#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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_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	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
CROCCP2	84809	broad.mit.edu	37	1	16946438	16946438	+	lincRNA	SNP	G	G	A	rs28392876	byFrequency	TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr1:16946438G>A	ENST00000412962.1	-	0	1081				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											GCCTTCCGCCGGGCCAGCAGC	0.672																																						ENST00000412962.1																			0																																																			0							g.chr1:16946438G>A	AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16946438G>A														0	1081	-								Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																						0.672	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1	NR_026752.1		4	22	0	0	0	1	0	4	22				
MFGE8	4240	broad.mit.edu	37	15	89453043	89453043	+	Missense_Mutation	SNP	G	G	A	rs34449331	byFrequency	TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr15:89453043G>A	ENST00000566497.1	-	2	246	c.185C>T	c.(184-186)gCg>gTg	p.A62V	MFGE8_ENST00000559997.1_Intron|MFGE8_ENST00000539437.1_Missense_Mutation_p.A54V|MFGE8_ENST00000542878.1_Intron|MFGE8_ENST00000268150.8_Missense_Mutation_p.A62V|MFGE8_ENST00000268151.7_Missense_Mutation_p.A62V			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	62	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					GTGGTTGCCCGCGTAGCCCTT	0.557													G|||	2	0.000399361	0.0	0.0	5008	,	,		22018	0.0		0.002	False		,,,				2504	0.0					ENST00000539437.1																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22						c.(160-162)gCg>gTg		milk fat globule-EGF factor 8 protein		G	VAL/ALA,VAL/ALA	4,4396	6.2+/-15.9	0,4,2196	166.0	129.0	142.0		185,185	-6.0	0.0	15	dbSNP_126	142	10,8588	7.7+/-29.5	0,10,4289	yes	missense,missense	MFGE8	NM_001114614.1,NM_005928.2	64,64	0,14,6485	AA,AG,GG		0.1163,0.0909,0.1077	benign,benign	62/336,62/388	89453043	14,12984	2200	4299	6499	SO:0001583	missense	4240				angiogenesis|cell adhesion|interspecies interaction between organisms|single fertilization			g.chr15:89453043G>A	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"""sperm surface protein hP47"""	602281	"""sperm associated antigen 10"""	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.185C>T	15.37:g.89453043G>A	ENSP00000456281:p.Ala62Val					MFGE8_ENST00000542878.1_Intron|MFGE8_ENST00000268151.7_Missense_Mutation_p.A62V|MFGE8_ENST00000559997.1_Intron|MFGE8_ENST00000268150.8_Missense_Mutation_p.A62V|MFGE8_ENST00000566497.1_Missense_Mutation_p.A62V	p.A54V			Q08431	MFGM_HUMAN			3	297	-	Lung NSC(78;0.0392)|all_lung(78;0.077)		62			EGF-like.		B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Missense_Mutation	SNP	ENST00000566497.1	37	c.161C>T	CCDS10347.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	12.88	2.069097	0.36470	9.09E-4	0.001163	ENSG00000140545	ENST00000268150;ENST00000268151;ENST00000539437	D;D;D	0.92545	-3.06;-3.06;-3.06	5.39	-6.03	0.02185	EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.864442	0.10595	N	0.656338	T	0.76891	0.4051	N	0.11131	0.1	0.09310	N	1	B;B;B;B	0.27140	0.075;0.169;0.005;0.028	B;B;B;B	0.22386	0.039;0.017;0.004;0.022	T	0.66548	-0.5896	10	0.20519	T	0.43	-0.113	6.3419	0.21327	0.3322:0.0:0.5003:0.1675	rs34449331	54;54;62;62	B3KTQ2;F5H7N9;Q08431-3;Q08431	.;.;.;MFGM_HUMAN	V	62;62;54	ENSP00000268150:A62V;ENSP00000268151:A62V;ENSP00000442386:A54V	ENSP00000268150:A62V	A	-	2	0	MFGE8	87254047	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.189000	0.17037	-0.550000	0.06183	-0.459000	0.05422	GCG		0.557	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928		5	130	0	0	0	1	0	5	130				
