#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_Algorithm	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_Confidence	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_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	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_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	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_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
CELF3	11189	hgsc.bcm.edu	37	1	151679166	151679166	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr1:151679166C>T	ENST00000290583.4	-	9	1760	c.967G>A	c.(967-969)Gcg>Acg	p.A323T	CELF3_ENST00000392706.3_Intron|CELF3_ENST00000470688.1_5'UTR|CELF3_ENST00000290585.4_Missense_Mutation_p.A273T|RP11-98D18.1_ENST00000457548.1_RNA	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	323					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						TGCATCCCCGCGTAGGCCTGC	0.687																																					p.A323T		Atlas-SNP	.											.	CELF3	49	.	0			c.G967A						PASS	.						9.0	10.0	9.0					1																	151679166		1879	3579	5458	SO:0001583	missense	11189	exon9			TCCCCGCGTAGGC	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"""Trinucleotide (CAG) repeat containing"", ""RNA binding motif (RRM) containing"""	11967	protein-coding gene	gene with protein product	"""expanded repeat domain, CAG/CTG 4"", ""CAG repeat domain"", ""CUG-BP and ETR-3 like factor 3"""	612678	"""trinucleotide repeat containing 4"""	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.967G>A	chr1.hg19:g.151679166C>T	ENSP00000290583:p.Ala323Thr	170.0	0.0	.		101.0	44.0	.	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	hg19	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	15.89	2.966802	0.53507	.	.	ENSG00000159409	ENST00000290585;ENST00000290583	T;T	0.16897	2.31;2.32	4.49	4.49	0.54785	.	0.126953	0.53938	D	0.000048	T	0.04272	0.0118	N	0.16567	0.415	0.80722	D	1	B;B;B;B	0.33826	0.006;0.01;0.063;0.427	B;B;B;B	0.23419	0.005;0.013;0.008;0.046	T	0.37009	-0.9724	10	0.22109	T	0.4	-7.7777	15.906	0.79430	0.0:1.0:0.0:0.0	.	273;323;323;322	Q5SZQ7;Q5SZQ8-2;Q5SZQ8;Q5SZQ8-3	.;.;CELF3_HUMAN;.	T	273;323	ENSP00000290585:A273T;ENSP00000290583:A323T	ENSP00000290583:A323T	A	-	1	0	CELF3	149945790	0.182000	0.23173	0.988000	0.46212	0.985000	0.73830	0.640000	0.24705	2.325000	0.78763	0.561000	0.74099	GCG	.	.	.	none		0.687	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185	
C1orf74	148304	hgsc.bcm.edu	37	1	209956222	209956222	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr1:209956222G>A	ENST00000294811.1	-	2	1014	c.758C>T	c.(757-759)gCt>gTt	p.A253V		NM_152485.2	NP_689698.1	Q96LT6	CA074_HUMAN	chromosome 1 open reading frame 74	253										endometrium(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	15				OV - Ovarian serous cystadenocarcinoma(81;0.0328)		GCTGAGATCAGCAAAGTCATT	0.478																																					p.A253V		Atlas-SNP	.											.	C1orf74	30	.	0			c.C758T						PASS	.						107.0	113.0	111.0					1																	209956222		2203	4300	6503	SO:0001583	missense	148304	exon2			AGATCAGCAAAGT	AK057807	CCDS1491.1	1q32.2	2008-02-05			ENSG00000162757	ENSG00000162757			26319	protein-coding gene	gene with protein product						12477932	Standard	NM_152485		Approved	FLJ25078	uc001hhp.1	Q96LT6	OTTHUMG00000036483	ENST00000294811.1:c.758C>T	chr1.hg19:g.209956222G>A	ENSP00000294811:p.Ala253Val	79.0	0.0	.		80.0	4.0	.	NM_152485		Missense_Mutation	SNP	ENST00000294811.1	hg19	CCDS1491.1	.	.	.	.	.	.	.	.	.	.	G	14.81	2.646718	0.47258	.	.	ENSG00000162757	ENST00000294811	T	0.47869	0.83	5.75	3.87	0.44632	.	0.659417	0.14008	N	0.347653	T	0.36524	0.0970	L	0.36672	1.1	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.27262	-1.0079	10	0.51188	T	0.08	-1.6294	7.8075	0.29211	0.1481:0.0:0.7188:0.1331	.	253	Q96LT6	CA074_HUMAN	V	253	ENSP00000294811:A253V	ENSP00000294811:A253V	A	-	2	0	C1orf74	208022845	0.493000	0.26035	0.984000	0.44739	0.988000	0.76386	2.185000	0.42584	0.763000	0.33175	0.655000	0.94253	GCT	.	.	.	none		0.478	C1orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088745.1	NM_152485	
CELSR3	1951	hgsc.bcm.edu	37	3	48687979	48687979	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr3:48687979C>A	ENST00000164024.4	-	16	6686	c.6406G>T	c.(6406-6408)Ggt>Tgt	p.G2136C	CELSR3_ENST00000544264.1_Missense_Mutation_p.G2136C	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	2136					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CACCACACACCAGATCTCAGG	0.607																																					p.G2136C		Atlas-SNP	.											.	CELSR3	237	.	0			c.G6406T						PASS	.						63.0	56.0	59.0					3																	48687979		2202	4300	6502	SO:0001583	missense	1951	exon16			ACACACCAGATCT	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.6406G>T	chr3.hg19:g.48687979C>A	ENSP00000164024:p.Gly2136Cys	295.0	0.0	.		168.0	53.0	.	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.448586	0.63178	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.57273	0.41;0.41	5.42	4.55	0.56014	GPCR, family 2, extracellular hormone receptor domain (3);	.	.	.	.	T	0.75620	0.3874	M	0.91818	3.245	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.69654	0.965;0.947	T	0.80730	-0.1252	9	0.87932	D	0	.	11.6972	0.51551	0.0:0.8515:0.0:0.1485	.	2136;2206	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	C	2136	ENSP00000164024:G2136C;ENSP00000445694:G2136C	ENSP00000164024:G2136C	G	-	1	0	CELSR3	48662983	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	4.669000	0.61575	1.285000	0.44548	0.643000	0.83706	GGT	.	.	.	none		0.607	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
