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 PLCE1 51196 broad.mit.edu 37 10 95791760 95791760 + Frame_Shift_Del DEL G G - TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr10:95791760delG ENST00000371380.3 + 1 1192 c.957delG c.(955-957)aagfs p.K319fs PLCE1_ENST00000260766.3_Frame_Shift_Del_p.K319fs Q9P212 PLCE1_HUMAN phospholipase C, epsilon 1 8 Colorectal(252;0.0458) AAAGCAAAAAGGAGCGATCCA 0.388000 0 SO:0001589 frameshift_variant ENST00000371380.3 1 1 hg19 CCDS41552.1 TCGA-2L-AAQJ-01A-12D-A397-08 PLCE1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000049469.3 1 0 0 57 448 0 88 0 3.586020e-14 0 1 0 88 2 0 0 0 0 0 0 1 0.997694 66 446 3 89 33 0 0 0 0 0 0 -19.750740 1 1 0 0 1 1 2 3 2.067720 0 0.440000 1.870000 0.441229 0.510000 0.390000 0.650000 0.510000 0.519832 0.510000 0 4.500000e-01 5.800000e-01 SETD1A 9739 broad.mit.edu 37 16 30977566 30977567 + Frame_Shift_Del DEL AG AG - TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr16:30977566_30977567delAG ENST00000262519.8 + 8 3050_3051 c.2364_2365delAG c.(2362-2367)gcaggcfs p.G789fs NM_014712.1 NP_055527.1 O15047 SET1A_HUMAN SET domain containing 1A 59 TCCCGACAGCAGGCACCGTGGG 0.658000 0 SO:0001589 frameshift_variant ENST00000262519.8 1 1 hg19 CCDS32435.1 TCGA-2L-AAQJ-01A-12D-A397-08 SETD1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318244.2 1 0 0 34 145 0 35 1 9.520197e-01 3 21 0 35 2 0 0 0 0 0 0 1 1.000000 35 145 0 35 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 0 0 2.044786 0 0.440000 1.870000 0.437525 0.850000 0.620000 1.000000 1.000000 0.856636 0.850000 1 7.300000e-01 1 GAS7 8522 broad.mit.edu 37 17 9923188 9923189 + Frame_Shift_Ins INS - - A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr17:9923188_9923189insA ENST00000432992.2 - 2 369_370 c.209_210insT c.(208-210)ccgfs p.P70fs GAS7_ENST00000542249.1_Frame_Shift_Ins_p.P6fs|GAS7_ENST00000540214.1_Frame_Shift_Ins_p.P6fs|GAS7_ENST00000585266.1_Frame_Shift_Ins_p.P10fs|GAS7_ENST00000578655.1_5'UTR|GAS7_ENST00000323816.4_Frame_Shift_Ins_p.P10fs|GAS7_ENST00000437099.2_Frame_Shift_Ins_p.P6fs|GAS7_ENST00000579158.1_Frame_Shift_Ins_p.P6fs|GAS7_ENST00000396115.2_Frame_Shift_Ins_p.P6fs NM_201433.1 NP_958839.1 O60861 GAS7_HUMAN growth arrest-specific 7 39 TTTCTTCTCCCGGCGGAGGGGG 0.540000 T MLL AML* Dom yes 17 17p 8522 growth arrest-specific 7 L 0 SO:0001589 frameshift_variant ENST00000432992.2 0 1 hg19 CCDS11152.1 TCGA-2L-AAQJ-01A-12D-A397-08 GAS7-017 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000439883.1 1 0 0 66 234 0 38 0 5.564741e-01 0 8 0 38 2 0 0 0 0 0 0 1 1.000000 71 234 0 38 2 0 0 0 0 0 0 -3.071452 1 1 0 0 1 0 1 1 1.685553 1 0.440000 1.870000 0.282051 0.770000 0.610000 0.930000 0.770000 0.778383 0.770000 0 6.900000e-01 8.600000e-01 HSPA12A 259217 broad.mit.edu 37 10 118434408 118434408 + Missense_Mutation SNP C C T rs41284376 TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr10:118434408C>T ENST00000369209.3 - 12 2016 c.1912G>A c.(1912-1914)Gcc>Acc p.A638T RP11-498B4.5_ENST00000433600.1_RNA NM_025015.2 NP_079291.2 O43301 HS12A_HUMAN heat shock 70kDa protein 12A 32 TCCCTCCGGGCGGGCACCGCA 0.577000 0 SO:0001583 missense ENST00000369209.3 1 0 hg19 CCDS41569.1 11 0.005036630036630037 0 0.0 2 0.0055248618784530384 0 0.0 9 0.011873350923482849 C 0.572 -0.840640 0.02692 5.07E-4 0.004221 ENSG00000165868 ENST00000369209 T 0.41758 0.99 6.02 -1.03 0.10102 . 0.615275 0.18234 N 0.147479 T 0.11367 0.0277 N 0.08118 0 0.19945 N 0.99994 B 0.02656 0.0 B 0.06405 0.002 T 0.23084 -1.0198 10 0.11485 T 0.65 . 5.9177 0.19063 0.0:0.3231:0.366:0.311 rs41284376 638 O43301 HS12A_HUMAN T 638 ENSP00000358211:A638T ENSP00000358211:A638T A - 1 0 HSPA12A 118424398 0.006000 0.16342 0.315000 0.25238 0.186000 0.23388 0.029000 0.13666 -0.068000 0.12953 0.655000 0.94253 GCC TCGA-2L-AAQJ-01A-12D-A397-08 HSPA12A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050530.1 1 0 1 62 237 0 68 0 4.435546e-02 1 1 0 68 2 0 0 0 0 0 2 1 1.000000 60 237 0 67 2 0 0 0 0 0 2 -2.305815 0 1 120908 586 59 1 1 2 3 2.067720 0 0.440000 1.870000 0.441229 0.940000 0.740000 1.000000 1.000000 0.927086 0.940000 1 8.300000e-01 1 MYO3A 53904 broad.mit.edu 37 10 26434386 26434386 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr10:26434386G>A ENST00000265944.5 + 22 2594 c.2428G>A c.(2428-2430)Ggt>Agt p.G810S MYO3A_ENST00000543632.1_Intron NM_017433.4 NP_059129.3 Q8NEV4 MYO3A_HUMAN myosin IIIA 146 AAAATTTGAAGGTAACCTGAA 0.313000 0 SO:0001583 missense ENST00000265944.5 1 1 hg19 CCDS7148.1 . . . . . . . . . . G 17.19 3.325787 0.60743 . . ENSG00000095777 ENST00000265944 T 0.70164 -0.46 5.72 3.72 0.42706 Myosin head, motor domain (2); 0.357715 0.33144 N 0.005222 T 0.48223 0.1488 N 0.11023 0.085 0.80722 D 1 B 0.26547 0.152 B 0.32928 0.155 T 0.44205 -0.9343 10 0.34782 T 0.22 . 11.4508 0.50151 0.1574:0.0:0.8426:0.0 . 810 Q8NEV4 MYO3A_HUMAN S 810 ENSP00000265944:G810S ENSP00000265944:G810S G + 1 0 MYO3A 26474392 1.000000 0.71417 0.957000 0.39632 0.999000 0.98932 5.647000 0.67923 1.276000 0.44395 0.655000 0.94253 GGT TCGA-2L-AAQJ-01A-12D-A397-08 MYO3A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047259.1 1 0 1 22 127 0 27 0 0 0 1 0 27 2 0 0 0 0 0 2 1 0.999999 22 127 0 27 2 0 0 0 0 0 2 -3.169113 1 1 0 0 1 0 0 0 2.040737 0 0.440000 1.870000 0.435028 0.660000 0.430000 0.930000 0.660000 0.679641 0.660000 0 5.400000e-01 8.000000e-01 KIAA1462 57608 broad.mit.edu 37 10 30336573 30336573 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr10:30336573G>A ENST00000375377.1 - 2 270 c.169C>T c.(169-171)Cgt>Tgt p.R57C NM_020848.2 NP_065899.1 Q9P266 JCAD_HUMAN KIAA1462 75 GACGTCTTACGATGTGCGAGG 0.662000 0 SO:0001583 missense ENST00000375377.1 1 1 hg19 CCDS41500.1 . . . . . . . . . . G 14.49 2.551265 0.45383 . . ENSG00000165757 ENST00000375377 T 0.12569 2.67 5.06 1.48 0.22813 . 0.673294 0.14424 N 0.320462 T 0.08088 0.0202 N 0.14661 0.345 0.09310 N 1 D 0.56521 0.976 P 0.44696 0.458 T 0.22626 -1.0211 10 0.56958 D 0.05 -6.0436 4.5512 0.12114 0.0:0.1942:0.1909:0.6149 . 57 Q9P266 K1462_HUMAN C 57 ENSP00000364526:R57C ENSP00000364526:R57C R - 1 0 KIAA1462 30376579 0.000000 0.05858 0.000000 0.03702 0.005000 0.04900 0.567000 0.23608 0.069000 0.16605 0.467000 0.42956 CGT TCGA-2L-AAQJ-01A-12D-A397-08 KIAA1462-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047409.1 1 0 1 55 210 0 71 0 1.145889e-01 0 3 0 71 2 0 0 0 0 0 2 1 1.000000 54 206 0 71 2 0 0 0 0 0 2 -3.668932 1 1 120938 1 31 1 0 0 0 2.040737 0 0.440000 1.870000 0.435028 0.930000 0.720000 1.000000 1.000000 0.918833 0.930000 1 8.200000e-01 1 DYNC2H1 79659 broad.mit.edu 37 11 102980335 102980335 + Missense_Mutation SNP T T C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr11:102980335T>C ENST00000375735.2 + 1 176 c.32T>C c.(31-33)cTc>cCc p.L11P DYNC2H1_ENST00000334267.7_Missense_Mutation_p.L11P|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.L11P NM_001080463.1|NM_001377.2 NP_001073932.1|NP_001368.2 Q8NCM8 DYHC2_HUMAN dynein, cytoplasmic 2, heavy chain 1 33 Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348) GTTCGGAAGCTCTTCATCTTC 0.507000 0 SO:0001583 missense ENST00000375735.2 1 1 hg19 CCDS53701.1 . . . . . . . . . . T 11.60 1.686710 0.29962 . . ENSG00000187240 ENST00000375735;ENST00000334267;ENST00000398093 T;T;T 0.30182 1.67;1.54;1.67 5.63 3.2 0.36748 . 0.568065 0.12492 U 0.464170 T 0.26738 0.0654 L 0.36672 1.1 0.24814 N 0.992625 B;B;B 0.29590 0.25;0.082;0.066 B;B;B 0.37091 0.241;0.05;0.079 T 0.15578 -1.0432 10 0.30854 T 0.27 . 8.7491 0.34605 0.1029:0.0:0.2424:0.6546 . 11;11;11 Q8NCM8-3;Q8NCM8;Q8NCM8-2 .;DYHC2_HUMAN;. P 11 ENSP00000364887:L11P;ENSP00000334021:L11P;ENSP00000381167:L11P ENSP00000334021:L11P L + 2 0 DYNC2H1 102485545 0.140000 0.22579 0.989000 0.46669 0.993000 0.82548 0.695000 0.25527 2.137000 0.66172 0.482000 0.46254 CTC TCGA-2L-AAQJ-01A-12D-A397-08 DYNC2H1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387196.1 1 0 0 10 103 0 24 0 0 0 0 24 2 0 0 0 0 0 2 1 0.997309 10 103 0 24 2 0 0 0 0 0 2 -15.664810 1 1 0 0 1 0 0 0 2.041626 0 0.440000 1.870000 0.435028 0.400000 0.210000 0.670000 0.390000 0.426042 0.400000 0 3.000000e-01 5.400000e-01 ADAMTS15 170689 broad.mit.edu 37 11 130343367 130343367 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr11:130343367C>T ENST00000299164.2 + 8 2504 c.2504C>T c.(2503-2505)cCg>cTg p.P835L NM_139055.2 NP_620686.1 Q8TE58 ATS15_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 15 36 all_hematologic(175;0.0429) Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837) GTGGAGCAGCCGGACGACAGG 0.697000 0 SO:0001583 missense ENST00000299164.2 1 1 hg19 CCDS8488.1 0 0.0 0 0.0 0 0.0 0 0.0 0 0.0 C 11.83 1.754593 0.31046 . . ENSG00000166106 ENST00000299164 T 0.61742 0.08 5.69 4.77 0.60923 . . . . . T 0.35393 0.0930 N 0.08118 0 0.37764 D 0.926416 B 0.25105 0.118 B 0.14578 0.011 T 0.24870 -1.0148 9 0.19147 T 0.46 . 14.1591 0.65434 0.1583:0.8417:0.0:0.0 . 835 Q8TE58 ATS15_HUMAN L 835 ENSP00000299164:P835L ENSP00000299164:P835L P + 2 0 ADAMTS15 129848577 0.000000 0.05858 0.681000 0.30009 0.939000 0.58152 1.050000 0.30404 1.373000 0.46208 0.655000 0.94253 CCG TCGA-2L-AAQJ-01A-12D-A397-08 ADAMTS15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385638.1 0 0 0 112 376 0 117 0 0 0 1 0 117 2 0 0 0 0 0 2 1 1.000000 110 371 0 115 2 0 0 0 0 0 2 -4.375662 1 1 121108 16 45 1 0 0 0 2.059310 0 0.440000 1.870000 0.440000 0.990000 0.870000 1.000000 1.000000 0.983884 0.990000 1 9.500000e-01 1 OR51I1 390063 broad.mit.edu 37 11 5462461 5462461 + Missense_Mutation SNP G G A rs115148889 TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr11:5462461G>A ENST00000380211.1 - 1 283 c.284C>T c.(283-285)gCg>gTg p.A95V HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron NM_001005288.2 NP_001005288.1 Q9H343 O51I1_HUMAN olfactory receptor, family 51, subfamily I, member 1 30 Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675) AGCATTAAACGCAACATGGTT 0.458000 0 SO:0001583 missense ENST00000380211.1 1 1 hg19 CCDS31382.1 . . . . . . . . . . C 14.42 2.529926 0.45073 . . ENSG00000167359 ENST00000317283;ENST00000321307;ENST00000380211 T 0.37235 1.21 5.78 -2.31 0.06765 GPCR, rhodopsin-like superfamily (1); 0.518492 0.17730 N 0.163931 T 0.19366 0.0465 L 0.39898 1.24 0.09310 N 1 B 0.27700 0.186 B 0.19148 0.024 T 0.12708 -1.0537 10 0.62326 D 0.03 . 0.4262 0.00464 0.2041:0.2902:0.1998:0.3058 . 95 Q9H343 O51I1_HUMAN V 80;92;95 ENSP00000369559:A95V ENSP00000348350:A80V A - 2 0 OR51I1 5419037 0.000000 0.05858 0.025000 0.17156 0.074000 0.17049 -2.368000 0.01077 -0.628000 0.05582 -0.231000 0.12243 GCG TCGA-2L-AAQJ-01A-12D-A397-08 OR51I1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000143399.1 1 0 1 52 153 0 60 0 0 0 0 60 2 0 0 0 0 0 2 1 1.000000 51 151 0 60 2 0 0 0 0 0 2 -20.000000 1 1 121408 3 40 1 0 0 0 2.041626 0 0.440000 1.870000 0.435028 0.990000 0.880000 1.000000 1.000000 0.991182 0.990000 1 9.900000e-01 1 OR5J2 282775 broad.mit.edu 37 11 55944377 55944377 + Missense_Mutation SNP C C G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr11:55944377C>G ENST00000312298.1 + 1 284 c.284C>G c.(283-285)tCt>tGt p.S95C NM_001005492.1 NP_001005492.1 Q8NH18 OR5J2_HUMAN olfactory receptor, family 5, subfamily J, member 2 44 Esophageal squamous(21;0.00693) ATTTCTTTCTCTGCTTGCATG 0.458000 0 SO:0001583 missense ENST00000312298.1 0 1 hg19 CCDS31522.1 . . . . . . . . . . C 13.69 2.311684 0.40895 . . ENSG00000174957 ENST00000312298 T 0.00408 7.54 4.67 -0.729 0.11158 GPCR, rhodopsin-like superfamily (1); 0.831860 0.10480 N 0.669723 T 0.00496 0.0016 L 0.46670 1.46 0.09310 N 1 D 0.67145 0.996 P 0.55785 0.784 T 0.53746 -0.8395 10 0.38643 T 0.18 . 6.1701 0.20412 0.1189:0.5225:0.0:0.3586 . 95 Q8NH18 OR5J2_HUMAN C 95 ENSP00000310788:S95C ENSP00000310788:S95C S + 2 0 OR5J2 55700953 0.000000 0.05858 0.000000 0.03702 0.006000 0.05464 -0.352000 0.07701 -0.056000 0.13221 0.584000 0.79450 TCT TCGA-2L-AAQJ-01A-12D-A397-08 OR5J2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391544.1 0 0 0 9 409 0 56 0 0 0 0 56 2 0 0 0 0 0 2 1 0.994269 9 409 0 56 2 0 0 0 0 0 2 -2.407337 0 1 0 0 1 0 0 0 2.041626 0 0.440000 1.870000 0.435028 0.090000 0.040000 0.180000 0.100000 0.106941 0.090000 0 6.000000e-02 1.400000e-01 SYT12 91683 broad.mit.edu 37 11 66807576 66807576 + Nonsense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr11:66807576C>T ENST00000393946.2 + 7 1685 c.523C>T c.(523-525)Cag>Tag p.Q175* SYT12_ENST00000527043.1_Nonsense_Mutation_p.Q175*|SYT12_ENST00000525457.1_Nonsense_Mutation_p.Q175*|SYT12_ENST00000526281.1_3'UTR Q8IV01 SYT12_HUMAN synaptotagmin XII 20 GGCGGTGATGCAGGGCAAGGA 0.632000 Ovarian(65;2862 3307) 0 SO:0001587 stop_gained ENST00000393946.2 0 1 hg19 CCDS8154.1 . . . . . . . . . . C 22.3 4.273932 0.80580 . . ENSG00000173227 ENST00000393946;ENST00000525457;ENST00000527043 . . . 5.63 5.63 0.86233 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.06494 T 0.89 . 17.1708 0.86830 0.0:1.0:0.0:0.0 . . . . X 175 . ENSP00000377520:Q175X Q + 1 0 SYT12 66564152 1.000000 0.71417 1.000000 0.80357 0.569000 0.35902 7.797000 0.85911 2.655000 0.90218 0.462000 0.41574 CAG TCGA-2L-AAQJ-01A-12D-A397-08 SYT12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393129.1 0 0 0 5 231 0 57 0 2.165887e-03 0 3 0 57 2 0 0 0 0 0 2 1 0.933143 5 224 0 55 2 0 0 0 0 0 2 -3.865519 1 1 0 0 1 0 0 0 2.041626 0 0.440000 1.870000 0.435028 0.100000 0.030000 0.210000 0.100000 0.112963 0.100000 0 6.000000e-02 1.600000e-01 PDE2A 5138 broad.mit.edu 37 11 72295749 72295749 + Silent SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr11:72295749G>A ENST00000334456.5 - 18 1628 c.1383C>T c.(1381-1383)gcC>gcT p.A461A PDE2A_ENST00000418754.2_Silent_p.A346A|PDE2A_ENST00000444035.2_Silent_p.A452A|RP11-169D4.2_ENST00000545254.1_RNA|PDE2A_ENST00000544570.1_Silent_p.A454A|PDE2A_ENST00000540345.1_Silent_p.A452A|PDE2A_ENST00000376450.3_Silent_p.A205A NM_002599.4 NP_002590.1 O00408 PDE2A_HUMAN phosphodiesterase 2A, cGMP-stimulated 36 BRCA - Breast invasive adenocarcinoma(5;3.55e-05) Caffeine(DB00201)|Tofisopam(DB08811) TGCCCTGATCGGCCGGGATGC 0.622000 0 SO:0001819 synonymous_variant ENST00000334456.5 1 1 hg19 CCDS8216.1 TCGA-2L-AAQJ-01A-12D-A397-08 PDE2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219839.2 1 0 0 36 135 0 40 0 5.327078e-01 0 8 0 40 2 0 0 0 0 0 2 1 1.000000 34 134 0 40 2 0 0 0 0 0 2 -19.999450 1 1 0 0 1 0 0 0 2.041626 0 0.440000 1.870000 0.435028 0.940000 0.690000 1.000000 1.000000 0.919394 0.940000 1 8.100000e-01 1 USP35 57558 broad.mit.edu 37 11 77907359 77907359 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr11:77907359G>A ENST00000529308.1 + 2 329 c.68G>A c.(67-69)cGg>cAg p.R23Q USP35_ENST00000530267.1_Intron|USP35_ENST00000441408.2_5'Flank|USP35_ENST00000530535.1_Intron|USP35_ENST00000526425.1_5'Flank NM_020798.2 NP_065849.1 Q9P2H5 UBP35_HUMAN ubiquitin specific peptidase 35 23 all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152) OV - Ovarian serous cystadenocarcinoma(8;1.04e-25) GGGCTGGTTCGGCGCGTGCTG 0.716000 0 SO:0001583 missense ENST00000529308.1 1 1 hg19 CCDS41693.1 . . . . . . . . . . G 14.83 2.652237 0.47362 . . ENSG00000118369 ENST00000529308 T 0.05649 3.41 4.31 3.38 0.38709 . 0.000000 0.41823 D 0.000817 T 0.04588 0.0125 L 0.29908 0.895 0.80722 D 1 P 0.35155 0.487 B 0.22152 0.038 T 0.50583 -0.8811 10 0.27785 T 0.31 -28.6736 13.2753 0.60184 0.0:0.0:0.8307:0.1693 . 23 Q9P2H5 UBP35_HUMAN Q 23 ENSP00000431876:R23Q ENSP00000431876:R23Q R + 2 0 USP35 77585007 1.000000 0.71417 1.000000 0.80357 0.624000 0.37722 6.220000 0.72237 0.989000 0.38761 0.313000 0.20887 CGG TCGA-2L-AAQJ-01A-12D-A397-08 USP35-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000390026.1 1 0 0 59 229 0 46 0 0 1 0 0 46 2 0 0 0 0 0 2 1 1.000000 59 225 0 44 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.041626 0 0.440000 1.870000 0.435028 0.910000 0.720000 1.000000 1.000000 0.911448 0.910000 1 8.100000e-01 1 BTBD11 121551 broad.mit.edu 37 12 108051434 108051434 + Missense_Mutation SNP G G T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr12:108051434G>T ENST00000280758.5 + 17 3782 c.3254G>T c.(3253-3255)aGg>aTg p.R1085M BTBD11_ENST00000420571.2_Missense_Mutation_p.R966M|BTBD11_ENST00000494235.2_Missense_Mutation_p.R164M|BTBD11_ENST00000357167.4_Missense_Mutation_p.R622M NM_001018072.1 NP_001018082.1 A6QL63 BTBDB_HUMAN BTB (POZ) domain containing 11 53 GACTTACAGAGGACGTTGGCC 0.493000 0 SO:0001583 missense ENST00000280758.5 1 1 hg19 CCDS31893.1 . . . . . . . . . . G 23.3 4.402325 0.83230 . . ENSG00000151136 ENST00000280758;ENST00000420571;ENST00000357167;ENST00000494235 T;T;T;T 0.39997 1.26;1.39;1.05;1.17 5.84 5.84 0.93424 . 0.085133 0.85682 D 0.000000 T 0.41026 0.1141 N 0.22421 0.69 0.58432 D 0.999994 D;D 0.56521 0.976;0.976 P;P 0.47744 0.459;0.556 T 0.22103 -1.0226 10 0.48119 T 0.1 . 20.1551 0.98106 0.0:0.0:1.0:0.0 . 622;1085 E9PHS4;A6QL63 .;BTBDB_HUMAN M 1085;966;622;164 ENSP00000280758:R1085M;ENSP00000413889:R966M;ENSP00000349690:R622M;ENSP00000448322:R164M ENSP00000280758:R1085M R + 2 0 BTBD11 106575564 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 5.694000 0.68272 2.760000 0.94817 0.655000 0.94253 AGG TCGA-2L-AAQJ-01A-12D-A397-08 BTBD11-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000318003.1 1 0 1 38 184 0 63 1 2.105079e-01 2 3 0 63 2 0 0 0 0 0 2 1 1.000000 38 181 0 63 2 0 0 0 0 0 2 -3.294152 1 1 0 0 1 1 2 3 2.095273 0 0.440000 1.870000 0.446093 0.790000 0.570000 1.000000 1.000000 0.801056 0.790000 0 6.700000e-01 9.300000e-01 PRDM4 11108 broad.mit.edu 37 12 108138409 108138409 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr12:108138409G>A ENST00000228437.5 - 7 1765 c.1306C>T c.(1306-1308)Cgg>Tgg p.R436W RP11-864J10.4_ENST00000546714.1_RNA NM_012406.3 NP_036538.3 Q9UKN5 PRDM4_HUMAN PR domain containing 4 20 AAGCAAGTCCGCACAGGAATG 0.463000 0 SO:0001583 missense ENST00000228437.5 0 1 hg19 CCDS9115.1 . . . . . . . . . . G 21.2 4.108122 0.77096 . . ENSG00000110851 ENST00000228437;ENST00000550659 T;T 0.41758 0.99;0.99 5.88 4.98 0.66077 SET domain (2); 0.000000 0.85682 D 0.000000 T 0.44746 0.1308 M 0.78049 2.395 0.53688 D 0.999977 D 0.62365 0.991 B 0.43331 0.416 T 0.50980 -0.8763 10 0.54805 T 0.06 -1.7026 8.8668 0.35291 0.0726:0.0:0.6819:0.2455 . 436 Q9UKN5 PRDM4_HUMAN W 436;188 ENSP00000228437:R436W;ENSP00000449295:R188W ENSP00000228437:R436W R - 1 2 PRDM4 106662539 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 3.390000 0.52523 1.481000 0.48307 0.655000 0.94253 CGG TCGA-2L-AAQJ-01A-12D-A397-08 PRDM4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406546.1 0 0 0 5 256 0 47 0 3.273736e-02 0 12 0 47 2 0 0 0 0 0 2 1 0.938133 5 256 0 47 2 0 0 0 0 0 2 -2.578033 1 1 121412 3 34 1 1 2 3 2.095273 0 0.440000 1.870000 0.446093 0.090000 0.030000 1.000000 0.090000 0.138354 0.090000 0 5.000000e-02 1.500000e-01 TRPV4 59341 broad.mit.edu 37 12 110221488 110221488 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr12:110221488G>A ENST00000418703.2 - 15 2648 c.2554C>T c.(2554-2556)Cgc>Tgc p.R852C TRPV4_ENST00000544971.1_Missense_Mutation_p.R745C|TRPV4_ENST00000392719.2_Missense_Mutation_p.R805C|TRPV4_ENST00000541794.1_Missense_Mutation_p.R805C|TRPV4_ENST00000346520.2_Missense_Mutation_p.R792C|TRPV4_ENST00000536838.1_Missense_Mutation_p.R818C|TRPV4_ENST00000537083.1_Missense_Mutation_p.R792C|TRPV4_ENST00000261740.2_Missense_Mutation_p.R852C NM_001177431.1 NP_001170902.1 Q9HBA0 TRPV4_HUMAN transient receptor potential cation channel, subfamily V, member 4 35 CCATCGCAGCGGGGGTTCCCC 0.642000 0 SO:0001583 missense ENST00000418703.2 1 1 hg19 CCDS9134.1 . . . . . . . . . . G 12.34 1.909237 0.33721 0.0 1.16E-4 ENSG00000111199 ENST00000418703;ENST00000261740;ENST00000392719;ENST00000346520;ENST00000544971;ENST00000537083;ENST00000541794;ENST00000536838 D;D;D;D;D;D;D;D 0.89343 -2.5;-2.5;-2.29;-2.5;-2.29;-2.5;-2.29;-2.5 5.39 1.7 0.24286 . 0.722577 0.14111 N 0.340695 T 0.72028 0.3410 N 0.08118 0 0.28470 N 0.915481 P;B;P;B;B 0.41546 0.754;0.389;0.584;0.34;0.167 B;B;B;B;B 0.34722 0.188;0.083;0.13;0.097;0.123 T 0.67604 -0.5628 10 0.62326 D 0.03 -0.0455 4.314 0.10984 0.0:0.2373:0.1878:0.5749 . 792;852;745;805;818 Q9HBA0-2;Q9HBA0;Q9HBA0-6;Q9HBA0-4;Q9HBA0-5 .;TRPV4_HUMAN;.;.;. C 852;852;805;792;745;792;805;818 ENSP00000406191:R852C;ENSP00000261740:R852C;ENSP00000376480:R805C;ENSP00000319003:R792C;ENSP00000443611:R745C;ENSP00000442738:R792C;ENSP00000442167:R805C;ENSP00000444336:R818C ENSP00000261740:R852C R - 1 0 TRPV4 108705871 0.983000 0.35010 0.998000 0.56505 0.533000 0.34776 0.091000 0.15046 0.356000 0.24157 -0.397000 0.06425 CGC TCGA-2L-AAQJ-01A-12D-A397-08 TRPV4-006 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403270.1 1 0 1 34 141 0 34 1 9.859692e-01 14 17 0 34 2 0 0 0 0 0 2 1 1.000000 34 140 0 33 2 0 0 0 0 0 2 -3.406252 1 1 121408 3 33 1 1 2 3 2.095273 0 0.440000 1.870000 0.446093 0.890000 0.640000 1.000000 1.000000 0.886737 0.890000 1 7.600000e-01 1 CLIP1 6249 broad.mit.edu 37 12 122825945 122825945 + Silent SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr12:122825945G>A ENST00000540338.1 - 10 1847 c.1806C>T c.