#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
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	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_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	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
PCDH11X	27328	genome.wustl.edu	37	X	91133089	91133089	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chrX:91133089C>T	ENST00000373094.1	+	2	2695	c.1850C>T	c.(1849-1851)aCc>aTc	p.T617I	PCDH11X_ENST00000298274.8_Missense_Mutation_p.T617I|PCDH11X_ENST00000504220.2_Missense_Mutation_p.T617I|PCDH11X_ENST00000395337.2_Missense_Mutation_p.T617I|PCDH11X_ENST00000361655.2_Missense_Mutation_p.T617I|PCDH11X_ENST00000373097.1_Missense_Mutation_p.T617I|PCDH11X_ENST00000373088.1_Missense_Mutation_p.T617I|PCDH11X_ENST00000361724.1_Missense_Mutation_p.T617I|PCDH11X_ENST00000406881.1_Missense_Mutation_p.T617I	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	617	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						GATGACTTCACCATTGATTCA	0.388																																					NSCLC(38;925 1092 2571 38200 45895)	dbGAP											0			X											24.0	22.0	23.0					X																	91133089		2186	4263	6449	91019745	SO:0001583	missense	0			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"""Cadherins / Protocadherins : Non-clustered"""	8656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 119"""	300246	"""protocadherin 11"""	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.1850C>T	X.37:g.91133089C>T	ENSP00000362186:p.Thr617Ile	Somatic	15	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	91019745	9	74.36	29	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,HMMPfam_Protocadherin,superfamily_Cadherin-like	p.T617I	ENST00000373094.1	37	c.1850	CCDS14461.1	X	.	.	.	.	.	.	.	.	.	.	C	3.089	-0.187402	0.06299	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	5.35	4.36	0.52297	Cadherin (4);Cadherin-like (1);	0.050673	0.85682	D	0.000000	T	0.27731	0.0682	N	0.11845	0.185	0.30467	N	0.773675	B;B;B;B;B;B;B;B	0.09022	0.001;0.0;0.001;0.001;0.001;0.002;0.0;0.0	B;B;B;B;B;B;B;B	0.14023	0.006;0.004;0.006;0.006;0.006;0.01;0.006;0.006	T	0.08229	-1.0732	10	0.25106	T	0.35	.	3.3638	0.07196	0.0:0.6:0.0:0.4	.	617;617;617;617;617;617;617;617	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	I	617	ENSP00000378746:T617I;ENSP00000362186:T617I;ENSP00000362189:T617I;ENSP00000355040:T617I;ENSP00000362180:T617I;ENSP00000423762:T617I;ENSP00000355105:T617I;ENSP00000384758:T617I;ENSP00000298274:T617I	ENSP00000298274:T617I	T	+	2	0	PCDH11X	91019745	1.000000	0.71417	0.997000	0.53966	0.295000	0.27426	3.853000	0.55941	2.212000	0.71576	0.415000	0.27848	ACC	-	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like		0.388	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PCDH11X	protein_coding	OTTHUMT00000057436.1	C	NM_032969		91019745	+1	no_errors	NM_032968.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
