#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
RP11-24M17.5	0	broad.mit.edu	37	15	76074441	76074441	+	RNA	SNP	A	A	T			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr15:76074441A>T	ENST00000395215.3	+	0	620																											CGAGCTGCAGAGAAGCGGTCC	0.557																																						ENST00000395215.3																			0																																																			0							g.chr15:76074441A>T																													15.37:g.76074441A>T														0	620	+									RNA	SNP	ENST00000395215.3	37			.	.	.	.	.	.	.	.	.	.	.	3.651	-0.071454	0.07228	.	.	ENSG00000187812	ENST00000395215	.	.	.	0.437	0.437	0.16555	.	.	.	.	.	T	0.15478	0.0373	.	.	.	.	.	.	B	0.02656	0.0	B	0.04013	0.001	T	0.38001	-0.9681	6	0.02654	T	1	.	3.7635	0.08613	0.6336:0.0:0.0:0.3664	.	193	B4DZE6	.	S	193	.	ENSP00000378641:R193S	R	+	3	2	AC019294.2	73861496	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.070000	0.14573	-0.824000	0.04295	-1.485000	0.00982	AGA		0.557	RP11-24M17.5-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000420501.1			3	38	0	0	0	1	0	3	38				
GSTA1	2938	broad.mit.edu	37	6	52658986	52658986	+	Silent	SNP	T	T	C			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr6:52658986T>C	ENST00000334575.5	-	5	506	c.351A>G	c.(349-351)aaA>aaG	p.K117K	GSTA1_ENST00000493331.1_5'UTR	NM_145740.3	NP_665683.1	P08263	GSTA1_HUMAN	glutathione S-transferase alpha 1	117	GST C-terminal.		K -> Q (in dbSNP:rs1051757).		epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|metabolic process (GO:0008152)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	12	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Glutathione(DB00143)	GCTTGGCATCTTTTTCCTCAG	0.398																																						ENST00000334575.5																			0				large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	12						c.(349-351)aaA>aaG		glutathione S-transferase alpha 1	Amsacrine(DB00276)|Busulfan(DB01008)|Glutathione(DB00143)						209.0	202.0	205.0					6																	52658986		2203	4300	6503	SO:0001819	synonymous_variant	2938				glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity	g.chr6:52658986T>C		CCDS4945.1	6p12.2	2012-06-21	2008-11-26		ENSG00000243955	ENSG00000243955	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4626	protein-coding gene	gene with protein product		138359	"""glutathione S-transferase A1"""			9503014	Standard	NM_145740		Approved		uc003paz.3	P08263	OTTHUMG00000014861	ENST00000334575.5:c.351A>G	6.37:g.52658986T>C						GSTA1_ENST00000493331.1_5'UTR	p.K117K	NM_145740.3	NP_665683.1	P08263	GSTA1_HUMAN			5	506	-	Lung NSC(77;0.118)		117		K -> Q (in dbSNP:rs1051757).	GST C-terminal.		Q14750|Q5GHF8|Q5SZC1	Silent	SNP	ENST00000334575.5	37	c.351A>G	CCDS4945.1																																																																																				0.398	GSTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040922.1			4	194	0	0	0	1	0	4	194				
RP11-24M17.5	0	broad.mit.edu	37	15	76074431	76074431	+	RNA	SNP	C	C	T	rs371238897		TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr15:76074431C>T	ENST00000395215.3	+	0	610																		p.S190L(2)									CTCCAGTCCTCGAGCTGCAGA	0.547																																						ENST00000395215.3																			2	Substitution - Missense(2)	p.S190L(2)	endometrium(2)																																																0							g.chr15:76074431C>T																													15.37:g.76074431C>T														0	610	+									RNA	SNP	ENST00000395215.3	37			.	.	.	.	.	.	.	.	.	.	.	3.205	-0.162863	0.06502	.	.	ENSG00000187812	ENST00000395215	.	.	.	0.789	0.789	0.18607	.	.	.	.	.	T	0.29850	0.0746	.	.	.	.	.	.	B	0.20550	0.046	B	0.15870	0.014	T	0.30208	-0.9986	6	0.27082	T	0.32	.	7.4893	0.27452	0.0:0.9999:0.0:1.0E-4	.	190	B4DZE6	.	L	190	.	ENSP00000378641:S190L	S	+	2	0	AC019294.2	73861486	0.987000	0.35691	0.013000	0.15412	0.024000	0.10985	3.310000	0.51911	0.745000	0.32763	0.274000	0.19336	TCG		0.547	RP11-24M17.5-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000420501.1			3	34	0	0	0	1	0	3	34				
