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 HIP1R 9026 broad.mit.edu 37 12 123333155 123333170 + Splice_Site DEL TGTGAGTAGCAGCTGC TGTGAGTAGCAGCTGC - TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr12:123333155_123333170delTGTGAGTAGCAGCTGC ENST00000253083.4 + 3 425 c.300delTGTGAGTAGCAGCTGC c.(298-300)aat>aa p.N100fs NM_003959.1 NP_003950.1 O75146 HIP1R_HUMAN huntingtin interacting protein 1 related 26 all_neural(191;0.0837)|Medulloblastoma(191;0.163) GGCACCCCAATGTGAGTAGCAGCTGCTGCCTCTGCT 0.662000 0 SO:0001630 splice_region_variant ENST00000253083.4 1 1 hg19 CCDS31922.1 TCGA-LB-A8F3-01A-11D-A36O-08 HIP1R-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400935.1 0 0 0 17 180 0 80 0 6.571390e-01 0 25 0 80 2 0 0 0 0 0 0 1 0.657441 38 200 3 80 19 0 0 0 0 0 0 -19.999570 1 1 0 0 1 0 2 2 1.790666 1 0.330000 3.010000 0.330000 0.530000 3.200000e-01 1.000000 0.520000 0.564014 0.530000 0 4.200000e-01 6.900000e-01 HELB 92797 broad.mit.edu 37 12 66709127 66709128 + Frame_Shift_Ins INS - - A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr12:66709127_66709128insA ENST00000247815.4 + 6 2023_2024 c.1964_1965insA c.(1963-1968)agagcafs p.A656fs NM_033647.3 NP_387467.2 Q8NG08 HELB_HUMAN helicase (DNA) B 40 GBM - Glioblastoma multiforme(2;0.000142) ACAAACCATAGAGCAGAATCTC 0.342000 0 SO:0001589 frameshift_variant ENST00000247815.4 0 1 hg19 CCDS8976.1 TCGA-LB-A8F3-01A-11D-A36O-08 HELB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401919.1 1 0 0 54 627 0 164 0 0 0 164 0 0 0 0 0 0 1 1.000000 54 616 0 160 2 0 0 0 0 0 0 -2.966611 1 1 0 0 1 1 2 3 1.998260 1 0.330000 3.010000 0.424077 0.550000 4.200000e-01 0.720000 0.560000 0.566635 0.550000 0 4.800000e-01 6.400000e-01 WDFY3 23001 broad.mit.edu 37 4 85678099 85678099 + Frame_Shift_Del DEL G G - rs138292353 TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr4:85678099delG ENST00000295888.4 - 33 5811 c.5404delC c.(5404-5406)cggfs p.R1802fs WDFY3_ENST00000322366.6_Frame_Shift_Del_p.R1802fs NM_014991.4 NP_055806.2 Q8IZQ1 WDFY3_HUMAN WD repeat and FYVE domain containing 3 134 Hepatocellular(203;0.114) TGCTTACTCCGGCAGCTGATG 0.488000 0 SO:0001589 frameshift_variant ENST00000295888.4 0 1 hg19 CCDS3609.1 TCGA-LB-A8F3-01A-11D-A36O-08 WDFY3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252811.2 1 0 0 75 924 0 248 0 0 0 248 0 0 0 0 0 0 1 0.999961 83 918 5 244 36 0 0 0 0 0 0 -3.221883 1 1 0 0 1 1 2 3 1.943468 0 0.330000 3.010000 0.410704 0.520000 4.100000e-01 1.000000 0.510000 0.585698 0.520000 0 4.600000e-01 6.400000e-01 SP4 6671 broad.mit.edu 37 7 21469543 21469544 + Frame_Shift_Ins INS - - T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr7:21469543_21469544insT ENST00000222584.3 + 3 978_979 c.760_761insT c.(760-762)gtafs p.V254fs NM_003112.3 NP_003103.2 Q02446 SP4_HUMAN Sp4 transcription factor 35 GGCTCAAGTTGTAACAACCCTA 0.500000 0 SO:0001589 frameshift_variant ENST00000222584.3 0 1 hg19 CCDS5373.1 TCGA-LB-A8F3-01A-11D-A36O-08 SP4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000211617.2 1 0 0 46 365 0 114 0 0 0 114 0 0 0 0 0 0 1 1.000000 49 363 0 114 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 3 4 2.209617 1 0.330000 3.010000 0.480781 0.890000 6.600000e-01 1.000000 1.000000 0.886725 0.890000 1 7.600000e-01 1 LZTS2 84445 broad.mit.edu 37 10 102763860 102763860 + Silent SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr10:102763860C>T ENST00000370220.1 + 2 4068 c.1005C>T c.(1003-1005)gaC>gaT p.D335D LZTS2_ENST00000370223.3_Silent_p.D335D leucine zipper, putative tumor suppressor 2 22 AGCTCCGAGACCGGGAGGCAG 0.632000 Esophageal Squamous(8;38 437 13604 19902 37640) 0 SO:0001819 synonymous_variant ENST00000370220.1 1 1 hg19 CCDS7507.1 TCGA-LB-A8F3-01A-11D-A36O-08 LZTS2-001 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049872.1 0 0 0 9 246 0 86 1 9.851449e-01 10 192 0 86 2 0 0 0 0 0 2 1 0.993925 9 241 0 85 2 0 0 0 0 0 0 -10.580220 1 1 0 0 1 2 2 4 2.031040 0 0.330000 3.010000 0.436074 0.300000 1.300000e-01 1.000000 0.250000 0.450094 0.300000 0 2.000000e-01 1 ATE1 11101 broad.mit.edu 37 10 123503198 123503198 + Silent SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr10:123503198G>A ENST00000224652.6 - 12 1639 c.1554C>T c.(1552-1554)aaC>aaT p.N518N ATE1_ENST00000369040.3_Silent_p.N422N|ATE1_ENST00000540606.1_Silent_p.N511N|ATE1_ENST00000543447.1_Silent_p.N403N|ATE1_ENST00000369043.3_Silent_p.N518N|ATE1_ENST00000535655.1_Silent_p.N219N NM_001001976.1 NP_001001976.1 O95260 ATE1_HUMAN arginyltransferase 1 14 all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212) GAACAGGTCAGTTTCTGAACA 0.522000 0 SO:0001819 synonymous_variant ENST00000224652.6 1 1 hg19 CCDS31300.1 TCGA-LB-A8F3-01A-11D-A36O-08 ATE1-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding 1 0 0 11 183 0 36 0 8.528621e-02 0 8 0 36 2 0 0 0 0 0 2 1 0.998391 11 181 0 36 2 0 0 0 0 0 0 -14.619200 1 1 0 0 1 2 2 4 2.031040 0 0.330000 3.010000 0.436074 0.470000 2.300000e-01 1.000000 0.400000 0.571444 0.470000 0 3.300000e-01 1 CALCA 796 broad.mit.edu 37 11 14991575 14991575 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr11:14991575C>T ENST00000486207.1 - 2 141 c.133G>A c.(133-135)Gac>Aac p.D45N CALCA_ENST00000361010.3_Missense_Mutation_p.D45N|CALCA_ENST00000396372.2_Missense_Mutation_p.D45N|CALCB_ENST00000523376.1_Intron|CALCA_ENST00000359642.3_Missense_Mutation_p.D45N|CALCA_ENST00000331587.4_Missense_Mutation_p.D45N P06881 CALCA_HUMAN calcitonin-related polypeptide alpha 8 CGCGCTTCGTCCTCACTGAGC 0.647000 OREG0020791 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000486207.1 1 1 hg19 CCDS31432.1 . . . . . . . . . . C 14.19 2.460413 0.43736 . . ENSG00000110680 ENST00000486207;ENST00000361010;ENST00000359642;ENST00000331587;ENST00000396372 T;T;T;T;T 0.21543 2.0;2.0;2.0;2.0;2.0 4.83 3.86 0.44501 . 0.545783 0.21140 N 0.079485 T 0.14313 0.0346 L 0.31926 0.97 0.80722 D 1 B;B 0.27316 0.175;0.084 B;B 0.27170 0.052;0.077 T 0.08472 -1.0720 10 0.30078 T 0.28 -17.1724 6.4121 0.21696 0.2889:0.6144:0.0:0.0967 . 45;45 P01258;P06881 CALC_HUMAN;CALCA_HUMAN N 45 ENSP00000417833:D45N;ENSP00000354286:D45N;ENSP00000352663:D45N;ENSP00000331746:D45N;ENSP00000379657:D45N ENSP00000331746:D45N D - 1 0 CALCA 14948151 0.968000 0.33430 0.098000 0.21074 0.081000 0.17604 2.326000 0.43849 1.312000 0.45043 0.655000 0.94253 GAC TCGA-LB-A8F3-01A-11D-A36O-08 CALCA-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357068.1 1 0 1 46 114 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 1.000000 46 112 0 29 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 3 3 2.028607 1 0.330000 3.010000 0.421616 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 ALX4 60529 broad.mit.edu 37 11 44286499 44286499 + Missense_Mutation SNP C C G TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr11:44286499C>G ENST00000329255.3 - 4 1244 c.1141G>C c.(1141-1143)Gag>Cag p.E381Q NM_021926.3 NP_068745.2 Q9H161 ALX4_HUMAN ALX homeobox 4 16 CCGTTGAGCTCGTAGCCATTG 0.652000 0 SO:0001583 missense ENST00000329255.3 1 1 hg19 CCDS31468.1 . . . . . . . . . . C 23.8 4.455312 0.84209 . . ENSG00000052850 ENST00000329255 D 0.90563 -2.69 5.19 5.19 0.71726 . 0.059235 0.64402 D 0.000002 D 0.90903 0.7141 L 0.46157 1.445 0.42428 D 0.992668 D 0.53312 0.959 P 0.54759 0.76 D 0.89026 0.3438 10 0.28530 T 0.3 . 13.9861 0.64337 0.1515:0.8485:0.0:0.0 . 381 Q9H161 ALX4_HUMAN Q 381 ENSP00000332744:E381Q ENSP00000332744:E381Q E - 1 0 ALX4 44243075 1.000000 0.71417 1.000000 0.80357 0.948000 0.59901 5.538000 0.67193 2.575000 0.86900 0.561000 0.74099 GAG TCGA-LB-A8F3-01A-11D-A36O-08 ALX4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390399.1 0 0 0 15 356 0 94 0 0 0 0 94 2 0 0 0 0 0 2 1 0.999868 14 353 0 93 2 0 0 0 0 0 0 -3.094407 1 1 121380 1 32 1 1 3 4 2.093733 1 0.330000 3.010000 0.451314 0.330000 1.800000e-01 1.000000 0.300000 0.462232 0.330000 0 2.400000e-01 1 OR8K1 390157 broad.mit.edu 37 11 56113884 56113884 + Missense_Mutation SNP A A G TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr11:56113884A>G ENST00000279783.2 + 1 464 c.370A>G c.(370-372)Atg>Gtg p.M124V NM_001002907.1 NP_001002907.1 Q8NGG5 OR8K1_HUMAN olfactory receptor, family 8, subfamily K, member 1 33 Esophageal squamous(21;0.00448) TCTATCAGCAATGGCCTATGA 0.403000 HNSCC(65;0.19) 0 SO:0001583 missense ENST00000279783.2 1 1 hg19 CCDS31528.1 . . . . . . . . . . A 18.01 3.528822 0.64860 . . ENSG00000150261 ENST00000279783 T 0.00995 5.46 5.0 5.0 0.66597 GPCR, rhodopsin-like superfamily (1); 0.000000 0.64402 D 0.000007 T 0.04227 0.0117 H 0.94964 3.605 0.45216 D 0.99822 P 0.51537 0.946 P 0.44647 0.456 T 0.08700 -1.0709 10 0.87932 D 0 -28.0834 14.7062 0.69191 1.0:0.0:0.0:0.0 . 124 Q8NGG5 OR8K1_HUMAN V 124 ENSP00000279783:M124V ENSP00000279783:M124V M + 1 0 OR8K1 55870460 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 8.771000 0.91751 1.862000 0.54008 0.448000 0.29417 ATG TCGA-LB-A8F3-01A-11D-A36O-08 OR8K1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391605.1 1 0 1 245 796 0 313 0 0 0 0 313 2 0 0 0 0 0 2 1 1.000000 244 783 0 313 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 3 4 2.093733 1 0.330000 3.010000 0.451314 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 CACNA1C 775 broad.mit.edu 37 12 2566843 2566843 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr12:2566843G>A ENST00000347598.4 + 5 728 c.728G>A c.(727-729)cGc>cAc p.R243H CACNA1C_ENST00000399637.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000399644.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000399603.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000480911.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000327702.7_Missense_Mutation_p.R243H|CACNA1C_ENST00000399641.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000399655.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000399597.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000399617.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000402845.3_Missense_Mutation_p.R243H|CACNA1C_ENST00000399638.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000399591.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000399634.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000399629.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000399606.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000399621.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000335762.5_Missense_Mutation_p.R243H|CACNA1C_ENST00000399649.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000344100.3_Missense_Mutation_p.R243H|CACNA1C_ENST00000399601.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000399595.1_Missense_Mutation_p.R243H|CACNA1C_ENST00000406454.3_Missense_Mutation_p.R243H NM_001129827.1|NM_199460.2 NP_001123299.1|NP_955630.2 Q13936 CAC1C_HUMAN calcium channel, voltage-dependent, L type, alpha 1C subunit 132 OV - Ovarian serous cystadenocarcinoma(31;0.00256) Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661) CGCGTGCTGCGCCCCCTGCGG 0.562000 0 SO:0001583 missense ENST00000347598.4 1 1 hg19 CCDS44788.1 . . . . . . . . . . G 27.5 4.834960 0.91036 . . ENSG00000151067 ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.99591 -6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24;-6.24 4.15 4.15 0.48705 Ion transport (1); 0.000000 0.85682 D 0.000000 D 0.99869 0.9938 H 0.99965 5.09 0.80722 D 1 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.97110 0.995;0.996;1.0;0.997;0.998;0.993;0.998;1.0;1.0;0.998;0.994;0.998;1.0;0.998;1.0;0.989;0.998;0.998;0.993;0.993 D 0.95822 0.8850 10 0.87932 D 0 . 