TTN	7273	genome.wustl.edu	37	2	179606055	179606055	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr2:179606055C>T	ENST00000591111.1	-	46	11178	c.10954G>A	c.(10954-10956)Gtt>Att	p.V3652I	TTN_ENST00000359218.5_Missense_Mutation_p.V3731I|TTN_ENST00000460472.2_Missense_Mutation_p.V3606I|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V3969I|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V3798I			Q8WZ42	TITIN_HUMAN	titin	13958	Ig-like 22.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AACCATGTAACAGTAGGGGCA	0.443																																						dbGAP											0			2											126.0	122.0	123.0					2																	179606055		1923	4132	6055	179314300	SO:0001583	missense	0			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10954G>A	2.37:g.179606055C>T	ENSP00000465570:p.Val3652Ile	Somatic	102	1.92	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	179314300	143	42.00	105	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	PatternScan_IG_MHC,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_I-set,HMMPfam_ig,HMMPfam_Titin_Z,PatternScan_FGGY_KINASES_1	p.V3800I	ENST00000591111.1	37	c.11398		2	.	.	.	.	.	.	.	.	.	.	C	12.10	1.835896	0.32421	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.72282	-0.64;-0.64;-0.64	5.87	2.53	0.30540	.	.	.	.	.	T	0.59004	0.2162	L	0.35593	1.075	0.22081	N	0.999375	B;B;B	0.12630	0.006;0.006;0.006	B;B;B	0.14023	0.01;0.01;0.01	T	0.54781	-0.8242	9	0.87932	D	0	.	9.2993	0.37835	0.0:0.6071:0.0:0.3929	.	3606;3731;3798	D3DPF9;E7EQE6;E7ET18	.;.;.	I	3606;3798;3731;3606	ENSP00000434586:V3606I;ENSP00000340554:V3798I;ENSP00000352154:V3731I	ENSP00000340554:V3798I	V	-	1	0	TTN	179314300	0.117000	0.22190	0.925000	0.36789	0.868000	0.49771	0.540000	0.23191	0.869000	0.35703	-0.150000	0.13652	GTT	-	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set		0.443	TTN-019	PUTATIVE	basic	protein_coding	TTN	protein_coding	OTTHUMT00000460310.1	C	NM_133378		179314300	-1	no_stop_codon	ENST00000286104	ensembl	human	known	54_36p	missense	SNP	0.951	T
DCHS2	54798	genome.wustl.edu	37	4	155156598	155156598	+	Missense_Mutation	SNP	G	G	A	rs149548848	byFrequency	TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr4:155156598G>A	ENST00000357232.4	-	25	7840	c.7841C>T	c.(7840-7842)cCg>cTg	p.P2614L		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2614					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CAACCATTCCGGAGTGGCATC	0.488													G|||	5	0.000998403	0.0	0.0029	5008	,	,		19330	0.0		0.003	False		,,,				2504	0.0					dbGAP											0			4						G	LEU/PRO	0,4406		0,0,2203	122.0	121.0	121.0		7841	5.8	0.5	4	dbSNP_134	121	12,8588	9.1+/-34.3	0,12,4288	yes	missense	DCHS2	NM_017639.3	98	0,12,6491	AA,AG,GG		0.1395,0.0,0.0923	possibly-damaging	2614/2917	155156598	12,12994	2203	4300	6503	155376048	SO:0001583	missense	0			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.7841C>T	4.37:g.155156598G>A	ENSP00000349768:p.Pro2614Leu	Somatic	117	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	155376048	103	40.23	70	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like	p.P2614L	ENST00000357232.4	37	c.7841	CCDS3785.1	4	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	9.936	1.216217	0.22373	0.0	0.001395	ENSG00000197410	ENST00000357232	T	0.55930	0.49	5.82	5.82	0.92795	.	0.166857	0.42053	D	0.000766	T	0.53753	0.1816	M	0.63843	1.955	0.80722	D	1	B	0.26258	0.145	B	0.21151	0.033	T	0.48293	-0.9048	10	0.36615	T	0.2	.	20.0951	0.97834	0.0:0.0:1.0:0.0	.	2614	Q6V1P9	PCD23_HUMAN	L	2614	ENSP00000349768:P2614L	ENSP00000349768:P2614L	P	-	2	0	DCHS2	155376048	0.168000	0.22989	0.478000	0.27316	0.025000	0.11179	2.923000	0.48868	2.753000	0.94483	0.467000	0.42956	CCG	-	NULL		0.488	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DCHS2	protein_coding	OTTHUMT00000365281.2	G	NM_001142552		155376048	-1	no_errors	NM_017639.1	genbank	human	validated	54_36p	missense	SNP	0.038	A