LINC00969	440993	broad.mit.edu	37	3	195400728	195400728	+	lincRNA	SNP	A	A	G	rs12107841	byFrequency	TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr3:195400728A>G	ENST00000445430.1	+	0	1324									long intergenic non-protein coding RNA 969																		GATTGTGCCCAGCCTGTACGC	0.587																																						ENST00000445430.1																			0																																																			440993							g.chr3:195400728A>G	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195400728A>G														0	1324	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.587	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			4	23	0	0	0	1	0	4	23				
ARSI	340075	broad.mit.edu	37	5	149677492	149677492	+	Missense_Mutation	SNP	G	G	T			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr5:149677492G>T	ENST00000328668.7	-	2	1574	c.995C>A	c.(994-996)cCc>cAc	p.P332H		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	332					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTTGAGCAGGGGACTGTGGAC	0.637																																						ENST00000328668.7																			0				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	23						c.(994-996)cCc>cAc		arylsulfatase family, member I							42.0	42.0	42.0					5																	149677492		2203	4300	6503	SO:0001583	missense	340075					endoplasmic reticulum|extracellular region	arylsulfatase activity|metal ion binding	g.chr5:149677492G>T	AY875937	CCDS34275.1	5q32	2014-03-03	2006-03-07			ENSG00000183876		"""Arylsulfatase family"""	32521	protein-coding gene	gene with protein product		610009	"""arylsulfatase I"""			16174644, 24482476	Standard	NM_001012301		Approved	FLJ16069, SPG66	uc003lrv.2	Q5FYB1		ENST00000328668.7:c.995C>A	5.37:g.149677492G>T	ENSP00000333395:p.Pro332His						p.P332H	NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		2	1574	-			332					A1L3B0|B3KV22|B7XD03	Missense_Mutation	SNP	ENST00000328668.7	37	c.995C>A	CCDS34275.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.001068	0.74818	.	.	ENSG00000183876	ENST00000328668;ENST00000515301	D;D	0.99488	-6.0;-6.0	4.46	4.46	0.54185	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.99680	0.9880	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97370	0.9975	10	0.72032	D	0.01	.	17.6599	0.88189	0.0:0.0:1.0:0.0	.	332	Q5FYB1	ARSI_HUMAN	H	332;189	ENSP00000333395:P332H;ENSP00000426879:P189H	ENSP00000333395:P332H	P	-	2	0	ARSI	149657685	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.601000	0.98297	2.460000	0.83146	0.561000	0.74099	CCC		0.637	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301		7	31	1	0	3.09899e-07	1	3.09899e-07	7	31				
SF3A3	10946	broad.mit.edu	37	1	38455621	38455621	+	Missense_Mutation	SNP	T	T	C			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr1:38455621T>C	ENST00000373019.4	-	1	972	c.17A>G	c.(16-18)gAg>gGg	p.E6G	RNU6-510P_ENST00000391239.1_RNA|SF3A3_ENST00000448721.2_Missense_Mutation_p.E6G|SF3A3_ENST00000489537.1_5'Flank	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	6					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CCGCTGCTGCTCCAGTATTGT	0.592											OREG0013386	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000373019.4																			0				breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12						c.