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 MRVI1 10335 broad.mit.edu 37 11 10645395 10645395 + Silent SNP G G T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr11:10645395G>T ENST00000436272.1 - 9 1374 c.1296C>A c.(1294-1296)atC>atA p.I432I MRVI1_ENST00000534266.2_Silent_p.I144I|MRVI1_ENST00000545852.1_Silent_p.I144I|MRVI1_ENST00000531107.1_Silent_p.I451I|MRVI1_ENST00000547195.1_Silent_p.I368I|MRVI1_ENST00000423302.2_Silent_p.I459I|MRVI1_ENST00000527509.2_Silent_p.I368I|MRVI1_ENST00000541483.1_Silent_p.I253I|MRVI1_ENST00000558540.1_Silent_p.I144I|MRVI1_ENST00000552103.1_Silent_p.I368I|MRVI1_ENST00000424001.1_Silent_p.I144I|MRVI1_ENST00000421747.1_Silent_p.I450I Q9Y6F6 MRVI1_HUMAN murine retrovirus integration site 1 homolog 22 TTCTCATCAGGATGTGCTCCT 0.483000 0 SO:0001819 synonymous_variant ENST00000436272.1 1 1 hg19 TCGA-IB-7885-01A-11D-2154-08 MRVI1-203 KNOWN basic protein_coding protein_coding 1 0 0 16 192 0 49 0 7.221349e-01 0 32 0 49 2 0 0 0 0 0 2 1 0.999937 15 190 0 48 2 -19.955600 1 1 0 0 1 0 1 1 1.882662 1 0.160000 1.730000 0.086957 0.790000 0.500000 0.990000 0.850000 0.790965 0.790000 0 0.640000 0.930000 NCAM1 4684 broad.mit.edu 37 11 113126681 113126681 + Silent SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr11:113126681C>T ENST00000533760.1 + 15 2126 c.1527C>T c.(1525-1527)gaC>gaT p.D509D NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000316851.7_Silent_p.D627D NM_001242608.1 NP_001229537.1 P13591 NCAM1_HUMAN neural cell adhesion molecule 1 49 all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207) AGCAGGATGACGGCGGCTCCC 0.552000 0 SO:0001819 synonymous_variant ENST00000533760.1 0 1 hg19 TCGA-IB-7885-01A-11D-2154-08 NCAM1-003 NOVEL basic|appris_principal protein_coding protein_coding OTTHUMT00000394068.2 1 0 1 6 57 0 18 0 3.565390e-02 0 3 0 18 2 0 0 0 0 0 2 1 0.965808 6 56 0 18 2 -11.619810 1 1 120884 2 26 1 1 2 3 2.052473 0 0.160000 1.730000 0.164678 0.990000 0.520000 1.000000 1.000000 0.934168 0.990000 1 0.810000 1.000000 HIPK3 10114 broad.mit.edu 37 11 33373261 33373261 + Missense_Mutation SNP A A T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr11:33373261A>T ENST00000303296.4 + 15 3220 c.2915A>T c.(2914-2916)gAc>gTc p.D972V HIPK3_ENST00000525975.1_Missense_Mutation_p.D951V|AL122015.1_ENST00000411202.1_RNA|HIPK3_ENST00000379016.3_Missense_Mutation_p.D951V|HIPK3_ENST00000456517.1_Missense_Mutation_p.D951V NM_005734.3 NP_005725.3 Q9H422 HIPK3_HUMAN homeodomain interacting protein kinase 3 39 TTTGTGGAGGACACTCATGAA 0.478000 0 SO:0001583 missense ENST00000303296.4 1 1 hg19 CCDS7884.1 . . . . . . . . . . A 12.95 2.091829 0.36952 . . ENSG00000110422 ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517 T;T;T;T 0.52526 0.67;0.66;0.67;0.67 6.05 3.75 0.43078 . 0.268050 0.31821 N 0.007020 T 0.33702 0.0872 N 0.14661 0.345 0.30727 N 0.747639 B;B 0.33103 0.397;0.042 B;B 0.41571 0.36;0.056 T 0.34129 -0.9841 10 0.19147 T 0.46 . 10.2146 0.43160 0.8652:0.0:0.1348:0.0 . 951;972 Q9H422-2;Q9H422 .;HIPK3_HUMAN V 951;972;951;951 ENSP00000431710:D951V;ENSP00000304226:D972V;ENSP00000368301:D951V;ENSP00000398241:D951V ENSP00000304226:D972V D + 2 0 HIPK3 33329837 0.998000 0.40836 0.138000 0.22173 0.108000 0.19459 3.844000 0.55873 0.538000 0.28769 -0.263000 0.10527 GAC TCGA-IB-7885-01A-11D-2154-08 HIPK3-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000255358.1 1 0 1 25 283 0 76 1 9.780475e-01 10 62 0 76 2 0 0 0 0 0 2 1 1.000000 25 279 0 76 2 -8.730358 1 1 0 0 1 1 2 3 2.059562 0 0.160000 1.730000 0.166005 0.990000 0.690000 1.000000 1.000000 0.945648 0.990000 1 0.840000 1.000000 CAPRIN1 4076 broad.mit.edu 37 11 34107957 34107957 + Missense_Mutation SNP C C G TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr11:34107957C>G ENST00000341394.4 + 11 1417 c.1228C>G c.(1228-1230)Cca>Gca p.P410A CAPRIN1_ENST00000389645.3_Missense_Mutation_p.P410A|CAPRIN1_ENST00000532820.1_Missense_Mutation_p.P410A|CAPRIN1_ENST00000529307.1_Missense_Mutation_p.P329A|CAPRIN1_ENST00000530820.1_Missense_Mutation_p.P410A NM_005898.4 NP_005889.3 Q14444 CAPR1_HUMAN cell cycle associated protein 1 18 Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016) GGTTTGCCCTCCAGGTTAGTA 0.363000 0 SO:0001583 missense ENST00000341394.4 1 1 hg19 CCDS31453.1 . . . . . . . . . . C 17.01 3.278865 0.59758 . . ENSG00000135387 ENST00000341394;ENST00000389645;ENST00000532820;ENST00000530820;ENST00000529307 T;T;T;T;T 0.36520 1.25;1.25;1.25;1.25;1.25 6.03 6.03 0.97812 . 0.098488 0.64402 D 0.000001 T 0.31513 0.0799 L 0.35414 1.06 0.80722 D 1 B;B 0.25850 0.136;0.023 B;B 0.21151 0.033;0.019 T 0.04621 -1.0938 10 0.21540 T 0.41 -6.388 20.5753 0.99366 0.0:1.0:0.0:0.0 . 410;410 Q14444;Q14444-2 CAPR1_HUMAN;. A 410;410;410;410;329 ENSP00000340329:P410A;ENSP00000374296:P410A;ENSP00000434150:P410A;ENSP00000434204:P410A;ENSP00000431581:P329A ENSP00000340329:P410A P + 1 0 CAPRIN1 34064533 1.000000 0.71417 1.000000 0.80357 0.939000 0.58152 4.642000 0.61383 2.868000 0.98415 0.557000 0.71058 CCA TCGA-IB-7885-01A-11D-2154-08 CAPRIN1-001 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000388680.2 1 0 0 20 182 0 63 1 1 84 242 0 63 2 0 0 0 0 0 2 1 0.999995 19 177 0 62 2 -3.075787 1 1 121412 1 30 1 1 2 3 2.059562 0 0.160000 1.730000 0.166005 0.990000 0.800000 1.000000 1.000000 0.984349 0.990000 1 0.990000 1.000000 PACSIN3 29763 broad.mit.edu 37 11 47203984 47203984 + Missense_Mutation SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr11:47203984C>T ENST00000539589.1 - 4 523 c.181G>A c.(181-183)Gcc>Acc p.A61T PACSIN3_ENST00000298838.6_Missense_Mutation_p.A61T NM_001184975.1 NP_001171904.1 Q9UKS6 PACN3_HUMAN protein kinase C and casein kinase substrate in neurons 3 11 CACTTTCGGGCCCAGTCAGCC 0.677000 0 SO:0001583 missense ENST00000539589.1 1 1 hg19 CCDS31481.1 . . . . . . . . . . C 17.88 3.497427 0.64186 . . ENSG00000165912 ENST00000298838;ENST00000415232;ENST00000539589;ENST00000528462;ENST00000531226;ENST00000525725;ENST00000530405;ENST00000524509 T;T;T;T;T;T;T 0.52526 2.31;2.31;2.31;0.66;0.66;0.66;0.66 5.01 5.01 0.66863 Fps/Fes/Fer/CIP4 homology (3); 0.167650 0.52532 D 0.000063 T 0.40932 0.1137 L 0.46885 1.475 0.58432 D 0.999998 P 0.45531 0.86 B 0.43838 0.433 T 0.26849 -1.0091 10 0.40728 T 0.16 -13.7472 7.1565 0.25641 0.218:0.6951:0.0:0.0869 . 61 Q9UKS6 PACN3_HUMAN T 61 ENSP00000298838:A61T;ENSP00000440945:A61T;ENSP00000437252:A61T;ENSP00000434699:A61T;ENSP00000435638:A61T;ENSP00000435672:A61T;ENSP00000431861:A61T ENSP00000298838:A61T A - 1 0 PACSIN3 47160560 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 2.895000 0.48648 2.511000 0.84671 0.561000 0.74099 GCC TCGA-IB-7885-01A-11D-2154-08 PACSIN3-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391632.1 1 0 1 32 359 0 116 1 9.885684e-01 31 50 0 116 2 0 0 0 0 0 2 1 1.000000 31 345 0 112 2 -9.718165 1 1 0 0 1 1 2 3 2.059562 0 0.160000 1.730000 0.166005 0.990000 0.720000 1.000000 1.000000 0.954953 0.990000 1 0.870000 1.000000 ZFP91 80829 broad.mit.edu 37 11 58347089 58347089 + Missense_Mutation SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr11:58347089G>A ENST00000316059.6 + 1 506 c.335G>A c.(334-336)cGa>cAa p.R112Q LPXN_ENST00000528954.1_5'Flank|ZFP91-CNTF_ENST00000389919.4_Missense_Mutation_p.R112Q|LPXN_ENST00000528489.1_5'Flank NM_001197051.1|NM_053023.4 NP_001183980.1|NP_444251.1 Q96JP5 ZFP91_HUMAN ZFP91 zinc finger protein 26 Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24) AAGAGTCCGCGACTCCTGTGA 0.672000 OREG0020976 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000316059.6 1 1 hg19 CCDS31553.1 . . . . . . . . . . G 15.18 2.756859 0.49362 . . ENSG00000186660 ENST00000316059;ENST00000389918 T 0.13901 2.55 3.77 3.77 0.43336 . . . . . T 0.07908 0.0198 N 0.19112 0.55 0.41174 D 0.986189 P;P 0.44241 0.829;0.738 B;B 0.33339 0.162;0.078 T 0.24083 -1.0170 9 0.59425 D 0.04 -2.8941 11.4656 0.50237 0.0:0.0:1.0:0.0 . 112;112 Q96JP5-2;Q96JP5 .;ZFP91_HUMAN Q 112 ENSP00000339030:R112Q ENSP00000374569:R112Q R + 2 0 ZFP91 58103665 1.000000 0.71417 1.000000 0.80357 0.709000 0.40893 4.412000 0.59787 1.815000 0.52974 0.313000 0.20887 CGA TCGA-IB-7885-01A-11D-2154-08 ZFP91-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268674.1 1 0 0 12 90 0 23 1 9.224812e-01 7 29 0 23 2 0 0 0 0 0 2 1 0.999172 12 87 0 22 2 -19.331180 1 1 117550 1 16 1 1 2 3 2.059562 0 0.160000 1.730000 0.166005 0.990000 0.820000 1.000000 1.000000 0.989192 0.990000 1 0.990000 1.000000 MYO7A 4647 broad.mit.edu 37 11 76918417 76918417 + Silent SNP A A G TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr11:76918417A>G ENST00000409709.3 + 42 6098 c.5826A>G c.(5824-5826)ggA>ggG p.G1942G MYO7A_ENST00000458637.2_Silent_p.G1904G|MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Silent_p.G1893G NM_000260.3 NP_000251.3 Q13402 MYO7A_HUMAN myosin VIIA 64 CCTCAGAGGGATTCAGCCTCT 0.572000 0 SO:0001819 synonymous_variant ENST00000409709.3 0 1 hg19 CCDS53683.1 TCGA-IB-7885-01A-11D-2154-08 MYO7A-001 KNOWN non_canonical_conserved|basic|CCDS protein_coding protein_coding OTTHUMT00000328133.1 0 0 0 4 63 0 23 1 2.957550e-01 4 11 0 23 2 0 0 0 0 0 2 1 0.885216 4 61 0 23 2 -8.532400 1 1 0 0 1 1 2 3 2.052473 0 0.160000 1.730000 0.164678 0.810000 0.280000 1.000000 1.000000 0.773573 0.810000 0 0.500000 1.000000 ENDOD1 23052 broad.mit.edu 37 11 94862206 94862206 + Silent SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr11:94862206G>A ENST00000278505.4 + 2 1084 c.966G>A c.