#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_ ensembl_gene_id	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_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_GMAF	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_dbSNP	i_default_gene_name	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_name_source	i_gene_type	i_havana_transcript	i_n_alt_count	i_n_alt_count_full	i_n_alt_count_val	i_n_ref_count	i_n_ref_count_full	i_n_ref_count_val	i_normal_vaf	i_normal_vaf_val	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_t_alt_count_full	i_t_alt_count_val	i_t_ref_count_full	i_t_ref_count_val	i_tier	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_vaf	i_tumor_vaf_val	i_type	i_ucsc_cons	i_variant	t_alt_count	t_ref_count
RDH16	8608	genome.wustl.edu	37	12	57346713	57346713	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A3U6-01A-11D-A29N-09	TCGA-DX-A3U6-10A-01D-A29N-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	db650eff-4e2c-4ce3-9124-7697b6e03359	7536cf00-aed9-4045-94e7-e562e7ec6b34	g.chr12:57346713C>T	ENST00000398138.3	-	3	1490	c.634G>A	c.(634-636)Gct>Act	p.A212T	RDH16_ENST00000360752.4_5'UTR	NM_003708.3	NP_003699.3	O75452	RDH16_HUMAN	retinol dehydrogenase 16 (all-trans)	212					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	electron carrier activity (GO:0009055)|retinol dehydrogenase activity (GO:0004745)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)	16						CTGGTCACAGCAGTCTTGAAA	0.507													ENSG00000139547																									GBM(179;741 2921 43105 45298)												0													129.0	127.0	127.0					12																	57346713		1889	4112	6001	SO:0001583	missense	0			-		CCDS41797.1	12q13.3	2011-09-14	2006-05-09			ENSG00000139547		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	29674	protein-coding gene	gene with protein product	"""microsomal NAD+ dependent retinol dehydrogenase 4"", ""short chain dehydrogenase/reductase family 9C, member 8"""		"""retinol dehydrogenase 16 (all-trans and 13-cis)"""			9677409, 10329026, 19027726	Standard	NM_003708		Approved	RODH-4, SDR9C8	uc001smi.4	O75452		ENST00000398138.3:c.634G>A	12.37:g.57346713C>T	ENSP00000381206:p.Ala212Thr		Q9UNV2	Missense_Mutation	SNP	pfam_DH_sc/Rdtase_SDR,prints_Glc/ribitol_DH,prints_DH_sc/Rdtase_SDR	p.A212T	ENST00000398138.3	37	c.634	CCDS41797.1	12	.	.	.	.	.	.	.	.	.	.	C	10.29	1.309970	0.23821	.	.	ENSG00000139547	ENST00000398138	D	0.93189	-3.18	5.17	-6.91	0.01649	NAD(P)-binding domain (1);	5.594590	0.00166	N	0.000001	D	0.83839	0.5341	N	0.20881	0.62	0.09310	N	1	B;B	0.28082	0.2;0.001	B;B	0.17098	0.017;0.006	T	0.76035	-0.3106	10	0.22109	T	0.4	.	4.4822	0.11773	0.1014:0.1302:0.2006:0.5677	.	88;212	Q59FX7;O75452	.;RDH16_HUMAN	T	212	ENSP00000381206:A212T	ENSP00000353980:A88T	A	-	1	0	RDH16	55632980	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.985000	0.00319	-1.366000	0.02155	-0.345000	0.07892	GCT	-	RDH16	-	prints_Glc/ribitol_DH		0.507	RDH16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	RDH16	HGNC	protein_coding	OTTHUMT00000410898.1	0	0	0	23	23	91	0.00	0.00	C	NM_003708		57346713	-1	10	100	24	97	tier1	no_errors	ENST00000398138	ensembl	human	known	74_37	missense	29.41	50.76	SNP	0.000	T	10	24
