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 LDB1 8861 broad.mit.edu 37 10 103868035 103868035 + Missense_Mutation SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr10:103868035C>T ENST00000425280.1 - 11 1393 c.1051G>A c.(1051-1053)Ggg>Agg p.G351R LDB1_ENST00000361198.5_Missense_Mutation_p.G315R|LDB1_ENST00000490751.1_5'Flank NM_001113407.1 NP_001106878.1 Q86U70 LDB1_HUMAN LIM domain binding 1 21 Colorectal(252;0.122) TCCTCGTCCCCGAACTCCCCG 0.632000 0 SO:0001583 missense ENST00000425280.1 1 1 hg19 CCDS44472.1 . . . . . . . . . . C 21.900000 4.210721 0.792400 . . ENSG00000198728 ENST00000361198;ENST00000425280 T;T 0.27890 1.64;1.64 5.490000 5.490000 0.811920 . 0.000000 0.85682 D 0.000000 T 0.40322 0.1112 M 0.85777 2.775 0.807220 D 1.000000 D 0.54772 0.968 B 0.37144 0.242 T 0.58120 -0.7692 10 0.87932 D 0 -3.4047 19.337900 0.943260 0.0:1.0:0.0:0.0 . 351 Q86U70 LDB1_HUMAN R 315;351 ENSP00000354616:G315R;ENSP00000392466:G351R ENSP00000354616:G315R G - 1 0 LDB1 103858025 1 0.714170 1 0.803570 9.960000e-01 0.888480 7.776000 0.855600 2.742000 0.940160 0.455000 0.322230 GGG TCGA-IB-AAUM-01A-11D-A377-08 LDB1-201 KNOWN basic|CCDS protein_coding protein_coding 0 0 0 9 216 0 41 1 8.434276e-01 8 75 0 41 2 0 0 0 0 0 2 1 0.994381 9 215 0 41 2 0 0 0 0 41 2 -2.947337 1 1 0 0 1 0 1 1 1.992979 0 0.080000 2.040000 0.071832 0.980000 0.490000 1.000000 1.000000 0.889537 0.980000 1 0.710000 1.000000 DSCAML1 57453 broad.mit.edu 37 11 117307881 117307881 + Silent SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr11:117307881G>A ENST00000321322.6 - 26 4858 c.4857C>T c.(4855-4857)tgC>tgT p.C1619C DSCAML1_ENST00000527706.1_Silent_p.C1349C NM_020693.2 NP_065744.2 Q8TD84 DSCL1_HUMAN Down syndrome cell adhesion molecule like 1 p.C1619C(1) 110 all_hematologic(175;0.0487) Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232) TTTCATTGCCGCAGCCCGCAC 0.632000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000321322.6 0 1 hg19 CCDS8384.1 TCGA-IB-AAUM-01A-11D-A377-08 DSCAML1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000392907.2 0 0 0 6 400 0 59 0 1.955125e-03 0 4 0 59 2 0 0 0 0 0 2 1 0.964437 6 397 0 58 2 0 0 0 0 59 2 -2.172429 0 1 121412 5 37 1 0 1 1 1.991255 0 0.080000 2.040000 0.071457 0.380000 0.160000 0.730000 0.350000 0.411276 0.380000 0 0.250000 0.550000 GRIK4 2900 broad.mit.edu 37 11 120769305 120769305 + Missense_Mutation SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr11:120769305C>T ENST00000527524.2 + 12 1516 c.1229C>T c.(1228-1230)tCg>tTg p.S410L GRIK4_ENST00000438375.2_Missense_Mutation_p.S410L NM_001282470.1 NP_001269399.1 Q16099 GRIK4_HUMAN glutamate receptor, ionotropic, kainate 4 69 Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21) TCCAACATCTCGGACACTCTC 0.612000 0 SO:0001583 missense ENST00000527524.2 1 1 hg19 CCDS8433.1 . . . . . . . . . . C 14.400000 2.523560 0.448660 . . ENSG00000149403 ENST00000527524;ENST00000438375 T;T 0.13657 2.57;2.57 5.030000 5.030000 0.673930 . 0.297347 0.40385 N 0.001116 T 0.17195 0.0413 M 0.62723 1.935 0.517670 D 0.999930 B;P 0.39376 0.239;0.67 B;B 0.31869 0.078;0.137 T 0.04360 -1.0957 10 0.72032 D 0.01 . 18.362300 0.903790 0.0:1.0:0.0:0.0 . 410;410 A6H8K8;Q16099 .;GRIK4_HUMAN L 410 ENSP00000435648:S410L;ENSP00000404063:S410L ENSP00000404063:S410L S + 2 0 GRIK4 120274515 1 0.714170 9.070000e-01 0.357230 1.800000e-02 0.096640 7.480000 0.811090 2.323000 0.785720 0.462000 0.415740 TCG TCGA-IB-AAUM-01A-11D-A377-08 GRIK4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109760.4 1 0 0 7 139 0 29 0 0 0 0 29 2 0 0 0 0 0 2 1 0.981434 7 139 0 29 2 0 0 0 0 29 2 -3.017763 1 1 121412 1 27 1 0 1 1 1.991255 0 0.080000 2.040000 0.071457 0.990000 0.530000 1.000000 1.000000 0.926943 0.990000 1 0.790000 1.000000 CDON 50937 broad.mit.edu 37 11 125871630 125871630 + Silent SNP G G C TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr11:125871630G>C ENST00000392693.3 - 11 2269 c.2142C>G c.(2140-2142)tcC>tcG p.S714S CDON_ENST00000531738.1_Silent_p.S91S|CDON_ENST00000263577.7_Silent_p.S714S NM_001243597.1|NM_016952.4 NP_001230526.1|NP_058648.4 Q4KMG0 CDON_HUMAN cell adhesion associated, oncogene regulated 61 all_hematologic(175;0.177) Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) TGTGCCTAGAGGAATCTGTAA 0.433000 0 SO:0001819 synonymous_variant ENST00000392693.3 1 1 hg19 CCDS58192.1 TCGA-IB-AAUM-01A-11D-A377-08 CDON-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000386749.2 1 0 0 17 343 0 81 0 1.441973e-02 0 4 0 81 2 0 0 0 0 0 2 1 0.999966 17 341 0 78 2 0 0 0 0 81 2 -2.725401 1 1 0 0 1 0 1 1 1.991255 0 0.080000 2.040000 0.071457 0.990000 0.700000 1.000000 1.000000 0.964896 0.990000 1 0.910000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.400000 4.409094 0.833400 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.680000 5.680000 0.881260 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.807220 D 1.000000 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 . 18.371900 0.904090 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 0.714170 1 0.803570 9.980000e-01 0.957120 7.743000 0.850200 2.668000 0.907890 0.563000 0.778840 GGT TCGA-IB-AAUM-01A-11D-A377-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 19 308 0 86 0 1.649818e-01 1 11 0 86 2 1 9.999007e-01 21 477 1 346 7 1 0.999992 19 308 0 85 2 1 1 462 7563 0 86 2 -5.925615 1 1 121404 2 44 1 1 2 3 2.001720 0 0.080000 2.040000 0.088387 0.990000 0.930000 1.000000 1.000000 0.995854 0.990000 1 0.990000 1.000000 NUP107 57122 broad.mit.edu 37 12 69082833 69082833 + Splice_Site SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr12:69082833C>T ENST00000229179.4 + 2 432 c.100C>T c.(100-102)Ctt>Ttt p.L34F RP11-637A17.2_ENST00000500695.2_lincRNA|NUP107_ENST00000539906.1_5'UTR|NUP107_ENST00000378905.2_5'UTR NM_020401.2 NP_065134.1 P57740 NU107_HUMAN nucleoporin 107kDa NUP107/LGR5(2) 39 Breast(13;6.25e-06) Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694) AAGAGTTTTACGTATCCTTTG 0.378000 0 SO:0001630 splice_region_variant ENST00000229179.4 0 1 hg19 CCDS8985.1 . . . . . . . . . . C 11.250000 1.583042 0.282680 . . ENSG00000111581 ENST00000229179 . . . 5.450000 1.620000 0.237400 . 0.364773 0.29515 N 0.011933 T 0.28764 0.0713 N 0.19112 0.55 0.807220 D 1.000000 B 0.33288 0.406 B 0.26614 0.071 T 0.03875 -1.0996 8 . . . -14.2674 7.303500 0.264340 0.4774:0.4454:0.0772:0.0 . 34 P57740 NU107_HUMAN F 34 . . L + 1 0 NUP107 67369100 1 0.714170 9.980000e-01 0.565050 8.450000e-01 0.480190 0.680000 0.253060 0.084000 0.170770 -0.541000 0.042450 CTT TCGA-IB-AAUM-01A-11D-A377-08 NUP107-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403195.1 0 0 0 9 170 0 33 0 1.437079e-01 0 12 0 33 2 0 0 0 0 0 2 1 0.994443 9 169 0 33 2 0 0 0 0 33 2 -4.353979 1 1 121412 7 37 1 1 2 3 2.001720 0 0.080000 2.040000 0.088387 0.990000 0.660000 1.000000 1.000000 0.967084 0.990000 1 0.950000 1.000000 HERC2 8924 broad.mit.edu 37 15 28518096 28518096 + Missense_Mutation SNP G G C TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr15:28518096G>C ENST00000261609.7 - 8 963 c.855C>G c.