HEG1	57493	hgsc.bcm.edu	37	3	124732410	124732410	+	Silent	SNP	A	A	G			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr3:124732410A>G	ENST00000311127.4	-	6	2080	c.2013T>C	c.(2011-2013)tcT>tcC	p.S671S	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	671	Ser-rich.				cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						GAGGCCCTgaagaagaagaag	0.473																																					p.S671S		Atlas-SNP	.											.	HEG1	109	.	0			c.T2013C						PASS	.						46.0	52.0	50.0					3																	124732410		2119	4239	6358	SO:0001819	synonymous_variant	57493	exon6			CCCTGAAGAAGAA	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.2013T>C	chr3.hg19:g.124732410A>G		71.0	0.0	.		84.0	11.0	.	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Silent	SNP	ENST00000311127.4	hg19	CCDS46898.1																																																																																			.	.	.	none		0.473	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
PCYT1A	5130	hgsc.bcm.edu	37	3	195968896	195968896	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr3:195968896G>A	ENST00000292823.2	-	8	803	c.631C>T	c.(631-633)Cgg>Tgg	p.R211W	PCYT1A_ENST00000431016.1_Missense_Mutation_p.R211W|PCYT1A_ENST00000419333.1_Missense_Mutation_p.R211W	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	211					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	TCATAATCCCGCACAATTCGG	0.488																																					p.R211W		Atlas-SNP	.											.	PCYT1A	34	.	0			c.C631T						PASS	.						147.0	123.0	131.0					3																	195968896		2203	4300	6503	SO:0001583	missense	5130	exon8			AATCCCGCACAAT	L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	123695	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.631C>T	chr3.hg19:g.195968896G>A	ENSP00000292823:p.Arg211Trp	118.0	0.0	.		91.0	4.0	.	NM_005017	A9LYK9|D3DXB1|Q86Y88	Missense_Mutation	SNP	ENST00000292823.2	hg19	CCDS3315.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.813714	0.90790	.	.	ENSG00000161217	ENST00000419333;ENST00000292823;ENST00000416798;ENST00000431016;ENST00000411591;ENST00000433733;ENST00000430755	.	.	.	5.65	5.65	0.86999	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.72590	0.3479	M	0.87381	2.88	0.80722	D	1	D	0.71674	0.998	P	0.48654	0.585	T	0.79004	-0.1980	9	0.87932	D	0	-1.6477	13.7119	0.62674	0.0:0.0:0.8461:0.1538	.	211	P49585	PCY1A_HUMAN	W	211;211;172;211;211;84;145	.	ENSP00000292823:R211W	R	-	1	2	PCYT1A	197453293	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.185000	0.72013	2.685000	0.91497	0.650000	0.86243	CGG	.	.	.	none		0.488	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017	
BMP2K	55589	hgsc.bcm.edu	37	4	79792157	79792157	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr4:79792157G>C	ENST00000335016.5	+	11	1618	c.1452G>C	c.(1450-1452)caG>caC	p.Q484H	BMP2K_ENST00000502871.1_Missense_Mutation_p.Q484H	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	484	Gln/His-rich.			Missing (in Ref. 2; CAB70863). {ECO:0000305}.	regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						agcagcagcagcagcagcacc	0.498																																					p.Q484H		Atlas-SNP	.											.	BMP2K	169	.	0			c.G1452C						PASS	.						19.0	23.0	21.0					4																	79792157		2101	4115	6216	SO:0001583	missense	55589	exon11			GCAGCAGCAGCAG	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.1452G>C	chr4.hg19:g.79792157G>C	ENSP00000334836:p.Gln484His	11.0	0.0	.		10.0	5.0	.	NM_017593	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	hg19	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.194|3.194	-0.165237|-0.165237	0.06461|0.06461	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000502613|ENST00000502871;ENST00000335016;ENST00000264889	.|T;T	.|0.74002	.|0.91;-0.8	0.515|0.515	0.515|0.515	0.17013|0.17013	.|.	.|3.723490	.|0.01123	.|N	.|0.005826	T|T	0.56688|0.56688	0.2002|0.2002	N|N	0.19112|0.19112	0.55|0.55	0.21325|0.21325	N|N	0.999728|0.999728	.|B;B	.|0.23540	.|0.087;0.032	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.41413|0.41413	-0.9510|-0.9510	5|10	.|0.26408	.|T	.|0.33	.|.	2.8589|2.8589	0.05580|0.05580	0.3668:0.0:0.6332:0.0|0.3668:0.0:0.6332:0.0	.|.	.|484;484	.|Q9NSY1;Q4W5H2	.|BMP2K_HUMAN;.	P|H	177|484;484;498	.|ENSP00000421768:Q484H;ENSP00000334836:Q484H	.|ENSP00000264889:Q498H	A|Q	+|+	1|3	0|2	BMP2K|BMP2K	80011181|80011181	0.879000|0.879000	0.30193|0.30193	0.126000|0.126000	0.21872|0.21872	0.036000|0.036000	0.12997|0.12997	1.288000|1.288000	0.33296|0.33296	0.550000|0.550000	0.28991|0.28991	0.163000|0.163000	0.16589|0.16589	GCA|CAG	.	.	.	none		0.498	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
BMP2K	55589	hgsc.bcm.edu	37	4	79792160	79792160	+	Missense_Mutation	SNP	G	G	C	rs202184856|rs575644040	byFrequency	TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr4:79792160G>C	ENST00000335016.5	+	11	1621	c.1455G>C	c.(1453-1455)caG>caC	p.Q485H	BMP2K_ENST00000502871.1_Missense_Mutation_p.Q485H	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	485	Gln/His-rich.			Missing (in Ref. 2; CAB70863). {ECO:0000305}.	regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						agcagcagcagcagcaccacc	0.493													G|||	44	0.00878594	0.0015	0.0043	5008	,	,		11170	0.0159		0.0219	False		,,,				2504	0.001				p.Q485H		Atlas-SNP	.											.	BMP2K	169	.	0			c.G1455C						PASS	.						19.0	23.0	22.0					4																	79792160		2144	4181	6325	SO:0001583	missense	55589	exon11			GCAGCAGCAGCAC	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.1455G>C	chr4.hg19:g.79792160G>C	ENSP00000334836:p.Gln485His	11.0	0.0	.		11.0	5.0	.	