#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_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	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
PIK3CD	5293	hgsc.bcm.edu;bcgsc.ca	37	1	9779982	9779982	+	Missense_Mutation	SNP	T	T	C			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:9779982T>C	ENST00000377346.4	+	10	1441	c.1246T>C	c.(1246-1248)Tgc>Cgc	p.C416R	PIK3CD_ENST00000536656.1_Missense_Mutation_p.C381R|PIK3CD_ENST00000543390.1_Missense_Mutation_p.C83R|PIK3CD_ENST00000361110.2_Missense_Mutation_p.C381R	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	416	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	TCTGCAGGACTGCCCCATTGC	0.647																																					p.C416R													.	.			0			c.T1246C												133.0	120.0	124.0					1																	9779982		2203	4300	6503	SO:0001583	missense	5293	exon10			CAGGACTGCCCCA		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase, catalytic, delta polypeptide"", ""phosphoinositide-3-kinase C"""	602839	"""phosphoinositide-3-kinase, catalytic, delta polypeptide"""			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.1246T>C	1.37:g.9779982T>C	ENSP00000366563:p.Cys416Arg		140	0	0		118	0.09	11	NM_005026	35	0.34	12	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	37	CCDS104.1	.	.	.	.	.	.	.	.	.	.	T	14.55	2.569189	0.45798	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563;ENST00000543390	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	5.23	5.23	0.72850	C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (1);	0.000000	0.85682	D	0.000000	T	0.74906	0.3778	L	0.45581	1.43	0.80722	D	1	P;D;D	0.76494	0.907;0.999;0.983	P;D;P	0.70487	0.664;0.969;0.88	T	0.71856	-0.4466	10	0.25751	T	0.34	-40.0069	15.123	0.72460	0.0:0.0:0.0:1.0	.	416;381;416	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	R	381;416;381;381;83	ENSP00000446444:C381R;ENSP00000366563:C416R;ENSP00000354410:C381R;ENSP00000443811:C83R	ENSP00000353766:C381R	C	+	1	0	PIK3CD	9702569	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	6.179000	0.71974	1.975000	0.57531	0.379000	0.24179	TGC			0.647	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000004235.1		NM_005026	
PRAMEF35P	100419649	bcgsc.ca	37	1	13171989	13171989	+	IGR	SNP	G	G	A	rs201114138		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:13171989G>A								RP13-221M14.3 (7521 upstream) : PRAMEF26 (44366 downstream)																							GCCATTGGCCGCTCACGTATA	0.453																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTGGCCGCTCACG																													1.37:g.13171989G>A			110	0	0		124	0.08	10	.	0		0		RNA	SNP		37																																																																																					0	0.453										
PRAMEF18	391003	bcgsc.ca;mdanderson.org	37	1	13474974	13474974	+	Silent	SNP	G	G	A	rs201607561	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:13474974G>A	ENST00000376126.2	-	3	1154	c.1155C>T	c.(1153-1155)caC>caT	p.H385H		NM_001099850.1	NP_001093320.1	Q5VWM3	PRA18_HUMAN	PRAME family member 18	385					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					lung(2)|ovary(1)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGTCATTGCCGTGAAAGCAGA	0.572													g|||	396	0.0790735	0.0061	0.0173	5008	,	,		15994	0.2659		0.0388	False		,,,				2504	0.0706				p.H385H													.	PRAMEF19	6		0			c.C1155T							G		81,4243		3,75,2084	30.0	33.0	32.0		1155	-1.3	0.0	1	dbSNP_134	32	371,8123		9,353,3885	no	coding-synonymous	PRAMEF18	NM_001099850.1		12,428,5969	AA,AG,GG		4.3678,1.8733,3.5263		385/480	13474974	452,12366	2162	4247	6409	SO:0001819	synonymous_variant	391003	exon3			ATTGCCGTGAAAG			1p36.21	2013-01-17			ENSG00000204491			"""-"""	30693	protein-coding gene	gene with protein product							Standard			Approved	OTTHUMG00000002932		Q5VWM3	OTTHUMG00000002932	ENST00000376126.2:c.1155C>T	1.37:g.13474974G>A			700	0	0		670	0.04	24	NM_001099790	0		0		Silent	SNP	ENST00000376126.2	37	CCDS41258.1																																																																																					0.572	PRAMEF18-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000008177.2		NM_001099850	
KAZN	23254	hgsc.bcm.edu	37	1	15439098	15439098	+	Intron	SNP	C	C	T	rs114844404		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:15439098C>T	ENST00000376030.2	+	14	2457					NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein						keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						CTTTTTTTCTCCTCCCGGGAG	0.587																																					.													.	.			0			.																																									SO:0001627	intron_variant	200197	.			TTTTCTCCTCCCG	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"""Sterile alpha motif (SAM) domain containing"""	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.2163+61C>T	1.37:g.15439098C>T			72	0	0		75	0.36	27	.	9	0.00	0	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	RNA	SNP	ENST00000376030.2	37	CCDS152.2																																																																																					0.587	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000005690.2		NM_001017999	
FAM46B	115572	bcgsc.ca	37	1	27332465	27332466	+	Missense_Mutation	DNP	GT	GT	AC	rs61737591|rs61737590	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:27332465_27332466GT>AC	ENST00000289166.5	-	2	1412_1413	c.1247_1248AC>GT	c.(1246-1248)cAC>cGT	p.H416R		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	416										breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		TGGGATAGGCGTGAGCCAGGAG	0.653																																					p.H416R													.	FAM46B	44		0			c.A1247G																																									SO:0001583	missense	115572	exon2			ATAGGCGTGAGCC	AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.1247_1248delinsAC	1.37:g.27332465_27332466delinsAC	ENSP00000289166:p.His416Arg		226	0	0		218	0.04	9	NM_052943	582	0.00	0		Missense_Mutation	DNP	ENST00000289166.5	37	CCDS294.2																																																																																					0.653	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000012347.2		NM_052943	
FAM183A	440585	broad.mit.edu;ucsc.edu	37	1	43610910	43610910	+	5'Flank	SNP	T	T	G	rs626842	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:43610910T>G	ENST00000335282.4	+	0	0				FAM183A_ENST00000410048.1_De_novo_Start_OutOfFrame	NM_001101376.2	NP_001094846.2	A6NL82	F183A_HUMAN	family with sequence similarity 183, member A											kidney(1)|large_intestine(1)|lung(2)|ovary(3)	7						TGCAGGGCCATTGACAGAGAA	0.512													G|||	2626	0.524361	0.857	0.5058	5008	,	,		20644	0.3274		0.4175	False		,,,				2504	0.4008				.													.	.			0			.																																									SO:0001631	upstream_gene_variant	440585	.			GGGCCATTGACAG	AI192630, AI375550, AL139138	CCDS44126.1	1p34.2	2008-08-11			ENSG00000186973	ENSG00000186973			34347	protein-coding gene	gene with protein product						11181995	Standard	NM_001101376		Approved	LOC440585, hCG23177	uc009vwo.3	A6NL82	OTTHUMG00000007286		1.37:g.43610910T>G	Exception_encountered		60	0	0		44	0.20	9	.	0		0	B7ZBL8	Translation_Start_Site	SNP	ENST00000335282.4	37	CCDS44126.1																																																																																					0.512	FAM183A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000019024.3		NM_001101376	
BTBD19	149478	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	45275921	45275921	+	Silent	SNP	G	G	A			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:45275921G>A	ENST00000450269.1	+	2	462	c.123G>A	c.(121-123)gaG>gaA	p.E41E	BTBD19_ENST00000409335.2_Silent_p.E41E|TCTEX1D4_ENST00000372200.1_5'Flank|BTBD19_ENST00000453418.1_Silent_p.E41E	NM_001136537.1	NP_001130009.1	C9JJ37	BTBDJ_HUMAN	BTB (POZ) domain containing 19	41	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									breast(1)|endometrium(1)	2						AACGGCAGGAGGTATTTGCCC	0.602																																					p.E41E													.	.			0			c.G123A												66.0	59.0	62.0					1																	45275921		692	1591	2283	SO:0001819	synonymous_variant	149478	exon2			GCAGGAGGTATTT			1p34.1	2013-01-08			ENSG00000222009	ENSG00000222009		"""BTB/POZ domain containing"""	27145	protein-coding gene	gene with protein product							Standard	NM_001136537		Approved		uc010ole.1	C9JJ37	OTTHUMG00000008493	ENST00000450269.1:c.123G>A	1.37:g.45275921G>A			57	0	0		62	0.10	6	NM_001136537	0		0	B4E384|B7ZC36|B7ZC37	Silent	SNP	ENST00000450269.1	37																																																																																						0.602	BTBD19-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				NM_001136537	
JAK1	3716	hgsc.bcm.edu	37	1	65330611	65330611	+	Frame_Shift_Del	DEL	T	T	-			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:65330611delT	ENST00000342505.4	-	8	1283	c.1035delA	c.(1033-1035)aaafs	p.K345fs		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	345	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TATTTTCCAGTTTTTTCCGCT	0.343			Mis		ALL																																p.L346fs				Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.,1	JAK1	209		0			c.1036delC												136.0	125.0	128.0					1																	65330611		1825	4079	5904	SO:0001589	frameshift_variant	3716	exon8			TTCCAGTTTTTTC	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.1035delA	1.37:g.65330611delT	ENSP00000343204:p.Lys345fs		146	0	0		141	0.07	10	NM_002227	38	0.00	0	Q59GQ2|Q9UD26	Frame_Shift_Del	DEL	ENST00000342505.4	37	CCDS41346.1																																																																																					0.343	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000025791.1		NM_002227	
Unknown	0	bcgsc.ca	37	1	79215138	79215138	+	IGR	SNP	G	G	T	rs12135932	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:79215138G>T								AC104837.1 (62293 upstream) : ELTD1 (140310 downstream)																							ACTTGCAAAGGCCCGATGAAG	0.433													G|||	1715	0.342452	0.3797	0.4856	5008	,	,		20401	0.2351		0.3429	False		,,,				2504	0.3006				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCAAAGGCCCGAT																													1.37:g.79215138G>T			48	0	0		44	0.14	6	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.433										
PSAT1P3	729779	bcgsc.ca	37	1	79520923	79520923	+	IGR	SNP	T	T	C	rs17131734	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:79520923T>C								ELTD1 (48520 upstream) : AC093430.1 (79894 downstream)																							ATTTGAGATTTGATGGAGCTA	0.433													T|||	969	0.19349	0.1369	0.2522	5008	,	,		20467	0.1548		0.174	False		,,,				2504	0.2883				.													.	.			0			.																																									SO:0001628	intergenic_variant	729779	.			GAGATTTGATGGA																													1.37:g.79520923T>C			31	0	0		59	0.10	6	.	0		0		RNA	SNP		37																																																																																					0	0.433										
Unknown	0	bcgsc.ca	37	1	157679691	157679691	+	IGR	SNP	C	C	T	rs17676303	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:157679691C>T								FCRL3 (9044 upstream) : FCRL2 (35831 downstream)																							GGATTGATGCCTGGGCTCAGC	0.473													C|||	788	0.157348	0.062	0.1945	5008	,	,		16245	0.2103		0.2346	False		,,,				2504	0.1258				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGATGCCTGGGCT																													1.37:g.157679691C>T			181	0	0		163	0.09	15	.	45	0.00	0		RNA	SNP		37																																																																																					0	0.473										
Unknown	0	bcgsc.ca	37	1	157679783	157679783	+	IGR	SNP	A	A	G	rs17727309	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:157679783A>G								FCRL3 (9136 upstream) : FCRL2 (35739 downstream)																							ACTGGTGCCCAACCTGGATTA	0.493													A|||	788	0.157348	0.062	0.1945	5008	,	,		19384	0.2103		0.2346	False		,,,				2504	0.1258				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTGCCCAACCTGG																													1.37:g.157679783A>G			195	0	0		171	0.06	11	.	6	0.17	1		RNA	SNP		37																																																																																					0	0.493										
Unknown	0	bcgsc.ca	37	1	157680114	157680114	+	IGR	SNP	T	T	C	rs17727339	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:157680114T>C								FCRL3 (9467 upstream) : FCRL2 (35408 downstream)																							CCCTGATCATTGCAAACGTTT	0.423													t|||	788	0.157348	0.062	0.1945	5008	,	,		20322	0.2103		0.2346	False		,,,				2504	0.1258				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GATCATTGCAAAC																													1.37:g.157680114T>C			65	0	0		60	0.10	6	.	85	1.00	85		RNA	SNP		37																																																																																					0	0.423										
Unknown	0	bcgsc.ca	37	1	158493554	158493554	+	IGR	SNP	A	A	G	rs6656837	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:158493554A>G								RP11-144L1.4 (28878 upstream) : OR6Y1 (23363 downstream)																							AGTTGATGTCACTGATCATCA	0.413													A|||	317	0.0632987	0.1006	0.062	5008	,	,		16870	0.0		0.0984	False		,,,				2504	0.0429				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GATGTCACTGATC																													1.37:g.158493554A>G			49	0	0		58	0.09	5	.	0		0		RNA	SNP		37																																																																																					0	0.413										
Unknown	0	bcgsc.ca	37	1	160865612	160865612	+	IGR	SNP	A	A	C	rs112211905	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:160865612A>C								ITLN1 (10652 upstream) : RP11-312J18.6 (35916 downstream)																							AGCTGTTCCAATCTCCACGTC	0.393													-|||	90	0.0179712	0.0053	0.0418	5008	,	,		20868	0.0		0.0497	False		,,,				2504	0.0041				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTTCCAATCTCCA																													1.37:g.160865612A>C			141	0	0		136	0.08	11	.	196	0.00	0		RNA	SNP		37																																																																																					0	0.393										
SDCCAG3P2	646891	bcgsc.ca	37	1	175013936	175013936	+	IGR	SNP	T	T	A	rs3737935	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:175013936T>A								MRPS14 (21375 upstream) : TNN (23057 downstream)																							GCTTCACCACTGTCAGGCTGG	0.577													T|||	830	0.165735	0.1649	0.0965	5008	,	,		10150	0.3006		0.1342	False		,,,				2504	0.1094				.													.	.			0			.																																									SO:0001628	intergenic_variant	646891	.			CACCACTGTCAGG																													1.37:g.175013936T>A			82	0	0		92	0.07	6	.	0		0		RNA	SNP		37																																																																																					0	0.577										
Unknown	0	bcgsc.ca	37	1	240136251	240136251	+	IGR	SNP	C	C	G	rs4659558	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr1:240136251C>G								RP11-35L17.3 (55996 upstream) : FMN2 (118928 downstream)																							ATTGCACTGGCCGACTGGAAG	0.433													G|||	715	0.142772	0.1641	0.1801	5008	,	,		20071	0.1429		0.0447	False		,,,				2504	0.1881				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CACTGGCCGACTG																													1.37:g.240136251C>G			27	0	0		28	0.14	4	.	0		0		RNA	SNP		37																																																																																					0	0.433										
