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 EXPH5 23086 broad.mit.edu 37 11 108382677 108382678 + Frame_Shift_Ins INS - - G TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr11:108382677_108382678insG ENST00000265843.4 - 6 3666_3667 c.3556_3557insC c.(3556-3558)caafs p.Q1186fs EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000443411.1_Frame_Shift_Ins_p.Q998fs|EXPH5_ENST00000428840.1_Frame_Shift_Ins_p.Q1110fs|EXPH5_ENST00000525344.1_Frame_Shift_Ins_p.Q1179fs NM_015065.2 NP_055880 Q8NEV8 EXPH5_HUMAN exophilin 5 91 all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16) AGTGTATTCTTGGAAGTTTTCC 0.416000 0 SO:0001589 frameshift_variant ENST00000265843.4 0 1 hg19 CCDS8341.1 TCGA-2J-AAB1-01A-11D-A40W-08 EXPH5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390279.1 1 0 0 76 554 0 91 0 4.117291e-02 0 3 0 91 2 0 0 0 0 0 0 1 1.000000 77 550 0 89 2 -2.841672 1 1 0 0 1 1 2 3 2.042490 0 0.380000 1.940000 0.382347 0.630000 5.000000e-01 0.800000 0.630000 0.645534 0.630000 0 0.560000 0.710000 MBD6 114785 broad.mit.edu 37 12 57919654 57919666 + Frame_Shift_Del DEL GGGGCCCCTGGGA GGGGCCCCTGGGA - TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr12:57919654_57919666delGGGGCCCCTGGGA ENST00000355673.3 + 6 1259_1271 c.903_915delGGGGCCCCTGGGA c.(901-915)ctggggcccctgggafs p.LGPLG301fs MBD6_ENST00000431731.2_Frame_Shift_Del_p.LGPLG301fs NM_052897.3 NP_443129.3 Q96DN6 MBD6_HUMAN methyl-CpG binding domain protein 6 31 CCCTGGTCCTGGGGCCCCTGGGAGGGGCCCCCA 0.695000 0 SO:0001589 frameshift_variant ENST00000355673.3 0 1 hg19 CCDS8944.1 TCGA-2J-AAB1-01A-11D-A40W-08 MBD6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407250.1 1 0 0 24 247 0 39 0 9.626537e-01 0 58 0 39 2 0 0 0 0 0 0 2 0.004121 73 292 5 42 59 -2.841673 1 1 0 0 1 0 0 0 1.993904 0 0.380000 1.940000 0.370431 0.460000 3.000000e-01 0.650000 0.460000 0.471682 0.460000 0 0.370000 0.560000 PLEK 5341 broad.mit.edu 37 2 68622834 68622834 + Frame_Shift_Del DEL C C - TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr2:68622834delC ENST00000234313.7 + 9 1118 c.939delC c.(937-939)aacfs p.N313fs NM_002664.2 NP_002655.2 P08567 PLEK_HUMAN pleckstrin 24 Ovarian(717;0.0129) AGGAAGAGAACCTTTTTGAGA 0.542000 0 SO:0001589 frameshift_variant ENST00000234313.7 1 1 hg19 CCDS1887.1 TCGA-2J-AAB1-01A-11D-A40W-08 PLEK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251755.1 1 0 0 86 597 0 121 0 6.824359e-01 0 18 0 121 2 0 0 0 0 0 0 1 0.999916 91 591 5 118 46 -20.000000 1 1 0 0 1 0 0 0 2.015667 0 0.380000 1.940000 0.377635 0.650000 5.300000e-01 0.790000 0.660000 0.664314 0.650000 0 0.590000 0.730000 NT5C2 22978 broad.mit.edu 37 10 104934648 104934648 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr10:104934648G>A ENST00000404739.3 - 1 91 c.68C>T c.(67-69)gCc>gTc p.A23V NT5C2_ENST00000343289.5_Missense_Mutation_p.A23V|NT5C2_ENST00000369857.4_Intron|NT5C2_ENST00000470299.1_Missense_Mutation_p.A23V P49902 5NTC_HUMAN 5'-nucleotidase, cytosolic II 16 all_hematologic(284;0.176)|Colorectal(252;0.178) Adenosine triphosphate(DB00171)|Ribavirin(DB00811) CTTTTTCAGGGCATGCTTATC 0.378000 0 SO:0001583 missense ENST00000404739.3 0 1 hg19 CCDS7544.1 . . . . . . . . . . G 16.87 3.240896 0.58995 . . ENSG00000076685 ENST00000343289;ENST00000404739;ENST00000452156 T;T;T 0.18502 2.21;2.21;2.22 5.39 4.49 0.54785 . 0.159024 0.56097 D 0.000039 T 0.10637 0.0260 N 0.14661 0.345 0.80722 D 1 B 0.02656 0.0 B 0.01281 0.0 T 0.12142 -1.0559 10 0.24483 T 0.36 -2.4411 13.313 0.60390 0.0782:0.0:0.9218:0.0 . 23 P49902 5NTC_HUMAN V 23 ENSP00000339479:A23V;ENSP00000383960:A23V;ENSP00000396468:A23V ENSP00000339479:A23V A - 2 0 NT5C2 104924638 1.000000 0.71417 0.998000 0.56505 0.984000 0.73092 5.904000 0.69886 1.256000 0.44068 0.650000 0.86243 GCC TCGA-2J-AAB1-01A-11D-A40W-08 NT5C2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050121.1 0 0 0 7 804 0 141 0 1.651182e-01 0 72 0 141 2 0 0 0 0 0 2 1 0.979851 7 795 0 138 2 -2.186632 0 1 0 0 1 1 2 3 2.036995 0 0.380000 1.940000 0.382347 0.040000 1.000000e-02 0.100000 0.040000 0.061253 0.040000 0 0.020000 0.070000 WDR37 22884 broad.mit.edu 37 10 1149626 1149626 + Missense_Mutation SNP C C A rs150728900 TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr10:1149626C>A ENST00000358220.1 + 10 955 c.811C>A c.(811-813)Cgc>Agc p.R271S WDR37_ENST00000263150.4_Missense_Mutation_p.R271S Q9Y2I8 WDR37_HUMAN WD repeat domain 37 17 all_epithelial(10;0.0449)|Colorectal(49;0.142) CCCCACCATCCGCGTCCCACT 0.622000 0 SO:0001583 missense ENST00000358220.1 1 1 hg19 CCDS7057.1 . . . . . . . . . . C 20.4 3.976358 0.74360 . . ENSG00000047056 ENST00000358220;ENST00000263150 T;T 0.01265 5.08;5.08 5.95 4.98 0.66077 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.000000 0.85682 D 0.000000 T 0.10981 0.0268 M 0.92604 3.325 0.80722 D 1 D;D 0.63046 0.992;0.992 P;D 0.65987 0.9;0.94 T 0.00033 -1.2272 10 0.72032 D 0.01 . 13.835 0.63404 0.2572:0.7428:0.0:0.0 . 272;271 A8K976;Q9Y2I8 .;WDR37_HUMAN S 271 ENSP00000350954:R271S;ENSP00000263150:R271S ENSP00000263150:R271S R + 1 0 WDR37 1139626 1.000000 0.71417 0.536000 0.28039 0.675000 0.39556 2.057000 0.41365 2.811000 0.96726 0.655000 0.94253 CGC TCGA-2J-AAB1-01A-11D-A40W-08 WDR37-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046418.1 1 0 1 52 246 0 47 1 6.913251e-01 2 11 0 47 2 0 0 0 0 0 2 1 1.000000 52 243 0 46 2 -2.733687 1 1 0 0 1 0 1 1 2.022886 0 0.380000 1.940000 0.378820 0.910000 7.000000e-01 1.000000 1.000000 0.904915 0.910000 1 0.800000 1.000000 NEBL 10529 broad.mit.edu 37 10 21098813 21098813 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr10:21098813G>A ENST00000377122.4 - 25 2929 c.2533C>T c.(2533-2535)Cgc>Tgc p.R845C NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron NM_006393.2 NP_006384.1 O76041 NEBL_HUMAN nebulette p.R845C(1) 70 GGATCTGTGCGCCAAACTTTG 0.383000 1 Substitution - Missense(1) SO:0001583 missense ENST00000377122.4 1 1 hg19 CCDS7134.1 . . . . . . . . . . G 25.7 4.664498 0.88251 . . ENSG00000078114 ENST00000377122 T 0.09538 2.97 6.05 6.05 0.98169 . 0.000000 0.85682 D 0.000000 T 0.30759 0.0775 L 0.55990 1.75 0.80722 D 1 D 0.89917 1.0 D 0.66351 0.943 T 0.00069 -1.2136 10 0.62326 D 0.03 . 20.6087 0.99469 0.0:0.0:1.0:0.0 . 845 O76041 NEBL_HUMAN C 845 ENSP00000366326:R845C ENSP00000366326:R845C R - 1 0 NEBL 21138819 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 4.001000 0.57046 2.866000 0.98385 0.650000 0.86243 CGC TCGA-2J-AAB1-01A-11D-A40W-08 NEBL-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000047113.1 1 0 1 68 220 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 67 215 0 42 2 -4.142076 1 1 121412 5 36 1 0 1 1 2.022886 0 0.380000 1.940000 0.378820 0.990000 9.900000e-01 1.000000 1.000000 0.998819 0.990000 1 0.990000 1.000000 FDX1 2230 broad.mit.edu 37 11 110327723 110327723 + Missense_Mutation SNP C C A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr11:110327723C>A ENST00000260270.2 + 3 630 c.392C>A c.(391-393)aCt>aAt p.T131N NM_004109.4 NP_004100.1 P10109 ADX_HUMAN ferredoxin 1 2 all_cancers(61;1.59e-12)|all_epithelial(67;8.38e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544) Mitotane(DB00648) GATGCAATCACTGATGAGGAG 0.403000 0 SO:0001583 missense ENST00000260270.2 0 1 hg19 CCDS8344.1 . . . . . . . . . . C 21.9 4.222520 0.79464 . . ENSG00000137714 ENST00000260270 . . . 5.46 4.55 0.56014 Beta-grasp fold, ferredoxin-type (1);Ferredoxin (3); 0.049070 0.85682 D 0.000000 T 0.66886 0.2835 L 0.52759 1.655 0.49483 D 0.999795 P 0.41366 0.747 P 0.49301 0.606 T 0.66284 -0.5962 9 0.39692 T 0.17 -2.2088 16.052 0.80772 0.0:0.8654:0.1346:0.0 . 131 P10109 ADX_HUMAN N 131 . ENSP00000260270:T131N T + 2 0 FDX1 109832933 1.000000 0.71417 0.999000 0.59377 0.837000 0.47467 4.678000 0.61641 1.304000 0.44892 0.561000 0.74099 ACT TCGA-2J-AAB1-01A-11D-A40W-08 FDX1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390590.1 0 0 0 12 691 0 109 1 4.030271e-01 4 72 0 109 2 0 0 0 0 0 2 1 0.999014 12 678 0 107 2 -3.231405 1 1 0 0 1 1 2 3 2.042490 0 0.380000 1.940000 0.382347 0.090000 4.000000e-02 0.170000 0.090000 0.106037 0.090000 0 0.060000 0.130000 UBASH3B 84959 broad.mit.edu 37 11 122659916 122659916 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr11:122659916G>A ENST00000284273.5 + 6 1255 c.880G>A c.(880-882)Ggt>Agt p.G294S NM_032873.4 NP_116262.2 Q8TF42 UBS3B_HUMAN ubiquitin associated and SH3 domain containing B 26 Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104) CACCAGCGAGGGTTGGATCTA 0.532000 0 SO:0001583 missense ENST00000284273.5 1 1 hg19 CCDS31694.1 . . . . . . . . . . G 36 5.789502 0.96945 . . ENSG00000154127 ENST00000284273 T 0.58797 0.31 5.86 5.86 0.93980 Src homology-3 domain (4); 0.000000 0.85682 D 0.000000 T 0.82042 0.4951 M 0.89840 3.065 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.84720 0.0739 10 0.87932 D 0 -7.8749 20.1931 0.98233 0.0:0.0:1.0:0.0 . 294 Q8TF42 UBS3B_HUMAN S 294 ENSP00000284273:G294S ENSP00000284273:G294S G + 1 0 UBASH3B 122165126 1.000000 0.71417 1.000000 0.80357 0.956000 0.61745 9.476000 0.97823 2.771000 0.95319 0.563000 0.77884 GGT TCGA-2J-AAB1-01A-11D-A40W-08 UBASH3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387499.1 1 0 1 194 820 0 176 1 4.007568e-01 2 5 0 176 2 0 0 0 0 0 2 1 1.000000 191 810 0 172 2 -20.000000 1 1 0 0 1 1 2 3 2.042490 0 0.380000 1.940000 0.382347 0.990000 8.800000e-01 1.000000 1.000000 0.979838 0.990000 1 0.940000 1.000000 UBASH3B 84959 broad.mit.edu 37 11 122667627 122667627 + Missense_Mutation SNP A A G TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr11:122667627A>G ENST00000284273.5 + 9 1618 c.1243A>G c.(1243-1245)Ata>Gta p.I415V NM_032873.4 NP_116262.2 Q8TF42 UBS3B_HUMAN ubiquitin associated and SH3 domain containing B 26 Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104) AGGCCGCTACATACGCACCAA 0.473000 0 SO:0001583 missense ENST00000284273.5 1 1 hg19 CCDS31694.1 . . . . . . . . . . A 8.583 0.882830 0.17467 . . ENSG00000154127 ENST00000284273 T 0.04917 3.53 5.94 3.61 0.41365 Histidine phosphatase superfamily, clade-1 (1); 0.337134 0.34110 N 0.004260 T 0.01835 0.0058 N 0.00677 -1.265 0.31402 N 0.676504 B 0.02656 0.0 B 0.01281 0.0 T 0.33343 -0.9872 10 0.15066 T 0.55 -1.7035 9.0924 0.36619 0.6732:0.0:0.3268:0.0 . 415 Q8TF42 UBS3B_HUMAN V 415 ENSP00000284273:I415V ENSP00000284273:I415V I + 1 0 UBASH3B 122172837 0.980000 0.34600 0.994000 0.49952 0.906000 0.53458 0.760000 0.26475 0.495000 0.27882 0.528000 0.53228 ATA TCGA-2J-AAB1-01A-11D-A40W-08 UBASH3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387499.1 1 0 0 16 288 0 74 0 1.057222e-01 0 10 0 74 2 0 0 0 0 0 2 1 0.999932 16 284 0 73 2 -18.273270 1 1 0 0 1 1 2 3 2.042490 0 0.380000 1.940000 0.382347 0.280000 1.600000e-01 0.460000 0.280000 0.298889 0.280000 0 0.210000 0.360000 OR51I2 390064 broad.mit.edu 37 11 5475025 5475025 + Missense_Mutation SNP C C A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr11:5475025C>A ENST00000341449.2 + 1 388 c.307C>A c.(307-309)Ctt>Att p.L103I HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron NM_001004754.2 NP_001004754.1 Q9H344 O51I2_HUMAN olfactory receptor, family 51, subfamily I, member 2 29 Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675) TCAGATGTTTCTTATTCACTT 0.483000 0 SO:0001583 missense ENST00000341449.2 1 1 hg19 CCDS31383.1 . . . . . . . . . . C 14.77 2.634332 0.47049 . . ENSG00000187918 ENST00000341449 T 0.40756 1.02 5.57 0.255 0.15561 GPCR, rhodopsin-like superfamily (1); 0.460534 0.20519 N 0.090739 T 0.22975 0.0555 L 0.28344 0.845 0.25272 N 0.989505 P 0.39665 0.682 B 0.31390 0.129 T 0.13202 -1.0518 10 0.87932 D 0 . 7.8771 0.29599 0.0:0.4244:0.0:0.5756 . 103 Q9H344 O51I2_HUMAN I 103 ENSP00000341987:L103I ENSP00000341987:L103I L + 1 0 OR51I2 5431601 0.000000 0.05858 0.991000 0.47740 0.981000 0.71138 -0.078000 0.11375 0.162000 0.19483 0.650000 0.86243 CTT TCGA-2J-AAB1-01A-11D-A40W-08 OR51I2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000143385.1 1 0 1 95 425 0 100 0 0 0 0 100 2 0 0 0 0 0 2 1 1.000000 93 422 0 100 2 -20.000000 1 1 0 0 1 1 2 3 2.042490 0 0.380000 1.940000 0.382347 0.960000 7.900000e-01 1.000000 1.000000 0.946672 0.960000 1 0.870000 1.000000 OR51I2 390064 broad.mit.edu 37 11 5475027 5475027 + Silent SNP T T A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr11:5475027T>A ENST00000341449.2 + 1 390 c.309T>A c.(307-309)ctT>ctA p.L103L HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron NM_001004754.2 NP_001004754.1 Q9H344 O51I2_HUMAN olfactory receptor, family 51, subfamily I, member 2 29 Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675) AGATGTTTCTTATTCACTTCT 0.483000 0 SO:0001819 synonymous_variant ENST00000341449.2 1 1 hg19 CCDS31383.1 TCGA-2J-AAB1-01A-11D-A40W-08 OR51I2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000143385.1 1 0 1 92 431 0 101 0 0 0 0 101 2 0 0 0 0 0 2 1 1.000000 91 428 0 101 2 -20.000000 1 1 0 0 1 1 2 3 2.042490 0 0.380000 1.940000 0.382347 0.920000 7.600000e-01 1.000000 1.000000 0.921979 0.920000 1 0.840000 1.000000 OR8J3 81168 broad.mit.edu 37 11 55905125 55905125 + Missense_Mutation SNP G G T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr11:55905125G>T ENST00000301529.1 - 1 69 c.70C>A c.(70-72)Cag>Aag p.Q24K NM_001004064.1 NP_001004064.1 Q8NGG0 OR8J3_HUMAN olfactory receptor, family 8, subfamily J, member 3 59 Esophageal squamous(21;0.00693) AGGGGAATCTGGAGCTCTGGA 0.488000 0 SO:0001583 missense ENST00000301529.1 1 1 hg19 CCDS31520.1 . . . . . . . . . . G 15.62 2.887120 0.52014 . . ENSG00000167822 ENST00000301529 T 0.00591 6.35 3.26 3.26 0.37387 . 0.000000 0.64402 D 0.000017 T 0.00998 0.0033 L 0.51422 1.61 0.21782 N 0.999543 P 0.47350 0.894 P 0.49853 0.624 T 0.51834 -0.8655 10 0.48119 T 0.1 . 8.7991 0.34898 0.0:0.1604:0.6748:0.1647 . 24 Q8NGG0 OR8J3_HUMAN K 24 ENSP00000301529:Q24K ENSP00000301529:Q24K Q - 1 0 OR8J3 55661701 0.879000 0.30193 0.274000 0.24659 0.245000 0.25701 1.766000 0.38491 1.548000 0.49413 0.289000 0.19496 CAG TCGA-2J-AAB1-01A-11D-A40W-08 OR8J3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391542.1 1 0 1 110 441 0 104 0 0 0 0 104 2 0 0 0 0 0 2 1 1.000000 109 430 0 104 2 -3.384226 1 1 0 0 1 1 2 3 2.042490 0 0.380000 1.940000 0.382347 0.990000 8.800000e-01 1.000000 1.000000 0.986273 0.990000 1 0.960000 1.000000 DNAJC4 3338 broad.mit.edu 37 11 63999972 63999972 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr11:63999972G>A ENST00000321685.3 + 4 716 c.251G>A c.(250-252)cGt>cAt p.R84H RP11-783K16.14_ENST00000539963.1_RNA|VEGFB_ENST00000309422.2_5'Flank|VEGFB_ENST00000426086.2_5'Flank|DNAJC4_ENST00000355040.4_Intron|RP11-783K16.14_ENST00000534988.1_RNA|DNAJC4_ENST00000321460.5_Missense_Mutation_p.R84H NM_005528.3 NP_005519.2 Q9NNZ3 DNJC4_HUMAN DnaJ (Hsp40) homolog, subfamily C, member 4 3 GAGGCATACCGTGTGCTCAGC 0.632000 0 SO:0001583 missense ENST00000321685.3 1 1 hg19 CCDS41666.1 . . . . . . . . . . G 11.20 1.569823 0.28003 . . ENSG00000110011 ENST00000321685;ENST00000321460 T;T 0.29917 1.55;1.55 4.04 -6.62 0.01813 Heat shock protein DnaJ, N-terminal (5); 0.346876 0.25135 N 0.032869 T 0.14614 0.0353 N 0.25890 0.77 0.25398 N 0.98846 P;B 0.38565 0.637;0.029 B;B 0.25506 0.061;0.011 T 0.02220 -1.1193 10 0.59425 D 0.04 -0.004 15.2131 0.73241 0.2268:0.0:0.7732:0.0 . 84;84 Q6PIN0;Q9NNZ3 .;DNJC4_HUMAN H 84 ENSP00000396896:R84H;ENSP00000320548:R84H ENSP00000320548:R84H R + 2 0 DNAJC4 63756548 0.063000 0.20901 0.002000 0.10522 0.787000 0.44495 0.222000 0.17699 -1.482000 0.01860 -0.448000 0.05591 CGT TCGA-2J-AAB1-01A-11D-A40W-08 DNAJC4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396305.1 1 0 0 7 182 0 35 1 9.383940e-01 7 124 0 35 2 0 0 0 0 0 2 1 0.980095 7 179 0 35 2 -9.110572 1 1 121126 1 26 1 1 2 3 2.042490 0 0.380000 1.940000 0.382347 0.200000 9.000000e-02 0.410000 0.200000 0.227048 0.200000 0 0.140000 0.300000 TMEM116 89894 broad.mit.edu 37 12 112374530 112374530 + Missense_Mutation SNP A A T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr12:112374530A>T ENST00000550831.3 - 7 646 c.278T>A c.(277-279)cTg>cAg p.L93Q TMEM116_ENST00000552374.2_Missense_Mutation_p.L185Q|TMEM116_ENST00000354825.3_Missense_Mutation_p.L93Q|TMEM116_ENST00000437003.2_Missense_Mutation_p.L93Q|TMEM116_ENST00000549537.2_Intron|TMEM116_ENST00000355445.3_Missense_Mutation_p.L150Q NM_138341.2 NP_612350.1 Q8NCL8 TM116_HUMAN transmembrane protein 116 8 AAAGCTGCCCAGGAAAATGGC 0.478000 0 SO:0001583 missense ENST00000550831.3 1 1 hg19 CCDS9157.1 . . . . . . . . . . a 19.40 3.819870 0.71028 . . ENSG00000198270 ENST00000355445;ENST00000354825;ENST00000550831;ENST00000437003;ENST00000552374 T;T;T;T;T 0.41758 0.99;0.99;0.99;0.99;0.99 5.12 5.12 0.69794 . 0.000000 0.64402 D 0.000014 T 0.58921 0.2156 L 0.59436 1.845 0.40890 D 0.98406 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.91635 0.999;0.999;0.999 T 0.63501 -0.6623 10 0.87932 D 0 -6.5126 11.3186 0.49407 1.0:0.0:0.0:0.0 . 150;185;93 G5E985;G3V1W7;Q8NCL8 .;.;TM116_HUMAN Q 150;93;93;93;185 ENSP00000347620:L150Q;ENSP00000346883:L93Q;ENSP00000450377:L93Q;ENSP00000395861:L93Q;ENSP00000447731:L185Q ENSP00000346883:L93Q L - 2 0 TMEM116 110858913 1.000000 0.71417 1.000000 0.80357 0.795000 0.44927 4.791000 0.62460 1.939000 0.56221 0.383000 0.25322 CTG TCGA-2J-AAB1-01A-11D-A40W-08 TMEM116-005 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000405026.3 1 0 1 52 228 0 43 1 7.611682e-01 6 8 0 43 2 0 0 0 0 0 2 1 1.000000 51 224 0 42 2 -20.000000 1 1 0 0 1 0 0 0 1.993904 0 0.380000 1.940000 0.370431 0.950000 7.300000e-01 1.000000 1.000000 0.934309 0.950000 1 0.840000 1.000000 TPCN1 53373 broad.mit.edu 37 12 113711435 113711435 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr12:113711435G>A ENST00000335509.6 + 10 1218 c.904G>A c.(904-906)Gtg>Atg p.V302M TPCN1_ENST00000550785.1_Missense_Mutation_p.V374M|TPCN1_ENST00000541517.1_Missense_Mutation_p.V374M|TPCN1_ENST00000392569.4_Missense_Mutation_p.V234M NM_017901.4 NP_060371.2 Q9ULQ1 TPC1_HUMAN two pore segment channel 1 40 CTTCTTCATCGTGTACCTCTC 0.557000 0 SO:0001583 missense ENST00000335509.6 1 1 hg19 CCDS31908.1 . . . . . . . . . . G 24.5 4.538199 0.85917 . . ENSG00000186815 ENST00000335509;ENST00000550785;ENST00000541517;ENST00000392569 D;D;D;D 0.98701 -5.08;-5.08;-5.08;-5.08 5.64 5.64 0.86602 Ion transport (1); 0.000000 0.85682 D 0.000000 D 0.98576 0.9524 L 0.60845 1.875 0.47214 D 0.999354 D;D;D 0.76494 0.999;0.999;0.998 D;D;P 0.66847 0.947;0.919;0.848 D 0.98287 1.0511 10 0.48119 T 0.1 -26.0173 12.9637 0.58472 0.0742:0.0:0.9258:0.0 . 