NM_017593	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	hg19	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.107|0.107	-1.144327|-1.144327	0.01728|0.01728	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000502613|ENST00000502871;ENST00000335016;ENST00000264889	.|T;T	.|0.73897	.|0.94;-0.79	.|.	.|.	.|.	.|.	.|2.710950	.|0.01643	.|U	.|0.024172	T|T	0.51941|0.51941	0.1704|0.1704	N|N	0.08118|0.08118	0|0	0.27818|0.27818	N|N	0.94189|0.94189	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.39210|0.39210	-0.9625|-0.9625	4|9	.|0.44086	.|T	.|0.13	.|.	5.0772|5.0772	0.14638|0.14638	0.0:0.6216:0.3784:0.0|0.0:0.6216:0.3784:0.0	.|.	.|485;485	.|Q9NSY1;Q4W5H2	.|BMP2K_HUMAN;.	P|H	178|485;485;499	.|ENSP00000421768:Q485H;ENSP00000334836:Q485H	.|ENSP00000264889:Q499H	A|Q	+|+	1|3	0|2	BMP2K|BMP2K	80011184|80011184	0.113000|0.113000	0.22115|0.22115	0.097000|0.097000	0.21041|0.21041	0.022000|0.022000	0.10575|0.10575	-0.733000|-0.733000	0.04898|0.04898	-1.546000|-1.546000	0.01717|0.01717	-1.555000|-1.555000	0.00892|0.00892	GCA|CAG	.	.	.	none		0.493	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
TUBB	203068	hgsc.bcm.edu	37	6	30691726	30691726	+	Missense_Mutation	SNP	C	C	G			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr6:30691726C>G	ENST00000327892.8	+	4	1193	c.887C>G	c.(886-888)gCc>gGc	p.A296G	TUBB_ENST00000396389.1_Missense_Mutation_p.A278G|TUBB_ENST00000330914.3_Missense_Mutation_p.A224G|TUBB_ENST00000396384.1_Missense_Mutation_p.A224G|TUBB_ENST00000435534.1_Intron|XXbac-BPG252P9.9_ENST00000607476.1_RNA	NM_178014.2	NP_821133.1	P07437	TBB5_HUMAN	tubulin, beta class I	296					cell division (GO:0051301)|cellular component movement (GO:0006928)|cellular process (GO:0009987)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|natural killer cell mediated cytotoxicity (GO:0042267)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cell body (GO:0044297)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nuclear envelope lumen (GO:0005641)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|kidney(8)|large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	16					Colchicine(DB01394)|Podofilox(DB01179)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)	GTCTTCGATGCCAAGAACATG	0.592																																					p.A296G		Atlas-SNP	.											.	TUBB	30	.	0			c.C887G						PASS	.						63.0	62.0	62.0					6																	30691726		2203	4300	6503	SO:0001583	missense	203068	exon4			TCGATGCCAAGAA	AB062393	CCDS4687.1	6p21.33	2011-10-10	2011-10-10		ENSG00000196230	ENSG00000196230		"""Tubulins"""	20778	protein-coding gene	gene with protein product	"""class I beta-tubulin"", ""beta1-tubulin"""	191130	"""tubulin, beta polypeptide"", ""tubulin, beta"""			11504633, 8270253	Standard	NM_001293212		Approved	OK/SW-cl.56, MGC16435, M40, Tubb5	uc003nrl.3	P07437	OTTHUMG00000031059	ENST00000327892.8:c.887C>G	chr6.hg19:g.30691726C>G	ENSP00000339001:p.Ala296Gly	39.0	0.0	.		47.0	16.0	.	NM_178014	P05218|Q8WUC1|Q9CY33	Missense_Mutation	SNP	ENST00000327892.8	hg19	CCDS4687.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.291594	0.40494	.	.	ENSG00000196230	ENST00000327892;ENST00000422827;ENST00000330914;ENST00000396389;ENST00000396384;ENST00000538863	D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52	4.25	4.25	0.50352	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87877	0.6288	H	0.97103	3.94	0.80722	D	1	B;B	0.20550	0.046;0.038	B;B	0.40782	0.34;0.23	D	0.89650	0.3869	10	0.87932	D	0	.	14.1681	0.65490	0.0:1.0:0.0:0.0	.	296;296	P07437;F8VW92	TBB5_HUMAN;.	G	296;205;224;278;224;150	ENSP00000339001:A296G;ENSP00000365578:A224G;ENSP00000379672:A278G;ENSP00000379668:A224G	ENSP00000339001:A296G	A	+	2	0	TUBB	30799705	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.377000	0.79668	2.204000	0.70986	0.591000	0.81541	GCC	.	.	.	none		0.592	TUBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076074.2	NM_178014	
SPDEF	25803	hgsc.bcm.edu	37	6	34506127	34506127	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr6:34506127T>C	ENST00000374037.3	-	6	1346	c.932A>G	c.(931-933)cAg>cGg	p.Q311R	SPDEF_ENST00000544425.1_Missense_Mutation_p.Q295R	NM_012391.2	NP_036523.1	O95238	SPDEF_HUMAN	SAM pointed domain containing ETS transcription factor	311					cell differentiation (GO:0030154)|intestinal epithelial cell development (GO:0060576)|lung goblet cell differentiation (GO:0060480)|multicellular organismal development (GO:0007275)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell fate commitment (GO:0010455)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)	15						CTTGTAATACTGGCGGATGGA	0.597																																					p.Q311R		Atlas-SNP	.											.	SPDEF	34	.	0			c.A932G						PASS	.						194.0	179.0	184.0					6																	34506127		2203	4300	6503	SO:0001583	missense	25803	exon6			TAATACTGGCGGA	AF071538	CCDS4794.1, CCDS59013.1	6p21.3	2013-08-07	2013-08-07		ENSG00000124664	ENSG00000124664			17257	protein-coding gene	gene with protein product		608144	"""SAM pointed domain containing ets transcription factor"""			10625666, 6857767	Standard	NM_012391		Approved	PDEF, bA375E1.3	uc003ojq.2	O95238	OTTHUMG00000014548	ENST00000374037.3:c.932A>G	chr6.hg19:g.34506127T>C	ENSP00000363149:p.Gln311Arg	180.0	0.0	.		94.0	11.0	.	NM_012391	B4DWH8|F5H778	Missense_Mutation	SNP	ENST00000374037.3	hg19	CCDS4794.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.045373	0.93685	.	.	ENSG00000124664	ENST00000374037;ENST00000544425	T;T	0.13307	2.6;2.6	5.55	5.55	0.83447	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (5);	0.000000	0.85682	D	0.000000	T	0.26340	0.0643	M	0.63428	1.95	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.996	T	0.01476	-1.1345	10	0.56958	D	0.05	.	15.6884	0.77430	0.0:0.0:0.0:1.0	.	295;311	F5H778;O95238	.;SPDEF_HUMAN	R	311;295	ENSP00000363149:Q311R;ENSP00000442715:Q295R	ENSP00000363149:Q311R	Q	-	2	0	SPDEF	34614105	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.027000	0.88791	2.108000	0.64289	0.533000	0.62120	CAG	.	.	.	none		0.597	SPDEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040246.1	NM_012391	