(853-855)gaC>gaG p.D285E NM_004667.5 NP_004658.3 HECT and RLD domain containing E3 ubiquitin protein ligase 2 204 all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227) CCAAGTGCTGGTCCTGCAGGG 0.612000 0 SO:0001583 missense ENST00000261609.7 0 1 hg19 CCDS10021.1 . . . . . . . . . . G 27.900000 4.875355 0.916640 . . ENSG00000128731 ENST00000261609 T 0.56611 0.45 5.230000 4.300000 0.512180 . 0.000000 0.85682 D 0.000000 T 0.70491 0.3230 M 0.75615 2.305 0.807220 D 1.000000 D 0.58970 0.984 D 0.68192 0.956 T 0.73902 -0.3836 10 0.54805 T 0.06 . 14.424100 0.672020 0.0718:0.0:0.9282:0.0 . 285 O95714 HERC2_HUMAN E 285 ENSP00000261609:D285E ENSP00000261609:D285E D - 3 2 HERC2 26191691 1 0.714170 1 0.803570 9.970000e-01 0.918780 3.274000 0.516310 1.424000 0.472170 0.644000 0.839320 GAC TCGA-IB-AAUM-01A-11D-A377-08 HERC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251358.2 0 0 0 12 221 1 37 1 3.598134e-02 4 9 1 37 3 0 0 0 0 0 2 0 0.119264 12 217 1 37 19 0 0 0 1 37 2 -2.117427 0 0 121412 7 23 1 0 1 1 1.978553 0 0.080000 2.040000 0.068449 0.990000 0.680000 1.000000 1.000000 0.965227 0.990000 1 0.920000 1.000000 KLHL25 64410 broad.mit.edu 37 15 86311613 86311613 + Missense_Mutation SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr15:86311613C>T ENST00000337975.5 - 2 1703 c.1429G>A c.(1429-1431)Gag>Aag p.E477K KLHL25_ENST00000536947.1_Missense_Mutation_p.E477K|KLHL25_ENST00000559131.1_Intron|MIR1276_ENST00000408707.1_RNA NM_022480.3 NP_071925.2 Q9H0H3 KLH25_HUMAN kelch-like family member 25 25 TGGGGGCACTCGGCCTTGATC 0.612000 0 SO:0001583 missense ENST00000337975.5 1 1 hg19 CCDS10339.1 . . . . . . . . . . C 11.800000 1.745761 0.309550 0.0 1.16E-4 ENSG00000183655 ENST00000337975;ENST00000538153;ENST00000536947 T;T 0.78003 -1.14;-1.14 5.710000 5.710000 0.891250 Kelch-type beta propeller (1); 0.056938 0.64402 D 0.000002 T 0.73877 0.3643 L 0.39147 1.195 0.448520 D 0.997868 B 0.28470 0.213 B 0.29862 0.108 T 0.71991 -0.4425 10 0.59425 D 0.04 . 18.831400 0.921410 0.0:1.0:0.0:0.0 . 477 Q9H0H3 ENC2_HUMAN K 477;446;477 ENSP00000336800:E477K;ENSP00000444739:E477K ENSP00000336800:E477K E - 1 0 KLHL25 84112617 9.900000e-01 0.363640 9.930000e-01 0.491080 2.570000e-01 0.261270 3.248000 0.514300 2.700000 0.922000 0.462000 0.415740 GAG TCGA-IB-AAUM-01A-11D-A377-08 KLHL25-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000309023.1 1 0 0 23 479 0 93 0 8.073680e-02 1 9 0 93 2 0 0 0 0 0 2 1 0.999999 23 471 0 88 2 0 0 0 0 93 2 -2.907014 1 1 0 0 1 0 1 1 1.983979 0 0.080000 2.040000 0.069579 0.990000 0.730000 1.000000 1.000000 0.967363 0.990000 1 0.910000 1.000000 MAN2A2 4122 broad.mit.edu 37 15 91454724 91454724 + Missense_Mutation SNP G G A rs146632780 byFrequency TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr15:91454724G>A ENST00000559717.1 + 14 2512 c.2053G>A c.(2053-2055)Gtg>Atg p.V685M MAN2A2_ENST00000360468.3_Missense_Mutation_p.V685M|MAN2A2_ENST00000431652.2_Missense_Mutation_p.V193M|MAN2A2_ENST00000430376.2_5'Flank P49641 MA2A2_HUMAN mannosidase, alpha, class 2A, member 2 47 Lung NSC(78;0.0771)|all_lung(78;0.137) Lung(145;0.229) GCCCCTGGCCGTGCAGATCAG 0.647000 0 SO:0001583 missense ENST00000559717.1 0 1 hg19 CCDS32332.1 . . . . . . . . . . G 14.640000 2.595953 0.463180 0.00182 0.0 ENSG00000196547 ENST00000360468;ENST00000431652 T;T 0.79247 -1.25;-1.25 5.490000 5.490000 0.811920 Glycosyl hydrolases 38, C-terminal (1);Glycosyl hydrolase, family 13, all-beta (1);Glycoside hydrolase-type carbohydrate-binding (1); 0.112697 0.64402 D 0.000012 D 0.83899 0.5354 M 0.81942 2.565 0.807220 D 1.000000 P;P;P 0.41848 0.577;0.763;0.763 B;P;P 0.48901 0.278;0.594;0.594 D 0.83927 0.0304 10 0.41790 T 0.15 -8.4381 15.856600 0.789830 0.0:0.0:0.8639:0.1361 . 193;313;685 B4DEU9;B4DIK4;P49641 .;.;MA2A2_HUMAN M 685;193 ENSP00000353655:V685M;ENSP00000388221:V193M ENSP00000353655:V685M V + 1 0 MAN2A2 89255728 1 0.714170 9.590000e-01 0.398830 3.900000e-02 0.134160 4.364000 0.594790 2.622000 0.888050 0.549000 0.686330 GTG TCGA-IB-AAUM-01A-11D-A377-08 MAN2A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000418246.5 0 0 0 4 235 0 39 0 2.412919e-01 0 45 0 39 2 0 0 0 0 0 2 1 0.885054 4 229 0 38 2 0 0 0 0 39 2 -2.946643 1 1 121412 20 45 1 0 1 1 1.983979 0 0.080000 2.040000 0.069579 0.440000 0.150000 0.930000 1.000000 0.481573 0.440000 0 0.270000 0.680000 ADCY9 115 broad.mit.edu 37 16 4163864 4163864 + Missense_Mutation SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr16:4163864C>T ENST00000294016.3 - 2 2118 c.1580G>A c.(1579-1581)gGc>gAc p.G527D NM_001116.3 NP_001107.2 O60503 ADCY9_HUMAN adenylate cyclase 9 47 GTGAACTTTGCCGGCCACTCC 0.522000 0 SO:0001583 missense ENST00000294016.3 0 1 hg19 CCDS32382.1 . . . . . . . . . . C 20.600000 4.018606 0.752750 . . ENSG00000162104 ENST00000294016 D 0.86562 -2.14 5.390000 5.390000 0.778230 Adenylyl cyclase class-3/4/guanylyl cyclase (4); 0.000000 0.85682 D 0.000000 D 0.93713 0.7991 M 0.78049 2.395 0.807220 D 1.000000 D 0.89917 1.0 D 0.97110 1.0 D 0.94090 0.7352 10 0.72032 D 0.01 . 19.201700 0.937130 0.0:1.0:0.0:0.0 . 527 O60503 ADCY9_HUMAN D 527 ENSP00000294016:G527D ENSP00000294016:G527D G - 2 0 ADCY9 4103865 1 0.714170 9.950000e-01 0.509660 9.920000e-01 0.810270 7.818000 0.864160 2.552000 0.860800 0.555000 0.697020 GGC TCGA-IB-AAUM-01A-11D-A377-08 ADCY9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438076.1 0 0 0 5 539 0 129 0 2.249191e-02 0 20 0 129 2 0 0 0 0 0 2 1 0.934392 5 528 0 128 2 0 0 0 0 129 2 -2.130388 0 1 0 0 1 1 2 3 2.010337 0 0.080000 2.040000 0.090190 0.280000 0.090000 1.000000 0.230000 0.413484 0.280000 0 0.170000 1.000000 ITFG1 81533 broad.mit.edu 37 16 47195677 47195677 + Missense_Mutation SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr16:47195677G>A ENST00000320640.6 - 16 1873 c.1645C>T c.(1645-1647)Cac>Tac p.H549Y ITFG1_ENST00000568047.1_5'UTR|RP11-329J18.2_ENST00000564705.1_RNA|RP11-329J18.2_ENST00000565694.1_RNA|ITFG1_ENST00000544001.2_Missense_Mutation_p.H436Y NM_030790.3 NP_110417.2 Q8TB96 TIP_HUMAN integrin alpha FG-GAP repeat containing 1 19 all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227) GGGACATTGTGAGGGTATGGA 0.373000 0 SO:0001583 missense ENST00000320640.6 1 1 hg19 CCDS10728.1 . . . . . . . . . . G 17.780000 3.474395 0.637370 . . ENSG00000129636 ENST00000320640;ENST00000537184;ENST00000542691;ENST00000544001 . . . 5.590000 5.590000 0.848120 . 0.050252 0.85682 D 0.000000 T 0.52948 0.1766 L 0.44542 1.39 0.807220 D 1.000000 P;B 0.35612 0.512;0.225 B;B 0.37047 0.24;0.158 T 0.46247 -0.9205 9 0.16420 T 0.52 -18.2506 19.599200 0.955520 0.0:0.0:1.0:0.0 . 436;549 F5GXC5;Q8TB96 .;TIP_HUMAN Y 549;209;294;436 . ENSP00000319918:H549Y H - 1 0 ITFG1 45753178 1 0.714170 9.970000e-01 0.539660 9.950000e-01 0.863560 7.229000 0.780880 2.640000 0.895330 0.467000 0.429560 CAC TCGA-IB-AAUM-01A-11D-A377-08 ITFG1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256768.3 1 0 0 24 429 0 101 1 9.939297e-01 10 135 0 101 2 0 0 0 0 0 2 1 1.000000 24 428 0 101 2 0 0 0 0 101 2 -3.316108 1 1 0 0 1 1 2 3 1.998329 0 0.080000 2.040000 0.087664 0.990000 0.890000 1.000000 1.000000 0.993929 0.990000 1 0.990000 1.000000 PIGQ 9091 broad.mit.edu 37 16 633162 633162 + Missense_Mutation SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr16:633162G>A ENST00000026218.5 + 10 1899 c.1811G>A c.