TELO2	9894	broad.mit.edu	37	16	1550606	1550606	+	Missense_Mutation	SNP	A	A	G			TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr16:1550606A>G	ENST00000262319.6	+	9	1466	c.1187A>G	c.(1186-1188)gAc>gGc	p.D396G		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	396					regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				TGCCGCCTGGACAGTAGCCTG	0.701																																						ENST00000262319.6																			0				NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19						c.(1186-1188)gAc>gGc		telomere maintenance 2							30.0	33.0	32.0					16																	1550606		2196	4297	6493	SO:0001583	missense	9894					chromosome, telomeric region|cytoplasm|membrane|nucleus	protein binding	g.chr16:1550606A>G	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"""TEL2, telomere maintenance 2, homolog (S. cerevisiae)"""			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.1187A>G	16.37:g.1550606A>G	ENSP00000262319:p.Asp396Gly						p.D396G	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN			9	1466	+		Hepatocellular(780;0.219)	396					D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	c.1187A>G	CCDS32363.1	.	.	.	.	.	.	.	.	.	.	a	23.4	4.406855	0.83230	.	.	ENSG00000100726	ENST00000437914;ENST00000262319	D	0.84660	-1.88	4.93	4.93	0.64822	.	0.044947	0.85682	D	0.000000	D	0.90086	0.6903	M	0.76002	2.32	0.58432	D	0.999999	D	0.76494	0.999	D	0.67103	0.949	D	0.87903	0.2692	10	0.15499	T	0.54	-36.8244	13.6054	0.62044	1.0:0.0:0.0:0.0	.	396	Q9Y4R8	TELO2_HUMAN	G	10;396	ENSP00000262319:D396G	ENSP00000262319:D396G	D	+	2	0	TELO2	1490607	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.877000	0.63086	1.866000	0.54105	0.529000	0.55759	GAC		0.701	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111		3	26	0	0	0	1	0	3	26				
ATXN7	6314	broad.mit.edu	37	3	63981655	63981655	+	Silent	SNP	C	C	T	rs377376951	byFrequency	TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr3:63981655C>T	ENST00000295900.6	+	12	2707	c.2157C>T	c.(2155-2157)tcC>tcT	p.S719S	ATXN7_ENST00000487717.1_Silent_p.S719S|ATXN7_ENST00000484332.1_Silent_p.S574S|ATXN7_ENST00000538065.1_Silent_p.S719S|ATXN7_ENST00000398590.3_Silent_p.S719S	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	719	Poly-Ser.|Ser-rich.				cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		Actcttcctcctcctcttcct	0.498													C|||	2	0.000399361	0.0	0.0	5008	,	,		17985	0.0		0.002	False		,,,				2504	0.0					ENST00000398590.3																			0				NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35						c.(2155-2157)tcC>tcT		ataxin 7		C	,,	0,4326		0,0,2163	56.0	67.0	63.0		2157,1722,2157	1.2	0.2	3		63	11,8547		0,11,4268	no	coding-synonymous,coding-synonymous,coding-synonymous	ATXN7	NM_000333.3,NM_001128149.2,NM_001177387.1	,,	0,11,6431	TT,TC,CC		0.1285,0.0,0.0854	,,	719/893,574/748,719/946	63981655	11,12873	2163	4279	6442	SO:0001819	synonymous_variant	6314				cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding	g.chr3:63981655C>T	AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"""Ataxins"""	10560	protein-coding gene	gene with protein product		607640	"""spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"""	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.2157C>T	3.37:g.63981655C>T						ATXN7_ENST00000295900.6_Silent_p.S719S|ATXN7_ENST00000538065.1_Silent_p.S719S|ATXN7_ENST00000487717.1_Silent_p.S719S|ATXN7_ENST00000484332.1_Silent_p.S574S	p.S719S	NM_001177387.1	NP_001170858.1	O15265	ATX7_HUMAN		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)	12	2710	+		Prostate(884;0.0181)	719			Poly-Ser.|Ser-rich.		B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Silent	SNP	ENST00000295900.6	37	c.2157C>T	CCDS43102.1																																																																																				0.498	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333		4	70	0	0	0	1	0	4	70				