DNAH8	1769	hgsc.bcm.edu	37	6	38835956	38835956	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr6:38835956T>C	ENST00000359357.3	+	46	6415	c.6161T>C	c.(6160-6162)aTg>aCg	p.M2054T	DNAH8_ENST00000449981.2_Missense_Mutation_p.M2271T|DNAH8_ENST00000441566.1_Missense_Mutation_p.M2018T			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2054					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CTAAGAGATATGAACCTTTCC	0.358																																					p.M2271T		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T6812C						PASS	.						110.0	109.0	109.0					6																	38835956		2203	4300	6503	SO:0001583	missense	1769	exon48			GAGATATGAACCT	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.6161T>C	chr6.hg19:g.38835956T>C	ENSP00000352312:p.Met2054Thr	44.0	0.0	.		104.0	20.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.4|21.4	4.149799|4.149799	0.78001|0.78001	.|.	.|.	ENSG00000124721|ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566|ENST00000394393	T;T;T|.	0.18960|.	2.18;2.18;2.18|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.69342|.	0.3100|.	M|M	0.76328|0.76328	2.33|2.33	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|.	0.70753|.	-0.4786|.	10|.	0.87932|.	D|.	0|.	.|.	16.1376|16.1376	0.81497|0.81497	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2054|.	Q96JB1|.	DYH8_HUMAN|.	T|R	2259;2259;2054;2018|100	ENSP00000333363:M2259T;ENSP00000352312:M2054T;ENSP00000402294:M2018T|.	ENSP00000333363:M2259T|.	M|X	+|+	2|1	0|0	DNAH8|DNAH8	38943934|38943934	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	8.010000|8.010000	0.88615|0.88615	2.212000|2.212000	0.71576|0.71576	0.533000|0.533000	0.62120|0.62120	ATG|TGA	.	.	.	none		0.358	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
DST	667	hgsc.bcm.edu	37	6	56382076	56382076	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr6:56382076T>C	ENST00000361203.3	-	66	17324	c.17317A>G	c.(17317-17319)Aag>Gag	p.K5773E	DST_ENST00000370788.2_Missense_Mutation_p.K3687E|DST_ENST00000312431.6_3'UTR|DST_ENST00000421834.2_Missense_Mutation_p.K3796E|DST_ENST00000370754.5_Missense_Mutation_p.K6062E|DST_ENST00000340834.4_5'UTR|DST_ENST00000446842.2_Missense_Mutation_p.K5558E|DST_ENST00000370769.4_Missense_Mutation_p.K5884E|DST_ENST00000244364.6_Missense_Mutation_p.K3470E			Q03001	DYST_HUMAN	dystonin	5773					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ATAATATCCTTGTGTCTCAAA	0.328																																					p.K3470E		Atlas-SNP	.											.	DST	1427	.	0			c.A10408G						PASS	.						190.0	183.0	185.0					6																	56382076		1876	4096	5972	SO:0001583	missense	667	exon52			TATCCTTGTGTCT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.17317A>G	chr6.hg19:g.56382076T>C	ENSP00000354508:p.Lys5773Glu	14.0	0.0	.		34.0	11.0	.	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	T	19.78	3.891493	0.72524	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.45	5.45	0.79879	.	0.000000	0.53938	D	0.000044	T	0.59088	0.2168	M	0.71581	2.175	0.30416	N	0.778577	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.994	D;D;D;D;D	0.87578	0.998;0.992;0.998;0.998;0.941	T	0.58509	-0.7624	9	0.31617	T	0.26	.	15.8029	0.78471	0.0:0.0:0.0:1.0	.	3796;5884;6062;5882;3470	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	E	3470;6062;5884;3796;5558;3687;5773	ENSP00000244364:K3470E;ENSP00000359790:K6062E;ENSP00000359805:K5884E;ENSP00000400883:K3796E;ENSP00000393645:K5558E;ENSP00000359824:K3687E;ENSP00000354508:K5773E	ENSP00000244364:K3470E	K	-	1	0	DST	56490035	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.189000	0.69895	0.533000	0.62120	AAG	.	.	.	none		0.328	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
FAM46A	55603	hgsc.bcm.edu	37	6	82461742	82461742	+	Silent	SNP	G	G	A			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr6:82461742G>A	ENST00000320172.6	-	2	431	c.117C>T	c.(115-117)ggC>ggT	p.G39G	FAM46A_ENST00000369756.3_Silent_p.G120G|FAM46A_ENST00000369754.3_Silent_p.G58G	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	39			Missing. {ECO:0000269|PubMed:12054608, ECO:0000269|PubMed:16545789}.		regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		cgaagtcgccgccgccgaagt	0.667																																					p.G39G		Atlas-SNP	.											.	FAM46A	37	.	0			c.C117T						PASS	.						7.0	8.0	8.0					6																	82461742		1601	3424	5025	SO:0001819	synonymous_variant	55603	exon2			GTCGCCGCCGCCG	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"""chromosome 6 open reading frame 37"""	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.117C>T	chr6.hg19:g.82461742G>A		43.0	0.0	.		37.0	5.0	.	NM_017633	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Silent	SNP	ENST00000320172.6	hg19	CCDS34489.1																																																																																			.	.	.	none		0.667	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1		