(964-966)gaG>gaA p.E322E NM_015036.2 NP_055851.1 O94919 ENDD1_HUMAN endonuclease domain containing 1 11 Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824) AGGCATCTGAGGGAAGTAGTA 0.433000 0 SO:0001819 synonymous_variant ENST00000278505.4 1 1 hg19 CCDS41699.1 TCGA-IB-7885-01A-11D-2154-08 ENDOD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396545.1 1 0 1 27 328 0 69 1 9.984022e-01 54 69 0 69 2 0 0 0 0 0 2 1 1.000000 26 322 0 68 2 -2.376787 0 1 0 0 1 1 2 3 2.052473 0 0.160000 1.730000 0.164678 0.970000 0.650000 1.000000 1.000000 0.919209 0.970000 1 0.790000 1.000000 SLCO1C1 53919 broad.mit.edu 37 12 20854341 20854341 + Missense_Mutation SNP G G T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr12:20854341G>T ENST00000266509.2 + 3 587 c.219G>T c.(217-219)agG>agT p.R73S SLCO1C1_ENST00000545102.1_Intron|SLCO1C1_ENST00000545604.1_Missense_Mutation_p.R73S|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.R73S|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.R73S NM_017435.4 NP_059131.1 Q9NYB5 SO1C1_HUMAN solute carrier organic anion transporter family, member 1C1 60 Esophageal squamous(101;0.149) Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032) TAGAGAGAAGGTTTGATATCC 0.393000 0 SO:0001583 missense ENST00000266509.2 1 1 hg19 CCDS8683.1 . . . . . . . . . . G 18.38 3.611539 0.66558 . . ENSG00000139155 ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552 T;T;T;T 0.56941 0.43;0.43;0.43;0.43 5.09 2.07 0.26955 Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1); 0.000000 0.85682 D 0.000000 T 0.76040 0.3932 H 0.95611 3.695 0.45205 D 0.998213 D;D;D 0.89917 1.0;0.999;0.999 D;D;D 0.87578 0.998;0.996;0.995 T 0.76691 -0.2866 10 0.87932 D 0 . 6.9954 0.24779 0.3913:0.0:0.6087:0.0 . 73;73;73 B7Z3Q3;Q5JPA4;Q9NYB5 .;.;SO1C1_HUMAN S 73 ENSP00000444149:R73S;ENSP00000438665:R73S;ENSP00000266509:R73S;ENSP00000370964:R73S ENSP00000266509:R73S R + 3 2 SLCO1C1 20745608 0.996000 0.38824 1.000000 0.80357 0.997000 0.91878 0.428000 0.21395 0.740000 0.32651 0.655000 0.94253 AGG TCGA-IB-7885-01A-11D-2154-08 SLCO1C1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401765.1 1 0 0 35 418 0 106 0 0 0 0 106 2 0 0 0 0 0 2 1 1.000000 35 408 0 106 2 -20.000000 1 1 0 0 1 1 2 3 2.113570 1 0.160000 1.730000 0.177116 0.990000 0.710000 1.000000 1.000000 0.947826 0.990000 1 0.850000 1.000000 ABCC9 10060 broad.mit.edu 37 12 21997786 21997786 + Missense_Mutation SNP A A T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr12:21997786A>T ENST00000261201.4 - 25 3159 c.3160T>A c.(3160-3162)Tcc>Acc p.S1054T RP11-729I10.2_ENST00000539874.1_RNA|ABCC9_ENST00000345162.2_Missense_Mutation_p.S1018T|ABCC9_ENST00000261200.4_Missense_Mutation_p.S1054T NM_005691.2 NP_005682.2 O60706 ABCC9_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 9 118 Adenosine triphosphate(DB00171)|Glyburide(DB01016) ACAGTGAGGGATGTAACAAGG 0.413000 0 SO:0001583 missense ENST00000261201.4 1 1 hg19 CCDS8694.1 . . . . . . . . . . A 19.31 3.803647 0.70682 . . ENSG00000069431 ENST00000261200;ENST00000544039;ENST00000261201;ENST00000345162 D;D;D;D 0.90620 -2.7;-2.7;-2.7;-2.7 5.27 5.27 0.74061 ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1); 0.278617 0.37393 N 0.002119 D 0.87877 0.6288 L 0.35723 1.085 0.58432 D 0.999994 B;B 0.32382 0.368;0.291 B;B 0.39152 0.292;0.091 D 0.85757 0.1347 10 0.30854 T 0.27 -13.5709 15.2233 0.73330 1.0:0.0:0.0:0.0 . 1054;1054 O60706;O60706-2 ABCC9_HUMAN;. T 1054;681;1054;1018 ENSP00000261200:S1054T;ENSP00000440521:S681T;ENSP00000261201:S1054T;ENSP00000261202:S1018T ENSP00000261200:S1054T S - 1 0 ABCC9 21889053 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 9.092000 0.94157 1.985000 0.57927 0.528000 0.53228 TCC TCGA-IB-7885-01A-11D-2154-08 ABCC9-002 KNOWN not_organism_supported|basic|CCDS protein_coding protein_coding OTTHUMT00000402230.1 1 0 1 44 389 0 67 0 4.665557e-01 0 15 0 67 2 0 0 0 0 0 2 1 1.000000 41 385 0 66 2 -15.104770 1 1 0 0 1 1 2 3 2.113570 1 0.160000 1.730000 0.177116 0.990000 0.970000 1.000000 1.000000 0.998013 0.990000 1 0.990000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V 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 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-IB-7885-01A-11D-2154-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 7 88 0 38 1 6.948953e-01 7 24 0 38 2 1 9.999989e-01 33 540 0 408 2 1 0.981954 7 88 0 37 2 -5.394511 1 1 0 0 1 1 2 3 2.113570 1 0.160000 1.730000 0.177116 0.990000 0.460000 1.000000 1.000000 0.892419 0.990000 1 0.700000 1.000000 NIN 51199 broad.mit.edu 37 14 51288700 51288700 + Silent SNP T T G TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr14:51288700T>G ENST00000382041.3 - 3 265 c.75A>C c.(73-75)acA>acC p.T25T NIN_ENST00000530997.2_Silent_p.T25T|NIN_ENST00000382043.4_Silent_p.T25T|NIN_ENST00000453196.1_Silent_p.T25T|NIN_ENST00000389868.3_Silent_p.T25T|NIN_ENST00000324330.9_Silent_p.T25T|NIN_ENST00000245441.5_Silent_p.T25T|RP11-286O18.1_ENST00000555966.1_RNA NM_016350.4|NM_182946.1 NP_057434.4|NP_891991 Q8N4C6 NIN_HUMAN ninein (GSK3B interacting protein) 71 all_epithelial(31;0.00244)|Breast(41;0.127) CCAGGGACCCTGTGCCCGTCG 0.582000 T PDGFRB MPD Dom yes 14 14q24 51199 ninein (GSK3B interacting protein) L 0 SO:0001819 synonymous_variant ENST00000382041.3 1 1 hg19 CCDS32079.1 TCGA-IB-7885-01A-11D-2154-08 NIN-016 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000395207.2 1 0 0 112 1138 0 334 0 9.589758e-02 1 5 0 334 2 0 0 0 0 0 2 1 1.000000 110 1098 0 331 2 -20.000000 1 1 0 0 1 0 0 0 2.027661 0 0.160000 1.730000 0.150485 0.990000 0.910000 1.000000 1.000000 0.993917 0.990000 1 0.990000 1.000000 ACAN 176 broad.mit.edu 37 15 89386782 89386782 + Silent SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr15:89386782C>T ENST00000561243.1 + 5 954 c.954C>T c.(952-954)tgC>tgT p.C318C ACAN_ENST00000559004.1_Silent_p.C318C|ACAN_ENST00000558207.1_Silent_p.C318C|ACAN_ENST00000352105.7_Silent_p.C318C|ACAN_ENST00000439576.2_Silent_p.C318C P16112 PGCA_HUMAN aggrecan 93 Lung NSC(78;0.0392)|all_lung(78;0.077) BRCA - Breast invasive adenocarcinoma(143;0.146) GGCCCAACTGCGGTGGCAACC 0.677000 0 SO:0001819 synonymous_variant ENST00000561243.1 0 1 hg19 CCDS53970.1 TCGA-IB-7885-01A-11D-2154-08 ACAN-006 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416267.2 0 0 0 11 194 0 50 0 1.028708e-02 0 3 0 50 2 0 0 0 0 0 2 1 0.997743 10 181 0 50 2 -14.007260 1 1 0 0 1 0 1 1 2.032754 0 0.160000 1.730000 0.154589 0.670000 0.360000 1.000000 1.000000 0.692504 0.670000 0 0.500000 0.890000 MRPL12 6182 broad.mit.edu 37 17 79673938 79673938 + Silent SNP G G A rs140892819 TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr17:79673938G>A ENST00000333676.3 + 4 493 c.348G>A c.(346-348)gcG>gcA p.A116A SLC25A10_ENST00000571730.1_Silent_p.A116A|SLC25A10_ENST00000541223.1_Silent_p.A116A NM_002949.3 NP_002940.2 P52815 RM12_HUMAN mitochondrial ribosomal protein L12 4 all_neural(118;0.0878)|all_lung(278;0.23) BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955) TCCCTAAGGCGGTGGAAGAAG 0.577000 0 SO:0001819 synonymous_variant ENST00000333676.3 1 1 hg19 CCDS11785.1 TCGA-IB-7885-01A-11D-2154-08 MRPL12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000440812.1 0 0 0 12 154 0 44 1 9.999998e-01 118 368 0 44 2 0 0 0 0 0 2 1 0.999104 12 150 0 44 2 -3.222626 1 1 0 0 1 0 1 1 2.032483 0 0.160000 1.730000 0.154589 0.900000 0.500000 1.000000 1.000000 0.861200 0.900000 1 0.680000 1.000000 DSC1 1823 broad.mit.edu 37 18 28736086 28736086 + Missense_Mutation SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr18:28736086G>A ENST00000257198.5 - 4 652 c.391C>T c.(391-393)Cgc>Tgc p.R131C DSC1_ENST00000257197.3_Missense_Mutation_p.R131C|RP11-408H20.2_ENST00000581836.1_RNA NM_024421.2 NP_077739.1 Q08554 DSC1_HUMAN desmocollin 1 p.R131C(2) 53 OV - Ovarian serous cystadenocarcinoma(10;0.00778) CTCTTGCTGCGCTTGAGGGCT 0.418000 2 Substitution - Missense(2) SO:0001583 missense ENST00000257198.5 1 1 hg19 CCDS11894.1 . . . . . . . . . . G 23.6 4.435632 0.83885 . . ENSG00000134765 ENST00000257197;ENST00000257198 T;T 0.63744 -0.06;-0.06 5.66 3.76 0.43208 Cadherin-like (1); 0.277613 0.24083 N 0.041706 T 0.80732 0.4679 M 0.91561 3.22 0.80722 D 1 D;D 0.89917 0.999;1.0 P;P 0.60609 0.791;0.877 D 0.86178 0.1604 10 0.87932 D 0 . 14.689 0.69070 0.0:0.0:0.74:0.26 . 131;131 Q08554;Q9HB00 DSC1_HUMAN;. C 131 ENSP00000257197:R131C;ENSP00000257198:R131C ENSP00000257197:R131C R - 1 0 DSC1 26990084 0.989000 0.36119 0.953000 0.39169 0.987000 0.75469 2.123000 0.41996 1.502000 0.48669 0.655000 0.94253 CGC TCGA-IB-7885-01A-11D-2154-08 DSC1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000254946.1 0 0 0 11 347 1 78 0 0 0 1 78 2 0 0 0 0 0 2 0 0.207915 11 344 1 77 16 -3.481508 1 1 121412 3 30 1 0 1 1 1.867096 1 0.160000 1.730000 0.086957 0.350000 0.180000 0.580000 0.340000 0.372116 0.350000 0 0.260000 0.470000 FBXO15 201456 broad.mit.edu 37 18 71790624 71790624 + Missense_Mutation SNP G G A rs144253482 byFrequency TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr18:71790624G>A ENST00000419743.2 - 8 1196 c.1117C>T c.