NMUR2	56923	genome.wustl.edu	37	5	151784257	151784257	+	Missense_Mutation	SNP	C	C	T	rs200145877		TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr5:151784257C>T	ENST00000255262.3	-	1	583	c.418G>A	c.(418-420)Gtc>Atc	p.V140I	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	140					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			TCCACGCTGACGGTGGTGATG	0.642																																						dbGAP											0			5											60.0	64.0	63.0					5																	151784257		2203	4300	6503	151764450	SO:0001583	missense	0			AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"""GPCR / Class A : Neuromedin U receptors"""	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.418G>A	5.37:g.151784257C>T	ENSP00000255262:p.Val140Ile	Somatic	18	5.26	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	151764450	70	48.15	65	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like	p.V140I	ENST00000255262.3	37	c.418	CCDS4321.1	5	.	.	.	.	.	.	.	.	.	.	C	11.54	1.669807	0.29693	.	.	ENSG00000132911	ENST00000255262	T	0.60299	0.2	5.45	2.59	0.31030	GPCR, rhodopsin-like superfamily (1);	0.174283	0.39210	N	0.001439	T	0.41119	0.1145	N	0.10760	0.04	0.23293	N	0.997962	P	0.51653	0.947	P	0.45998	0.5	T	0.37957	-0.9683	10	0.54805	T	0.06	-18.0088	12.8575	0.57894	0.0:0.6219:0.3138:0.0643	.	140	Q9GZQ4	NMUR2_HUMAN	I	140	ENSP00000255262:V140I	ENSP00000255262:V140I	V	-	1	0	NMUR2	151764450	0.373000	0.25073	0.115000	0.21578	0.267000	0.26476	1.573000	0.36472	0.004000	0.14682	-0.797000	0.03246	GTC	-	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like		0.642	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NMUR2	protein_coding	OTTHUMT00000252439.1	C	NM_020167		151764450	-1	no_errors	NM_020167.4	genbank	human	reviewed	54_36p	missense	SNP	0.391	T
SPDEF	25803	genome.wustl.edu	37	6	34508852	34508852	+	Silent	SNP	C	C	T			TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr6:34508852C>T	ENST00000374037.3	-	3	957	c.543G>A	c.(541-543)aaG>aaA	p.K181K	SPDEF_ENST00000544425.1_Silent_p.K181K	NM_012391.2	NP_036523.1	O95238	SPDEF_HUMAN	SAM pointed domain containing ETS transcription factor	181	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				cell differentiation (GO:0030154)|intestinal epithelial cell development (GO:0060576)|lung goblet cell differentiation (GO:0060480)|multicellular organismal development (GO:0007275)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell fate commitment (GO:0010455)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)	15						CGCACAGCTCCTTGCCCGCCA	0.647																																						dbGAP											0			6											34.0	32.0	33.0					6																	34508852		2201	4300	6501	34616830	SO:0001819	synonymous_variant	0			AF071538	CCDS4794.1, CCDS59013.1	6p21.3	2013-08-07	2013-08-07		ENSG00000124664	ENSG00000124664			17257	protein-coding gene	gene with protein product		608144	"""SAM pointed domain containing ets transcription factor"""			10625666, 6857767	Standard	NM_012391		Approved	PDEF, bA375E1.3	uc003ojq.2	O95238	OTTHUMG00000014548	ENST00000374037.3:c.543G>A	6.37:g.34508852C>T		Somatic	6	0.00	0		0	0.00	0	WXS	Illumina HiSeq	Phase_IV	34616830	29	36.96	17	B4DWH8|F5H778	Silent	SNP	