#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_IGV	i_Mutation_Status	i_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVaf_SOL	i_TVarCov_SOL	i_Transcript_Id	i_Ttot_rna	i_Tvaf_rna	i_Tvar_rna	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_germline-maf-frequency	i_havana_transcript	i_note	i_refseq_mrna_id	i_secondary_variant_classification
NOL9	79707	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	6586826	6586826	+	Missense_Mutation	SNP	T	T	A			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr1:6586826T>A	ENST00000377705.5	-	11	1921	c.1889A>T	c.(1888-1890)gAa>gTa	p.E630V		NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	630					maturation of 5.8S rRNA (GO:0000460)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|polynucleotide 5'-hydroxyl-kinase activity (GO:0051731)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(2)|urinary_tract(1)	19	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)		CCTTAGCTCTTCCGGGGGCAC	0.542																																					p.E630V													.	.			0			c.A1889T												128.0	113.0	118.0					1																	6586826		2203	4300	6503	SO:0001583	missense	79707	exon11			AGCTCTTCCGGGG	AK091284	CCDS80.1	1p36.31	2012-05-02			ENSG00000162408	ENSG00000162408			26265	protein-coding gene	gene with protein product	"""polynucleotide 5'-kinase"""					21063389	Standard	NM_024654		Approved	FLJ23323, NET6, Grc3	uc001ans.3	Q5SY16	OTTHUMG00000000904	ENST00000377705.5:c.1889A>T	1.37:g.6586826T>A	ENSP00000366934:p.Glu630Val		Somatic	124	0	0		WXS	Illumina HiSeq	.	130	0.22	28	NM_024654	70	0.19	13	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	Missense_Mutation	SNP	ENST00000377705.5	37	CCDS80.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.588116	0.46110	.	.	ENSG00000162408	ENST00000377705	T	0.51325	0.71	5.24	5.24	0.73138	Pre-mRNA cleavage complex II Clp1 (1);	0.224729	0.40640	N	0.001041	T	0.67268	0.2875	M	0.77103	2.36	0.09310	N	1	D	0.76494	0.999	D	0.72982	0.979	T	0.61959	-0.6955	10	0.42905	T	0.14	-20.5329	13.0942	0.59182	0.0:0.0:0.0:1.0	.	630	Q5SY16	NOL9_HUMAN	V	630	ENSP00000366934:E630V	ENSP00000366934:E630V	E	-	2	0	NOL9	6509413	0.881000	0.30235	0.044000	0.18714	0.417000	0.31264	3.395000	0.52558	1.984000	0.57885	0.460000	0.39030	GAA			0.542	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000002625.1		NM_024654	
PIK3CD	5293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	9775907	9775907	+	Splice_Site	SNP	G	G	A			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr1:9775907G>A	ENST00000377346.4	+	5	566	c.371G>A	c.(370-372)gGc>gAc	p.G124D	PIK3CD_ENST00000361110.2_Splice_Site_p.G124D|PIK3CD_ENST00000536656.1_Splice_Site_p.G124D|PIK3CD_ENST00000543390.1_5'Flank	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	124					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)	CACCCCGCAGGCCTCCACGAG	0.682																																					p.G124D													.	.			0			c.G371A												13.0	15.0	15.0					1																	9775907		2196	4294	6490	SO:0001630	splice_region_variant	5293	exon5			CCGCAGGCCTCCA		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.371-1G>A	1.37:g.9775907G>A			Somatic	77	0	0		WXS	Illumina HiSeq	.	82	0.15	12	NM_005026	86	0.10	9	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	37	CCDS104.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.931385	0.73442	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	T;T;T	0.45668	0.89;0.89;0.89	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.62429	0.2427	L	0.60455	1.87	0.80722	D	1	P;D;D	0.89917	0.823;1.0;1.0	B;D;D	0.74674	0.414;0.984;0.984	T	0.58482	-0.7629	9	.	.	.	.	19.5625	0.95378	0.0:0.0:1.0:0.0	.	124;124;124	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	D	124	ENSP00000446444:G124D;ENSP00000366563:G124D;ENSP00000354410:G124D	.	G	+	2	0	PIK3CD	9698494	1.000000	0.71417	1.000000	0.80357	0.194000	0.23727	9.424000	0.97464	2.620000	0.88729	0.563000	0.77884	GGC			0.682	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000004235.1		NM_005026	Missense_Mutation
PSAT1P3	729779	bcgsc.ca	37	1	79521355	79521355	+	IGR	SNP	C	C	T	rs3795404	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr1:79521355C>T								ELTD1 (48952 upstream) : AC093430.1 (79462 downstream)																							TGTATAACTCCCAAGTTTAGG	0.468													C|||	1101	0.219848	0.1422	0.2738	5008	,	,		20164	0.3313		0.2406	False		,,,				2504	0.1503				.													.	.			0			.																																									SO:0001628	intergenic_variant	729779	.			TAACTCCCAAGTT																													1.37:g.79521355C>T			Somatic	83	0	0		WXS	Illumina HiSeq	Phase_1	89	0.08	7	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.468										
EEF1A1P11	440595	bcgsc.ca	37	1	96913449	96913449	+	IGR	SNP	C	C	T	rs11165631	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr1:96913449C>T								RP5-898J17.1 (73768 upstream) : RN7SL831P (135315 downstream)																							GGATGTTCATCGTGGCAACGT	0.468													C|||	884	0.176518	0.1014	0.1527	5008	,	,		22163	0.3145		0.2137	False		,,,				2504	0.1145				.													.	.			0			.																																									SO:0001628	intergenic_variant	440595	.			GTTCATCGTGGCA																													1.37:g.96913449C>T			Somatic	118	0	0		WXS	Illumina HiSeq	Phase_1	116	0.05	6	.	85	0.00	0		RNA	SNP		37																																																																																					0	0.468										
Unknown	0	bcgsc.ca	37	1	106435772	106435772	+	IGR	SNP	T	T	G	rs12066937	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr1:106435772T>G								RP11-251P6.1 (274192 upstream) : RP11-24P14.1 (34473 downstream)																							CCAGTGAGAGTTCATTTATCC	0.423													T|||	768	0.153355	0.0832	0.1614	5008	,	,		17463	0.2391		0.1332	False		,,,				2504	0.1748				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGAGAGTTCATTT																													1.37:g.106435772T>G			Somatic	174	0	0		WXS	Illumina HiSeq	Phase_1	173	0.07	12	.	25	0.00	0		RNA	SNP		37																																																																																					0	0.423										
NRAS	4893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																											p.Q61R				Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"""L, E"""	NRAS,NS,haematopoietic_neoplasm,-1,2068	NRAS	-1	2068	1016	Substitution - Missense(1016)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)	c.A182G												180.0	156.0	164.0					1																	115256529		2203	4300	6503	SO:0001583	missense	4893	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	TCTTCTTGTCCAG	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>G	1.37:g.115256529T>C	ENSP00000358548:p.Gln61Arg		Somatic	151	0	0		WXS	Illumina HiSeq	.	136	0.13	18	NM_002524	53	0.26	14	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004139	0.74932	.	.	ENSG00000213281	ENST00000369535	D	0.83673	-1.75	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.86489	0.5945	M	0.92604	3.325	0.80722	D	1	B	0.28512	0.214	B	0.39590	0.304	D	0.88255	0.2919	10	0.66056	D	0.02	.	15.0132	0.71565	0.0:0.0:0.0:1.0	rs11554290;rs11554290	61	P01111	RASN_HUMAN	R	61	ENSP00000358548:Q61R	ENSP00000358548:Q61R	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA			0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000033395.2		NM_002524	
LOC728989	728989	bcgsc.ca	37	1	146523045	146523045	+	IGR	SNP	A	A	G	rs580852	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr1:146523045A>G								RP4-704D21.2 (47868 upstream) : RNVU1-8 (28249 downstream)																							AACATCACTAAGTAGACCCAG	0.502													.|||	1044	0.208466	0.2247	0.2046	5008	,	,		18152	0.1389		0.2445	False		,,,				2504	0.2239				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCACTAAGTAGAC																													1.37:g.146523045A>G			Somatic	86	0	0		WXS	Illumina HiSeq	Phase_1	81	0.07	6	.	0		0		RNA	SNP		37																																																																																					0	0.502										
Unknown	0	bcgsc.ca	37	1	146791020	146791020	+	IGR	SNP	A	A	G	rs4950399	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr1:146791020A>G								CHD1L (23577 upstream) : Y_RNA (100905 downstream)																							AAGTGGCCAGATTTGTGGAAA	0.478													A|||	717	0.143171	0.0076	0.1888	5008	,	,		18965	0.0923		0.2326	False		,,,				2504	0.2546				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGCCAGATTTGTG																													1.37:g.146791020A>G			Somatic	184	0	0		WXS	Illumina HiSeq	Phase_1	129	0.04	5	.	0		0		RNA	SNP		37																																																																																					0	0.478										
Unknown	0	bcgsc.ca	37	1	157679783	157679783	+	IGR	SNP	A	A	G	rs17727309	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	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			Somatic	228	0	0		WXS	Illumina HiSeq	Phase_1	197	0.05	9	.	12	0.08	1		RNA	SNP		37																																																																																					0	0.493										
OBSCN	84033	bcgsc.ca	37	1	228412227	228412228	+	Missense_Mutation	DNP	TG	TG	CA	rs386640006|rs1757153|rs1771480	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	TG	TG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr1:228412227_228412228TG>CA	ENST00000422127.1	+	9	2765_2766	c.2721_2722TG>CA	c.(2719-2724)agTGcc>agCAcc	p.A908T	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.A908T|OBSCN_ENST00000570156.2_Missense_Mutation_p.A1000T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	908	Ig-like 9.		A -> T (in dbSNP:rs1757153).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CAGGAGCCAGTGCCACACTGAG	0.614																																					p.A908T													.	OBSCN	2142		0			c.G2998A																																									SO:0001583	missense	84033	exon10			AGCCAGTGCCACA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	Exception_encountered	1.37:g.228412227_228412228delinsCA	ENSP00000409493:p.Ala908Thr		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_1	98	0.08	8	NM_001271223	10	0.00	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	DNP	ENST00000422127.1	37	CCDS58065.1																																																																																					0.614	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding				NM_052843	
OBSCN	84033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	228480321	228480321	+	Silent	SNP	G	G	T			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr1:228480321G>T	ENST00000422127.1	+	40	10745	c.10701G>T	c.(10699-10701)gtG>gtT	p.V3567V	OBSCN_ENST00000359599.6_Silent_p.V2414V|OBSCN_ENST00000570156.2_Silent_p.V3996V|OBSCN_ENST00000366707.4_Silent_p.V686V|OBSCN_ENST00000366709.4_Silent_p.V686V|OBSCN_ENST00000284548.11_Silent_p.V3567V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3567	Ig-like 36.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CAGCCCCTGTGGAGTGGAGAA	0.572																																					p.V3996V													.	.			0			c.G11988T												114.0	113.0	114.0					1																	228480321		2016	4185	6201	SO:0001819	synonymous_variant	84033	exon45			CCCTGTGGAGTGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.10701G>T	1.37:g.228480321G>T			Somatic	185	0	0		WXS	Illumina HiSeq	.	168	0.14	24	NM_001271223	3	0.33	1	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																					0.572	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding				NM_052843	