(1117-1119)Cgc>Tgc p.R373C FBXO15_ENST00000269500.5_Missense_Mutation_p.R297C NM_001142958.1 NP_001136430.1 Q8NCQ5 FBX15_HUMAN F-box protein 15 27 Esophageal squamous(42;0.103)|Prostate(75;0.173) AAGAGATTGCGAAATGTACCA 0.428000 0 SO:0001583 missense ENST00000419743.2 1 1 hg19 CCDS45884.1 . . . . . . . . . . G 12.05 1.822669 0.32237 2.27E-4 1.16E-4 ENSG00000141665 ENST00000269500;ENST00000419743 T;T 0.46063 0.88;0.88 5.45 4.58 0.56647 . 0.718217 0.13850 N 0.358421 T 0.50837 0.1639 L 0.59436 1.845 0.09310 N 0.999999 D;D 0.76494 0.999;0.998 P;P 0.50490 0.642;0.549 T 0.46775 -0.9167 10 0.87932 D 0 -24.4827 14.1359 0.65287 0.0:0.1514:0.8486:0.0 . 373;297 B3KST3;Q8NCQ5 .;FBX15_HUMAN C 297;373 ENSP00000269500:R297C;ENSP00000393154:R373C ENSP00000269500:R297C R - 1 0 FBXO15 69941604 0.793000 0.28825 0.007000 0.13788 0.007000 0.05969 1.823000 0.39062 1.290000 0.44636 0.655000 0.94253 CGC TCGA-IB-7885-01A-11D-2154-08 FBXO15-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000444223.1 1 0 0 24 271 0 65 1 3.894504e-02 4 0 0 65 2 0 0 0 0 0 2 1 1.000000 24 265 0 65 2 -8.069414 1 1 121412 20 42 1 0 1 1 1.867096 1 0.160000 1.730000 0.086957 0.840000 0.580000 0.990000 0.910000 0.836188 0.840000 0 0.710000 0.950000 KIR3DL3 115653 broad.mit.edu 37 19 55247491 55247491 + Silent SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr19:55247491C>T ENST00000291860.1 + 8 1179 c.1161C>T c.(1159-1161)tgC>tgT p.C387C KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR2DL3_ENST00000434419.2_5'Flank|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR2DL3_ENST00000342376.3_5'Flank NM_153443.3 NP_703144.2 Q8N743 KI3L3_HUMAN killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3 21 TGAATCACTGCGTTTTCACAC 0.517000 0 SO:0001819 synonymous_variant ENST00000291860.1 0 1 hg19 CCDS12903.1 TCGA-IB-7885-01A-11D-2154-08 KIR3DL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000141147.1 0 0 0 56 254 0 104 0 0 0 0 104 2 0 0 0 0 0 2 1 1.000000 37 135 0 199 2 -20.000000 1 1 108008 1 35 1 0 0 0 1.999485 0 0.160000 1.730000 0.137931 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 NGF 4803 broad.mit.edu 37 1 115829233 115829233 + Missense_Mutation SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr1:115829233G>A ENST00000369512.2 - 3 352 c.184C>T c.(184-186)Cgc>Tgc p.R62C RP4-663N10.1_ENST00000425449.1_RNA NM_002506.2 NP_002497.2 P01138 NGF_HUMAN nerve growth factor (beta polypeptide) 13 Lung SC(450;0.211) all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05) Clenbuterol(DB01407) CCCGCCACGCGTGCAGCTATC 0.632000 0 SO:0001583 missense ENST00000369512.2 1 1 hg19 CCDS882.1 . . . . . . . . . . G 12.46 1.943321 0.34283 . . ENSG00000134259 ENST00000369512 T 0.63417 -0.04 5.06 -0.0542 0.13815 . 0.100578 0.42548 D 0.000686 T 0.58206 0.2106 M 0.77486 2.375 0.09310 N 0.999997 D 0.76494 0.999 P 0.51806 0.68 T 0.63184 -0.6694 10 0.87932 D 0 -22.5746 14.8749 0.70488 0.0:0.0:0.6922:0.3078 . 62 P01138 NGF_HUMAN C 62 ENSP00000358525:R62C ENSP00000358525:R62C R - 1 0 NGF 115630756 0.066000 0.20996 0.543000 0.28128 0.207000 0.24258 1.510000 0.35790 0.104000 0.17725 0.467000 0.42956 CGC TCGA-IB-7885-01A-11D-2154-08 NGF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032832.1 1 0 0 20 251 0 62 0 1.749579e-02 0 3 0 62 2 0 0 0 0 0 2 1 0.999995 19 247 0 60 2 -19.999990 1 1 121410 2 35 1 1 2 3 2.045242 0 0.160000 1.730000 0.163347 0.930000 0.590000 1.000000 1.000000 0.895037 0.930000 1 0.750000 1.000000 ETV3L 440695 broad.mit.edu 37 1 157068532 157068532 + Missense_Mutation SNP C C T rs147712441 byFrequency TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr1:157068532C>T ENST00000454449.2 - 3 736 c.452G>A c.(451-453)cGg>cAg p.R151Q NM_001004341.2 NP_001004341.1 Q6ZN32 ETV3L_HUMAN ets variant 3-like 24 Hepatocellular(266;0.158) Prostate(1639;0.184) CAGCGCTGGCCGACACAGGGC 0.647000 0 SO:0001583 missense ENST00000454449.2 1 1 hg19 CCDS30893.1 . . . . . . . . . . C 1.717 -0.497505 0.04291 4.54E-4 1.16E-4 ENSG00000253831 ENST00000454449 T 0.08193 3.12 4.3 -1.01 0.10169 . . . . . T 0.01124 0.0037 N 0.11201 0.11 0.09310 N 1 B 0.13594 0.008 B 0.06405 0.002 T 0.46470 -0.9189 9 0.16896 T 0.51 . 10.2253 0.43222 0.0:0.5723:0.0:0.4277 . 151 Q6ZN32 ETV3L_HUMAN Q 151 ENSP00000430271:R151Q ENSP00000430271:R151Q R - 2 0 ETV3L 155335156 0.960000 0.32886 0.459000 0.27081 0.103000 0.19146 -1.036000 0.03560 -0.603000 0.05767 -0.797000 0.03246 CGG TCGA-IB-7885-01A-11D-2154-08 ETV3L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000099024.2 1 0 0 41 396 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 1.000000 41 391 0 70 2 -3.221883 1 1 121392 25 44 1 1 2 3 2.051566 0 0.160000 1.730000 0.164678 0.990000 0.860000 1.000000 1.000000 0.990165 0.990000 1 0.990000 1.000000 SPTA1 6708 broad.mit.edu 37 1 158596687 158596687 + Missense_Mutation SNP T T G TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr1:158596687T>G ENST00000368147.4 - 41 5955 c.5775A>C c.(5773-5775)gaA>gaC p.E1925D NM_003126.2 NP_003117.2 P02549 SPTA1_HUMAN spectrin, alpha, erythrocytic 1 307 all_hematologic(112;0.0378) CATAATCGTCTTCCAATTGCA 0.453000 0 SO:0001583 missense ENST00000368147.4 1 1 hg19 CCDS41423.1 . . . . . . . . . . T 1.984 -0.433334 0.04669 . . ENSG00000163554 ENST00000368148;ENST00000368147 T;T 0.39997 1.05;1.05 5.41 -3.96 0.04106 . 0.513432 0.14584 N 0.310658 T 0.04634 0.0126 N 0.17564 0.495 0.21416 N 0.999695 B 0.06786 0.001 B 0.09377 0.004 T 0.33854 -0.9852 10 0.09338 T 0.73 . 0.247 0.00200 0.2871:0.2601:0.2146:0.2382 . 1925 P02549 SPTA1_HUMAN D 1925;1922 ENSP00000357130:E1925D;ENSP00000357129:E1922D ENSP00000357129:E1922D E - 3 2 SPTA1 156863311 0.995000 0.38212 0.001000 0.08648 0.340000 0.28889 0.254000 0.18314 -0.327000 0.08551 0.460000 0.39030 GAA TCGA-IB-7885-01A-11D-2154-08 SPTA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051851.3 1 0 0 47 652 0 146 0 0 0 1 0 146 2 0 0 0 0 0 2 1 1.000000 46 637 0 146 2 -9.487158 1 1 0 0 1 1 2 3 2.051566 0 0.160000 1.730000 0.164678 0.850000 0.630000 1.000000 1.000000 0.855499 0.850000 1 0.730000 1.000000 FCER1A 2205 broad.mit.edu 37 1 159273851 159273851 + Silent SNP T T A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr1:159273851T>A ENST00000368115.1 + 4 309 c.210T>A c.(208-210)ctT>ctA p.L70L FCER1A_ENST00000368114.1_Silent_p.L37L NM_002001.3 NP_001992.1 P12319 FCERA_HUMAN Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide 33 all_hematologic(112;0.0429) Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043) ATGGCAGCCTTTCAGAAGAGA 0.368000 0 SO:0001819 synonymous_variant ENST00000368115.1 1 1 hg19 CCDS1184.1 TCGA-IB-7885-01A-11D-2154-08 FCER1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090328.2 1 0 1 36 343 0 84 0 2.904795e-01 0 11 0 84 2 0 0 0 1 0 0 2 1 1.000000 36 337 0 84 2 -20.000000 1 1 0 0 1 1 2 3 2.051566 0 0.160000 1.730000 0.164678 0.990000 0.860000 1.000000 1.000000 0.989658 0.990000 1 0.990000 1.000000 SEC16B 89866 broad.mit.edu 37 1 177934213 177934213 + Missense_Mutation SNP G G C TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr1:177934213G>C ENST00000308284.6 - 4 591 c.502C>G c.(502-504)Cca>Gca p.P168A SEC16B_ENST00000464631.2_Missense_Mutation_p.P168A|RP4-798P15.3_ENST00000354921.3_RNA NM_033127.2 NP_149118.2 Q96JE7 SC16B_HUMAN SEC16 homolog B (S. cerevisiae) 35 GTTCCAAATGGACTGTGCTGG 0.448000 0 SO:0001583 missense ENST00000308284.6 0 1 hg19 CCDS44281.1 . . . . . . . . . . G 9.492 1.100919 0.20552 . . ENSG00000120341 ENST00000308284;ENST00000464631 T;T 0.44482 2.51;0.92 5.49 -8.05 0.01106 . 1.562370 0.03228 N 0.178526 T 0.26412 0.0645 L 0.50333 1.59 0.09310 N 1 B;B;B 0.25563 0.129;0.055;0.055 B;B;B 0.21151 0.033;0.03;0.03 T 0.16394 -1.0404 10 0.15066 T 0.55 5.5521 1.2287 0.01939 0.4395:0.1985:0.1517:0.2103 . 168;168;168 E9PK14;B1AM08;Q96JE7 .;.;SC16B_HUMAN A 168 ENSP00000308339:P168A;ENSP00000431727:P168A ENSP00000308339:P168A P - 1 0 AL359075.1 176200836 0.000000 0.05858 0.000000 0.03702 0.003000 0.03518 -0.828000 0.04419 -1.710000 0.01397 -0.909000 0.02823 CCA TCGA-IB-7885-01A-11D-2154-08 SEC16B-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084773.16 1 0 0 6 87 0 21 1 7.178126e-02 3 3 0 21 2 0 0 0 0 0 2 1 0.966631 6 87 0 21 2 -10.253800 1 1 0 0 1 1 2 3 2.051566 0 0.160000 1.730000 0.164678 0.860000 0.360000 1.000000 1.000000 0.810494 0.860000 1 0.570000 1.000000 OSBPL9 114883 broad.mit.edu 37 1 52249642 52249642 + Missense_Mutation SNP C C G rs61743086 byFrequency TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr1:52249642C>G ENST00000428468.1 + 18 1571 c.1569C>G c.