GPR124	25960	hgsc.bcm.edu	37	8	37690712	37690712	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr8:37690712T>C	ENST00000412232.2	+	9	1295	c.1282T>C	c.(1282-1284)Tac>Cac	p.Y428H	GPR124_ENST00000315215.7_Missense_Mutation_p.Y428H	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	428					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			CAGGGTGCTGTACACCTTCGT	0.667																																					p.Y428H		Atlas-SNP	.											.	GPR124	85	.	0			c.T1282C						PASS	.						41.0	37.0	38.0					8																	37690712		2203	4297	6500	SO:0001583	missense	25960	exon9			GTGCTGTACACCT	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17849	protein-coding gene	gene with protein product	"""tumor endothelial marker 5"""	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.1282T>C	chr8.hg19:g.37690712T>C	ENSP00000406367:p.Tyr428His	51.0	0.0	.		27.0	8.0	.	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	T	12.84	2.058746	0.36277	.	.	ENSG00000020181	ENST00000416514;ENST00000315215;ENST00000412232	T;T	0.59502	0.26;0.26	5.11	5.11	0.69529	.	0.144593	0.47852	N	0.000209	T	0.41858	0.1177	N	0.16743	0.435	0.47094	D	0.999312	B;B	0.27416	0.178;0.009	B;B	0.29862	0.108;0.009	T	0.29119	-1.0022	10	0.15499	T	0.54	-21.7041	14.9163	0.70801	0.0:0.0:0.0:1.0	.	428;428	Q96PE1-2;Q96PE1	.;GP124_HUMAN	H	421;428;428	ENSP00000323508:Y428H;ENSP00000406367:Y428H	ENSP00000323508:Y428H	Y	+	1	0	GPR124	37809870	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.087000	0.50167	1.924000	0.55735	0.533000	0.62120	TAC	.	.	.	none		0.667	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2		
VPS13A	23230	hgsc.bcm.edu	37	9	79936242	79936242	+	Splice_Site	SNP	A	A	G			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr9:79936242A>G	ENST00000360280.3	+	43	5833	c.5573A>G	c.(5572-5574)aAg>aGg	p.K1858R	VPS13A_ENST00000376636.3_Splice_Site_p.K1819R|VPS13A_ENST00000376634.4_Splice_Site_p.K1858R|VPS13A_ENST00000357409.5_Splice_Site_p.K1858R	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1858					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AATTTAGTCAAGGTAAGAAAA	0.279																																					p.K1858R		Atlas-SNP	.											.	VPS13A	735	.	0			c.A5573G						PASS	.						26.0	26.0	26.0					9																	79936242		2195	4278	6473	SO:0001630	splice_region_variant	23230	exon43			TAGTCAAGGTAAG	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.5574+1A>G	chr9.hg19:g.79936242A>G		88.0	0.0	.		221.0	75.0	.	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.69|16.69	3.193752|3.193752	0.58017|0.58017	.|.	.|.	ENSG00000197969|ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409|ENST00000419472	T;T;T;T|.	0.50813|.	0.73;0.73;0.73;0.73|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.551714|.	0.20291|.	N|.	0.095247|.	T|T	0.63295|0.63295	0.2499|0.2499	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	B;P;B;B;B|.	0.44877|.	0.376;0.845;0.411;0.404;0.404|.	B;P;B;B;B|.	0.48677|.	0.108;0.586;0.055;0.234;0.234|.	T|T	0.61855|0.61855	-0.6977|-0.6977	10|5	0.44086|.	T|.	0.13|.	.|.	12.3993|12.3993	0.55404|0.55404	0.821:0.179:0.0:0.0|0.821:0.179:0.0:0.0	.|.	110;1819;1858;1858;1858|.	B1ALW4;Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4|.	.;.;VP13A_HUMAN;.;.|.	R|G	1858;1819;1858;1858|111	ENSP00000365821:K1858R;ENSP00000365823:K1819R;ENSP00000353422:K1858R;ENSP00000349985:K1858R|.	ENSP00000349985:K1858R|.	K|R	+|+	2|1	0|2	VPS13A|VPS13A	79126062|79126062	0.998000|0.998000	0.40836|0.40836	0.940000|0.940000	0.37924|0.37924	0.835000|0.835000	0.47333|0.47333	1.435000|1.435000	0.34969|0.34969	2.214000|2.214000	0.71695|0.71695	0.477000|0.477000	0.44152|0.44152	AAG|AGG	.	.	.	none		0.279	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	Missense_Mutation
ALKBH8	91801	hgsc.bcm.edu	37	11	107427686	107427686	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr11:107427686C>T	ENST00000428149.2	-	3	324	c.173G>A	c.(172-174)cGg>cAg	p.R58Q	ALKBH8_ENST00000389568.3_Missense_Mutation_p.R58Q|ALKBH8_ENST00000429370.1_Missense_Mutation_p.R58Q|ALKBH8_ENST00000417449.2_Missense_Mutation_p.R61Q|ALKBH8_ENST00000530933.1_5'UTR	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	58	RRM.				cellular response to DNA damage stimulus (GO:0006974)|tRNA methylation (GO:0030488)	cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|RNA binding (GO:0003723)|tRNA (uracil) methyltransferase activity (GO:0016300)			breast(2)|large_intestine(2)|lung(5)	9		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00512)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.53e-05)|Epithelial(105;0.00029)|all cancers(92;0.00518)		CAGCTGGTTCCGACTCACACC	0.433																																					p.R58Q		Atlas-SNP	.											.	ALKBH8	88	.	0			c.G173A						PASS	.						96.0	94.0	94.0					11																	107427686		2201	4298	6499	SO:0001583	missense	91801	exon3			TGGTTCCGACTCA	AF086489	CCDS8337.2, CCDS73376.1	11q22.3	2013-10-04			ENSG00000137760	ENSG00000137760	2.1.1.229	"""Alkylation repair homologs"", ""RNA binding motif (RRM) containing"""	25189	protein-coding gene	gene with protein product		613306				20123966	Standard	NM_138775		Approved	MGC10235	uc009yxp.3	Q96BT7	OTTHUMG00000157008	ENST00000428149.2:c.173G>A	chr11.hg19:g.107427686C>T	ENSP00000415885:p.Arg58Gln	74.0	0.0	.		139.0	48.0	.	NM_138775	B1Q2M0|B4DEF6|Q8N989	Missense_Mutation	SNP	ENST00000428149.2	hg19	CCDS8337.2	.	.	.	.	.	.	.	.	.	.	C	30	5.054614	0.93793	.	.	ENSG00000137760	ENST00000428149;ENST00000429370;ENST00000389568;ENST00000417449	T;T;T;T	0.45276	0.9;2.44;0.9;0.9	5.67	5.67	0.87782	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.64193	0.2576	M	0.61703	1.905	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.63919	-0.6528	10	0.59425	D	0.04	-18.0663	18.7588	0.91842	0.0:1.0:0.0:0.0	.	58	Q96BT7	ALKB8_HUMAN	Q	58;58;58;61	ENSP00000415885:R58Q;ENSP00000391225:R58Q;ENSP00000374219:R58Q;ENSP00000397673:R61Q	ENSP00000260318:R58Q	R	-	2	0	ALKBH8	106932896	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	6.676000	0.74498	2.697000	0.92050	0.655000	0.94253	CGG	.	.	.	none		0.433	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775	