OR14A2	388761	bcgsc.ca;mdanderson.org	37	1	247886949	247886949	+	Missense_Mutation	SNP	T	T	C	rs36075193	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr1:247886949T>C	ENST00000366485.1	-	1	396	c.397A>G	c.(397-399)Atc>Gtc	p.I133V	RP11-634B7.5_ENST00000426444.1_RNA|RP11-634B7.4_ENST00000449298.1_RNA			Q96R54	O14A2_HUMAN	olfactory receptor, family 14, subfamily A, member 2	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										GTATTCATGATTACCTCGTAG	0.468													T|||	189	0.0377396	0.0053	0.0476	5008	,	,		21772	0.001		0.1272	False		,,,				2504	0.0204				.													.	.			0			.																																									SO:0001583	missense	388761	.			TCATGATTACCTC	AB065620		1q44	2013-01-16	2008-04-02	2008-04-02	ENSG00000241128	ENSG00000241128		"""GPCR / Class A : Olfactory receptors"""	15024	other	unknown			"""olfactory receptor, family 5, subfamily AX, member 1 pseudogene"", ""olfactory receptor, family 5, subfamily AX, member 1"""	OR5AX1P, OR5AX1			Standard	NG_002409		Approved			Q96R54	OTTHUMG00000040207	ENST00000366485.1:c.397A>G	1.37:g.247886949T>C	ENSP00000355441:p.Ile133Val		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_1	123	0.07	8	.	0		0		Missense_Mutation	SNP	ENST00000366485.1	37		111	0.050824175824175824	4	0.008130081300813009	21	0.058011049723756904	1	0.0017482517482517483	85	0.11213720316622691	T	1.446	-0.566297	0.03910	.	.	ENSG00000241128	ENST00000366485	T	0.19669	2.13	3.18	0.633	0.17712	.	0.314707	0.23017	N	0.052889	T	0.00271	0.0008	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.24476	-1.0159	7	0.27785	T	0.31	.	5.1576	0.15044	0.1374:0.1898:0.0:0.6729	rs36075193	.	.	.	V	133	ENSP00000355441:I133V	ENSP00000355441:I133V	I	-	1	0	OR14A2	245953572	0.000000	0.05858	0.027000	0.17364	0.150000	0.21749	-0.517000	0.06275	-0.322000	0.08615	-1.139000	0.01908	ATC			0.468	OR14A2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000096864.1		NG_002409	
ANKRD30A	91074	bcgsc.ca	37	10	37626786	37626786	+	Intron	SNP	G	G	A	rs144068387	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr10:37626786G>A	ENST00000602533.1	+	37	4405				LINC00993_ENST00000426471.1_lincRNA			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A						regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						TTTTGCAATCGAAGTTCTATT	0.348													g|||	25	0.00499201	0.0182	0.0014	5008	,	,		18726	0.0		0.0	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001627	intron_variant	0	.			GCAATCGAAGTTC	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.4024-46201G>A	10.37:g.37626786G>A			Somatic	219	0	0		WXS	Illumina HiSeq	Phase_1	189	0.04	8	.	0		0	Q5W025	RNA	SNP	ENST00000602533.1	37																																																																																						0.348	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000047588.2		NM_052997	
DYNC1I2P1	728532	bcgsc.ca	37	10	52026055	52026055	+	IGR	SNP	C	C	T	rs138093924	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr10:52026055C>T								ASAH2 (17685 upstream) : SGMS1 (39304 downstream)																							GGCAGCAAAGCTGGAATCAGT	0.473													-|||	48	0.00958466	0.0008	0.0043	5008	,	,		23554	0.0		0.0179	False		,,,				2504	0.0266				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCAAAGCTGGAAT																													10.37:g.52026055C>T			Somatic	197	0	0		WXS	Illumina HiSeq	Phase_1	169	0.04	6	.	82	0.00	0		RNA	SNP		37																																																																																					0	0.473										
Unknown	0	bcgsc.ca	37	11	4233016	4233016	+	IGR	SNP	A	A	C	rs75810507|rs386749974	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr11:4233016A>C								RP11-23F23.2 (9131 upstream) : OR52B4 (155476 downstream)																							CAAGAAGAAGAGTCTCTGGGT	0.363													N|||	1900	0.379393	0.3041	0.4625	5008	,	,		18824	0.4405		0.3588	False		,,,				2504	0.3804				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAGAAGAGTCTCT																													11.37:g.4233016A>C			Somatic	96	0	0		WXS	Illumina HiSeq	Phase_1	86	0.08	7	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.363										
OR51H1P	401663	bcgsc.ca;mdanderson.org	37	11	4880892	4880892	+	Silent	SNP	T	T	C	rs11034368	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr11:4880892T>C	ENST00000322059.1	-	1	902	c.903A>G	c.(901-903)caA>caG	p.Q301Q	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron			Q8NH63	O51H1_HUMAN	olfactory receptor, family 51, subfamily H, member 1 pseudogene	301						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			lung(1)	1						TTCTTCAAATTTGCTTGGTCT	0.423													C|||	1409	0.28135	0.2451	0.2594	5008	,	,		20858	0.0774		0.4175	False		,,,				2504	0.4162				.													.	.			0			.																																									SO:0001819	synonymous_variant	401663	.			TCAAATTTGCTTG			11p15.4	2013-09-24		2004-03-10	ENSG00000176904	ENSG00000176904		"""GPCR / Class A : Olfactory receptors"""	14833	pseudogene	pseudogene				OR51H1			Standard	NG_004388		Approved			Q8NH63	OTTHUMG00000066512	ENST00000322059.1:c.903A>G	11.37:g.4880892T>C			Somatic	59	0	0		WXS	Illumina HiSeq	Phase_1	46	0.09	4	.	0		0	Q6IFI3	Silent	SNP	ENST00000322059.1	37																																																																																						0.423	OR51H1P-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000142185.1			
C11orf48	79081	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	62434994	62434994	+	Splice_Site	DEL	C	C	-			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr11:62434994delC	ENST00000431002.2	-	2	2350		c.e2+1		C11orf48_ENST00000354588.3_Splice_Site|C11orf48_ENST00000532208.1_Splice_Site|C11orf83_ENST00000531323.1_5'Flank|C11orf48_ENST00000524958.1_5'Flank|C11orf48_ENST00000525675.1_5'Flank|RP11-831H9.11_ENST00000528405.1_5'Flank|METTL12_ENST00000532971.1_3'UTR|SNORA57_ENST00000383870.1_RNA			Q9BQE6	CK048_HUMAN	chromosome 11 open reading frame 48											endometrium(1)|lung(5)|urinary_tract(1)	7						ACAATACTTACCCTCAAAGCT	0.468																																					.													.	C11orf48	18		0			c.538+2G>-												84.0	87.0	86.0					11																	62434994		2202	4299	6501	SO:0001630	splice_region_variant	79081	exon5			TACTTACCCTCAA	BC001434	CCDS8028.1	11q12.3	2014-02-12			ENSG00000162194	ENSG00000162194			28351	protein-coding gene	gene with protein product						12477932	Standard	NM_024099		Approved	MGC2477	uc001nuf.3	Q9BQE6	OTTHUMG00000167588	ENST00000431002.2:c.616+1G>-	11.37:g.62434994delC			Somatic	142	0	0		WXS	Illumina HiSeq	.	134	0.12	16	NM_024099	1	0.00	0	Q96NA4	Splice_Site	DEL	ENST00000431002.2	37																																																																																						0.468	C11orf48-004	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000395233.1		NM_024099	Intron
Unknown	0	bcgsc.ca	37	11	67524358	67524358	+	IGR	SNP	A	A	G	rs140614895	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr11:67524358A>G								AP003385.1 (22279 upstream) : FAM86C2P (34896 downstream)																							GTAGAATGCCAAGGGCACTGT	0.453													.|||	411	0.0820687	0.0204	0.062	5008	,	,		21185	0.2034		0.0636	False		,,,				2504	0.0736				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AATGCCAAGGGCA																													11.37:g.67524358A>G			Somatic	26	0	0		WXS	Illumina HiSeq	Phase_1	32	0.19	6	.	0		0		RNA	SNP		37																																																																																					0	0.453										
LOC101927058	101927058	bcgsc.ca	37	12	43030796	43030796	+	lincRNA	SNP	G	G	A	rs79463838	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr12:43030796G>A	ENST00000550337.1	-	0	405																											TTGTCTTTCTGGATGTGAAGG	0.408													G|||	539	0.107628	0.0091	0.0807	5008	,	,		21735	0.2272		0.1074	False		,,,				2504	0.137				.													.	.			0			.																																											0	.			CTTTCTGGATGTG																													12.37:g.43030796G>A			Somatic	130	0	0		WXS	Illumina HiSeq	Phase_1	115	0.05	6	.	0		0		RNA	SNP	ENST00000550337.1	37																																																																																						0.408	RP11-609L23.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000404160.2			
OR8S1	341568	bcgsc.ca	37	12	48919659	48919660	+	Missense_Mutation	DNP	TG	TG	CA	rs35367885|rs4075258|rs71439450	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	TG	TG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr12:48919659_48919660TG>CA	ENST00000310194.1	+	1	245_246	c.245_246TG>CA	c.(244-246)cTG>cCA	p.L82P	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	82			L -> P (in dbSNP:rs4075258).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|skin(4)	22						CCCAAGATGCTGGAGAACCTCC	0.485																																					p.L82P													.	OR8S1	47		0			c.G246A																																									SO:0001583	missense	341568	exon1			AGATGCTGGAGAA		CCDS31789.1	12q13.2	2012-08-09				ENSG00000197376		"""GPCR / Class A : Olfactory receptors"""	19628	protein-coding gene	gene with protein product							Standard	NM_001005203		Approved		uc010slu.2	Q8NH09		Exception_encountered	12.37:g.48919659_48919660delinsCA	ENSP00000310632:p.Leu82Pro		Somatic	136	0.0073529412	1		WXS	Illumina HiSeq	Phase_1	111	0.09	10	NM_001005203	0		0		Missense_Mutation	DNP	ENST00000310194.1	37	CCDS31789.1																																																																																					0.485	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000406881.1			
LOC100507377	100507377	bcgsc.ca	37	12	74565295	74565295	+	IGR	SNP	C	C	T	rs6582210	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr12:74565295C>T								RP11-711C17.2 (125687 upstream) : RP11-81H3.2 (28056 downstream)																							TGGAAATCCTCAAGGCCCTGA	0.547													C|||	1419	0.283347	0.5991	0.1744	5008	,	,		20120	0.0526		0.2555	False		,,,				2504	0.2004				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AATCCTCAAGGCC																													12.37:g.74565295C>T			Somatic	23	0	0		WXS	Illumina HiSeq	Phase_1	28	0.18	5	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.547										
HECTD4	283450	hgsc.bcm.edu	37	12	112628625	112628625	+	Missense_Mutation	SNP	G	G	T	rs151280588		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr12:112628625G>T	ENST00000430131.2	-	59	9316	c.8171C>A	c.(8170-8172)cCg>cAg	p.P2724Q	HECTD4_ENST00000550722.1_Missense_Mutation_p.P3000Q|HECTD4_ENST00000377560.5_Missense_Mutation_p.P2974Q			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2724					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										GACGGATGTCGGAATGGTGTC	0.607																																					p.P3012Q													.	.			0			c.C9035A												44.0	50.0	48.0					12																	112628625		2120	4224	6344	SO:0001583	missense	283450	exon60			GATGTCGGAATGG	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.8171C>A	12.37:g.112628625G>T	ENSP00000404379:p.Pro2724Gln		Somatic	123	0	0		WXS	Illumina HiSeq	.	115	0.04	5	NM_001109662	39	0.00	0	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	G	33	5.198855	0.94997	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.50548	0.74;0.75;0.74	5.73	5.73	0.89815	.	.	.	.	.	T	0.55577	0.1929	N	0.14661	0.345	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.62709	-0.6797	9	0.87932	D	0	.	19.8966	0.96963	0.0:0.0:1.0:0.0	.	2724	Q9Y4D8	K0614_HUMAN	Q	2974;2724;3000	ENSP00000366783:P2974Q;ENSP00000404379:P2724Q;ENSP00000449784:P3000Q	ENSP00000366783:P2974Q	P	-	2	0	C12orf51	111113008	1.000000	0.71417	0.845000	0.33349	0.843000	0.47879	9.422000	0.97458	2.700000	0.92200	0.655000	0.94253	CCG			0.607	HECTD4-202	KNOWN	basic	protein_coding	protein_coding				NM_173813	
LRRC43	254050	ucsc.edu	37	12	122685163	122685164	+	Missense_Mutation	DNP	AA	AA	GG	rs199718757|rs200955000	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	AA	AA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr12:122685163_122685164AA>GG	ENST00000339777.4	+	9	1604_1605	c.1576_1577AA>GG	c.(1576-1578)AAg>GGg	p.K526G	LRRC43_ENST00000537733.1_3'UTR|B3GNT4_ENST00000324189.4_5'Flank|LRRC43_ENST00000425921.1_Missense_Mutation_p.K341G	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	526	Lys-rich.									NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		caagaaagggaaggagaaagac	0.579																																					p.K526G													.	LRRC43	105		0			c.A1577G																																									SO:0001583	missense	254050	exon9			AAAGGGAAGGAGA	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	Exception_encountered	12.37:g.122685163_122685164delinsGG	ENSP00000344233:p.Lys526Gly		Somatic	52	0	0		WXS	Illumina HiSeq		64	0.34	22	NM_001098519	2	0.00	0	Q6ZVT9	Missense_Mutation	DNP	ENST00000339777.4	37	CCDS45001.1																																																																																					0.579	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000401589.1		NM_152759	