(1567-1569)atC>atG p.I523M OSBPL9_ENST00000462759.1_Missense_Mutation_p.I345M|OSBPL9_ENST00000447887.1_Missense_Mutation_p.I533M|OSBPL9_ENST00000453295.1_Missense_Mutation_p.I506M|OSBPL9_ENST00000371710.3_Missense_Mutation_p.I541M|OSBPL9_ENST00000486942.1_Missense_Mutation_p.I345M|OSBPL9_ENST00000531828.1_Missense_Mutation_p.I358M|OSBPL9_ENST00000371714.1_Missense_Mutation_p.I510M|OSBPL9_ENST00000337809.4_Missense_Mutation_p.I528M|OSBPL9_ENST00000361556.5_Missense_Mutation_p.I413M|OSBPL9_ENST00000530544.1_Missense_Mutation_p.I442M|OSBPL9_ENST00000435686.2_Missense_Mutation_p.I358M Q96SU4 OSBL9_HUMAN oxysterol binding protein-like 9 18 ATGCTCATATCTGGACCAAAT 0.368000 0 SO:0001583 missense ENST00000428468.1 1 1 hg19 CCDS41332.3 . . . . . . . . . . C 16.28 3.078450 0.55753 . . ENSG00000117859 ENST00000371714;ENST00000371710;ENST00000337809;ENST00000447887;ENST00000435686;ENST00000428468;ENST00000453295;ENST00000530544;ENST00000531828;ENST00000361556;ENST00000462759;ENST00000486942 T;T;T;T;T;T;T;T;T;T;T;T 0.32753 1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44 5.24 4.27 0.50696 . 0.000000 0.85682 D 0.000000 T 0.65037 0.2653 M 0.93594 3.435 0.58432 D 0.999993 D;D;D;D;D 0.76494 0.996;0.991;0.996;0.993;0.999 D;D;D;D;D 0.78314 0.991;0.952;0.969;0.969;0.984 T 0.76353 -0.2990 10 0.87932 D 0 -10.3454 14.7454 0.69488 0.2284:0.7716:0.0:0.0 . 506;413;539;523;528 Q86YQ3;Q96SU4-3;B1AKJ7;Q96SU4;B1AKJ6 .;.;.;OSBL9_HUMAN;. M 510;541;528;533;358;523;506;442;358;413;345;345 ENSP00000360779:I510M;ENSP00000360775:I541M;ENSP00000337265:I528M;ENSP00000412733:I533M;ENSP00000402646:I358M;ENSP00000407168:I523M;ENSP00000413263:I506M;ENSP00000433675:I442M;ENSP00000433083:I358M;ENSP00000354970:I413M;ENSP00000433279:I345M;ENSP00000431980:I345M ENSP00000337265:I528M I + 3 3 OSBPL9 52022230 0.999000 0.42202 1.000000 0.80357 0.998000 0.95712 0.768000 0.26590 1.362000 0.46000 0.555000 0.69702 ATC TCGA-IB-7885-01A-11D-2154-08 OSBPL9-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000022584.4 1 0 0 19 337 0 80 1 9.974191e-01 14 157 0 80 2 0 0 0 0 0 2 1 0.999989 18 330 0 80 2 -5.424052 1 0 0 0 1 1 2 3 2.045242 0 0.160000 1.730000 0.163347 0.680000 0.420000 1.000000 1.000000 0.700700 0.680000 0 0.540000 0.860000 OSBPL9 114883 broad.mit.edu 37 1 52249653 52249653 + Missense_Mutation SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr1:52249653C>T ENST00000428468.1 + 18 1582 c.1580C>T c.(1579-1581)tCa>tTa p.S527L OSBPL9_ENST00000462759.1_Missense_Mutation_p.S349L|OSBPL9_ENST00000447887.1_Missense_Mutation_p.S537L|OSBPL9_ENST00000453295.1_Missense_Mutation_p.S510L|OSBPL9_ENST00000371710.3_Missense_Mutation_p.S545L|OSBPL9_ENST00000486942.1_Missense_Mutation_p.S349L|OSBPL9_ENST00000531828.1_Missense_Mutation_p.S362L|OSBPL9_ENST00000371714.1_Missense_Mutation_p.S514L|OSBPL9_ENST00000337809.4_Missense_Mutation_p.S532L|OSBPL9_ENST00000361556.5_Missense_Mutation_p.S417L|OSBPL9_ENST00000530544.1_Missense_Mutation_p.S446L|OSBPL9_ENST00000435686.2_Missense_Mutation_p.S362L Q96SU4 OSBL9_HUMAN oxysterol binding protein-like 9 18 TGGACCAAATCAAAATTCCTT 0.348000 0 SO:0001583 missense ENST00000428468.1 1 1 hg19 CCDS41332.3 . . . . . . . . . . C 33 5.236229 0.95240 . . ENSG00000117859 ENST00000371714;ENST00000371710;ENST00000337809;ENST00000447887;ENST00000435686;ENST00000428468;ENST00000453295;ENST00000530544;ENST00000531828;ENST00000361556;ENST00000462759;ENST00000486942 T;T;T;T;T;T;T;T;T;T;T;T 0.32753 1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44;1.44 5.24 5.24 0.73138 . 0.000000 0.85682 D 0.000000 T 0.60534 0.2276 M 0.80332 2.49 0.80722 D 1 D;D;D;D;D 0.89917 0.994;1.0;1.0;1.0;1.0 D;D;D;D;D 0.91635 0.985;0.997;0.994;0.997;0.999 T 0.64753 -0.6333 10 0.87932 D 0 -18.1822 19.0133 0.92882 0.0:1.0:0.0:0.0 . 510;417;543;527;532 Q86YQ3;Q96SU4-3;B1AKJ7;Q96SU4;B1AKJ6 .;.;.;OSBL9_HUMAN;. L 514;545;532;537;362;527;510;446;362;417;349;349 ENSP00000360779:S514L;ENSP00000360775:S545L;ENSP00000337265:S532L;ENSP00000412733:S537L;ENSP00000402646:S362L;ENSP00000407168:S527L;ENSP00000413263:S510L;ENSP00000433675:S446L;ENSP00000433083:S362L;ENSP00000354970:S417L;ENSP00000433279:S349L;ENSP00000431980:S349L ENSP00000337265:S532L S + 2 0 OSBPL9 52022241 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 7.576000 0.82467 2.729000 0.93468 0.555000 0.69702 TCA TCGA-IB-7885-01A-11D-2154-08 OSBPL9-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000022584.4 1 0 0 16 346 0 81 1 9.968445e-01 13 192 0 81 2 0 0 0 0 0 2 1 0.999923 15 338 0 81 2 -3.297894 1 0 0 0 1 1 2 3 2.045242 0 0.160000 1.730000 0.163347 0.560000 0.330000 1.000000 0.550000 0.593653 0.560000 0 0.440000 0.740000 OSBPL9 114883 broad.mit.edu 37 1 52249970 52249970 + Silent SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr1:52249970C>T ENST00000428468.1 + 19 1661 c.1659C>T c.(1657-1659)taC>taT p.Y553Y OSBPL9_ENST00000462759.1_Silent_p.Y375Y|OSBPL9_ENST00000447887.1_Silent_p.Y563Y|OSBPL9_ENST00000453295.1_Silent_p.Y536Y|OSBPL9_ENST00000371710.3_Silent_p.Y571Y|OSBPL9_ENST00000486942.1_Silent_p.Y375Y|OSBPL9_ENST00000531828.1_Silent_p.Y388Y|OSBPL9_ENST00000371714.1_Silent_p.Y540Y|OSBPL9_ENST00000337809.4_Silent_p.Y558Y|OSBPL9_ENST00000361556.5_Silent_p.Y443Y|OSBPL9_ENST00000530544.1_Silent_p.Y472Y|OSBPL9_ENST00000435686.2_Silent_p.Y388Y Q96SU4 OSBL9_HUMAN oxysterol binding protein-like 9 18 ATGAACATTACATTCTCACAT 0.488000 0 SO:0001819 synonymous_variant ENST00000428468.1 1 1 hg19 CCDS41332.3 TCGA-IB-7885-01A-11D-2154-08 OSBPL9-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000022584.4 1 0 0 47 464 0 140 1 9.999991e-01 8 194 0 140 2 0 0 0 0 0 2 1 1.000000 46 453 0 139 2 -14.003430 1 1 0 0 1 1 2 3 2.045242 0 0.160000 1.730000 0.163347 0.990000 0.860000 1.000000 1.000000 0.989262 0.990000 1 0.990000 1.000000 ZSWIM3 140831 broad.mit.edu 37 20 44506266 44506266 + Missense_Mutation SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr20:44506266G>A ENST00000255152.2 + 2 1278 c.1069G>A c.(1069-1071)Gta>Ata p.V357I ZSWIM3_ENST00000454862.2_Missense_Mutation_p.V351I NM_080752.3 NP_542790.2 Q96MP5 ZSWM3_HUMAN zinc finger, SWIM-type containing 3 35 Myeloproliferative disorder(115;0.0122) GTCCCAGGCCGTACTGGATGA 0.522000 0 SO:0001583 missense ENST00000255152.2 1 1 hg19 CCDS13381.1 . . . . . . . . . . g 3.393 -0.123988 0.06795 . . ENSG00000132801 ENST00000255152;ENST00000454862 T;T 0.21734 2.01;1.99 5.65 2.64 0.31445 . 0.413487 0.22779 N 0.055752 T 0.09555 0.0235 N 0.14661 0.345 0.09310 N 1 B;B 0.24882 0.048;0.113 B;B 0.13407 0.006;0.009 T 0.33854 -0.9852 10 0.16896 T 0.51 -3.9801 6.6767 0.23098 0.12:0.4609:0.3521:0.067 . 351;357 E7ETT6;Q96MP5 .;ZSWM3_HUMAN I 357;351 ENSP00000255152:V357I;ENSP00000406313:V351I ENSP00000255152:V357I V + 1 0 ZSWIM3 43939673 0.000000 0.05858 0.265000 0.24526 0.985000 0.73830 -0.175000 0.09825 0.464000 0.27142 -0.123000 0.14984 GTA TCGA-IB-7885-01A-11D-2154-08 ZSWIM3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079540.1 1 0 0 20 338 0 78 0 1.538057e-01 0 12 0 78 2 0 0 0 0 0 2 1 0.999995 20 336 0 78 2 -2.807658 1 1 0 0 1 1 2 3 2.063923 0 0.160000 1.730000 0.167328 0.720000 0.450000 1.000000 1.000000 0.746403 0.720000 0 0.570000 0.950000 RTEL1 51750 broad.mit.edu 37 20 62292776 62292776 + Silent SNP G G A rs116624637 by1000genomes TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr20:62292776G>A ENST00000360203.5 + 3 553 c.228G>A c.(226-228)gcG>gcA p.A76A RTEL1_ENST00000370018.3_Silent_p.A76A|RTEL1_ENST00000508582.2_Silent_p.A76A|RTEL1_ENST00000318100.4_Silent_p.A76A|RTEL1-TNFRSF6B_ENST00000482936.1_Silent_p.A76A|RTEL1_ENST00000488316.1_3'UTR regulator of telomere elongation helicase 1 24 all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13) Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107) CCGAGAGGGCGCAAGGAGAGC 0.637000 0 SO:0001819 synonymous_variant ENST00000360203.5 1 1 hg19 TCGA-IB-7885-01A-11D-2154-08 RTEL1-011 NOVEL not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000289781.1 1 0 0 14 229 0 56 0 1.664135e-01 0 12 0 56 2 0 0 0 0 0 2 1 0.999760 14 227 0 55 2 -16.926990 1 1 121410 2 35 1 1 2 3 2.063923 0 0.160000 1.730000 0.167328 0.750000 0.430000 1.000000 1.000000 0.767260 0.750000 0 0.570000 1.000000 SNAP29 9342 broad.mit.edu 37 22 21213614 21213614 + Silent SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr22:21213614G>A ENST00000215730.7 + 1 344 c.216G>A c.(214-216)aaG>aaA p.K72K PI4KA_ENST00000255882.6_5'Flank|PI4KA_ENST00000572273.1_5'Flank NM_004782.3 NP_004773.1 O95721 SNP29_HUMAN synaptosomal-associated protein, 29kDa 9 all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117) AGTCCGAGAAGGTTGGGGTCG 0.637000 0 SO:0001819 synonymous_variant ENST00000215730.7 1 1 hg19 CCDS13784.1 TCGA-IB-7885-01A-11D-2154-08 SNAP29-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320000.4 0 0 0 10 120 0 42 1 8.682270e-01 10 36 0 42 2 0 0 0 0 0 2 1 0.997019 10 118 0 40 2 -3.222820 1 1 0 0 1 0 1 1 2.035408 0 0.160000 1.730000 0.155270 0.950000 0.500000 1.000000 1.000000 0.883533 0.950000 1 0.700000 1.000000 EP300 2033 broad.mit.edu 37 22 41533755 41533755 + Missense_Mutation SNP A A G TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr22:41533755A>G ENST00000263253.7 + 8 2940 c.1721A>G c.(1720-1722)gAt>gGt p.D574G NM_001429.3 NP_001420.2 Q09472 EP300_HUMAN E1A binding protein p300 171 TGGCACGAAGATATTACTCAG 0.438000 T, N, F, Mis, O MLL, RUNXBP2 colorectal, breast, pancreatic, AML, ALL, DLBCL Rubinstein-Taybi syndrome Rec yes 22 22q13 2033 300 kd E1A-Binding protein gene L, E 0 SO:0001583 missense Familial Cancer Database Broad Thumb-Hallux syndrome ENST00000263253.7 1 1 hg19 CCDS14010.1 . . . . . . . . . . A 23.2 4.391655 0.83011 . . ENSG00000100393 ENST00000263253 D 0.83591 -1.74 5.85 5.85 0.93711 Coactivator CBP, KIX (4); 0.000000 0.47852 D 0.000203 T 0.77870 0.4195 N 0.03608 -0.345 0.54753 D 0.999982 P 0.46987 0.888 P 0.58620 0.842 T 0.78183 -0.2303 10 0.20046 T 0.44 -11.8926 16.2444 0.82434 1.0:0.0:0.0:0.0 . 