302;374;302 A5PKY2;Q9ULQ1-3;Q9ULQ1 .;.;TPC1_HUMAN M 302;374;374;234 ENSP00000335300:V302M;ENSP00000448083:V374M;ENSP00000438125:V374M;ENSP00000376350:V234M ENSP00000335300:V302M V + 1 0 TPCN1 112195818 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 7.600000 0.82769 2.656000 0.90262 0.655000 0.94253 GTG TCGA-2J-AAB1-01A-11D-A40W-08 TPCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405156.3 1 0 1 117 609 0 147 1 9.973635e-01 6 42 0 147 2 0 0 0 0 0 2 1 1.000000 115 597 0 143 2 -20.000000 1 1 0 0 1 0 0 0 1.993904 0 0.380000 1.940000 0.370431 0.830000 6.900000e-01 0.970000 0.830000 0.837777 0.830000 0 0.760000 0.910000 RSRC2 65117 broad.mit.edu 37 12 123005948 123005948 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr12:123005948C>T ENST00000331738.7 - 3 336 c.191G>A c.(190-192)cGg>cAg p.R64Q RSRC2_ENST00000354654.2_Missense_Mutation_p.G9R NM_023012.5 NP_075388.2 Q7L4I2 RSRC2_HUMAN arginine/serine-rich coiled-coil 2 24 all_neural(191;0.0837)|Medulloblastoma(191;0.163) GCTTCTGCTCCGGCTCCTGTG 0.308000 0 SO:0001583 missense ENST00000331738.7 0 1 hg19 CCDS31920.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 14.99|14.99 2.700233|2.700233 0.48307|0.48307 .|. .|. ENSG00000111011|ENSG00000111011 ENST00000354654;ENST00000528279|ENST00000331738;ENST00000418773 T|T 0.46063|0.20332 0.88|2.08 5.44|5.44 5.44|5.44 0.79542|0.79542 .|. .|0.220291 .|0.47852 .|D .|0.000206 T|T 0.16599|0.16599 0.0399|0.0399 N|N 0.19112|0.19112 0.55|0.55 0.26343|0.26343 N|N 0.977338|0.977338 P|D;D 0.41673|0.56521 0.759|0.976;0.976 B|B;B 0.30495|0.40825 0.116|0.341;0.341 T|T 0.07520|0.07520 -1.0768|-1.0768 9|10 0.41790|0.39692 T|T 0.15|0.17 .|. 19.2639|19.2639 0.93979|0.93979 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 9|64;64 Q7L4I2-2|F5GXM2;Q7L4I2 .|.;RSRC2_HUMAN R|Q 9|64 ENSP00000346678:G9R|ENSP00000330188:R64Q ENSP00000346678:G9R|ENSP00000330188:R64Q G|R -|- 1|2 0|0 RSRC2|RSRC2 121571901|121571901 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.998000|0.998000 0.95712|0.95712 5.313000|5.313000 0.65798|0.65798 2.541000|2.541000 0.85698|0.85698 0.555000|0.555000 0.69702|0.69702 GGA|CGG TCGA-2J-AAB1-01A-11D-A40W-08 RSRC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000395096.3 0 0 0 4 254 0 52 0 7.612298e-01 1 169 0 52 2 0 0 0 0 0 2 1 0.886451 4 249 0 50 2 -2.796904 1 1 121398 1 38 1 0 0 0 1.993904 0 0.380000 1.940000 0.370431 0.080000 2.000000e-02 0.190000 0.080000 0.099011 0.080000 0 0.050000 0.140000 NOC4L 79050 broad.mit.edu 37 12 132635870 132635870 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr12:132635870C>T ENST00000330579.1 + 11 1071 c.1030C>T c.(1030-1032)Cgc>Tgc p.R344C NOC4L_ENST00000535343.1_3'UTR|NOC4L_ENST00000538784.1_5'UTR NM_024078.1 NP_076983.1 Q9BVI4 NOC4L_HUMAN nucleolar complex associated 4 homolog (S. cerevisiae) 14 all_neural(191;0.0982)|Medulloblastoma(191;0.163) CGTCAAGTACCGCGCCCGCTT 0.652000 0 SO:0001583 missense ENST00000330579.1 1 1 hg19 CCDS9277.1 . . . . . . . . . . C 15.18 2.755773 0.49362 . . ENSG00000184967 ENST00000330579 T 0.65178 -0.14 5.2 4.3 0.51218 CCAAT-binding factor (1); 0.000000 0.85682 D 0.000000 D 0.83908 0.5356 M 0.93978 3.48 0.80722 D 1 D 0.89917 1.0 D 0.83275 0.996 D 0.88477 0.3066 10 0.87932 D 0 -22.5329 15.3287 0.74190 0.0:0.8591:0.1409:0.0 . 344 Q9BVI4 NOC4L_HUMAN C 344 ENSP00000328854:R344C ENSP00000328854:R344C R + 1 0 NOC4L 131201823 1.000000 0.71417 0.489000 0.27452 0.056000 0.15407 2.615000 0.46368 1.165000 0.42670 0.561000 0.74099 CGC TCGA-2J-AAB1-01A-11D-A40W-08 NOC4L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398999.1 0 0 1 101 486 0 135 1 9.999963e-01 26 61 0 135 2 0 0 0 0 0 2 1 1.000000 99 477 1 129 16 -2.827600 1 1 121290 9 44 1 0 0 0 1.993904 0 0.380000 1.940000 0.370431 0.880000 7.300000e-01 1.000000 1.000000 0.890903 0.880000 1 0.800000 0.970000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 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-2J-AAB1-01A-11D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 8 199 0 53 0 1.537874e-01 1 15 0 53 2 1 9.993325e-01 11 354 0 365 2 1 0.989787 8 199 0 51 2 -4.074507 1 1 121404 2 44 1 0 0 0 1.993904 0 0.380000 1.940000 0.370431 0.200000 9.000000e-02 0.370000 0.200000 0.221373 0.200000 0 0.140000 0.290000 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 C G C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr12:25398285C>G ENST00000256078.4 - 2 97 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) CCTACGCCACCAGCTCCAACT 0.348000 G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 5144 Substitution - Missense(5142)|Insertion - In frame(2) GRCh37 CM076251 KRAS M rs121913530 SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 28.6 4.930538 0.92389 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78246 -1.16;-1.16;-1.16;-1.16 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.84893 0.5573 M 0.84082 2.675 0.80722 D 1 P;P 0.43287 0.802;0.741 B;P 0.47941 0.36;0.562 D 0.86658 0.1902 10 0.66056 D 0.02 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN R 12 ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R ENSP00000256078:G12R G - 1 0 KRAS 25289552 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-2J-AAB1-01A-11D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 26 181 0 55 1 6.511692e-01 10 7 0 55 2 1 1 47 316 0 364 2 1 1.000000 26 181 0 53 2 -12.853510 1 1 0 0 1 0 0 0 1.993904 0 0.380000 1.940000 0.370431 0.650000 4.400000e-01 0.890000 0.640000 0.663868 0.650000 0 0.540000 0.780000 ARNTL2 56938 broad.mit.edu 37 12 27533278 27533278 + Missense_Mutation SNP G G A rs149871988 TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr12:27533278G>A ENST00000266503.5 + 5 443 c.425G>A c.(424-426)cGt>cAt p.R142H ARNTL2_ENST00000261178.5_Missense_Mutation_p.R94H|ARNTL2_ENST00000395901.2_Missense_Mutation_p.R105H|ARNTL2_ENST00000542388.1_Missense_Mutation_p.R57H|ARNTL2_ENST00000311001.5_Missense_Mutation_p.R128H|ARNTL2_ENST00000544915.1_Missense_Mutation_p.R108H|ARNTL2_ENST00000546179.1_Missense_Mutation_p.R105H Q8WYA1 BMAL2_HUMAN aryl hydrocarbon receptor nuclear translocator-like 2 21 Colorectal(261;0.0847)|Lung SC(9;0.184) CCCATGGCGCGTAAACTGGAC 0.418000 0 SO:0001583 missense ENST00000266503.5 0 1 hg19 CCDS8712.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 15.36|15.36 2.809399|2.809399 0.50421|0.50421 0.0|0.0 1.16E-4|1.16E-4 ENSG00000029153|ENSG00000029153 ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000542388|ENST00000457040 D;D;D;D;D;D;D|. 0.98044|. -4.68;-4.68;-4.68;-4.68;-4.68;-4.68;-4.68|. 3.33|3.33 2.41|2.41 0.29592|0.29592 Helix-loop-helix DNA-binding (5);|. 0.166448|. 0.41294|. N|. 0.000915|. T|T 0.52933|0.52933 0.1765|0.1765 L|L 0.43701|0.43701 1.375|1.375 0.45962|0.45962 D|D 0.998786|0.998786 P;P;P;P;P;P|. 0.46578|. 0.507;0.708;0.647;0.647;0.501;0.88|. B;B;B;B;B;P|. 0.44696|. 0.169;0.329;0.233;0.233;0.109;0.458|. T|T 0.42932|0.42932 -0.9422|-0.9422 10|5 0.54805|. T|. 0.06|. .|. 8.1033|8.1033 0.30870|0.30870 0.1179:0.0:0.8821:0.0|0.1179:0.0:0.8821:0.0 .|. 105;108;105;94;128;142|. F5H402;Q8WYA1-5;Q8WYA1-3;Q8WYA1-4;Q8WYA1-2;Q8WYA1|. .;.;.;.;.;BMAL2_HUMAN|. H|I 108;105;105;128;94;142;57|94 ENSP00000442438:R108H;ENSP00000379238:R105H;ENSP00000438545:R105H;ENSP00000312247:R128H;ENSP00000261178:R94H;ENSP00000266503:R142H;ENSP00000445836:R57H|. ENSP00000261178:R94H|. R|V +|+ 2|1 0|0 ARNTL2|ARNTL2 27424545|27424545 0.987000|0.987000 0.35691|0.35691 0.059000|0.059000 0.19551|0.19551 0.969000|0.969000 0.65631|0.65631 6.556000|6.556000 0.73932|0.73932 0.728000|0.728000 0.32382|0.32382 0.655000|0.655000 0.94253|0.94253 CGT|GTA TCGA-2J-AAB1-01A-11D-A40W-08 ARNTL2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000403162.1 0 0 0 5 450 0 86 0 2.298764e-02 0 17 0 86 2 0 0 0 0 0 2 1 0.932983 5 437 0 84 2 -2.520841 1 1 121412 4 39 1 0 0 0 1.993904 0 0.380000 1.940000 0.370431 0.050000 1.000000e-02 0.130000 0.060000 0.067790 0.050000 0 0.030000 0.090000 SLC6A15 55117 broad.mit.edu 37 12 85255590 85255590 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr12:85255590C>T ENST00000266682.5 - 12 2555 c.2014G>A c.(2014-2016)Gat>Aat p.D672N SLC6A15_ENST00000309283.7_3'UTR|SLC6A15_ENST00000552192.1_Missense_Mutation_p.D565N NM_182767.5 NP_877499.1 Q9H2J7 S6A15_HUMAN solute carrier family 6 (neutral amino acid transporter), member 15 44 CTTGTATCATCGCCCTCTAAG 0.423000 0 SO:0001583 missense ENST00000266682.5 1 1 hg19 CCDS9026.1 . . . . . . . . . . C 26.0 4.699502 0.88830 . . ENSG00000072041 ENST00000266682;ENST00000552192;ENST00000548267 T;T 0.77620 -0.93;-1.11 5.85 5.85 0.93711 . 0.182364 0.64402 D 0.000018 D 0.86581 0.5967 L 0.54323 1.7 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.85436 0.1152 10 0.49607 T 0.09 . 20.1649 0.98147 0.0:1.0:0.0:0.0 . 672 Q9H2J7 S6A15_HUMAN N 672;565;150 ENSP00000266682:D672N;ENSP00000450145:D565N ENSP00000266682:D672N D - 1 0 SLC6A15 83779721 1.000000 0.71417 1.000000 0.80357 0.915000 0.54546 5.665000 0.68052 2.753000 0.94483 0.655000 0.94253 GAT TCGA-2J-AAB1-01A-11D-A40W-08 SLC6A15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405678.1 1 0 1 126 511 0 142 0 0 0 0 142 2 0 0 0 0 0 2 1 1.000000 125 506 0 135 2 -20.000000 1 1 0 0 1 0 0 0 1.993904 0 0.380000 1.940000 0.370431 0.990000 8.600000e-01 1.000000 1.000000 0.979447 0.990000 1 0.940000 1.000000 USP44 84101 broad.mit.edu 37 12 95922666 95922666 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr12:95922666G>A ENST00000258499.3 - 3 1829 c.1541C>T c.(1540-1542)cCa>cTa p.P514L USP44_ENST00000552440.1_Intron|USP44_ENST00000537435.2_Missense_Mutation_p.P514L|USP44_ENST00000393091.2_Missense_Mutation_p.P514L NM_001278393.1|NM_032147.2 NP_001265322.1|NP_115523.2 Q9H0E7 UBP44_HUMAN ubiquitin specific peptidase 44 36 AACCAGACATGGCTGGGAAGC 0.393000 0 SO:0001583 missense ENST00000258499.3 1 1 hg19 CCDS9053.1 . . . . . . . . . . G 19.23 3.787659 0.70337 . . ENSG00000136014 ENST00000258499;ENST00000393091;ENST00000537435 T;T;T 0.02631 4.22;4.22;4.22 5.94 5.94 0.96194 Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2); 0.049563 0.85682 D 0.000000 T 0.06050 0.0157 L 0.31371 0.925 0.58432 D 0.999998 P 0.37731 0.607 P 0.45913 0.497 T 0.52845 -0.8521 10 0.35671 T 0.21 . 20.3632 0.98871 0.0:0.0:1.0:0.0 . 514 Q9H0E7 UBP44_HUMAN L 514 ENSP00000258499:P514L;ENSP00000376806:P514L;ENSP00000442629:P514L ENSP00000258499:P514L P - 2 0 USP44 94446797 1.000000 0.71417 1.000000 0.80357 0.863000 0.49368 6.662000 0.74426 2.826000 0.97356 0.561000 0.74099 CCA TCGA-2J-AAB1-01A-11D-A40W-08 USP44-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408312.1 1 0 1 50 247 0 57 0 1.385372e-01 0 4 0 57 2 0 0 0 0 0 2 1 1.000000 50 244 0 57 2 -20.000000 1 0 0 0 1 0 0 0 1.993904 0 0.380000 1.940000 0.370431 0.860000 6.600000e-01 1.000000 1.000000 0.870168 0.860000 1 0.760000 0.990000 LRCH1 23143 broad.mit.edu 37 13 47266683 47266683 + Missense_Mutation SNP G G T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr13:47266683G>T ENST00000389798.3 + 8 1224 c.1027G>T c.(1027-1029)Gac>Tac p.D343Y LRCH1_ENST00000311191.6_Missense_Mutation_p.D343Y|LRCH1_ENST00000389797.3_Missense_Mutation_p.D343Y NM_015116.2 NP_055931 Q9Y2L9 LRCH1_HUMAN leucine-rich repeats and calponin homology (CH) domain containing 1 26 all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556) KIRC - Kidney renal clear cell carcinoma(16;0.234) TTCTGACGAAGACACTGTTAG 0.418000 0 SO:0001583 missense ENST00000389798.3 1 1 hg19 CCDS31972.1 . . . . . . . . . . G 19.73 3.882904 0.72410 . . ENSG00000136141 ENST00000311191;ENST00000389798;ENST00000389797;ENST00000463929 T;T;T 0.59906 0.35;0.39;0.23 5.83 5.83 0.93111 . 0.000000 0.85682 D 0.000000 T 0.77928 0.4204 M 0.82630 2.6 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.999;0.994;0.999;0.999 T 0.73448 -0.3979 10 0.21540 T 0.41 -24.1686 19.122 0.93367 0.0:0.0:1.0:0.0 . 343;343;343;343 Q17R43;Q9Y2L9-2;F8W6F0;Q9Y2L9 .;.;.;LRCH1_HUMAN Y 343;343;343;89 ENSP00000308493:D343Y;ENSP00000374448:D343Y;ENSP00000374447:D343Y ENSP00000308493:D343Y D + 1 0 LRCH1 46164684 1.000000 0.71417 1.000000 0.80357 0.640000 0.38277 7.924000 0.87555 2.770000 0.95276 0.655000 0.94253 GAC TCGA-2J-AAB1-01A-11D-A40W-08 LRCH1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000044824.2 1 0 1 113 468 0 90 1 9.994734e-01 14 34 0 90 2 0 0 0 0 0 2 1 1.000000 112 467 0 89 2 -20.000000 1 1 0 0 1 0 0 0 2.015661 0 0.380000 1.940000 0.377635 0.990000 8.500000e-01 1.000000 1.000000 0.975856 0.990000 1 0.930000 1.000000 PCDH9 5101 broad.mit.edu 37 13 66878827 66878827 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr13:66878827G>A ENST00000377865.2 - 4 3808 c.3674C>T c.(3673-3675)gCa>gTa p.A1225V PCDH9-AS1_ENST00000430861.1_RNA|PCDH9_ENST00000328454.5_Missense_Mutation_p.A1191V|PCDH9_ENST00000456367.1_Missense_Mutation_p.A1191V|PCDH9_ENST00000544246.1_Missense_Mutation_p.A1225V Q9HC56 PCDH9_HUMAN protocadherin 9 p.A1225E(1) 103 Hepatocellular(98;0.0906)|Breast(118;0.107) AGCACCTCCTGCTTGCTTATA 0.438000 1 Substitution - Missense(1) SO:0001583 missense ENST00000377865.2 1 1 hg19 CCDS9444.1 . . . . . . . . . . G 15.84 2.950604 0.53186 . . ENSG00000184226 ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454 T;T;T;T 0.57907 0.47;0.47;0.37;0.37 6.05 5.2 0.72013 . 0.461993 0.18412 N 0.142037 T 0.38374 0.1038 N 0.19112 0.55 0.32371 N 0.555834 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.04013 0.001;0.001;0.001 T 0.46803 -0.9165 10 0.56958 D 0.05 . 11.2657 0.49110 0.1389:0.0:0.8611:0.0 . 1183;1191;1225 B7ZM79;Q9HC56-2;Q9HC56 .;.;PCDH9_HUMAN V 1225;1225;1191;1191 ENSP00000442186:A1225V;ENSP00000367096:A1225V;ENSP00000401699:A1191V;ENSP00000332060:A1191V ENSP00000332060:A1191V A - 2 0 PCDH9 65776828 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 3.884000 0.56175 1.561000 0.49584 0.650000 0.86243 GCA TCGA-2J-AAB1-01A-11D-A40W-08 PCDH9-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000276387.1 1 0 1 59 221 0 56 0 1.175597e-01 0 3 0 56 2 0 0 0 0 0 2 1 1.000000 59 218 0 56 2 -20.000000 1 1 0 0 1 0 0 0 2.015661 0 0.380000 1.940000 0.377635 0.990000 8.600000e-01 1.000000 1.000000 0.987129 0.990000 1 0.970000 1.000000 KLHL1 57626 broad.mit.edu 37 13 70535555 70535555 + Silent SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr13:70535555G>A ENST00000377844.4 - 3 1461 c.702C>T c.(700-702)tcC>tcT p.S234S KLHL1_ENST00000545028.1_Silent_p.S41S NM_020866.2 NP_065917.1 Q9NR64 KLHL1_HUMAN kelch-like family member 1 p.S234S(1) 84 Breast(118;0.000162) CAAAATAGTCGGAGACTGAAC 0.453000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000377844.4 1 1 hg19 CCDS9445.1 TCGA-2J-AAB1-01A-11D-A40W-08 KLHL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045231.3 1 0 1 29 204 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 1.000000 29 200 0 48 2 -2.691054 1 1 121388 2 38 1 0 0 0 2.015661 0 0.380000 1.940000 0.377635 0.650000 4.500000e-01 0.880000 0.640000 0.664462 0.650000 0 0.540000 0.770000 DIO3 1735 broad.mit.edu 37 14 102028329 102028329 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr14:102028329G>A ENST00000510508.4 + 1 642 c.496G>A c.(496-498)Ggc>Agc p.G166S DIO3_ENST00000359323.3_Missense_Mutation_p.G140S|DIO3OS_ENST00000408206.1_lincRNA P55073 IOD3_HUMAN deiodinase, iodothyronine, type III 22 all_neural(303;0.185) TCTCAATTTCGGCAGCTGCAC 0.627000 0 SO:0001583 missense ENST00000510508.4 1 1 hg19 CCDS41992.2 . . . . . . . . . . G 29.7 5.030514 0.93575 . . ENSG00000197406;ENSG00000258865 ENST00000359323;ENST00000510508 T;T 0.57907 0.37;0.37 3.51 3.51 0.40186 Thioredoxin-like fold (1); 0.000000 0.47852 U 0.000217 T 0.75184 0.3815 M 0.91510 3.215 0.46927 D 0.999255 D 0.89917 1.0 D 0.64877 0.93 T 0.82051 -0.0649 10 0.59425 D 0.04 -16.4547 14.2065 0.65737 0.0:0.0:1.0:0.0 . 140 P55073 IOD3_HUMAN S 140;166 ENSP00000352273:G140S;ENSP00000427336:G166S ENSP00000352273:G166S G + 1 0 DIO3;AL049836.1 101098082 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 9.515000 0.98015 1.799000 0.52666 0.462000 0.41574 GGC TCGA-2J-AAB1-01A-11D-A40W-08 DIO3-001 KNOWN upstream_ATG|basic|appris_principal|CCDS|seleno protein_coding protein_coding OTTHUMT00000361712.4 0 0 0 13 238 0 54 0 3.817580e-01 0 24 0 54 2 0 0 0 0 0 2 1 0.999525 13 234 0 52 2 -3.328041 1 1 0 0 1 0 0 0 2.012091 0 0.380000 1.940000 0.377635 0.270000 1.500000e-01 0.440000 0.270000 0.288239 0.270000 0 0.200000 0.360000 OR4M1 441670 broad.mit.edu 37 14 20248817 20248817 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr14:20248817G>A ENST00000315957.4 + 1 417 c.336G>A c.(334-336)atG>atA p.M112I NM_001005500.1 NP_001005500.1 Q8NGD0 OR4M1_HUMAN olfactory receptor, family 4, subfamily M, member 1 42 all_cancers(95;0.00108) Epithelial(56;9.96e-07)|all cancers(55;2.95e-06) CTTCGGAGATGTTCTTGCTCA 0.478000 0 SO:0001583 missense ENST00000315957.4 1 1 hg19 CCDS32021.1 . . . . . . . . . . . 1.041 -0.678902 0.03378 . . ENSG00000176299 ENST00000315957 T 0.00388 7.59 4.33 4.33 0.51752 GPCR, rhodopsin-like superfamily (1); 0.000000 0.64402 D 0.000014 T 0.00210 0.0006 L 0.31207 0.915 0.27921 N 0.938258 B 0.30439 0.279 B 0.27608 0.081 T 0.41945 -0.9480 10 0.05959 T 0.93 -21.4932 14.6986 0.69139 0.0:0.0:1.0:0.0 . 112 Q8NGD0 OR4M1_HUMAN I 112 ENSP00000319654:M112I ENSP00000319654:M112I M + 3 0 OR4M1 19318657 0.000000 0.05858 1.000000 0.80357 0.945000 0.59286 -0.007000 0.12810 2.407000 0.81776 0.506000 0.49869 ATG TCGA-2J-AAB1-01A-11D-A40W-08 OR4M1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000409770.1 0 0 0 130 1897 0 354 0 0 0 0 354 2 0 0 0 0 0 2 1 1.000000 129 1880 0 346 2 -18.041860 1 1 0 0 1 1 2 3 2.350241 1 0.380000 1.940000 0.478992 0.390000 3.300000e-01 0.470000 0.390000 0.404155 0.390000 0 0.360000 0.440000 FBN1 2200 broad.mit.edu 37 15 48704920 48704920 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr15:48704920C>T ENST00000316623.5 - 65 8527 c.8072G>A c.