#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_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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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_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_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
ABCA2	20	genome.wustl.edu	37	9	139915379	139915379	+	Silent	SNP	G	G	T			TCGA-C5-A2LT-01A-11D-A18J-09	TCGA-C5-A2LT-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6b355e-3898-4be6-be97-da0c3840a4ed	aff606ff-0c62-4adf-b137-275bf4aafa5a	g.chr9:139915379G>T	ENST00000371605.3	-	8	1176	c.1029C>A	c.(1027-1029)gcC>gcA	p.A343A	ABCA2_ENST00000341511.6_Silent_p.A344A|ABCA2_ENST00000492260.1_5'UTR|ABCA2_ENST00000265662.5_Silent_p.A344A			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	343					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		GCAGTAGCAGGGCCAGGGCCG	0.716																																																	0													4.0	6.0	6.0					9																	139915379		1865	3993	5858	SO:0001819	synonymous_variant	20			U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"""ATP binding cassette transporters / subfamily A"""	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.1029C>A	9.37:g.139915379G>T		Somatic		WXS	Illumina HiSeq	Phase_IV	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	pfam_ABC_transporter-like,smart_AAA+_ATPase,pfscan_ABC_transporter-like	p.A344	ENST00000371605.3	37	c.1032		9																																																																																			ABCA2	-	NULL		0.716	ABCA2-202	KNOWN	basic	protein_coding	ABCA2	HGNC	protein_coding		G	NM_001606		139915379	-1	no_errors	ENST00000265662	ensembl	human	known	70_37	silent	SNP	0.997	T
ALG13	79868	genome.wustl.edu	37	X	110988036	110988036	+	Missense_Mutation	SNP	G	G	T			TCGA-C5-A2LT-01A-11D-A18J-09	TCGA-C5-A2LT-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6b355e-3898-4be6-be97-da0c3840a4ed	aff606ff-0c62-4adf-b137-275bf4aafa5a	g.chrX:110988036G>T	ENST00000394780.3	+	24	2848	c.2836G>T	c.(2836-2838)Gct>Tct	p.A946S	ALG13_ENST00000470971.1_3'UTR|ALG13_ENST00000251943.4_Intron	NM_001099922.2|NM_001257231.1	NP_001093392.1|NP_001244160.1	Q9NP73	ALG13_HUMAN	ALG13, UDP-N-acetylglucosaminyltransferase subunit	946	Pro-rich.				cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipid glycosylation (GO:0030259)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	carbohydrate binding (GO:0030246)|cysteine-type peptidase activity (GO:0008234)|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity (GO:0004577)|poly(A) RNA binding (GO:0044822)			endometrium(2)|lung(10)|skin(1)	13						tcctcctcctgctcTTGATGT	0.567																																																	0													47.0	34.0	38.0					X																	110988036		1567	3579	5146	SO:0001583	missense	79868			AF220051	CCDS14559.1, CCDS55477.1, CCDS59173.1, CCDS76011.1, CCDS76012.1, CCDS76013.1	Xq23	2014-02-24	2013-02-21	2006-11-07	ENSG00000101901	ENSG00000101901	2.4.1.141	"""Tudor domain containing"", ""OTU domain containing"""	30881	protein-coding gene	gene with protein product	"""tudor domain containing 13"", ""N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase"""	300776	"""glycosyltransferase 28 domain containing 1"", ""chromosome X open reading frame 45"", ""asparagine-linked glycosylation 13 homolog (S. cerevisiae)"""	GLT28D1, CXorf45		12477932	Standard	NM_018466		Approved	MDS031, YGL047W, FLJ23018, TDRD13	uc011msy.2	Q9NP73	OTTHUMG00000022209	ENST00000394780.3:c.2836G>T	X.37:g.110988036G>T	ENSP00000378260:p.Ala946Ser	Somatic		WXS	Illumina HiSeq	Phase_IV	B1AKD6|B1AKM1|B2R5L5|B7Z6J0|B7Z804|B7Z847|B7Z9A8|B7ZAJ1|B7ZB57|Q17RC3|Q5JXY9|Q9H5U8	Missense_Mutation	SNP	pfam_Glyco_trans_28_C,pfam_OTU,pfscan_OTU,pfscan_Tudor	p.A946S	ENST00000394780.3	37	c.2836	CCDS55477.1	X	.	