574 Q09472 EP300_HUMAN G 574 ENSP00000263253:D574G ENSP00000263253:D574G D + 2 0 EP300 39863701 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.339000 0.96797 2.233000 0.73108 0.455000 0.32223 GAT TCGA-IB-7885-01A-11D-2154-08 EP300-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320600.1 1 0 1 29 338 0 66 1 8.226205e-01 8 31 0 66 2 0 0 0 0 0 2 1 1.000000 29 324 0 66 2 -20.000000 1 1 0 0 1 0 0 0 2.026679 0 0.160000 1.730000 0.149109 0.970000 0.670000 1.000000 1.000000 0.924872 0.970000 1 0.810000 1.000000 SMPD4 55627 broad.mit.edu 37 2 130921950 130921950 + Missense_Mutation SNP G G C TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr2:130921950G>C ENST00000452225.2 - 4 357 c.119C>G c.(118-120)cCa>cGa p.P40R SMPD4_ENST00000339679.7_Silent_p.A213A|SMPD4_ENST00000443958.2_Silent_p.A19A|SMPD4_ENST00000409031.1_Silent_p.A326A|SMPD4_ENST00000453750.1_Silent_p.A104A|SMPD4_ENST00000351288.6_Silent_p.A326A|SMPD4_ENST00000426662.2_Missense_Mutation_p.P40R|SMPD4_ENST00000431183.2_Silent_p.A253A|SMPD4_ENST00000473720.1_5'UTR Q9NXE4 NSMA3_HUMAN sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3) 29 Colorectal(110;0.1) Phosphatidylserine(DB00144) AACATACCTTGGCATGAGGGG 0.448000 0 SO:0001583 missense ENST00000452225.2 0 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. 4.526|4.526 0.097659|0.097659 0.08681|0.08681 .|. .|. ENSG00000136699|ENSG00000136699 ENST00000439886;ENST00000452225;ENST00000426662|ENST00000430682 .|. .|. .|. 4.17|4.17 3.28|3.28 0.37604|0.37604 .|. .|. .|. .|. .|. T|T 0.53932|0.53932 0.1827|0.1827 .|. .|. .|. 0.80722|0.80722 D|D 1|1 B;P|. 0.41131|. 0.035;0.739|. B;B|. 0.33121|. 0.017;0.158|. T|T 0.47156|0.47156 -0.9139|-0.9139 7|4 0.41790|. T|. 0.15|. .|. 5.3514|5.3514 0.16038|0.16038 0.1079:0.0:0.6939:0.1982|0.1079:0.0:0.6939:0.1982 .|. 40;40|. B4E0L6;B4DQ31|. .;.|. R|E 155;40;40|116 .|. ENSP00000397479:P40R|. P|Q -|- 2|1 0|0 SMPD4|SMPD4 130638420|130638420 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.941000|0.941000 0.58515|0.58515 0.994000|0.994000 0.29693|0.29693 0.733000|0.733000 0.32492|0.32492 0.557000|0.557000 0.71058|0.71058 CCA|CAA TCGA-IB-7885-01A-11D-2154-08 SMPD4-205 KNOWN basic protein_coding protein_coding 0 0 0 7 263 1 71 0 5.227636e-02 1 61 1 71 5 0 0 0 0 0 2 0 0.084692 7 260 1 71 14 -7.823359 1 1 0 0 1 1 2 3 2.054193 0 0.160000 1.730000 0.165342 0.350000 0.150000 1.000000 0.330000 0.404076 0.350000 0 0.230000 0.530000 TPO 7173 broad.mit.edu 37 2 1497799 1497799 + Missense_Mutation SNP G G A rs140124953 TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr2:1497799G>A ENST00000345913.4 + 11 2085 c.1994G>A c.(1993-1995)cGg>cAg p.R665Q TPO_ENST00000382198.1_Missense_Mutation_p.R492Q|TPO_ENST00000329066.4_Missense_Mutation_p.R665Q|TPO_ENST00000382201.3_Missense_Mutation_p.R608Q|TPO_ENST00000337415.3_Missense_Mutation_p.R665Q|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000349624.3_Missense_Mutation_p.R492Q|TPO_ENST00000346956.3_Missense_Mutation_p.R665Q NM_000547.5 NP_000538.3 P07202 PERT_HUMAN thyroid peroxidase 95 all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627) all_cancers(51;0.0338) Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550) AAGGCTCTGCGGGACGGTGAC 0.577000 0 GRCh37 CM035088 TPO M rs140124953 SO:0001583 missense ENST00000345913.4 1 1 hg19 CCDS1643.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 21.5|21.5 4.152346|4.152346 0.78001|0.78001 0.0|0.0 1.16E-4|1.16E-4 ENSG00000115705|ENSG00000115705 ENST00000446278|ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607 .|T;T;T;T;T;T;T;T;T .|0.72282 .|-0.64;-0.64;-0.64;-0.64;-0.64;-0.64;-0.64;-0.64;-0.64 4.84|4.84 4.84|4.84 0.62591|0.62591 .|. .|0.000000 .|0.85682 .|D .|0.000000 D|D 0.85643|0.85643 0.5744|0.5744 M|M 0.82716|0.82716 2.605|2.605 0.80722|0.80722 D|D 1|1 .|D;D;D;D .|0.89917 .|1.0;1.0;1.0;1.0 .|D;D;D;D .|0.97110 .|1.0;0.999;0.999;1.0 D|D 0.88101|0.88101 0.2819|0.2819 5|10 .|0.87932 .|D .|0 -34.9581|-34.9581 18.3104|18.3104 0.90197|0.90197 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|665;492;608;665 .|P07202-4;P07202-5;P07202-2;P07202 .|.;.;.;PERT_HUMAN R|Q 140|665;665;665;492;665;608;492;594;139 .|ENSP00000337263:R665Q;ENSP00000318820:R665Q;ENSP00000263886:R665Q;ENSP00000332044:R492Q;ENSP00000329869:R665Q;ENSP00000371636:R608Q;ENSP00000371633:R492Q;ENSP00000405788:R594Q;ENSP00000419461:R139Q .|ENSP00000329869:R665Q G|R +|+ 1|2 0|0 TPO|TPO 1476806|1476806 1.000000|1.000000 0.71417|0.71417 0.998000|0.998000 0.56505|0.56505 0.175000|0.175000 0.22909|0.22909 7.143000|7.143000 0.77348|0.77348 2.399000|2.399000 0.81585|0.81585 0.561000|0.561000 0.74099|0.74099 GGG|CGG TCGA-IB-7885-01A-11D-2154-08 TPO-202 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000206594.2 0 0 0 24 268 0 88 0 3.969151e-02 0 4 0 88 2 0 0 0 0 0 2 1 1.000000 24 266 0 88 2 -2.429493 0 1 121410 3 35 1 1 2 3 2.049419 0 0.160000 1.730000 0.164013 0.990000 0.680000 1.000000 1.000000 0.946472 0.990000 1 0.850000 1.000000 PARD3B 117583 broad.mit.edu 37 2 205829959 205829959 + Missense_Mutation SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr2:205829959G>A ENST00000406610.2 + 3 514 c.307G>A c.(307-309)Gct>Act p.A103T PARD3B_ENST00000349953.3_Missense_Mutation_p.A103T|PARD3B_ENST00000462231.1_Missense_Mutation_p.A103T|PARD3B_ENST00000351153.1_Missense_Mutation_p.A103T|PARD3B_ENST00000358768.2_Missense_Mutation_p.A103T NM_057177.6|NM_152526.5|NM_205863.3 NP_476518.4|NP_689739.4|NP_995585.2 Q8TEW8 PAR3L_HUMAN par-3 family cell polarity regulator beta 65 all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06) GAGCCCAGATGCTTTTGAGAC 0.478000 0 SO:0001583 missense ENST00000406610.2 1 1 hg19 . . . . . . . . . . G 17.38 3.375436 0.61735 . . ENSG00000116117 ENST00000406610;ENST00000358768;ENST00000351153;ENST00000349953 T;T;T;T 0.43688 0.94;0.94;0.94;0.94 5.61 3.73 0.42828 . 0.220595 0.39020 N 0.001496 T 0.29355 0.0731 N 0.14661 0.345 0.26617 N 0.972736 P;P;P;P;P 0.49358 0.814;0.923;0.87;0.716;0.818 P;P;P;B;B 0.46796 0.458;0.527;0.525;0.407;0.167 T 0.08027 -1.0742 10 0.28530 T 0.3 . 11.2408 0.48968 0.0:0.2451:0.5704:0.1845 . 103;103;103;103;103 Q8TEW8-3;Q8TEW8;E9PE87;Q8TEW8-2;Q8TEW8-5 .;PAR3L_HUMAN;.;.;. T 103 ENSP00000385848:A103T;ENSP00000351618:A103T;ENSP00000317261:A103T;ENSP00000340280:A103T ENSP00000340280:A103T A + 1 0 PARD3B 205538204 0.558000 0.26554 1.000000 0.80357 0.984000 0.73092 1.066000 0.30604 2.635000 0.89317 0.563000 0.77884 GCT TCGA-IB-7885-01A-11D-2154-08 PARD3B-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000335992.1 1 0 0 14 199 0 57 1 4.369838e-02 3 2 0 57 2 0 0 0 0 0 2 1 0.999754 14 196 0 56 2 -5.727956 1 1 0 0 1 0 0 0 2.018080 0 0.160000 1.730000 0.146341 0.810000 0.470000 1.000000 1.000000 0.806768 0.810000 0 0.620000 1.000000 GTF2A1L 11036 broad.mit.edu 37 2 48873884 48873884 + Silent SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr2:48873884C>T ENST00000403751.3 + 6 718 c.681C>T c.(679-681)atC>atT p.I227I STON1-GTF2A1L_ENST00000394751.3_Silent_p.I884I|LHCGR_ENST00000420913.3_Intron|STON1-GTF2A1L_ENST00000405008.1_Silent_p.I931I|GTF2A1L_ENST00000430487.2_Silent_p.I193I|STON1-GTF2A1L_ENST00000394754.1_Silent_p.I931I|STON1-GTF2A1L_ENST00000402114.2_Silent_p.I931I|STON1-GTF2A1L_ENST00000309827.2_Silent_p.I931I NM_006872.3 NP_006863.2 Q9UNN4 TF2AY_HUMAN general transcription factor IIA, 1-like 7 all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) AGCATAAAATCGTGCCTGAAG 0.413000 0 SO:0001819 synonymous_variant ENST00000403751.3 1 1 hg19 CCDS46281.1 TCGA-IB-7885-01A-11D-2154-08 GTF2A1L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323852.4 1 0 0 21 378 0 82 0 2.782107e-02 0 5 0 82 2 0 0 0 0 0 2 1 0.999997 21 373 0 82 2 -3.142702 1 1 121412 2 36 1 1 2 3 2.049419 0 0.160000 1.730000 0.164013 0.670000 0.420000 1.000000 0.660000 0.694075 0.670000 0 0.530000 0.850000 FBLN2 2199 broad.mit.edu 37 3 13612273 13612273 + Missense_Mutation SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr3:13612273G>A ENST00000295760.7 + 2 487 c.418G>A c.(418-420)Gtc>Atc p.V140I FBLN2_ENST00000492059.1_Missense_Mutation_p.V140I|FBLN2_ENST00000404922.3_Missense_Mutation_p.V140I|FBLN2_ENST00000535798.1_Missense_Mutation_p.V166I NM_001998.2 NP_001989.2 P98095 FBLN2_HUMAN fibulin 2 24 UCEC - Uterine corpus endometrioid carcinoma (1;0.00416) GGTGGGCTGCGTCCACGCGGG 0.677000 0 SO:0001583 missense ENST00000295760.7 0 1 hg19 CCDS46762.1 . . . . . . . . . . G 6.919 0.539238 0.13250 . . ENSG00000163520 ENST00000535798;ENST00000404922;ENST00000295760;ENST00000465610;ENST00000492059 T;T;T;T;T 0.65916 -0.18;-0.18;-0.18;1.44;-0.18 5.05 -4.8 0.03190 . 0.992466 0.08188 N 0.984342 T 0.46054 0.1373 L 0.46157 1.445 0.09310 N 1 B;B;B 0.14805 0.011;0.007;0.003 B;B;B 0.09377 0.004;0.003;0.002 T 0.38650 -0.9651 10 0.45353 T 0.12 . 2.9868 0.05971 0.4092:0.2291:0.2727:0.089 . 