ITPR2	3709	hgsc.bcm.edu	37	12	26810812	26810812	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr12:26810812G>A	ENST00000381340.3	-	18	2436	c.2020C>T	c.(2020-2022)Caa>Taa	p.Q674*		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	674					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TTGTCTGCTTGCATTGAGACC	0.373																																					p.Q674X		Atlas-SNP	.											.	ITPR2	270	.	0			c.C2020T						PASS	.						100.0	91.0	94.0					12																	26810812		1861	4097	5958	SO:0001587	stop_gained	3709	exon18			CTGCTTGCATTGA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.2020C>T	chr12.hg19:g.26810812G>A	ENSP00000370744:p.Gln674*	80.0	0.0	.		106.0	30.0	.	NM_002223	O94773	Nonsense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	43	10.411246	0.99400	.	.	ENSG00000123104	ENST00000381340	.	.	.	4.4	4.4	0.53042	.	0.380582	0.29908	N	0.010886	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	17.5669	0.87922	0.0:0.0:1.0:0.0	.	.	.	.	X	674	.	ENSP00000370744:Q674X	Q	-	1	0	ITPR2	26702079	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.467000	0.66737	2.448000	0.82819	0.655000	0.94253	CAA	.	.	.	none		0.373	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
SIRT7	51547	hgsc.bcm.edu	37	17	79871988	79871988	+	Missense_Mutation	SNP	G	G	A	rs560137203		TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr17:79871988G>A	ENST00000328666.6	-	8	934	c.872C>T	c.(871-873)cCg>cTg	p.P291L	PCYT2_ENST00000570391.1_5'Flank|PCYT2_ENST00000538936.2_5'Flank|PCYT2_ENST00000571105.1_5'Flank|PCYT2_ENST00000331285.3_5'Flank|PCYT2_ENST00000538721.2_5'Flank|PCYT2_ENST00000570388.1_5'Flank	NM_016538.2	NP_057622.1	Q9NRC8	SIR7_HUMAN	sirtuin 7	291	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription on exit from mitosis (GO:0007072)|rRNA transcription (GO:0009303)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleolus organizer region (GO:0005731)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			GTAAAGCTTCGGCCGCCGGCT	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		19606	0.001		0.0	False		,,,				2504	0.0				p.P291L		Atlas-SNP	.											.	SIRT7	37	.	0			c.C872T						PASS	.						58.0	59.0	59.0					17																	79871988		2203	4300	6503	SO:0001583	missense	51547	exon8			AGCTTCGGCCGCC	AF233395	CCDS11792.1	17q25.3	2010-06-25	2010-06-25			ENSG00000187531			14935	protein-coding gene	gene with protein product		606212	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 7"", ""sirtuin (silent mating type information regulation 2 homolog) 7 (S. cerevisiae)"""			10873683, 16618798	Standard	NM_016538		Approved		uc002kcj.2	Q9NRC8		ENST00000328666.6:c.872C>T	chr17.hg19:g.79871988G>A	ENSP00000329466:p.Pro291Leu	145.0	0.0	.		82.0	4.0	.	NM_016538	A8K2K0|B3KSU8|Q3MIK4|Q9NSZ6|Q9NUS6	Missense_Mutation	SNP	ENST00000328666.6	hg19	CCDS11792.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.857274	0.71834	.	.	ENSG00000187531	ENST00000328666;ENST00000536038	T	0.15834	2.39	4.27	3.3	0.37823	.	0.000000	0.85682	D	0.000000	T	0.31389	0.0795	M	0.75884	2.315	0.80722	D	1	P;D	0.53151	0.953;0.958	B;P	0.52793	0.372;0.709	T	0.12091	-1.0561	10	0.56958	D	0.05	-21.8466	12.1883	0.54252	0.0829:0.0:0.9171:0.0	.	291;291	A8K2K0;Q9NRC8	.;SIRT7_HUMAN	L	291;274	ENSP00000329466:P291L	ENSP00000329466:P291L	P	-	2	0	SIRT7	77465280	1.000000	0.71417	0.992000	0.48379	0.659000	0.38960	9.121000	0.94375	1.034000	0.39945	0.549000	0.68633	CCG	.	.	.	none		0.572	SIRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439961.1	NM_016538	
MUC16	94025	hgsc.bcm.edu	37	19	9062897	9062897	+	Silent	SNP	G	G	A			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr19:9062897G>A	ENST00000397910.4	-	3	24752	c.24549C>T	c.(24547-24549)atC>atT	p.I8183I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8185	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGAGTCTGGTGATGGTTTCTG	0.488																																					p.I8183I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C24549T						PASS	.						121.0	116.0	118.0					19																	9062897		2075	4211	6286	SO:0001819	synonymous_variant	94025	exon3			TCTGGTGATGGTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.24549C>T	chr19.hg19:g.9062897G>A		43.0	0.0	.		54.0	24.0	.	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.	.	none		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PRDM15	63977	hgsc.bcm.edu	37	21	43230577	43230577	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr21:43230577T>G	ENST00000269844.3	-	28	3793	c.3683A>C	c.(3682-3684)cAg>cCg	p.Q1228P	PRDM15_ENST00000398548.1_Missense_Mutation_p.Q899P|PRDM15_ENST00000422911.1_Missense_Mutation_p.Q919P|PRDM15_ENST00000538201.1_Missense_Mutation_p.Q882P|PRDM15_ENST00000447207.2_Missense_Mutation_p.Q862P|PRDM15_ENST00000470586.1_5'UTR	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1228					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						CCCGCACAGCTGGCAGCTCTG	0.647																																					p.Q1228P		Atlas-SNP	.											.	PRDM15	110	.	0			c.A3683C						PASS	.						91.0	60.0	71.0					21																	43230577		2203	4299	6502	SO:0001583	missense	63977	exon28			CACAGCTGGCAGC	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.3683A>C	chr21.hg19:g.43230577T>G	ENSP00000269844:p.Gln1228Pro	76.0	0.0	.		38.0	13.0	.	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	hg19	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	t	21.2	4.114809	0.77210	.	.	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000538201;ENST00000447207;ENST00000269844	T;T;T;T;T	0.08008	4.82;4.82;4.82;4.82;3.14	4.11	4.11	0.48088	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	.	.	.	.	T	0.11067	0.0270	N	0.14661	0.345	0.43868	D	0.996471	D;D;D	0.62365	0.961;0.989;0.991	P;P;P	0.57468	0.815;0.767;0.821	T	0.16600	-1.0397	9	0.54805	T	0.06	-30.9208	12.2904	0.54815	0.0:0.0:0.0:1.0	.	1228;919;899	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	P	919;899;882;862;1228	ENSP00000408592:Q919P;ENSP00000381556:Q899P;ENSP00000444044:Q882P;ENSP00000390245:Q862P;ENSP00000269844:Q1228P	ENSP00000269844:Q1228P	Q	-	2	0	PRDM15	42103646	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.744000	0.85034	1.496000	0.48567	0.255000	0.18592	CAG	.	.	.	none		0.647	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