HMMPfam_Ets,HMMSmart_ETS,PatternScan_ETS_DOMAIN_1,PatternScan_ETS_DOMAIN_2,HMMPfam_SAM_PNT,HMMSmart_SAM_PNT,superfamily_SAM_homology,superfamily_SSF46785	p.K181	ENST00000374037.3	37	c.543	CCDS4794.1	6																																																																																			-	HMMPfam_SAM_PNT,HMMSmart_SAM_PNT,superfamily_SAM_homology		0.647	SPDEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPDEF	protein_coding	OTTHUMT00000040246.1	C	NM_012391		34616830	-1	no_errors	NM_012391.1	genbank	human	provisional	54_36p	silent	SNP	1.000	T
TJAP1	93643	genome.wustl.edu	37	6	43466819	43466819	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr6:43466819G>T	ENST00000372445.5	+	4	456	c.80G>T	c.(79-81)gGa>gTa	p.G27V	TJAP1_ENST00000259751.1_Missense_Mutation_p.G27V|TJAP1_ENST00000372449.1_Missense_Mutation_p.G27V|TJAP1_ENST00000372452.1_Missense_Mutation_p.G27V|TJAP1_ENST00000436109.2_Missense_Mutation_p.G27V|TJAP1_ENST00000438588.2_Missense_Mutation_p.G27V|TJAP1_ENST00000372444.2_Missense_Mutation_p.G27V|TJAP1_ENST00000483640.1_3'UTR	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	27					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			GAAATTCCTGGATCCCGGCTT	0.602																																						dbGAP											0			6											91.0	74.0	80.0					6																	43466819		2203	4300	6503	43574797	SO:0001583	missense	0			AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"""tight junction protein 4 (peripheral)"""	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.80G>T	6.37:g.43466819G>T	ENSP00000361522:p.Gly27Val	Somatic	51	0.00	0		11	56.00	14	WXS	Illumina HiSeq	Phase_IV	43574797	109	36.93	65	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Missense_Mutation	SNP	NULL	p.G27V	ENST00000372445.5	37	c.80	CCDS55004.1	6	.	.	.	.	.	.	.	.	.	.	G	6.122	0.390813	0.11581	.	.	ENSG00000137221	ENST00000372444;ENST00000372445;ENST00000436109;ENST00000442878;ENST00000259751;ENST00000372454;ENST00000372452;ENST00000372449;ENST00000438588	T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	5.31	2.21	0.28008	.	0.534276	0.18371	N	0.143248	T	0.09202	0.0227	N	0.15975	0.35	0.28496	N	0.914233	B;B;B	0.18166	0.001;0.026;0.006	B;B;B	0.17098	0.001;0.017;0.011	T	0.27191	-1.0081	10	0.21014	T	0.42	-9.4904	4.0602	0.09834	0.0945:0.2995:0.4617:0.1443	.	27;27;27	E2QRK7;Q5JTD0;Q5JTD0-2	.;TJAP1_HUMAN;.	V	27	ENSP00000361521:G27V;ENSP00000361522:G27V;ENSP00000407080:G27V;ENSP00000390981:G27V;ENSP00000259751:G27V;ENSP00000361530:G27V;ENSP00000361527:G27V;ENSP00000408769:G27V	ENSP00000259751:G27V	G	+	2	0	TJAP1	43574797	0.948000	0.32251	0.571000	0.28486	0.721000	0.41392	1.359000	0.34113	0.575000	0.29434	0.655000	0.94253	GGA	-	NULL		0.602	TJAP1-202	KNOWN	basic|CCDS	protein_coding	TJAP1	protein_coding	OTTHUMT00000040629.1	G	NM_080604		43574797	+1	no_errors	NM_080604.1	genbank	human	reviewed	54_36p	missense	SNP	0.026	T
SCAF8	22828	genome.wustl.edu	37	6	155153900	155153900	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr6:155153900C>A	ENST00000367178.3	+	20	3763	c.3187C>A	c.