#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_AAChange	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_IGV	i_Mutation_Status	i_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVaf_SOL	i_TVarCov_SOL	i_Transcript_Id	i_Ttot_rna	i_Tvaf_rna	i_Tvar_rna	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	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_dbSNPPopFreq	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_germline-maf-frequency	i_havana_transcript	i_note	i_refseq_mrna_id	i_secondary_variant_classification
CCDC18	343099	broad.mit.edu	37	1	93744309	93744310	+	IGR	INS	-	-	T	rs372723050		TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr1:93744309_93744310insT	ENST00000343253.7	+	0	4867				RP4-717I23.3_ENST00000427669.1_RNA|RP4-717I23.3_ENST00000429859.1_RNA|RP4-717I23.3_ENST00000457025.1_RNA|RP4-717I23.3_ENST00000455474.1_RNA|RP4-717I23.3_ENST00000414430.1_RNA|RP4-717I23.3_ENST00000413606.1_RNA|RP4-717I23.3_ENST00000451302.2_RNA|RP4-717I23.3_ENST00000447577.1_RNA|RP4-717I23.3_ENST00000446528.2_RNA|RP4-717I23.3_ENST00000442860.1_RNA|RP4-717I23.3_ENST00000415150.1_RNA|RP4-717I23.3_ENST00000424517.3_RNA			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18											breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		AGGAATGCaaattttttttttt	0.277																																					.													.	CCDC18	93		0			.																																									SO:0001628	intergenic_variant	0	.			ATGCAAATTTTTT			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598		1.37:g.93744320_93744320dupT			Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	6	0.50	3	.	0		0	Q6ZU17	RNA	INS	ENST00000343253.7	37																																																																																						0.277	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000382327.1		NM_206886	
IGSF3	3321	ucsc.edu;bcgsc.ca	37	1	117142641	117142641	+	Missense_Mutation	SNP	G	G	A	rs76417519	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr1:117142641G>A	ENST00000369486.3	-	7	2716	c.1951C>T	c.(1951-1953)Cgg>Tgg	p.R651W	IGSF3_ENST00000318837.6_Missense_Mutation_p.R671W|IGSF3_ENST00000369483.1_Missense_Mutation_p.R671W	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	651	Ig-like C2-type 5.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		TAGTTCTTCCGCCACAGCTCT	0.607																																					p.R671W													.	IGSF3	294		0			c.C2011T												75.0	56.0	63.0					1																	117142641		2203	4300	6503	SO:0001583	missense	3321	exon8			TCTTCCGCCACAG	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.1951C>T	1.37:g.117142641G>A	ENSP00000358498:p.Arg651Trp		Somatic	70	0.0428571429	3		WXS	Illumina HiSeq		83	0.12	10	NM_001542	49	0.00	0	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	G	18.98	3.738507	0.69304	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.03386	3.95;3.95;3.95	4.56	3.57	0.40892	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.06005	0.0156	L	0.43152	1.355	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.993;1.0;0.996	T	0.08848	-1.0702	10	0.66056	D	0.02	-40.6149	9.1987	0.37244	0.0:0.0:0.6762:0.3238	.	671;651;671	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	W	651;671;671	ENSP00000358498:R651W;ENSP00000358495:R671W;ENSP00000321184:R671W	ENSP00000321184:R671W	R	-	1	2	IGSF3	116944164	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	1.391000	0.34475	2.356000	0.79943	0.455000	0.32223	CGG			0.607	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000059040.1		NM_001542	
SEC22B	9554	broad.mit.edu	37	1	145116147	145116148	+	RNA	INS	-	-	A	rs56026824|rs113058116	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr1:145116147_145116148insA	ENST00000453618.1	+	0	1233_1234							O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B (S. cerevisiae) (gene/pseudogene)						ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											AGTAGATTGTTATTTCGTTTTT	0.416													A|A|AA|insertion	2465	0.492212	0.497	0.4914	5008	,	,		69600	0.4891		0.4891	False		,,,				2504	0.4928				.													.	.			0			.																																											9554	.			GATTGTTATTTCG	AF047442		1q21.1	2012-04-20	2010-03-12	2006-04-25	ENSG00000223380				10700	protein-coding gene	gene with protein product		604029	"""SEC22, vesicle trafficking protein (S. cerevisiae)-like 1"", ""SEC22 vesicle trafficking protein-like 1 (S. cerevisiae)"", ""SEC22 vesicle trafficking protein homolog B (S. cerevisiae)"""	SEC22L1		9094723, 16354670	Standard	NM_004892		Approved	sec22b, ERS-24	uc031poa.1	O75396	OTTHUMG00000013745		1.37:g.145116148_145116148dupA			Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	91	0.00	0	A8K1G0	RNA	INS	ENST00000453618.1	37																																																																																						0.416	SEC22B-001	KNOWN	basic	processed_transcript	processed_transcript		OTTHUMT00000038523.5		NM_004892	
HRNR	388697	bcgsc.ca	37	1	152188062	152188062	+	Missense_Mutation	SNP	T	T	C	rs79940627	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr1:152188062T>C	ENST00000368801.2	-	3	6118	c.6043A>G	c.(6043-6045)Acc>Gcc	p.T2015A	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2015					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCCCATGGGTAGAGGAATGA	0.567																																					p.T2015A													.	HRNR	403		0			c.A6043G							T	ALA/THR	25,4297		0,25,2136	379.0	540.0	485.0		6043	-5.8	0.0	1	dbSNP_131	485	206,8166		0,206,3980	no	missense	HRNR	NM_001009931.1	58	0,231,6116	CC,CT,TT		2.4606,0.5784,1.8198	benign	2015/2851	152188062	231,12463	2161	4186	6347	SO:0001583	missense	388697	exon3			CATGGGTAGAGGA	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6043A>G	1.37:g.152188062T>C	ENSP00000357791:p.Thr2015Ala		Somatic	237	0.0084388186	2		WXS	Illumina HiSeq	Phase_1	227	0.05	11	NM_001009931	0		0	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	T	6.886	0.532947	0.13188	0.005784	0.024606	ENSG00000197915	ENST00000368801	T	0.01629	4.72	3.9	-5.76	0.02376	.	.	.	.	.	T	0.00328	0.0010	L	0.29908	0.895	0.09310	N	1	B	0.17268	0.021	B	0.12837	0.008	T	0.48293	-0.9048	9	0.05436	T	0.98	.	6.6385	0.22897	0.0:0.3528:0.414:0.2332	.	2015	Q86YZ3	HORN_HUMAN	A	2015	ENSP00000357791:T2015A	ENSP00000357791:T2015A	T	-	1	0	HRNR	150454686	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.431000	0.02432	-1.305000	0.02327	-0.573000	0.04149	ACC			0.567	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000034016.1		XM_373868	
BROX	148362	hgsc.bcm.edu;broad.mit.edu;mdanderson.org	37	1	222903028	222903028	+	Nonsense_Mutation	SNP	C	C	T			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr1:222903028C>T	ENST00000340934.5	+	10	1229	c.823C>T	c.(823-825)Caa>Taa	p.Q275*	BROX_ENST00000539697.1_Nonsense_Mutation_p.Q243*|BROX_ENST00000537020.1_Nonsense_Mutation_p.Q275*	NM_144695.2	NP_653296.2	Q5VW32	BROX_HUMAN	BRO1 domain and CAAX motif containing	275	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|stomach(1)	14						CAGGTCTCTCCAAGAAGCAGA	0.323																																					p.Q275X													.	.			0			c.C823T												81.0	85.0	84.0					1																	222903028		2203	4300	6503	SO:0001587	stop_gained	148362	exon10			TCTCTCCAAGAAG		CCDS1534.1, CCDS73036.1, CCDS73037.1	1q41	2010-11-30	2010-11-30	2010-11-30	ENSG00000162819	ENSG00000162819			26512	protein-coding gene	gene with protein product	"""BRO1 domain containing protein"""		"""chromosome 1 open reading frame 58"""	C1orf58		18190528	Standard	XM_005273065		Approved	FLJ32421	uc001hnq.1	Q5VW32	OTTHUMG00000037650	ENST00000340934.5:c.823C>T	1.37:g.222903028C>T	ENSP00000343742:p.Gln275*		Somatic	124	0	0		WXS	Illumina HiSeq	.	95	0.08	8	NM_144695	27	0.04	1	B7Z9G5|Q96MG1	Nonsense_Mutation	SNP	ENST00000340934.5	37	CCDS1534.1	.	.	.	.	.	.	.	.	.	.	c	37	6.187790	0.97357	.	.	ENSG00000162819	ENST00000340934;ENST00000537020;ENST00000539697	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-12.8277	20.5827	0.99408	0.0:1.0:0.0:0.0	.	.	.	.	X	275;275;243	.	ENSP00000343742:Q275X	Q	+	1	0	BROX	220969651	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.100000	0.76989	2.941000	0.99782	0.655000	0.94253	CAA			0.323	BROX-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000091815.2		NM_144695	
