L-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000252844.1 1 0 1 85 207 0 64 1 9.995103e-01 9 22 0 64 2 0 0 0 0 0 2 1 1 83 205 0 63 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 2.043824 0 0.580000 1.910000 0.578778 0.990000 8.200000e-01 1.000000 1.000000 0.965253 0.990000 1 9.000000e-01 1.000000 ILDR1 286676 broad.mit.edu 37 3 121720701 121720701 + Silent SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr3:121720701G>A ENST00000344209.5 - 4 516 c.390C>T c.(388-390)ctC>ctT p.L130L ILDR1_ENST00000273691.3_Silent_p.L130L|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Intron|ILDR1_ENST00000462014.1_Silent_p.L142L NM_001199799.1 NP_001186728.1 Q86SU0 ILDR1_HUMAN immunoglobulin-like domain containing receptor 1 25 CATTTATCACGAGATCTGCTC 0.517000 0 SO:0001819 synonymous_variant ENST00000344209.5 1 1 hg19 CCDS56271.1 TCGA-3A-A9IU-01A-11D-A397-08 ILDR1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000355666.1 1 0 1 58 151 0 25 1 9.083933e-01 3 10 0 25 2 0 0 0 0 0 2 1 1 58 148 0 25 2 0 0 0 0 0 2 -5.535798 1 1 121412 1 27 1 0 0 0 2.055893 0 0.580000 1.910000 0.580000 0.950000 7.500000e-01 1.000000 1.000000 0.934903 0.950000 1 8.400000e-01 1.000000 TNIK 23043 broad.mit.edu 37 3 170786732 170786732 + Missense_Mutation SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr3:170786732C>T ENST00000436636.2 - 30 3948 c.3604G>A c.(3604-3606)Ggt>Agt p.G1202S TNIK_ENST00000538048.1_Missense_Mutation_p.G1154S|TNIK_ENST00000341852.6_Missense_Mutation_p.G1118S|TNIK_ENST00000470834.1_Missense_Mutation_p.G1165S|TNIK_ENST00000460047.1_Missense_Mutation_p.G1139S|TNIK_ENST00000475336.1_Missense_Mutation_p.G1110S|TNIK_ENST00000369326.5_Missense_Mutation_p.G1180S|TNIK_ENST00000488470.1_Missense_Mutation_p.G1147S|TNIK_ENST00000357327.5_Missense_Mutation_p.G1173S|TNIK_ENST00000284483.8_Missense_Mutation_p.G1194S NM_015028.2 NP_055843.1 Q9UKE5 TNIK_HUMAN TRAF2 and NCK interacting kinase 62 all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122) LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14) AATCTTTGACCTTCTTCTACC 0.388000 0 SO:0001583 missense ENST00000436636.2 1 1 hg19 CCDS46956.1 . . . . . . . . . . C 28.8 4.954878 0.92726 . . ENSG00000154310 ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834 T;T;T;T;T;T;T;T;T;T 0.75154 -0.89;-0.88;-0.9;-0.9;-0.89;-0.89;-0.9;-0.9;-0.91;-0.89 6.06 6.06 0.98353 Citron-like (3); 0.000000 0.85682 D 0.000000 D 0.86108 0.5854 M 0.77616 2.38 0.80722 D 1 D;P;P;P;P;D;P;P;D 0.61080 0.979;0.748;0.863;0.884;0.748;0.986;0.936;0.884;0.989 P;B;B;B;B;P;B;B;P 0.61003 0.882;0.319;0.437;0.41;0.319;0.8;0.437;0.41;0.874 D 0.86263 0.1656 10 0.72032 D 0.01 . 20.6208 0.99490 0.0:1.0:0.0:0.0 . 1154;1110;1165;1139;1118;1194;1173;1147;1202 F5H5M9;Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5 .;.;.;.;.;.;.;.;TNIK_HUMAN S 1202;1180;1154;1118;1194;1110;1173;1139;1147;1165 ENSP00000399511:G1202S;ENSP00000358332:G1180S;ENSP00000443278:G1154S;ENSP00000345352:G1118S;ENSP00000284483:G1194S;ENSP00000418156:G1110S;ENSP00000349880:G1173S;ENSP00000418916:G1139S;ENSP00000418378:G1147S;ENSP00000419990:G1165S ENSP00000284483:G1194S G - 1 0 TNIK 172269426 1.000000 0.71417 1.000000 0.80357 0.756000 0.42949 5.920000 0.70017 2.882000 0.98803 0.655000 0.94253 GGT TCGA-3A-A9IU-01A-11D-A397-08 TNIK-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000352973.2 1 0 1 114 303 0 54 1 9.052270e-01 5 8 0 54 2 0 0 0 0 0 2 1 1 113 301 0 54 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.055893 0 0.580000 1.910000 0.580000 0.930000 7.900000e-01 1.000000 1.000000 0.934338 0.930000 1 8.600000e-01 1.000000 PCYT1A 5130 broad.mit.edu 37 3 195975170 195975170 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr3:195975170G>A ENST00000292823.2 - 5 414 c.242C>T c.