FIBCD1	84929	genome.wustl.edu	37	9	133779553	133779553	+	Silent	SNP	G	G	A			TCGA-DX-A3U6-01A-11D-A29N-09	TCGA-DX-A3U6-10A-01D-A29N-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	db650eff-4e2c-4ce3-9124-7697b6e03359	7536cf00-aed9-4045-94e7-e562e7ec6b34	g.chr9:133779553G>A	ENST00000372338.4	-	7	1526	c.1284C>T	c.(1282-1284)caC>caT	p.H428H	FIBCD1_ENST00000448616.1_Silent_p.H428H|FIBCD1_ENST00000372337.2_Silent_p.H270H|FIBCD1_ENST00000253018.4_Intron	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	428	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitin binding (GO:0008061)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|prostate(5)|urinary_tract(1)	12	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		CATAGGAGGCGTGCGCACCGC	0.627													ENSG00000130720																																					0													128.0	108.0	115.0					9																	133779553		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AK027716	CCDS6937.1	9q34.2	2013-02-06			ENSG00000130720	ENSG00000130720		"""Fibrinogen C domain containing"""	25922	protein-coding gene	gene with protein product		613357				12975309	Standard	NM_001145106		Approved	FLJ14810	uc004bzz.3	Q8N539	OTTHUMG00000020814	ENST00000372338.4:c.1284C>T	9.37:g.133779553G>A			A3KFK0|Q6UXK6|Q96SJ7	Silent	SNP	pfam_Fibrinogen_a/b/g_C_dom,superfamily_Fibrinogen_a/b/g_C_dom,smart_Fibrinogen_a/b/g_C_dom	p.H428	ENST00000372338.4	37	c.1284	CCDS6937.1	9																																																																																			-	FIBCD1	-	pfam_Fibrinogen_a/b/g_C_dom,superfamily_Fibrinogen_a/b/g_C_dom,smart_Fibrinogen_a/b/g_C_dom		0.627	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FIBCD1	HGNC	protein_coding	OTTHUMT00000054687.2	0	0	0	46	46	21	0.00	0.00	G	NM_032843		133779553	-1	4	3	23	18	tier1	no_errors	ENST00000372338	ensembl	human	known	74_37	silent	14.81	14.29	SNP	1.000	A	4	23
PRELID1P1	728666	genome.wustl.edu	37	6	126964903	126964903	+	RNA	SNP	G	G	A	rs538763841		TCGA-DX-A3U6-01A-11D-A29N-09	TCGA-DX-A3U6-10A-01D-A29N-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	db650eff-4e2c-4ce3-9124-7697b6e03359	7536cf00-aed9-4045-94e7-e562e7ec6b34	g.chr6:126964903G>A	ENST00000567272.1	+	0	270									PRELI domain containing 1 pseudogene 1																		GGAAGACATAGTACACCGGGA	0.597													ENSG00000217325																																					0																																												0			-			6q22.32	2012-04-23			ENSG00000217325	ENSG00000217325			43886	pseudogene	pseudogene							Standard	NG_022903		Approved				OTTHUMG00000015520		6.37:g.126964903G>A				R	SNP	-	NULL	ENST00000567272.1	37	NULL		6																																																																																			-	PRELID1P1	-	-		0.597	PRELID1P1-002	KNOWN	basic	processed_transcript	PRELID1P1	HGNC	pseudogene	OTTHUMT00000436205.1	0	0	0	50	50	12	0.00	0.00	G	NG_022903		126964903	+1	13	4	52	7	tier1	no_errors	ENST00000567272	ensembl	human	known	74_37	rna	20.00	36.36	SNP	1.000	A	13	52
TBC1D22A	25771	genome.wustl.edu	37	22	47243848	47243855	+	Intron	DEL	GTGTGCGC	GTGTGCGC	-	rs143664618|rs146524849|rs62233855|rs62233856|rs62233857|rs111929620|rs137955823	byFrequency	TCGA-DX-A3U6-01A-11D-A29N-09	TCGA-DX-A3U6-10A-01D-A29N-09	GTGTGCGC	GTGTGCGC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	db650eff-4e2c-4ce3-9124-7697b6e03359	7536cf00-aed9-4045-94e7-e562e7ec6b34	g.chr22:47243848_47243855delGTGTGCGC	ENST00000337137.4	+	5	803				TBC1D22A_ENST00000407381.3_Intron|TBC1D22A_ENST00000406733.1_Intron|TBC1D22A_ENST00000355704.3_Intron|Z97351.1_ENST00000408745.1_RNA|TBC1D22A_ENST00000380995.1_Intron	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A								protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		gtgtgtgtgtgtgtgCGCGCGCGCACGC	0.486													ENSG00000221672																																					