(1804-1806)aaC>aaT p.N602N CLIP1_ENST00000361654.4_Silent_p.N556N|CLIP1_ENST00000545889.1_Silent_p.N292N|CLIP1_ENST00000537178.1_Silent_p.N556N|CLIP1_ENST00000302528.7_Silent_p.N591N|CLIP1_ENST00000358808.2_Silent_p.N591N P30622 CLIP1_HUMAN CAP-GLY domain containing linker protein 1 60 all_neural(191;0.0837)|Medulloblastoma(191;0.163) TCAATGACTCGTTCTCTTTGG 0.468000 0 SO:0001819 synonymous_variant ENST00000540338.1 1 1 hg19 CCDS58285.1 TCGA-2L-AAQJ-01A-12D-A397-08 CLIP1-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000401625.1 0 0 1 103 603 0 115 1 9.991301e-01 11 51 0 115 2 0 0 0 0 0 2 1 1.000000 102 601 0 114 2 0 0 0 0 0 2 -20.000000 1 1 121412 27 49 1 1 2 3 2.095273 0 0.440000 1.870000 0.446093 0.670000 0.550000 1.000000 0.670000 0.686238 0.670000 0 6.000000e-01 7.400000e-01 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-2L-AAQJ-01A-12D-A397-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 55 181 0 58 1 9.792503e-01 22 1 0 58 2 1 1 56 211 0 208 2 1 1.000000 55 181 0 57 2 1 1 2326 5689 14 7988 25 -20.000000 1 1 121404 2 44 1 0 1 1 1.726764 1 0.440000 1.870000 0.282051 0.810000 0.630000 0.970000 0.820000 0.816580 0.810000 0 7.200000e-01 9.100000e-01 VWF 7450 broad.mit.edu 37 12 6138548 6138548 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr12:6138548C>T ENST00000261405.5 - 22 3181 c.2927G>A c.(2926-2928)cGc>cAc p.R976H NM_000552.3 NP_000543 P04275 VWF_HUMAN von Willebrand factor 129 Antihemophilic Factor(DB00025) GCTCAGGTGGCGGTCCCAGAC 0.557000 0 SO:0001583 missense ENST00000261405.5 1 1 hg19 CCDS8539.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 C 4.964 0.178991 0.09443 . . ENSG00000110799 ENST00000261405 T 0.59364 0.27 4.58 -4.91 0.03085 von Willebrand factor, type D domain (3); 1.340220 0.05412 N 0.542595 T 0.42471 0.1204 L 0.31578 0.945 0.09310 N 0.999998 B 0.14012 0.009 B 0.10450 0.005 T 0.30268 -0.9984 10 0.32370 T 0.25 . 10.1299 0.42672 0.111:0.1943:0.0:0.6948 . 976 P04275 VWF_HUMAN H 976 ENSP00000261405:R976H ENSP00000261405:R976H R - 2 0 VWF 6008809 0.000000 0.05858 0.141000 0.22245 0.187000 0.23431 -0.956000 0.03865 -1.024000 0.03338 -0.347000 0.07816 CGC TCGA-2L-AAQJ-01A-12D-A397-08 VWF-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399020.1 1 0 1 76 247 0 90 0 9.999972e-01 0 64 0 90 2 0 0 0 0 0 2 1 1.000000 76 240 0 90 2 0 0 0 0 0 2 -20.000000 1 1 121412 3 41 1 0 1 1 1.630284 1 0.440000 1.870000 0.282051 0.820000 0.670000 0.970000 0.830000 0.828196 0.820000 0 7.400000e-01 9.100000e-01 IRAK3 11213 broad.mit.edu 37 12 66641598 66641598 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr12:66641598G>A ENST00000261233.4 + 12 1859 c.1438G>A c.(1438-1440)Gaa>Aaa p.E480K IRAK3_ENST00000457197.2_Missense_Mutation_p.E419K NM_007199.2 NP_009130.2 interleukin-1 receptor-associated kinase 3 36 TATTCCAGTGGAAGATGATGA 0.428000 0 SO:0001583 missense ENST00000261233.4 1 1 hg19 CCDS8975.1 . . . . . . . . . . G 28.8 4.955128 0.92726 . . ENSG00000090376 ENST00000261233;ENST00000457197 T;T 0.73258 -0.69;-0.73 5.77 5.77 0.91146 . 0.000000 0.85682 D 0.000000 T 0.77458 0.4133 L 0.36672 1.1 0.40471 D 0.980346 D;D 0.89917 1.0;0.999 D;D 0.87578 0.998;0.994 T 0.75628 -0.3252 9 . . . -27.7703 15.4984 0.75677 0.0:0.0:1.0:0.0 . 419;480 Q9Y616-2;Q9Y616 .;IRAK3_HUMAN K 480;419 ENSP00000261233:E480K;ENSP00000409852:E419K . E + 1 0 IRAK3 64927865 1.000000 0.71417 1.000000 0.80357 0.946000 0.59487 4.853000 0.62911 2.724000 0.93272 0.561000 0.74099 GAA TCGA-2L-AAQJ-01A-12D-A397-08 IRAK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401908.1 1 0 1 65 210 0 42 0 9.901520e-01 1 25 0 42 2 0 0 0 0 0 2 1 1.000000 65 208 0 42 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.095273 0 0.440000 1.870000 0.446093 0.990000 0.860000 1.000000 1.000000 0.986344 0.990000 1 9.700000e-01 1 CAND1 55832 broad.mit.edu 37 12 67691335 67691335 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr12:67691335C>T ENST00000545606.1 + 5 1077 c.640C>T c.(640-642)Ctt>Ttt p.L214F NM_018448.3 NP_060918.2 Q86VP6 CAND1_HUMAN cullin-associated and neddylation-dissociated 1 35 GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196) TTTTGTAGATCTTATTGAACA 0.403000 0 SO:0001583 missense ENST00000545606.1 1 1 hg19 CCDS8977.1 . . . . . . . . . . C 28.9 4.963385 0.92791 . . ENSG00000111530 ENST00000545606;ENST00000299218;ENST00000540047 T 0.67865 -0.29 5.61 5.61 0.85477 Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.79575 0.4469 L 0.55834 1.745 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.76940 -0.2773 9 . . . -12.9708 19.6379 0.95744 0.0:1.0:0.0:0.0 . 214 Q86VP6 CAND1_HUMAN F 214;214;56 ENSP00000442318:L214F . L + 1 0 CAND1 65977602 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.818000 0.86416 2.657000 0.90304 0.655000 0.94253 CTT TCGA-2L-AAQJ-01A-12D-A397-08 CAND1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402105.1 0 0 1 87 291 1 69 1 8.890906e-01 5 16 1 69 3 0 0 0 0 0 2 1 1.000000 86 288 1 68 18 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.095273 0 0.440000 1.870000 0.446093 0.990000 0.860000 1.000000 1.000000 0.984623 0.990000 1 9.500000e-01 1 LPCAT3 10162 broad.mit.edu 37 12 7086376 7086376 + Missense_Mutation SNP G G C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr12:7086376G>C ENST00000261407.4 - 12 1481 c.1396C>G c.(1396-1398)Cta>Gta p.L466V U47924.30_ENST00000606112.1_lincRNA|LPCAT3_ENST00000535021.1_5'UTR NM_005768.5 NP_005759.4 Q6P1A2 MBOA5_HUMAN lysophosphatidylcholine acyltransferase 3 17 AATATGAATAGTAGGCTCAGG 0.418000 0 SO:0001583 missense ENST00000261407.4 1 1 hg19 CCDS8572.1 . . . . . . . . . . G 10.54 1.379121 0.24944 . . ENSG00000111684 ENST00000261407 T 0.73897 -0.79 4.77 2.95 0.34219 . 0.147474 0.46758 D 0.000278 T 0.63698 0.2533 L 0.39898 1.24 0.48696 D 0.999699 P 0.49090 0.919 B 0.42087 0.375 T 0.58994 -0.7537 10 0.32370 T 0.25 -13.8297 10.1817 0.42972 0.2237:0.0:0.7763:0.0 . 466 Q6P1A2 MBOA5_HUMAN V 466 ENSP00000261407:L466V ENSP00000261407:L466V L - 1 2 LPCAT3 6956637 0.980000 0.34600 0.277000 0.24703 0.895000 0.52256 1.816000 0.38992 0.627000 0.30340 -0.258000 0.10820 CTA TCGA-2L-AAQJ-01A-12D-A397-08 LPCAT3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401812.1 1 0 1 62 158 0 44 1 1 57 29 0 44 2 0 0 0 0 0 2 1 1.000000 62 157 0 44 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.630284 1 0.440000 1.870000 0.282051 0.920000 0.760000 1.000000 0.990000 0.917278 0.920000 1 8.400000e-01 9.800000e-01 SACS 26278 broad.mit.edu 37 13 23912096 23912096 + Missense_Mutation SNP T T G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr13:23912096T>G ENST00000382292.3 - 9 6192 c.5919A>C c.(5917-5919)aaA>aaC p.K1973N SACS_ENST00000402364.1_Missense_Mutation_p.K1223N|SACS_ENST00000382298.3_Missense_Mutation_p.K1973N Q9NZJ4 SACS_HUMAN sacsin molecular chaperone 189 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) TGGTCAGTTCTTTCCCTTTTC 0.363000 0 SO:0001583 missense ENST00000382292.3 1 1 hg19 CCDS9300.2 . . . . . . . . . . T 6.072 0.381555 0.11524 . . ENSG00000151835 ENST00000382292;ENST00000402364;ENST00000382298 D;D;D 0.88354 -2.22;-2.37;-2.22 5.93 -1.21 0.09524 . 0.145938 0.64402 D 0.000008 T 0.78817 0.4343 N 0.25647 0.755 0.30667 N 0.753783 B 0.13594 0.008 B 0.11329 0.006 T 0.66048 -0.6020 10 0.33940 T 0.23 . 10.3333 0.43835 0.0:0.4088:0.0:0.5912 . 1973 Q9NZJ4 SACS_HUMAN N 1973;1223;1973 ENSP00000371729:K1973N;ENSP00000385844:K1223N;ENSP00000371735:K1973N ENSP00000371729:K1973N K - 3 2 SACS 22810096 1.000000 0.71417 0.742000 0.31022 0.119000 0.20118 0.854000 0.27791 -0.412000 0.07519 -0.353000 0.07706 AAA TCGA-2L-AAQJ-01A-12D-A397-08 SACS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044148.3 1 0 1 39 222 0 41 0 2.362023e-02 1 1 0 41 2 0 0 0 0 0 2 1 1.000000 39 219 0 41 2 0 0 0 0 0 2 -19.408850 1 1 0 0 1 0 1 1 1.931512 0 0.440000 1.870000 0.406025 0.630000 0.460000 0.830000 0.640000 0.648128 0.630000 0 5.400000e-01 7.400000e-01 FREM2 341640 broad.mit.edu 37 13 39262875 39262875 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr13:39262875C>T ENST00000280481.7 + 1 1610 c.1394C>T c.(1393-1395)cCg>cTg p.P465L NM_207361.4 NP_997244.3 Q5SZK8 FREM2_HUMAN FRAS1 related extracellular matrix protein 2 p.P465L(1) 148 Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114) GGCAGTGGTCCGCAAAACTTG 0.582000 1 Substitution - Missense(1) SO:0001583 missense ENST00000280481.7 1 1 hg19 CCDS31960.1 . . . . . . . . . . C 3.698 -0.062202 0.07317 . . ENSG00000150893 ENST00000280481 T 0.18174 2.23 5.6 2.0 0.26442 . 0.505278 0.18484 N 0.139857 T 0.13756 0.0333 L 0.43152 1.355 0.09310 N 0.999998 B 0.13145 0.007 B 0.06405 0.002 T 0.21621 -1.0240 10 0.34782 T 0.22 . 8.9993 0.36072 0.0:0.6923:0.0:0.3077 . 465 Q5SZK8 FREM2_HUMAN L 465 ENSP00000280481:P465L ENSP00000280481:P465L P + 2 0 FREM2 38160875 0.000000 0.05858 0.001000 0.08648 0.248000 0.25809 0.505000 0.22642 0.063000 0.16370 -1.036000 0.02392 CCG TCGA-2L-AAQJ-01A-12D-A397-08 FREM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044599.2 1 0 1 24 168 0 49 0 0 0 0 49 2 0 0 0 0 0 2 1 1.000000 24 167 0 49 2 0 0 0 0 0 2 -2.968319 1 1 121412 3 35 1 0.440000 1.870000 0 0 SIAH3 283514 broad.mit.edu 37 13 46357678 46357678 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr13:46357678G>A ENST00000400405.2 - 2 756 c.650C>T c.(649-651)aCg>aTg p.T217M NM_198849.2 NP_942146.2 Q8IW03 SIAH3_HUMAN siah E3 ubiquitin protein ligase family member 3 12 AGACCGGGGCGTGGCCTCCCA 0.612000 0 SO:0001583 missense ENST00000400405.2 1 1 hg19 CCDS41883.1 . . . . . . . . . . G 19.04 3.748952 0.69533 . . ENSG00000215475 ENST00000400405 T 0.27256 1.68 5.07 5.07 0.68467 TRAF-type (1);Seven-in-absentia protein, TRAF-like domain (1);TRAF-like (1); 0.000000 0.85682 U 0.000000 T 0.44767 0.1309 L 0.44542 1.39 0.51482 D 0.999923 D 0.89917 1.0 D 0.91635 0.999 T 0.31223 -0.9951 10 0.51188 T 0.08 -19.0347 17.4324 0.87543 0.0:0.0:1.0:0.0 . 217 Q8IW03 SIAH3_HUMAN M 217 ENSP00000383256:T217M ENSP00000383256:T217M T - 2 0 SIAH3 45255679 1.000000 0.71417 0.987000 0.45799 0.493000 0.33554 9.719000 0.98760 2.369000 0.80426 0.561000 0.74099 ACG TCGA-2L-AAQJ-01A-12D-A397-08 SIAH3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044788.2 1 0 1 37 168 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 1.000000 37 168 0 36 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 2 2 4 2.196026 1 0.440000 1.870000 0.474672 0.890000 0.640000 1.000000 1.000000 0.885740 0.890000 1 7.600000e-01 1 DIO3 1735 broad.mit.edu 37 14 102028119 102028119 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr14:102028119G>A ENST00000510508.4 + 1 432 c.286G>A c.(286-288)Gat>Aat p.D96N DIO3_ENST00000359323.3_Missense_Mutation_p.D70N|DIO3OS_ENST00000408206.1_lincRNA P55073 IOD3_HUMAN deiodinase, iodothyronine, type III 22 all_neural(303;0.185) GGTGCCTCCCGATGACCCGCC 0.642000 0 SO:0001583 missense ENST00000510508.4 1 1 hg19 CCDS41992.2 . . . . . . . . . . g 18.36 3.607744 0.66558 . . ENSG00000197406;ENSG00000258865 ENST00000359323;ENST00000510508 T;T 0.35236 1.37;1.32 3.21 3.21 0.36854 . 0.000000 0.40302 U 0.001121 T 0.54565 0.1866 M 0.80028 2.48 0.28273 N 0.924327 D 0.89917 1.0 D 0.70227 0.968 T 0.46679 -0.9174 10 0.34782 T 0.22 . 7.8692 0.29556 0.124:0.0:0.876:0.0 . 70 P55073 IOD3_HUMAN N 70;96 ENSP00000352273:D70N;ENSP00000427336:D96N ENSP00000352273:D96N D + 1 0 DIO3;AL049836.1 101097872 1.000000 0.71417 1.000000 0.80357 0.815000 0.46073 6.208000 0.72165 1.608000 0.50180 0.457000 0.33378 GAT TCGA-2L-AAQJ-01A-12D-A397-08 DIO3-001 KNOWN upstream_ATG|basic|appris_principal|CCDS|seleno protein_coding protein_coding OTTHUMT00000361712.4 0 0 0 53 271 0 84 0 2.786064e-02 1 1 0 84 2 0 0 0 0 0 2 1 1.000000 52 267 0 82 2 0 0 0 0 0 2 -3.342333 1 1 0 0 1 0 0 0 2.042068 0 0.440000 1.870000 0.437525 0.730000 0.560000 0.920000 0.740000 0.746465 0.730000 0 6.400000e-01 8.400000e-01 KIF26A 26153 broad.mit.edu 37 14 104618363 104618363 + Silent SNP C C A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr14:104618363C>A ENST00000423312.2 + 3 300 c.300C>A c.(298-300)ctC>ctA p.L100L KIF26A_ENST00000315264.7_5'UTR NM_015656.1 NP_056471.1 Q9ULI4 KI26A_HUMAN kinesin family member 26A 21 all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767) Epithelial(46;0.152) ATCCTTGCCTCTCTGCCCTGC 0.672000 0 SO:0001819 synonymous_variant ENST00000423312.2 1 1 hg19 CCDS45171.1 TCGA-2L-AAQJ-01A-12D-A397-08 KIF26A-002 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414356.1 1 0 1 55 172 0 50 0 1.501976e-01 0 3 0 50 2 0 0 0 0 0 2 1 1.000000 55 170 0 50 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.042068 0 0.440000 1.870000 0.437525 0.990000 0.850000 1.000000 1.000000 0.985077 0.990000 1 9.600000e-01 1 ARHGAP5 394 broad.mit.edu 37 14 32623887 32623887 + Nonsense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr14:32623887G>A ENST00000345122.3 + 7 4557 c.4242G>A c.(4240-4242)tgG>tgA p.W1414* ARHGAP5_ENST00000396582.2_Nonsense_Mutation_p.W149*|ARHGAP5_ENST00000432921.1_Nonsense_Mutation_p.W1413*|ARHGAP5_ENST00000539826.2_Nonsense_Mutation_p.W1414*|ARHGAP5_ENST00000433497.1_Nonsense_Mutation_p.W153*|ARHGAP5_ENST00000556611.1_Nonsense_Mutation_p.W1413* NM_001030055.1 NP_001025226.1 Q13017 RHG05_HUMAN Rho GTPase activating protein 5 55 Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186) LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173) TCTGTTTTTGGCCAACCTTGA 0.338000 NSCLC(9;77 350 3443 29227 41353) 0 SO:0001587 stop_gained ENST00000345122.3 0 1 hg19 CCDS32062.1 . . . . . . . . . . G 45 11.775769 0.99601 . . ENSG00000100852 ENST00000556611;ENST00000539826;ENST00000396582;ENST00000345122;ENST00000432921;ENST00000433497 . . . 4.93 4.93 0.64822 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 18.5752 0.91153 0.0:0.0:1.0:0.0 . . . . X 1413;1414;149;1414;1413;153 . ENSP00000371897:W1414X W + 3 0 ARHGAP5 31693638 1.000000 0.71417 1.000000 0.80357 0.954000 0.61252 9.748000 0.98867 2.475000 0.83589 0.549000 0.68633 TGG TCGA-2L-AAQJ-01A-12D-A397-08 ARHGAP5-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000409735.1 1 0 1 84 279 0 79 1 9.999999e-01 54 30 0 79 2 0 0 0 0 0 2 1 1.000000 83 277 0 78 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.042068 0 0.440000 1.870000 0.437525 0.990000 0.850000 1.000000 1.000000 0.980703 0.990000 1 9.400000e-01 1 AKAP6 9472 broad.mit.edu 37 14 33291973 33291973 + Nonsense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr14:33291973C>T ENST00000280979.4 + 13 5124 c.4954C>T c.(4954-4956)Cga>Tga p.R1652* AKAP6_ENST00000557272.1_Intron NM_004274.4 NP_004265.3 Q13023 AKAP6_HUMAN A kinase (PRKA) anchor protein 6 122 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) AAAGATAAAACGAAGTGTTTC 0.418000 Melanoma(49;821 1200 7288 13647 42351) 0 SO:0001587 stop_gained ENST00000280979.4 0 1 hg19 CCDS9644.1 . . . . . . . . . . C 44 10.633637 0.99441 . . ENSG00000151320 ENST00000280979 . . . 5.98 3.08 0.35506 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -9.6398 15.1411 0.72612 0.3707:0.6293:0.0:0.0 . . . . X 1652 . ENSP00000280979:R1652X R + 1 2 AKAP6 32361724 1.000000 0.71417 0.998000 0.56505 0.979000 0.70002 4.452000 0.60054 0.371000 0.24564 -0.188000 0.12872 CGA TCGA-2L-AAQJ-01A-12D-A397-08 AKAP6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276617.2 1 0 1 55 216 0 51 0 0 0 0 51 2 0 0 0 0 0 2 1 1.000000 55 213 0 51 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.042068 0 0.440000 1.870000 0.437525 0.910000 0.710000 1.000000 1.000000 0.907275 0.910000 1 8.000000e-01 1 VPS39 23339 broad.mit.edu 37 15 42457994 42457994 + Silent SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr15:42457994C>T ENST00000348544.4 - 18 1733 c.1734G>A c.(1732-1734)ccG>ccA p.P578P VPS39_ENST00000318006.5_Silent_p.P567P Q96JC1 VPS39_HUMAN vacuolar protein sorting 39 homolog (S. cerevisiae) 28 all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152) ACTCCACTTCCGGGAGATCTT 0.473000 0 SO:0001819 synonymous_variant ENST00000348544.4 0 1 hg19 CCDS10083.1 TCGA-2L-AAQJ-01A-12D-A397-08 VPS39-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000420472.1 0 0 0 4 287 0 65 0 1.844012e-01 0 45 0 65 2 0 0 0 0 0 2 1 0.889409 4 285 0 65 2 0 0 0 0 0 2 -3.166510 1 1 121412 2 31 1 0 0 0 2.049200 0 0.440000 1.870000 0.437525 0.060000 0.010000 0.150000 0.060000 0.076844 0.060000 0 3.000000e-02 1.100000e-01 MORF4L1 10933 broad.mit.edu 37 15 79186408 79186408 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr15:79186408C>T ENST00000331268.5 + 11 959 c.755C>T c.(754-756)gCg>gTg p.A252V MORF4L1_ENST00000559345.1_Missense_Mutation_p.A125V|MORF4L1_ENST00000561171.1_Intron|MORF4L1_ENST00000558502.1_Missense_Mutation_p.A125V|MORF4L1_ENST00000426013.2_Missense_Mutation_p.A213V|MORF4L1_ENST00000558746.1_Missense_Mutation_p.A186V|MORF4L1_ENST00000379535.4_Missense_Mutation_p.A238V NM_206839.2 NP_996670.1 Q9UBU8 MO4L1_HUMAN mortality factor 4 like 1 10 AGGGAGTATGCGGTTAATGAA 0.333000 0 SO:0001583 missense ENST00000331268.5 0 1 hg19 CCDS10307.1 . . . . . . . . . . C 19.10 3.761130 0.69763 . . ENSG00000185787 ENST00000379535;ENST00000426013;ENST00000331268 T;T;T 0.08458 3.09;3.09;3.09 4.36 4.36 0.52297 . 0.000000 0.85682 D 0.000000 T 0.11580 0.0282 L 0.48174 1.505 0.80722 D 1 D;D 0.67145 0.996;0.978 P;B 0.48840 0.592;0.366 T 0.20107 -1.0285 10 0.09590 T 0.72 -22.9863 15.8341 0.78787 0.0:1.0:0.0:0.0 . 213;252 Q9UBU8-2;Q9UBU8 .;MO4L1_HUMAN V 238;213;252 ENSP00000368850:A238V;ENSP00000408880:A213V;ENSP00000331310:A252V ENSP00000331310:A252V A + 2 0 MORF4L1 76973463 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 7.604000 0.82830 2.123000 0.65237 0.650000 0.86243 GCG TCGA-2L-AAQJ-01A-12D-A397-08 MORF4L1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000290131.4 0 0 0 7 522 0 95 0 9.977517e-01 0 886 0 95 2 0 0 0 0 0 2 1 0.975966 7 490 0 94 2 0 0 0 0 0 2 -1.807614 0 1 0 0 1 0 0 0 2.049200 0 0.440000 1.870000 0.437525 0.060000 0.020000 0.120000 0.060000 0.068044 0.060000 0 3.000000e-02 9.000000e-02 ADAMTSL3 57188 broad.mit.edu 37 15 84705713 84705713 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr15:84705713G>A ENST00000286744.5 + 29 5167 c.4943G>A c.(4942-4944)cGg>cAg p.R1648Q ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R1648Q NM_207517.2 NP_997400.2 P82987 ATL3_HUMAN ADAMTS-like 3 130 BRCA - Breast invasive adenocarcinoma(143;0.211) ATTTCCTGGCGGCACTGTCTT 0.527000 0 SO:0001583 missense ENST00000286744.5 1 1 hg19 CCDS10326.1 . . . . . . . . . . G 6.948 0.544751 0.13312 . . ENSG00000156218 ENST00000286744 T 0.61274 0.12 5.19 2.26 0.28386 . 1.096740 0.07323 N 0.878014 T 0.31888 0.0811 N 0.11364 0.135 0.27026 N 0.964354 B;B 0.21452 0.033;0.056 B;B 0.10450 0.005;0.002 T 0.22661 -1.0210 10 0.02654 T 1 . 7.0906 0.25282 0.4565:0.0:0.5435:0.0 . 1648;1648 P82987-2;P82987 .;ATL3_HUMAN Q 1648 ENSP00000286744:R1648Q ENSP00000286744:R1648Q R + 2 0 ADAMTSL3 82496717 1.000000 0.71417 0.966000 0.40874 0.998000 0.95712 1.780000 0.38634 0.701000 0.31803 0.655000 0.94253 CGG TCGA-2L-AAQJ-01A-12D-A397-08 ADAMTSL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000304007.2 1 0 1 47 164 0 37 0 0 0 1 0 37 2 0 0 0 0 0 2 1 1.000000 47 159 0 36 2 0 0 0 0 0 2 -4.041260 1 1 121410 2 32 1 0 0 0 2.049200 0 0.440000 1.870000 0.437525 0.990000 0.760000 1.000000 1.000000 0.955385 0.990000 1 8.700000e-01 1 DNAH3 55567 broad.mit.edu 37 16 21080832 21080832 + Silent SNP T T A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr16:21080832T>A ENST00000261383.3 - 23 3284 c.3285A>T c.(3283-3285)ccA>ccT p.P1095P DNAH3_ENST00000415178.1_Silent_p.P1095P NM_017539.1 NP_060009.1 Q8TD57 DYH3_HUMAN dynein, axonemal, heavy chain 3 202 AACTGAAGATTGGTTCCAGGT 0.433000 0 SO:0001819 synonymous_variant ENST00000261383.3 0 1 hg19 CCDS10594.1 TCGA-2L-AAQJ-01A-12D-A397-08 DNAH3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207361.1 0 0 0 9 628 0 129 0 0 0 0 129 2 0 0 0 0 0 2 1 0.993969 9 621 0 128 2 0 0 0 0 0 2 -3.225134 1 1 0 0 1 0 0 0 2.042094 0 0.440000 1.870000 0.437525 0.060000 0.020000 0.120000 0.060000 0.070680 0.060000 0 4.000000e-02 9.000000e-02 PRSS36 146547 broad.mit.edu 37 16 31152793 31152793 + Missense_Mutation SNP A A G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr16:31152793A>G ENST00000268281.4 - 12 1956 c.1898T>C c.(1897-1899)cTc>cCc p.L633P PRSS36_ENST00000418068.2_Missense_Mutation_p.L633P|PRSS36_ENST00000569305.1_Missense_Mutation_p.L628P NM_001258290.1|NM_173502.4 NP_001245219.1|NP_775773.2 Q5K4E3 POLS2_HUMAN protease, serine, 36 17 GACCCACCTGAGGACACAGTG 0.547000 0 SO:0001583 missense ENST00000268281.4 0 1 hg19 CCDS32436.1 . . . . . . . . . . A 16.81 3.225929 0.58668 . . ENSG00000178226 ENST00000268281;ENST00000418068 D;D 0.88818 -2.43;-1.57 5.29 3.99 0.46301 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); . . . . D 0.85435 0.5696 N 0.05554 -0.025 0.53005 D 0.999966 D;D;D 0.76494 0.999;0.999;0.999 D;D;D 0.87578 0.998;0.985;0.985 T 0.82182 -0.0584 9 0.27785 T 0.31 . 7.6216 0.28189 0.8891:0.0:0.1109:0.0 . 633;628;633 E7EX56;B7ZMK8;Q5K4E3 .;.;POLS2_HUMAN P 633 ENSP00000268281:L633P;ENSP00000407160:L633P ENSP00000268281:L633P L - 2 0 PRSS36 31060294 1.000000 0.71417 1.000000 0.80357 0.940000 0.58332 2.959000 0.49153 1.996000 0.58369 0.374000 0.22700 CTC TCGA-2L-AAQJ-01A-12D-A397-08 PRSS36-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000433542.1 0 0 0 6 464 0 91 0 7.429741e-04 0 3 0 91 2 0 0 0 0 0 2 1 0.964016 6 459 0 90 2 0 0 0 0 0 2 -5.813833 1 1 0 0 1 0 0 0 2.044786 0 0.440000 1.870000 0.437525 0.050000 0.010000 0.120000 0.060000 0.066957 0.050000 0 3.000000e-02 9.000000e-02 DNASE1 1773 broad.mit.edu 37 16 3706107 3706107 + Missense_Mutation SNP G G A rs140530129 by1000genomes TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr16:3706107G>A ENST00000246949.5 + 4 3450 c.241G>A c.