(8071-8073)gGc>gAc p.G2691D FBN1_ENST00000561429.1_5'UTR NM_000138.4 NP_000129 P35555 FBN1_HUMAN fibrillin 1 139 all_lung(180;0.00279) TCGGCCCATGCCCATTCCAGA 0.502000 0 SO:0001583 missense ENST00000316623.5 0 1 hg19 CCDS32232.1 . . . . . . . . . . C 25.5 4.647484 0.87958 . . ENSG00000166147 ENST00000316623 D 0.81821 -1.54 5.38 5.38 0.77491 Growth factor, receptor (1); 0.000000 0.85682 D 0.000000 D 0.88599 0.6480 M 0.73598 2.24 0.80722 D 1 D 0.69078 0.997 D 0.66196 0.942 D 0.85789 0.1366 10 0.27785 T 0.31 . 18.926 0.92544 0.0:1.0:0.0:0.0 . 2691 P35555 FBN1_HUMAN D 2691 ENSP00000325527:G2691D ENSP00000325527:G2691D G - 2 0 FBN1 46492212 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.651000 0.83577 2.793000 0.96121 0.655000 0.94253 GGC TCGA-2J-AAB1-01A-11D-A40W-08 FBN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000417355.1 0 0 0 6 718 0 127 0 4.193274e-01 0 152 0 127 2 0 0 0 0 0 2 1 0.963687 6 709 0 125 2 -1.655459 0 1 0 0 1 1 2 3 2.029824 0 0.380000 1.940000 0.381176 0.040000 0 0.100000 0.040000 0.050708 0.040000 0 0.020000 0.070000 ANPEP 290 broad.mit.edu 37 15 90334315 90334315 + Silent SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr15:90334315G>A ENST00000300060.6 - 19 2851 c.2538C>T c.(2536-2538)agC>agT p.S846S NM_001150.2 NP_001141.2 P15144 AMPN_HUMAN alanyl (membrane) aminopeptidase 57 Lung NSC(78;0.0221)|all_lung(78;0.0448) BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169) Ezetimibe(DB00973)|Icatibant(DB06196) TCAGGGTGTAGCTCAGGTACC 0.532000 NSCLC(30;827 977 2459 19669 26125) 0 SO:0001819 synonymous_variant ENST00000300060.6 1 1 hg19 CCDS10356.1 TCGA-2J-AAB1-01A-11D-A40W-08 ANPEP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313425.1 0 0 0 13 366 0 80 1 9.447764e-01 2 139 0 80 2 0 0 0 0 0 2 1 0.999529 13 363 0 79 2 -3.816047 1 1 0 0 1 1 2 3 2.029824 0 0.380000 1.940000 0.381176 0.180000 9.000000e-02 0.300000 0.180000 0.192936 0.180000 0 0.130000 0.240000 CACNA1H 8912 broad.mit.edu 37 16 1256207 1256207 + Missense_Mutation SNP C C A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr16:1256207C>A ENST00000348261.5 + 12 2955 c.2707C>A c.(2707-2709)Cgc>Agc p.R903S CACNA1H_ENST00000565831.1_Missense_Mutation_p.R903S|RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000358590.4_Missense_Mutation_p.R903S NM_021098.2 NP_066921.2 O95180 CAC1H_HUMAN calcium channel, voltage-dependent, T type, alpha 1H subunit 34 Hepatocellular(780;0.00369) Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909) AGCCCTGCGGCGCCAGCTCGT 0.632000 0 SO:0001583 missense ENST00000348261.5 1 1 hg19 CCDS45375.1 . . . . . . . . . . C 19.72 3.880727 0.72294 . . ENSG00000196557 ENST00000348261;ENST00000358590 D;D 0.98474 -4.95;-4.95 3.96 3.96 0.45880 Ion transport (1); 0.127635 0.51477 N 0.000098 D 0.98632 0.9542 M 0.71920 2.185 0.35343 D 0.786673 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 D 0.99970 1.1986 10 0.87932 D 0 . 15.1886 0.73025 0.0:1.0:0.0:0.0 . 903;903 O95180-2;O95180 .;CAC1H_HUMAN S 903 ENSP00000334198:R903S;ENSP00000351401:R903S ENSP00000334198:R903S R + 1 0 CACNA1H 1196208 0.986000 0.35501 0.999000 0.59377 0.794000 0.44872 2.180000 0.42537 2.050000 0.60909 0.561000 0.74099 CGC TCGA-2J-AAB1-01A-11D-A40W-08 CACNA1H-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000421601.1 1 0 1 9 39 0 14 0 3.444169e-01 0 6 0 14 2 0 0 0 0 0 2 1 0.995741 9 39 0 14 2 -17.915760 1 1 0 0 1 1 2 3 2.023473 0 0.380000 1.940000 0.381176 0.990000 5.100000e-01 1.000000 1.000000 0.896701 0.990000 1 0.730000 1.000000 CACNA1H 8912 broad.mit.edu 37 16 1256208 1256208 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr16:1256208G>A ENST00000348261.5 + 12 2956 c.2708G>A c.(2707-2709)cGc>cAc p.R903H CACNA1H_ENST00000565831.1_Missense_Mutation_p.R903H|RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000358590.4_Missense_Mutation_p.R903H NM_021098.2 NP_066921.2 O95180 CAC1H_HUMAN calcium channel, voltage-dependent, T type, alpha 1H subunit 34 Hepatocellular(780;0.00369) Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909) GCCCTGCGGCGCCAGCTCGTG 0.632000 0 SO:0001583 missense ENST00000348261.5 1 1 hg19 CCDS45375.1 . . . . . . . . . . G 29.2 4.982149 0.93044 . . ENSG00000196557 ENST00000348261;ENST00000358590 D;D 0.98474 -4.95;-4.95 3.96 3.96 0.45880 Ion transport (1); 0.127635 0.51477 D 0.000098 D 0.98896 0.9626 M 0.85542 2.76 0.40805 D 0.98337 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 D 0.99884 1.1119 10 0.87932 D 0 . 15.1886 0.73025 0.0:0.0:1.0:0.0 . 903;903 O95180-2;O95180 .;CAC1H_HUMAN H 903 ENSP00000334198:R903H;ENSP00000351401:R903H ENSP00000334198:R903H R + 2 0 CACNA1H 1196209 1.000000 0.71417 0.993000 0.49108 0.785000 0.44390 9.153000 0.94687 2.050000 0.60909 0.561000 0.74099 CGC TCGA-2J-AAB1-01A-11D-A40W-08 CACNA1H-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000421601.1 1 0 1 9 38 0 14 0 4.285151e-01 0 7 0 14 2 0 0 0 0 0 2 1 0.995774 9 38 0 14 2 -17.943830 1 1 0 0 1 1 2 3 2.023473 0 0.380000 1.940000 0.381176 0.990000 5.200000e-01 1.000000 1.000000 0.904532 0.990000 1 0.740000 1.000000 CYLD 1540 broad.mit.edu 37 16 50827516 50827516 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr16:50827516G>A ENST00000427738.3 + 16 2615 c.2410G>A c.(2410-2412)Gac>Aac p.D804N CYLD_ENST00000398568.2_Missense_Mutation_p.D801N|CYLD_ENST00000566206.1_Missense_Mutation_p.D801N|CYLD_ENST00000568704.2_Missense_Mutation_p.D619N|RP11-327F22.4_ENST00000575917.1_RNA|CYLD_ENST00000564326.1_Missense_Mutation_p.D801N|CYLD_ENST00000540145.1_Missense_Mutation_p.D804N|RP11-327F22.4_ENST00000564510.1_RNA|CYLD_ENST00000569418.1_Missense_Mutation_p.D801N|CYLD_ENST00000311559.9_Missense_Mutation_p.D804N Q9NQC7 CYLD_HUMAN cylindromatosis (turban tumor syndrome) 62 all_cancers(37;0.0156) AGAATGCTACGACGATCCGGA 0.438000 Mis, N, F, S cylindroma cylindroma Multiple Trichoepithelioma, Familial;Familial Cylindromatosis yes Rec yes Familial cylindromatosis 16 16q12-q13 1540 familial cylindromatosis gene E 0 SO:0001583 missense Familial Cancer Database ;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s. ENST00000427738.3 0 1 hg19 CCDS45482.1 . . . . . . . . . . G 20.8 4.052407 0.75960 . . ENSG00000083799 ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568 T;T;T 0.74002 -0.8;-0.8;-0.8 5.25 5.25 0.73442 . 0.188320 0.56097 D 0.000035 T 0.62183 0.2407 N 0.14661 0.345 0.58432 D 0.999999 P;P 0.45176 0.852;0.821 B;B 0.40165 0.321;0.215 T 0.67011 -0.5778 10 0.45353 T 0.12 -19.1886 19.2041 0.93723 0.0:0.0:1.0:0.0 . 801;801 A8KAB0;Q9NQC7-2 .;. N 804;804;801;801 ENSP00000445447:D804N;ENSP00000308928:D804N;ENSP00000381574:D801N ENSP00000308928:D804N D + 1 0 CYLD 49385017 1.000000 0.71417 0.273000 0.24645 0.846000 0.48090 7.522000 0.81844 2.620000 0.88729 0.655000 0.94253 GAC TCGA-2J-AAB1-01A-11D-A40W-08 CYLD-010 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000422998.2 0 0 0 14 618 0 129 0 4.095970e-01 1 59 0 129 2 0 0 0 0 0 2 1 0.999751 14 616 0 126 2 -2.758398 1 1 0 0 1 1 2 3 2.027735 0 0.380000 1.940000 0.381176 0.110000 6.000000e-02 0.200000 0.120000 0.124440 0.110000 0 0.080000 0.160000 C16orf11 0 broad.mit.edu 37 16 615296 615296 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr16:615296G>A ENST00000409413.3 + 3 1984 c.1705G>A c.(1705-1707)Gcc>Acc p.A569T NHLRC4_ENST00000424439.2_5'Flank|NHLRC4_ENST00000540585.1_5'Flank|PIGQ_ENST00000409527.2_5'Flank NM_145270.2 NP_660313.1 P0CG20 PRR35_HUMAN 10 CCCCCAGGGCGCCGAGGTCTG 0.677000 0 SO:0001583 missense ENST00000409413.3 1 1 hg19 CCDS45365.1 . . . . . . . . . . G 13.28 2.189481 0.38707 . . ENSG00000161992 ENST00000409413 . . . 5.25 1.61 0.23674 . 1.152320 0.06446 N 0.726940 T 0.23766 0.0575 N 0.20986 0.625 0.09310 N 1 B 0.30021 0.265 B 0.20577 0.03 T 0.26573 -1.0099 9 0.87932 D 0 . 6.6076 0.22734 0.1873:0.0:0.6619:0.1507 . 569 P0CG20 CP011_HUMAN T 569 . ENSP00000386499:A569T A + 1 0 C16orf11 555297 0.000000 0.05858 0.006000 0.13384 0.021000 0.10359 0.126000 0.15769 0.554000 0.29061 0.491000 0.48974 GCC TCGA-2J-AAB1-01A-11D-A40W-08 C16orf11-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000333913.1 1 0 1 11 37 0 12 0 0 0 0 12 2 0 0 0 0 0 2 1 0.998993 11 37 0 12 2 -19.998620 1 1 117812 5 30 1 1 2 3 2.023473 0 0.380000 1.940000 0.381176 0.990000 6.700000e-01 1.000000 1.000000 0.963165 0.990000 1 0.910000 1.000000 CES3 23491 broad.mit.edu 37 16 67006841 67006841 + Silent SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr16:67006841C>T ENST00000303334.4 + 13 1676 c.1605C>T c.(1603-1605)gcC>gcT p.A535A CES3_ENST00000543856.1_Silent_p.A174A|CES3_ENST00000394037.1_Silent_p.A532A NM_024922.5 NP_079198.2 Q6UWW8 EST3_HUMAN carboxylesterase 3 24 Ovarian(137;0.0563) TGCCACGGGCCGGACAGAAGT 0.582000 0 SO:0001819 synonymous_variant ENST00000303334.4 1 1 hg19 CCDS10826.1 TCGA-2J-AAB1-01A-11D-A40W-08 CES3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000268848.1 1 0 0 18 368 0 63 0 5.348096e-01 1 36 0 63 2 0 0 0 0 0 2 1 0.999978 18 357 0 62 2 -4.545027 1 1 121412 2 34 1 1 2 3 2.027735 0 0.380000 1.940000 0.381176 0.240000 1.500000e-01 0.380000 0.240000 0.257139 0.240000 0 0.190000 0.310000 SMYD4 114826 broad.mit.edu 37 17 1703597 1703597 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr17:1703597C>T ENST00000305513.7 - 5 1258 c.1091G>A c.(1090-1092)cGc>cAc p.R364H NM_052928.2 NP_443160.2 Q8IYR2 SMYD4_HUMAN SET and MYND domain containing 4 21 TATGATTTTGCGAACATCCTC 0.453000 0 SO:0001583 missense ENST00000305513.7 0 1 hg19 CCDS11013.1 . . . . . . . . . . C 10.27 1.304550 0.23736 . . ENSG00000186532 ENST00000305513 T 0.10099 2.91 6.17 3.9 0.45041 SET domain (2); 0.633514 0.19290 N 0.117933 T 0.06280 0.0162 N 0.08118 0 0.09310 N 1 P 0.40660 0.726 P 0.44860 0.462 T 0.19224 -1.0312 10 0.45353 T 0.12 -4.1382 2.4272 0.04462 0.1423:0.5342:0.1385:0.1849 . 364 Q8IYR2 SMYD4_HUMAN H 364 ENSP00000304360:R364H ENSP00000304360:R364H R - 2 0 SMYD4 1650347 0.000000 0.05858 0.001000 0.08648 0.006000 0.05464 0.710000 0.25748 0.647000 0.30713 0.655000 0.94253 CGC TCGA-2J-AAB1-01A-11D-A40W-08 SMYD4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207108.4 0 0 0 6 365 1 78 0 7.781872e-03 0 7 1 78 2 0 0 0 0 0 2 0 0.023796 6 363 1 78 16 -2.303287 0 1 121412 4 38 1 0 0 0 1.952011 0 0.380000 1.940000 0.355509 0.080000 3.000000e-02 0.170000 0.080000 0.094556 0.080000 0 0.050000 0.130000 RTN4RL1 146760 broad.mit.edu 37 17 1840902 1840902 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr17:1840902C>T ENST00000331238.6 - 2 693 c.214G>A c.(214-216)Ggc>Agc p.G72S NM_178568.2 NP_848663.1 reticulon 4 receptor-like 1 11 CTGAAGTGGCCGGGCTGGAGG 0.637000 GBM(68;949 1139 14865 32798 38342) 0 SO:0001583 missense ENST00000331238.6 1 1 hg19 CCDS45569.1 . . . . . . . . . . C 22.1 4.242161 0.79912 . . ENSG00000185924 ENST00000331238 T 0.02323 4.34 5.49 5.49 0.81192 . 0.000000 0.40064 N 0.001187 T 0.10895 0.0266 L 0.53780 1.695 0.80722 D 1 D 0.55605 0.972 P 0.59012 0.85 T 0.03051 -1.1078 10 0.38643 T 0.18 . 19.4381 0.94806 0.0:1.0:0.0:0.0 . 72 Q86UN2 R4RL1_HUMAN S 72 ENSP00000330631:G72S ENSP00000330631:G72S G - 1 0 RTN4RL1 1787652 1.000000 0.71417 0.998000 0.56505 0.576000 0.36127 7.813000 0.86123 2.606000 0.88127 0.650000 0.86243 GGC TCGA-2J-AAB1-01A-11D-A40W-08 RTN4RL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000450155.2 1 0 1 29 139 0 32 0 4.859141e-01 0 9 0 32 2 0 0 0 0 0 2 1 1.000000 23 135 0 31 2 -20.000000 1 1 121282 2 33 1 0 0 0 1.952011 0 0.380000 1.940000 0.355509 0.870000 6.100000e-01 1.000000 1.000000 0.864865 0.870000 1 0.730000 1.000000 MAP2K3 5606 broad.mit.edu 37 17 21208417 21208417 + Missense_Mutation SNP G G A rs150613942 byFrequency TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr17:21208417G>A ENST00000342679.4 + 9 1000 c.751G>A c.(751-753)Gtc>Atc p.V251I MAP2K3_ENST00000361818.5_Missense_Mutation_p.V222I|MAP2K3_ENST00000316920.6_Missense_Mutation_p.V222I NM_145109.2 NP_659731.1 P46734 MP2K3_HUMAN mitogen-activated protein kinase kinase 3 p.V255I(1) CAAGTCCGACGTCTGGAGCCT 0.637000 1 Substitution - Missense(1) SO:0001583 missense ENST00000342679.4 1 1 hg19 CCDS11217.1 . . . . . . . . . . G 13.88 2.369435 0.42003 2.27E-4 0.001395 ENSG00000034152 ENST00000342679;ENST00000395491;ENST00000361818;ENST00000316920 T;T 0.40756 1.02;1.02 5.13 5.13 0.70059 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.085299 0.46758 D 0.000277 T 0.19565 0.0470 N 0.02345 -0.59 0.58432 D 0.99999 B 0.10296 0.003 B 0.11329 0.006 T 0.08351 -1.0726 10 0.32370 T 0.25 -49.0281 11.9966 0.53206 0.0796:0.0:0.9204:0.0 . 251 P46734 MP2K3_HUMAN I 251;222;222;255 ENSP00000345083:V251I;ENSP00000355081:V222I ENSP00000319139:V255I V + 1 0 MAP2K3 21149010 1.000000 0.71417 0.951000 0.38953 0.735000 0.41995 3.362000 0.52314 2.387000 0.81309 0.462000 0.41574 GTC TCGA-2J-AAB1-01A-11D-A40W-08 MAP2K3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000259374.2 1 0 0 27 549 0 129 0 9.997718e-01 0 262 0 129 2 0 0 0 0 0 2 1 1.000000 27 537 0 128 2 -2.281329 0 1 121412 273 50 1 1 2 3 2.024650 0 0.380000 1.940000 0.381176 0.240000 1.600000e-01 0.360000 0.240000 0.254729 0.240000 0 0.200000 0.300000 TOP2A 7153 broad.mit.edu 37 17 38564781 38564781 + Missense_Mutation SNP G G C TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr17:38564781G>C ENST00000423485.1 - 11 1463 c.1305C>G c.(1303-1305)atC>atG p.I435M NM_001067.3 NP_001058.2 P11388 TOP2A_HUMAN topoisomerase (DNA) II alpha 170kDa 39 Breast(137;0.00328) STAD - Stomach adenocarcinoma(5;0.00183) Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385) GAATTCCCTTGATTCTATTAT 0.338000 0 SO:0001583 missense ENST00000423485.1 1 1 hg19 CCDS45672.1 . . . . . . . . . . G 18.48 3.632601 0.67015 . . ENSG00000131747 ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601 T 0.25250 1.81 5.5 4.51 0.55191 DNA topoisomerase, type IIA, subunit B/N-terminal, alpha-beta (1);DNA topoisomerase, type IIA, central (1);DNA topoisomerase, type IIA, subunit B/N-terminal (1); 0.000000 0.85682 D 0.000000 T 0.38401 0.1039 M 0.73372 2.23 0.58432 D 0.999992 P 0.50443 0.935 P 0.54460 0.753 T 0.14227 -1.0480 10 0.35671 T 0.21 . 8.5579 0.33492 0.232:0.0:0.7679:0.0 . 435 P11388 TOP2A_HUMAN M 435;515;458;471 ENSP00000411532:I435M ENSP00000269577:I515M I - 3 3 TOP2A 35818307 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 3.709000 0.54853 1.277000 0.44412 0.591000 0.81541 ATC TCGA-2J-AAB1-01A-11D-A40W-08 TOP2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000338035.1 0 0 0 9 250 0 47 1 1.024245e-01 2 12 0 47 2 0 0 0 0 0 2 1 0.994037 9 246 0 47 2 -3.733343 1 1 0 0 1 1 2 3 2.039392 0 0.380000 1.940000 0.382347 0.190000 9.000000e-02 0.360000 0.180000 0.208987 0.190000 0 0.130000 0.270000 KRT38 8687 broad.mit.edu 37 17 39596894 39596894 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr17:39596894C>T ENST00000246646.3 - 1 279 c.280G>A c.(280-282)Gcc>Acc p.A94T NM_006771.3 NP_006762.3 O76015 KRT38_HUMAN keratin 38 29 Breast(137;0.000496) TCACCATAGGCCCCACAGATT 0.602000 0 SO:0001583 missense ENST00000246646.3 1 1 hg19 CCDS11392.1 . . . . . . . . . . C 10.97 1.500176 0.26861 . . ENSG00000171360 ENST00000246646 T 0.81330 -1.48 4.89 -9.78 0.00496 . 1.660260 0.03712 N 0.250436 T 0.55986 0.1955 N 0.11064 0.09 0.09310 N 1 B 0.14438 0.01 B 0.10450 0.005 T 0.48139 -0.9061 10 0.26408 T 0.33 . 4.3812 0.11295 0.2664:0.4535:0.1747:0.1055 . 94 O76015 KRT38_HUMAN T 94 ENSP00000246646:A94T ENSP00000246646:A94T A - 1 0 KRT38 36850420 0.000000 0.05858 0.000000 0.03702 0.177000 0.22998 -1.774000 0.01784 -2.506000 0.00507 -0.912000 0.02778 GCC TCGA-2J-AAB1-01A-11D-A40W-08 KRT38-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257307.2 1 0 1 70 313 0 62 0 0 0 0 62 2 0 0 0 0 0 2 1 1.000000 68 306 0 60 2 -3.992291 1 1 121412 5 39 1 1 2 3 2.039392 0 0.380000 1.940000 0.382347 0.960000 7.600000e-01 1.000000 1.000000 0.942156 0.960000 1 0.860000 1.000000 DHX58 79132 broad.mit.edu 37 17 40263826 40263826 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr17:40263826C>T ENST00000251642.3 - 3 307 c.85G>A c.(85-87)Ggg>Agg p.G29R NM_024119.2 NP_077024.2 Q96C10 DHX58_HUMAN DEXH (Asp-Glu-X-His) box polypeptide 58 16 all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143) CGGGTCTTCCCGGCACCCGTG 0.592000 0 SO:0001583 missense ENST00000251642.3 0 1 hg19 CCDS11416.1 . . . . . . . . . . C 21.0 4.089390 0.76756 0.0 1.16E-4 ENSG00000108771 ENST00000251642;ENST00000423748;ENST00000413196;ENST00000430773 D;D;D 0.95554 -3.23;-3.74;-3.74 4.99 4.02 0.46733 DEAD-like helicase (2);Helicase/UvrB domain (1); 0.000000 0.85682 D 0.000000 D 0.98673 0.9555 H 0.99169 4.455 0.58432 D 0.999993 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.98660 1.0683 10 0.87932 D 0 -2.8477 12.3178 0.54966 0.0:0.9172:0.0:0.0828 . 29;29 B7Z455;Q96C10 .;DHX58_HUMAN R 29 ENSP00000251642:G29R;ENSP00000416389:G29R;ENSP00000404639:G29R ENSP00000251642:G29R G - 1 0 DHX58 37517352 1.000000 0.71417 0.836000 0.33094 0.493000 0.33554 5.333000 0.65917 1.348000 0.45733 0.455000 0.32223 GGG TCGA-2J-AAB1-01A-11D-A40W-08 DHX58-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257396.1 0 0 0 6 482 0 93 0 1.308777e-01 0 43 0 93 2 0 0 0 0 1 2 1 0.963816 6 476 0 89 2 -2.414314 0 1 121412 4 40 1 1 2 3 2.039392 0 0.380000 1.940000 0.382347 0.060000 2.000000e-02 0.150000 0.060000 0.084300 0.060000 0 0.040000 0.110000 ALOX15 246 broad.mit.edu 37 17 4544868 4544868 + Missense_Mutation SNP C C G TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr17:4544868C>G ENST00000570836.1 - 2 175 c.79G>C c.(79-81)Gtc>Ctc p.V27L ALOX15_ENST00000293761.3_Missense_Mutation_p.V27L|ALOX15_ENST00000545513.1_Missense_Mutation_p.V49L|ALOX15_ENST00000574640.1_Missense_Mutation_p.V27L P16050 LOX15_HUMAN arachidonate 15-lipoxygenase 20 TGCTGGCCGACCAGCCACAGC 0.687000 0 SO:0001583 missense ENST00000570836.1 1 1 hg19 CCDS11049.1 . . . . . . . . . . C 18.79 3.698666 0.68501 . . ENSG00000161905 ENST00000293761;ENST00000545513 T;T 0.65549 -0.16;-0.16 5.33 3.31 0.37934 Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1); 0.294429 0.26891 N 0.021975 T 0.68979 0.3060 M 0.88906 2.99 0.27340 N 0.956541 B;B;B 0.31859 0.106;0.343;0.129 B;B;B 0.38712 0.169;0.125;0.28 T 0.65940 -0.6046 10 0.66056 D 0.02 -16.6582 9.0593 0.36425 0.0:0.8459:0.0:0.1541 . 