#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_CAF	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_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_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_ORegAnno_bin	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_normal_ref_reads	i_normal_ref_reads_val	i_normal_vaf	i_normal_vaf_val	i_normal_var_reads	i_normal_var_reads_val	i_reference	i_refseq_mrna_id	i_rsID	i_rsID_ref_var_alleles	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_tumor_ref_reads	i_tumor_ref_reads_val	i_tumor_vaf	i_tumor_vaf_val	i_tumor_var_reads	i_tumor_var_reads_val	i_type	i_ucsc_cons	i_variant
SDAD1	55153	genome.wustl.edu	37	4	76879002	76879002	+	Missense_Mutation	SNP	T	T	C			TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chr4:76879002T>C	ENST00000356260.5	-	18	1694	c.1576A>G	c.(1576-1578)Atc>Gtc	p.I526V	SDAD1_ENST00000395711.4_Missense_Mutation_p.I489V|SDAD1_ENST00000513089.1_5'Flank	NM_018115.2	NP_060585.2	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	526					actin cytoskeleton organization (GO:0030036)|protein transport (GO:0015031)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal large subunit export from nucleus (GO:0000055)	nucleolus (GO:0005730)				breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	19			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			AGACTTACGATTTCTTGCTGT	0.423																																							0											0													156.0	149.0	152.0					4																	76879002		2203	4300	6503	SO:0001583	missense	0			AF132198	CCDS3573.2, CCDS75147.1	4q21.21	2010-11-24			ENSG00000198301	ENSG00000198301			25537	protein-coding gene	gene with protein product						11483580	Standard	NM_001288984		Approved	FLJ10498	uc003hje.4	Q9NVU7	OTTHUMG00000130111	ENST00000356260.5:c.1576A>G	4.37:g.76879002T>C	ENSP00000348596:p.Ile526Val		Q32Q11|Q68D52|Q7Z5U4|Q9H831|Q9H9P6	Missense_Mutation	SNP	pfam_SDA1_dom,pfam_Uncharacterised_NUC130/133_N,superfamily_ARM-type_fold	p.I526V	ENST00000356260.5	37	c.1576	CCDS3573.2	4	.	.	.	.	.	.	.	.	.	.	T	7.416	0.635647	0.14322	.	.	ENSG00000198301	ENST00000356260;ENST00000395711	T;D	0.85484	2.01;-1.99	5.41	1.54	0.23209	SDA1 (2);	0.241030	0.41500	N	0.000866	T	0.64832	0.2634	N	0.11560	0.145	0.26367	N	0.976959	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.49862	-0.8894	10	0.28530	T	0.3	-7.2709	3.2564	0.06834	0.1651:0.2535:0.0:0.5814	.	489;526	E7EW05;Q9NVU7	.;SDA1_HUMAN	V	526;489	ENSP00000348596:I526V;ENSP00000379061:I489V	ENSP00000348596:I526V	I	-	1	0	SDAD1	77098026	0.998000	0.40836	0.968000	0.41197	0.695000	0.40330	0.765000	0.26546	0.326000	0.23384	0.454000	0.30748	ATC	0	pfam_SDA1_dom		0.423	SDAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SDAD1	protein_coding	OTTHUMT00000252418.3	69	153	0	0.00	0	0	T	NM_018115	0	0		76879002	-1	no_errors	ENST00000356260	ensembl	human	known	74_37	missense	56	127	9.68	8.63	6	12	SNP	1	C
FCHO2	115548	genome.wustl.edu	37	5	72348254	72348254	+	Missense_Mutation	SNP	A	A	T			TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chr5:72348254A>T	ENST00000430046.2	+	13	1209	c.1093A>T	c.(1093-1095)Aat>Tat	p.N365Y	FCHO2_ENST00000512348.1_Missense_Mutation_p.N332Y|FCHO2_ENST00000341845.6_Missense_Mutation_p.N365Y	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	365					clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		TATGCATCCAAATAACTCACA	0.368																																							0											0													96.0	90.0	92.0					5																	72348254		1860	4106	5966	SO:0001583	missense	0			AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.1093A>T	5.37:g.72348254A>T	ENSP00000393776:p.Asn365Tyr		A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Missense_Mutation	SNP	pfam_Muniscin_C-term_mu_dom,pfam_FCH_dom,smart_FCH_dom,pfscan_FCH_dom	p.N365Y	ENST00000430046.2	37	c.1093	CCDS47230.1	5	.	.	.	.	.	.	.	.	.	.	A	14.76	2.630614	0.46944	.	