(241-243)gCc>gTc p.A81V PCYT1A_ENST00000419333.1_Missense_Mutation_p.A81V|RP11-447L10.1_ENST00000431391.1_3'UTR|AC069257.8_ENST00000425275.1_RNA|PCYT1A_ENST00000431016.1_Missense_Mutation_p.A81V|AC069257.8_ENST00000608995.1_RNA|PCYT1A_ENST00000491544.1_5'UTR NM_005017.2 NP_005008.2 P49585 PCY1A_HUMAN phosphate cytidylyltransferase 1, choline, alpha 18 all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206) Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06) Choline(DB00122)|Lamivudine(DB00709) TATTCCATCGGCATAAACTCT 0.383000 0 SO:0001583 missense ENST00000292823.2 0 1 hg19 CCDS3315.1 . . . . . . . . . . g 26.8 4.769299 0.90020 . . ENSG00000161217 ENST00000441879;ENST00000419333;ENST00000292823;ENST00000416798;ENST00000431016;ENST00000411591;ENST00000430755;ENST00000412869;ENST00000443555 D;D;D;D;D;D;D;D 0.96913 -4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17;-4.17 5.67 5.67 0.87782 Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);Cytidyltransferase-related (1); 0.044612 0.85682 D 0.000000 D 0.97334 0.9128 L 0.48260 1.515 0.80722 D 1 D 0.89917 1.0 D 0.80764 0.994 D 0.98016 1.0368 10 0.87932 D 0 -4.6307 18.8171 0.92081 0.0:0.0:1.0:0.0 . 81 P49585 PCY1A_HUMAN V 81;81;81;42;81;81;15;81;81 ENSP00000392397:A81V;ENSP00000390968:A81V;ENSP00000292823:A81V;ENSP00000394617:A81V;ENSP00000400430:A81V;ENSP00000402283:A15V;ENSP00000402015:A81V;ENSP00000393341:A81V ENSP00000292823:A81V A - 2 0 PCYT1A 197459567 1.000000 0.71417 0.998000 0.56505 0.423000 0.31445 9.472000 0.97709 2.686000 0.91538 0.645000 0.84053 GCC TCGA-3A-A9IU-01A-11D-A397-08 PCYT1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000341147.1 0 0 0 5 347 0 74 0 1.301313e-01 0 36 0 74 2 0 0 0 0 0 2 1 9.365585e-01 5 344 0 73 2 0 0 0 0 0 2 -2.659890 1 1 0 0 1 1 2 3 2.065867 0 0.580000 1.910000 0.581214 0.050000 1.000000e-02 0.110000 0.050000 0.058442 0.050000 0 2.000000e-02 0.080000 GRM2 2912 broad.mit.edu 37 3 51743211 51743211 + Missense_Mutation SNP G G A rs144180122 by1000genomes TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr3:51743211G>A ENST00000395052.3 + 2 446 c.212G>A c.(211-213)cGc>cAc p.R71H GRM2_ENST00000442933.2_Missense_Mutation_p.R71H|GRM2_ENST00000475478.1_Intron NM_000839.3 NP_000830.2 Q14416 GRM2_HUMAN glutamate receptor, metabotropic 2 33 GCACTGGACCGCATCAACCGT 0.632000 0 SO:0001583 missense ENST00000395052.3 0 1 hg19 CCDS2834.1 . . . . . . . . . . G 22.1 4.247197 0.80024 . . ENSG00000164082 ENST00000395052;ENST00000442933 D;D 0.86497 -2.13;-2.13 5.28 4.41 0.53225 Extracellular ligand-binding receptor (1); 0.167226 0.46758 D 0.000274 T 0.81093 0.4751 L 0.56199 1.76 0.42153 D 0.991563 B 0.28419 0.211 B 0.21917 0.037 T 0.78252 -0.2276 10 0.62326 D 0.03 . 5.1701 0.15105 0.2123:0.1632:0.6245:0.0 . 71 Q14416 GRM2_HUMAN H 71 ENSP00000378492:R71H;ENSP00000408906:R71H ENSP00000296479:R71H R + 2 0 GRM2 51718251 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 3.691000 0.54720 1.245000 0.43885 -0.137000 0.14449 CGC TCGA-3A-A9IU-01A-11D-A397-08 GRM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346542.1 0 0 0 6 671 0 148 0 0 0 0 148 2 0 0 0 0 0 2 1 9.644367e-01 6 667 0 147 2 0 0 0 0 0 2 -1.831932 0 1 0 0 1 0 0 0 2.055893 0 0.580000 1.910000 0.580000 0.020000 0 0.070000 0.040000 0.034823 0.020000 0 1.000000e-02 0.050000 STAB1 23166 broad.mit.edu 37 3 52555958 52555958 + Missense_Mutation SNP G G A rs144247661 byFrequency TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr3:52555958G>A ENST00000321725.6 + 58 6338 c.6262G>A c.(6262-6264)Gtg>Atg p.V2088M NM_015136.2 NP_055951.2 Q9NY15 STAB1_HUMAN stabilin 1 p.V2088L(1) 76 GGATGGCCGTGTGTGTACAGG 0.642000 1 Substitution - Missense(1) SO:0001583 missense ENST00000321725.6 1 1 hg19 CCDS33768.1 . . . . . . . . . . G 7.022 0.558925 0.13436 6.81E-4 0.0 ENSG00000010327 ENST00000321725 D 0.87571 -2.27 5.75 -2.33 0.06724 Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1); 1.447070 0.03638 N 0.239087 T 0.71005 0.3289 N 0.08118 0 0.09310 N 1 P 0.38148 0.62 B 0.36885 0.235 T 0.64597 -0.6370 10 0.66056 D 0.02 . 