49;27;27 F5H0G8;B7ZA11;P16050 .;.;LOX15_HUMAN L 27;49 ENSP00000293761:V27L;ENSP00000439855:V49L ENSP00000293761:V27L V - 1 0 ALOX15 4491617 1.000000 0.71417 0.921000 0.36526 0.960000 0.62799 2.813000 0.48002 0.607000 0.29982 0.655000 0.94253 GTC TCGA-2J-AAB1-01A-11D-A40W-08 ALOX15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207487.2 1 0 1 36 155 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 1.000000 36 153 0 32 2 -20.000000 1 1 0 0 1 0 0 0 1.952011 0 0.380000 1.940000 0.355509 0.940000 6.900000e-01 1.000000 1.000000 0.921623 0.940000 1 0.810000 1.000000 ABCA9 10350 broad.mit.edu 37 17 67016614 67016614 + Missense_Mutation SNP C C T rs61740908 TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr17:67016614C>T ENST00000340001.4 - 19 2726 c.2515G>A c.(2515-2517)Gtg>Atg p.V839M ABCA9_ENST00000370732.2_Missense_Mutation_p.V839M|ABCA9_ENST00000453985.2_Missense_Mutation_p.V839M|ABCA9-AS1_ENST00000458677.1_RNA NM_080283.3 NP_525022.2 Q8IUA7 ABCA9_HUMAN ATP-binding cassette, sub-family A (ABC1), member 9 p.V839M(1) 91 Breast(10;1.47e-12) CAGAGCGCCACGCCACTGATT 0.443000 1 Substitution - Missense(1) SO:0001583 missense ENST00000340001.4 0 1 hg19 CCDS11681.1 . . . . . . . . . . c 0.305 -0.971160 0.02232 . . ENSG00000154258 ENST00000340001;ENST00000453985;ENST00000370732;ENST00000453749 T;T 0.75938 -0.98;-0.98 5.08 -4.05 0.03998 . 0.703590 0.12727 N 0.444186 T 0.26593 0.0650 N 0.00413 -1.525 0.22684 N 0.998856 B;B 0.11235 0.004;0.001 B;B 0.08055 0.003;0.001 T 0.45205 -0.9277 10 0.02654 T 1 . 2.4227 0.04452 0.1895:0.1485:0.43:0.232 . 839;839 Q8IUA7-3;Q8IUA7 .;ABCA9_HUMAN M 839;822;839;834 ENSP00000342216:V839M;ENSP00000359767:V839M ENSP00000342216:V839M V - 1 0 ABCA9 64528209 0.000000 0.05858 0.810000 0.32431 0.644000 0.38419 -0.621000 0.05559 -0.594000 0.05836 -0.464000 0.05259 GTG TCGA-2J-AAB1-01A-11D-A40W-08 ABCA9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000277072.2 0 0 0 10 546 0 86 0 4.231827e-04 0 2 0 86 2 0 0 0 0 0 2 1 0.996753 10 540 0 83 2 -3.166621 1 1 121410 6 41 1 0 1 1 2.019142 0 0.380000 1.940000 0.378820 0.090000 4.000000e-02 0.170000 0.100000 0.103253 0.090000 0 0.060000 0.130000 POLR2A 5430 broad.mit.edu 37 17 7401414 7401414 + Missense_Mutation SNP G G A rs141769858 byFrequency TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr17:7401414G>A ENST00000322644.6 + 8 1619 c.1220G>A c.(1219-1221)cGc>cAc p.R407H POLR2A_ENST00000572844.1_Missense_Mutation_p.R407H NM_000937.4 NP_000928 P24928 RPB1_HUMAN polymerase (RNA) II (DNA directed) polypeptide A, 220kDa 50 Prostate(122;0.173) GAACTAGTGCGCAGGGGGAAC 0.517000 0 SO:0001583 missense ENST00000322644.6 0 1 hg19 CCDS32548.1 . . . . . . . . . . G 20.3 3.969615 0.74246 0.00227 0.0 ENSG00000181222 ENST00000535204;ENST00000322644 T 0.68765 -0.35 5.6 5.6 0.85130 RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1); 0.000000 0.85682 D 0.000000 T 0.73567 0.3603 M 0.86343 2.81 0.58432 D 0.999999 B;B 0.23490 0.086;0.024 B;B 0.22152 0.038;0.014 T 0.73572 -0.3940 10 0.62326 D 0.03 -11.3406 18.3894 0.90477 0.0:0.0:1.0:0.0 . 407;407 P24928;Q6NX41 RPB1_HUMAN;. H 363;407 ENSP00000314949:R407H ENSP00000314949:R407H R + 2 0 SLC35G6 7342138 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 8.828000 0.92047 2.653000 0.90120 0.563000 0.77884 CGC TCGA-2J-AAB1-01A-11D-A40W-08 POLR2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000437967.1 0 0 0 5 339 1 51 0 2.325891e-03 0 80 1 51 7 0 0 0 0 0 2 0 0.000960 5 337 1 51 21 -3.238978 1 1 121412 27 45 1 0 0 0 1.959757 0 0.380000 1.940000 0.358045 0.070000 2.000000e-02 0.160000 0.070000 0.087686 0.070000 0 0.040000 0.120000 TP53 7157 broad.mit.edu 37 17 7578406 7578406 + Missense_Mutation SNP C C T rs28934578 TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr17:7578406C>T ENST00000269305.4 - 5 713 c.524G>A c.(523-525)cGc>cAc p.R175H TP53_ENST00000445888.2_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GTGGGGGCAGCGCCTCACAAC 0.652000 R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY) 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 980 Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3) GRCh37 CM062017|CM951224 TP53 M rs28934578 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . C 31 5.079737 0.94050 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 D;D;D;D;D;D;D;D 0.99889 -7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55 5.41 5.41 0.78517 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.101149 0.64402 D 0.000008 D 0.99908 0.9956 M 0.92784 3.345 0.80722 A 1 D;P;D;D;P;B;D 0.89917 0.999;0.578;1.0;0.998;0.632;0.213;0.999 D;B;D;D;B;B;D 0.91635 0.985;0.26;0.999;0.921;0.378;0.144;0.939 D 0.96278 0.9204 9 0.87932 D 0 -11.8679 17.0767 0.86588 0.0:1.0:0.0:0.0 rs28934578 136;175;175;82;175;175;175 B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. H 175;175;175;175;175;175;164;82;43;82;43 ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H ENSP00000269305:R175H R - 2 0 TP53 7519131 1.000000 0.71417 0.989000 0.46669 0.795000 0.44927 6.042000 0.70996 2.702000 0.92279 0.655000 0.94253 CGC TCGA-2J-AAB1-01A-11D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 13 238 0 49 1 8.920237e-01 8 66 0 49 2 1 9.999992e-01 52 1018 1 857 7 1 0.999538 13 235 0 48 2 -3.027011 1 1 121412 1 41 1 0 0 0 1.959757 0 0.380000 1.940000 0.358045 0.260000 1.400000e-01 0.420000 0.260000 0.279280 0.260000 0 0.200000 0.350000 LAMA1 284217 broad.mit.edu 37 18 7023334 7023334 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr18:7023334C>T ENST00000389658.3 - 19 2623 c.2530G>A c.(2530-2532)Gaa>Aaa p.E844K NM_005559.3 NP_005550.2 P25391 LAMA1_HUMAN laminin, alpha 1 205 Colorectal(10;0.172) ACACAAGATTCGCCAGGCACT 0.532000 0 SO:0001583 missense ENST00000389658.3 1 1 hg19 CCDS32787.1 . . . . . . . . . . C 11.87 1.767948 0.31320 0.0 1.16E-4 ENSG00000101680 ENST00000389658 T 0.61392 0.11 5.47 4.61 0.57282 EGF-like, laminin (4); 0.325995 0.26971 N 0.021577 T 0.49440 0.1557 L 0.52573 1.65 0.22745 N 0.99879 B 0.12013 0.005 B 0.10450 0.005 T 0.38478 -0.9659 10 0.31617 T 0.26 . 10.5047 0.44826 0.0:0.753:0.1702:0.0769 . 844 P25391 LAMA1_HUMAN K 844 ENSP00000374309:E844K ENSP00000374309:E844K E - 1 0 LAMA1 7013334 0.334000 0.24739 0.677000 0.29947 0.127000 0.20565 3.215000 0.51169 1.323000 0.45263 -0.149000 0.13747 GAA TCGA-2J-AAB1-01A-11D-A40W-08 LAMA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257369.1 1 0 1 49 171 0 39 0 0 0 1 0 39 2 0 0 0 0 0 2 1 1.000000 48 168 0 38 2 -3.749639 1 1 121412 4 38 1 1 2 3 2.043860 0 0.380000 1.940000 0.384676 0.990000 9.000000e-01 1.000000 1.000000 0.993917 0.990000 1 0.990000 1.000000 C19orf57 79173 broad.mit.edu 37 19 14006194 14006194 + Missense_Mutation SNP G G A rs145142690 TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr19:14006194G>A ENST00000586783.1 - 2 196 c.197C>T c.(196-198)gCc>gTc p.A66V C19orf57_ENST00000346736.2_Missense_Mutation_p.A66V|C19orf57_ENST00000454313.1_Missense_Mutation_p.A66V|C19orf57_ENST00000591586.1_Missense_Mutation_p.A66V Q0VDD7 CS057_HUMAN chromosome 19 open reading frame 57 14 OV - Ovarian serous cystadenocarcinoma(19;2e-21) CCTGGAGACGGCCTTTCCTGG 0.562000 0 SO:0001583 missense ENST00000586783.1 1 1 hg19 . . . . . . . . . . G 5.727 0.318640 0.10845 2.27E-4 0.0 ENSG00000132016 ENST00000454313;ENST00000346736 T;T 0.35605 1.3;1.3 4.03 -0.708 0.11241 . 0.461071 0.16102 N 0.229524 T 0.15825 0.0381 N 0.12746 0.255 0.09310 N 1 B 0.16603 0.018 B 0.17433 0.018 T 0.12243 -1.0555 10 0.38643 T 0.18 -3.5745 3.3117 0.07018 0.2027:0.0:0.4413:0.356 . 66 Q0VDD7-2 . V 66 ENSP00000404382:A66V;ENSP00000254336:A66V ENSP00000254336:A66V A - 2 0 C19orf57 13867194 0.000000 0.05858 0.000000 0.03702 0.007000 0.05969 -0.281000 0.08456 -0.011000 0.14247 -0.137000 0.14449 GCC TCGA-2J-AAB1-01A-11D-A40W-08 C19orf57-003 NOVEL basic protein_coding protein_coding OTTHUMT00000457947.1 1 0 1 78 408 0 77 0 2.648429e-02 0 2 0 77 2 0 0 0 0 0 2 1 1.000000 76 401 0 77 2 -20.000000 1 1 121412 2 37 1 1 2 3 2.047246 0 0.380000 1.940000 0.384676 0.850000 6.800000e-01 1.000000 1.000000 0.857597 0.850000 1 0.760000 0.950000 SARS2 54938 broad.mit.edu 37 19 39421234 39421234 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr19:39421234G>A ENST00000221431.6 - 1 302 c.143C>T c.(142-144)gCg>gTg p.A48V MRPS12_ENST00000308018.4_5'UTR|MRPS12_ENST00000402029.3_5'Flank|SARS2_ENST00000600042.1_Missense_Mutation_p.A48V|SARS2_ENST00000430193.3_Missense_Mutation_p.A48V|MRPS12_ENST00000407800.2_5'Flank|SARS2_ENST00000448145.2_Intron|CTC-360G5.8_ENST00000599996.1_Intron|SARS2_ENST00000594171.1_5'Flank NM_017827.3 NP_060297.1 Q9NP81 SYSM_HUMAN seryl-tRNA synthetase 2, mitochondrial 15 all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454) Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554) GCCCTCGCGCGCATACTCGTA 0.627000 OREG0025455 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000221431.6 0 1 hg19 CCDS33017.1 . . . . . . . . . . G 14.36 2.512002 0.44660 . . ENSG00000104835 ENST00000430193;ENST00000221431;ENST00000455102 T;T;T 0.55588 0.51;0.51;1.49 5.65 4.57 0.56435 . 0.122893 0.53938 D 0.000045 T 0.40979 0.1139 L 0.43923 1.385 . . . D;B;B 0.56746 0.977;0.206;0.257 B;B;B 0.43623 0.425;0.014;0.007 T 0.44952 -0.9294 9 0.16896 T 0.51 . 8.6175 0.33840 0.1027:0.0:0.8973:0.0 . 48;48;48 B4DJP6;B4DE10;Q9NP81 .;.;SYSM_HUMAN V 48 ENSP00000406754:A48V;ENSP00000221431:A48V;ENSP00000414954:A48V ENSP00000221431:A48V A - 2 0 FBXO17 44113074 1.000000 0.71417 1.000000 0.80357 0.672000 0.39443 3.764000 0.55264 2.941000 0.99782 0.655000 0.94253 GCG TCGA-2J-AAB1-01A-11D-A40W-08 SARS2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000463139.1 0 0 0 6 597 0 129 0 3.925745e-02 0 26 0 129 2 0 0 0 0 0 2 1 0.963070 6 586 0 127 2 -1.740918 0 1 121412 2 37 1 1 2 3 2.030287 0 0.380000 1.940000 0.381176 0.050000 1.000000e-02 0.110000 0.060000 0.060873 0.050000 0 0.030000 0.080000 ZNF404 342908 broad.mit.edu 37 19 44388109 44388109 + Splice_Site SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr19:44388109C>T ENST00000587539.1 - 1 7 c.8G>A c.(7-9)cGg>cAg p.R3Q ZNF404_ENST00000588094.1_5'UTR NM_001033719.2 NP_001028891.2 Q494X3 ZN404_HUMAN zinc finger protein 404 17 Prostate(69;0.0352) TCAACTCACCCGGGCCATGGT 0.388000 0 SO:0001630 splice_region_variant ENST00000587539.1 1 0 hg19 CCDS59394.1 TCGA-2J-AAB1-01A-11D-A40W-08 ZNF404-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000460019.1 0 0 1 41 169 0 40 0 0 0 1 0 40 2 0 0 0 0 0 2 1 1.000000 41 162 0 40 2 -2.534310 1 1 119076 132 49 1 0 0 0 1.990385 0 0.380000 1.940000 0.367992 0.990000 7.400000e-01 1.000000 1.000000 0.951392 0.990000 1 0.860000 1.000000 ZNF227 7770 broad.mit.edu 37 19 44739673 44739673 + Missense_Mutation SNP A A T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr19:44739673A>T ENST00000313040.7 + 6 1295 c.1090A>T c.(1090-1092)Agt>Tgt p.S364C ZNF227_ENST00000589005.1_Missense_Mutation_p.S313C|ZNF227_ENST00000391961.2_Missense_Mutation_p.S313C NM_182490.1 NP_872296.1 Q86WZ6 ZN227_HUMAN zinc finger protein 227 24 Prostate(69;0.0435) CTTTAGTCAAAGTTCAAATTT 0.423000 0 SO:0001583 missense ENST00000313040.7 0 1 hg19 CCDS12636.1 . . . . . . . . . . A 15.35 2.808701 0.50421 . . ENSG00000131115 ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980;ENST00000377916 T;T 0.16743 2.32;3.13 4.54 4.54 0.55810 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.27027 0.0662 M 0.78285 2.405 0.18873 N 0.999988 B;B;D;B 0.64830 0.238;0.114;0.994;0.114 B;B;P;B 0.47402 0.016;0.023;0.546;0.023 T 0.21484 -1.0244 9 0.52906 T 0.07 . 8.7324 0.34507 0.8306:0.0:0.0:0.1694 . 285;343;316;364 B7Z6M2;Q658S5;Q9NS43;Q86WZ6 .;.;.;ZN227_HUMAN C 364;321;313;343;65 ENSP00000321049:S364C;ENSP00000375823:S313C ENSP00000321049:S364C S + 1 0 ZNF227 49431513 0.062000 0.20869 0.998000 0.56505 0.993000 0.82548 1.890000 0.39728 1.801000 0.52704 0.460000 0.39030 AGT TCGA-2J-AAB1-01A-11D-A40W-08 ZNF227-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000460720.1 0 0 0 5 327 0 43 0 4.043804e-02 0 17 0 43 2 0 0 0 0 0 2 1 0.935993 4 324 0 43 2 -5.855425 1 0 0 0 1 0 0 0 1.990385 0 0.380000 1.940000 0.367992 0.080000 2.000000e-02 0.170000 0.080000 0.092276 0.080000 0 0.050000 0.130000 ZNF114 163071 broad.mit.edu 37 19 48789674 48789674 + Missense_Mutation SNP A A C TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr19:48789674A>C ENST00000595607.1 + 6 1287 c.793A>C c.(793-795)Atg>Ctg p.M265L ZNF114_ENST00000315849.1_Missense_Mutation_p.M265L|ZNF114_ENST00000597695.1_Missense_Mutation_p.M231L|ZNF114_ENST00000600687.1_Missense_Mutation_p.M265L Q8NC26 ZN114_HUMAN zinc finger protein 114 18 all_epithelial(76;8.01e-05)|all_lung(116;0.000112)|Lung NSC(112;0.000192)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113) AATTCACGCCATGCAGATGCA 0.463000 0 SO:0001583 missense ENST00000595607.1 1 1 hg19 CCDS12713.1 . . . . . . . . . . G 1.280 -0.610640 0.03690 . . ENSG00000178150 ENST00000315849 T 0.04502 3.61 2.01 0.895 0.19247 . . . . . T 0.02304 0.0071 N 0.08118 0 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.48234 -0.9053 9 0.24483 T 0.36 . 4.187 0.10402 0.1438:0.0:0.6304:0.2258 . 265 Q8NC26 ZN114_HUMAN L 265 ENSP00000318898:M265L ENSP00000318898:M265L M + 1 0 ZNF114 53481486 0.000000 0.05858 0.000000 0.03702 0.005000 0.04900 -0.407000 0.07178 0.016000 0.14998 -0.349000 0.07799 ATG TCGA-2J-AAB1-01A-11D-A40W-08 ZNF114-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465601.1 0 0 0 12 385 1 95 0 0 0 1 95 2 0 0 0 0 0 2 0 0.333234 12 380 1 95 15 -12.119060 1 1 0 0 1 0 0 0 1.990385 0 0.380000 1.940000 0.367992 0.150000 8.000000e-02 0.260000 0.150000 0.167493 0.150000 0 0.110000 0.210000 RPL28 6158 broad.mit.edu 37 19 55899358 55899358 + Missense_Mutation SNP C C T rs150642428 TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr19:55899358C>T ENST00000344063.2 + 4 895 c.266C>T c.(265-267)aCg>aTg p.T89M RPL28_ENST00000558815.1_Missense_Mutation_p.T89M|RPL28_ENST00000458349.2_Missense_Mutation_p.T89M|RPL28_ENST00000560055.1_Missense_Mutation_p.T89M|RPL28_ENST00000558131.1_Missense_Mutation_p.R83C|RPL28_ENST00000559463.1_Missense_Mutation_p.T89M|RPL28_ENST00000560583.1_Missense_Mutation_p.T89M P46779 RL28_HUMAN ribosomal protein L28 6 Breast(117;0.191) Renal(1328;0.245) LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209) GCTCGCGCCACGCTCAGCAGC 0.622000 0 SO:0001583 missense ENST00000344063.2 1 1 hg19 CCDS12924.1 . . . . . . . . . . C 16.19 3.054549 0.55218 . . ENSG00000108107 ENST00000344063;ENST00000426763;ENST00000458349 T;T 0.44881 0.91;0.91 3.44 3.44 0.39384 . 0.000000 0.85682 D 0.000000 T 0.51075 0.1653 L 0.53617 1.68 0.58432 D 0.999996 D;D;P 0.65815 0.978;0.995;0.607 P;P;B 0.56042 0.543;0.79;0.427 T 0.54925 -0.8220 10 0.52906 T 0.07 . 13.1887 0.59697 0.0:1.0:0.0:0.0 . 89;89;89 B4DEP9;E9PB24;P46779 .;.;RL28_HUMAN M 89 ENSP00000342787:T89M;ENSP00000401450:T89M ENSP00000342787:T89M T + 2 0 RPL28 60591170 1.000000 0.71417 1.000000 0.80357 0.651000 0.38670 7.107000 0.77047 1.864000 0.54056 0.462000 0.41574 ACG TCGA-2J-AAB1-01A-11D-A40W-08 RPL28-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416277.2 1 0 0 17 386 0 80 1 1 326 6836 0 80 2 0 0 0 0 0 2 1 0.999960 17 377 0 75 2 -4.410952 1 1 121410 9 41 1 0 0 0 2.014203 0 0.380000 1.940000 0.377635 0.220000 1.300000e-01 0.340000 0.220000 0.232081 0.220000 0 0.170000 0.280000 DCLRE1B 64858 broad.mit.edu 37 1 114454068 114454068 + Missense_Mutation SNP T T G TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:114454068T>G ENST00000369563.3 + 4 1300 c.854T>G c.(853-855)tTt>tGt p.F285C DCLRE1B_ENST00000466480.1_3'UTR NM_022836.3 NP_073747.1 Q9H816 DCR1B_HUMAN DNA cross-link repair 1B 18 Lung SC(450;0.184) all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518) CTTCGTGCCTTTGTCGCAGCA 0.567000 Other identified genes with known or suspected DNA repair function 0 SO:0001583 missense ENST00000369563.3 1 1 hg19 CCDS866.1 . . . . . . . . . . T 22.5 4.298120 0.81025 . . ENSG00000118655 ENST00000369563 T 0.61980 0.06 6.02 4.9 0.64082 DNA repair metallo-beta-lactamase (1); 0.000000 0.85682 D 0.000000 T 0.70439 0.3224 M 0.85630 2.765 0.58432 D 0.999998 D 0.63046 0.992 P 0.59357 0.856 T 0.75983 -0.3125 10 0.59425 D 0.04 -9.6429 11.9514 0.52956 0.0:0.0672:0.0:0.9328 . 285 Q9H816 DCR1B_HUMAN C 285 ENSP00000358576:F285C ENSP00000358576:F285C F + 2 0 DCLRE1B 114255591 1.000000 0.71417 0.988000 0.46212 0.939000 0.58152 7.967000 0.87967 1.116000 0.41820 0.533000 0.62120 TTT TCGA-2J-AAB1-01A-11D-A40W-08 DCLRE1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033020.2 1 0 1 64 300 0 61 1 6.953711e-01 3 10 0 61 2 0 0 0 0 0 2 1 1.000000 63 292 0 60 2 -20.000000 1 1 0 0 1 1 2 3 2.038935 0 0.380000 1.940000 0.382347 0.920000 7.300000e-01 1.000000 1.000000 0.917342 0.920000 1 0.820000 1.000000 SPAG17 200162 broad.mit.edu 37 1 118550780 118550780 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:118550780G>A ENST00000336338.5 - 31 4539 c.4474C>T c.(4474-4476)Cgg>Tgg p.R1492W NM_206996.2 NP_996879.1 Q6Q759 SPG17_HUMAN sperm associated antigen 17 123 Esophageal squamous(2;0.0106) all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01) CTTTCTACCCGCATACACTTC 0.493000 0 SO:0001583 missense ENST00000336338.5 1 1 hg19 CCDS899.1 . . . . . . . . . . G 11.93 1.785810 0.31593 . . ENSG00000155761 ENST00000336338 T 0.23348 1.91 5.83 2.83 0.33086 . 0.346719 0.27932 N 0.017261 T 0.26048 0.0635 L 0.41961 1.31 0.30207 N 0.798109 D 0.89917 1.0 D 0.66196 0.942 T 0.11470 -1.0586 10 0.62326 D 0.03 . 14.1367 0.65291 0.0:0.0:0.6081:0.3919 . 