16.6608 0.85240 0.0:0.0:1.0:0.0 . 243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243 Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-11;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12 .;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;. H 243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;243;84 ENSP00000336982:R243H;ENSP00000382563:R243H;ENSP00000437936:R243H;ENSP00000382552:R243H;ENSP00000382547:R243H;ENSP00000382506:R243H;ENSP00000382530:R243H;ENSP00000382546:R243H;ENSP00000382500:R243H;ENSP00000382549:R243H;ENSP00000266376:R243H;ENSP00000382515:R243H;ENSP00000382510:R243H;ENSP00000341092:R243H;ENSP00000382537:R243H;ENSP00000329877:R243H;ENSP00000382557:R243H;ENSP00000385724:R243H;ENSP00000382512:R243H;ENSP00000382542:R243H;ENSP00000382526:R243H;ENSP00000385896:R243H;ENSP00000382504:R243H ENSP00000323129:R84H R + 2 0 CACNA1C 2437104 1.000000 0.71417 0.997000 0.53966 0.807000 0.45602 9.542000 0.98086 2.139000 0.66308 0.563000 0.77884 CGC TCGA-LB-A8F3-01A-11D-A36O-08 CACNA1C-017 KNOWN non_canonical_conserved|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000317035.1 0 0 0 66 1002 1 366 0 0 0 1 366 2 0 0 0 0 0 2 1 1.000000 65 981 1 361 12 0 0 0 0 0 0 -9.918375 1 1 0 0 1 2 2 4 2.238903 1 0.330000 3.010000 0.488628 0.490000 3.700000e-01 1.000000 0.500000 0.520366 0.490000 0 4.300000e-01 5.700000e-01 TSPAN11 441631 broad.mit.edu 37 12 31116773 31116773 + Missense_Mutation SNP G G T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr12:31116773G>T ENST00000261177.9 + 3 156 c.97G>T c.(97-99)Gcc>Tcc p.A33S TSPAN11_ENST00000544427.1_Missense_Mutation_p.A23S|TSPAN11_ENST00000535215.1_5'UTR|TSPAN11_ENST00000546076.1_Missense_Mutation_p.A33S NM_001080509.2 NP_001073978.1 A1L157 TSN11_HUMAN tetraspanin 11 11 all_lung(12;3.11e-10)|Lung NSC(12;5.24e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233) CGGGGGAGCAGCCGTCCTGGC 0.662000 0 SO:0001583 missense ENST00000261177.9 1 1 hg19 CCDS31765.1 . . . . . . . . . . G 12.64 1.999666 0.35320 . . ENSG00000110900 ENST00000546076;ENST00000544427;ENST00000261177 T;T;T 0.80738 -1.41;-1.41;-1.41 3.5 2.6 0.31112 . 0.149427 0.43919 U 0.000512 T 0.79112 0.4391 M 0.76328 2.33 0.20489 N 0.999896 P;B 0.35155 0.487;0.083 B;B 0.39465 0.3;0.177 T 0.68977 -0.5267 10 0.41790 T 0.15 . 8.7712 0.34733 0.1194:0.0:0.8806:0.0 . 23;33 F5H0F0;A1L157 .;TSN11_HUMAN S 33;23;33 ENSP00000437403:A33S;ENSP00000439895:A23S;ENSP00000261177:A33S ENSP00000261177:A33S A + 1 0 TSPAN11 31008040 0.999000 0.42202 0.004000 0.12327 0.645000 0.38454 6.020000 0.70826 0.571000 0.29365 0.457000 0.33378 GCC TCGA-LB-A8F3-01A-11D-A36O-08 TSPAN11-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399888.1 0 0 0 9 332 0 97 0 0 0 1 0 97 2 0 0 0 0 0 2 1 0.993981 9 327 0 94 2 0 0 0 0 0 0 -9.287503 1 1 0 0 1 2 2 4 2.302934 1 0.330000 3.010000 0.496241 0.220000 1.000000e-01 0.380000 0.200000 0.234310 0.220000 0 1.500000e-01 3.000000e-01 KCNA6 3742 broad.mit.edu 37 12 4920759 4920759 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr12:4920759C>T ENST00000280684.3 + 1 2418 c.1552C>T c.(1552-1554)Cgg>Tgg p.R518W RP11-234B24.4_ENST00000542988.1_lincRNA|KCNA6_ENST00000433855.1_Missense_Mutation_p.R518W P17658 KCNA6_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 6 49 Dalfampridine(DB06637) TACACCACATCGGGCCTATGC 0.597000 HNSCC(72;0.22) 0 SO:0001583 missense ENST00000280684.3 1 1 hg19 CCDS8534.1 . . . . . . . . . . C 12.43 1.935726 0.34189 . . ENSG00000151079 ENST00000433855;ENST00000280684 D;D 0.97553 -4.43;-4.43 4.97 4.01 0.46588 . 0.394655 0.23474 N 0.047785 D 0.95027 0.8390 N 0.19112 0.55 0.31860 N 0.62104 D 0.76494 0.999 P 0.53809 0.735 D 0.93607 0.6935 10 0.31617 T 0.26 . 14.9663 0.71196 0.1522:0.8478:0.0:0.0 . 518 P17658 KCNA6_HUMAN W 518 ENSP00000408321:R518W;ENSP00000280684:R518W ENSP00000280684:R518W R + 1 2 KCNA6 4791020 1.000000 0.71417 1.000000 0.80357 0.119000 0.20118 5.194000 0.65125 2.578000 0.87016 0.655000 0.94253 CGG TCGA-LB-A8F3-01A-11D-A36O-08 KCNA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398909.1 0 0 0 12 337 0 106 0 0 0 0 106 2 0 0 0 0 0 2 1 0.999124 12 336 0 106 2 0 0 0 0 0 0 -3.291887 1 1 0 0 1 2 2 4 2.238903 1 0.330000 3.010000 0.488628 0.280000 1.400000e-01 1.000000 0.270000 0.326409 0.280000 0 2.100000e-01 3.900000e-01 KRT74 121391 broad.mit.edu 37 12 52964517 52964517 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr12:52964517C>T ENST00000305620.2 - 5 991 c.944G>A c.(943-945)cGc>cAc p.R315H KRT74_ENST00000549343.1_Missense_Mutation_p.R315H NM_175053.3 NP_778223.2 Q7RTS7 K2C74_HUMAN keratin 74 28 ATAATGCATGCGGACCTCAGC 0.592000 0 SO:0001583 missense ENST00000305620.2 0 1 hg19 CCDS8832.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 C 9.276 1.046988 0.19748 . . ENSG00000170484 ENST00000549343;ENST00000305620 D;D 0.93307 -3.2;-3.2 4.49 3.56 0.40772 Filament (1); 0.000000 0.34291 N 0.004087 D 0.93973 0.8070 H 0.95187 3.635 0.09310 N 1 P 0.36633 0.562 B 0.36186 0.219 D 0.90228 0.4277 10 0.87932 D 0 . 6.036 0.19708 0.0:0.6265:0.0:0.3735 . 315 Q7RTS7 K2C74_HUMAN H 315 ENSP00000447447:R315H;ENSP00000307240:R315H ENSP00000307240:R315H R - 2 0 KRT74 51250784 0.000000 0.05858 0.644000 0.29465 0.067000 0.16453 -0.672000 0.05244 1.137000 0.42214 0.655000 0.94253 CGC TCGA-LB-A8F3-01A-11D-A36O-08 KRT74-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405324.1 0 0 0 5 217 0 84 0 0 0 0 84 2 0 0 0 0 0 2 1 0.936758 5 215 0 83 2 0 0 0 0 0 0 -2.557965 1 1 121412 1 34 1 1 2 3 2.012148 1 0.330000 3.010000 0.420791 0.170000 6.000000e-02 1.000000 0.150000 0.217510 0.170000 0 1.000000e-01 2.700000e-01 MTMR6 9107 broad.mit.edu 37 13 25826043 25826043 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr13:25826043C>T ENST00000381801.5 - 12 2187 c.1426G>A c.(1426-1428)Gaa>Aaa p.E476K MTMR6_ENST00000540661.1_Missense_Mutation_p.E476K NM_004685.3 NP_004676.3 Q9Y217 MTMR6_HUMAN myotubularin related protein 6 36 Lung SC(185;0.0225)|Breast(139;0.0351) CTGTGAGATTCGGAACTGTAG 0.328000 0 SO:0001583 missense ENST00000381801.5 0 1 hg19 CCDS9313.1 . . . . . . . . . . C 3.298 -0.143515 0.06627 0.0 1.16E-4 ENSG00000139505 ENST00000540661;ENST00000541021;ENST00000381801;ENST00000319298 D;D 0.90133 -2.62;-2.62 5.63 -5.02 0.02982 Myotubularin phosphatase domain (1); 0.741247 0.14353 N 0.324976 T 0.78130 0.4235 L 0.31926 0.97 0.09310 N 1 B;B 0.06786 0.0;0.001 B;B 0.04013 0.001;0.0 T 0.65717 -0.6100 10 0.07030 T 0.85 . 7.079 0.25221 0.0:0.2984:0.3046:0.397 . 476;476 Q9Y217;Q9Y217-2 MTMR6_HUMAN;. K 476;476;476;44 ENSP00000443161:E476K;ENSP00000371221:E476K ENSP00000317987:E44K E - 1 0 MTMR6 24724043 0.000000 0.05858 0.002000 0.10522 0.740000 0.42216 -0.079000 0.11357 -0.861000 0.04094 -0.385000 0.06624 GAA TCGA-LB-A8F3-01A-11D-A36O-08 MTMR6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044225.1 0 0 0 16 1042 1 293 0 1.586151e-02 0 12 1 293 2 0 0 0 0 0 2 1 0.690666 14 1026 1 288 14 0 0 0 0 0 0 -2.034964 0 1 121402 7 42 1 1 2 3 1.973208 1 0.330000 3.010000 0.418302 0.100000 5.000000e-02 1.000000 0.110000 0.168968 0.100000 0 7.000000e-02 1.500000e-01 KBTBD6 89890 broad.mit.edu 37 13 41705888 41705888 + Missense_Mutation SNP G G A rs61999308 TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr13:41705888G>A ENST00000379485.1 - 1 994 c.760C>T c.(760-762)Cgg>Tgg p.R254W KBTBD6_ENST00000499385.2_Missense_Mutation_p.R188W NM_152903.4 NP_690867.3 Q86V97 KBTB6_HUMAN kelch repeat and BTB (POZ) domain containing 6 43 Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114) CTGGGACCCCGCTCTTTGGGA 0.582000 0 SO:0001583 missense ENST00000379485.1 1 1 hg19 CCDS9376.1 . . . . . . . . . . g 15.36 2.811259 0.50527 . . ENSG00000165572 ENST00000379485;ENST00000499385 T;T 0.74209 -0.82;-0.82 3.69 3.69 0.42338 BTB/Kelch-associated (2); 0.227860 0.29980 N 0.010714 D 0.84479 0.5481 M 0.84326 2.69 0.38841 D 0.956059 D;D 0.89917 1.0;1.0 D;D 0.78314 0.989;0.991 D 0.86451 0.1773 10 0.87932 D 0 . 8.6734 0.34165 0.0:0.0:0.7723:0.2277 . 188;254 F5GZN7;Q86V97 .;KBTB6_HUMAN W 254;188 ENSP00000368799:R254W;ENSP00000444326:R188W ENSP00000368799:R254W R - 1 2 KBTBD6 40603888 0.465000 0.25815 0.999000 0.59377 0.991000 0.79684 0.528000 0.23002 2.065000 0.61736 0.462000 0.41574 CGG TCGA-LB-A8F3-01A-11D-A36O-08 KBTBD6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044657.1 1 0 1 102 278 0 114 0 0 0 0 114 2 0 0 0 0 0 2 1 1.000000 100 278 1 125 12 0 0 0 0 0 0 -2.341083 0 1 0 0 1 1 2 3 1.973208 1 0.330000 3.010000 0.418302 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 DOCK9 23348 broad.mit.edu 37 13 99566593 99566593 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr13:99566593C>T ENST00000376460.1 - 9 1029 c.949G>A c.(949-951)Gaa>Aaa p.E317K DOCK9_ENST00000448493.2_Missense_Mutation_p.E329K|DOCK9_ENST00000339416.2_Missense_Mutation_p.E318K|DOCK9_ENST00000442173.1_Missense_Mutation_p.E317K NM_001130048.1|NM_015296.2 NP_001123520.1|NP_056111.1 Q9BZ29 DOCK9_HUMAN dedicator of cytokinesis 9 59 all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) TTGGCAAGTTCCGGCAGGTAG 0.393000 0 SO:0001583 missense ENST00000376460.1 0 1 hg19 CCDS45062.1 . . . . . . . . . . C 22.1 4.243118 0.79912 . . ENSG00000088387 ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173 T;T;T;T 0.20598 2.41;2.49;2.06;2.06 6.16 6.16 0.99307 . 0.695998 0.14892 N 0.292369 T 0.29620 0.0739 M 0.68317 2.08 0.54753 D 0.999985 B;B;B;B;B 0.22983 0.038;0.032;0.078;0.004;0.008 B;B;B;B;B 0.23018 0.043;0.013;0.013;0.018;0.01 T 0.04840 -1.0923 9 . . . . 19.848 0.96722 0.0:1.0:0.0:0.0 . 318;317;317;317;318 A6H8Z6;E9PFM9;B3KX25;Q9BZ29-5;Q9BZ29 .;.;.;.;DOCK9_HUMAN K 317;318;318;318;317;318;329;317 ENSP00000365643:E317K;ENSP00000341086:E318K;ENSP00000401958:E329K;ENSP00000406883:E317K . E - 1 0 DOCK9 98364594 1.000000 0.71417 1.000000 0.80357 0.937000 0.57800 5.097000 0.64542 2.937000 0.99478 0.650000 0.86243 GAA TCGA-LB-A8F3-01A-11D-A36O-08 DOCK9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045566.1 0 0 0 6 56 0 20 0 0 0 1 0 20 2 0 0 0 0 0 2 1 0.967542 6 56 0 20 2 0 0 0 0 0 0 -11.503030 1 1 0 0 1 2 2 4 2.236121 1 0.330000 3.010000 0.487336 0.830000 3.500000e-01 1.000000 1.000000 0.798564 0.830000 0 5.500000e-01 1 ACIN1 22985 broad.mit.edu 37 14 23528647 23528647 + Missense_Mutation SNP T T G TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 T G T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr14:23528647T>G ENST00000262710.1 - 19 4063 c.3736A>C c.(3736-3738)Aag>Cag p.K1246Q ACIN1_ENST00000357481.2_Missense_Mutation_p.K488Q|ACIN1_ENST00000457657.1_Missense_Mutation_p.K1206Q|ACIN1_ENST00000397341.3_Missense_Mutation_p.K488Q|ACIN1_ENST00000557515.1_Missense_Mutation_p.K487Q|ACIN1_ENST00000338631.6_Missense_Mutation_p.K519Q|ACIN1_ENST00000555053.1_Missense_Mutation_p.K1233Q|CDH24_ENST00000487137.2_5'Flank|CDH24_ENST00000397359.3_5'Flank|ACIN1_ENST00000605057.1_Missense_Mutation_p.K1188Q NM_001164814.1|NM_014977.3 NP_001158286.1|NP_055792 Q9UKV3 ACINU_HUMAN apoptotic chromatin condensation inducer 1 37 all_cancers(95;1.36e-05) tcccgctccttGGCCCGTTCG 0.582000 0 SO:0001583 missense ENST00000262710.1 1 1 hg19 CCDS9587.1 . . . . . . . . . . T 14.24 2.476246 0.44044 . . ENSG00000100813 ENST00000557515;ENST00000338631;ENST00000357481;ENST00000262710;ENST00000457657;ENST00000397341;ENST00000555053 T;T;T;T;T;T;T 0.40756 1.02;1.02;1.02;1.02;1.02;1.02;1.02 4.18 4.18 0.49190 . 