(3187-3189)Cct>Act	p.P1063T	TIAM2_ENST00000461783.3_5'UTR|SCAF8_ENST00000367186.4_Missense_Mutation_p.P1129T|SCAF8_ENST00000417268.1_Missense_Mutation_p.P1063T	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	1063	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						TTTTGGAAGACCTCCTGTAGA	0.502																																						dbGAP											0			6											50.0	52.0	51.0					6																	155153900		2203	4300	6503	155195592	SO:0001583	missense	0			AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"""RNA binding motif (RRM) containing"""	20959	protein-coding gene	gene with protein product			"""RNA binding motif protein 16"""	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.3187C>A	6.37:g.155153900C>A	ENSP00000356146:p.Pro1063Thr	Somatic	54	3.51	2		39	26.42	14	WXS	Illumina HiSeq	Phase_IV	155195592	134	48.88	131	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	HMMPfam_RRM_1,HMMSmart_RRM,HMMSmart_RPR,HMMPfam_DUF618,superfamily_ENTH_VHS,superfamily_SSF54928	p.P1063T	ENST00000367178.3	37	c.3187	CCDS5247.1	6	.	.	.	.	.	.	.	.	.	.	C	17.27	3.347102	0.61183	.	.	ENSG00000213079;ENSG00000213079;ENSG00000213079;ENSG00000146426	ENST00000367178;ENST00000417268;ENST00000367186;ENST00000528928	T;T;T	0.51071	0.75;0.75;0.72	5.46	5.46	0.80206	.	0.000000	0.64402	U	0.000001	T	0.53658	0.1810	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.976	D;D;P	0.85130	0.997;0.996;0.761	T	0.57717	-0.7763	10	0.66056	D	0.02	.	19.3175	0.94220	0.0:1.0:0.0:0.0	.	1108;1129;1063	B7Z876;B7Z888;Q9UPN6	.;.;SCAF8_HUMAN	T	1063;1063;1129;24	ENSP00000356146:P1063T;ENSP00000413098:P1063T;ENSP00000356154:P1129T	ENSP00000356146:P1063T	P	+	1	0	TIAM2;SCAF8	155195592	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.932000	0.56537	2.563000	0.86464	0.655000	0.94253	CCT	-	NULL		0.502	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RBM16	protein_coding	OTTHUMT00000042798.1	C	NM_014892		155195592	+1	no_errors	NM_014892.3	genbank	human	validated	54_36p	missense	SNP	1.000	A
LRRC4	64101	genome.wustl.edu	37	7	127669227	127669227	+	Silent	SNP	G	G	A			TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr7:127669227G>A	ENST00000249363.3	-	2	1724	c.1467C>T	c.(1465-1467)acC>acT	p.T489T	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	489	Thr-rich.				postsynaptic density protein 95 clustering (GO:0097119)|regulation of synapse organization (GO:0050807)|synapse organization (GO:0050808)	cell junction (GO:0030054)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26				Lung(243;0.124)		CCGTGGTAGAGGTGGTATATG	0.562																																						dbGAP											0			7											160.0	126.0	138.0					7																	127669227		2203	4300	6503	127456463	SO:0001819	synonymous_variant	0			AF196976	CCDS5799.1	7q31	2013-01-14	2003-11-19		ENSG00000128594	ENSG00000128594		"""Immunoglobulin superfamily / I-set domain containing"""	15586	protein-coding gene	gene with protein product		610486	"""leucine-rich repeat-containing 4"""			12969517	Standard	NM_022143		Approved	NAG14	uc003vmk.3	Q9HBW1	OTTHUMG00000157563	ENST00000249363.3:c.1467C>T	7.37:g.127669227G>A		Somatic	12	0.00	0		12	0.00	0	WXS	Illumina HiSeq	Phase_IV	127456463	69	15.85	13	A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	Silent	SNP	HMMPfam_LRRNT,HMMSmart_SM00013,HMMSmart_SM00082,HMMPfam_LRR_1,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin,superfamily_L domain-like	p.T489	ENST00000249363.3	37	c.1467	CCDS5799.1	7																																																																																			-	NULL		0.562	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRRC4	protein_coding	OTTHUMT00000349170.1	G	NM_022143		127456463	-1	no_errors	NM_022143.4	genbank	human	validated	54_36p	silent	SNP	1.000	A