C10orf105	414152	ucsc.edu	37	10	73497499	73497499	+	5'UTR	SNP	G	G	A	rs377075213|rs534466092|rs559098698	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr10:73497499G>A	ENST00000398786.2	-	0	82				CDH23_ENST00000224721.6_Intron	NM_001168390.1	NP_001161862.1	Q8TEF2	CJ105_HUMAN	chromosome 10 open reading frame 105							integral component of membrane (GO:0016021)											GATTCCAGCCGCAGTGGCCTG	0.612													G|||	6	0.00119808	0.0	0.0	5008	,	,		15724	0.0		0.001	False		,,,				2504	0.0051				.													.	C10orf105	11		0			.																																									SO:0001623	5_prime_UTR_variant	414152	.			CCAGCCGCAGTGG	AK074172	CCDS44430.1	10q22.1	2012-06-01			ENSG00000214688	ENSG00000214688			20304	protein-coding gene	gene with protein product							Standard	NM_001164375		Approved	FLJ00245	uc001jsa.2	Q8TEF2	OTTHUMG00000018427	ENST00000398786.2:c.-20C>T	10.37:g.73497499G>A			48	0	0		45	0.09	4	.	0		0		Missense_Mutation	SNP	ENST00000398786.2	37	CCDS44430.1	.	.	.	.	.	.	.	.	.	.	G	8.726	0.915416	0.17907	.	.	ENSG00000214688	ENST00000398786	.	.	.	3.02	-6.05	0.02172	.	.	.	.	.	T	0.23532	0.0569	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30937	-0.9961	5	0.54805	T	0.06	.	1.2896	0.02058	0.4046:0.1057:0.2994:0.1903	.	.	.	.	V	28	.	ENSP00000381766:A28V	A	-	2	0	C10orf105	73167505	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.122000	0.03267	-1.713000	0.01392	-1.543000	0.00907	GCG			0.612	C10orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000048551.2		NM_001164375	
PAPSS2	9060	bcgsc.ca	37	10	89473069	89473069	+	Splice_Site	SNP	T	T	A	rs375158238|rs367885911		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr10:89473069T>A	ENST00000361175.4	+	3	750		c.e3+2		PAPSS2_ENST00000427144.2_Splice_Site|PAPSS2_ENST00000456849.1_Splice_Site	NM_004670.3	NP_004661.2	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|blood coagulation (GO:0007596)|bone development (GO:0060348)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)	p.?(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	20		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		TTCGCAAAGGTaaaaaaaaaa	0.458																																					.													PAPSS2,NS,lymphoid_neoplasm,0,2	PAPSS2	46	2	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.381+2T>A												33.0	31.0	32.0					10																	89473069		2203	4299	6502	SO:0001630	splice_region_variant	9060	exon3			CAAAGGTAAAAAA	AF091242	CCDS7385.1, CCDS44453.1	10q24	2008-02-07			ENSG00000198682	ENSG00000198682	2.7.7.4, 2.7.1.25		8604	protein-coding gene	gene with protein product		603005				9771708	Standard	NM_004670		Approved	ATPSK2	uc001kex.3	O95340	OTTHUMG00000018683	ENST00000361175.4:c.381+2T>A	10.37:g.89473069T>A			90	0.0888888889	8		88	0.22	19	NM_004670	0		0	Q9BZL2|Q9P0G6|Q9UHM1|Q9UKD3|Q9UP30	Splice_Site	SNP	ENST00000361175.4	37	CCDS7385.1	.	.	.	.	.	.	.	.	.	.	T	13.05	2.122187	0.37436	.	.	ENSG00000198682	ENST00000361175;ENST00000456849;ENST00000427144;ENST00000371981	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9515	0.52959	0.0:0.0693:0.0:0.9307	.	.	.	.	.	-1	.	.	.	+	.	.	PAPSS2	89463049	1.000000	0.71417	0.962000	0.40283	0.179000	0.23085	5.984000	0.70548	2.210000	0.71456	0.482000	0.46254	.			0.458	PAPSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000049229.1			Intron
PIK3C2A	5286	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	17170258	17170258	+	Silent	SNP	G	G	A			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr11:17170258G>A	ENST00000265970.7	-	4	1403	c.1404C>T	c.(1402-1404)ggC>ggT	p.G468G	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Silent_p.G88G	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	468	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						GAACATAGCTGCCAACATCTA	0.343																																					p.G468G													.	.			0			c.C1404T												109.0	99.0	102.0					11																	17170258		2200	4293	6493	SO:0001819	synonymous_variant	5286	exon4			ATAGCTGCCAACA	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"""phosphoinositide-3-kinase, class 2, alpha polypeptide"""			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.1404C>T	11.37:g.17170258G>A			59	0	0		77	0.10	8	NM_002645	6	0.17	1	B0LPH2|B4E2G4|Q14CQ9	Silent	SNP	ENST00000265970.7	37	CCDS7824.1																																																																																					0.343	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000387553.1		NM_002645	
Unknown	0	bcgsc.ca	37	11	49329521	49329521	+	IGR	SNP	T	T	C	rs1164671	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr11:49329521T>C								FOLH1 (99299 upstream) : CTD-2026G22.1 (58101 downstream)																							ATTTTGGTCATAAGTCATCCC	0.428													T|||	1043	0.208267	0.09	0.196	5008	,	,		15218	0.2639		0.1899	False		,,,				2504	0.3384				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGGTCATAAGTCA																													11.37:g.49329521T>C			132	0	0		119	0.04	5	.	0		0		RNA	SNP		37																																																																																					0	0.428										
RP11-360K13.1	0	broad.mit.edu	37	11	96514998	96514999	+	lincRNA	INS	-	-	A	rs67317023|rs149392521		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr11:96514998_96514999insA	ENST00000527528.1	+	0	158																											GCTTAGTTATTaaaaaaaaaaa	0.366																																					.													.	.			0			.																																											0	.			AGTTATTAAAAAA																													11.37:g.96515009_96515009dupA			11	0	0		9	0.33	3	.	1	0.00	0		RNA	INS	ENST00000527528.1	37																																																																																						0.366	RP11-360K13.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000395474.1			
OR8G3P	387815	bcgsc.ca	37	11	124086175	124086175	+	IGR	SNP	T	T	C	rs2508890	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr11:124086175T>C								OR10D3 (29223 upstream) : OR8G1 (34247 downstream)																							CCAAAGCCTTTAGCACTTGCA	0.493																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	387815	.			AGCCTTTAGCACT																													11.37:g.124086175T>C			90	0	0		79	0.08	6	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.493										
SCNN1A	6337	bcgsc.ca	37	12	6472752	6472753	+	Missense_Mutation	DNP	GC	GC	AA	rs55859427|rs55797039	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr12:6472752_6472753GC>AA	ENST00000228916.2	-	3	638_639	c.540_541GC>TT	c.(538-543)ctGCgg>ctTTgg	p.R181W	SCNN1A_ENST00000396966.2_Missense_Mutation_p.R181W|SCNN1A_ENST00000358945.3_Missense_Mutation_p.R181W|SCNN1A_ENST00000540037.1_5'UTR|SCNN1A_ENST00000543768.1_Missense_Mutation_p.R204W|SCNN1A_ENST00000360168.3_Missense_Mutation_p.R240W|SCNN1A_ENST00000538979.1_Intron	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	181			R -> W (functional polymorphism; significant increase of amiloride- sensitive sodium currents; dbSNP:rs55797039). {ECO:0000269|PubMed:16207733, ECO:0000269|PubMed:19462466}.		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	AGAGTCCCCCGCAGGTCGCGAC	0.678																																					p.R240W													.	SCNN1A	54		0			c.G717T	GRCh37	CM055536	SCNN1A	M	rs55797039																																				SO:0001583	missense	6337	exon2			TCCCCCGCAGGTC	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10599	protein-coding gene	gene with protein product		600228	"""sodium channel, nonvoltage-gated 1 alpha"", ""sodium channel, non-voltage-gated 1 alpha"""	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.540_541delinsAA	12.37:g.6472752_6472753delinsAA	ENSP00000228916:p.Arg181Trp		33	0	0		81	0.10	8	NM_001159576	3	0.00	0	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	DNP	ENST00000228916.2	37	CCDS8543.1																																																																																					0.678	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000399055.1			
MUC19	283463	bcgsc.ca;mdanderson.org	37	12	40834376	40834376	+	Splice_Site	SNP	C	C	G	rs10878592	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr12:40834376C>G	ENST00000454784.4	+	22	2449	c.1716C>G	c.(1714-1716)tgC>tgG	p.C572W	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	572					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						TTATTTCCAGCGTCTGTCGGG	0.343													C|||	2594	0.517971	0.3601	0.5648	5008	,	,		19095	0.4742		0.5447	False		,,,				2504	0.7157				.													.	.			0			.																																									SO:0001630	splice_region_variant	283463	.			TTCCAGCGTCTGT	AY236870		12q12	2012-04-20	2006-03-14		ENSG00000205592	ENSG00000205592		"""Mucins"""	14362	protein-coding gene	gene with protein product		612170				12882755	Standard	NM_173600		Approved	FLJ35746	uc021qxa.1	Q7Z5P9	OTTHUMG00000060732	ENST00000454784.4:c.1716-1C>G	12.37:g.40834376C>G			319	0	0		351	0.08	27	.	0		0	Q8NA85	Missense_Mutation	SNP	ENST00000454784.4	37		1086	0.49725274725274726	198	0.4024390243902439	215	0.5939226519337016	247	0.4318181818181818	426	0.5620052770448549	C	12.41	1.930900	0.34096	.	.	ENSG00000205592	ENST00000425730	.	.	.	5.44	0.143	0.14820	.	.	.	.	.	T	0.00012	0.0000	M	0.90814	3.15	0.09310	P	0.9999999999658039	.	.	.	.	.	.	T	0.43702	-0.9375	4	.	.	.	.	5.5996	0.17347	0.0:0.3108:0.1367:0.5525	rs10878592;rs17445029;rs17521264;rs52833400;rs10878592	.	.	.	W	801	.	.	C	+	3	2	MUC19	39120643	0.983000	0.35010	0.976000	0.42696	0.471000	0.32888	0.078000	0.14761	-0.209000	0.10156	-1.068000	0.02270	TGC			0.343	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	Missense_Mutation
MUC19	283463	bcgsc.ca	37	12	40835734	40835734	+	Missense_Mutation	SNP	C	C	G	rs7966110	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr12:40835734C>G	ENST00000454784.4	+	25	2815	c.2082C>G	c.(2080-2082)atC>atG	p.I694M	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	694	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.		I -> M (in dbSNP:rs7966110).		cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						TCTGCCACATCTATGGGGAAG	0.368													C|||	2596	0.518371	0.3601	0.5663	5008	,	,		16912	0.4742		0.5447	False		,,,				2504	0.7168				.													.	.			0			.																																									SO:0001583	missense	283463	.			CCACATCTATGGG	AY236870		12q12	2012-04-20	2006-03-14		ENSG00000205592	ENSG00000205592		"""Mucins"""	14362	protein-coding gene	gene with protein product		612170				12882755	Standard	NM_173600		Approved	FLJ35746	uc021qxa.1	Q7Z5P9	OTTHUMG00000060732	ENST00000454784.4:c.2082C>G	12.37:g.40835734C>G	ENSP00000476404:p.Ile694Met		171	0	0		193	0.05	10	.	0		0	Q8NA85	Missense_Mutation	SNP	ENST00000454784.4	37		1086	0.49725274725274726	198	0.4024390243902439	215	0.5939226519337016	247	0.4318181818181818	426	0.5620052770448549	C	15.04	2.715889	0.48622	.	.	ENSG00000205592	ENST00000425730	.	.	.	4.95	3.09	0.35607	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	0.09310	P	0.999999999999998	.	.	.	.	.	.	T	0.49234	-0.8961	5	0.72032	D	0.01	.	8.9957	0.36050	0.0:0.7499:0.0:0.2501	rs7966110;rs17445043;rs52818908;rs7966110	.	.	.	M	923	.	ENSP00000395253:I923M	I	+	3	3	MUC19	39122001	0.303000	0.24463	1.000000	0.80357	0.976000	0.68499	-0.406000	0.07187	1.210000	0.43336	-0.439000	0.05793	ATC			0.368	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca	37	12	40951596	40951596	+	Intron	SNP	A	A	G	rs3751167	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr12:40951596A>G	ENST00000454784.4	+	70	18503							Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric						cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						CATCTTTTCCACTTTTCTTGA	0.318													A|||	788	0.157348	0.2065	0.1484	5008	,	,		18058	0.1706		0.161	False		,,,				2504	0.0798				.													.	.			0			.																																									SO:0001627	intron_variant	283463	.			TTTTCCACTTTTC	AY236870		12q12	2012-04-20	2006-03-14		ENSG00000205592	ENSG00000205592		"""Mucins"""	14362	protein-coding gene	gene with protein product		612170				12882755	Standard	NM_173600		Approved	FLJ35746	uc021qxa.1	Q7Z5P9	OTTHUMG00000060732	ENST00000454784.4:c.10890+277A>G	12.37:g.40951596A>G			129	0	0		134	0.07	10	.	0		0	Q8NA85	Silent	SNP	ENST00000454784.4	37																																																																																						0.318	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca	37	12	40951605	40951605	+	Intron	SNP	G	G	A	rs3751168	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr12:40951605G>A	ENST00000454784.4	+	70	18503							Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric						cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						CACTTTTCTTGATTTGCTCTT	0.323													A|||	997	0.199081	0.3585	0.1571	5008	,	,		17969	0.1706		0.163	False		,,,				2504	0.0798				.													.	.			0			.																																									SO:0001627	intron_variant	283463	.			TTTCTTGATTTGC	AY236870		12q12	2012-04-20	2006-03-14		ENSG00000205592	ENSG00000205592		"""Mucins"""	14362	protein-coding gene	gene with protein product		612170				12882755	Standard	NM_173600		Approved	FLJ35746	uc021qxa.1	Q7Z5P9	OTTHUMG00000060732	ENST00000454784.4:c.10890+286G>A	12.37:g.40951605G>A			140	0	0		137	0.07	10	.	0		0	Q8NA85	Silent	SNP	ENST00000454784.4	37																																																																																						0.323	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
Unknown	0	bcgsc.ca	37	12	43965108	43965108	+	IGR	SNP	T	T	A	rs11611126	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr12:43965108T>A								ADAMTS20 (19384 upstream) : RP11-350F4.2 (147687 downstream)																							TCTTCTCCAATACAGTTCTCA	0.433													T|||	802	0.160144	0.0204	0.2651	5008	,	,		20799	0.2768		0.1352	False		,,,				2504	0.18				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTCCAATACAGTT																													12.37:g.43965108T>A			84	0	0		126	0.06	7	.	0		0		RNA	SNP		37																																																																																					0	0.433										
BEST3	144453	bcgsc.ca	37	12	70037520	70037520	+	Missense_Mutation	SNP	G	G	A	rs61747221	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr12:70037520G>A	ENST00000331471.4	-	10	1319	c.1148C>T	c.(1147-1149)cCa>cTa	p.P383L		NM_001282614.1	NP_001269543.1	Q8N1M1	BEST3_HUMAN	bestrophin 3	0					negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			ctgagggagtgggatttttat	0.443													G|||	691	0.137979	0.1694	0.062	5008	,	,		21522	0.2341		0.0875	False		,,,				2504	0.1022				.													.	.			0			.																																									SO:0001583	missense	144453	.			GGGAGTGGGATTT	AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17105	protein-coding gene	gene with protein product		607337	"""vitelliform macular dystrophy 2-like 3"""	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000331471.4:c.1148C>T	12.37:g.70037520G>A	ENSP00000329064:p.Pro383Leu		137	0	0		167	0.04	7	.	0		0	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Missense_Mutation	SNP	ENST00000331471.4	37		318	0.14560439560439561	81	0.16463414634146342	29	0.08011049723756906	140	0.24475524475524477	68	0.08970976253298153	G	9.433	1.086090	0.20390	.	.	ENSG00000127325	ENST00000331471	D	0.98192	-4.78	3.74	-0.249	0.13011	.	.	.	.	.	T	0.00412	0.0013	.	.	.	0.80722	P	0.0	B	0.19583	0.037	B	0.20955	0.032	T	0.54384	-0.8302	7	0.48119	T	0.1	.	3.8985	0.09150	0.3062:0.1853:0.5085:0.0	.	383	Q8N1M1-1	.	L	383	ENSP00000329064:P383L	ENSP00000329064:P383L	P	-	2	0	BEST3	68323787	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.112000	0.15479	-0.057000	0.13199	-0.137000	0.14449	CCA			0.443	BEST3-008	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000403865.1		NM_152439	