SKIDA1	387640	mdanderson.org	37	10	21806050	21806050	+	Silent	SNP	A	A	G			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr10:21806050A>G	ENST00000449193.2	-	4	2954	c.702T>C	c.(700-702)gcT>gcC	p.A234A	SKIDA1_ENST00000487107.1_5'Flank|SKIDA1_ENST00000444772.3_Intron	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	234	Ala-rich.			Missing (in Ref. 2; BAD18601). {ECO:0000305}.		nucleus (GO:0005634)											cggcggcggcagcagcggcgg	0.761																																					p.A234A													.	.			0			c.T702C																																									SO:0001819	synonymous_variant	387640	exon4			GGCGGCAGCAGCG	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 140"""	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.702T>C	10.37:g.21806050A>G			Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	19	0.42	8	NM_207371	0		0	B1ANA5|Q6ZMX4|Q8N3C3	Silent	SNP	ENST00000449193.2	37	CCDS44363.1																																																																																					0.761	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000286950.2		NM_207371	
SKIDA1	387640	mdanderson.org	37	10	21806056	21806056	+	Silent	SNP	G	G	A			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr10:21806056G>A	ENST00000449193.2	-	4	2948	c.696C>T	c.(694-696)gcC>gcT	p.A232A	SKIDA1_ENST00000487107.1_5'Flank|SKIDA1_ENST00000444772.3_Intron	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	232	Ala-rich.			Missing (in Ref. 2; BAD18601). {ECO:0000305}.		nucleus (GO:0005634)											cggcagcagcggcggcggcgg	0.766																																					p.A232A													.	.			0			c.C696T												1.0	1.0	1.0					10																	21806056		64	241	305	SO:0001819	synonymous_variant	387640	exon4			AGCAGCGGCGGCG	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 140"""	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.696C>T	10.37:g.21806056G>A			Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	25	0.48	12	NM_207371	0		0	B1ANA5|Q6ZMX4|Q8N3C3	Silent	SNP	ENST00000449193.2	37	CCDS44363.1																																																																																					0.766	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000286950.2		NM_207371	
C10orf131	100127889	hgsc.bcm.edu	37	10	97684298	97684298	+	Intron	SNP	T	T	A			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr10:97684298T>A	ENST00000423344.2	+	5	346				ENTPD1-AS1_ENST00000452728.1_RNA|ENTPD1-AS1_ENST00000451364.1_RNA|ENTPD1-AS1_ENST00000454638.1_RNA|RP11-248J23.7_ENST00000491114.1_Intron|ENTPD1-AS1_ENST00000416301.1_RNA	NM_001130446.2	NP_001123918.2	A6NCD4	CJ131_HUMAN	chromosome 10 open reading frame 131											endometrium(1)|kidney(1)	2						ATATATATATTTTCCTTTTGT	0.313																																					.													.	.			0			.																																									SO:0001627	intron_variant	0	.			ATATATTTTCCTT		CCDS58090.1	10q24.1	2012-05-30			ENSG00000173088	ENSG00000173088			31667	protein-coding gene	gene with protein product							Standard	NM_001130446		Approved	bA690P14.3	uc010qoo.2	A6NCD4	OTTHUMG00000018824	ENST00000423344.2:c.150+151T>A	10.37:g.97684298T>A			Somatic	168	0	0		WXS	Illumina HiSeq	.	134	0.06	8	.	0		0	B1AMZ2|B4DG41	RNA	SNP	ENST00000423344.2	37	CCDS58090.1																																																																																					0.313	C10orf131-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000468148.1		NM_001098847	
RPL13AP5	728658	bcgsc.ca	37	10	98510149	98510149	+	IGR	SNP	T	T	C	rs186308547	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr10:98510149T>C								RNU6-1274P (7119 upstream) : MIR607 (78276 downstream)																							AGGTGGTGGTTGTACGCTGTG	0.572													-|||	3	0.000599042	0.0008	0.0	5008	,	,		15131	0.002		0.0	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	728658	.			GGTGGTTGTACGC																													10.37:g.98510149T>C			Somatic	52	0	0		WXS	Illumina HiSeq	Phase_1	53	0.13	7	.	144	0.72	104		RNA	SNP		37																																																																																					0	0.572										
RPL13AP5	728658	bcgsc.ca	37	10	98510250	98510250	+	IGR	SNP	T	T	G			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr10:98510250T>G								RNU6-1274P (7220 upstream) : MIR607 (78175 downstream)																							CCTTCCCGAGTCCCCTACCAC	0.587																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	728658	.			CCCGAGTCCCCTA																													10.37:g.98510250T>G			Somatic	85	0	0		WXS	Illumina HiSeq	Phase_1	67	0.18	12	.	191	0.43	82		RNA	SNP		37																																																																																					0	0.587										
MUC6	4588	bcgsc.ca	37	11	1017900	1017900	+	Missense_Mutation	SNP	G	G	T	rs77920671	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr11:1017900G>T	ENST00000421673.2	-	31	4951	c.4901C>A	c.(4900-4902)cCt>cAt	p.P1634H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1634	Approximate repeats.|Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGCATGGGTAGGGGTGATGAC	0.557																																					p.P1634H													.	MUC6	408		0			c.C4901A												542.0	517.0	525.0					11																	1017900		2199	4295	6494	SO:0001583	missense	4588	exon31			TGGGTAGGGGTGA	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4901C>A	11.37:g.1017900G>T	ENSP00000406861:p.Pro1634His		Somatic	286	0.013986014	4		WXS	Illumina HiSeq	Phase_1	184	0.05	9	NM_005961	0		0	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	8.763	0.924154	0.18056	.	.	ENSG00000184956	ENST00000421673	T	0.27256	1.68	2.39	1.37	0.22104	.	.	.	.	.	T	0.41903	0.1179	M	0.69358	2.11	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.18777	-1.0326	9	0.72032	D	0.01	.	3.2668	0.06868	0.1581:0.0:0.5815:0.2604	.	1634	Q6W4X9	MUC6_HUMAN	H	1634	ENSP00000406861:P1634H	ENSP00000406861:P1634H	P	-	2	0	MUC6	1007900	0.000000	0.05858	0.006000	0.13384	0.016000	0.09150	0.395000	0.20850	0.255000	0.21593	0.297000	0.19635	CCT			0.557	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000382120.2		XM_290540	