0.7708 0.01024 0.384:0.1181:0.262:0.2359 . 2088 Q9NY15 STAB1_HUMAN M 2088 ENSP00000312946:V2088M ENSP00000312946:V2088M V + 1 0 STAB1 52530998 0.000000 0.05858 0.003000 0.11579 0.000000 0.00434 0.653000 0.24902 -0.277000 0.09193 -1.130000 0.01982 GTG TCGA-3A-A9IU-01A-11D-A397-08 STAB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351380.2 1 0 1 66 169 0 50 0 9.986905e-01 0 29 0 50 2 0 0 0 0 0 2 1 1 65 167 0 50 2 0 0 0 0 0 2 -20.000000 1 1 121220 24 45 1 0 0 0 2.055893 0 0.580000 1.910000 0.580000 0.960000 7.700000e-01 1.000000 1.000000 0.943979 0.960000 1 8.600000e-01 1.000000 SORCS2 57537 broad.mit.edu 37 4 7533314 7533314 + Silent SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr4:7533314C>T ENST00000507866.2 + 3 715 c.606C>T c.(604-606)acC>acT p.T202T SORCS2_ENST00000511199.1_3'UTR|SORCS2_ENST00000329016.9_Silent_p.T30T NM_020777.2 NP_065828.2 Q96PQ0 SORC2_HUMAN sortilin-related VPS10 domain containing receptor 2 42 GTGTCACCACCGTCATCGACA 0.602000 0 SO:0001819 synonymous_variant ENST00000507866.2 1 1 hg19 CCDS47008.1 TCGA-3A-A9IU-01A-11D-A397-08 SORCS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000358685.4 1 0 0 49 127 1 20 0 3.997764e-01 0 8 1 20 3 0 0 0 0 0 2 1 9.997850e-01 49 125 1 20 23 0 0 0 0 0 2 -5.351211 1 1 121052 50 45 1 1 2 3 2.100555 0 0.580000 1.910000 0.584816 0.970000 7.500000e-01 1.000000 1.000000 0.941796 0.970000 1 8.500000e-01 1.000000 ACOT12 134526 broad.mit.edu 37 5 80667586 80667586 + Missense_Mutation SNP A A G TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr5:80667586A>G ENST00000307624.3 - 3 269 c.241T>C c.(241-243)Ttc>Ctc p.F81L ACOT12_ENST00000513751.1_Missense_Mutation_p.F81L NM_130767.2 NP_570123.1 Q8WYK0 ACO12_HUMAN acyl-CoA thioesterase 12 23 Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135) CTTGTGCTGAATGCTCTAGTA 0.393000 0 SO:0001583 missense ENST00000307624.3 1 1 hg19 CCDS4055.1 . . . . . . . . . . A 24.4 4.532595 0.85812 . . ENSG00000172497 ENST00000307624;ENST00000513751 T;T 0.21734 1.99;1.99 5.8 5.8 0.92144 Thioesterase superfamily (1); 0.000000 0.85682 D 0.000000 T 0.53190 0.1781 M 0.90650 3.135 0.52099 D 0.999946 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.998 T 0.60120 -0.7325 10 0.46703 T 0.11 -10.442 13.6838 0.62504 1.0:0.0:0.0:0.0 . 81;81 Q5FWE9;Q8WYK0 .;ACO12_HUMAN L 81 ENSP00000303246:F81L;ENSP00000421628:F81L ENSP00000303246:F81L F - 1 0 ACOT12 80703342 1.000000 0.71417 0.982000 0.44146 0.992000 0.81027 5.817000 0.69229 2.227000 0.72691 0.460000 0.39030 TTC TCGA-3A-A9IU-01A-11D-A397-08 ACOT12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254074.1 1 0 1 64 176 0 25 0 0 0 0 25 2 0 0 0 0 0 2 1 1 64 176 0 25 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.074995 0 0.580000 1.910000 0.581214 0.910000 7.300000e-01 1.000000 1.000000 0.912756 0.910000 1 8.200000e-01 1.000000 GPR98 84059 broad.mit.edu 37 5 90046453 90046453 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr5:90046453G>A ENST00000405460.2 + 53 11156 c.11060G>A c.(11059-11061)cGt>cAt p.R3687H NM_032119.3 NP_115495.3 Q8WXG9 GPR98_HUMAN G protein-coupled receptor 98 269 all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192) ACATATGGCCGTATAACCATA 0.343000 0 SO:0001583 missense ENST00000405460.2 0 1 hg19 CCDS47246.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 12.95|12.95 2.092138|2.092138 0.36952|0.36952 .|. .|. ENSG00000164199|ENSG00000164199 ENST00000405460;ENST00000296619|ENST00000509621 T|. 0.27720|. 1.65|. 5.52|5.52 1.66|1.66 0.24008|0.24008 .|. 0.152878|. 0.64402|. N|. 0.000017|. T|T 0.55097|0.55097 0.1899|0.1899 L|L 0.45051|0.45051 1.395|1.395 0.80722|0.80722 D|D 1|1 B;B|. 0.26483|. 0.15;0.101|. B;B|. 0.18561|. 0.022;0.01|. T|T 0.43653|0.43653 -0.9378|-0.9378 10|5 0.37606|. T|. 