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 CELF2 10659 broad.mit.edu 37 10 11363283 11363283 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr10:11363283G>A ENST00000379261.4 + 11 1281 c.1189G>A c.(1189-1191)Gcg>Acg p.A397T CELF2_ENST00000537122.1_Missense_Mutation_p.A292T|CELF2_ENST00000608830.1_Missense_Mutation_p.A377T|CELF2-AS1_ENST00000379256.3_RNA|CELF2_ENST00000417956.2_Missense_Mutation_p.A377T|CELF2_ENST00000542579.1_Missense_Mutation_p.A410T|CELF2_ENST00000609692.1_Missense_Mutation_p.A377T|CELF2_ENST00000354440.2_Missense_Mutation_p.A379T|CELF2_ENST00000315874.4_Missense_Mutation_p.A379T|CELF2_ENST00000450189.1_Missense_Mutation_p.A410T|CELF2_ENST00000416382.2_Missense_Mutation_p.A397T|CELF2_ENST00000354897.3_Missense_Mutation_p.A391T|CELF2_ENST00000399850.3_Missense_Mutation_p.A379T|CELF2_ENST00000427450.1_Missense_Mutation_p.A379T NM_001025077.2 NP_001020248.1 O95319 CELF2_HUMAN CUGBP, Elav-like family member 2 16 CGCAGCCGCCGCGCTGCCCAC 0.657000 0 SO:0001583 missense ENST00000379261.4 1 1 hg19 CCDS44354.1 . . . . . . . . . . G 22.7 4.318107 0.81469 . . ENSG00000048740 ENST00000379261;ENST00000416382;ENST00000450189;ENST00000542579;ENST00000399850;ENST00000417956;ENST00000315874;ENST00000354440;ENST00000354897;ENST00000427450;ENST00000537122;ENST00000538632 T;T;T;T;T;T;T;T;T;T 0.67345 -0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26 5.33 5.33 0.75918 . 0.186321 0.32753 N 0.005686 T 0.79094 0.4388 M 0.62723 1.935 0.80722 D 1 P;P;B;D;P;D 0.76494 0.802;0.802;0.078;0.999;0.898;0.991 P;P;B;D;B;P 0.68621 0.471;0.471;0.029;0.959;0.378;0.776 T 0.73836 -0.3857 10 0.25106 T 0.35 -1.3418 19.2874 0.94084 0.0:0.0:1.0:0.0 . 385;403;398;410;410;397 B4DDE7;B4DS31;B2RA86;E9PC62;O95319-3;O95319 .;.;.;.;.;CELF2_HUMAN T 397;397;410;410;379;377;379;379;387;379;292;203 ENSP00000368563:A397T;ENSP00000406451:A397T;ENSP00000389951:A410T;ENSP00000443926:A410T;ENSP00000382743:A379T;ENSP00000404834:A377T;ENSP00000315328:A379T;ENSP00000346426:A379T;ENSP00000388530:A379T;ENSP00000438884:A292T ENSP00000315328:A379T A + 1 0 CELF2 11403289 1.000000 0.71417 0.344000 0.25628 0.982000 0.71751 9.591000 0.98241 2.789000 0.95967 0.558000 0.71614 GCG TCGA-IB-8126-01A-11D-2396-08 CELF2-201 KNOWN basic|CCDS protein_coding protein_coding 0 0 0 11 293 0 52 0 1.186448e-01 0 15 0 52 2 0 0 0 0 0 2 1 0.998292 11 289 0 52 2 0 0 0 0 52 2 -11.920220 1 1 120968 7 39 1 1 2 3 1.940731 0 0.090000 3.970000 0.122003 0.900000 4.600000e-01 1.000000 1.000000 0.852733 0.900000 1 6.500000e-01 1 KNDC1 85442 broad.mit.edu 37 10 134997481 134997481 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr10:134997481G>A ENST00000304613.3 + 5 634 c.613G>A c.(613-615)Gga>Aga p.G205R KNDC1_ENST00000368572.2_Missense_Mutation_p.G205R|KNDC1_ENST00000368571.2_Missense_Mutation_p.G140R Q76NI1 VKIND_HUMAN kinase non-catalytic C-lobe domain (KIND) containing 1 60 all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203) CGAGTCCTTCGGAGCGCTGCA 0.582000 0 SO:0001583 missense ENST00000304613.3 1 1 hg19 CCDS7674.1 . . . . . . . . . . G 17.87 3.494056 0.64186 . . ENSG00000171798 ENST00000304613;ENST00000368572;ENST00000368571 T;T;T 0.20598 2.54;2.54;2.06 4.15 4.15 0.48705 KIND (2); 0.492334 0.17935 U 0.157032 T 0.41766 0.1173 L 0.57536 1.79 0.38641 D 0.951614 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.998 T 0.41520 -0.9504 10 0.87932 D 0 -17.3865 12.7092 0.57080 0.0:0.0:1.0:0.0 . 140;205 Q76NI1-2;Q76NI1 .;VKIND_HUMAN R 205;205;140 ENSP00000304437:G205R;ENSP00000357561:G205R;ENSP00000357560:G140R ENSP00000304437:G205R G + 1 0 KNDC1 134847471 0.995000 0.38212 0.998000 0.56505 0.682000 0.39822 3.501000 0.53325 2.255000 0.74692 0.450000 0.29827 GGA TCGA-IB-8126-01A-11D-2396-08 KNDC1-006 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000277044.3 0 0 0 13 304 0 60 0 5.966550e-03 0 3 0 60 2 0 0 0 0 0 2 1 0.999532 13 301 0 60 2 0 0 0 0 60 2 -3.064027 1 1 121378 3 34 1 1 2 3 2.008180 0 0.090000 3.970000 0.129187 0.960000 5.400000e-01 1.000000 1.000000 0.895549 0.960000 1 7.300000e-01 1 CHAT 1103 broad.mit.edu 37 10 50827783 50827783 + Silent SNP C C T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr10:50827783C>T ENST00000337653.2 + 3 553 c.400C>T c.(400-402)Ctg>Ttg p.L134L CHAT_ENST00000460699.1_3'UTR|CHAT_ENST00000455728.2_Silent_p.L16L|CHAT_ENST00000395559.2_Silent_p.L16L|CHAT_ENST00000395562.2_Silent_p.L52L|CHAT_ENST00000339797.1_Silent_p.L16L|CHAT_ENST00000351556.3_Silent_p.L16L NM_001142929.1|NM_020549.4 NP_001136401.1|NP_065574 P28329 CLAT_HUMAN choline O-acetyltransferase 56 all_neural(218;0.107) Choline(DB00122)|Nicotine(DB00184) GCTGCCCAAACTGCCCGTGCC 0.577000 0 SO:0001819 synonymous_variant ENST00000337653.2 1 1 hg19 CCDS7232.1 TCGA-IB-8126-01A-11D-2396-08 CHAT-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047997.1 1 0 0 6 137 0 24 0 0 0 1 0 24 2 0 0 0 0 0 2 1 0.966001 6 137 0 23 2 0 0 0 0 24 2 -8.996124 1 1 0 0 1 1 2 3 2.016533 0 0.090000 3.970000 0.129187 0.990000 4.300000e-01 1.000000 1.000000 0.880847 0.990000 1 6.800000e-01 1 OR5D18 219438 broad.mit.edu 37 11 55587727 55587727 + Nonsense_Mutation SNP G G T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr11:55587727G>T ENST00000333976.4 + 1 642 c.622G>T c.(622-624)Gaa>Taa p.E208* NM_001001952.1 NP_001001952.1 Q8NGL1 OR5DI_HUMAN olfactory receptor, family 5, subfamily D, member 18 55 all_epithelial(135;0.208) CACCTTTAATGAAATCAGCAC 0.448000 0 SO:0001587 stop_gained ENST00000333976.4 0 1 hg19 CCDS31510.1 . . . . . . . . . . . 10.04 1.242711 0.22796 . . ENSG00000186119 ENST00000333976 . . . 4.85 3.92 0.45320 . 1.005710 0.08015 N 0.991100 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.17369 T 0.5 0.2984 7.6562 0.28377 0.0887:0.0:0.7453:0.166 . . . . X 208 . ENSP00000335025:E208X E + 1 0 OR5D18 55344303 0.000000 0.05858 0.891000 0.34965 0.219000 0.24729 0.634000 0.24614 2.462000 0.83206 0.567000 0.79289 GAA TCGA-IB-8126-01A-11D-2396-08 OR5D18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391515.1 0 0 0 14 496 0 108 0 0 0 0 108 2 0 0 0 0 0 2 1 0.999742 14 491 0 108 2 0 0 0 0 108 2 -12.233260 1 1 0 0 1 1 2 3 1.968950 0 0.090000 3.970000 0.128811 0.650000 3.700000e-01 1.000000 1.000000 0.667472 0.650000 0 4.900000e-01 8.400000e-01 ARAP1 116985 broad.mit.edu 37 11 72422096 72422096 + Nonsense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr11:72422096G>A ENST00000393609.3 - 9 1385 c.1183C>T c.(1183-1185)Cga>Tga p.R395* ARAP1_ENST00000429686.1_Nonsense_Mutation_p.R150*|ARAP1_ENST00000426523.1_Nonsense_Mutation_p.R150*|ARAP1_ENST00000334211.8_Nonsense_Mutation_p.R150*|ARAP1_ENST00000393605.3_Nonsense_Mutation_p.R155*|ARAP1_ENST00000455638.2_Nonsense_Mutation_p.R395*|ARAP1_ENST00000359373.5_Nonsense_Mutation_p.R395* NM_001040118.2 NP_001035207.1 Q96P48 ARAP1_HUMAN ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 27 GCAAAGGTTCGGTTGTTTGTG 0.547000 Ovarian(102;1198 1520 13195 17913 37529) 0 SO:0001587 stop_gained ENST00000393609.3 0 1 hg19 CCDS41687.1 . . . . . . . . . . G 45 11.461141 0.99564 . . ENSG00000186635 ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000340247 . . . 5.52 4.61 0.57282 . 0.000000 0.64402 D 0.000002 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 13.6244 0.62155 0.0:0.0:0.8439:0.1561 . . . . X 395;395;155;150;395;150;150;184 . ENSP00000335506:R150X R - 1 2 ARAP1 72099744 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 3.092000 0.50207 1.343000 0.45638 -0.152000 0.13540 CGA TCGA-IB-8126-01A-11D-2396-08 ARAP1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000347428.1 1 0 0 31 629 0 98 0 7.937185e-01 0 62 0 98 2 0 0 0 0 0 2 1 1.000000 31 622 0 98 2 0 0 0 0 98 2 -2.607054 1 1 0 0 1 1 2 3 2.014809 0 0.090000 3.970000 0.129187 0.990000 7.600000e-01 1.000000 1.000000 0.968826 0.990000 1 9.100000e-01 1 DENND5A 23258 broad.mit.edu 37 11 9225319 9225319 + Silent SNP A A G TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr11:9225319A>G ENST00000328194.3 - 4 1157 c.837T>C c.(835-837)ctT>ctC p.L279L DENND5A_ENST00000530044.1_Silent_p.L279L NM_001243254.1|NM_015213.3 NP_001230183.1|NP_056028.2 Q6IQ26 DEN5A_HUMAN DENN/MADD domain containing 5A 39 CAAATAGGGGAAGCTCATTGG 0.498000 0 SO:0001819 synonymous_variant ENST00000328194.3 0 1 hg19 CCDS31423.1 TCGA-IB-8126-01A-11D-2396-08 DENND5A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385910.2 0 0 0 5 575 0 93 0 9.677867e-02 0 49 0 93 2 0 0 0 0 0 2 1 0.936643 5 571 0 93 2 0 0 0 0 93 2 -4.554739 1 1 0 0 1 1 2 3 1.968950 0 0.090000 3.970000 0.128811 0.210000 7.000000e-02 0.460000 0.200000 0.236516 0.210000 0 1.300000e-01 3.300000e-01 HSP90B1 7184 broad.mit.edu 37 12 104327988 104327988 + Silent SNP C C A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr12:104327988C>A ENST00000299767.5 + 5 848 c.666C>A c.