OR52A4	390053	bcgsc.ca;mdanderson.org	37	11	5141902	5141902	+	RNA	SNP	T	T	C	rs10837374|rs386750110	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr11:5141902T>C	ENST00000498233.1	-	0	1014							A6NMU1	O52A4_HUMAN	olfactory receptor, family 52, subfamily A, member 4							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(1)|lung(12)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.7e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		CTCTAATGTGTTTGGTCTTTA	0.353													C|||	3760	0.750799	0.9175	0.7334	5008	,	,		18621	0.5675		0.7276	False		,,,				2504	0.7505				.													.	.			0			.							C		3920,482	224.3+/-240.5	1745,430,26	81.0	81.0	81.0			-1.5	0.8	11	dbSNP_120	81	6106,2490	407.3+/-349.1	2182,1742,374	no	intergenic				3927,2172,400	CC,CT,TT		28.967,10.9496,22.8651			5141902	10026,2972	2201	4298	6499			390053	.			AATGTGTTTGGTC			11p15.4	2012-10-03	2012-10-03	2012-10-03	ENSG00000205494	ENSG00000205494		"""GPCR / Class A : Olfactory receptors"""	19579	pseudogene	pseudogene							Standard	NG_029079		Approved			A6NMU1	OTTHUMG00000066610		11.37:g.5141902T>C			Somatic	108	0	0		WXS	Illumina HiSeq	Phase_1	75	0.07	5	.	0		0		RNA	SNP	ENST00000498233.1	37		1603	0.7339743589743589	460	0.9349593495934959	265	0.7320441988950276	329	0.5751748251748252	549	0.7242744063324539	C	10.75	1.437222	0.25900	0.890504	0.71033	ENSG00000248953	ENST00000380369	.	.	.	3.94	-1.51	0.08664	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.20306	-1.0279	6	0.87932	D	0	.	6.5847	0.22614	0.1455:0.1996:0.0:0.6549	rs10837374	303	A6NMU1	O52A4_HUMAN	A	303	.	ENSP00000369727:T303A	T	-	1	0	OR52A4	5098478	0.000000	0.05858	0.799000	0.32177	0.705000	0.40729	-1.714000	0.01881	-0.351000	0.08249	-0.119000	0.15052	ACA			0.353	OR52A4-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000268565.1		NG_029079	
MMP1	4312	mdanderson.org	37	11	102668807	102668807	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr11:102668807G>T	ENST00000315274.6	-	1	84	c.17C>A	c.(16-18)cCa>cAa	p.P6Q	WTAPP1_ENST00000525739.2_RNA	NM_001145938.1|NM_002421.3	NP_001139410.1|NP_002412.1	P03956	MMP1_HUMAN	matrix metallopeptidase 1 (interstitial collagenase)	6					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|proteolysis (GO:0006508)|viral process (GO:0016032)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)	Marimastat(DB00786)	CAGCAGCAGTGGAGGAAAGCT	0.517																																					p.P6Q													.	.			0			c.C17A												68.0	58.0	62.0					11																	102668807		2203	4299	6502	SO:0001583	missense	4312	exon1			AGCAGTGGAGGAA	X54925	CCDS8322.1	11q21-q22	2014-01-30	2005-08-08		ENSG00000196611	ENSG00000196611	3.4.24.7	"""Endogenous ligands"""	7155	protein-coding gene	gene with protein product		120353	"""matrix metalloproteinase 1 (interstitial collagenase)"""	CLG			Standard	NM_002421		Approved		uc001phi.2	P03956	OTTHUMG00000048192	ENST00000315274.6:c.17C>A	11.37:g.102668807G>T	ENSP00000322788:p.Pro6Gln		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	33	0.09	3	NM_002421	1	0.00	0	P08156	Missense_Mutation	SNP	ENST00000315274.6	37	CCDS8322.1	.	.	.	.	.	.	.	.	.	.	G	4.015	0.000223	0.07819	.	.	ENSG00000196611	ENST00000315274	T	0.13657	2.57	0.235	0.235	0.15431	.	1.876360	0.02289	N	0.070092	T	0.07234	0.0183	N	0.08118	0	0.09310	N	1	B	0.29115	0.233	B	0.15484	0.013	T	0.27971	-1.0058	9	0.56958	D	0.05	.	.	.	.	.	6	P03956	MMP1_HUMAN	Q	6	ENSP00000322788:P6Q	ENSP00000322788:P6Q	P	-	2	0	MMP1	102174017	0.089000	0.21612	0.021000	0.16686	0.041000	0.13682	1.596000	0.36718	0.308000	0.22923	0.313000	0.20887	CCA			0.517	MMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000109632.1		NM_002421	
NACA	4666	bcgsc.ca	37	12	57110530	57110530	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr12:57110530G>T	ENST00000454682.1	-	3	5065	c.4784C>A	c.(4783-4785)tCc>tAc	p.S1595Y	NACA_ENST00000356769.3_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000550952.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1595	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						CTCTTTGGGGGATGGGGCCCC	0.592			T	BCL6	NHL																																.				Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131		0			.												20.0	21.0	20.0					12																	57110530		1567	3575	5142	SO:0001583	missense	4666	.			TTGGGGGATGGGG	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.4784C>A	12.37:g.57110530G>T	ENSP00000403817:p.Ser1595Tyr		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_1	98	0.06	6	.	1	0.00	0		Missense_Mutation	SNP	ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	G	3.870	-0.028161	0.07589	.	.	ENSG00000196531	ENST00000454682	T	0.49139	0.79	2.76	1.84	0.25277	.	.	.	.	.	T	0.32763	0.0840	.	.	.	0.09310	N	1	D	0.54964	0.969	B	0.41332	0.354	T	0.12451	-1.0547	7	.	.	.	.	5.1543	0.15027	0.1305:0.2118:0.6577:0.0	.	1595	E9PAV3	.	Y	1595	ENSP00000403817:S1595Y	.	S	-	2	0	NACA	55396797	0.655000	0.27376	0.015000	0.15790	0.045000	0.14185	0.209000	0.17435	0.264000	0.21851	0.430000	0.28490	TCC			0.592	NACA-201	KNOWN	basic	protein_coding	protein_coding				NM_005594	
IGHV3-11	28450	broad.mit.edu	37	14	106573362	106573364	+	RNA	DEL	ACC	ACC	-	rs2003432|rs367875175	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	ACC	ACC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr14:106573362_106573364delACC	ENST00000390601.2	-	0	339_341									immunoglobulin heavy variable 3-11 (gene/pseudogene)																		ATATGGTACTACCACTACTACTA	0.522																																					.													.	.			0			.																																											0	.			GGTACTACCACTA	M99652		14q32.33	2012-02-08	2008-09-12		ENSG00000211941	ENSG00000211941		"""Immunoglobulins / IGH locus"""	5580	other	immunoglobulin gene			"""immunoglobulin heavy variable 3-11"""				Standard	NG_001019		Approved				OTTHUMG00000152277		14.37:g.106573362_106573364delACC			Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	326	0.01	3	.	96	0.00	0		RNA	DEL	ENST00000390601.2	37																																																																																						0.522	IGHV3-11-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325665.1		NG_001019	
HERC2P3	283755	broad.mit.edu	37	15	20588563	20588563	+	RNA	SNP	A	A	G	rs2291972	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr15:20588563A>G	ENST00000428453.1	-	0	4187							Q9BVR0	HRC23_HUMAN	hect domain and RLD 2 pseudogene 3								metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(1)|lung(14)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35						GCGGTTGCAGAAGCCCAGTAG	0.463																																					.													.	.			0			.							G		1850,2504		163,1524,490	125.0	96.0	106.0			1.1	0.0	15	dbSNP_100	106	2056,6422		76,1904,2259	no	intergenic				239,3428,2749	GG,GA,AA		24.251,42.4897,30.4395			20588563	3906,8926	2177	4239	6416			0	.			TTGCAGAAGCCCA	AF041081		15q11.2	2010-08-02			ENSG00000180229	ENSG00000180229			4871	pseudogene	pseudogene						9730612	Standard	NR_036432		Approved	D15F37S4, LOC283755	uc001ytg.3	Q9BVR0	OTTHUMG00000157175		15.37:g.20588563A>G			Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	70	0.06	4	.	17	0.00	0		RNA	SNP	ENST00000428453.1	37																																																																																						0.463	HERC2P3-014	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000347772.2		NG_008269	
Unknown	0	bcgsc.ca	37	16	32626855	32626855	+	IGR	SNP	A	A	G	rs28446891	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr16:32626855A>G								RP11-652G5.1 (7308 upstream) : RP11-586K12.11 (34607 downstream)																							AAGCACAGACATGCCCATGTT	0.478																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACAGACATGCCCA																													16.37:g.32626855A>G			Somatic	181	0.0055248619	1		WXS	Illumina HiSeq	Phase_1	160	0.04	7	.	0		0		RNA	SNP		37																																																																																					0	0.478										