DMD	1756	hgsc.bcm.edu	37	X	31462641	31462641	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chrX:31462641A>C	ENST00000357033.4	-	60	9247	c.9041T>G	c.(9040-9042)cTc>cGc	p.L3014R	DMD_ENST00000541735.1_Missense_Mutation_p.L554R|DMD_ENST00000378677.2_Missense_Mutation_p.L3010R|DMD_ENST00000343523.2_Missense_Mutation_p.L554R|DMD_ENST00000359836.1_Missense_Mutation_p.L554R|DMD_ENST00000474231.1_Missense_Mutation_p.L554R|DMD_ENST00000378707.3_Missense_Mutation_p.L554R	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3014					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				CAGAGTGCTGAGGTTATACGG	0.448																																					p.L3014R		Atlas-SNP	.											.	DMD	2127	.	0			c.T9041G	GRCh37	CD054319	DMD	D		PASS	.						148.0	119.0	129.0					X																	31462641		2202	4300	6502	SO:0001583	missense	1756	exon60			GTGCTGAGGTTAT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.9041T>G	chrX.hg19:g.31462641A>C	ENSP00000354923:p.Leu3014Arg	37.0	0.0	.		123.0	58.0	.	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.625732	0.66901	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231	T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	5.56	5.56	0.83823	.	0.000000	0.30911	U	0.008637	T	0.61160	0.2325	M	0.62723	1.935	0.49213	D	0.999766	P;D;D;D;D;B;P;P;D;D;P	0.76494	0.951;0.999;0.986;0.997;0.997;0.185;0.741;0.741;0.999;0.999;0.934	P;D;P;D;D;B;P;B;D;D;P	0.71184	0.699;0.969;0.876;0.952;0.952;0.187;0.67;0.395;0.972;0.952;0.685	T	0.58487	-0.7628	10	0.10902	T	0.67	.	13.5718	0.61851	1.0:0.0:0.0:0.0	.	3006;3014;3010;1673;1670;554;554;554;554;554;2891	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3	.;DMD_HUMAN;.;.;.;.;.;.;.;.;.	R	3006;1673;1670;710;3010;3014;554;554;3014;2891;554;554;554	ENSP00000350765:L710R;ENSP00000367948:L3010R;ENSP00000354923:L3014R;ENSP00000352894:L554R;ENSP00000340057:L554R;ENSP00000367979:L554R;ENSP00000444119:L554R;ENSP00000417123:L554R	ENSP00000340057:L554R	L	-	2	0	DMD	31372562	1.000000	0.71417	0.982000	0.44146	0.871000	0.50021	6.407000	0.73280	1.848000	0.53677	0.437000	0.28790	CTC	.	.	.	none		0.448	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
TIMP1	7076	hgsc.bcm.edu	37	X	47445924	47445924	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chrX:47445924T>G	ENST00000218388.4	+	6	628	c.458T>G	c.(457-459)tTt>tGt	p.F153C	MIR4769_ENST00000584126.1_RNA|SYN1_ENST00000340666.4_Intron|SYN1_ENST00000295987.7_Intron|TIMP1_ENST00000377017.1_Missense_Mutation_p.F89C	NM_003254.2	NP_003245.1	P01033	TIMP1_HUMAN	TIMP metallopeptidase inhibitor 1	153					aging (GO:0007568)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of trophoblast cell migration (GO:1901164)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell proliferation (GO:0008284)|regulation of integrin-mediated signaling pathway (GO:2001044)|response to cytokine (GO:0034097)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	cytokine activity (GO:0005125)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|large_intestine(2)	3						TTCCAGGTGTTTCCCTGTTTA	0.577																																					p.F153C		Atlas-SNP	.											.	TIMP1	12	.	0			c.T458G						PASS	.						138.0	106.0	117.0					X																	47445924		2203	4300	6503	SO:0001583	missense	7076	exon6			AGGTGTTTCCCTG		CCDS14281.1	Xp11.3-p11.23	2008-07-29	2005-08-08		ENSG00000102265	ENSG00000102265			11820	protein-coding gene	gene with protein product		305370	"""tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor)"""	TIMP, CLGI			Standard	XM_005272645		Approved	EPO	uc004dif.3	P01033	OTTHUMG00000021447	ENST00000218388.4:c.458T>G	chrX.hg19:g.47445924T>G	ENSP00000218388:p.Phe153Cys	79.0	0.0	.		46.0	18.0	.	NM_003254	Q14252|Q9UCU1	Missense_Mutation	SNP	ENST00000218388.4	hg19	CCDS14281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.76|15.76	2.929866|2.929866	0.52759|0.52759	.|.	.|.	ENSG00000102265|ENSG00000102265	ENST00000218388;ENST00000377017|ENST00000445623	D;D|D	0.93307|0.92858	-3.2;-3.2|-3.12	5.35|5.35	4.05|4.05	0.47172|0.47172	Tissue inhibitor of metalloproteinases-like, OB-fold (1);|.	0.712428|0.712428	0.12937|0.12937	N|N	0.426934|0.426934	D|D	0.91412|0.91412	0.7290|0.7290	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.64506|.	0.926|.	D|D	0.85916|0.85916	0.1443|0.1443	10|8	0.38643|0.14252	T|T	0.18|0.57	.|.	7.9867|7.9867	0.30216|0.30216	0.1993:0.0:0.0:0.8007|0.1993:0.0:0.0:0.8007	.|.	153|.	P01033|.	TIMP1_HUMAN|.	C|V	153;89|111	ENSP00000218388:F153C;ENSP00000366216:F89C|ENSP00000410983:F111V	ENSP00000218388:F153C|ENSP00000410983:F111V	F|F	+|+	2|1	0|0	TIMP1|TIMP1	47330868|47330868	0.944000|0.944000	0.32072|0.32072	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	1.733000|1.733000	0.38156|0.38156	1.793000|1.793000	0.52555|0.52555	0.425000|0.425000	0.28330|0.28330	TTT|TTC	.	.	.	