AGAP10	728127	broad.mit.edu	37	10	47207813	47207813	+	Splice_Site	SNP	T	T	C	rs202014361	byFrequency	TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr10:47207813T>C	ENST00000452145.2	-	4	506	c.395A>G	c.(394-396)cAt>cGt	p.H132R	AGAP10_ENST00000413193.2_Splice_Site_p.H228R|AGAP10_ENST00000355232.3_Splice_Site_p.H157R|RP11-144G6.12_ENST00000605970.1_RNA			Q5T2P9	AGA10_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 10	132					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.H228R(20)		endometrium(5)|kidney(3)|lung(1)|prostate(2)|urinary_tract(1)	12						TTTACTTACATGGTTTGTACA	0.294																																						ENST00000355232.3																			20	Substitution - Missense(20)	p.H228R(20)	endometrium(10)|prostate(4)|kidney(4)|urinary_tract(2)	endometrium(5)|kidney(3)|lung(1)|prostate(2)|urinary_tract(1)	12						c.e5+1		ArfGAP with GTPase domain, ankyrin repeat and PH domain 10																																				SO:0001630	splice_region_variant	728127							g.chr10:47207813T>C	BC075841		10q11.22	2013-01-11	2008-09-22	2008-09-22	ENSG00000204172	ENSG00000204172		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23462	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 7"""	CTGLF7			Standard	XM_006709937		Approved	bA144G6.2		Q5T2P9	OTTHUMG00000018115	ENST00000452145.2:c.396+1A>G	10.37:g.47207813T>C						RP11-144G6.12_ENST00000605970.1_RNA|AGAP10_ENST00000452145.2_Splice_Site_p.H132_splice|AGAP10_ENST00000413193.2_Splice_Site_p.H228_splice	p.H157_splice							5	3482	-									Splice_Site	SNP	ENST00000452145.2	37	c.471_splice		.	.	.	.	.	.	.	.	.	.	t	0.012	-1.675265	0.00751	.	.	ENSG00000204172	ENST00000452145;ENST00000413193;ENST00000355232	D;T;D	0.87966	-2.32;2.68;-2.32	1.4	1.4	0.22301	.	0.264128	0.34555	N	0.003879	T	0.72486	0.3466	.	.	.	0.20764	N	0.999856	B	0.22003	0.063	B	0.19666	0.026	T	0.55471	-0.8136	9	0.16896	T	0.51	.	6.9024	0.24291	0.0:0.0:0.0:1.0	.	132	Q5T2P9	AGA10_HUMAN	R	132;228;157	ENSP00000392206:H132R;ENSP00000407436:H228R;ENSP00000347372:H157R	ENSP00000347372:H157R	H	-	2	0	AGAP10	46627819	1.000000	0.71417	1.000000	0.80357	0.105000	0.19272	3.704000	0.54815	0.898000	0.36418	0.163000	0.16589	CAT		0.294	AGAP10-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000047845.2	XM_001714786.2	Missense_Mutation	5	26	0	0	0	1	0	5	26				
TMEM50B	757	broad.mit.edu	37	21	34841166	34841166	+	Silent	SNP	A	A	G	rs201411977		TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr21:34841166A>G	ENST00000542230.2	-	2	241	c.27T>C	c.(25-27)cgT>cgC	p.R9R		NM_006134.6	NP_006125.2	P56557	TM50B_HUMAN	transmembrane protein 50B	9						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|ovary(1)|skin(1)	4						ATTCTGGCCAACGAAAATTAT	0.368													A|||	1	0.000199681	0.0	0.0	5008	,	,		17183	0.001		0.0	False		,,,				2504	0.0					ENST00000542230.2																			0				breast(1)|kidney(1)|ovary(1)|skin(1)	4						c.(25-27)cgT>cgC		transmembrane protein 50B							120.0	110.0	114.0					21																	34841166		2203	4300	6503	SO:0001819	synonymous_variant	757					endoplasmic reticulum|integral to membrane|plasma membrane		g.chr21:34841166A>G	AF045606	CCDS13625.1	21q22.1	2008-07-29	2005-06-02	2005-06-02	ENSG00000142188	ENSG00000142188			1280	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 4"""	C21orf4			Standard	NR_040016		Approved		uc002yrs.2	P56557	OTTHUMG00000065286	ENST00000542230.2:c.27T>C	21.37:g.34841166A>G							p.R9R	NM_006134.6	NP_006125.2	P56557	TM50B_HUMAN			2	241	-			9					B2R4L4|D3DSF1|O60537|Q5PY47	Silent	SNP	ENST00000542230.2	37	c.27T>C	CCDS13625.1																																																																																				0.368	TMEM50B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140080.5			4	88	0	0	0	1	0	4	88				