PGAM5	192111	hgsc.bcm.edu;mdanderson.org	37	12	133291445	133291445	+	Splice_Site	SNP	C	C	T	rs374915398		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr12:133291445C>T	ENST00000498926.2	+	2	251	c.193C>T	c.(193-195)Cga>Tga	p.R65*	PGAM5_ENST00000454808.2_5'UTR|RP13-672B3.2_ENST00000537262.1_Splice_Site_p.A104V|PGAM5_ENST00000317555.2_Splice_Site_p.R65*|PXMP2_ENST00000545677.1_Splice_Site_p.A104V|PGAM5_ENST00000543955.1_5'UTR	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	65					dephosphorylation (GO:0016311)|necroptotic process (GO:0070266)|positive regulation of GTPase activity (GO:0043547)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein complex binding (GO:0032403)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		CAACATCAGGCGAGAACCACT	0.473																																					p.R65X													.	.			0			c.C193T							C	stop/ARG,stop/ARG,stop/ARG	0,4406		0,0,2203	124.0	106.0	112.0		193,193,193	2.7	1.0	12		112	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained-near-splice,stop-gained-near-splice,stop-gained-near-splice	PGAM5	NM_001170543.1,NM_001170544.1,NM_138575.3	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	65/290,65/289,65/256	133291445	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	192111	exon2			ATCAGGCGAGAAC	BC008196	CCDS9280.1, CCDS53845.1	12q24.33	2011-07-28			ENSG00000247077	ENSG00000247077			28763	protein-coding gene	gene with protein product		614939				11283018	Standard	NM_001170543		Approved	MGC5352, BXLBv68	uc009zyv.3	Q96HS1	OTTHUMG00000168021	ENST00000498926.2:c.192-1C>T	12.37:g.133291445C>T			Somatic	93	0	0		WXS	Illumina HiSeq	.	107	0.09	10	NM_138575	37	0.11	4	A9LN06|C9IZY7|Q96JB0	Nonsense_Mutation	SNP	ENST00000498926.2	37	CCDS53845.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.39|17.39	3.377555|3.377555	0.61735|0.61735	0.0|0.0	1.16E-4|1.16E-4	ENSG00000176894;ENSG00000256632|ENSG00000247077	ENST00000545677;ENST00000537262|ENST00000317555;ENST00000498926	.|.	.|.	.|.	4.64|4.64	2.68|2.68	0.31781|0.31781	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.33933|.	0.0880|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.13845|.	-1.0494|.	5|.	0.87932|0.02654	D|T	0|1	-22.8648|-22.8648	12.8006|12.8006	0.57584|0.57584	0.3097:0.6903:0.0:0.0|0.3097:0.6903:0.0:0.0	.|.	.|.	.|.	.|.	V|X	104|65	.|.	ENSP00000442747:A104V|ENSP00000321503:R65X	A|R	+|+	2|1	0|2	RP13-672B3.2;PXMP2|PGAM5	131801518|131801518	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.490000|0.490000	0.33462|0.33462	2.830000|2.830000	0.48136|0.48136	0.920000|0.920000	0.36970|0.36970	0.462000|0.462000	0.41574|0.41574	GCG|CGA			0.473	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000397562.1		NM_138575	Nonsense_Mutation
DOCK11P1	100132537	bcgsc.ca	37	14	45330721	45330721	+	IGR	SNP	A	A	T	rs7149683	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr14:45330721A>T								RP11-398E10.1 (78689 upstream) : RP11-857B24.1 (15355 downstream)																							TCCTTCTTCAACTATATTGGG	0.388													T|||	1301	0.259784	0.6604	0.1311	5008	,	,		18711	0.1002		0.1093	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTTCAACTATAT																													14.37:g.45330721A>T			Somatic	141	0	0		WXS	Illumina HiSeq	Phase_1	129	0.05	7	.	0		0		RNA	SNP		37																																																																																					0	0.388										
DOCK11P1	100132537	bcgsc.ca	37	14	45331290	45331290	+	IGR	SNP	C	C	T	rs73345244	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr14:45331290C>T								RP11-398E10.1 (79258 upstream) : RP11-857B24.1 (14786 downstream)																							TAAAACCTCACAGCAAAATGC	0.373													T|||	1301	0.259784	0.6604	0.1311	5008	,	,		21313	0.1002		0.1093	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACCTCACAGCAAA																													14.37:g.45331290C>T			Somatic	166	0	0		WXS	Illumina HiSeq	Phase_1	143	0.04	6	.	0		0		RNA	SNP		37																																																																																					0	0.373										
DOCK11P1	100132537	bcgsc.ca	37	14	45331397	45331397	+	IGR	SNP	T	T	C	rs12323568	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	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			Somatic	285	0	0		WXS	Illumina HiSeq	Phase_1	282	0.03	9	.	0		0		RNA	SNP		37																																																																																					0	0.368										
DOCK11P1	100132537	bcgsc.ca	37	14	45331633	45331633	+	IGR	SNP	T	T	G	rs12323575	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	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			Somatic	332	0.0030120482	1		WXS	Illumina HiSeq	Phase_1	293	0.03	10	.	1	1.00	1		RNA	SNP		37																																																																																					0	0.413								rescued with RNA-seq		
DOCK11P1	100132537	bcgsc.ca	37	14	45332387	45332387	+	IGR	SNP	C	C	G	rs7161626	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	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			Somatic	278	0	0		WXS	Illumina HiSeq	Phase_1	242	0.06	15	.	0		0		RNA	SNP		37																																																																																					0	0.358										
IGHV3-7	28452	bcgsc.ca	37	14	106518415	106518415	+	RNA	SNP	C	C	A	rs188349361	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr14:106518415C>A	ENST00000390598.2	-	0	414									immunoglobulin heavy variable 3-7																		CACAGTAATACACAGCCGTGT	0.567													.|||	68	0.0135783	0.025	0.0187	5008	,	,		12199	0.004		0.008	False		,,,				2504	0.0102				.													.	.			0			.												140.0	130.0	133.0					14																	106518415		1852	4062	5914			28452	.			GTAATACACAGCC	M99649		14q32.33	2012-02-08			ENSG00000211938	ENSG00000211938		"""Immunoglobulins / IGH locus"""	5620	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152271		14.37:g.106518415C>A			Somatic	242	0.020661157	5		WXS	Illumina HiSeq	Phase_1	224	0.11	25	.	2416	0.16	381		RNA	SNP	ENST00000390598.2	37																																																																																						0.567	IGHV3-7-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325659.1		NG_001019	
Unknown	0	bcgsc.ca	37	15	22298279	22298279	+	IGR	SNP	G	G	A	rs11856712	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr15:22298279G>A								RP11-928F19.5 (98309 upstream) : RP11-69H14.6 (4904 downstream)																							TGACGTCGCCGGTCACACCAC	0.458													.|||	1461	0.291733	0.3472	0.1945	5008	,	,		34404	0.2738		0.2863	False		,,,				2504	0.3098				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTCGCCGGTCACA																													15.37:g.22298279G>A			Somatic	191	0	0		WXS	Illumina HiSeq	Phase_1	146	0.07	10	.	0		0		RNA	SNP		37																																																																																					0	0.458										
RP11-143J24.1	0	bcgsc.ca	37	15	30297737	30297737	+	lincRNA	SNP	C	C	T	rs2015398	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr15:30297737C>T	ENST00000561392.1	-	0	393																											CTGGCTTATCCGGTGTTAGCT	0.438													C|||	892	0.178115	0.1778	0.281	5008	,	,		20844	0.0218		0.2515	False		,,,				2504	0.1912				.													.	.			0			.																																											0	.			CTTATCCGGTGTT																													15.37:g.30297737C>T			Somatic	121	0	0		WXS	Illumina HiSeq	Phase_1	144	0.05	7	.	0		0		RNA	SNP	ENST00000561392.1	37																																																																																						0.438	RP11-143J24.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000417288.1			
ADAMTS7P3	400406	bcgsc.ca	37	15	78272318	78272318	+	IGR	SNP	C	C	G	rs12439777	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr15:78272318C>G								RP11-114H24.3 (16322 upstream) : RP11-114H24.5 (8015 downstream)																							AGCACCAGGGCCCTCCCCTCC	0.677																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCAGGGCCCTCCC																													15.37:g.78272318C>G			Somatic	551	0	0		WXS	Illumina HiSeq	Phase_1	489	0.06	31	.	0		0		RNA	SNP		37																																																																																					0	0.677										
ADAMTS7P4	642935	bcgsc.ca	37	15	85806001	85806001	+	IGR	SNP	C	C	T	rs2002507	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr15:85806001C>T								RP11-561C5.4 (27985 upstream) : RP11-561C5.5 (63623 downstream)																							CCCCTGTCCCCGCCAGGTCTA	0.642													.|||	1033	0.20627	0.0847	0.1873	5008	,	,		15133	0.2887		0.2296	False		,,,				2504	0.2751				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGTCCCCGCCAGG																													15.37:g.85806001C>T			Somatic	41	0	0		WXS	Illumina HiSeq	Phase_1	37	0.11	4	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.642										
PKMYT1	9088	bcgsc.ca	37	16	3025413	3025413	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr16:3025413G>T	ENST00000262300.8	-	4	1287	c.779C>A	c.(778-780)aCa>aAa	p.T260K	PKMYT1_ENST00000431515.2_Missense_Mutation_p.T260K|PKMYT1_ENST00000574730.1_Missense_Mutation_p.T191K|PKMYT1_ENST00000574385.1_Missense_Mutation_p.T251K|PKMYT1_ENST00000440027.2_Missense_Mutation_p.T260K|PKMYT1_ENST00000573944.1_Missense_Mutation_p.T251K	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	260	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						AGCTCCTGCTGTACCCAGCTC	0.657																																					p.T260K													.	PKMYT1	23		0			c.C779A												37.0	40.0	39.0					16																	3025413		2198	4299	6497	SO:0001583	missense	9088	exon4			CCTGCTGTACCCA	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"""membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase"", ""protein phosphatase 1, regulatory subunit 126"""	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.779C>A	16.37:g.3025413G>T	ENSP00000262300:p.Thr260Lys		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_1	117	0.05	6	NM_182687	135	0.00	0	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000262300.8	37	CCDS10486.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.070215	0.00379	.	.	ENSG00000127564	ENST00000431515;ENST00000262300;ENST00000440027;ENST00000402679;ENST00000382240	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	5.41	1.01	0.19927	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.047250	0.07472	N	0.902445	T	0.43634	0.1256	L	0.38692	1.165	0.09310	N	1	B;B;B;B	0.10296	0.003;0.0;0.001;0.002	B;B;B;B	0.17098	0.005;0.007;0.012;0.017	T	0.29518	-1.0009	10	0.05351	T	0.99	1.1777	3.5492	0.07840	0.0778:0.2699:0.3752:0.2771	.	251;191;260;260	A6NHV6;B4DXD4;Q99640;F8W164	.;.;PMYT1_HUMAN;.	K	260;260;260;260;251	ENSP00000392855:T260K;ENSP00000262300:T260K;ENSP00000397739:T260K;ENSP00000371675:T251K	ENSP00000262300:T260K	T	-	2	0	PKMYT1	2965414	0.000000	0.05858	0.000000	0.03702	0.215000	0.24574	0.619000	0.24388	-0.022000	0.13986	0.650000	0.86243	ACA			0.657	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000250963.2		NM_004203	
FUK	197258	mdanderson.org	37	16	70508475	70508475	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr16:70508475G>T	ENST00000288078.6	+	17	2265	c.2033G>T	c.(2032-2034)gGt>gTt	p.G678V	FUK_ENST00000571514.1_Missense_Mutation_p.G169V|FUK_ENST00000378912.2_Missense_Mutation_p.G710V	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	678						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				GAGGGGGCTGGTCAGATCCTG	0.652																																					p.G678V													.	.			0			c.G2033T												21.0	26.0	24.0					16																	70508475		2004	4151	6155	SO:0001583	missense	197258	exon17			GGGCTGGTCAGAT		CCDS10891.2	16q22.1	2008-02-05			ENSG00000157353	ENSG00000157353	2.7.1.52		29500	protein-coding gene	gene with protein product	"""L-fucose kinase"""	608675				12056818	Standard	XM_006721161		Approved	FLJ39408	uc002eyy.3	Q8N0W3	OTTHUMG00000074085	ENST00000288078.6:c.2033G>T	16.37:g.70508475G>T	ENSP00000288078:p.Gly678Val		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	23	0.13	3	NM_145059	14	0.00	0	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	37	CCDS10891.2	.	.	.	.	.	.	.	.	.	.	G	13.02	2.113331	0.37339	.	.	ENSG00000157353	ENST00000288078;ENST00000378912	T;T	0.07800	3.19;3.16	5.77	1.78	0.24846	.	0.420263	0.26919	N	0.021839	T	0.04952	0.0133	L	0.38838	1.175	0.80722	D	1	B;P;P	0.43477	0.196;0.808;0.808	B;B;B	0.33121	0.158;0.154;0.154	T	0.44267	-0.9339	10	0.56958	D	0.05	-16.2604	4.4782	0.11753	0.5651:0.1838:0.2511:0.0	.	710;584;678	Q8N0W3-2;B2RDL5;Q8N0W3	.;.;FUK_HUMAN	V	678;710	ENSP00000288078:G678V;ENSP00000368192:G710V	ENSP00000288078:G678V	G	+	2	0	FUK	69065976	1.000000	0.71417	0.977000	0.42913	0.991000	0.79684	1.981000	0.40628	0.502000	0.28037	0.655000	0.94253	GGT			0.652	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000157291.2		NM_145059	