0.19|. .|. 11.2443|11.2443 0.48987|0.48987 0.2377:0.0:0.7623:0.0|0.2377:0.0:0.7623:0.0 .|. 3687;3687|. E7ETI5;Q8WXG9|. .;GPR98_HUMAN|. H|I 3687|1253 ENSP00000384582:R3687H|. ENSP00000296619:R3687H|. R|V +|+ 2|1 0|0 GPR98|GPR98 90082209|90082209 0.096000|0.096000 0.21769|0.21769 0.050000|0.050000 0.19076|0.19076 0.779000|0.779000 0.44077|0.44077 0.982000|0.982000 0.29539|0.29539 0.028000|0.028000 0.15324|0.15324 -0.123000|-0.123000 0.14984|0.14984 CGT|GTA TCGA-3A-A9IU-01A-11D-A397-08 GPR98-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000369993.2 0 0 0 5 602 0 72 0 0 0 0 72 2 0 0 0 0 0 2 1 9.369563e-01 5 599 0 72 2 0 0 0 0 0 2 -1.922761 0 1 120822 8 41 1 1 2 3 2.074995 0 0.580000 1.910000 0.581214 0.020000 0 0.070000 0.030000 0.033299 0.020000 0 1.000000e-02 0.050000 LNPEP 4012 broad.mit.edu 37 5 96342191 96342191 + Silent SNP A A G TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr5:96342191A>G ENST00000231368.5 + 11 2699 c.2007A>G c.(2005-2007)caA>caG p.Q669Q LNPEP_ENST00000395770.3_Silent_p.Q655Q NM_005575.2 NP_005566.2 Q9UIQ6 LCAP_HUMAN leucyl/cystinyl aminopeptidase 34 all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244) CAAAATATCAATCGGTATCAT 0.308000 0 SO:0001819 synonymous_variant ENST00000231368.5 1 1 hg19 CCDS4087.1 TCGA-3A-A9IU-01A-11D-A397-08 LNPEP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250624.1 1 0 1 101 271 0 35 1 7.476668e-01 3 6 0 35 2 0 0 0 0 0 2 1 1 100 270 0 34 2 0 0 0 0 0 2 -20.000000 1 1 121386 5 36 1 1 2 3 2.074995 0 0.580000 1.910000 0.581214 0.930000 7.800000e-01 1.000000 1.000000 0.930317 0.930000 1 8.500000e-01 1.000000 ELOVL2 54898 broad.mit.edu 37 6 10984107 10984107 + Missense_Mutation SNP C C A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr6:10984107C>A ENST00000354666.3 - 8 881 c.798G>T c.(796-798)atG>atT p.M266I NM_017770.3 NP_060240.3 Q9NXB9 ELOV2_HUMAN ELOVL fatty acid elongase 2 14 Breast(50;0.0418)|Ovarian(93;0.0919) all_hematologic(90;0.117) Epithelial(50;0.176) GTGGCTCTTGCATATCTTTCT 0.353000 0 SO:0001583 missense ENST00000354666.3 1 1 hg19 CCDS4518.1 . . . . . . . . . . C 11.38 1.622984 0.28889 . . ENSG00000197977 ENST00000354666 T 0.21191 2.02 5.2 1.35 0.21983 . . . . . T 0.02727 0.0082 N 0.08118 0 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.44847 -0.9301 9 0.38643 T 0.18 1.9891 4.5775 0.12241 0.0:0.4456:0.1567:0.3977 . 266 Q9NXB9 ELOV2_HUMAN I 266 ENSP00000346693:M266I ENSP00000346693:M266I M - 3 0 ELOVL2 11092093 0.000000 0.05858 0.000000 0.03702 0.709000 0.40893 -0.408000 0.07169 0.020000 0.15106 0.650000 0.86243 ATG TCGA-3A-A9IU-01A-11D-A397-08 ELOVL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039849.1 1 0 1 64 186 0 41 0 1.663651e-01 0 3 0 41 2 0 0 0 0 0 2 1 1 63 183 0 41 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.026811 0 0.580000 1.910000 0.575071 0.860000 6.900000e-01 1.000000 1.000000 0.871958 0.860000 1 7.700000e-01 0.970000 ABCA13 154664 broad.mit.edu 37 7 48411864 48411864 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr7:48411864G>A ENST00000435803.1 + 33 10927 c.10903G>A c.(10903-10905)Gtt>Att p.V3635I NM_152701.3 NP_689914.2 Q86UQ4 ABCAD_HUMAN ATP-binding cassette, sub-family A (ABC1), member 13 p.V3635I(1)|p.V3580I(1) 270 TCTGGCCATCGTTCTGAAAAC 0.468000 2 Substitution - Missense(2) SO:0001583 missense ENST00000435803.1 1 1 hg19 CCDS47584.1 . . . . . . . . . . G 1.351 -0.591282 0.03799 . . ENSG00000179869 ENST00000435803 D 0.87491 -2.26 5.77 -1.16 0.09678 . 0.381500 0.22125 N 0.064274 T 0.55114 0.1900 N 0.00801 -1.175 0.49582 D 0.999804 B;B 0.06786 0.0;0.001 B;B 0.06405 0.002;0.002 T 0.54543 -0.8278 10 0.02654 T 1 . 6.8687 0.24108 0.4762:0.128:0.3958:0.0 . 