(664-666)atC>atA p.I222I NM_003299.2 NP_003290.1 P14625 ENPL_HUMAN heat shock protein 90kDa beta (Grp94), member 1 29 Rifabutin(DB00615) CCCAGCACATCTGGGAGTCTG 0.433000 0 SO:0001819 synonymous_variant ENST00000299767.5 1 1 hg19 CCDS9094.1 TCGA-IB-8126-01A-11D-2396-08 HSP90B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000407349.1 0 0 0 11 277 0 54 1 9.999966e-01 16 680 0 54 2 0 0 0 0 0 2 1 0.998325 11 275 0 55 2 0 0 0 0 54 2 -12.315890 1 1 0 0 1 1 2 3 2.001934 0 0.090000 3.970000 0.129187 0.900000 4.800000e-01 1.000000 1.000000 0.859484 0.900000 1 6.700000e-01 1 CAPZA3 93661 broad.mit.edu 37 12 18891852 18891852 + Missense_Mutation SNP A A G TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr12:18891852A>G ENST00000317658.3 + 1 808 c.650A>G c.(649-651)aAc>aGc p.N217S PLCZ1_ENST00000539875.1_5'Flank|PLCZ1_ENST00000435379.1_5'Flank|PLCZ1_ENST00000447925.2_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000266505.7_5'Flank NM_033328.2 NP_201585.1 Q96KX2 CAZA3_HUMAN capping protein (actin filament) muscle Z-line, alpha 3 19 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241) Hepatocellular(102;0.194) GAAATAGTTAACCAAGCTCAA 0.398000 0 SO:0001583 missense ENST00000317658.3 1 1 hg19 CCDS8681.1 . . . . . . . . . . A 15.91 2.972165 0.53614 0.0 1.16E-4 ENSG00000177938 ENST00000317658 . . . 4.8 4.8 0.61643 . 0.288858 0.31673 N 0.007253 T 0.61850 0.2380 L 0.41906 1.305 0.37992 D 0.933951 D 0.59767 0.986 P 0.58928 0.848 T 0.65158 -0.6236 9 0.40728 T 0.16 -22.2602 11.8334 0.52309 1.0:0.0:0.0:0.0 . 217 Q96KX2 CAZA3_HUMAN S 217 . ENSP00000326238:N217S N + 2 0 CAPZA3 18783119 1.000000 0.71417 0.997000 0.53966 0.988000 0.76386 5.478000 0.66806 2.021000 0.59480 0.379000 0.24179 AAC TCGA-IB-8126-01A-11D-2396-08 CAPZA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401902.1 0 0 0 8 251 0 61 0 0 0 1 0 61 2 0 0 0 0 0 2 1 0.989175 8 248 0 61 2 0 0 0 0 61 2 -9.764521 1 1 121406 1 28 1 1 2 3 2.003616 0 0.090000 3.970000 0.129187 0.740000 3.500000e-01 1.000000 1.000000 0.747274 0.740000 0 5.200000e-01 1 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-IB-8126-01A-11D-2396-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 0 0 80 0 25 0 15 0 25 7 371 0 365 0 79 0 25 1055 6830 0 25 -2.752535 1 1 121404 2 44 1 1 2 3 2.003616 0 0.090000 3.970000 0.129187 0.180000 0 1.000000 0.010000 0.287707 0.180000 0 4.000000e-02 5.500000e-01 KRT7 3855 broad.mit.edu 37 12 52639299 52639299 + Missense_Mutation SNP G G T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr12:52639299G>T ENST00000331817.5 + 7 1271 c.1088G>T c.(1087-1089)cGg>cTg p.R363L RP3-416H24.1_ENST00000546686.1_RNA|KRT7_ENST00000552322.1_3'UTR NM_005556.3 NP_005547.3 P08729 K2C7_HUMAN keratin 7 14 Primaquine(DB01087) GCCCTGCAGCGGGGCAAGCAG 0.647000 0 SO:0001583 missense ENST00000331817.5 0 1 hg19 CCDS8822.1 . . . . . . . . . . G 11.78 1.739868 0.30865 . . ENSG00000135480 ENST00000331817;ENST00000422319 D 0.89050 -2.46 4.4 1.11 0.20524 Filament (1); 1.896280 0.03317 N 0.191374 D 0.86447 0.5935 L 0.47190 1.495 0.29184 N 0.876328 P 0.43701 0.815 B 0.40477 0.33 T 0.75634 -0.3250 10 0.87932 D 0 . 8.4518 0.32875 0.7315:0.0:0.2685:0.0 . 363 P08729 K2C7_HUMAN L 363;339 ENSP00000329243:R363L ENSP00000329243:R363L R + 2 0 KRT7 50925566 0.867000 0.29959 0.022000 0.16811 0.005000 0.04900 1.090000 0.30902 0.096000 0.17463 -0.258000 0.10820 CGG TCGA-IB-8126-01A-11D-2396-08 KRT7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404897.1 0 0 0 5 448 0 57 0 8.057674e-01 0 271 0 57 2 0 0 0 0 0 2 1 0.935277 5 441 0 57 2 0 0 0 0 57 2 -4.429121 1 1 0 0 1 1 2 3 2.001934 0 0.090000 3.970000 0.129187 0.270000 1.000000e-01 0.560000 0.250000 0.301673 0.270000 0 1.700000e-01 4.200000e-01 C3AR1 719 broad.mit.edu 37 12 8211546 8211546 + Silent SNP A A C TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr12:8211546A>C ENST00000307637.4 - 2 1439 c.1236T>G c.(1234-1236)acT>acG p.T412T NM_004054.2 NP_004045.1 Q16581 C3AR_HUMAN complement component 3a receptor 1 20 AGGACATCAGAGTTTTCCCCA 0.468000 0 SO:0001819 synonymous_variant ENST00000307637.4 1 1 hg19 CCDS8588.1 TCGA-IB-8126-01A-11D-2396-08 C3AR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400254.1 0 0 0 10 285 0 70 0 5.366142e-01 0 50 0 70 2 0 0 0 0 0 2 1 0.996800 10 281 0 69 2 0 0 0 0 70 2 -11.397040 1 1 0 0 1 1 2 3 2.003616 0 0.090000 3.970000 0.129187 0.800000 4.100000e-01 1.000000 1.000000 0.797415 0.800000 0 5.900000e-01 1 CCDC70 83446 broad.mit.edu 37 13 52439917 52439917 + Missense_Mutation SNP T T A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr13:52439917T>A ENST00000242819.4 + 2 699 c.403T>A c.(403-405)Ttc>Atc p.F135I NM_031290.2 NP_112580.2 Q6NSX1 CCD70_HUMAN coiled-coil domain containing 70 15 Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.0107)|Hepatocellular(98;0.065)|all_neural(104;0.19) GGATAAGGCCTTCTGGAAAGA 0.478000 0 SO:0001583 missense ENST00000242819.4 1 1 hg19 CCDS9431.1 . . . . . . . . . . T 12.48 1.949934 0.34377 . . ENSG00000123171 ENST00000242819 T 0.20738 2.05 5.78 -0.997 0.10215 . 0.097664 0.45606 D 0.000357 T 0.30230 0.0758 M 0.70595 2.14 0.09310 N 1 D 0.56287 0.975 P 0.53035 0.716 T 0.17077 -1.0381 10 0.42905 T 0.14 -25.4087 10.0609 0.42275 0.0:0.3629:0.0:0.6371 . 135 Q6NSX1 CCD70_HUMAN I 135 ENSP00000242819:F135I ENSP00000242819:F135I F + 1 0 CCDC70 51337918 0.963000 0.33076 0.000000 0.03702 0.005000 0.04900 1.723000 0.38053 -0.085000 0.12573 -0.256000 0.11100 TTC TCGA-IB-8126-01A-11D-2396-08 CCDC70-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045033.2 1 0 0 45 947 0 118 0 0 0 0 118 2 0 0 0 0 0 2 1 1.000000 44 939 0 117 2 0 0 0 0 118 2 -5.262018 1 1 0 0 1 1 2 3 1.946162 0 0.090000 3.970000 0.123145 0.990000 7.800000e-01 1.000000 1.000000 0.969733 0.990000 1 9.100000e-01 1 TGM5 9333 broad.mit.edu 37 15 43527834 43527834 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr15:43527834G>A ENST00000220420.5 - 10 1554 c.1547C>T c.(1546-1548)cCg>cTg p.P516L TGM5_ENST00000349114.4_Missense_Mutation_p.P434L NM_201631.3 NP_963925.2 O43548 TGM5_HUMAN transglutaminase 5 44 all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216) L-Glutamine(DB00130) CATGTTGGGCGGGTCGAGCAG 0.567000 0 SO:0001583 missense ENST00000220420.5 1 1 hg19 CCDS32212.1 . . . . . . . . . . G 6.234 0.411308 0.11812 . . ENSG00000104055 ENST00000220420;ENST00000349114;ENST00000396996 T;T 0.68624 -0.34;-0.34 5.58 3.58 0.41010 Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1); 0.439796 0.24666 N 0.036588 T 0.54838 0.1883 L 0.47016 1.485 0.09310 N 1 B;B 0.30937 0.136;0.301 B;B 0.24269 0.024;0.052 T 0.49041 -0.8980 10 0.39692 T 0.17 -0.4586 10.2275 0.43233 0.0:0.1477:0.6995:0.1528 . 434;516 O43548-2;O43548 .;TGM5_HUMAN L 516;434;515 ENSP00000220420:P516L;ENSP00000220419:P434L ENSP00000220420:P516L P - 2 0 TGM5 41315126 0.094000 0.21725 0.008000 0.14137 0.083000 0.17756 2.334000 0.43920 1.351000 0.45789 -0.165000 0.13383 CCG TCGA-IB-8126-01A-11D-2396-08 TGM5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000432257.1 1 0 0 11 238 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.998441 12 237 0 36 2 0 0 0 0 36 2 -2.901027 1 1 121412 4 33 1 1 2 3 2.011097 0 0.090000 3.970000 0.129187 0.990000 5.600000e-01 1.000000 1.000000 0.918569 0.990000 1 7.700000e-01 1 IL16 3603 broad.mit.edu 37 15 81592482 81592482 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr15:81592482G>A ENST00000302987.4 + 13 2815 c.2815G>A c.(2815-2817)Gac>Aac p.D939N IL16_ENST00000394660.2_Missense_Mutation_p.D939N|IL16_ENST00000394652.2_Missense_Mutation_p.D238N Q14005 IL16_HUMAN interleukin 16 57 CCCTGGCCCGGACCCGCTCCT 0.657000 0 SO:0001583 missense ENST00000302987.4 0 1 hg19 CCDS42069.1 . . . . . . . . . . G 21.9 4.211166 0.79240 . . ENSG00000172349 ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653;ENST00000394652;ENST00000394656 T;T;T 0.11495 2.77;2.78;3.37 4.85 4.85 0.62838 . 0.267702 0.26731 N 0.022788 T 0.24928 0.0605 L 0.46157 1.445 0.36294 D 0.856591 D;D;D;D;B;D 0.89917 0.997;0.965;1.0;1.0;0.166;0.991 P;P;D;D;B;P 0.83275 0.844;0.703;0.994;0.996;0.017;0.798 T 0.08126 -1.0737 10 0.62326 D 0.03 . 