DDX10P2	401533	genome.wustl.edu	37	9	84703415	84703415	+	IGR	SNP	C	C	T			TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr9:84703415C>T								SPATA31D1 (93244 upstream) : RP11-15B24.5 (184255 downstream)																							AGTTACCAAACGGTACTGAGC	0.388																																						dbGAP											0			9																																								83893235	SO:0001628	intergenic_variant	0																															9.37:g.84703415C>T		Somatic	74	0.00	0		3	0.00	0	WXS	Illumina HiSeq	Phase_IV	83893235	18	76.19	64		RNA	SNP	-	NULL		37	NULL		9																																																																																			-	-	0	0.388					LOC401533			C			83893235	-1	pseudogene	XR_016904.2	genbank	human	model	54_36p	rna	SNP	0.975	T
CTNNA3	29119	genome.wustl.edu	37	10	68040231	68040231	+	Silent	SNP	A	A	T			TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr10:68040231A>T	ENST00000433211.2	-	13	2055	c.1881T>A	c.(1879-1881)atT>atA	p.I627I	CTNNA3_ENST00000373744.4_Silent_p.I627I	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						AACTTACCCGAATCATCATGA	0.358																																						dbGAP											0			10											169.0	163.0	165.0					10																	68040231		2203	4299	6502	67710237	SO:0001819	synonymous_variant	0			AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.1881T>A	10.37:g.68040231A>T		Somatic	102	0.96	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	67710237	114	43.07	87		Silent	SNP	HMMPfam_Vinculin,superfamily_alpha-catenin/vinculin	p.I627	ENST00000433211.2	37	c.1881	CCDS7269.1	10																																																																																			-	HMMPfam_Vinculin		0.358	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CTNNA3	protein_coding	OTTHUMT00000048282.2	A	NM_013266		67710237	-1	no_errors	NM_013266.1	genbank	human	validated	54_36p	silent	SNP	1.000	T
DYRK4	8798	genome.wustl.edu	37	12	4705861	4705861	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr12:4705861C>T	ENST00000540757.2	+	6	686	c.526C>T	c.(526-528)Cgc>Tgc	p.R176C	DYRK4_ENST00000010132.5_Missense_Mutation_p.R176C|DYRK4_ENST00000543431.1_Missense_Mutation_p.R176C	NM_001282285.1|NM_001282286.1|NM_003845.1	NP_001269214.1|NP_001269215.1|NP_003836.1	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.R578C(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27			Colorectal(7;0.103)			TTTCTACTTTCGCAATCACTT	0.443																																						dbGAP											1	Substitution - Missense(1)	endometrium(1)	12											177.0	155.0	162.0					12																	4705861		2203	4300	6503	4576122	SO:0001583	missense	0			Y09305	CCDS8530.1	12p13.32	2014-09-11			ENSG00000010219	ENSG00000010219			3095	protein-coding gene	gene with protein product		609181				9748265	Standard	NM_003845		Approved		uc001qmx.3	Q9NR20	OTTHUMG00000168204	ENST00000540757.2:c.526C>T	12.37:g.4705861C>T	ENSP00000441755:p.Arg176Cys	Somatic	111	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	4576122	157	38.76	100	A8K8F7|Q8NEF2|Q92631	Missense_Mutation	SNP	HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase	p.R176C	ENST00000540757.2	37	c.526	CCDS8530.1	12	.	.	.	.	.	.	.	.	.	.	C	23.3	4.400752	0.83120	.	.	