HYDIN	54768	broad.mit.edu	37	16	70868034	70868034	+	Missense_Mutation	SNP	G	G	T	rs202145562		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr16:70868034G>T	ENST00000393567.2	-	79	13585	c.13435C>A	c.(13435-13437)Ctg>Atg	p.L4479M		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4479					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TTGGGCTTCAGTGTGATGTTG	0.557																																					p.L4479M													.	HYDIN	788		0			c.C13435A							G	MET/LEU	0,3784		0,0,1892	58.0	56.0	56.0		13432	3.0	0.8	16		56	5,8225		0,5,4110	no	missense	HYDIN	NM_032821.2	15	0,5,6002	TT,TG,GG		0.0608,0.0,0.0416	possibly-damaging	4478/5121	70868034	5,12009	1892	4115	6007	SO:0001583	missense	54768	exon79			GCTTCAGTGTGAT	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.13435C>A	16.37:g.70868034G>T	ENSP00000377197:p.Leu4479Met		Somatic	60	0.0166666667	1		WXS	Illumina HiSeq	Phase_I	49	0.12	6	NM_001270974	0		0	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.811995	0.50527	0.0	6.08E-4	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01335	5.0	5.06	3.01	0.34805	.	0.341082	0.15584	N	0.254722	T	0.03220	0.0094	L	0.54323	1.7	0.80722	D	1	P	0.40638	0.725	P	0.49387	0.609	T	0.55166	-0.8183	10	0.49607	T	0.09	.	7.4448	0.27205	0.144:0.0:0.7147:0.1413	.	4478	F8WD23	.	M	4479;4478	ENSP00000377197:L4479M	ENSP00000313052:L4478M	L	-	1	2	HYDIN	69425535	1.000000	0.71417	0.794000	0.32065	0.684000	0.39900	3.438000	0.52871	1.073000	0.40885	0.511000	0.50034	CTG			0.557	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000398624.3			
GAS8	2622	broad.mit.edu;mdanderson.org	37	16	90110027	90110027	+	3'UTR	SNP	G	G	A	rs3743824	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr16:90110027G>A	ENST00000268699.4	+	0	1833				URAHP_ENST00000517889.1_RNA	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		CACAGTCGGCGGCACCTTCTC	0.662													A|||	2895	0.578075	0.7466	0.5476	5008	,	,		18958	0.8224		0.2962	False		,,,				2504	0.41				.													.	.			0			.																																									SO:0001624	3_prime_UTR_variant	0	.			GTCGGCGGCACCT	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.*274G>A	16.37:g.90110027G>A			Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	26	0.15	4	.	8	0.00	0	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	1235	0.5654761904761905	358	0.7276422764227642	176	0.4861878453038674	462	0.8076923076923077	239	0.3153034300791557	A	0.005	-2.157125	0.00321	.	.	ENSG00000222019	ENST00000517889	.	.	.	1.76	-3.52	0.04682	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.26710	-1.0095	5	.	.	.	.	5.0846	0.14675	0.2622:0.0:0.5809:0.1568	rs3743824;rs61392914;rs3743824	160	B7Z8Y8	.	L	160	.	.	P	-	2	0	AC133919.6	88637528	0.003000	0.15002	0.000000	0.03702	0.001000	0.01503	1.352000	0.34033	-2.351000	0.00617	-1.818000	0.00600	CCG			0.662	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000272877.2			
SENP3	26168	bcgsc.ca	37	17	7466636	7466636	+	Silent	SNP	G	G	A			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr17:7466636G>A	ENST00000429205.2	+	2	292	c.243G>A	c.(241-243)gaG>gaA	p.E81E	SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000321337.7_Silent_p.E81E|SENP3_ENST00000578868.1_3'UTR			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	81	Glu-rich.					cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				aggaagaagaggaggaggagg	0.622																																					p.E81E													.	SENP3	18		0			c.G243A																																									SO:0001819	synonymous_variant	26168	exon2			AGAAGAGGAGGAG	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.243G>A	17.37:g.7466636G>A			Somatic	102	0.0196078431	2		WXS	Illumina HiSeq	Phase_1	90	0.06	5	NM_015670	131	0.01	1	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	37																																																																																						0.622	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				NM_015670	
FLCN	201163	bcgsc.ca	37	17	17118366	17118366	+	Missense_Mutation	SNP	T	T	C			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr17:17118366T>C	ENST00000285071.4	-	13	1925	c.1471A>G	c.(1471-1473)Acc>Gcc	p.T491A	RP11-45M22.4_ENST00000427497.3_3'UTR	NM_144997.5	NP_659434.2	Q8NFG4	FLCN_HUMAN	folliculin	491					cell-cell junction assembly (GO:0007043)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|negative regulation of ATP biosynthetic process (GO:2001170)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in kidney development (GO:1901723)|negative regulation of energy homeostasis (GO:2000506)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of gene expression (GO:0010629)|negative regulation of mitochondrion organization (GO:0010823)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of gene expression (GO:0010628)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cytokinesis (GO:0032465)|regulation of histone acetylation (GO:0035065)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|regulation of TOR signaling (GO:0032006)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|stomach(1)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TTCTGGTTGGTCAGAGCCGCT	0.602									Familial Non-VHL Clear Cell Renal Cancer;Birt-Hogg-Dub syndrome																												p.T491A													.	FLCN	87		0			c.A1471G												92.0	83.0	86.0					17																	17118366		2203	4300	6503	SO:0001583	missense	201163	exon13	Familial Cancer Database	Familial Clear Cell Renal Cell Cancer, FcRCC, Familial Non-VHL Non-Papillary Clear Cell Renal Cancer;BHD, Fibrofolliculomas with Trichodiscomas and Acrochordons, incl.: Hornstein-Knickenberg syndrome, Perifollicular Fibromatosis	GGTTGGTCAGAGC	AF517523	CCDS32579.1, CCDS32580.1	17p11.2	2014-09-17			ENSG00000154803	ENSG00000154803			27310	protein-coding gene	gene with protein product		607273					Standard	NM_144997		Approved	BHD, MGC17998, MGC23445	uc002gra.4	Q8NFG4	OTTHUMG00000059275	ENST00000285071.4:c.1471A>G	17.37:g.17118366T>C	ENSP00000285071:p.Thr491Ala		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_1	64	0.08	5	NM_144997	80	0.00	0	A6NJJ8|Q6ZRX1|Q96BD2|Q96BE4	Missense_Mutation	SNP	ENST00000285071.4	37	CCDS32579.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.483047	0.26598	.	.	ENSG00000154803	ENST00000285071	D	0.92348	-3.02	5.36	4.28	0.50868	.	0.096735	0.64402	D	0.000001	T	0.78773	0.4336	N	0.03608	-0.345	0.80722	D	1	B	0.13145	0.007	B	0.06405	0.002	T	0.70306	-0.4908	10	0.09084	T	0.74	-25.5544	11.2889	0.49239	0.0:0.0719:0.0:0.9281	.	491	Q8NFG4	FLCN_HUMAN	A	491	ENSP00000285071:T491A	ENSP00000285071:T491A	T	-	1	0	FLCN	17059091	1.000000	0.71417	0.999000	0.59377	0.719000	0.41307	4.472000	0.60189	0.991000	0.38814	0.533000	0.62120	ACC			0.602	FLCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000131577.1		NM_144606	
KRT17P6	284196	broad.mit.edu	37	17	20418724	20418728	+	RNA	DEL	TCAGC	TCAGC	-			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	TCAGC	TCAGC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr17:20418724_20418728delTCAGC	ENST00000581013.1	-	0	391_395																											CTGGCCAGGGTCAGCTCATCCAGCA	0.6																																					.													.	.			0			.																																											0	.			CCAGGGTCAGCTC																													17.37:g.20418724_20418728delTCAGC			Somatic	413	0	0		WXS	Illumina HiSeq	Phase_I	352	0.03	10	.	1	0.00	0		RNA	DEL	ENST00000581013.1	37																																																																																						0.600	AC025627.9-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000443766.1			
Unknown	0	bcgsc.ca	37	17	60324448	60324448	+	IGR	SNP	C	C	T	rs12325728	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr17:60324448C>T								Y_RNA (124666 upstream) : TBC1D3P2 (17617 downstream)																							GGATGCCTTACTTCCTCCAGA	0.378													.|||	1482	0.295927	0.1619	0.3141	5008	,	,		18009	0.5506		0.2833	False		,,,				2504	0.2147				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCCTTACTTCCTC																													17.37:g.60324448C>T			Somatic	246	0	0		WXS	Illumina HiSeq	Phase_1	212	0.06	12	.	0		0		RNA	SNP		37																																																																																					0	0.378										
NPC1	4864	ucsc.edu;bcgsc.ca	37	18	21114422	21114422	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr18:21114422G>T	ENST00000269228.5	-	23	4133	c.3579C>A	c.(3577-3579)caC>caA	p.H1193Q	NPC1_ENST00000412552.2_Missense_Mutation_p.H875Q	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	1193					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)					AGCTGCCCATGTGGGCAAGTG	0.597																																					p.H1193Q													.	NPC1	114		0			c.C3579A												61.0	53.0	56.0					18																	21114422		2203	4300	6503	SO:0001583	missense	4864	exon23			GCCCATGTGGGCA	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.3579C>A	18.37:g.21114422G>T	ENSP00000269228:p.His1193Gln		Somatic	57	0	0		WXS	Illumina HiSeq		53	0.09	5	NM_000271	94	0.00	0	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.270441	0.40194	.	.	ENSG00000141458	ENST00000269228;ENST00000412552	D;D	0.84873	-1.91;-1.91	5.84	4.97	0.65823	.	0.231620	0.51477	D	0.000095	T	0.76659	0.4018	L	0.35593	1.075	0.80722	D	1	B;B	0.14012	0.008;0.009	B;B	0.19666	0.026;0.026	T	0.69269	-0.5189	10	0.20046	T	0.44	-14.6805	10.8001	0.46483	0.1434:0.0:0.8566:0.0	.	1204;1193	Q59GR1;O15118	.;NPC1_HUMAN	Q	1193;875	ENSP00000269228:H1193Q;ENSP00000408606:H875Q	ENSP00000269228:H1193Q	H	-	3	2	NPC1	19368420	1.000000	0.71417	0.981000	0.43875	0.982000	0.71751	3.040000	0.49799	1.469000	0.48083	0.643000	0.83706	CAC			0.597	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254823.2		NM_000271	
GPR108	56927	hgsc.bcm.edu	37	19	6737580	6737580	+	Missense_Mutation	SNP	A	A	C			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr19:6737580A>C	ENST00000264080.7	-	1	34	c.8T>G	c.(7-9)gTg>gGg	p.V3G	GPR108_ENST00000430424.4_5'Flank|TRIP10_ENST00000600428.1_5'Flank|TRIP10_ENST00000313244.9_5'Flank|TRIP10_ENST00000313285.8_5'Flank|TRIP10_ENST00000596758.1_5'Flank	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	3						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						CCTCTCGCTCACTGCCATCTC	0.736																																					p.V3G													.	.			0			c.T8G												4.0	8.0	7.0					19																	6737580		1774	3879	5653	SO:0001583	missense	56927	exon1			TCGCTCACTGCCA		CCDS42479.1	19p13.3	2014-01-30				ENSG00000125734		"""GPCR / Unclassified : 7TM orphan receptors"""	17829	protein-coding gene	gene with protein product							Standard	NM_001080452		Approved	LUSTR2	uc002mfp.3	Q9NPR9	OTTHUMG00000170129	ENST00000264080.7:c.8T>G	19.37:g.6737580A>C	ENSP00000264080:p.Val3Gly		Somatic	6	0	0		WXS	Illumina HiSeq	.	17	0.29	5	NM_001080452	6	0.17	1	B9EJD7	Missense_Mutation	SNP	ENST00000264080.7	37	CCDS42479.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	17.94|17.94	3.512348|3.512348	0.64522|0.64522	.|.	.|.	ENSG00000125734|ENSG00000125734	ENST00000549846|ENST00000264080	.|T	.|0.25912	.|1.77	4.16|4.16	-1.1|-1.1	0.09872|0.09872	.|.	.|0.470653	.|0.15619	.|U	.|0.252989	T|T	0.20414|0.20414	0.0491|0.0491	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	D|D	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.04013	.|0.001	T|T	0.05649|0.05649	-1.0872|-1.0872	5|10	.|0.33141	.|T	.|0.24	-5.7848|-5.7848	4.8976|4.8976	0.13759|0.13759	0.324:0.1597:0.0:0.5162|0.324:0.1597:0.0:0.5162	.|.	.|3	.|Q9NPR9	.|GP108_HUMAN	R|G	2|3	.|ENSP00000264080:V3G	.|ENSP00000264080:V3G	S|V	-|-	3|2	2|0	GPR108|GPR108	6688580|6688580	0.997000|0.997000	0.39634|0.39634	0.998000|0.998000	0.56505|0.56505	0.986000|0.986000	0.74619|0.74619	0.214000|0.214000	0.17541|0.17541	-0.117000|-0.117000	0.11872|0.11872	-0.373000|-0.373000	0.07131|0.07131	AGT|GTG			0.736	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000407508.2			