0.336627 0.21615 N 0.071728 T 0.33933 0.0880 L 0.29908 0.895 0.42293 D 0.992148 P;P;P;P;P 0.51351 0.944;0.906;0.906;0.476;0.476 P;B;B;B;B 0.47470 0.548;0.346;0.346;0.071;0.071 T 0.03795 -1.1003 10 0.23302 T 0.38 -11.8368 9.4065 0.38464 0.0:0.0:0.1791:0.8209 . 1233;1246;1206;519;488 G3V3M7;Q9UKV3;E7EQT4;Q9UKV3-2;Q9UKV3-3 .;ACINU_HUMAN;.;.;. Q 487;519;488;1246;1206;488;1233 ENSP00000451138:K487Q;ENSP00000345541:K519Q;ENSP00000350073:K488Q;ENSP00000262710:K1246Q;ENSP00000405677:K1206Q;ENSP00000380502:K488Q;ENSP00000451328:K1233Q ENSP00000262710:K1246Q K - 1 0 ACIN1 22598487 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 4.190000 0.58365 1.881000 0.54492 0.379000 0.24179 AAG TCGA-LB-A8F3-01A-11D-A36O-08 ACIN1-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000071707.3 1 0 1 55 180 0 69 1 1 224 134 0 69 2 0 0 0 0 0 2 1 1.000000 55 174 0 67 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 2 2 1.729271 1 0.330000 3.010000 0.330000 0.990000 9.900000e-01 1.000000 1.000000 0.999879 0.990000 1 9.900000e-01 1 AMFR 267 broad.mit.edu 37 16 56401435 56401435 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr16:56401435G>A ENST00000290649.5 - 12 1730 c.1520C>T c.(1519-1521)tCa>tTa p.S507L NM_001144.5 NP_001135.3 Q9UKV5 AMFR_HUMAN autocrine motility factor receptor, E3 ubiquitin protein ligase 17 GATGCTATCTGACCGCTGGAA 0.498000 Pancreas(2;144 323 39528) 0 SO:0001583 missense ENST00000290649.5 1 1 hg19 CCDS10758.1 . . . . . . . . . . G 13.45 2.241135 0.39598 . . ENSG00000159461 ENST00000290649 T 0.14266 2.52 5.8 5.8 0.92144 . 0.647010 0.15443 N 0.262073 T 0.15825 0.0381 L 0.44542 1.39 0.39616 D 0.96996 B;B 0.06786 0.001;0.0 B;B 0.04013 0.001;0.001 T 0.07424 -1.0773 10 0.27785 T 0.31 -7.4232 18.2436 0.89977 0.0:0.0:1.0:0.0 . 507;156 Q9UKV5;Q1RN03 AMFR2_HUMAN;. L 507 ENSP00000290649:S507L ENSP00000290649:S507L S - 2 0 AMFR 54958936 1.000000 0.71417 1.000000 0.80357 0.431000 0.31685 4.726000 0.61986 2.735000 0.93741 0.655000 0.94253 TCA TCGA-LB-A8F3-01A-11D-A36O-08 AMFR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256978.2 0 0 0 25 1016 0 325 1 6.526957e-01 2 89 0 325 2 0 0 0 0 0 2 1 1.000000 26 987 0 321 2 0 0 0 0 0 0 -2.558441 1 1 0 0 1 1 2 3 1.989453 0 0.330000 3.010000 0.382943 0.170000 1.000000e-01 1.000000 0.150000 0.366231 0.170000 0 1.300000e-01 1 NLRC5 84166 broad.mit.edu 37 16 57075463 57075463 + Missense_Mutation SNP C C G TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr16:57075463C>G ENST00000262510.6 + 18 3231 c.3006C>G c.(3004-3006)tgC>tgG p.C1002W NLRC5_ENST00000539144.1_Missense_Mutation_p.C1002W|NLRC5_ENST00000308149.7_Missense_Mutation_p.C1002W|NLRC5_ENST00000436936.1_Missense_Mutation_p.C1002W NM_032206.4 NP_115582.4 Q86WI3 NLRC5_HUMAN NLR family, CARD domain containing 5 75 all_neural(199;0.225) GAGGAAGCTGCCACCTCGGTC 0.552000 0 SO:0001583 missense ENST00000262510.6 1 1 hg19 CCDS10773.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 11.80|11.80 1.746925|1.746925 0.30955|0.30955 .|. .|. ENSG00000140853|ENSG00000140853 ENST00000262510;ENST00000308149;ENST00000436936;ENST00000327982;ENST00000539144;ENST00000538110;ENST00000543030|ENST00000538805 T;T;T;T;T;T|. 0.54479|. 0.57;0.57;0.57;0.57;0.57;0.57|. 3.98|3.98 -2.66|-2.66 0.06077|0.06077 .|. 1.053610|. 0.07584|. N|. 0.920873|. T|T 0.38081|0.38081 0.1027|0.1027 L|L 0.56769|0.56769 1.78|1.78 0.09310|0.09310 N|N 1|1 D;D;D;D|. 0.57571|. 0.966;0.972;0.98;0.978|. P;P;P;P|. 0.56474|. 0.62;0.697;0.706;0.799|. T|T 0.40403|0.40403 -0.9565|-0.9565 10|5 0.49607|. T|. 0.09|. .|. 4.9157|4.9157 0.13844|0.13844 0.0:0.3487:0.1617:0.4897|0.0:0.3487:0.1617:0.4897 .|. 1002;1002;1002;1002|. Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3|. .;.;.;NLRC5_HUMAN|. W|A 1002;1002;1002;476;1002;509;301|755 ENSP00000262510:C1002W;ENSP00000308886:C1002W;ENSP00000389739:C1002W;ENSP00000441727:C1002W;ENSP00000441597:C509W;ENSP00000440153:C301W|. ENSP00000262510:C1002W|. C|P +|+ 3|1 2|0 NLRC5|NLRC5 55632964|55632964 0.000000|0.000000 0.05858|0.05858 0.000000|0.000000 0.03702|0.03702 0.263000|0.263000 0.26337|0.26337 -0.740000|-0.740000 0.04861|0.04861 -0.493000|-0.493000 0.06678|0.06678 -0.136000|-0.136000 0.14681|0.14681 TGC|CCA TCGA-LB-A8F3-01A-11D-A36O-08 NLRC5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257346.1 1 0 1 28 178 0 52 1 7.252738e-01 9 9 0 52 2 0 0 0 0 0 2 1 1.000000 25 176 0 52 2 0 0 0 0 0 0 -3.323170 1 1 0 0 1 1 2 3 1.989453 0 0.330000 3.010000 0.382943 0.960000 6.300000e-01 1.000000 1.000000 0.910081 0.960000 1 7.700000e-01 1 TMEM104 54868 broad.mit.edu 37 17 72832228 72832228 + Missense_Mutation SNP C C G TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr17:72832228C>G ENST00000335464.5 + 10 1055 c.893C>G c.(892-894)tCc>tGc p.S298C TMEM104_ENST00000582330.1_Missense_Mutation_p.S298C|TMEM104_ENST00000582773.1_Intron|TMEM104_ENST00000417024.2_Intron NM_017728.3 NP_060198.3 Q8NE00 TM104_HUMAN transmembrane protein 104 19 all_lung(278;0.23) ACCCCCGTCTCCTCCAAGCGC 0.622000 0 SO:0001583 missense ENST00000335464.5 1 1 hg19 CCDS32723.1 . . . . . . . . . . C 19.67 3.870313 0.72065 . . ENSG00000109066 ENST00000335464 T 0.02369 4.32 5.21 4.23 0.50019 . 0.000000 0.85682 D 0.000000 T 0.13286 0.0322 M 0.72894 2.215 0.80722 D 1 D 0.89917 1.0 D 0.74023 0.982 T 0.00482 -1.1713 10 0.72032 D 0.01 -45.754 13.9219 0.63937 0.0:0.9256:0.0:0.0744 . 298 Q8NE00 TM104_HUMAN C 298 ENSP00000334849:S298C ENSP00000334849:S298C S + 2 0 TMEM104 70343823 1.000000 0.71417 0.949000 0.38748 0.895000 0.52256 7.384000 0.79751 1.319000 0.45190 0.561000 0.74099 TCC TCGA-LB-A8F3-01A-11D-A36O-08 TMEM104-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000444442.1 1 0 0 32 287 0 126 0 2.751977e-01 1 9 0 126 2 0 0 0 0 0 2 1 1.000000 31 280 0 125 2 0 0 0 0 0 0 -3.318794 1 1 0 0 1 1 3 4 2.174750 1 0.330000 3.010000 0.474056 0.800000 5.500000e-01 1.000000 1.000000 0.815025 0.800000 0 6.600000e-01 1 TLE2 7089 broad.mit.edu 37 19 3002419 3002419 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr19:3002419C>T ENST00000262953.6 - 18 2241 c.1979G>A c.(1978-1980)cGc>cAc p.R660H TLE2_ENST00000426948.2_Missense_Mutation_p.R674H|TLE2_ENST00000447365.2_Missense_Mutation_p.R327H|TLE2_ENST00000455444.2_Missense_Mutation_p.R538H|TLE2_ENST00000443826.3_Missense_Mutation_p.R538H|TLE2_ENST00000590536.1_Missense_Mutation_p.R661H|TLE2_ENST00000591529.1_Missense_Mutation_p.R674H|TLE2_ENST00000586422.1_Intron NM_003260.4 NP_003251.2 Q04725 TLE2_HUMAN transducin-like enhancer of split 2 13 CTCCGGCTTGCGGACGTGCAG 0.617000 0 SO:0001583 missense ENST00000262953.6 0 1 hg19 CCDS45911.1 . . . . . . . . . . C 13.03 2.115899 0.37339 . . ENSG00000065717 ENST00000262953;ENST00000455444;ENST00000360654;ENST00000450017;ENST00000447365;ENST00000443826;ENST00000426948 T;T;T;T;T 0.13420 2.59;2.59;2.59;2.59;2.59 3.79 3.79 0.43588 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.130101 0.52532 D 0.000070 T 0.07999 0.0200 N 0.04880 -0.145 0.35702 D 0.815685 D;P;B;D;D 0.56287 0.975;0.859;0.102;0.975;0.975 B;B;B;P;P 0.45232 0.375;0.172;0.13;0.474;0.474 T 0.20806 -1.0264 10 0.87932 D 0 -10.9012 9.5891 0.39534 0.0:0.7853:0.2147:0.0 . 538;327;674;538;660 E9PEV7;B4DE62;F8WCH2;B4DE03;Q04725 .;.;.;.;TLE2_HUMAN H 660;538;209;654;327;538;674 ENSP00000262953:R660H;ENSP00000413107:R538H;ENSP00000406523:R327H;ENSP00000392427:R538H;ENSP00000392869:R674H ENSP00000262953:R660H R - 2 0 TLE2 2953419 0.999000 0.42202 0.973000 0.42090 0.829000 0.46940 3.176000 0.50863 2.128000 0.65567 0.455000 0.32223 CGC TCGA-LB-A8F3-01A-11D-A36O-08 TLE2-004 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000452194.2 0 0 0 5 103 0 40 0 9.942826e-01 1 223 0 40 2 0 0 0 0 0 2 1 0.937529 4 103 0 40 2 0 0 0 0 0 0 -7.998348 1 0 121276 7 24 1 1 2 3 1.978307 0 0.330000 3.010000 0.409848 0.370000 1.300000e-01 1.000000 0.310000 0.457875 0.370000 0 2.300000e-01 7.100000e-01 ANKRD27 84079 broad.mit.edu 37 19 33134064 33134064 + Silent SNP A A T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr19:33134064A>T ENST00000306065.4 - 9 905 c.747T>A c.(745-747)ctT>ctA p.L249L ANKRD27_ENST00000587352.1_Silent_p.L249L NM_032139.2 NP_115515.2 Q96NW4 ANR27_HUMAN ankyrin repeat domain 27 (VPS9 domain) 42 Esophageal squamous(110;0.137) CTTTCTGCTGAAGATCTTGAA 0.473000 0 SO:0001819 synonymous_variant ENST00000306065.4 1 1 hg19 CCDS32986.1 TCGA-LB-A8F3-01A-11D-A36O-08 ANKRD27-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000450329.1 0 0 0 14 411 0 133 0 1.212377e-02 0 5 0 133 2 0 0 0 0 0 2 1 0.999739 14 405 0 132 2 0 0 0 0 0 0 -13.726990 1 1 0 0 1 1 2 3 1.930400 0 0.330000 3.010000 0.407263 0.240000 1.300000e-01 1.000000 0.220000 0.359604 0.240000 0 1.800000e-01 4.400000e-01 ANKRD24 170961 broad.mit.edu 37 19 4216640 4216640 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr19:4216640G>A ENST00000600132.1 + 18 1759 c.1483G>A c.(1483-1485)Gag>Aag p.E495K ANKRD24_ENST00000318934.4_Missense_Mutation_p.E495K|ANKRD24_ENST00000262970.5_Missense_Mutation_p.E585K NM_133475.1 NP_597732.1 Q8TF21 ANR24_HUMAN ankyrin repeat domain 24 21 TCTCCGGGCCGAGTTTGACCA 0.607000 0 SO:0001583 missense ENST00000600132.1 1 1 hg19 CCDS45925.1 . . . . . . . . . . g 23.0 4.362717 0.82353 0.0 1.2E-4 ENSG00000089847 ENST00000318934;ENST00000262970 T;T 0.71817 0.38;-0.6 4.6 4.6 0.57074 . 0.000000 0.34460 N 0.003942 T 0.75213 0.3819 L 0.29908 0.895 0.45415 D 0.998398 D;D 0.89917 1.0;1.0 D;D 0.83275 0.995;0.996 T 0.74968 -0.3483 10 0.39692 T 0.17 -25.7121 14.5191 0.67840 0.0:0.0:1.0:0.0 . 495;585 Q8TF21;Q8TF21-2 ANR24_HUMAN;. K 495;585 ENSP00000321731:E495K;ENSP00000262970:E585K ENSP00000262970:E585K E + 1 0 ANKRD24 4167640 1.000000 0.71417 0.899000 0.35326 0.825000 0.46686 5.855000 0.69510 2.288000 0.76882 0.313000 0.20887 GAG TCGA-LB-A8F3-01A-11D-A36O-08 ANKRD24-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000458188.1 1 0 1 7 43 0 21 0 0 0 1 0 21 2 0 0 0 0 0 2 1 0.980586 7 41 0 21 2 0 0 0 0 0 0 -14.172920 1 1 120914 9 38 1 1 2 3 1.978307 0 0.330000 3.010000 0.409848 0.990000 4.700000e-01 1.000000 1.000000 0.899468 0.990000 1 7.200000e-01 1 TEAD2 8463 broad.mit.edu 37 19 49845730 49845730 + Missense_Mutation SNP T T A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr19:49845730T>A ENST00000311227.2 - 11 1285 c.1195A>T c.(1195-1197)Atg>Ttg p.M399L TEAD2_ENST00000377214.4_Missense_Mutation_p.M402L|TEAD2_ENST00000598810.1_Missense_Mutation_p.M403L|TEAD2_ENST00000593945.1_Missense_Mutation_p.M403L|TEAD2_ENST00000539846.1_Missense_Mutation_p.M271L|TEAD2_ENST00000601519.1_Missense_Mutation_p.M402L|CTC-301O7.4_ENST00000358234.4_lincRNA NM_001256659.1|NM_003598.1 NP_001243588.1|NP_003589.1 Q15562 TEAD2_HUMAN TEA domain family member 2 29 all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15) ACGCTGTTCATCATGTATCGC 0.587000 0 SO:0001583 missense ENST00000311227.2 1 1 hg19 CCDS12761.1 . . . . . . . . . . T 22.8 4.341581 0.81911 . . ENSG00000074219 ENST00000311227;ENST00000377214;ENST00000539846 T;T;T 0.33438 1.41;1.41;1.41 3.9 3.9 0.45041 . 