1337;3635 Q86UQ4-3;Q86UQ4 .;ABCAD_HUMAN I 3635 ENSP00000411096:V3635I ENSP00000411096:V3635I V + 1 0 ABCA13 48382410 0.853000 0.29707 0.008000 0.14137 0.914000 0.54420 0.853000 0.27777 -0.342000 0.08363 -0.294000 0.09567 GTT TCGA-3A-A9IU-01A-11D-A397-08 ABCA13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000341964.2 1 0 1 110 292 0 49 0 0 0 1 0 49 2 0 0 0 0 0 2 1 1 109 291 0 48 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.071627 0 0.580000 1.910000 0.581214 0.940000 7.900000e-01 1.000000 1.000000 0.936633 0.940000 1 8.600000e-01 1.000000 TYW1 55253 broad.mit.edu 37 7 66479413 66479413 + Silent SNP T T C rs145686658 by1000genomes TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr7:66479413T>C ENST00000359626.5 + 5 599 c.435T>C c.(433-435)acT>acC p.T145T NM_018264.2 NP_060734.2 Q9NV66 TYW1_HUMAN tRNA-yW synthesizing protein 1 homolog (S. cerevisiae) p.T145T(1) 46 Lung NSC(55;0.0846)|all_lung(88;0.183) GCCTACCAACTGAAAGTGCAG 0.428000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000359626.5 0 1 hg19 CCDS5538.1 TCGA-3A-A9IU-01A-11D-A397-08 TYW1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251932.2 0 0 0 7 609 0 101 0 5.418782e-02 0 28 0 101 2 0 0 0 0 0 2 1 9.797682e-01 7 601 0 100 2 0 0 0 0 0 2 -1.820533 0 1 121412 80 43 1 1 2 3 2.071627 0 0.580000 1.910000 0.581214 0.030000 0 0.080000 0.040000 0.044739 0.030000 0 2.000000e-02 0.060000 TG 7038 broad.mit.edu 37 8 133923730 133923730 + Missense_Mutation SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr8:133923730C>T ENST00000220616.4 + 19 4151 c.4111C>T c.(4111-4113)Cgg>Tgg p.R1371W TG_ENST00000377869.1_Missense_Mutation_p.R1371W NM_003235.4 NP_003226.4 P01266 THYG_HUMAN thyroglobulin 168 Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155) Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735) BRCA - Breast invasive adenocarcinoma(115;0.000701) ATGGAAATCACGGCTTGAGGA 0.478000 0 SO:0001583 missense ENST00000220616.4 0 1 hg19 CCDS34944.1 . . . . . . . . . . C 21.8 4.209064 0.79240 0.0 1.16E-4 ENSG00000042832 ENST00000377869;ENST00000543313;ENST00000220616 T;T 0.64803 -0.11;-0.12 5.51 5.51 0.81932 . 1.131830 0.06509 N 0.737751 T 0.58495 0.2126 L 0.40543 1.245 0.09310 N 1 D 0.69078 0.997 B 0.40534 0.332 T 0.57774 -0.7753 10 0.72032 D 0.01 . 14.9365 0.70960 0.0:1.0:0.0:0.0 . 1371 P01266 THYG_HUMAN W 1371;177;1371 ENSP00000367100:R1371W;ENSP00000220616:R1371W ENSP00000220616:R1371W R + 1 2 TG 133992912 0.036000 0.19791 0.006000 0.13384 0.514000 0.34195 3.406000 0.52637 2.582000 0.87167 0.557000 0.71058 CGG TCGA-3A-A9IU-01A-11D-A397-08 TG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000379606.1 0 0 0 9 625 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 9.937437e-01 9 613 0 70 2 0 0 0 0 0 2 -2.301031 0 1 121412 5 41 1 0 0 0 2.055610 0 0.580000 1.910000 0.580000 0.040000 1.000000e-02 0.090000 0.050000 0.054226 0.040000 0 3.000000e-02 0.070000 RALYL 138046 broad.mit.edu 37 8 85774611 85774611 + Missense_Mutation SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr8:85774611C>T ENST00000521268.1 + 6 1599 c.494C>T c.(493-495)aCg>aTg p.T165M RALYL_ENST00000518566.1_Missense_Mutation_p.T154M|RALYL_ENST00000521376.1_Missense_Mutation_p.T76M|RALYL_ENST00000522455.1_Missense_Mutation_p.T165M|RALYL_ENST00000523850.1_Missense_Mutation_p.T92M|RALYL_ENST00000521695.1_Missense_Mutation_p.T165M|RALYL_ENST00000517638.1_Missense_Mutation_p.T178M NM_173848.5 NP_776247.3 Q86SE5 RALYL_HUMAN RALY RNA binding protein-like 24 GCAGTCACAACGACTCGCAGG 0.483000 0 SO:0001583 missense ENST00000521268.1 1 1 hg19 CCDS55253.1 . . . . . . . . . . C 18.00 3.526572 0.64860 . . ENSG00000184672 ENST00000522455;ENST00000521695;ENST00000521268;ENST00000518566;ENST00000517638;ENST00000523850;ENST00000521376 T;T;T;T;T;T;T 0.18657 2.83;2.83;2.83;2.85;2.83;2.42;2.2 5.1 5.1 0.69264 . 0.214143 0.49305 D 0.000143 T 0.35941 0.0949 M 0.61703 1.905 0.09310 N 1 P;D;P;P;D 0.60160 0.791;0.987;0.939;0.93;0.987 B;P;B;P;P 0.51016 0.336;0.588;0.337;0.656;0.588 T 0.19192 -1.0313 10 0.62326 D 0.03 -3.4988 18.8851 0.92375 0.0:1.0:0.0:0.0 . 