#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
NUDCD2	134492	genome.wustl.edu	37	5	162884088	162884089	+	Splice_Site	INS	-	-	A			TCGA-XU-AAXY-01A-11D-A428-09	TCGA-XU-AAXY-10A-01D-A42B-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	2b99c573-4c13-45b8-bfc6-eac1400e57bd	a8e97066-ec44-4ffa-9346-6dd78d038388	g.chr5:162884088_162884089insA	ENST00000302764.4	-	3	328		c.e3-2		NUDCD2_ENST00000517501.1_Intron|NUDCD2_ENST00000519395.1_Splice_Site	NM_145266.4	NP_660309.1	Q8WVJ2	NUDC2_HUMAN	NudC domain containing 2							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)				large_intestine(1)|prostate(1)	2	Renal(175;0.000281)	Medulloblastoma(196;0.0207)|all_neural(177;0.0966)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0981)|OV - Ovarian serous cystadenocarcinoma(192;0.183)|Epithelial(171;0.247)		TTCTGTCCTCTAAAAAAAAAAC	0.366																																							0											0																																										SO:0001630	splice_region_variant	0			BX538290	CCDS4361.1	5q34	2008-02-05			ENSG00000170584	ENSG00000170584			30535	protein-coding gene	gene with protein product							Standard	NM_145266		Approved	DKFZp686E10109	uc003lze.3	Q8WVJ2	OTTHUMG00000130378	ENST00000302764.4:c.239-2->T	5.37:g.162884098_162884098dupA			B2R4V0	Splice_Site	INS	0	e3-2	ENST00000302764.4	37	c.239-3_239-2	CCDS4361.1	5																																																																																			0	0		0.366	NUDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NUDCD2	protein_coding	OTTHUMT00000252747.3	37	115	0	0.86	0	1	0	NM_145266	0	0	Intron	162884089	-1	no_errors	ENST00000302764	ensembl	human	known	74_37	splice_site_ins	18	99	14.29	4.81	3	5	INS	0.984:0.001	A
HLA-V	352962	genome.wustl.edu	37	6	29760077	29760077	+	RNA	SNP	G	G	T			TCGA-XU-AAXY-01A-11D-A428-09	TCGA-XU-AAXY-10A-01D-A42B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	2b99c573-4c13-45b8-bfc6-eac1400e57bd	a8e97066-ec44-4ffa-9346-6dd78d038388	g.chr6:29760077G>T	ENST00000457107.1	+	0	78									major histocompatibility complex, class I, V (pseudogene)																		ACCCAGACCTGGGCAGGTGAG	0.706																																							0											0																																												0			M96332		6p21.3	2012-10-05	2007-12-12	2007-12-12	ENSG00000181126	ENSG00000181126		"""Histocompatibility complex"""	23482	pseudogene	pseudogene			"""HLA-75 pseudogene"""	HLA-75			Standard	NG_002729		Approved	dJ377H14.4			OTTHUMG00000031277		6.37:g.29760077G>T				RNA	SNP	0	NULL	ENST00000457107.1	37	NULL		6																																																																																			0	0		0.706	HLA-V-003	KNOWN	basic	processed_transcript	HLA-V	pseudogene	OTTHUMT00000105231.1	36	11	0	0.00	0	0	G	NG_002729	0	0		29760077	1	no_errors	ENST00000446817	ensembl	human	known	74_37	rna	34	9	10.53	0.00	4	0	SNP	0.919	T
TMTC1	83857	genome.wustl.edu	37	12	29936577	29936577	+	Silent	SNP	T	T	C			TCGA-XU-AAXY-01A-11D-A428-09	TCGA-XU-AAXY-10A-01D-A42B-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	2b99c573-4c13-45b8-bfc6-eac1400e57bd	a8e97066-ec44-4ffa-9346-6dd78d038388	g.chr12:29936577T>C	ENST00000539277.1	-	1	166	c.108A>G	c.