11.7533 0.51862 0.0853:0.0:0.9147:0.0 . 771;432;476;329;939;939 F8W7Z5;Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2 .;.;.;.;IL16_HUMAN;. N 939;771;939;476;329;238;238 ENSP00000378155:D939N;ENSP00000302935:D939N;ENSP00000378147:D238N ENSP00000302935:D939N D + 1 0 IL16 79379537 0.986000 0.35501 0.367000 0.25926 0.037000 0.13140 3.537000 0.53590 2.236000 0.73375 0.655000 0.94253 GAC TCGA-IB-8126-01A-11D-2396-08 IL16-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000303952.1 0 0 0 6 304 0 61 0 3.659531e-01 0 58 0 61 2 0 0 0 0 0 2 1 0.962451 6 296 0 59 2 0 0 0 0 61 2 -6.807217 1 1 0 0 1 1 2 3 2.011097 0 0.090000 3.970000 0.129187 0.470000 2.000000e-01 0.900000 0.450000 0.508048 0.470000 0 3.100000e-01 6.900000e-01 SBK1 388228 broad.mit.edu 37 16 28331735 28331735 + Silent SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr16:28331735G>A ENST00000341901.4 + 4 1557 c.768G>A c.(766-768)gcG>gcA p.A256A NM_001024401.2 NP_001019572.1 Q52WX2 SBK1_HUMAN SH3 domain binding kinase 1 5 GGGAGGCGGCGTCGGGCGCCG 0.746000 0 SO:0001819 synonymous_variant ENST00000341901.4 1 1 hg19 CCDS32416.1 TCGA-IB-8126-01A-11D-2396-08 SBK1-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000387677.1 1 0 0 11 160 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 0.998456 10 160 0 44 2 0 0 0 0 44 2 -15.370900 1 1 0 0 1 1 2 3 2.017862 0 0.090000 3.970000 0.129187 0.990000 8.100000e-01 1.000000 1.000000 0.988269 0.990000 1 9.900000e-01 1 HSD17B2 3294 broad.mit.edu 37 16 82131809 82131809 + Missense_Mutation SNP A A G TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr16:82131809A>G ENST00000199936.4 + 5 1125 c.932A>G c.(931-933)aAc>aGc p.N311S RP11-510J16.5_ENST00000567021.1_RNA NM_002153.2 NP_002144.1 P37059 DHB2_HUMAN hydroxysteroid (17-beta) dehydrogenase 2 10 CTATTGATCAACTCGTTAGCC 0.542000 0 SO:0001583 missense ENST00000199936.4 1 1 hg19 CCDS10936.1 . . . . . . . . . . a 5.085 0.201396 0.09652 . . ENSG00000086696 ENST00000199936 D 0.83419 -1.72 5.57 -9.36 0.00629 NAD(P)-binding domain (1); 2.782280 0.00732 N 0.000947 T 0.56645 0.1999 N 0.11064 0.09 0.09310 N 1 B 0.06786 0.001 B 0.06405 0.002 T 0.57740 -0.7759 10 0.08837 T 0.75 . 0.9019 0.01276 0.281:0.2882:0.2436:0.1872 . 311 P37059 DHB2_HUMAN S 311 ENSP00000199936:N311S ENSP00000199936:N311S N + 2 0 HSD17B2 80689310 0.000000 0.05858 0.000000 0.03702 0.006000 0.05464 -1.845000 0.01677 -1.859000 0.01156 0.533000 0.62120 AAC TCGA-IB-8126-01A-11D-2396-08 HSD17B2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269057.2 0 0 0 20 504 0 110 1 9.769839e-01 10 146 0 110 2 0 0 0 0 0 2 1 0.999995 20 499 0 110 2 0 0 0 0 110 2 -4.258489 1 1 121412 1 32 1 1 2 3 2.012426 0 0.090000 3.970000 0.129187 0.890000 5.600000e-01 1.000000 1.000000 0.870578 0.890000 1 7.100000e-01 1 CDT1 81620 broad.mit.edu 37 16 88871873 88871873 + Missense_Mutation SNP C C T rs3218727 byFrequency TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr16:88871873C>T ENST00000301019.4 + 4 1133 c.514C>T c.(514-516)Cgc>Tgc p.R172C NM_030928.3 NP_112190.2 chromatin licensing and DNA replication factor 1 7 CGCCTACCAGCGCTTCCATGC 0.677000 Melanoma(159;511 3380 30971) 0 SO:0001583 missense ENST00000301019.4 0 1 hg19 CCDS32510.1 . . . . . . . . . . C 25.5 4.644116 0.87859 0.003412 0.0 ENSG00000167513 ENST00000301019 T 0.28255 1.62 4.68 3.66 0.41972 . 0.111388 0.64402 D 0.000007 T 0.56217 0.1970 M 0.77103 2.36 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 T 0.64089 -0.6489 10 0.87932 D 0 -22.4772 15.3458 0.74337 0.0:0.8602:0.1398:0.0 rs3218727 172 Q9H211 CDT1_HUMAN C 172 ENSP00000301019:R172C ENSP00000301019:R172C R + 1 0 CDT1 87399374 1.000000 0.71417 1.000000 0.80357 0.867000 0.49689 3.838000 0.55828 2.319000 0.78375 0.462000 0.41574 CGC TCGA-IB-8126-01A-11D-2396-08 CDT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000423215.1 0 0 0 9 354 0 45 0 4.727954e-03 1 3 0 45 2 0 0 0 0 0 2 1 0.994142 9 351 0 44 2 0 0 0 0 45 2 -8.880385 1 1 121224 43 47 1 1 2 3 2.012426 0 0.090000 3.970000 0.129187 0.590000 2.900000e-01 1.000000 1.000000 0.619910 0.590000 0 4.200000e-01 8.100000e-01 GRIN2A 2903 broad.mit.edu 37 16 9862737 9862737 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr16:9862737G>A ENST00000396573.2 - 13 2875 c.2566C>T c.(2566-2568)Cgg>Tgg p.R856W GRIN2A_ENST00000396575.2_Missense_Mutation_p.R856W|GRIN2A_ENST00000330684.3_Missense_Mutation_p.R856W|GRIN2A_ENST00000404927.2_Missense_Mutation_p.R856W|GRIN2A_ENST00000562109.1_Missense_Mutation_p.R856W|GRIN2A_ENST00000535259.1_Missense_Mutation_p.R699W NM_000833.3 NP_000824.1 Q12879 NMDE1_HUMAN glutamate receptor, ionotropic, N-methyl D-aspartate 2A 198 Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418) AACCCAGGCCGGTCGGAGCAC 0.567000 0 SO:0001583 missense ENST00000396573.2 1 1 hg19 CCDS10539.1 . . . . . . . . . . G 20.9 4.066263 0.76187 . . ENSG00000183454 ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575 T;T;T;T;T 0.12984 2.63;2.63;2.63;2.63;2.63 4.44 3.33 0.38152 Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1); 0.155509 0.56097 D 0.000031 T 0.28928 0.0718 M 0.64997 1.995 0.37896 D 0.930866 D;D;D 0.76494 0.998;0.999;0.999 D;D;D 0.70016 0.944;0.967;0.913 T 0.04885 -1.0920 9 . . . . 9.4317 0.38615 0.0:0.0:0.5699:0.4301 . 699;856;856 F5GZ52;Q17RZ6;Q12879 .;.;NMDE1_HUMAN W 856;856;699;856;856 ENSP00000379818:R856W;ENSP00000385872:R856W;ENSP00000441572:R699W;ENSP00000332549:R856W;ENSP00000379820:R856W . R - 1 2 GRIN2A 9770238 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 4.673000 0.61604 2.170000 0.68504 0.563000 0.77884 CGG TCGA-IB-8126-01A-11D-2396-08 GRIN2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251930.3 0 0 0 17 818 0 98 0 0 0 0 98 2 0 0 0 0 0 2 1 0.999961 17 809 0 98 2 0 0 0 0 98 2 -2.115213 0 1 121412 1 39 1 1 2 3 2.004762 0 0.090000 3.970000 0.129187 0.480000 2.800000e-01 0.720000 0.480000 0.495365 0.480000 0 3.700000e-01 6.100000e-01 KIAA0100 9703 broad.mit.edu 37 17 26946933 26946933 + Missense_Mutation SNP C C T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr17:26946933C>T ENST00000528896.2 - 30 5539 c.5465G>A c.(5464-5466)cGg>cAg p.R1822Q SPAG5-AS1_ENST00000424210.1_RNA|KIAA0100_ENST00000389003.3_Missense_Mutation_p.R1679Q|KIAA0100_ENST00000544884.1_Missense_Mutation_p.R1679Q|SPAG5-AS1_ENST00000414744.1_RNA|KIAA0100_ENST00000579924.2_5'Flank NM_014680.3 NP_055495.2 Q14667 K0100_HUMAN KIAA0100 68 Lung NSC(42;0.00431) CACATGCTGCCGCACAGCCTC 0.493000 0 SO:0001583 missense ENST00000528896.2 1 1 hg19 CCDS32595.1 . . . . . . . . . . C 33 5.208479 0.95069 . . ENSG00000007202 ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884 T;T 0.53423 0.62;0.62 5.53 5.53 0.82687 FMP27, C-terminal (1); 0.051185 0.64402 D 0.000001 T 0.71576 0.3356 M 0.80332 2.49 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 T 0.69826 -0.5040 10 0.38643 T 0.18 . 19.4358 0.94794 0.0:1.0:0.0:0.0 . 1822 Q14667 K0100_HUMAN Q 1822;1792;1822;1679 ENSP00000436773:R1822Q;ENSP00000446443:R1679Q ENSP00000005905:R1822Q R - 2 0 KIAA0100 23971060 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 5.448000 0.66612 2.768000 0.95171 0.655000 0.94253 CGG TCGA-IB-8126-01A-11D-2396-08 KIAA0100-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390571.3 0 0 0 13 385 0 62 1 7.877712e-01 3 85 0 62 2 0 0 0 0 0 2 1 0.999528 13 382 0 62 2 0 0 0 0 62 2 -2.516486 1 1 0 0 1 3 3 6 2.078682 0 0.090000 3.970000 0.198238 0.910000 4.800000e-01 1.000000 1.000000 0.859339 0.910000 1 6.600000e-01 1 NUFIP2 57532 broad.mit.edu 37 17 27613833 27613833 + Silent SNP T T C TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr17:27613833T>C ENST00000225388.4 - 2 1237 c.1179A>G c.(1177-1179)caA>caG p.Q393Q NUFIP2_ENST00000579665.1_Intron NM_020772.2 NP_065823.1 Q7Z417 NUFP2_HUMAN nuclear fragile X mental retardation protein interacting protein 2 24 BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551) GACTTGATGATTGGGTCTGAG 0.433000 0 SO:0001819 synonymous_variant ENST00000225388.4 1 1 hg19 CCDS32600.1 TCGA-IB-8126-01A-11D-2396-08 NUFIP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447015.2 1 0 0 47 597 0 105 1 9.812358e-01 2 79 0 105 2 0 0 0 0 0 2 1 1.000000 47 591 0 103 2 0 0 0 0 105 2 -10.949910 1 1 0 0 1 3 3 6 2.078682 0 0.090000 3.970000 0.198238 0.990000 9.900000e-01 1.000000 1.000000 0.999999 0.990000 1 9.900000e-01 1 CSH2 1443 broad.mit.edu 37 17 61949520 61949520 + Missense_Mutation SNP T T A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr17:61949520T>A ENST00000392886.2 - 5 771 c.620A>T c.