HSP90B1	7184	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	104336993	104336993	+	Missense_Mutation	SNP	G	G	C			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr12:104336993G>C	ENST00000299767.5	+	13	1968	c.1786G>C	c.(1786-1788)Gtg>Ctg	p.V596L		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	596					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	CAAGGAAGGAGTGAAGTTCGA	0.423																																					p.V596L													.	.			0			c.G1786C												71.0	73.0	72.0					12																	104336993		2203	4300	6503	SO:0001583	missense	7184	exon13			GAAGGAGTGAAGT	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"""Heat shock proteins / HSPC"""	12028	protein-coding gene	gene with protein product		191175	"""tumor rejection antigen (gp96) 1"""	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.1786G>C	12.37:g.104336993G>C	ENSP00000299767:p.Val596Leu		80	0	0		97	0.11	11	NM_003299	2786	0.23	635	Q96A97	Missense_Mutation	SNP	ENST00000299767.5	37	CCDS9094.1	.	.	.	.	.	.	.	.	.	.	G	6.633	0.485196	0.12641	.	.	ENSG00000166598	ENST00000299767;ENST00000421266	T	0.06142	3.34	5.85	4.97	0.65823	.	0.119952	0.56097	D	0.000025	T	0.01730	0.0055	N	0.00670	-1.27	0.58432	D	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.37454	-0.9705	10	0.02654	T	1	.	10.5807	0.45255	0.0691:0.1327:0.7982:0.0	.	596	P14625	ENPL_HUMAN	L	596;346	ENSP00000299767:V596L	ENSP00000299767:V596L	V	+	1	0	HSP90B1	102861123	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	4.705000	0.61838	1.622000	0.50330	0.643000	0.83706	GTG			0.423	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000407349.1		NM_003299	
VPS33A	65082	bcgsc.ca	37	12	122723203	122723203	+	Silent	SNP	G	G	A			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr12:122723203G>A	ENST00000267199.4	-	10	1345	c.1233C>T	c.(1231-1233)tgC>tgT	p.C411C	RP11-512M8.5_ENST00000535844.1_Silent_p.C372C	NM_022916.4	NP_075067.2	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33 homolog A (S. cerevisiae)	411					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of developmental pigmentation (GO:0048070)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	28	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)		CGGATTGGAGGCAAACTAGTC	0.343																																					p.C411C													.	VPS33A	61		0			c.C1233T												185.0	175.0	178.0					12																	122723203		2203	4300	6503	SO:0001819	synonymous_variant	65082	exon10			TTGGAGGCAAACT	AK026048	CCDS9231.1	12q24.31	2008-06-23	2006-04-04		ENSG00000139719	ENSG00000139719			18179	protein-coding gene	gene with protein product		610034	"""vacuolar protein sorting 33A (yeast)"""			11250079	Standard	NM_022916		Approved		uc001ucd.3	Q96AX1	OTTHUMG00000168920	ENST00000267199.4:c.1233C>T	12.37:g.122723203G>A			119	0	0		154	0.05	7	NM_022916	177	0.00	0	Q547V4|Q9H5Q0	Silent	SNP	ENST00000267199.4	37	CCDS9231.1																																																																																					0.343	VPS33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000401607.2			
RP11-556N21.1	0	bcgsc.ca	37	13	25144717	25144717	+	RNA	SNP	C	C	A	rs71218558|rs3742168	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr13:25144717C>A	ENST00000453498.1	+	0	258																											TTAACACAGCCCCTGCTGGTA	0.403													a|||	1419	0.283347	0.1566	0.3473	5008	,	,		15761	0.378		0.3151	False		,,,				2504	0.2791				.													.	.			0			.																																											374491	.			CACAGCCCCTGCT																													13.37:g.25144717C>A			105	0.0095238095	1		127	0.05	6	.	0		0		RNA	SNP	ENST00000453498.1	37																																																																																						0.403	RP11-556N21.1-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript		OTTHUMT00000044193.1			
COX17P1	81993	bcgsc.ca	37	13	47065127	47065127	+	IGR	SNP	G	G	A	rs200135094	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr13:47065127G>A								RP11-189B4.6 (31807 upstream) : LRCH1 (62175 downstream)																							GGCCGCTGAAGCCCTGCTGCA	0.557													g|||	2	0.000399361	0.0	0.0	5008	,	,		16040	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	81993	.			GCTGAAGCCCTGC																													13.37:g.47065127G>A			228	0	0		203	0.04	9	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.557										
TARDBPP2	440142	bcgsc.ca	37	13	60849048	60849048	+	IGR	SNP	C	C	T	rs9528094	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr13:60849048C>T								LINC00434 (59968 upstream) : TDRD3 (121542 downstream)																							TACAGAAATCCAGTGTCTCAG	0.512													C|||	2336	0.466454	0.3563	0.4207	5008	,	,		17887	0.5218		0.5139	False		,,,				2504	0.5419				.													.	.			0			.																																									SO:0001628	intergenic_variant	440142	.			GAAATCCAGTGTC																													13.37:g.60849048C>T			46	0	0		40	0.10	4	.	0		0		RNA	SNP		37																																																																																					0	0.512										
RP11-754I20.1	0	broad.mit.edu	37	14	19114215	19114215	+	RNA	DEL	T	T	-	rs142626582		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:19114215delT	ENST00000553170.1	+	0	71																											caagctcaagttgaactgaat	0.353																																					.													.	.			0			.																																											0	.			CTCAAGTTGAACT																													14.37:g.19114215delT			5	0	0		7	0.43	3	.	0		0		RNA	DEL	ENST00000553170.1	37																																																																																						0.353	RP11-754I20.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000408394.1			
DOCK11P1	100132537	bcgsc.ca	37	14	45329860	45329860	+	IGR	SNP	C	C	T	rs17115657	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:45329860C>T								RP11-398E10.1 (77828 upstream) : RP11-857B24.1 (16216 downstream)																							CCTGCATATGCTAATGGACCA	0.423													C|||	367	0.0732827	0.056	0.0375	5008	,	,		20819	0.1002		0.0497	False		,,,				2504	0.1186				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CATATGCTAATGG																													14.37:g.45329860C>T			138	0	0		169	0.04	7	.	0		0		RNA	SNP		37																																																																																					0	0.423										
DOCK11P1	100132537	bcgsc.ca	37	14	45329930	45329930	+	IGR	SNP	A	A	G	rs8016855	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:45329930A>G								RP11-398E10.1 (77898 upstream) : RP11-857B24.1 (16146 downstream)																							TCATGTCCACATAAACAGAGG	0.388													G|||	1358	0.271166	0.7012	0.1354	5008	,	,		21155	0.1002		0.1093	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTCCACATAAACA																													14.37:g.45329930A>G			113	0	0		157	0.08	12	.	0		0		RNA	SNP		37																																																																																					0	0.388										
DOCK11P1	100132537	bcgsc.ca	37	14	45330315	45330315	+	IGR	SNP	A	A	G	rs17633092	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:45330315A>G								RP11-398E10.1 (78283 upstream) : RP11-857B24.1 (15761 downstream)																							GACATTCGCCATACCAAATTT	0.353													A|||	298	0.0595048	0.0061	0.0331	5008	,	,		17282	0.1002		0.0497	False		,,,				2504	0.1186				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTCGCCATACCAA																													14.37:g.45330315A>G			323	0	0		394	0.04	14	.	0		0		RNA	SNP		37																																																																																					0	0.353										
DOCK11P1	100132537	bcgsc.ca	37	14	45330929	45330929	+	IGR	SNP	T	T	C	rs11846198	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:45330929T>C								RP11-398E10.1 (78897 upstream) : RP11-857B24.1 (15147 downstream)																							CTAAGCTACATTGGAGATCAG	0.433													t|||	1157	0.23103	0.559	0.1196	5008	,	,		20448	0.1022		0.1054	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCTACATTGGAGA																													14.37:g.45330929T>C			53	0	0		73	0.07	5	.	0		0		RNA	SNP		37																																																																																					0	0.433										
DOCK11P1	100132537	bcgsc.ca	37	14	45331397	45331397	+	IGR	SNP	T	T	C	rs12323568	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:45331397T>C								RP11-398E10.1 (79365 upstream) : RP11-857B24.1 (14679 downstream)																							ACACTTCAGATTGTCCATTTT	0.368													T|||	1355	0.270567	0.6997	0.134	5008	,	,		21690	0.1002		0.1093	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTCAGATTGTCCA																													14.37:g.45331397T>C			198	0	0		270	0.04	11	.	0		0		RNA	SNP		37																																																																																					0	0.368										
DOCK11P1	100132537	bcgsc.ca	37	14	45331633	45331633	+	IGR	SNP	T	T	G	rs12323575	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:45331633T>G								RP11-398E10.1 (79601 upstream) : RP11-857B24.1 (14443 downstream)																							CTACTAAGATTCTGAAGCCAG	0.413													G|||	1155	0.230631	0.559	0.1196	5008	,	,		19228	0.1002		0.1054	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TAAGATTCTGAAG																													14.37:g.45331633T>G			256	0	0		323	0.04	14	.	0		0		RNA	SNP		37																																																																																					0	0.413										
DOCK11P1	100132537	bcgsc.ca	37	14	45332387	45332387	+	IGR	SNP	C	C	G	rs7161626	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:45332387C>G								RP11-398E10.1 (80355 upstream) : RP11-857B24.1 (13689 downstream)																							CTCAGAAGTACACCAAACAAG	0.358													G|||	1157	0.23103	0.5605	0.1196	5008	,	,		21582	0.1002		0.1054	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAAGTACACCAAA																													14.37:g.45332387C>G			182	0	0		270	0.04	10	.	0		0		RNA	SNP		37																																																																																					0	0.358										
DOCK11P1	100132537	bcgsc.ca	37	14	45332752	45332752	+	IGR	SNP	G	G	A	rs74700367	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:45332752G>A								RP11-398E10.1 (80720 upstream) : RP11-857B24.1 (13324 downstream)																							ATATGCCTTGGGAAATCTCTG	0.388													G|||	103	0.0205671	0.0265	0.0303	5008	,	,		20994	0.0		0.0408	False		,,,				2504	0.0061				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCCTTGGGAAATC																													14.37:g.45332752G>A			119	0	0		155	0.05	8	.	0		0		RNA	SNP		37																																																																																					0	0.388										
DOCK11P1	100132537	bcgsc.ca	37	14	45334503	45334503	+	IGR	SNP	C	C	A	rs8014660	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:45334503C>A								RP11-398E10.1 (82471 upstream) : RP11-857B24.1 (11573 downstream)																							TTCTTTACATCAAATAAGGCA	0.418													C|||	1163	0.232228	0.562	0.1196	5008	,	,		18174	0.1091		0.1054	False		,,,				2504	0.1237				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTACATCAAATAA																													14.37:g.45334503C>A			113	0	0		146	0.04	6	.	0		0		RNA	SNP		37																																																																																					0	0.418										
IGHV3-38	28429	bcgsc.ca	37	14	106866565	106866565	+	RNA	SNP	C	C	A	rs551167779|rs58308167	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:106866565C>A	ENST00000390618.2	-	0	266									immunoglobulin heavy variable 3-38 (non-functional)																		CCCACTCCAGCCCCTTCCCTG	0.557													c|||	1147	0.229034	0.3381	0.1643	5008	,	,		15465	0.2867		0.1054	False		,,,				2504	0.1953				.													.	.			0			.							A		1941,2413		213,1515,449	196.0	149.0	165.0			-1.9	0.6	14	dbSNP_129	165	1550,6994		54,1442,2776	no	intergenic				267,2957,3225	AA,AC,CC		18.1414,44.5797,27.0662			106866565	3491,9407	2177	4272	6449			28429	.			CTCCAGCCCCTTC	M99669		14q32.33	2012-02-08	2008-08-22		ENSG00000211958	ENSG00000211958		"""Immunoglobulins / IGH locus"""	5601	other	immunoglobulin gene			"""immunoglobulin heavy variable 3-38"""				Standard	NG_001019		Approved				OTTHUMG00000152093		14.37:g.106866565C>A			124	0	0		162	0.05	8	.	7	0.00	0		RNA	SNP	ENST00000390618.2	37																																																																																						0.557	IGHV3-38-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325190.1		NG_001019	
IGHV3-38	28429	bcgsc.ca	37	14	106866588	106866588	+	RNA	SNP	T	T	C	rs73379082	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr14:106866588T>C	ENST00000390618.2	-	0	243									immunoglobulin heavy variable 3-38 (non-functional)																		GCCTGGCGGATCCAGCTCATC	0.587																																					.													.	.			0			.							T		1528,2796		2,1524,636	188.0	142.0	158.0			-4.8	0.3	14	dbSNP_130	158	837,7661		0,837,3412	no	intergenic				2,2361,4048	CC,CT,TT		9.8494,35.3377,18.4449			106866588	2365,10457	2162	4249	6411			28429	.			GGCGGATCCAGCT	M99669		14q32.33	2012-02-08	2008-08-22		ENSG00000211958	ENSG00000211958		"""Immunoglobulins / IGH locus"""	5601	other	immunoglobulin gene			"""immunoglobulin heavy variable 3-38"""				Standard	NG_001019		Approved				OTTHUMG00000152093		14.37:g.106866588T>C			122	0	0		144	0.06	8	.	1	0.00	0		RNA	SNP	ENST00000390618.2	37																																																																																						0.587	IGHV3-38-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325190.1		NG_001019	
DNM1P46	196968	hgsc.bcm.edu	37	15	100331823	100331823	+	RNA	SNP	G	G	C	rs543612334		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr15:100331823G>C	ENST00000341853.1	-	0	2368				AC090825.1_ENST00000408584.1_RNA|RN7SL484P_ENST00000462651.2_RNA	NR_003260.1		Q6ZS02	DMP46_HUMAN	DNM1 pseudogene 46							microtubule (GO:0005874)	GTPase activity (GO:0003924)										CAACCCAGAGGACCTGGAGAG	0.607													.|||	1	0.000199681	0.0	0.0	5008	,	,		18113	0.0		0.001	False		,,,				2504	0.0				.													ENSG00000214394,NS,haematopoietic_neoplasm,-2,1	ENSG00000214394	-2	1	0			.												73.0	74.0	74.0					15																	100331823		876	1991	2867			196968	.			CCAGAGGACCTGG	AJ576275		15q26.3	2013-04-25			ENSG00000182397	ENSG00000182397			35199	pseudogene	pseudogene			"""chromosome 15 open reading frame 51"""	DNM1DN14@, C15orf51			Standard	NR_003260		Approved	DNM1DN14.2, FLJ45937, DKFZp434I1020	uc021sxl.1	Q6ZS02	OTTHUMG00000149852		15.37:g.100331823G>C			12	0.0833333333	1		30	0.10	3	.	0		0	Q3ZCN3	RNA	SNP	ENST00000341853.1	37																																																																																						0.607	DNM1P46-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000313543.1		NR_003260	
RHBDF1	64285	ucsc.edu	37	16	108653	108653	+	Silent	SNP	G	G	A			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr16:108653G>A	ENST00000262316.6	-	18	2396	c.2254C>T	c.(2254-2256)Ctg>Ttg	p.L752L		NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	752					cell migration (GO:0016477)|cell proliferation (GO:0008283)|negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)|proteolysis (GO:0006508)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	18		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				ACCACAGCCAGCAGCTTGAAG	0.607																																					p.L752L													.	RHBDF1	54		0			c.C2254T												48.0	53.0	51.0					16																	108653		2203	4300	6503	SO:0001819	synonymous_variant	64285	exon18			CAGCCAGCAGCTT	BC014425	CCDS32344.1	16p13.3	2008-02-05	2006-02-22		ENSG00000007384	ENSG00000007384			20561	protein-coding gene	gene with protein product		614403	"""chromosome 16 open reading frame 8"", ""rhomboid family 1 (Drosophila)"""	C16orf8		8318735, 15965977	Standard	NM_022450		Approved	EGFR-RS, FLJ2235, Dist1	uc002cfl.4	Q96CC6	OTTHUMG00000060719	ENST00000262316.6:c.2254C>T	16.37:g.108653G>A			51	0	0		53	0.09	5	NM_022450	22	0.27	6	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Silent	SNP	ENST00000262316.6	37	CCDS32344.1																																																																																					0.607	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000134178.2		NM_022450	