1492 Q6Q759 SPG17_HUMAN W 1492 ENSP00000337804:R1492W ENSP00000337804:R1492W R - 1 2 SPAG17 118352303 0.805000 0.28982 0.998000 0.56505 0.340000 0.28889 1.437000 0.34991 0.326000 0.23384 0.563000 0.77884 CGG TCGA-2J-AAB1-01A-11D-A40W-08 SPAG17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033723.1 1 0 0 16 197 0 46 0 0 0 1 0 46 2 0 0 0 0 0 2 1 0.999932 15 193 0 46 2 -3.017764 1 1 121402 3 36 1 1 2 3 2.038935 0 0.380000 1.940000 0.382347 0.400000 2.400000e-01 0.650000 0.390000 0.420318 0.400000 0 0.310000 0.510000 SV2A 9900 broad.mit.edu 37 1 149877463 149877463 + Missense_Mutation SNP A A C TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:149877463A>C ENST00000369146.3 - 12 2504 c.2014T>G c.(2014-2016)Ttg>Gtg p.L672V SV2A_ENST00000369145.1_Missense_Mutation_p.L672V NM_001278719.1|NM_014849.3 NP_001265648.1|NP_055664.3 Q7L0J3 SV2A_HUMAN synaptic vesicle glycoprotein 2A 55 Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171) LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247) Levetiracetam(DB01202) TCAACAGTCAACACGTCCAGC 0.557000 0 SO:0001583 missense ENST00000369146.3 0 1 hg19 CCDS940.1 . . . . . . . . . . A 2.739 -0.262762 0.05754 . . ENSG00000159164 ENST00000369146;ENST00000369145 T;T 0.06371 3.31;3.31 3.89 -0.377 0.12501 Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1); 0.982908 0.08311 N 0.965306 T 0.00695 0.0023 N 0.02865 -0.47 0.48632 D 0.999689 B;B 0.16802 0.019;0.005 B;B 0.21360 0.034;0.023 T 0.48768 -0.9006 10 0.02654 T 1 -9.4314 8.0509 0.30577 0.3216:0.0:0.6784:0.0 . 124;672 B4E000;Q7L0J3 .;SV2A_HUMAN V 672 ENSP00000358142:L672V;ENSP00000358141:L672V ENSP00000358141:L672V L - 1 2 SV2A 148144087 0.954000 0.32549 0.999000 0.59377 0.960000 0.62799 0.088000 0.14979 0.030000 0.15379 0.247000 0.18012 TTG TCGA-2J-AAB1-01A-11D-A40W-08 SV2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033754.1 0 0 0 12 884 0 128 0 5.892605e-03 0 8 0 128 2 0 0 0 0 0 2 1 0.998968 11 863 0 125 2 -8.023559 1 1 0 0 1 1 2 3 2.040103 0 0.380000 1.940000 0.382347 0.070000 3.000000e-02 0.130000 0.070000 0.085386 0.070000 0 0.040000 0.100000 CRNN 49860 broad.mit.edu 37 1 152382863 152382863 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:152382863G>A ENST00000271835.3 - 3 757 c.695C>T c.(694-696)aCt>aTt p.T232I RP1-91G5.3_ENST00000411804.1_RNA NM_016190.2 NP_057274.1 Q9UBG3 CRNN_HUMAN cornulin 35 Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.206) CTGGGTCTGAGTTCCAGATCC 0.572000 0 SO:0001583 missense ENST00000271835.3 1 1 hg19 CCDS1010.1 . . . . . . . . . . G 12.31 1.900907 0.33535 . . ENSG00000143536 ENST00000271835 T 0.05025 3.51 4.93 1.99 0.26369 . 0.507715 0.18383 N 0.142896 T 0.01254 0.0041 L 0.43923 1.385 0.09310 N 0.999999 P 0.43431 0.807 B 0.35470 0.203 T 0.46176 -0.9210 10 0.16896 T 0.51 . 4.0875 0.09953 0.1931:0.0:0.6221:0.1848 . 232 Q9UBG3 CRNN_HUMAN I 232 ENSP00000271835:T232I ENSP00000271835:T232I T - 2 0 CRNN 150649487 0.996000 0.38824 0.242000 0.24170 0.021000 0.10359 2.827000 0.48112 0.255000 0.21593 -0.237000 0.12165 ACT TCGA-2J-AAB1-01A-11D-A40W-08 CRNN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000034503.1 1 0 1 186 817 0 194 0 0 0 0 194 2 0 0 0 0 0 2 1 1.000000 185 805 0 191 2 -20.000000 1 1 0 0 1 1 2 3 2.040103 0 0.380000 1.940000 0.382347 0.970000 8.500000e-01 1.000000 1.000000 0.963924 0.970000 1 0.910000 1.000000 S100A8 6279 broad.mit.edu 37 1 153362970 153362970 + Silent SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:153362970G>A ENST00000368733.3 - 2 211 c.42C>T c.(40-42)gaC>gaT p.D14D S100A8_ENST00000368732.1_Silent_p.D14D|S100A8_ENST00000477801.1_5'UTR NM_002964.4 NP_002955.2 P05109 S10A8_HUMAN S100 calcium binding protein A8 4 all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.171) TGTGGTAGACGTCGATGATAG 0.507000 0 SO:0001819 synonymous_variant ENST00000368733.3 0 1 hg19 CCDS1038.1 TCGA-2J-AAB1-01A-11D-A40W-08 S100A8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000036791.1 0 0 0 11 902 0 169 0 6.464373e-02 0 31 0 169 2 0 0 0 0 0 2 1 0.998115 10 884 0 166 2 -2.744861 1 1 121412 14 45 1 1 2 3 2.040103 0 0.380000 1.940000 0.382347 0.060000 2.000000e-02 0.120000 0.060000 0.078264 0.060000 0 0.040000 0.090000 OLFML2B 25903 broad.mit.edu 37 1 161953983 161953983 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:161953983G>A ENST00000294794.3 - 8 2158 c.1735C>T c.(1735-1737)Cgc>Tgc p.R579C OLFML2B_ENST00000367938.1_Missense_Mutation_p.R62C|OLFML2B_ENST00000367940.2_Missense_Mutation_p.R580C NM_015441.1 NP_056256.1 Q68BL8 OLM2B_HUMAN olfactomedin-like 2B 48 all_hematologic(112;0.156) BRCA - Breast invasive adenocarcinoma(70;0.0172) GTGAAGGCGCGATTGTAGTAG 0.597000 0 SO:0001583 missense ENST00000294794.3 1 1 hg19 CCDS1236.1 . . . . . . . . . . G 20.3 3.968748 0.74131 . . ENSG00000162745 ENST00000294794;ENST00000367940;ENST00000367938 D;D;D 0.90004 -2.6;-2.6;-2.6 5.06 5.06 0.68205 Olfactomedin-like (3); . . . . D 0.92453 0.7604 M 0.77313 2.365 0.46849 D 0.999222 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.977 D 0.93668 0.6987 8 0.87932 D 0 . 11.0657 0.47974 0.0:0.0:0.8145:0.1855 . 580;579 F2Z3N3;Q68BL8 .;OLM2B_HUMAN C 579;580;62 ENSP00000294794:R579C;ENSP00000356917:R580C;ENSP00000356915:R62C ENSP00000294794:R579C R - 1 0 OLFML2B 160220607 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 7.692000 0.84203 2.328000 0.79073 0.561000 0.74099 CGC TCGA-2J-AAB1-01A-11D-A40W-08 OLFML2B-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000060552.2 1 0 1 60 272 0 57 0 9.999855e-01 0 77 0 57 2 0 0 0 0 0 2 1 1.000000 60 265 0 56 2 -3.417237 1 1 0 0 1 1 2 3 2.040103 0 0.380000 1.940000 0.382347 0.950000 7.400000e-01 1.000000 1.000000 0.933171 0.950000 1 0.840000 1.000000 ELF3 1999 broad.mit.edu 37 1 201981145 201981145 + Nonsense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:201981145G>A ENST00000359651.3 + 2 3416 c.224G>A c.(223-225)tGg>tAg p.W75* RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367284.5_Nonsense_Mutation_p.W75*|ELF3_ENST00000495848.1_3'UTR|RP11-465N4.4_ENST00000419190.1_RNA|ELF3_ENST00000367283.3_Nonsense_Mutation_p.W75* E74-like factor 3 (ets domain transcription factor, epithelial-specific ) 20 GTTCTGGACTGGATCAGCTAC 0.577000 0 SO:0001587 stop_gained ENST00000359651.3 0 1 hg19 CCDS1419.1 . . . . . . . . . . G 38 6.948324 0.97956 . . ENSG00000163435 ENST00000359651;ENST00000367284;ENST00000367283;ENST00000310044;ENST00000446188 . . . 5.56 5.56 0.83823 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 19.5332 0.95237 0.0:0.0:1.0:0.0 . . . . X 75;75;75;75;73 . ENSP00000311348:W75X W + 2 0 ELF3 200247768 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 9.149000 0.94659 2.608000 0.88229 0.591000 0.81541 TGG TCGA-2J-AAB1-01A-11D-A40W-08 ELF3-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087360.1 1 0 1 123 616 0 131 1 1 465 1498 0 131 2 0 0 0 0 0 2 1 1.000000 117 599 0 128 2 -3.323569 1 1 0 0 1 1 2 3 2.040103 0 0.380000 1.940000 0.382347 0.870000 7.300000e-01 1.000000 1.000000 0.881466 0.870000 1 0.800000 0.960000 OPRD1 4985 broad.mit.edu 37 1 29189523 29189523 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:29189523G>A ENST00000234961.2 + 3 1089 c.847G>A c.(847-849)Gtc>Atc p.V283I NM_000911.3 NP_000902.3 P41143 OPRD_HUMAN opioid receptor, delta 1 15 Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123) Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193) CTTCGTCATCGTCTGGACGCT 0.662000 0 SO:0001583 missense ENST00000234961.2 0 1 hg19 CCDS329.1 . . . . . . . . . . G 16.11 3.029141 0.54790 . . ENSG00000116329 ENST00000234961;ENST00000536280 T 0.37235 1.21 4.06 4.06 0.47325 GPCR, rhodopsin-like superfamily (1); 0.149246 0.44688 D 0.000439 T 0.28499 0.0705 N 0.25992 0.78 0.80722 D 1 B 0.24768 0.111 B 0.32805 0.153 T 0.07673 -1.0760 10 0.23891 T 0.37 . 13.7884 0.63123 0.0:0.0:1.0:0.0 . 283 P41143 OPRD_HUMAN I 283;235 ENSP00000234961:V283I ENSP00000234961:V283I V + 1 0 OPRD1 29062110 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 6.554000 0.73923 2.097000 0.63578 0.462000 0.41574 GTC TCGA-2J-AAB1-01A-11D-A40W-08 OPRD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000010330.1 0 0 0 4 67 0 13 0 0 0 0 13 2 0 0 0 0 0 2 1 0.888999 4 66 0 13 2 -8.354660 1 1 0 0 1 0 1 1 1.664513 1 0.380000 1.940000 0.234568 0.250000 8.000000e-02 0.530000 0.230000 0.278751 0.250000 0 0.150000 0.390000 CSMD2 114784 broad.mit.edu 37 1 34286109 34286109 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:34286109C>T ENST00000373381.4 - 8 1336 c.1160G>A c.(1159-1161)gGc>gAc p.G387D NM_001281956.1|NM_052896.3 NP_001268885.1|NP_443128.2 Q7Z408 CSMD2_HUMAN CUB and Sushi multiple domains 2 246 Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249) TTCGGGTATGCCAGGGTCTGG 0.448000 0 SO:0001583 missense ENST00000373381.4 0 1 hg19 . . . . . . . . . . C 31 5.068273 0.93950 . . ENSG00000121904 ENST00000373381 T 0.63417 -0.04 5.81 5.81 0.92471 Complement control module (2);Sushi/SCR/CCP (3); 0.000000 0.85682 D 0.000000 T 0.78194 0.4245 M 0.76938 2.355 0.80722 D 1 D;B 0.57257 0.979;0.07 P;B 0.60473 0.875;0.102 T 0.76310 -0.3006 10 0.38643 T 0.18 . 19.0707 0.93134 0.0:1.0:0.0:0.0 . 347;387 Q7Z408;E7EUA6 CSMD2_HUMAN;. D 387 ENSP00000362479:G387D ENSP00000241312:G347D G - 2 0 CSMD2 34058696 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 6.069000 0.71209 2.746000 0.94184 0.655000 0.94253 GGC TCGA-2J-AAB1-01A-11D-A40W-08 CSMD2-201 KNOWN basic|appris_principal protein_coding protein_coding 0 0 0 7 842 0 148 0 0 0 0 148 2 0 0 0 0 0 2 1 0.978267 7 815 0 144 2 -1.872151 0 1 0 0 1 1 2 3 2.045202 0 0.380000 1.940000 0.384676 0.040000 0 1.000000 0.040000 0.077185 0.040000 0 0.020000 0.070000 RNF207 388591 broad.mit.edu 37 1 6279452 6279452 + Silent SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:6279452G>A ENST00000377939.4 + 18 2017 c.1890G>A c.(1888-1890)agG>agA p.R630R RNF207_ENST00000377948.2_3'UTR|ICMT_ENST00000495791.1_5'Flank NM_207396.2 NP_997279.2 Q6ZRF8 RN207_HUMAN ring finger protein 207 16 Ovarian(185;0.0634) all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211) CCACATGGAGGGAACACCCGA 0.532000 0 SO:0001819 synonymous_variant ENST00000377939.4 1 1 hg19 CCDS59.2 TCGA-2J-AAB1-01A-11D-A40W-08 RNF207-001 NOVEL not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000003669.2 1 0 1 29 99 0 26 1 9.609944e-01 11 10 0 26 2 0 0 0 0 0 2 1 1.000000 29 98 0 25 2 -20.000000 1 1 0 0 1 1 2 3 2.041574 0 0.380000 1.940000 0.382347 0.990000 8.400000e-01 1.000000 1.000000 0.987780 0.990000 1 0.990000 1.000000 LHX8 431707 broad.mit.edu 37 1 75622617 75622617 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:75622617G>A ENST00000294638.5 + 9 1514 c.850G>A c.(850-852)Gtc>Atc p.V284I LHX8_ENST00000356261.3_Missense_Mutation_p.V274I NM_001001933.1 NP_001001933.1 Q68G74 LHX8_HUMAN LIM homeobox 8 30 CAAGAAACACGTCAGTCCTAA 0.502000 0 SO:0001583 missense ENST00000294638.5 1 1 hg19 CCDS30756.1 . . . . . . . . . . G 15.50 2.852331 0.51270 . . ENSG00000162624 ENST00000294638;ENST00000356261 D;D 0.86097 -2.07;-2.06 5.12 5.12 0.69794 Homeodomain-related (1);Homeobox (1);Homeodomain-like (1); 0.000000 0.85682 D 0.000000 T 0.70185 0.3195 L 0.29908 0.895 0.80722 D 1 B 0.22480 0.07 B 0.16722 0.016 T 0.66400 -0.5933 10 0.27785 T 0.31 . 18.9441 0.92615 0.0:0.0:1.0:0.0 . 284 Q68G74 LHX8_HUMAN I 284;274 ENSP00000294638:V284I;ENSP00000348597:V274I ENSP00000294638:V284I V + 1 0 LHX8 75395205 1.000000 0.71417 0.990000 0.47175 0.940000 0.58332 7.404000 0.79996 2.556000 0.86216 0.455000 0.32223 GTC TCGA-2J-AAB1-01A-11D-A40W-08 LHX8-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000026700.1 0 0 0 23 710 0 123 0 0 0 0 123 2 0 0 0 0 0 2 1 0.999999 23 702 0 120 2 -3.184890 1 1 121412 2 36 1 1 2 3 2.045202 0 0.380000 1.940000 0.384676 0.160000 1.000000e-01 1.000000 0.160000 0.196597 0.160000 0 0.130000 0.210000 ABCA4 24 broad.mit.edu 37 1 94497517 94497517 + Silent SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:94497517C>T ENST00000370225.3 - 27 4031 c.3945G>A c.(3943-3945)caG>caA p.Q1315Q NM_000350.2 NP_000341.2 P78363 ABCA4_HUMAN ATP-binding cassette, sub-family A (ABC1), member 4 147 all_lung(203;0.000757)|Lung NSC(277;0.00335) CATTGGAGTCCTGGGGTGTCT 0.632000 0 SO:0001819 synonymous_variant ENST00000370225.3 1 1 hg19 CCDS747.1 TCGA-2J-AAB1-01A-11D-A40W-08 ABCA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029320.1 1 0 0 19 388 0 62 0 0 0 1 0 62 2 0 0 0 0 0 2 1 0.999989 19 378 0 59 2 -3.308679 1 1 0 0 1 1 2 3 2.045202 0 0.380000 1.940000 0.384676 0.250000 1.500000e-01 1.000000 0.250000 0.279655 0.250000 0 0.190000 0.320000 DPYD 1806 broad.mit.edu 37 1 98205957 98205957 + Missense_Mutation SNP A A C TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr1:98205957A>C ENST00000370192.3 - 4 412 c.312T>G c.(310-312)atT>atG p.I104M DPYD_ENST00000306031.5_Missense_Mutation_p.I104M|DPYD_ENST00000423006.2_Missense_Mutation_p.I67M NM_000110.3 NP_000101 Q12882 DPYD_HUMAN dihydropyrimidine dehydrogenase 83 all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994) Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544) CCTTGTTTGCAATACTTGTGA 0.343000 0 SO:0001583 missense ENST00000370192.3 1 1 hg19 CCDS30777.1 . . . . . . . . . . A 18.70 3.679197 0.68042 . . ENSG00000188641 ENST00000370192;ENST00000423006;ENST00000306031 T;T;T 0.76186 -1.0;-1.0;-1.0 5.69 -5.09 0.02920 Fumarate reductase, C-terminal (1);Alpha-helical ferredoxin (1); 0.000000 0.85682 D 0.000000 D 0.83464 0.5260 H 0.96604 3.85 0.54753 D 0.999984 D;D 0.89917 1.0;1.0 D;D 0.91635 0.993;0.999 T 0.82926 -0.0215 10 0.87932 D 0 -18.9959 7.7046 0.28642 0.5443:0.0:0.3574:0.0983 . 104;104 E9PFN1;Q12882 .;DPYD_HUMAN M 104;67;104 ENSP00000359211:I104M;ENSP00000398884:I67M;ENSP00000307107:I104M ENSP00000307107:I104M I - 3 3 DPYD 97978545 0.973000 0.33851 0.958000 0.39756 0.987000 0.75469 0.190000 0.17057 -0.884000 0.03976 -0.361000 0.07541 ATT TCGA-2J-AAB1-01A-11D-A40W-08 DPYD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095698.3 1 0 1 72 326 0 89 1 9.786672e-01 2 28 0 89 2 0 0 0 0 0 2 1 1.000000 70 325 0 88 2 -20.000000 1 1 121408 2 32 1 1 2 3 2.045202 0 0.380000 1.940000 0.384676 0.950000 7.600000e-01 1.000000 1.000000 0.940137 0.950000 1 0.850000 1.000000 DHX35 60625 broad.mit.edu 37 20 37653909 37653909 + Missense_Mutation SNP C C G TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr20:37653909C>G ENST00000252011.3 + 18 1741 c.1708C>G c.(1708-1710)Ctg>Gtg p.L570V DHX35_ENST00000373325.2_Missense_Mutation_p.L570V|DHX35_ENST00000373323.4_Missense_Mutation_p.L539V NM_021931.3 NP_068750.2 Q9H5Z1 DHX35_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 35 40 Myeloproliferative disorder(115;0.00878) GGAACATTTCCTGAATTACAA 0.418000 0 SO:0001583 missense ENST00000252011.3 1 1 hg19 CCDS13310.1 . . . . . . . . . . C 15.64 2.894638 0.52121 . . ENSG00000101452 ENST00000373325;ENST00000252011;ENST00000373323;ENST00000373321;ENST00000449559 T;T;T;T 0.41758 3.7;3.65;3.59;0.99 5.41 4.46 0.54185 . 0.000000 0.85682 D 0.000000 T 0.43545 0.1252 L 0.45228 1.405 0.80722 D 1 P;B 0.40534 0.72;0.429 P;B 0.49752 0.621;0.088 T 0.19778 -1.0295 10 0.25751 T 0.34 . 9.8859 0.41262 0.0:0.834:0.0:0.166 . 539;570 F5GXM6;Q9H5Z1 .;DHX35_HUMAN V 570;570;539;50;34 ENSP00000362422:L570V;ENSP00000252011:L570V;ENSP00000362420:L539V;ENSP00000397997:L34V ENSP00000252011:L570V L + 1 2 DHX35 37087323 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 2.399000 0.44495 1.269000 0.44280 0.655000 0.94253 CTG TCGA-2J-AAB1-01A-11D-A40W-08 DHX35-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079212.2 1 0 1 184 782 0 157 1 9.285829e-01 6 15 0 157 2 0 0 0 0 0 2 1 1.000000 181 773 0 155 2 -2.997715 1 1 0 0 1 0 0 0 2.013459 0 0.380000 1.940000 0.377635 0.990000 8.600000e-01 1.000000 1.000000 0.973634 0.990000 1 0.920000 1.000000 CHD6 84181 broad.mit.edu 37 20 40085993 40085993 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr20:40085993C>T ENST00000373233.3 - 18 2917 c.2740G>A c.(2740-2742)Gag>Aag p.E914K CHD6_ENST00000309279.7_Intron NM_032221.3 NP_115597.3 Q8TD26 CHD6_HUMAN chromodomain helicase DNA binding protein 6 129 Myeloproliferative disorder(115;0.00425) ATCTCGCGCTCGTAGGAATTT 0.542000 0 SO:0001583 missense ENST00000373233.3 1 1 hg19 CCDS13317.1 . . . . . . . . . . C 33 5.210518 0.95069 . . ENSG00000124177 ENST00000373233 D 0.85088 -1.94 5.42 5.42 0.78866 Helicase, C-terminal (1); 0.000000 0.56097 D 0.000021 D 0.95449 0.8522 H 0.97077 3.935 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.96602 0.9445 10 0.87932 D 0 -28.0288 19.5951 0.95533 0.0:1.0:0.0:0.0 . 914 Q8TD26 CHD6_HUMAN K 914 ENSP00000362330:E914K ENSP00000362330:E914K E - 1 0 CHD6 39519407 1.000000 0.71417 0.998000 0.56505 0.479000 0.33129 7.729000 0.84864 2.705000 0.92388 0.591000 0.81541 GAG TCGA-2J-AAB1-01A-11D-A40W-08 CHD6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079270.1 1 0 1 58 231 0 44 0 5.026555e-01 0 8 0 44 2 0 0 0 0 0 2 1 1.000000 55 231 0 43 2 -20.000000 1 1 0 0 1 0 0 0 2.013459 0 0.380000 1.940000 0.377635 0.990000 8.200000e-01 1.000000 1.000000 0.974932 0.990000 1 0.920000 1.000000 GNAS 2778 broad.mit.edu 37 20 57484421 57484421 + Missense_Mutation SNP G G A rs121913495 TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr20:57484421G>A ENST00000371085.3 + 8 1026 c.602G>A c.(601-603)cGt>cAt p.R201H GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.R186H|GNAS_ENST00000371102.4_Missense_Mutation_p.R830H|GNAS_ENST00000354359.7_Missense_Mutation_p.R202H|GNAS_ENST00000371095.3_Missense_Mutation_p.R187H|GNAS_ENST00000306090.10_Missense_Mutation_p.R187H|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371100.4_Missense_Mutation_p.R844H NM_000516.4 NP_000507.1 P63092 GNAS2_HUMAN GNAS complex locus p.R201H(81)|p.R844H(4)|p.R201L(2)|p.R844L(1) 441 all_lung(29;0.0104) BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109) CTTCGCTGCCGTGTCCTGACT 0.423000 Mis pituitary adenoma McCune-Albright syndrome; pseudohypoparathyroidism, type IA TSP Lung(22;0.16) Colon(117;935 1597 6045 8307 46442) Dom yes 20 20q13.2 2778 guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1 yes E 88 Substitution - Missense(88) SO:0001583 missense ENST00000371085.3 0 1 hg19 CCDS13472.1 . . . . . . . . . . G 35 5.430570 0.96150 . . ENSG00000087460 ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090 D;D;D;D;D;D;D 0.99458 -5.93;-5.93;-5.93;-5.93;-5.93;-2.96;-5.93 5.53 5.53 0.82687 G protein alpha subunit, helical insertion (2); 0.000000 0.85682 D 0.000000 D 0.99799 0.9914 H 0.98965 4.385 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 0.997;0.994;0.983;1.0 D 0.96812 0.9597 10 0.87932 D 0 . 