ZNF276	92822	hgsc.bcm.edu	37	16	89793728	89793728	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr16:89793728G>T	ENST00000443381.2	+	5	1145	c.1048G>T	c.(1048-1050)Gat>Tat	p.D350Y	ZNF276_ENST00000289816.5_Missense_Mutation_p.D275Y|ZNF276_ENST00000446326.2_Missense_Mutation_p.M146I|ZNF276_ENST00000568064.1_Missense_Mutation_p.M268I	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	350					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)	14		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		AACCTCGGATGATCGGGTAAA	0.473																																					p.D350Y													.	.			0			c.G1048T												184.0	165.0	171.0					16																	89793728		2198	4300	6498	SO:0001583	missense	92822	exon5			TCGGATGATCGGG	AK026482	CCDS10986.1, CCDS45554.1	16q24.3	2014-02-17	2006-02-10	2006-02-10	ENSG00000158805	ENSG00000158805		"""Zinc fingers, C2H2-type"""	23330	protein-coding gene	gene with protein product	"""centromere protein Z"", ""zinc finger, AD-type"""	608460	"""zinc finger protein 276 homolog (mouse)"""	ZFP276		10936049, 20813266	Standard	NM_152287		Approved	MGC45417, ZNF477, CENPZ, CENP-Z, ZADT	uc002fos.4	Q8N554	OTTHUMG00000138050	ENST00000443381.2:c.1048G>T	16.37:g.89793728G>T	ENSP00000415836:p.Asp350Tyr		Somatic	128	0	0		WXS	Illumina HiSeq	.	117	0.04	5	NM_001113525	20	0.00	0	Q0VGA1|Q2TBE8|Q3B7H7	Missense_Mutation	SNP	ENST00000443381.2	37	CCDS45554.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.3|23.3	4.403579|4.403579	0.83230|0.83230	.|.	.|.	ENSG00000158805|ENSG00000158805	ENST00000289816;ENST00000443381|ENST00000446326	T;T|T	0.07216|0.05139	3.21;3.25|3.49	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	0.168593|.	0.49916|.	D|.	0.000125|.	T|T	0.17492|0.17492	0.0420|0.0420	L|L	0.32530|0.32530	0.975|0.975	0.30710|0.30710	N|N	0.749363|0.749363	D;D|D	0.89917|0.63880	0.998;1.0|0.993	D;D|D	0.67231|0.70227	0.945;0.95|0.968	T|T	0.00920|0.00920	-1.1514|-1.1514	10|9	0.56958|0.46703	D|T	0.05|0.11	-20.1344|-20.1344	18.4672|18.4672	0.90760|0.90760	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	188;350|146	B4DIT3;Q8N554|A8K186	.;ZN276_HUMAN|.	Y|I	275;350|146	ENSP00000289816:D275Y;ENSP00000415836:D350Y|ENSP00000415999:M146I	ENSP00000289816:D275Y|ENSP00000415999:M146I	D|M	+|+	1|3	0|0	ZNF276|ZNF276	88321229|88321229	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.444000|6.444000	0.73452|0.73452	2.596000|2.596000	0.87737|0.87737	0.655000|0.655000	0.94253|0.94253	GAT|ATG			0.473	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000422517.1		NM_152287	
Unknown	0	bcgsc.ca	37	17	26794863	26794863	+	IGR	SNP	T	T	C			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr17:26794863T>C								CTD-2350C19.2 (61049 upstream) : SLC13A2 (5447 downstream)																							GCGCCAAGATTGTGAAGCCCA	0.547																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	388363	.			CAAGATTGTGAAG																													17.37:g.26794863T>C			Somatic	80	0	0		WXS	Illumina HiSeq	Phase_1	84	0.06	5	.	48	0.79	38		RNA	SNP		37																																																																																					0	0.547										
TXNDC2	84203	hgsc.bcm.edu	37	18	9886918	9886918	+	Missense_Mutation	SNP	A	A	G	rs142946305		TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr18:9886918A>G	ENST00000306084.6	+	2	641	c.442A>G	c.(442-444)Aac>Gac	p.N148D	TXNDC2_ENST00000426718.3_3'UTR|TXNDC2_ENST00000357775.5_Missense_Mutation_p.N81D|TXNDC2_ENST00000536353.2_Missense_Mutation_p.N81D	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	148	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						CAAAGAGAGTAACATCCCCAA	0.557																																					p.N148D													TXNDC2_ENST00000306084,NS,carcinoma,0,4	TXNDC2_ENST00000306084	0	4	0			c.A442G							A	ASP/ASN,ASP/ASN	1,4405		0,1,2202	134.0	138.0	137.0		442,241	-6.2	0.0	18	dbSNP_134	137	0,8600		0,0,4300	yes	missense,missense	TXNDC2	NM_001098529.1,NM_032243.5	23,23	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign,benign	148/554,81/487	9886918	1,13005	2203	4300	6503	SO:0001583	missense	84203	exon2			GAGAGTAACATCC	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.442A>G	18.37:g.9886918A>G	ENSP00000304908:p.Asn148Asp		Somatic	120	0.0083333333	1		WXS	Illumina HiSeq	.	71	0.06	4	NM_001098529	0		0	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	.	.	.	.	.	.	.	.	.	.	a	2.139	-0.397257	0.04899	2.27E-4	0.0	ENSG00000168454	ENST00000536353;ENST00000357775;ENST00000306084;ENST00000426718	T;T;T	0.16743	2.44;2.32;2.32	3.49	-6.25	0.02039	.	2.476990	0.01833	N	0.034859	T	0.06554	0.0168	N	0.01188	-0.97	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.33471	-0.9867	9	.	.	.	.	15.0384	0.71767	0.8494:0.0:0.1506:0.0	.	148	Q86VQ3	TXND2_HUMAN	D	81;81;148;148	ENSP00000437393:N81D;ENSP00000350419:N81D;ENSP00000304908:N148D	.	N	+	1	0	TXNDC2	9876918	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.078000	0.03413	-1.562000	0.01682	-1.345000	0.01243	AAC	0		0.557	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000254487.1			
ATCAY	85300	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	3909500	3909500	+	Frame_Shift_Del	DEL	T	T	-			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr19:3909500delT	ENST00000450849.2	+	7	1131	c.664delT	c.(664-666)ttafs	p.L222fs	ATCAY_ENST00000398448.3_Frame_Shift_Del_p.L228fs|ATCAY_ENST00000600960.1_Frame_Shift_Del_p.L222fs|ATCAY_ENST00000301260.6_Frame_Shift_Del_p.L222fs	NM_033064.4	NP_149053.1	Q86WG3	ATCAY_HUMAN	ataxia, cerebellar, Cayman type	222	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Mediates interaction with GLS.				apoptotic process (GO:0006915)|mitochondrion distribution (GO:0048311)|negative regulation of glutamate metabolic process (GO:2000212)|neuron projection development (GO:0031175)|regulation of protein localization (GO:0032880)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|synapse (GO:0045202)	kinesin binding (GO:0019894)	p.L222L(1)		breast(1)|endometrium(2)|kidney(2)|lung(2)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		CATCAGCAGCTTAGAGCTCCT	0.632																																					p.S221fs													.	ATCAY	84		1	Substitution - coding silent(1)	breast(1)	c.663delC												59.0	62.0	61.0					19																	3909500		2114	4210	6324	SO:0001589	frameshift_variant	85300	exon7			AGCAGCTTAGAGC		CCDS45923.1	19p13.3	2014-06-24	2008-07-18		ENSG00000167654	ENSG00000167654			779	protein-coding gene	gene with protein product	"""Cayman ataxia"", ""caytaxin"""	608179				8845847, 14556008	Standard	NM_033064		Approved		uc002lyy.4	Q86WG3	OTTHUMG00000181836	ENST00000450849.2:c.664delT	19.37:g.3909500delT	ENSP00000390941:p.Leu222fs		Somatic	81	0	0		WXS	Illumina HiSeq	.	54	0.30	16	NM_033064	8	0.00	0	Q8NAQ2|Q8TAQ3|Q96HC6|Q96JF5	Frame_Shift_Del	DEL	ENST00000450849.2	37	CCDS45923.1																																																																																					0.632	ATCAY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000457872.2			
