#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	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_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_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
FOXB2	442425	broad.mit.edu	37	9	79635214	79635214	+	Missense_Mutation	SNP	G	G	A			TCGA-EJ-A46H-01A-31D-A26M-08	TCGA-EJ-A46H-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32e768ca-262b-4887-831d-be38e2fbded6	4a1b4f8f-a455-4055-bc01-504f65df35b8	g.chr9:79635214G>A	ENST00000376708.1	+	1	644	c.644G>A	c.(643-645)gGc>gAc	p.G215D		NM_001013735.1	NP_001013757.1	Q5VYV0	FOXB2_HUMAN	forkhead box B2	215					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|lung(8)|ovary(1)	10						TCTCACCCCGGCAAGATGCAG	0.761																																						ENST00000376708.1																			0				breast(1)|lung(8)|ovary(1)	10						c.(643-645)gGc>gAc		forkhead box B2							5.0	7.0	7.0					9																	79635214		1849	3728	5577	SO:0001583	missense	442425				brain development|embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding	g.chr9:79635214G>A		CCDS35045.1	9q21.2	2008-02-05			ENSG00000204612	ENSG00000204612		"""Forkhead boxes"""	23315	protein-coding gene	gene with protein product							Standard	NM_001013735		Approved	bA159H20.4	uc004ako.1	Q5VYV0	OTTHUMG00000020051	ENST00000376708.1:c.644G>A	9.37:g.79635214G>A	ENSP00000365898:p.Gly215Asp						p.G215D	NM_001013735.1	NP_001013757.1	Q5VYV0	FOXB2_HUMAN			1	644	+			215						Missense_Mutation	SNP	ENST00000376708.1	37	c.644G>A	CCDS35045.1	.	.	.	.	.	.	.	.	.	.	G	13.32	2.203221	0.38905	.	.	ENSG00000204612	ENST00000376708	T	0.41065	1.01	2.79	2.79	0.32731	.	1.887600	0.03453	U	0.210908	T	0.26159	0.0638	N	0.22421	0.69	0.36692	D	0.879617	P	0.47762	0.9	B	0.36244	0.22	T	0.43877	-0.9364	10	0.23891	T	0.37	.	5.4513	0.16566	0.1587:0.0:0.8413:0.0	.	215	Q5VYV0	FOXB2_HUMAN	D	215	ENSP00000365898:G215D	ENSP00000365898:G215D	G	+	2	0	FOXB2	78825034	.	.	0.999000	0.59377	0.468000	0.32798	.	.	1.378000	0.46305	0.313000	0.20887	GGC		0.761	FOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052745.1	NM_001013735		3	20	0	0	0	1	0	3	20				
GOLGA6L17P	642402	broad.mit.edu	37	15	85053124	85053124	+	RNA	SNP	G	G	T	rs192508624	byFrequency	TCGA-EJ-A46H-01A-31D-A26M-08	TCGA-EJ-A46H-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32e768ca-262b-4887-831d-be38e2fbded6	4a1b4f8f-a455-4055-bc01-504f65df35b8	g.chr15:85053124G>T	ENST00000414190.2	-	0	328					NR_003246.2																						TAAATGTTTTGTTTTTTTTTT	0.353																																						ENST00000414190.2																			0																																																			0							g.chr15:85053124G>T																													15.37:g.85053124G>T								NR_003246.2						0	328	-									RNA	SNP	ENST00000414190.2	37																																																																																						0.353	GOLGA6L5-003	KNOWN	mRNA_end_NF|basic	processed_transcript	pseudogene	OTTHUMT00000418579.1			3	11	1	0	0.00116845	1	0.00116845	3	11				