.	.	.	.	.	.	.	.	.	G	3.833	-0.035362	0.07497	.	.	ENSG00000101901	ENST00000394780	T	0.14766	2.48	4.28	-2.32	0.06745	.	0.890365	0.08781	U	0.894689	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.39860	-0.9593	10	0.26408	T	0.33	0.6604	1.9557	0.03375	0.1269:0.2411:0.375:0.257	.	868;946	Q9NP73-3;Q9NP73	.;ALG13_HUMAN	S	946	ENSP00000378260:A946S	ENSP00000378260:A946S	A	+	1	0	ALG13	110874692	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-0.461000	0.06712	-0.887000	0.03961	-0.427000	0.05922	GCT	ALG13	-	NULL		0.567	ALG13-011	PUTATIVE	basic|appris_principal|CCDS	protein_coding	ALG13	HGNC	protein_coding	OTTHUMT00000272895.1	G	NM_018466		110988036	+1	no_errors	ENST00000394780	ensembl	human	putative	70_37	missense	SNP	0.003	T
CTC-360P9.5	0	genome.wustl.edu	37	19	32417514	32417515	+	lincRNA	INS	-	-	G			TCGA-C5-A2LT-01A-11D-A18J-09	TCGA-C5-A2LT-10A-01D-A18J-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6b355e-3898-4be6-be97-da0c3840a4ed	aff606ff-0c62-4adf-b137-275bf4aafa5a	g.chr19:32417514_32417515insG	ENST00000593211.1	-	0	543				AC011456.1_ENST00000408577.1_RNA																							GTGTGatatatatatatatata	0.248																																																	0																																												0																															19.37:g.32417514_32417515insG		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	INS	-	NULL	ENST00000593211.1	37	NULL		19																																																																																			AC011456.1	-	-		0.248	CTC-360P9.5-001	KNOWN	basic	lincRNA	ENSG00000221504	Clone_based_ensembl_gene	lincRNA	OTTHUMT00000451919.1	-			32417515	+1	no_errors	ENST00000408577	ensembl	human	novel	70_37	rna	INS	0.182:0.173	G
GOLGA6L6	727832	genome.wustl.edu	37	15	20740459	20740461	+	In_Frame_Del	DEL	TCG	TCG	-			TCGA-C5-A2LT-01A-11D-A18J-09	TCGA-C5-A2LT-10A-01D-A18J-09	TCG	TCG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6b355e-3898-4be6-be97-da0c3840a4ed	aff606ff-0c62-4adf-b137-275bf4aafa5a	g.chr15:20740459_20740461delTCG	ENST00000427390.2	-	8	1379_1381	c.1289_1291delCGA	c.(1288-1293)gcgaag>gag	p.430_431AK>E		NM_001145004.1	NP_001138476.1	A8MZA4	GG6L6_HUMAN	golgin A6 family-like 6	430	Gln-rich.|Glu-rich.									NS(3)|endometrium(4)|kidney(1)|skin(3)	11						ctccacatcttcgcctcctgctc	0.552																																																	0										16,452		5,6,223							0.0			1	60,546		25,10,268	no	coding	GOLGA6L6	NM_001145004.1		30,16,491	A1A1,A1R,RR		9.901,3.4188,7.0764				76,998				SO:0001651	inframe_deletion	727832			AK093450	CCDS45184.1	15q11.2	2014-02-12	2010-02-12		ENSG00000215405	ENSG00000277322			37225	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 6"""				Standard	NM_001145004		Approved	FLJ36131	uc001ytk.2	A8MZA4	OTTHUMG00000171663	ENST00000427390.2:c.1289_1291delCGA	15.37:g.20740459_20740461delTCG	ENSP00000398615:p.Ala430_Lys431delinsGlu	Somatic		WXS	Illumina HiSeq	Phase_IV	D3YTC0	In_Frame_Del	DEL	superfamily_Ribosomal_L7/12_C/ClpS-like,prints_Tropomyosin	p.AK430in_frame_delE	ENST00000427390.2	37	c.1291_1289	CCDS45184.1	15																																																																																			GOLGA6L6	-	NULL		0.552	GOLGA6L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GOLGA6L6	HGNC	protein_coding	OTTHUMT00000414660.3	TCG	NM_001145004		20740461	-1	no_errors	ENST00000427390	ensembl	human	known	70_37	in_frame_del	DEL	0.966:0.963:0.960	-