0.000000 0.64402 D 0.000001 T 0.30510 0.0767 L 0.49571 1.57 0.80722 D 1 B;B;B 0.16396 0.003;0.017;0.0 B;B;B 0.27608 0.01;0.081;0.002 T 0.21143 -1.0254 10 0.87932 D 0 -25.0067 11.3375 0.49513 0.0:0.0:0.0:1.0 . 271;399;402 B4DTJ6;Q15562;Q8NA25 .;TEAD2_HUMAN;. L 399;402;271 ENSP00000310701:M399L;ENSP00000366419:M402L;ENSP00000437928:M271L ENSP00000310701:M399L M - 1 0 TEAD2 54537542 1.000000 0.71417 1.000000 0.80357 0.971000 0.66376 7.971000 0.88012 1.730000 0.51580 0.496000 0.49642 ATG TCGA-LB-A8F3-01A-11D-A36O-08 TEAD2-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000465465.1 1 0 1 27 286 0 100 1 9.999419e-01 36 128 0 100 2 0 0 0 0 0 2 1 1.000000 26 280 0 100 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.929141 0 0.330000 3.010000 0.412410 0.610000 4.100000e-01 1.000000 0.600000 0.657595 0.610000 0 5.000000e-01 8.100000e-01 ACTL9 284382 broad.mit.edu 37 19 8807880 8807880 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr19:8807880C>T ENST00000324436.3 - 1 1292 c.1172G>A c.(1171-1173)cGc>cAc p.R391H NM_178525.3 NP_848620.3 Q8TC94 ACTL9_HUMAN actin-like 9 36 CTGGAAGGCGCGCAGGGAGGC 0.652000 0 SO:0001583 missense ENST00000324436.3 1 1 hg19 CCDS12207.1 . . . . . . . . . . c 12.78 2.040034 0.35989 . . ENSG00000181786 ENST00000324436 T 0.07800 3.16 4.51 2.32 0.28847 . 0.317190 0.22565 U 0.058402 T 0.05456 0.0144 N 0.20845 0.615 0.25834 N 0.984134 B 0.25521 0.128 B 0.23419 0.046 T 0.30650 -0.9971 10 0.87932 D 0 . 7.217 0.25965 0.0:0.5778:0.3287:0.0934 . 391 Q8TC94 ACTL9_HUMAN H 391 ENSP00000316674:R391H ENSP00000316674:R391H R - 2 0 ACTL9 8668880 0.005000 0.15991 0.279000 0.24732 0.748000 0.42578 0.594000 0.24014 0.592000 0.29728 0.457000 0.33378 CGC TCGA-LB-A8F3-01A-11D-A36O-08 ACTL9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459953.1 1 0 1 36 221 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 1.000000 36 219 0 69 2 0 0 0 0 0 0 -3.322053 1 1 121402 1 32 1 1 2 3 1.944477 0 0.330000 3.010000 0.414105 0.990000 7.100000e-01 1.000000 1.000000 0.939070 0.990000 1 8.400000e-01 1 CD1B 910 broad.mit.edu 37 1 158299919 158299919 + Splice_Site SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr1:158299919G>A ENST00000368168.3 - 3 437 c.330C>T c.(328-330)taC>taT p.Y110Y NM_001764.2 NP_001755.1 P29016 CD1B_HUMAN CD1b molecule 30 all_hematologic(112;0.0378) TCTCAAAGGGGTCTATGTAGA 0.428000 0 SO:0001630 splice_region_variant ENST00000368168.3 0 1 hg19 CCDS1176.1 . . . . . . . . . . G 1.531 -0.544230 0.04024 . . ENSG00000158485 ENST00000451207 . . . 4.45 -3.42 0.04825 . . . . . T 0.25717 0.0626 . . . 0.38491 D 0.947979 . . . . . . T 0.31081 -0.9956 4 . . . . 5.1937 0.15225 0.5354:0.0:0.3163:0.1484 . . . . S 78 . . P - 1 0 CD1B 156566543 0.141000 0.22595 0.289000 0.24876 0.417000 0.31264 -1.396000 0.02513 -0.854000 0.04131 0.655000 0.94253 CCC TCGA-LB-A8F3-01A-11D-A36O-08 CD1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046350.2 0 0 0 34 1296 0 215 0 0 0 0 215 2 0 0 0 0 0 2 1 1.000000 31 1274 0 213 2 0 0 0 0 0 0 -3.315004 1 1 121408 5 40 1 2 9 11 3.398783 1 0.330000 3.010000 0.661633 0.320000 1.900000e-01 1.000000 0.320000 0.463680 0.320000 0 2.500000e-01 1 MAEL 84944 broad.mit.edu 37 1 166987189 166987189 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr1:166987189G>A ENST00000367872.4 + 10 1278 c.1034G>A c.(1033-1035)cGt>cAt p.R345H MAEL_ENST00000491055.1_3'UTR|MAEL_ENST00000367870.2_Missense_Mutation_p.R314H NM_032858.1 NP_116247.1 Q96JY0 MAEL_HUMAN maelstrom spermatogenic transposon silencer 28 GATGCAGGGCGTTACCAGGTA 0.443000 0 SO:0001583 missense ENST00000367872.4 0 1 hg19 CCDS1257.1 . . . . . . . . . . G 17.31 3.356516 0.61293 . . ENSG00000143194 ENST00000367872;ENST00000367870;ENST00000447624;ENST00000537744 T;T;T 0.60040 0.22;0.27;0.6 5.69 4.76 0.60689 . 0.000000 0.64402 D 0.000015 T 0.32071 0.0817 L 0.29908 0.895 0.44816 D 0.997822 D;P 0.57257 0.979;0.954 B;B 0.42995 0.328;0.404 T 0.20571 -1.0271 10 0.46703 T 0.11 . 11.9142 0.52755 0.0:0.0:0.8258:0.1742 . 314;345 E9JVC3;Q96JY0 .;MAEL_HUMAN H 345;314;314;67 ENSP00000356846:R345H;ENSP00000356844:R314H;ENSP00000402143:R314H ENSP00000356844:R314H R + 2 0 MAEL 165253813 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 5.141000 0.64814 1.381000 0.46364 0.555000 0.69702 CGT TCGA-LB-A8F3-01A-11D-A36O-08 MAEL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000083239.1 0 0 0 14 716 0 99 0 0 0 1 0 99 2 0 0 0 0 0 2 1 0.999721 14 703 0 97 2 0 0 0 0 0 0 -2.786466 1 1 121392 2 35 1 2 8 10 3.503479 1 0.330000 3.010000 0.674125 0.260000 1.100000e-01 1.000000 0.250000 0.367869 0.260000 0 1.800000e-01 4.500000e-01 PIK3C2B 5287 broad.mit.edu 37 1 204412697 204412697 + Nonsense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr1:204412697G>A ENST00000367187.3 - 20 3452 c.2896C>T c.(2896-2898)Cag>Tag p.Q966* PIK3C2B_ENST00000424712.2_Nonsense_Mutation_p.Q938* NM_002646.3 NP_002637.3 O00750 P3C2B_HUMAN phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta 52 all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227) GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193) ATGCTGAACTGAGAGTCCTTG 0.567000 0 SO:0001587 stop_gained ENST00000367187.3 0 1 hg19 CCDS1446.1 . . . . . . . . . . G 46 12.910723 0.99705 . . ENSG00000133056 ENST00000367187;ENST00000424712 . . . 5.98 5.98 0.97165 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.09843 T 0.71 . 13.2926 0.60278 0.0728:0.0:0.9272:0.0 . . . . X 966;938 . ENSP00000356155:Q966X Q - 1 0 PIK3C2B 202679320 1.000000 0.71417 0.976000 0.42696 0.995000 0.86356 4.809000 0.62591 2.847000 0.97988 0.591000 0.81541 CAG TCGA-LB-A8F3-01A-11D-A36O-08 PIK3C2B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087965.1 0 0 0 59 1534 0 244 0 1.327794e-02 0 5 0 244 2 0 0 0 0 0 2 1 1.000000 60 1514 0 242 2 0 0 0 0 0 0 -3.261609 1 1 0 0 1 2 9 11 3.493699 1 0.330000 3.010000 0.671488 0.480000 3.400000e-01 1.000000 0.490000 0.572935 0.480000 0 4.000000e-01 1 OBSCN 84033 broad.mit.edu 37 1 228495118 228495118 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr1:228495118C>T ENST00000422127.1 + 46 12396 c.12352C>T c.(12352-12354)Cgg>Tgg p.R4118W OBSCN_ENST00000284548.11_Missense_Mutation_p.R4118W|OBSCN_ENST00000366707.4_Missense_Mutation_p.R1752W|OBSCN_ENST00000570156.2_Missense_Mutation_p.R5075W|OBSCN_ENST00000366709.4_Missense_Mutation_p.R1237W NM_001098623.2 NP_001092093.2 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF 223 Prostate(94;0.0405) GTACGAGATGCGGAGCCAGGG 0.662000 0 SO:0001583 missense ENST00000422127.1 0 1 hg19 CCDS58065.1 . . . . . . . . . . C 15.65 2.897492 0.52121 . . ENSG00000154358 ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709 T;T;T;T 0.68479 -0.33;-0.33;-0.33;-0.33 5.79 1.41 0.22369 Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 1.288780 0.05292 N 0.521231 T 0.76572 0.4006 L 0.53729 1.69 0.24836 N 0.992496 D;B 0.89917 1.0;0.37 D;B 0.78314 0.991;0.059 T 0.57505 -0.7800 10 0.54805 T 0.06 . 6.5659 0.22511 0.5717:0.2742:0.0:0.154 . 4118;4118 Q5VST9;Q5VST9-3 OBSCN_HUMAN;. W 4118;4118;1752;1237 ENSP00000284548:R4118W;ENSP00000409493:R4118W;ENSP00000355668:R1752W;ENSP00000355670:R1237W ENSP00000284548:R4118W R + 1 2 OBSCN 226561741 0.809000 0.29036 0.030000 0.17652 0.186000 0.23388 0.384000 0.20668 0.364000 0.24374 -0.515000 0.04445 CGG TCGA-LB-A8F3-01A-11D-A36O-08 OBSCN-204 KNOWN basic|CCDS protein_coding protein_coding 0 0 0 4 175 0 27 0 2.633681e-03 0 3 0 27 2 0 0 0 0 0 2 1 0.883149 4 170 0 27 2 0 0 0 0 0 0 -5.866944 1 1 121030 3 28 1 2 8 10 3.619451 1 0.330000 3.010000 0.684260 0.350000 1.000000e-01 1.000000 0.270000 0.430789 0.350000 0 2.000000e-01 6.600000e-01 SLC12A5 57468 broad.mit.edu 37 20 44675062 44675062 + Nonsense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr20:44675062C>T ENST00000454036.2 + 14 1892 c.1843C>T c.(1843-1845)Cga>Tga p.R615* SLC12A5_ENST00000243964.3_Nonsense_Mutation_p.R592* NM_001134771.1 NP_001128243.1 Q9H2X9 S12A5_HUMAN solute carrier family 12 (potassium/chloride transporter), member 5 80 Myeloproliferative disorder(115;0.0122) Bumetanide(DB00887)|Potassium Chloride(DB00761) GCCACGCTTTCGATATTACCA 0.552000 0 SO:0001587 stop_gained ENST00000454036.2 0 1 hg19 CCDS46610.1 . . . . . . . . . . C 38 7.042841 0.98021 . . ENSG00000124140 ENST00000454036;ENST00000243964 . . . 4.33 4.33 0.51752 . 0.075781 0.52532 D 0.000070 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.18710 T 0.47 . 10.9059 0.47079 0.1878:0.8122:0.0:0.0 . . . . X 615;592 . ENSP00000243964:R592X R + 1 2 SLC12A5 44108469 1.000000 0.71417 1.000000 0.80357 0.911000 0.54048 4.103000 0.57783 2.253000 0.74438 0.467000 0.42956 CGA TCGA-LB-A8F3-01A-11D-A36O-08 SLC12A5-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000471538.1 1 0 0 13 359 0 91 0 0 0 0 91 2 0 0 0 0 0 2 1 0.999466 13 349 0 86 2 0 0 0 0 0 0 -12.894970 1 1 0 0 1 3 3 6 2.405922 1 0.330000 3.010000 0.522316 0.330000 1.700000e-01 1.000000 0.310000 0.474609 0.330000 0 2.400000e-01 1 OGFR 11054 broad.mit.edu 37 20 61444217 61444217 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr20:61444217G>A ENST00000290291.6 + 7 1275 c.1250G>A c.(1249-1251)tGt>tAt p.C417Y OGFR_ENST00000370461.1_Missense_Mutation_p.C365Y NM_007346.2 NP_031372.2 Q9NZT2 OGFR_HUMAN opioid growth factor receptor 17 Breast(26;3.65e-08) TTGGAGGGGTGTGCCCTCAGC 0.682000 0 SO:0001583 missense ENST00000290291.6 1 1 hg19 CCDS13504.1 . . . . . . . . . . G 14.58 2.577779 0.45902 . . ENSG00000060491 ENST00000290291;ENST00000370468;ENST00000357163;ENST00000370469;ENST00000370461 T;T;T 0.64085 0.56;0.05;-0.08 4.98 3.99 0.46301 . 0.131453 0.51477 D 0.000099 T 0.71685 0.3369 M 0.66939 2.045 0.09310 N 0.999996 D;D;D 0.60160 0.987;0.987;0.987 P;P;P 0.57371 0.819;0.819;0.819 T 0.65434 -0.6169 10 0.72032 D 0.01 -13.4023 13.2842 0.60232 0.0:0.0:0.7181:0.2819 . 417;400;417 B3KMQ6;Q05BV5;Q9NZT2 .;.;OGFR_HUMAN Y 417;417;417;272;365 ENSP00000290291:C417Y;ENSP00000359499:C417Y;ENSP00000359491:C365Y ENSP00000290291:C417Y C + 2 0 OGFR 60914662 0.964000 0.33143 0.980000 0.43619 0.665000 0.39181 1.485000 0.35519 2.278000 0.76064 0.555000 0.69702 TGT TCGA-LB-A8F3-01A-11D-A36O-08 OGFR-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000080067.1 1 0 0 11 191 0 55 1 9.977942e-01 4 185 0 55 2 0 0 0 0 0 2 1 0.998194 11 185 0 54 2 0 0 0 0 0 0 -13.979590 1 1 0 0 1 3 3 6 2.405922 1 0.330000 3.010000 0.522316 0.530000 2.600000e-01 1.000000 0.460000 0.613356 0.530000 0 3.700000e-01 1 C21orf2 755 broad.mit.edu 37 21 45753071 45753071 + Missense_Mutation SNP C C T rs140451304 TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr21:45753071C>T ENST00000339818.4 - 4 425 c.218G>A c.(217-219)cGc>cAc p.R73H C21orf2_ENST00000325223.7_Missense_Mutation_p.R73H|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000397956.3_Missense_Mutation_p.R73H|C21orf2_ENST00000496321.1_5'UTR NM_001271440.1|NM_004928.2 NP_001258369.1|NP_004919.1 O43822 CU002_HUMAN chromosome 21 open reading frame 2 2 GCTGGGGATGCGGTTCCTCCG 0.677000 0 SO:0001583 missense ENST00000339818.4 0 1 hg19 CCDS13709.1 . . . . . . . . . . C 13.19 2.164124 0.38217 . . ENSG00000160226 ENST00000339818;ENST00000380160;ENST00000397956;ENST00000325223 T;T;T 0.09911 2.93;2.93;2.93 4.99 2.04 0.26737 . 