(619-621)cAg>cTg p.Q207L CSH2_ENST00000336844.5_3'UTR|CSH2_ENST00000345366.7_Missense_Mutation_p.Q112L|CSH2_ENST00000560142.1_Missense_Mutation_p.Q150L NM_020991.3 NP_066271.1 P0DML3 CSH2_HUMAN chorionic somatomammotropin hormone 2 6 AGAGCGGCACTGCACCATGCG 0.592000 0 SO:0001583 missense ENST00000392886.2 1 1 hg19 CCDS42369.1 . . . . . . . . . . N 14.32 2.499020 0.44455 . . ENSG00000213218 ENST00000345366;ENST00000392886 D;T 0.90676 -2.71;0.93 3.97 2.88 0.33553 Somatotropin hormone, conserved site (1);Four-helical cytokine-like, core (1);Four-helical cytokine, core (1); 1.587450 0.04964 N 0.462618 D 0.95529 0.8547 M 0.85630 2.765 0.32011 N 0.602031 D;D;P 0.64830 0.994;0.994;0.728 D;D;B 0.74674 0.984;0.984;0.42 D 0.84470 0.0599 10 0.87932 D 0 . 8.0549 0.30600 0.0:0.101:0.0:0.899 . 207;207;112 P01243;A8K6C2;B1A4H9 CSH_HUMAN;.;. L 112;207 ENSP00000308396:Q112L;ENSP00000376623:Q207L ENSP00000308396:Q112L Q - 2 0 CSH2 59303252 1.000000 0.71417 0.999000 0.59377 0.018000 0.09664 3.847000 0.55895 0.570000 0.29347 0.379000 0.24179 CAG TCGA-IB-8126-01A-11D-2396-08 CSH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000417657.1 0 0 0 20 437 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 0.999990 20 402 0 94 2 0 0 0 0 87 2 -4.636657 1 1 0 0 1 1 2 3 1.941436 0 0.090000 3.970000 0.122003 0.990000 6.500000e-01 1.000000 1.000000 0.940701 0.990000 1 8.300000e-01 1 RNF213 57674 broad.mit.edu 37 17 78363984 78363984 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr17:78363984G>A ENST00000582970.1 + 67 15601 c.15458G>A c.(15457-15459)cGc>cAc p.R5153H CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.R5202H|CTD-2047H16.4_ENST00000573394.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.R3226H|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000427003.3_3'UTR NM_001256071.1 NP_001243000.1 Q63HN8 RN213_HUMAN ring finger protein 213 130 all_neural(118;0.0538) BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057) GAGCGCTTCCGCCCTCAGTGG 0.483000 0 SO:0001583 missense ENST00000582970.1 1 1 hg19 CCDS58606.1 . . . . . . . . . . G 9.024 0.985660 0.18889 . . ENSG00000173821 ENST00000508628;ENST00000411702;ENST00000336301;ENST00000427003 T;T 0.23147 1.95;1.92 5.67 2.26 0.28386 . 0.954721 0.08773 N 0.896005 T 0.17704 0.0425 L 0.43152 1.355 0.20926 N 0.999826 D;P 0.53619 0.961;0.713 B;B 0.35240 0.198;0.139 T 0.16305 -1.0407 10 0.44086 T 0.13 . 6.2579 0.20884 0.6156:0.1201:0.2643:0.0 . 5153;3226 D6RI12;Q63HN8 .;RN213_HUMAN H 5153;5202;3226;503 ENSP00000425956:R5153H;ENSP00000338218:R3226H ENSP00000338218:R3226H R + 2 0 RNF213 75978579 0.010000 0.17322 0.026000 0.17262 0.011000 0.07611 0.138000 0.16016 0.092000 0.17331 -0.294000 0.09567 CGC TCGA-IB-8126-01A-11D-2396-08 RNF213-020 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000443298.1 0 0 0 27 655 0 90 1 9.073145e-01 5 96 0 90 2 0 4.463657e-01 1 36 0 40 2 1 1.000000 27 650 0 87 2 0 0 0 0 90 2 -3.010969 1 1 121392 4 38 1 1 2 3 1.941436 0 0.090000 3.970000 0.122003 0.950000 6.200000e-01 1.000000 1.000000 0.907002 0.950000 1 7.700000e-01 1 VPS13D 55187 broad.mit.edu 37 1 12423195 12423195 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr1:12423195G>A ENST00000358136.3 + 52 10470 c.10340G>A c.(10339-10341)cGg>cAg p.R3447Q VPS13D_ENST00000356315.4_Missense_Mutation_p.R3422Q NM_015378.2 NP_056193.2 vacuolar protein sorting 13 homolog D (S. cerevisiae) p.R3447Q(1) 130 Ovarian(185;0.249) Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) CACTGGCCTCGGAATGACTAT 0.453000 1 Substitution - Missense(1) SO:0001583 missense ENST00000358136.3 1 1 hg19 CCDS30588.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 36|36 5.752959|5.752959 0.96890|0.96890 .|. .|. ENSG00000048707|ENSG00000048707 ENST00000011700|ENST00000356315;ENST00000358136 .|T;T .|0.33438 .|1.41;1.41 6.06|6.06 6.06|6.06 0.98353|0.98353 .|Vacuolar protein sorting-associated protein (1); .|0.000000 .|0.85682 .|D .|0.000000 T|T 0.55561|0.55561 0.1928|0.1928 M|M 0.64997|0.64997 1.995|1.995 0.80722|0.80722 D|D 1|1 .|D;D .|0.89917 .|0.994;1.0 .|D;D .|0.87578 .|0.956;0.998 T|T 0.35943|0.35943 -0.9768|-0.9768 5|10 .|0.31617 .|T .|0.26 .|. 20.6208|20.6208 0.99490|0.99490 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|3422;3446 .|Q5THJ4-2;Q5THJ4 .|.;VP13D_HUMAN R|Q 2269|3422;3447 .|ENSP00000348666:R3422Q;ENSP00000350854:R3447Q .|ENSP00000348666:R3422Q G|R +|+ 1|2 0|0 VPS13D|VPS13D 12345782|12345782 1.000000|1.000000 0.71417|0.71417 0.986000|0.986000 0.45419|0.45419 0.863000|0.863000 0.49368|0.49368 9.434000|9.434000 0.97515|0.97515 2.882000|2.882000 0.98803|0.98803 0.655000|0.655000 0.94253|0.94253 GGA|CGG TCGA-IB-8126-01A-11D-2396-08 VPS13D-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000036897.2 0 0 0 16 438 0 119 0 1.082953e-01 0 15 0 119 2 0 0 0 0 0 2 1 0.999931 16 434 0 119 2 0 0 0 0 119 2 -2.331684 0 1 121412 1 35 1 1 2 3 1.951197 0 0.090000 3.970000 0.124284 0.850000 4.900000e-01 1.000000 1.000000 0.837303 0.850000 1 6.500000e-01 1 TNN 63923 broad.mit.edu 37 1 175086325 175086325 + Silent SNP C C T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr1:175086325C>T ENST00000239462.4 + 10 2483 c.2370C>T c.(2368-2370)gaC>gaT p.D790D NM_022093.1 NP_071376.1 Q9UQP3 TENN_HUMAN tenascin N 156 Breast(1374;0.000962) AGAAGGCTGACACCAAGGCCC 0.537000 0 SO:0001819 synonymous_variant ENST00000239462.4 1 1 hg19 CCDS30943.1 TCGA-IB-8126-01A-11D-2396-08 TNN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084422.1 0 0 0 19 481 0 82 0 0 0 1 0 82 2 0 0 0 0 0 2 1 0.999989 19 474 0 82 2 0 0 0 0 82 2 -17.804350 1 1 0 0 1 1 2 3 2.018194 0 0.090000 3.970000 0.129187 0.890000 5.500000e-01 1.000000 1.000000 0.867287 0.890000 1 7.000000e-01 1 HMCN1 83872 broad.mit.edu 37 1 185931765 185931765 + Silent SNP C C T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr1:185931765C>T ENST00000271588.4 + 12 2173 c.1944C>T c.(1942-1944)aaC>aaT p.N648N HMCN1_ENST00000367492.2_Silent_p.N648N|HMCN1_ENST00000485744.1_3'UTR NM_031935.2 NP_114141.2 Q96RW7 HMCN1_HUMAN hemicentin 1 308 GGACCGTTAACGATATGTTTA 0.413000 0 SO:0001819 synonymous_variant ENST00000271588.4 0 1 hg19 CCDS30956.1 TCGA-IB-8126-01A-11D-2396-08 HMCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131848.1 0 0 0 9 391 0 91 0 1.996626e-03 0 2 0 91 2 0 0 0 0 0 2 1 0.994275 9 390 0 91 2 0 0 0 0 91 2 -2.758881 1 1 121412 5 41 1 1 2 3 2.018194 0 0.090000 3.970000 0.129187 0.540000 2.600000e-01 0.930000 0.510000 0.566283 0.540000 0 3.800000e-01 7.300000e-01 SNAP47 116841 broad.mit.edu 37 1 227968309 227968309 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr1:227968309G>A ENST00000366759.4 + 5 1744 c.1330G>A c.(1330-1332)Gca>Aca p.A444T SNAP47_ENST00000366760.1_Missense_Mutation_p.A202T NM_053052.3 NP_444280.2 Q5SQN1 SNP47_HUMAN synaptosomal-associated protein, 47kDa 17 TGGCGTTGCAGCAGCTGTGGA 0.597000 0 SO:0001583 missense ENST00000366759.4 0 1 hg19 CCDS1562.1 . . . . . . . . . . G 0.015 -1.565409 0.00903 . . ENSG00000143740 ENST00000366760;ENST00000366759 T;T 0.42513 0.97;2.28 4.67 -2.54 0.06307 Target SNARE coiled-coil domain (1); 0.884135 0.10124 N 0.713045 T 0.17109 0.0411 N 0.11560 0.145 0.09310 N 1 B 0.09022 0.002 B 0.10450 0.005 T 0.28681 -1.0036 10 0.10636 T 0.68 -15.287 4.493 0.11822 0.3799:0.0:0.2016:0.4185 . 444 Q5SQN1 SNP47_HUMAN T 202;444 ENSP00000355722:A202T;ENSP00000355721:A444T ENSP00000355721:A444T A + 1 0 SNAP47 226034932 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.403000 0.07214 -0.674000 0.05253 -0.258000 0.10820 GCA TCGA-IB-8126-01A-11D-2396-08 SNAP47-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000091961.1 0 0 0 5 337 0 54 0 1.774911e-01 0 43 0 54 2 0 0 0 0 0 2 1 0.936531 5 334 0 54 2 0 0 0 0 54 2 -4.407505 1 1 0 0 1 1 2 3 2.013594 0 0.090000 3.970000 0.129187 0.360000 1.400000e-01 0.730000 0.330000 0.396879 0.360000 0 2.300000e-01 5.500000e-01 EPB41 2035 broad.mit.edu 37 1 29314163 29314163 + Missense_Mutation SNP C C T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr1:29314163C>T ENST00000343067.4 + 2 341 c.214C>T c.