140;140;166 P98095;P98095-2;F5H1F3 FBLN2_HUMAN;.;. I 166;140;140;140;140 ENSP00000445705:V166I;ENSP00000384169:V140I;ENSP00000295760:V140I;ENSP00000420164:V140I;ENSP00000420042:V140I ENSP00000295760:V140I V + 1 0 FBLN2 13587273 0.000000 0.05858 0.001000 0.08648 0.112000 0.19704 -0.627000 0.05521 -0.614000 0.05687 -0.252000 0.11476 GTC TCGA-IB-7885-01A-11D-2154-08 FBLN2-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000340083.3 0 0 0 6 61 0 16 0 9.854772e-01 0 85 0 16 2 1 9.999954e-01 36 396 0 426 2 1 0.964065 6 59 0 15 2 -13.853710 1 1 120224 5 29 1 0 1 1 1.900460 0 0.160000 1.730000 0.094828 0.820000 0.390000 1.000000 1.000000 0.797588 0.820000 0 0.590000 1.000000 TGFBR2 7048 broad.mit.edu 37 3 30686373 30686373 + Missense_Mutation SNP T T A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 T A T T Valid Somatic Phase_I WXS targeted Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr3:30686373T>A ENST00000295754.5 + 2 611 c.229T>A c.(229-231)Tgt>Agt p.C77S TGFBR2_ENST00000359013.4_Missense_Mutation_p.C102S NM_003242.5 NP_003233.4 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II (70/80kDa) 53 CACCTCCATCTGTGAGAAGCC 0.408000 0 SO:0001583 missense ENST00000295754.5 1 1 hg19 CCDS2648.1 . . . . . . . . . . T 24.4 4.530383 0.85706 . . ENSG00000163513 ENST00000295754;ENST00000359013 D;D 0.89123 -2.47;-2.47 5.66 5.66 0.87406 Transforming growth factor beta receptor 2 ectodomain (1); 0.000000 0.85682 D 0.000000 D 0.93953 0.8064 M 0.74881 2.28 0.80722 D 1 D;D 0.76494 0.999;0.999 D;D 0.97110 1.0;1.0 D 0.94419 0.7639 10 0.66056 D 0.02 . 14.8777 0.70507 0.0:0.0:0.0:1.0 . 77;102 P37173;D2JYI1 TGFR2_HUMAN;. S 77;102 ENSP00000295754:C77S;ENSP00000351905:C102S ENSP00000295754:C77S C + 1 0 TGFBR2 30661377 1.000000 0.71417 1.000000 0.80357 0.968000 0.65278 6.321000 0.72881 2.147000 0.66899 0.533000 0.62120 TGT TCGA-IB-7885-01A-11D-2154-08 TGFBR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252994.2 1 0 1 13 189 0 71 1 9.989650e-01 66 109 0 71 2 1 9.999955e-01 23 339 0 294 2 1 0.999544 12 187 0 71 2 -16.661990 1 1 0 0 1 0 1 1 1.900460 0 0.160000 1.730000 0.094828 0.720000 0.410000 1.000000 1.000000 0.733316 0.720000 0 0.550000 0.910000 DCLK2 166614 broad.mit.edu 37 4 151168835 151168835 + Missense_Mutation SNP T T C TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr4:151168835T>C ENST00000296550.7 + 13 2613 c.1859T>C c.(1858-1860)aTc>aCc p.I620T DCLK2_ENST00000506325.1_Missense_Mutation_p.I619T|DCLK2_ENST00000302176.8_Missense_Mutation_p.I637T NM_001040260.3 NP_001035350.2 Q8N568 DCLK2_HUMAN doublecortin-like kinase 2 26 all_hematologic(180;0.151) TGGGATAACATCACGGACTCT 0.527000 GBM(195;186 2215 13375 16801 37459) 0 SO:0001583 missense ENST00000296550.7 0 1 hg19 CCDS34076.1 . . . . . . . . . . T 31 5.059723 0.93846 . . ENSG00000170390 ENST00000296550;ENST00000506325;ENST00000302176 T;T;T 0.42900 0.96;0.96;0.96 6.17 6.17 0.99709 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.049932 0.85682 D 0.000000 T 0.64681 0.2620 M 0.74647 2.275 0.80722 D 1 D;P;D 0.62365 0.986;0.873;0.991 P;B;D 0.64877 0.885;0.385;0.93 T 0.67868 -0.5559 10 0.87932 D 0 . 16.8222 0.85835 0.0:0.0:0.0:1.0 . 637;619;620 Q8N568-3;Q8N568-2;Q8N568 .;.;DCLK2_HUMAN T 620;619;637 ENSP00000296550:I620T;ENSP00000427235:I619T;ENSP00000303887:I637T ENSP00000296550:I620T I + 2 0 DCLK2 151388285 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.698000 0.84413 2.371000 0.80710 0.533000 0.62120 ATC TCGA-IB-7885-01A-11D-2154-08 DCLK2-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000364952.1 0 0 0 7 197 0 71 0 1.313011e-01 0 16 0 71 2 0 0 0 0 0 2 1 0.980123 7 194 0 71 2 -9.423048 1 1 0 0 1 0 1 1 2.044131 0 0.160000 1.730000 0.156627 0.440000 0.200000 0.800000 0.410000 0.470447 0.440000 0 0.300000 0.620000 TXNDC15 79770 broad.mit.edu 37 5 134232006 134232006 + Missense_Mutation SNP G G A rs139088311 TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr5:134232006G>A ENST00000358387.4 + 4 1403 c.778G>A c.(778-780)Gta>Ata p.V260I TXNDC15_ENST00000546290.1_Missense_Mutation_p.V237I NM_024715.3 NP_078991.3 Q96J42 TXD15_HUMAN thioredoxin domain containing 15 17 KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233) GTTTGGCACCGTAGCTGTTCC 0.338000 0 SO:0001583 missense ENST00000358387.4 1 1 hg19 CCDS4180.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 35|35 5.437679|5.437679 0.96168|0.96168 2.27E-4|2.27E-4 0.0|0.0 ENSG00000113621|ENSG00000113621 ENST00000509954|ENST00000441965;ENST00000358387;ENST00000546290 .|T;T .|0.03301 .|3.98;3.98 6.17|6.17 6.17|6.17 0.99709|0.99709 .|Thioredoxin domain (1);Thioredoxin-like fold (3); .|0.000000 .|0.85682 .|D .|0.000000 T|T 0.14442|0.14442 0.0349|0.0349 L|L 0.41415|0.41415 1.275|1.275 0.80722|0.80722 D|D 1|1 .|D .|0.89917 .|1.0 .|D .|0.87578 .|0.998 T|T 0.00137|0.00137 -1.2004|-1.2004 5|10 .|0.54805 .|T .|0.06 2.2193|2.2193 20.8794|20.8794 0.99867|0.99867 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|260 .|Q96J42 .|TXD15_HUMAN H|I 14|244;260;237 .|ENSP00000351157:V260I;ENSP00000443942:V237I .|ENSP00000351157:V260I R|V +|+ 2|1 0|0 TXNDC15|TXNDC15 134259905|134259905 1.000000|1.000000 0.71417|0.71417 0.850000|0.850000 0.33497|0.33497 0.972000|0.972000 0.66771|0.66771 9.476000|9.476000 0.97823|0.97823 2.941000|2.941000 0.99782|0.99782 0.655000|0.655000 0.94253|0.94253 CGT|GTA TCGA-IB-7885-01A-11D-2154-08 TXNDC15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251160.1 1 0 0 40 548 0 84 1 9.999057e-01 17 171 0 84 2 0 0 0 0 0 2 1 1.000000 39 540 0 84 2 -3.075755 1 1 121410 3 37 1 1 2 3 2.045984 0 0.160000 1.730000 0.163347 0.860000 0.620000 1.000000 1.000000 0.858709 0.860000 1 0.730000 1.000000 PCDHGA7 56108 broad.mit.edu 37 5 140763117 140763117 + Silent SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr5:140763117C>T ENST00000518325.1 + 1 651 c.651C>T c.(649-651)ggC>ggT p.G217G PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron NM_018920.2 NP_061743.1 Q9Y5G6 PCDG7_HUMAN protocadherin gamma subfamily A, 7 49 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CCTCTGATGGCGGCGACCCGC 0.607000 0 SO:0001819 synonymous_variant ENST00000518325.1 0 1 hg19 CCDS54927.1 TCGA-IB-7885-01A-11D-2154-08 PCDHGA7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374744.1 0 0 0 5 109 0 23 0 3.094607e-03 0 2 0 23 2 0 0 0 0 0 2 1 0.932972 5 105 0 21 2 -4.195660 1 0 0 0 1 1 2 3 2.045984 0 0.160000 1.730000 0.163347 0.590000 0.230000 1.000000 1.000000 0.623540 0.590000 0 0.380000 0.900000 GPRIN1 114787 broad.mit.edu 37 5 176025336 176025336 + Silent SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr5:176025336C>T ENST00000303991.4 - 2 1677 c.1500G>A c.(1498-1500)ttG>ttA p.L500L NM_052899.2 NP_443131.2 Q7Z2K8 GRIN1_HUMAN G protein regulated inducer of neurite outgrowth 1 35 all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142) Medulloblastoma(196;0.0208)|all_neural(177;0.0416) Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) CTGCTGTCCCCAAGGACCTGG 0.547000 0 SO:0001819 synonymous_variant ENST00000303991.4 1 1 hg19 CCDS4405.1 TCGA-IB-7885-01A-11D-2154-08 GPRIN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253149.1 1 0 0 29 535 0 151 1 2.670764e-01 2 17 0 151 2 0 0 0 0 0 2 1 1.000000 29 523 0 151 2 -2.599005 1 1 121408 2 35 1 1 2 3 2.045984 0 0.160000 1.730000 0.163347 0.650000 0.440000 1.000000 0.640000 0.671888 0.650000 0 0.540000 0.790000 BTNL9 153579 broad.mit.edu 37 5 180475168 180475168 + Silent SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr5:180475168C>T ENST00000327705.9 + 3 582 c.351C>T c.(349-351)gtC>gtT p.V117V BTNL9_ENST00000376841.2_Silent_p.V117V|BTNL9_ENST00000515271.1_Silent_p.V48V|BTNL9_ENST00000376842.3_Silent_p.V117V NM_152547.4 NP_689760.2 Q6UXG8 BTNL9_HUMAN butyrophilin-like 9 19 all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114) all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GCAGCGTGGTCCTGCAGCTTC 0.597000 0 SO:0001819 synonymous_variant ENST00000327705.9 1 1 hg19 CCDS4460.2 TCGA-IB-7885-01A-11D-2154-08 BTNL9-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000157342.3 1 0 0 13 209 0 65 0 5.165357e-02 0 6 0 65 2 0 0 0 0 0 2 1 0.999527 12 206 0 65 2 -16.360060 1 1 0 0 1 1 2 3 2.045984 0 0.160000 1.730000 0.163347 0.750000 0.420000 1.000000 1.000000 0.760977 0.750000 0 0.570000 0.990000 THEMIS 387357 broad.mit.edu 37 6 128134640 128134640 + Silent SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr6:128134640G>A ENST00000368248.2 - 4 1294 c.1146C>T c.(1144-1146)tcC>tcT p.S382S THEMIS_ENST00000368250.1_Silent_p.S303S|THEMIS_ENST00000537166.1_Silent_p.S347S|THEMIS_ENST00000543064.1_Silent_p.S382S NM_001010923.2 NP_001010923.1 Q8N1K5 THMS1_HUMAN thymocyte selection associated 60 CAACAGATACGGATGACAGCT 0.488000 0 SO:0001819 synonymous_variant ENST00000368248.2 1 1 hg19 CCDS34534.1 TCGA-IB-7885-01A-11D-2154-08 THEMIS-201 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding 1 0 0 38 320 0 96 0 3.329201e-02 0 3 0 96 2 0 0 0 0 0 2 1 1.000000 37 317 0 96 2 -2.402340 0 1 0 0 1 0 1 1 1.873866 1 0.160000 1.730000 0.086957 0.930000 0.760000 1.000000 0.990000 0.926958 0.930000 1 0.850000 0.990000 NRSN1 140767 broad.mit.edu 37 6 24145857 24145857 + Missense_Mutation SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr6:24145857G>A ENST00000378491.4 + 4 572 c.271G>A c.