ZNF849P	100130108	bcgsc.ca	37	19	22868665	22868665	+	RNA	SNP	A	A	G	rs148261119	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr19:22868665A>G	ENST00000601860.1	-	0	340																											AACCCTTACTACACATAAGAT	0.373													t|||	65	0.0129792	0.0008	0.0245	5008	,	,		18778	0.0		0.0298	False		,,,				2504	0.0174				.													.	.			0			.																																											0	.			CTTACTACACATA																													19.37:g.22868665A>G			Somatic	105	0	0		WXS	Illumina HiSeq	Phase_1	90	0.06	5	.	1	0.00	0		Missense_Mutation	SNP	ENST00000601860.1	37		37	0.01694139194139194	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	26	0.03430079155672823	.	0.013	-1.621094	0.00820	.	.	ENSG00000198153	ENST00000340708	.	.	.	0.819	-1.64	0.08318	.	.	.	.	.	T	0.04272	0.0118	.	.	.	.	.	.	.	.	.	.	.	.	T	0.26224	-1.0109	4	0.10902	T	0.67	.	2.1998	0.03920	0.5068:0.2456:0.0:0.2475	.	.	.	.	A	233	.	ENSP00000342595:T233A	T	+	1	0	AC011467.1	22660505	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-3.708000	0.00387	-1.136000	0.02892	-1.225000	0.01585	ACA			0.373	CTC-457E21.9-001	KNOWN	basic	antisense	antisense		OTTHUMT00000464586.1			
GPR42	2866	bcgsc.ca;mdanderson.org	37	19	35863014	35863014	+	Silent	SNP	C	C	T	rs145254622	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr19:35863014C>T	ENST00000454971.1	+	2	954	c.753C>T	c.(751-753)tgC>tgT	p.C251C	GPR42_ENST00000597214.1_Silent_p.C251C			O15529	GPR42_HUMAN	G protein-coupled receptor 42 (gene/pseudogene)	251						integral component of plasma membrane (GO:0005887)	signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|skin(2)	4	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			GCTATATCTGCGGTGAAAGCC	0.607													C|||	50	0.00998403	0.0008	0.0288	5008	,	,		6479	0.001		0.0278	False		,,,				2504	0.0				.													.	.			0			.							C		30,2802		13,4,1399	33.0	50.0	45.0			2.2	0.0	19	dbSNP_134	45	276,5620		117,42,2789	no	intergenic				130,46,4188	TT,TC,CC		4.6811,1.0593,3.506			35863014	306,8422	1416	2948	4364	SO:0001819	synonymous_variant	2866	.			TATCTGCGGTGAA	AF024689		19q13.12	2012-08-20	2010-02-09	2010-02-09	ENSG00000126251	ENSG00000126251		"""GPCR / Class A : Fatty acid receptors"""	4500	protein-coding gene	gene with protein product		603822	"""G protein-coupled receptor 42 pseudogene"""	GPR42P		9344866, 19630535	Standard	NG_008348		Approved	GPR41L, FFAR3L		O15529	OTTHUMG00000157124	ENST00000454971.1:c.753C>T	19.37:g.35863014C>T			Somatic	109	0	0		WXS	Illumina HiSeq	Phase_1	74	0.08	6	.	0		0		Silent	SNP	ENST00000454971.1	37																																																																																						0.607	GPR42-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000347518.1		NM_005305	
Unknown	0	bcgsc.ca	37	19	41414408	41414408	+	IGR	SNP	C	C	G	rs17656995	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr19:41414408C>G								CYP2G1P (7995 upstream) : CYP2B7P1 (15715 downstream)																							GGTGTAGTTTCGTGGGATTGT	0.602													c|||	38	0.00758786	0.0015	0.0159	5008	,	,		13994	0.0		0.0219	False		,,,				2504	0.0031				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TAGTTTCGTGGGA																													19.37:g.41414408C>G			Somatic	135	0	0		WXS	Illumina HiSeq	Phase_1	115	0.06	7	.	1	0.00	0		Missense_Mutation	SNP		37		20	0.009157509157509158	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	15	0.01978891820580475	C	0.006	-2.062499	0.00386	.	.	ENSG00000198251	ENST00000412510	.	.	.	2.76	-5.51	0.02568	.	.	.	.	.	T	0.07863	0.0197	.	.	.	.	.	.	.	.	.	.	.	.	T	0.42515	-0.9447	4	0.02654	T	1	.	11.1773	0.48607	0.0:0.6969:0.172:0.1311	rs17656995;rs17656995	.	.	.	P	210	.	ENSP00000388274:R210P	R	-	2	0	AC008537.2	46106248	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.767000	0.00782	-1.309000	0.02315	-2.158000	0.00328	CGA		0	0.602										
BCKDHA	593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	41932262	41932262	+	IGR	SNP	C	C	G			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr19:41932262C>G	ENST00000269980.2	+	0	2103				B3GNT8_ENST00000601379.1_5'UTR|CTC-435M10.6_ENST00000598887.1_RNA|B3GNT8_ENST00000321702.2_Missense_Mutation_p.S141T	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide						branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						ATCTGAGCAGCTGGAGACTTG	0.622																																					p.S141T													.	.			0			c.G422C												45.0	46.0	45.0					19																	41932262		2203	4300	6503	SO:0001628	intergenic_variant	374907	exon3			GAGCAGCTGGAGA	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128		19.37:g.41932262C>G			Somatic	113	0	0		WXS	Illumina HiSeq	.	68	0.34	23	NM_198540	3	0.00	0	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	37	CCDS12581.1	.	.	.	.	.	.	.	.	.	.	C	8.143	0.785755	0.16189	.	.	ENSG00000177191	ENST00000321702	T	0.35605	1.3	4.21	3.16	0.36331	.	1.351940	0.04817	N	0.436211	T	0.27419	0.0673	N	0.25647	0.755	0.23923	N	0.996454	B	0.27498	0.18	B	0.26969	0.075	T	0.24693	-1.0153	10	0.48119	T	0.1	.	5.4879	0.16759	0.1956:0.7008:0.0:0.1036	.	141	Q7Z7M8	B3GN8_HUMAN	T	141	ENSP00000312700:S141T	ENSP00000312700:S141T	S	-	2	0	B3GNT8	46624102	0.347000	0.24853	0.932000	0.37286	0.560000	0.35617	0.697000	0.25556	1.127000	0.42034	0.462000	0.41574	AGC			0.622	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000398313.3		NM_000709	
PSG7	5676	broad.mit.edu	37	19	43440069	43440070	+	RNA	INS	-	-	AA	rs147024666		TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr19:43440069_43440070insAA	ENST00000406070.2	-	0	161				PSG7_ENST00000471557.1_RNA|PSG7_ENST00000446844.3_RNA	NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)						female pregnancy (GO:0007565)	extracellular region (GO:0005576)							Prostate(69;0.00682)				cacacacaaacacacacacaca	0.495																																					.													.	.			0			.																																											5676	.			CACAAACACACAC			19q13.2	2013-01-29	2010-02-26		ENSG00000221878	ENSG00000221878		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9524	protein-coding gene	gene with protein product		176396	"""pregnancy specific beta-1-glycoprotein 7"""				Standard	NM_002783		Approved		uc010xwl.2	Q13046	OTTHUMG00000151125		19.37:g.43440069_43440070insAA			Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	12	0.42	5	.	0		0	Q15232	RNA	INS	ENST00000406070.2	37																																																																																						0.495	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene		OTTHUMT00000321431.2		NM_001206650	
RPLP0P6	220717	broad.mit.edu	37	2	38709067	38709067	+	lincRNA	SNP	A	A	G	rs113173138		TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr2:38709067A>G	ENST00000417039.1	-	0	696																											ATGATTATCCAAAATGTTTCA	0.537																																					.													.	.			0			.																																											0	.			TTATCCAAAATGT																													2.37:g.38709067A>G			Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	32	0.13	4	.	54	0.93	50		RNA	SNP	ENST00000417039.1	37																																																																																						0.537	AC016995.3-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000331173.1			
RPLP0P6	220717	broad.mit.edu	37	2	38709079	38709079	+	lincRNA	SNP	C	C	T	rs111340107		TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr2:38709079C>T	ENST00000417039.1	-	0	696																											AATGTTTCATCGTGGGAGCAG	0.537																																					.													.	.			0			.																																											0	.			TTTCATCGTGGGA																													2.37:g.38709079C>T			Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	35	0.11	4	.	48	0.54	26		RNA	SNP	ENST00000417039.1	37																																																																																						0.537	AC016995.3-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000331173.1			