(1810-1812)gGc>gAc p.G604D PIGQ_ENST00000321878.5_3'UTR NM_148920.2 NP_683721.1 Q9BRB3 PIGQ_HUMAN phosphatidylinositol glycan anchor biosynthesis, class Q 13 Hepatocellular(780;0.00335) CCTGAACACGGCAGGCCCTGC 0.642000 0 SO:0001583 missense ENST00000026218.5 0 1 hg19 CCDS10411.1 . . . . . . . . . . G 10.540000 1.379045 0.249440 . . ENSG00000007541 ENST00000026218 T 0.25912 1.77 3.180000 -0.830000 0.107920 . . . . . T 0.09686 0.0238 N 0.08118 0 0.193000 N 0.999972 B;B 0.18013 0.025;0.001 B;B 0.15870 0.014;0.001 T 0.34725 -0.9817 8 . . . 0.0578 3.077300 0.062510 0.4718:0.0:0.3279:0.2004 . 174;604 B3KRR7;Q9BRB3 .;PIGQ_HUMAN D 604 ENSP00000026218:G604D . G + 2 0 PIGQ 573163 0 0.058580 1.020000e-01 0.211980 2.800000e-02 0.117280 -0.042000 0.120630 -0.023000 0.139630 -0.481000 0.048170 GGC TCGA-IB-AAUM-01A-11D-A377-08 PIGQ-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000239270.2 0 0 0 5 657 0 138 0 4.413348e-01 0 173 0 138 2 0 0 0 0 0 2 1 0.934447 5 644 0 138 2 0 0 0 0 138 2 -1.963791 0 1 0 0 1 1 2 3 2.010337 0 0.080000 2.040000 0.090190 0.230000 0.080000 1.000000 0.180000 0.375018 0.230000 0 0.140000 1.000000 TP53I13 90313 broad.mit.edu 37 17 27898646 27898646 + Missense_Mutation SNP A A T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr17:27898646A>T ENST00000301057.7 + 4 336 c.221A>T c.(220-222)cAt>cTt p.H74L RP11-68I3.2_ENST00000581474.1_RNA|RP11-68I3.4_ENST00000579050.1_RNA NM_138349.2 NP_612358.3 Q8NBR0 P5I13_HUMAN tumor protein p53 inducible protein 13 4 CCCTGTGCCCATCCCTGGCTG 0.577000 0 SO:0001583 missense ENST00000301057.7 1 1 hg19 CCDS42289.1 . . . . . . . . . . A 12.340000 1.907199 0.336280 . . ENSG00000167543 ENST00000301057 . . . 4.620000 4.620000 0.575010 . 0.078468 0.51477 D 0.000094 T 0.71264 0.3319 M 0.72118 2.19 0.400650 D 0.975940 D 0.71674 0.998 D 0.68943 0.961 T 0.74127 -0.3765 9 0.52906 T 0.07 -16.3851 10.723600 0.460550 1.0:0.0:0.0:0.0 . 74 Q8NBR0 P5I13_HUMAN L 74 . ENSP00000301057:H74L H + 2 0 TP53I13 24922772 9.850000e-01 0.353260 1 0.803570 9.150000e-01 0.545460 2.593000 0.461800 1.844000 0.535880 0.374000 0.227000 CAT TCGA-IB-AAUM-01A-11D-A377-08 TP53I13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447804.2 0 0 1 9 278 0 70 1 7.623299e-01 10 76 0 70 2 0 0 0 0 0 2 1 0.993648 9 270 0 69 2 0 0 0 0 70 2 -10.282210 1 1 0 0 1 1 2 3 2.004719 0 0.080000 2.040000 0.089109 0.880000 0.410000 1.000000 1.000000 0.831743 0.880000 1 0.610000 1.000000 RHOT1 55288 broad.mit.edu 37 17 30521098 30521098 + Missense_Mutation SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr17:30521098G>A ENST00000333942.6 + 11 1080 c.841G>A c.(841-843)Gat>Aat p.D281N RHOT1_ENST00000545287.2_Missense_Mutation_p.D281N|RHOT1_ENST00000358365.3_Missense_Mutation_p.D281N|RHOT1_ENST00000580976.1_3'UTR|RHOT1_ENST00000354266.3_Missense_Mutation_p.D260N|RHOT1_ENST00000583994.1_Missense_Mutation_p.D154N|RHOT1_ENST00000581094.1_Missense_Mutation_p.D281N|RHOT1_ENST00000394692.2_Missense_Mutation_p.D281N NM_018307.3 NP_060777.3 Q8IXI2 MIRO1_HUMAN ras homolog family member T1 28 Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182) TGATGACCTGGATTTGACACC 0.363000 0 SO:0001583 missense ENST00000333942.6 0 1 hg19 CCDS32612.1 . . . . . . . . . . G 19.010000 3.743488 0.694180 . . ENSG00000126858 ENST00000358365;ENST00000354266;ENST00000394692;ENST00000333942 T;T;T 0.42131 0.98;0.98;0.98 5.970000 5.970000 0.969550 EF hand associated, type-2 (1); 0.088643 0.85682 D 0.000000 T 0.22166 0.0534 N 0.01352 -0.895 0.807220 D 1.000000 B;B;B;B 0.24317 0.101;0.0;0.0;0.0 B;B;B;B 0.24394 0.053;0.002;0.006;0.002 T 0.18745 -1.0327 10 0.38643 T 0.18 -6.5042 20.413500 0.990230 0.0:0.0:1.0:0.0 . 281;281;281;281 Q8IXI2-2;Q8IXI2;Q8IXI2-5;Q8IXI2-3 .;MIRO1_HUMAN;.;. N 281 ENSP00000351132:D281N;ENSP00000378184:D281N;ENSP00000334724:D281N ENSP00000334724:D281N D + 1 0 RHOT1 27545211 1 0.714170 1 0.803570 9.970000e-01 0.918780 9.869000 0.998100 2.835000 0.976880 0.591000 0.815410 GAT TCGA-IB-AAUM-01A-11D-A377-08 RHOT1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000447097.1 0 0 0 21 1713 0 477 0 4.385822e-02 1 25 0 477 2 0 0 0 0 0 2 1 0.999996 22 1664 0 475 2 0 0 0 0 477 2 -3.017764 1 1 0 0 1 1 2 3 2.004719 0 0.080000 2.040000 0.089109 0.320000 0.190000 1.000000 0.310000 0.440418 0.320000 0 0.250000 1.000000 DVL2 1856 broad.mit.edu 37 17 7137472 7137472 + Missense_Mutation SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr17:7137472C>T ENST00000005340.5 - 1 392 c.110G>A c.(109-111)cGc>cAc p.R37H DVL2_ENST00000575458.1_Missense_Mutation_p.R37H|PHF23_ENST00000570753.1_5'Flank NM_004422.2 NP_004413.1 O14641 DVL2_HUMAN dishevelled segment polarity protein 2 25 GAGGGTGATGCGCTCGGCGGG 0.602000 0 SO:0001583 missense ENST00000005340.5 0 1 hg19 CCDS11091.1 . . . . . . . . . . C 27.300000 4.821401 0.908730 . . ENSG00000004975 ENST00000005340 T 0.43294 0.95 4.510000 4.510000 0.551910 DIX (3); 0.287347 0.32640 N 0.005840 T 0.51652 0.1687 L 0.53249 1.67 0.361700 D 0.848736 D;D;D 0.69078 0.997;0.996;0.997 P;P;P 0.60789 0.879;0.703;0.879 T 0.61787 -0.6991 10 0.56958 D 0.05 -13.7627 8.550400 0.334490 0.0:0.8922:0.0:0.1078 . 37;37;37 B4DLQ0;B4E2D6;O14641 .;.;DVL2_HUMAN H 37 ENSP00000005340:R37H ENSP00000005340:R37H R - 2 0 DVL2 7078196 1 0.714170 1 0.803570 9.920000e-01 0.810270 3.334000 0.520970 2.055000 0.611980 0.484000 0.476210 CGC TCGA-IB-AAUM-01A-11D-A377-08 DVL2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000219999.2 0 0 0 6 809 0 147 0 2.621717e-02 0 28 0 147 2 0 0 0 0 0 2 1 0.963820 6 801 0 142 2 0 0 0 0 147 2 -1.929403 0 1 0 0 1 1 2 3 1.998392 0 0.080000 2.040000 0.087664 0.210000 0.080000 1.000000 0.180000 0.337202 0.210000 0 0.130000 0.500000 SMAD4 4089 broad.mit.edu 37 18 48604703 48604703 + Missense_Mutation SNP T T G TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 T G T T Valid Somatic Phase_I WXS targeted Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr18:48604703T>G ENST00000342988.3 + 12 2063 c.1525T>G c.(1525-1527)Tgg>Ggg p.W509G SMAD4_ENST00000588745.1_Missense_Mutation_p.W413G|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Missense_Mutation_p.W509G NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(2) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) TGTGAAAGGCTGGGGACCGGA 0.473000 38 Whole gene deletion(36)|Unknown(2) SO:0001583 missense ENST00000342988.3 1 1 hg19 CCDS11950.1 . . . . . . . . . . T 17.730000 3.460910 0.635130 . . ENSG00000141646 ENST00000342988;ENST00000398417 D;D 0.99113 -5.44;-5.44 6.080000 6.080000 0.989890 SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3); 0.000000 0.85682 D 0.000000 D 0.99515 0.9827 H 0.95539 3.685 0.807220 D 1.000000 D 0.89917 1.0 D 0.97110 1.0 D 0.98200 1.0467 10 0.87932 D 0 . 15.625500 0.768510 0.0:0.0:0.0:1.0 . 509 Q13485 SMAD4_HUMAN G 509 ENSP00000341551:W509G;ENSP00000381452:W509G ENSP00000341551:W509G W + 1 0 SMAD4 46858701 1 0.714170 1 0.803570 9.960000e-01 0.888480 7.819000 0.866210 2.330000 0.791610 0.533000 0.621200 TGG TCGA-IB-AAUM-01A-11D-A377-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 1 20 253 0 56 1 9.830782e-01 15 71 0 56 2 1 1 58 1111 0 898 2 1 0.999995 20 248 0 56 2 0 0 0 0 56 2 -19.999990 1 1 0 0 1 0 0 0 1.895056 1 0.080000 2.040000 0.022109 0.490000 0.400000 1.000000 0.510000 0.520576 0.490000 0 0.450000 0.520000 TSHZ1 10194 broad.mit.edu 37 18 72998573 72998573 + Missense_Mutation SNP A A G TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr18:72998573A>G ENST00000580243.1 + 2 1559 c.1211A>G c.