0																																										SO:0001627	intron_variant	0				AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 4"""	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.638-30694GTGTGCGC>-	22.37:g.47243848_47243855delGTGTGCGC			B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	R	DEL	-	NULL	ENST00000337137.4	37	NULL	CCDS14078.1	22																																																																																				Z97351.1	-	-		0.486	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000221672	Clone_based_ensembl_gene	protein_coding	OTTHUMT00000317600.3	0	0	0	8	8	8	0.00	0.00	GTGTGCGC	NM_014346		47243855	+1	0	0	4	4	tier1	no_errors	ENST00000408745	ensembl	human	novel	74_37	rna	0.00	0.00	DEL	0.003:0.002:0.002:0.003:0.004:0.001:0.001:0.001	-	0	4
AGAP1	116987	genome.wustl.edu	37	2	236480576	236480577	+	Intron	INS	-	-	TGTGTGTGTGTG	rs141898525|rs371400174	byFrequency	TCGA-DX-A3U6-01A-11D-A29N-09	TCGA-DX-A3U6-10A-01D-A29N-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	db650eff-4e2c-4ce3-9124-7697b6e03359	7536cf00-aed9-4045-94e7-e562e7ec6b34	g.chr2:236480576_236480577insTGTGTGTGTGTG	ENST00000304032.8	+	1	743				AC012305.1_ENST00000408777.1_RNA|AGAP1_ENST00000409457.1_Intron|AGAP1_ENST00000336665.5_Intron	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1						protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TGCCCACACTTtgtgtgtgtgt	0.441													ENSG00000221704		1304	0.260383	0.1762	0.2925	5008	,	,		11270	0.1776		0.3121	False		,,,				2504	0.3834																0																																										SO:0001627	intron_variant	0				AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.163+77083->TGTGTGTGTGTG	2.37:g.236480576_236480577insTGTGTGTGTGTG			B2RTX7|Q541S5|Q6P9D7|Q9NV93	R	INS	-	NULL	ENST00000304032.8	37	NULL	CCDS33408.1	2																																																																																				AC012305.1	-	-		0.441	AGAP1-001	KNOWN	basic|CCDS	protein_coding	ENSG00000221704	Clone_based_ensembl_gene	protein_coding	OTTHUMT00000257076.2	0	0	0	0	0	0	0.00	0.00	-	NM_014914		236480577	+1	0	0	0	0	tier1	no_errors	ENST00000408777	ensembl	human	novel	74_37	rna	0.00	0.00	INS	0.083:0.055	TGTGTGTGTGTG	0	0
POTEM	641455	genome.wustl.edu	37	14	20012850	20012850	+	Intron	SNP	A	A	T	rs201036322		TCGA-DX-A3U6-01A-11D-A29N-09	TCGA-DX-A3U6-10A-01D-A29N-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	db650eff-4e2c-4ce3-9124-7697b6e03359	7536cf00-aed9-4045-94e7-e562e7ec6b34	g.chr14:20012850A>T	ENST00000551509.1	-	4	862				RP11-244H18.1_ENST00000547584.1_lincRNA	NM_001145442.1	NP_001138914.1	A6NI47	POTEM_HUMAN	POTE ankyrin domain family, member M											endometrium(4)|kidney(1)|lung(4)	9						actgaggttgaggttggagga	0.398													ENSG00000187537																																					0																																										SO:0001627	intron_variant	0			-		CCDS73609.1	14q11.2	2013-01-10			ENSG00000187537	ENSG00000187537		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	37096	protein-coding gene	gene with protein product	"""prostate-specific P704P"""					16364570	Standard	NM_001145442		Approved	POTE14beta, P704P, ACT	uc001vwc.3	A6NI47		ENST00000551509.1:c.811-1193T>A	14.37:g.20012850A>T				Silent	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_Ankyrin_rpt	p.P302	ENST00000551509.1	37	c.906	CCDS45076.1	14																																																																																			rs201036322	POTEM	-	NULL		0.398	POTEM-001	NOVEL	basic|appris_principal|CCDS	protein_coding	POTEM	HGNC	protein_coding	OTTHUMT00000409490.3	0	0	0	12	12	0	0.00	0.00	A	NM_001145442		20012850	-1	6	0	11	0	tier1	no_errors	ENST00000547722	ensembl	human	known	74_37	silent	35.29	0.00	SNP	0.030	T	6	11