GYPC	2995	bcgsc.ca	37	2	127413734	127413734	+	5'UTR	SNP	C	C	G	rs11542968	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr2:127413734C>G	ENST00000259254.4	+	0	226				GYPC_ENST00000356887.7_5'UTR|GYPC_ENST00000409836.3_5'Flank	NM_002101.4	NP_002092.1	P04921	GLPC_HUMAN	glycophorin C (Gerbich blood group)							cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|prostate(2)|urinary_tract(1)	13	Colorectal(110;0.0533)			BRCA - Breast invasive adenocarcinoma(221;0.075)		GGTGCCGCTTCCTCTCGCCGC	0.711													C|||	12	0.00239617	0.0	0.0014	5008	,	,		11539	0.001		0.006	False		,,,				2504	0.0041				.	Melanoma(110;806 1600 6704 9981 33404)												.	GYPC	27		0			.																																									SO:0001623	5_prime_UTR_variant	2995	.			CCGCTTCCTCTCG		CCDS2136.1, CCDS46402.1, CCDS58724.1	2q14-q21	2014-07-19			ENSG00000136732	ENSG00000136732		"""CD molecules"", ""Blood group antigens"""	4704	protein-coding gene	gene with protein product		110750					Standard	NM_016815		Approved	GPC, GYPD, Ge, CD236, CD236R	uc002tnq.4	P04921	OTTHUMG00000131464	ENST00000259254.4:c.-106C>G	2.37:g.127413734C>G			Somatic	25	0	0		WXS	Illumina HiSeq	Phase_1	29	0.14	4	.	3	0.00	0	B2R522|Q53SV9|Q92642	Missense_Mutation	SNP	ENST00000259254.4	37	CCDS2136.1																																																																																					0.711	GYPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000254297.1		NM_002101	
AC103564.7	0	bcgsc.ca	37	2	132591478	132591478	+	lincRNA	SNP	T	T	C	rs7597931	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr2:132591478T>C	ENST00000437330.1	-	0	0																											CAGGGCCCAGTCCAGGGACCA	0.682													.|||	2782	0.555511	0.6286	0.4683	5008	,	,		17513	0.749		0.3588	False		,,,				2504	0.5215				.													.	.			0			.																																											0	.			GCCCAGTCCAGGG																													2.37:g.132591478T>C			Somatic	24	0	0		WXS	Illumina HiSeq	Phase_1	19	0.21	4	.	0		0		RNA	SNP	ENST00000437330.1	37																																																																																						0.682	AC103564.7-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000332207.1			
NECAB3	63941	mdanderson.org	37	20	32247749	32247749	+	Silent	SNP	G	G	T			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr20:32247749G>T	ENST00000246190.6	-	7	640	c.585C>A	c.(583-585)cgC>cgA	p.R195R	NECAB3_ENST00000375238.4_Silent_p.R195R|NECAB3_ENST00000606525.1_5'UTR|C20orf144_ENST00000375222.3_5'Flank|RP1-63M2.6_ENST00000607224.1_RNA	NM_031232.3	NP_112509.3	Q96P71	NECA3_HUMAN	N-terminal EF-hand calcium binding protein 3	195					protein metabolic process (GO:0019538)|protein secretion (GO:0009306)|regulation of amyloid precursor protein biosynthetic process (GO:0042984)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|Golgi cis cisterna (GO:0000137)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			large_intestine(3)|lung(5)|skin(2)	10						TCAGGGCTCGGCGTCCTGCCC	0.706																																					p.R195R													.	.			0			c.C585A												5.0	8.0	7.0					20																	32247749		1915	4029	5944	SO:0001819	synonymous_variant	63941	exon7			GGCTCGGCGTCCT	AB039947	CCDS42866.1, CCDS42867.1	20q11.21	2013-01-10	2007-12-06	2007-12-06	ENSG00000125967	ENSG00000125967		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	15851	protein-coding gene	gene with protein product	"""EF-hand calcium binding protein 3"""	612478	"""amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein"""	SYTIP2, APBA2BP		10833507	Standard	NM_031232		Approved	XB51, dJ63M2.4, NIP1, dJ63M2.5, EFCBP3	uc002wzn.4	Q96P71	OTTHUMG00000032264	ENST00000246190.6:c.585C>A	20.37:g.32247749G>T			Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	36	0.08	3	NM_031231	41	0.02	1	A8K780|E1P5N2|Q5JWF5|Q5JWF6|Q5JWF7|Q86VV1|Q9H433|Q9H8G8|Q9HBW7|Q9HCQ9	Silent	SNP	ENST00000246190.6	37	CCDS42866.1																																																																																					0.706	NECAB3-010	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000078724.2			
ELMO2	63916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	45017782	45017782	+	Silent	SNP	C	C	T			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr20:45017782C>T	ENST00000290246.6	-	7	515	c.321G>A	c.(319-321)ctG>ctA	p.L107L	ELMO2_ENST00000445496.2_5'UTR|ELMO2_ENST00000439931.2_Silent_p.L107L|ELMO2_ENST00000352077.2_Silent_p.L107L|ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000372176.1_Silent_p.L19L|ELMO2_ENST00000396391.1_Silent_p.L107L	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	107					apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				AGAGCTTGGCCAGCTCCTTCA	0.557																																					p.L107L													.	.			0			c.G321A												136.0	106.0	116.0					20																	45017782		2203	4300	6503	SO:0001819	synonymous_variant	63916	exon6			CTTGGCCAGCTCC	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"""Engulfment and cell motility proteins"""	17233	protein-coding gene	gene with protein product		606421	"""engulfment and cell motility 2 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.321G>A	20.37:g.45017782C>T			Somatic	64	0	0		WXS	Illumina HiSeq	.	94	0.20	19	NM_182764	35	0.23	8	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Silent	SNP	ENST00000290246.6	37	CCDS13398.1																																																																																					0.557	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000080466.1		NM_022086	
LIME1	54923	mdanderson.org	37	20	62369750	62369750	+	Silent	SNP	C	C	T			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr20:62369750C>T	ENST00000309546.3	+	5	570	c.483C>T	c.(481-483)agC>agT	p.S161S	SLC2A4RG_ENST00000266077.2_5'Flank|RP4-583P15.14_ENST00000467211.1_Missense_Mutation_p.A43V|LIME1_ENST00000490824.1_3'UTR|RP4-583P15.15_ENST00000490623.2_3'UTR	NM_017806.2	NP_060276.2	Q9H400	LIME1_HUMAN	Lck interacting transmembrane adaptor 1	161					B cell receptor signaling pathway (GO:0050853)|T cell receptor signaling pathway (GO:0050852)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|liver(1)	3	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					TGGCGGCCAGCCCTGTGGTGG	0.706																																					p.S161S													.	.			0			c.C483T												4.0	4.0	4.0					20																	62369750		1946	3942	5888	SO:0001819	synonymous_variant	54923	exon5			GGCCAGCCCTGTG	AK000413	CCDS13536.1	20q13.33	2010-05-11			ENSG00000203896	ENSG00000203896			26016	protein-coding gene	gene with protein product		609809				12477932	Standard	NM_017806		Approved	FLJ20406, dJ583P15.4, LIME	uc002ygp.4	Q9H400	OTTHUMG00000032999	ENST00000309546.3:c.483C>T	20.37:g.62369750C>T			Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	26	0.12	3	NM_017806	44	0.00	0	E1P5K5|E1P5K6|Q5JWJ2|Q6XYB3|Q9NX69	Silent	SNP	ENST00000309546.3	37	CCDS13536.1																																																																																					0.706	LIME1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000080225.1		NM_017806	