CYP4F9P	100506916	bcgsc.ca	37	19	16091763	16091763	+	IGR	SNP	T	T	C	rs8103740	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr19:16091763T>C								OR10H4 (30995 upstream) : LINC00661 (34680 downstream)																							GTGATCTCTCTTTGCTATTCT	0.562													C|||	279	0.0557109	0.1399	0.036	5008	,	,		18019	0.001		0.0378	False		,,,				2504	0.0307				.													.	.			0			.																																									SO:0001628	intergenic_variant	100506916	.			TCTCTCTTTGCTA																													19.37:g.16091763T>C			Somatic	36	0	0		WXS	Illumina HiSeq	Phase_1	27	0.15	4	.	0		0		RNA	SNP		37																																																																																					0	0.562										
FKBP8	23770	hgsc.bcm.edu;broad.mit.edu;mdanderson.org	37	19	18650505	18650505	+	Silent	SNP	C	C	A	rs370114965		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr19:18650505C>A	ENST00000596558.2	-	3	427	c.318G>T	c.(316-318)acG>acT	p.T106T	FKBP8_ENST00000610101.1_Intron|FKBP8_ENST00000222308.4_Silent_p.T106T|FKBP8_ENST00000608443.1_Silent_p.T106T|FKBP8_ENST00000597960.3_Silent_p.T106T|FKBP8_ENST00000453489.2_Silent_p.T135T			Q14318	FKBP8_HUMAN	FK506 binding protein 8, 38kDa	106					apoptotic process (GO:0006915)|camera-type eye development (GO:0043010)|cell fate specification (GO:0001708)|chaperone-mediated protein folding (GO:0061077)|dorsal/ventral neural tube patterning (GO:0021904)|intracellular signal transduction (GO:0035556)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|positive regulation of BMP signaling pathway (GO:0030513)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of gene expression (GO:0010468)|smoothened signaling pathway (GO:0007224)|viral process (GO:0016032)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	FK506 binding (GO:0005528)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	15						CTGGGACCAGCGTCTTCTTCC	0.667																																					p.T106T													FKBP8,NS,carcinoma,0,1	FKBP8	0	1	0			c.G318T												110.0	116.0	114.0					19																	18650505		2203	4300	6503	SO:0001819	synonymous_variant	23770	exon3			GACCAGCGTCTTC	L37033	CCDS32961.1	19p12	2013-01-10	2002-08-29		ENSG00000105701	ENSG00000105701		"""Tetratricopeptide (TTC) repeat domain containing"""	3724	protein-coding gene	gene with protein product	"""FK506-binding protein 8 (38kD)"""	604840	"""FK506-binding protein 8 (38kD)"""			7543869	Standard	NM_012181		Approved	FKBP38, FKBPr38	uc002njj.1	Q14318		ENST00000596558.2:c.318G>T	19.37:g.18650505C>A			Somatic	31	0	0		WXS	Illumina HiSeq	.	35	0.14	5	NM_012181	401	0.22	87	C8C9T5|Q53GU3|Q7Z349|Q86YK6	Silent	SNP	ENST00000596558.2	37																																																																																						0.667	FKBP8-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate	protein_coding	protein_coding		OTTHUMT00000466374.3		NM_012181	
CRIM1	51232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	36623892	36623892	+	Missense_Mutation	SNP	G	G	A			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr2:36623892G>A	ENST00000280527.2	+	2	834	c.467G>A	c.(466-468)aGt>aAt	p.S156N		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	156					insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				GAGTTTCCAAGTCAGGATATG	0.383																																					p.S156N													.	.			0			c.G467A												140.0	133.0	135.0					2																	36623892		2203	4300	6503	SO:0001583	missense	51232	exon2			TTCCAAGTCAGGA	AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"""cysteine-rich motor neuron 1"""	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.467G>A	2.37:g.36623892G>A	ENSP00000280527:p.Ser156Asn		Somatic	163	0	0		WXS	Illumina HiSeq	.	142	0.15	22	NM_016441	19	0.21	4	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Missense_Mutation	SNP	ENST00000280527.2	37	CCDS1783.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.125147	0.37533	.	.	ENSG00000150938	ENST00000280527	T	0.04275	3.66	5.08	5.08	0.68730	.	0.223984	0.44097	D	0.000493	T	0.05227	0.0139	N	0.26042	0.785	0.32894	D	0.512233	B	0.09022	0.002	B	0.09377	0.004	T	0.14615	-1.0466	10	0.30078	T	0.28	-7.1481	17.4683	0.87639	0.0:0.0:1.0:0.0	.	156	Q9NZV1	CRIM1_HUMAN	N	156	ENSP00000280527:S156N	ENSP00000280527:S156N	S	+	2	0	CRIM1	36477396	1.000000	0.71417	0.998000	0.56505	0.813000	0.45954	5.122000	0.64697	2.361000	0.80049	0.460000	0.39030	AGT			0.383	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000216878.2		NM_016441	
AC105399.2	0	broad.mit.edu	37	2	78019879	78019880	+	RNA	INS	-	-	T	rs369659281		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr2:78019879_78019880insT	ENST00000422418.1	+	0	130																											GTAAAAATTCCTTTTTTTTTTT	0.391																																					.													.	.			0			.																																											0	.			AAATTCCTTTTTT																													2.37:g.78019890_78019890dupT			Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	7	0.43	3	.	1	0.00	0		RNA	INS	ENST00000422418.1	37																																																																																						0.391	AC105399.2-002	PUTATIVE	basic	processed_transcript	pseudogene		OTTHUMT00000328256.1			
ANKRD36BP2	645784	broad.mit.edu	37	2	89104503	89104504	+	RNA	INS	-	-	C	rs149625899|rs67367050	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr2:89104503_89104504insC	ENST00000393525.3	+	0	4868									ankyrin repeat domain 36B pseudogene 2																		gtagatttttttcagattttgg	0.307													-|-|C|insertion	512	0.102236	0.1067	0.0965	5008	,	,		29304	0.0694		0.1064	False		,,,				2504	0.1299				.													.	.			0			.																																											0	.			ATTTTTTTCAGAT			2q11.2	2010-09-30			ENSG00000230006	ENSG00000230006			33607	pseudogene	pseudogene							Standard	NR_015424		Approved		uc010fhg.4		OTTHUMG00000151690		2.37:g.89104503_89104504insC			Somatic	17	0.2941176471	5		WXS	Illumina HiSeq	Phase_I	23	0.61	14	.	2	0.00	0		RNA	INS	ENST00000393525.3	37																																																																																						0.307	ANKRD36BP2-003	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000323523.1			
GPR45	11250	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	2	105859305	105859305	+	Missense_Mutation	SNP	A	A	T			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr2:105859305A>T	ENST00000258456.1	+	1	1106	c.990A>T	c.(988-990)aaA>aaT	p.K330N		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	330						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						GAATCAAAAAATTCCGCGAGG	0.557																																					p.K330N													.	.			0			c.A990T												87.0	92.0	90.0					2																	105859305		2203	4300	6503	SO:0001583	missense	11250	exon1			CAAAAAATTCCGC	AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"""GPCR / Class A : Orphans"""	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.990A>T	2.37:g.105859305A>T	ENSP00000258456:p.Lys330Asn		Somatic	120	0	0		WXS	Illumina HiSeq	.	131	0.08	11	NM_007227	6	0.17	1	Q6NWS4|Q6NXU6	Missense_Mutation	SNP	ENST00000258456.1	37	CCDS2066.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.451686	0.63290	.	.	ENSG00000135973	ENST00000258456	T	0.37411	1.2	4.84	-2.17	0.07059	.	0.000000	0.85682	D	0.000000	T	0.47875	0.1469	L	0.54323	1.7	0.47065	D	0.999304	D	0.89917	1.0	D	0.78314	0.991	T	0.40961	-0.9535	10	0.52906	T	0.07	-11.1348	11.0662	0.47976	0.5683:0.0:0.4317:0.0	.	330	Q9Y5Y3	GPR45_HUMAN	N	330	ENSP00000258456:K330N	ENSP00000258456:K330N	K	+	3	2	GPR45	105225737	0.995000	0.38212	0.794000	0.32065	0.990000	0.78478	0.461000	0.21940	-0.376000	0.07943	0.374000	0.22700	AAA			0.557	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000253348.1		NM_007227	
ERICH2	285141	bcgsc.ca;mdanderson.org	37	2	171649402	171649402	+	Silent	SNP	C	C	T	rs3764916	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr2:171649402C>T	ENST00000409885.1	+	3	299	c.246C>T	c.(244-246)taC>taT	p.Y82Y				A1L162	ERIC2_HUMAN	glutamate-rich 2	82																	CCCGAGAGTACCAGCTGGCAA	0.303													C|||	1448	0.289137	0.0734	0.2752	5008	,	,		18432	0.5933		0.2873	False		,,,				2504	0.2791				.													.	.			0			.																																									SO:0001819	synonymous_variant	0	.			AGAGTACCAGCTG	BC127676, BC150546		2q31.1	2012-09-25			ENSG00000204334	ENSG00000204334			44395	protein-coding gene	gene with protein product							Standard	XM_001714892		Approved		uc002ugg.3	A1L162	OTTHUMG00000154074	ENST00000409885.1:c.246C>T	2.37:g.171649402C>T			Somatic	258	0.003875969	1		WXS	Illumina HiSeq	Phase_1	262	0.04	11	.	14	0.00	0	A7E2T7	Silent	SNP	ENST00000409885.1	37																																																																																						0.303	ERICH2-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000333723.1			
CDH22	64405	broad.mit.edu;mdanderson.org	37	20	44839036	44839036	+	Missense_Mutation	SNP	C	C	T	rs573144704		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr20:44839036C>T	ENST00000372262.3	-	6	1596	c.1196G>A	c.(1195-1197)gGc>gAc	p.G399D	CDH22_ENST00000474438.1_5'UTR|CDH22_ENST00000537909.1_Missense_Mutation_p.G399D	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	399	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				CTCCAGGAGGCCGGAGGGCGG	0.766													C|||	1	0.000199681	0.0	0.0014	5008	,	,		11168	0.0		0.0	False		,,,				2504	0.0				p.G399D													.	CDH22	112		0			c.G1196A																																									SO:0001583	missense	64405	exon7			AGGAGGCCGGAGG	AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"""Cadherins / Major cadherins"""	13251	protein-coding gene	gene with protein product		609920	"""cadherin-like 22"""	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.1196G>A	20.37:g.44839036C>T	ENSP00000361336:p.Gly399Asp		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	36	0.14	5	NM_021248	1	0.00	0	B9EGK7|O43205	Missense_Mutation	SNP	ENST00000372262.3	37	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.056400	0.55325	.	.	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.60672	0.17;0.17	3.96	3.96	0.45880	Cadherin (2);Cadherin-like (1);	0.189523	0.44483	D	0.000445	T	0.36468	0.0968	N	0.11427	0.14	0.25298	N	0.989307	B	0.31611	0.331	B	0.32928	0.155	T	0.35475	-0.9787	10	0.66056	D	0.02	.	8.8653	0.35282	0.0:0.8829:0.0:0.1171	.	399	Q9UJ99	CAD22_HUMAN	D	399	ENSP00000361336:G399D;ENSP00000437790:G399D	ENSP00000361336:G399D	G	-	2	0	CDH22	44272443	0.947000	0.32204	1.000000	0.80357	0.913000	0.54294	2.593000	0.46180	2.059000	0.61396	0.555000	0.69702	GGC			0.766	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000080491.1		NM_021248	
THOC5	8563	broad.mit.edu	37	22	29932681	29932681	+	Frame_Shift_Del	DEL	G	G	-			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr22:29932681delG	ENST00000490103.1	-	7	768	c.646delC	c.(646-648)ctcfs	p.L216fs	THOC5_ENST00000397871.1_Frame_Shift_Del_p.L216fs|THOC5_ENST00000397872.1_Frame_Shift_Del_p.L216fs|THOC5_ENST00000397873.2_Frame_Shift_Del_p.L216fs|CTA-256D12.11_ENST00000411969.1_RNA	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	216					blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)	p.L216V(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						ATCTCCTTGAGAATCTTCTCC	0.537																																					p.L216fs													THOC5,NS,carcinoma,0,2	THOC5	58	2	1	Substitution - Missense(1)	breast(1)	c.646delC												188.0	156.0	167.0					22																	29932681		2203	4300	6503	SO:0001589	frameshift_variant	8563	exon8			CCTTGAGAATCTT	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"""THO complex subunits"""	19074	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 79"""	612733	"""chromosome 22 open reading frame 19"""	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.646delC	22.37:g.29932681delG	ENSP00000420306:p.Leu216fs		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	105	0.09	9	NM_001002878	92	0.13	12	O60839|Q9UPZ5	Frame_Shift_Del	DEL	ENST00000490103.1	37	CCDS13859.1																																																																																					0.537	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000322097.1		NM_003678	