(16-18)gAg>gGg		splicing factor 3a, subunit 3, 60kDa							114.0	104.0	107.0					1																	38455621		2203	4300	6503	SO:0001583	missense	10946				nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nuclear speck	nucleic acid binding|protein binding|zinc ion binding	g.chr1:38455621T>C	U08815	CCDS428.1	1p34.3	2012-06-07	2002-08-29		ENSG00000183431	ENSG00000183431			10767	protein-coding gene	gene with protein product		605596	"""splicing factor 3a, subunit 3, 60kD"""			7816610, 8022796	Standard	NM_006802		Approved	SF3a60, SAP61, PRP9, PRPF9	uc001cci.3	Q12874	OTTHUMG00000004438	ENST00000373019.4:c.17A>G	1.37:g.38455621T>C	ENSP00000362110:p.Glu6Gly		OREG0013386	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	878	SF3A3_ENST00000448721.2_Missense_Mutation_p.E6G	p.E6G	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN			1	972	-	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)	6					D3DPT5|Q15460|Q5VT87	Missense_Mutation	SNP	ENST00000373019.4	37	c.17A>G	CCDS428.1	.	.	.	.	.	.	.	.	.	.	T	32	5.127112	0.94429	.	.	ENSG00000183431	ENST00000373019;ENST00000448721	.	.	.	4.86	4.86	0.63082	.	0.047751	0.85682	D	0.000000	D	0.85869	0.5797	M	0.93328	3.405	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.979	D	0.89739	0.3932	9	0.87932	D	0	-24.9809	14.9046	0.70709	0.0:0.0:0.0:1.0	.	6;6	E7EUT8;Q12874	.;SF3A3_HUMAN	G	6	.	ENSP00000362110:E6G	E	-	2	0	SF3A3	38228208	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	7.532000	0.81985	2.171000	0.68590	0.377000	0.23210	GAG		0.592	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802		6	63	0	0	0	1	0	6	63				
ARNTL	406	broad.mit.edu	37	11	13402802	13402802	+	Splice_Site	SNP	G	G	A			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr11:13402802G>A	ENST00000403290.1	+	18	1972		c.e18+1		ARNTL_ENST00000401424.1_Splice_Site|ARNTL_ENST00000389707.4_Splice_Site|ARNTL_ENST00000361003.4_Splice_Site|ARNTL_ENST00000396441.3_Splice_Site|ARNTL_ENST00000389708.3_Splice_Site|ARNTL_ENST00000403482.3_Splice_Site|ARNTL_ENST00000403510.3_Splice_Site			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like						circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of cell cycle (GO:0051726)|regulation of cellular senescence (GO:2000772)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|nuclear body (GO:0016604)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|Hsp90 protein binding (GO:0051879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|signal transducer activity (GO:0004871)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20				Epithelial(150;0.0243)		AGGCAAGAAGGTAAGACTGAT	0.502																																						ENST00000389708.3																			0				breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20						c.e18+1		aryl hydrocarbon receptor nuclear translocator-like							111.0	98.0	103.0					11																	13402802		2200	4294	6494	SO:0001630	splice_region_variant	406				circadian rhythm|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	aryl hydrocarbon receptor binding|DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity	g.chr11:13402802G>A	D89722	CCDS31430.1, CCDS44543.1, CCDS73259.1	11p15	2013-05-21			ENSG00000133794	ENSG00000133794		"""Basic helix-loop-helix proteins"""	701	protein-coding gene	gene with protein product		602550				9144434, 9079689	Standard	XM_005252930		Approved	MOP3, JAP3, BMAL1, PASD3, bHLHe5	uc001mkp.3	O00327	OTTHUMG00000150623	ENST00000403290.1:c.1617+1G>A	11.37:g.13402802G>A						ARNTL_ENST00000403510.3_Splice_Site|ARNTL_ENST00000403482.3_Splice_Site|ARNTL_ENST00000401424.1_Splice_Site|ARNTL_ENST00000396441.3_Splice_Site|ARNTL_ENST00000389707.4_Splice_Site|ARNTL_ENST00000361003.4_Splice_Site|ARNTL_ENST00000403290.1_Splice_Site				O00327	BMAL1_HUMAN		Epithelial(150;0.0243)	18	2067	+								A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	Splice_Site	SNP	ENST00000403290.1	37			.	.	.	.	.	.	.	.	.	.	G	28.2	4.899610	0.91962	.	.	ENSG00000133794	ENST00000396441;ENST00000389707;ENST00000401424;ENST00000403290;ENST00000361003;ENST00000403510;ENST00000339640;ENST00000403482	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3418	0.94344	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARNTL	13359378	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.340000	0.97038	2.731000	0.93534	0.650000	0.86243	.		0.502	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178	Intron	3	37	0	0	0	1	0	3	37				