TCF20	6942	bcgsc.ca;mdanderson.org	37	22	42608414	42608414	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr22:42608414G>T	ENST00000359486.3	-	1	3034	c.2898C>A	c.(2896-2898)agC>agA	p.S966R	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Missense_Mutation_p.S966R	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	966					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						CTGCTCCAGGGCTGGCATTGC	0.547																																					p.S966R													.	TCF20	164		0			c.C2898A												97.0	94.0	95.0					22																	42608414		2203	4300	6503	SO:0001583	missense	6942	exon1			TCCAGGGCTGGCA	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.2898C>A	22.37:g.42608414G>T	ENSP00000352463:p.Ser966Arg		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_1	125	0.06	7	NM_181492	41	0.00	0	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Missense_Mutation	SNP	ENST00000359486.3	37	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.716340	0.48622	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	T;T	0.63580	-0.05;-0.05	5.77	-1.07	0.09968	.	0.059736	0.64402	D	0.000002	T	0.62270	0.2414	N	0.24115	0.695	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.986	T	0.62632	-0.6813	10	0.72032	D	0.01	-10.5029	11.3661	0.49673	0.3877:0.0:0.6123:0.0	.	966;966	Q9UGU0-2;Q9UGU0	.;TCF20_HUMAN	R	966	ENSP00000352463:S966R;ENSP00000335561:S966R	ENSP00000335561:S966R	S	-	3	2	TCF20	40938358	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	0.534000	0.23098	0.005000	0.14708	0.655000	0.94253	AGC			0.547	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000320531.1		NM_181492	
PSMD12P	317753	bcgsc.ca	37	3	72926390	72926390	+	IGR	SNP	A	A	G	rs7610496	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr3:72926390A>G								SHQ1 (28759 upstream) : GXYLT2 (10833 downstream)																							CCACTTATTCAGTGAACCAAA	0.413													G|||	1460	0.291534	0.4917	0.2824	5008	,	,		19096	0.0437		0.3608	False		,,,				2504	0.2117				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTATTCAGTGAAC																													3.37:g.72926390A>G			Somatic	208	0	0		WXS	Illumina HiSeq	Phase_1	229	0.04	9	.	0		0		RNA	SNP		37																																																																																					0	0.413										
TLR1	7096	broad.mit.edu	37	4	38798148	38798148	+	Frame_Shift_Del	DEL	A	A	-			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr4:38798148delA	ENST00000502213.2	-	3	2534	c.2305delT	c.(2305-2307)tggfs	p.W769fs	TLR1_ENST00000308979.2_Frame_Shift_Del_p.W769fs|TLR1_ENST00000510552.1_5'Flank			Q15399	TLR1_HUMAN	toll-like receptor 1	769	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						AAGTTAGCCCAAAAAAGGCCA	0.418																																					p.W769fs	GBM(5;216 373 40795 46382)												.	TLR1	70		0			c.2305delT												85.0	80.0	82.0					4																	38798148		2203	4300	6503	SO:0001589	frameshift_variant	7096	exon4			TAGCCCAAAAAAG	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.2305delT	4.37:g.38798148delA	ENSP00000421259:p.Trp769fs		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	164	0.04	7	NM_003263	10	0.00	0	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Frame_Shift_Del	DEL	ENST00000502213.2	37	CCDS33973.1																																																																																					0.418	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000360510.3			
CDYL	9425	bcgsc.ca;mdanderson.org	37	6	4735071	4735071	+	Missense_Mutation	SNP	C	C	G	rs28360500	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr6:4735071C>G	ENST00000328908.5	+	3	310	c.179C>G	c.(178-180)gCt>gGt	p.A60G				Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	60			A -> G (in dbSNP:rs28360500). {ECO:0000269|PubMed:10192397}.		regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)	p.A60G(1)		breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		CAGCCTCCCGCTTTACAGGTA	0.552													G|||	1326	0.264776	0.2791	0.3285	5008	,	,		16619	0.2937		0.2734	False		,,,				2504	0.1616				.													CDYL,NS,carcinoma,0,1	.		1	1	Substitution - Missense(1)	lung(1)	.							G		1318,3088	697.1+/-406.2	201,916,1086	70.0	69.0	69.0			-1.9	0.0	6	dbSNP_125	69	2278,6322	707.2+/-405.6	314,1650,2336	no	intergenic				515,2566,3422	GG,GC,CC		26.4884,29.9138,27.6488			4735071	3596,9410	2203	4300	6503	SO:0001583	missense	9425	.			CTCCCGCTTTACA	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"""CDY-like, autosomal"", ""testis-specific chromodomain Y-like protein"""	603778	"""chromodomain protein, Y chromosome-like"""			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.179C>G	6.37:g.4735071C>G	ENSP00000330512:p.Ala60Gly		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_1	65	0.08	5	.	0		0	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	37		633	0.28983516483516486	158	0.32113821138211385	120	0.3314917127071823	155	0.270979020979021	200	0.2638522427440633	G	0.007	-1.995926	0.00435	0.299138	0.264884	ENSG00000153046	ENST00000328908	T	0.44083	0.93	0.923	-1.85	0.07784	Chromo domain-like (1);Chromo domain/shadow (1);	.	.	.	.	T	0.07234	0.0183	.	.	.	0.80722	P	0.0	B	0.19817	0.039	B	0.18871	0.023	T	0.29181	-1.0020	7	0.22109	T	0.4	.	3.1919	0.06620	0.3542:0.24:0.4058:0.0	rs28360500;rs57339934	60	Q9Y232	CDYL1_HUMAN	G	60	ENSP00000330512:A60G	ENSP00000330512:A60G	A	+	2	0	CDYL	4680070	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.774000	0.04684	-1.574000	0.01657	-1.394000	0.01149	GCT			0.552	CDYL-001	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000039736.1		NM_004824	
ITPR3	3710	hgsc.bcm.edu;mdanderson.org	37	6	33638140	33638140	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr6:33638140G>T	ENST00000374316.5	+	20	3288	c.2228G>T	c.(2227-2229)cGc>cTc	p.R743L	ITPR3_ENST00000605930.1_Missense_Mutation_p.R743L			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	743					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	TGCTTGGACCGCCAGTACTTG	0.627																																					p.R743L													.	.			0			c.G2228T												109.0	100.0	103.0					6																	33638140		2203	4300	6503	SO:0001583	missense	3710	exon19			TGGACCGCCAGTA	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.2228G>T	6.37:g.33638140G>T	ENSP00000363435:p.Arg743Leu		Somatic	89	0	0		WXS	Illumina HiSeq	.	60	0.07	4	NM_002224	58	0.00	0	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	G	33	5.286877	0.95517	.	.	ENSG00000096433	ENST00000374316	D	0.96073	-3.9	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	D	0.97732	0.9256	M	0.84511	2.7	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98753	1.0721	10	0.87932	D	0	-30.0789	17.8678	0.88801	0.0:0.0:1.0:0.0	.	743	Q14573	ITPR3_HUMAN	L	743	ENSP00000363435:R743L	ENSP00000363435:R743L	R	+	2	0	ITPR3	33746118	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.748000	0.98867	2.209000	0.71365	0.563000	0.77884	CGC			0.627	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000040204.2		NM_002224	
CCDC170	80129	mdanderson.org	37	6	151815308	151815308	+	Silent	SNP	G	G	A			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr6:151815308G>A	ENST00000239374.7	+	1	144	c.45G>A	c.(43-45)tcG>tcA	p.S15S	CCDC170_ENST00000367290.5_Silent_p.S15S	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	15																	GTGCCGCTTCGCCAGCGCCCG	0.746																																					p.S15S													.	.			0			c.G45A												2.0	3.0	3.0					6																	151815308		1400	3244	4644	SO:0001819	synonymous_variant	80129	exon1			CGCTTCGCCAGCG	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.45G>A	6.37:g.151815308G>A			Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	13	0.15	2	NM_025059	0		0	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Silent	SNP	ENST00000239374.7	37	CCDS43515.1																																																																																					0.746	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000042727.2		NM_025059	