RNA5-8SP6	100873336	genome.wustl.edu	37	Y	10037863	10037863	+	RNA	DEL	C	C	-	rs373540942		TCGA-DX-A3U6-01A-11D-A29N-09	TCGA-DX-A3U6-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	db650eff-4e2c-4ce3-9124-7697b6e03359	7536cf00-aed9-4045-94e7-e562e7ec6b34	g.chrY:10037863delC	ENST00000515896.1	+	0	100									RNA, 5.8S ribosomal pseudogene 6																		ATCGACACTTCGAACGCACTT	0.552													ENSG00000251705																																					0																																												0						Yp11.2	2012-08-07	2012-08-07	2012-08-07	ENSG00000251705	ENSG00000251705			41960	pseudogene	RNA, pseudogene			"""RNA, 5.8S ribosomal 6"""	RN5-8S6			Standard	NG_033474		Approved						Y.37:g.10037863delC				R	DEL	-	NULL	ENST00000515896.1	37	NULL		Y																																																																																				R5-8SP6	-	-		0.552	RNA5-8SP6-201	KNOWN	basic	rRNA	R5-8SP6	HGNC	rRNA		0	0	0	40	40	2	0.00	0.00	C			10037863	+1	8	0	48	3	tier1	no_errors	ENST00000515896	ensembl	human	known	74_37	rna	14.29	0.00	DEL	1.000	-	8	48
SMC6	79677	genome.wustl.edu	37	2	17927101	17927101	+	Missense_Mutation	SNP	G	G	A	rs143978525	byFrequency	TCGA-DX-A3U6-01A-11D-A29N-09	TCGA-DX-A3U6-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	db650eff-4e2c-4ce3-9124-7697b6e03359	7536cf00-aed9-4045-94e7-e562e7ec6b34	g.chr2:17927101G>A	ENST00000448223.2	-	3	382	c.113C>T	c.(112-114)aCt>aTt	p.T38I	SMC6_ENST00000402989.1_Missense_Mutation_p.T38I|SMC6_ENST00000381272.4_Missense_Mutation_p.T38I|SMC6_ENST00000351948.4_Missense_Mutation_p.T38I	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	38					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TACCAAAGTAGTACCTTTACA	0.303													ENSG00000163029																																					0													174.0	161.0	165.0					2																	17927101		2203	4298	6501	SO:0001583	missense	0			-	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"""Structural maintenance of chromosomes proteins"""	20466	protein-coding gene	gene with protein product		609387	"""SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"""	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.113C>T	2.37:g.17927101G>A	ENSP00000404092:p.Thr38Ile		A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	superfamily_P-loop_NTPase	p.T38I	ENST00000448223.2	37	c.113	CCDS1690.1	2	.	.	.	.	.	.	.	.	.	.	G	10.71	1.426349	0.25726	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852;ENST00000428868	T;T;T;T;T	0.32988	2.65;2.65;2.15;2.65;1.43	3.96	3.06	0.35304	.	0.738632	0.13264	N	0.401074	T	0.16128	0.0388	N	0.08118	0	0.22240	N	0.999264	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.11329	0.001;0.001;0.006	T	0.17776	-1.0358	10	0.37606	T	0.19	.	9.5596	0.39360	0.0:0.2139:0.7861:0.0	.	38;38;38	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	I	38	ENSP00000404092:T38I;ENSP00000323439:T38I;ENSP00000370672:T38I;ENSP00000384539:T38I;ENSP00000408644:T38I	ENSP00000323439:T38I	T	-	2	0	SMC6	17790582	0.998000	0.40836	0.998000	0.56505	0.656000	0.38851	2.039000	0.41193	1.215000	0.43411	0.561000	0.74099	ACT	-	SMC6	-	NULL		0.303	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	SMC6	HGNC	protein_coding	OTTHUMT00000207359.1	0	0	0	44	44	135	0.00	0.00	G	NM_024624		17927101	-1	4	3	37	142	tier1	no_errors	ENST00000381272	ensembl	human	known	74_37	missense	9.76	2.05	SNP	0.998	A	4	37