154;165;92;178;165 B3KT61;B3KSX3;Q86SE5-2;G3V129;Q86SE5 .;.;.;.;RALYL_HUMAN M 165;165;165;154;178;92;76 ENSP00000430394:T165M;ENSP00000428667:T165M;ENSP00000430367:T165M;ENSP00000430065:T154M;ENSP00000430128:T178M;ENSP00000428807:T92M;ENSP00000428310:T76M ENSP00000430128:T178M T + 2 0 RALYL 85937166 0.679000 0.27596 0.011000 0.14972 0.798000 0.45092 5.613000 0.67688 2.511000 0.84671 0.551000 0.68910 ACG TCGA-3A-A9IU-01A-11D-A397-08 RALYL-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000379448.1 1 0 1 36 89 0 18 0 0 0 0 18 2 0 0 0 0 0 2 1 1 36 85 0 18 2 0 0 0 0 0 2 -20.000000 1 1 120836 3 28 1 0 0 0 2.055610 0 0.580000 1.910000 0.580000 0.980000 7.300000e-01 1.000000 1.000000 0.944361 0.980000 1 8.500000e-01 1.000000 TNKS 8658 broad.mit.edu 37 8 9609296 9609296 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr8:9609296G>A ENST00000310430.6 + 19 3036 c.3010G>A c.(3010-3012)Gta>Ata p.V1004I TNKS_ENST00000518281.1_Missense_Mutation_p.V767I NM_003747.2 NP_003738.2 O95271 TNKS1_HUMAN tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 49 AGAGTTGGCCGTAGGAGGAGC 0.542000 0 SO:0001583 missense ENST00000310430.6 0 1 hg19 CCDS5974.1 . . . . . . . . . . G 9.102 1.004279 0.19199 0.0 1.16E-4 ENSG00000173273 ENST00000310430;ENST00000518281 T;T 0.61859 0.07;0.14 5.73 5.73 0.89815 . 0.331114 0.32055 N 0.006645 T 0.45034 0.1322 N 0.19112 0.55 0.54753 D 0.999982 B 0.16396 0.017 B 0.09377 0.004 T 0.29941 -0.9995 10 0.18276 T 0.48 . 19.9054 0.97006 0.0:0.0:1.0:0.0 . 1004 O95271 TNKS1_HUMAN I 1004;767 ENSP00000311579:V1004I;ENSP00000429890:V767I ENSP00000311579:V1004I V + 1 0 TNKS 9646706 1.000000 0.71417 0.901000 0.35422 0.191000 0.23601 6.449000 0.73473 2.698000 0.92095 0.655000 0.94253 GTA TCGA-3A-A9IU-01A-11D-A397-08 TNKS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206935.1 0 0 0 6 526 0 75 0 1.353191e-02 0 13 0 75 2 0 0 0 0 0 2 1 9.632581e-01 6 517 0 74 2 0 0 0 0 0 2 -2.164740 0 1 121412 3 37 1 0 0 0 2.055610 0 0.580000 1.910000 0.580000 0.030000 0 0.080000 0.040000 0.045001 0.030000 0 2.000000e-02 0.060000 TNC 3371 broad.mit.edu 37 9 117848514 117848514 + Missense_Mutation SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr9:117848514C>T ENST00000350763.4 - 3 1907 c.1496G>A c.(1495-1497)cGc>cAc p.R499H TNC_ENST00000535648.1_Missense_Mutation_p.R499H|TNC_ENST00000346706.3_Missense_Mutation_p.R499H|TNC_ENST00000345230.3_Missense_Mutation_p.R499H|TNC_ENST00000423613.2_Missense_Mutation_p.R499H|TNC_ENST00000340094.3_Missense_Mutation_p.R499H|TNC_ENST00000341037.4_Missense_Mutation_p.R499H|TNC_ENST00000542877.1_Missense_Mutation_p.R499H|TNC_ENST00000537320.1_Missense_Mutation_p.R499H NM_002160.3 NP_002151.2 P24821 TENA_HUMAN tenascin C p.R499H(1) 120 GGGGCATTGGCGATCCCGGCA 0.597000 1 Substitution - Missense(1) SO:0001583 missense ENST00000350763.4 0 1 hg19 CCDS6811.1 . . . . . . . . . . C 8.572 0.880360 0.17467 . . ENSG00000041982 ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877 T;T;T;T;T;T;T;T;T 0.03524 3.9;3.9;3.9;3.9;3.9;3.9;3.9;3.9;3.9 5.82 -2.57 0.06248 . 0.783888 0.11926 N 0.516193 T 0.03959 0.0111 L 0.59436 1.845 0.09310 N 1 B;B 0.15719 0.014;0.001 B;B 0.08055 0.003;0.001 T 0.37407 -0.9707 10 0.59425 D 0.04 . 4.1099 0.10053 0.5463:0.2293:0.0677:0.1566 . 499;499 E9PC84;P24821 .;TENA_HUMAN H 499 ENSP00000344400:R499H;ENSP00000438152:R499H;ENSP00000344555:R499H;ENSP00000345861:R499H;ENSP00000265131:R499H;ENSP00000339553:R499H;ENSP00000411406:R499H;ENSP00000443478:R499H;ENSP00000442242:R499H ENSP00000344400:R499H R - 2 0 TNC 116888335 0.000000 0.05858 0.001000 0.08648 0.323000 0.28346 -0.002000 0.12924 -0.330000 0.08514 0.462000 0.41574 CGC TCGA-3A-A9IU-01A-11D-A397-08 TNC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055418.2 0 0 0 6 564 0 101 0 7.643824e-02 0 35 0 101 2 0 2.951098e-01 2 702 1 279 11 1 9.645545e-01 6 561 0 98 2 0 0 0 0 0 2 -2.068723 0 1 121412 2 38 1 0 0 0 2.054451 0 0.580000 1.910000 0.580000 0.030000 0 0.080000 0.040000 0.041898 0.030000 0 1.000000e-02 0.060000 CERCAM 51148 broad.mit.edu 37 9 131193524 131193524 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr9:131193524G>A ENST00000372838.4 + 9 1543 c.1145G>A c.