ENSG00000010219	ENST00000542744;ENST00000540757;ENST00000010132;ENST00000543431	T;T;T;T	0.21191	2.02;2.02;2.02;2.02	5.47	5.47	0.80525	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	0.85682	D	0.000000	T	0.49508	0.1561	M	0.74467	2.265	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;P;D	0.79108	0.992;0.877;0.963	T	0.51228	-0.8732	10	0.87932	D	0	.	18.9413	0.92607	0.0:1.0:0.0:0.0	.	291;176;176	F5H6L9;Q9NR20-2;Q9NR20	.;.;DYRK4_HUMAN	C	291;176;176;176	ENSP00000437534:R291C;ENSP00000441755:R176C;ENSP00000010132:R176C;ENSP00000439697:R176C	ENSP00000010132:R176C	R	+	1	0	DYRK4	4576122	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	4.634000	0.61325	2.570000	0.86706	0.655000	0.94253	CGC	-	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase		0.443	DYRK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	DYRK4	protein_coding	OTTHUMT00000398780.2	C			4576122	+1	no_errors	NM_003845.1	genbank	human	provisional	54_36p	missense	SNP	1.000	T
TCL1A	8115	genome.wustl.edu	37	14	96180354	96180354	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr14:96180354C>T	ENST00000402399.1	-	1	179	c.50G>A	c.(49-51)cGc>cAc	p.R17H	RP11-164H13.1_ENST00000556386.1_RNA|TCL1A_ENST00000556450.1_Missense_Mutation_p.R17H|RP11-164H13.1_ENST00000553445.1_RNA|RP11-164H13.1_ENST00000547644.2_RNA|TCL1A_ENST00000554012.1_Missense_Mutation_p.R17H|TCL1A_ENST00000555202.1_Missense_Mutation_p.R17H	NM_021966.2	NP_068801.1	P56279	TCL1A_HUMAN	T-cell leukemia/lymphoma 1A	17					multicellular organismal development (GO:0007275)|stem cell maintenance (GO:0019827)	cell cortex (GO:0005938)|endoplasmic reticulum (GO:0005783)|pronucleus (GO:0045120)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	12		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		GGCCCACAGGCGGTCCGGGTG	0.647			T	TRA@	T-CLL																																Ovarian(96;1068 2019 35393 39316)	dbGAP		Dom	yes		14	14q32.1	8115	T-cell leukemia/lymphoma 1A		L	0			14											88.0	80.0	83.0					14																	96180354		2203	4300	6503	95250107	SO:0001583	missense	0			X82240	CCDS9941.1	14q32.1	2008-07-03				ENSG00000100721			11648	protein-coding gene	gene with protein product		186960				2783489, 7809072	Standard	NM_021966		Approved	TCL1	uc001yfb.4	P56279		ENST00000402399.1:c.50G>A	14.37:g.96180354C>T	ENSP00000385036:p.Arg17His	Somatic	26	0.00	0		6	0.00	0	WXS	Illumina HiSeq	Phase_IV	95250107	53	32.91	26	Q6IBK7	Missense_Mutation	SNP	HMMPfam_TCL1_MTCP1,superfamily_TCL1_MTCP1	p.R17H	ENST00000402399.1	37	c.50	CCDS9941.1	14	.	.	.	.	.	.	.	.	.	.	C	11.94	1.789766	0.31685	.	.	ENSG00000100721	ENST00000554012;ENST00000402399;ENST00000556450;ENST00000555202	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	3.07	1.08	0.20341	.	0.538685	0.15407	N	0.263985	T	0.13200	0.0320	N	0.16066	0.365	0.32243	N	0.572405	B	0.23185	0.081	B	0.19148	0.024	T	0.27088	-1.0084	10	0.15066	T	0.55	-14.5898	4.3469	0.11138	0.0:0.6247:0.0:0.3753	.	17	P56279	TCL1A_HUMAN	H	17	ENSP00000451506:R17H;ENSP00000385036:R17H;ENSP00000450701:R17H;ENSP00000450496:R17H	ENSP00000385036:R17H	R	-	2	0	TCL1A	95250107	0.965000	0.33210	0.841000	0.33234	0.414000	0.31173	0.225000	0.17757	0.257000	0.21650	0.455000	0.32223	CGC	-	HMMPfam_TCL1_MTCP1,superfamily_TCL1_MTCP1		0.647	TCL1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	TCL1A	protein_coding	OTTHUMT00000413246.1	C			95250107	-1	no_errors	NM_001098725.1	genbank	human	validated	54_36p	missense	SNP	0.953	T