EPAS1	2034	broad.mit.edu	37	2	46607406	46607406	+	Missense_Mutation	SNP	A	A	G			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr2:46607406A>G	ENST00000263734.3	+	12	2105	c.1595A>G	c.(1594-1596)tAt>tGt	p.Y532C		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	532	NTAD.				angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			CTGGCACCCTATATCCCCATG	0.587																																						ENST00000263734.3																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						c.(1594-1596)tAt>tGt		endothelial PAS domain protein 1							84.0	92.0	89.0					2																	46607406		2203	4300	6503	SO:0001583	missense	2034				angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia	transcription factor complex	histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding	g.chr2:46607406A>G	U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"""Basic helix-loop-helix proteins"""	3374	protein-coding gene	gene with protein product	"""HIF-1 alpha-like factor"""	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.1595A>G	2.37:g.46607406A>G	ENSP00000263734:p.Tyr532Cys						p.Y532C	NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	LUSC - Lung squamous cell carcinoma(58;0.151)		12	2105	+		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	532			NTAD.		Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	37	c.1595A>G	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.246852	0.80024	.	.	ENSG00000116016	ENST00000263734	D	0.98400	-4.91	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.98673	0.9555	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99861	1.1083	10	0.87932	D	0	.	14.8316	0.70153	1.0:0.0:0.0:0.0	.	532	Q99814	EPAS1_HUMAN	C	532	ENSP00000263734:Y532C	ENSP00000263734:Y532C	Y	+	2	0	EPAS1	46460910	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.335000	0.96500	1.915000	0.55452	0.402000	0.26972	TAT		0.587	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430		75	10	0	0	0	1	0	75	10				
KRTAP4-11	653240	broad.mit.edu	37	17	39274214	39274214	+	Missense_Mutation	SNP	G	G	C			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr17:39274214G>C	ENST00000391413.2	-	1	392	c.354C>G	c.(352-354)agC>agG	p.S118R		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	118	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gtctgcagcagctggacacac	0.652																																						ENST00000391413.2																			0				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33						c.(352-354)agC>agG		keratin associated protein 4-11							4.0	8.0	7.0					17																	39274214		642	1521	2163	SO:0001583	missense	653240					keratin filament		g.chr17:39274214G>C	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.354C>G	17.37:g.39274214G>C	ENSP00000375232:p.Ser118Arg						p.S118R	NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	STAD - Stomach adenocarcinoma(17;0.000371)		1	392	-		Breast(137;0.000496)	118			27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	c.354C>G	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	11.65	1.702454	0.30232	.	.	ENSG00000212721	ENST00000391413	T	0.01963	4.53	3.63	2.63	0.31362	.	.	.	.	.	T	0.05914	0.0154	M	0.92691	3.335	0.25757	N	0.984995	B	0.18166	0.026	B	0.19391	0.025	T	0.23013	-1.0200	9	0.37606	T	0.19	.	5.3088	0.15819	0.1185:0.2126:0.6689:0.0	.	118	Q9BYQ6	KR411_HUMAN	R	118	ENSP00000375232:S118R	ENSP00000375232:S118R	S	-	3	2	KRTAP4-11	36527740	0.000000	0.05858	0.722000	0.30670	0.015000	0.08874	0.147000	0.16202	0.630000	0.30394	-0.413000	0.06143	AGC		0.652	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			3	28	0	0	0	1	0	3	28				