LUC7L	55692	bcgsc.ca	37	16	239209	239209	+	Silent	SNP	G	G	A	rs535303746		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr16:239209G>A	ENST00000293872.8	-	10	1214	c.1104C>T	c.(1102-1104)gcC>gcT	p.A368A	LUC7L_ENST00000337351.4_3'UTR|LA16c-OS12.2_ENST00000595428.1_lincRNA|LUC7L_ENST00000397783.1_3'UTR	NM_201412.1	NP_958815.1	Q9NQ29	LUC7L_HUMAN	LUC7-like (S. cerevisiae)	368					mRNA splice site selection (GO:0006376)|negative regulation of striated muscle tissue development (GO:0045843)	U1 snRNP (GO:0005685)	identical protein binding (GO:0042802)|mRNA binding (GO:0003729)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	11		all_cancers(16;1.1e-06)|all_epithelial(16;2.71e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.0138)|all_lung(18;0.0306)				AGATCTCGCCGGCCTCCTTCT	0.537													G|||	1	0.000199681	0.0	0.0	5008	,	,		17071	0.001		0.0	False		,,,				2504	0.0				p.A368A													.	LUC7L	46		0			c.C1104T												113.0	128.0	123.0					16																	239209		2203	4300	6503	SO:0001819	synonymous_variant	55692	exon10			CTCGCCGGCCTCC	AY005111	CCDS10401.1, CCDS32348.1	16p13.3	2010-01-25	2001-11-28		ENSG00000007392	ENSG00000007392			6723	protein-coding gene	gene with protein product		607782	"""LUC7 (S. cerevisiae)-like"""				Standard	NM_201412		Approved	LUC7B1, hLuc7B1, Luc7	uc002cgc.1	Q9NQ29	OTTHUMG00000060730	ENST00000293872.8:c.1104C>T	16.37:g.239209G>A			43	0	0		66	0.08	5	NM_201412	218	0.00	1	B8ZZ13|Q96S32|Q9NPH4	Silent	SNP	ENST00000293872.8	37	CCDS32348.1																																																																																					0.537	LUC7L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000134239.1			
HERC2P4	100289574	broad.mit.edu;bcgsc.ca	37	16	32163525	32163525	+	IGR	SNP	G	G	A	rs461744	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr16:32163525G>A								RP11-1166P10.6 (67419 upstream) : HERC2P4 (17779 downstream)																							TGCCAGTCACGGTGCCTTCTC	0.567																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGTCACGGTGCCT																													16.37:g.32163525G>A			98	0	0		102	0.09	9	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.567										
RP11-652G5.1	0	bcgsc.ca	37	16	32617196	32617196	+	RNA	SNP	G	G	A	rs28503299	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr16:32617196G>A	ENST00000562976.1	+	0	383																											TTTGTATAGAGGAAGGTGCTG	0.448																																					.													.	.			0			.																																											0	.			TATAGAGGAAGGT																													16.37:g.32617196G>A			41	0	0		50	0.12	6	.	0		0		RNA	SNP	ENST00000562976.1	37																																																																																						0.448	RP11-652G5.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000432347.1			
CCDC102A	92922	ucsc.edu	37	16	57550226	57550226	+	Silent	SNP	C	C	T			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr16:57550226C>T	ENST00000258214.2	-	7	1644	c.1398G>A	c.(1396-1398)gaG>gaA	p.E466E		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	466										endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						CCTGGGCCAGCTCCTTCTTGA	0.667																																					p.E466E													.	CCDC102A	22		0			c.G1398A												65.0	50.0	55.0					16																	57550226		2198	4300	6498	SO:0001819	synonymous_variant	92922	exon7			GGCCAGCTCCTTC	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.1398G>A	16.37:g.57550226C>T			34	0	0		27	0.07	2	NM_033212	57	0.26	15	Q9BT74	Silent	SNP	ENST00000258214.2	37	CCDS10784.1																																																																																					0.667	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000257348.1		NM_033212	
RP11-434D2.11	0	broad.mit.edu	37	17	20459719	20459719	+	RNA	DEL	A	A	-	rs57794427|rs149462269		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr17:20459719delA	ENST00000579603.1	-	0	63																											atatatatatatatatatata	0.353																																					.													.	.			0			.																																											0	.			ATATATATATATA																													17.37:g.20459719delA			92	0.0108695652	1		50	0.18	9	.	0		0		RNA	DEL	ENST00000579603.1	37																																																																																						0.353	RP11-434D2.11-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000448286.1			
RP11-259G18.1	0	bcgsc.ca	37	17	44344738	44344749	+	RNA	DEL	GCTGGTGACCCT	GCTGGTGACCCT	-	rs67539917|rs200890045	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	GCTGGTGACCCT	GCTGGTGACCCT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr17:44344738_44344749delGCTGGTGACCCT	ENST00000570002.2	+	0	336_347																											CGGGCATCTGGCTGGTGACCCTGCTGGTGGAT	0.59														368	0.0734824	0.0113	0.1412	5008	,	,		20359	0.001		0.2008	False		,,,				2504	0.0532				.													.	.			0			.																																											0	.			CATCTGGCTGGTG																													17.37:g.44344738_44344749delGCTGGTGACCCT			119	0	0		117	0.03	4	.	7	0.00	0		RNA	DEL	ENST00000570002.2	37																																																																																						0.590	RP11-259G18.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000431423.2			
RP11-259G18.1	0	bcgsc.ca	37	17	44344810	44344810	+	RNA	SNP	T	T	G	rs2732649	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr17:44344810T>G	ENST00000570002.2	+	0	408																											ACCCCCGACGTCTTCTTCTTC	0.562													.|||	434	0.0866613	0.0166	0.1556	5008	,	,		20931	0.001		0.2396	False		,,,				2504	0.0634				.													.	.			0			.																																											0	.			CCGACGTCTTCTT																													17.37:g.44344810T>G			149	0	0		169	0.05	8	.	2	0.00	0		RNA	SNP	ENST00000570002.2	37																																																																																						0.562	RP11-259G18.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000431423.2			
RP11-259G18.1	0	bcgsc.ca	37	17	44344822	44344822	+	RNA	SNP	G	G	A	rs76934998	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr17:44344822G>A	ENST00000570002.2	+	0	420																											TTCTTCTTCCGAGTCCACATG	0.542													.|||	368	0.0734824	0.0113	0.1412	5008	,	,		22066	0.001		0.2008	False		,,,				2504	0.0532				.													.	.			0			.																																											0	.			TCTTCCGAGTCCA																													17.37:g.44344822G>A			155	0	0		180	0.04	8	.	3	0.00	0		RNA	SNP	ENST00000570002.2	37																																																																																						0.542	RP11-259G18.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000431423.2			
RP11-259G18.1	0	bcgsc.ca	37	17	44344858	44344858	+	RNA	SNP	A	A	G	rs74358353	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr17:44344858A>G	ENST00000570002.2	+	0	456																											TCCAGCTGCAATAAACCGTGT	0.517													.|||	368	0.0734824	0.0113	0.1412	5008	,	,		24369	0.001		0.2008	False		,,,				2504	0.0532				.													.	.			0			.																																											0	.			GCTGCAATAAACC																													17.37:g.44344858A>G			145	0	0		156	0.06	9	.	4	0.00	0		RNA	SNP	ENST00000570002.2	37																																																																																						0.517	RP11-259G18.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000431423.2			
RP11-51L5.7	0	bcgsc.ca	37	17	60361652	60361652	+	5'Flank	SNP	C	C	G	rs139504127	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr17:60361652C>G	ENST00000602932.1	-	0	0				RP11-51L5.5_ENST00000602493.1_RNA																							CTGTGTTGGACTAGAAGCTGA	0.378													.|||	701	0.139976	0.1157	0.1556	5008	,	,		18016	0.0288		0.2664	False		,,,				2504	0.1462				.													.	.			0			.																																									SO:0001631	upstream_gene_variant	0	.			GTTGGACTAGAAG																													17.37:g.60361652C>G	Exception_encountered		228	0	0		235	0.06	15	.	0		0		RNA	SNP	ENST00000602932.1	37																																																																																						0.378	RP11-51L5.7-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding		OTTHUMT00000467667.1			
ANAPC11	51529	bcgsc.ca	37	17	79857807	79857807	+	Missense_Mutation	SNP	G	G	T	rs535288823		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr17:79857807G>T	ENST00000575195.2	+	2	301	c.121G>T	c.(121-123)Ggc>Tgc	p.G41C	NPB_ENST00000573081.1_5'Flank|ANAPC11_ENST00000344877.5_Missense_Mutation_p.G41C|ANAPC11_ENST00000571024.2_Missense_Mutation_p.G41C|ANAPC11_ENST00000577425.1_3'UTR|ANAPC11_ENST00000571570.1_Missense_Mutation_p.G41C|ANAPC11_ENST00000571874.2_Missense_Mutation_p.G41C|ANAPC11_ENST00000579133.1_3'UTR|ANAPC11_ENST00000578550.1_Missense_Mutation_p.G41C|ANAPC11_ENST00000583839.1_Missense_Mutation_p.G41C|ANAPC11_ENST00000578544.1_3'UTR|ANAPC11_ENST00000572851.2_Missense_Mutation_p.G41C|ANAPC11_ENST00000392376.3_Missense_Mutation_p.G41C|ANAPC11_ENST00000577747.1_Missense_Mutation_p.G41C|ANAPC11_ENST00000572639.1_Missense_Mutation_p.G41C|ANAPC11_ENST00000574924.2_Missense_Mutation_p.G41C|ANAPC11_ENST00000357385.3_Missense_Mutation_p.R141L|NPB_ENST00000333383.7_5'Flank|ANAPC11_ENST00000579978.1_Missense_Mutation_p.G41C			Q9NYG5	APC11_HUMAN	anaphase promoting complex subunit 11	41					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)	2	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			CAAGGTGCCCGGCGACGACTG	0.647																																					p.R141L													.	ANAPC11	1		0			c.G422T												111.0	78.0	89.0					17																	79857807		2202	4300	6502	SO:0001583	missense	51529	exon4			GTGCCCGGCGACG	AF247565	CCDS11789.1, CCDS32769.1, CCDS74180.1	17q25.3	2011-06-15	2008-10-30			ENSG00000141552		"""Anaphase promoting complex subunits"""	14452	protein-coding gene	gene with protein product		614534	"""anaphase promoting complex subunit 11 (yeast APC11 homolog)"""			10922056	Standard	NM_001002245		Approved	HSPC214, APC11, Apc11p, MGC882	uc002kby.1	Q9NYG5		ENST00000575195.2:c.121G>T	17.37:g.79857807G>T	ENSP00000458515:p.Gly41Cys		49	0	0		57	0.07	4	NM_001002244	621	0.00	1	A8MTT2|B7ZW64|Q502X9|Q9BW64|Q9P0R2	Missense_Mutation	SNP	ENST00000575195.2	37	CCDS11789.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.27|11.27	1.589008|1.589008	0.28357|0.28357	.|.	.|.	ENSG00000141552|ENSG00000141552	ENST00000344877;ENST00000392376|ENST00000357385	.|.	.|.	.|.	4.65|4.65	4.65|4.65	0.58169|0.58169	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);|.	.|.	.|.	.|.	.|.	T|T	0.59595|0.59595	0.2205|0.2205	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D|B	0.89917|0.27416	1.0|0.178	D|B	0.91635|0.28916	0.999|0.096	T|T	0.63189|0.63189	-0.6693|-0.6693	7|7	0.87932|0.87932	D|D	0|0	-2.7225|-2.7225	17.7226|17.7226	0.88356|0.88356	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	41|141	Q9NYG5|Q9NYG5-2	APC11_HUMAN|.	C|L	41|141	.|.	ENSP00000339695:G41C|ENSP00000349957:R141L	G|R	+|+	1|2	0|0	ANAPC11|ANAPC11	77451099|77451099	1.000000|1.000000	0.71417|0.71417	0.723000|0.723000	0.30687|0.30687	0.264000|0.264000	0.26372|0.26372	8.844000|8.844000	0.92147|0.92147	2.424000|2.424000	0.82194|0.82194	0.655000|0.655000	0.94253|0.94253	GGC|CGG			0.647	ANAPC11-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000440106.2		NM_016476	
NPC1	4864	hgsc.bcm.edu;bcgsc.ca	37	18	21134853	21134853	+	Silent	SNP	C	C	T	rs367900403		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr18:21134853C>T	ENST00000269228.5	-	9	1976	c.1422G>A	c.(1420-1422)ccG>ccA	p.P474P	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_Silent_p.P224P	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	474			P -> L (in NPC1). {ECO:0000269|PubMed:12401890, ECO:0000269|PubMed:16098014}.		adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TCGTGTTATACGGTGAAAGAG	0.443																																					p.P474P													.	.			0			c.G1422A							C		0,4406		0,0,2203	166.0	132.0	143.0		1422	-9.8	0.0	18		143	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	NPC1	NM_000271.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		474/1279	21134853	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4864	exon9			GTTATACGGTGAA	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.1422G>A	18.37:g.21134853C>T			178	0	0		139	0.04	6	NM_000271	17	0.00	0	B4DET3|Q9P130	Silent	SNP	ENST00000269228.5	37	CCDS11878.1																																																																																					0.443	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254823.2		NM_000271	
AZU1	566	broad.mit.edu	37	19	827874	827874	+	Frame_Shift_Del	DEL	C	C	-			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr19:827874delC	ENST00000233997.2	+	1	49	c.28delC	c.(28-30)ctgfs	p.L10fs		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	10					cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTGGCCCTGCTGGCTGGTCT	0.687																																					p.L10fs													.	AZU1	31		0			c.28delC												18.0	21.0	20.0					19																	827874		2103	4168	6271	SO:0001589	frameshift_variant	566	exon1			GCCCTGCTGGCTG	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.28delC	19.37:g.827874delC	ENSP00000233997:p.Leu10fs		11	0	0		6	0.50	3	NM_001700	0		0	P80014|Q52LG4|Q9UCM1|Q9UCT5	Frame_Shift_Del	DEL	ENST00000233997.2	37	CCDS12044.1																																																																																					0.687	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000457472.2		NM_001700	
PSPN	5623	broad.mit.edu	37	19	6375401	6375401	+	Silent	SNP	C	C	A			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr19:6375401C>A	ENST00000245810.1	-	2	374	c.375G>T	c.(373-375)cgG>cgT	p.R125R	PSPN_ENST00000597721.1_Missense_Mutation_p.A154S	NM_004158.2	NP_004149.1	O60542	PSPN_HUMAN	persephin	125					axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|central nervous system development (GO:0007417)|nervous system development (GO:0007399)	extracellular space (GO:0005615)	receptor binding (GO:0005102)			lung(1)|ovary(1)|skin(1)	3						AGCGAGTGGGCCGGCAGCAGG	0.766																																					p.R125R													.	PSPN	5		0			c.G375T												1.0	2.0	1.0					19																	6375401		1041	2253	3294	SO:0001819	synonymous_variant	5623	exon2			AGTGGGCCGGCAG	AF040962	CCDS12164.1	19p13.3	2014-01-30				ENSG00000125650		"""Endogenous ligands"""	9579	protein-coding gene	gene with protein product		602921				10072588	Standard	NM_004158		Approved	PSP	uc010xja.2	O60542		ENST00000245810.1:c.375G>T	19.37:g.6375401C>A			14	0.0714285714	1		20	0.30	6	NM_004158	0		0		Missense_Mutation	SNP	ENST00000245810.1	37	CCDS12164.1	.	.	.	.	.	.	.	.	.	.	C	7.807	0.714977	0.15306	.	.	ENSG00000125650	ENST00000545374	.	.	.	4.21	1.87	0.25490	.	.	.	.	.	T	0.71195	0.3311	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.75811	-0.3186	5	0.87932	D	0	-1.939	12.3574	0.55184	0.0:0.4667:0.5333:0.0	.	.	.	.	S	154	.	ENSP00000438257:A154S	A	-	1	0	PSPN	6326401	0.346000	0.24844	0.884000	0.34674	0.010000	0.07245	-0.010000	0.12743	1.130000	0.42092	0.313000	0.20887	GCC			0.766	PSPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000398032.1		NM_004158	
LOC113230	113230	bcgsc.ca	37	19	14181974	14181974	+	5'Flank	SNP	T	T	A	rs13346822	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr19:14181974T>A	ENST00000587086.1	+	0	0				hsa-mir-1199_ENST00000269720.2_5'Flank																							AGGTGGGGACTTACTTGCTGG	0.542													A|||	305	0.0609026	0.1369	0.0144	5008	,	,		15892	0.0298		0.0219	False		,,,				2504	0.0634				.													.	.			0			.																																									SO:0001631	upstream_gene_variant	126037	.			GGGGACTTACTTG																													19.37:g.14181974T>A	Exception_encountered		59	0	0		74	0.08	6	.	2	1.00	2		RNA	SNP	ENST00000587086.1	37																																																																																						0.542	hsa-mir-1199.1-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000458552.1			