0.730148 0.13311 N 0.397507 T 0.05960 0.0155 L 0.33245 0.995 0.09310 N 0.999998 B;P;B;B 0.36378 0.04;0.55;0.049;0.001 B;B;B;B 0.24541 0.007;0.054;0.011;0.001 T 0.34254 -0.9836 10 0.34782 T 0.22 -18.6603 4.4168 0.11461 0.17:0.583:0.0:0.247 . 73;73;73;32 G5E952;Q8N5X6;O43822;O43822-2 .;.;CU002_HUMAN;. H 73;109;73;73 ENSP00000344566:R73H;ENSP00000381047:R73H;ENSP00000317302:R73H ENSP00000317302:R73H R - 2 0 C21orf2 44577499 0.135000 0.22499 0.996000 0.52242 0.789000 0.44602 -0.042000 0.12063 0.587000 0.29643 -0.126000 0.14955 CGC TCGA-LB-A8F3-01A-11D-A36O-08 C21orf2-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000195799.1 0 0 0 4 96 0 26 0 8.383465e-01 0 82 0 26 2 0 0 0 0 0 2 1 0.876685 4 90 0 26 2 0 0 0 0 0 0 -3.261623 1 1 121316 38 43 1 1 2 3 1.912912 0 0.330000 3.010000 0.403782 0.340000 1.000000e-01 1.000000 0.270000 0.449314 0.340000 0 1.900000e-01 1 CECR1 51816 broad.mit.edu 37 22 17669277 17669277 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr22:17669277C>T ENST00000399839.1 - 7 1303 c.1033G>A c.(1033-1035)Gcc>Acc p.A345T CECR1_ENST00000449907.2_Missense_Mutation_p.A303T|CECR1_ENST00000262607.3_Missense_Mutation_p.A345T|CECR1_ENST00000330232.4_Missense_Mutation_p.A104T|CECR1_ENST00000399837.2_Missense_Mutation_p.A345T|CECR1_ENST00000480276.1_5'Flank NM_001282227.1|NM_001282228.1 NP_001269156.1|NP_001269157.1 Q9NZK5 CECR1_HUMAN cat eye syndrome chromosome region, candidate 1 25 all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106) CCATCCTTGGCGGGGATCATC 0.607000 0 SO:0001583 missense ENST00000399839.1 0 1 hg19 CCDS13742.1 . . . . . . . . . . C 2.897 -0.228346 0.06022 . . ENSG00000093072 ENST00000399839;ENST00000330232;ENST00000262607;ENST00000449907;ENST00000399837 D;D;D;D;D 0.82984 -1.67;-1.67;-1.67;-1.67;-1.67 4.24 -1.32 0.09201 Adenosine/AMP deaminase (1); 0.973928 0.08462 N 0.942354 T 0.68081 0.2962 L 0.38838 1.175 0.09310 N 1 B;B 0.20887 0.049;0.008 B;B 0.10450 0.005;0.002 T 0.49224 -0.8962 10 0.12766 T 0.61 . 3.2155 0.06697 0.2619:0.3322:0.0:0.406 . 345;104 Q9NZK5;Q9NZK5-2 CECR1_HUMAN;. T 345;104;345;303;345 ENSP00000382733:A345T;ENSP00000332871:A104T;ENSP00000262607:A345T;ENSP00000406443:A303T;ENSP00000382731:A345T ENSP00000262607:A345T A - 1 0 CECR1 16049277 0.000000 0.05858 0.001000 0.08648 0.011000 0.07611 0.129000 0.15830 0.143000 0.18926 0.561000 0.74099 GCC TCGA-LB-A8F3-01A-11D-A36O-08 CECR1-002 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316079.1 0 0 0 8 326 0 99 0 3.010218e-02 0 10 0 99 2 0 0 0 0 0 2 1 0.988784 8 320 0 99 2 0 0 0 0 0 0 -2.953949 1 1 121412 8 39 1 1 2 3 2.011614 0 0.330000 3.010000 0.410704 0.180000 7.000000e-02 1.000000 0.170000 0.291938 0.180000 0 1.200000e-01 3.100000e-01 FAM171B 165215 broad.mit.edu 37 2 187626909 187626909 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr2:187626909C>T ENST00000304698.5 + 8 2043 c.1840C>T c.(1840-1842)Cca>Tca p.P614S NM_177454.3 NP_803237.3 Q6P995 F171B_HUMAN family with sequence similarity 171, member B 54 ACAGAGCCTGCCATCCCAGGC 0.483000 0 SO:0001583 missense ENST00000304698.5 1 1 hg19 CCDS33347.1 . . . . . . . . . . C 8.496 0.863233 0.17250 . . ENSG00000144369 ENST00000304698 T 0.27890 1.64 5.85 5.85 0.93711 . 0.072813 0.56097 D 0.000025 T 0.23410 0.0566 N 0.25647 0.755 0.32038 N 0.598562 B;B 0.18461 0.028;0.028 B;B 0.24848 0.056;0.056 T 0.15780 -1.0425 10 0.26408 T 0.33 -16.0957 12.8401 0.57797 0.0:0.884:0.0:0.116 . 614;615 Q6P995;A8K122 F171B_HUMAN;. S 614 ENSP00000304108:P614S ENSP00000304108:P614S P + 1 0 FAM171B 187335154 0.101000 0.21875 1.000000 0.80357 0.980000 0.70556 1.693000 0.37742 2.753000 0.94483 0.655000 0.94253 CCA TCGA-LB-A8F3-01A-11D-A36O-08 FAM171B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000334679.1 1 0 1 33 289 0 91 0 0 0 0 91 2 0 0 0 0 0 2 1 1.000000 33 284 0 90 2 0 0 0 0 0 0 -12.732200 1 1 0 0 1 1 2 3 1.965871 0 0.330000 3.010000 0.410704 0.730000 5.000000e-01 1.000000 0.700000 0.756409 0.730000 0 6.000000e-01 9.500000e-01 MYO1B 4430 broad.mit.edu 37 2 192261178 192261178 + Silent SNP A A G TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr2:192261178A>G ENST00000392318.3 + 21 2497 c.2250A>G c.(2248-2250)acA>acG p.T750T MYO1B_ENST00000392316.1_Silent_p.T750T|MYO1B_ENST00000304164.4_Silent_p.T750T|MYO1B_ENST00000439065.2_Silent_p.T24T|MYO1B_ENST00000339514.4_Silent_p.T750T NM_001130158.1 NP_001123630.1 O43795 MYO1B_HUMAN myosin IB 55 OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236) ACCAGCAGACAAAGAGTTCCG 0.368000 0 SO:0001819 synonymous_variant ENST00000392318.3 1 1 hg19 CCDS46477.1 TCGA-LB-A8F3-01A-11D-A36O-08 MYO1B-010 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000334774.1 0 0 1 20 548 0 169 1 7.094443e-01 6 63 0 169 2 0 0 0 0 0 2 1 0.999995 20 540 0 168 2 0 0 0 0 0 0 -18.085410 1 1 0 0 1 1 2 3 1.965871 0 0.330000 3.010000 0.410704 0.250000 1.500000e-01 1.000000 0.250000 0.352180 0.250000 0 1.900000e-01 3.600000e-01 MPP4 58538 broad.mit.edu 37 2 202552087 202552087 + Missense_Mutation SNP T T C TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr2:202552087T>C ENST00000409474.3 - 5 494 c.287A>G c.(286-288)gAg>gGg p.E96G MPP4_ENST00000359962.5_Missense_Mutation_p.E96G|MPP4_ENST00000315506.7_Missense_Mutation_p.E96G|MPP4_ENST00000428900.2_Missense_Mutation_p.E96G|MPP4_ENST00000447335.2_Missense_Mutation_p.E96G|MPP4_ENST00000409143.1_Intron|MPP4_ENST00000396886.3_Missense_Mutation_p.E96G NM_033066.2 NP_149055 Q96JB8 MPP4_HUMAN membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4) 12 ACGTAATAACTCCACTACCTG 0.393000 0 SO:0001583 missense ENST00000409474.3 0 1 hg19 CCDS46491.1 . . . . . . . . . . T 12.24 1.877332 0.33162 . . ENSG00000082126 ENST00000409474;ENST00000315506;ENST00000396886;ENST00000359962;ENST00000315549;ENST00000428900;ENST00000447335 T;T;T;T;T 0.06687 3.28;3.27;3.28;3.28;3.28 5.88 3.43 0.39272 L27, C-terminal (1);L27 (2); 0.697165 0.13777 N 0.363487 T 0.08044 0.0201 L 0.43757 1.38 0.09310 N 0.999996 B;B;B;B;B;B;B;B;B 0.10296 0.003;0.002;0.002;0.002;0.001;0.002;0.003;0.001;0.001 B;B;B;B;B;B;B;B;B 0.13407 0.008;0.006;0.002;0.002;0.001;0.002;0.009;0.001;0.005 T 0.32079 -0.9920 10 0.52906 T 0.07 . 5.6829 0.17786 0.0:0.1486:0.1428:0.7086 . 96;96;96;96;96;96;109;96;96 B4DUF3;E7ET46;B7ZM19;Q96JB8-2;E7EUL8;F8WC25;F8WBH8;Q96JB8;Q96JB8-4 .;.;.;.;.;.;.;MPP4_HUMAN;. G 96 ENSP00000387278:E96G;ENSP00000319363:E96G;ENSP00000353047:E96G;ENSP00000416781:E96G;ENSP00000406160:E96G ENSP00000319363:E96G E - 2 0 MPP4 202260332 0.937000 0.31787 0.005000 0.12908 0.084000 0.17831 2.824000 0.48088 0.445000 0.26639 0.533000 0.62120 GAG TCGA-LB-A8F3-01A-11D-A36O-08 MPP4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000335748.2 0 0 0 3 54 0 10 0 0 0 0 10 2 0 0 0 0 0 2 1 0.782304 2 50 0 9 2 0 0 0 0 0 0 -7.301237 1 0 0 0 1 1 2 3 1.965871 0 0.330000 3.010000 0.410704 0.460000 1.200000e-01 1.000000 1.000000 0.525470 0.460000 0 2.500000e-01 9.300000e-01 SLC1A4 6509 broad.mit.edu 37 2 65243676 65243676 + Silent SNP T T A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr2:65243676T>A ENST00000234256.3 + 5 1146 c.903T>A c.(901-903)tcT>tcA p.S301S SLC1A4_ENST00000531327.1_Intron|SLC1A4_ENST00000493121.1_3'UTR NM_003038.4 NP_003029.2 P43007 SATT_HUMAN solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 13 L-Alanine(DB00160) TCTTCGCATCTATATTGGGCC 0.458000 0 SO:0001819 synonymous_variant ENST00000234256.3 1 1 hg19 CCDS1879.1 TCGA-LB-A8F3-01A-11D-A36O-08 SLC1A4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251726.2 0 0 0 18 477 0 170 0 1.650680e-01 1 18 0 170 2 0 0 0 0 0 2 1 0.999981 18 472 0 168 2 0 0 0 0 0 0 -17.052850 1 1 0 0 1 1 2 3 1.922617 0 0.330000 3.010000 0.406397 0.260000 1.500000e-01 1.000000 0.250000 0.381474 0.260000 0 2.000000e-01 1 CNGA3 1261 broad.mit.edu 37 2 99013711 99013711 + Missense_Mutation SNP A A G TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr2:99013711A>G ENST00000272602.2 + 7 2117 c.2078A>G c.(2077-2079)cAa>cGa p.Q693R CNGA3_ENST00000393504.1_Missense_Mutation_p.Q693R|CNGA3_ENST00000409937.1_Missense_Mutation_p.Q697R|CNGA3_ENST00000436404.2_Missense_Mutation_p.Q675R Q16281 CNGA3_HUMAN cyclic nucleotide gated channel alpha 3 49 GAGGACAAACAACAGTGAAAA 0.562000 0 SO:0001583 missense ENST00000272602.2 0 1 hg19 CCDS2034.1 . . . . . . . . . . A 17.02 3.281297 0.59758 . . ENSG00000144191 ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937 D;D;D;D 0.97553 -4.27;-4.21;-4.27;-4.43 5.18 -1.08 0.09936 . 1.144930 0.06868 N 0.800336 D 0.90195 0.6935 L 0.29908 0.895 0.09310 N 1 B;B;B 0.29716 0.255;0.0;0.0 B;B;B 0.16722 0.016;0.001;0.001 T 0.81933 -0.0706 10 0.10377 T 0.69 . 0.7756 0.01031 0.4129:0.1827:0.2527:0.1518 . 697;675;693 E9PF93;Q4VAP7;Q16281 .;.;CNGA3_HUMAN R 693;675;693;697 ENSP00000377140:Q693R;ENSP00000410070:Q675R;ENSP00000272602:Q693R;ENSP00000386761:Q697R ENSP00000272602:Q693R Q + 2 0 CNGA3 98380143 0.000000 0.05858 0.000000 0.03702 0.853000 0.48598 0.012000 0.13287 -0.316000 0.08690 0.533000 0.62120 CAA TCGA-LB-A8F3-01A-11D-A36O-08 CNGA3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000252986.1 0 0 0 7 144 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 0.979508 7 140 0 45 2 0 0 0 0 0 0 -10.201140 1 1 0 0 1 1 2 3 1.939341 0 0.330000 3.010000 0.414105 0.350000 1.500000e-01 1.000000 0.320000 0.425818 0.350000 0 2.300000e-01 5.600000e-01 GATA2 2624 broad.mit.edu 37 3 128200783 128200783 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr3:128200783G>A ENST00000341105.2 - 5 1353 c.1022C>T c.(1021-1023)gCc>gTc p.A341V GATA2_ENST00000430265.2_Intron|GATA2_ENST00000487848.1_Missense_Mutation_p.A341V|GATA2_ENST00000489987.1_5'UTR NM_032638.4 NP_116027.2 P23769 GATA2_HUMAN GATA binding protein 2 p.A341_G346del(1) 79 TCTTCTGGCGGCCGACTGGGA 0.667000 Mis AML(CML blast transformation) Dom yes 3 3q21.3 2624 GATA binding protein 2 L 1 Deletion - In frame(1) SO:0001583 missense ENST00000341105.2 0 1 hg19 CCDS3049.1 . . . . . . . . . . G 27.9 4.871747 0.91587 . . ENSG00000179348 ENST00000341105;ENST00000487848 D;D 0.97710 -4.5;-4.5 4.95 4.95 0.65309 Zinc finger, NHR/GATA-type (1);Zinc finger, GATA-type (1); 0.000000 0.85682 D 0.000000 D 0.97142 0.9066 L 0.31926 0.97 0.80722 D 1 P 0.50528 0.936 P 0.56434 0.798 D 0.97318 0.9942 10 0.42905 T 0.14 -6.4427 18.1809 0.89777 0.0:0.0:1.0:0.0 . 341 P23769 GATA2_HUMAN V 341 ENSP00000345681:A341V;ENSP00000417074:A341V ENSP00000345681:A341V A - 2 0 GATA2 129683473 1.000000 0.71417 0.857000 0.33713 0.977000 0.68977 9.778000 0.99011 2.271000 0.75665 0.591000 0.81541 GCC TCGA-LB-A8F3-01A-11D-A36O-08 GATA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356925.1 0 0 0 4 161 0 82 0 3.119290e-03 0 3 0 82 2 0 0 0 0 0 2 1 0.891348 5 160 0 81 2 0 0 0 0 0 0 -5.911514 1 1 0 0 1 0 2 2 1.700345 1 0.330000 3.010000 0.330000 0.170000 5.000000e-02 1.000000 0.140000 0.264770 0.170000 0 1.000000e-01 3.100000e-01 RFTN1 23180 broad.mit.edu 37 3 16475415 16475415 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr3:16475415C>T ENST00000334133.4 - 3 547 c.275G>A c.