none		0.577	TIMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056423.1	NM_003254	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350751	50350751	+	Missense_Mutation	SNP	G	G	C	rs201290098		TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chrX:50350751G>C	ENST00000289292.7	-	6	3674	c.3391C>G	c.(3391-3393)Cag>Gag	p.Q1131E	SHROOM4_ENST00000376020.2_Missense_Mutation_p.Q1131E|SHROOM4_ENST00000460112.3_Missense_Mutation_p.Q1015E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1131	Gln-rich.			KQQ -> QQQQKQQE (in Ref. 1; BAA86516 and 3; AAI51241). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					tcctcctcctgttgcttctgc	0.582																																					p.Q1131E		Atlas-SNP	.											.	SHROOM4	171	.	0			c.C3391G						PASS	.						15.0	14.0	15.0					X																	50350751		2199	4294	6493	SO:0001583	missense	57477	exon6			CCTCCTGTTGCTT	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3391C>G	chrX.hg19:g.50350751G>C	ENSP00000289292:p.Gln1131Glu	50.0	0.0	.		125.0	5.0	.	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.554911	0.00918	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.06449	3.3;3.3;3.3	4.89	-0.0454	0.13851	.	1.383290	0.04423	N	0.367895	T	0.03827	0.0108	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36456	-0.9747	10	0.02654	T	1	.	4.0399	0.09746	0.093:0.4322:0.3193:0.1556	.	1131	Q9ULL8	SHRM4_HUMAN	E	1131;1131;1015	ENSP00000289292:Q1131E;ENSP00000365188:Q1131E;ENSP00000421450:Q1015E	ENSP00000289292:Q1131E	Q	-	1	0	SHROOM4	50367491	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.374000	0.20501	-0.047000	0.13423	-0.434000	0.05882	CAG	.	.	.	weak		0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
HUWE1	10075	hgsc.bcm.edu	37	X	53627271	53627271	+	Splice_Site	SNP	T	T	C			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chrX:53627271T>C	ENST00000342160.3	-	28	3429		c.e28-2		HUWE1_ENST00000218328.8_Splice_Site|HUWE1_ENST00000262854.6_Splice_Site			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase						base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						GTTCCCCATCTACAGATGTAT	0.453																																					.		Atlas-SNP	.											.	HUWE1	724	.	0			c.2972-2A>G						PASS	.						60.0	49.0	53.0					X																	53627271		2201	4299	6500	SO:0001630	splice_region_variant	10075	exon30			CCCATCTACAGAT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.2972-2A>G	chrX.hg19:g.53627271T>C		30.0	0.0	.		98.0	4.0	.	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Splice_Site	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.757675	0.49468	.	.	ENSG00000086758	ENST00000342160;ENST00000427052;ENST00000262854;ENST00000218328	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6011	0.62020	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	HUWE1	53643996	1.000000	0.71417	0.883000	0.34634	0.741000	0.42261	5.399000	0.66314	1.855000	0.53841	0.425000	0.28330	.	.	.	.	none		0.453	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	Intron
SYVN1	84447	hgsc.bcm.edu	37	11	64898172	64898173	+	Frame_Shift_Ins	INS	-	-	G			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr11:64898172_64898173insG	ENST00000377190.3	-	11	1158_1159	c.1064_1065insC	c.(1063-1065)cctfs	p.P355fs	SYVN1_ENST00000526121.1_5'Flank|SYVN1_ENST00000526060.1_Frame_Shift_Ins_p.P355fs|SYVN1_ENST00000294256.8_Frame_Shift_Ins_p.P355fs|SYVN1_ENST00000307289.6_Frame_Shift_Ins_p.P304fs	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	355	Pro-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						GGTGGGGGGCAGGGGGTGGCCC	0.673																																					p.P355fs		Atlas-INDEL	.											.	SYVN1	55	.	0			c.1065_1066insC						PASS	.																																			SO:0001589	frameshift_variant	84447	exon11			.	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"""RING-type (C3HC4) zinc fingers"""	20738	protein-coding gene	gene with protein product	"""HMG-coA reductase degradation 1 homolog (S. cerevisiae)"""	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.1065dupC	chr11.hg19:g.64898177_64898177dupG	ENSP00000366395:p.Pro355fs	48.0	0.0	0		31.0	14.0	0.451613	NM_032431	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Frame_Shift_Ins	INS	ENST00000377190.3	hg19	CCDS31605.1																																																																																			.	.	.	none		0.673	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431	
ABCB5	340273	hgsc.bcm.edu	37	7	20739491	20739492	+	Frame_Shift_Ins	INS	-	-	T			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr7:20739491_20739492insT	ENST00000404938.2	+	18	2850_2851	c.2198_2199insT	c.(2197-2202)gaaattfs	p.EI733fs	ABCB5_ENST00000258738.6_Frame_Shift_Ins_p.EI288fs	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	733	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						CATGATGCAGAAATTTATTCCA	0.307																																					p.E733fs		Atlas-Indel,Pindel	.											.	ABCB5	357	.	0			c.2198_2199insT						PASS	.																																			SO:0001589	frameshift_variant	340273	exon18			.	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"""ATP binding cassette transporters / subfamily B"""	46	protein-coding gene	gene with protein product	"""P-glycoprotein ABCB5"", ""ATP-binding cassette protein"""	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	Exception_encountered	chr7.hg19:g.20739491_20739492insT	ENSP00000384881:p.Glu733fs	48.0	0.0	0		78.0	17.0	0.217949	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Frame_Shift_Ins	INS	ENST00000404938.2	hg19	CCDS55090.1																																																																																			.	.	.	none		0.307	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