(241-243)Gca>Aca p.A81T DNASE1_ENST00000414110.2_Start_Codon_SNP_p.M1I|DNASE1_ENST00000407479.1_Missense_Mutation_p.A81T NM_005223.3 NP_005214.2 P24855 DNAS1_HUMAN deoxyribonuclease I 1 Ovarian(90;0.0261) ATCCAGGGATGCACCAGACAC 0.597000 0 SO:0001583 missense ENST00000246949.5 0 1 hg19 CCDS10507.1 2|2 9.157509157509158E-4|9.157509157509158E-4 2|2 0.0040650406504065045|0.0040650406504065045 0|0 0.0|0.0 0|0 0.0|0.0 0|0 0.0|0.0 G|G 12.44|12.44 1.938101|1.938101 0.34189|0.34189 .|. .|. ENSG00000213918|ENSG00000213918 ENST00000407479;ENST00000246949|ENST00000414110 T;T|T 0.51071|0.40476 0.72;0.72|1.03 5.06|5.06 -0.503|-0.503 0.12000|0.12000 Endonuclease/exonuclease/phosphatase (2);|. 1.806170|. 0.02552|. N|. 0.095796|. T|T 0.23806|0.23806 0.0576|0.0576 N|N 0.12182|0.12182 0.205|0.205 0.09310|0.09310 N|N 1|1 B|. 0.14438|. 0.01|. B|. 0.12837|. 0.008|. T|T 0.29027|0.29027 -1.0025|-1.0025 10|7 0.42905|0.87932 T|D 0.14|0 -7.8118|-7.8118 4.4516|4.4516 0.11623|0.11623 0.3473:0.0:0.4251:0.2276|0.3473:0.0:0.4251:0.2276 .|. 81|. P24855|. DNAS1_HUMAN|. T|I 81|1 ENSP00000385905:A81T;ENSP00000246949:A81T|ENSP00000416699:M1I ENSP00000246949:A81T|ENSP00000416699:M1I A|M +|+ 1|3 0|0 DNASE1|DNASE1 3646108|3646108 0.000000|0.000000 0.05858|0.05858 0.001000|0.001000 0.08648|0.08648 0.028000|0.028000 0.11728|0.11728 -0.075000|-0.075000 0.11431|0.11431 0.527000|0.527000 0.28560|0.28560 -0.291000|-0.291000 0.09656|0.09656 GCA|ATG TCGA-2L-AAQJ-01A-12D-A397-08 DNASE1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251585.2 1 0 1 57 241 0 49 1 4.752164e-01 3 5 0 49 2 0 0 0 0 0 2 1 1.000000 57 239 0 49 2 0 0 0 0 0 2 -20.000000 1 1 121412 3 33 1 0 0 0 2.042094 0 0.440000 1.870000 0.437525 0.860000 0.670000 1.000000 1.000000 0.865328 0.860000 1 7.600000e-01 9.700000e-01 ZNF423 23090 broad.mit.edu 37 16 49671084 49671084 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr16:49671084C>T ENST00000561648.1 - 4 2032 c.1979G>A c.(1978-1980)cGg>cAg p.R660Q ZNF423_ENST00000562871.1_Missense_Mutation_p.R600Q|ZNF423_ENST00000562520.1_Missense_Mutation_p.R600Q|ZNF423_ENST00000567169.1_Missense_Mutation_p.R543Q|ZNF423_ENST00000262383.2_Missense_Mutation_p.R660Q|ZNF423_ENST00000563137.2_Missense_Mutation_p.R600Q|ZNF423_ENST00000535559.1_Missense_Mutation_p.R543Q NM_001271620.1 NP_001258549.1 Q2M1K9 ZN423_HUMAN zinc finger protein 423 89 all_cancers(37;0.0155) CGCTTGCTTCCGCAGCAGCAG 0.552000 0 SO:0001583 missense ENST00000561648.1 1 1 hg19 CCDS32445.1 . . . . . . . . . . C 16.81 3.225160 0.58668 . . ENSG00000102935 ENST00000262383;ENST00000535559 T;T 0.30714 1.52;1.52 4.86 4.86 0.63082 . 0.000000 0.85682 D 0.000000 T 0.27313 0.0670 L 0.42529 1.33 0.48830 D 0.999718 B 0.29862 0.259 B 0.23150 0.044 T 0.04454 -1.0950 9 . . . . 18.0121 0.89227 0.0:1.0:0.0:0.0 . 660 Q2M1K9 ZN423_HUMAN Q 660;543 ENSP00000262383:R660Q;ENSP00000442321:R543Q . R - 2 0 ZNF423 48228585 1.000000 0.71417 1.000000 0.80357 0.949000 0.60115 4.679000 0.61649 2.250000 0.74265 0.462000 0.41574 CGG TCGA-2L-AAQJ-01A-12D-A397-08 ZNF423-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000423258.1 1 0 1 37 177 0 51 0 2.156132e-01 0 4 0 51 2 0 0 0 0 0 2 1 1.000000 37 172 0 50 2 0 0 0 0 0 2 -3.004217 1 1 121412 3 37 1 0 0 0 2.044786 0 0.440000 1.870000 0.437525 0.780000 0.570000 1.000000 1.000000 0.789052 0.780000 0 6.600000e-01 9.000000e-01 ABAT 18 broad.mit.edu 37 16 8858595 8858595 + Splice_Site SNP G G T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr16:8858595G>T ENST00000396600.2 + 8 1386 c.448G>T c.(448-450)Gtg>Ttg p.V150L ABAT_ENST00000425191.2_Splice_Site_p.V150L|ABAT_ENST00000567812.1_Splice_Site_p.V165L|ABAT_ENST00000569156.1_Splice_Site_p.V150L|ABAT_ENST00000268251.8_Splice_Site_p.V150L NM_000663.4 NP_000654.2 P80404 GABT_HUMAN 4-aminobutyrate aminotransferase 26 L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080) CTCCCCACAGGTGGCTCCCAA 0.597000 0 SO:0001630 splice_region_variant ENST00000396600.2 0 1 hg19 CCDS10534.1 . . . . . . . . . . G 19.06 3.754306 0.69648 . . ENSG00000183044 ENST00000268251;ENST00000396600;ENST00000425191 T;T;T 0.74315 -0.83;-0.83;-0.83 5.63 5.63 0.86233 Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1); 0.057206 0.64402 D 0.000001 T 0.76485 0.3994 L 0.60455 1.87 0.80722 D 1 B 0.17268 0.021 B 0.35182 0.197 T 0.69964 -0.5002 9 . . . -19.9755 18.7245 0.91710 0.0:0.0:1.0:0.0 . 150 P80404 GABT_HUMAN L 150 ENSP00000268251:V150L;ENSP00000379845:V150L;ENSP00000411916:V150L . V + 1 0 ABAT 8766096 1.000000 0.71417 1.000000 0.80357 0.815000 0.46073 6.063000 0.71162 2.661000 0.90470 0.650000 0.86243 GTG TCGA-2L-AAQJ-01A-12D-A397-08 ABAT-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000433620.2 0 0 0 8 276 0 62 0 1.015284e-02 0 5 0 62 2 0 0 0 0 0 2 1 0.989023 6 274 0 61 2 0 0 0 0 0 2 -9.039571 1 1 0 0 1 0 0 0 2.042094 0 0.440000 1.870000 0.437525 0.130000 0.050000 0.240000 0.130000 0.141766 0.130000 0 9.000000e-02 1.900000e-01 MYO15A 51168 broad.mit.edu 37 17 18043920 18043920 + Silent SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr17:18043920G>A ENST00000205890.5 + 20 5639 c.5301G>A c.(5299-5301)gcG>gcA p.A1767A MYO15A_ENST00000412324.1_3'UTR NM_016239.3 NP_057323.3 Q9UKN7 MYO15_HUMAN myosin XVA 99 all_neural(463;0.228) TCTACAAGGCGCACACTGTGG 0.662000 OREG0024223 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001819 synonymous_variant ENST00000205890.5 0 1 hg19 CCDS42271.1 TCGA-2L-AAQJ-01A-12D-A397-08 MYO15A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000132048.1 0 0 0 6 413 0 131 0 0 0 0 131 2 0 0 0 0 0 2 1 0.963093 6 405 0 131 2 0 0 0 0 0 2 -2.400880 0 1 120914 6 43 1 0 1 1 1.685553 1 0.440000 1.870000 0.282051 0.050000 0.010000 0.100000 0.050000 0.058585 0.050000 0 3.000000e-02 8.000000e-02 TIAF1 9220 broad.mit.edu 37 17 27401145 27401145 + Missense_Mutation SNP G G A rs151013388 TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr17:27401145G>A ENST00000359450.6 - 1 4730 c.73C>T c.(73-75)Cgg>Tgg p.R25W MYO18A_ENST00000527372.1_3'UTR|MYO18A_ENST00000533112.1_3'UTR|MYO18A_ENST00000529578.1_5'UTR|MYO18A_ENST00000531253.1_3'UTR|MYO18A_ENST00000354329.4_3'UTR|TIAF1_ENST00000408971.2_Missense_Mutation_p.R25W NM_004740.3 NP_004731.2 O95411 TIAF1_HUMAN TGFB1-induced anti-apoptotic factor 1 3 Lung NSC(42;0.015) Epithelial(11;1.19e-05)|all cancers(11;6.57e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000153)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031) ACCTGGACCCGGCTCTCCTCA 0.592000 0 SO:0001583 missense ENST00000359450.6 1 1 hg19 CCDS32599.1 . . . . . . . . . . G 4.088 0.014265 0.07959 2.27E-4 0.0 ENSG00000221995 ENST00000408971;ENST00000511177 . . . 5.99 -10.5 0.00291 . . . . . T 0.18215 0.0437 N 0.08118 0 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.42068 -0.9473 8 0.87932 D 0 . 9.1113 0.36730 0.3327:0.2671:0.4002:0.0 . 25 O95411 TIAF1_HUMAN W 25 . ENSP00000386130:R25W R - 1 2 TIAF1 24425271 0.001000 0.12720 0.001000 0.08648 0.008000 0.06430 -0.869000 0.04232 -1.616000 0.01572 -1.595000 0.00837 CGG TCGA-2L-AAQJ-01A-12D-A397-08 TIAF1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372394.2 1 0 1 39 248 0 47 1 1 86 209 0 47 2 0 0 0 0 0 2 1 1.000000 39 245 0 47 2 0 0 0 0 0 2 -3.076960 1 1 121412 2 38 1 1 2 3 2.152119 0 0.440000 1.870000 0.453232 0.640000 0.460000 1.000000 0.630000 0.673497 0.640000 0 5.400000e-01 7.800000e-01 AP2B1 163 broad.mit.edu 37 17 33954713 33954713 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr17:33954713C>T ENST00000262325.7 + 9 1676 c.1123C>T c.(1123-1125)Cgg>Tgg p.R375W AP2B1_ENST00000589344.1_Missense_Mutation_p.R375W|AP2B1_ENST00000538556.1_Missense_Mutation_p.R318W|AP2B1_ENST00000312678.8_Missense_Mutation_p.R375W|AP2B1_ENST00000592545.1_Missense_Mutation_p.R337W|AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000537622.2_Missense_Mutation_p.R375W NM_001282.2 NP_001273.1 P63010 AP2B1_HUMAN adaptor-related protein complex 2, beta 1 subunit 28 Ovarian(249;0.17) AAAAGCTGTGCGGGCCATTGG 0.438000 0 SO:0001583 missense ENST00000262325.7 0 1 hg19 CCDS32622.1 . . . . . . . . . . C 17.82 3.483673 0.63962 . . ENSG00000006125 ENST00000262325;ENST00000312678;ENST00000538556;ENST00000537622;ENST00000545922 T;T;T;T 0.27402 1.67;1.67;1.67;1.67 5.74 2.04 0.26737 Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.67420 0.2891 H 0.97158 3.95 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 0.998;0.999;1.0;0.996 T 0.77787 -0.2457 10 0.87932 D 0 -0.402 14.3775 0.66889 0.4861:0.5139:0.0:0.0 . 112;337;375;375 F5GYG9;B4DWG4;P63010;P63010-2 .;.;AP2B1_HUMAN;. W 375;375;318;375;112 ENSP00000262325:R375W;ENSP00000314414:R375W;ENSP00000440563:R318W;ENSP00000437413:R375W ENSP00000262325:R375W R + 1 2 AP2B1 30978826 0.999000 0.42202 1.000000 0.80357 0.992000 0.81027 1.241000 0.32743 0.128000 0.18479 -1.036000 0.02392 CGG TCGA-2L-AAQJ-01A-12D-A397-08 AP2B1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000448969.1 0 0 0 4 278 0 60 0 7.505153e-01 1 179 0 60 2 0 0 0 0 0 2 1 0.890211 4 277 0 60 2 0 0 0 0 0 2 -2.364776 0 1 0 0 1 1 2 3 2.152119 0 0.440000 1.870000 0.453232 0.070000 0.010000 1.000000 0.070000 0.163183 0.070000 0 4.000000e-02 1.400000e-01 BECN1 8678 broad.mit.edu 37 17 40967986 40967986 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr17:40967986G>A ENST00000361523.4 - 8 902 c.770C>T c.(769-771)gCc>gTc p.A257V BECN1_ENST00000438274.3_Missense_Mutation_p.A181V|BECN1_ENST00000590099.1_Missense_Mutation_p.A257V NM_003766.3 NP_003757.1 Q14457 BECN1_HUMAN beclin 1, autophagy related 13 Breast(137;0.00104) CTGCGTCTGGGCATAACGCAT 0.463000 0 SO:0001583 missense ENST00000361523.4 0 1 hg19 CCDS11441.1 . . . . . . . . . . G 15.43 2.830695 0.50845 . . ENSG00000126581 ENST00000361523;ENST00000438274;ENST00000543382 T;T 0.46451 0.87;2.55 5.95 5.95 0.96441 . 0.171847 0.52532 D 0.000064 T 0.34978 0.0916 L 0.33339 1.005 0.58432 D 0.999994 B;B 0.32188 0.359;0.024 B;B 0.29663 0.105;0.094 T 0.07083 -1.0791 10 0.18710 T 0.47 . 20.3931 0.98965 0.0:0.0:1.0:0.0 . 181;257 E7EV84;Q14457 .;BECN1_HUMAN V 257;181;170 ENSP00000355231:A257V;ENSP00000416173:A181V ENSP00000355231:A257V A - 2 0 BECN1 38221512 1.000000 0.71417 1.000000 0.80357 0.144000 0.21451 6.847000 0.75404 2.824000 0.97209 0.655000 0.94253 GCC TCGA-2L-AAQJ-01A-12D-A397-08 BECN1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452405.1 0 0 0 7 376 0 92 0 6.875938e-01 0 124 0 92 2 0 0 0 0 0 2 1 0.981016 8 376 0 92 2 0 0 0 0 0 2 -1.737995 0 1 0 0 1 0 1 1 1.664854 1 0.440000 1.870000 0.282051 0.060000 0.020000 0.130000 0.060000 0.073175 0.060000 0 4.000000e-02 1.000000e-01 AMZ2 51321 broad.mit.edu 37 17 66253070 66253070 + Missense_Mutation SNP A A C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr17:66253070A>C ENST00000359904.3 + 7 2175 c.1043A>C c.(1042-1044)aAa>aCa p.K348T ARSG_ENST00000448504.2_5'Flank|AMZ2_ENST00000359783.4_Missense_Mutation_p.K290T|AMZ2_ENST00000580753.1_Missense_Mutation_p.K348T|AMZ2_ENST00000577273.1_3'UTR|AMZ2_ENST00000392720.2_Missense_Mutation_p.K348T|AMZ2_ENST00000577866.1_Missense_Mutation_p.K348T|AMZ2_ENST00000577985.1_Missense_Mutation_p.K348T NM_016627.4 NP_057711.3 Q86W34 AMZ2_HUMAN archaelysin family metallopeptidase 2 9 all_cancers(12;1.12e-09) BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24) AAGGAATGGAAAGAGTGGATA 0.398000 0 SO:0001583 missense ENST00000359904.3 1 1 hg19 CCDS11674.1 . . . . . . . . . . A 6.893 0.534347 0.13188 . . ENSG00000196704 ENST00000359904;ENST00000359783;ENST00000392720 T;T;T 0.33865 1.39;1.39;1.39 3.42 -3.74 0.04385 . 0.527164 0.15835 N 0.242322 T 0.28928 0.0718 L 0.54323 1.7 0.40767 D 0.983057 B;B 0.32245 0.181;0.361 B;B 0.31686 0.134;0.134 T 0.06110 -1.0845 10 0.51188 T 0.08 -21.1054 10.9082 0.47092 0.2793:0.0:0.7207:0.0 . 290;348 A6NLD9;Q86W34 .;AMZ2_HUMAN T 348;290;348 ENSP00000352976:K348T;ENSP00000352831:K290T;ENSP00000376481:K348T ENSP00000352831:K290T K + 2 0 AMZ2 63764665 0.719000 0.27986 0.392000 0.26245 0.101000 0.19017 0.235000 0.17948 -0.834000 0.04239 -0.353000 0.07706 AAA TCGA-2L-AAQJ-01A-12D-A397-08 AMZ2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000448261.1 1 0 1 57 418 0 85 1 9.999999e-01 27 152 0 85 2 0 0 0 0 0 2 1 1.000000 57 412 0 85 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 2 5 7 2.566464 1 0.440000 1.870000 0.553073 0.700000 0.530000 1.000000 0.690000 0.743462 0.700000 0 6.100000e-01 1 GPR142 350383 broad.mit.edu 37 17 72363648 72363648 + Missense_Mutation SNP A A T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr17:72363648A>T ENST00000335666.4 + 1 52 c.4A>T c.(4-6)Agt>Tgt p.S2C NM_181790.1 NP_861455.1 Q7Z601 GP142_HUMAN G protein-coupled receptor 142 35 GTTAGCAATGAGTATTATGAT 0.527000 0 SO:0001583 missense ENST00000335666.4 1 1 hg19 CCDS11698.1 . . . . . . . . . . A 10.68 1.417868 0.25552 . . ENSG00000257008 ENST00000335666 T 0.71817 -0.6 2.61 1.45 0.22620 . . . . . T 0.46776 0.1410 N 0.08118 0 0.27124 N 0.962078 P 0.51653 0.947 B 0.40741 0.339 T 0.42032 -0.9475 9 0.87932 D 0 . 6.1442 0.20276 0.773:0.0:0.0:0.227 . 2 Q7Z601 GP142_HUMAN C 2 ENSP00000335158:S2C ENSP00000335158:S2C S + 1 0 GPR142 69875243 1.000000 0.71417 0.001000 0.08648 0.000000 0.00434 4.243000 0.58721 0.062000 0.16340 -0.343000 0.07986 AGT TCGA-2L-AAQJ-01A-12D-A397-08 GPR142-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000442545.1 1 0 1 51 324 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 1.000000 51 320 0 67 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 2 5 7 2.566464 1 0.440000 1.870000 0.553073 0.800000 0.590000 1.000000 0.780000 0.819603 0.800000 0 6.800000e-01 1 TP53 7157 broad.mit.edu 37 17 7577141 7577141 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr17:7577141C>T ENST00000269305.4 - 8 986 c.797G>A c.(796-798)gGa>gAa p.G266E TP53_ENST00000445888.2_Missense_Mutation_p.G266E|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.G266E|TP53_ENST00000420246.2_Missense_Mutation_p.G266E|TP53_ENST00000359597.4_Missense_Mutation_p.G266E|TP53_ENST00000413465.2_Intron NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.G266E(50)|p.G266V(42)|p.0?(8)|p.?(3)|p.G266fs*79(3)|p.G262_F270delGNLLGRNSF(2)|p.G266A(2)|p.G266_E271delGRNSFE(2)|p.G262_S269delGNLLGRNS(2)|p.G266fs*4(1)|p.G266T(1)|p.L265_K305del41(1)|p.E258fs*71(1)|p.L265_R267delLGR(1)|p.G266_N268delGRN(1)|p.G262fs*2(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GCTGTTCCGTCCCAGTAGATT 0.517000 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 121 Substitution - Missense(95)|Deletion - In frame(9)|Whole gene deletion(8)|Deletion - Frameshift(6)|Unknown(3) SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 0 1 hg19 CCDS11118.1 . . . . . . . . . . C 25.2 4.614795 0.87359 . . ENSG00000141510 ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690 D;D;D;D;D;D 0.99898 -7.61;-7.61;-7.61;-7.61;-7.61;-7.61 5.13 5.13 0.70059 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99906 0.9955 M 0.92367 3.3 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 0.999;1.0;0.999;0.998 D 0.96190 0.9137 10 0.87932 D 0 -13.0798 16.1198 0.81342 0.0:1.0:0.0:0.0 . 266;266;266;266 P04637-2;P04637-3;P04637;Q1MSW8 .;.;P53_HUMAN;. E 266;266;266;266;266;255;134 ENSP00000352610:G266E;ENSP00000269305:G266E;ENSP00000398846:G266E;ENSP00000391127:G266E;ENSP00000391478:G266E;ENSP00000425104:G134E ENSP00000269305:G266E G - 2 0 TP53 7517866 1.000000 0.71417 0.996000 0.52242 0.744000 0.42396 7.587000 0.82613 2.667000 0.90743 0.462000 0.41574 GGA TCGA-2L-AAQJ-01A-12D-A397-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 15 43 0 13 1 9.996204e-01 33 12 0 13 2 1 1 271 512 0 468 2 1 0.999936 14 43 0 13 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.685553 1 0.440000 1.870000 0.282051 0.820000 0.530000 0.990000 0.880000 0.810034 0.820000 0 6.700000e-01 9.400000e-01 AFMID 125061 broad.mit.edu 37 17 76187132 76187132 + Nonsense_Mutation SNP G G T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr17:76187132G>T ENST00000586731.1 + 2 115 c.94G>T c.(94-96)Gga>Tga p.G32* AFMID_ENST00000589256.1_Nonsense_Mutation_p.G49*|AFMID_ENST00000327898.5_Nonsense_Mutation_p.G49*|AFMID_ENST00000588800.1_Nonsense_Mutation_p.G49*|AFMID_ENST00000409257.5_Nonsense_Mutation_p.G49*|AFMID_ENST00000591952.1_Nonsense_Mutation_p.G49* arylformamidase 19 BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.134) CTCACAGATAGGAATTGAAGG 0.557000 0 SO:0001587 stop_gained ENST00000586731.1 0 1 hg19 . . . . . . . . . . G 34 5.309732 0.95629 . . ENSG00000183077 ENST00000409257;ENST00000409431;ENST00000409722;ENST00000392388;ENST00000327898 . . . 4.9 3.86 0.44501 . 0.483859 0.21363 N 0.075763 . . . . . . 0.38453 D 0.947022 . . . . . . . . . . 0.25751 T 0.34 -12.3045 4.8598 0.13577 0.1436:0.2108:0.6456:0.0 . . . . X 49 . ENSP00000328938:G49X G + 1 0 AFMID 73698727 0.755000 0.28372 0.050000 0.19076 0.691000 0.40173 1.557000 0.36299 2.224000 0.72417 0.609000 0.83330 GGA TCGA-2L-AAQJ-01A-12D-A397-08 AFMID-015 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000438866.1 0 0 0 6 184 0 21 1 9.167167e-01 4 135 0 21 2 0 0 0 0 0 2 1 0.965142 6 183 0 20 2 0 0 0 0 0 2 -8.053794 1 1 0 0 1 2 5 7 2.566464 1 0.440000 1.870000 0.553073 0.210000 0.070000 1.000000 0.190000 0.340724 0.210000 0 1.300000e-01 1 DNAH17 8632 broad.mit.edu 37 17 76567670 76567670 + Splice_Site SNP A A T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr17:76567670A>T ENST00000585328.1 - 4 857 c.e4+1 DNAH17_ENST00000389840.5_Splice_Site NM_173628.3 NP_775899.3 Q9UFH2 DYH17_HUMAN dynein, axonemal, heavy chain 17 116 BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656) AGGAGGCCGTACCTGTTCATG 0.667000 0 SO:0001630 splice_region_variant ENST00000585328.1 1 0 hg19 . . . . . . . . . . A 16.21 3.058575 0.55325 . . ENSG00000187775 ENST00000300671;ENST00000389840 . . . 5.13 5.13 0.70059 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 13.1577 0.59527 1.0:0.0:0.0:0.0 . . . . . -1 . . . - . . DNAH17 74079265 1.000000 0.71417 0.965000 0.40720 0.502000 0.33828 7.753000 0.85153 1.922000 0.55676 0.459000 0.35465 . TCGA-2L-AAQJ-01A-12D-A397-08 DNAH17-001 PUTATIVE not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000318962.2 1 0 0 113 218 0 56 0 0 0 0 56 2 0 0 0 0 0 2 1 1.000000 112 217 0 54 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 2 5 7 2.566464 1 0.440000 1.870000 0.553073 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 PIK3R5 23533 broad.mit.edu 37 17 8791989 8791989 + Missense_Mutation SNP G G C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr17:8791989G>C ENST00000447110.1 - 10 1239 c.1115C>G c.(1114-1116)tCg>tGg p.S372W PIK3R5_ENST00000584803.1_Missense_Mutation_p.S372W|PIK3R5_ENST00000581552.1_Missense_Mutation_p.S372W NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1 NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1 Q8WYR1 PI3R5_HUMAN phosphoinositide-3-kinase, regulatory subunit 5 34 CAGATGGCGCGAGAGGGCCGG 0.632000 NSCLC(18;589 615 7696 20311 50332) 0 SO:0001583 missense ENST00000447110.1 1 1 hg19 CCDS11147.1 . . . . . . . . . . G 4.122 0.020770 0.08006 . . ENSG00000141506 ENST00000269300;ENST00000447110 T 0.80304 -1.36 5.51 4.53 0.55603 . 0.440169 0.25296 N 0.031685 T 0.81664 0.4870 N 0.24115 0.695 0.48452 D 0.99965 D 0.61697 0.99 P 0.61275 0.886 D 0.84368 0.0542 10 0.87932 D 0 -10.1214 15.3433 0.74314 0.0:0.0:0.8589:0.141 . 372 Q8WYR1 PI3R5_HUMAN W 372 ENSP00000392812:S372W ENSP00000269300:S372W S - 2 0 PIK3R5 8732714 0.943000 0.32029 0.003000 0.11579 0.023000 0.10783 2.226000 0.42963 1.312000 0.45043 0.650000 0.86243 TCG TCGA-2L-AAQJ-01A-12D-A397-08 PIK3R5-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000227003.2 1 0 1 18 121 0 40 0 9.285503e-02 0 4 0 40 2 0 0 0 0 0 2 1 0.999987 18 120 0 38 2 0 0 0 0 0 2 -3.326904 1 1 0 0 1 0 1 1 1.685553 1 0.440000 1.870000 0.282051 0.450000 0.280000 0.660000 0.450000 0.469066 0.450000 0 3.600000e-01 5.600000e-01 DLGAP1 9229 broad.mit.edu 37 18 3879329 3879329 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr18:3879329G>A ENST00000315677.3 - 4 1335 c.740C>T c.(739-741)gCg>gTg p.A247V DLGAP1-AS3_ENST00000577649.1_RNA|DLGAP1_ENST00000515196.2_Missense_Mutation_p.A247V|DLGAP1_ENST00000581527.1_Missense_Mutation_p.A247V|DLGAP1_ENST00000584874.1_Missense_Mutation_p.A247V NM_004746.3 NP_004737.2 O14490 DLGP1_HUMAN discs, large (Drosophila) homolog-associated protein 1 56 Colorectal(8;0.0257) GGCCTTCACCGCCTGCTCGCT 0.657000 0 SO:0001583 missense ENST00000315677.3 1 1 hg19 CCDS11836.1 . . . . . . . . . . G 18.74 3.688161 0.68271 . . ENSG00000170579 ENST00000315677;ENST00000515196 T;T 0.16597 2.33;2.33 5.51 5.51 0.81932 . 0.118257 0.64402 D 0.000017 T 0.16642 0.0400 L 0.40543 1.245 0.53688 D 0.999975 B;P;B 0.40931 0.384;0.733;0.181 B;B;B 0.33339 0.038;0.162;0.069 T 0.01993 -1.1233 10 0.62326 D 0.03 -12.462 19.4162 0.94700 0.0:0.0:1.0:0.0 . 