(274-276)cGg>cAg p.R92Q RFTN1_ENST00000432519.1_Missense_Mutation_p.R56Q NM_015150.1 NP_055965.1 Q14699 RFTN1_HUMAN raftlin, lipid raft linker 1 p.R92L(1) 38 CGTCTTCTCCCGCTCATGGGT 0.632000 1 Substitution - Missense(1) SO:0001583 missense ENST00000334133.4 0 1 hg19 CCDS33712.1 . . . . . . . . . . C 5.639 0.302648 0.10678 . . ENSG00000131378 ENST00000432519;ENST00000334133;ENST00000451036;ENST00000449415;ENST00000441460;ENST00000431547 T;T;T;T;T;T 0.30714 1.52;1.52;1.52;1.52;1.52;1.52 5.21 -8.08 0.01094 . 1.391410 0.04296 N 0.346433 T 0.13884 0.0336 N 0.16790 0.44 0.09310 N 1 B;B 0.20261 0.043;0.014 B;B 0.12837 0.008;0.003 T 0.13845 -1.0494 10 0.19147 T 0.46 0.1934 4.5627 0.12168 0.1791:0.1421:0.0834:0.5953 . 56;92 G3XAJ6;Q14699 .;RFTN1_HUMAN Q 56;92;92;92;92;92 ENSP00000403926:R56Q;ENSP00000334153:R92Q;ENSP00000403997:R92Q;ENSP00000409427:R92Q;ENSP00000388718:R92Q;ENSP00000393216:R92Q ENSP00000334153:R92Q R - 2 0 RFTN1 16450419 0.012000 0.17670 0.001000 0.08648 0.415000 0.31203 0.128000 0.15810 -2.466000 0.00533 -0.367000 0.07326 CGG TCGA-LB-A8F3-01A-11D-A36O-08 RFTN1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000346908.1 0 0 0 10 676 0 267 0 3.135803e-02 0 17 0 267 2 0 0 0 0 0 2 1 0.996516 9 661 0 264 2 0 0 0 0 0 0 -1.792441 0 1 121412 1 38 1 0 2 2 1.700345 1 0.330000 3.010000 0.330000 0.090000 4.000000e-02 1.000000 0.090000 0.190757 0.090000 0 6.000000e-02 1.500000e-01 SAMD7 344658 broad.mit.edu 37 3 169644499 169644499 + Missense_Mutation SNP T T C TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr3:169644499T>C ENST00000428432.2 + 6 838 c.449T>C c.(448-450)cTg>cCg p.L150P SAMD7_ENST00000335556.3_Missense_Mutation_p.L150P NM_182610.2 NP_872416.1 Q7Z3H4 SAMD7_HUMAN sterile alpha motif domain containing 7 31 all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169) Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106) GCCGGTGACCTGCATTTTCAC 0.592000 0 SO:0001583 missense ENST00000428432.2 1 1 hg19 CCDS3209.1 . . . . . . . . . . T 9.381 1.072926 0.20147 . . ENSG00000187033 ENST00000428432;ENST00000335556 T;T 0.55588 0.51;0.51 6.16 3.76 0.43208 . 0.394431 0.24664 N 0.036603 T 0.35451 0.0932 N 0.21448 0.665 0.51012 D 0.999903 B 0.24533 0.105 B 0.20384 0.029 T 0.09058 -1.0692 10 0.40728 T 0.16 -0.459 8.2492 0.31706 0.1197:0.065:0.0:0.8154 . 150 Q7Z3H4 SAMD7_HUMAN P 150 ENSP00000391299:L150P;ENSP00000334668:L150P ENSP00000334668:L150P L + 2 0 SAMD7 171127193 1.000000 0.71417 0.997000 0.53966 0.051000 0.14879 3.078000 0.50096 0.541000 0.28827 0.528000 0.53228 CTG TCGA-LB-A8F3-01A-11D-A36O-08 SAMD7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351959.1 1 0 1 44 248 0 90 0 0 0 0 90 2 0 0 0 0 0 2 1 1.000000 44 245 0 89 2 0 0 0 0 0 0 -19.986190 1 1 0 0 1 0 2 2 1.700345 1 0.330000 3.010000 0.330000 0.930000 6.800000e-01 1.000000 1.000000 0.910262 0.930000 1 7.900000e-01 1 CPE 1363 broad.mit.edu 37 4 166418761 166418761 + Nonstop_Mutation SNP A A T rs34858186 TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr4:166418761A>T ENST00000402744.4 + 9 1710 c.1430A>T c.(1429-1431)tAa>tTa p.*477L NM_001873.2 NP_001864.1 P16870 CBPE_HUMAN carboxypeptidase E 26 all_hematologic(180;0.221) Prostate(90;0.0962)|Melanoma(52;0.18) """Insulin(DB00071)|Insulin Regular(DB00030)" TTAAATTTTTAAAAAGGCTTC 0.299000 0 SO:0001578 stop_lost ENST00000402744.4 0 1 hg19 CCDS3810.1 . . . . . . . . . . A 12.01 1.808900 0.31961 . . ENSG00000109472 ENST00000402744 . . . 5.76 4.59 0.56863 . . . . . . . . . . . 0.09310 N 1 . . . . . . . . . . . . . . 8.884 0.35392 0.8565:0.0:0.1435:0.0 . . . . L 477 . . X + 2 2 CPE 166638211 1.000000 0.71417 0.896000 0.35187 0.550000 0.35303 3.556000 0.53734 1.019000 0.39547 -0.250000 0.11733 TAA TCGA-LB-A8F3-01A-11D-A36O-08 CPE-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317094.2 0 0 1 37 114 0 42 1 9.999967e-01 7 59 0 42 2 0 0 0 0 0 2 1 1.000000 37 114 0 42 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.984231 1 0.330000 3.010000 0.416630 0.990000 9.900000e-01 1.000000 1.000000 0.999981 0.990000 1 9.900000e-01 1 FRAS1 80144 broad.mit.edu 37 4 79396679 79396679 + Silent SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr4:79396679C>T ENST00000264895.6 + 54 8210 c.7770C>T c.(7768-7770)cgC>cgT p.R2590R NM_025074.6 NP_079350.5 Q86XX4 FRAS1_HUMAN Fraser extracellular matrix complex subunit 1 103 TCCTGTGTCGCACCGAGCAAG 0.582000 0 SO:0001819 synonymous_variant ENST00000264895.6 0 1 hg19 CCDS54771.1 . . . . . . . . . . C 1.648 -0.514788 0.04200 . . ENSG00000138759 ENST00000512123 . . . 5.44 0.23 0.15372 . . . . . T 0.41534 0.1163 . . . 0.80722 D 1 . . . . . . T 0.20338 -1.0278 4 . . . . 1.4158 0.02301 0.2395:0.4251:0.1163:0.219 . . . . Y 819 . . H + 1 0 FRAS1 79615703 0.998000 0.40836 0.409000 0.26459 0.132000 0.20833 0.632000 0.24583 -0.322000 0.08615 -0.194000 0.12790 CAC TCGA-LB-A8F3-01A-11D-A36O-08 FRAS1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 5 284 0 80 0 4.942805e-04 0 2 0 80 2 0 0 0 0 0 2 1 0.933971 5 277 0 80 2 0 0 0 0 0 0 -5.894410 1 0 0 0 1 1 2 3 1.943468 0 0.330000 3.010000 0.410704 0.140000 4.000000e-02 1.000000 0.120000 0.255151 0.140000 0 8.000000e-02 2.700000e-01 SH3TC1 54436 broad.mit.edu 37 4 8230216 8230216 + Missense_Mutation SNP T T A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr4:8230216T>A ENST00000245105.3 + 12 2862 c.2795T>A c.(2794-2796)cTg>cAg p.L932Q SH3TC1_ENST00000539824.1_Missense_Mutation_p.L856Q NM_018986.3 NP_061859 Q8TE82 S3TC1_HUMAN SH3 domain and tetratricopeptide repeats 1 33 GCCGTGCGGCTGTTCTCGAGG 0.706000 NSCLC(145;2298 2623 35616 37297) 0 SO:0001583 missense ENST00000245105.3 1 1 hg19 CCDS3399.1 . . . . . . . . . . T 13.09 2.134594 0.37630 . . ENSG00000125089 ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265 T;T 0.69306 -0.39;-0.39 4.63 3.4 0.38934 Tetratricopeptide-like helical (1); 0.234828 0.36303 N 0.002670 T 0.79575 0.4469 M 0.78049 2.395 0.44485 D 0.997427 D 0.89917 1.0 D 0.77557 0.99 T 0.79694 -0.1696 10 0.87932 D 0 -16.7905 10.304 0.43670 0.1479:0.0:0.0:0.8521 . 932 Q8TE82 S3TC1_HUMAN Q 670;932;856;761 ENSP00000245105:L932Q;ENSP00000441045:L856Q ENSP00000245105:L932Q L + 2 0 SH3TC1 8281116 1.000000 0.71417 0.885000 0.34714 0.007000 0.05969 7.019000 0.76412 0.585000 0.29608 0.459000 0.35465 CTG TCGA-LB-A8F3-01A-11D-A36O-08 SH3TC1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000206991.2 1 0 1 23 134 0 49 1 9.927851e-01 13 36 0 49 2 0 0 0 0 0 2 1 0.999999 22 129 0 48 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.932073 0 0.330000 3.010000 0.411558 0.990000 6.800000e-01 1.000000 1.000000 0.946202 0.990000 1 8.500000e-01 1 SLC6A19 340024 broad.mit.edu 37 5 1201792 1201792 + Silent SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr5:1201792C>T ENST00000304460.10 + 1 83 c.27C>T c.(25-27)ccC>ccT p.P9P NM_001003841.2 NP_001003841.1 Q695T7 S6A19_HUMAN solute carrier family 6 (neutral amino acid transporter), member 19 44 all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10) Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185) TGCCCAACCCCGGCCTAGACG 0.697000 0 SO:0001819 synonymous_variant ENST00000304460.10 1 1 hg19 CCDS34130.1 TCGA-LB-A8F3-01A-11D-A36O-08 SLC6A19-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365557.1 1 0 1 9 74 0 31 1 4.009623e-02 3 0 0 31 2 0 0 0 0 0 2 1 0.994166 9 71 0 30 2 0 0 0 0 0 0 -15.304850 1 1 120904 15 36 1 1 2 3 1.943568 0 0.330000 3.010000 0.409848 0.810000 4.000000e-01 1.000000 1.000000 0.798889 0.810000 0 5.700000e-01 1 ACTBL2 345651 broad.mit.edu 37 5 56778497 56778497 + Missense_Mutation SNP T T C TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr5:56778497T>C ENST00000423391.1 - 1 139 c.38A>G c.(37-39)aAt>aGt p.N13S AC025470.1_ENST00000584598.1_RNA|CTD-2023N9.1_ENST00000506106.1_RNA NM_001017992.3 NP_001017992.1 Q562R1 ACTBL_HUMAN actin, beta-like 2 28 Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182) CCCTGACCCATTATCCACTAC 0.542000 0 SO:0001583 missense ENST00000423391.1 1 1 hg19 CCDS34163.1 . . . . . . . . . . T 15.83 2.949343 0.53186 . . ENSG00000169067 ENST00000423391 D 0.97665 -4.48 5.16 5.16 0.70880 . 0.000000 0.64402 D 0.000002 D 0.98040 0.9354 M 0.93854 3.465 0.49798 D 0.999821 B 0.26318 0.146 B 0.40741 0.339 D 0.98614 1.0664 10 0.87932 D 0 . 12.977 0.58542 0.0:0.0:0.0:1.0 . 13 Q562R1 ACTBL_HUMAN S 13 ENSP00000416706:N13S ENSP00000416706:N13S N - 2 0 ACTBL2 56814254 1.000000 0.71417 1.000000 0.80357 0.945000 0.59286 6.054000 0.71096 2.156000 0.67533 0.460000 0.39030 AAT TCGA-LB-A8F3-01A-11D-A36O-08 ACTBL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000368579.1 1 0 1 18 149 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 0.999985 17 147 0 46 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.943568 0 0.330000 3.010000 0.409848 0.780000 4.700000e-01 1.000000 1.000000 0.792426 0.780000 0 6.100000e-01 1 GPR98 84059 broad.mit.edu 37 5 89979973 89979973 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr5:89979973C>T ENST00000405460.2 + 28 6331 c.6235C>T c.(6235-6237)Ctc>Ttc p.L2079F NM_032119.3 NP_115495.3 Q8WXG9 GPR98_HUMAN G protein-coupled receptor 98 269 all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192) TATCGAACTACTCAACTCTAC 0.363000 0 SO:0001583 missense ENST00000405460.2 1 1 hg19 CCDS47246.1 . . . . . . . . . . C 6.792 0.515177 0.12944 . . ENSG00000164199 ENST00000405460;ENST00000296619;ENST00000399043 T 0.28069 1.63 5.71 1.34 0.21922 Na-Ca exchanger/integrin-beta4 (1); 0.425070 0.27821 N 0.017719 T 0.13756 0.0333 N 0.16307 0.4 0.42111 D 0.991388 B 0.20368 0.044 B 0.24006 0.05 T 0.10382 -1.0632 10 0.13853 T 0.58 . 3.4706 0.07566 0.1498:0.5324:0.0958:0.2221 . 2079 Q8WXG9 GPR98_HUMAN F 2079 ENSP00000384582:L2079F ENSP00000296619:L2079F L + 1 0 GPR98 90015729 0.004000 0.15560 0.946000 0.38457 0.893000 0.52053 0.320000 0.19540 0.319000 0.23209 0.591000 0.81541 CTC TCGA-LB-A8F3-01A-11D-A36O-08 GPR98-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000369993.2 1 0 1 20 143 0 52 0 0 0 0 52 2 0 0 0 0 0 2 1 0.999997 20 142 0 52 2 0 0 0 0 0 0 -20.000000 1 1 120792 2 37 1 1 2 3 1.943568 0 0.330000 3.010000 0.409848 0.880000 5.500000e-01 1.000000 1.000000 0.864492 0.880000 1 7.000000e-01 1 TAS2R1 50834 broad.mit.edu 37 5 9629850 9629850 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr5:9629850G>A ENST00000382492.2 - 1 613 c.295C>T c.(295-297)Ctc>Ttc p.L99F CTD-2001E22.1_ENST00000504182.2_RNA NM_019599.2 NP_062545.1 Q9NYW7 TA2R1_HUMAN taste receptor, type 2, member 1 39 AAAACGCCGAGCCATGTGGCA 0.433000 0 SO:0001583 missense ENST00000382492.2 0 1 hg19 CCDS3876.1 . . . . . . . . . . G 21.7 4.185783 0.78789 . . ENSG00000169777 ENST00000382492 T 0.02216 4.39 5.32 5.32 0.75619 . 0.000000 0.64402 D 0.000004 T 0.14917 0.0360 M 0.84773 2.715 0.48135 D 0.999591 D 0.89917 1.0 D 0.97110 1.0 T 0.00059 -1.2166 9 . . . . 16.5409 0.84384 0.0:0.0:1.0:0.0 . 99 Q9NYW7 TA2R1_HUMAN F 99 ENSP00000371932:L99F . L - 1 0 TAS2R1 9682850 1.000000 0.71417 0.995000 0.50966 0.692000 0.40212 6.136000 0.71703 2.767000 0.95098 0.655000 0.94253 CTC TCGA-LB-A8F3-01A-11D-A36O-08 TAS2R1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206988.2 0 0 0 6 175 0 39 0 0 0 0 39 2 0 0 0 0 0 2 1 0.964546 6 173 0 38 2 0 0 0 0 0 0 -8.629536 1 1 0 0 1 1 2 3 1.943568 0 0.330000 3.010000 0.409848 0.260000 1.000000e-01 1.000000 0.230000 0.363873 0.260000 0 1.600000e-01 4.800000e-01 IYD 389434 broad.mit.edu 37 6 150715311 150715311 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr6:150715311G>A ENST00000344419.3 + 4 747 c.607G>A c.