FANCD2P2	101929530	bcgsc.ca	37	3	11926467	11926467	+	IGR	SNP	A	A	G	rs2055282	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr3:11926467A>G								TAMM41 (38074 upstream) : RN7SL147P (67796 downstream)																							CTGAGACTTTATGTGGAGAGA	0.403													-|||	1690	0.33746	0.4085	0.2695	5008	,	,		20541	0.4107		0.2346	False		,,,				2504	0.32				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GACTTTATGTGGA																													3.37:g.11926467A>G			Somatic	61	0	0		WXS	Illumina HiSeq	Phase_1	40	0.10	4	.	0		0		RNA	SNP		37																																																																																					0	0.403										
RP11-767C1.1	0	bcgsc.ca	37	3	12926399	12926399	+	lincRNA	SNP	C	C	T	rs61739284	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr3:12926399C>T	ENST00000448129.1	-	0	311																											AAGACCCTGACCTCGGAGGTG	0.572													c|||	128	0.0255591	0.003	0.049	5008	,	,		17547	0.0		0.0467	False		,,,				2504	0.044				.													.	.			0			.																																											0	.			CCCTGACCTCGGA																													3.37:g.12926399C>T			Somatic	20	0	0		WXS	Illumina HiSeq	Phase_1	20	0.20	4	.	0		0		RNA	SNP	ENST00000448129.1	37																																																																																						0.572	RP11-767C1.1-001	KNOWN	basic|exp_conf	lincRNA	lincRNA		OTTHUMT00000340089.1			
OR5H4P	79299	bcgsc.ca	37	3	97940932	97940932	+	IGR	SNP	A	A	G	rs35658290	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr3:97940932A>G								OR5H15 (52447 upstream) : RP11-325B23.2 (11562 downstream)																							TTGTTCTCACAGGATTTTTAT	0.358													A|||	1260	0.251597	0.2587	0.2334	5008	,	,		19215	0.0387		0.4185	False		,,,				2504	0.3027				.													.	.			0			.																																									SO:0001628	intergenic_variant	79299	.			TCTCACAGGATTT																													3.37:g.97940932A>G			Somatic	40	0	0		WXS	Illumina HiSeq	Phase_1	47	0.21	10	.	0		0		RNA	SNP		37																																																																																					0	0.358										
OR5H4P	79299	bcgsc.ca	37	3	97941104	97941104	+	IGR	SNP	A	A	G	rs13063850	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr3:97941104A>G								OR5H15 (52619 upstream) : RP11-325B23.2 (11390 downstream)																							TTTTGTGGATACTTGGTTATC	0.393													A|||	1292	0.257987	0.2791	0.2392	5008	,	,		20534	0.0387		0.4195	False		,,,				2504	0.3027				.													.	.			0			.																																									SO:0001628	intergenic_variant	79299	.			GTGGATACTTGGT																													3.37:g.97941104A>G			Somatic	110	0	0		WXS	Illumina HiSeq	Phase_1	92	0.08	7	.	0		0		RNA	SNP		37																																																																																					0	0.393										
OR5H7P	79291	bcgsc.ca	37	3	97957490	97957490	+	lincRNA	SNP	G	G	A	rs6439724	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr3:97957490G>A	ENST00000508616.1	+	0	26																											TGAATGCATGGTACAATTTTT	0.378													A|||	1660	0.33147	0.5386	0.2666	5008	,	,		19860	0.0387		0.4254	False		,,,				2504	0.3027				.													.	.			0			.																																											79291	.			TGCATGGTACAAT																													3.37:g.97957490G>A			Somatic	123	0	0		WXS	Illumina HiSeq	Phase_1	117	0.08	9	.	0		0		RNA	SNP	ENST00000508616.1	37																																																																																						0.378	RP11-325B23.2-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000359282.1			
KIAA2018	205717	hgsc.bcm.edu	37	3	113376107	113376107	+	Silent	SNP	C	C	T			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr3:113376107C>T	ENST00000478658.1	-	5	4439	c.4422G>A	c.(4420-4422)caG>caA	p.Q1474Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q1474Q			Q68DE3	K2018_HUMAN	KIAA2018	1474	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						gttgttgttgctgttgctgct	0.493																																					p.Q1474Q													KIAA2018,colon,carcinoma,0,1	KIAA2018	0	1	0			c.G4422A												88.0	96.0	93.0					3																	113376107		2193	4279	6472	SO:0001819	synonymous_variant	205717	exon7			TTGTTGCTGTTGC	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4422G>A	3.37:g.113376107C>T			Somatic	53	0	0		WXS	Illumina HiSeq	.	59	0.10	6	NM_001009899	1	0.00	0	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																					0.493	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000354591.1		NM_001009899	
UBQLN4P1	285329	bcgsc.ca	37	3	148703787	148703787	+	IGR	SNP	T	T	G	rs3732559	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr3:148703787T>G								RP11-680B3.2 (25888 upstream) : GYG1 (5340 downstream)																							AAATCTCACTTCTGACGTCTG	0.547													T|||	2088	0.416933	0.677	0.3429	5008	,	,		20971	0.3641		0.3479	False		,,,				2504	0.2434				.													.	.			0			.																																									SO:0001628	intergenic_variant	285329	.			CTCACTTCTGACG																													3.37:g.148703787T>G			Somatic	118	0.0084745763	1		WXS	Illumina HiSeq	Phase_1	107	0.08	9	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.547										
Unknown	0	bcgsc.ca	37	3	195345872	195345872	+	IGR	SNP	A	A	C	rs199805117		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr3:195345872A>C								APOD (34796 upstream) : RP11-141C7.4 (20988 downstream)																							ACATCTCTGAAGAGGCAAAGA	0.562																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	200958	.			CTCTGAAGAGGCA																													3.37:g.195345872A>C			Somatic	772	0	0		WXS	Illumina HiSeq	Phase_1	593	0.03	16	.	1	0.00	0		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	.	12.62	1.993804	0.35131	.	.	ENSG00000176945	ENST00000381954	.	.	.	0.682	0.682	0.17992	.	.	.	.	.	T	0.62877	0.2464	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.64097	-0.6487	4	0.51188	T	0.08	.	.	.	.	.	.	.	.	D	115	.	ENSP00000371380:E115D	E	+	3	2	MUC20	196827161	0.948000	0.32251	0.886000	0.34754	0.214000	0.24535	0.912000	0.28597	0.556000	0.29098	0.331000	0.21540	GAA		0	0.562										
ZNF721	170960	ucsc.edu	37	4	437132	437132	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr4:437132G>T	ENST00000338977.5	-	2	1136	c.1088C>A	c.(1087-1089)gCc>gAc	p.A363D	ZNF721_ENST00000511833.2_Missense_Mutation_p.A375D|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000507078.1_Intron|ZNF721_ENST00000506646.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	363				A -> D (in Ref. 1; CAH10687). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						TTGATTCAGGGCTGTGTACCG	0.408																																					p.F375Y													.	ZNF721	205		0			c.T1124A												102.0	109.0	106.0					4																	437132		2141	4276	6417	SO:0001583	missense	170960	exon3			TTCAGGGCTGTGT	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"""Zinc fingers, C2H2-type"", ""-"""	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.1088C>A	4.37:g.437132G>T	ENSP00000340524:p.Ala363Asp		Somatic	93	0	0		RNA-Seq	Illumina HiSeq		86	0.05	4	NM_133474	28	0.29	8	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	G	0.011	-1.694654	0.00731	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.07444	3.19;3.19	0.71	-1.42	0.08913	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02267	0.0070	N	0.02286	-0.61	0.09310	N	1	B;B;B	0.11235	0.004;0.004;0.003	B;B;B	0.09377	0.002;0.004;0.002	T	0.43702	-0.9375	9	0.16420	T	0.52	.	0.3204	0.00302	0.2125:0.2447:0.2974:0.2454	.	363;375;375	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	D	363;375	ENSP00000340524:A363D;ENSP00000428878:A375D	ENSP00000340524:A363D	A	-	2	0	ZNF721	427132	0.000000	0.05858	0.012000	0.15200	0.016000	0.09150	-6.835000	0.00052	-0.929000	0.03757	-1.052000	0.02337	GCC			0.408	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding		OTTHUMT00000357939.1		NM_133474	
EXOC5P1	644548	bcgsc.ca	37	4	63682706	63682706	+	IGR	SNP	A	A	T	rs11946403	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr4:63682706A>T								AC110810.1 (221526 upstream) : RP11-257A22.1 (311322 downstream)																							GGAACTCCAGATAATGGATGA	0.413													A|||	312	0.0623003	0.0136	0.085	5008	,	,		16970	0.002		0.1451	False		,,,				2504	0.089				.													.	.			0			.																																									SO:0001628	intergenic_variant	644548	.			CTCCAGATAATGG																													4.37:g.63682706A>T			Somatic	156	0	0		WXS	Illumina HiSeq	Phase_1	125	0.06	7	.	0		0		RNA	SNP		37																																																																																					0	0.413										
EXOC5P1	644548	bcgsc.ca	37	4	63683038	63683038	+	IGR	SNP	C	C	T	rs6852768	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr4:63683038C>T								AC110810.1 (221858 upstream) : RP11-257A22.1 (310990 downstream)																							AGAAGTTGCACCTAATTGCCC	0.323													C|||	1164	0.232428	0.118	0.1643	5008	,	,		19845	0.3938		0.1948	False		,,,				2504	0.3078				.													.	.			0			.																																									SO:0001628	intergenic_variant	644548	.			GTTGCACCTAATT																													4.37:g.63683038C>T			Somatic	214	0	0		WXS	Illumina HiSeq	Phase_1	183	0.04	7	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.323										
Unknown	0	bcgsc.ca	37	4	189659777	189659777	+	IGR	SNP	G	G	A	rs6553227	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr4:189659777G>A								RNU7-192P (21898 upstream) : RP11-756P10.4 (19055 downstream)																							GAGAATGAAGGTTTAAGGAAA	0.458													-|||	1685	0.336462	0.4531	0.1974	5008	,	,		15480	0.3145		0.2237	False		,,,				2504	0.4162				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATGAAGGTTTAAG																													4.37:g.189659777G>A			Somatic	167	0	0		WXS	Illumina HiSeq	Phase_1	170	0.04	7	.	5	1.00	5		RNA	SNP		37																																																																																					0	0.458										
Unknown	0	bcgsc.ca	37	4	189660025	189660025	+	IGR	SNP	G	G	C	rs6553229	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr4:189660025G>C								RNU7-192P (22146 upstream) : RP11-756P10.4 (18807 downstream)																							TCCAAGTGAAGTAGGTGGCCT	0.408													-|||	541	0.108027	0.2103	0.0937	5008	,	,		18404	0.006		0.0954	False		,,,				2504	0.0982				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGTGAAGTAGGTG																													4.37:g.189660025G>C			Somatic	120	0	0		WXS	Illumina HiSeq	Phase_1	90	0.06	5	.	0		0		RNA	SNP		37																																																																																					0	0.408										
DHX29	54505	hgsc.bcm.edu;bcgsc.ca	37	5	54581236	54581236	+	Missense_Mutation	SNP	A	A	G			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr5:54581236A>G	ENST00000251636.5	-	10	1389	c.1241T>C	c.(1240-1242)gTa>gCa	p.V414A	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	414						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				AGACTTGATTACCCTAACCCT	0.373																																					p.V414A													.	.			0			c.T1241C												67.0	59.0	62.0					5																	54581236		2203	4300	6503	SO:0001583	missense	54505	exon10			TTGATTACCCTAA	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"""DEAH-boxes"""	15815	protein-coding gene	gene with protein product		612720	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"""	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.1241T>C	5.37:g.54581236A>G	ENSP00000251636:p.Val414Ala		Somatic	151	0	0		WXS	Illumina HiSeq	.	124	0.06	7	NM_019030	20	0.25	5	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Missense_Mutation	SNP	ENST00000251636.5	37	CCDS34158.1	.	.	.	.	.	.	.	.	.	.	A	15.43	2.832463	0.50845	.	.	ENSG00000067248	ENST00000251636	T	0.03386	3.95	5.76	5.76	0.90799	.	0.168219	0.53938	D	0.000058	T	0.03608	0.0103	N	0.24115	0.695	0.26791	N	0.969397	P	0.46395	0.877	B	0.40741	0.339	T	0.50285	-0.8846	10	0.16896	T	0.51	.	15.7411	0.77899	1.0:0.0:0.0:0.0	.	414	Q7Z478	DHX29_HUMAN	A	414	ENSP00000251636:V414A	ENSP00000251636:V414A	V	-	2	0	DHX29	54616993	1.000000	0.71417	0.734000	0.30879	0.642000	0.38348	8.437000	0.90302	2.201000	0.70794	0.533000	0.62120	GTA			0.373	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000368532.1		NM_019030	