IGFL4	444882	genome.wustl.edu	37	19	46543439	46543439	+	Silent	SNP	G	G	T			TCGA-C5-A2LT-01A-11D-A18J-09	TCGA-C5-A2LT-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6b355e-3898-4be6-be97-da0c3840a4ed	aff606ff-0c62-4adf-b137-275bf4aafa5a	g.chr19:46543439G>T	ENST00000377697.1	-	3	359	c.306C>A	c.(304-306)tcC>tcA	p.S102S	IGFL4_ENST00000595006.1_5'Flank|IGFL4_ENST00000601672.1_Silent_p.S8S	NM_001002923.1	NP_001002923.1	Q6B9Z1	IGFL4_HUMAN	IGF-like family member 4	102						extracellular space (GO:0005615)				cervix(1)|kidney(1)|lung(1)	3		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.0036)|GBM - Glioblastoma multiforme(486;0.022)|Epithelial(262;0.208)		TGGTGATAGGGGAGGACTTGC	0.582																																																	0													103.0	101.0	102.0					19																	46543439		2203	4300	6503	SO:0001819	synonymous_variant	444882			AY672114	CCDS33057.1	19q13.32	2006-07-14							32931	protein-coding gene	gene with protein product		610547				14702039	Standard	NM_001002923		Approved		uc002pdy.1	Q6B9Z1		ENST00000377697.1:c.306C>A	19.37:g.46543439G>T		Somatic		WXS	Illumina HiSeq	Phase_IV		Silent	SNP	NULL	p.S102	ENST00000377697.1	37	c.306	CCDS33057.1	19																																																																																			IGFL4	-	NULL		0.582	IGFL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	IGFL4	HGNC	protein_coding	OTTHUMT00000461698.1	G	NM_001002923		46543439	-1	no_errors	ENST00000377697	ensembl	human	known	70_37	silent	SNP	0.001	T
KCNJ13	3769	genome.wustl.edu	37	2	233633435	233633435	+	Silent	SNP	G	G	T			TCGA-C5-A2LT-01A-11D-A18J-09	TCGA-C5-A2LT-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6b355e-3898-4be6-be97-da0c3840a4ed	aff606ff-0c62-4adf-b137-275bf4aafa5a	g.chr2:233633435G>T	ENST00000233826.3	-	3	688	c.549C>A	c.(547-549)ggC>ggA	p.G183G	GIGYF2_ENST00000409451.3_Intron|KCNJ13_ENST00000409779.1_3'UTR|GIGYF2_ENST00000373566.3_Intron|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000452341.2_Intron|KCNJ13_ENST00000410029.1_Silent_p.G183G|GIGYF2_ENST00000409547.1_Intron|GIGYF2_ENST00000373563.4_Intron|AC064852.4_ENST00000427571.1_RNA	NM_002242.4	NP_002233.2	O60928	KCJ13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	183					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	inward rectifier potassium channel activity (GO:0005242)			endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		GATTAGGTTTGCCATCCATGT	0.458																																																	0													121.0	123.0	122.0					2																	233633435		2203	4300	6503	SO:0001819	synonymous_variant	3769			AJ006128	CCDS2498.1, CCDS54437.1	2q37	2014-01-28			ENSG00000115474	ENSG00000115474		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6259	protein-coding gene	gene with protein product		603208				9878260, 9620703, 16382105	Standard	NM_002242		Approved	Kir7.1, Kir1.4, LCA16	uc002vtp.3	O60928	OTTHUMG00000153292	ENST00000233826.3:c.549C>A	2.37:g.233633435G>T		Somatic		WXS	Illumina HiSeq	Phase_IV	A0PGH1|O76023|Q53SA1|Q8N3Y4	Silent	SNP	pfam_K_chnl_inward-rec_Kir,superfamily_Ig_E-set,pirsf_K_chnl_inward-rec_Kir,prints_K_chnl_inward-rec_Kir7,prints_K_chnl_inward-rec_Kir	p.G183	ENST00000233826.3	37	c.549	CCDS2498.1	2																																																																																			KCNJ13	-	pfam_K_chnl_inward-rec_Kir,superfamily_Ig_E-set,pirsf_K_chnl_inward-rec_Kir,prints_K_chnl_inward-rec_Kir7		0.458	KCNJ13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNJ13	HGNC	protein_coding	OTTHUMT00000257036.1	G	NM_002242		233633435	-1	no_errors	ENST00000233826	ensembl	human	known	70_37	silent	SNP	1.000	T