COL19A1	1310	broad.mit.edu	37	6	70854156	70854156	+	Splice_Site	SNP	G	G	A			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr6:70854156G>A	ENST00000322773.4	+	24	1782		c.e24+1		COL19A1_ENST00000393344.1_Splice_Site	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1						cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						AGGAGAAAAGGTATAGTTTAC	0.398																																						ENST00000322773.4																			0				breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						c.e24+1		collagen, type XIX, alpha 1							94.0	91.0	92.0					6																	70854156		2203	4300	6503	SO:0001630	splice_region_variant	1310				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging	g.chr6:70854156G>A		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.1680+1G>A	6.37:g.70854156G>A						COL19A1_ENST00000393344.1_Splice_Site		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN			24	1782	+								Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Splice_Site	SNP	ENST00000322773.4	37		CCDS4970.1	.	.	.	.	.	.	.	.	.	.	G	12.54	1.968438	0.34754	.	.	ENSG00000082293	ENST00000322773;ENST00000393344	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0673	0.86562	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL19A1	70910877	1.000000	0.71417	1.000000	0.80357	0.180000	0.23129	6.643000	0.74334	2.529000	0.85273	0.650000	0.86243	.		0.398	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		Intron	41	60	0	0	0	1	0	41	60				
EPS8	2059	broad.mit.edu	37	12	15800190	15800190	+	Missense_Mutation	SNP	G	G	C			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr12:15800190G>C	ENST00000281172.5	-	15	1875	c.1439C>G	c.(1438-1440)tCc>tGc	p.S480C	EPS8_ENST00000542903.1_Missense_Mutation_p.S220C|EPS8_ENST00000543523.1_Missense_Mutation_p.S480C|EPS8_ENST00000543612.1_Missense_Mutation_p.S480C|EPS8_ENST00000540613.1_Missense_Mutation_p.S220C	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	480					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		TGATACACTGGAATGCTGAAA	0.428																																						ENST00000281172.5																			0				NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						c.(1438-1440)tCc>tGc		epidermal growth factor receptor pathway substrate 8							114.0	108.0	110.0					12																	15800190		2203	4300	6503	SO:0001583	missense	2059				cell proliferation|epidermal growth factor receptor signaling pathway		SH3/SH2 adaptor activity	g.chr12:15800190G>C	U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.1439C>G	12.37:g.15800190G>C	ENSP00000281172:p.Ser480Cys					EPS8_ENST00000542903.1_Missense_Mutation_p.S220C|EPS8_ENST00000540613.1_Missense_Mutation_p.S220C|EPS8_ENST00000543612.1_Missense_Mutation_p.S480C|EPS8_ENST00000543523.1_Missense_Mutation_p.S480C	p.S480C	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)	15	1875	-		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)	480					A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Missense_Mutation	SNP	ENST00000281172.5	37	c.1439C>G	CCDS31753.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.183135	0.78677	.	.	ENSG00000151491	ENST00000543523;ENST00000281172;ENST00000543612;ENST00000540613;ENST00000542903;ENST00000543223	T;T;T;T;T	0.07800	3.3;3.3;3.3;3.16;3.16	4.26	4.26	0.50523	.	0.611997	0.16676	N	0.204157	T	0.20333	0.0489	L	0.55481	1.735	0.34207	D	0.673825	D	0.53885	0.963	P	0.55391	0.775	T	0.13899	-1.0492	10	0.52906	T	0.07	-3.756	17.2305	0.86983	0.0:0.0:1.0:0.0	.	480	Q12929	EPS8_HUMAN	C	480;480;480;220;220;480	ENSP00000441867:S480C;ENSP00000281172:S480C;ENSP00000442388:S480C;ENSP00000441888:S220C;ENSP00000437806:S220C	ENSP00000281172:S480C	S	-	2	0	EPS8	15691457	1.000000	0.71417	0.604000	0.28916	0.979000	0.70002	5.554000	0.67294	2.373000	0.80994	0.563000	0.77884	TCC		0.428	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			15	43	0	0	0	1	0	15	43				