UVRAG	7405	broad.mit.edu	37	11	75827023	75827023	+	Missense_Mutation	SNP	T	T	C			TCGA-EJ-A46H-01A-31D-A26M-08	TCGA-EJ-A46H-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32e768ca-262b-4887-831d-be38e2fbded6	4a1b4f8f-a455-4055-bc01-504f65df35b8	g.chr11:75827023T>C	ENST00000356136.3	+	14	1602	c.1361T>C	c.(1360-1362)cTg>cCg	p.L454P	UVRAG_ENST00000539288.1_Missense_Mutation_p.L82P|UVRAG_ENST00000533454.1_Missense_Mutation_p.L82P|UVRAG_ENST00000531818.1_Missense_Mutation_p.L82P|UVRAG_ENST00000532130.1_Missense_Mutation_p.L82P|UVRAG_ENST00000538870.1_5'UTR|UVRAG_ENST00000528420.1_Missense_Mutation_p.L353P	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	454					DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						CTTCCCAACCTGAAAAACTTC	0.393																																						ENST00000356136.3																			0				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						c.(1360-1362)cTg>cCg		UV radiation resistance associated							87.0	76.0	80.0					11																	75827023		2200	4293	6493	SO:0001583	missense	7405				DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding	g.chr11:75827023T>C	X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382			12640	protein-coding gene	gene with protein product	"""beclin 1 binding protein"""	602493	"""UV radiation resistance associated gene"""			9169138, 16799551, 18843052	Standard	NM_003369		Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000356136.3:c.1361T>C	11.37:g.75827023T>C	ENSP00000348455:p.Leu454Pro					UVRAG_ENST00000531818.1_Missense_Mutation_p.L82P|UVRAG_ENST00000539288.1_Missense_Mutation_p.L82P|UVRAG_ENST00000533454.1_Missense_Mutation_p.L82P|UVRAG_ENST00000528420.1_Missense_Mutation_p.L353P|UVRAG_ENST00000538870.1_5'UTR|UVRAG_ENST00000532130.1_Missense_Mutation_p.L82P	p.L454P	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN			14	1602	+			454					B3KTC1|O00392	Missense_Mutation	SNP	ENST00000356136.3	37	c.1361T>C	CCDS8241.1	.	.	.	.	.	.	.	.	.	.	T	17.02	3.282267	0.59867	.	.	ENSG00000198382	ENST00000356136;ENST00000528420;ENST00000533454;ENST00000531818;ENST00000532130;ENST00000539288	T	0.74421	-0.84	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.87954	0.6308	M	0.88377	2.95	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90059	0.4155	10	0.87932	D	0	-8.4706	14.1947	0.65662	0.0:0.0:0.0:1.0	.	454	Q9P2Y5	UVRAG_HUMAN	P	454;353;82;82;82;82	ENSP00000348455:L454P	ENSP00000348455:L454P	L	+	2	0	UVRAG	75504671	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.942000	0.75928	2.291000	0.77112	0.533000	0.62120	CTG		0.393	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	NM_003369		3	24	0	0	0	1	0	3	24				
GTF2H2B	653238	broad.mit.edu	37	5	69715976	69715977	+	RNA	INS	-	-	T	rs201035823	byFrequency	TCGA-EJ-A46H-01A-31D-A26M-08	TCGA-EJ-A46H-10A-01D-A26K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32e768ca-262b-4887-831d-be38e2fbded6	4a1b4f8f-a455-4055-bc01-504f65df35b8	g.chr5:69715976_69715977insT	ENST00000513202.1	+	0	108					NR_033417.1				general transcription factor IIH, polypeptide 2B (pseudogene)																		CTGGCATTCCATTTTTTTTTAC	0.238													|||unknown(NO_COVERAGE)	72	0.014377	0.0484	0.0043	5008	,	,		17491	0.002		0.001	False		,,,				2504	0.002					ENST00000513202.1																			0																																																			0							g.chr5:69715976_69715977insT			5q13.2	2011-09-01	2011-09-01		ENSG00000226259	ENSG00000226259		"""General transcription factors"""	31393	pseudogene	pseudogene			"""general transcription factor IIH, polypeptide 2B"""				Standard	NR_033417		Approved	DKFZP686M0199	uc021yab.1		OTTHUMG00000162394		5.37:g.69715985_69715985dupT								NR_033417.1						0	108	+									RNA	INS	ENST00000513202.1	37																																																																																						0.238	GTF2H2B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000396209.1	NM_001098729		3	4						3	4	---	---	---	---