ANKHD1	54882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	139907915	139907915	+	Missense_Mutation	SNP	G	G	A			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr5:139907915G>A	ENST00000360839.2	+	29	5538	c.5384G>A	c.(5383-5385)gGa>gAa	p.G1795E	ANKHD1_ENST00000544120.1_Missense_Mutation_p.G178E|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.G1795E|SNORD45_ENST00000363181.1_RNA|ANKHD1_ENST00000297183.6_Missense_Mutation_p.G1795E	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1795						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCTCATCTGGAGTAGGTACC	0.438																																					p.G1795E													.	.			0			c.G5384A												143.0	135.0	137.0					5																	139907915		2203	4300	6503	SO:0001583	missense	54882	exon29			CATCTGGAGTAGG	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"""Ankyrin repeat domain containing"""	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.5384G>A	5.37:g.139907915G>A	ENSP00000354085:p.Gly1795Glu		Somatic	128	0	0		WXS	Illumina HiSeq	.	91	0.14	13	NM_017747	67	0.36	24	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.51|12.51	1.960098|1.960098	0.34565|0.34565	.|.	.|.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996|ENSG00000131503	ENST00000360839;ENST00000297183;ENST00000253810;ENST00000431508;ENST00000536646;ENST00000433049;ENST00000544120;ENST00000532219|ENST00000435794;ENST00000432301	T;T;T;T;T;T|.	0.66460|.	-0.17;-0.21;1.85;1.86;1.44;-0.21|.	5.09|5.09	4.21|4.21	0.49690|0.49690	.|.	0.204155|.	0.43110|.	D|.	0.000605|.	T|.	0.57504|.	0.2058|.	L|L	0.36672|0.36672	1.1|1.1	0.40053|0.40053	D|D	0.975793|0.975793	D;B;B;P;B|.	0.65815|.	0.995;0.319;0.392;0.501;0.18|.	P;B;B;B;B|.	0.61328|.	0.887;0.096;0.149;0.157;0.112|.	T|.	0.56214|.	-0.8016|.	10|.	0.51188|.	T|.	0.08|.	.|.	15.7297|15.7297	0.77792|0.77792	0.0:0.1368:0.8632:0.0|0.0:0.1368:0.8632:0.0	.|.	178;225;1795;1795;1795|.	Q8IWG5;Q9H059;E9PF56;Q8IWZ2;Q8IWZ3|.	.;.;.;.;ANKH1_HUMAN|.	E|X	1795;1795;1795;451;230;317;178;1795|285;245	ENSP00000354085:G1795E;ENSP00000297183:G1795E;ENSP00000393204:G451E;ENSP00000390034:G317E;ENSP00000437687:G178E;ENSP00000432016:G1795E|.	ENSP00000432016:G1795E|.	G|W	+|+	2|3	0|0	ANKHD1-EIF4EBP3;ANKHD1|ANKHD1	139888099|139888099	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.347000|4.347000	0.59373|0.59373	1.360000|1.360000	0.45960|0.45960	0.655000|0.655000	0.94253|0.94253	GGA|TGG			0.438	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000251672.1		NM_017747	
PCDHA3	56145	ucsc.edu	37	5	140182571	140182571	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr5:140182571G>T	ENST00000522353.2	+	1	1789	c.1789G>T	c.(1789-1791)Gtg>Ttg	p.V597L	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.V597L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000520672.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	597	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGCGCGCAGTGGATGCAGA	0.677																																					p.V597L													.	PCDHA3	396		0			c.G1789T												102.0	99.0	100.0					5																	140182571		2203	4300	6503	SO:0001583	missense	56145	exon1			CGCGCAGTGGATG	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1789G>T	5.37:g.140182571G>T	ENSP00000429808:p.Val597Leu		Somatic	54	0	0		WXS	Illumina HiSeq		43	0.09	4	NM_031497	0		0	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	g	9.629	1.135862	0.21123	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.51817	0.69;0.69	4.32	4.32	0.51571	Cadherin (4);Cadherin-like (1);	0.000000	0.30781	U	0.008884	T	0.45875	0.1364	L	0.35723	1.085	0.18873	N	0.999987	P;P	0.43607	0.717;0.812	B;P	0.50109	0.333;0.631	T	0.38134	-0.9675	10	0.66056	D	0.02	.	8.6292	0.33908	0.0841:0.0:0.7641:0.1518	.	597;597	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	L	597	ENSP00000429808:V597L;ENSP00000434086:V597L	ENSP00000429808:V597L	V	+	1	0	PCDHA3	140162755	0.709000	0.27886	0.984000	0.44739	0.055000	0.15305	1.023000	0.30065	2.117000	0.64856	0.467000	0.42956	GTG			0.677	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000372848.2		NM_018906	
ERVFRD-1	405754	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	11105023	11105023	+	Missense_Mutation	SNP	T	T	A			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr6:11105023T>A	ENST00000472091.1	-	2	896	c.521A>T	c.(520-522)aAa>aTa	p.K174I	SMIM13_ENST00000416247.2_Intron|ERVFRD-1_ENST00000542862.1_Missense_Mutation_p.K174I	NM_207582.2	NP_997465.1	P60508	SYCY2_HUMAN	endogenous retrovirus group FRD, member 1	174					syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(4)|stomach(1)	15						ATTTGGAGGTTTGGGGAATCT	0.443																																					p.K174I													.	.			0			c.A521T												154.0	168.0	163.0					6																	11105023		2203	4300	6503	SO:0001583	missense	405754	exon2			GGAGGTTTGGGGA	AK075092, AK123938, AY358244	CCDS4519.1	6p24.2	2014-05-02			ENSG00000244476	ENSG00000244476			33823	other	endogenous retrovirus		610524				12970426, 14557543, 15476554, 21542922	Standard	NM_207582		Approved	HERV-W/FRD, HERV-FRD, envFRD, ERVFRDE1, syncytin-2	uc003mzt.3	P60508	OTTHUMG00000159193	ENST00000472091.1:c.521A>T	6.37:g.11105023T>A	ENSP00000420174:p.Lys174Ile		Somatic	133	0	0		WXS	Illumina HiSeq	.	116	0.08	9	NM_207582	1	0.00	0		Missense_Mutation	SNP	ENST00000472091.1	37	CCDS4519.1	.	.	.	.	.	.	.	.	.	.	T	17.61	3.433184	0.62844	.	.	ENSG00000244476	ENST00000472091;ENST00000542862	T;T	0.15834	2.39;2.39	0.235	0.235	0.15431	.	.	.	.	.	T	0.03434	0.0099	N	0.14661	0.345	0.21416	N	0.999691	P	0.42993	0.797	B	0.40901	0.343	T	0.32666	-0.9898	8	0.66056	D	0.02	.	.	.	.	.	174	P60508	EFRD1_HUMAN	I	174	ENSP00000420174:K174I;ENSP00000444461:K174I	ENSP00000420174:K174I	K	-	2	0	ERVFRD-1	11213009	0.753000	0.28349	0.872000	0.34217	0.873000	0.50193	0.310000	0.19356	0.263000	0.21812	0.260000	0.18958	AAA			0.443	ERVFRD-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000353776.1		NM_207582	
HLA-C	3107	ucsc.edu	37	6	31238898	31238898	+	Missense_Mutation	SNP	A	A	C	rs281860533|rs201707949|rs281860528	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr6:31238898A>C	ENST00000376228.5	-	3	585	c.571T>G	c.(571-573)Tgg>Ggg	p.W191G	HLA-C_ENST00000383329.3_Missense_Mutation_p.W191G	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	191	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)	p.W191G(2)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CTGCGGAGCCACTCCACGCAC	0.677													a|||	46	0.0091853	0.0091	0.0101	5008	,	,		14074	0.0119		0.003	False		,,,				2504	0.0123				p.W191G													HLA-C_ENST00000383329,NS,carcinoma,0,4	HLA-C	92	4	2	Substitution - Missense(2)	prostate(2)	c.T571G												52.0	41.0	45.0					6																	31238898		2201	4297	6498	SO:0001583	missense	3107	exon3			GGAGCCACTCCAC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.571T>G	6.37:g.31238898A>C	ENSP00000365402:p.Trp191Gly		Somatic	57	0.0350877193	2		RNA-Seq	Illumina HiSeq		50	0.02	1	NM_002117	2926	0.17	507	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	6.739|6.739	0.505074|0.505074	0.12822|0.12822	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.00014	.|9.21;9.21	2.71|2.71	1.5|1.5	0.22942|0.22942	.|MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|2.640200	.|0.01822	.|U	.|0.034101	T|T	0.00109|0.00109	0.0003|0.0003	M|M	0.77486|0.77486	2.375|2.375	0.09310|0.09310	N|N	1|1	.|P;B;B;B	.|0.44877	.|0.845;0.393;0.152;0.393	.|P;B;B;P	.|0.53450	.|0.726;0.394;0.394;0.474	T|T	0.45366|0.45366	-0.9266|-0.9266	5|10	.|0.66056	.|D	.|0.02	.|.	6.5885|6.5885	0.22634|0.22634	0.7861:0.0:0.0:0.2139|0.7861:0.0:0.0:0.2139	.|.	.|191;191;191;191	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	G|G	190|191;191;191;228	.|ENSP00000365402:W191G;ENSP00000372819:W191G	.|ENSP00000365402:W191G	V|W	-|-	2|1	0|0	HLA-C|HLA-C	31346877|31346877	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.000000|0.000000	0.00434|0.00434	0.361000|0.361000	0.20267|0.20267	0.433000|0.433000	0.26313|0.26313	-1.026000|-1.026000	0.02426|0.02426	GTG|TGG			0.677	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000076281.3		NM_002117	
HLA-DRB6	3128	broad.mit.edu	37	6	32523273	32523274	+	RNA	DEL	GA	GA	-	rs142054686		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	GA	GA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr6:32523273_32523274delGA	ENST00000411500.1	-	0	458					NR_001298.1				major histocompatibility complex, class II, DR beta 6 (pseudogene)																		ATTCCACTGTGAGAGGGCTCAT	0.396																																					.													.	.			0			.																																											0	.			CACTGTGAGAGGG	L76566		6p21.3	2011-07-08			ENSG00000229391	ENSG00000229391		"""Histocompatibility complex"""	4954	pseudogene	pseudogene						1529427, 10436177	Standard	NR_001298		Approved		uc003obn.1		OTTHUMG00000031028		6.37:g.32523275_32523276delGA			Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	10	0.40	4	.	16	0.00	0		RNA	DEL	ENST00000411500.1	37																																																																																						0.396	HLA-DRB6-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000272900.1		NR_001298	
SEPT7P2	641977	broad.mit.edu	37	7	45787002	45787002	+	RNA	DEL	A	A	-			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr7:45787002delA	ENST00000429741.1	-	0	822									septin 7 pseudogene 2																		CAGATTAGCCAAAAAAAATTA	0.259																																					.													.	.			0			.																																											0	.			TTAGCCAAAAAAA	AL133216		7p12.3	2010-03-24	2010-03-24	2010-03-24	ENSG00000214765	ENSG00000214765			32339	pseudogene	pseudogene		611563	"""septin 7B"", ""septin 13"""	SEPT7B, SEPT13		15915442	Standard	NR_024271		Approved	DKFZp313J1114	uc003tnf.4		OTTHUMG00000155423		7.37:g.45787002delA			Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	6	0.50	3	.	0		0		RNA	DEL	ENST00000429741.1	37																																																																																						0.259	SEPT7P2-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000340060.1		NR_024271	
HAUS6P1	653175	bcgsc.ca	37	7	53255471	53255471	+	IGR	SNP	A	A	G	rs6943510	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr7:53255471A>G								POM121L12 (150854 upstream) : RNU1-14P (178279 downstream)																							AGTTAAGCAGATACGAAACTT	0.313													G|||	4348	0.868211	0.9773	0.8228	5008	,	,		17983	0.9415		0.7147	False		,,,				2504	0.8354				.													.	.			0			.																																									SO:0001628	intergenic_variant	653175	.			AAGCAGATACGAA																													7.37:g.53255471A>G			Somatic	198	0	0		WXS	Illumina HiSeq	Phase_1	247	0.05	13	.	0		0		RNA	SNP		37																																																																																					0	0.313										
HAUS6P1	653175	bcgsc.ca	37	7	53256265	53256265	+	IGR	SNP	G	G	A	rs11972016	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr7:53256265G>A								POM121L12 (151648 upstream) : RNU1-14P (177485 downstream)																							CTTTCTTGTCGCAGTCAGTTT	0.398													A|||	1461	0.291733	0.3215	0.219	5008	,	,		18594	0.1935		0.332	False		,,,				2504	0.363				.													.	.			0			.																																									SO:0001628	intergenic_variant	653175	.			CTTGTCGCAGTCA																													7.37:g.53256265G>A			Somatic	244	0.0040983607	1		WXS	Illumina HiSeq	Phase_1	262	0.03	8	.	12	0.00	0		RNA	SNP		37																																																																																					0	0.398										
OR2A15P	135942	bcgsc.ca	37	7	143815744	143815744	+	IGR	SNP	T	T	C	rs10263904	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr7:143815744T>C								OR2A2 (8087 upstream) : OR2A14 (10406 downstream)																							AAAGAAGAACTCCACCACACA	0.577													-|||	2502	0.499601	0.3525	0.6095	5008	,	,		20857	0.7381		0.3191	False		,,,				2504	0.5603				.													.	.			0			.																																									SO:0001628	intergenic_variant	135942	.			AAGAACTCCACCA																													7.37:g.143815744T>C			Somatic	75	0.0133333333	1		WXS	Illumina HiSeq	Phase_1	74	0.08	6	.	0		0		RNA	SNP		37																																																																																					0	0.577										