(271-273)Gaa>Aaa p.E91K NM_080723.4 NP_542454.3 neurensin 1 p.E91K(2) 22 CCCCAAAATCGAAGCATTTGG 0.488000 2 Substitution - Missense(2) SO:0001583 missense ENST00000378491.4 1 1 hg19 CCDS4549.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 32 5.178898 0.94846 . . ENSG00000152954 ENST00000378491;ENST00000378477 T 0.24151 1.87 5.37 5.37 0.77165 . 0.000000 0.85682 D 0.000000 T 0.45597 0.1350 M 0.79475 2.455 0.80722 D 1 D 0.89917 1.0 D 0.63877 0.919 T 0.50432 -0.8829 10 0.87932 D 0 5.9041 19.1095 0.93312 0.0:0.0:1.0:0.0 . 91 Q8IZ57 NRSN1_HUMAN K 91 ENSP00000367752:E91K ENSP00000367738:E91K E + 1 0 NRSN1 24253836 1.000000 0.71417 1.000000 0.80357 0.703000 0.40648 9.620000 0.98373 2.524000 0.85096 0.557000 0.71058 GAA TCGA-IB-7885-01A-11D-2154-08 NRSN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043866.1 1 0 0 37 435 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 1.000000 37 425 0 86 2 -9.986972 1 1 121412 1 37 1 0 0 0 2.030817 0 0.160000 1.730000 0.151858 0.960000 0.690000 1.000000 1.000000 0.928917 0.960000 1 0.820000 1.000000 TRIM26 7726 broad.mit.edu 37 6 30166741 30166741 + Missense_Mutation SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr6:30166741G>A ENST00000454678.2 - 4 576 c.140C>T c.(139-141)tCa>tTa p.S47L TRIM26_ENST00000453195.1_Missense_Mutation_p.S47L|TRIM26_ENST00000437089.1_Missense_Mutation_p.S47L|TRIM26_ENST00000487829.1_5'UTR NM_003449.4 NP_003440.1 Q12899 TRI26_HUMAN tripartite motif containing 26 3 GCGGCTCCCTGAGATGGGGCG 0.602000 0 SO:0001583 missense ENST00000454678.2 1 1 hg19 CCDS4678.1 . . . . . . . . . . G 11.95 1.790254 0.31685 . . ENSG00000234127 ENST00000453195;ENST00000454678;ENST00000437089;ENST00000416596;ENST00000420345;ENST00000418026;ENST00000434785 T;T;T;T;T;T 0.08458 3.09;3.09;3.09;3.09;3.09;3.09 5.59 3.8 0.43715 Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1); 0.676716 0.12973 N 0.423994 T 0.02929 0.0087 L 0.33485 1.01 0.09310 N 1 P 0.50369 0.934 P 0.47864 0.559 T 0.38457 -0.9660 10 0.21540 T 0.41 . 5.4594 0.16607 0.1742:0.1654:0.6604:0.0 . 47 Q12899 TRI26_HUMAN L 47 ENSP00000391879:S47L;ENSP00000410446:S47L;ENSP00000395491:S47L;ENSP00000413673:S47L;ENSP00000387530:S47L;ENSP00000400920:S47L ENSP00000413673:S47L S - 2 0 TRIM26 30274720 0.007000 0.16637 0.015000 0.15790 0.052000 0.14988 1.758000 0.38410 1.363000 0.46019 -0.163000 0.13421 TCA TCGA-IB-7885-01A-11D-2154-08 TRIM26-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253442.1 1 0 1 25 215 0 46 1 9.988622e-01 20 74 0 46 2 0 0 0 0 0 2 1 1.000000 25 205 0 46 2 -20.000000 1 1 0 0 1 0 0 0 2.030817 0 0.160000 1.730000 0.151858 0.990000 0.860000 1.000000 1.000000 0.990903 0.990000 1 0.990000 1.000000 CFB 629 broad.mit.edu 37 6 31918989 31918989 + Missense_Mutation SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr6:31918989C>T ENST00000425368.2 + 15 2437 c.1924C>T c.(1924-1926)Cgg>Tgg p.R642W CFB_ENST00000456570.1_Missense_Mutation_p.R1144W|CFB_ENST00000477310.1_Missense_Mutation_p.R993W|CFB_ENST00000556679.1_Missense_Mutation_p.R1144W NM_001710.5 NP_001701.2 P00751 CFAB_HUMAN complement factor B 21 AAAGCTGACTCGGAAGGAGGT 0.502000 0 SO:0001583 missense ENST00000425368.2 1 1 hg19 CCDS4729.1 . . . . . . . . . . C 20.9 4.068731 0.76301 . . ENSG00000243649;ENSG00000243649;ENSG00000244255;ENSG00000244255 ENST00000556679;ENST00000425368;ENST00000456570;ENST00000477310 D;D;D;D 0.88818 -2.43;-2.43;-2.43;-2.43 5.41 5.41 0.78517 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 0.166558 0.28865 N 0.013890 D 0.90126 0.6915 L 0.48260 1.515 0.37642 D 0.922095 D;D 0.89917 1.0;1.0 D;D 0.80764 0.994;0.989 D 0.91549 0.5255 10 0.87932 D 0 -23.6051 11.7828 0.52023 0.1755:0.8245:0.0:0.0 . 1144;642 B4E1Z4;P00751 .;CFAB_HUMAN W 1144;642;1144;993 ENSP00000451848:R1144W;ENSP00000416561:R642W;ENSP00000410815:R1144W;ENSP00000418996:R993W ENSP00000416561:R642W R + 1 2 CFB;XXbac-BPG116M5.17 32026968 0.986000 0.35501 0.957000 0.39632 0.975000 0.68041 2.981000 0.49329 2.535000 0.85469 0.591000 0.81541 CGG TCGA-IB-7885-01A-11D-2154-08 CFB-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000076395.3 1 0 1 39 339 0 101 1 1 645 968 0 101 2 0 0 0 0 0 2 1 1.000000 38 331 0 100 2 -2.920854 1 1 0 0 1 0 0 0 2.030817 0 0.160000 1.730000 0.151858 0.990000 0.920000 1.000000 1.000000 0.995846 0.990000 1 0.990000 1.000000 ZNF292 23036 broad.mit.edu 37 6 87969936 87969936 + Missense_Mutation SNP C C A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr6:87969936C>A ENST00000369577.3 + 8 6632 c.6589C>A c.(6589-6591)Cat>Aat p.H2197N ZNF292_ENST00000339907.4_Missense_Mutation_p.H2192N NM_015021.1 NP_055836.1 O60281 ZN292_HUMAN zinc finger protein 292 89 all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05) CATGAAACTTCATGAAATGAC 0.353000 0 SO:0001583 missense ENST00000369577.3 1 1 hg19 CCDS47457.1 . . . . . . . . . . C 24.6 4.546126 0.86022 . . ENSG00000188994 ENST00000369577;ENST00000339907;ENST00000496806 T;T;T 0.63744 -0.06;-0.06;-0.06 5.42 5.42 0.78866 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2); 0.000000 0.85682 D 0.000000 T 0.82061 0.4955 M 0.92268 3.29 0.54753 D 0.99998 D 0.69078 0.997 D 0.73380 0.98 D 0.85022 0.0912 10 0.52906 T 0.07 . 19.21 0.93749 0.0:1.0:0.0:0.0 . 2197 O60281 ZN292_HUMAN N 2197;2192;115 ENSP00000358590:H2197N;ENSP00000342847:H2192N;ENSP00000428857:H115N ENSP00000342847:H2192N H + 1 0 ZNF292 88026655 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.487000 0.81328 2.541000 0.85698 0.591000 0.81541 CAT TCGA-IB-7885-01A-11D-2154-08 ZNF292-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000376192.2 1 0 1 56 737 0 216 1 6.016087e-01 10 18 0 216 2 0 0 0 0 0 2 1 1.000000 56 719 0 215 2 -10.916610 1 1 0 0 1 0 1 1 1.873866 1 0.160000 1.730000 0.086957 0.790000 0.610000 0.970000 0.800000 0.803415 0.790000 0 0.700000 0.900000 PSMC2 5701 broad.mit.edu 37 7 102996160 102996160 + Silent SNP T T C TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr7:102996160T>C ENST00000435765.1 + 5 621 c.210T>C c.(208-210)acT>acC p.T70T PSMC2_ENST00000544811.1_Intron|PSMC2_ENST00000292644.3_Silent_p.T70T|SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000339444.6_Intron|SLC26A5_ENST00000356767.4_Intron NM_002803.3 NP_002794.1 P35998 PRS7_HUMAN proteasome (prosome, macropain) 26S subunit, ATPase, 2 21 AATCTGACACTGGCCTGGCCC 0.448000 0 SO:0001819 synonymous_variant ENST00000435765.1 1 1 hg19 CCDS5731.1 TCGA-IB-7885-01A-11D-2154-08 PSMC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347922.1 1 0 1 14 168 0 59 1 9.999969e-01 90 214 0 59 2 0 0 0 0 0 2 1 0.999746 13 164 0 59 2 -19.052120 1 1 0 0 1 1 2 3 2.060044 0 0.160000 1.730000 0.166667 0.990000 0.570000 1.000000 1.000000 0.909920 0.990000 1 0.760000 1.000000 SSPO 23145 broad.mit.edu 37 7 149524951 149524951 + RNA SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr7:149524951G>A ENST00000378016.2 + 0 14862 A2VEC9 SSPO_HUMAN SCO-spondin Melanoma(164;0.165)|Ovarian(565;0.177) OV - Ovarian serous cystadenocarcinoma(82;0.00625) CAAAGACCCAGAGTAACTGCA 0.682000 0 ENST00000378016.2 1 1 hg19 TCGA-IB-7885-01A-11D-2154-08 SSPO-202 KNOWN basic processed_transcript processed_transcript 0 0 0 14 204 0 54 0 0 0 1 0 54 2 0 0 0 0 0 2 1 0.999728 14 197 0 53 2 -17.801970 1 1 0 0 1 1 2 3 2.060044 0 0.160000 1.730000 0.166667 0.840000 0.470000 1.000000 1.000000 0.825327 0.840000 0 0.630000 1.000000 HECW1 23072 broad.mit.edu 37 7 43447240 43447240 + Silent SNP A A G TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr7:43447240A>G ENST00000395891.2 + 8 1316 c.711A>G c.(709-711)aaA>aaG p.K237K HECW1_ENST00000453890.1_Silent_p.K237K|HECW1_ENST00000471043.1_3'UTR NM_015052.3 NP_055867.3 Q76N89 HECW1_HUMAN HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 125 AGCCTGGGAAACACAGCATCT 0.493000 0 SO:0001819 synonymous_variant ENST00000395891.2 1 1 hg19 CCDS5469.2 TCGA-IB-7885-01A-11D-2154-08 HECW1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250893.2 1 0 0 19 204 0 52 0 8.259587e-03 0 2 0 52 2 0 0 0 0 0 2 1 0.999990 18 198 0 52 2 -7.731963 1 1 0 0 1 1 2 3 2.060044 0 0.160000 1.730000 0.166667 0.990000 0.680000 1.000000 1.000000 0.953745 0.990000 1 0.870000 1.000000 PCLO 27445 broad.mit.edu 37 7 82584750 82584750 + Missense_Mutation SNP T T C TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr7:82584750T>C ENST00000333891.9 - 5 5856 c.5519A>G c.(5518-5520)gAa>gGa p.E1840G PCLO_ENST00000423517.2_Missense_Mutation_p.E1840G NM_033026.5 NP_149015.2 piccolo presynaptic cytomatrix protein 259 ACGTAACTCTTCTGTCGGAGA 0.438000 0 SO:0001583 missense ENST00000333891.9 1 1 hg19 CCDS47630.1 . . . . . . . . . . T 12.16 1.855731 0.32791 . . ENSG00000186472 ENST00000431819;ENST00000333891;ENST00000423517 T;T 0.30448 1.53;1.55 5.57 5.57 0.84162 . . . . . T 0.42585 0.1209 L 0.27053 0.805 0.80722 D 1 D;D 0.76494 0.999;0.999 D;D 0.67382 0.951;0.951 T 0.41645 -0.9497 9 0.87932 D 0 . 15.7247 0.77747 0.0:0.0:0.0:1.0 . 