19.4606 0.94915 0.0:0.0:1.0:0.0 . 201;202;186;844 P63092;A6NI00;P63092-3;Q5JWF2 GNAS2_HUMAN;.;.;GNAS1_HUMAN H 844;830;187;201;202;186;187 ENSP00000360141:R844H;ENSP00000360143:R830H;ENSP00000360136:R187H;ENSP00000360126:R201H;ENSP00000346328:R202H;ENSP00000265620:R186H;ENSP00000304472:R187H ENSP00000265620:R186H R + 2 0 GNAS 56917816 1.000000 0.71417 0.963000 0.40424 0.936000 0.57629 9.291000 0.96070 2.596000 0.87737 0.563000 0.77884 CGT TCGA-2J-AAB1-01A-11D-A40W-08 GNAS-015 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000080431.2 0 0 0 5 315 0 50 1 9.999926e-01 24 2779 0 50 2 1 8.695476e-01 6 622 1 545 6 1 0.933250 5 307 0 48 2 -2.938661 1 1 121412 10 32 1 0 0 0 2.013459 0 0.380000 1.940000 0.377635 0.080000 2.000000e-02 0.180000 0.080000 0.097200 0.080000 0 0.050000 0.130000 DIDO1 11083 broad.mit.edu 37 20 61525110 61525110 + Silent SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr20:61525110C>T ENST00000266070.4 - 12 3334 c.3009G>A c.(3007-3009)ttG>ttA p.L1003L DIDO1_ENST00000395340.1_Silent_p.L1003L|DIDO1_ENST00000395335.2_Silent_p.L1003L|DIDO1_ENST00000395343.1_Silent_p.L1003L NM_033081.2 NP_149072.2 Q9BTC0 DIDO1_HUMAN death inducer-obliterator 1 99 Breast(26;5.68e-08) TCACAGAAGTCAAGACAGGCT 0.567000 Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095) 0 SO:0001819 synonymous_variant ENST00000266070.4 0 1 hg19 CCDS33506.1 TCGA-2J-AAB1-01A-11D-A40W-08 DIDO1-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000080091.2 0 0 0 6 482 1 92 0 8.715306e-03 0 27 1 92 3 0 0 0 0 0 2 0 0.009572 6 476 1 92 18 -2.880596 1 1 121412 1 29 1 0 0 0 2.013459 0 0.380000 1.940000 0.377635 0.060000 2.000000e-02 0.130000 0.060000 0.074668 0.060000 0 0.040000 0.100000 CHAF1B 8208 broad.mit.edu 37 21 37783861 37783861 + Silent SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr21:37783861C>T ENST00000314103.5 + 11 1171 c.1020C>T c.(1018-1020)taC>taT p.Y340Y NM_005441.2 NP_005432.1 Q13112 CAF1B_HUMAN chromatin assembly factor 1, subunit B (p60) 20 CTTTTGGTTACGTGTCTAATA 0.522000 0 SO:0001819 synonymous_variant ENST00000314103.5 0 1 hg19 CCDS13644.1 TCGA-2J-AAB1-01A-11D-A40W-08 CHAF1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000194616.2 0 0 0 6 762 1 145 0 5.719412e-03 0 12 1 145 2 0 0 0 0 0 2 0 0.006037 5 751 1 139 19 -2.614970 1 1 121412 1 37 1 0 0 0 2.008296 0 0.380000 1.940000 0.375252 0.040000 0 0.090000 0.040000 0.047333 0.040000 0 0.020000 0.070000 BRWD1 54014 broad.mit.edu 37 21 40578077 40578077 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr21:40578077G>A ENST00000333229.2 - 37 4648 c.4321C>T c.(4321-4323)Cgg>Tgg p.R1441W BRWD1_ENST00000342449.3_Missense_Mutation_p.R1441W|BRWD1_ENST00000380800.3_Missense_Mutation_p.R1441W NM_018963.4 NP_061836.2 Q9NSI6 BRWD1_HUMAN bromodomain and WD repeat domain containing 1 58 Prostate(19;8.44e-08)|all_epithelial(19;0.223) CAATTTTGCCGTTGCTTGAAC 0.328000 Melanoma(170;988 1986 4794 16843 39731) 0 SO:0001583 missense ENST00000333229.2 1 1 hg19 CCDS13662.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 14.62|14.62 2.589350|2.589350 0.46214|0.46214 .|. .|. ENSG00000185658|ENSG00000185658 ENST00000333229;ENST00000342449;ENST00000380800;ENST00000380783|ENST00000424441 T;T;T|. 0.59638|. 0.25;0.28;0.34|. 4.87|4.87 -4.09|-4.09 0.03951|0.03951 .|. 0.173450|. 0.35970|. N|. 0.002879|. T|T 0.47432|0.47432 0.1445|0.1445 L|L 0.58101|0.58101 1.795|1.795 0.09310|0.09310 N|N 0.999995|0.999995 D;D;B|. 0.71674|. 0.997;0.998;0.009|. P;P;B|. 0.56474|. 0.799;0.785;0.003|. T|T 0.52366|0.52366 -0.8585|-0.8585 10|5 0.87932|. D|. 0|. -0.1605|-0.1605 11.4109|11.4109 0.49925|0.49925 0.0715:0.0:0.3738:0.5547|0.0715:0.0:0.3738:0.5547 .|. 1441;1441;1441|. Q9NSI6-3;Q9NSI6-2;Q9NSI6|. .;.;BRWD1_HUMAN|. W|M 1441;1441;1441;397|378 ENSP00000330753:R1441W;ENSP00000344333:R1441W;ENSP00000370178:R1441W|. ENSP00000330753:R1441W|. R|T -|- 1|2 2|0 BRWD1|BRWD1 39499947|39499947 0.044000|0.044000 0.20184|0.20184 0.347000|0.347000 0.25668|0.25668 0.557000|0.557000 0.35523|0.35523 0.106000|0.106000 0.15354|0.15354 -0.524000|-0.524000 0.06400|0.06400 -0.215000|-0.215000 0.12644|0.12644 CGG|ACG TCGA-2J-AAB1-01A-11D-A40W-08 BRWD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000141398.3 1 0 1 141 661 0 125 0 8.499323e-01 1 17 0 125 2 0 0 0 0 0 2 1 1.000000 138 644 1 124 21 -20.000000 1 1 121412 4 43 1 0 0 0 2.008296 0 0.380000 1.940000 0.375252 0.910000 7.800000e-01 1.000000 1.000000 0.915689 0.910000 1 0.840000 0.990000 DSCAM 1826 broad.mit.edu 37 21 41559185 41559185 + Splice_Site SNP C C A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr21:41559185C>A ENST00000400454.1 - 14 3129 c.2652G>T c.(2650-2652)gaG>gaT p.E884D NM_001271534.1|NM_001389.3 NP_001258463.1|NP_001380.2 O60469 DSCAM_HUMAN Down syndrome cell adhesion molecule 142 all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103) GGTCTGGGGGCTCTGTGCCAT 0.483000 Melanoma(134;970 1778 1785 21664 32388) 0 SO:0001630 splice_region_variant ENST00000400454.1 0 1 hg19 CCDS42929.1 . . . . . . . . . . C 13.91 2.378979 0.42207 . . ENSG00000171587 ENST00000400454;ENST00000404019 T;T 0.39229 1.09;1.09 5.18 2.29 0.28610 Fibronectin, type III (1);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 T 0.28863 0.0716 N 0.25332 0.735 0.40427 D 0.979904 B 0.17465 0.022 B 0.12156 0.007 T 0.12993 -1.0526 10 0.62326 D 0.03 . 10.457 0.44557 0.0:0.6553:0.0:0.3447 . 884 O60469 DSCAM_HUMAN D 884;636 ENSP00000383303:E884D;ENSP00000385342:E636D ENSP00000383303:E884D E - 3 2 DSCAM 40481055 0.293000 0.24371 1.000000 0.80357 0.973000 0.67179 -0.338000 0.07842 0.659000 0.30945 0.561000 0.74099 GAG TCGA-2J-AAB1-01A-11D-A40W-08 DSCAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195029.1 0 0 0 5 131 0 26 0 0 0 0 26 2 0 0 0 0 0 2 1 0.933734 4 128 0 26 2 -8.004621 1 1 0 0 1 0 0 0 2.008296 0 0.380000 1.940000 0.375252 0.200000 7.000000e-02 0.410000 0.190000 0.224334 0.200000 0 0.130000 0.310000 SEZ6L 23544 broad.mit.edu 37 22 26736580 26736580 + Missense_Mutation SNP T T C TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr22:26736580T>C ENST00000248933.6 + 10 2289 c.2194T>C c.(2194-2196)Ttt>Ctt p.F732L SEZ6L_ENST00000403121.1_Missense_Mutation_p.F505L|SEZ6L_ENST00000360929.3_Missense_Mutation_p.F732L|SEZ6L_ENST00000404234.3_Missense_Mutation_p.F732L|SEZ6L_ENST00000343706.4_Missense_Mutation_p.F732L|SEZ6L_ENST00000529632.2_Missense_Mutation_p.F732L|SEZ6L_ENST00000402979.1_Missense_Mutation_p.F505L Q9BYH1 SE6L1_HUMAN seizure related 6 homolog (mouse)-like 80 GGGCCAGGGATTTATCATGAA 0.458000 0 SO:0001583 missense ENST00000248933.6 1 1 hg19 CCDS13833.1 . . . . . . . . . . T 17.70 3.455009 0.63290 . . ENSG00000100095 ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979 T;T;T;T;T;T;T 0.66638 -0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22 5.01 5.01 0.66863 CUB (4); 0.000000 0.56097 D 0.000031 T 0.73916 0.3648 M 0.91663 3.23 0.80722 D 1 B;B;B;B;B;B;B 0.22480 0.007;0.07;0.007;0.056;0.05;0.07;0.07 B;B;B;B;B;B;B 0.23574 0.022;0.046;0.024;0.027;0.047;0.046;0.046 T 0.75761 -0.3204 10 0.56958 D 0.05 . 14.0549 0.64761 0.0:0.0:0.0:1.0 . 732;732;505;732;732;732;732 B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1 .;.;.;.;.;.;SE6L1_HUMAN L 732;732;732;732;732;505;505 ENSP00000384772:F732L;ENSP00000437037:F732L;ENSP00000354185:F732L;ENSP00000248933:F732L;ENSP00000342661:F732L;ENSP00000384838:F505L;ENSP00000384733:F505L ENSP00000248933:F732L F + 1 0 SEZ6L 25066580 1.000000 0.71417 0.959000 0.39883 0.971000 0.66376 7.350000 0.79385 2.104000 0.64026 0.260000 0.18958 TTT TCGA-2J-AAB1-01A-11D-A40W-08 SEZ6L-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000320359.3 1 0 1 33 194 0 47 0 0 0 1 0 47 2 0 0 0 0 0 2 1 1.000000 33 192 0 47 2 -17.006960 1 1 0 0 1 1 2 3 2.064369 0 0.380000 1.940000 0.386988 0.780000 5.500000e-01 1.000000 1.000000 0.792180 0.780000 0 0.660000 0.930000 RANGAP1 5905 broad.mit.edu 37 22 41650338 41650338 + Missense_Mutation SNP G G A rs139571477 byFrequency TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr22:41650338G>A ENST00000455915.2 - 10 2703 c.1234C>T c.(1234-1236)Cgg>Tgg p.R412W RANGAP1_ENST00000405486.1_Missense_Mutation_p.R412W|RANGAP1_ENST00000356244.3_Missense_Mutation_p.R412W|RANGAP1_ENST00000407260.4_Missense_Mutation_p.R357W P46060 RAGP1_HUMAN Ran GTPase activating protein 1 19 AGAATCTTCCGTGAGGGCGTG 0.552000 0 SO:0001583 missense ENST00000455915.2 1 0 hg19 CCDS14012.1 . . . . . . . . . . G 12.98 2.101483 0.37048 2.27E-4 0.001395 ENSG00000100401 ENST00000405486;ENST00000356244;ENST00000405383;ENST00000455915;ENST00000407260 T;T;T;T 0.42131 0.98;0.98;0.98;0.98 4.39 2.17 0.27698 Ran-GTPase activating protein 1, C-terminal (1); 1.014230 0.07853 N 0.965026 T 0.45975 0.1369 L 0.36672 1.1 0.19775 N 0.999959 D;D 0.76494 0.999;0.995 P;P 0.54372 0.711;0.75 T 0.34054 -0.9844 10 0.72032 D 0.01 -21.7601 8.6119 0.33808 0.0:0.0:0.4106:0.5894 . 357;412 F8W7I9;P46060 .;RAGP1_HUMAN W 412;412;412;412;357 ENSP00000385866:R412W;ENSP00000348577:R412W;ENSP00000401470:R412W;ENSP00000385354:R357W ENSP00000348577:R412W R - 1 2 RANGAP1 39980284 0.792000 0.28813 0.401000 0.26359 0.093000 0.18481 0.893000 0.28336 0.297000 0.22615 -0.521000 0.04368 CGG TCGA-2J-AAB1-01A-11D-A40W-08 RANGAP1-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320606.1 0 0 1 63 253 0 79 1 1 56 157 0 79 2 0 0 0 0 0 2 1 1.000000 63 249 0 77 2 -2.933500 1 1 121412 35 55 1 1 2 3 2.064369 0 0.380000 1.940000 0.386988 0.990000 8.300000e-01 1.000000 1.000000 0.979999 0.990000 1 0.940000 1.000000 MOV10L1 54456 broad.mit.edu 37 22 50538027 50538027 + Silent SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr22:50538027C>T ENST00000262794.5 + 3 521 c.438C>T c.(436-438)tgC>tgT p.C146C MOV10L1_ENST00000540615.1_Silent_p.C126C|MOV10L1_ENST00000395858.3_Silent_p.C146C|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000545383.1_Silent_p.C146C|MOV10L1_ENST00000475190.1_3'UTR NM_018995.2 NP_061868.1 Q9BXT6 M10L1_HUMAN Mov10 RISC complex RNA helicase like 1 67 all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114) AGAGTGTGTGCGAAGGTATGC 0.512000 0 SO:0001819 synonymous_variant ENST00000262794.5 1 1 hg19 CCDS14084.1 TCGA-2J-AAB1-01A-11D-A40W-08 MOV10L1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000075009.2 1 0 0 47 229 0 70 0 0 0 1 0 70 2 0 0 0 0 0 2 1 1.000000 46 228 0 68 2 -19.999990 1 1 121412 4 35 1 1 2 3 2.064369 0 0.380000 1.940000 0.386988 0.910000 6.800000e-01 1.000000 1.000000 0.901233 0.910000 1 0.790000 1.000000 GLI2 2736 broad.mit.edu 37 2 121740416 121740416 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr2:121740416C>T ENST00000452319.1 + 11 1703 c.1643C>T c.(1642-1644)tCg>tTg p.S548L GLI2_ENST00000361492.4_Missense_Mutation_p.S548L|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_Missense_Mutation_p.S220L GLI family zinc finger 2 64 Renal(3;0.0496) Prostate(154;0.0623) TCCAACGCCTCGGACCGCGCC 0.637000 0 SO:0001583 missense ENST00000452319.1 1 1 hg19 CCDS33283.1 . . . . . . . . . . C 33 5.240212 0.95240 . . ENSG00000074047 ENST00000452319;ENST00000361492;ENST00000314490 T;T;T 0.52526 0.66;0.66;0.66 4.59 4.59 0.56863 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.85682 D 0.000000 T 0.67126 0.2860 M 0.64676 1.99 0.80722 D 1 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.91635 0.996;0.994;0.998;0.999;0.994 T 0.70967 -0.4728 10 0.87932 D 0 . 17.9271 0.88987 0.0:1.0:0.0:0.0 . 548;531;203;203;220 P10070;Q0VGA0;P10070-2;P10070-4;P10070-3 GLI2_HUMAN;.;.;.;. L 548;548;220 ENSP00000390436:S548L;ENSP00000354586:S548L;ENSP00000312694:S220L ENSP00000312694:S220L S + 2 0 GLI2 121456886 1.000000 0.71417 0.998000 0.56505 0.850000 0.48378 7.599000 0.82757 2.536000 0.85505 0.484000 0.47621 TCG TCGA-2J-AAB1-01A-11D-A40W-08 GLI2-009 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000332293.3 1 0 1 50 282 0 51 0 3.510172e-01 0 8 0 51 2 0 0 0 0 0 2 1 1.000000 48 279 0 48 2 -3.022880 1 1 0 0 1 0 0 0 2.015667 0 0.380000 1.940000 0.377635 0.780000 6.000000e-01 0.990000 0.790000 0.795310 0.780000 0 0.680000 0.900000 EPC2 26122 broad.mit.edu 37 2 149542414 149542414 + Missense_Mutation SNP A A G TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr2:149542414A>G ENST00000258484.6 + 13 2229 c.2195A>G c.(2194-2196)cAc>cGc p.H732R NM_015630.3 NP_056445.3 Q52LR7 EPC2_HUMAN enhancer of polycomb homolog 2 (Drosophila) 13 AATGCAGTGCACCTCAATAAT 0.473000 0 SO:0001583 missense ENST00000258484.6 1 1 hg19 CCDS46422.1 . . . . . . . . . . A 12.37 1.916638 0.33815 . . ENSG00000135999 ENST00000258484 . . . 5.93 5.93 0.95920 . 0.105505 0.64402 D 0.000005 T 0.68449 0.3002 L 0.44542 1.39 0.80722 D 1 D 0.54772 0.968 D 0.67900 0.954 T 0.65713 -0.6101 9 0.34782 T 0.22 -2.9627 16.3783 0.83418 1.0:0.0:0.0:0.0 . 732 Q52LR7 EPC2_HUMAN R 732 . ENSP00000258484:H732R H + 2 0 EPC2 149258884 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 6.746000 0.74866 2.261000 0.74972 0.477000 0.44152 CAC TCGA-2J-AAB1-01A-11D-A40W-08 EPC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000332278.1 1 0 1 23 187 0 34 1 9.015453e-01 8 27 0 34 2 0 0 0 0 0 2 1 1.000000 22 186 0 34 2 -10.431350 1 1 0 0 1 0 0 0 2.015667 0 0.380000 1.940000 0.377635 0.570000 3.800000e-01 0.810000 0.570000 0.588896 0.570000 0 0.470000 0.700000 TANC1 85461 broad.mit.edu 37 2 160087288 160087288 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr2:160087288C>T ENST00000263635.6 + 27 5588 c.5351C>T c.(5350-5352)aCc>aTc p.T1784I TANC1_ENST00000454300.1_Missense_Mutation_p.T1678I NM_001145909.1|NM_033394.2 NP_001139381.1|NP_203752.2 Q9C0D5 TANC1_HUMAN tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1 77 CAAGCCAAAACCTGTTCTGTT 0.498000 0 SO:0001583 missense ENST00000263635.6 1 1 hg19 CCDS42766.1 . . . . . . . . . . C 9.077 0.998461 0.19121 . . ENSG00000115183 ENST00000454300;ENST00000263635 T;T 0.69685 -0.42;-0.42 5.96 4.9 0.64082 . 0.635444 0.17407 N 0.175331 T 0.50939 0.1645 N 0.22421 0.69 0.18873 N 0.999989 B 0.15473 0.013 B 0.16289 0.015 T 0.24261 -1.0165 9 . . . . 12.4187 0.55508 0.0:0.8581:0.0:0.1419 . 1784 Q9C0D5 TANC1_HUMAN I 1678;1784 ENSP00000396339:T1678I;ENSP00000263635:T1784I . T + 2 0 TANC1 159795534 0.992000 0.36948 0.283000 0.24790 0.386000 0.30323 0.906000 0.28517 2.823000 0.97156 0.655000 0.94253 ACC TCGA-2J-AAB1-01A-11D-A40W-08 TANC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000333135.1 1 0 1 40 138 0 26 1 9.994377e-01 18 25 0 26 2 0 0 0 0 0 2 1 1.000000 40 134 0 26 2 -20.000000 1 1 0 0 1 0 0 0 2.015667 0 0.380000 1.940000 0.377635 0.990000 8.700000e-01 1.000000 1.000000 0.990875 0.990000 1 0.990000 1.000000 PDE11A 50940 broad.mit.edu 37 2 178762794 178762794 + Silent SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr2:178762794G>A ENST00000286063.6 - 4 1610 c.1293C>T c.(1291-1293)atC>atT p.I431I PDE11A_ENST00000409504.1_Silent_p.I73I|PDE11A_ENST00000449286.2_Silent_p.I73I|PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000358450.4_Silent_p.I181I NM_016953.3 NP_058649.3 Q9HCR9 PDE11_HUMAN phosphodiesterase 11A p.I431I(2)|p.I181I(2) 58 OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02) Caffeine(DB00201)|Tadalafil(DB00820) CTGGTGATTCGATGTCCTCTA 0.348000 Primary Pigmented Nodular Adrenocortical Disease, Familial 4 Substitution - coding silent(4) SO:0001819 synonymous_variant Familial Cancer Database iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2 ENST00000286063.6 1 1 hg19 CCDS33334.1 . . . . . . . . . . G 9.329 1.059928 0.19987 . . ENSG00000128655 ENST00000433879 . . . 5.89 0.569 0.17340 . . . . . T 0.57417 0.2052 . . . 0.80722 D 1 . . . . . . T 0.49808 -0.8900 4 . . . . 9.715 0.40270 0.7158:0.0:0.2842:0.0 . . . . L 70 . . S - 2 0 PDE11A 178471040 0.922000 0.31269 0.995000 0.50966 0.966000 0.64601 0.180000 0.16860 -0.128000 0.11641 -0.302000 0.09304 TCG TCGA-2J-AAB1-01A-11D-A40W-08 PDE11A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000334313.2 1 0 1 94 338 0 77 0 4.830764e-02 1 1 0 77 2 0 0 0 0 0 2 1 1.000000 93 336 0 77 2 -3.842923 1 1 121412 2 32 1 0 0 0 2.015667 0 0.380000 1.940000 0.377635 0.990000 9.400000e-01 1.000000 1.000000 0.996523 0.990000 1 0.990000 1.000000 SF3B1 23451 broad.mit.edu 37 2 198267359 198267359 + Missense_Mutation SNP C C G TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 C G C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr2:198267359C>G ENST00000335508.6 - 14 2089 c.1998G>C c.(1996-1998)aaG>aaC p.K666N SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank NM_012433.2 NP_036565.2 O75533 SF3B1_HUMAN splicing factor 3b, subunit 1, 155kDa p.K666N(19) 633 OV - Ovarian serous cystadenocarcinoma(117;0.246) GTTGTACAATCTTAATACCAG 0.413000 Mis myelodysplastic syndrome Dom yes 2 2q33.1 23451 splicing factor 3b, subunit 1, 155kDa L 19 Substitution - Missense(19) SO:0001583 missense ENST00000335508.6 1 1 hg19 CCDS33356.1 . . . . . . . . . . C 21.5 4.159735 0.78226 0.0 1.16E-4 ENSG00000115524 ENST00000335508 T 0.65732 -0.17 5.68 4.81 0.61882 Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 D 0.83575 0.5284 H 0.95645 3.7 0.80722 D 1 D 0.89917 1.0 D 0.79108 0.992 D 0.87121 0.2191 10 0.87932 D 0 . 11.0204 0.47715 0.0:0.8576:0.0:0.1424 . 666 O75533 SF3B1_HUMAN N 666 ENSP00000335321:K666N ENSP00000335321:K666N K - 3 2 SF3B1 197975604 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.643000 0.46604 1.410000 0.46936 0.561000 0.74099 AAG TCGA-2J-AAB1-01A-11D-A40W-08 SF3B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335245.2 0 0 0 11 319 0 56 1 9.944347e-01 7 253 0 56 2 1 9.999981e-01 15 840 0 794 2 1 0.998349 11 317 0 55 2 -3.187404 1 1 121412 7 39 1 0 0 0 2.015667 0 0.380000 1.940000 0.377635 0.170000 9.000000e-02 0.300000 0.180000 0.188569 0.170000 0 0.130000 0.240000 ZDBF2 57683 broad.mit.edu 37 2 207175041 207175041 + Missense_Mutation SNP A A G TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr2:207175041A>G ENST00000374423.3 + 5 6175 c.5789A>G c.