BIRC8	112401	bcgsc.ca	37	19	53792954	53792955	+	Missense_Mutation	DNP	GC	GC	AT	rs35700345|rs34683072|rs386810666	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr19:53792954_53792955GC>AT	ENST00000426466.1	-	1	1920_1921	c.673_674GC>AT	c.(673-675)GCg>ATg	p.A225M		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	225			A -> T (in dbSNP:rs35700345).|A -> V (in dbSNP:rs34683072).		apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|urinary_tract(1)	19				GBM - Glioblastoma multiforme(134;0.00304)		ATCAATAACCGCGCTGCACATG	0.401																																					p.A225M													.	BIRC8	54		0			c.G673A																																									SO:0001583	missense	112401	exon1			ATAACCGCGCTGC	AF164682	CCDS12863.1	19q13.3-q13.4	2011-01-25	2011-01-25			ENSG00000163098		"""Baculoviral IAP repeat containing"""	14878	protein-coding gene	gene with protein product	"""IAP-like protein 2"", ""inhibitor of apoptosis-like protein 2"""		"""baculoviral IAP repeat-containing 8"""			11390657	Standard	NM_033341		Approved	ILP-2, hILP2	uc002qbk.3	Q96P09		ENST00000426466.1:c.673_674delinsAT	19.37:g.53792954_53792955delinsAT	ENSP00000412957:p.Ala225Met		125	0	0		155	0.05	8	NM_033341	0		0	Q6IPY1|Q96RW5	Missense_Mutation	DNP	ENST00000426466.1	37	CCDS12863.1																																																																																					0.401	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000464357.1		NM_033341	
ZNF525	170958	broad.mit.edu	37	19	53879109	53879109	+	Silent	SNP	G	G	A			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr19:53879109G>A	ENST00000475179.1	+	3	216	c.102G>A	c.(100-102)agG>agA	p.R34R	ZNF525_ENST00000474037.1_Silent_p.R34R|ZNF525_ENST00000467003.1_5'UTR|ZNF525_ENST00000593918.1_Silent_p.R34R|ZNF525_ENST00000491101.1_Silent_p.R34R			Q8N782	ZN525_HUMAN	zinc finger protein 525	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R34R(6)		endometrium(3)|kidney(3)|lung(3)	9						CTCTATACAGGGACGTGATGC	0.473																																					.													.	ZNF525	35		6	Substitution - coding silent(6)	kidney(6)	.																																									SO:0001819	synonymous_variant	170958	.			ATACAGGGACGTG	AB075859		19q13.42	2013-01-16			ENSG00000203326	ENSG00000203326		"""Zinc fingers, C2H2-type"", ""-"""	29423	protein-coding gene	gene with protein product						11853319	Standard	NR_003699		Approved	KIAA1979	uc010eqn.3	Q8N782	OTTHUMG00000158277	ENST00000475179.1:c.102G>A	19.37:g.53879109G>A			37	0	0		62	0.08	5	.	13	0.00	0	Q8TF23	Silent	SNP	ENST00000475179.1	37																																																																																						0.473	ZNF525-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding		OTTHUMT00000350553.1		NR_003699	
LINC01122	400955	bcgsc.ca	37	2	58688907	58688907	+	lincRNA	SNP	G	G	A	rs2075171	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr2:58688907G>A	ENST00000452840.1	+	0	127																											TTCCTCCTTCGTGCAGCTGGG	0.507													G|||	827	0.165136	0.0386	0.183	5008	,	,		22101	0.2391		0.2644	False		,,,				2504	0.1452				.													.	.			0			.																																											0	.			TCCTTCGTGCAGC																													2.37:g.58688907G>A			166	0.0120481928	2		142	0.04	6	.	123	0.00	0		RNA	SNP	ENST00000452840.1	37																																																																																						0.507	AC007092.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000327022.1			
PLGLA	285189	broad.mit.edu	37	2	107007467	107007467	+	RNA	SNP	G	G	A	rs7575679	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr2:107007467G>A	ENST00000484422.1	+	0	316							Q15195	PLGA_HUMAN	plasminogen-like A (pseudogene)							extracellular region (GO:0005576)											ACTTCTCCCCGCAGACCTAGG	0.468													.|||	1467	0.292931	0.0772	0.3213	5008	,	,		21059	0.7312		0.1183	False		,,,				2504	0.2924				.													.	.			0			.																																											0	.			CTCCCCGCAGACC	U67178, M86872, M86873		2q12.2	2013-03-28	2013-03-28	2008-02-07	ENSG00000240935	ENSG00000240935			9074	pseudogene	pseudogene		612212	"""plasminogen pseudogene 2"", ""plasminogen-like A1"", ""plasminogen-like A"""	PLGP2, PLGLA1		1986355	Standard	NR_003506		Approved		uc002tdp.4	Q15195	OTTHUMG00000153188		2.37:g.107007467G>A			61	0	0		61	0.10	6	.	0		0		RNA	SNP	ENST00000484422.1	37																																																																																						0.468	PLGLA-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000331219.1		NR_003506.2	
CTAGE14P	401018	bcgsc.ca	37	2	168570749	168570749	+	IGR	SNP	G	G	A	rs12987185	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr2:168570749G>A								RNU7-148P (82698 upstream) : AC016723.4 (100534 downstream)																							TGATTGTCCTGGTGGAGGAAA	0.473													G|||	849	0.169529	0.1513	0.1268	5008	,	,		20302	0.0446		0.2654	False		,,,				2504	0.2546				.													.	.			0			.																																									SO:0001628	intergenic_variant	401018	.			TGTCCTGGTGGAG																													2.37:g.168570749G>A			151	0.0066225166	1		130	0.05	7	.	0		0		RNA	SNP		37																																																																																					0	0.473										
MFF	56947	bcgsc.ca	37	2	228194480	228194481	+	Missense_Mutation	DNP	AG	AG	TT	rs3211098|rs3211097|rs386655869	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr2:228194480_228194481AG>TT	ENST00000353339.3	+	3	460_461	c.19_20AG>TT	c.(19-21)AGt>TTt	p.S7F	MFF_ENST00000337110.7_Intron|MFF_ENST00000349901.7_Intron|MFF_ENST00000524634.1_Intron|MFF_ENST00000392059.1_Missense_Mutation_p.S7F|MFF_ENST00000409565.1_Intron|MFF_ENST00000354503.6_Intron|MFF_ENST00000304593.9_Intron|MFF_ENST00000476924.1_Intron|MFF_ENST00000409616.1_5'UTR	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	7			S -> C (in dbSNP:rs3211097).|S -> I (in dbSNP:rs3211098).		mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)			breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						AGGAACAAGCAGTGACACATCA	0.366																																					p.S7F													.	MFF	48		0			c.G20T																																									SO:0001583	missense	56947	exon3			ACAAGCAGTGACA	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"""chromosome 2 open reading frame 33"""	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	Exception_encountered	2.37:g.228194480_228194481delinsTT	ENSP00000302037:p.Ser7Phe		228	0	0		216	0.03	7	NM_020194	6	0.00	0	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Missense_Mutation	DNP	ENST00000353339.3	37	CCDS2465.1																																																																																					0.366	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000256887.2		NM_020194	
MROH2A	339766	bcgsc.ca	37	2	234717839	234717839	+	Missense_Mutation	SNP	C	C	A	rs188948269	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr2:234717839C>A	ENST00000389758.3	+	22	2529	c.2363C>A	c.(2362-2364)tCc>tAc	p.S788Y				A6NES4	MRO2A_HUMAN	maestro heat-like repeat family member 2A	818																	TGCGTGGCCTCCTACTGCCAC	0.562													C|||	3	0.000599042	0.0	0.0	5008	,	,		18683	0.0		0.003	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001583	missense	339766	.			TGGCCTCCTACTG		CCDS74674.1	2q37.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000185038	ENSG00000185038		"""maestro heat-like repeat containing"""	27936	protein-coding gene	gene with protein product			"""HEAT repeat containing 7B1"""	HEATR7B1		12477932	Standard	NM_001287395		Approved			A6NES4	OTTHUMG00000059037	ENST00000389758.3:c.2363C>A	2.37:g.234717839C>A	ENSP00000374408:p.Ser788Tyr		129	0	0		137	0.05	7	.	0		0		Missense_Mutation	SNP	ENST00000389758.3	37		4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	17.78	3.474553	0.63737	.	.	ENSG00000185038	ENST00000389758	T	0.66815	-0.23	5.7	3.9	0.45041	.	0.575228	0.14561	N	0.312068	T	0.58075	0.2097	L	0.57536	1.79	0.23784	N	0.996851	.	.	.	.	.	.	T	0.51498	-0.8698	8	0.30854	T	0.27	.	8.6584	0.34077	0.0:0.8244:0.0:0.1756	.	.	.	.	Y	788	ENSP00000374408:S788Y	ENSP00000374408:S788Y	S	+	2	0	HEATR7B1	234382578	0.002000	0.14202	0.922000	0.36590	0.994000	0.84299	0.187000	0.16998	0.754000	0.32968	0.603000	0.83216	TCC			0.562	MROH2A-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000130646.6		XM_291007	
UBE2D3P1	100037280	bcgsc.ca	37	20	5273253	5273253	+	IGR	SNP	G	G	A	rs7271296	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr20:5273253G>A								CDS2 (94720 upstream) : PROKR2 (9063 downstream)																							TAATATTTGGGTGATAAATTC	0.368													N|||	2865	0.572085	0.6596	0.5086	5008	,	,		20515	0.5784		0.506	False		,,,				2504	0.5603				.													.	.			0			.																																									SO:0001628	intergenic_variant	100037280	.			ATTTGGGTGATAA																													20.37:g.5273253G>A			122	0	0		145	0.05	7	.	6	0.67	4		RNA	SNP		37																																																																																					0	0.368										
BAK1	578	bcgsc.ca	37	20	31277958	31277958	+	IGR	SNP	G	G	A	rs117063806	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr20:31277958G>A								C20orf203 (16215 upstream) : COMMD7 (12534 downstream)																							TCTGAACTGGGACCCCAAAGG	0.537													-|||	12	0.00239617	0.0008	0.0058	5008	,	,		20257	0.0		0.007	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	600	.			AACTGGGACCCCA																													20.37:g.31277958G>A			104	0	0		115	0.08	9	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.537										
RARB	5915	bcgsc.ca	37	3	25502825	25502825	+	Missense_Mutation	SNP	G	G	A			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr3:25502825G>A	ENST00000404969.1	+	2	320	c.320G>A	c.(319-321)gGa>gAa	p.G107E	RARB_ENST00000330688.4_Missense_Mutation_p.G100E|RARB_ENST00000458646.1_De_novo_Start_OutOfFrame|RARB_ENST00000462272.1_3'UTR|RARB_ENST00000437042.2_De_novo_Start_OutOfFrame			P10826	RARB_HUMAN	retinoic acid receptor, beta	107					embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	GCCTGTGAGGGATGTAAGGTG	0.517																																					p.G100E													.	RARB	123		0			c.G299A												115.0	113.0	114.0					3																	25502825		2203	4300	6503	SO:0001583	missense	5915	exon2			GTGAGGGATGTAA	Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"""Nuclear hormone receptors"""	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.320G>A	3.37:g.25502825G>A	ENSP00000385865:p.Gly107Glu		75	0	0		73	0.07	5	NM_000965	34	0.06	2	P12891|Q00989|Q15298|Q9UN48	Missense_Mutation	SNP	ENST00000404969.1	37		.	.	.	.	.	.	.	.	.	.	G	32	5.187730	0.94923	.	.	ENSG00000077092	ENST00000383772;ENST00000404969;ENST00000538226;ENST00000330688	D;D;D	0.98221	-4.8;-4.8;-4.8	5.71	5.71	0.89125	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.000000	0.85682	D	0.000000	D	0.99515	0.9827	H	0.99169	4.455	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.989	D	0.97889	1.0296	10	0.87932	D	0	.	19.9109	0.97025	0.0:0.0:1.0:0.0	.	107;100	P10826;F1D8S6	RARB_HUMAN;.	E	107;107;107;100	ENSP00000373282:G107E;ENSP00000385865:G107E;ENSP00000332296:G100E	ENSP00000332296:G100E	G	+	2	0	RARB	25477829	1.000000	0.71417	0.988000	0.46212	0.935000	0.57460	9.869000	0.99810	2.723000	0.93209	0.644000	0.83932	GGA			0.517	RARB-201	KNOWN	basic	protein_coding	protein_coding				NM_000965, NM_016152	
WDR48	57599	hgsc.bcm.edu;bcgsc.ca	37	3	39130788	39130788	+	Missense_Mutation	SNP	G	G	T			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr3:39130788G>T	ENST00000302313.5	+	16	1675	c.1647G>T	c.(1645-1647)tgG>tgT	p.W549C	WDR48_ENST00000396258.3_Missense_Mutation_p.W467C|WDR48_ENST00000544962.1_Missense_Mutation_p.W274C|WDR48_ENST00000418020.1_5'UTR	NM_020839.2	NP_065890.1	Q8TAF3	WDR48_HUMAN	WD repeat domain 48	549					double-strand break repair via homologous recombination (GO:0000724)|embryonic organ development (GO:0048568)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|positive regulation of epithelial cell proliferation (GO:0050679)|protein deubiquitination (GO:0016579)|regulation of protein monoubiquitination (GO:1902525)|seminiferous tubule development (GO:0072520)|single fertilization (GO:0007338)|skeletal system morphogenesis (GO:0048705)|skin development (GO:0043588)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)				breast(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TGCCACAATGGGTAATTGACA	0.388																																					p.W549C													.	.			0			c.G1647T												217.0	201.0	206.0					3																	39130788		2203	4300	6503	SO:0001583	missense	57599	exon16			ACAATGGGTAATT	AF468833	CCDS33738.1	3p21.33	2014-06-16			ENSG00000114742	ENSG00000114742		"""WD repeat domain containing"""	30914	protein-coding gene	gene with protein product		612167				10819331, 12196293, 24482476	Standard	NM_020839		Approved	KIAA1449, P80, SPG60	uc003cit.3	Q8TAF3	OTTHUMG00000155972	ENST00000302313.5:c.1647G>T	3.37:g.39130788G>T	ENSP00000307491:p.Trp549Cys		105	0	0		109	0.05	5	NM_020839	56	0.00	0	B4DM86|B4DQI2|B4DY84|Q63HJ2|Q658Y1|Q8N3Z1|Q9NSK8|Q9P279	Missense_Mutation	SNP	ENST00000302313.5	37	CCDS33738.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.862403	0.91511	.	.	ENSG00000114742	ENST00000302313;ENST00000544962;ENST00000396258	D;D;D	0.99571	-2.52;-6.19;-2.68	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.99697	0.9885	M	0.89095	3.005	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.99;1.0;1.0;1.0	D	0.97994	1.0356	10	0.87932	D	0	-8.3527	20.1634	0.98142	0.0:0.0:1.0:0.0	.	274;467;540;549	Q8TAF3-5;Q8TAF3-4;Q8TAF3-3;Q8TAF3	.;.;.;WDR48_HUMAN	C	549;274;467	ENSP00000307491:W549C;ENSP00000445187:W274C;ENSP00000379557:W467C	ENSP00000307491:W549C	W	+	3	0	WDR48	39105792	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.830000	0.99415	2.773000	0.95371	0.655000	0.94253	TGG			0.388	WDR48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000342529.1		NM_020839	
SERBP1P3	553148	bcgsc.ca	37	3	53098775	53098775	+	Intron	SNP	A	A	G	rs1811351	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr3:53098775A>G	ENST00000607203.1	-	3	317																											AAGTCAGTTAATTCATCTTTG	0.443													A|||	991	0.197883	0.1369	0.1902	5008	,	,		21692	0.1538		0.325	False		,,,				2504	0.2004				.													.	.			0			.																																									SO:0001627	intron_variant	0	.			CAGTTAATTCATC																												ENST00000607203.1:c.74+12928T>C	3.37:g.53098775A>G			93	0	0		119	0.07	8	.	2	0.00	0		RNA	SNP	ENST00000607203.1	37																																																																																						0.443	RP11-894J14.5-003	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_candidate|readthrough_transcript	nonsense_mediated_decay	protein_coding		OTTHUMT00000470877.1			
PPATP1	100289640	bcgsc.ca	37	3	87100988	87100988	+	IGR	SNP	T	T	C	rs2256479	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr3:87100988T>C								VGLL3 (60719 upstream) : MIR4795 (174350 downstream)																							ACGACGGTATTTTATTGTATA	0.418													C|||	3363	0.671526	0.3911	0.8112	5008	,	,		19551	0.6766		0.8439	False		,,,				2504	0.7689				.													.	.			0			.																																									SO:0001628	intergenic_variant	100289640	.			CGGTATTTTATTG																													3.37:g.87100988T>C			80	0	0		60	0.08	5	.	0		0		RNA	SNP		37																																																																																					0	0.418										
ABCF2P1	344653	bcgsc.ca	37	3	88367906	88367906	+	IGR	SNP	C	C	T	rs1350410	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr3:88367906C>T								C3orf38 (160788 upstream) : Y_RNA (112434 downstream)																							GCAGAACCCCCACATGCTCTT	0.537													N|||	1663	0.332069	0.0257	0.5346	5008	,	,		20220	0.3065		0.4284	False		,,,				2504	0.5297				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AACCCCCACATGC																													3.37:g.88367906C>T			63	0	0		60	0.10	6	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.537										