247;247;247 B7Z9Y4;Q6IS01;O14490 .;.;DLGP1_HUMAN V 247 ENSP00000316377:A247V;ENSP00000445973:A247V ENSP00000316377:A247V A - 2 0 DLGAP1 3869329 1.000000 0.71417 0.999000 0.59377 0.995000 0.86356 7.431000 0.80335 2.605000 0.88082 0.655000 0.94253 GCG TCGA-2L-AAQJ-01A-12D-A397-08 DLGAP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254394.4 1 0 1 68 260 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 1.000000 68 258 0 68 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.061695 0 0.440000 1.870000 0.441229 0.940000 0.750000 1.000000 1.000000 0.928370 0.940000 1 8.400000e-01 1 SETBP1 26040 broad.mit.edu 37 18 42530405 42530405 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr18:42530405G>A ENST00000282030.5 + 4 1396 c.1100G>A c.(1099-1101)gGg>gAg p.G367E NM_015559.2 NP_056374.2 Q9Y6X0 SETBP_HUMAN SET binding protein 1 104 AATACAGAAGGGAAAAGGGAA 0.448000 Schinzel-Giedion syndrome 0 SO:0001583 missense Familial Cancer Database SGC, Schinzel-Giedion Midface Retraction syndrome ENST00000282030.5 1 1 hg19 CCDS11923.2 . . . . . . . . . . G 15.00 2.702158 0.48307 . . ENSG00000152217 ENST00000282030 T 0.37058 1.22 5.78 5.78 0.91487 . 0.166529 0.53938 D 0.000041 T 0.31358 0.0794 L 0.27053 0.805 0.36681 D 0.87903 P 0.38597 0.639 B 0.35655 0.207 T 0.34551 -0.9824 10 0.87932 D 0 . 20.3668 0.98882 0.0:0.0:1.0:0.0 . 367 Q9Y6X0 SETBP_HUMAN E 367 ENSP00000282030:G367E ENSP00000282030:G367E G + 2 0 SETBP1 40784403 1.000000 0.71417 1.000000 0.80357 0.678000 0.39670 3.539000 0.53604 2.894000 0.99253 0.655000 0.94253 GGG TCGA-2L-AAQJ-01A-12D-A397-08 SETBP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255854.4 1 0 1 61 173 0 45 0 3.937572e-01 0 5 0 45 2 0 0 0 0 0 2 1 1.000000 60 172 0 44 2 0 0 0 0 0 2 -4.890624 1 1 0 0 1 0 1 1 1.704625 1 0.440000 1.870000 0.323998 0.960000 0.770000 1.000000 1.000000 0.946051 0.960000 1 8.600000e-01 1 MBD2 8932 broad.mit.edu 37 18 51691000 51691000 + Silent SNP C C A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr18:51691000C>A ENST00000256429.3 - 5 1230 c.1002G>T c.(1000-1002)gcG>gcT p.A334A NM_003927.4 NP_003918.1 Q9UBB5 MBD2_HUMAN methyl-CpG binding domain protein 2 8 CTGTGATTGGCGCAGAGCTTG 0.473000 0 SO:0001819 synonymous_variant ENST00000256429.3 0 1 hg19 CCDS11953.1 TCGA-2L-AAQJ-01A-12D-A397-08 MBD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256003.2 0 0 0 4 217 0 41 0 8.811227e-01 0 212 0 41 2 0 0 0 0 0 2 1 0.889020 4 215 0 41 2 0 0 0 0 0 2 -3.112260 1 1 121412 1 33 1 0 1 1 1.704625 1 0.440000 1.870000 0.323998 0.070000 0.020000 0.160000 0.070000 0.083634 0.070000 0 4.000000e-02 1.200000e-01 GPI 2821 broad.mit.edu 37 19 34884838 34884838 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr19:34884838C>T ENST00000356487.5 + 12 1170 c.929C>T c.(928-930)aCg>aTg p.T310M GPI_ENST00000415930.3_Missense_Mutation_p.T321M|GPI_ENST00000586425.1_Missense_Mutation_p.T310M NM_000175.3 NP_000166.2 P06744 G6PI_HUMAN glucose-6-phosphate isomerase 25 Esophageal squamous(110;0.162) TTCCGCACGACGCCCCTGGAG 0.627000 0 SO:0001583 missense ENST00000356487.5 1 1 hg19 CCDS12437.1 . . . . . . . . . . C 13.96 2.394367 0.42410 . . ENSG00000105220 ENST00000415930;ENST00000356487 D;D 0.93763 -3.28;-3.28 5.65 4.6 0.57074 . 0.386357 0.32868 N 0.005554 D 0.96030 0.8707 M 0.75085 2.285 0.44454 D 0.997381 B;D;B;B 0.56746 0.05;0.977;0.299;0.286 B;D;B;B 0.64144 0.094;0.922;0.094;0.157 D 0.96395 0.9292 10 0.72032 D 0.01 -0.4064 15.9577 0.79898 0.1361:0.8639:0.0:0.0 . 282;321;283;310 B4DE36;B4DG39;B4DVJ0;P06744 .;.;.;G6PI_HUMAN M 321;310 ENSP00000405573:T321M;ENSP00000348877:T310M ENSP00000348877:T310M T + 2 0 GPI 39576678 0.815000 0.29118 0.084000 0.20598 0.007000 0.05969 7.487000 0.81328 1.371000 0.46172 -0.188000 0.12872 ACG TCGA-2L-AAQJ-01A-12D-A397-08 GPI-006 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000451693.3 1 0 1 147 636 0 165 1 1 173 393 0 165 2 0 0 0 0 0 2 1 1.000000 148 621 0 162 2 0 0 0 0 0 2 -20.000000 1 1 121410 3 37 1 0 0 0 2.024636 0 0.440000 1.870000 0.429967 0.830000 0.710000 0.960000 0.840000 0.840314 0.830000 0 7.700000e-01 9.000000e-01 HPN 3249 broad.mit.edu 37 19 35556925 35556925 + Missense_Mutation SNP C C G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr19:35556925C>G ENST00000262626.2 + 12 2029 c.1204C>G c.(1204-1206)Cag>Gag p.Q402E HPN_ENST00000392226.1_Missense_Mutation_p.Q402E|HPN-AS1_ENST00000392227.2_RNA|HPN_ENST00000597419.1_Missense_Mutation_p.Q244E NM_182983.2 NP_892028.1 P05981 HEPS_HUMAN hepsin 19 all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0849) Coagulation factor VIIa(DB00036) GTGGATCTTCCAGGCCATAAA 0.562000 0 SO:0001583 missense ENST00000262626.2 0 1 hg19 CCDS32993.1 . . . . . . . . . . C 11.21 1.570793 0.28003 . . ENSG00000105707 ENST00000262626;ENST00000392226;ENST00000541345 D;D 0.87887 -2.31;-2.31 4.86 3.81 0.43845 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1); 0.194075 0.40908 D 0.000999 T 0.62575 0.2439 N 0.01656 -0.775 0.80722 D 1 B;B;B 0.23249 0.024;0.067;0.082 B;B;B 0.13407 0.003;0.006;0.009 T 0.62558 -0.6829 10 0.02654 T 1 . 10.3731 0.44066 0.3539:0.6461:0.0:0.0 . 374;402;402 B7Z1L4;B2ZDQ2;P05981 .;.;HEPS_HUMAN E 402;402;374 ENSP00000262626:Q402E;ENSP00000376060:Q402E ENSP00000262626:Q402E Q + 1 0 HPN 40248765 0.966000 0.33281 1.000000 0.80357 0.970000 0.65996 1.161000 0.31773 1.252000 0.44001 0.455000 0.32223 CAG TCGA-2L-AAQJ-01A-12D-A397-08 HPN-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461573.1 0 0 0 11 615 0 145 1 3.861395e-02 2 14 0 145 2 0 0 0 0 0 2 1 0.998276 11 610 0 145 2 0 0 0 0 0 2 -2.290691 0 1 0 0 1 0 0 0 2.024636 0 0.440000 1.870000 0.429967 0.070000 0.030000 0.140000 0.080000 0.085148 0.070000 0 5.000000e-02 1.100000e-01 PLEKHG2 64857 broad.mit.edu 37 19 39914871 39914871 + Nonsense_Mutation SNP C C G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr19:39914871C>G ENST00000409794.3 + 19 3948 c.3098C>G c.(3097-3099)tCa>tGa p.S1033* PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000425673.1_Nonsense_Mutation_p.S1004*|PLEKHG2_ENST00000458508.2_Nonsense_Mutation_p.S974*|CTB-60E11.4_ENST00000601124.1_lincRNA NM_022835.2 NP_073746.2 Q9H7P9 PKHG2_HUMAN pleckstrin homology domain containing, family G (with RhoGef domain) member 2 40 all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569) Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657) TTCACAGTTTCAGTCACCACC 0.547000 0 SO:0001587 stop_gained ENST00000409794.3 0 1 hg19 CCDS33022.2 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 37|37 6.087494|6.087494 0.97271|0.97271 .|. .|. ENSG00000090924|ENSG00000090924 ENST00000205135|ENST00000409794;ENST00000425673;ENST00000458508 .|. .|. .|. 3.08|3.08 -3.41|-3.41 0.04839|0.04839 .|. .|1.788450 .|0.03467 .|N .|0.213043 T|. 0.31513|. 0.0799|. .|. .|. .|. 0.09310|0.09310 N|N 1|1 .|. .|. .|. .|. .|. .|. T|. 0.26538|. -1.0100|. 4|. .|0.28530 .|T .|0.3 .|. 9.007|9.007 0.36117|0.36117 0.0:0.6787:0.0:0.3213|0.0:0.6787:0.0:0.3213 .|. .|. .|. .|. E|X 901|1033;1004;974 .|. .|ENSP00000386733:S1033X Q|S +|+ 1|2 0|0 PLEKHG2|PLEKHG2 44606711|44606711 0.000000|0.000000 0.05858|0.05858 0.000000|0.000000 0.03702|0.03702 0.725000|0.725000 0.41563|0.41563 -0.142000|-0.142000 0.10311|0.10311 -0.739000|-0.739000 0.04809|0.04809 0.491000|0.491000 0.48974|0.48974 CAG|TCA TCGA-2L-AAQJ-01A-12D-A397-08 PLEKHG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000326802.1 1 0 1 69 286 0 66 1 9.710426e-01 3 23 0 66 2 0 0 0 0 0 2 1 1.000000 69 283 0 65 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.024636 0 0.440000 1.870000 0.429967 0.860000 0.690000 1.000000 1.000000 0.868087 0.860000 1 7.700000e-01 9.600000e-01 PSG6 5675 broad.mit.edu 37 19 43411814 43411814 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr19:43411814G>A ENST00000292125.2 - 4 943 c.899C>T c.(898-900)aCg>aTg p.T300M PSG6_ENST00000187910.2_Missense_Mutation_p.T300M|PSG6_ENST00000402603.4_Intron NM_002782.4 NP_002773.1 Q00889 PSG6_HUMAN pregnancy specific beta-1-glycoprotein 6 44 Prostate(69;0.00899) TTCATTTCTCGTGACACTGGG 0.488000 0 SO:0001583 missense ENST00000292125.2 1 1 hg19 CCDS12613.1 . . . . . . . . . . N 8.993 0.978199 0.18812 . . ENSG00000170848 ENST00000187910;ENST00000292125 T;T 0.15603 2.41;2.41 1.42 -0.067 0.13762 Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); . . . . T 0.30665 0.0772 H 0.95745 3.715 0.09310 N 0.999998 B;P 0.39520 0.331;0.676 B;B 0.40864 0.146;0.342 T 0.33523 -0.9865 9 0.72032 D 0.01 . 4.8586 0.13571 0.0:0.397:0.603:0.0 . 300;300 Q00889;Q00889-2 PSG6_HUMAN;. M 300 ENSP00000187910:T300M;ENSP00000292125:T300M ENSP00000187910:T300M T - 2 0 PSG6 48103654 0.000000 0.05858 0.347000 0.25668 0.098000 0.18820 -0.625000 0.05534 0.792000 0.33850 0.134000 0.15878 ACG TCGA-2L-AAQJ-01A-12D-A397-08 PSG6-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000321436.1 1 0 1 199 650 0 178 0 0 0 0 178 2 0 0 0 0 0 2 1 1.000000 187 606 0 183 2 0 0 0 0 0 2 -20.000000 1 1 121350 1 34 1 0 0 0 2.024636 0 0.440000 1.870000 0.429967 0.990000 0.910000 1.000000 1.000000 0.991422 0.990000 1 9.700000e-01 1 FPR2 2358 broad.mit.edu 37 19 52272706 52272706 + Silent SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr19:52272706C>T ENST00000598776.1 + 2 1567 c.795C>T c.(793-795)acC>acT p.T265T FPR2_ENST00000598953.1_Silent_p.T265T|FPR2_ENST00000340023.6_Silent_p.T265T NM_001462.3 NP_001453.1 P25090 FPR2_HUMAN formyl peptide receptor 2 33 TTCTGGGCACCGTCTGGCTCA 0.502000 0 SO:0001819 synonymous_variant ENST00000598776.1 1 1 hg19 CCDS12840.1 TCGA-2L-AAQJ-01A-12D-A397-08 FPR2-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466912.2 1 0 1 45 160 0 28 0 1.275764e-01 0 3 0 28 2 0 0 0 0 0 2 1 1.000000 45 159 0 27 2 0 0 0 0 0 2 -3.870410 1 1 0 0 1 0 0 0 2.024636 0 0.440000 1.870000 0.429967 0.970000 0.740000 1.000000 1.000000 0.941424 0.970000 1 8.500000e-01 1 PTPRS 5802 broad.mit.edu 37 19 5244288 5244288 + Silent SNP G G A rs144956737 TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr19:5244288G>A ENST00000587303.1 - 10 1293 c.1194C>T c.(1192-1194)taC>taT p.Y398Y PTPRS_ENST00000348075.2_Silent_p.Y385Y|PTPRS_ENST00000372412.4_Silent_p.Y399Y|PTPRS_ENST00000592099.1_Silent_p.Y385Y|PTPRS_ENST00000357368.4_Silent_p.Y398Y|PTPRS_ENST00000353284.2_Silent_p.Y385Y|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000588012.1_Silent_p.Y385Y|PTPRS_ENST00000262963.6_Silent_p.Y394Y Q13332 PTPRS_HUMAN protein tyrosine phosphatase, receptor type, S 61 Alendronate(DB00630)|Etidronic acid(DB01077) CCCAGATCTCGTACTCCGAGT 0.637000 0 SO:0001819 synonymous_variant ENST00000587303.1 1 1 hg19 CCDS45930.1 TCGA-2L-AAQJ-01A-12D-A397-08 PTPRS-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000450762.2 1 0 1 64 205 0 54 0 1.460317e-01 0 3 0 54 2 0 0 0 0 0 2 1 1.000000 63 202 0 53 2 0 0 0 0 0 2 -20.000000 1 1 121410 3 34 1 0 0 0 2.031251 0 0.440000 1.870000 0.435028 0.990000 0.850000 1.000000 1.000000 0.982518 0.990000 1 9.500000e-01 1 ZNF835 90485 broad.mit.edu 37 19 57175831 57175831 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr19:57175831C>T ENST00000537055.2 - 2 967 c.736G>A c.(736-738)Ggt>Agt p.G246S NM_001005850.2 NP_001005850.2 Q9Y2P0 ZN835_HUMAN zinc finger protein 835 47 GGCTTCTCACCGGTGTGGATG 0.692000 0 SO:0001583 missense ENST00000537055.2 1 1 hg19 CCDS56105.1 . . . . . . . . . . C 33 5.267381 0.95399 . . ENSG00000127903 ENST00000342088;ENST00000537055 T 0.25085 1.82 2.12 2.12 0.27331 Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.39963 0.1098 L 0.43152 1.355 0.31918 N 0.61385 D 0.89917 1.0 D 0.83275 0.996 T 0.46857 -0.9161 9 0.87932 D 0 . 10.2869 0.43573 0.0:1.0:0.0:0.0 . 268 Q9Y2P0 ZN835_HUMAN S 268;246 ENSP00000444747:G246S ENSP00000341756:G268S G - 1 0 ZNF835 61867643 0.002000 0.14202 0.005000 0.12908 0.717000 0.41224 1.681000 0.37618 1.506000 0.48736 0.561000 0.74099 GGT TCGA-2L-AAQJ-01A-12D-A397-08 ZNF835-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459800.1 1 0 1 16 123 0 25 0 0 0 1 0 25 2 0 0 0 0 0 2 1 0.999949 16 122 0 25 2 0 0 0 0 0 2 -3.321058 1 1 121392 2 28 1 0 0 0 2.024636 0 0.440000 1.870000 0.429967 0.510000 0.310000 0.770000 0.500000 0.533266 0.510000 0 4.000000e-01 6.500000e-01 ATP5F1 515 broad.mit.edu 37 1 111992194 111992194 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr1:111992194G>A ENST00000369722.3 + 1 637 c.31G>A c.(31-33)Gcc>Acc p.A11T ATP5F1_ENST00000483994.1_Missense_Mutation_p.A11T|Y_RNA_ENST00000363020.1_RNA|ATP5F1_ENST00000369721.4_3'UTR|WDR77_ENST00000411751.2_5'Flank|WDR77_ENST00000497278.1_5'Flank|WDR77_ENST00000235090.5_5'Flank NM_001688.4 NP_001679.2 P24539 AT5F1_HUMAN ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1 8 all_cancers(81;8.16e-06)|all_epithelial(167;5.63e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301) TTCCGCCGCCGCCACAGCGGG 0.577000 0 SO:0001583 missense ENST00000369722.3 0 1 hg19 CCDS836.1 . . . . . . . . . . G 19.52 3.843991 0.71488 . . ENSG00000116459 ENST00000369722;ENST00000483994 T;T 0.31510 1.49;1.51 5.73 4.82 0.62117 . 0.250346 0.33650 N 0.004681 T 0.09202 0.0227 L 0.54323 1.7 0.20074 N 0.999938 P;P 0.48640 0.913;0.913 B;B 0.28385 0.089;0.089 T 0.11817 -1.0572 10 0.24483 T 0.36 . 11.2813 0.49197 0.0844:0.0:0.9156:0.0 . 11;11 Q08ET0;P24539 .;AT5F1_HUMAN T 11 ENSP00000358737:A11T;ENSP00000420366:A11T ENSP00000358737:A11T A + 1 0 ATP5F1 111793717 0.986000 0.35501 1.000000 0.80357 0.867000 0.49689 2.836000 0.48183 1.562000 0.49601 0.655000 0.94253 GCC TCGA-2L-AAQJ-01A-12D-A397-08 ATP5F1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032455.1 0 0 0 6 454 0 105 1 9.088540e-01 2 324 0 105 2 0 0 0 0 0 2 1 0.964964 5 454 0 105 2 0 0 0 0 0 2 -2.421037 0 0 0 0 1 0 1 1 1.798735 1 0.440000 1.870000 0.338061 0.050000 0.010000 0.100000 0.050000 0.058021 0.050000 0 3.000000e-02 8.000000e-02 KPRP 448834 broad.mit.edu 37 1 152733552 152733552 + Silent SNP C C A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr1:152733552C>A ENST00000606109.1 + 1 1516 c.1488C>A c.(1486-1488)cgC>cgA p.R496R KPRP_ENST00000368773.1_Silent_p.R496R Q5T749 KPRP_HUMAN keratinocyte proline-rich protein 60 Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.206) AGACTTGGCGCAGCCCCAGCC 0.647000 0 SO:0001819 synonymous_variant ENST00000606109.1 0 1 hg19 CCDS30862.1 TCGA-2L-AAQJ-01A-12D-A397-08 KPRP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000034522.2 0 0 0 9 296 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 0.994053 9 292 0 52 2 0 0 0 0 0 2 -9.944246 1 1 0 0 1 2 2 4 2.219696 1 0.440000 1.870000 0.481097 0.150000 0.070000 1.000000 0.140000 0.276156 0.150000 0 1.000000e-01 2.700000e-01 FDPS 2224 broad.mit.edu 37 1 155289625 155289625 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr1:155289625G>A ENST00000356657.6 + 10 1127 c.965G>A c.(964-966)gGc>gAc p.G322D RUSC1-AS1_ENST00000450199.1_RNA|RUSC1_ENST00000368352.5_5'Flank|FDPS_ENST00000368356.4_Missense_Mutation_p.G322D|FDPS_ENST00000447866.1_Missense_Mutation_p.G256D|RUSC1-AS1_ENST00000543656.1_RNA|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1_ENST00000368354.3_5'Flank NM_001135821.1 NP_001129293.1 P14324 FPPS_HUMAN farnesyl diphosphate synthase 10 Hepatocellular(266;0.0877)|all_hematologic(923;0.145) Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127) Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399) AGTGTGACCGGCAAAATTGGC 0.567000 0 SO:0001583 missense ENST00000356657.6 0 1 hg19 CCDS1110.1 . . . . . . . . . . G 21.4 4.143251 0.77888 . . ENSG00000160752 ENST00000447866;ENST00000368356;ENST00000356657 T;T;T 0.73681 -0.77;-0.77;-0.77 4.28 4.28 0.50868 Terpenoid synthase (2); 0.000000 0.44688 D 0.000439 D 0.88250 0.6386 H 0.94698 3.57 0.80722 D 1 D 0.76494 0.999 D 0.85130 0.997 D 0.90597 0.4541 10 0.87932 D 0 -1.7784 14.6536 0.68817 0.0:0.0:1.0:0.0 . 322 P14324 FPPS_HUMAN D 256;322;322 ENSP00000391755:G256D;ENSP00000357340:G322D;ENSP00000349078:G322D ENSP00000349078:G322D G + 2 0 FDPS 153556249 1.000000 0.71417 0.997000 0.53966 0.488000 0.33401 9.276000 0.95745 2.673000 0.90976 0.561000 0.74099 GGC TCGA-2L-AAQJ-01A-12D-A397-08 FDPS-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000039053.1 0 0 0 7 586 1 114 0 2.698581e-02 2 947 1 114 26 0 0 0 0 0 2 0 0.018526 7 577 1 111 18 0 0 0 0 0 2 -1.788477 0 1 0 0 1 2 2 4 2.219696 1 0.440000 1.870000 0.481097 0.060000 0.020000 1.000000 0.060000 0.195827 0.060000 0 3.000000e-02 1.200000e-01 BCAN 63827 broad.mit.edu 37 1 156621427 156621427 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr1:156621427G>A ENST00000329117.5 + 7 1579 c.1243G>A c.(1243-1245)Gga>Aga p.G415R RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.G415R NM_021948.4 NP_068767.3 Q96GW7 PGCB_HUMAN brevican 55 all_hematologic(923;0.088)|Hepatocellular(266;0.158) GGAGGACGGAGGAGGTGGAAG 0.557000 0 SO:0001583 missense ENST00000329117.5 1 1 hg19 CCDS1149.1 . . . . . . . . . . G 10.23 1.292944 0.23564 . . ENSG00000132692 ENST00000255029;ENST00000329117;ENST00000361588 T;T 0.13196 2.61;3.33 5.17 3.16 0.36331 . 0.777525 0.10979 N 0.612889 T 0.02193 0.0068 N 0.11201 0.11 0.09310 N 1 B;B 0.15473 0.006;0.013 B;B 0.14578 0.005;0.011 T 0.43940 -0.9360 10 0.15066 T 0.55 -0.351 11.1054 0.48199 0.1755:0.0:0.8245:0.0 . 415;415 Q96GW7;Q96GW7-2 PGCB_HUMAN;. R 354;415;415 ENSP00000331210:G415R;ENSP00000354925:G415R ENSP00000255029:G354R G + 1 0 BCAN 154888051 0.011000 0.17503 0.672000 0.29872 0.985000 0.73830 1.976000 0.40579 1.418000 0.47098 0.655000 0.94253 GGA TCGA-2L-AAQJ-01A-12D-A397-08 BCAN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000081844.2 1 0 1 88 438 0 84 0 0 0 0 84 2 0 0 0 0 0 2 1 1.000000 88 434 0 84 2 0 0 0 0 0 2 -20.000000 1 1 121410 7 41 1 2 2 4 2.219696 1 0.440000 1.870000 0.481097 0.830000 0.670000 1.000000 0.820000 0.848985 0.830000 0 7.400000e-01 9.900000e-01 TNN 63923 broad.mit.edu 37 1 175105027 175105027 + Missense_Mutation SNP G G T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr1:175105027G>T ENST00000239462.4 + 16 3490 c.3377G>T c.(3376-3378)tGg>tTg p.W1126L NM_022093.1 NP_071376.1 Q9UQP3 TENN_HUMAN tenascin N p.W1126*(1) 156 Breast(1374;0.000962) TTCAAGCGATGGAGGAGCTAT 0.537000 1 Substitution - Nonsense(1) SO:0001583 missense ENST00000239462.4 1 1 hg19 CCDS30943.1 . . . . . . . . . . G 28.4 4.912742 0.92178 . . ENSG00000120332 ENST00000239462;ENST00000539081 D 0.86865 -2.18 5.5 5.5 0.81552 Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1); 0.115488 0.64402 D 0.000005 D 0.96614 0.8895 H 0.98818 4.34 0.80722 D 1 D 0.76494 0.999 D 0.75484 0.986 D 0.98254 1.0495 10 0.87932 D 0 . 19.003 0.92841 0.0:0.0:1.0:0.0 . 1126 Q9UQP3 TENN_HUMAN L 1126;949 ENSP00000239462:W1126L ENSP00000239462:W1126L W + 2 0 TNN 173371650 1.000000 0.71417 1.000000 0.80357 0.947000 0.59692 9.420000 0.97426 2.555000 0.86185 0.655000 0.94253 TGG TCGA-2L-AAQJ-01A-12D-A397-08 TNN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084422.1 1 0 1 106 395 0 97 0 0 0 0 97 2 0 0 0 0 0 2 1 1.000000 104 389 0 97 2 0 0 0 0 0 2 -3.575378 1 1 0 0 1 2 2 4 2.219696 1 0.440000 1.870000 0.481097 0.990000 0.870000 1.000000 1.000000 0.984020 0.990000 1 9.500000e-01 1 TNR 7143 broad.mit.edu 37 1 175365862 175365862 + Missense_Mutation SNP G G A rs138654492 TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr1:175365862G>A ENST00000367674.2 - 5 1766 c.1058C>T c.(1057-1059)aCg>aTg p.T353M TNR_ENST00000263525.2_Missense_Mutation_p.T353M Q92752 TENR_HUMAN tenascin R 177 Renal(580;0.146) CACATATTCCGTCACTGCCAT 0.617000 0 SO:0001583 missense ENST00000367674.2 0 1 hg19 CCDS1318.1 . . . . . . . . . . G 28.3 4.905250 0.92035 2.27E-4 0.0 ENSG00000116147 ENST00000367674;ENST00000263525;ENST00000367673 T;T 0.60171 0.21;0.21 5.96 5.96 0.96718 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.055941 0.64402 D 0.000001 T 0.77805 0.4185 M 0.78344 2.41 0.80722 D 1 D 0.89917 1.0 D 0.72075 0.976 T 0.76277 -0.3018 10 0.46703 T 0.11 . 19.9958 0.97383 0.0:0.0:1.0:0.0 . 353 Q92752 TENR_HUMAN M 353 ENSP00000356646:T353M;ENSP00000263525:T353M ENSP00000263525:T353M T - 2 0 TNR 173632485 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.328000 0.96403 2.826000 0.97356 0.655000 0.94253 ACG TCGA-2L-AAQJ-01A-12D-A397-08 TNR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084414.4 0 0 0 7 540 0 86 0 0 0 0 86 2 0 0 0 0 0 2 1 0.979406 7 529 0 86 2 0 0 0 0 0 2 -5.621657 1 1 121412 7 42 1 2 2 4 2.219696 1 0.440000 1.870000 0.481097 0.060000 0.020000 1.000000 0.070000 0.200547 0.060000 0 4.000000e-02 1.300000e-01 PM20D1 148811 broad.mit.edu 37 1 205819140 205819140 + Missense_Mutation SNP T T G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr1:205819140T>G ENST00000367136.4 - 1 105 c.61A>C c.(61-63)Acc>Ccc p.T21P PM20D1_ENST00000460624.1_5'UTR NM_152491.4 NP_689704.4 Q6GTS8 P20D1_HUMAN peptidase M20 domain containing 1 28 Breast(84;0.201) BRCA - Breast invasive adenocarcinoma(75;0.0252) CTGGAGACGGTAGGGAAAACT 0.602000 0 SO:0001583 missense ENST00000367136.4 1 1 hg19 CCDS1460.1 . . . . . . . . . . T 12.71 2.018274 0.35606 . . ENSG00000162877 ENST00000367136 T 0.07327 3.2 5.44 0.353 0.16058 . 0.566255 0.20291 N 0.095250 T 0.08714 0.0216 L 0.59436 1.845 0.09310 N 1 P 0.49961 0.93 P 0.44860 0.462 T 0.20874 -1.0262 10 0.36615 T 0.2 . 3.7543 0.08579 0.1477:0.2187:0.0:0.6336 . 21 Q6GTS8 P20D1_HUMAN P 21 ENSP00000356104:T21P ENSP00000356104:T21P T - 1 0 PM20D1 204085763 0.961000 0.32948 0.001000 0.08648 0.039000 0.13416 0.604000 0.24164 -0.105000 0.12132 0.533000 0.62120 ACC TCGA-2L-AAQJ-01A-12D-A397-08 PM20D1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087736.1 1 0 1 28 245 0 58 0 0 0 1 0 58 2 0 0 0 0 0 2 1 1.000000 27 245 0 57 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 2 2 4 2.219696 1 0.440000 1.870000 0.481097 0.520000 0.350000 1.000000 0.500000 0.582681 0.520000 0 4.200000e-01 7.100000e-01 KIAA1522 57648 broad.mit.edu 37 1 33237860 33237860 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr1:33237860G>A ENST00000373480.1 + 6 3006 c.2903G>A c.