ZNF507	22847	broad.mit.edu	37	19	32845169	32845169	+	Missense_Mutation	SNP	C	C	T			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr19:32845169C>T	ENST00000311921.4	+	2	1625	c.1433C>T	c.(1432-1434)gCc>gTc	p.A478V	ZNF507_ENST00000355898.5_Missense_Mutation_p.A478V|ZNF507_ENST00000544431.1_Missense_Mutation_p.A478V	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	478					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31	Esophageal squamous(110;0.162)					GATGAGAATGCCCCACCAGGC	0.448																																						ENST00000311921.3																			0				NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	31						c.(1432-1434)gCc>gTc		zinc finger protein 507							81.0	83.0	82.0					19																	32845169		2203	4300	6503	SO:0001583	missense	22847				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:32845169C>T	AB029007	CCDS32985.1	19q13.12	2008-02-05				ENSG00000168813		"""Zinc fingers, C2H2-type"""	23783	protein-coding gene	gene with protein product							Standard	NM_014910		Approved	KIAA1084	uc002ntd.3	Q8TCN5		ENST00000311921.4:c.1433C>T	19.37:g.32845169C>T	ENSP00000312277:p.Ala478Val					ZNF507_ENST00000587084.1_3'UTR|ZNF507_ENST00000355898.5_Missense_Mutation_p.A478V|ZNF507_ENST00000544431.1_Missense_Mutation_p.A478V	p.A478V	NM_001136156.1|NM_014910.4	NP_001129628.1|NP_055725.2	Q8TCN5	ZN507_HUMAN			2	1625	+	Esophageal squamous(110;0.162)		478					A8K911|Q2TBF1|Q6MZU0|Q9UPR8	Missense_Mutation	SNP	ENST00000311921.4	37	c.1433C>T	CCDS32985.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.579196	0.46006	.	.	ENSG00000168813	ENST00000355898;ENST00000311921;ENST00000544431	T;T;T	0.04603	3.9;3.9;3.59	5.79	5.79	0.91817	.	0.225147	0.47852	D	0.000220	T	0.05823	0.0152	L	0.49640	1.575	0.37926	D	0.931849	B;B	0.26400	0.06;0.148	B;B	0.27380	0.017;0.079	T	0.34551	-0.9824	10	0.12430	T	0.62	.	11.3463	0.49563	0.0:0.8607:0.0:0.1393	.	478;478	Q8TCN5;Q8TCN5-2	ZN507_HUMAN;.	V	478	ENSP00000348162:A478V;ENSP00000312277:A478V;ENSP00000441549:A478V	ENSP00000312277:A478V	A	+	2	0	ZNF507	37537009	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	4.366000	0.59492	2.722000	0.93159	0.655000	0.94253	GCC		0.448	ZNF507-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450301.3	NM_014910		3	45	0	0	0	1	0	3	45				
FAM159A	348378	broad.mit.edu	37	1	53108560	53108560	+	Missense_Mutation	SNP	G	G	A	rs557241775	byFrequency	TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr1:53108560G>A	ENST00000517870.1	+	2	358	c.208G>A	c.(208-210)Gta>Ata	p.V70I	FAM159A_ENST00000401050.3_3'UTR	NM_001042693.1	NP_001036158.1	Q6UWV7	F159A_HUMAN	family with sequence similarity 159, member A	70						integral component of membrane (GO:0016021)				endometrium(3)|lung(6)|upper_aerodigestive_tract(1)	10						AGGCCTGTCCGTAGCAGCAGT	0.522													g|||	2	0.000399361	0.0	0.0	5008	,	,		17083	0.0		0.0	False		,,,				2504	0.002					ENST00000517870.1																			0				endometrium(3)|lung(6)|upper_aerodigestive_tract(1)	10						c.(208-210)Gta>Ata		family with sequence similarity 159, member A							268.0	258.0	261.0					1																	53108560		2085	4199	6284	SO:0001583	missense	348378					integral to membrane		g.chr1:53108560G>A		CCDS41336.1	1p32.3	2008-08-08			ENSG00000182183	ENSG00000182183			28757	protein-coding gene	gene with protein product						12477932	Standard	NM_001042693		Approved	MGC52498	uc001cuf.3	Q6UWV7	OTTHUMG00000008330	ENST00000517870.1:c.208G>A	1.37:g.53108560G>A	ENSP00000429726:p.Val70Ile					FAM159A_ENST00000401050.3_3'UTR	p.V70I	NM_001042693.1	NP_001036158.1	Q6UWV7	F159A_HUMAN			2	358	+			70					Q6ZRG4	Missense_Mutation	SNP	ENST00000517870.1	37	c.208G>A	CCDS41336.1	.	