WWP1P1	339843	bcgsc.ca	37	3	98378701	98378701	+	IGR	SNP	A	A	G	rs3796139	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr3:98378701A>G								AC021660.1 (35813 upstream) : ST3GAL6-AS1 (54472 downstream)																							CTACAAGCATATGTTAAGTAA	0.318													A|||	1181	0.235823	0.3525	0.2147	5008	,	,		21985	0.2361		0.159	False		,,,				2504	0.1718				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAGCATATGTTAA																													3.37:g.98378701A>G			71	0	0		75	0.08	6	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.318										
LOC653712	653712	bcgsc.ca	37	3	128580585	128580585	+	RNA	SNP	C	C	A	rs789247	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr3:128580585C>A	ENST00000498297.1	-	0	868				RP11-723O4.2_ENST00000480931.1_RNA|RP11-723O4.9_ENST00000567253.1_lincRNA	NR_034179.1																						GGCACCTCCACGGCAGAAATG	0.587													C|||	1641	0.327676	0.3525	0.2695	5008	,	,		20008	0.5645		0.1879	False		,,,				2504	0.2352				.													.	.			0			.																																											0	.			CCTCCACGGCAGA																													3.37:g.128580585C>A			88	0	0		96	0.06	6	.	1	0.00	0		RNA	SNP	ENST00000498297.1	37																																																																																						0.587	RP11-723O4.2-001	KNOWN	basic	antisense	antisense		OTTHUMT00000357491.1			
Unknown	0	bcgsc.ca	37	3	132106634	132106634	+	IGR	SNP	G	G	A	rs10935006	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr3:132106634G>A								ACPP (19492 upstream) : DNAJC13 (29735 downstream)																							AGTAGCATACGTTATTGAAAA	0.343													G|||	1204	0.240415	0.1263	0.2867	5008	,	,		21679	0.2867		0.2724	False		,,,				2504	0.2812				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCATACGTTATTG																													3.37:g.132106634G>A			83	0	0		78	0.09	7	.	0		0		RNA	SNP		37																																																																																					0	0.343										
Unknown	0	bcgsc.ca	37	3	180042256	180042256	+	IGR	SNP	A	A	G	rs9867767	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr3:180042256A>G								RNA5SP149 (162491 upstream) : RP11-420J11.2 (89705 downstream)																							AACCAAGATTACACAAAAGAT	0.338													G|||	2267	0.452676	0.5522	0.4611	5008	,	,		19912	0.3948		0.336	False		,,,				2504	0.4918				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAGATTACACAAA																													3.37:g.180042256A>G			111	0	0		94	0.09	8	.	0		0		RNA	SNP		37																																																																																					0	0.338										
WDR19	57728	bcgsc.ca	37	4	39257506	39257506	+	Missense_Mutation	SNP	G	G	T			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr4:39257506G>T	ENST00000399820.3	+	27	3194	c.3040G>T	c.(3040-3042)Gcc>Tcc	p.A1014S	WDR19_ENST00000288634.7_Missense_Mutation_p.A854S	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	1014					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						TCAAAGCATTGCCTTATACTT	0.338																																					p.A1014S													.	WDR19	96		0			c.G3040T												63.0	60.0	61.0					4																	39257506		1861	4112	5973	SO:0001583	missense	57728	exon27			AGCATTGCCTTAT	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.3040G>T	4.37:g.39257506G>T	ENSP00000382717:p.Ala1014Ser		86	0	0		69	0.07	5	NM_025132	21	0.00	0	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Missense_Mutation	SNP	ENST00000399820.3	37	CCDS47042.1	.	.	.	.	.	.	.	.	.	.	G	35	5.456147	0.96223	.	.	ENSG00000157796	ENST00000399820;ENST00000288634	D;D	0.84660	-1.8;-1.88	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.94473	0.8221	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94679	0.7863	10	0.72032	D	0.01	-14.9373	20.3184	0.98660	0.0:0.0:1.0:0.0	.	1014	Q8NEZ3	WDR19_HUMAN	S	1014;854	ENSP00000382717:A1014S;ENSP00000288634:A854S	ENSP00000288634:A854S	A	+	1	0	WDR19	38933901	1.000000	0.71417	0.980000	0.43619	0.993000	0.82548	9.323000	0.96364	2.807000	0.96579	0.549000	0.68633	GCC			0.338	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000360689.1			
KIT	3815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	55593603	55593603	+	Missense_Mutation	SNP	T	T	C	rs121913234|rs121913235		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr4:55593603T>C	ENST00000288135.5	+	11	1766	c.1669T>C	c.(1669-1671)Tgg>Cgg	p.W557R		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	557			Missing (in GIST; somatic mutation). {ECO:0000269|PubMed:15824741, ECO:0000269|PubMed:9438854}.		actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.W557_K558del(120)|p.W557R(28)|p.W557G(23)|p.W557_E561del(17)|p.Y553_K558>(8)|p.E554_K558del(8)|p.M552_W557del(8)|p.K550_K558del(7)|p.W557_V559del(7)|p.Q556_V560del(6)|p.Y553_K558del(4)|p.W557del(4)|p.V555_K558del(3)|p.Y553_T574>S(3)|p.Y553_W557del(3)|p.V555_I571del(3)|p.V555_V560del(3)|p.V555_P573del(3)|p.Q556_V560>H(3)|p.V555_V559del(3)|p.W557_K558>E(2)|p.Q556_L576del(2)|p.K550_V559del(2)|p.W557_Q575del(2)|p.K550fs*6(2)|p.Q556_K558del(2)|p.V555_E562del(2)|p.W557_V560del(2)|p.Q556_V559del(2)|p.V555_G565del(1)|p.M552_W557>R(1)|p.Q556_W557del(1)|p.P551_K558del(1)|p.Q556_V559>H(1)|p.M552_E561>K(1)|p.V555_I563del(1)|p.W557_K558>S(1)|p.Q556_K558>HPCR(1)|p.E554_I571del(1)|p.Q556_V560>F(1)|p.V555_Y570del(1)|p.Q556_N566>SNNLQLY(1)|p.M552_T574>TESA(1)|p.Q556_D572>PS(1)|p.Q556_D572del(1)|p.W557_E562del(1)|p.V555_N566>D(1)|p.V555_V560>V(1)|p.Q556_V560>HNLQLY(1)|p.M552_K558del(1)|p.Q556_E561del(1)|p.Q556_K558>H(1)|p.Q556_E561>HH(1)|p.W557_I571del(1)|p.Q556_K558>R(1)|p.Q556_W557>R(1)|p.E554_N564del(1)|p.Q556_V560>TTF(1)|p.K550_W557del(1)|p.Q556_D572>H(1)|p.W557_V559>I(1)|p.M552_D572del(1)|p.Y553_V559>E(1)|p.Q556_T574del(1)|p.P551_V559del>L(1)|p.Q556_P573del(1)|p.E554_D572del(1)|p.Q556_V559>HT(1)|p.E554_E562del(1)|p.Y553_V559del(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGAAGTACAGTGGAAGGTTGT	0.388		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.W557R			yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	KIT,NS,germ_cell_tumour,0,64	KIT	0	64	323	Deletion - In frame(233)|Substitution - Missense(51)|Complex - deletion inframe(34)|Complex - insertion inframe(3)|Deletion - Frameshift(2)	soft_tissue(308)|skin(6)|haematopoietic_and_lymphoid_tissue(5)|testis(3)|genital_tract(1)	c.T1669C	GRCh37	CM005329	KIT	M	rs121913235							80.0	82.0	82.0					4																	55593603		2203	4300	6503	SO:0001583	missense	3815	exon11	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	GTACAGTGGAAGG	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1669T>C	4.37:g.55593603T>C	ENSP00000288135:p.Trp557Arg		87	0	0		95	0.12	11	NM_000222	97	0.08	8	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.382011	0.82792	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.95554	-3.74;-3.74	6.06	6.06	0.98353	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000016	D	0.97974	0.9333	M	0.87617	2.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.991	D	0.98792	1.0736	10	0.87932	D	0	.	16.6003	0.84812	0.0:0.0:0.0:1.0	.	64;553;557	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	R	557;553	ENSP00000288135:W557R;ENSP00000390987:W553R	ENSP00000288135:W557R	W	+	1	0	KIT	55288360	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	7.880000	0.87243	2.319000	0.78375	0.533000	0.62120	TGG			0.388	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000250618.1			
UGT2B7	7364	bcgsc.ca	37	4	69964337	69964338	+	Missense_Mutation	DNP	AT	AT	TC	rs7438284|rs7439366|rs386675647	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	AT	AT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr4:69964337_69964338AT>TC	ENST00000508661.1	+	2	828_829	c.801_802AT>TC	c.(799-804)ccATat>ccTCat	p.Y268H	UGT2B7_ENST00000305231.7_Missense_Mutation_p.Y268H|UGT2B7_ENST00000509763.1_3'UTR			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	268			H -> Y (in allele UGT2B7*2; dbSNP:rs7439366). {ECO:0000269|PubMed:11186130, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15815621, ECO:0000269|Ref.3}.		androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)	p.P267P(1)		autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TTCAGTTTCCATATCCACTCTT	0.396																																					p.Y268H													.	UGT2B7	79		1	Substitution - coding silent(1)	prostate(1)	c.T802C	GRCh37	CM057512	UGT2B7	M	rs7439366																																				SO:0001583	missense	7364	exon2			GTTTCCATATCCA	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	Exception_encountered	4.37:g.69964337_69964338delinsTC	ENSP00000427659:p.Tyr268His		123	0	0		143	0.05	7	NM_001074	0		0	B2R810|Q6GTW0	Missense_Mutation	DNP	ENST00000508661.1	37																																																																																						0.396	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding		OTTHUMT00000362103.1		NM_001074	
ACTN4P1	344978	bcgsc.ca	37	4	117519499	117519499	+	IGR	SNP	T	T	C	rs4834570	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr4:117519499T>C								RP11-55L3.1 (83197 upstream) : RNU6-119P (240935 downstream)																							TGGATTACTATGACTCCCACA	0.607													C|||	1234	0.246406	0.5204	0.3285	5008	,	,		17872	0.0298		0.1143	False		,,,				2504	0.1769				.													.	.			0			.																																									SO:0001628	intergenic_variant	344978	.			TTACTATGACTCC																													4.37:g.117519499T>C			71	0	0		86	0.06	5	.	0		0		RNA	SNP		37																																																																																					0	0.607										
OTUD4	54726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	146085375	146085375	+	Missense_Mutation	SNP	T	T	A			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr4:146085375T>A	ENST00000447906.2	-	5	532	c.345A>T	c.(343-345)aaA>aaT	p.K115N	OTUD4_ENST00000296579.6_Missense_Mutation_p.K50N|OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000454497.2_Missense_Mutation_p.K50N|OTUD4_ENST00000509620.2_Missense_Mutation_p.K50N			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	115	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					TTATAAAATCTTTCCTGAAAA	0.279																																					p.K50N													.	.			0			c.A150T												10.0	10.0	10.0					4																	146085375		2085	4160	6245	SO:0001583	missense	54726	exon4			AAAATCTTTCCTG		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"""OTU domain containing"""	24949	protein-coding gene	gene with protein product		611744	"""OTU domain containing 4"""			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.345A>T	4.37:g.146085375T>A	ENSP00000395487:p.Lys115Asn		174	0	0		136	0.12	16	NM_017493	16	0.19	3	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	ENST00000447906.2	37		.	.	.	.	.	.	.	.	.	.	T	19.71	3.878151	0.72294	.	.	ENSG00000164164	ENST00000454497;ENST00000447906;ENST00000514973;ENST00000509620;ENST00000296579;ENST00000504501	T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53;1.53	5.45	5.45	0.79879	Ovarian tumour, otubain (2);	0.000000	0.53938	D	0.000053	T	0.51483	0.1677	M	0.71581	2.175	0.50467	D	0.999873	D;D	0.67145	0.988;0.996	P;D	0.63957	0.827;0.92	T	0.48269	-0.9050	10	0.30854	T	0.27	-23.4416	15.1776	0.72927	0.0:0.0:0.0:1.0	.	115;115	G3V0I6;Q01804	.;OTUD4_HUMAN	N	50;115;50;50;50;50	ENSP00000409279:K50N;ENSP00000395487:K115N;ENSP00000425972:K50N;ENSP00000424192:K50N;ENSP00000296579:K50N;ENSP00000423453:K50N	ENSP00000296579:K50N	K	-	3	2	OTUD4	146304825	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.106000	0.31098	2.062000	0.61559	0.482000	0.46254	AAA			0.279	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000365117.2		NM_017493	
Unknown	0	bcgsc.ca	37	5	119016414	119016414	+	IGR	SNP	C	C	G	rs330203	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr5:119016414C>G								FAM170A (45637 upstream) : CTC-552D5.1 (564728 downstream)																							ACCAAAATCTCCTGCCCCTTT	0.522													G|||	2109	0.421126	0.5779	0.2795	5008	,	,		21264	0.506		0.2873	False		,,,				2504	0.3599				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAATCTCCTGCCC																													5.37:g.119016414C>G			78	0	0		80	0.09	7	.	0		0		RNA	SNP		37																																																																																					0	0.522										
CDKAL1	54901	bcgsc.ca	37	6	21065449	21065450	+	Missense_Mutation	DNP	CA	CA	TG	rs77152992|rs56087852	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr6:21065449_21065450CA>TG	ENST00000378610.1	+	10	1236_1237	c.1226_1227CA>TG	c.(1225-1227)cCA>cTG	p.P409L	CDKAL1_ENST00000274695.4_Missense_Mutation_p.P409L|CDKAL1_ENST00000378624.4_Missense_Mutation_p.P339L			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	409					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)	p.P409P(1)|p.P409Q(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			GAACAAGTTCCAGCACAAGTGG	0.391																																					p.P409L													CDKAL1,NS,carcinoma,0,1	CDKAL1	55	1	2	Substitution - Missense(1)|Substitution - coding silent(1)	stomach(1)|lung(1)	c.A1227G																																									SO:0001583	missense	54901	exon12			AAGTTCCAGCACA	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	Exception_encountered	6.37:g.21065449_21065450delinsTG	ENSP00000367873:p.Pro409Leu		96	0	0		112	0.07	8	NM_017774	49	0.00	0	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Missense_Mutation	DNP	ENST00000378610.1	37	CCDS4546.1																																																																																					0.391	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000039986.1		NM_017774	
GFRAL	389400	hgsc.bcm.edu;bcgsc.ca	37	6	55216242	55216242	+	Missense_Mutation	SNP	T	T	C			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr6:55216242T>C	ENST00000340465.2	+	5	648	c.562T>C	c.(562-564)Ttt>Ctt	p.F188L		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	188					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			GATGTTGGCTTTTTGTGACTG	0.443																																					p.F188L													.	.			0			c.T562C												181.0	172.0	175.0					6																	55216242		2203	4300	6503	SO:0001583	missense	389400	exon5			TTGGCTTTTTGTG	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 144"""	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.562T>C	6.37:g.55216242T>C	ENSP00000343636:p.Phe188Leu		131	0	0		149	0.05	8	NM_207410	1	0.00	0	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	37	CCDS4957.1	.	.	.	.	.	.	.	.	.	.	T	17.80	3.479228	0.63849	.	.	ENSG00000187871	ENST00000340465	T	0.37915	1.17	5.75	3.37	0.38596	GDNF/GAS1 (2);	0.175156	0.50627	D	0.000110	T	0.12178	0.0296	N	0.20986	0.625	0.43222	D	0.995104	P	0.41978	0.767	B	0.40782	0.34	T	0.04140	-1.0974	10	0.33141	T	0.24	-8.6933	10.207	0.43118	0.0:0.1343:0.0:0.8657	.	188	Q6UXV0	GFRAL_HUMAN	L	188	ENSP00000343636:F188L	ENSP00000343636:F188L	F	+	1	0	GFRAL	55324201	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	3.175000	0.50855	0.536000	0.28733	0.528000	0.53228	TTT			0.443	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000040995.2		NM_207410	
RNU4-70P	106480548	bcgsc.ca	37	6	97096688	97096688	+	RNA	SNP	T	T	C	rs11759390	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr6:97096688T>C	ENST00000384579.1	-	0	139									RNA, U4 small nuclear 70, pseudogene																		TGCTTCCCACTGAACTTTTTC	0.423													T|||	172	0.034345	0.0257	0.0562	5008	,	,		20467	0.0		0.0577	False		,,,				2504	0.0419				.													.	.			0			.																																											442237	.			TCCCACTGAACTT			6q16.1	2013-04-03			ENSG00000207309	ENSG00000207309			47006	pseudogene	RNA, pseudogene							Standard			Approved						6.37:g.97096688T>C			110	0	0		125	0.06	7	.	0		0		RNA	SNP	ENST00000384579.1	37																																																																																						0.423	RNU4-70P-201	KNOWN	basic	snRNA	snRNA					