(2902-2904)cGc>cAc p.R968H YARS_ENST00000469100.1_5'Flank|KIAA1522_ENST00000401073.2_Missense_Mutation_p.R1027H|KIAA1522_ENST00000373481.3_Missense_Mutation_p.R979H|KIAA1522_ENST00000294521.3_Intron NM_001198972.1 NP_001185901.1 Q9P206 K1522_HUMAN KIAA1522 24 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244) CCTGTGGCCCGCAAGCCGTCT 0.662000 0 SO:0001583 missense ENST00000373480.1 0 1 hg19 CCDS55588.1 . . . . . . . . . . G 20.8 4.043295 0.75732 . . ENSG00000162522 ENST00000401073;ENST00000373481;ENST00000373480 T;T;T 0.16597 2.33;2.34;2.35 5.05 4.14 0.48551 . 0.086750 0.45867 D 0.000333 T 0.20941 0.0504 M 0.61703 1.905 0.30845 N 0.73524 D;D;D 0.57257 0.979;0.979;0.979 P;P;P 0.46049 0.502;0.502;0.502 T 0.16541 -1.0399 10 0.46703 T 0.11 -11.6125 8.9717 0.35910 0.2107:0.0:0.7892:0.0 . 979;968;1027 Q9P206-3;Q9P206;Q9P206-2 .;K1522_HUMAN;. H 1027;979;968 ENSP00000383851:R1027H;ENSP00000362580:R979H;ENSP00000362579:R968H ENSP00000362579:R968H R + 2 0 KIAA1522 33010447 1.000000 0.71417 1.000000 0.80357 0.937000 0.57800 3.416000 0.52707 1.503000 0.48686 0.650000 0.86243 CGC TCGA-2L-AAQJ-01A-12D-A397-08 KIAA1522-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000022130.1 0 0 0 4 182 1 56 0 3.529645e-02 0 168 1 56 11 0 0 0 0 0 2 0 0.031157 4 178 1 55 12 0 0 0 0 0 2 -2.521368 1 1 120800 4 33 1 0 1 1 1.756461 1 0.440000 1.870000 0.323998 0.080000 0.020000 0.190000 0.080000 0.099028 0.080000 0 5.000000e-02 1.400000e-01 ENO1 2023 broad.mit.edu 37 1 8926458 8926458 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr1:8926458G>A ENST00000234590.4 - 7 666 c.547C>T c.(547-549)Cgc>Tgc p.R183C NM_001428.3 NP_001419.1 P06733 ENOA_HUMAN enolase 1, (alpha) 10 Ovarian(185;0.0661)|all_lung(157;0.127) all_epithelial(116;2.54e-20)|all_lung(118;2.99e-06)|Lung NSC(185;6.25e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) GCTCCAATGCGCATGGCTTCC 0.512000 Esophageal Squamous(21;302 608 19946 22210 33560) 0 SO:0001583 missense ENST00000234590.4 0 1 hg19 CCDS97.1 . . . . . . . . . . G 19.56 3.849934 0.71603 . . ENSG00000074800 ENST00000234590 T 0.58358 0.34 5.33 5.33 0.75918 Enolase, C-terminal (1); 0.052249 0.85682 N 0.000000 T 0.63792 0.2541 M 0.87097 2.86 0.80722 D 1 B;B;B;B;B 0.31769 0.194;0.238;0.339;0.161;0.194 B;B;B;B;B 0.34991 0.102;0.123;0.193;0.061;0.102 T 0.69720 -0.5069 10 0.87932 D 0 -2.9305 18.013 0.89230 0.0:0.0:1.0:0.0 . 87;150;21;90;183 E2DRY6;A4UCS8;Q9BT62;P06733-2;P06733 .;.;.;.;ENOA_HUMAN C 183 ENSP00000234590:R183C ENSP00000234590:R183C R - 1 0 ENO1 8849045 1.000000 0.71417 1.000000 0.80357 0.968000 0.65278 7.984000 0.88150 2.492000 0.84095 0.563000 0.77884 CGC TCGA-2L-AAQJ-01A-12D-A397-08 ENO1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000004945.1 0 0 0 6 452 0 104 0 9.994856e-01 0 1288 0 104 2 0 0 0 0 0 2 1 0.964240 6 448 0 103 2 0 0 0 0 0 2 -2.202556 0 1 121412 2 37 1 0 1 1 1.797343 1 0.440000 1.870000 0.343186 0.050000 0.010000 0.110000 0.050000 0.058738 0.050000 0 3.000000e-02 8.000000e-02 RBM12 10137 broad.mit.edu 37 20 34240896 34240896 + Silent SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr20:34240896C>T ENST00000374114.3 - 3 2612 c.2349G>A c.(2347-2349)tcG>tcA p.S783S CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000317677.5_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|RBM12_ENST00000374104.3_Silent_p.S783S|RBM12_ENST00000359646.1_Silent_p.S783S|CPNE1_ENST00000397445.1_Intron NM_001198838.1|NM_001198840.1|NM_006047.5 NP_001185767.1|NP_001185769.1|NP_006038.2 Q9NTZ6 RBM12_HUMAN RNA binding motif protein 12 36 Lung NSC(9;0.00608)|all_lung(11;0.00918) BRCA - Breast invasive adenocarcinoma(18;0.00953) CTCCAAATCCCGATGGCCCAC 0.562000 0 SO:0001819 synonymous_variant ENST00000374114.3 1 1 hg19 CCDS13261.1 TCGA-2L-AAQJ-01A-12D-A397-08 RBM12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078894.1 1 0 0 79 246 0 67 1 9.999997e-01 29 42 0 67 2 0 0 0 0 0 2 1 1.000000 77 245 0 66 2 0 0 0 0 0 2 -4.091664 1 1 0 0 1 0 0 0 2.020317 0 0.440000 1.870000 0.427403 0.990000 0.870000 1.000000 1.000000 0.987650 0.990000 1 9.700000e-01 1 SIGLEC1 6614 broad.mit.edu 37 20 3673686 3673686 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr20:3673686C>T ENST00000344754.4 - 14 3600 c.3601G>A c.(3601-3603)Gcc>Acc p.A1201T SIGLEC1_ENST00000202578.4_Missense_Mutation_p.A1201T NM_023068.3 NP_075556.1 Q9BZZ2 SN_HUMAN sialic acid binding Ig-like lectin 1, sialoadhesin 70 GCCAGCTGGGCGGGCGGGCGG 0.721000 0 SO:0001583 missense ENST00000344754.4 1 1 hg19 CCDS13060.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 17.66|17.66 3.443368|3.443368 0.63067|0.63067 .|. .|. ENSG00000088827|ENSG00000088827 ENST00000344754;ENST00000202578|ENST00000419548 T;T|. 0.75154|. -0.91;-0.91|. 4.74|4.74 4.74|4.74 0.60224|0.60224 Immunoglobulin subtype (1);Immunoglobulin-like fold (1);|. 0.000000|. 0.39615|. N|. 0.001309|. T|T 0.73992|0.73992 0.3658|0.3658 M|M 0.78223|0.78223 2.4|2.4 0.36727|0.36727 D|D 0.88151|0.88151 D;D|. 0.89917|. 1.0;1.0|. D;D|. 0.75484|. 0.986;0.966|. T|T 0.79339|0.79339 -0.1844|-0.1844 10|5 0.30078|. T|. 0.28|. .|. 13.088|13.088 0.59153|0.59153 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 1201;1201|. Q9BZZ2;Q9BZZ2-3|. SN_HUMAN;.|. T|H 1201|14 ENSP00000341141:A1201T;ENSP00000202578:A1201T|. ENSP00000202578:A1201T|. A|R -|- 1|2 0|0 SIGLEC1|SIGLEC1 3621686|3621686 0.045000|0.045000 0.20229|0.20229 0.979000|0.979000 0.43373|0.43373 0.294000|0.294000 0.27393|0.27393 0.222000|0.222000 0.17699|0.17699 2.477000|2.477000 0.83638|0.83638 0.655000|0.655000 0.94253|0.94253 GCC|CGC TCGA-2L-AAQJ-01A-12D-A397-08 SIGLEC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077761.2 1 0 0 48 104 0 22 0 0 0 1 0 22 2 0 0 0 0 0 2 1 1.000000 48 103 0 21 2 0 0 0 0 0 2 -6.835376 1 1 119828 1 27 1 0 1 1 1.597628 1 0.440000 1.870000 0.282051 0.940000 0.780000 1.000000 0.990000 0.934704 0.940000 1 8.700000e-01 9.900000e-01 BAGE2 85319 broad.mit.edu 37 21 11098773 11098773 + RNA SNP G G A rs77771067 TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr21:11098773G>A ENST00000470054.1 - 0 152 Q86Y30 BAGE2_HUMAN B melanoma antigen family, member 2 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) cgctcaggccgccctcctaac 0.627000 0 ENST00000470054.1 1 1 hg19 TCGA-2L-AAQJ-01A-12D-A397-08 BAGE2-001 KNOWN basic processed_transcript pseudogene OTTHUMT00000157417.3 0 0 0 54 747 0 183 0 0 0 0 183 2 0 0 0 0 0 2 1 1.000000 51 677 0 177 2 0 0 0 0 0 2 -2.966611 1 1 121250 21 43 1 0 0 0 2.026235 0 0.440000 1.870000 0.429967 0.290000 0.220000 0.380000 0.300000 0.305350 0.290000 0 2.500000e-01 3.400000e-01 ADARB1 104 broad.mit.edu 37 21 46596475 46596475 + Missense_Mutation SNP C C T rs142476560 TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr21:46596475C>T ENST00000360697.3 + 2 874 c.859C>T c.(859-861)Cgg>Tgg p.R287W ADARB1_ENST00000389863.4_Missense_Mutation_p.R287W|ADARB1_ENST00000539173.1_Missense_Mutation_p.R287W|ADARB1_ENST00000348831.4_Missense_Mutation_p.R287W|ADARB1_ENST00000437626.1_Intron P78563 RED1_HUMAN adenosine deaminase, RNA-specific, B1 17 TGCCAAGGCCCGGGCTGCGCA 0.572000 0 SO:0001583 missense ENST00000360697.3 1 1 hg19 CCDS33589.1 . . . . . . . . . . C 21.0 4.077779 0.76528 . . ENSG00000197381 ENST00000539173;ENST00000539917;ENST00000389863;ENST00000348831;ENST00000360697 T;T;T;T 0.77750 -1.12;-1.12;-1.12;-1.12 5.14 5.14 0.70334 Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1); 0.061314 0.64402 D 0.000003 D 0.86727 0.6002 M 0.77486 2.375 0.80722 D 1 D;D;D;D;D 0.89917 0.999;1.0;0.999;0.998;0.998 D;D;D;D;D 0.77004 0.957;0.989;0.975;0.957;0.957 D 0.87690 0.2553 10 0.72032 D 0.01 -46.512 11.5532 0.50733 0.1787:0.8213:0.0:0.0 . 314;287;287;315;287 P78563-4;P78563;Q4AE77;G5E9B4;P78563-3 .;RED1_HUMAN;.;.;. W 287 ENSP00000441897:R287W;ENSP00000374513:R287W;ENSP00000015877:R287W;ENSP00000353920:R287W ENSP00000015877:R287W R + 1 2 ADARB1 45420903 0.994000 0.37717 1.000000 0.80357 0.976000 0.68499 2.697000 0.47060 2.552000 0.86080 0.655000 0.94253 CGG TCGA-2L-AAQJ-01A-12D-A397-08 ADARB1-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000206648.2 1 0 1 87 230 0 57 0 1.861163e-01 0 3 0 57 2 0 0 0 0 0 2 1 1.000000 86 229 0 57 2 0 0 0 0 0 2 -5.924463 1 1 0 0 1 0 0 0 2.026235 0 0.440000 1.870000 0.429967 0.990000 0.990000 1.000000 1.000000 0.999360 0.990000 1 9.900000e-01 1 CECR2 27443 broad.mit.edu 37 22 18021889 18021889 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr22:18021889C>T ENST00000400585.2 + 16 2006 c.1568C>T c.(1567-1569)aCa>aTa p.T523I CECR2_ENST00000400573.5_Missense_Mutation_p.T664I|CECR2_ENST00000262608.8_Missense_Mutation_p.T665I Q9BXF3 CECR2_HUMAN cat eye syndrome chromosome region, candidate 2 59 all_epithelial(15;0.139) AGGCTAGGCACACCAGAGGAG 0.547000 0 SO:0001583 missense ENST00000400585.2 0 1 hg19 . . . . . . . . . . C 4.046 0.006138 0.07866 . . ENSG00000099954 ENST00000400585;ENST00000400573;ENST00000262608 T;T;T 0.26223 1.88;1.87;1.75 5.28 3.1 0.35709 . 1.079560 0.07208 N 0.858745 T 0.25195 0.0612 L 0.51422 1.61 0.09310 N 1 B;B;B 0.23442 0.085;0.049;0.029 B;B;B 0.14023 0.01;0.01;0.01 T 0.17684 -1.0361 10 0.29301 T 0.29 -0.0068 10.7002 0.45922 0.0:0.7801:0.0:0.2199 . 706;523;664 Q9BXF3;B7WPH3;E2QRE6 CECR2_HUMAN;.;. I 523;664;665 ENSP00000383428:T523I;ENSP00000383417:T664I;ENSP00000262608:T665I ENSP00000262608:T665I T + 2 0 CECR2 16401889 0.000000 0.05858 0.002000 0.10522 0.005000 0.04900 0.558000 0.23469 1.467000 0.48044 0.655000 0.94253 ACA TCGA-2L-AAQJ-01A-12D-A397-08 CECR2-002 NOVEL basic|appris_candidate|exp_conf protein_coding protein_coding OTTHUMT00000316226.2 0 0 0 9 77 0 21 0 0 0 1 0 21 2 0 0 0 0 0 2 1 0.994775 9 76 0 20 2 0 0 0 0 0 2 -15.383410 1 1 0 0 1 1 2 3 2.062546 0 0.440000 1.870000 0.441229 0.490000 0.240000 0.840000 0.470000 0.509919 0.490000 0 3.500000e-01 6.600000e-01 TRMU 55687 broad.mit.edu 37 22 46742405 46742405 + Missense_Mutation SNP G G A rs34012206 byFrequency TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr22:46742405G>A ENST00000290846.4 + 4 782 c.442G>A c.(442-444)Gaa>Aaa p.E148K TRMU_ENST00000424260.2_Missense_Mutation_p.E113K|TRMU_ENST00000381019.3_Missense_Mutation_p.E148K NM_018006.4 NP_060476.2 O75648 MTU1_HUMAN tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase p.E148K(1) 10 Ovarian(80;0.00965)|Breast(42;0.0194)|all_neural(38;0.0416) TAAGAAGCCCGAAGGGCTTTT 0.443000 1 Substitution - Missense(1) SO:0001583 missense ENST00000290846.4 1 0 hg19 CCDS14075.1 35 0.016025641025641024 34 0.06910569105691057 1 0.0027624309392265192 0 0.0 0 0.0 g 11.94 1.787630 0.31593 0.047208 4.65E-4 ENSG00000100416 ENST00000290846;ENST00000381019;ENST00000424260 T;T;T 0.74106 -0.49;-0.81;0.01 5.41 0.554 0.17241 Rossmann-like alpha/beta/alpha sandwich fold (1); 0.611098 0.17383 N 0.176250 T 0.06962 0.0177 N 0.08118 0 0.09310 N 1 B;B;B 0.10296 0.002;0.003;0.002 B;B;B 0.06405 0.002;0.001;0.001 T 0.10359 -1.0633 10 0.38643 T 0.18 -16.2804 10.4278 0.44389 0.1212:0.5516:0.3271:0.0 rs34012206 148;148;148 B4DHM1;O75648-2;O75648 .;.;MTU1_HUMAN K 148;148;113 ENSP00000290846:E148K;ENSP00000370407:E148K;ENSP00000406038:E113K ENSP00000290846:E148K E + 1 0 TRMU 45121069 0.055000 0.20627 0.331000 0.25455 0.916000 0.54674 0.716000 0.25836 0.616000 0.30141 0.651000 0.88453 GAA TCGA-2L-AAQJ-01A-12D-A397-08 TRMU-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318042.2 0 0 1 93 319 0 87 1 9.710165e-01 2 20 0 87 2 0 0 0 0 0 2 1 1.000000 93 318 0 86 2 0 0 0 0 0 2 -2.046559 0 1 121412 561 60 1 0 1 1 2.056367 0 0.440000 1.870000 0.438765 0.990000 0.840000 1.000000 1.000000 0.974810 0.990000 1 9.200000e-01 1 APOB 338 broad.mit.edu 37 2 21231133 21231133 + Silent SNP A A G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr2:21231133A>G ENST00000233242.1 - 26 8734 c.8607T>C c.(8605-8607)ctT>ctC p.L2869L NM_000384.2 NP_000375 P04114 APOB_HUMAN apolipoprotein B 305 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) CTCCATTACTAAGCTCCAGTG 0.393000 0 SO:0001819 synonymous_variant ENST00000233242.1 0 1 hg19 CCDS1703.1 TCGA-2L-AAQJ-01A-12D-A397-08 APOB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207571.1 0 0 0 9 686 0 112 0 0 0 0 112 2 0 0 0 0 0 2 1 0.994141 8 684 0 112 2 0 0 0 0 0 2 -6.972063 1 1 0 0 1 0 0 0 2.058326 0 0.440000 1.870000 0.440000 0.050000 0.020000 0.110000 0.060000 0.065084 0.050000 0 3.000000e-02 9.000000e-02 GLB1L 79411 broad.mit.edu 37 2 220101856 220101856 + Missense_Mutation SNP T T C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr2:220101856T>C ENST00000295759.7 - 17 2216 c.1903A>G c.(1903-1905)Atc>Gtc p.I635V GLB1L_ENST00000356283.3_Missense_Mutation_p.I545V|GLB1L_ENST00000409640.1_Missense_Mutation_p.I545V|GLB1L_ENST00000392089.2_Missense_Mutation_p.I635V|GLB1L_ENST00000497855.1_5'UTR Q6UWU2 GLB1L_HUMAN galactosidase, beta 1-like 22 all_lung(227;1.19e-05)|Lung NSC(271;2.76e-05)|Medulloblastoma(418;0.0208)|Esophageal squamous(248;0.0559) AGGGAATTGATATGTGTCCTG 0.468000 0 SO:0001583 missense ENST00000295759.7 1 1 hg19 CCDS2437.1 . . . . . . . . . . T 4.871 0.161916 0.09287 . . ENSG00000163521 ENST00000295759;ENST00000409640;ENST00000392089;ENST00000356283 D;D;D;D 0.96992 -4.2;-3.93;-4.2;-3.93 4.93 -9.86 0.00473 Galactose-binding domain-like (1); 3.089320 0.00575 N 0.000313 D 0.86112 0.5855 N 0.04959 -0.14 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.81204 -0.1039 10 0.21540 T 0.41 0.3857 2.6931 0.05126 0.1812:0.3995:0.1959:0.2234 . 545;635 Q6UWU2-2;Q6UWU2 .;GLB1L_HUMAN V 635;545;635;545 ENSP00000295759:I635V;ENSP00000386354:I545V;ENSP00000375939:I635V;ENSP00000348628:I545V ENSP00000295759:I635V I - 1 0 GLB1L 219810100 0.000000 0.05858 0.000000 0.03702 0.008000 0.06430 -1.053000 0.03500 -2.213000 0.00735 -0.256000 0.11100 ATC TCGA-2L-AAQJ-01A-12D-A397-08 GLB1L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256822.2 1 0 1 99 398 0 107 1 9.999935e-01 20 51 0 107 2 0 0 0 0 0 2 1 1.000000 98 394 0 106 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.022512 0 0.440000 1.870000 0.429967 0.880000 0.730000 1.000000 1.000000 0.888803 0.880000 1 8.000000e-01 9.700000e-01 ITSN2 50618 broad.mit.edu 37 2 24533237 24533237 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr2:24533237C>T ENST00000355123.4 - 7 1012 c.569G>A c.(568-570)gGg>gAg p.G190E ITSN2_ENST00000406921.3_Missense_Mutation_p.G190E|ITSN2_ENST00000361999.3_Missense_Mutation_p.G190E|ITSN2_ENST00000407704.1_5'Flank NM_006277.2 NP_006268.2 Q9NZM3 ITSN2_HUMAN intersectin 2 61 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) ATAAGATGACCCATGAGGCAA 0.343000 0 SO:0001583 missense ENST00000355123.4 1 1 hg19 CCDS1710.2 . . . . . . . . . . C 12.21 1.868542 0.32977 . . ENSG00000198399 ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011;ENST00000443927 T;T;T;T;T;T 0.59906 0.25;0.23;0.25;0.65;0.74;1.57 4.98 4.1 0.47936 . 0.809232 0.09677 U 0.770329 T 0.49779 0.1577 N 0.14661 0.345 0.24743 N 0.993024 B;B;B;P 0.40050 0.131;0.131;0.314;0.7 B;B;B;P 0.44477 0.028;0.028;0.041;0.451 T 0.48410 -0.9038 10 0.56958 D 0.05 . 13.9001 0.63797 0.0:0.1599:0.8401:0.0 . 190;190;190;190 Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 .;.;.;ITSN2_HUMAN E 190;190;190;189;190;190;176 ENSP00000354561:G190E;ENSP00000347244:G190E;ENSP00000370250:G190E;ENSP00000384499:G190E;ENSP00000391224:G190E;ENSP00000391715:G176E ENSP00000347244:G190E G - 2 0 ITSN2 24386741 1.000000 0.71417 0.889000 0.34880 0.766000 0.43426 3.658000 0.54482 1.218000 0.43458 -0.499000 0.04595 GGG TCGA-2L-AAQJ-01A-12D-A397-08 ITSN2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000207620.2 1 0 1 123 844 0 166 1 6.229116e-01 4 12 0 166 2 0 0 0 0 0 2 1 1.000000 123 838 0 165 2 0 0 0 0 0 2 -3.142702 1 1 121412 1 36 1 0 0 0 2.058326 0 0.440000 1.870000 0.440000 0.570000 0.480000 0.670000 0.580000 0.580895 0.570000 0 5.200000e-01 6.300000e-01 BCL11A 53335 broad.mit.edu 37 2 60688782 60688782 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr2:60688782C>T ENST00000335712.6 - 4 1492 c.1265G>A c.(1264-1266)cGc>cAc p.R422H BCL11A_ENST00000538214.1_Missense_Mutation_p.R388H|BCL11A_ENST00000537768.1_Missense_Mutation_p.R91H|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000358510.4_Missense_Mutation_p.R388H|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000356842.4_Missense_Mutation_p.R422H NM_022893.3 NP_075044.2 Q9H165 BC11A_HUMAN B-cell CLL/lymphoma 11A (zinc finger protein) 59 LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199) CTTCATGTGGCGCTTCAGCTT 0.647000 T IGH@ B-CLL Dom yes 2 2p13 53335 B-cell CLL/lymphoma 11A L 0 SO:0001583 missense ENST00000335712.6 0 1 hg19 CCDS1862.1 . . . . . . . . . . C 13.62 2.291279 0.40494 . . ENSG00000119866 ENST00000356842;ENST00000378117;ENST00000538214;ENST00000537768;ENST00000335712;ENST00000358510 T;T;T;T;T 0.16743 3.17;3.17;2.32;5.19;5.19 5.27 4.37 0.52481 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.062434 0.64402 D 0.000010 T 0.41396 0.1157 M 0.73217 2.22 0.80722 D 1 D;D;D;D;D 0.89917 1.0;0.999;1.0;1.0;1.0 D;D;D;D;D 0.87578 0.998;0.98;0.997;0.998;0.997 T 0.34153 -0.9840 10 0.56958 D 0.05 -2.2443 15.0016 0.71476 0.1436:0.8564:0.0:0.0 . 388;91;388;422;422 F5H2Y4;B4DT16;Q9H165-6;Q9H165;D9YZV9 .;.;.;BC11A_HUMAN;. H 422;458;388;91;422;388 ENSP00000349300:R422H;ENSP00000438303:R388H;ENSP00000443712:R91H;ENSP00000338774:R422H;ENSP00000351307:R388H ENSP00000338774:R422H R - 2 0 BCL11A 60542286 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 7.818000 0.86416 1.173000 0.42796 0.655000 0.94253 CGC TCGA-2L-AAQJ-01A-12D-A397-08 BCL11A-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000251579.2 0 0 0 8 421 0 85 0 0 0 1 0 85 2 0 0 0 0 0 2 1 0.988998 8 416 0 84 2 0 0 0 0 0 2 -2.615840 1 1 0 0 1 0 0 0 2.046845 0 0.440000 1.870000 0.437525 0.080000 0.030000 0.160000 0.080000 0.094216 0.080000 0 5.000000e-02 1.200000e-01 ADCY5 111 broad.mit.edu 37 3 123021980 123021980 + Silent SNP C C T rs148384901 TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr3:123021980C>T ENST00000462833.1 - 14 3858 c.2646G>A c.(2644-2646)gcG>gcA p.A882A ADCY5_ENST00000309879.5_Silent_p.A532A|ADCY5_ENST00000491190.1_Silent_p.A515A NM_183357.2 NP_899200.1 O95622 ADCY5_HUMAN adenylate cyclase 5 60 CGGCCGACTCCGCCACGTGAC 0.652000 0 SO:0001819 synonymous_variant ENST00000462833.1 1 1 hg19 CCDS3022.1 TCGA-2L-AAQJ-01A-12D-A397-08 ADCY5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000355889.4 1 0 1 43 169 0 44 0 4.371882e-01 0 7 0 44 2 0 0 0 0 0 2 1 1.000000 43 166 0 42 2 0 0 0 0 0 2 -3.683136 1 1 121410 3 37 1 1 2 3 2.071607 0 0.440000 1.870000 0.441229 0.920000 0.690000 1.000000 1.000000 0.907529 0.920000 1 8.000000e-01 1 TGFBR2 7048 broad.mit.edu 37 3 30713171 30713171 + Nonsense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr3:30713171C>T ENST00000295754.5 + 4 878 c.496C>T c.(496-498)Caa>Taa p.Q166* TGFBR2_ENST00000359013.4_Nonsense_Mutation_p.Q191* NM_003242.5 NP_003233.4 P37173 TGFR2_HUMAN transforming growth factor, beta receptor II (70/80kDa) 53 AGTCATATTTCAAGTGACAGG 0.473000 0 SO:0001587 stop_gained ENST00000295754.5 0 1 hg19 CCDS2648.1 . . . . . . . . . . C 38 6.940423 0.97952 . . ENSG00000163513 ENST00000295754;ENST00000359013;ENST00000383765;ENST00000439925 . . . 4.86 3.91 0.45181 . 0.557577 0.20898 N 0.083695 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.07325 T 0.83 . 12.5905 0.56439 0.231:0.769:0.0:0.0 . . . . X 166;191;68;32 . ENSP00000295754:Q166X Q + 1 0 TGFBR2 30688175 1.000000 0.71417 0.989000 0.46669 0.920000 0.55202 2.769000 0.47654 2.508000 0.84585 0.655000 0.94253 CAA TCGA-2L-AAQJ-01A-12D-A397-08 TGFBR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252994.2 1 0 1 50 148 0 49 1 9.999827e-01 6 47 0 49 2 1 1 76 223 0 191 2 1 1.000000 49 148 0 49 2 0 0 0 0 0 2 -4.720671 1 1 0 0 1 0 1 1 1.610984 1 0.440000 1.870000 0.282051 0.860000 0.670000 0.990000 0.880000 0.861450 0.860000 1 7.600000e-01 9.500000e-01 LRRC2 79442 broad.mit.edu 37 3 46563080 46563080 + Missense_Mutation SNP C C G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr3:46563080C>G ENST00000395905.3 - 8 1390 c.998G>C c.(997-999)aGt>aCt p.S333T LRRC2_ENST00000296144.3_Missense_Mutation_p.S333T NM_024512.4 NP_078788.2 Q9BYS8 LRRC2_HUMAN leucine rich repeat containing 2 17 Ovarian(412;0.0563) ATCCCGTTCACTTTCCATTAT 0.328000 0 SO:0001583 missense ENST00000395905.3 0 1 hg19 CCDS2741.1 . . . . . . . . . . C 11.15 1.554666 0.27739 . . ENSG00000163827 ENST00000395905;ENST00000296144 T;T 0.17854 2.25;2.25 4.56 3.67 0.42095 . 0.161627 0.41097 N 0.000942 T 0.13457 0.0326 L 0.40543 1.245 0.32701 N 0.512847 B 0.06786 0.001 B 0.08055 0.003 T 0.13845 -1.0494 10 0.14656 T 0.56 . 12.2733 0.54719 0.0:0.8089:0.1911:0.0 . 