(214-216)Cgg>Tgg p.R72W EPB41_ENST00000398863.2_Missense_Mutation_p.R72W|EPB41_ENST00000373797.1_Missense_Mutation_p.R72W|EPB41_ENST00000349460.4_5'UTR|Y_RNA_ENST00000383977.1_RNA|EPB41_ENST00000356093.2_Missense_Mutation_p.R72W|EPB41_ENST00000347529.3_Missense_Mutation_p.R72W|EPB41_ENST00000373798.1_Missense_Mutation_p.R72W|EPB41_ENST00000373800.3_5'UTR NM_001166005.1 NP_001159477.1 P11171 41_HUMAN erythrocyte membrane protein band 4.1 14 Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123) GAACAAGGAGCGGACATCAGA 0.453000 0 SO:0001583 missense ENST00000343067.4 0 1 hg19 CCDS53288.1 . . . . . . . . . . C 21.6 4.179746 0.78564 . . ENSG00000159023 ENST00000358989;ENST00000343067;ENST00000356093;ENST00000398863;ENST00000398861;ENST00000398865;ENST00000347529;ENST00000373798;ENST00000373797 D;D;D;D;D;D 0.85258 -1.96;-1.95;-1.78;-1.69;-1.96;-1.94 5.6 5.6 0.85130 . 0.070962 0.56097 D 0.000035 D 0.89150 0.6633 L 0.32530 0.975 0.44500 D 0.997445 D;D;D;D;D 0.89917 1.0;0.999;1.0;1.0;1.0 D;D;D;D;D 0.97110 0.997;0.988;0.999;1.0;0.999 D 0.90061 0.4156 10 0.72032 D 0.01 . 18.6548 0.91448 0.0:1.0:0.0:0.0 . 72;72;72;72;72 C9JTS2;P11171;P11171-2;P11171-7;P11171-5 .;41_HUMAN;.;.;. W 89;72;72;72;72;72;72;72;72 ENSP00000345259:R72W;ENSP00000348397:R72W;ENSP00000381839:R72W;ENSP00000290100:R72W;ENSP00000362904:R72W;ENSP00000362903:R72W ENSP00000345259:R72W R + 1 2 EPB41 29186750 0.998000 0.40836 0.978000 0.43139 0.926000 0.56050 3.068000 0.50018 2.633000 0.89246 0.650000 0.86243 CGG TCGA-IB-8126-01A-11D-2396-08 EPB41-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000010312.1 0 0 0 6 954 0 134 0 1.695685e-02 0 26 0 134 2 0 0 0 0 0 2 1 0.963858 6 944 0 134 2 0 0 0 0 134 2 -2.077858 0 1 121412 2 37 1 1 2 3 1.944733 0 0.090000 3.970000 0.122765 0.160000 6.000000e-02 1.000000 0.140000 0.276944 0.160000 0 1.000000e-01 3.000000e-01 PPT1 5538 broad.mit.edu 37 1 40539758 40539758 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr1:40539758G>A ENST00000433473.3 - 9 1360 c.896C>T c.(895-897)gCc>gTc p.A299V PPT1_ENST00000372775.2_5'UTR|PPT1_ENST00000449045.2_Missense_Mutation_p.A196V|PPT1_ENST00000530076.1_Missense_Mutation_p.A80V NM_000310.3 NP_000301.1 P50897 PPT1_HUMAN palmitoyl-protein thioesterase 1 11 Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204) TATGATGTGGGCATAAAACCA 0.483000 0 SO:0001583 missense ENST00000433473.3 0 1 hg19 CCDS447.1 . . . . . . . . . . G 11.43 1.636756 0.29068 . . ENSG00000131238 ENST00000433473;ENST00000449045;ENST00000439754;ENST00000530076 D;D;D;D 0.97404 -4.37;-4.37;-3.51;-4.37 5.78 3.84 0.44239 . 0.619388 0.16981 N 0.191714 D 0.95541 0.8551 L 0.59436 1.845 0.20196 N 0.999925 B;B;B 0.29571 0.249;0.119;0.01 B;B;B 0.32583 0.024;0.148;0.007 D 0.89878 0.4028 10 0.51188 T 0.08 -0.8945 12.7764 0.57451 0.0:0.0:0.5698:0.4302 . 196;225;299 P50897-2;B4DWU3;P50897 .;.;PPT1_HUMAN V 299;196;170;80 ENSP00000394863:A299V;ENSP00000392293:A196V;ENSP00000403207:A170V;ENSP00000434007:A80V ENSP00000394863:A299V A - 2 0 PPT1 40312345 0.795000 0.28851 1.000000 0.80357 0.476000 0.33039 1.039000 0.30266 0.720000 0.32209 -0.182000 0.12963 GCC TCGA-IB-8126-01A-11D-2396-08 PPT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000013126.2 0 0 0 6 823 0 155 0 4.526501e-01 0 189 0 155 2 0 0 0 0 0 2 1 0.964245 8 816 0 155 2 0 0 0 0 155 2 -2.111416 0 1 121412 1 32 1 1 2 3 1.944733 0 0.090000 3.970000 0.122765 0.190000 7.000000e-02 1.000000 0.170000 0.299513 0.190000 0 1.200000e-01 3.500000e-01 CAMTA1 23261 broad.mit.edu 37 1 7796575 7796575 + Silent SNP C C T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr1:7796575C>T ENST00000303635.7 + 13 3445 c.3238C>T c.(3238-3240)Cta>Tta p.L1080L CAMTA1_ENST00000439411.2_Silent_p.L1080L NM_015215.2 NP_056030.1 Q9Y6Y1 CMTA1_HUMAN calmodulin binding transcription activator 1 85 Ovarian(185;0.0634) all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388) CTATGCCACCCTAATCCAGAC 0.607000 T WWTR1 epitheliod hemangioendothelioma Dom yes 1 1p36.31-p36.23 611501 calmodulin binding transcription activator 1 M 0 SO:0001819 synonymous_variant ENST00000303635.7 1 1 hg19 CCDS30576.1 TCGA-IB-8126-01A-11D-2396-08 CAMTA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000003588.3 0 0 0 24 568 0 89 0 5.350727e-03 0 3 0 89 2 0 0 0 0 0 2 1 1.000000 24 564 0 88 2 0 0 0 0 89 2 -2.771097 1 1 0 0 1 1 2 3 1.951197 0 0.090000 3.970000 0.124284 0.970000 6.200000e-01 1.000000 1.000000 0.912950 0.970000 1 7.800000e-01 1 RPRD1B 58490 broad.mit.edu 37 20 36694636 36694636 + Missense_Mutation SNP C C T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr20:36694636C>T ENST00000373433.4 + 6 1211 c.809C>T c.(808-810)tCg>tTg p.S270L NM_021215.3 NP_067038.1 Q9NQG5 RPR1B_HUMAN regulation of nuclear pre-mRNA domain containing 1B 12 GATGTTTTGTCGGAGAAGGAG 0.502000 0 SO:0001583 missense ENST00000373433.4 1 1 hg19 CCDS13301.1 . . . . . . . . . . C 14.45 2.538823 0.45176 . . ENSG00000101413 ENST00000373433;ENST00000449186 . . . 5.35 5.35 0.76521 . 0.313199 0.35207 N 0.003367 T 0.45377 0.1339 L 0.27053 0.805 0.41599 D 0.988848 B 0.13594 0.008 B 0.10450 0.005 T 0.30208 -0.9986 9 0.39692 T 0.17 -5.9908 14.2206 0.65823 0.0:0.851:0.149:0.0 . 270 Q9NQG5 RPR1B_HUMAN L 270;152 . ENSP00000362532:S270L S + 2 0 RPRD1B 36128050 0.996000 0.38824 1.000000 0.80357 0.966000 0.64601 0.953000 0.29162 2.941000 0.99782 0.655000 0.94253 TCG TCGA-IB-8126-01A-11D-2396-08 RPRD1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079142.2 0 0 0 12 482 0 80 0 3.733316e-01 0 50 0 80 2 0 0 0 0 0 2 1 0.999067 12 476 0 79 2 0 0 0 0 80 2 -2.823549 1 1 0 0 1 1 2 3 1.991956 0 0.090000 3.970000 0.129187 0.570000 3.100000e-01 0.930000 0.570000 0.598965 0.570000 0 4.300000e-01 7.600000e-01 TIAM1 7074 broad.mit.edu 37 21 32493078 32493078 + Missense_Mutation SNP C C T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr21:32493078C>T ENST00000286827.3 - 29 4855 c.4384G>A c.(4384-4386)Gtc>Atc p.V1462I TIAM1_ENST00000541036.1_Missense_Mutation_p.V1402I NM_003253.2 NP_003244.2 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 115 CTTGCGGAGACGGCATCAGAA 0.562000 0 SO:0001583 missense ENST00000286827.3 1 1 hg19 CCDS13609.1 . . . . . . . . . . C 9.128 1.010725 0.19277 0.0 1.16E-4 ENSG00000156299 ENST00000286827;ENST00000541036 T;T 0.39056 1.1;1.11 5.14 2.2 0.27929 . 0.290368 0.32147 N 0.006505 T 0.20981 0.0505 N 0.13235 0.315 0.27602 N 0.948927 B;B 0.09022 0.002;0.001 B;B 0.06405 0.002;0.001 T 0.17471 -1.0368 10 0.20046 T 0.44 . 6.7271 0.23363 0.0:0.5879:0.0:0.4121 . 1402;1462 F5GZ53;Q13009 .;TIAM1_HUMAN I 1462;1402 ENSP00000286827:V1462I;ENSP00000441570:V1402I ENSP00000286827:V1462I V - 1 0 TIAM1 31414949 0.308000 0.24509 0.735000 0.30896 0.916000 0.54674 0.220000 0.17660 0.129000 0.18514 -0.140000 0.14226 GTC TCGA-IB-8126-01A-11D-2396-08 TIAM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000192552.1 0 0 0 14 392 0 84 0 8.310043e-02 0 13 0 84 2 0 0 0 0 0 2 1 0.999743 14 387 0 82 2 0 0 0 0 84 2 -13.580230 1 1 121410 14 45 1 1 2 3 2.002735 0 0.090000 3.970000 0.129187 0.810000 4.600000e-01 1.000000 1.000000 0.808561 0.810000 0 6.200000e-01 1 MFSD9 84804 broad.mit.edu 37 2 103335481 103335481 + Missense_Mutation SNP G G A rs144200432 by1000genomes TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr2:103335481G>A ENST00000258436.5 - 6 866 c.823C>T c.(823-825)Cgg>Tgg p.R275W MFSD9_ENST00000496253.1_5'Flank NM_032718.3 NP_116107.3 Q8NBP5 MFSD9_HUMAN major facilitator superfamily domain containing 9 20 TTCATGTTCCGCAAGGCCAAC 0.557000 0 SO:0001583 missense ENST00000258436.5 0 1 hg19 CCDS2063.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 G 13.25 2.181450 0.38511 . . ENSG00000135953 ENST00000258436 D 0.83250 -1.7 4.97 1.47 0.22746 Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1); 0.665977 0.15409 N 0.263908 T 0.71745 0.3376 L 0.34521 1.04 0.09310 N 1 B 0.18013 0.025 B 0.17098 0.017 T 0.62062 -0.6933 10 0.52906 T 0.07 -5.4226 7.0595 0.25117 0.0938:0.0:0.3214:0.5847 . 275 Q8NBP5 MFSD9_HUMAN W 275 ENSP00000258436:R275W ENSP00000258436:R275W R - 1 2 MFSD9 102701913 0.437000 0.25593 0.068000 0.19968 0.045000 0.14185 1.372000 0.34261 0.571000 0.29365 0.644000 0.83932 CGG TCGA-IB-8126-01A-11D-2396-08 MFSD9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253295.2 0 0 0 7 436 1 93 0 1.118152e-02 0 24 1 93 3 0 0 0 0 0 2 0 0.040460 7 430 1 93 16 0 0 0 1 93 2 -2.414887 0 1 121412 8 40 1 1 2 3 2.009564 0 0.090000 3.970000 0.129187 0.380000 1.700000e-01 0.710000 0.360000 0.411070 0.380000 0 2.600000e-01 5.500000e-01 FIGN 55137 broad.mit.edu 37 2 164466495 164466495 + Missense_Mutation SNP A A G TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr2:164466495A>G ENST00000333129.3 - 3 2161 c.1847T>C c.