.	ENSG00000157107	ENST00000430046;ENST00000341845;ENST00000512348	T;T;T	0.18338	2.22;2.22;2.22	5.47	3.03	0.35002	.	0.208128	0.48286	D	0.000181	T	0.14227	0.0344	L	0.59436	1.845	0.46774	D	0.999199	P;P	0.43287	0.802;0.561	B;B	0.32980	0.156;0.125	T	0.02789	-1.1110	10	0.66056	D	0.02	-7.9291	8.3042	0.32032	0.7973:0.1334:0.0692:0.0	.	332;365	E9PG79;Q0JRZ9	.;FCHO2_HUMAN	Y	365;365;332	ENSP00000393776:N365Y;ENSP00000344034:N365Y;ENSP00000427296:N332Y	ENSP00000344034:N365Y	N	+	1	0	FCHO2	72384010	1.000000	0.71417	0.949000	0.38748	0.972000	0.66771	4.564000	0.60830	0.354000	0.24105	-0.321000	0.08615	AAT	0	NULL		0.368	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	FCHO2	protein_coding	OTTHUMT00000368795.3	95	403	0	0.00	0	0	A	XM_291142	0	0		72348254	1	no_errors	ENST00000341845	ensembl	human	known	74_37	missense	97	309	9.35	9.12	10	31	SNP	1	T
TEAD2	8463	genome.wustl.edu	37	19	49859215	49859215	+	Intron	SNP	C	C	T			TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chr19:49859215C>T	ENST00000311227.2	-	5	451				TEAD2_ENST00000539846.1_Splice_Site|TEAD2_ENST00000598397.1_Intron|TEAD2_ENST00000601519.1_Intron|TEAD2_ENST00000377214.4_Intron|TEAD2_ENST00000598810.1_Splice_Site|AC010524.4_ENST00000596488.1_RNA|TEAD2_ENST00000593945.1_Splice_Site	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2						gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		GAGGAACTTACCACGTTCAGA	0.632																																							0											0																																										SO:0001627	intron_variant	0			X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.361-539G>A	19.37:g.49859215C>T			B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Splice_Site	SNP	0	e0+1	ENST00000311227.2	37	c.1+1	CCDS12761.1	19																																																																																			0	0		0.632	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	TEAD2	protein_coding	OTTHUMT00000465465.1	107	35	0	0.00	0	0	C	NM_003598	0	0		49859215	-1	no_errors	ENST00000539846	ensembl	human	putative	74_37	splice_site	92	28	7.07	17.65	7	6	SNP	1	T
DSCR10	259234	genome.wustl.edu	37	21	39580413	39580413	+	lincRNA	SNP	C	C	A			TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chr21:39580413C>A	ENST00000432141.1	+	0	535					NR_027695.1		P59022	DSC10_HUMAN	Down syndrome critical region gene 10 (non-protein coding)																		CCCTCCGCTTCCTGTCAGGGT	0.587																																							0											0													265.0	220.0	235.0					21																	39580413		2203	4300	6503			0			AB066291		21q22.13	2012-10-16	2011-02-24		ENSG00000233316	ENSG00000233316		"""Long non-coding RNAs"""	16302	non-coding RNA	RNA, long non-coding			"""Down syndrome critical region gene 10"""			12168953	Standard	NR_027695		Approved		uc010gnt.2	P59022	OTTHUMG00000090611		21.37:g.39580413C>A			Q52LN2	RNA	SNP	0	NULL	ENST00000432141.1	37	NULL		21																																																																																			0	0		0.587	DSCR10-001	KNOWN	basic	lincRNA	DSCR10	lincRNA	OTTHUMT00000207199.1	49	105	0	0.00	0	0	C	NR_027695.1	0	0		39580413	1	no_errors	ENST00000432141	ensembl	human	known	74_37	rna	42	99	8.7	5.71	4	6	SNP	0.001	A
PKNOX1	5316	genome.wustl.edu	37	21	44450115	44450115	+	Silent	SNP	G	G	A			TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chr21:44450115G>A	ENST00000291547.5	+	11	1426	c.1215G>A	c.