SDHAP1	255812	broad.mit.edu	37	3	195690118	195690118	+	RNA	SNP	G	G	A	rs189722989	byFrequency	TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr3:195690118G>A	ENST00000427841.1	-	0	2325					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		GTGCAGAAGCGTATAAAGACA	0.463													g|||	324	0.0646965	0.0257	0.1052	5008	,	,		18108	0.0952		0.0408	False		,,,				2504	0.0818				Ovarian(67;1158 1227 12109 20189 43170)	ENST00000427841.1																			0																																																			0							g.chr3:195690118G>A	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195690118G>A								NR_003264.2						0	2325	-									RNA	SNP	ENST00000427841.1	37																																																																																						0.463	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			2	2	0	0	0	1	0	2	2				
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	RNA	SNP	A	A	G	rs2257765		TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr10:38654432A>G	ENST00000494540.1	+	0	599					NR_003086.1				hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2																		TCATCTCGCAATGCAAGGAAA	0.453																																						ENST00000494540.1																			0																																																			0							g.chr10:38654432A>G			10p11.1	2011-06-29			ENSG00000099251	ENSG00000099251			28120	pseudogene	pseudogene						10544267	Standard	NR_003086		Approved	HSD17B7, bA291L22.1	uc010qex.1		OTTHUMG00000017993		10.37:g.38654432A>G								NR_003086.1						0	599	+									RNA	SNP	ENST00000494540.1	37																																																																																						0.453	HSD17B7P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000047631.2	NR_003086		4	45	0	0	0	1	0	4	45				
LOC101927924	101927924	broad.mit.edu	37	2	130697560	130697560	+	lincRNA	DEL	A	A	-			TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr2:130697560delA	ENST00000450840.1	+	0	346																											TATCTTTTGGAAAAAGGCACC	0.403																																						ENST00000450840.1																			0																																																			0							g.chr2:130697560delA																													2.37:g.130697560delA														0	346	+									RNA	DEL	ENST00000450840.1	37																																																																																						0.403	AC079776.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000331345.1			2	4						2	4	---	---	---	---
CNPY3	10695	broad.mit.edu	37	6	42897358	42897360	+	In_Frame_Del	DEL	TGC	TGC	-	rs570105218	byFrequency	TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr6:42897358_42897360delTGC	ENST00000372836.4	+	1	421_423	c.50_52delTGC	c.(49-54)ttgctg>ttg	p.17_18LL>L	CNPY3_ENST00000394142.3_In_Frame_Del_p.17_18LL>L	NM_006586.3	NP_006577.2	Q9BT09	CNPY3_HUMAN	canopy FGF signaling regulator 3	17					innate immune response (GO:0045087)|toll-like receptor signaling pathway (GO:0002224)	endoplasmic reticulum lumen (GO:0005788)		p.L25delL(1)		central_nervous_system(1)|endometrium(1)|lung(3)|ovary(1)	6	Colorectal(47;0.196)		all cancers(41;0.000954)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			CTTCTTCCCTtgctgctgctgct	0.695																																						ENST00000372836.4																			1	Deletion - In frame(1)	p.L25delL(1)	central_nervous_system(1)	central_nervous_system(1)|endometrium(1)|lung(3)|ovary(1)	6						c.