(1144-1146)cGc>cAc p.R382H RP11-339B21.10_ENST00000610052.1_RNA|CERCAM_ENST00000372842.1_Missense_Mutation_p.R304H NM_016174.4 NP_057258.3 Q5T4B2 GT253_HUMAN cerebral endothelial cell adhesion molecule 20 TACTCGGGCCGCACTCTGACC 0.627000 0 SO:0001583 missense ENST00000372838.4 0 1 hg19 CCDS6901.2 . . . . . . . . . . G 19.24 3.789219 0.70337 . . ENSG00000167123 ENST00000372842;ENST00000372838;ENST00000413863 T;T 0.80653 -1.37;-1.4 5.02 4.1 0.47936 . 0.055960 0.64402 N 0.000001 D 0.86293 0.5898 M 0.74546 2.27 0.80722 D 1 D 0.59767 0.986 P 0.57679 0.825 D 0.87600 0.2496 10 0.72032 D 0.01 -20.9121 12.8845 0.58036 0.0818:0.0:0.9182:0.0 . 382 Q5T4B2 GT253_HUMAN H 304;382;335 ENSP00000361933:R304H;ENSP00000361929:R382H ENSP00000361929:R382H R + 2 0 CERCAM 130233345 1.000000 0.71417 1.000000 0.80357 0.715000 0.41141 7.668000 0.83897 1.197000 0.43143 0.491000 0.48974 CGC TCGA-3A-A9IU-01A-11D-A397-08 CERCAM-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054435.2 0 0 0 6 406 0 71 0 8.631611e-01 0 244 0 71 2 0 0 0 0 0 2 1 9.649787e-01 6 405 0 70 2 0 0 0 0 0 2 -2.041438 0 1 0 0 1 0 0 0 2.054451 0 0.580000 1.910000 0.580000 0.050000 1.000000e-02 0.110000 0.050000 0.058204 0.050000 0 3.000000e-02 0.080000 CDKN2A 1029 broad.mit.edu 37 9 21971000 21971000 + Nonsense_Mutation SNP C C A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr9:21971000C>A ENST00000304494.5 - 2 628 c.358G>T c.(358-360)Gag>Tag p.E120* CDKN2A_ENST00000530628.2_3'UTR|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.E120*|CDKN2A_ENST00000579755.1_3'UTR|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.E69*|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.E69*|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.E69*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.E120*|CDKN2A_ENST00000361570.3_3'UTR|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.E69*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.E120*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.E69* NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.?(13)|p.E120*(9)|p.E120K(4)|p.0(1)|p.A118fs*10(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) TGGCCCAGCTCCTCAGCCAGG 0.726000 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1343 Whole gene deletion(1316)|Unknown(13)|Substitution - Nonsense(9)|Substitution - Missense(4)|Deletion - Frameshift(1) GRCh37 CD972119 CDKN2A D SO:0001587 stop_gained ENST00000304494.5 0 1 hg19 CCDS6510.1 . . . . . . . . . . C 37 6.320898 0.97471 . . ENSG00000147889 ENST00000304494;ENST00000446177 . . . 5.93 5.03 0.67393 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . 0.40728 T 0.16 -15.0988 14.364 0.66792 0.0:0.8518:0.1482:0.0 . . . . X 120 . ENSP00000307101:E120X E - 1 0 CDKN2A 21961000 0.585000 0.26774 1.000000 0.80357 0.613000 0.37349 1.323000 0.33701 1.489000 0.48450 0.655000 0.94253 GAG TCGA-3A-A9IU-01A-11D-A397-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 51 81 0 55 1 1 81 14 0 55 2 1 1 84 151 0 269 2 1 1 51 79 0 55 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.459422 1 0.580000 1.910000 0.408451 0.890000 7.200000e-01 1.000000 0.940000 0.894260 0.890000 1 8.100000e-01 0.970000 KDM4C 23081 broad.mit.edu 37 9 7049110 7049110 + Silent SNP C C T TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr9:7049110C>T ENST00000381309.3 + 17 2899 c.2334C>T c.