(5788-5790)aAg>aGg p.K1930R NM_020923.1 NP_065974.1 Q9HCK1 ZDBF2_HUMAN zinc finger, DBF-type containing 2 95 CCTAAGCAAAAGGGGCGTGTG 0.428000 0 SO:0001583 missense ENST00000374423.3 0 1 hg19 CCDS46501.1 . . . . . . . . . . A 4.060 0.008959 0.07912 . . ENSG00000204186 ENST00000374423 T 0.44482 0.92 5.64 -2.84 0.05751 . . . . . T 0.19525 0.0469 N 0.22421 0.69 0.09310 N 1 P 0.40144 0.704 B 0.33799 0.17 T 0.22556 -1.0213 9 0.16896 T 0.51 . 5.9471 0.19225 0.1465:0.6094:0.0829:0.1612 . 1930 Q9HCK1 ZDBF2_HUMAN R 1930 ENSP00000363545:K1930R ENSP00000363545:K1930R K + 2 0 ZDBF2 206883286 0.023000 0.18921 0.000000 0.03702 0.003000 0.03518 0.647000 0.24812 -0.083000 0.12618 0.456000 0.33151 AAG TCGA-2J-AAB1-01A-11D-A40W-08 ZDBF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336458.1 0 0 0 4 360 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 0.876406 4 339 0 52 2 -3.207332 1 1 0 0 1 0 0 0 2.015667 0 0.380000 1.940000 0.377635 0.060000 1.000000e-02 0.140000 0.060000 0.071245 0.060000 0 0.030000 0.100000 ACADL 33 broad.mit.edu 37 2 211070474 211070474 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr2:211070474G>A ENST00000233710.3 - 6 877 c.650C>T c.(649-651)gCg>gTg p.A217V AC006994.2_ENST00000412065.1_RNA NM_001608.3 NP_001599.1 P28330 ACADL_HUMAN acyl-CoA dehydrogenase, long chain 14 Renal(323;0.202) ATTTGTGACCGCAACTACAAT 0.398000 0 SO:0001583 missense ENST00000233710.3 0 1 hg19 CCDS2389.1 . . . . . . . . . . G 11.41 1.630025 0.28978 . . ENSG00000115361 ENST00000233710 D 0.97505 -4.41 5.28 4.41 0.53225 Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (2); 0.208411 0.49305 D 0.000151 D 0.95500 0.8538 L 0.46885 1.475 0.43141 D 0.994895 P 0.45594 0.862 P 0.44772 0.46 D 0.94867 0.8027 10 0.51188 T 0.08 . 14.1005 0.65051 0.0727:0.0:0.9273:0.0 . 217 P28330 ACADL_HUMAN V 217 ENSP00000233710:A217V ENSP00000233710:A217V A - 2 0 ACADL 210778719 1.000000 0.71417 0.009000 0.14445 0.008000 0.06430 7.334000 0.79224 1.240000 0.43803 -0.137000 0.14449 GCG TCGA-2J-AAB1-01A-11D-A40W-08 ACADL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256561.2 0 0 0 6 349 0 65 0 0 0 0 65 2 0 0 0 0 0 2 1 0.964691 6 347 0 64 2 -2.517377 1 1 121400 3 38 1 0 0 0 2.015667 0 0.380000 1.940000 0.377635 0.090000 3.000000e-02 0.180000 0.090000 0.102334 0.090000 0 0.050000 0.140000 DNPEP 23549 broad.mit.edu 37 2 220239025 220239025 + Missense_Mutation SNP A A C TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr2:220239025A>C ENST00000273075.4 - 15 1667 c.1447T>G c.(1447-1449)Tta>Gta p.L483V DNPEP_ENST00000490371.1_5'UTR|DNPEP_ENST00000523282.1_Missense_Mutation_p.L491V|DNPEP_ENST00000373972.1_Missense_Mutation_p.L408V NM_012100.2 NP_036232 Q9ULA0 DNPEP_HUMAN aspartyl aminopeptidase 17 Renal(207;0.0474) CAATCCACTAAGAGATTATGG 0.473000 0 SO:0001583 missense ENST00000273075.4 1 1 hg19 CCDS42823.1 . . . . . . . . . . A 2.901 -0.227412 0.06022 . . ENSG00000123992 ENST00000273075;ENST00000373972;ENST00000523282;ENST00000535056 . . . 5.44 -10.9 0.00192 . 1.368830 0.04681 N 0.412341 T 0.11495 0.0280 N 0.11023 0.085 0.09310 N 0.999999 B;B;B;B 0.02656 0.0;0.0;0.0;0.0 B;B;B;B 0.04013 0.001;0.001;0.0;0.001 T 0.13388 -1.0511 9 0.13470 T 0.59 1.4126 0.5348 0.00635 0.2362:0.1861:0.301:0.2768 . 491;491;473;483 E7ETB3;B7Z7F0;Q9ULA0;Q53SB6 .;.;DNPEP_HUMAN;. V 483;408;491;376 . ENSP00000273075:L483V L - 1 2 DNPEP 219947269 0.000000 0.05858 0.016000 0.15963 0.364000 0.29643 -1.670000 0.01956 -1.757000 0.01316 -0.333000 0.08304 TTA TCGA-2J-AAB1-01A-11D-A40W-08 DNPEP-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000130212.1 1 0 1 51 256 0 50 1 1 75 140 0 50 2 0 0 0 0 0 2 1 1.000000 51 254 0 49 2 -20.000000 1 1 0 0 1 0 0 0 2.015667 0 0.380000 1.940000 0.377635 0.860000 6.600000e-01 1.000000 1.000000 0.869195 0.860000 1 0.760000 0.980000 TBC1D23 55773 broad.mit.edu 37 3 100016873 100016873 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr3:100016873C>T ENST00000394144.4 + 9 990 c.983C>T c.(982-984)gCg>gTg p.A328V TBC1D23_ENST00000475134.1_Missense_Mutation_p.A191V|TBC1D23_ENST00000344949.5_Missense_Mutation_p.A328V|TBC1D23_ENST00000486274.1_3'UTR NM_001199198.2 NP_001186127.1 Q9NUY8 TBC23_HUMAN TBC1 domain family, member 23 25 ATCCTTCAAGCGAATCAGCTA 0.443000 0 SO:0001583 missense ENST00000394144.4 0 1 hg19 CCDS56265.1 . . . . . . . . . . C 34 5.350043 0.95830 2.27E-4 0.0 ENSG00000036054 ENST00000344949;ENST00000394144;ENST00000475134 T;T;T 0.32988 1.43;1.43;1.43 5.76 5.76 0.90799 Rhodanese-like (2); 0.000000 0.85682 D 0.000000 T 0.41282 0.1152 N 0.22421 0.69 0.80722 D 1 D;D 0.71674 0.998;0.997 P;P 0.62885 0.908;0.851 T 0.09058 -1.0692 9 . . . . 19.9533 0.97211 0.0:1.0:0.0:0.0 . 328;328 Q9NUY8;Q9NUY8-2 TBC23_HUMAN;. V 328;328;191 ENSP00000340693:A328V;ENSP00000377700:A328V;ENSP00000418059:A191V . A + 2 0 TBC1D23 101499563 1.000000 0.71417 1.000000 0.80357 0.934000 0.57294 7.086000 0.76885 2.725000 0.93324 0.585000 0.79938 GCG TCGA-2J-AAB1-01A-11D-A40W-08 TBC1D23-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000353150.1 0 0 0 8 184 0 32 0 4.577688e-01 1 33 0 32 2 0 0 0 0 0 2 1 0.988665 8 179 0 29 2 -3.966471 1 1 121410 3 33 1 0 1 1 2.022971 0 0.380000 1.940000 0.378820 0.220000 1.000000e-01 0.400000 0.220000 0.241633 0.220000 0 0.150000 0.320000 EIF2B5 8893 broad.mit.edu 37 3 183855998 183855998 + Silent SNP T T C TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr3:183855998T>C ENST00000273783.3 + 5 851 c.729T>C c.(727-729)gaT>gaC p.D243D RP11-778D9.12_ENST00000608135.1_RNA|EIF2B5_ENST00000444495.1_Silent_p.D243D NM_003907.2 NP_003898.2 Q13144 EI2BE_HUMAN eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa 27 all_cancers(143;7.59e-11)|Ovarian(172;0.0303) Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22) TTCGATATGATTTACTGGATT 0.478000 0 SO:0001819 synonymous_variant ENST00000273783.3 1 1 hg19 CCDS3252.1 TCGA-2J-AAB1-01A-11D-A40W-08 EIF2B5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346168.1 1 0 0 20 441 0 76 1 5.750939e-01 4 39 0 76 2 0 0 0 0 0 2 1 0.999995 20 436 0 76 2 -19.700530 1 1 0 0 1 0 1 1 2.022971 0 0.380000 1.940000 0.378820 0.220000 1.400000e-01 0.340000 0.220000 0.237419 0.220000 0 0.180000 0.290000 TGFBR2 7048 broad.mit.edu 37 3 30732957 30732957 + Missense_Mutation SNP G G T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 G T G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr3:30732957G>T ENST00000295754.5 + 7 1952 c.1570G>T c.(1570-1572)Gac>Tac p.D524Y TGFBR2_ENST00000359013.4_Missense_Mutation_p.D549Y NM_003242.5 NP_003233.4 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II (70/80kDa) p.D524N(1)|p.D524Y(1) 53 CTGGGACCACGACCCAGAGGC 0.607000 2 Substitution - Missense(2) GRCh37 CM064328 TGFBR2 M SO:0001583 missense ENST00000295754.5 1 1 hg19 CCDS2648.1 . . . . . . . . . . G 29.4 5.005083 0.93287 . . ENSG00000163513 ENST00000295754;ENST00000359013;ENST00000439925 D;D 0.95103 -3.61;-3.61 5.91 5.91 0.95273 Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 D 0.98018 0.9347 M 0.91663 3.23 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.98294 1.0515 10 0.87932 D 0 . 20.3052 0.98627 0.0:0.0:1.0:0.0 . 524;549 P37173;D2JYI1 TGFR2_HUMAN;. Y 524;549;354 ENSP00000295754:D524Y;ENSP00000351905:D549Y ENSP00000295754:D524Y D + 1 0 TGFBR2 30707961 1.000000 0.71417 0.974000 0.42286 0.985000 0.73830 9.869000 0.99810 2.808000 0.96608 0.655000 0.94253 GAC TCGA-2J-AAB1-01A-11D-A40W-08 TGFBR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252994.2 1 0 1 107 174 0 57 1 1 103 153 0 57 2 1 1 286 423 0 575 2 1 1.000000 105 168 0 56 2 -20.000000 1 1 0 0 1 0 2 2 2.018562 1 0.380000 1.940000 0.380000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 DOCK3 1795 broad.mit.edu 37 3 51400102 51400102 + Nonsense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr3:51400102C>T ENST00000266037.9 + 49 5313 c.5290C>T c.(5290-5292)Cga>Tga p.R1764* NM_004947.4 NP_004938.1 Q8IZD9 DOCK3_HUMAN dedicator of cytokinesis 3 45 TTCCAGTGCCCGAGGTAAGGA 0.562000 0 SO:0001587 stop_gained ENST00000266037.9 0 1 hg19 CCDS46835.1 . . . . . . . . . . C 44 10.689336 0.99450 . . ENSG00000088538 ENST00000266037;ENST00000402669 . . . 5.26 5.26 0.73747 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.10377 T 0.69 . 15.6164 0.76769 0.1379:0.862:0.0:0.0 . . . . X 1764;560 . ENSP00000266037:R1764X R + 1 2 DOCK3 51375142 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 3.049000 0.49869 2.605000 0.88082 0.563000 0.77884 CGA TCGA-2J-AAB1-01A-11D-A40W-08 DOCK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346478.5 1 0 1 26 50 0 16 0 0 0 1 0 16 2 1 1 185 678 0 739 2 1 1.000000 26 50 0 15 2 -6.053581 1 1 0 0 1 0 1 1 2.022556 0 0.380000 1.940000 0.378820 0.990000 9.900000e-01 1.000000 1.000000 0.999933 0.990000 1 0.990000 1.000000 GABRA4 2557 broad.mit.edu 37 4 46979145 46979145 + Silent SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr4:46979145C>T ENST00000264318.3 - 5 1492 c.510G>A c.(508-510)gcG>gcA p.A170A NM_000809.3|NM_001204266.1|NM_001204267.1 NP_000800.2|NP_001191195.1|NP_001191196.1 P48169 GBRA4_HUMAN gamma-aminobutyric acid (GABA) A receptor, alpha 4 45 Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897) TGGGACACTCCGCACTTATGG 0.343000 Ovarian(6;283 369 8234 12290 33402) 0 SO:0001819 synonymous_variant ENST00000264318.3 1 1 hg19 CCDS3473.1 TCGA-2J-AAB1-01A-11D-A40W-08 GABRA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000216893.1 0 0 1 33 183 1 38 0 0 0 1 38 2 0 0 0 0 0 2 1 0.989151 32 179 1 38 18 -2.684716 1 1 121372 4 36 1 0 1 1 2.022977 0 0.380000 1.940000 0.378820 0.800000 5.700000e-01 1.000000 1.000000 0.807961 0.800000 0 0.680000 0.940000 TMPRSS11D 9407 broad.mit.edu 37 4 68699089 68699089 + Silent SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr4:68699089G>A ENST00000283916.6 - 7 623 c.525C>T c.(523-525)gcC>gcT p.A175A TMPRSS11D_ENST00000545541.1_Silent_p.A58A|TMPRSS11D_ENST00000509584.1_5'UTR|UBA6-AS1_ENST00000500538.2_RNA NM_004262.2 NP_004253.1 O60235 TM11D_HUMAN transmembrane protease, serine 11D 23 GGTCTGGACCGGCCCCACATT 0.463000 0 SO:0001819 synonymous_variant ENST00000283916.6 0 1 hg19 CCDS3518.1 TCGA-2J-AAB1-01A-11D-A40W-08 TMPRSS11D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251430.3 0 0 0 22 697 0 115 0 0 0 0 115 2 0 0 0 0 0 2 1 0.999999 21 686 0 115 2 -2.764799 1 1 121340 9 44 1 0 1 1 2.022977 0 0.380000 1.940000 0.378820 0.150000 9.000000e-02 0.240000 0.160000 0.167193 0.150000 0 0.120000 0.200000 APC 324 broad.mit.edu 37 5 112176765 112176765 + Missense_Mutation SNP A A G TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr5:112176765A>G ENST00000457016.1 + 16 5854 c.5474A>G c.(5473-5475)gAt>gGt p.D1825G APC_ENST00000508376.2_Missense_Mutation_p.D1825G|APC_ENST00000257430.4_Missense_Mutation_p.D1825G|CTC-554D6.1_ENST00000520401.1_Intron P25054 APC_HUMAN adenomatous polyposis coli p.K1192fs*3(1)|p.?(1) 3261 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) GTCTTCAATGATAAGCTCCCA 0.333000 12 D, Mis, N, F, S colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis TSP Lung(16;0.13) NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115) yes Rec yes Adenomatous polyposis coli; Turcot syndrome 5 5q21 324 adenomatous polyposis of the colon gene E, M, O 2 Unknown(1)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s, ENST00000457016.1 1 1 hg19 CCDS4107.1 . . . . . . . . . . A 11.59 1.683218 0.29872 . . ENSG00000134982 ENST00000457016;ENST00000257430;ENST00000508376 D;D;D 0.90197 -2.63;-2.63;-2.63 6.07 6.07 0.98685 . 0.322819 0.37955 N 0.001867 D 0.84822 0.5557 L 0.27053 0.805 0.39105 D 0.961357 B;B 0.02656 0.0;0.0 B;B 0.04013 0.001;0.001 T 0.80569 -0.1324 9 . . . -12.6701 16.6277 0.84984 1.0:0.0:0.0:0.0 . 1827;1825 Q4LE70;P25054 .;APC_HUMAN G 1825 ENSP00000413133:D1825G;ENSP00000257430:D1825G;ENSP00000427089:D1825G . D + 2 0 APC 112204664 1.000000 0.71417 0.582000 0.28627 0.778000 0.44026 7.395000 0.79876 2.330000 0.79161 0.528000 0.53228 GAT TCGA-2J-AAB1-01A-11D-A40W-08 APC-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250738.2 1 0 1 49 203 0 37 0 1.771917e-01 1 3 0 37 2 0 0 0 0 0 2 1 1.000000 47 200 0 35 2 -20.000000 1 1 0 0 1 1 2 3 2.028143 0 0.380000 1.940000 0.381176 0.990000 7.800000e-01 1.000000 1.000000 0.962495 0.990000 1 0.890000 1.000000 ETF1 2107 broad.mit.edu 37 5 137844426 137844426 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr5:137844426G>A ENST00000360541.5 - 10 1384 c.1163C>T c.(1162-1164)aCg>aTg p.T388M ETF1_ENST00000499810.2_Missense_Mutation_p.T355M|ETF1_ENST00000503014.1_Missense_Mutation_p.T374M NM_004730.3 NP_004721.1 P62495 ERF1_HUMAN eukaryotic translation termination factor 1 18 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325) AATTTCCAACGTAGCTCCAAA 0.413000 0 SO:0001583 missense ENST00000360541.5 0 1 hg19 CCDS4207.1 . . . . . . . . . . G 21.4 4.150639 0.78001 . . ENSG00000120705 ENST00000499810;ENST00000360541;ENST00000503014 . . . 6.17 6.17 0.99709 eRF1 domain 3 (1); 0.000000 0.85682 D 0.000000 D 0.83229 0.5209 M 0.88640 2.97 0.80722 D 1 D;P 0.64830 0.994;0.607 P;B 0.57324 0.818;0.087 D 0.83814 0.0243 9 0.51188 T 0.08 -6.0305 20.4745 0.99168 0.0:0.0:1.0:0.0 . 374;388 B7Z7P8;P62495 .;ERF1_HUMAN M 355;388;374 . ENSP00000353741:T388M T - 2 0 ETF1 137872325 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 9.857000 0.99534 2.941000 0.99782 0.655000 0.94253 ACG TCGA-2J-AAB1-01A-11D-A40W-08 ETF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251276.2 0 0 0 6 878 0 162 0 2.975263e-01 0 139 0 162 2 0 0 0 0 0 2 1 0.964533 6 874 0 162 2 -2.489483 0 1 0 0 1 1 2 3 2.028143 0 0.380000 1.940000 0.381176 0.030000 0 0.080000 0.040000 0.041317 0.030000 0 0.010000 0.060000 PCDHA9 9752 broad.mit.edu 37 5 140229874 140229874 + Silent SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr5:140229874C>T ENST00000532602.1 + 1 2827 c.1794C>T c.(1792-1794)gaC>gaT p.D598D PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.D598D|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron NM_031857.1 NP_114063.1 Q9Y5H5 PCDA9_HUMAN protocadherin alpha 9 59 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GCGCAGTGGACGCCGACTCGG 0.672000 Melanoma(55;1800 1972 14909) 0 SO:0001819 synonymous_variant ENST00000532602.1 1 1 hg19 CCDS54920.1 TCGA-2J-AAB1-01A-11D-A40W-08 PCDHA9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372896.2 1 0 1 76 318 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 1.000000 74 312 0 73 2 -20.000000 1 1 120728 1 17 1 1 2 3 2.028143 0 0.380000 1.940000 0.381176 0.990000 8.100000e-01 1.000000 1.000000 0.968228 0.990000 1 0.910000 1.000000 PCDHA9 9752 broad.mit.edu 37 5 140230003 140230003 + Silent SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr5:140230003C>T ENST00000532602.1 + 1 2956 c.1923C>T c.(1921-1923)gaC>gaT p.D641D PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.D641D|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron NM_031857.1 NP_114063.1 Q9Y5H5 PCDA9_HUMAN protocadherin alpha 9 59 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) ACGAAACGGACGCACCGCGCC 0.682000 Melanoma(55;1800 1972 14909) 0 SO:0001819 synonymous_variant ENST00000532602.1 1 1 hg19 CCDS54920.1 TCGA-2J-AAB1-01A-11D-A40W-08 PCDHA9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372896.2 1 0 1 53 325 0 91 0 0 0 0 91 2 0 0 0 0 0 2 1 1.000000 53 321 0 90 2 -19.999890 1 1 0 0 1 1 2 3 2.028143 0 0.380000 1.940000 0.381176 0.730000 5.600000e-01 0.940000 0.740000 0.745922 0.730000 0 0.640000 0.840000 GLRA1 2741 broad.mit.edu 37 5 151271898 151271898 + Missense_Mutation SNP T T A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr5:151271898T>A ENST00000455880.2 - 2 444 c.158A>T c.(157-159)gAt>gTt p.D53V GLRA1_ENST00000545569.1_Intron|GLRA1_ENST00000471351.2_5'UTR|GLRA1_ENST00000274576.4_Missense_Mutation_p.D53V P23415 GLRA1_HUMAN glycine receptor, alpha 1 23 all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912) Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785) Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236) GATCCTGGCATCATATCCGGA 0.498000 0 SO:0001583 missense ENST00000455880.2 1 1 hg19 CCDS54942.1 . . . . . . . . . . T 25.0 4.590090 0.86851 . . ENSG00000145888 ENST00000274576;ENST00000455880 T;T 0.81415 -1.49;-1.49 5.48 5.48 0.80851 Neurotransmitter-gated ion-channel ligand-binding (3); 0.116646 0.56097 D 0.000030 D 0.91506 0.7318 M 0.91612 3.225 0.80722 D 1 D;D 0.69078 0.996;0.997 D;D 0.72982 0.979;0.964 D 0.93395 0.6755 10 0.87932 D 0 . 15.5709 0.76337 0.0:0.0:0.0:1.0 . 53;53 P23415;P23415-2 GLRA1_HUMAN;. V 53 ENSP00000274576:D53V;ENSP00000411593:D53V ENSP00000274576:D53V D - 2 0 GLRA1 151252091 1.000000 0.71417 0.993000 0.49108 0.943000 0.58893 7.516000 0.81772 2.089000 0.63090 0.482000 0.46254 GAT TCGA-2J-AAB1-01A-11D-A40W-08 GLRA1-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000373959.1 0 0 0 14 369 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 0.999753 14 366 0 59 2 -3.703570 1 1 0 0 1 1 2 3 2.028143 0 0.380000 1.940000 0.381176 0.190000 1.000000e-01 0.320000 0.200000 0.204579 0.190000 0 0.140000 0.260000 GEMIN5 25929 broad.mit.edu 37 5 154292538 154292538 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr5:154292538G>A ENST00000285873.7 - 14 1991 c.1916C>T c.(1915-1917)aCg>aTg p.T639M NM_001252156.1|NM_015465.4 NP_001239085.1|NP_056280.2 Q8TEQ6 GEMI5_HUMAN gem (nuclear organelle) associated protein 5 38 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.147) KIRC - Kidney renal clear cell carcinoma(527;0.00112) AATCTTGGCCGTATGCCCTGA 0.522000 0 SO:0001583 missense ENST00000285873.7 0 1 hg19 CCDS4330.1 . . . . . . . . . . G 19.12 3.766113 0.69878 . . ENSG00000082516 ENST00000285873 T 0.65549 -0.16 5.37 5.37 0.77165 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.000000 0.85682 D 0.000000 T 0.80742 0.4681 M 0.78637 2.42 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 T 0.82647 -0.0354 10 0.87932 D 0 -17.564 19.0919 0.93229 0.0:0.0:1.0:0.0 . 