(1210-1212)tAc>tGc p.Y404C TSHZ1_ENST00000322038.5_Missense_Mutation_p.Y359C Q6ZSZ6 TSH1_HUMAN teashirt zinc finger homeobox 1 42 Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211) GGCGCCAGCTACACCTGGCAG 0.612000 0 SO:0001583 missense ENST00000580243.1 0 1 hg19 . . . . . . . . . . A 10.700000 1.424041 0.256390 . . ENSG00000179981 ENST00000322038 T 0.20463 2.07 5.120000 5.120000 0.697940 . 0.000000 0.85682 D 0.000000 T 0.47229 0.1434 M 0.74647 2.275 0.452160 D 0.998227 D 0.89917 1.0 D 0.85130 0.997 T 0.49570 -0.8926 10 0.87932 D 0 -30.001 14.940200 0.709890 1.0:0.0:0.0:0.0 . 404 Q6ZSZ6 TSH1_HUMAN C 359 ENSP00000323584:Y359C ENSP00000323584:Y359C Y + 2 0 TSHZ1 71127561 1 0.714170 1 0.803570 9.010000e-01 0.528970 8.794000 0.918670 2.371000 0.807100 0.561000 0.740990 TAC TCGA-IB-AAUM-01A-11D-A377-08 TSHZ1-005 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000444913.1 0 0 0 4 197 0 39 0 4.421781e-02 0 13 0 39 2 0 0 0 0 0 2 1 0.890045 4 196 0 39 2 0 0 0 0 39 2 -6.245539 1 1 0 0 1 0 0 0 1.895056 1 0.080000 2.040000 0.022109 0.350000 0.130000 0.510000 0.400000 0.354990 0.350000 0 0.230000 0.470000 KRI1 65095 broad.mit.edu 37 19 10671101 10671101 + Silent SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr19:10671101G>A ENST00000312962.6 - 9 724 c.705C>T c.(703-705)aaC>aaT p.N235N KRI1_ENST00000361821.5_Silent_p.N231N|KRI1_ENST00000537964.1_5'Flank NM_023008.3 NP_075384.3 Q8N9T8 KRI1_HUMAN KRI1 homolog (S. cerevisiae) 26 Epithelial(33;9.2e-06)|all cancers(31;3.9e-05) ACTCAGGGTCGTTCCAGTATT 0.552000 0 SO:0001819 synonymous_variant ENST00000312962.6 1 1 hg19 CCDS12242.1 . . . . . . . . . . G 9.792000 1.178289 0.217870 . . ENSG00000129347 ENST00000543682 . . . 5.360000 3.240000 0.371750 . . . . . T 0.56001 0.1956 . . . 0.807220 D 1.000000 . . . . . . T 0.49133 -0.8971 4 . . . -58.2916 7.286200 0.263400 0.3358:0.0:0.6642:0.0 . . . . M 173 . . T - 2 0 KRI1 10532101 1.440000e-01 0.226410 9.930000e-01 0.491080 9.250000e-01 0.559040 0.275000 0.186980 0.652000 0.308060 0.563000 0.778840 ACG TCGA-IB-AAUM-01A-11D-A377-08 KRI1-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317705.1 0 0 0 39 492 1 98 1 6.788818e-01 7 55 1 98 4 0 0 0 0 0 2 1 0.998288 37 481 1 96 18 0 0 0 1 98 2 -9.896644 1 1 121412 3 35 1 1 2 3 2.007831 0 0.080000 2.040000 0.089830 0.990000 0.990000 1.000000 1.000000 0.999994 0.990000 1 0.990000 1.000000 ZNF781 163115 broad.mit.edu 37 19 38160168 38160168 + Missense_Mutation SNP C C A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr19:38160168C>A ENST00000590008.1 - 5 1734 c.882G>T c.(880-882)ttG>ttT p.L294F ZNF781_ENST00000593040.1_5'Flank|ZNF781_ENST00000358582.4_Missense_Mutation_p.L294F|ZFP30_ENST00000586732.1_Intron Q8N8C0 ZN781_HUMAN zinc finger protein 781 24 GGACAGGAGACAAAAACCTTC 0.383000 0 SO:0001583 missense ENST00000590008.1 1 1 hg19 CCDS12507.1 . . . . . . . . . . C 8.075000 0.771033 0.160510 . . ENSG00000196381 ENST00000358582;ENST00000545586 T 0.06142 3.34 2.070000 -4.150000 0.038810 . . . . . T 0.03305 0.0096 L 0.35341 1.055 0.093100 N 1.000000 B 0.14805 0.011 B 0.13407 0.009 T 0.48305 -0.9047 9 0.02654 T 1 -0.7011 4.050700 0.097930 0.4516:0.3457:0.0:0.2027 . 294 Q8N8C0 ZN781_HUMAN F 294 ENSP00000351391:L294F ENSP00000351391:L294F L - 3 2 ZNF781 42852008 0 0.058580 0 0.037020 0 0.004340 -1.780000 0.017750 -1.890000 0.011110 -1.760000 0.006710 TTG TCGA-IB-AAUM-01A-11D-A377-08 ZNF781-002 KNOWN alternative_5_UTR|basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000459495.2 0 0 0 25 422 0 145 0 0 0 1 0 145 2 0 0 1 0 0 0 2 1 1.000000 25 419 0 143 2 0 0 0 0 145 2 -20.000000 1 1 121410 1 34 1 1 2 3 2.007831 0 0.080000 2.040000 0.089830 0.990000 0.960000 1.000000 1.000000 0.997019 0.990000 1 0.990000 1.000000 IZUMO1 284359 broad.mit.edu 37 19 49248495 49248495 + Missense_Mutation SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr19:49248495G>A ENST00000332955.2 - 3 833 c.286C>T c.(286-288)Cgc>Tgc p.R96C NM_182575.2 NP_872381.2 Q8IYV9 IZUM1_HUMAN izumo sperm-egg fusion 1 17 all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113) TCTGTGATGCGTTTCAGATCC 0.507000 0 SO:0001583 missense ENST00000332955.2 1 1 hg19 CCDS12732.1 . . . . . . . . . . G 20.200000 3.951427 0.737870 . . ENSG00000182264 ENST00000332955 T 0.25749 1.78 5.100000 2.880000 0.335530 . 0.237333 0.30101 N 0.010409 T 0.42720 0.1215 L 0.59436 1.845 0.393810 D 0.966252 D 0.89917 1.0 D 0.97110 1.0 T 0.33727 -0.9857 10 0.87932 D 0 -9.5316 8.523600 0.332910 0.0:0.1681:0.6575:0.1744 . 96 Q8IYV9 IZUM1_HUMAN C 96 ENSP00000327786:R96C ENSP00000327786:R96C R - 1 0 IZUMO1 53940307 9.940000e-01 0.377170 9.960000e-01 0.522420 9.940000e-01 0.842990 2.965000 0.492000 0.624000 0.302860 0.491000 0.489740 CGC TCGA-IB-AAUM-01A-11D-A377-08 IZUMO1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466189.1 1 0 0 13 284 0 51 0 6.774520e-03 0 3 0 51 2 0 0 0 0 0 2 1 0.999564 13 284 0 50 2 0 0 0 0 51 2 -3.221883 1 1 0 0 1 1 2 3 2.016145 0 0.080000 2.040000 0.091627 0.990000 0.650000 1.000000 1.000000 0.956904 0.990000 1 0.880000 1.000000 ZNF544 27300 broad.mit.edu 37 19 58773981 58773981 + Nonsense_Mutation SNP C C G TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr19:58773981C>G ENST00000596652.1 + 6 2243 c.2009C>G c.(2008-2010)tCa>tGa p.S670* ZNF544_ENST00000600220.1_Nonsense_Mutation_p.S642*|ZNF544_ENST00000596929.1_Intron|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000600044.1_Nonsense_Mutation_p.S642*|ZNF544_ENST00000269829.4_Nonsense_Mutation_p.S670*|ZNF544_ENST00000415203.2_Nonsense_Mutation_p.S642*|ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000599953.1_Nonsense_Mutation_p.S528*|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000595981.1_Intron Q6NX49 ZN544_HUMAN zinc finger protein 544 18 all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156) AAAGCCTTTTCAGGGAGCTCT 0.453000 0 SO:0001587 stop_gained ENST00000596652.1 0 1 hg19 CCDS12973.1 . . . . . . . . . . C 37.000000 6.545208 0.976540 . . ENSG00000198131 ENST00000269829;ENST00000415203;ENST00000441758 . . . 2.940000 -1.630000 0.083450 . . . . . . . . . . . 0.188730 N 0.999988 . . . . . . . . . . 0.45353 T 0.12 . 8.056500 0.306080 0.1591:0.4408:0.4:0.0 . . . . X 670;642;222 . ENSP00000269829:S670X S + 2 0 ZNF544 63465793 0 0.058580 0 0.037020 3.920000e-01 0.305060 -2.916000 0.006960 -0.330000 0.085140 0.563000 0.778840 TCA TCGA-IB-AAUM-01A-11D-A377-08 ZNF544-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466754.1 0 0 0 10 692 0 237 1 4.828061e-02 2 20 0 237 2 0 0 0 0 0 2 1 0.996745 9 686 0 237 2 0 0 0 0 237 2 -3.078061 1 1 0 0 1 1 2 3 2.012541 0 0.080000 2.040000 0.090909 0.410000 0.190000 1.000000 0.350000 0.513031 0.410000 0 0.280000 1.000000 AMPD1 270 broad.mit.edu 37 1 115217379 115217379 + Missense_Mutation SNP T T A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr1:115217379T>A ENST00000520113.2 - 13 1908 c.1893A>T c.