(607-609)Gca>Aca p.A203T IYD_ENST00000500320.3_Missense_Mutation_p.A203T|IYD_ENST00000392255.3_Missense_Mutation_p.A203T|IYD_ENST00000392256.2_Missense_Mutation_p.A203T|IYD_ENST00000229447.5_Missense_Mutation_p.A203T|IYD_ENST00000425615.3_Missense_Mutation_p.A148T NM_203395.2 NP_981932.1 Q6PHW0 IYD1_HUMAN iodotyrosine deiodinase 15 Ovarian(120;0.028) BRCA - Breast invasive adenocarcinoma(37;0.215) TGGTTTCGCCGCAAATGGCAA 0.433000 0 SO:0001583 missense ENST00000344419.3 0 1 hg19 CCDS5227.1 . . . . . . . . . . g 5.689 0.311597 0.10789 2.27E-4 0.0 ENSG00000009765 ENST00000229447;ENST00000344419;ENST00000392256;ENST00000392255;ENST00000500320;ENST00000425615 T;T;T;T;T;T 0.76578 -1.03;-1.03;-1.03;-1.03;-1.03;-1.03 6.17 2.1 0.27182 Nitroreductase-like (3); 0.509560 0.22264 N 0.062376 T 0.43055 0.1230 L 0.46885 1.475 0.09310 N 1 B;B;B;B 0.20261 0.004;0.043;0.001;0.002 B;B;B;B 0.18561 0.003;0.022;0.001;0.005 T 0.24548 -1.0157 10 0.27785 T 0.31 -23.7178 1.2452 0.01971 0.2372:0.2256:0.3896:0.1475 . 121;203;203;203 Q2VPV9;C9JFW2;Q6PHW0-3;Q6PHW0 .;.;.;IYD1_HUMAN T 203;203;203;203;203;148 ENSP00000229447:A203T;ENSP00000343763:A203T;ENSP00000376085:A203T;ENSP00000376084:A203T;ENSP00000441276:A203T;ENSP00000390081:A148T ENSP00000229447:A203T A + 1 0 IYD 150757004 0.019000 0.18553 0.001000 0.08648 0.174000 0.22865 0.255000 0.18333 0.496000 0.27904 -0.119000 0.15052 GCA TCGA-LB-A8F3-01A-11D-A36O-08 IYD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043754.3 0 0 0 8 572 0 127 0 0 0 1 0 127 2 0 0 0 0 0 2 1 0.988910 8 565 0 126 2 0 0 0 0 0 0 -1.969494 0 1 121412 3 38 1 2 2 4 2.129274 1 0.330000 3.010000 0.461501 0.110000 4.000000e-02 1.000000 0.110000 0.279275 0.110000 0 7.000000e-02 1 HIST1H2BO 8348 broad.mit.edu 37 6 27861401 27861401 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr6:27861401G>A ENST00000303806.4 + 1 199 c.161G>A c.(160-162)gGc>gAc p.G54D HIST1H3J_ENST00000479986.1_5'Flank|HIST1H3J_ENST00000359303.2_5'Flank|HIST1H2AM_ENST00000359611.2_5'Flank NM_003527.4 NP_003518.2 P23527 H2B1O_HUMAN histone cluster 1, H2bo CCCGACACCGGCATCTCATCG 0.557000 0 SO:0001583 missense ENST00000303806.4 0 1 hg19 CCDS4640.1 . . . . . . . . . . G 19.99 3.928991 0.73327 . . ENSG00000196331 ENST00000303806 T 0.69435 -0.4 3.55 3.55 0.40652 Histone-fold (2);Histone core (1); . . . . T 0.82240 0.4994 M 0.93150 3.385 0.51767 D 0.999939 D 0.61697 0.99 D 0.64595 0.927 D 0.87114 0.2187 9 0.87932 D 0 . 14.9186 0.70818 0.0:0.0:1.0:0.0 . 54 P23527 H2B1O_HUMAN D 54 ENSP00000303408:G54D ENSP00000303408:G54D G + 2 0 HIST1H2BO 27969380 1.000000 0.71417 1.000000 0.80357 0.528000 0.34623 7.022000 0.76431 2.275000 0.75901 0.561000 0.74099 GGC TCGA-LB-A8F3-01A-11D-A36O-08 HIST1H2BO-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040161.1 0 0 0 6 791 0 249 0 0 0 0 249 2 0 0 0 0 0 2 1 0.963366 6 779 0 247 2 0 0 0 0 0 0 -1.757050 0 1 0 0 1 2 2 4 2.129274 1 0.330000 3.010000 0.461501 0.060000 1.000000e-02 1.000000 0.070000 0.237457 0.060000 0 3.000000e-02 1 LRRN3 54674 broad.mit.edu 37 7 110763403 110763403 + Missense_Mutation SNP T T C TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr7:110763403T>C ENST00000422987.3 + 2 1406 c.575T>C c.(574-576)aTt>aCt p.I192T IMMP2L_ENST00000331762.3_Intron|LRRN3_ENST00000308478.5_Missense_Mutation_p.I192T|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000405709.2_Intron|LRRN3_ENST00000451085.1_Missense_Mutation_p.I192T|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000415362.1_Intron NM_018334.4 NP_060804.3 Q9H3W5 LRRN3_HUMAN leucine rich repeat neuronal 3 55 AATCTAGAGATTCTGATGATT 0.373000 0 SO:0001583 missense ENST00000422987.3 1 1 hg19 CCDS5754.1 . . . . . . . . . . T 17.33 3.362159 0.61403 . . ENSG00000173114 ENST00000308478;ENST00000451085;ENST00000422987;ENST00000421101 T;T;T;T 0.23348 1.91;1.91;1.91;4.37 5.94 5.94 0.96194 . 0.000000 0.64402 D 0.000013 T 0.35653 0.0939 L 0.55017 1.72 0.58432 D 0.999999 D 0.56968 0.978 P 0.51974 0.686 T 0.05666 -1.0871 10 0.15499 T 0.54 . 16.4075 0.83691 0.0:0.0:0.0:1.0 . 192 Q9H3W5 LRRN3_HUMAN T 192 ENSP00000312001:I192T;ENSP00000397312:I192T;ENSP00000412417:I192T;ENSP00000407927:I192T ENSP00000312001:I192T I + 2 0 LRRN3 110550639 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 8.040000 0.89188 2.275000 0.75901 0.528000 0.53228 ATT TCGA-LB-A8F3-01A-11D-A36O-08 LRRN3-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000338171.2 1 0 1 60 304 0 116 0 0 0 0 116 2 0 0 0 0 0 2 1 1.000000 57 301 0 116 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.729580 0 0.330000 3.010000 0.334393 0.990000 7.800000e-01 1.000000 1.000000 0.959597 0.990000 1 8.900000e-01 1 OR2A7 401427 broad.mit.edu 37 7 143956698 143956698 + Silent SNP G G T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr7:143956698G>T ENST00000493325.1 - 1 117 c.24C>A c.(22-24)atC>atA p.I8I OR2A1-AS1_ENST00000487102.1_RNA|OR2A1-AS1_ENST00000489488.1_RNA|OR2A1-AS1_ENST00000463561.1_RNA|RP4-545C24.1_ENST00000460955.1_RNA|OR2A1-AS1_ENST00000461843.1_RNA|ARHGEF35_ENST00000543357.1_Intron|OR2A1-AS1_ENST00000478806.1_RNA|OR2A1-AS1_ENST00000476560.1_RNA NM_001005328.1 NP_001005328.1 Q96R45 OR2A7_HUMAN olfactory receptor, family 2, subfamily A, member 7 6 Melanoma(164;0.14) GGAACTCTGTGATGGATGTTA 0.448000 0 SO:0001819 synonymous_variant ENST00000493325.1 1 1 hg19 CCDS55177.1 TCGA-LB-A8F3-01A-11D-A36O-08 OR2A7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000349979.1 1 0 0 60 440 0 127 0 1.497786e-02 1 1 0 127 2 0 0 0 0 0 2 1 1.000000 57 435 0 126 2 0 0 0 0 0 0 -19.996180 1 1 0 0 1 0.330000 3.010000 0 0 WBSCR28 135886 broad.mit.edu 37 7 73279489 73279489 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr7:73279489G>A ENST00000320531.2 + 2 275 c.239G>A c.(238-240)gGg>gAg p.G80E NM_182504.3 NP_872310.2 Q6UE05 WBS28_HUMAN Williams-Beuren syndrome chromosome region 28 11 Lung NSC(55;0.159) CTCTGGGCTGGGCTGGCTCTG 0.697000 0 SO:0001583 missense ENST00000320531.2 1 1 hg19 CCDS43597.1 . . . . . . . . . . G 15.17 2.755009 0.49362 . . ENSG00000175877 ENST00000320531 T 0.36699 1.24 4.63 2.63 0.31362 . 0.340255 0.21598 N 0.071982 T 0.45458 0.1343 L 0.36672 1.1 0.09310 N 1 D 0.76494 0.999 D 0.72075 0.976 T 0.16600 -1.0397 10 0.87932 D 0 -14.5081 9.5408 0.39251 0.0:0.0:0.622:0.378 . 80 Q6UE05 WBS28_HUMAN E 80 ENSP00000316775:G80E ENSP00000316775:G80E G + 2 0 WBSCR28 72917425 0.201000 0.23410 0.191000 0.23289 0.093000 0.18481 1.085000 0.30840 1.121000 0.41925 0.650000 0.86243 GGG TCGA-LB-A8F3-01A-11D-A36O-08 WBSCR28-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000348130.1 1 0 1 58 459 0 176 0 0 0 0 176 2 0 0 0 0 0 2 1 1.000000 57 447 0 176 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 3 4 2.213029 1 0.330000 3.010000 0.478112 0.890000 6.700000e-01 1.000000 1.000000 0.887982 0.890000 1 7.700000e-01 1 SAMD12 401474 broad.mit.edu 37 8 119391680 119391680 + Silent SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr8:119391680G>A ENST00000314727.4 - 4 718 c.582C>T c.(580-582)atC>atT p.I194I AC023590.1_ENST00000430457.1_Intron|SAMD12_ENST00000527515.1_Intron|SAMD12_ENST00000409003.4_Intron NM_207506.2 NP_997389.2 Q8N8I0 SAM12_HUMAN sterile alpha motif domain containing 12 9 all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249) STAD - Stomach adenocarcinoma(47;0.00391) TATTTTCTATGATGGAAATTC 0.368000 0 SO:0001819 synonymous_variant ENST00000314727.4 0 1 hg19 CCDS6325.1 TCGA-LB-A8F3-01A-11D-A36O-08 SAMD12-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000132989.3 0 0 0 5 234 0 78 0 0 0 0 78 2 0 0 0 0 0 2 1 0.936107 5 231 0 78 2 0 0 0 0 0 0 -3.289897 1 1 0 0 1 0 2 2 1.737975 1 0.330000 3.010000 0.330000 0.140000 5.000000e-02 1.000000 0.120000 0.238232 0.140000 0 8.000000e-02 2.500000e-01 ADAM2 2515 broad.mit.edu 37 8 39626997 39626997 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr8:39626997G>A ENST00000265708.4 - 12 1229 c.1126C>T c.(1126-1128)Cgc>Tgc p.R376C ADAM2_ENST00000379853.2_Missense_Mutation_p.R250C|ADAM2_ENST00000347580.4_Missense_Mutation_p.R357C|ADAM2_ENST00000521880.1_Missense_Mutation_p.R376C NM_001464.3 NP_001455.3 Q99965 ADAM2_HUMAN ADAM metallopeptidase domain 2 53 all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246) LUSC - Lung squamous cell carcinoma(45;0.000149) GGATCTAAGCGAGGCTGATTG 0.433000 0 SO:0001583 missense ENST00000265708.4 1 1 hg19 CCDS34884.1 . . . . . . . . . . G 13.10 2.134834 0.37728 . . ENSG00000104755 ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880 T;T;T;T 0.02258 4.99;4.37;5.23;5.19 5.11 3.29 0.37713 Metallopeptidase, catalytic domain (1); . . . . T 0.08044 0.0201 M 0.81802 2.56 0.09310 N 0.999999 P;D;D;P 0.69078 0.955;0.997;0.973;0.955 P;P;P;P 0.55667 0.608;0.649;0.781;0.608 T 0.18241 -1.0343 8 . . . . 6.5366 0.22357 0.0932:0.0:0.7281:0.1787 . 376;250;357;376 B4DWY7;Q6P2G0;Q99965-2;Q99965 .;.;.;ADAM2_HUMAN C 357;250;376;376 ENSP00000343854:R357C;ENSP00000369182:R250C;ENSP00000265708:R376C;ENSP00000429352:R376C . R - 1 0 ADAM2 39746154 0.001000 0.12720 0.048000 0.18961 0.292000 0.27327 0.361000 0.20267 0.635000 0.30488 0.650000 0.86243 CGC TCGA-LB-A8F3-01A-11D-A36O-08 ADAM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376926.1 1 0 0 11 215 0 62 0 0 0 0 62 2 0 0 0 0 0 2 1 0.998417 11 214 0 62 2 0 0 0 0 0 0 -2.939794 1 1 0 0 1 0 2 2 1.737975 1 0.330000 3.010000 0.330000 0.310000 1.600000e-01 1.000000 0.300000 0.387395 0.310000 0 2.200000e-01 4.600000e-01 MUSK 4593 broad.mit.edu 37 9 113547892 113547892 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr9:113547892C>T ENST00000374448.4 + 13 1806 c.1672C>T c.(1672-1674)Ccg>Tcg p.P558S MUSK_ENST00000416899.2_Missense_Mutation_p.P550S|MUSK_ENST00000189978.5_Missense_Mutation_p.P558S|MUSK_ENST00000374438.1_Missense_Mutation_p.P74S NM_001166281.1|NM_005592.3 NP_001159753.1|NP_005583.1 O15146 MUSK_HUMAN muscle, skeletal, receptor tyrosine kinase 49 CCAGAGGATGCCGCTCCTTCT 0.498000 0 SO:0001583 missense ENST00000374448.4 0 1 hg19 CCDS48005.1 . . . . . . . . . . C 21.0 4.084498 0.76642 . . ENSG00000030304 ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000374441;ENST00000416899;ENST00000374438 T;D 0.88664 -0.83;-2.41 5.86 5.86 0.93980 . 0.000000 0.85682 D 0.000000 D 0.92394 0.7586 L 0.45228 1.405 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.90595 0.4540 10 0.33940 T 0.23 . 19.1684 0.93567 0.0:1.0:0.0:0.0 . 558 O15146 MUSK_HUMAN S 564;558;558;472;472;74;556;74 ENSP00000363571:P558S;ENSP00000363561:P74S ENSP00000189978:P564S P + 1 0 MUSK 112587713 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.487000 0.81328 2.777000 0.95525 0.655000 0.94253 CCG TCGA-LB-A8F3-01A-11D-A36O-08 MUSK-202 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding 0 0 0 6 856 0 246 0 0 0 0 246 2 0 0 0 0 0 2 1 0.963081 6 841 0 245 2 0 0 0 0 0 0 -1.858213 0 1 0 0 1 1 2 3 1.943401 0 0.330000 3.010000 0.409848 0.050000 0 1.000000 0.060000 0.186542 0.050000 0 2.000000e-02 1.100000e-01 ANAPC2 29882 broad.mit.edu 37 9 140082360 140082360 + Missense_Mutation SNP G G C TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr9:140082360G>C ENST00000323927.2 - 2 317 c.313C>G c.