333 Q9BYS8 LRRC2_HUMAN T 333 ENSP00000379241:S333T;ENSP00000296144:S333T ENSP00000296144:S333T S - 2 0 LRRC2 46538084 0.998000 0.40836 0.863000 0.33907 0.897000 0.52465 0.599000 0.24089 1.245000 0.43885 0.591000 0.81541 AGT TCGA-2L-AAQJ-01A-12D-A397-08 LRRC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257375.2 0 0 0 5 189 0 45 0 0 0 1 0 45 2 0 0 0 0 0 2 1 0.937509 5 188 0 45 2 0 0 0 0 0 2 -7.000087 1 1 0 0 1 0 1 1 1.610984 1 0.440000 1.870000 0.282051 0.090000 0.030000 0.200000 0.090000 0.107110 0.090000 0 5.000000e-02 1.500000e-01 DOCK3 1795 broad.mit.edu 37 3 51378785 51378785 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr3:51378785G>A ENST00000266037.9 + 38 3907 c.3884G>A c.(3883-3885)cGg>cAg p.R1295Q NM_004947.4 NP_004938.1 Q8IZD9 DOCK3_HUMAN dedicator of cytokinesis 3 45 GGACTGTGCCGGAAGATCATT 0.532000 0 SO:0001583 missense ENST00000266037.9 0 1 hg19 CCDS46835.1 . . . . . . . . . . G 15.93 2.977405 0.53720 . . ENSG00000088538 ENST00000266037;ENST00000402669 T 0.04603 3.59 5.5 5.5 0.81552 . 0.000000 0.85682 D 0.000000 T 0.08891 0.0220 N 0.20766 0.605 0.58432 D 0.999999 D 0.67145 0.996 P 0.55087 0.768 T 0.47032 -0.9148 10 0.28530 T 0.3 . 19.4028 0.94637 0.0:0.0:1.0:0.0 . 1295 Q8IZD9 DOCK3_HUMAN Q 1295;91 ENSP00000266037:R1295Q ENSP00000266037:R1295Q R + 2 0 DOCK3 51353825 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.863000 0.87023 2.574000 0.86865 0.655000 0.94253 CGG TCGA-2L-AAQJ-01A-12D-A397-08 DOCK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346478.5 0 0 0 5 117 0 23 0 0 0 0 23 2 0 9.898736e-01 4 773 2 543 10 1 0.937523 5 116 0 22 2 0 0 0 0 0 2 -3.045236 1 1 121008 3 31 1 0 1 1 1.610984 1 0.440000 1.870000 0.282051 0.150000 0.050000 0.310000 0.140000 0.167997 0.150000 0 9.000000e-02 2.300000e-01 CACNA1D 776 broad.mit.edu 37 3 53752385 53752385 + Missense_Mutation SNP G G T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr3:53752385G>T ENST00000350061.5 + 10 1959 c.1448G>T c.(1447-1449)gGc>gTc p.G483V CACNA1D_ENST00000288139.4_Missense_Mutation_p.G483V|CACNA1D_ENST00000422281.2_Missense_Mutation_p.G483V NM_001128840.1 NP_001122312.1 Q01668 CAC1D_HUMAN calcium channel, voltage-dependent, L type, alpha 1D subunit 90 Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661) AGCGGTGAAGGCGAGAACCGA 0.592000 0 SO:0001583 missense ENST00000350061.5 1 1 hg19 CCDS46848.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 10.02|10.02 1.235118|1.235118 0.22626|0.22626 .|. .|. ENSG00000157388|ENSG00000157388 ENST00000481085|ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478 .|D;D;D;D .|0.93712 .|-3.27;-3.27;-3.27;-3.27 5.44|5.44 4.57|4.57 0.56435|0.56435 .|. .|153.860000 .|0.00166 .|N .|0.000000 D|D 0.89853|0.89853 0.6835|0.6835 N|N 0.19112|0.19112 0.55|0.55 0.80722|0.80722 D|D 1|1 .|B;B;B;B .|0.25486 .|0.01;0.001;0.002;0.127 .|B;B;B;B .|0.28305 .|0.01;0.002;0.008;0.088 T|T 0.69544|0.69544 -0.5117|-0.5117 5|10 .|0.39692 .|T .|0.17 .|. 10.5212|10.5212 0.44920|0.44920 0.0:0.1448:0.7048:0.1504|0.0:0.1448:0.7048:0.1504 .|. .|483;156;483;483 .|B0FYA3;Q59GD8;Q01668;Q01668-2 .|.;.;CAC1D_HUMAN;. S|V 197|483;483;483;156 .|ENSP00000288133:G483V;ENSP00000288139:G483V;ENSP00000409174:G483V;ENSP00000418014:G156V .|ENSP00000288139:G483V A|G +|+ 1|2 0|0 CACNA1D|CACNA1D 53727425|53727425 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.433000|0.433000 0.31745|0.31745 3.391000|3.391000 0.52530|0.52530 1.292000|1.292000 0.44672|0.44672 -0.150000|-0.150000 0.13652|0.13652 GCG|GGC TCGA-2L-AAQJ-01A-12D-A397-08 CACNA1D-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350557.1 1 0 1 76 236 0 96 0 0 1 0 0 96 2 0 0 0 0 0 2 1 1.000000 75 233 0 93 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.610984 1 0.440000 1.870000 0.282051 0.840000 0.690000 0.980000 0.860000 0.851812 0.840000 0 7.600000e-01 9.300000e-01 OXTR 5021 broad.mit.edu 37 3 8794835 8794835 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr3:8794835G>A ENST00000316793.3 - 4 1622 c.998C>T c.(997-999)aCg>aTg p.T333M CAV3_ENST00000472766.1_Intron NM_000916.3 NP_000907.2 P30559 OXYR_HUMAN oxytocin receptor 13 Carbetocin(DB01282)|Oxytocin(DB00107) GAGGTGGCCCGTGAACAGCAT 0.617000 0 SO:0001583 missense ENST00000316793.3 1 1 hg19 CCDS2570.1 1 4.578754578754579E-4 0 0.0 1 0.0027624309392265192 0 0.0 0 0.0 G 23.0 4.366953 0.82463 2.27E-4 1.16E-4 ENSG00000180914 ENST00000316793 T 0.38560 1.13 5.13 4.23 0.50019 . 0.052718 0.85682 D 0.000000 T 0.55449 0.1921 M 0.63428 1.95 0.41902 D 0.990422 D 0.71674 0.998 P 0.57204 0.815 T 0.62158 -0.6913 10 0.87932 D 0 -32.9382 14.1848 0.65598 0.0:0.1509:0.8491:0.0 . 333 P30559 OXYR_HUMAN M 333 ENSP00000324270:T333M ENSP00000324270:T333M T - 2 0 OXTR 8769835 1.000000 0.71417 0.845000 0.33349 0.985000 0.73830 5.333000 0.65917 1.330000 0.45394 0.655000 0.94253 ACG TCGA-2L-AAQJ-01A-12D-A397-08 OXTR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207061.2 0 0 0 61 152 1 47 1 3.283906e-01 2 2 1 47 2 0 0 0 0 0 2 1 1.000000 61 150 1 46 15 0 0 0 0 0 2 -6.283823 1 1 121412 4 35 1 0 1 1 1.610984 1 0.440000 1.870000 0.282051 0.920000 0.770000 1.000000 0.990000 0.921743 0.920000 1 8.500000e-01 9.800000e-01 LDB2 9079 broad.mit.edu 37 4 16504411 16504411 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr4:16504411G>A ENST00000304523.5 - 8 1300 c.977C>T c.(976-978)aCg>aTg p.T326M LDB2_ENST00000441778.2_3'UTR|LDB2_ENST00000515064.1_Missense_Mutation_p.T324M|LDB2_ENST00000502640.1_3'UTR|RP11-446J8.1_ENST00000512370.1_RNA NM_001290.3 NP_001281.1 O43679 LDB2_HUMAN LIM domain binding 2 33 ATCATATTGCGTGTTTTCTAA 0.537000 0 SO:0001583 missense ENST00000304523.5 1 1 hg19 CCDS3420.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 16.11|16.11 3.030178|3.030178 0.54790|0.54790 .|. .|. ENSG00000169744|ENSG00000169744 ENST00000507464|ENST00000515064;ENST00000304523 .|T;T .|0.26810 .|1.71;1.71 5.48|5.48 5.48|5.48 0.80851|0.80851 .|. .|0.000000 .|0.64402 .|D .|0.000002 T|T 0.50531|0.50531 0.1621|0.1621 M|M 0.68952|0.68952 2.095|2.095 0.80722|0.80722 D|D 1|1 .|D;D;D;D .|0.89917 .|1.0;0.998;1.0;1.0 .|D;P;P;D .|0.75020 .|0.985;0.899;0.891;0.949 T|T 0.43491|0.43491 -0.9388|-0.9388 5|10 .|0.45353 .|T .|0.12 -13.6093|-13.6093 18.3199|18.3199 0.90234|0.90234 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|290;324;326;300 .|B7Z6D0;G5E9Y7;O43679;O43679-3 .|.;.;LDB2_HUMAN;. C|M 247|324;326 .|ENSP00000422552:T324M;ENSP00000306772:T326M .|ENSP00000306772:T326M R|T -|- 1|2 0|0 LDB2|LDB2 16113509|16113509 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.998000|0.998000 0.95712|0.95712 9.869000|9.869000 0.99810|0.99810 2.558000|2.558000 0.86282|0.86282 0.655000|0.655000 0.94253|0.94253 CGC|ACG TCGA-2L-AAQJ-01A-12D-A397-08 LDB2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000250321.2 1 0 1 126 513 1 131 0 9.571750e-01 0 31 1 131 3 0 0 0 0 0 2 1 1.000000 125 504 1 130 17 0 0 0 0 0 2 -20.000000 1 1 121412 1 35 1 0 1 1 2.055782 0 0.440000 1.870000 0.438765 0.880000 0.750000 1.000000 1.000000 0.894130 0.880000 1 8.200000e-01 9.700000e-01 COX7B2 170712 broad.mit.edu 37 4 46737152 46737152 + Missense_Mutation SNP G G C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr4:46737152G>C ENST00000396533.1 - 4 308 c.58C>G c.(58-60)Caa>Gaa p.Q20E COX7B2_ENST00000355591.3_Missense_Mutation_p.Q20E|COX7B2_ENST00000543208.1_Missense_Mutation_p.Q19E|COX7B2_ENST00000302930.5_Missense_Mutation_p.Q20E Q8TF08 CX7B2_HUMAN cytochrome c oxidase subunit VIIb2 5 GCCATGCTTTGCAGAATGCTT 0.423000 0 SO:0001583 missense ENST00000396533.1 0 1 hg19 CCDS3472.2 . . . . . . . . . . G 5.784 0.329026 0.10956 . . ENSG00000170516 ENST00000355591;ENST00000396533;ENST00000302930;ENST00000543208;ENST00000505102 T;T;T;T;T 0.45276 0.9;0.9;0.9;0.9;0.9 4.22 1.33 0.21861 . 0.393840 0.25771 N 0.028415 T 0.29256 0.0728 . . . 0.09310 N 1 B 0.14438 0.01 B 0.14023 0.01 T 0.24368 -1.0162 9 0.72032 D 0.01 -8.2035 6.926 0.24416 0.0:0.3509:0.4531:0.1959 . 20 Q8TF08 CX7B2_HUMAN E 20;20;20;19;20 ENSP00000347799:Q20E;ENSP00000379784:Q20E;ENSP00000305964:Q20E;ENSP00000437439:Q19E;ENSP00000423519:Q20E ENSP00000305964:Q20E Q - 1 0 COX7B2 46431909 0.003000 0.15002 0.019000 0.16419 0.193000 0.23685 1.002000 0.29796 0.255000 0.21593 0.585000 0.79938 CAA TCGA-2L-AAQJ-01A-12D-A397-08 COX7B2-002 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000313899.1 0 0 0 5 397 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 0.936259 5 393 0 71 2 0 0 0 0 0 2 -3.317288 1 1 0 0 1 0 1 1 2.055782 0 0.440000 1.870000 0.438765 0.050000 0.010000 0.130000 0.060000 0.067131 0.050000 0 3.000000e-02 9.000000e-02 CEP135 9662 broad.mit.edu 37 4 56877620 56877620 + Nonsense_Mutation SNP G G T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr4:56877620G>T ENST00000257287.4 + 20 2672 c.2548G>T c.(2548-2550)Gaa>Taa p.E850* NM_025009.4 NP_079285.2 Q66GS9 CP135_HUMAN centrosomal protein 135kDa 50 Glioma(25;0.08)|all_neural(26;0.101) AGAAAAAGAAGAAATGAAGAG 0.333000 0 SO:0001587 stop_gained ENST00000257287.4 0 1 hg19 CCDS33986.1 . . . . . . . . . . G 41 8.869519 0.98984 . . ENSG00000174799 ENST00000257287 . . . 5.11 5.11 0.69529 . 0.046328 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.27785 T 0.31 . 18.5341 0.91002 0.0:0.0:1.0:0.0 . . . . X 850 . ENSP00000257287:E850X E + 1 0 CEP135 56572377 1.000000 0.71417 1.000000 0.80357 0.975000 0.68041 7.811000 0.86092 2.373000 0.80994 0.591000 0.81541 GAA TCGA-2L-AAQJ-01A-12D-A397-08 CEP135-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000362092.2 1 0 1 38 178 0 37 0 4.945258e-01 1 8 0 37 2 0 0 0 0 0 2 1 1.000000 38 175 0 37 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 2.055782 0 0.440000 1.870000 0.438765 0.790000 0.580000 1.000000 1.000000 0.803493 0.790000 0 6.800000e-01 9.200000e-01 NAA11 84779 broad.mit.edu 37 4 80246531 80246531 + Silent SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr4:80246531G>A ENST00000286794.4 - 1 673 c.501C>T c.(499-501)ggC>ggT p.G167G NAA11_ENST00000513733.1_5'UTR NM_032693.2 NP_116082.1 Q9BSU3 NAA11_HUMAN N(alpha)-acetyltransferase 11, NatA catalytic subunit 23 CCACATACCCGCCCTTCTTCA 0.532000 0 SO:0001819 synonymous_variant ENST00000286794.4 1 1 hg19 CCDS47084.1 TCGA-2L-AAQJ-01A-12D-A397-08 NAA11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000362922.1 1 0 1 42 127 0 31 0 0 0 0 31 2 0 0 0 0 0 2 1 1.000000 41 126 0 31 2 0 0 0 0 0 2 -4.581958 1 1 0 0 1 0 1 1 2.055782 0 0.440000 1.870000 0.438765 0.990000 0.840000 1.000000 1.000000 0.985715 0.990000 1 9.700000e-01 1 PDHA2 5161 broad.mit.edu 37 4 96762066 96762066 + Missense_Mutation SNP G G T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr4:96762066G>T ENST00000295266.4 + 1 828 c.765G>T c.(763-765)atG>atT p.M255I NM_005390.4 NP_005381.1 P29803 ODPAT_HUMAN pyruvate dehydrogenase (lipoamide) alpha 2 46 Hepatocellular(203;0.114) TCGATGGAATGGATGTTCTGT 0.463000 0 SO:0001583 missense ENST00000295266.4 1 1 hg19 CCDS3644.1 . . . . . . . . . . G 17.34 3.365331 0.61513 . . ENSG00000163114 ENST00000295266 D 0.97209 -4.29 4.91 4.91 0.64330 Dehydrogenase, E1 component (1); 0.000000 0.85682 D 0.000000 D 0.98848 0.9611 H 0.94264 3.515 0.80722 D 1 D 0.76494 0.999 D 0.91635 0.999 D 0.99282 1.0896 10 0.87932 D 0 -26.8691 16.0034 0.80327 0.0:0.0:1.0:0.0 . 255 P29803 ODPAT_HUMAN I 255 ENSP00000295266:M255I ENSP00000295266:M255I M + 3 0 PDHA2 96981089 1.000000 0.71417 0.992000 0.48379 0.523000 0.34469 4.138000 0.58017 2.733000 0.93635 0.467000 0.42956 ATG TCGA-2L-AAQJ-01A-12D-A397-08 PDHA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253608.1 1 0 1 48 171 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 1.000000 48 171 0 38 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 2.055782 0 0.440000 1.870000 0.438765 0.980000 0.750000 1.000000 1.000000 0.949661 0.980000 1 8.600000e-01 1 TCERG1 10915 broad.mit.edu 37 5 145886749 145886749 + Silent SNP A A G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr5:145886749A>G ENST00000296702.5 + 19 2927 c.2889A>G c.(2887-2889)caA>caG p.Q963Q TCERG1_ENST00000394421.2_Silent_p.Q942Q NM_006706.3 NP_006697.2 O14776 TCRG1_HUMAN transcription elongation regulator 1 46 Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) ACTTTAGGCAACTTCTGGATG 0.338000 0 SO:0001819 synonymous_variant ENST00000296702.5 1 1 hg19 CCDS4282.1 TCGA-2L-AAQJ-01A-12D-A397-08 TCERG1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000251886.1 1 0 1 72 265 0 72 1 1 31 63 0 72 2 0 0 0 0 0 2 1 1.000000 71 264 0 72 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.075514 0 0.440000 1.870000 0.442453 0.970000 0.780000 1.000000 1.000000 0.948660 0.970000 1 8.700000e-01 1 STK32A 202374 broad.mit.edu 37 5 146750320 146750320 + Nonsense_Mutation SNP C C A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr5:146750320C>A ENST00000397936.3 + 9 1097 c.764C>A c.(763-765)tCa>tAa p.S255* STK32A_ENST00000398523.3_Nonsense_Mutation_p.S255* NM_001112724.1 NP_001106195.1 Q8WU08 ST32A_HUMAN serine/threonine kinase 32A 13 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GAAATGGTGTCACTTCTTAAA 0.418000 0 SO:0001587 stop_gained ENST00000397936.3 0 1 hg19 CCDS47299.1 . . . . . . . . . . C 38 6.721010 0.97788 . . ENSG00000169302 ENST00000397936;ENST00000398523 . . . 5.52 5.52 0.82312 . 0.191964 0.25885 N 0.027664 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 18.563 0.91107 0.0:1.0:0.0:0.0 . . . . X 255 . ENSP00000381030:S255X S + 2 0 STK32A 146730513 0.999000 0.42202 1.000000 0.80357 0.977000 0.68977 4.191000 0.58372 2.761000 0.94854 0.655000 0.94253 TCA TCGA-2L-AAQJ-01A-12D-A397-08 STK32A-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000373306.1 1 0 0 70 309 0 68 0 0 0 1 0 68 2 0 0 0 0 0 2 1 1.000000 70 304 0 68 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.075514 0 0.440000 1.870000 0.442453 0.840000 0.670000 1.000000 1.000000 0.847287 0.840000 0 7.500000e-01 9.400000e-01 GM2A 2760 broad.mit.edu 37 5 150639359 150639359 + Missense_Mutation SNP G G C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr5:150639359G>C ENST00000357164.3 + 2 450 c.125G>C c.(124-126)gGg>gCg p.G42A NM_000405.4|NM_001167607.1 NP_000396.2|NP_001161079.1 P17900 SAP3_HUMAN GM2 ganglioside activator 8 Medulloblastoma(196;0.091)|all_hematologic(541;0.207) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) TGTGATGAAGGGAAGGACCCT 0.527000 0 SO:0001583 missense ENST00000357164.3 0 1 hg19 CCDS4313.1 . . . . . . . . . . G 2.987 -0.209025 0.06140 . . ENSG00000196743 ENST00000523466;ENST00000357164 T;T 0.71579 -0.58;-0.58 4.96 2.14 0.27477 MD-2-related lipid-recognition (1); 0.306608 0.35772 N 0.002992 T 0.57417 0.2052 L 0.47716 1.5 0.09310 N 1 P;P 0.46142 0.797;0.873 B;B 0.39027 0.117;0.288 T 0.48570 -0.9024 10 0.29301 T 0.29 -7.8707 8.4518 0.32875 0.0857:0.4541:0.4602:0.0 . 42;42 B4DQM5;P17900 .;SAP3_HUMAN A 57;42 ENSP00000429100:G57A;ENSP00000349687:G42A ENSP00000349687:G42A G + 2 0 GM2A 150619552 0.006000 0.16342 0.021000 0.16686 0.165000 0.22458 0.193000 0.17116 0.140000 0.18849 -0.136000 0.14681 GGG TCGA-2L-AAQJ-01A-12D-A397-08 GM2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252432.1 0 0 0 4 176 0 28 0 4.868203e-01 1 62 0 28 2 0 0 0 0 0 2 1 0.888650 4 174 0 28 2 0 0 0 0 0 2 -3.315606 1 1 0 0 1 1 2 3 2.075514 0 0.440000 1.870000 0.442453 0.110000 0.030000 0.270000 0.100000 0.133120 0.110000 0 6.000000e-02 1.800000e-01 FAM71B 153745 broad.mit.edu 37 5 156590194 156590194 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr5:156590194G>A ENST00000302938.4 - 2 1177 c.1082C>T c.(1081-1083)gCg>gTg p.A361V NM_130899.2 NP_570969.2 Q8TC56 FA71B_HUMAN family with sequence similarity 71, member B 68 Renal(175;0.00212) Medulloblastoma(196;0.0523)|all_neural(177;0.21) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) GGCGGCCCCCGCCATCGAGGT 0.567000 0 SO:0001583 missense ENST00000302938.4 1 1 hg19 CCDS4335.1 . . . . . . . . . . G 8.201 0.798141 0.16397 . . ENSG00000170613 ENST00000302938 T 0.04156 3.69 3.83 -0.0601 0.13790 . 2.284610 0.01796 N 0.032639 T 0.01695 0.0054 N 0.08118 0 0.09310 N 1 P 0.35628 0.513 B 0.14023 0.01 T 0.32929 -0.9888 10 0.02654 T 1 0.1287 1.1705 0.01824 0.2063:0.1729:0.4431:0.1777 . 361 Q8TC56 FA71B_HUMAN V 361 ENSP00000305596:A361V ENSP00000305596:A361V A - 2 0 FAM71B 156522772 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.879000 0.04188 -0.036000 0.13669 -0.224000 0.12420 GCG TCGA-2L-AAQJ-01A-12D-A397-08 FAM71B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252570.2 1 0 1 49 201 0 59 0 0 0 0 59 2 0 0 0 0 0 2 1 1.000000 49 198 0 57 2 0 0 0 0 0 2 -2.671760 1 1 121412 4 34 1 1 2 3 2.075514 0 0.440000 1.870000 0.442453 0.890000 0.680000 1.000000 1.000000 0.889361 0.890000 1 7.800000e-01 1 TPD52L1 7164 broad.mit.edu 37 6 125541274 125541274 + Missense_Mutation SNP A A T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr6:125541274A>T ENST00000534000.1 + 2 366 c.70A>T c.(70-72)Agt>Tgt p.S24C TPD52L1_ENST00000368402.5_Missense_Mutation_p.S24C|TPD52L1_ENST00000304877.13_Missense_Mutation_p.S24C|TPD52L1_ENST00000368388.2_Missense_Mutation_p.S24C|TPD52L1_ENST00000532429.1_5'UTR|TPD52L1_ENST00000528193.1_Missense_Mutation_p.S24C|HDDC2_ENST00000608456.1_5'UTR|TPD52L1_ENST00000392482.2_5'UTR|TPD52L1_ENST00000524679.1_5'UTR|TPD52L1_ENST00000534199.1_5'UTR|TPD52L1_ENST00000527711.1_Missense_Mutation_p.S24C NM_003287.2 NP_003278.1 Q16890 TPD53_HUMAN tumor protein D52-like 1 5 LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828) TGCAGTAGCCAGTGCTGACTT 0.378000 0 SO:0001583 missense ENST00000534000.1 0 1 hg19 CCDS5130.1 . . . . . . . . . . A 16.93 3.258538 0.59321 . . ENSG00000111907 ENST00000304877;ENST00000534000;ENST00000368402;ENST00000368388;ENST00000527711;ENST00000528193;ENST00000392484 T;T;T;T;T;T 0.26518 1.73;1.73;1.73;1.73;1.73;1.73 5.26 -0.253 0.12996 . 0.282976 0.43919 D 0.000514 T 0.12263 0.0298 L 0.38175 1.15 0.38267 D 0.942041 P;P;P 0.51537 0.844;0.844;0.946 B;B;P 0.50590 0.416;0.416;0.645 T 0.06058 -1.0848 10 0.56958 D 0.05 -0.967 5.6478 0.17598 0.4559:0.1515:0.3926:0.0 . 24;24;24 Q16890-3;Q16890-2;Q16890 .;.;TPD53_HUMAN C 24 ENSP00000306285:S24C;ENSP00000434142:S24C;ENSP00000357387:S24C;ENSP00000357373:S24C;ENSP00000436953:S24C;ENSP00000434743:S24C ENSP00000306285:S24C S + 1 0 TPD52L1 125582973 0.999000 0.42202 0.993000 0.49108 0.840000 0.47671 1.953000 0.40352 0.087000 0.17167 -0.250000 0.11733 AGT TCGA-2L-AAQJ-01A-12D-A397-08 TPD52L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042065.2 0 0 0 4 288 0 54 0 2.010071e-01 0 48 0 54 2 0 0 0 0 0 2 1 0.890225 4 287 0 54 2 0 0 0 0 0 2 -5.096504 1 0 0 0 1 0 0 0 2.005955 0 0.440000 1.870000 0.424815 0.060000 0.010000 0.150000 0.060000 0.074888 0.060000 0 3.000000e-02 1.100000e-01 KIAA0408 9729 broad.mit.edu 37 6 127771349 127771349 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr6:127771349G>A ENST00000483725.3 - 3 620 c.284C>T c.(283-285)aCg>aTg p.T95M SOGA3_ENST00000368268.2_3'UTR|SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR NM_014702.4 NP_055517.3 Q6ZU52 K0408_HUMAN KIAA0408 p.T95M(1) 28 TTTGTGATTCGTCCTTATAAA 0.358000 1 Substitution - Missense(1) SO:0001583 missense ENST00000483725.3 0 1 hg19 CCDS34531.1 . . . . . . . . . . G 0.313 -0.966787 0.02232 . . ENSG00000189367 ENST00000483725;ENST00000487331 T;T 0.43294 0.95;0.95 5.7 3.22 0.36961 . 0.603786 0.12642 N 0.451213 T 0.04952 0.0133 N 0.00926 -1.1 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.38628 -0.9652 10 0.30078 T 0.28 0.4989 7.4927 0.27471 0.766:0.0:0.234:0.0 . 95 Q6ZU52 K0408_HUMAN M 95;107 ENSP00000435150:T95M;ENSP00000434384:T107M ENSP00000435150:T95M T - 2 0 KIAA0408 127813042 0.001000 0.12720 0.008000 0.14137 0.002000 0.02628 0.957000 0.29215 0.978000 0.38470 -0.300000 0.09419 ACG TCGA-2L-AAQJ-01A-12D-A397-08 KIAA0408-003 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042145.3 0 0 0 6 430 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 0.965221 6 430 0 68 2 0 0 0 0 0 2 -2.781143 1 1 121406 6 42 1 0 0 0 2.005955 0 0.440000 1.870000 0.424815 0.060000 0.020000 0.130000 0.060000 0.070535 0.060000 0 3.000000e-02 1.000000e-01 NOTCH4 4855 broad.mit.edu 37 6 32168996 32168996 + Missense_Mutation SNP C C T rs116359968 byFrequency TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr6:32168996C>T ENST00000375023.3 - 22 4175 c.4037G>A c.(4036-4038)cGg>cAg p.R1346Q NM_004557.3 NP_004548.3 Q99466 NOTC4_HUMAN notch 4 100 TTCTTCAGCCCGGGCCCCAGG 0.617000 0 SO:0001583 missense ENST00000375023.3 1 0 hg19 CCDS34420.1 . . . . . . . . . . C 10.61 1.397977 0.25205 . . ENSG00000204301 ENST00000375023 T 0.80824 -1.42 4.37 1.09 0.20402 . 0.581966 0.13081 N 0.415340 T 0.35098 0.0920 N 0.03608 -0.345 0.80722 D 1 B;B 0.18741 0.03;0.001 B;B 0.17979 0.02;0.0 T 0.08534 -1.0717 10 0.25106 T 0.35 . 5.443 0.16519 0.0:0.4431:0.0:0.5569 . 1346;1345 Q99466;B0S882 NOTC4_HUMAN;. Q 1346 ENSP00000364163:R1346Q ENSP00000364163:R1346Q R - 2 0 NOTCH4 32276974 0.999000 0.42202 0.990000 0.47175 0.931000 0.56810 1.224000 0.32539 0.052000 0.16007 0.456000 0.33151 CGG TCGA-2L-AAQJ-01A-12D-A397-08 NOTCH4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076045.2 1 0 0 19 338 0 54 0 4.943782e-01 0 30 0 54 2 0 0 0 0 0 2 1 0.999990 19 332 0 54 2 0 0 0 0 0 2 -2.484114 0 1 0 0 1 0 0 0 2.030214 0 0.440000 1.870000 0.435028 0.240000 0.140000 0.360000 0.240000 0.250089 0.240000 0 1.900000e-01 3.000000e-01 PGC 5225 broad.mit.edu 37 6 41704646 41704646 + Missense_Mutation SNP A A G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr6:41704646A>G ENST00000373025.3 - 9 1173 c.1111T>C c.