(1891-1893)ttA>ttT p.L631F AMPD1_ENST00000353928.6_Missense_Mutation_p.L598F|AMPD1_ENST00000369538.3_Missense_Mutation_p.L627F P23109 AMPD1_HUMAN adenosine monophosphate deaminase 1 p.L598F(2)|p.L631F(1) 45 all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211) all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05) Adenosine monophosphate(DB00131) TCACCTTTTTTAAATTTAGGC 0.418000 3 Substitution - Missense(3) SO:0001583 missense ENST00000520113.2 1 1 hg19 CCDS876.2 . . . . . . . . . . T 18.120000 3.552218 0.653110 2.27E-4 0.0 ENSG00000116748 ENST00000520113;ENST00000369538;ENST00000353928 D;D;D 0.88046 -2.33;-2.33;-2.33 5.990000 3.680000 0.422160 Adenosine/AMP deaminase (1); 0.000000 0.85682 D 0.000000 D 0.92964 0.7761 H 0.95224 3.64 0.807220 D 1.000000 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.92592 0.6084 10 0.87932 D 0 -11.4622 6.261100 0.209010 0.0:0.2024:0.1353:0.6624 . 627;598 Q5TF02;P23109 .;AMPD1_HUMAN F 631;627;598 ENSP00000430075:L631F;ENSP00000358551:L627F;ENSP00000316520:L598F ENSP00000316520:L598F L - 3 2 AMPD1 115018902 1 0.714170 1 0.803570 7.700000e-01 0.436240 0.599000 0.240890 1.100000 0.415170 0.533000 0.621200 TTA TCGA-IB-AAUM-01A-11D-A377-08 AMPD1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000032860.4 0 0 0 10 310 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 0.997000 10 310 0 69 2 0 0 0 0 69 2 -10.785210 1 1 121412 19 46 1 0 1 1 1.983845 0 0.080000 2.040000 0.069579 0.770000 0.400000 1.000000 1.000000 0.776424 0.770000 0 0.560000 1.000000 FLG 2312 broad.mit.edu 37 1 152282688 152282688 + Silent SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr1:152282688C>T ENST00000368799.1 - 3 4709 c.4674G>A c.(4672-4674)ggG>ggA p.G1558G FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA NM_002016.1 NP_002007.1 P20930 FILA_HUMAN filaggrin 424 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) GGTGACGTGACCCTGAGTGCC 0.592000 Ichthyosis 0 SO:0001819 synonymous_variant Familial Cancer Database X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris ENST00000368799.1 1 1 hg19 CCDS30860.1 TCGA-IB-AAUM-01A-11D-A377-08 FLG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033742.1 1 0 0 60 1268 0 365 0 0 0 0 365 2 0 0 0 0 0 2 1 1.000000 58 1241 0 364 2 0 0 0 0 365 2 -6.047627 1 1 0 0 1 1 3 4 2.186804 1 0.080000 2.040000 0.148148 0.990000 0.940000 1.000000 1.000000 0.996667 0.990000 1 0.990000 1.000000 SNRPE 6635 broad.mit.edu 37 1 203831342 203831342 + Missense_Mutation SNP T T A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr1:203831342T>A ENST00000414487.2 + 2 118 c.73T>A c.(73-75)Tta>Ata p.L25I SNRPE_ENST00000483099.1_3'UTR|SNRPE_ENST00000367208.1_5'Flank NM_003094.2 NP_003085.1 P62304 RUXE_HUMAN small nuclear ribonucleoprotein polypeptide E 5 all_cancers(21;0.103) BRCA - Breast invasive adenocarcinoma(75;0.109) CTTCAGATACTTACAAAATGT 0.403000 Ovarian(83;324 1318 17952 32395 39614) 0 SO:0001583 missense ENST00000414487.2 1 1 hg19 CCDS30979.1 . . . . . . . . . . T 24.200000 4.501065 0.851760 . . ENSG00000182004 ENST00000414487 T 0.59772 0.24 5.250000 1.230000 0.212490 Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1); 0.000000 0.64402 D 0.000001 T 0.68044 0.2958 . . . 0.807220 D 1.000000 D 0.63880 0.993 D 0.64506 0.926 T 0.66917 -0.5802 9 0.87932 D 0 . 6.643600 0.229230 0.0:0.5457:0.0:0.4543 . 25 P62304 RUXE_HUMAN I 25 ENSP00000400591:L25I ENSP00000400591:L25I L + 1 2 SNRPE 202097965 1 0.714170 1 0.803570 9.900000e-01 0.784780 1.606000 0.368260 0.394000 0.252300 0.402000 0.269720 TTA TCGA-IB-AAUM-01A-11D-A377-08 SNRPE-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087703.1 0 0 0 14 358 0 80 1 9.946299e-01 22 201 0 80 2 0 0 0 0 0 2 1 0.999758 13 357 0 80 2 0 0 0 0 80 2 -3.725384 1 1 0 0 1 1 4 5 2.190197 1 0.080000 2.040000 0.162418 0.990000 0.620000 1.000000 1.000000 0.940842 0.990000 1 0.830000 1.000000 LPHN2 23266 broad.mit.edu 37 1 82421570 82421570 + Missense_Mutation SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr1:82421570G>A ENST00000370728.1 + 13 2476 c.1831G>A c.(1831-1833)Gac>Aac p.D611N LPHN2_ENST00000370717.2_Missense_Mutation_p.D611N|LPHN2_ENST00000359929.3_Missense_Mutation_p.D598N|LPHN2_ENST00000370721.1_Missense_Mutation_p.D536N|LPHN2_ENST00000335786.5_Missense_Mutation_p.D611N|LPHN2_ENST00000469377.2_Intron|LPHN2_ENST00000370725.1_Missense_Mutation_p.D611N|LPHN2_ENST00000271029.4_Missense_Mutation_p.D611N|LPHN2_ENST00000394879.1_Missense_Mutation_p.D598N|LPHN2_ENST00000370723.1_Missense_Mutation_p.D598N|LPHN2_ENST00000370715.1_Missense_Mutation_p.D598N|LPHN2_ENST00000370713.1_Missense_Mutation_p.D598N|LPHN2_ENST00000370727.1_Missense_Mutation_p.D611N|LPHN2_ENST00000319517.6_Missense_Mutation_p.D598N|LPHN2_ENST00000370730.1_Missense_Mutation_p.D611N O95490 LPHN2_HUMAN latrophilin 2 119 GGCAATTGTTGACACAGTGGA 0.358000 0 SO:0001583 missense ENST00000370728.1 1 1 hg19 . . . . . . . . . . G 19.100000 3.761933 0.697630 . . ENSG00000117114 ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000370715;ENST00000370713;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786 T;T;T;T;T;T;T;T;T;T;T;T;T;T 0.08984 3.03;3.03;3.03;3.03;3.03;3.03;3.03;3.03;3.03;3.03;3.03;3.03;3.03;3.03 5.620000 5.620000 0.858410 . 0.000000 0.85682 D 0.000000 T 0.18173 0.0436 L 0.60455 1.87 0.807220 D 1.000000 P;D;D 0.71674 0.837;0.998;0.969 P;D;P 0.65987 0.535;0.94;0.709 T 0.00394 -1.1767 10 0.45353 T 0.12 . 19.654800 0.958320 0.0:0.0:1.0:0.0 . 598;598;598 O95490-3;O95490-4;O95490-2 .;.;. N 536;611;611;611;611;598;598;598;598;598;611;598;611;611 ENSP00000359756:D536N;ENSP00000359763:D611N;ENSP00000359765:D611N;ENSP00000359762:D611N;ENSP00000359760:D611N;ENSP00000359758:D598N;ENSP00000353006:D598N;ENSP00000359750:D598N;ENSP00000359748:D598N;ENSP00000322270:D598N;ENSP00000359752:D611N;ENSP00000378344:D598N;ENSP00000271029:D611N;ENSP00000337306:D611N ENSP00000271029:D611N D + 1 0 LPHN2 82194158 1 0.714170 1 0.803570 9.740000e-01 0.676020 9.476000 0.978230 2.648000 0.898790 0.467000 0.429560 GAC TCGA-IB-AAUM-01A-11D-A377-08 LPHN2-007 KNOWN non_canonical_conserved|not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000027188.1 1 0 0 20 321 0 105 0 4.704669e-01 0 26 0 105 2 0 0 0 0 0 2 1 0.999995 20 315 0 105 2 0 0 0 0 105 2 -3.222668 1 1 0 0 1 0 1 1 1.974596 0 0.080000 2.040000 0.067315 0.990000 0.880000 1.000000 1.000000 0.993056 0.990000 1 0.990000 1.000000 JAM2 58494 broad.mit.edu 37 21 27066110 27066110 + Missense_Mutation SNP G G T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr21:27066110G>T ENST00000480456.1 + 4 834 c.284G>T c.(283-285)cGg>cTg p.R95L JAM2_ENST00000400532.1_Missense_Mutation_p.R95L|JAM2_ENST00000425221.2_Missense_Mutation_p.R59L|JAM2_ENST00000312957.5_Missense_Mutation_p.R95L NM_001270407.1|NM_021219.3 NP_001257336.1|NP_067042.1 P57087 JAM2_HUMAN junctional adhesion molecule 2 19 TTCAATATCCGGATCAAAAAT 0.378000 0 SO:0001583 missense ENST00000480456.1 1 1 hg19 CCDS42911.1 . . . . . . . . . . G 19.310000 3.802133 0.706820 . . ENSG00000154721 ENST00000480456;ENST00000400533;ENST00000400532;ENST00000400537;ENST00000312957;ENST00000425221 T;T;T;T 0.64803 -0.12;-0.12;-0.12;-0.12 5.560000 5.560000 0.838230 Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.122923 0.52532 D 0.000074 T 0.69115 0.3075 L 0.47716 1.5 0.360130 D 0.838181 D;D;D;D;D 0.64830 0.983;0.994;0.994;0.992;0.987 P;D;D;P;P 0.65233 0.866;0.933;0.933;0.9;0.9 T 0.73078 -0.4096 10 0.44086 T 0.13 . 