LAMA2	3908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	129785566	129785566	+	Missense_Mutation	SNP	C	C	T			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr6:129785566C>T	ENST00000421865.2	+	50	7173	c.7124C>T	c.(7123-7125)gCt>gTt	p.A2375V		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2375	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TCTTCGAGTGCTCTTCTGATG	0.428																																					p.A2375V													.	.			0			c.C7124T												269.0	219.0	236.0					6																	129785566		2203	4300	6503	SO:0001583	missense	3908	exon50			CGAGTGCTCTTCT	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.7124C>T	6.37:g.129785566C>T	ENSP00000400365:p.Ala2375Val		114	0	0		148	0.13	19	NM_000426	9	0.33	3	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	C	36	5.756019	0.96898	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.81415	-1.49	5.6	5.6	0.85130	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.200652	0.52532	D	0.000065	D	0.85544	0.5721	L	0.55990	1.75	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.72625	0.978;0.959	D	0.83659	0.0160	9	.	.	.	.	19.6113	0.95607	0.0:1.0:0.0:0.0	.	2376;2375	A6NF00;P24043	.;LAMA2_HUMAN	V	2375;2374;2375;393	ENSP00000400365:A2375V	.	A	+	2	0	LAMA2	129827259	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.394000	0.79862	2.618000	0.88619	0.655000	0.94253	GCT			0.428	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000042180.1			
SRP72P2	153932	bcgsc.ca	37	6	158658937	158658937	+	IGR	SNP	T	T	C	rs7753292	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr6:158658937T>C								GTF2H5 (38561 upstream) : RP11-732M18.3 (44357 downstream)																							TGAATATCTTTTGGATTTTGT	0.403													t|||	1656	0.330671	0.1044	0.4611	5008	,	,		19022	0.4573		0.4185	False		,,,				2504	0.3231				.													.	.			0			.																																									SO:0001628	intergenic_variant	153932	.			TATCTTTTGGATT																													6.37:g.158658937T>C			52	0	0		55	0.07	4	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.403										
Unknown	0	bcgsc.ca	37	7	35473	35473	+	IGR	SNP	T	T	C			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr7:35473T>C								None (None upstream) : AC093627.7 (35498 downstream)																							ctgctgctgctgccgccgccg	0.547																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGCTGCTGCCGCC																													7.37:g.35473T>C			256	0.01171875	3		343	0.05	16	.	0		0		RNA	SNP		37																																																																																					0	0.547										
DPY19L2P3	442524	bcgsc.ca	37	7	29757664	29757664	+	IGR	SNP	G	G	A	rs111261285	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr7:29757664G>A								AC007276.5 (29805 upstream) : WIPF3 (88437 downstream)																							AATCTTAGGCGTTTCAGACCA	0.308													.|||	143	0.0285543	0.0083	0.0432	5008	,	,		14950	0.0188		0.0268	False		,,,				2504	0.0573				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTAGGCGTTTCAG																													7.37:g.29757664G>A			182	0	0		220	0.05	10	.	0		0		RNA	SNP		37																																																																																					0	0.308										
ANLN	54443	broad.mit.edu	37	7	36446171	36446171	+	Missense_Mutation	SNP	C	C	T			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr7:36446171C>T	ENST00000265748.2	+	4	1090	c.869C>T	c.(868-870)tCt>tTt	p.S290F	ANLN_ENST00000495714.1_3'UTR|ANLN_ENST00000396068.2_Missense_Mutation_p.S290F	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	290	Interaction with F-actin.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						ATTTCCAGCTCTGTGGTAAGT	0.428																																					p.S290F													.	ANLN	101		0			c.C869T												222.0	215.0	217.0					7																	36446171		2203	4300	6503	SO:0001583	missense	54443	exon4			CCAGCTCTGTGGT	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"""Pleckstrin homology (PH) domain containing"""	14082	protein-coding gene	gene with protein product			"""anillin (Drosophila Scraps homolog), actin binding protein"", ""anillin, actin binding protein (scraps homolog, Drosophila)"""			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.869C>T	7.37:g.36446171C>T	ENSP00000265748:p.Ser290Phe		18	0	0		28	0.14	4	NM_018685	29	0.21	6	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Missense_Mutation	SNP	ENST00000265748.2	37	CCDS5447.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496939	0.44352	.	.	ENSG00000011426	ENST00000265748;ENST00000396068	T;T	0.03212	4.01;4.01	4.2	3.32	0.38043	.	0.659026	0.16308	N	0.220131	T	0.04092	0.0114	L	0.44542	1.39	0.44555	D	0.997514	P;P;P;P	0.43519	0.664;0.71;0.809;0.71	B;B;B;B	0.38954	0.156;0.149;0.286;0.149	T	0.47598	-0.9105	10	0.72032	D	0.01	-0.7616	7.653	0.28358	0.0:0.7404:0.1671:0.0925	.	167;290;290;290	B4DSL6;A8K5D9;Q9NQW6-2;Q9NQW6	.;.;.;ANLN_HUMAN	F	290	ENSP00000265748:S290F;ENSP00000379380:S290F	ENSP00000265748:S290F	S	+	2	0	ANLN	36412696	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.015000	0.29963	1.371000	0.46172	0.650000	0.86243	TCT			0.428	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000218582.3		NM_018685	
Unknown	0	bcgsc.ca	37	7	55002841	55002841	+	IGR	SNP	T	T	G	rs564664705|rs2330916|rs374147543|rs58809495	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr7:55002841T>G								SNORA73 (69124 upstream) : EGFR (83872 downstream)																							TAGTTGAAAATCCAAAGAAAA	0.333																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGAAAATCCAAAG																													7.37:g.55002841T>G			55	0.0181818182	1		59	0.08	5	.	0		0		RNA	SNP		37																																																																																					0	0.333										
Unknown	0	bcgsc.ca	37	7	55005265	55005265	+	IGR	SNP	A	A	G	rs2192264	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr7:55005265A>G								SNORA73 (71548 upstream) : EGFR (81448 downstream)																							CCGTGTTAGCAGGAACGAAAC	0.388													a|||	2839	0.566893	0.764	0.4107	5008	,	,		20691	0.7173		0.2813	False		,,,				2504	0.5501				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTTAGCAGGAACG																													7.37:g.55005265A>G			101	0	0		133	0.05	7	.	0		0		RNA	SNP		37																																																																																					0	0.388										
YWHAEP1	649395	bcgsc.ca	37	7	63894558	63894558	+	IGR	SNP	A	A	C	rs73125103	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr7:63894558A>C								ZNF736 (79320 upstream) : ZNF680 (85703 downstream)																							TGTACTGGACAAAAACCTCAT	0.403													.|||	516	0.103035	0.0719	0.1167	5008	,	,		19365	0.005		0.1958	False		,,,				2504	0.1411				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTGGACAAAAACC																													7.37:g.63894558A>C			135	0	0		189	0.03	6	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.403										
ZNF680	340252	ucsc.edu	37	7	63981631	63981631	+	Missense_Mutation	SNP	G	G	A			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr7:63981631G>A	ENST00000309683.6	-	4	1652	c.1501C>T	c.(1501-1503)Cgg>Tgg	p.R501W	ZNF680_ENST00000476563.1_5'Flank	NM_178558.4	NP_848653.2	Q8NEM1	ZN680_HUMAN	zinc finger protein 680	501					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	27		Lung NSC(55;0.118)|all_lung(88;0.243)				TGTGAGGACCGGTTAAAAGCT	0.358																																					p.R501W													ZNF680,NS,carcinoma,+1,1	ZNF680	58	1	0			c.C1501T												65.0	69.0	67.0					7																	63981631		2203	4300	6503	SO:0001583	missense	340252	exon4			AGGACCGGTTAAA	AK074911	CCDS34644.1, CCDS47594.1	7q11.21	2013-01-08			ENSG00000173041	ENSG00000173041		"""Zinc fingers, C2H2-type"", ""-"""	26897	protein-coding gene	gene with protein product	"""hypothetical protein FLJ90430"""					12477932	Standard	NM_178558		Approved	FLJ90430	uc003tta.2	Q8NEM1	OTTHUMG00000156542	ENST00000309683.6:c.1501C>T	7.37:g.63981631G>A	ENSP00000309330:p.Arg501Trp		97	0	0		120	0.02	2	NM_178558	44	0.57	25	B3KVJ4|Q6ZNF3|Q8NC79	Missense_Mutation	SNP	ENST00000309683.6	37	CCDS34644.1	.	.	.	.	.	.	.	.	.	.	g	16.13	3.035027	0.54896	.	.	ENSG00000173041	ENST00000309683	T	0.58210	0.35	1.31	-2.46	0.06461	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.51466	0.1676	L	0.45285	1.41	0.09310	N	1	D	0.89917	1.0	D	0.64877	0.93	T	0.41142	-0.9525	9	0.27082	T	0.32	.	2.0402	0.03549	0.2511:0.0:0.4566:0.2924	.	501	Q8NEM1	ZN680_HUMAN	W	501	ENSP00000309330:R501W	ENSP00000309330:R501W	R	-	1	2	ZNF680	63619066	0.000000	0.05858	0.000000	0.03702	0.125000	0.20455	0.133000	0.15912	-0.859000	0.04105	-0.359000	0.07587	CGG			0.358	ZNF680-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000344568.1	rescued with RNA-seq	NM_178558	
CDK5PS	392265	bcgsc.ca	37	8	123782133	123782133	+	IGR	SNP	C	C	T	rs6992158	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr8:123782133C>T								RP11-973F15.2 (66471 upstream) : RP11-44N11.2 (10076 downstream)																							CAGGCAATGACGTCGATGACC	0.542													T|||	3186	0.636182	0.7231	0.6052	5008	,	,		21838	0.6617		0.5885	False		,,,				2504	0.5634				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAATGACGTCGAT																													8.37:g.123782133C>T			39	0	0		32	0.16	5	.	0		0		RNA	SNP		37																																																																																					0	0.542										
TRBV25OR9-2	6960	bcgsc.ca	37	9	33662557	33662557	+	IGR	SNP	G	G	C	rs41302224	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr9:33662557G>C								TRBV23OR9-2 (24065 upstream) : PTENP1 (10944 downstream)																							GGAGATCTTTGCTCTGAGTCA	0.493													C|||	408	0.0814696	0.1929	0.0476	5008	,	,		21046	0.002		0.0676	False		,,,				2504	0.0511				.													.	.			0			.																																									SO:0001628	intergenic_variant	6960	.			ATCTTTGCTCTGA																													9.37:g.33662557G>C			51	0	0		50	0.08	4	.	0		0		Missense_Mutation	SNP		37		149	0.06822344322344322	77	0.1565040650406504	21	0.058011049723756904	0	0.0	51	0.06728232189973615	C	2.947	-0.217511	0.06101	.	.	ENSG00000240215	ENST00000438417	.	.	.	2.79	1.86	0.25419	.	.	.	.	.	T	0.00109	0.0003	.	.	.	.	.	.	.	.	.	.	.	.	T	0.17592	-1.0364	4	0.23302	T	0.38	.	4.1671	0.10312	0.0:0.6141:0.2414:0.1446	rs41302224	.	.	.	S	78	.	ENSP00000403609:C78S	C	+	2	0	TRBV25OR9-2	33652557	0.000000	0.05858	0.001000	0.08648	0.103000	0.19146	0.227000	0.17795	0.082000	0.17018	-1.201000	0.01664	TGC		0	0.493										
Unknown	0	bcgsc.ca	37	9	40610136	40610136	+	IGR	SNP	G	G	A	rs3739627		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr9:40610136G>A								RN7SL422P (93072 upstream) : SPATA31A3 (90154 downstream)																							AGGCCAGTGGGGCATCACAGT	0.478																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGTGGGGCATCA																													9.37:g.40610136G>A			225	0	0		255	0.04	10	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.478										
LOC105376072	105376072	bcgsc.ca	37	9	71224796	71224796	+	lincRNA	SNP	G	G	C	rs10781073	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr9:71224796G>C	ENST00000413269.3	+	0	460																											ATGATGGATGGCTCCCTCTAT	0.458													G|||	2448	0.488818	0.3154	0.4726	5008	,	,		22108	0.4345		0.6481	False		,,,				2504	0.6268				.													.	.			0			.																																											0	.			TGGATGGCTCCCT																													9.37:g.71224796G>C			40	0	0		44	0.09	4	.	0		0		RNA	SNP	ENST00000413269.3	37																																																																																						0.458	RP11-274B18.4-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000052555.2			
SPATA31D5P	347127	broad.mit.edu	37	9	84532319	84532319	+	RNA	DEL	G	G	-			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr9:84532319delG	ENST00000527857.1	+	0	2341					NR_026851.1				SPATA31 subfamily D, member 5, pseudogene																		TGCTTTCCATGGAGAATGTGG	0.468																																					.													.	.			0			.																																											0	.			TTCCATGGAGAAT			9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000240632	ENSG00000240632			38602	pseudogene	pseudogene			"""family with sequence similarity 75, member D5"", ""family with sequence similarity 75, member D5, pseudogene"""	FAM75D5			Standard	NR_026851		Approved	FLJ43950, FAM75D5P	uc011lst.2		OTTHUMG00000020087		9.37:g.84532319delG			260	0	0		257	0.05	14	.	0		0		RNA	DEL	ENST00000527857.1	37																																																																																						0.468	SPATA31D5P-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000052810.2		NR_026851	
RP11-435O5.2	0	broad.mit.edu	37	9	98180677	98180678	+	lincRNA	INS	-	-	GTGTGT	rs376542879|rs575031246|rs10685762|rs113946320	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr9:98180677_98180678insGTGTGT	ENST00000433644.2	-	0	73																											gtatgggtgtggtgtgtgtgtg	0.406																																					.													.	.			0			.																																											0	.			GGGTGTGGTGTGT																													9.37:g.98180678_98180683dupGTGTGT			4	0	0		6	0.33	2	.	0		0		RNA	INS	ENST00000433644.2	37																																																																																						0.406	RP11-435O5.2-001	KNOWN	basic|exp_conf	lincRNA	lincRNA		OTTHUMT00000053234.2			
KRT8P11	347265	bcgsc.ca;mdanderson.org	37	9	102068058	102068058	+	IGR	SNP	A	A	G	rs184437	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr9:102068058A>G								RN7SKP225 (21403 upstream) : NAMA (49633 downstream)																							GCTTACATGAACAAGGCAGAA	0.483													A|||	806	0.160942	0.2027	0.1643	5008	,	,		25508	0.1052		0.2147	False		,,,				2504	0.1043				.													.	.			0			.																																									SO:0001628	intergenic_variant	347265	.			ACATGAACAAGGC																													9.37:g.102068058A>G			81	0	0		81	0.09	7	.	5	0.00	0		Missense_Mutation	SNP		37		379	0.17353479853479853	88	0.17886178861788618	75	0.20718232044198895	49	0.08566433566433566	167	0.22031662269129287	A	9.168	1.020494	0.19433	.	.	ENSG00000222039	ENST00000409686	D	0.88431	-2.38	0.522	0.522	0.17053	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.26420	P	0.9761123	.	.	.	.	.	.	T	0.11591	-1.0581	5	0.48119	T	0.1	.	5.277	0.15655	0.9999:0.0:1.0E-4:0.0	rs184437;rs184554;rs16918468;rs52833471;rs184437	.	.	.	S	222	ENSP00000404011:N222S	ENSP00000404011:N222S	N	+	2	0	KRT8P11	101107879	1.000000	0.71417	0.330000	0.25442	0.032000	0.12392	1.824000	0.39072	0.428000	0.26173	0.260000	0.18958	AAC		0	0.483										
UBAC1	10422	ucsc.edu;bcgsc.ca	37	9	138830111	138830111	+	Missense_Mutation	SNP	G	G	T			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chr9:138830111G>T	ENST00000371756.3	-	9	1276	c.1059C>A	c.(1057-1059)aaC>aaA	p.N353K	UBAC1_ENST00000465873.1_5'Flank	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	353	STI1.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		GCACCACCGGGTTATCCAGGA	0.612																																					p.N353K	NSCLC(78;973 1398 27381 29552 42415)												.	UBAC1	40		0			c.C1059A												123.0	113.0	117.0					9																	138830111		2203	4300	6503	SO:0001583	missense	10422	exon9			CACCGGGTTATCC	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"""ubiquitin associated domain containing 1"""	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.1059C>A	9.37:g.138830111G>T	ENSP00000360821:p.Asn353Lys		41	0	0		32	0.13	4	NM_016172	211	0.00	0	O75500|Q9UMW7	Missense_Mutation	SNP	ENST00000371756.3	37	CCDS35177.1	.	.	.	.	.	.	.	.	.	.	G	18.68	3.676623	0.67928	.	.	ENSG00000130560	ENST00000371756	T	0.25250	1.81	4.8	2.95	0.34219	Heat shock chaperonin-binding (1);	0.000000	0.85682	D	0.000000	T	0.39545	0.1082	L	0.50333	1.59	0.80722	D	1	D	0.76494	0.999	D	0.66196	0.942	T	0.10917	-1.0609	10	0.72032	D	0.01	-45.2288	9.668	0.39996	0.1688:0.0:0.8312:0.0	.	353	Q9BSL1	UBAC1_HUMAN	K	353	ENSP00000360821:N353K	ENSP00000360821:N353K	N	-	3	2	UBAC1	137969932	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	3.638000	0.54332	0.443000	0.26582	0.561000	0.74099	AAC			0.612	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000055034.1		NM_016172	