OR2A15P	135942	bcgsc.ca	37	7	143815780	143815780	+	IGR	SNP	G	G	T	rs10274340	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr7:143815780G>T								OR2A2 (8123 upstream) : OR2A14 (10370 downstream)																							GGTAGAGAAGGCCTTTCTGCG	0.592													-|||	2500	0.499201	0.351	0.6095	5008	,	,		20716	0.7381		0.3191	False		,,,				2504	0.5603				.													.	.			0			.																																									SO:0001628	intergenic_variant	135942	.			GAGAAGGCCTTTC																													7.37:g.143815780G>T			Somatic	60	0	0		WXS	Illumina HiSeq	Phase_1	68	0.07	5	.	0		0		RNA	SNP		37																																																																																					0	0.592										
LINC00583	100113404	broad.mit.edu	37	9	13928081	13928084	+	lincRNA	DEL	ATTC	ATTC	-	rs35583621|rs147030758|rs185868809	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	ATTC	ATTC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr9:13928081_13928084delATTC	ENST00000381010.3	+	0	91					NR_038194.1				long intergenic non-protein coding RNA 583																		TTTAAAACATATTCAATTTGGGGA	0.255														330	0.0658946	0.0121	0.1167	5008	,	,		15895	0.0198		0.1402	False		,,,				2504	0.0736				.													.	LINC00583	1		0			.																																											0	.			AAACATATTCAAT			9p23	2012-10-12	2012-04-03	2012-04-03	ENSG00000205636	ENSG00000205636		"""Long non-coding RNAs"""	31437	non-coding RNA	RNA, long non-coding			"""chromosome 9 open reading frame 146"""	C9orf146			Standard	NR_038194		Approved		uc022bdn.1		OTTHUMG00000019564		9.37:g.13928081_13928084delATTC			Somatic	566	0	0		WXS	Illumina HiSeq	Phase_I	541	0.02	12	.	0		0		RNA	DEL	ENST00000381010.3	37																																																																																						0.255	LINC00583-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000051738.1		NR_038194	
Unknown	0	bcgsc.ca	37	9	68433564	68433564	+	IGR	SNP	C	C	A			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr9:68433564C>A								MIR4477B (18176 upstream) : CR786580.2 (78781 downstream)																							AAGCCATTTTCCCCTAAGTGA	0.338																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CATTTTCCCCTAA																													9.37:g.68433564C>A			Somatic	167	0.0179640719	3		WXS	Illumina HiSeq	Phase_1	167	0.05	9	.	11	0.00	0		RNA	SNP		37																																																																																					0	0.338										
NUP188	23511	ucsc.edu	37	9	131735464	131735464	+	Missense_Mutation	SNP	G	G	T			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chr9:131735464G>T	ENST00000372577.2	+	12	1160	c.1139G>T	c.(1138-1140)tGt>tTt	p.C380F		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	380					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						GCATGCATGTGTGTCTATGGA	0.502																																					p.C380F													.	NUP188	140		0			c.G1139T												169.0	129.0	143.0					9																	131735464		2203	4300	6503	SO:0001583	missense	23511	exon12			GCATGTGTGTCTA	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.1139G>T	9.37:g.131735464G>T	ENSP00000361658:p.Cys380Phe		Somatic	46	0	0		WXS	Illumina HiSeq		37	0.11	4	NM_015354	68	0.00	0	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	37	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.836094	0.71373	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.65732	-0.17	5.01	5.01	0.66863	.	0.091610	0.85682	D	0.000000	T	0.68824	0.3043	N	0.24115	0.695	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.73452	-0.3978	10	0.72032	D	0.01	3.3229	17.7641	0.88471	0.0:0.0:1.0:0.0	.	380	Q5SRE5	NU188_HUMAN	F	269;380	ENSP00000361658:C380F	ENSP00000349125:C269F	C	+	2	0	NUP188	130775285	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	8.787000	0.91830	2.487000	0.83934	0.551000	0.68910	TGT			0.502	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000054529.2			
MT-ND5	4540	broad.mit.edu;bcgsc.ca	37	M	13812	13812	+	Silent	SNP	T	T	C			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chrM:13812T>C	ENST00000361567.2	+	1	1476	c.1476T>C	c.(1474-1476)gcT>gcC	p.A492A	MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	492					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						ACAGCCCTCGCTGTCACTTTC	0.443																																					p.A492A													.	.			0			c.T1476C																																									SO:0001819	synonymous_variant	4540	exon1			CCTCGCTGTCACT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1476T>C	M.37:g.13812T>C			Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	12	0.58	7	ENST00000361567	0		0	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																						0.443	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				YP_003024036	
KDM6A	7403	broad.mit.edu	37	X	44918601	44918602	+	Frame_Shift_Del	DEL	TA	TA	-			TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	TA	TA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chrX:44918601_44918602delTA	ENST00000377967.4	+	12	1125_1126	c.1084_1085delTA	c.(1084-1086)tatfs	p.Y362fs	KDM6A_ENST00000382899.4_Frame_Shift_Del_p.Y362fs|KDM6A_ENST00000536777.1_Frame_Shift_Del_p.Y362fs|KDM6A_ENST00000543216.1_Frame_Shift_Del_p.Y362fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	362	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.0(2)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						AGGCACTCTCTATGAATCCTGC	0.455			"""D, N, F, S"""		"""renal, oesophageal SCC, MM"""																																p.362_362del	Colon(129;1273 1667 15230 27352 52914)			Rec	yes		X	Xp11.2	7403	"""lysine (K)-specific demethylase 6A, UTX"""		"""E, L"""	.	KDM6A	274		8	Whole gene deletion(6)|No detectable mRNA/protein(2)	haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|breast(2)|pancreas(2)	c.1084_1085del																																									SO:0001589	frameshift_variant	7403	exon12			ACTCTCTATGAAT	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"""Chromatin-modifying enzymes / K-demethylases"", ""Tetratricopeptide (TTC) repeat domain containing"""	12637	protein-coding gene	gene with protein product		300128	"""ubiquitously transcribed tetratricopeptide repeat, X chromosome"""	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.1084_1085delTA	X.37:g.44918601_44918602delTA	ENSP00000367203:p.Tyr362fs		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	208	0.03	7	NM_021140	30	0.00	0	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	37	CCDS14265.1																																																																																					0.455	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000056324.1		NM_021140	
FAM104B	90736	ucsc.edu	37	X	55172630	55172630	+	Nonsense_Mutation	SNP	G	G	A	rs113263757		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chrX:55172630G>A	ENST00000358460.4	-	3	388	c.235C>T	c.(235-237)Cag>Tag	p.Q79*	FAM104B_ENST00000478918.1_5'Flank|FAM104B_ENST00000332132.4_Nonsense_Mutation_p.Q80*|FAM104B_ENST00000477847.2_Nonsense_Mutation_p.Q76*|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000489298.1_Nonsense_Mutation_p.Q78*|FAM104B_ENST00000425133.2_Nonsense_Mutation_p.Q80*			Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	79										endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						TGCAAGAACTGGGGAAAGTTT	0.493																																					p.Q80X													.	FAM104B	28		0			c.C238T												127.0	104.0	112.0					X																	55172630		2203	4300	6503	SO:0001587	stop_gained	90736	exon3			AGAACTGGGGAAA	BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518			25085	protein-coding gene	gene with protein product			"""chromosome X open reading frame 44"""	CXorf44		12477932	Standard	NM_138362		Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000358460.4:c.235C>T	X.37:g.55172630G>A	ENSP00000364101:p.Gln79*		Somatic	38	0.0526315789	2		WXS	Illumina HiSeq		37	0.19	7	NM_001166699	66	0.00	0	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	Nonsense_Mutation	SNP	ENST00000358460.4	37	CCDS35305.2	.	.	.	.	.	.	.	.	.	.	g	11.17	1.559418	0.27827	.	.	ENSG00000182518	ENST00000358460;ENST00000332132;ENST00000425133;ENST00000477847;ENST00000489298	.	.	.	1.6	1.6	0.23607	.	0.325359	0.21941	U	0.066869	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-0.2487	6.0913	0.19995	0.0:0.0:1.0:0.0	.	.	.	.	X	79;80;80;76;78	.	ENSP00000333394:Q80X	Q	-	1	0	FAM104B	55189355	0.905000	0.30787	0.015000	0.15790	0.033000	0.12548	1.600000	0.36762	1.084000	0.41184	0.436000	0.28706	CAG			0.493	FAM104B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000056851.1		NM_138362	
FAM104B	90736	ucsc.edu;mdanderson.org	37	X	55172645	55172645	+	Missense_Mutation	SNP	C	C	G	rs1047042	byFrequency	TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chrX:55172645C>G	ENST00000358460.4	-	3	373	c.220G>C	c.(220-222)Gat>Cat	p.D74H	FAM104B_ENST00000478918.1_5'Flank|FAM104B_ENST00000332132.4_Missense_Mutation_p.D75H|FAM104B_ENST00000477847.2_Missense_Mutation_p.D71H|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000489298.1_Missense_Mutation_p.D73H|FAM104B_ENST00000425133.2_Missense_Mutation_p.D75H			Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	74				D -> V (in Ref. 1; BAG61768). {ECO:0000305}.						endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						AAGTTTGCATCGGGTTCAGTA	0.468													C|||	5	0.0013245	0.0023	0.0	3775	,	,		14416	0.0		0.0	False		,,,				2504	0.002				p.D75H													.	FAM104B	28		0			c.G223C												136.0	110.0	119.0					X																	55172645		2203	4300	6503	SO:0001583	missense	90736	exon3			TTGCATCGGGTTC	BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518			25085	protein-coding gene	gene with protein product			"""chromosome X open reading frame 44"""	CXorf44		12477932	Standard	NM_138362		Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000358460.4:c.220G>C	X.37:g.55172645C>G	ENSP00000364101:p.Asp74His		Somatic	38	0.0263157895	1		WXS	Illumina HiSeq		39	0.21	8	NM_001166699	77	0.00	0	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	Missense_Mutation	SNP	ENST00000358460.4	37	CCDS35305.2	.	.	.	.	.	.	.	.	.	.	c	3.193	-0.165363	0.06461	.	.	ENSG00000182518	ENST00000358460;ENST00000332132;ENST00000425133;ENST00000477847;ENST00000489298	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	1.59	-1.04	0.10068	.	0.505297	0.17523	U	0.171170	T	0.25044	0.0608	N	0.14661	0.345	0.09310	N	1	B;P;P	0.46859	0.002;0.774;0.885	B;P;B	0.46479	0.001;0.518;0.241	T	0.15065	-1.0450	10	0.56958	D	0.05	-1.547	4.2247	0.10575	0.0:0.4679:0.0:0.5321	.	75;74;75	Q5XKR9-3;Q5XKR9;Q5XKR9-2	.;F104B_HUMAN;.	H	74;75;75;71;73	ENSP00000364101:D74H;ENSP00000333394:D75H;ENSP00000397188:D75H;ENSP00000421161:D71H;ENSP00000423164:D73H	ENSP00000333394:D75H	D	-	1	0	FAM104B	55189370	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.019000	0.12546	-0.355000	0.08199	-0.556000	0.04195	GAT			0.468	FAM104B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000056851.1		NM_138362	
RP11-1007I13.4	0	broad.mit.edu	37	X	151290002	151290003	+	RNA	INS	-	-	T	rs200557971		TCGA-WZ-A7V4-01A-11D-A435-10	TCGA-WZ-A7V4-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7bea22d-c914-41c9-bb43-0b1785b36b5b	5d280fa0-3f46-444a-8d3f-bc1be8090d47	g.chrX:151290002_151290003insT	ENST00000509345.2	-	0	172																											TGCTGATATTGTTTTTTTTTTT	0.391																																					.													.	.			0			.																																											0	.			GATATTGTTTTTT																													X.37:g.151290013_151290013dupT			Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	12	0.33	4	.	2	0.00	0		RNA	INS	ENST00000509345.2	37																																																																																						0.391	RP11-1007I13.4-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript		OTTHUMT00000445981.1			