10.280800 0.435390 0.0869:0.0:0.9131:0.0 . 59;95;95;95;95 B4DGT9;A8MQ45;A8MXS1;A8MTB0;P57087 .;.;.;.;JAM2_HUMAN L 95;95;95;95;95;59 ENSP00000420419:R95L;ENSP00000383376:R95L;ENSP00000318416:R95L;ENSP00000392611:R59L ENSP00000318416:R95L R + 2 0 JAM2 25987981 9.780000e-01 0.343610 1 0.803570 8.700000e-01 0.499360 4.018000 0.571740 2.890000 0.991280 0.655000 0.942530 CGG TCGA-IB-AAUM-01A-11D-A377-08 JAM2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000171347.1 1 0 0 9 230 0 66 0 4.709052e-01 0 39 0 66 2 0 0 0 0 0 2 1 0.994256 9 228 0 66 2 0 0 0 0 66 2 -2.725326 1 1 0 0 1 0 1 1 1.980546 0 0.080000 2.040000 0.068826 0.920000 0.460000 1.000000 1.000000 0.863201 0.920000 1 0.660000 1.000000 HMGXB4 10042 broad.mit.edu 37 22 35660888 35660888 + Silent SNP G G A rs148445726 TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr22:35660888G>A ENST00000216106.5 + 5 635 c.507G>A c.(505-507)tcG>tcA p.S169S HMGXB4_ENST00000444518.2_Silent_p.S60S NM_001003681.2 NP_001003681.1 Q9UGU5 HMGX4_HUMAN HMG box domain containing 4 19 CCCACAAATCGAAAAAAATGA 0.463000 0 SO:0001819 synonymous_variant ENST00000216106.5 1 1 hg19 CCDS33641.1 TCGA-IB-AAUM-01A-11D-A377-08 HMGXB4-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000318104.2 0 0 0 16 411 0 133 1 1.197135e-01 2 13 0 133 2 0 0 0 0 0 2 1 0.999926 16 403 0 133 2 0 0 0 0 133 2 -3.073026 1 1 121412 3 37 1 0 1 1 1.992321 0 0.080000 2.040000 0.071832 0.920000 0.550000 1.000000 1.000000 0.883516 0.920000 1 0.720000 1.000000 ZAP70 7535 broad.mit.edu 37 2 98349783 98349783 + Missense_Mutation SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr2:98349783G>A ENST00000264972.5 + 7 1029 c.814G>A c.(814-816)Gcc>Acc p.A272T ZAP70_ENST00000451498.2_5'Flank|ZAP70_ENST00000463643.1_3'UTR|ZAP70_ENST00000442208.1_Missense_Mutation_p.A146T NM_001079.3 NP_001070.2 P43403 ZAP70_HUMAN zeta-chain (TCR) associated protein kinase 70kDa 29 CACACTCCCAGCCCACCCATC 0.706000 0 SO:0001583 missense ENST00000264972.5 0 1 hg19 CCDS33254.1 . . . . . . . . . . G 10.980000 1.504992 0.269490 . . ENSG00000115085 ENST00000264972;ENST00000442208 T;T 0.72615 -0.67;-0.67 5.360000 4.470000 0.543850 . 0.582850 0.15303 N 0.269546 T 0.55130 0.1901 N 0.21448 0.665 0.342490 D 0.678521 B;B 0.13145 0.007;0.003 B;B 0.17433 0.018;0.002 T 0.58222 -0.7674 10 0.23891 T 0.37 . 10.219200 0.431880 0.0926:0.0:0.9074:0.0 . 146;272 P43403-3;P43403 .;ZAP70_HUMAN T 272;146 ENSP00000264972:A272T;ENSP00000411141:A146T ENSP00000264972:A272T A + 1 0 ZAP70 97716215 9.520000e-01 0.324450 9.970000e-01 0.539660 4.870000e-01 0.333710 2.503000 0.454070 1.384000 0.464240 0.655000 0.942530 GCC TCGA-IB-AAUM-01A-11D-A377-08 ZAP70-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000329278.1 1 0 0 9 113 0 19 0 1.916094e-01 0 10 0 19 2 0 0 0 0 0 2 1 0.994152 9 110 0 19 2 0 0 0 0 19 2 -13.692320 1 1 0 0 1 1 2 3 2.005760 0 0.080000 2.040000 0.089109 0.990000 0.920000 1.000000 1.000000 0.994581 0.990000 1 0.990000 1.000000 CCDC80 151887 broad.mit.edu 37 3 112324383 112324383 + Missense_Mutation SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr3:112324383G>A ENST00000206423.3 - 8 3687 c.2734C>T c.(2734-2736)Cgc>Tgc p.R912C CCDC80_ENST00000439685.2_Missense_Mutation_p.R912C NM_199511.1|NM_199512.1 NP_955805.1|NP_955806.1 Q76M96 CCD80_HUMAN coiled-coil domain containing 80 51 TCTGGGCAGCGCATCCCCAGT 0.473000 0 SO:0001583 missense ENST00000206423.3 0 1 hg19 CCDS2968.1 . . . . . . . . . . G 20.500000 4.003686 0.749320 . . ENSG00000091986 ENST00000206423;ENST00000439685;ENST00000444594;ENST00000479368 T;T;T 0.52754 0.65;0.65;0.81 5.830000 4.870000 0.633300 . 0.099290 0.64402 D 0.000001 T 0.56978 0.2022 L 0.27053 0.805 0.807220 D 1.000000 D;D 0.89917 1.0;1.0 D;D 0.76575 0.988;0.973 T 0.61038 -0.7143 10 0.87932 D 0 -11.0485 16.814200 0.857290 0.0:0.0:0.8076:0.1924 . 923;912 Q76M96-2;Q76M96 .;CCD80_HUMAN C 912;912;513;190 ENSP00000206423:R912C;ENSP00000411814:R912C;ENSP00000418188:R190C ENSP00000206423:R912C R - 1 0 CCDC80 113807073 1 0.714170 1 0.803570 9.980000e-01 0.957120 5.439000 0.665560 2.753000 0.944830 0.585000 0.799380 CGC TCGA-IB-AAUM-01A-11D-A377-08 CCDC80-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354219.1 0 0 0 5 281 1 81 0 5.793511e-02 0 414 1 81 17 0 0 0 0 0 2 0 0.042690 5 278 1 81 13 0 0 0 1 81 2 -2.608490 1 1 121412 1 36 1 0 1 1 1.987942 0 0.080000 2.040000 0.070707 0.450000 0.170000 0.900000 0.420000 0.490193 0.450000 0 0.290000 0.680000 CNTN6 27255 broad.mit.edu 37 3 1415695 1415695 + Missense_Mutation SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr3:1415695G>A ENST00000446702.2 + 16 2660 c.2033G>A c.(2032-2034)gGc>gAc p.G678D CNTN6_ENST00000350110.2_Missense_Mutation_p.G678D|CNTN6_ENST00000539053.1_Missense_Mutation_p.G606D Q9UQ52 CNTN6_HUMAN contactin 6 p.G678D(1) 90 all_cancers(2;0.000164)|all_epithelial(2;0.107) GTTGTTGCCGGCAACAGCATT 0.383000 1 Substitution - Missense(1) SO:0001583 missense ENST00000446702.2 0 1 hg19 CCDS2557.1 . . . . . . . . . . G 14.440000 2.535149 0.450730 . . ENSG00000134115 ENST00000446702;ENST00000539053;ENST00000350110 T;T;T 0.56776 0.44;0.44;0.44 4.840000 3.890000 0.449020 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.107766 0.41823 D 0.000811 T 0.50017 0.1591 L 0.29908 0.895 0.193000 N 0.999973 D 0.54772 0.968 P 0.54629 0.757 T 0.36432 -0.9748 10 0.42905 T 0.14 . 10.048500 0.422010 0.0:0.1484:0.6981:0.1535 . 678 Q9UQ52 CNTN6_HUMAN D 678;606;678 ENSP00000407822:G678D;ENSP00000442791:G606D;ENSP00000341882:G678D ENSP00000341882:G678D G + 2 0 CNTN6 1390695 9.380000e-01 0.318260 9.990000e-01 0.593770 9.850000e-01 0.738300 2.160000 0.423480 2.379000 0.811260 0.655000 0.942530 GGC TCGA-IB-AAUM-01A-11D-A377-08 CNTN6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000239235.2 0 0 0 5 385 0 94 0 0 0 0 94 2 0 0 0 0 0 2 0 0.017065 5 377 1 94 15 0 0 0 0 94 2 -2.718292 1 1 121412 1 28 1 0 1 1 1.992217 0 0.080000 2.040000 0.071832 0.340000 0.120000 0.680000 0.310000 0.366685 0.340000 0 0.210000 0.500000 XIRP1 165904 broad.mit.edu 37 3 39227663 39227663 + Missense_Mutation SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr3:39227663C>T ENST00000340369.3 - 2 3502 c.3274G>A c.(3274-3276)Ggt>Agt p.G1092S XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Missense_Mutation_p.G1092S NM_194293.2 NP_919269.2 Q702N8 XIRP1_HUMAN xin actin-binding repeat containing 1 71 TTCCGAAGACCGTCCTGGATG 0.602000 0 SO:0001583 missense ENST00000340369.3 1 1 hg19 CCDS2683.1 . . . . . . . . . . C 1.886000 -0.456684 0.045400 . . ENSG00000168334 ENST00000396251;ENST00000340369 T;T 0.05580 3.42;3.74 4.720000 0.745000 0.183590 . 7.244150 0.01698 U 0.027049 T 0.06050 0.0157 L 0.47716 1.5 0.093100 N 1.000000 B;B 0.24882 0.113;0.062 B;B 0.13407 0.004;0.009 T 0.37709 -0.9694 10 0.09084 T 0.74 . 3.123000 0.063970 0.1423:0.557:0.1381:0.1626 . 