NHS	4810	hgsc.bcm.edu	37	X	17750309	17750309	+	Missense_Mutation	SNP	G	G	A			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:17750309G>A	ENST00000380060.3	+	8	4956	c.4618G>A	c.(4618-4620)Gat>Aat	p.D1540N	NHS_ENST00000398097.3_Missense_Mutation_p.D1384N	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1561					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TCAGAGCACCGATGATGCCCA	0.562																																					p.D1540N													.	.			0			c.G4618A												86.0	79.0	81.0					X																	17750309		2203	4300	6503	SO:0001583	missense	4810	exon8			AGCACCGATGATG		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.4618G>A	X.37:g.17750309G>A	ENSP00000369400:p.Asp1540Asn		161	0	0		182	0.04	8	NM_198270	1	0.00	0	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	37	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.251357	0.59212	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.45276	0.9;0.91	5.69	4.83	0.62350	.	0.488362	0.23724	N	0.045192	T	0.29588	0.0738	L	0.43152	1.355	0.46749	D	0.999188	P;B;B;P	0.40681	0.519;0.229;0.229;0.727	B;B;B;B	0.24269	0.052;0.052;0.052;0.049	T	0.06285	-1.0835	10	0.29301	T	0.29	-2.2614	14.3458	0.66662	0.0:0.1917:0.8083:0.0	.	1561;1382;1384;1540	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	N	1540;1384;1382	ENSP00000369400:D1540N;ENSP00000381170:D1384N	ENSP00000369397:D1382N	D	+	1	0	NHS	17660230	1.000000	0.71417	0.521000	0.27850	0.819000	0.46315	6.833000	0.75334	1.293000	0.44690	0.600000	0.82982	GAT			0.562	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000059120.1		NM_198270	
PTCHD1	139411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	23411681	23411681	+	Missense_Mutation	SNP	C	C	G			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:23411681C>G	ENST00000379361.4	+	3	2906	c.2046C>G	c.(2044-2046)ttC>ttG	p.F682L		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	682					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						TCATCGTCTTCAATCCGTCCT	0.493																																					p.F682L													.	.			0			c.C2046G												91.0	82.0	85.0					X																	23411681		2203	4300	6503	SO:0001583	missense	139411	exon3			CGTCTTCAATCCG	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.2046C>G	X.37:g.23411681C>G	ENSP00000368666:p.Phe682Leu		55	0	0		96	0.11	11	NM_173495	1	0.00	0	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	37	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	C	16.52	3.145132	0.57044	.	.	ENSG00000165186	ENST00000379361	D	0.90788	-2.73	5.34	2.05	0.26809	.	0.000000	0.85682	D	0.000000	D	0.92606	0.7651	L	0.57536	1.79	0.48087	D	0.99958	D	0.60160	0.987	D	0.69824	0.966	D	0.90484	0.4462	10	0.87932	D	0	.	9.0092	0.36131	0.0:0.7193:0.0:0.2807	.	682	Q96NR3	PTHD1_HUMAN	L	682	ENSP00000368666:F682L	ENSP00000368666:F682L	F	+	3	2	PTCHD1	23321602	0.998000	0.40836	0.992000	0.48379	0.996000	0.88848	0.666000	0.25097	-0.011000	0.14247	0.529000	0.55759	TTC			0.493	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000056047.2		NM_173495	
SALL1P1	139163	bcgsc.ca	37	X	49432879	49432880	+	IGR	DNP	CA	CA	TG	rs147747838|rs181522811		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:49432879_49432880CA>TG								GAGE1 (61921 upstream) : PAGE1 (19172 downstream)																							AGGTTGTGATCACTGAGGTATC	0.554																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	139163	.			TGTGATCACTGAG																													X.37:g.49432879_49432880delinsTG			41	0	0		49	0.12	6	.	0		0		RNA	DNP		37																																																																																					0	0.554										
SALL1P1	139163	bcgsc.ca	37	X	49432943	49432943	+	IGR	SNP	T	T	C	rs6608907	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:49432943T>C								GAGE1 (61985 upstream) : PAGE1 (19109 downstream)																							gctgtggctgtggctggaagt	0.562													C||||C|||	146|146	0.0386755|0.0386755	0.025|0.025	0.0231|0.0231	3775|3775	,|,	,|,		12283|12283	0.0476|0.0476		0.0129|0.0129	False|False		,,,|,,,				2504|2504	0.0368|0.0368				.													.	.			0			.																																									SO:0001628	intergenic_variant	139163	.			TGGCTGTGGCTGG																													X.37:g.49432943T>C			33	0	0		40	0.13	5	.	0		0		RNA	SNP		37																																																																																					0	0.562										
SERBP1P1	389866	bcgsc.ca	37	X	68003320	68003320	+	IGR	SNP	T	T	C	rs12012713	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:68003320T>C								STARD8 (57638 upstream) : EFNB1 (45519 downstream)																							CCATCATGCCTGGGCACTTAC	0.607													t|||	345	0.0913907	0.2496	0.0187	3775	,	,		11335	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CATGCCTGGGCAC																													X.37:g.68003320T>C			59	0	0		58	0.09	5	.	0		0		RNA	SNP		37																																																																																					0	0.607										
SERBP1P1	389866	bcgsc.ca	37	X	68004148	68004148	+	IGR	SNP	T	T	C	rs7061948	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:68004148T>C								STARD8 (58466 upstream) : EFNB1 (44691 downstream)																							GCGACCACCTTGTGAACGAAG	0.408													N|||	251	0.0664901	0.1815	0.013	3775	,	,		13910	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCACCTTGTGAAC																													X.37:g.68004148T>C			75	0	0		89	0.09	8	.	0		0		RNA	SNP		37																																																																																					0	0.408										
SERBP1P1	389866	bcgsc.ca	37	X	68004230	68004230	+	IGR	SNP	A	A	C	rs7058210		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:68004230A>C								STARD8 (58548 upstream) : EFNB1 (44609 downstream)																							ATTGACCGACATATTCGAGGT	0.478													C|||	254	0.0672848	0.1838	0.013	3775	,	,		15308	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACCGACATATTCG																													X.37:g.68004230A>C			172	0	0		187	0.09	16	.	0		0		RNA	SNP		37																																																																																					0	0.478										
SERBP1P1	389866	bcgsc.ca	37	X	68004333	68004333	+	IGR	SNP	G	G	T	rs111708563		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:68004333G>T								STARD8 (58651 upstream) : EFNB1 (44506 downstream)																							AATTTGATAGGCATAGTGGAA	0.502													G|||	254	0.0672848	0.1838	0.013	3775	,	,		14968	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGATAGGCATAGT																													X.37:g.68004333G>T			172	0	0		184	0.09	16	.	33	0.00	0		RNA	SNP		37																																																																																					0	0.502										
SERBP1P1	389866	bcgsc.ca	37	X	68004709	68004709	+	IGR	SNP	C	C	T	rs16990731	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:68004709C>T								STARD8 (59027 upstream) : EFNB1 (44130 downstream)																							GGTTATGGACCGTCATTTCCG	0.507													C|||	174	0.0460927	0.1256	0.0086	3775	,	,		14153	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATGGACCGTCATT																													X.37:g.68004709C>T			87	0	0		127	0.13	17	.	0		0		RNA	SNP		37																																																																																					0	0.507										
Unknown	0	bcgsc.ca	37	X	89294856	89294856	+	IGR	SNP	G	G	T			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:89294856G>T								TGIF2LX (116974 upstream) : RNU6-555P (557377 downstream)																							ATTCTGGTCCGGCCTTGACTA	0.428																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGGTCCGGCCTTG																													X.37:g.89294856G>T			24	0	0		40	0.28	11	.	0		0		RNA	SNP		37																																																																																					0	0.428										
USP12PX	254700	bcgsc.ca	37	X	89368606	89368606	+	IGR	SNP	G	G	T	rs5941478		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:89368606G>T								TGIF2LX (190724 upstream) : RNU6-555P (483627 downstream)																							ATTATATTGCGATAGTTAAGA	0.398													G||||G|||	932|932	0.246887|0.246887	0.1127|0.1127	0.1888|0.1888	3775|3775	,|,	,|,		13450|13450	0.0109|0.0109		0.4085|0.4085	False|False		,,,|,,,				2504|2504	0.2352|0.2352				.													.	.			0			.																																									SO:0001628	intergenic_variant	254700	.			TATTGCGATAGTT																													X.37:g.89368606G>T			68	0	0		73	0.07	5	.	0		0		RNA	SNP		37																																																																																					0	0.398										
FRMPD3	84443	bcgsc.ca	37	X	106796084	106796084	+	Silent	SNP	T	T	C	rs12011630	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:106796084T>C	ENST00000276185.4	+	8	669	c.669T>C	c.(667-669)ctT>ctC	p.L223L	FRMPD3_ENST00000477796.1_3'UTR			Q5JV73	FRPD3_HUMAN	FERM and PDZ domain containing 3	223	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(16)|ovary(2)|urinary_tract(1)	28						ACTTTGCTCTTGTCCTTGAGT	0.458													t|||	669	0.177219	0.3971	0.1095	3775	,	,		14784	0.0327		0.005	False		,,,				2504	0.0307				.													.	.			0			.									653,765		119,260,155,163,179	47.0	41.0	42.0		804	-3.5	1.0	X	dbSNP_120	42	20,3087		1,14,4,1101,871	no	coding-synonymous	FRMPD3	XM_042978.7		120,274,159,1264,1050	CC,CT,C,TT,T		0.6437,46.0508,14.8729		268/1856	106796084	673,3852	876	1991	2867	SO:0001819	synonymous_variant	84443	.			TGCTCTTGTCCTT	AB058720	CCDS76006.1	Xq22	2008-02-05			ENSG00000147234	ENSG00000147234			29382	protein-coding gene	gene with protein product						11347906	Standard	NM_032428		Approved	RP5-1070B1.1, KIAA1817		Q5JV73	OTTHUMG00000022165	ENST00000276185.4:c.669T>C	X.37:g.106796084T>C			77	0	0		65	0.08	5	.	0		0	Q96JK8	Silent	SNP	ENST00000276185.4	37																																																																																						0.458	FRMPD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				XM_042978	
NCBP2L	392517	bcgsc.ca;mdanderson.org	37	X	107037795	107037795	+	Silent	SNP	C	C	A	rs5962885	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:107037795C>A	ENST00000509000.2	+	2	543	c.345C>A	c.(343-345)gtC>gtA	p.V115V	NCBP2L_ENST00000372379.2_Silent_p.V115V			A6PVI3	NCB2L_HUMAN	nuclear cap binding protein subunit 2-like	115	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA cis splicing, via spliceosome (GO:0045292)	nuclear cap binding complex (GO:0005846)	nucleotide binding (GO:0000166)|RNA cap binding (GO:0000339)			large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	5						ATTGGGATGTCGGTTTTAGAG	0.463													A|||	1171	0.310199	0.6006	0.1052	3775	,	,		12995	0.1012		0.1093	False		,,,				2504	0.0941				.													.	.			0			.							A		999,419		262,234,241,46,93	134.0	120.0	124.0			-2.0	0.0	X	dbSNP_114	124	391,2716		23,242,103,851,772	no	intergenic				285,476,344,897,865	AA,AC,A,CC,C		12.5845,29.5487,30.7182			107037795	1390,3135	876	1991	2867	SO:0001819	synonymous_variant	392517	.			GGATGTCGGTTTT			Xq22.3	2013-02-12			ENSG00000170935	ENSG00000170935		"""RNA binding motif (RRM) containing"""	31795	protein-coding gene	gene with protein product							Standard	NG_011409		Approved			A6PVI3	OTTHUMG00000022169	ENST00000509000.2:c.345C>A	X.37:g.107037795C>A			71	0	0		88	0.08	7	.	0		0		Silent	SNP	ENST00000509000.2	37																																																																																						0.463	NCBP2L-001	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000057850.2		XM_373362	
API5P1	642812	bcgsc.ca	37	X	115239675	115239675	+	IGR	SNP	G	G	C	rs7057314	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:115239675G>C								RN7SL712P (130575 upstream) : AGTR2 (62299 downstream)																							GCTCCTCTACGTTCGGCACAG	0.547													C|||	1547	0.409801	0.5401	0.3098	3775	,	,		12755	0.1052		0.3579	False		,,,				2504	0.1554				.													.	.			0			.																																									SO:0001628	intergenic_variant	642812	.			CTCTACGTTCGGC																													X.37:g.115239675G>C			90	0	0		72	0.11	8	.	0		0		RNA	SNP		37																																																																																					0	0.547										
MRRFP1	286423	bcgsc.ca	37	X	122250996	122250996	+	IGR	SNP	G	G	T	rs6648942	byFrequency	TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:122250996G>T								U3 (276499 upstream) : GRIA3 (67009 downstream)																							TAAAGAGTATGTGGCCTTGTT	0.468													T|||	2076	0.549934	0.3631	0.4769	3775	,	,		16291	0.5635		0.2008	False		,,,				2504	0.5061				.													.	.			0			.																																									SO:0001628	intergenic_variant	286423	.			GAGTATGTGGCCT																													X.37:g.122250996G>T			147	0	0		199	0.05	10	.	0		0		Missense_Mutation	SNP		37		808	0.487040385774563	122	0.3193717277486911	98	0.3656716417910448	217	0.5896739130434783	119	0.1803030303030303	T	6.412	0.444056	0.12164	.	.	ENSG00000224236	ENST00000435941	.	.	.	1.49	1.49	0.22878	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	.	.	.	0.58432	P	6.999999999979245E-6	.	.	.	.	.	.	T	0.46345	-0.9198	5	0.02654	T	1	-1.3317	5.4932	0.16787	0.0:0.0:0.2846:0.7154	rs6648942;rs16997095;rs52801655;rs56738867;rs6648942	.	.	.	K	205	.	ENSP00000387841:T205K	T	-	2	0	MRRFP1	122078677	1.000000	0.71417	0.164000	0.22755	0.098000	0.18820	2.795000	0.47861	-0.130000	0.11599	-1.794000	0.00625	ACA		0	0.468										
CT55	54967	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	134294393	134294393	+	Missense_Mutation	SNP	C	C	T			TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:134294393C>T	ENST00000276241.6	-	3	593	c.367G>A	c.(367-369)Gaa>Aaa	p.E123K	CXorf48_ENST00000344129.2_Missense_Mutation_p.E123K	NM_001031705.2	NP_001026875.1	Q8WUE5	CT55_HUMAN		123										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)	5	Acute lymphoblastic leukemia(192;0.000127)					ATATTATCTTCATTTATAGAA	0.313																																					p.E123K													.	.			0			c.G367A												20.0	19.0	20.0					X																	134294393		2202	4286	6488	SO:0001583	missense	54967	exon3			TATCTTCATTTAT																												ENST00000276241.6:c.367G>A	X.37:g.134294393C>T	ENSP00000276241:p.Glu123Lys		278	0	0		291	0.15	45	NM_017863	5	0.20	1	Q9NWY8	Missense_Mutation	SNP	ENST00000276241.6	37	CCDS35400.1	.	.	.	.	.	.	.	.	.	.	C	9.595	1.127090	0.20959	.	.	ENSG00000169551	ENST00000276241;ENST00000344129	T;T	0.44083	0.93;0.93	2.93	-5.86	0.02304	.	0.530450	0.15689	N	0.249532	T	0.24353	0.0590	L	0.33339	1.005	0.09310	N	1	B	0.22080	0.064	B	0.11329	0.006	T	0.03443	-1.1036	10	0.30854	T	0.27	-2.9105	9.4264	0.38583	0.0:0.6726:0.1416:0.1859	.	123	Q8WUE5	CX048_HUMAN	K	123	ENSP00000276241:E123K;ENSP00000343893:E123K	ENSP00000276241:E123K	E	-	1	0	CXorf48	134122059	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.709000	0.05030	-2.254000	0.00697	-0.351000	0.07748	GAA			0.313	CXorf48-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000058404.1			
Unknown	0	bcgsc.ca	37	X	134345975	134345975	+	IGR	SNP	G	G	A	rs147984738		TCGA-VF-A8AA-01A-11D-A435-10	TCGA-VF-A8AA-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	59db8d85-3daa-42af-8649-41c53d90e9ce	5cf5995d-4ad7-4c93-858b-1e46e9cb6bfb	g.chrX:134345975G>A								AL590282.1 (5398 upstream) : ZNF75D (36891 downstream)																							AGTTTTAATTGGATGTGTTAC	0.353													g|||	22	0.00582781	0.0015	0.0029	3775	,	,		14366	0.0		0.0119	False		,,,				2504	0.0061				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTAATTGGATGTG																													X.37:g.134345975G>A			214	0	0		230	0.06	13	.	0		0		RNA	SNP		37																																																																																					0	0.353										