(1846-1848)gTa>gCa p.V616A FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron NM_018086.2 NP_060556.2 Q5HY92 FIGN_HUMAN fidgetin 47 CGAAGTTAGTACAGTGTCCAG 0.423000 0 SO:0001583 missense ENST00000333129.3 1 1 hg19 CCDS2221.2 . . . . . . . . . . A 4.122 0.020814 0.08006 . . ENSG00000182263 ENST00000333129 D 0.94897 -3.55 5.77 5.77 0.91146 ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1); 0.062004 0.64402 D 0.000004 D 0.93324 0.7872 L 0.27975 0.815 0.58432 D 0.999999 P 0.41366 0.747 P 0.55161 0.77 D 0.90675 0.4601 10 0.08837 T 0.75 -17.6067 16.0953 0.81117 1.0:0.0:0.0:0.0 . 616 Q5HY92 FIGN_HUMAN A 616 ENSP00000333836:V616A ENSP00000333836:V616A V - 2 0 FIGN 164174741 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 6.116000 0.71571 2.204000 0.70986 0.383000 0.25322 GTA TCGA-IB-8126-01A-11D-2396-08 FIGN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000157220.2 0 0 0 14 481 0 97 0 9.619238e-04 0 2 0 97 2 0 0 0 0 0 2 1 0.999743 13 478 0 96 2 0 0 0 0 97 2 -12.729920 1 1 0 0 1 1 2 3 2.009564 0 0.090000 3.970000 0.129187 0.660000 3.800000e-01 1.000000 1.000000 0.686332 0.660000 0 5.100000e-01 8.600000e-01 WDFY1 57590 broad.mit.edu 37 2 224758990 224758990 + Silent SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr2:224758990G>A ENST00000233055.4 - 8 894 c.792C>T c.(790-792)ggC>ggT p.G264G NM_020830.3 NP_065881.1 Q8IWB7 WDFY1_HUMAN WD repeat and FYVE domain containing 1 18 all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189) CTGCAATTCCGCCGTCCGAGG 0.557000 0 SO:0001819 synonymous_variant ENST00000233055.4 0 1 hg19 CCDS33387.1 TCGA-IB-8126-01A-11D-2396-08 WDFY1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000330908.1 0 0 0 8 306 0 53 0 3.522196e-01 1 43 0 53 2 0 0 0 0 0 2 1 0.988900 8 301 0 52 2 0 0 0 0 53 2 -2.887808 1 1 121412 6 36 1 1 2 3 2.009564 0 0.090000 3.970000 0.129187 0.610000 2.900000e-01 1.000000 1.000000 0.639248 0.610000 0 4.300000e-01 8.500000e-01 ALK 238 broad.mit.edu 37 2 30143012 30143012 + Missense_Mutation SNP C C T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr2:30143012C>T ENST00000389048.3 - 1 1420 c.514G>A c.(514-516)Gag>Aag p.E172K ALK_ENST00000431873.1_Missense_Mutation_p.E172K NM_004304.4 NP_004295.2 Q9UM73 ALK_HUMAN anaplastic lymphoma receptor tyrosine kinase ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9) 340 Acute lymphoblastic leukemia(172;0.155) Adenosine triphosphate(DB00171)|Crizotinib(DB08865) CTGAACAGCTCGCTGAGATTG 0.647000 T, Mis, A NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22 ALCL, NSCLC, Neuroblastoma neuroblastoma Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome yes Dom yes Familial neuroblastoma 2 2p23 238 anaplastic lymphoma kinase (Ki-1) L, E, M 0 SO:0001583 missense Familial Cancer Database Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease ENST00000389048.3 0 1 hg19 CCDS33172.1 . . . . . . . . . . C 18.26 3.585036 0.66105 . . ENSG00000171094 ENST00000389048;ENST00000431873 T;T 0.80033 -1.33;2.7 5.33 5.33 0.75918 . . . . . T 0.69886 0.3161 N 0.24115 0.695 0.32250 N 0.571579 B 0.28258 0.205 B 0.19666 0.026 T 0.68503 -0.5391 8 . . . . 17.9759 0.89127 0.0:1.0:0.0:0.0 . 172 Q9UM73 ALK_HUMAN K 172 ENSP00000373700:E172K;ENSP00000414027:E172K . E - 1 0 ALK 29996516 1.000000 0.71417 1.000000 0.80357 0.973000 0.67179 2.012000 0.40932 2.652000 0.90054 0.655000 0.94253 GAG TCGA-IB-8126-01A-11D-2396-08 ALK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324994.1 0 0 0 6 248 1 44 0 0 0 1 44 2 0 0 0 0 0 2 0 0.009554 6 248 1 44 18 0 0 0 1 44 2 -3.329602 1 1 0 0 1 1 2 3 2.009564 0 0.090000 3.970000 0.129187 0.580000 2.400000e-01 1.000000 1.000000 0.609013 0.580000 0 3.800000e-01 8.300000e-01 ATG3 64422 broad.mit.edu 37 3 112267472 112267472 + Missense_Mutation SNP C C T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr3:112267472C>T ENST00000283290.5 - 5 685 c.251G>A c.(250-252)cGg>cAg p.R84Q ATG3_ENST00000495756.1_5'UTR|ATG3_ENST00000402314.2_Missense_Mutation_p.R84Q NM_022488.3 NP_071933.2 Q9NT62 ATG3_HUMAN autophagy related 3 9 CTGTTTGCACCGCTTATAGCA 0.378000 0 SO:0001583 missense ENST00000283290.5 0 1 hg19 CCDS2966.1 . . . . . . . . . . C 35 5.539479 0.96474 . . ENSG00000144848 ENST00000283290;ENST00000402314 . . . 5.32 5.32 0.75619 Autophagy-related protein 3, N-terminal (1); 0.000000 0.85682 D 0.000000 D 0.86690 0.5993 M 0.93638 3.44 0.80722 D 1 D;D 0.76494 0.998;0.999 D;D 0.74023 0.982;0.974 D 0.90176 0.4239 9 0.87932 D 0 0.0444 18.5844 0.91183 0.0:1.0:0.0:0.0 . 84;84 Q9NT62;Q9NT62-2 ATG3_HUMAN;. Q 84 . ENSP00000283290:R84Q R - 2 0 ATG3 113750162 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 5.416000 0.66417 2.482000 0.83794 0.591000 0.81541 CGG TCGA-IB-8126-01A-11D-2396-08 ATG3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354147.1 0 0 0 7 212 0 45 1 9.255595e-01 5 137 0 45 2 0 0 0 0 0 2 1 0.980474 7 210 0 45 2 0 0 0 0 45 2 -2.925876 1 1 121406 2 30 1 1 2 3 2.028119 0 0.090000 3.970000 0.129187 0.770000 3.500000e-01 1.000000 1.000000 0.766263 0.770000 0 5.300000e-01 1 ARHGAP31 57514 broad.mit.edu 37 3 119128441 119128441 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr3:119128441G>A ENST00000264245.4 + 11 2276 c.1744G>A c.(1744-1746)Gcc>Acc p.A582T NM_020754.2 NP_065805.2 Q2M1Z3 RHG31_HUMAN Rho GTPase activating protein 31 67 GGAGCCAGGCGCCCACCTGGA 0.542000 Pancreas(7;176 297 5394 51128 51241) 0 SO:0001583 missense ENST00000264245.4 0 1 hg19 CCDS43135.1 . . . . . . . . . . G 0.018 -1.477473 0.01035 . . ENSG00000031081 ENST00000264245;ENST00000543280 T 0.05925 3.37 5.27 -10.5 0.00291 . 1.661360 0.03193 N 0.173588 T 0.02083 0.0065 N 0.04880 -0.145 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.32348 -0.9910 10 0.02654 T 1 . 5.8933 0.18925 0.5415:0.2715:0.1077:0.0793 . 582 Q2M1Z3 RHG31_HUMAN T 582 ENSP00000264245:A582T ENSP00000264245:A582T A + 1 0 ARHGAP31 120611131 0.000000 0.05858 0.000000 0.03702 0.006000 0.05464 -3.506000 0.00448 -3.278000 0.00198 -1.594000 0.00841 GCC TCGA-IB-8126-01A-11D-2396-08 ARHGAP31-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354942.2 1 0 0 8 156 0 21 0 3.883010e-01 0 25 0 21 2 0 0 0 0 0 2 1 0.988848 7 153 0 21 2 0 0 0 0 21 2 -10.989630 1 1 120840 4 34 1 1 2 3 2.028119 0 0.090000 3.970000 0.129187 0.990000 5.500000e-01 1.000000 1.000000 0.935818 0.990000 1 8.100000e-01 1 COL6A6 131873 broad.mit.edu 37 3 130284081 130284081 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr3:130284081G>A ENST00000358511.6 + 3 936 c.905G>A c.(904-906)cGa>cAa p.R302Q COL6A6_ENST00000453409.2_Missense_Mutation_p.R302Q NM_001102608.1 NP_001096078.1 A6NMZ7 CO6A6_HUMAN collagen, type VI, alpha 6 134 CTTTCTCCCCGAACTGGGAAG 0.478000 0 SO:0001583 missense ENST00000358511.6 0 1 hg19 CCDS46911.1 . . . . . . . . . . G 0.090 -1.169073 0.01660 . . ENSG00000206384 ENST00000358511;ENST00000453409 T;T 0.78364 -1.17;-1.17 5.01 -2.32 0.06745 von Willebrand factor, type A (3); 1.188040 0.06089 N 0.663415 T 0.57036 0.2026 N 0.04387 -0.21 0.09310 N 1 B 0.02656 0.0 B 0.06405 0.002 T 0.38178 -0.9673 10 0.26408 T 0.33 . 12.8264 0.57723 0.4013:0.0:0.5987:0.0 . 302 A6NMZ7 CO6A6_HUMAN Q 302 ENSP00000351310:R302Q;ENSP00000399236:R302Q ENSP00000351310:R302Q R + 2 0 COL6A6 131766771 0.000000 0.05858 0.000000 0.03702 0.025000 0.11179 -0.959000 0.03853 -0.497000 0.06641 -0.459000 0.05422 CGA TCGA-IB-8126-01A-11D-2396-08 COL6A6-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000356705.5 0 0 0 11 430 0 96 0 2.329450e-03 0 3 0 96 2 0 0 0 0 0 2 1 0.998335 11 428 0 95 2 0 0 0 0 96 2 -1.996802 0 1 120804 4 39 1 1 2 3 2.028119 0 0.090000 3.970000 0.129187 0.590000 3.100000e-01 0.970000 1.000000 0.616869 0.590000 0 4.400000e-01 7.900000e-01 LRRIQ4 344657 broad.mit.edu 37 3 169539979 169539979 + Silent SNP G G T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr3:169539979G>T ENST00000340806.6 + 1 270 c.270G>T c.(268-270)ctG>ctT p.L90L NM_001080460.1 NP_001073929.1 A6NIV6 LRIQ4_HUMAN leucine-rich repeats and IQ motif containing 4 30 GCCCGGCGCTGGGGCTGCTGA 0.567000 0 SO:0001819 synonymous_variant ENST00000340806.6 0 1 hg19 CCDS46951.1 TCGA-IB-8126-01A-11D-2396-08 LRRIQ4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378698.1 0 0 0 10 635 0 119 0 0 0 0 119 2 0 0 0 0 0 2 1 0.996737 9 629 0 118 2 0 0 0 0 119 2 -2.272507 0 1 0 0 1 1 2 3 2.028119 0 0.090000 3.970000 0.129187 0.370000 1.800000e-01 0.630000 0.360000 0.390689 0.370000 0 2.600000e-01 5.000000e-01 THRB 7068 broad.mit.edu 37 3 24231773 24231773 + Silent SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr3:24231773G>A ENST00000356447.4 - 4 359 c.75C>T c.