1092;1092 Q702N8;Q702N8-2 XIRP1_HUMAN;. S 1092 ENSP00000379550:G1092S;ENSP00000343140:G1092S ENSP00000343140:G1092S G - 1 0 XIRP1 39202667 0 0.058580 0 0.037020 1.110000e-01 0.196430 0.016000 0.133770 0.030000 0.153790 0.650000 0.862430 GGT TCGA-IB-AAUM-01A-11D-A377-08 XIRP1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000254065.1 0 0 0 14 332 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 0.999749 14 328 0 71 2 0 0 0 0 73 2 -2.985372 1 1 121412 1 28 1 0 1 1 1.992217 0 0.080000 2.040000 0.071832 0.990000 0.570000 1.000000 1.000000 0.911982 0.990000 1 0.760000 1.000000 PI16 221476 broad.mit.edu 37 6 36930968 36930968 + Missense_Mutation SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr6:36930968G>A ENST00000373674.3 + 5 1178 c.850G>A c.(850-852)Gta>Ata p.V284I PI16_ENST00000491324.1_Intron NM_001199159.1|NM_153370.2 NP_001186088.1|NP_699201.2 Q6UXB8 PI16_HUMAN peptidase inhibitor 16 p.V284I(2) 30 TCCACCTTGCGTAACAACTGA 0.567000 2 Substitution - Missense(2) SO:0001583 missense ENST00000373674.3 1 1 hg19 CCDS34440.1 . . . . . . . . . . G 10.020000 1.235618 0.226260 . . ENSG00000164530 ENST00000373674;ENST00000539035 T 0.06933 3.24 5.800000 -7.550000 0.013270 . 1.505140 0.04117 N 0.315674 T 0.00875 0.0029 N 0.08118 0 0.093100 N 0.999999 B 0.30211 0.273 B 0.17722 0.019 T 0.41052 -0.9530 10 0.66056 D 0.02 . 1.694900 0.028590 0.1826:0.2985:0.3241:0.1948 . 284 Q6UXB8 PI16_HUMAN I 284;136 ENSP00000362778:V284I ENSP00000362778:V284I V + 1 0 PI16 37038946 0 0.058580 0 0.037020 8.000000e-03 0.064300 -0.569000 0.059020 -1.245000 0.025130 -0.127000 0.149210 GTA TCGA-IB-AAUM-01A-11D-A377-08 PI16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040380.1 1 0 0 24 286 0 85 0 2.198886e-01 0 11 0 85 2 0 0 0 0 0 2 1 1.000000 24 285 0 83 2 0 0 0 0 85 2 -3.318783 1 1 121412 5 46 1 0 1 1 1.986508 0 0.080000 2.040000 0.070331 0.990000 0.990000 1.000000 1.000000 0.999701 0.990000 1 0.990000 1.000000 RPP40 10799 broad.mit.edu 37 6 5004223 5004223 + Missense_Mutation SNP C C G TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr6:5004223C>G ENST00000380051.2 - 1 58 c.14G>C c.(13-15)cGc>cCc p.R5P RPP40_ENST00000464646.1_5'Flank|RPP40_ENST00000319533.5_Missense_Mutation_p.R5P NM_006638.2 NP_006629.2 O75818 RPP40_HUMAN ribonuclease P/MRP 40kDa subunit 14 Ovarian(93;0.11) all_hematologic(90;0.0895) CCGAAGCCGGCGCAGCGTGGC 0.697000 OREG0017160 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000380051.2 1 1 hg19 CCDS34333.1 . . . . . . . . . . C 15.950000 2.984604 0.539340 . . ENSG00000124787 ENST00000380051;ENST00000319533 T;T 0.51071 0.81;0.72 4.530000 4.530000 0.556030 . 0.509013 0.19657 N 0.109065 T 0.41026 0.1141 L 0.37630 1.12 0.807220 D 1.000000 D;P 0.53885 0.963;0.938 P;B 0.52454 0.699;0.422 T 0.36016 -0.9765 10 0.52906 T 0.07 -11.2996 16.002400 0.803060 0.0:1.0:0.0:0.0 . 5;5 O75818-2;O75818 .;RPP40_HUMAN P 5 ENSP00000369391:R5P;ENSP00000317998:R5P ENSP00000317998:R5P R - 2 0 RPP40 4949222 8.460000e-01 0.295900 8.900000e-02 0.207740 9.000000e-03 0.068530 1.435000 0.349690 2.338000 0.795400 0.557000 0.710580 CGC TCGA-IB-AAUM-01A-11D-A377-08 RPP40-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039733.2 1 0 0 16 214 0 31 1 1.397310e-01 3 6 0 31 2 0 0 0 0 0 2 1 0.999934 16 210 0 29 2 0 0 0 0 31 2 -3.221823 1 1 0 0 1 0 1 1 1.979522 0 0.080000 2.040000 0.068826 0.990000 0.940000 1.000000 1.000000 0.996132 0.990000 1 0.990000 1.000000 KEL 3792 broad.mit.edu 37 7 142641797 142641797 + Missense_Mutation SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr7:142641797G>A ENST00000355265.2 - 12 1820 c.1346C>T c.(1345-1347)gCc>gTc p.A449V KEL_ENST00000479768.2_5'Flank NM_000420.2 NP_000411.1 P23276 KELL_HUMAN Kell blood group, metallo-endopeptidase 60 Melanoma(164;0.059) AGTGATGAGGGCATCCCGGAT 0.617000 0 SO:0001583 missense ENST00000355265.2 0 1 hg19 CCDS34766.1 . . . . . . . . . . G 11.470000 1.648408 0.293360 . . ENSG00000197993 ENST00000355265 T 0.78924 -1.22 4.870000 3.990000 0.463010 Peptidase M13 (1); 0.518330 0.17628 N 0.167488 T 0.75162 0.3812 M 0.76328 2.33 0.296590 N 0.843357 P 0.38617 0.64 B 0.38616 0.277 T 0.71137 -0.4680 10 0.34782 T 0.22 -7.2386 8.948600 0.357730 0.1008:0.0:0.8992:0.0 . 449 P23276 KELL_HUMAN V 449 ENSP00000347409:A449V ENSP00000347409:A449V A - 2 0 KEL 142351919 7.210000e-01 0.280070 7.000000e-01 0.303050 4.200000e-02 0.138120 3.694000 0.547420 1.297000 0.447610 -0.373000 0.071310 GCC TCGA-IB-AAUM-01A-11D-A377-08 KEL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347671.2 0 0 0 4 196 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 0.883926 4 190 0 45 2 0 0 0 0 45 2 -3.218095 1 1 0 0 1 1 2 3 2.014320 0 0.080000 2.040000 0.091268 0.640000 0.200000 1.000000 1.000000 0.668295 0.640000 0 0.360000 1.000000 PDE1C 5137 broad.mit.edu 37 7 31793127 31793127 + Silent SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr7:31793127G>A ENST00000396191.1 - 18 2456 c.2001C>T c.(1999-2001)taC>taT p.Y667Y PDE1C_ENST00000396193.1_Silent_p.Y727Y|PDE1C_ENST00000321453.7_Silent_p.Y667Y NM_001191057.1 NP_001177986.1 Q14123 PDE1C_HUMAN phosphodiesterase 1C, calmodulin-dependent 70kDa 81 GBM - Glioblastoma multiforme(11;0.216) Caffeine(DB00201) AGCTAGATGCGTAAGCAGGGC 0.478000 0 SO:0001819 synonymous_variant ENST00000396191.1 0 1 hg19 CCDS55099.1 TCGA-IB-AAUM-01A-11D-A377-08 PDE1C-006 KNOWN alternative_5_UTR|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000328458.1 0 0 0 5 375 0 132 0 0 0 0 132 2 0 0 0 0 0 2 1 0.936628 5 372 0 132 2 0 0 0 0 132 2 -2.550590 1 1 116166 15 44 1 1 2 3 2.002752 0 0.080000 2.040000 0.088387 0.400000 0.140000 1.000000 0.320000 0.489206 0.400000 0 0.240000 1.000000 TYW1 55253 broad.mit.edu 37 7 66479413 66479413 + Silent SNP T T C rs145686658 by1000genomes TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr7:66479413T>C ENST00000359626.5 + 5 599 c.435T>C c.(433-435)acT>acC p.T145T NM_018264.2 NP_060734.2 Q9NV66 TYW1_HUMAN tRNA-yW synthesizing protein 1 homolog (S. cerevisiae) p.T145T(1) 46 Lung NSC(55;0.0846)|all_lung(88;0.183) GCCTACCAACTGAAAGTGCAG 0.428000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000359626.5 0 1 hg19 CCDS5538.1 TCGA-IB-AAUM-01A-11D-A377-08 TYW1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251932.2 0 0 0 6 609 0 148 0 2.134904e-02 0 19 0 148 2 0 0 0 0 0 2 1 0.962914 6 597 0 148 2 0 0 0 0 148 2 -1.819237 0 1 121412 80 43 1 1 2 3 2.004904 0 0.080000 2.040000 0.089109 0.290000 0.110000 1.000000 0.250000 0.410555 0.290000 0 0.180000 1.000000 AZGP1 563 broad.mit.edu 37 7 99565782 99565782 + Silent SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr7:99565782C>T ENST00000292401.4 - 3 745 c.609G>A c.(607-609)cgG>cgA p.R203R AZGP1_ENST00000411734.1_Silent_p.R200R|AZGP1_ENST00000483612.1_5'Flank NM_001185.3 NP_001176.1 P25311 ZA2G_HUMAN alpha-2-glycoprotein 1, zinc-binding 16 Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323) GAGTACCTTGCCGGTCCAGGA 0.532000 0 SO:0001819 synonymous_variant ENST00000292401.4 0 1 hg19 CCDS5680.1 TCGA-IB-AAUM-01A-11D-A377-08 AZGP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059387.4 0 0 0 5 279 0 83 0 9.996924e-01 1 1173 0 83 2 0 0 0 0 0 2 1 0.937504 5 278 0 81 2 0 0 0 0 83 2 -2.624971 1 1 121412 3 35 1 1 2 3 2.004904 0 0.080000 2.040000 0.089109 0.530000 0.190000 1.000000 1.000000 0.596286 0.530000 0 0.320000 1.000000 ZFAT 57623 broad.mit.edu 37 8 135614834 135614834 + Silent SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr8:135614834C>T ENST00000377838.3 - 6 1302 c.1128G>A c.