(1213-1215)gaG>gaA	p.E405E	PKNOX1_ENST00000432907.2_Silent_p.E288E	NM_004571.3	NP_004562.2	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	405					angiogenesis (GO:0001525)|camera-type eye development (GO:0043010)|erythrocyte differentiation (GO:0030218)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|prostate(1)	22						GGCAGAGCGAGGACGAGTCTG	0.647																																							0											0													87.0	76.0	79.0					21																	44450115		2203	4300	6503	SO:0001819	synonymous_variant	0				CCDS13692.1, CCDS68211.1	21q22.3	2011-06-20			ENSG00000160199	ENSG00000160199		"""Homeoboxes / TALE class"""	9022	protein-coding gene	gene with protein product		602100				9479508	Standard	NM_001286258		Approved	PREP1	uc002zcq.1	P55347	OTTHUMG00000086833	ENST00000291547.5:c.1215G>A	21.37:g.44450115G>A			O00528|Q8IWT7	Silent	SNP	pfam_Homeobox_dom,pfam_Homeobox_KN_domain,superfamily_Homeodomain-like,smart_Homeobox_dom,pfscan_Homeobox_dom	p.E405	ENST00000291547.5	37	c.1215	CCDS13692.1	21																																																																																			0	NULL		0.647	PKNOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PKNOX1	protein_coding	OTTHUMT00000195520.3	38	53	0	0.00	0	0	G		0	0		44450115	1	no_errors	ENST00000291547	ensembl	human	known	74_37	silent	32	38	13.51	7.32	5	3	SNP	1	A
PLXNB2	23654	genome.wustl.edu	37	22	50719926	50719926	+	Silent	SNP	C	C	T			TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chr22:50719926C>T	ENST00000449103.1	-	22	3665	c.3525G>A	c.(3523-3525)gtG>gtA	p.V1175V	PLXNB2_ENST00000359337.4_Silent_p.V1175V|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	1175					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		AGCCGAACTTCACCTGTGTGG	0.682																																							0											0													20.0	28.0	26.0					22																	50719926		2128	4217	6345	SO:0001819	synonymous_variant	0				CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.3525G>A	22.37:g.50719926C>T			A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	pfam_Plexin_cytoplasmic_RasGAP_dom,pfam_IPT,pfam_Semap_dom,pfam_Plexin_repeat,superfamily_Semap_dom,superfamily_Rho_GTPase_activation_prot,superfamily_Ig_E-set,superfamily_Plexin-like_fold,smart_Semap_dom,smart_Plexin-like_fold,smart_IPT,pfscan_Semap_dom	p.V1175	ENST00000449103.1	37	c.3525	CCDS43035.1	22																																																																																			0	NULL		0.682	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLXNB2	protein_coding	OTTHUMT00000316874.3	60	47	0	0.00	0	0	C	NM_012401	0	0		50719926	-1	no_errors	ENST00000359337	ensembl	human	known	74_37	silent	30	39	16.67	9.30	6	4	SNP	1	T
NT5C1B	93034	genome.wustl.edu	37	2	18765869	18765871	+	In_Frame_Del	DEL	GCT	GCT	-	rs145060005		TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	GCT	GCT	GCT	-	GCT	GCT	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chr2:18765869_18765871delGCT	ENST00000359846.2	-	5	889_891	c.812_814delAGC	c.(811-816)cagcgg>cgg	p.Q271del	NT5C1B_ENST00000600945.1_In_Frame_Del_p.Q271del|NT5C1B-RDH14_ENST00000532967.1_In_Frame_Del_p.Q271del|NT5C1B_ENST00000304081.4_In_Frame_Del_p.Q211del|NT5C1B_ENST00000460052.1_5'Flank|RNU6-1215P_ENST00000384441.1_RNA	NM_001002006.2|NM_001199086.1|NM_001199087.1|NM_001199088.1	NP_001002006.1|NP_001186015.1|NP_001186016.1|NP_001186017.1	Q96P26	5NT1B_HUMAN	5'-nucleotidase, cytosolic IB	271	Poly-Gln.				nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				TCGTCCTCCCGCTGCTGCTGCTG	0.67																																							0											0																																										SO:0001651	inframe_deletion	0			AF356185	CCDS33149.1, CCDS33150.1	2p24.2	2010-08-13			ENSG00000185013	ENSG00000185013	3.1.3.5		17818	protein-coding gene	gene with protein product		610526				11690631	Standard	NM_033253		Approved	AIRP, CN-IB		Q96P26	OTTHUMG00000151765	ENST00000359846.2:c.812_814delAGC	2.37:g.18765878_18765880delGCT	ENSP00000352904:p.Gln271del		B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	In_Frame_Del	DEL	pfam_5-nucleotidase	p.Q271in_frame_del	ENST00000359846.2	37	c.814_812	CCDS33150.1	2																																																																																			0	NULL		0.670	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NT5C1B	protein_coding	OTTHUMT00000323822.1	54	57	0	0.00	0	0	GCT		rs145060005	CGCT->C		18765871	-1	no_errors	ENST00000359846	ensembl	human	known	74_37	in_frame_del	34	44	10.53	4.35	4	2	DEL	0.009:0.011:0.004	0