PSMD9	5715	genome.wustl.edu	37	12	122353787	122353787	+	Missense_Mutation	SNP	G	G	T			TCGA-C5-A2LT-01A-11D-A18J-09	TCGA-C5-A2LT-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0f6b355e-3898-4be6-be97-da0c3840a4ed	aff606ff-0c62-4adf-b137-275bf4aafa5a	g.chr12:122353787G>T	ENST00000541212.1	+	5	707	c.581G>T	c.(580-582)cGc>cTc	p.R194L	PSMD9_ENST00000261817.2_Missense_Mutation_p.R193L|PSMD9_ENST00000542602.1_Missense_Mutation_p.R89L|WDR66_ENST00000397454.2_5'Flank|WDR66_ENST00000288912.4_5'Flank|RP11-87C12.2_ENST00000546333.1_Intron			O00233	PSMD9_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	194	PDZ.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|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)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion (GO:0046676)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of insulin secretion (GO:0032024)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome regulatory particle assembly (GO:0070682)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome regulatory particle (GO:0005838)	bHLH transcription factor binding (GO:0043425)|transcription coactivator activity (GO:0003713)			endometrium(1)|large_intestine(1)|lung(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000117)|Epithelial(86;0.000415)|BRCA - Breast invasive adenocarcinoma(302;0.231)		ACAGTGATCCGCAGGGGGGAA	0.478																																																	0													48.0	46.0	47.0					12																	122353787		2203	4300	6503	SO:0001583	missense	5715			AB003177	CCDS9225.1, CCDS58284.1	12q24.31-q24.32	2008-05-22			ENSG00000110801	ENSG00000110801		"""Proteasome (prosome, macropain) subunits"""	9567	protein-coding gene	gene with protein product		603146				9653651	Standard	NM_002813		Approved	p27, Rpn4	uc001ubl.4	O00233	OTTHUMG00000168945	ENST00000541212.1:c.581G>T	12.37:g.122353787G>T	ENSP00000440485:p.Arg194Leu	Somatic		WXS	Illumina HiSeq	Phase_IV	B2RD35|G3V1Q6|Q9BQ42	Missense_Mutation	SNP	pfam_PDZ,superfamily_PDZ,smart_PDZ	p.R194L	ENST00000541212.1	37	c.581	CCDS9225.1	12	.	.	.	.	.	.	.	.	.	.	G	18.30	3.594624	0.66219	.	.	ENSG00000110801;ENSG00000110801;ENSG00000110801;ENSG00000256950	ENST00000541212;ENST00000261817;ENST00000544724;ENST00000542602	D;T;D;T	0.86627	-2.15;0.78;-2.15;2.09	5.31	5.31	0.75309	PDZ/DHR/GLGF (2);	0.000000	0.85682	D	0.000000	D	0.96331	0.8803	H	0.99058	4.415	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.97927	1.0318	10	0.87932	D	0	-21.8991	15.736	0.77842	0.0:0.0:1.0:0.0	.	194	O00233	PSMD9_HUMAN	L	194;193;105;89	ENSP00000440485:R194L;ENSP00000261817:R193L;ENSP00000443929:R105L;ENSP00000443772:R89L	ENSP00000261817:R193L	R	+	2	0	RP11-87C12.2;PSMD9	120838170	1.000000	0.71417	0.991000	0.47740	0.069000	0.16628	5.024000	0.64090	2.484000	0.83849	0.655000	0.94253	CGC	PSMD9	-	superfamily_PDZ,smart_PDZ		0.478	PSMD9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PSMD9	HGNC	protein_coding	OTTHUMT00000401686.1	G	NM_002813		122353787	+1	no_errors	ENST00000541212	ensembl	human	known	70_37	missense	SNP	0.992	T