(2332-2334)tgC>tgT p.C778C KDM4C_ENST00000536108.1_Intron|KDM4C_ENST00000442236.2_Silent_p.C523C|KDM4C_ENST00000381306.3_Silent_p.C778C|KDM4C_ENST00000535193.1_Silent_p.C800C|KDM4C_ENST00000543771.1_Silent_p.C778C|KDM4C_ENST00000428870.2_Silent_p.C465C NM_015061.3 NP_055876.2 Q9H3R0 KDM4C_HUMAN lysine (K)-specific demethylase 4C 43 ATGTCATGTGCGCCGTTGCGG 0.433000 0 SO:0001819 synonymous_variant ENST00000381309.3 1 1 hg19 CCDS6471.1 TCGA-3A-A9IU-01A-11D-A397-08 KDM4C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051692.1 1 0 1 71 124 0 32 1 9.985734e-01 11 10 0 32 2 0 0 0 0 0 2 1 1 69 124 0 32 2 0 0 0 0 0 2 -10.332930 1 1 121410 3 34 1 0 1 1 1.459422 1 0.580000 1.910000 0.408451 0.870000 7.200000e-01 0.990000 0.890000 0.873098 0.870000 1 7.900000e-01 0.950000 RORB 6096 broad.mit.edu 37 9 77282784 77282784 + Missense_Mutation SNP G G A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chr9:77282784G>A ENST00000396204.2 + 8 1111 c.1111G>A c.(1111-1113)Gct>Act p.A371T RORB_ENST00000376896.3_Missense_Mutation_p.A360T Q92753 RORB_HUMAN RAR-related orphan receptor B 12 Melatonin(DB01065) GGAGGAGATCGCTTTGTTCTC 0.388000 0 SO:0001583 missense ENST00000396204.2 1 1 hg19 . . . . . . . . . . G 36 5.715486 0.96830 . . ENSG00000198963 ENST00000376896;ENST00000396204 D;D 0.97575 -4.44;-4.44 6.17 6.17 0.99709 Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2); 0.092611 0.64402 D 0.000001 D 0.98689 0.9560 M 0.86178 2.8 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.85130 0.995;0.997 D 0.98965 1.0799 10 0.87932 D 0 . 20.8794 0.99867 0.0:0.0:1.0:0.0 . 371;360 Q92753;Q58EY0 RORB_HUMAN;. T 360;371 ENSP00000366093:A360T;ENSP00000379507:A371T ENSP00000366093:A360T A + 1 0 RORB 76472604 1.000000 0.71417 1.000000 0.80357 0.973000 0.67179 9.775000 0.98995 2.941000 0.99782 0.655000 0.94253 GCT TCGA-3A-A9IU-01A-11D-A397-08 RORB-201 KNOWN basic protein_coding protein_coding 1 0 1 150 379 0 59 0 0 0 0 59 2 0 0 0 0 0 2 1 1 148 376 0 58 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.054451 0 0.580000 1.910000 0.580000 0.970000 8.400000e-01 1.000000 1.000000 0.961213 0.970000 1 9.000000e-01 1.000000 GPR112 139378 broad.mit.edu 37 X 135429875 135429875 + Missense_Mutation SNP C C A TCGA-3A-A9IU-01A-11D-A397-08 TCGA-3A-A9IU-10A-01D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 912bafe3-1218-44c3-ba4e-16aeac4f598e c7a38788-c7eb-42b3-a1f2-75d82c600d91 g.chrX:135429875C>A ENST00000394143.1 + 6 4301 c.4010C>A c.(4009-4011)aCa>aAa p.T1337K GPR112_ENST00000412101.1_Missense_Mutation_p.T1132K|GPR112_ENST00000370652.1_Missense_Mutation_p.T1337K|GPR112_ENST00000394141.1_Missense_Mutation_p.T1132K|GPR112_ENST00000287534.4_Missense_Mutation_p.T1274K NM_153834.3 NP_722576.3 Q8IZF6 GP112_HUMAN G protein-coupled receptor 112 199 Acute lymphoblastic leukemia(192;0.000127) TCTGGAAGCACACAGATTACA 0.463000 0 SO:0001583 missense ENST00000394143.1 1 1 hg19 CCDS35409.1 . . . . . . . . . . c 3.929 -0.016606 0.07681 . . ENSG00000156920 ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141 T;T;T;T;T 0.31510 1.53;1.53;1.49;1.62;1.49 2.81 -0.405 0.12392 . . . . . T 0.16811 0.0404 L 0.29908 0.895 0.09310 N 1 P;P;B 0.45827 0.867;0.642;0.421 B;B;B 0.38020 0.263;0.26;0.081 T 0.12066 -1.0562 9 0.54805 T 0.06 . 3.1011 0.06327 0.2101:0.5296:0.0:0.2603 . 1274;1132;1337 Q8IZF6-2;Q8IZF6-3;Q8IZF6 .;.;GP112_HUMAN K 1337;1337;1132;1274;1132 ENSP00000377699:T1337K;ENSP00000359686:T1337K;ENSP00000416526:T1132K;ENSP00000287534:T1274K;ENSP00000377697:T1132K ENSP00000287534:T1274K T + 2 0 GPR112 135257541 0.001000 0.12720 0.001000 0.08648 0.070000 0.16714 0.046000 0.14035 -0.387000 0.07809 0.525000 0.51046 ACA TCGA-3A-A9IU-01A-11D-A397-08 GPR112-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000286639.1 1 0 1 121 105 0 24 0 0 0 0 24 2 0 0 0 0 0 2 1 1 121 105 0 24 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 0.580000 1.910000 0.580000 0.900000 8.000000e-01 0.990000 0.920000 0.911088 0.900000 1 8.500000e-01 0.960000