(1111-1113)Tac>Cac p.Y371H TFEB_ENST00000230323.4_5'Flank|TFEB_ENST00000420312.1_5'Flank|TFEB_ENST00000403298.4_5'Flank|TFEB_ENST00000373033.1_5'Flank|TFEB_ENST00000358871.2_5'Flank|RP11-298J23.5_ENST00000438967.1_RNA NM_002630.3 NP_002621.1 P20142 PEPC_HUMAN progastricsin (pepsinogen C) 16 Ovarian(28;0.0355)|Colorectal(47;0.121) Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507) ACGGAATAGTAGGACCTGAGG 0.602000 0 SO:0001583 missense ENST00000373025.3 1 1 hg19 CCDS4859.1 . . . . . . . . . . A 14.87 2.663054 0.47572 . . ENSG00000096088 ENST00000373025 T 0.34275 1.37 4.82 4.82 0.62117 Peptidase aspartic (1);Peptidase aspartic, catalytic (1); 0.000000 0.64402 D 0.000001 T 0.64136 0.2571 H 0.94620 3.56 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.76091 -0.3086 10 0.87932 D 0 . 14.2156 0.65790 1.0:0.0:0.0:0.0 . 371 P20142 PEPC_HUMAN H 371 ENSP00000362116:Y371H ENSP00000362116:Y371H Y - 1 0 PGC 41812624 1.000000 0.71417 0.967000 0.41034 0.048000 0.14542 6.504000 0.73704 2.013000 0.59113 0.459000 0.35465 TAC TCGA-2L-AAQJ-01A-12D-A397-08 PGC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040521.2 1 0 0 10 198 0 39 1 1 11 1109 0 39 2 0 0 0 0 0 2 1 0.997020 10 197 0 39 2 0 0 0 0 0 2 -12.524860 1 1 0 0 1 0 0 0 2.005955 0 0.440000 1.870000 0.424815 0.210000 0.110000 0.370000 0.210000 0.230305 0.210000 0 1.500000e-01 2.900000e-01 DOCK4 9732 broad.mit.edu 37 7 111368508 111368508 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr7:111368508C>T ENST00000437633.1 - 52 5979 c.5723G>A c.(5722-5724)cGg>cAg p.R1908Q DOCK4_ENST00000428084.1_Missense_Mutation_p.R1917Q|DOCK4_ENST00000494651.2_Missense_Mutation_p.R791Q NM_014705.3 NP_055520.3 Q8N1I0 DOCK4_HUMAN dedicator of cytokinesis 4 72 Acute lymphoblastic leukemia(1;0.0441) CCGCAGAGTCCGCTCGTAGAC 0.731000 0 SO:0001583 missense ENST00000437633.1 1 1 hg19 CCDS47688.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 36|36 5.850010|5.850010 0.97023|0.97023 0.0|0.0 1.2E-4|1.2E-4 ENSG00000128512|ENSG00000128512 ENST00000423057;ENST00000445943|ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288 .|T;T;T .|0.32753 .|1.44;1.44;1.44 5.59|5.59 5.59|5.59 0.84812|0.84812 .|. .|0.000000 .|0.85682 .|D .|0.000000 T|T 0.53706|0.53706 0.1813|0.1813 L|L 0.57536|0.57536 1.79|1.79 0.46927|0.46927 D|D 0.999258|0.999258 .|D;P;D;D;D;D .|0.89917 .|0.994;0.951;0.981;0.994;0.997;1.0 .|D;B;B;D;D;D .|0.85130 .|0.921;0.404;0.391;0.921;0.964;0.997 T|T 0.40515|0.40515 -0.9559|-0.9559 5|10 .|0.33141 .|T .|0.24 .|. 19.5919|19.5919 0.95518|0.95518 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|777;791;1953;1908;1879;221 .|B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2;Q8N1I0-4 .|.;.;.;DOCK4_HUMAN;.;. R|Q 1331;1941|1896;1917;791;1908;1867 .|ENSP00000410746:R1917Q;ENSP00000440944:R791Q;ENSP00000404179:R1908Q .|ENSP00000345432:R1867Q G|R -|- 1|2 0|0 DOCK4|DOCK4 111155744|111155744 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.998000|0.998000 0.95712|0.95712 5.513000|5.513000 0.67037|0.67037 2.640000|2.640000 0.89533|0.89533 0.655000|0.655000 0.94253|0.94253 GGA|CGG TCGA-2L-AAQJ-01A-12D-A397-08 DOCK4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000338369.4 1 0 0 62 201 0 62 0 8.112629e-01 1 11 0 62 2 0 0 0 0 0 2 1 1.000000 62 198 0 59 2 0 0 0 0 0 2 -4.473540 1 1 120600 9 39 1 0 0 0 2.040935 0 0.440000 1.870000 0.435028 0.990000 0.830000 1.000000 1.000000 0.979552 0.990000 1 9.400000e-01 1 FAM71F1 84691 broad.mit.edu 37 7 128363345 128363345 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr7:128363345C>T ENST00000315184.5 + 4 835 c.782C>T c.(781-783)gCc>gTc p.A261V FAM71F1_ENST00000485070.1_Missense_Mutation_p.A162V|FAM71F1_ENST00000469348.1_3'UTR NM_001282788.1|NM_032599.2 NP_001269717.1|NP_115988.1 Q96KD3 F71F1_HUMAN family with sequence similarity 71, member F1 p.A261V(1) 18 CAGATTTTTGCCGACTTACAC 0.502000 1 Substitution - Missense(1) SO:0001583 missense ENST00000315184.5 0 1 hg19 CCDS5804.1 . . . . . . . . . . C 15.05 2.717581 0.48622 . . ENSG00000135248 ENST00000485070;ENST00000315184;ENST00000466842 T;T;T 0.24151 1.87;3.23;1.92 5.2 3.36 0.38483 . 0.643829 0.14692 N 0.304119 T 0.17365 0.0417 L 0.33485 1.01 0.26152 N 0.980124 B;B;B;B;B 0.18310 0.011;0.01;0.003;0.002;0.027 B;B;B;B;B 0.15052 0.012;0.006;0.004;0.002;0.006 T 0.17992 -1.0351 10 0.30854 T 0.27 -2.5683 6.5261 0.22303 0.1782:0.7313:0.0:0.0905 . 153;261;261;261;162 B4DY15;F8WC62;Q96KD3-2;Q96KD3;Q8NA48 .;.;.;F71F1_HUMAN;. V 162;261;117 ENSP00000418192:A162V;ENSP00000326652:A261V;ENSP00000417930:A117V ENSP00000326652:A261V A + 2 0 FAM71F1 128150581 0.133000 0.22466 0.998000 0.56505 0.995000 0.86356 0.071000 0.14594 0.862000 0.35528 0.555000 0.69702 GCC TCGA-2L-AAQJ-01A-12D-A397-08 FAM71F1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350544.2 0 0 0 6 412 0 81 0 0 0 0 81 2 0 0 0 0 0 2 1 0.964714 6 410 0 80 2 0 0 0 0 0 2 -1.790619 0 1 121412 5 39 1 0 0 0 2.040935 0 0.440000 1.870000 0.435028 0.060000 0.020000 0.130000 0.060000 0.074872 0.060000 0 4.000000e-02 1.000000e-01 PTPRN2 5799 broad.mit.edu 37 7 157926586 157926586 + Missense_Mutation SNP C C T rs142388788 TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr7:157926586C>T ENST00000389418.4 - 9 1348 c.1339G>A c.(1339-1341)Gtc>Atc p.V447I PTPRN2_ENST00000389413.3_Missense_Mutation_p.V447I|PTPRN2_ENST00000409483.1_Missense_Mutation_p.V409I|PTPRN2_ENST00000404321.2_Missense_Mutation_p.V470I|PTPRN2_ENST00000389416.4_Missense_Mutation_p.V430I NM_002847.3 NP_002838.2 Q92932 PTPR2_HUMAN protein tyrosine phosphatase, receptor type, N polypeptide 2 86 all_neural(206;0.181) all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132) OV - Ovarian serous cystadenocarcinoma(82;0.00463) TGGCTCTTGACGTTCTCCACT 0.612000 0 SO:0001583 missense ENST00000389418.4 1 1 hg19 CCDS5947.1 . . . . . . . . . . C 12.64 1.997688 0.35226 0.0 1.16E-4 ENSG00000155093 ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321 T;T;T;T;T 0.07327 3.29;3.2;3.26;3.29;3.25 3.78 2.88 0.33553 . 0.310886 0.20844 U 0.084645 T 0.05181 0.0138 L 0.32530 0.975 0.26315 N 0.977769 P;P;P;P;P 0.45902 0.868;0.792;0.868;0.792;0.792 B;B;B;B;B 0.30572 0.117;0.055;0.117;0.055;0.055 T 0.32214 -0.9915 10 0.56958 D 0.05 . 9.1024 0.36676 0.0:0.89:0.0:0.11 . 470;409;447;430;447 Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932 .;.;.;.;PTPR2_HUMAN I 409;447;430;447;470 ENSP00000387114:V409I;ENSP00000374064:V447I;ENSP00000374067:V430I;ENSP00000374069:V447I;ENSP00000385464:V470I ENSP00000374064:V447I V - 1 0 PTPRN2 157619347 0.443000 0.25641 0.048000 0.18961 0.043000 0.13939 1.614000 0.36911 0.681000 0.31386 0.585000 0.79938 GTC TCGA-2L-AAQJ-01A-12D-A397-08 PTPRN2-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000353214.1 1 0 1 123 487 0 122 1 9.999559e-01 36 23 0 122 2 0 0 0 0 0 2 1 1.000000 121 482 0 122 2 0 0 0 0 0 2 -20.000000 1 1 121412 1 36 1 0 0 0 2.040935 0 0.440000 1.870000 0.435028 0.900000 0.760000 1.000000 1.000000 0.906609 0.900000 1 8.300000e-01 9.800000e-01 CDK13 8621 broad.mit.edu 37 7 40027359 40027359 + Missense_Mutation SNP A A C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr7:40027359A>C ENST00000181839.4 + 2 1978 c.1373A>C c.(1372-1374)aAa>aCa p.K458T CDK13_ENST00000340829.5_Missense_Mutation_p.K458T NM_003718.4|NM_031267.3 NP_003709.3|NP_112557.2 Q14004 CDK13_HUMAN cyclin-dependent kinase 13 49 AAGAATAAAAAagcacgagca 0.488000 0 SO:0001583 missense ENST00000181839.4 0 1 hg19 CCDS5461.1 . . . . . . . . . . A 17.32 3.358737 0.61403 . . ENSG00000065883 ENST00000181839;ENST00000340829 T;T 0.66638 -0.22;-0.22 5.95 5.95 0.96441 . . . . . T 0.79924 0.4530 M 0.61703 1.905 0.58432 D 0.999998 D;D 0.89917 1.0;0.999 D;D 0.85130 0.997;0.994 T 0.79212 -0.1896 8 . . . -13.8654 16.4101 0.83708 1.0:0.0:0.0:0.0 . 458;458 Q14004-2;Q14004 .;CDK13_HUMAN T 458 ENSP00000181839:K458T;ENSP00000340557:K458T . K + 2 0 CDK13 39993884 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 6.281000 0.72632 2.280000 0.76307 0.460000 0.39030 AAA TCGA-2L-AAQJ-01A-12D-A397-08 CDK13-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000250726.2 0 0 0 4 226 0 48 0 3.325394e-01 1 55 0 48 2 0 0 0 0 0 2 1 0.891141 4 226 0 47 2 0 0 0 0 0 2 -7.210621 1 1 0 0 1 0 0 0 2.040935 0 0.440000 1.870000 0.435028 0.080000 0.020000 0.190000 0.080000 0.096540 0.080000 0 4.000000e-02 1.400000e-01 SDK1 221935 broad.mit.edu 37 7 4188979 4188979 + Silent SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr7:4188979C>T ENST00000404826.2 + 30 4648 c.4509C>T c.(4507-4509)agC>agT p.S1503S SDK1_ENST00000389531.3_Silent_p.S1503S NM_152744.3 NP_689957.3 Q7Z5N4 SDK1_HUMAN sidekick cell adhesion molecule 1 153 all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194) TCCCGGGCAGCGACGGGGCCT 0.677000 0 SO:0001819 synonymous_variant ENST00000404826.2 1 1 hg19 CCDS34590.1 TCGA-2L-AAQJ-01A-12D-A397-08 SDK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323702.1 1 0 1 10 50 0 17 0 3.588710e-01 0 7 0 17 2 0 0 0 0 0 2 1 0.997708 10 50 0 17 2 0 0 0 0 0 2 -19.021370 1 1 121250 1 26 1 0 0 0 2.040935 0 0.440000 1.870000 0.435028 0.750000 0.400000 1.000000 1.000000 0.762280 0.750000 0 5.600000e-01 9.800000e-01 GLI3 2737 broad.mit.edu 37 7 42005299 42005299 + Silent SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr7:42005299G>A ENST00000395925.3 - 15 3456 c.3372C>T c.(3370-3372)caC>caT p.H1124H GLI3_ENST00000479210.1_5'UTR NM_000168.5 NP_000159.3 P10071 GLI3_HUMAN GLI family zinc finger 3 112 CACCGGGCCCGTGGGGCACTT 0.657000 Pallister-Hall syndrome;Greig Cephalopolysyndactyly 0 SO:0001819 synonymous_variant Familial Cancer Database ; ENST00000395925.3 1 1 hg19 CCDS5465.1 TCGA-2L-AAQJ-01A-12D-A397-08 GLI3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250806.3 1 0 1 97 372 0 109 0 4.364137e-02 0 2 0 109 2 0 0 0 0 0 2 1 1.000000 96 366 0 109 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.040935 0 0.440000 1.870000 0.435028 0.920000 0.760000 1.000000 1.000000 0.923828 0.920000 1 8.400000e-01 1 OGDH 4967 broad.mit.edu 37 7 44715672 44715672 + Missense_Mutation SNP T T C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr7:44715672T>C ENST00000222673.5 + 9 1172 c.1130T>C c.(1129-1131)cTt>cCt p.L377P OGDH_ENST00000449767.1_Missense_Mutation_p.L373P|OGDH_ENST00000444676.1_Missense_Mutation_p.L392P|OGDH_ENST00000443864.2_Missense_Mutation_p.L377P|OGDH_ENST00000439616.2_Missense_Mutation_p.L227P|OGDH_ENST00000543843.1_Missense_Mutation_p.L328P|OGDH_ENST00000447398.1_Missense_Mutation_p.L388P NM_002541.3 NP_002532.2 Q02218 ODO1_HUMAN oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) 36 Valproic Acid(DB00313) CCTTCCCACCTTGAGGCCGCT 0.557000 0 SO:0001583 missense ENST00000222673.5 1 1 hg19 CCDS34627.1 . . . . . . . . . . T 22.6 4.306757 0.81247 . . ENSG00000105953 ENST00000439616;ENST00000443864;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843 D;T;D;D;D;D;D 0.95788 -3.81;2.0;-3.81;-3.81;-3.81;-3.81;-3.81 5.14 5.14 0.70334 Dehydrogenase, E1 component (1); 0.000000 0.85682 D 0.000000 D 0.98738 0.9576 H 0.98996 4.395 0.80722 D 1 D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D 0.97110 1.0;1.0;1.0;1.0;1.0;1.0;1.0 D 0.99521 1.0958 10 0.87932 D 0 -27.6918 14.9242 0.70862 0.0:0.0:0.0:1.0 . 172;227;373;388;279;377;377 B4E3E9;E9PFG7;E9PBM1;E9PDF2;A2VCT2;Q02218;Q96DD3 .;.;.;.;.;ODO1_HUMAN;. P 227;377;373;388;392;377;328 ENSP00000398576:L227P;ENSP00000388084:L377P;ENSP00000392878:L373P;ENSP00000388183:L388P;ENSP00000414662:L392P;ENSP00000222673:L377P;ENSP00000443821:L328P ENSP00000222673:L377P L + 2 0 OGDH 44682197 1.000000 0.71417 0.987000 0.45799 0.892000 0.51952 7.788000 0.85771 2.063000 0.61619 0.379000 0.24179 CTT TCGA-2L-AAQJ-01A-12D-A397-08 OGDH-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000339391.1 1 0 1 71 413 0 106 1 9.999272e-01 21 60 0 106 2 0 0 0 0 0 2 1 1.000000 71 408 0 106 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.040935 0 0.440000 1.870000 0.435028 0.650000 0.520000 0.800000 0.660000 0.665688 0.650000 0 5.800000e-01 7.400000e-01 C7orf57 136288 broad.mit.edu 37 7 48080979 48080979 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr7:48080979C>T ENST00000348904.3 + 3 316 c.104C>T c.(103-105)gCc>gTc p.A35V C7orf57_ENST00000430738.1_Missense_Mutation_p.A80V|C7orf57_ENST00000539619.1_Missense_Mutation_p.A35V|C7orf57_ENST00000420324.1_Missense_Mutation_p.A80V|C7orf57_ENST00000435376.1_5'UTR NM_001100159.2 NP_001093629.1 Q8NEG2 CG057_HUMAN chromosome 7 open reading frame 57 9 GCCGTGGATGCCCCACCAGCG 0.567000 0 SO:0001583 missense ENST00000348904.3 0 1 hg19 CCDS47583.1 . . . . . . . . . . C 0.418 -0.909812 0.02434 . . ENSG00000164746 ENST00000420324;ENST00000430738;ENST00000348904;ENST00000539619 T;T;T;T 0.54675 0.56;0.56;0.56;0.56 5.69 -1.12 0.09808 . 0.758231 0.12566 N 0.457767 T 0.29491 0.0735 N 0.11698 0.16 0.09310 N 1 B 0.14438 0.01 B 0.16722 0.016 T 0.22765 -1.0207 10 0.18710 T 0.47 -42.8651 9.8678 0.41154 0.0:0.4479:0.0:0.5521 . 35 Q8NEG2 CG057_HUMAN V 80;80;35;35 ENSP00000394648:A80V;ENSP00000410944:A80V;ENSP00000335500:A35V;ENSP00000442474:A35V ENSP00000335500:A35V A + 2 0 C7orf57 48047504 0.000000 0.05858 0.005000 0.12908 0.037000 0.13140 -0.525000 0.06214 -0.112000 0.11979 -0.251000 0.11542 GCC TCGA-2L-AAQJ-01A-12D-A397-08 C7orf57-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000341745.1 0 0 0 4 206 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 0.888935 4 204 0 48 2 0 0 0 0 0 2 -2.863991 1 1 0 0 1 0 0 0 2.040935 0 0.440000 1.870000 0.435028 0.090000 0.020000 0.200000 0.080000 0.105597 0.090000 0 5.000000e-02 1.500000e-01 WIPI2 26100 broad.mit.edu 37 7 5232787 5232787 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr7:5232787G>A ENST00000288828.4 + 2 345 c.113G>A c.(112-114)cGt>cAt p.R38H WIPI2_ENST00000382384.2_Intron|WIPI2_ENST00000404704.3_Missense_Mutation_p.R38H|WIPI2_ENST00000485854.1_Intron|WIPI2_ENST00000401525.3_Intron NM_001033518.1|NM_001278299.1|NM_015610.3 NP_001028690.1|NP_001265228.1|NP_056425.1 Q9Y4P8 WIPI2_HUMAN WD repeat domain, phosphoinositide interacting 2 16 Ovarian(82;0.0175) GGTCTTGGCCGTCGCGCTGTT 0.388000 0 SO:0001583 missense ENST00000288828.4 1 1 hg19 CCDS5339.1 . . . . . . . . . . G 7.818 0.717084 0.15372 . . ENSG00000157954 ENST00000288828;ENST00000404704 T;T 0.35973 1.28;1.28 3.42 -6.11 0.02131 . 608.758000 0.01314 U 0.010739 T 0.15782 0.0380 N 0.03608 -0.345 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.18967 -1.0320 10 0.40728 T 0.16 . 6.7201 0.23325 0.3457:0.1644:0.4899:0.0 . 38;38 Q9Y4P8-6;Q9Y4P8 .;WIPI2_HUMAN H 38 ENSP00000288828:R38H;ENSP00000385297:R38H ENSP00000288828:R38H R + 2 0 WIPI2 5199313 0.000000 0.05858 0.000000 0.03702 0.003000 0.03518 -2.087000 0.01360 -1.161000 0.02800 -1.223000 0.01593 CGT TCGA-2L-AAQJ-01A-12D-A397-08 WIPI2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000241669.2 0 0 1 97 377 1 86 1 9.065020e-01 7 11 1 86 2 0 0 0 0 0 2 1 1.000000 96 373 1 83 19 0 0 0 0 0 2 -20.000000 1 1 121412 1 35 1 0 0 0 2.040935 0 0.440000 1.870000 0.435028 0.910000 0.760000 1.000000 1.000000 0.916210 0.910000 1 8.300000e-01 1 FSCN1 6624 broad.mit.edu 37 7 5644983 5644983 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr7:5644983G>A ENST00000382361.3 + 5 1474 c.1360G>A c.(1360-1362)Gag>Aag p.E454K FSCN1_ENST00000340250.6_Missense_Mutation_p.E433K NM_003088.3 NP_003079.1 Q16658 FSCN1_HUMAN fascin actin-bundling protein 1 9 Ovarian(82;0.0694) CTTCTTCTTCGAGTTCTGCGA 0.617000 0 SO:0001583 missense ENST00000382361.3 1 1 hg19 CCDS5342.1 . . . . . . . . . . G 31 5.060521 0.93846 . . ENSG00000075618 ENST00000340250;ENST00000382361;ENST00000535097 T;T 0.52057 0.68;0.68 4.0 4.0 0.46444 Fascin domain (1);Actin cross-linking (1); 0.062034 0.64402 D 0.000007 T 0.45377 0.1339 M 0.62209 1.925 0.80722 D 1 P 0.50443 0.935 B 0.39068 0.289 T 0.59069 -0.7523 10 0.87932 D 0 -0.2446 15.5031 0.75716 0.0:0.0:1.0:0.0 . 454 Q16658 FSCN1_HUMAN K 433;454;176 ENSP00000339729:E433K;ENSP00000371798:E454K ENSP00000339729:E433K E + 1 0 FSCN1 5611509 1.000000 0.71417 0.998000 0.56505 0.878000 0.50629 9.420000 0.97426 1.944000 0.56390 0.549000 0.68633 GAG TCGA-2L-AAQJ-01A-12D-A397-08 FSCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207153.3 1 0 1 46 157 0 46 1 1 84 182 0 46 2 0 0 0 0 0 2 1 1.000000 45 156 0 44 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.040935 0 0.440000 1.870000 0.435028 0.990000 0.770000 1.000000 1.000000 0.960091 0.990000 1 8.800000e-01 1 MAGI2 9863 broad.mit.edu 37 7 77885649 77885649 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr7:77885649C>T ENST00000354212.4 - 10 1911 c.1658G>A c.(1657-1659)cGg>cAg p.R553Q MAGI2_ENST00000419488.1_Missense_Mutation_p.R553Q|MAGI2_ENST00000536571.1_Missense_Mutation_p.R385Q|MAGI2_ENST00000522391.1_Missense_Mutation_p.R553Q|MAGI2_ENST00000535697.1_Missense_Mutation_p.R390Q NM_012301.3 NP_036433.2 Q86UL8 MAGI2_HUMAN membrane associated guanylate kinase, WW and PDZ domain containing 2 84 all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236) CTGTGAGGTCCGAGAAATGTA 0.512000 0 SO:0001583 missense ENST00000354212.4 1 1 hg19 CCDS5594.1 . . . . . . . . . . C 14.28 2.488783 0.44249 . . ENSG00000187391 ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697 T;T;T;T;T 0.10382 2.97;2.98;2.88;3.82;3.83 5.94 5.06 0.68205 . 0.000000 0.33253 U 0.005115 T 0.12220 0.0297 N 0.16790 0.44 0.49130 D 0.999757 D;B;D;D;B;D 0.76494 0.988;0.145;0.998;0.998;0.376;0.999 P;B;P;P;B;P 0.55011 0.507;0.018;0.652;0.652;0.068;0.766 T 0.23940 -1.0174 10 0.11485 T 0.65 . 14.5211 0.67851 0.0:0.9297:0.0:0.0703 . 390;385;553;553;553;553 F5GWH1;F5GWK7;B7Z4H4;E7EWI0;Q86UL8-2;Q86UL8 .;.;.;.;.;MAGI2_HUMAN Q 553;553;553;553;385;390 ENSP00000405766:R553Q;ENSP00000346151:R553Q;ENSP00000428389:R553Q;ENSP00000441584:R385Q;ENSP00000441603:R390Q ENSP00000346151:R553Q R - 2 0 MAGI2 77723585 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 3.243000 0.51392 1.519000 0.48950 0.561000 0.74099 CGG TCGA-2L-AAQJ-01A-12D-A397-08 MAGI2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253197.3 1 0 1 38 163 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 1.000000 38 161 0 38 2 0 0 0 0 0 2 -2.948967 1 1 121408 3 36 1 0 0 0 2.040935 0 0.440000 1.870000 0.435028 0.840000 0.620000 1.000000 1.000000 0.851045 0.840000 0 7.300000e-01 9.800000e-01 COL14A1 7373 broad.mit.edu 37 8 121160087 121160087 + Missense_Mutation SNP G G T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr8:121160087G>T ENST00000297848.3 + 2 276 c.6G>T c.(4-6)aaG>aaT p.K2N COL14A1_ENST00000537875.1_Missense_Mutation_p.K2N|COL14A1_ENST00000247781.3_Missense_Mutation_p.K2N|COL14A1_ENST00000309791.4_Missense_Mutation_p.K2N|COL14A1_ENST00000432943.2_3'UTR NM_021110.1 NP_066933.1 collagen, type XIV, alpha 1 119 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) ATAAAATGAAGATTTTCCAGC 0.383000 0 SO:0001583 missense ENST00000297848.3 1 1 hg19 CCDS34938.1 . . . . . . . . . . G 11.64 1.697656 0.30142 . . ENSG00000187955 ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781 T;D;D;D 0.87966 0.45;-2.14;-2.16;-2.32 5.92 5.92 0.95590 . 0.536026 0.19314 N 0.117330 T 0.78214 0.4248 N 0.14661 0.345 0.26614 N 0.972785 B 0.19583 0.037 B 0.17098 0.017 T 0.64296 -0.6441 10 0.27082 T 0.32 . 15.8249 0.78690 0.0:0.0:1.0:0.0 . 2 Q05707 COEA1_HUMAN N 2 ENSP00000443974:K2N;ENSP00000311809:K2N;ENSP00000297848:K2N;ENSP00000247781:K2N ENSP00000247781:K2N K + 3 2 COL14A1 121229268 1.000000 0.71417 0.513000 0.27749 0.105000 0.19272 2.807000 0.47955 2.818000 0.97014 0.655000 0.94253 AAG TCGA-2L-AAQJ-01A-12D-A397-08 COL14A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313657.2 1 0 1 26 223 0 43 0 2.523345e-01 0 9 0 43 2 0 0 0 0 0 2 1 1.000000 27 222 0 43 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.477001 1 0.440000 1.870000 0.537649 0.580000 0.390000 1.000000 0.570000 0.601961 0.580000 0 4.800000e-01 7.100000e-01 ENTPD4 9583 broad.mit.edu 37 8 23294452 23294452 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr8:23294452C>T ENST00000358689.4 - 10 1604 c.1369G>A c.(1369-1371)Gca>Aca p.A457T ENTPD4_ENST00000417069.2_Missense_Mutation_p.A449T|ENTPD4_ENST00000521321.1_5'UTR|ENTPD4_ENST00000356206.6_Missense_Mutation_p.A449T NM_001128930.2|NM_004901.4 NP_001122402.1|NP_004892.1 Q9Y227 ENTP4_HUMAN ectonucleoside triphosphate diphosphohydrolase 4 25 Prostate(55;0.114) GGTACCTTTGCAGCTTTAGTA 0.483000 0 SO:0001583 missense ENST00000358689.4 1 1 hg19 CCDS6041.1 . . . . . . . . . . C 32 5.132882 0.94517 . . ENSG00000197217 ENST00000518471;ENST00000356206;ENST00000358689;ENST00000417069 T;T;T;T 0.11930 2.73;2.73;2.73;2.73 5.59 5.59 0.84812 . 0.000000 0.85682 D 0.000000 T 0.30759 0.0775 L 0.56340 1.77 0.80722 D 1 D;D;D 0.56521 0.976;0.97;0.976 P;P;P 0.61070 0.883;0.857;0.883 T 0.00236 -1.1891 10 0.35671 T 0.21 -17.3279 18.1443 0.89651 0.0:1.0:0.0:0.0 . 449;449;457 Q8NE73;Q9Y227-2;Q9Y227 .;.;ENTP4_HUMAN T 52;449;457;449 ENSP00000430579:A52T;ENSP00000348536:A449T;ENSP00000351520:A457T;ENSP00000408573:A449T ENSP00000348536:A449T A - 1 0 ENTPD4 23350397 1.000000 0.71417 0.998000 0.56505 0.955000 0.61496 7.818000 0.86416 2.631000 0.89168 0.462000 0.41574 GCA TCGA-2L-AAQJ-01A-12D-A397-08 ENTPD4-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000215142.1 1 0 1 99 433 0 98 1 9.998515e-01 17 41 0 98 2 0 0 0 0 0 2 1 1.000000 98 427 0 98 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.039724 0 0.440000 1.870000 0.435028 0.830000 0.690000 0.980000 0.840000 0.840971 0.830000 0 7.600000e-01 9.100000e-01 DOCK5 80005 broad.mit.edu 37 8 25193885 25193885 + Silent SNP T T C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr8:25193885T>C ENST00000276440.7 + 22 2367 c.2323T>C c.