ELFN1	392617	broad.mit.edu;bcgsc.ca;mdanderson.org	37	7	1733102	1733102	+	Intron	SNP	G	G	T	rs4720922	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr7:1733102G>T	ENST00000424383.2	+	1	32				AC074389.7_ENST00000450458.1_lincRNA|AC074389.6_ENST00000382528.1_Missense_Mutation_p.L144M			P0C7U0	ELFN1_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 1						negative regulation of phosphatase activity (GO:0010923)|synapse organization (GO:0050808)	dendrite (GO:0030425)|excitatory synapse (GO:0060076)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)	1						GGTGCACCCAGACAGGTGCGT	0.567													G|||	921	0.183906	0.0083	0.2824	5008	,	,		22706	0.1627		0.2744	False		,,,				2504	0.2802				.													.	.			0			.																																									SO:0001627	intron_variant	0	.			CACCCAGACAGGT		CCDS59046.1	7p22.3	2013-02-11	2011-10-27	2011-10-27	ENSG00000225968	ENSG00000225968		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	33154	protein-coding gene	gene with protein product		614964	"""extracellular leucine-rich repeat and fibronectin type III containing 1"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 1"", ""protein phosphatase 1, regulatory subunit 28"""	PPP1R28		17868438	Standard	NM_001128636		Approved		uc010ksg.2	P0C7U0	OTTHUMG00000151495	ENST00000424383.2:c.-456+5316G>T	7.37:g.1733102G>T			Somatic	228	0.0043859649	1		WXS	Illumina HiSeq	Phase_I	203	0.04	9	.	0		0	H3BS57	Missense_Mutation	SNP	ENST00000424383.2	37	CCDS59046.1	427	0.1955128205128205	3	0.006097560975609756	102	0.281767955801105	104	0.18181818181818182	218	0.287598944591029	G	8.260	0.810947	0.16537	.	.	ENSG00000205971	ENST00000382528	.	.	.	1.69	1.69	0.24217	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	D	0.65815	0.995	P	0.60682	0.878	T	0.05801	-1.0863	6	0.87932	D	0	.	6.8425	0.23971	0.0:0.0:1.0:0.0	rs4720922;rs58424792;rs4720922	144	A2RU56	.	M	144	.	ENSP00000371968:L144M	L	-	1	2	AC074389.6	1699628	0.002000	0.14202	0.007000	0.13788	0.025000	0.11179	0.495000	0.22483	1.237000	0.43756	0.462000	0.41574	CTG			0.567	ELFN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000322893.2		NM_001128636	
OR2A15P	135942	bcgsc.ca	37	7	143815824	143815824	+	IGR	SNP	C	C	T			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr7:143815824C>T								OR2A2 (8167 upstream) : OR2A14 (10326 downstream)																							GGATGGCCGCCAGGATGCCCA	0.587																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	135942	.			GGCCGCCAGGATG																													7.37:g.143815824C>T			Somatic	60	0	0		WXS	Illumina HiSeq	Phase_1	84	0.06	5	.	0		0		RNA	SNP		37																																																																																					0	0.587										
CDCA2	157313	ucsc.edu	37	8	25364715	25364715	+	Missense_Mutation	SNP	G	G	A			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr8:25364715G>A	ENST00000330560.3	+	15	3010	c.2533G>A	c.(2533-2535)Gaa>Aaa	p.E845K	CDCA2_ENST00000380665.3_Missense_Mutation_p.E830K|CDCA2_ENST00000521098.2_3'UTR	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	845					mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		TTTACATTTGGAAAAAAATGG	0.393																																					p.E845K													CDCA2,NS,carcinoma,0,3	CDCA2	78	3	0			c.G2533A												68.0	65.0	66.0					8																	25364715		2203	4300	6503	SO:0001583	missense	157313	exon15			CATTTGGAAAAAA	BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 81"""					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.2533G>A	8.37:g.25364715G>A	ENSP00000328228:p.Glu845Lys		Somatic	76	0	0		RNA-Seq	Illumina HiSeq		124	0.02	3	NM_152562	106	0.16	17	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Missense_Mutation	SNP	ENST00000330560.3	37	CCDS6049.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.307667	0.81247	.	.	ENSG00000184661	ENST00000330560;ENST00000380665;ENST00000434814	T;T	0.44083	0.94;0.93	5.8	5.8	0.92144	.	0.722011	0.13275	N	0.400205	T	0.57725	0.2073	L	0.52573	1.65	0.09310	N	1	D;D	0.67145	0.996;0.996	P;P	0.59948	0.866;0.866	T	0.52510	-0.8566	10	0.56958	D	0.05	-3.8489	16.783	0.85567	0.0:0.0:1.0:0.0	.	830;845	E9PEI0;Q69YH5	.;CDCA2_HUMAN	K	845;830;244	ENSP00000328228:E845K;ENSP00000370040:E830K	ENSP00000328228:E845K	E	+	1	0	CDCA2	25420632	0.005000	0.15991	0.014000	0.15608	0.017000	0.09413	1.294000	0.33365	2.751000	0.94390	0.650000	0.86243	GAA			0.393	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000216891.3	rescued with RNA-seq	NM_152562	
RBMXP2	441391	bcgsc.ca	37	9	30690221	30690221	+	IGR	SNP	G	G	C	rs12340776	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr9:30690221G>C								snoU13 (511646 upstream) : AL590726.2 (80873 downstream)																							AGCACCAAGCGGTGGTGGCTG	0.493													G|||	1099	0.219449	0.4357	0.1398	5008	,	,		17325	0.1438		0.1183	False		,,,				2504	0.1656				.													.	.			0			.																																									SO:0001628	intergenic_variant	441391	.			CCAAGCGGTGGTG																													9.37:g.30690221G>C			Somatic	276	0	0		WXS	Illumina HiSeq	Phase_1	222	0.07	15	.	0		0		RNA	SNP		37																																																																																					0	0.493										
Unknown	0	bcgsc.ca	37	9	90796001	90796001	+	IGR	SNP	G	G	A	rs3818707	byFrequency	TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chr9:90796001G>A								U6 (182751 upstream) : U3 (193182 downstream)																							GCTTTTCAAGGCCCTGTGAGT	0.458													G|||	1540	0.307508	0.3457	0.2896	5008	,	,		21211	0.2153		0.331	False		,,,				2504	0.3395				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTCAAGGCCCTGT																													9.37:g.90796001G>A			Somatic	93	0	0		WXS	Illumina HiSeq	Phase_1	70	0.09	6	.	0		0		RNA	SNP		37																																																																																					0	0.458										
MT-ND2	4536	hgsc.bcm.edu;broad.mit.edu	37	M	1824	1824	+	5'Flank	SNP	T	T	C			TCGA-W4-A7U4-01A-12D-A435-10	TCGA-W4-A7U4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93e5db42-7b98-42ed-bb10-42cc65aa7f42	3a394593-a286-4619-ac57-928781488648	g.chrM:1824T>C	ENST00000361453.3	+	0	0				MT-ND1_ENST00000361390.2_5'Flank|MT-TV_ENST00000387342.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TM_ENST00000387377.1_RNA|MT-TF_ENST00000387314.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TQ_ENST00000387372.1_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|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 I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|lung(1)	3						CCAAGCATAATATAGCAAGGA	0.383																																					.													.	.			0			.																																									SO:0001631	upstream_gene_variant	6053	.			ATAATATAGCAAG			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891			M.37:g.1824T>C	Exception_encountered		Somatic	23	0	0		WXS	Illumina HiSeq	.	23	0.35	8	.	0		0	Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	RNA	SNP	ENST00000361453.3	37																																																																																						0.383	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				YP_003024027	