EXD1	161829	genome.wustl.edu	37	15	41482302	41482302	+	Nonsense_Mutation	SNP	G	G	A	rs371217636		TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr15:41482302G>A	ENST00000314992.5	-	9	905	c.715C>T	c.(715-717)Cga>Tga	p.R239*	RN7SL497P_ENST00000476341.2_RNA|EXD1_ENST00000458580.2_Nonsense_Mutation_p.R297*	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	239							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						GAAACAGGTCGGATGAACCAT	0.428																																						dbGAP											0			15											110.0	113.0	112.0					15																	41482302		2203	4300	6503	39269594	SO:0001587	stop_gained	0			BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"""exonuclease 3'-5' domain-like 1"""	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.715C>T	15.37:g.41482302G>A	ENSP00000321029:p.Arg239*	Somatic	91	2.15	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	39269594	99	38.41	63	A8K909|B7Z839|Q6ZW94	Nonsense_Mutation	SNP	HMMPfam_3_5_exonuc,HMMSmart_SM00474,superfamily_Ribonuclease H-like	p.R239*	ENST00000314992.5	37	c.715	CCDS10072.1	15	.	.	.	.	.	.	.	.	.	.	G	37	6.432506	0.97564	.	.	ENSG00000178997	ENST00000314992;ENST00000458580	.	.	.	6.17	3.13	0.36017	.	0.162931	0.39146	N	0.001457	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.8542	8.6871	0.34245	0.0735:0.0:0.4973:0.4292	.	.	.	.	X	239;297	.	ENSP00000321029:R239X	R	-	1	2	EXD1	39269594	0.997000	0.39634	0.972000	0.41901	0.521000	0.34408	2.112000	0.41892	0.369000	0.24510	0.655000	0.94253	CGA	-	HMMSmart_SM00474,superfamily_Ribonuclease H-like		0.428	EXD1-001	KNOWN	basic|CCDS	protein_coding	EXD1	protein_coding	OTTHUMT00000252553.2	G	NM_152596		39269594	-1	no_errors	NM_152596.2	genbank	human	provisional	54_36p	nonsense	SNP	0.496	A
CALR	811	genome.wustl.edu	37	19	13051080	13051081	+	Frame_Shift_Ins	INS	-	-	A	rs141216842		TCGA-AB-2872-03A-01W-0732-08	TCGA-AB-2872-11A-01W-0761-09	-	-	-	A	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	495c3e6d-76f1-499d-894b-761d50b70566	6bf7d555-2afc-4865-9b8f-97a5dd6609bd	g.chr19:13051080_13051081insA	ENST00000316448.5	+	5	589_590	c.516_517insA	c.(517-519)acafs	p.T173fs		NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	173	N-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	CACACCTGTACACACTGATTGT	0.545																																						dbGAP											0			19																																								12912081	SO:0001589	frameshift_variant	0			M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"""Sicca syndrome antigen A (autoantigen Ro; calreticulin)"", ""autoantigen Ro"""	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.517dupA	19.37:g.13051081_13051081dupA	ENSP00000320866:p.Thr173fs	Somatic	43	4.44	2		3033	7.70	253	WXS	Illumina HiSeq	Phase_IV	12912080	82	29.31	34	Q6IAT4|Q9UDG2	Frame_Shift_Ins	INS	HMMPfam_Calreticulin,superfamily_Concanavalin A-like lectins/glucanases,PatternScan_CALRETICULIN_1,PatternScan_CALRETICULIN_2,PatternScan_CALRETICULIN_REPEAT	p.T172fs	ENST00000316448.5	37	c.516_517	CCDS12288.1	19																																																																																			-	HMMPfam_Calreticulin,superfamily_Concanavalin A-like lectins/glucanases		0.545	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CALR	protein_coding	OTTHUMT00000451952.1	-	NM_004343		12912081	+1	no_errors	NM_004343.3	genbank	human	reviewed	54_36p	frame_shift_ins	INS	1.000:1.000	A