MT-CO1	4512	genome.wustl.edu	37	M	6497	6497	+	Silent	SNP	T	T	C			TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chrM:6497T>C	ENST00000361624.2	+	1	594	c.594T>C	c.(592-594)tcT>tcC	p.S198S	MT-TW_ENST00000387382.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TC_ENST00000387405.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TM_ENST00000387377.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-TQ_ENST00000387372.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	198					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						CTTCTCCTATCTCTCCCAGTC	0.498																																							0											0																																										SO:0001819	synonymous_variant	0					mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.594T>C	M.37:g.6497T>C			Q34770	Silent	SNP	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom,prints_Cyt_c_Oxase_su1	p.S198	ENST00000361624.2	37	c.594		MT																																																																																			0	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom,prints_Cyt_c_Oxase_su1		0.498	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	MT-CO1	protein_coding		15	0	0	0.00	0	0	T	YP_003024028	0	0		6497	1	no_errors	ENST00000361624	ensembl	human	known	74_37	silent	2	0	66.67	0.00	4	0	SNP	NULL	C
LINC00200	399706	genome.wustl.edu	37	10	1205771	1205771	+	lincRNA	SNP	T	T	C	rs55923937		TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chr10:1205771T>C	ENST00000425630.1	+	0	64					NR_015376.2				long intergenic non-protein coding RNA 200																		ACGCTTTGCGTAGATGAGGGA	0.657																																							0											0													15.0	19.0	17.0					10																	1205771		691	1591	2282			0			AK097673		10p15.3	2012-10-12	2011-08-11	2011-08-11	ENSG00000229205	ENSG00000229205		"""Long non-coding RNAs"""	30974	non-coding RNA	RNA, long non-coding			"""chromosome 10 open reading frame 139"", ""non-protein coding RNA 200"""	C10orf139, NCRNA00200			Standard	NR_015376		Approved	FLJ40354	uc010qag.1		OTTHUMG00000017539		10.37:g.1205771T>C				RNA	SNP	0	NULL	ENST00000425630.1	37	NULL		10																																																																																			0	0		0.657	LINC00200-001	KNOWN	basic	lincRNA	LINC00200	lincRNA	OTTHUMT00000046417.2	30	0	3.23	0.00	1	0	T	NR_015376	rs55923937	T->C		1205771	1	no_errors	ENST00000425630	ensembl	human	known	74_37	rna	14	1	22.22	0.00	4	0	SNP	0.02	C
ZNF724P	440519	genome.wustl.edu	37	19	23405608	23405608	+	Missense_Mutation	SNP	C	C	T			TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chr19:23405608C>T	ENST00000418100.1	-	4	1556	c.1439G>A	c.(1438-1440)tGt>tAt	p.C480Y				A8MTY0	ZN724_HUMAN	zinc finger protein 724, pseudogene	480					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|lung(2)|ovary(2)	8						ACATTCTTCACATTTGTAGGG	0.373																																							0											0																																										SO:0001583	missense	0					19p12	2014-02-14	2010-08-03		ENSG00000196081	ENSG00000196081			32460	pseudogene	pseudogene			"""zinc finger protein 724 pseudogene"", ""zinc finger protein 724 (pseudogene)"""				Standard	NR_045525		Approved		uc021uru.1	A8MTY0	OTTHUMG00000183231	ENST00000418100.1:c.1439G>A	19.37:g.23405608C>T	ENSP00000413411:p.Cys480Tyr			Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.C480Y	ENST00000418100.1	37	c.1439		19	.	.	.	.	.	.	.	.	.	.	C	8.645	0.896892	0.17686	.	.	ENSG00000196081	ENST00000418100	D	0.85088	-1.94	1.08	1.08	0.20341	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.90270	0.6957	.	.	.	0.38013	D	0.934619	D	0.89917	1.0	D	0.77004	0.989	D	0.89693	0.3899	8	0.72032	D	0.01	.	8.9688	0.35894	0.0:1.0:0.0:0.0	.	480	A8MTY0	ZN724_HUMAN	Y	480	ENSP00000413411:C480Y	ENSP00000413411:C480Y	C	-	2	0	ZNF724P	23197448	0.958000	0.32768	0.043000	0.18650	0.040000	0.13550	3.666000	0.54540	0.482000	0.27582	0.484000	0.47621	TGT	0	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2		0.373	ZNF724P-001	NOVEL	basic|appris_principal	protein_coding	ZNF724P	protein_coding	OTTHUMT00000465743.1	25	8	0	0.00	0	0	C		0	0		23405608	-1	no_errors	ENST00000418100	ensembl	human	novel	74_37	missense	40	3	13.04	0.00	6	0	SNP	0.697	T