(73-75)caC>caT p.H25H THRB_ENST00000396671.2_Silent_p.H25H|THRB_ENST00000416420.1_Silent_p.H25H NM_000461.4|NM_001128177.1 NP_000452.2|NP_001121649.1 P10828 THB_HUMAN thyroid hormone receptor, beta 19 Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583) GCTTCCAGTCGTGTTCTCGGT 0.493000 Melanoma(21;896 1043 15021 37958) 0 SO:0001819 synonymous_variant ENST00000356447.4 0 1 hg19 CCDS2641.1 . . . . . . . . . . G 7.584 0.669381 0.14776 . . ENSG00000151090 ENST00000416811 . . . 5.93 2.09 0.27110 . . . . . T 0.63414 0.2509 . . . 0.38566 D 0.949829 . . . . . . T 0.64236 -0.6455 5 0.87932 D 0 . 8.5522 0.33458 0.0713:0.5866:0.2416:0.1005 . . . . M 25 . ENSP00000414401:T25M T - 2 0 THRB 24206777 0.992000 0.36948 0.664000 0.29753 0.990000 0.78478 0.216000 0.17585 0.095000 0.17434 -0.175000 0.13238 ACG TCGA-IB-8126-01A-11D-2396-08 THRB-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000252877.3 0 0 0 5 405 0 107 0 3.516292e-03 0 6 0 107 2 0 0 0 0 0 2 1 0.935872 5 400 0 107 2 0 0 0 0 107 2 -2.881296 1 1 121412 3 37 1 1 2 3 1.940226 0 0.090000 3.970000 0.122003 0.330000 1.100000e-01 1.000000 0.280000 0.427044 0.330000 0 2.000000e-01 6.700000e-01 TET2 54790 broad.mit.edu 37 4 106157130 106157130 + Nonsense_Mutation SNP T T A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr4:106157130T>A ENST00000540549.1 + 3 2891 c.2031T>A c.(2029-2031)tgT>tgA p.C677* TET2_ENST00000380013.4_Nonsense_Mutation_p.C677*|TET2_ENST00000413648.2_Nonsense_Mutation_p.C677*|TET2_ENST00000305737.2_Nonsense_Mutation_p.C677*|TET2_ENST00000513237.1_Nonsense_Mutation_p.C698*|TET2_ENST00000394764.1_Nonsense_Mutation_p.C677*|TET2_ENST00000545826.1_Nonsense_Mutation_p.C677* Q6N021 TET2_HUMAN tet methylcytosine dioxygenase 2 1314 Myeloproliferative disorder(5;0.0393) AGTCACTGTGTGGCACTAGAT 0.438000 Mis N, F MDS Rec yes 4 4q24 54790 tet oncogene family member 2 L 0 SO:0001587 stop_gained ENST00000540549.1 0 1 hg19 CCDS47120.1 . . . . . . . . . . T 29.6 5.020328 0.93462 . . ENSG00000168769 ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648 . . . 5.6 -6.08 0.02151 . 0.621347 0.15973 N 0.235671 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.38643 T 0.18 . 10.1181 0.42603 0.0:0.5241:0.1056:0.3704 . . . . X 677;677;677;698;677;677;677 . ENSP00000265149:C677X C + 3 2 TET2 106376579 0.000000 0.05858 0.000000 0.03702 0.027000 0.11550 -0.340000 0.07821 -0.678000 0.05224 0.533000 0.62120 TGT TCGA-IB-8126-01A-11D-2396-08 TET2-202 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000253952.2 0 0 0 5 398 1 76 0 1.249650e-02 0 11 1 76 2 0 0 0 0 0 2 0 0.004463 5 395 1 76 18 0 0 0 1 76 2 -2.971831 1 1 0 0 1 1 2 3 2.015993 0 0.090000 3.970000 0.129187 0.310000 1.100000e-01 0.620000 0.280000 0.338266 0.310000 0 1.900000e-01 4.700000e-01 SHROOM3 57619 broad.mit.edu 37 4 77661903 77661903 + Silent SNP C C G TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr4:77661903C>G ENST00000296043.6 + 5 3530 c.2577C>G c.(2575-2577)tcC>tcG p.S859S NM_020859.3 NP_065910.3 Q8TF72 SHRM3_HUMAN shroom family member 3 60 Lung(101;0.0903) AAGAGGCTTCCCGGCAGCCCT 0.632000 0 SO:0001819 synonymous_variant ENST00000296043.6 0 1 hg19 CCDS3579.2 TCGA-IB-8126-01A-11D-2396-08 SHROOM3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252408.2 0 0 0 13 369 0 52 1 1.797514e-01 2 19 0 52 2 0 0 0 0 0 2 1 0.999512 13 364 0 52 2 0 0 0 0 52 2 -3.150672 1 1 0 0 1 1 2 3 2.015993 0 0.090000 3.970000 0.129187 0.800000 4.500000e-01 1.000000 1.000000 0.800599 0.800000 0 6.100000e-01 1 SYNE1 23345 broad.mit.edu 37 6 152777116 152777116 + Missense_Mutation SNP T T G TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr6:152777116T>G ENST00000367255.5 - 23 3233 c.2632A>C c.(2632-2634)Agt>Cgt p.S878R SYNE1_ENST00000341594.5_Missense_Mutation_p.S930R|SYNE1_ENST00000495090.2_Missense_Mutation_p.S445R|SYNE1_ENST00000265368.4_Missense_Mutation_p.S878R|SYNE1_ENST00000448038.1_Missense_Mutation_p.S885R|SYNE1_ENST00000367253.4_Missense_Mutation_p.S878R|SYNE1_ENST00000413186.2_Missense_Mutation_p.S878R|SYNE1_ENST00000367248.3_Missense_Mutation_p.S868R|SYNE1_ENST00000423061.1_Missense_Mutation_p.S885R NM_182961.3 NP_892006.3 Q8NF91 SYNE1_HUMAN spectrin repeat containing, nuclear envelope 1 524 Ovarian(120;0.0955) BRCA - Breast invasive adenocarcinoma(37;0.243) TTTTGAACACTTTGACTGCCT 0.363000 HNSCC(10;0.0054) 0 SO:0001583 missense ENST00000367255.5 0 1 hg19 CCDS5236.2 . . . . . . . . . . T 15.54 2.865046 0.51482 . . ENSG00000131018 ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000495090 T;T;T;T;T;T;T;T;T 0.52983 1.44;1.44;1.44;1.44;0.64;1.44;1.44;1.44;1.44 5.25 4.09 0.47781 . 0.427135 0.21974 N 0.066416 T 0.20861 0.0502 L 0.34521 1.04 0.80722 D 1 B;B;B;P;B;B;B 0.35077 0.112;0.215;0.404;0.483;0.321;0.215;0.21 B;B;B;B;B;B;B 0.36244 0.074;0.063;0.22;0.203;0.146;0.063;0.146 T 0.05937 -1.0855 10 0.52906 T 0.07 . 8.2238 0.31558 0.0:0.1536:0.0:0.8464 . 861;878;445;868;878;878;885 B3W695;Q8NF91;F5H422;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4 .;SYNE1_HUMAN;.;.;.;.;. R 878;885;878;885;930;878;868;878;445 ENSP00000356224:S878R;ENSP00000396024:S885R;ENSP00000265368:S878R;ENSP00000390975:S885R;ENSP00000341887:S930R;ENSP00000356222:S878R;ENSP00000356217:S868R;ENSP00000414510:S878R;ENSP00000438508:S445R ENSP00000265368:S878R S - 1 0 SYNE1 152818809 0.025000 0.19082 0.998000 0.56505 0.967000 0.64934 1.554000 0.36266 0.845000 0.35118 0.533000 0.62120 AGT TCGA-IB-8126-01A-11D-2396-08 SYNE1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000334755.2 0 0 0 6 380 0 92 0 3.691253e-04 0 2 0 92 2 0 0 0 0 0 2 1 0.964987 6 379 0 92 2 0 0 0 0 92 2 -3.099545 1 1 0 0 1 1 2 3 2.005936 0 0.090000 3.970000 0.129187 0.380000 1.500000e-01 0.730000 0.360000 0.411515 0.380000 0 2.500000e-01 5.600000e-01 SEPT14 346288 broad.mit.edu 37 7 55872990 55872990 + Silent SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr7:55872990G>A ENST00000388975.3 - 9 1196 c.1080C>T c.(1078-1080)gtC>gtT p.V360V NM_207366.2 NP_997249.2 Q6ZU15 SEP14_HUMAN septin 14 23 Breast(14;0.214) Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099) CTTTCTCCTTGACTCGCTGCA 0.343000 0 SO:0001819 synonymous_variant ENST00000388975.3 0 1 hg19 CCDS5519.2 TCGA-IB-8126-01A-11D-2396-08 SEPT14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251489.2 0 0 0 6 201 0 37 0 0 0 0 37 2 0 0 0 0 0 2 1 0.965117 6 200 0 37 2 0 0 0 0 37 2 -3.682513 1 1 0 0 1 1 2 3 2.016128 0 0.090000 3.970000 0.129187 0.710000 3.000000e-01 1.000000 1.000000 0.717387 0.710000 0 4.700000e-01 1 BAI1 575 broad.mit.edu 37 8 143603440 143603440 + Missense_Mutation SNP C C T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr8:143603440C>T ENST00000517894.1 + 21 4033 c.3139C>T c.(3139-3141)Cgc>Tgc p.R1047C BAI1_ENST00000323289.5_Missense_Mutation_p.R1047C O14514 BAI1_HUMAN brain-specific angiogenesis inhibitor 1 57 all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155) CCTCCGGAACCGCCTCATCCG 0.657000 0 SO:0001583 missense ENST00000517894.1 1 1 hg19 . . . . . . . . . . C 14.72 2.619636 0.46736 . . ENSG00000181790 ENST00000517894;ENST00000323289 T;T 0.50813 0.73;0.73 3.78 2.89 0.33648 . 0.162599 0.41938 U 0.000782 T 0.49762 0.1576 M 0.83603 2.65 0.58432 D 0.999992 B 0.16802 0.019 B 0.17433 0.018 T 0.51593 -0.8686 10 0.72032 D 0.01 . 9.8607 0.41112 0.0:0.897:0.0:0.103 . 1047 E9PBK0 . C 1047 ENSP00000430945:R1047C;ENSP00000313046:R1047C ENSP00000313046:R1047C R + 1 0 BAI1 143600442 1.000000 0.71417 1.000000 0.80357 0.962000 0.63368 4.563000 0.60823 0.558000 0.29135 0.305000 0.20034 CGC TCGA-IB-8126-01A-11D-2396-08 BAI1-001 KNOWN non_canonical_conserved|not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000379963.3 0 0 0 11 227 0 32 0 0 0 1 0 32 2 0 0 0 0 0 2 1 0.997009 11 200 0 31 2 0 0 0 0 32 2 -2.992802 1 1 121348 2 33 1 1 2 3 2.017890 0 0.090000 3.970000 0.129187 0.990000 5.800000e-01 1.000000 1.000000 0.932854 0.990000 1 8.100000e-01 1 XKR4 114786 broad.mit.edu 37 8 56436505 56436505 + Missense_Mutation SNP G G A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr8:56436505G>A ENST00000327381.6 + 3 1772 c.1672G>A c.