638;639 B7ZLC9;Q8TEQ6 .;GEMI5_HUMAN M 639 ENSP00000285873:T639M ENSP00000285873:T639M T - 2 0 GEMIN5 154272731 1.000000 0.71417 1.000000 0.80357 0.298000 0.27526 8.881000 0.92415 2.667000 0.90743 0.561000 0.74099 ACG TCGA-2J-AAB1-01A-11D-A40W-08 GEMIN5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252507.1 0 0 0 5 319 0 60 0 1.266467e-02 0 9 0 60 2 0 0 0 0 0 2 1 0.934364 5 312 0 59 2 -2.742171 1 1 121412 5 34 1 1 2 3 2.028143 0 0.380000 1.940000 0.381176 0.080000 2.000000e-02 0.190000 0.080000 0.096572 0.080000 0 0.050000 0.140000 GRM6 2916 broad.mit.edu 37 5 178413623 178413623 + Silent SNP G G A rs139758482 TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr5:178413623G>A ENST00000517717.1 - 9 1670 c.1632C>T c.(1630-1632)gaC>gaT p.D544D RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Silent_p.D544D O15303 GRM6_HUMAN glutamate receptor, metabotropic 6 55 all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351) all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) AGCGGTACCCGTCACAGGCCT 0.682000 0 SO:0001819 synonymous_variant ENST00000517717.1 0 1 hg19 CCDS4442.1 TCGA-2J-AAB1-01A-11D-A40W-08 GRM6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253474.2 0 0 0 8 245 1 44 0 0 0 1 44 2 0 0 0 0 0 2 0 0.031009 8 242 1 43 18 -9.201594 1 1 121358 41 47 1 1 2 3 2.028143 0 0.380000 1.940000 0.381176 0.170000 7.000000e-02 0.320000 0.160000 0.184922 0.170000 0 0.120000 0.240000 ADAMTS16 170690 broad.mit.edu 37 5 5242275 5242275 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr5:5242275G>A ENST00000274181.7 + 17 2771 c.2633G>A c.(2632-2634)cGc>cAc p.R878H NM_139056.2 NP_620687.2 Q8TE57 ATS16_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 16 107 GCCATCGTGCGCTCTGAGTGC 0.642000 0 SO:0001583 missense ENST00000274181.7 1 1 hg19 CCDS43299.1 . . . . . . . . . . G 10.82 1.458019 0.26161 . . ENSG00000145536 ENST00000274181;ENST00000536857 T 0.61274 0.12 5.73 2.91 0.33838 . 0.432157 0.23055 N 0.052451 T 0.45796 0.1360 L 0.52759 1.655 0.42913 D 0.994269 B;B 0.20550 0.046;0.021 B;B 0.12837 0.006;0.008 T 0.35351 -0.9792 10 0.49607 T 0.09 . 4.6802 0.12731 0.3127:0.152:0.5352:0.0 . 878;878 Q8TE57;Q8TE57-2 ATS16_HUMAN;. H 878 ENSP00000274181:R878H ENSP00000274181:R878H R + 2 0 ADAMTS16 5295275 0.049000 0.20398 0.169000 0.22859 0.931000 0.56810 1.271000 0.33098 0.328000 0.23435 0.644000 0.83932 CGC TCGA-2J-AAB1-01A-11D-A40W-08 ADAMTS16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365657.1 0 0 1 30 173 0 49 0 0 0 1 0 49 2 0 0 0 0 0 2 1 1.000000 29 170 0 49 2 -20.000000 1 1 121060 1 31 1 1 2 3 2.028143 0 0.380000 1.940000 0.381176 0.780000 5.400000e-01 1.000000 1.000000 0.786994 0.780000 0 0.650000 0.920000 SEMA5A 9037 broad.mit.edu 37 5 9197372 9197372 + Missense_Mutation SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr5:9197372C>T ENST00000382496.5 - 10 1641 c.976G>A c.(976-978)Gcc>Acc p.A326T NM_003966.2 NP_003957.2 Q13591 SEM5A_HUMAN sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A 81 TGCGCGATGGCGCTCAGGTTG 0.597000 0 SO:0001583 missense ENST00000382496.5 1 1 hg19 CCDS3875.1 . . . . . . . . . . C 19.89 3.910739 0.72983 0.0 1.16E-4 ENSG00000112902 ENST00000382496 T 0.22539 1.95 5.35 4.48 0.54585 WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4); 0.049884 0.85682 N 0.000000 T 0.34978 0.0916 L 0.43701 1.375 0.58432 D 0.999998 D 0.89917 1.0 D 0.73708 0.981 T 0.03017 -1.1082 10 0.34782 T 0.22 . 11.7948 0.52093 0.0:0.9145:0.0:0.0855 . 326 Q13591 SEM5A_HUMAN T 326 ENSP00000371936:A326T ENSP00000371936:A326T A - 1 0 SEMA5A 9250372 1.000000 0.71417 0.971000 0.41717 0.171000 0.22731 4.769000 0.62300 1.385000 0.46445 0.650000 0.86243 GCC TCGA-2J-AAB1-01A-11D-A40W-08 SEMA5A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206989.2 1 0 1 55 391 0 97 0 0 0 0 97 2 0 0 0 0 0 2 1 1.000000 55 386 0 92 2 -19.983910 1 1 121412 1 35 1 1 2 3 2.028143 0 0.380000 1.940000 0.381176 0.640000 4.900000e-01 0.830000 0.640000 0.656748 0.640000 0 0.560000 0.740000 T 6862 broad.mit.edu 37 6 166574388 166574388 + Missense_Mutation SNP C C A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr6:166574388C>A ENST00000296946.2 - 8 1439 c.971G>T c.(970-972)gGa>gTa p.G324V T_ENST00000366871.3_Missense_Mutation_p.G266V NM_003181.3 NP_003172.1 O15178 BRAC_HUMAN T, brachyury homolog (mouse) 39 Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559) GGCAGGCATTCCAAGGCTGGA 0.522000 Chordoma, Familial Clustering of 0 SO:0001583 missense Familial Cancer Database ENST00000296946.2 0 1 hg19 CCDS5290.1 . . . . . . . . . . C 8.205 0.798999 0.16397 . . ENSG00000164458 ENST00000366876;ENST00000296946;ENST00000366871 D;D 0.83837 -1.75;-1.77 4.88 4.88 0.63580 . 0.142303 0.47852 D 0.000214 T 0.72179 0.3428 M 0.64997 1.995 0.58432 D 0.999998 P;P;P 0.37914 0.611;0.57;0.565 B;B;B 0.38106 0.265;0.142;0.146 T 0.73341 -0.4013 10 0.33141 T 0.24 . 10.9779 0.47478 0.0:0.9145:0.0:0.0855 . 266;324;266 E7ERD6;O15178;Q4KMP4 .;BRAC_HUMAN;. V 324;324;266 ENSP00000296946:G324V;ENSP00000355836:G266V ENSP00000296946:G324V G - 2 0 T 166494378 0.999000 0.42202 0.077000 0.20336 0.013000 0.08279 3.928000 0.56506 2.409000 0.81822 0.655000 0.94253 GGA TCGA-2J-AAB1-01A-11D-A40W-08 T-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043037.2 0 0 0 9 313 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 0.994142 9 310 0 51 2 -2.858768 1 1 0 0 1 0 1 1 1.673221 1 0.380000 1.940000 0.252111 0.120000 5.000000e-02 0.220000 0.120000 0.133428 0.120000 0 0.080000 0.170000 EEF1A1 1915 broad.mit.edu 37 6 74227973 74227973 + Missense_Mutation SNP G G T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 G T G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr6:74227973G>T ENST00000316292.9 - 6 2035 c.1044C>A c.(1042-1044)aaC>aaA p.N348K EEF1A1_ENST00000331523.2_Missense_Mutation_p.N348K|EEF1A1_ENST00000309268.6_Missense_Mutation_p.N348K|EEF1A1_ENST00000491404.1_Intron NM_001402.5 NP_001393.1 P68104 EF1A1_HUMAN eukaryotic translation elongation factor 1 alpha 1 18 GGCCTGGATGGTTCAGGATAA 0.423000 0 SO:0001583 missense ENST00000316292.9 1 0 hg19 CCDS4980.1 . . . . . . . . . . G 13.71 2.319688 0.41096 . . ENSG00000156508 ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977 T;T;T 0.43688 0.94;0.94;0.94 4.71 3.84 0.44239 Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (2);Translation elongation factor EFTu/EF1A, C-terminal (2); 0.000000 0.85682 U 0.000000 T 0.52354 0.1729 H 0.98866 4.355 0.80722 D 1 B;B;B 0.26483 0.027;0.027;0.15 B;B;B 0.30316 0.074;0.074;0.114 T 0.65533 -0.6145 10 0.87932 D 0 . 13.2814 0.60216 0.0779:0.0:0.9221:0.0 . 348;348;348 P68104;Q6IPS9;Q5VTE0 EF1A1_HUMAN;.;EF1A3_HUMAN K 348;346;348;348;327 ENSP00000339063:N348K;ENSP00000339053:N348K;ENSP00000330054:N348K ENSP00000339053:N348K N - 3 2 EEF1A1 74284694 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 3.738000 0.55067 1.107000 0.41642 0.556000 0.70494 AAC TCGA-2J-AAB1-01A-11D-A40W-08 EEF1A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041210.2 0 0 1 30 189 0 38 0 1 0 3972 0 38 2 0 0 0 0 0 2 1 1.000000 27 189 0 36 2 -1.194063 0 1 121368 961 47 1 0 1 1 1.673221 1 0.380000 1.940000 0.252111 0.590000 4.100000e-01 0.800000 0.590000 0.603762 0.590000 0 0.490000 0.700000 KCND2 3751 broad.mit.edu 37 7 119914985 119914985 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr7:119914985G>A ENST00000331113.4 + 1 1264 c.299G>A c.(298-300)cGc>cAc p.R100H NM_012281.2 NP_036413.1 Q9NZV8 KCND2_HUMAN potassium voltage-gated channel, Shal-related subfamily, member 2 75 all_neural(327;0.117) Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458) AATTTCTACCGCACTGGGAAG 0.522000 0 SO:0001583 missense ENST00000331113.4 0 1 hg19 CCDS5776.1 . . . . . . . . . . G 27.5 4.840334 0.91117 . . ENSG00000184408 ENST00000331113 T 0.55760 0.5 5.71 5.71 0.89125 BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1); 0.000000 0.85682 D 0.000000 T 0.81669 0.4871 H 0.94808 3.585 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 D 0.86200 0.1618 9 . . . . 19.8677 0.96824 0.0:0.0:1.0:0.0 . 100 Q9NZV8 KCND2_HUMAN H 100 ENSP00000333496:R100H . R + 2 0 KCND2 119702221 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 8.062000 0.89475 2.709000 0.92574 0.655000 0.94253 CGC TCGA-2J-AAB1-01A-11D-A40W-08 KCND2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346996.1 0 0 0 19 899 0 177 0 4.946053e-04 0 2 0 177 2 0 0 0 0 0 2 1 0.999988 20 878 0 172 2 -2.188806 0 1 0 0 1 1 2 3 2.111304 0 0.380000 1.940000 0.393821 0.110000 6.000000e-02 1.000000 0.110000 0.202197 0.110000 0 0.080000 0.160000 SSPO 23145 broad.mit.edu 37 7 149513539 149513539 + RNA SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr7:149513539G>A ENST00000378016.2 + 0 11160 A2VEC9 SSPO_HUMAN SCO-spondin Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CCCACGTCACGCAGCAGGTGG 0.692000 0 ENST00000378016.2 0 1 hg19 TCGA-2J-AAB1-01A-11D-A40W-08 SSPO-202 KNOWN basic processed_transcript processed_transcript 0 0 0 8 45 0 17 0 0 0 1 0 17 2 0 0 0 0 0 2 1 0.989769 8 43 0 17 2 -15.999350 1 1 117776 2 20 1 1 2 3 2.111304 0 0.380000 1.940000 0.393821 0.860000 4.100000e-01 1.000000 1.000000 0.824554 0.860000 1 0.600000 1.000000 USP42 84132 broad.mit.edu 37 7 6185257 6185257 + Silent SNP C C T TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr7:6185257C>T ENST00000306177.5 + 10 1259 c.1101C>T c.(1099-1101)tgC>tgT p.C367C NM_032172.2 NP_115548.1 Q9H9J4 UBP42_HUMAN ubiquitin specific peptidase 42 35 Ovarian(82;0.0423) GTTTTAATTGCCATGCTGGCC 0.423000 0 SO:0001819 synonymous_variant ENST00000306177.5 0 1 hg19 CCDS47535.1 TCGA-2J-AAB1-01A-11D-A40W-08 USP42-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324262.3 0 0 0 4 155 0 37 0 1.520467e-02 0 6 0 37 2 0 0 0 0 0 2 1 0.882168 4 150 0 36 2 -3.500347 1 1 120832 2 31 1 1 2 3 2.111304 0 0.380000 1.940000 0.393821 0.160000 4.000000e-02 1.000000 0.130000 0.246221 0.160000 0 0.090000 0.280000 EPB41L4B 54566 broad.mit.edu 37 9 111970268 111970268 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr9:111970268G>A ENST00000374566.3 - 18 2331 c.1814C>T c.(1813-1815)gCg>gTg p.A605V NM_019114.3 NP_061987.3 Q9H329 E41LB_HUMAN erythrocyte membrane protein band 4.1 like 4B 39 CACATGATCCGCAACAGGGGA 0.423000 0 SO:0001583 missense ENST00000374566.3 0 1 hg19 CCDS43859.1 . . . . . . . . . . G 15.03 2.711206 0.48517 0.0 4.86E-4 ENSG00000095203 ENST00000262536;ENST00000374566 D 0.84516 -1.86 5.49 5.49 0.81192 . 0.000000 0.39834 N 0.001248 T 0.78130 0.4235 N 0.22421 0.69 0.80722 D 1 B 0.22541 0.071 B 0.12156 0.007 T 0.75255 -0.3382 10 0.87932 D 0 . 16.9032 0.86118 0.0:0.0:1.0:0.0 . 605 Q9H329 E41LB_HUMAN V 290;605 ENSP00000363694:A605V ENSP00000262536:A290V A - 2 0 EPB41L4B 111010089 0.984000 0.35163 0.130000 0.21974 0.350000 0.29205 4.611000 0.61162 2.583000 0.87209 0.561000 0.74099 GCG TCGA-2J-AAB1-01A-11D-A40W-08 EPB41L4B-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000053592.1 0 0 0 5 536 0 89 0 0 0 0 89 2 0 0 0 0 0 2 1 0.935959 5 530 0 89 2 -1.952813 0 1 120806 18 46 1 0 0 0 2.014026 0 0.380000 1.940000 0.377635 0.040000 1.000000e-02 0.110000 0.050000 0.057708 0.040000 0 0.020000 0.080000 KIF24 347240 broad.mit.edu 37 9 34256356 34256356 + Missense_Mutation SNP C C G TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chr9:34256356C>G ENST00000402558.2 - 10 3273 c.3249G>C c.(3247-3249)gaG>gaC p.E1083D KIF24_ENST00000345050.2_Missense_Mutation_p.E949D|KIF24_ENST00000379166.2_Missense_Mutation_p.E1083D|KIF24_ENST00000379174.3_Missense_Mutation_p.E949D Q5T7B8 KIF24_HUMAN kinesin family member 24 32 LUSC - Lung squamous cell carcinoma(29;0.0107) CCCCTGTGCTCTCTGCCACTA 0.602000 0 SO:0001583 missense ENST00000402558.2 1 1 hg19 CCDS6551.2 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 12.10|12.10 1.837588|1.837588 0.32513|0.32513 .|. .|. ENSG00000186638|ENSG00000186638 ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050;ENST00000420188|ENST00000443226 T;T;T;T|. 0.73152|. -0.5;-0.72;-0.5;-0.72|. 4.71|4.71 -2.5|-2.5 0.06384|0.06384 .|. 0.770342|0.770342 0.11063|0.11063 N|N 0.603757|0.603757 T|T 0.30135|0.30135 0.0755|0.0755 L|L 0.39898|0.39898 1.24|1.24 0.09310|0.09310 N|N 1|1 B|. 0.06786|. 0.001|. B|. 0.06405|. 0.002|. T|T 0.34527|0.34527 -0.9825|-0.9825 10|7 0.40728|0.20046 T|T 0.16|0.44 .|. 6.1763|6.1763 0.20444|0.20444 0.123:0.3985:0.0:0.4785|0.123:0.3985:0.0:0.4785 .|. 1083|. Q5T7B8|. KIF24_HUMAN|. D|Q 1083;949;1083;949;1083|129 ENSP00000384433:E1083D;ENSP00000368472:E949D;ENSP00000368464:E1083D;ENSP00000340179:E949D|. ENSP00000340179:E949D|ENSP00000414628:E129Q E|E -|- 3|1 2|0 KIF24|KIF24 34246356|34246356 0.000000|0.000000 0.05858|0.05858 0.000000|0.000000 0.03702|0.03702 0.120000|0.120000 0.20174|0.20174 -0.917000|-0.917000 0.04025|0.04025 -0.108000|-0.108000 0.12066|0.12066 0.563000|0.563000 0.77884|0.77884 GAG|GAG TCGA-2J-AAB1-01A-11D-A40W-08 KIF24-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052150.5 1 0 0 13 195 0 45 0 4.739336e-03 0 2 0 45 2 0 0 0 0 0 2 1 0.999558 13 193 0 45 2 -16.899190 1 1 0 0 1 0 2 2 2.027475 1 0.380000 1.940000 0.380000 0.330000 1.800000e-01 0.530000 0.320000 0.348125 0.330000 0 0.250000 0.430000 CUL4B 8450 broad.mit.edu 37 X 119674244 119674244 + Missense_Mutation SNP A A C TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chrX:119674244A>C ENST00000404115.3 - 13 2072 c.1671T>G c.(1669-1671)aaT>aaG p.N557K CUL4B_ENST00000336592.6_Missense_Mutation_p.N544K|CUL4B_ENST00000371322.5_Missense_Mutation_p.N539K NM_003588.3 NP_003579.3 Q13620 CUL4B_HUMAN cullin 4B 36 CAGCTGGTTTATTTGGTCTTT 0.308000 0 SO:0001583 missense ENST00000404115.3 1 1 hg19 CCDS35379.1 . . . . . . . . . . A 11.67 1.707788 0.30322 . . ENSG00000158290 ENST00000371322;ENST00000336592;ENST00000404115 T;T;T 0.73363 -0.74;-0.74;-0.74 5.6 2.54 0.30619 Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);Cullin homology (1); 0.000000 0.85682 D 0.000000 D 0.84088 0.5395 M 0.83118 2.625 0.58432 D 0.999999 P;D;D 0.89917 0.535;1.0;1.0 B;D;D 0.83275 0.398;0.996;0.993 T 0.82067 -0.0641 9 . . . -17.2501 7.9584 0.30057 0.5235:0.0:0.4765:0.0 . 361;557;539 Q13620-3;Q13620;Q13620-1 .;CUL4B_HUMAN;. K 539;544;557 ENSP00000360373:N539K;ENSP00000338919:N544K;ENSP00000384109:N557K . N - 3 2 CUL4B 119558272 1.000000 0.71417 1.000000 0.80357 0.233000 0.25261 1.401000 0.34589 0.413000 0.25759 -0.509000 0.04479 AAT TCGA-2J-AAB1-01A-11D-A40W-08 CUL4B-001 KNOWN non_canonical_conserved|basic|CCDS protein_coding protein_coding OTTHUMT00000058103.1 1 0 1 44 87 0 14 1 9.999798e-01 23 15 0 14 2 0 0 0 0 0 2 1 1.000000 44 86 0 14 2 -20.000000 1 1 0 0 1 0 1 1 0.380000 1.940000 0.380000 0.850000 6.600000e-01 0.990000 0.870000 0.853511 0.850000 1 0.750000 0.940000 BMX 660 broad.mit.edu 37 X 15526493 15526493 + Missense_Mutation SNP T T C TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chrX:15526493T>C ENST00000357607.2 + 2 205 c.17T>C c.(16-18)aTt>aCt p.I6T BMX_ENST00000463891.1_Intron|BMX_ENST00000342014.6_Missense_Mutation_p.I6T|BMX_ENST00000348343.6_Missense_Mutation_p.I6T P51813 BMX_HUMAN BMX non-receptor tyrosine kinase 30 Hepatocellular(33;0.183) ACAAAATCTATTCTAGAAGAA 0.294000 0 SO:0001583 missense ENST00000357607.2 0 1 hg19 CCDS14168.1 . . . . . . . . . . T 18.97 3.735041 0.69189 . . ENSG00000102010 ENST00000357607;ENST00000348343;ENST00000342014 D;D;D 0.94232 -3.38;-3.38;-3.38 5.67 5.67 0.87782 Pleckstrin homology-type (1);Pleckstrin homology domain (3); 0.097450 0.44483 D 0.000449 D 0.95169 0.8434 M 0.79926 2.475 0.37061 D 0.89808 P 0.50819 0.939 P 0.53988 0.739 D 0.96917 0.9671 10 0.87932 D 0 . 11.1504 0.48455 0.0:0.0:0.0:1.0 . 6 P51813 BMX_HUMAN T 6 ENSP00000350224:I6T;ENSP00000308774:I6T;ENSP00000340082:I6T ENSP00000340082:I6T I + 2 0 BMX 15436414 1.000000 0.71417 1.000000 0.80357 0.882000 0.50991 5.182000 0.65059 1.904000 0.55121 0.486000 0.48141 ATT TCGA-2J-AAB1-01A-11D-A40W-08 BMX-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055877.1 0 0 0 6 236 0 38 0 1.741371e-02 0 7 0 38 2 0 0 0 0 0 2 1 0.962730 6 230 0 38 2 -7.588117 1 1 0 0 1 0 1 1 0.380000 1.940000 0.380000 0.060000 2.000000e-02 0.130000 0.070000 0.074981 0.060000 0 0.040000 0.100000 OGT 8473 broad.mit.edu 37 X 70757810 70757810 + Missense_Mutation SNP G G A TCGA-2J-AAB1-01A-11D-A40W-08 TCGA-2J-AAB1-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 3654586b-e1d2-42e7-8560-b339bd5e3488 8a1fecb6-04f4-413a-bed8-63fce4ac7072 g.chrX:70757810G>A ENST00000373719.3 + 3 567 c.350G>A c.(349-351)cGt>cAt p.R117H OGT_ENST00000373701.3_Missense_Mutation_p.R107H|OGT_ENST00000498566.1_3'UTR NM_181672.2|NM_181673.2 NP_858058.1|NP_858059.1 O15294 OGT1_HUMAN O-linked N-acetylglucosamine (GlcNAc) transferase p.R117H(1)|p.R107H(1) 43 Renal(35;0.156) CATGCATTGCGTCTCAAACCT 0.493000 2 Substitution - Missense(2) SO:0001583 missense ENST00000373719.3 1 1 hg19 CCDS14414.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. g|g 20.1|20.1 3.937205|3.937205 0.73557|0.73557 .|. .|. ENSG00000147162|ENSG00000147162 ENST00000373719;ENST00000373701;ENST00000444774|ENST00000455587 T;T;T|. 0.60920|. 0.15;0.15;0.15|. 4.86|4.86 4.86|4.86 0.63082|0.63082 Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|. 0.105470|. 0.64402|. D|. 0.000011|. T|T 0.73297|0.73297 0.3569|0.3569 M|M 0.66560|0.66560 2.04|2.04 0.80722|0.80722 D|D 1|1 D;D;B|. 0.71674|. 0.998;0.997;0.369|. D;P;B|. 0.64042|. 0.921;0.832;0.045|. T|T 0.73275|0.73275 -0.4034|-0.4034 10|5 0.46703|. T|. 0.11|. -19.0221|-19.0221 17.2684|17.2684 0.87093|0.87093 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 117;107;117|. B4DTL6;O15294-3;O15294|. .;.;OGT1_HUMAN|. H|I 117;107;100|77 ENSP00000362824:R117H;ENSP00000362805:R107H;ENSP00000399729:R100H|. ENSP00000362805:R107H|. R|V +|+ 2|1 0|0 OGT|OGT 70674535|70674535 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.996000|0.996000 0.88848|0.88848 9.502000|9.502000 0.97981|0.97981 2.259000|2.259000 0.74868|0.74868 0.525000|0.525000 0.51046|0.51046 CGT|GTC TCGA-2J-AAB1-01A-11D-A40W-08 OGT-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000081829.3 1 0 1 75 106 0 30 1 9.999572e-01 11 15 0 30 2 0 0 0 0 0 2 1 1.000000 74 105 0 29 2 -20.000000 1 1 0 0 1 0 1 1 0.380000 1.940000 0.380000 0.950000 8.400000e-01 1.000000 0.990000 0.952522 0.950000 1 0.900000 0.990000