(1126-1128)gcG>gcA p.A376A ZFAT_ENST00000520214.1_Silent_p.A364A|ZFAT_ENST00000429442.2_Silent_p.A364A|ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000523399.1_Silent_p.A314A|ZFAT_ENST00000520356.1_Silent_p.A364A|ZFAT_ENST00000520727.1_Silent_p.A364A NM_001174157.1|NM_020863.3 NP_001167628.1|NP_065914.2 Q9P243 ZFAT_HUMAN zinc finger and AT hook domain containing 54 all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.0432) GTGGGTCATGCGCGTCTCGGA 0.552000 0 SO:0001819 synonymous_variant ENST00000377838.3 0 1 hg19 CCDS47924.1 TCGA-IB-AAUM-01A-11D-A377-08 ZFAT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378272.1 0 0 0 5 383 0 89 0 2.643777e-03 0 5 0 89 2 0 0 0 0 0 2 1 0.937076 6 380 0 88 2 0 0 0 0 89 2 -2.073560 0 1 121082 2 34 1 1 2 3 1.999017 0 0.080000 2.040000 0.087664 0.380000 0.130000 1.000000 0.320000 0.475467 0.380000 0 0.230000 0.930000 RB1CC1 9821 broad.mit.edu 37 8 53555118 53555118 + Missense_Mutation SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr8:53555118C>T ENST00000025008.5 - 18 4653 c.4130G>A c.(4129-4131)cGt>cAt p.R1377H RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Missense_Mutation_p.R1377H|RB1CC1_ENST00000435644.2_Missense_Mutation_p.R1377H NM_014781.4 NP_055596.3 Q8TDY2 RBCC1_HUMAN RB1-inducible coiled-coil 1 60 all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023) CTCAAGCAAACGAGCTCGATC 0.358000 GBM(180;1701 2102 13475 42023 52570) 0 SO:0001583 missense ENST00000025008.5 1 1 hg19 CCDS34892.1 . . . . . . . . . . C 27.400000 4.831119 0.910360 . . ENSG00000023287 ENST00000025008;ENST00000435644;ENST00000539297 T;T;T 0.15487 2.42;2.42;2.42 5.610000 5.610000 0.854770 . 0.053357 0.85682 D 0.000000 T 0.30823 0.0777 L 0.32530 0.975 0.441040 D 0.996878 D;D 0.76494 0.999;0.998 P;P 0.61592 0.891;0.781 T 0.01460 -1.1349 10 0.72032 D 0.01 -13.615 18.620100 0.913180 0.0:1.0:0.0:0.0 . 1377;1377 Q8TDY2-2;Q8TDY2 .;RBCC1_HUMAN H 1377 ENSP00000025008:R1377H;ENSP00000396067:R1377H;ENSP00000445960:R1377H ENSP00000025008:R1377H R - 2 0 RB1CC1 53717671 9.980000e-01 0.408360 9.940000e-01 0.499520 9.980000e-01 0.957120 3.761000 0.552420 2.632000 0.892090 0.655000 0.942530 CGT TCGA-IB-AAUM-01A-11D-A377-08 RB1CC1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000378011.1 1 0 0 16 344 0 121 1 5.132124e-01 2 35 0 121 2 0 0 0 0 0 2 1 0.999933 16 341 0 119 2 0 0 0 0 121 2 -16.928200 1 1 121404 6 37 1 1 2 3 1.999017 0 0.080000 2.040000 0.087664 0.990000 0.680000 1.000000 1.000000 0.962232 0.990000 1 0.900000 1.000000 KCNB2 9312 broad.mit.edu 37 8 73480147 73480147 + Missense_Mutation SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr8:73480147C>T ENST00000523207.1 + 2 766 c.178C>T c.(178-180)Cgc>Tgc p.R60C NM_004770.2 NP_004761.2 Q92953 KCNB2_HUMAN potassium voltage-gated channel, Shab-related subfamily, member 2 85 Breast(64;0.137) Epithelial(68;0.105) Dalfampridine(DB06637) GCCCAGGACGCGCCTGGGGAA 0.542000 0 SO:0001583 missense ENST00000523207.1 1 1 hg19 CCDS6209.1 . . . . . . . . . . C 20.800000 4.048690 0.758460 . . ENSG00000182674 ENST00000523207 T 0.78481 -1.18 5.710000 4.840000 0.625910 BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1); . . . . D 0.90703 0.7083 H 0.95950 3.745 0.807220 D 1.000000 D 0.89917 1.0 D 0.97110 1.0 D 0.91904 0.5534 9 0.87932 D 0 . 9.681300 0.400720 0.1398:0.7897:0.0:0.0705 . 60 Q92953 KCNB2_HUMAN C 60 ENSP00000430846:R60C ENSP00000430846:R60C R + 1 0 KCNB2 73642701 9.960000e-01 0.388240 6.350000e-01 0.293380 9.850000e-01 0.738300 3.471000 0.531070 1.432000 0.473750 0.655000 0.942530 CGC TCGA-IB-AAUM-01A-11D-A377-08 KCNB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378998.1 1 0 0 21 376 0 104 0 0 0 0 104 2 0 0 0 0 0 2 1 0.999997 21 369 0 104 2 0 0 0 0 104 2 -3.077950 1 1 0 0 1 1 2 3 1.999017 0 0.080000 2.040000 0.087664 0.990000 0.870000 1.000000 1.000000 0.992103 0.990000 1 0.990000 1.000000 MPDZ 8777 broad.mit.edu 37 9 13140072 13140072 + Missense_Mutation SNP G G A TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr9:13140072G>A ENST00000319217.7 - 28 4164 c.3917C>T c.(3916-3918)gCc>gTc p.A1306V MPDZ_ENST00000540202.1_5'UTR|MPDZ_ENST00000536827.1_Missense_Mutation_p.A1273V|MPDZ_ENST00000546205.1_Missense_Mutation_p.A1320V|MPDZ_ENST00000447879.1_Missense_Mutation_p.A1273V|MPDZ_ENST00000381022.2_Missense_Mutation_p.A1306V|MPDZ_ENST00000381015.4_Missense_Mutation_p.A1306V|MPDZ_ENST00000538841.1_Missense_Mutation_p.A165V|MPDZ_ENST00000541718.1_Missense_Mutation_p.A1306V NM_001261406.1 NP_001248335.1 O75970 MPDZ_HUMAN multiple PDZ domain protein 61 ACCCATTTCGGCAAAGGCTGA 0.493000 0 SO:0001583 missense ENST00000319217.7 0 1 hg19 . . . . . . . . . . G 10.050000 1.244722 0.227960 . . ENSG00000107186 ENST00000319217;ENST00000541718;ENST00000381022;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205;ENST00000433359 T;T;T;T;T;T;T;T;T;T 0.45276 2.88;2.83;2.83;2.71;2.73;2.74;2.78;2.88;2.88;0.9 5.900000 3.990000 0.463010 . 0.701509 0.12341 N 0.477536 T 0.33614 0.0869 L 0.29908 0.895 0.255140 N 0.987437 B;B;B;B;B 0.28055 0.126;0.019;0.199;0.126;0.199 B;B;B;B;B 0.33620 0.055;0.028;0.167;0.08;0.117 T 0.27806 -1.0063 10 0.28530 T 0.3 . 10.109300 0.425520 0.0648:0.0:0.6902:0.245 . 1273;165;1273;1186;1306 B7ZMI4;B7ZB24;O75970-3;E7EPZ1;O75970-2 .;.;.;.;. V 1306;1306;1306;242;165;1273;1273;1306;1186;1320;128 ENSP00000320006:A1306V;ENSP00000439807:A1306V;ENSP00000370410:A1306V;ENSP00000444230:A242V;ENSP00000444717:A165V;ENSP00000444151:A1273V;ENSP00000415208:A1273V;ENSP00000370403:A1306V;ENSP00000446358:A1320V;ENSP00000389705:A128V ENSP00000320006:A1306V A - 2 0 MPDZ 13130072 9.940000e-01 0.377170 2.390000e-01 0.241220 7.080000e-01 0.408520 1.599000 0.367510 0.765000 0.332210 0.552000 0.689910 GCC TCGA-IB-AAUM-01A-11D-A377-08 MPDZ-001 KNOWN not_organism_supported|basic protein_coding protein_coding OTTHUMT00000055485.2 0 0 0 6 602 0 133 0 8.995884e-03 0 12 0 133 2 0 0 0 0 0 2 1 0.963649 6 594 0 130 2 0 0 0 0 133 2 -1.966308 0 1 0 0 1 0 1 1 1.992647 0 0.080000 2.040000 0.071832 0.250000 0.100000 0.490000 0.240000 0.278327 0.250000 0 0.170000 0.380000 DOLK 22845 broad.mit.edu 37 9 131708515 131708515 + Silent SNP C C T TCGA-IB-AAUM-01A-11D-A377-08 TCGA-IB-AAUM-10A-01D-A37A-08 Untested Somatic Phase_I WXS none Illumina GAIIx b61630e4-5b3e-455b-b6df-ca8b76a678cd 3323a86b-52b7-46b7-aa03-cdfd4a3bb710 g.chr9:131708515C>T ENST00000372586.3 - 1 1383 c.1068G>A c.(1066-1068)cgG>cgA p.R356R NUP188_ENST00000372577.2_5'Flank|RP11-101E3.5_ENST00000482796.1_Intron NM_014908.3 NP_055723.1 Q9UPQ8 DOLK_HUMAN dolichol kinase 11 AGAGCAGTGGCCGGTCAAAGA 0.547000 0 SO:0001819 synonymous_variant ENST00000372586.3 0 1 hg19 CCDS6915.1 TCGA-IB-AAUM-01A-11D-A377-08 DOLK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054515.1 0 0 0 8 720 0 126 0 6.586118e-02 0 33 0 126 2 0 0 0 0 0 2 1 0.988665 7 709 0 118 2 0 0 0 0 126 2 -2.239572 0 1 121412 1 30 1 0 1 1 1.992647 0 0.080000 2.040000 0.071832 0.280000 0.130000 0.500000 0.270000 0.300092 0.280000 0 0.190000 0.390000