ONECUT1	3175	genome.wustl.edu	37	15	53081865	53081867	+	In_Frame_Del	DEL	GGT	GGT	-			TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	GGT	GGT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chr15:53081865_53081867delGGT	ENST00000305901.5	-	1	342_344	c.215_217delACC	c.(214-219)caccgg>cgg	p.H72del	ONECUT1_ENST00000561401.2_Intron	NM_004498.2	NP_004489.1	Q9UBC0	HNF6_HUMAN	one cut homeobox 1	72	Poly-His.				B cell differentiation (GO:0030183)|cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|endoderm development (GO:0007492)|epithelial cell development (GO:0002064)|glucose metabolic process (GO:0006006)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription, DNA-templated (GO:0006355)|spleen development (GO:0048536)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	17				all cancers(107;0.0708)		TCAGGGGCCCGGTGGTGGTGGTG	0.719																																							0											0																																										SO:0001651	inframe_deletion	0			U77975	CCDS10150.1	15q21.3	2012-03-09	2007-07-16		ENSG00000169856	ENSG00000169856		"""Homeoboxes / CUT class"""	8138	protein-coding gene	gene with protein product		604164	"""one cut domain, family member 1"""	HNF6, HNF6A		8887657, 8790352	Standard	NM_004498		Approved	HNF-6	uc002aci.2	Q9UBC0	OTTHUMG00000131899	ENST00000305901.5:c.215_217delACC	15.37:g.53081874_53081876delGGT	ENSP00000302630:p.His72del		B2RTV4|Q99744|Q9UMR6	In_Frame_Del	DEL	pfam_Hmoeo_CUT,pfam_Homeobox_dom,superfamily_Lambda_DNA-bd_dom,superfamily_Homeodomain-like,smart_Homeobox_dom,pfscan_Homeobox_dom,pfscan_Hmoeo_CUT	p.H72in_frame_del	ENST00000305901.5	37	c.217_215	CCDS10150.1	15																																																																																			0	NULL		0.719	ONECUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ONECUT1	protein_coding	OTTHUMT00000254849.2	43	11	2.27	0.00	1	0	GGT		0	0		53081867	-1	no_errors	ENST00000305901	ensembl	human	known	74_37	in_frame_del	32	5	13.51	0.00	5	0	DEL	1.000:1.000:1.000	0
KRTAP10-2	386679	genome.wustl.edu	37	21	45971380	45971381	+	5'UTR	INS	-	-	GTGAGTGAGTGT	rs6147532|rs61660473|rs375322622|rs587605229|rs375670763|rs62220863	byFrequency	TCGA-XM-A8R9-01A-31D-A423-09	TCGA-XM-A8R9-10A-01D-A426-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	af0ac1c2-2335-4517-96b0-96f4c804eab6	4d060e5b-e384-403d-a14a-1fe57d89d74e	g.chr21:45971380_45971381insGTGAGTGAGTGT	ENST00000391621.1	-	0	7_8				TSPEAR_ENST00000397916.1_Intron|KRTAP10-2_ENST00000498210.1_5'UTR|TSPEAR_ENST00000323084.4_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2							keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						GAGgtgtgtgagtgagtgagtg	0.599														3966	0.791933	0.8343	0.7262	5008	,	,		18766	0.7609		0.7773	False		,,,				2504	0.8282						0.1847,.,0.0007987,0.7919,0.02256											0																																										SO:0001623	5_prime_UTR_variant	0			AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.-40->ACACTCACTCAC	21.37:g.45971380_45971381insGTGAGTGAGTGT			Q70LJ5	RNA	INS	0	NULL	ENST00000391621.1	37	NULL	CCDS42955.1	21																																																																																			0	0		0.599	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRTAP10-2	protein_coding	OTTHUMT00000128027.1	24	5	4	0.00	1	0	0		rs6147532	A->AAG,AGTGAGTGAGTGAGTGAGTGAGTGT,AGTGAGTGAGTGT,AGTGAGTGT		45971381	-1	no_errors	ENST00000498210	ensembl	human	known	74_37	rna	34	6	22.73	0.00	10	0	INS	0.018:0.138	GTGAGTGAGTGT