(1672-1674)Gac>Aac p.D558N RP11-628E19.2_ENST00000522918.1_RNA NM_052898.1 NP_443130.1 Q5GH76 XKR4_HUMAN XK, Kell blood group complex subunit-related family, member 4 34 Epithelial(17;0.000117)|all cancers(17;0.000836) TGTTGTCAGCGACCGCGATCA 0.587000 0 SO:0001583 missense ENST00000327381.6 0 1 hg19 CCDS34893.1 . . . . . . . . . . G 14.03 2.413709 0.42817 . . ENSG00000206579 ENST00000327381;ENST00000543752 D 0.82984 -1.67 5.95 5.95 0.96441 . 0.453459 0.26616 N 0.023398 T 0.77665 0.4164 L 0.43152 1.355 0.50813 D 0.99989 B 0.33748 0.423 B 0.26094 0.066 T 0.73445 -0.3980 10 0.21014 T 0.42 -4.3001 20.3931 0.98965 0.0:0.0:1.0:0.0 . 558 Q5GH76 XKR4_HUMAN N 558 ENSP00000328326:D558N ENSP00000328326:D558N D + 1 0 XKR4 56599059 1.000000 0.71417 0.862000 0.33874 0.008000 0.06430 7.863000 0.87023 2.824000 0.97209 0.655000 0.94253 GAC TCGA-IB-8126-01A-11D-2396-08 XKR4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378129.2 0 0 0 5 331 0 66 0 0 0 1 0 66 2 0 0 0 0 0 2 1 0.936516 4 330 0 66 2 0 0 0 0 66 2 -5.345967 1 0 0 0 1 1 2 3 2.017890 0 0.090000 3.970000 0.129187 0.370000 1.400000e-01 0.740000 0.330000 0.403739 0.370000 0 2.300000e-01 5.600000e-01 KIAA1045 23349 broad.mit.edu 37 9 34971580 34971580 + Missense_Mutation SNP G G T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr9:34971580G>T ENST00000242315.3 + 2 367 c.285G>T c.(283-285)agG>agT p.R95S KIAA1045_ENST00000544237.1_Missense_Mutation_p.R95S|KIAA1045_ENST00000476115.2_Intron NM_015297.1 NP_056112.1 Q9UPV7 K1045_HUMAN KIAA1045 19 LUSC - Lung squamous cell carcinoma(32;0.00575) AGTTTGACAGGACAAGTCGAT 0.622000 0 SO:0001583 missense ENST00000242315.3 0 1 hg19 CCDS43796.1 . . . . . . . . . . g 11.00 1.510166 0.27036 . . ENSG00000122733 ENST00000544237;ENST00000242315 . . . 6.03 2.92 0.33932 . 0.366196 0.29046 N 0.013305 T 0.28134 0.0694 L 0.36672 1.1 0.21220 N 0.99976 B 0.19200 0.034 B 0.18561 0.022 T 0.13683 -1.0500 8 . . . -9.928 6.5955 0.22669 0.2802:0.0:0.5903:0.1295 . 95 Q9UPV7 K1045_HUMAN S 95 . . R + 3 2 KIAA1045 34961580 0.710000 0.27896 0.619000 0.29118 0.132000 0.20833 -0.067000 0.11579 0.885000 0.36088 0.655000 0.94253 AGG TCGA-IB-8126-01A-11D-2396-08 KIAA1045-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052256.2 0 0 0 12 1763 0 167 0 0 0 0 167 2 0 0 0 0 0 2 1 0.999048 11 1748 0 163 2 0 0 0 0 167 2 -2.804656 1 1 0 0 1 0.090000 3.970000 0 0 TRPM3 80036 broad.mit.edu 37 9 73151119 73151119 + Missense_Mutation SNP T T C TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chr9:73151119T>C ENST00000377110.3 - 25 5117 c.4874A>G c.(4873-4875)aAc>aGc p.N1625S TRPM3_ENST00000360823.2_Missense_Mutation_p.N1487S|TRPM3_ENST00000396285.1_Missense_Mutation_p.N1484S|TRPM3_ENST00000423814.3_Missense_Mutation_p.N1652S|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000396292.4_Missense_Mutation_p.N1497S|TRPM3_ENST00000377105.1_Missense_Mutation_p.N1484S|TRPM3_ENST00000358082.3_Missense_Mutation_p.N1487S|TRPM3_ENST00000408909.2_Missense_Mutation_p.N1484S|TRPM3_ENST00000396280.5_Missense_Mutation_p.N1474S|TRPM3_ENST00000377106.1_Missense_Mutation_p.N1497S|TRPM3_ENST00000357533.2_Missense_Mutation_p.N1629S Q9HCF6 TRPM3_HUMAN transient receptor potential cation channel, subfamily M, member 3 95 AGTGATGTTGTTGGACAGGGT 0.552000 0 SO:0001583 missense ENST00000377110.3 1 1 hg19 CCDS43835.1 . . . . . . . . . . T 11.08 1.534120 0.27475 . . ENSG00000083067 ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814 T;T;T;T;T;T;T;T;T;T 0.53640 0.66;0.64;0.64;0.61;0.66;0.61;0.64;0.64;0.64;0.65 5.77 4.62 0.57501 . 0.290243 0.39083 N 0.001479 T 0.51126 0.1656 N 0.24115 0.695 0.32672 N 0.516704 B;B;B;B;P;D;B 0.56035 0.318;0.318;0.213;0.378;0.73;0.974;0.213 B;B;B;B;B;D;B 0.67725 0.099;0.141;0.046;0.047;0.281;0.953;0.031 T 0.58194 -0.7679 10 0.25751 T 0.34 -32.5811 13.0652 0.59030 0.0:0.0:0.1343:0.8657 . 1625;1615;1629;1487;1484;1597;1484 Q9HCF6-2;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3 .;.;.;.;.;.;. S 1625;1497;1487;1484;1629;1484;1484;1497;1487;1652 ENSP00000366314:N1625S;ENSP00000366310:N1497S;ENSP00000354066:N1487S;ENSP00000366309:N1484S;ENSP00000350140:N1629S;ENSP00000386127:N1484S;ENSP00000379581:N1484S;ENSP00000379587:N1497S;ENSP00000350791:N1487S;ENSP00000389542:N1652S ENSP00000350140:N1629S N - 2 0 TRPM3 72340939 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.505000 0.66981 0.985000 0.38656 0.533000 0.62120 AAC TCGA-IB-8126-01A-11D-2396-08 TRPM3-008 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214158.3 0 0 0 97 2227 1 440 0 0 0 1 440 2 0 0 0 0 0 2 1 1.000000 97 2203 1 438 19 0 0 0 1 440 2 -6.187704 1 1 0 0 1 1 2 3 2.012233 0 0.090000 3.970000 0.129187 0.960000 7.800000e-01 1.000000 1.000000 0.947562 0.960000 1 8.700000e-01 1 P2RY8 286530 broad.mit.edu 37 X 1584602 1584602 + Missense_Mutation SNP G G T TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chrX:1584602G>T ENST00000381297.4 - 2 1060 c.850C>A c.(850-852)Ctc>Atc p.L284I P2RY8_ENST00000460672.1_5'Flank NM_178129.4 NP_835230.1 Q86VZ1 P2RY8_HUMAN purinergic receptor P2Y, G-protein coupled, 8 23 all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122) CAGTTGTTGAGGCAGCTGAGA 0.587000 T CRLF2 B-ALL, Downs associated ALL Dom yes X,Y Xp22.3; Yp11.3 286530 purinergic receptor P2Y, G-protein coupled, 8 L 0 SO:0001583 missense ENST00000381297.4 1 1 hg19 CCDS14115.1 . . . . . . . . . . g 11.73 1.724334 0.30593 . . ENSG00000182162 ENST00000381297 T 0.20598 2.06 2.73 2.73 0.32206 GPCR, rhodopsin-like superfamily (1); 0.191682 0.34110 U 0.004251 T 0.18551 0.0445 L 0.52759 1.655 0.09310 N 1 B 0.33494 0.414 B 0.38327 0.271 T 0.11275 -1.0594 10 0.23891 T 0.37 . 6.3011 0.21113 0.3491:0.0:0.6509:0.0 . 284 Q86VZ1 P2RY8_HUMAN I 284 ENSP00000370697:L284I ENSP00000370697:L284I L - 1 0 P2RY8 1544602 1.000000 0.71417 1.000000 0.80357 0.732000 0.41865 0.594000 0.24014 1.007000 0.39238 0.279000 0.19357 CTC TCGA-IB-8126-01A-11D-2396-08 P2RY8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055602.1 0 0 0 21 551 0 97 0 6.576327e-02 0 11 0 97 2 0 0 0 0 0 2 1 0.999997 20 544 0 96 2 0 0 0 0 97 2 -3.580398 1 1 0 0 1 0 1 1 0.090000 3.970000 0.090000 0.810000 5.200000e-01 1.000000 1.000000 0.817780 0.810000 0 6.500000e-01 1 AKAP4 8852 broad.mit.edu 37 X 49957303 49957303 + Silent SNP A A G TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chrX:49957303A>G ENST00000376056.2 - 5 2184 c.2034T>C c.(2032-2034)agT>agC p.S678S AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Silent_p.S304S|AKAP4_ENST00000358526.2_Silent_p.S687S|AKAP4_ENST00000376064.3_Silent_p.S678S A kinase (PRKA) anchor protein 4 41 Ovarian(276;0.236) GCTTCATCCCACTGGTACAGT 0.478000 0 SO:0001819 synonymous_variant ENST00000376056.2 1 1 hg19 CCDS14330.1 TCGA-IB-8126-01A-11D-2396-08 AKAP4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056552.1 0 0 0 9 282 1 84 0 0 0 1 84 2 0 0 0 0 0 2 0 0.252370 9 281 1 84 13 0 0 0 1 84 2 -10.280390 1 1 0 0 1 0 1 1 0.090000 3.970000 0.090000 0.700000 3.500000e-01 1.000000 1.000000 0.714435 0.700000 0 5.000000e-01 9.400000e-01 SLC7A3 84889 broad.mit.edu 37 X 70146816 70146816 + Missense_Mutation SNP C C A TCGA-IB-8126-01A-11D-2396-08 TCGA-IB-8126-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 39fccb1b-b1fb-4a1f-bb83-beaefa163ff1 6e08a2fc-e7b8-4811-a7c5-e676767d0e8a g.chrX:70146816C>A ENST00000374299.3 - 9 1506 c.1362G>T c.(1360-1362)gaG>gaT p.E454D SLC7A3_ENST00000298085.4_Missense_Mutation_p.E454D Q8WY07 CTR3_HUMAN solute carrier family 7 (cationic amino acid transporter, y+ system), member 3 31 Renal(35;0.156) L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129) GGGTCAACTTCTCTGATTCAG 0.468000 0 SO:0001583 missense ENST00000374299.3 1 1 hg19 CCDS14404.1 . . . . . . . . . . C 9.547 1.114898 0.20795 . . ENSG00000165349 ENST00000374299;ENST00000298085 D;D 0.88664 -2.41;-2.41 5.31 2.39 0.29439 . 0.537794 0.13865 U 0.357372 D 0.86301 0.5900 L 0.46157 1.445 0.09310 N 0.999999 B 0.23650 0.089 B 0.35727 0.209 T 0.76189 -0.3050 10 0.44086 T 0.13 . 9.0769 0.36527 0.0:0.7342:0.0:0.2658 . 454 Q8WY07 CTR3_HUMAN D 454 ENSP00000363417:E454D;ENSP00000298085:E454D ENSP00000298085:E454D E - 3 2 SLC7A3 70063541 0.579000 0.26725 0.881000 0.34555 0.226000 0.24999 0.230000 0.17852 0.158000 0.19367 0.529000 0.55759 GAG TCGA-IB-8126-01A-11D-2396-08 SLC7A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057080.1 1 0 0 17 313 0 68 0 0 0 1 0 68 2 0 0 0 0 0 2 1 0.999966 17 310 0 68 2 0 0 0 0 68 2 -18.789010 1 1 0 0 1 0 1 1 0.090000 3.970000 0.090000 0.990000 6.900000e-01 1.000000 1.000000 0.961782 0.990000 1 8.900000e-01 1