(49-54)ttg>t		canopy FGF signaling regulator 3																																				SO:0001651	inframe_deletion	10695				innate immune response	endoplasmic reticulum		g.chr6:42897358_42897360delTGC	U80744	CCDS4875.1	6p21.1	2013-09-19	2013-07-23	2007-10-22	ENSG00000137161	ENSG00000137161		"""Trinucleotide (CAG) repeat containing"""	11968	protein-coding gene	gene with protein product		610774	"""trinucleotide repeat containing 5"", ""canopy 3 homolog (zebrafish)"""	TNRC5		9225980	Standard	NM_006586		Approved	CAG4A	uc003ota.4	Q9BT09	OTTHUMG00000014708	ENST00000372836.4:c.50_52delTGC	6.37:g.42897367_42897369delTGC	ENSP00000361926:p.Leu25del					CNPY3_ENST00000394142.3_In_Frame_Del_p.LL23del	p.LL23del	NM_006586.3	NP_006577.2	Q9BT09	CNPY3_HUMAN	all cancers(41;0.000954)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)		1	421_423	+	Colorectal(47;0.196)		23					O15412|Q0P6I2|Q8NF54|Q8WTU8|Q9P0F2	In_Frame_Del	DEL	ENST00000372836.4	37	c.50_52delTGC	CCDS4875.1																																																																																				0.695	CNPY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040564.1	NM_006586		3	6						3	6	---	---	---	---
LMOD2	442721	broad.mit.edu	37	7	123301995	123301997	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr7:123301995_123301997delGAG	ENST00000458573.2	+	2	512_514	c.355_357delGAG	c.(355-357)gagdel	p.E124del	LMOD2_ENST00000456238.2_Intron	NM_207163.1	NP_997046.1	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	124	Glu-rich.					cytoskeleton (GO:0005856)											AGTGTATACAgaggaggaggagg	0.409																																						ENST00000458573.2																			0											c.(355-357)del		leiomodin 2 (cardiac)				66,3558		3,60,1749						-9.4	0.0			37	117,7687		5,107,3790	no	coding	LMOD2	NM_207163.1		8,167,5539	A1A1,A1R,RR		1.4992,1.8212,1.6013				183,11245				SO:0001651	inframe_deletion	442721					cytoskeleton	actin binding|tropomyosin binding	g.chr7:123301995_123301997delGAG	AC006333	CCDS47693.1	7q31.32	2008-08-08			ENSG00000170807	ENSG00000170807			6648	protein-coding gene	gene with protein product		608006					Standard	NM_207163		Approved		uc003vky.2	Q6P5Q4	OTTHUMG00000157149	ENST00000458573.2:c.355_357delGAG	7.37:g.123302004_123302006delGAG	ENSP00000411932:p.Glu124del					LMOD2_ENST00000456238.2_Intron	p.E124del	NM_207163.1	NP_997046.1	Q6P5Q4	LMOD2_HUMAN			2	512_514	+			124			Glu-rich.		A4D0W9|A4D0Y2|Q8WVJ8	In_Frame_Del	DEL	ENST00000458573.2	37	c.355_357delGAG	CCDS47693.1																																																																																				0.409	LMOD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348525.1			2	4						2	4	---	---	---	---
AGAP6	414189	broad.mit.edu	37	10	51748528	51748529	+	Frame_Shift_Ins	INS	-	-	C	rs555930275|rs375532834		TCGA-EJ-A46B-01A-31D-A257-08	TCGA-EJ-A46B-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71680fa7-bf45-4381-828f-0cc1f73a13c6	94207d64-f627-4ce4-b463-6ea128d2ad79	g.chr10:51748528_51748529insC	ENST00000374056.4	+	1	451_452	c.53_54insC	c.(52-57)gaccagfs	p.Q19fs	AGAP6_ENST00000412531.3_Frame_Shift_Ins_p.Q19fs			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	19					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						CTCGAGTTTGACCAGCAGCAGG	0.604																																						ENST00000374056.4																			0				NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						c.(52-54)gcafs		ArfGAP with GTPase domain, ankyrin repeat and PH domain 6																																				SO:0001589	frameshift_variant	414189				regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding	g.chr10:51748528_51748529insC		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.55dupC	10.37:g.51748530_51748530dupC	ENSP00000363168:p.Gln19fs					AGAP6_ENST00000412531.3_Frame_Shift_Ins_p.A18fs	p.A18fs			C9IYN2	C9IYN2_HUMAN			1	451_452	+			18						Frame_Shift_Ins	INS	ENST00000374056.4	37	c.53_54insC																																																																																					0.604	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665		4	5						4	5	---	---	---	---