(313-315)Ccc>Gcc p.P105A SSNA1_ENST00000322310.5_5'Flank NM_013366.3 NP_037498.1 Q9UJX6 ANC2_HUMAN anaphase promoting complex subunit 2 15 all_cancers(76;0.0926) STAD - Stomach adenocarcinoma(284;0.0698) AGGCACTGGGGCTCATCCGCA 0.582000 0 SO:0001583 missense ENST00000323927.2 1 1 hg19 CCDS7033.1 . . . . . . . . . . G 10.80 1.452889 0.26161 . . ENSG00000176248 ENST00000323927 T 0.70399 -0.48 5.09 5.09 0.68999 . 0.187678 0.48767 D 0.000169 T 0.57007 0.2024 L 0.40543 1.245 0.31326 N 0.685481 B 0.06786 0.001 B 0.04013 0.001 T 0.52003 -0.8633 10 0.07482 T 0.82 -30.4898 11.8137 0.52197 0.0:0.1774:0.8226:0.0 . 105 Q9UJX6 ANC2_HUMAN A 105 ENSP00000314004:P105A ENSP00000314004:P105A P - 1 0 ANAPC2 139202181 1.000000 0.71417 0.983000 0.44433 0.770000 0.43624 2.929000 0.48916 2.365000 0.80145 0.561000 0.74099 CCC TCGA-LB-A8F3-01A-11D-A36O-08 ANAPC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055315.1 1 0 1 30 192 0 80 1 9.351292e-01 9 23 0 80 2 0 0 0 0 0 2 1 1.000000 29 190 0 80 2 0 0 0 0 0 0 -14.950100 1 1 0 0 1 1 2 3 1.955606 0 0.330000 3.010000 0.406397 0.960000 6.500000e-01 1.000000 1.000000 0.918259 0.960000 1 7.900000e-01 1 VLDLR 7436 broad.mit.edu 37 9 2641436 2641436 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr9:2641436C>T ENST00000382100.3 + 4 741 c.385C>T c.(385-387)Cca>Tca p.P129S RP11-125B21.2_ENST00000599229.1_RNA|VLDLR_ENST00000382099.2_Missense_Mutation_p.P129S NM_003383.3 NP_003374.3 P98155 VLDLR_HUMAN very low density lipoprotein receptor 24 TCAGTGTATCCCAGTGTCCTG 0.433000 0 SO:0001583 missense ENST00000382100.3 0 1 hg19 CCDS6446.1 . . . . . . . . . . C 18.54 3.645424 0.67358 . . ENSG00000147852 ENST00000382100;ENST00000382099 D;D 0.95554 -3.74;-3.74 6.07 6.07 0.98685 Low-density lipoprotein (LDL) receptor class A, conserved site (1); 0.000000 0.52532 D 0.000066 D 0.96648 0.8906 L 0.50919 1.6 0.80722 D 1 B;B 0.33694 0.421;0.148 B;P 0.51055 0.429;0.657 D 0.95111 0.8238 10 0.49607 T 0.09 . 20.6439 0.99570 0.0:1.0:0.0:0.0 . 129;129 Q5VVF5;P98155 .;VLDLR_HUMAN S 129 ENSP00000371532:P129S;ENSP00000371531:P129S ENSP00000371531:P129S P + 1 0 VLDLR 2631436 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.635000 0.61332 2.884000 0.98904 0.655000 0.94253 CCA TCGA-LB-A8F3-01A-11D-A36O-08 VLDLR-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000051519.2 0 0 0 6 339 0 117 0 1.171486e-02 0 8 0 117 2 0 0 0 0 0 2 1 0.964364 6 336 0 116 2 0 0 0 0 0 0 -2.544284 1 1 0 0 1 0 2 2 1.718977 1 0.330000 3.010000 0.330000 0.110000 4.000000e-02 1.000000 0.100000 0.225867 0.110000 0 7.000000e-02 2.100000e-01 PRKACG 5568 broad.mit.edu 37 9 71628843 71628843 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chr9:71628843C>T ENST00000377276.2 - 1 196 c.166G>A c.(166-168)Ggg>Agg p.G56R NM_002732.3 NP_002723.2 P22612 KAPCG_HUMAN protein kinase, cAMP-dependent, catalytic, gamma 22 ATCACCCGCCCGAAGGAGCCC 0.592000 Esophageal Squamous(110;2236 2623 32146) 0 SO:0001583 missense ENST00000377276.2 0 1 hg19 CCDS6625.1 . . . . . . . . . . C 15.59 2.877235 0.51801 . . ENSG00000165059 ENST00000377276 T 0.80738 -1.41 1.32 1.32 0.21799 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.31531 U 0.007486 D 0.92120 0.7502 H 0.98682 4.3 0.36255 D 0.854184 D 0.89917 1.0 D 0.87578 0.998 D 0.92260 0.5816 10 0.87932 D 0 . 8.1306 0.31024 0.0:1.0:0.0:0.0 . 56 P22612 KAPCG_HUMAN R 56 ENSP00000366488:G56R ENSP00000366488:G56R G - 1 0 PRKACG 70818663 0.004000 0.15560 0.002000 0.10522 0.002000 0.02628 1.488000 0.35551 0.687000 0.31509 0.563000 0.77884 GGG TCGA-LB-A8F3-01A-11D-A36O-08 PRKACG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052559.1 0 0 0 7 269 0 105 0 0 0 0 105 2 0 0 0 0 0 2 1 0.979684 7 264 0 102 2 0 0 0 0 0 0 -2.935363 1 1 0 0 1 0 2 2 1.712697 1 0.330000 3.010000 0.330000 0.170000 7.000000e-02 1.000000 0.160000 0.265395 0.170000 0 1.100000e-01 2.800000e-01 STAG2 10735 broad.mit.edu 37 X 123176477 123176477 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chrX:123176477G>A ENST00000371160.1 + 7 734 c.444G>A c.(442-444)atG>atA p.M148I STAG2_ENST00000354548.5_Missense_Mutation_p.M79I|STAG2_ENST00000371157.3_Missense_Mutation_p.M148I|STAG2_ENST00000218089.9_Missense_Mutation_p.M148I|STAG2_ENST00000371145.3_Missense_Mutation_p.M148I|STAG2_ENST00000371144.3_Missense_Mutation_p.M148I|STAG2_ENST00000469481.1_Intron NM_001282418.1 NP_001269347.1 Q8N3U4 STAG2_HUMAN stromal antigen 2 78 TTCGAAAAATGACTGAAGAAT 0.299000 0 SO:0001583 missense ENST00000371160.1 1 1 hg19 CCDS14607.1 . . . . . . . . . . G 22.3 4.274155 0.80580 . . ENSG00000101972 ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000435103;ENST00000371157;ENST00000371145;ENST00000371144;ENST00000428941;ENST00000435215 T;T;T;T;T;T;T 0.42900 1.9;0.96;1.52;1.51;1.51;1.9;1.51 5.74 4.86 0.63082 . 0.077879 0.85682 D 0.000000 T 0.60958 0.2309 M 0.83603 2.65 0.80722 D 1 D;P 0.55172 0.97;0.884 P;P 0.56700 0.804;0.54 T 0.62817 -0.6774 10 0.29301 T 0.29 -15.651 15.262 0.73631 0.0:0.0:0.8586:0.1414 . 148;148 Q8N3U4-2;Q8N3U4 .;STAG2_HUMAN I 148;148;79;148;148;148;148;148;148;148 ENSP00000218089:M148I;ENSP00000397265:M148I;ENSP00000346555:M79I;ENSP00000360202:M148I;ENSP00000360199:M148I;ENSP00000360187:M148I;ENSP00000360186:M148I ENSP00000218089:M148I M + 3 0 STAG2 123004158 1.000000 0.71417 1.000000 0.80357 0.948000 0.59901 9.740000 0.98839 1.172000 0.42781 0.522000 0.50473 ATG TCGA-LB-A8F3-01A-11D-A36O-08 STAG2-018 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000156159.2 1 0 0 25 344 0 111 0 1.290434e-01 0 9 0 111 2 0 0 0 0 0 2 1 1.000000 25 339 0 111 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 0.330000 3.010000 0.330000 0.410000 2.700000e-01 0.580000 0.410000 0.422390 0.410000 0 3.300000e-01 5.000000e-01 CXorf23 256643 broad.mit.edu 37 X 19955570 19955570 + Nonsense_Mutation SNP G G T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chrX:19955570G>T ENST00000379682.4 - 8 1859 c.1826C>A c.(1825-1827)tCa>tAa p.S609* CXorf23_ENST00000379687.3_Intron|CXorf23_ENST00000356980.3_Intron A2AJT9 CX023_HUMAN chromosome X open reading frame 23 11 TCTAAAATTTGATTTTATAAA 0.289000 0 SO:0001587 stop_gained ENST00000379682.4 0 1 hg19 . . . . . . . . . . G 19.99 3.928330 0.73327 . . ENSG00000173681 ENST00000379682 . . . 5.49 5.49 0.81192 . . . . . . . . . . . 0.43480 D 0.995702 . . . . . . . . . . . . . . 10.6845 0.45835 0.0912:0.0:0.9088:0.0 . . . . X 609 . . S - 2 0 CXorf23 19865491 0.998000 0.40836 0.587000 0.28692 0.095000 0.18619 4.275000 0.58927 2.293000 0.77203 0.538000 0.68166 TCA TCGA-LB-A8F3-01A-11D-A36O-08 CXorf23-006 NOVEL basic protein_coding protein_coding OTTHUMT00000055991.2 0 0 1 28 190 0 48 0 1.789387e-02 0 2 0 48 2 0 0 0 0 0 2 1 1.000000 28 189 0 48 2 0 0 0 0 0 0 -13.818080 1 1 0 0 1 0 1 1 0.330000 3.010000 0.330000 0.770000 5.300000e-01 1.000000 1.000000 0.786483 0.770000 0 6.400000e-01 9.200000e-01 ZNF645 158506 broad.mit.edu 37 X 22292216 22292216 + Missense_Mutation SNP G G A TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chrX:22292216G>A ENST00000323684.1 + 1 1152 c.1108G>A c.(1108-1110)Gaa>Aaa p.E370K NM_152577.3 NP_689790.1 Q8N7E2 ZN645_HUMAN zinc finger protein 645 27 TCAGTTCACCGAAAATCAAGA 0.448000 0 SO:0001583 missense ENST00000323684.1 1 1 hg19 CCDS14205.1 . . . . . . . . . . G 12.38 1.921190 0.33908 . . ENSG00000175809 ENST00000323684 T 0.44881 0.91 2.9 2.03 0.26663 . 0.187414 0.44902 U 0.000420 T 0.44787 0.1310 L 0.50333 1.59 0.24531 N 0.994111 D 0.61080 0.989 P 0.54856 0.762 T 0.23547 -1.0185 10 0.46703 T 0.11 . 7.378 0.26839 0.143:0.0:0.857:0.0 . 370 Q8N7E2 ZN645_HUMAN K 370 ENSP00000323348:E370K ENSP00000323348:E370K E + 1 0 ZNF645 22202137 0.998000 0.40836 0.003000 0.11579 0.002000 0.02628 1.969000 0.40510 0.622000 0.30249 -0.191000 0.12829 GAA TCGA-LB-A8F3-01A-11D-A36O-08 ZNF645-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056037.1 1 0 0 32 406 0 127 0 0 0 0 127 2 0 0 0 0 0 2 1 1.000000 31 401 0 126 2 0 0 0 0 0 0 -3.318785 1 1 0 0 1 0 1 1 0.330000 3.010000 0.330000 0.440000 3.000000e-01 0.600000 0.440000 0.452432 0.440000 0 3.700000e-01 5.300000e-01 KIF4A 24137 broad.mit.edu 37 X 69607059 69607059 + Missense_Mutation SNP A A G TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chrX:69607059A>G ENST00000374403.3 + 20 2226 c.2144A>G c.(2143-2145)aAg>aGg p.K715R KIF4A_ENST00000374388.3_Missense_Mutation_p.K715R NM_012310.4 NP_036442.3 O95239 KIF4A_HUMAN kinesin family member 4A 51 AAGCGTCTCAAGGATGCTCTC 0.423000 0 SO:0001583 missense ENST00000374403.3 1 1 hg19 CCDS14401.1 . . . . . . . . . . A 14.78 2.637444 0.47049 . . ENSG00000090889 ENST00000374388;ENST00000374403;ENST00000544650 T;T 0.71461 2.54;-0.57 4.6 2.26 0.28386 . 0.203530 0.34460 N 0.003950 T 0.61048 0.2316 L 0.55990 1.75 0.54753 D 0.999982 B 0.19935 0.04 B 0.16722 0.016 T 0.56306 -0.8001 10 0.41790 T 0.15 . 7.6175 0.28167 0.803:0.0:0.197:0.0 . 715 O95239 KIF4A_HUMAN R 715;715;17 ENSP00000363509:K715R;ENSP00000363524:K715R ENSP00000363509:K715R K + 2 0 KIF4A 69523784 1.000000 0.71417 1.000000 0.80357 0.970000 0.65996 3.459000 0.53021 0.707000 0.31934 0.381000 0.24937 AAG TCGA-LB-A8F3-01A-11D-A36O-08 KIF4A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057068.1 1 0 1 12 36 0 11 0 7.137255e-02 1 1 0 11 2 0 0 0 0 0 2 1 0.999525 12 36 0 11 2 0 0 0 0 0 0 -19.999980 1 1 0 0 1 0 1 1 0.330000 3.010000 0.330000 0.990000 8.500000e-01 1.000000 1.000000 0.991401 0.990000 1 9.900000e-01 1 PCDH19 57526 broad.mit.edu 37 X 99662436 99662436 + Missense_Mutation SNP C C T TCGA-LB-A8F3-01A-11D-A36O-08 TCGA-LB-A8F3-10A-01D-A367-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5d875181-2048-4fa9-9dda-6fd59784c583 2bbbc64a-f365-4fcb-8de2-b6ca00f3cb4a g.chrX:99662436C>T ENST00000373034.4 - 1 2835 c.1160G>A c.(1159-1161)cGt>cAt p.R387H PCDH19_ENST00000420881.2_Missense_Mutation_p.R387H|PCDH19_ENST00000255531.7_Missense_Mutation_p.R387H NM_001184880.1 NP_001171809.1 Q8TAB3 PCD19_HUMAN protocadherin 19 68 GCCCAGCAAACGGCACTGCAC 0.607000 0 SO:0001583 missense ENST00000373034.4 1 1 hg19 CCDS55462.1 . . . . . . . . . . C 16.77 3.215554 0.58452 . . ENSG00000165194 ENST00000420881;ENST00000373034;ENST00000255531 T;T;T 0.53640 0.61;0.61;0.61 5.95 5.95 0.96441 Cadherin (4);Cadherin-like (1); 0.045907 0.85682 D 0.000000 T 0.53546 0.1803 L 0.39514 1.22 0.49389 D 0.99978 D;D;D 0.76494 0.999;0.999;0.999 D;D;D 0.71414 0.937;0.955;0.973 T 0.52983 -0.8502 10 0.32370 T 0.25 . 6.888 0.24214 0.0:0.7732:0.0:0.2268 . 387;387;387 Q8TAB3;Q8TAB3-2;E9PAM6 PCD19_HUMAN;.;. H 387 ENSP00000400327:R387H;ENSP00000362125:R387H;ENSP00000255531:R387H ENSP00000255531:R387H R - 2 0 PCDH19 99549092 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 3.536000 0.53582 2.498000 0.84270 0.513000 0.50165 CGT TCGA-LB-A8F3-01A-11D-A36O-08 PCDH19-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000057479.2 1 0 0 41 350 0 102 0 0 0 0 102 2 0 0 0 0 0 2 1 1.000000 41 347 0 100 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 0.330000 3.010000 0.330000 0.630000 4.600000e-01 0.820000 0.630000 0.644324 0.630000 0 5.400000e-01 7.300000e-01