1840;1840 Q9Y6V0-5;Q9Y6V0-6 .;. G 1771;1840;1840 ENSP00000334319:E1840G;ENSP00000388393:E1840G ENSP00000334319:E1840G E - 2 0 PCLO 82422686 1.000000 0.71417 1.000000 0.80357 0.947000 0.59692 8.013000 0.88655 2.116000 0.64780 0.533000 0.62120 GAA TCGA-IB-7885-01A-11D-2154-08 PCLO-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000337368.5 1 0 0 75 771 0 198 0 0 0 1 0 198 2 0 0 0 0 0 2 1 1.000000 74 754 0 196 2 -19.122090 1 1 0 0 1 1 2 3 2.060044 0 0.160000 1.730000 0.166667 0.990000 0.890000 1.000000 1.000000 0.991464 0.990000 1 0.990000 1.000000 SH2D4A 63898 broad.mit.edu 37 8 19250984 19250984 + Missense_Mutation SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr8:19250984G>A ENST00000265807.3 + 9 1615 c.1204G>A c.(1204-1206)Gcc>Acc p.A402T SH2D4A_ENST00000518040.1_Missense_Mutation_p.A357T|SH2D4A_ENST00000519207.1_Missense_Mutation_p.A402T NM_001174160.1|NM_022071.3 NP_001167631.1|NP_071354.2 Q9H788 SH24A_HUMAN SH2 domain containing 4A 16 CTCTGCAGACGCCTACAGCTT 0.498000 0 SO:0001583 missense ENST00000265807.3 1 1 hg19 CCDS6009.1 . . . . . . . . . . G 11.32 1.602992 0.28534 . . ENSG00000104611 ENST00000265807;ENST00000518040;ENST00000519207 T;T;T 0.62639 0.01;0.01;0.01 5.89 3.48 0.39840 SH2 motif (4); 0.143839 0.49916 D 0.000129 T 0.32315 0.0825 N 0.01656 -0.775 0.21740 N 0.999567 B;B 0.28026 0.198;0.064 B;B 0.28784 0.094;0.039 T 0.20672 -1.0268 10 0.19590 T 0.45 . 12.1602 0.54099 0.0:0.0:0.2721:0.7279 . 357;402 B4DDR1;Q9H788 .;SH24A_HUMAN T 402;357;402 ENSP00000265807:A402T;ENSP00000429482:A357T;ENSP00000428684:A402T ENSP00000265807:A402T A + 1 0 SH2D4A 19295264 1.000000 0.71417 0.996000 0.52242 0.276000 0.26787 3.207000 0.51106 0.468000 0.27243 -1.262000 0.01453 GCC TCGA-IB-7885-01A-11D-2154-08 SH2D4A-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000214094.1 1 0 1 27 299 0 81 1 9.992783e-01 52 74 0 81 2 0 0 0 1 0 0 2 1 1.000000 26 295 0 81 2 -3.142702 1 1 121412 1 26 1 1 2 3 2.046120 0 0.160000 1.730000 0.163347 0.990000 0.710000 1.000000 1.000000 0.951626 0.990000 1 0.860000 1.000000 HR 55806 broad.mit.edu 37 8 21985133 21985133 + Silent SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr8:21985133C>T ENST00000381418.4 - 3 2302 c.822G>A c.(820-822)gtG>gtA p.V274V HR_ENST00000312841.8_Silent_p.V274V|HR_ENST00000518377.1_5'Flank NM_005144.4 NP_005135.2 O43593 HAIR_HUMAN hair growth associated 27 Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116) AGGTCCAGGGCACAGTGTCTG 0.657000 0 SO:0001819 synonymous_variant ENST00000381418.4 1 1 hg19 CCDS6022.1 TCGA-IB-7885-01A-11D-2154-08 HR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214213.1 1 0 0 42 543 0 143 1 1.128829e-01 2 6 0 143 2 0 0 0 0 0 2 1 1.000000 41 531 0 141 2 -10.228010 1 1 0 0 1 1 2 3 2.046120 0 0.160000 1.730000 0.163347 0.900000 0.660000 1.000000 1.000000 0.893993 0.900000 1 0.770000 1.000000 FCN2 2220 broad.mit.edu 37 9 137772750 137772750 + Missense_Mutation SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr9:137772750C>T ENST00000291744.6 + 1 93 c.83C>T c.(82-84)gCg>gTg p.A28V FCN2_ENST00000350339.2_Missense_Mutation_p.A28V NM_004108.2 NP_004099.2 Q15485 FCN2_HUMAN ficolin (collagen/fibrinogen domain containing lectin) 2 20 Myeloproliferative disorder(178;0.0333) GCTCTCCAGGCGGCAGACACC 0.617000 0 SO:0001583 missense ENST00000291744.6 1 1 hg19 CCDS6983.1 . . . . . . . . . . C 9.967 1.224474 0.22457 2.27E-4 0.0 ENSG00000160339 ENST00000350339;ENST00000291744 T;T 0.58506 0.33;0.63 0.821 0.821 0.18799 . . . . . T 0.66597 0.2805 M 0.76574 2.34 0.09310 N 1 D;P 0.71674 0.998;0.718 P;B 0.60345 0.873;0.221 T 0.53823 -0.8384 9 0.62326 D 0.03 . 4.9504 0.14011 0.0:1.0:0.0:0.0 . 28;28 Q15485-2;Q15485 .;FCN2_HUMAN V 28 ENSP00000291741:A28V;ENSP00000291744:A28V ENSP00000291744:A28V A + 2 0 FCN2 136912571 0.001000 0.12720 0.084000 0.20598 0.162000 0.22319 0.255000 0.18333 0.713000 0.32060 0.467000 0.42956 GCG TCGA-IB-7885-01A-11D-2154-08 FCN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054960.1 1 0 0 8 99 0 22 0 0 0 0 22 2 0 0 0 0 0 2 1 0.989486 8 97 0 22 2 -12.752400 1 1 121366 11 39 1 1 2 3 2.054532 0 0.160000 1.730000 0.165342 0.980000 0.460000 1.000000 1.000000 0.879131 0.980000 1 0.680000 1.000000 TLN1 7094 broad.mit.edu 37 9 35699041 35699041 + Silent SNP C C T TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr9:35699041C>T ENST00000314888.9 - 52 7340 c.6987G>A c.(6985-6987)cgG>cgA p.R2329R TLN1_ENST00000540444.1_Silent_p.R2217R NM_006289.3 NP_006280.3 Q9Y490 TLN1_HUMAN talin 1 85 all_epithelial(49;0.167) Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194) TGGGTTTGGCCCGGGGCTTCA 0.567000 0 SO:0001819 synonymous_variant ENST00000314888.9 1 1 hg19 CCDS35009.1 TCGA-IB-7885-01A-11D-2154-08 TLN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052353.2 1 0 1 29 257 0 89 1 1 139 715 0 89 2 0 0 0 0 0 2 1 1.000000 27 245 0 87 2 -20.000000 1 1 0 0 1 0 1 1 1.880781 1 0.160000 1.730000 0.086957 0.910000 0.700000 1.000000 0.990000 0.904152 0.910000 1 0.810000 0.980000 PRUNE2 158471 broad.mit.edu 37 9 79325846 79325846 + Silent SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chr9:79325846G>A ENST00000376718.3 - 8 1467 c.1344C>T c.(1342-1344)gaC>gaT p.D448D PRUNE2_ENST00000428286.1_Silent_p.D89D NM_015225.2 NP_056040.2 Q8WUY3 PRUN2_HUMAN prune homolog 2 (Drosophila) 16 CGGGGCTGTCGTCACTGAGGA 0.602000 0 SO:0001819 synonymous_variant ENST00000376718.3 1 1 hg19 CCDS47982.1 TCGA-IB-7885-01A-11D-2154-08 PRUNE2-003 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052730.2 1 0 0 18 177 0 36 0 9.742091e-03 0 2 0 36 2 0 0 0 0 0 2 1 0.999984 18 174 0 34 2 -19.999990 1 1 120344 2 29 1 0 1 1 2.039043 0 0.160000 1.730000 0.155949 0.990000 0.710000 1.000000 1.000000 0.965137 0.990000 1 0.910000 1.000000 PLXNB3 5365 broad.mit.edu 37 X 153035996 153035996 + Missense_Mutation SNP G G A TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chrX:153035996G>A ENST00000361971.5 + 10 2023 c.1909G>A c.(1909-1911)Gtg>Atg p.V637M PLXNB3_ENST00000538282.1_Missense_Mutation_p.V247M|PLXNB3_ENST00000538776.1_Missense_Mutation_p.V290M|PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538966.1_Missense_Mutation_p.V660M NM_005393.2 NP_005384.2 Q9ULL4 PLXB3_HUMAN plexin B3 32 all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05) TCGCGCTTGCGTGGGCAGCAT 0.677000 0 SO:0001583 missense ENST00000361971.5 1 1 hg19 CCDS14729.1 . . . . . . . . . . g 15.37 2.812203 0.50527 . . ENSG00000198753 ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282 T;T;T;T 0.73789 4.84;4.8;4.25;-0.78 5.34 5.34 0.76211 . 0.000000 0.85682 D 0.000000 D 0.87309 0.6145 M 0.85630 2.765 0.37423 D 0.9137 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.999;0.999;0.994;0.999 D 0.90934 0.4792 10 0.66056 D 0.02 . 15.3352 0.74247 0.0:0.0:1.0:0.0 . 290;319;660;637 B7Z3H9;B7Z9A5;F5H773;Q9ULL4 .;.;.;PLXB3_HUMAN M 660;637;290;247 ENSP00000442736:V660M;ENSP00000355378:V637M;ENSP00000445569:V290M;ENSP00000441919:V247M ENSP00000355378:V637M V + 1 0 PLXNB3 152689190 1.000000 0.71417 0.991000 0.47740 0.032000 0.12392 3.590000 0.53979 2.212000 0.71576 0.525000 0.51046 GTG TCGA-IB-7885-01A-11D-2154-08 PLXNB3-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000061063.1 1 0 1 9 120 0 50 1 6.447181e-01 28 2 0 50 2 0 0 0 0 0 2 1 0.993475 9 115 0 44 2 -13.752160 1 1 120920 2 31 1 0 1 1 0.160000 1.730000 0.160000 0.880000 0.440000 1.000000 1.000000 0.840650 0.880000 1 0.630000 1.000000 TAF1 6872 broad.mit.edu 37 X 70627893 70627893 + Missense_Mutation SNP A A G TCGA-IB-7885-01A-11D-2154-08 TCGA-IB-7885-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx adfbadb2-fb88-49d5-84ea-5197b9c77c06 e89b13a9-1fd5-46a7-96f1-c0b8b932ddda g.chrX:70627893A>G ENST00000373790.4 + 28 4324 c.4273A>G c.(4273-4275)Atg>Gtg p.M1425V TAF1_ENST00000276072.3_Missense_Mutation_p.M1446V|TAF1_ENST00000423759.1_Missense_Mutation_p.M1446V|TAF1_ENST00000449580.1_Missense_Mutation_p.M1425V NM_004606.3|NM_138923.2 NP_004597.2|NP_620278.1 P21675 TAF1_HUMAN TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa 124 Renal(35;0.156) all_lung(315;0.000321) CACTCGGCCAATGGACCTACA 0.468000 0 SO:0001583 missense ENST00000373790.4 1 1 hg19 CCDS35325.1 . . . . . . . . . . . 17.06 3.293716 0.60086 . . ENSG00000147133 ENST00000373790;ENST00000449580;ENST00000423759;ENST00000395779;ENST00000538124;ENST00000276072 T;T;T;T 0.26067 1.76;1.76;1.76;1.76 4.17 2.92 0.33932 Bromodomain (5);Bromodomain, conserved site (1); 0.000000 0.85682 D 0.000000 T 0.50684 0.1630 M 0.89715 3.055 0.58432 D 0.99999 P;D;D 0.61080 0.939;0.989;0.964 P;P;P 0.62560 0.708;0.904;0.647 T 0.58934 -0.7548 10 0.72032 D 0.01 . 9.3206 0.37962 0.8382:0.0:0.0:0.1618 . 1425;1425;1446 P21675-4;P21675;P21675-2 .;TAF1_HUMAN;. V 1425;1425;1446;131;131;1446 ENSP00000362895:M1425V;ENSP00000389000:M1425V;ENSP00000406549:M1446V;ENSP00000276072:M1446V ENSP00000276072:M1446V M + 1 0 TAF1 70544618 1.000000 0.71417 1.000000 0.80357 0.887000 0.51463 8.757000 0.91657 1.535000 0.49220 0.345000 0.21793 ATG TCGA-IB-7885-01A-11D-2154-08 TAF1-009 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000058995.2 1 0 1 33 417 0 88 1 4.201906e-01 11 8 0 88 2 0 0 0 0 0 2 1 1.000000 33 405 0 87 2 -20.000000 1 1 0 0 1 0 1 1 0.160000 1.730000 0.160000 0.910000 0.640000 1.000000 1.000000 0.896093 0.910000 1 0.770000 1.000000