(2323-2325)Ttg>Ctg p.L775L NM_024940.6 NP_079216.4 Q9H7D0 DOCK5_HUMAN dedicator of cytokinesis 5 72 all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143) AGTGCTCTACTTGAGGTAATG 0.448000 Pancreas(145;34 1887 3271 10937 30165) 0 SO:0001819 synonymous_variant ENST00000276440.7 1 1 hg19 CCDS6047.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 T 9.240 1.038124 0.19669 . . ENSG00000147459 ENST00000444569 . . . 5.76 -4.24 0.03777 . 0.000000 0.64402 D 0.000001 T 0.64875 0.2638 . . . 0.80722 D 1 . . . . . . T 0.65348 -0.6190 5 . . . . 15.9667 0.79979 0.0:0.7662:0.0:0.2338 . . . . P 546 . . L + 2 0 DOCK5 25249802 0.795000 0.28851 0.949000 0.38748 0.803000 0.45373 -0.041000 0.12084 -0.567000 0.06046 -0.263000 0.10527 CTT TCGA-2L-AAQJ-01A-12D-A397-08 DOCK5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254955.2 0 0 1 19 94 0 30 1 5.841187e-01 4 7 0 30 2 0 0 0 0 0 2 1 0.999994 18 93 0 30 2 0 0 0 0 0 2 -12.972770 1 1 121410 8 38 1 0 0 0 2.039724 0 0.440000 1.870000 0.435028 0.750000 0.480000 1.000000 1.000000 0.767735 0.750000 0 6.100000e-01 9.200000e-01 CSMD1 64478 broad.mit.edu 37 8 3216706 3216706 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr8:3216706C>T ENST00000520002.1 - 22 3830 c.3275G>A c.(3274-3276)cGt>cAt p.R1092H CSMD1_ENST00000542608.1_Missense_Mutation_p.R1091H|CSMD1_ENST00000602557.1_Missense_Mutation_p.R1092H|CSMD1_ENST00000537824.1_Missense_Mutation_p.R1091H|CSMD1_ENST00000400186.3_Missense_Mutation_p.R1092H|CSMD1_ENST00000602723.1_Missense_Mutation_p.R1092H|CSMD1_ENST00000539096.1_Missense_Mutation_p.R1091H Q96PZ7 CSMD1_HUMAN CUB and Sushi multiple domains 1 25 all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234) ACTCCACACACGGCGGCCCCC 0.562000 0 SO:0001583 missense ENST00000520002.1 0 1 hg19 . . . . . . . . . . c 36 5.695321 0.96793 . . ENSG00000183117 ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096 T;T;T;T;T 0.64803 -0.12;-0.12;-0.12;-0.12;-0.12 5.34 5.34 0.76211 Complement control module (2);Sushi/SCR/CCP (3); 0.000000 0.64402 D 0.000001 D 0.84483 0.5482 M 0.92268 3.29 0.80722 D 1 D;D;D 0.89917 1.0;0.995;0.994 D;D;P 0.85130 0.997;0.957;0.837 D 0.87265 0.2282 10 0.52906 T 0.07 . 19.067 0.93116 0.0:1.0:0.0:0.0 . 1092;1092;1092 E5RIG2;Q96PZ7;Q96PZ7-4 .;CSMD1_HUMAN;. H 1092;1092;954;1091;1091;1091 ENSP00000383047:R1092H;ENSP00000430733:R1092H;ENSP00000441462:R1091H;ENSP00000446243:R1091H;ENSP00000441675:R1091H ENSP00000320445:R954H R - 2 0 CSMD1 3204113 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 4.762000 0.62250 2.489000 0.83994 0.550000 0.68814 CGT TCGA-2L-AAQJ-01A-12D-A397-08 CSMD1-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000374500.2 0 0 0 7 319 0 64 0 0 0 0 64 2 0 0 0 0 0 2 1 0.978882 7 310 0 61 2 0 0 0 0 0 2 -3.082203 1 1 121412 4 35 1 0 0 0 2.027595 0 0.440000 1.870000 0.429967 0.090000 0.040000 0.190000 0.100000 0.108472 0.090000 0 6.000000e-02 1.400000e-01 PAG1 55824 broad.mit.edu 37 8 81888976 81888976 + Missense_Mutation SNP T T G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr8:81888976T>G ENST00000220597.4 - 9 1812 c.1102A>C c.(1102-1104)Act>Cct p.T368P PAG1_ENST00000523463.1_5'Flank NM_018440.3 NP_060910.3 Q9NWQ8 PHAG1_HUMAN phosphoprotein membrane anchor with glycosphingolipid microdomains 1 11 Lung NSC(7;5.76e-06)|all_lung(9;2e-05) BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197) CTGTTTGGAGTTTTTTCGAAG 0.512000 0 SO:0001583 missense ENST00000220597.4 1 1 hg19 CCDS6227.1 . . . . . . . . . . T 3.651 -0.071468 0.07228 . . ENSG00000076641 ENST00000220597 . . . 5.05 -2.76 0.05896 . 0.702006 0.14361 N 0.324452 T 0.34687 0.0906 L 0.51422 1.61 0.09310 N 1 B 0.06786 0.001 B 0.08055 0.003 T 0.26815 -1.0092 9 0.45353 T 0.12 -1.9998 6.671 0.23068 0.0:0.1378:0.3656:0.4965 . 368 Q9NWQ8 PAG1_HUMAN P 368 . ENSP00000220597:T368P T - 1 0 PAG1 82051531 0.005000 0.15991 0.027000 0.17364 0.026000 0.11368 0.003000 0.13083 -0.242000 0.09667 -1.106000 0.02097 ACT TCGA-2L-AAQJ-01A-12D-A397-08 PAG1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000379352.3 1 0 0 30 269 0 39 1 1.587105e-01 4 3 0 39 2 0 0 0 0 0 2 1 1.000000 30 264 0 38 2 0 0 0 0 0 2 -11.301750 1 1 0 0 1 1 2 3 2.471346 1 0.440000 1.870000 0.540984 0.550000 0.380000 0.760000 0.550000 0.569510 0.550000 0 4.600000e-01 6.600000e-01 SH2D3C 10044 broad.mit.edu 37 9 130511512 130511512 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr9:130511512G>A ENST00000314830.8 - 5 1230 c.1117C>T c.(1117-1119)Cgc>Tgc p.R373C SH2D3C_ENST00000429553.1_Missense_Mutation_p.R19C|SH2D3C_ENST00000471939.1_Intron|SH2D3C_ENST00000373274.3_Missense_Mutation_p.R213C|SH2D3C_ENST00000420366.1_Missense_Mutation_p.R215C|SH2D3C_ENST00000373277.4_Missense_Mutation_p.R216C|SH2D3C_ENST00000373276.3_Missense_Mutation_p.R305C NM_170600.2 NP_733745.1 Q8N5H7 SH2D3_HUMAN SH2 domain containing 3C p.R373S(2) 28 CCATCGCTGCGGGTGACCTTG 0.617000 2 Substitution - Missense(2) SO:0001583 missense ENST00000314830.8 1 1 hg19 CCDS6877.1 . . . . . . . . . . G 12.60 1.986440 0.35036 . . ENSG00000095370 ENST00000373277;ENST00000420366;ENST00000373276;ENST00000373274;ENST00000429553;ENST00000314830;ENST00000414380 T;T;T;T;T;T;T 0.38722 2.55;2.56;2.3;2.56;1.68;2.51;1.12 5.37 3.42 0.39159 . 0.469026 0.24884 N 0.034822 T 0.33469 0.0864 L 0.51422 1.61 0.47123 D 0.999322 B;B;B;B;B 0.21821 0.007;0.061;0.033;0.007;0.005 B;B;B;B;B 0.14578 0.003;0.011;0.005;0.007;0.004 T 0.15867 -1.0422 10 0.38643 T 0.18 -28.0923 7.986 0.30212 0.0869:0.0:0.6601:0.253 . 213;373;305;216;215 E9PG48;Q8N5H7;E7EUN5;Q8N5H7-2;Q8N5H7-5 .;SH2D3_HUMAN;.;.;. C 216;215;305;213;19;373;190 ENSP00000362374:R216C;ENSP00000388536:R215C;ENSP00000362373:R305C;ENSP00000362371:R213C;ENSP00000394632:R19C;ENSP00000317817:R373C;ENSP00000413760:R190C ENSP00000317817:R373C R - 1 0 SH2D3C 129551333 1.000000 0.71417 0.993000 0.49108 0.615000 0.37417 2.677000 0.46892 1.413000 0.46997 0.561000 0.74099 CGC TCGA-2L-AAQJ-01A-12D-A397-08 SH2D3C-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000054264.1 1 0 1 59 337 0 84 0 9.225326e-01 0 27 0 84 2 0 0 0 0 0 2 1 1.000000 58 333 0 83 2 0 0 0 0 0 2 -2.475894 0 1 0 0 1 0 0 0 2.034520 0 0.440000 1.870000 0.435028 0.660000 0.520000 0.830000 0.670000 0.676990 0.660000 0 5.900000e-01 7.500000e-01 LRRC8A 56262 broad.mit.edu 37 9 131669884 131669884 + Silent SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr9:131669884G>A ENST00000259324.5 + 3 964 c.441G>A c.(439-441)ccG>ccA p.P147P LRRC8A_ENST00000372600.4_Silent_p.P147P|LRRC8A_ENST00000372599.3_Silent_p.P147P NM_001127244.1 NP_001120716.1 Q8IWT6 LRC8A_HUMAN leucine rich repeat containing 8 family, member A 28 TCAAATTCCCGCGCACCAGCT 0.572000 0 SO:0001819 synonymous_variant ENST00000259324.5 1 1 hg19 CCDS35155.1 TCGA-2L-AAQJ-01A-12D-A397-08 LRRC8A-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054516.2 1 0 1 43 159 0 51 1 1 80 147 0 51 2 0 0 0 0 0 2 1 1.000000 42 158 0 51 2 0 0 0 0 0 2 -3.840315 1 1 121412 1 31 1 0 0 0 2.034520 0 0.440000 1.870000 0.435028 0.950000 0.710000 1.000000 1.000000 0.929177 0.950000 1 8.300000e-01 1 ENTPD2 954 broad.mit.edu 37 9 139944888 139944888 + Missense_Mutation SNP A A T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chr9:139944888A>T ENST00000355097.2 - 6 924 c.877T>A c.(877-879)Ttc>Atc p.F293I ENTPD2_ENST00000312665.5_Missense_Mutation_p.F293I|RP11-229P13.15_ENST00000439076.1_RNA|ENTPD2_ENST00000460614.1_5'Flank NM_001246.3|NM_203468.2 NP_001237.1|NP_982293.1 Q9Y5L3 ENTP2_HUMAN ectonucleoside triphosphate diphosphohydrolase 2 12 all_cancers(76;0.0926) Myeloproliferative disorder(178;0.0511) STAD - Stomach adenocarcinoma(284;0.123) CTGCTGTTGAAGTTCTGGGGC 0.632000 OREG0019627 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000355097.2 1 1 hg19 CCDS7026.1 . . . . . . . . . . A 13.54 2.267428 0.40095 . . ENSG00000054179 ENST00000355097;ENST00000312665 T;T 0.11277 2.8;2.79 4.95 1.35 0.21983 . 0.427784 0.23684 N 0.045587 T 0.09905 0.0243 L 0.59436 1.845 0.09310 N 1 B;B 0.22541 0.058;0.071 B;B 0.24006 0.03;0.05 T 0.23261 -1.0193 10 0.42905 T 0.14 -9.6179 4.0512 0.09796 0.5803:0.0:0.262:0.1576 . 293;293 Q9Y5L3-2;Q9Y5L3 .;ENTP2_HUMAN I 293 ENSP00000347213:F293I;ENSP00000312494:F293I ENSP00000312494:F293I F - 1 0 ENTPD2 139064709 0.411000 0.25384 0.155000 0.22561 0.030000 0.12068 0.623000 0.24447 0.244000 0.21351 0.459000 0.35465 TTC TCGA-2L-AAQJ-01A-12D-A397-08 ENTPD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055169.1 1 0 1 40 141 0 35 1 9.999377e-01 30 26 0 35 2 0 0 0 0 0 2 1 1.000000 39 141 0 35 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 2.034520 0 0.440000 1.870000 0.435028 0.990000 0.740000 1.000000 1.000000 0.946237 0.990000 1 8.500000e-01 1 VSIG1 340547 broad.mit.edu 37 X 107316507 107316507 + Missense_Mutation SNP G G A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chrX:107316507G>A ENST00000217957.5 + 5 713 c.596G>A c.(595-597)gGa>gAa p.G199E VSIG1_ENST00000415430.3_Missense_Mutation_p.G235E NM_182607.4 NP_872413.1 Q86XK7 VSIG1_HUMAN V-set and immunoglobulin domain containing 1 17 TTGGTCATTGGAAATCTGACA 0.418000 0 SO:0001583 missense ENST00000217957.5 1 1 hg19 CCDS14535.1 . . . . . . . . . . G 19.23 3.786560 0.70337 . . ENSG00000101842 ENST00000415430;ENST00000217957 T;T 0.11495 2.77;2.77 5.27 4.41 0.53225 Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.207594 0.40908 D 0.000995 T 0.12944 0.0314 N 0.16790 0.44 0.42936 D 0.99433 D;D 0.89917 1.0;1.0 D;D 0.77557 0.99;0.985 T 0.13845 -1.0494 10 0.02654 T 1 . 9.9443 0.41600 0.0969:0.0:0.9031:0.0 . 235;199 C9J4P2;Q86XK7 .;VSIG1_HUMAN E 235;199 ENSP00000402219:G235E;ENSP00000217957:G199E ENSP00000217957:G199E G + 2 0 VSIG1 107203163 1.000000 0.71417 1.000000 0.80357 0.962000 0.63368 3.976000 0.56867 1.198000 0.43158 0.513000 0.50165 GGA TCGA-2L-AAQJ-01A-12D-A397-08 VSIG1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000057858.1 1 0 1 195 1012 0 282 1 1 8 425 0 282 2 0 0 0 0 0 2 1 1.000000 193 1004 0 280 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 0.440000 1.870000 0.440000 0.720000 0.630000 0.830000 0.740000 0.736116 0.720000 0 6.800000e-01 7.800000e-01 ARHGAP36 158763 broad.mit.edu 37 X 130218925 130218925 + Missense_Mutation SNP T T C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chrX:130218925T>C ENST00000276211.5 + 7 1187 c.842T>C c.(841-843)cTg>cCg p.L281P ARHGAP36_ENST00000370921.1_Missense_Mutation_p.L145P|ARHGAP36_ENST00000370922.1_Missense_Mutation_p.L269P NM_144967.3 NP_659404.2 Q6ZRI8 RHG36_HUMAN Rho GTPase activating protein 36 71 GATGTAGTGCTGGATGACAAT 0.488000 0 SO:0001583 missense ENST00000276211.5 1 1 hg19 CCDS14628.1 . . . . . . . . . . T 23.1 4.378294 0.82682 . . ENSG00000147256 ENST00000276211;ENST00000370922;ENST00000412432;ENST00000370921 T;T;T;T 0.46451 0.87;0.87;0.87;0.87 5.16 5.16 0.70880 Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1); 0.187606 0.26397 N 0.024602 T 0.65186 0.2667 M 0.85630 2.765 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.76575 0.988;0.988;0.987 T 0.68876 -0.5293 10 0.52906 T 0.07 . 10.0987 0.42491 0.0:0.0:0.0:1.0 . 250;269;281 Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8 .;.;RHG36_HUMAN P 281;269;250;145 ENSP00000276211:L281P;ENSP00000359960:L269P;ENSP00000408515:L250P;ENSP00000359959:L145P ENSP00000276211:L281P L + 2 0 ARHGAP36 130046606 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 6.818000 0.75257 1.909000 0.55274 0.356000 0.21956 CTG TCGA-2L-AAQJ-01A-12D-A397-08 ARHGAP36-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000355073.1 1 0 1 113 548 0 134 0 0 0 1 0 134 2 0 0 0 0 0 2 1 1.000000 113 547 0 134 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 0.440000 1.870000 0.440000 0.770000 0.640000 0.900000 0.780000 0.780044 0.770000 0 7.000000e-01 8.400000e-01 ARHGEF6 9459 broad.mit.edu 37 X 135789073 135789073 + Missense_Mutation SNP T T A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chrX:135789073T>A ENST00000250617.6 - 9 2245 c.1040A>T c.(1039-1041)cAg>cTg p.Q347L ARHGEF6_ENST00000370620.1_Missense_Mutation_p.Q193L|ARHGEF6_ENST00000535227.1_Missense_Mutation_p.Q220L|ARHGEF6_ENST00000370622.1_Missense_Mutation_p.Q193L NM_004840.2 NP_004831.1 Q15052 ARHG6_HUMAN Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 38 Acute lymphoblastic leukemia(192;0.000127) TTACCTGTGCTGAGTGAGCAC 0.408000 0 SO:0001583 missense ENST00000250617.6 0 1 hg19 CCDS14660.1 . . . . . . . . . . T 17.07 3.295049 0.60086 . . ENSG00000129675 ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227 T;T;T;T 0.63744 -0.06;-0.06;-0.06;-0.06 5.15 5.15 0.70609 Dbl homology (DH) domain (5); 0.210007 0.49916 D 0.000125 T 0.70718 0.3256 M 0.81802 2.56 0.42510 D 0.992962 P;P 0.43352 0.629;0.804 B;P 0.47346 0.326;0.544 T 0.76280 -0.3017 10 0.72032 D 0.01 . 13.1422 0.59440 0.0:0.0:0.0:1.0 . 220;347 B7Z3C7;Q15052 .;ARHG6_HUMAN L 347;193;193;193;220 ENSP00000250617:Q347L;ENSP00000359654:Q193L;ENSP00000359656:Q193L;ENSP00000439483:Q220L ENSP00000250617:Q347L Q - 2 0 ARHGEF6 135616739 1.000000 0.71417 0.995000 0.50966 0.557000 0.35523 7.138000 0.77305 1.813000 0.52934 0.486000 0.48141 CAG TCGA-2L-AAQJ-01A-12D-A397-08 ARHGEF6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058511.2 0 0 0 7 629 0 122 0 7.314050e-03 0 10 0 122 2 0 0 0 0 0 2 1 0.979906 5 624 0 122 2 0 0 0 0 0 2 -5.715155 1 0 0 0 1 0 1 1 0.440000 1.870000 0.440000 0.040000 0.010000 0.100000 0.050000 0.056928 0.040000 0 3.000000e-02 8.000000e-02 NR0B1 190 broad.mit.edu 37 X 30326930 30326930 + Missense_Mutation SNP T T G TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chrX:30326930T>G ENST00000378970.4 - 1 785 c.551A>C c.(550-552)aAa>aCa p.K184T NR0B1_ENST00000453287.1_Missense_Mutation_p.K184T|NR0B1_ENST00000378963.1_5'Flank NM_000475.4 NP_000466.2 P51843 NR0B1_HUMAN nuclear receptor subfamily 0, group B, member 1 24 Dexamethasone(DB01234)|Tretinoin(DB00755) TAGCGCCTCTTTACCCCCTGG 0.692000 OREG0019719 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000378970.4 1 1 hg19 CCDS14223.1 . . . . . . . . . . T 2.662 -0.279477 0.05642 . . ENSG00000169297 ENST00000378970;ENST00000453287 D;D 0.97752 -3.63;-4.52 4.32 0.238 0.15480 . 1.525170 0.04086 N 0.310508 D 0.91597 0.7345 N 0.03608 -0.345 0.09310 N 1 B 0.06786 0.001 B 0.01281 0.0 D 0.85206 0.1018 10 0.52906 T 0.07 0.6249 4.5457 0.12079 0.0:0.422:0.3572:0.2207 . 184 P51843 NR0B1_HUMAN T 184 ENSP00000368253:K184T;ENSP00000396403:K184T ENSP00000368253:K184T K - 2 0 NR0B1 30236851 0.000000 0.05858 0.000000 0.03702 0.025000 0.11179 -0.356000 0.07661 -0.201000 0.10284 -0.402000 0.06365 AAA TCGA-2L-AAQJ-01A-12D-A397-08 NR0B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056161.1 1 0 1 14 44 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 0.999843 14 42 0 22 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 0.440000 1.870000 0.440000 0.990000 0.660000 1.000000 1.000000 0.949802 0.990000 1 8.500000e-01 1 NR0B1 190 broad.mit.edu 37 X 30327066 30327066 + Missense_Mutation SNP G G C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chrX:30327066G>C ENST00000378970.4 - 1 649 c.415C>G c.(415-417)Cac>Gac p.H139D NR0B1_ENST00000453287.1_Missense_Mutation_p.H139D|NR0B1_ENST00000378963.1_5'Flank NM_000475.4 NP_000466.2 P51843 NR0B1_HUMAN nuclear receptor subfamily 0, group B, member 1 24 Dexamethasone(DB01234)|Tretinoin(DB00755) TGCCGCGGGTGGTCTTCACCA 0.692000 OREG0019719 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000378970.4 1 1 hg19 CCDS14223.1 . . . . . . . . . . G 17.92 3.507718 0.64410 . . ENSG00000169297 ENST00000378970;ENST00000453287 D;D 0.98164 -3.9;-4.76 3.96 3.96 0.45880 . 0.000000 0.42053 D 0.000762 D 0.98397 0.9467 M 0.66939 2.045 0.40318 D 0.978796 D 0.69078 0.997 D 0.69142 0.962 D 0.99107 1.0845 10 0.87932 D 0 -5.5412 12.706 0.57061 0.0:0.0:1.0:0.0 . 139 P51843 NR0B1_HUMAN D 139 ENSP00000368253:H139D;ENSP00000396403:H139D ENSP00000368253:H139D H - 1 0 NR0B1 30236987 1.000000 0.71417 0.998000 0.56505 0.979000 0.70002 3.474000 0.53129 2.222000 0.72286 0.513000 0.50165 CAC TCGA-2L-AAQJ-01A-12D-A397-08 NR0B1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056161.1 1 0 1 42 137 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 1.000000 41 136 0 39 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 0.440000 1.870000 0.440000 0.990000 0.800000 1.000000 1.000000 0.972910 0.990000 1 9.200000e-01 1 FAM47A 158724 broad.mit.edu 37 X 34148936 34148936 + Missense_Mutation SNP C C T TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chrX:34148936C>T ENST00000346193.3 - 1 1511 c.1460G>A c.(1459-1461)cGg>cAg p.R487Q NM_203408.3 NP_981953.2 Q5JRC9 FA47A_HUMAN family with sequence similarity 47, member A p.R487Q(1) 97 ACTGGACCTCCGACGTGTCTT 0.642000 1 Substitution - Missense(1) SO:0001583 missense ENST00000346193.3 1 1 hg19 CCDS43926.1 . . . . . . . . . . c 9.489 1.100058 0.20552 . . ENSG00000185448 ENST00000346193 T 0.16196 2.36 0.446 0.446 0.16602 . . . . . T 0.10380 0.0254 N 0.24115 0.695 0.09310 N 1 D 0.62365 0.991 P 0.44811 0.461 T 0.23762 -1.0179 8 0.13470 T 0.59 . . . . . 487 Q5JRC9 FA47A_HUMAN Q 487 ENSP00000345029:R487Q ENSP00000345029:R487Q R - 2 0 FAM47A 34058857 0.022000 0.18835 0.006000 0.13384 0.016000 0.09150 0.010000 0.13242 0.435000 0.26365 0.183000 0.17082 CGG TCGA-2L-AAQJ-01A-12D-A397-08 FAM47A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056205.1 1 0 1 76 304 0 85 0 0 0 0 85 2 0 0 0 0 0 2 1 1.000000 76 299 0 82 2 0 0 0 0 0 2 -3.239998 1 1 0 0 1 0 1 1 0.440000 1.870000 0.440000 0.900000 0.730000 1.000000 1.000000 0.903808 0.900000 1 8.100000e-01 1 MED14 9282 broad.mit.edu 37 X 40526067 40526067 + Missense_Mutation SNP A A C TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chrX:40526067A>C ENST00000324817.1 - 24 3288 c.3170T>G c.(3169-3171)tTg>tGg p.L1057W NM_004229.3 NP_004220.2 O60244 MED14_HUMAN mediator complex subunit 14 39 TGGGGCTCTCAAAGCCCCACT 0.493000 0 SO:0001583 missense ENST00000324817.1 0 1 hg19 CCDS14254.1 . . . . . . . . . . A 22.8 4.337558 0.81911 . . ENSG00000180182 ENST00000324817 . . . 5.64 5.64 0.86602 . 0.000000 0.64402 D 0.000001 T 0.75155 0.3811 L 0.53249 1.67 0.58432 D 0.999991 D 0.76494 0.999 D 0.77557 0.99 T 0.77587 -0.2532 9 0.72032 D 0.01 . 14.8838 0.70553 1.0:0.0:0.0:0.0 . 1057 O60244 MED14_HUMAN W 1057 . ENSP00000323720:L1057W L - 2 0 MED14 40411011 1.000000 0.71417 1.000000 0.80357 0.973000 0.67179 8.721000 0.91446 1.896000 0.54893 0.402000 0.26972 TTG TCGA-2L-AAQJ-01A-12D-A397-08 MED14-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060692.1 0 0 0 31 66 0 18 1 9.989050e-01 2 25 0 18 2 0 0 0 0 0 2 1 1.000000 30 65 0 18 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 0.440000 1.870000 0.440000 0.990000 0.990000 1.000000 1.000000 0.999291 0.990000 1 9.900000e-01 1 KCND1 3750 broad.mit.edu 37 X 48819916 48819916 + Missense_Mutation SNP C C T rs145016539 TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chrX:48819916C>T ENST00000218176.3 - 6 3167 c.1870G>A c.(1870-1872)Ggc>Agc p.G624S KCND1_ENST00000376477.1_Missense_Mutation_p.G247S NM_004979.4 NP_004970.3 Q9NSA2 KCND1_HUMAN potassium voltage-gated channel, Shal-related subfamily, member 1 24 Dalfampridine(DB06637) AGGGTGCTGCCGGCCCTGCCA 0.632000 0 SO:0001583 missense ENST00000218176.3 1 1 hg19 CCDS14314.1 . . . . . . . . . . c 1.827 -0.470870 0.04445 7.82E-4 0.0 ENSG00000102057 ENST00000376477;ENST00000218176 D;D 0.95918 -3.34;-3.85 5.32 -0.965 0.10323 . 1.211090 0.05587 N 0.573947 D 0.88919 0.6568 L 0.36672 1.1 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.77501 -0.2564 10 0.02654 T 1 . 3.4758 0.07583 0.197:0.4041:0.0:0.3989 . 624 Q9NSA2 KCND1_HUMAN S 247;624 ENSP00000365660:G247S;ENSP00000218176:G624S ENSP00000218176:G624S G - 1 0 KCND1 48704860 0.959000 0.32827 0.014000 0.15608 0.107000 0.19398 1.496000 0.35638 0.195000 0.20347 -0.743000 0.03520 GGC TCGA-2L-AAQJ-01A-12D-A397-08 KCND1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060774.1 1 0 1 24 84 0 25 0 4.925881e-01 0 7 0 25 2 0 0 0 0 0 2 1 1.000000 23 83 0 24 2 0 0 0 0 0 2 -20.000000 1 1 121348 33 41 1 0 1 1 0.440000 1.870000 0.440000 0.990000 0.680000 1.000000 1.000000 0.939084 0.990000 1 8.300000e-01 1 HDX 139324 broad.mit.edu 37 X 83724365 83724365 + Silent SNP T T A TCGA-2L-AAQJ-01A-12D-A397-08 TCGA-2L-AAQJ-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx de369dbb-736e-4970-998d-a0470029653f cb472e98-8801-40f4-9c2c-6ebb03b41c40 g.chrX:83724365T>A ENST00000297977.5 - 3 477 c.366A>T c.(364-366)acA>acT p.T122T HDX_ENST00000373177.2_Silent_p.T122T|HDX_ENST00000506585.2_Silent_p.T64T NM_001177479.1|NM_144657.4 NP_001170950.1|NP_653258.2 Q7Z353 HDX_HUMAN highly divergent homeobox 48 TATGTTTGTTTGTTCCTTGCC 0.403000 Pancreas(53;231 1169 36156 43751 51139) 0 SO:0001819 synonymous_variant ENST00000297977.5 1 1 hg19 CCDS35342.1 TCGA-2L-AAQJ-01A-12D-A397-08 HDX-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057379.2 1 0 1 66 376 0 84 0 6.204219e-02 0 3 0 84 2 0 0 0 0 0 2 1 1.000000 66 373 0 83 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 0.440000 1.870000 0.440000 0.670000 0.530000 0.830000 0.680000 0.683934 0.670000 0 6.000000e-01 7.600000e-01