(106-108)gcA>gcG	p.A36A	TMTC1_ENST00000552618.1_Silent_p.A36A|TMTC1_ENST00000256062.5_Intron|TMTC1_ENST00000381224.2_Intron|TMTC1_ENST00000551659.1_Silent_p.A36A	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	36						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					ACAGGCAGCTTGCCCCGGCCA	0.781																																							0											0																																										SO:0001819	synonymous_variant	0				CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"""Tetratricopeptide (TTC) repeat domain containing"""	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.108A>G	12.37:g.29936577T>C			D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Silent	SNP	pfam_TPR_1,pfam_TPR_2,pfam_DUF1736,pfam_PIK-rel_kinase_FAT,pfam_TPR-3,smart_HAT,smart_TPR_repeat,pfscan_TPR_repeat,pfscan_TPR-contain_dom	p.A36	ENST00000539277.1	37	c.108	CCDS53772.1	12																																																																																			0	NULL		0.781	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	TMTC1	protein_coding	OTTHUMT00000403509.1	25	1	0	0.00	0	0	T	NM_031920	0	0		29936577	-1	no_errors	ENST00000539277	ensembl	human	putative	74_37	silent	17	2	19.05	0.00	4	0	SNP	0.995	C
DNM1P47	100216544	genome.wustl.edu	37	15	102300309	102300309	+	RNA	SNP	C	C	G			TCGA-XU-AAXY-01A-11D-A428-09	TCGA-XU-AAXY-10A-01D-A42B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	2b99c573-4c13-45b8-bfc6-eac1400e57bd	a8e97066-ec44-4ffa-9346-6dd78d038388	g.chr15:102300309C>G	ENST00000561463.1	+	0	8355									DNM1 pseudogene 47																		GAGCTGCTGTCCAACCTGCAC	0.587																																							0											0																																												0			AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102300309C>G				RNA	SNP	0	NULL	ENST00000561463.1	37	NULL		15	.	.	.	.	.	.	.	.	.	.	.	0.485	-0.878010	0.02550	.	.	ENSG00000225587	ENST00000448059	.	.	.	1.31	1.31	0.21738	.	.	.	.	.	T	0.46425	0.1392	.	.	.	.	.	.	.	.	.	.	.	.	T	0.57159	-0.7859	4	0.66056	D	0.02	.	6.1587	0.20352	0.0:1.0:0.0:0.0	.	.	.	.	C	76	.	ENSP00000413267:S76C	S	+	2	0	AC107977.3	100117832	1.000000	0.71417	1.000000	0.80357	0.096000	0.18686	2.943000	0.49026	1.061000	0.40601	0.089000	0.15464	TCC	0	0		0.587	DNM1P47-001	KNOWN	basic	processed_transcript	DNM1P47	pseudogene	OTTHUMT00000417589.1	27	1	0	0.00	0	0	C	NG_009149	0	0		102300309	1	no_errors	ENST00000561463	ensembl	human	known	74_37	rna	15	3	31.82	0.00	7	0	SNP	1	G
PLEKHM1P	440456	genome.wustl.edu	37	17	62796799	62796799	+	RNA	SNP	G	G	A			TCGA-XU-AAXY-01A-11D-A428-09	TCGA-XU-AAXY-10A-01D-A42B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	2b99c573-4c13-45b8-bfc6-eac1400e57bd	a8e97066-ec44-4ffa-9346-6dd78d038388	g.chr17:62796799G>A	ENST00000582986.1	-	0	1121					NR_024386.1		Q69YJ1	PKHMP_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1 pseudogene						intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)										GAGGAGGCGCGCAGGGCCAGC	0.647																																							0											0																																												0					17q24.1	2012-10-03			ENSG00000214176	ENSG00000214176			35411	pseudogene	pseudogene							Standard	NR_024386		Approved	LOC440456	uc002jew.4	Q69YJ1	OTTHUMG00000179296		17.37:g.62796799G>A				RNA	SNP	0	NULL	ENST00000582986.1	37	NULL		17																																																																																			0	0		0.647	PLEKHM1P-002	KNOWN	basic	processed_transcript	PLEKHM1P	pseudogene	OTTHUMT00000445598.1	29	20	0	0.00	0	0	G	NR_024386	0	0		62796799	-1	no_errors	ENST00000578036	ensembl	human	known	74_37	rna	27	6	12.9	0.00	4	0	SNP	1	A