.	.	.	.	.	.	.	.	.	g	0.010	-1.750825	0.00663	.	.	ENSG00000182183	ENST00000517870	.	.	.	4.7	-3.8	0.04307	.	0.710719	0.11665	N	0.541468	T	0.05960	0.0155	N	0.00289	-1.7	0.18873	N	0.999985	B	0.02656	0.0	B	0.04013	0.001	T	0.41502	-0.9505	9	0.02654	T	1	.	12.7823	0.57485	0.6176:0.0:0.3824:0.0	.	70	Q6UWV7	F159A_HUMAN	I	70	.	ENSP00000429726:V70I	V	+	1	0	FAM159A	52881148	0.890000	0.30428	0.951000	0.38953	0.004000	0.04260	0.743000	0.26231	-0.564000	0.06070	-2.008000	0.00441	GTA		0.522	FAM159A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022934.2	NM_001042693		4	115	0	0	0	1	0	4	115				
LRRC37A4P	55073	broad.mit.edu	37	17	43587569	43587569	+	RNA	SNP	G	G	C	rs202189074		TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr17:43587569G>C	ENST00000579913.1	-	0	1444				RP11-798G7.5_ENST00000253803.2_RNA	NR_002940.2				leucine rich repeat containing 37, member A4, pseudogene																		aactccgtctgaaaagaaaag	0.443																																						ENST00000253803.2																			0																																																			100294341							g.chr17:43587569G>C	AK000982		17q21.31	2014-04-01	2012-03-07	2012-03-07	ENSG00000214425	ENSG00000214425			25479	pseudogene	pseudogene			"""leucine rich repeat containing 37, member A4 (pseudogene)"""	LRRC37A4			Standard	NR_002940		Approved	FLJ10120	uc031rhd.1		OTTHUMG00000179212		17.37:g.43587569G>C						LRRC37A4P_ENST00000579913.1_RNA								0	267	+									RNA	SNP	ENST00000579913.1	37																																																																																						0.443	LRRC37A4P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445300.1	NR_002940		3	34	0	0	0	1	0	3	34				
EHBP1	23301	broad.mit.edu	37	2	63220752	63220752	+	Missense_Mutation	SNP	G	G	A			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr2:63220752G>A	ENST00000263991.5	+	19	3516	c.3034G>A	c.(3034-3036)Gtc>Atc	p.V1012I	EHBP1_ENST00000405289.1_Missense_Mutation_p.V977I|EHBP1_ENST00000431489.1_Missense_Mutation_p.V941I|EHBP1_ENST00000354487.3_Missense_Mutation_p.V977I|EHBP1_ENST00000405015.3_Missense_Mutation_p.V941I|EHBP1_ENST00000496857.1_3'UTR	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	1012						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			AGATTCTACAGTCAGAAAAAC	0.338																																						ENST00000263991.5																			0				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47						c.(3034-3036)Gtc>Atc		EH domain binding protein 1							61.0	61.0	61.0					2																	63220752		2203	4299	6502	SO:0001583	missense	23301					cytoplasm|membrane		g.chr2:63220752G>A	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.3034G>A	2.37:g.63220752G>A	ENSP00000263991:p.Val1012Ile					EHBP1_ENST00000405289.1_Missense_Mutation_p.V977I|EHBP1_ENST00000354487.3_Missense_Mutation_p.V977I|EHBP1_ENST00000496857.1_3'UTR|EHBP1_ENST00000405015.3_Missense_Mutation_p.V941I|EHBP1_ENST00000431489.1_Missense_Mutation_p.V941I	p.V1012I	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)		19	3516	+	Lung NSC(7;0.0951)|all_lung(7;0.169)		1012					O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	37	c.3034G>A	CCDS1872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.981|9.981	1.228254|1.228254	0.22542|0.22542	.|.	.|.	ENSG00000115504|ENSG00000115504	ENST00000422032|ENST00000405015;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	.|T;T;T;T;T	.|0.75477	.|-0.82;-0.82;-0.92;-0.94;-0.94	5.92|5.92	4.1|4.1	0.47936|0.47936	.|.	.|0.067156	.|0.56097	.|N	.|0.000025	T|T	0.68540|0.68540	0.3012|0.3012	L|L	0.59436|0.59436	1.845|1.845	0.50632|0.50632	D|D	0.999889|0.999889	.|B;B;B	.|0.10296	.|0.003;0.003;0.002	.|B;B;B	.|0.15484	.|0.013;0.01;0.006	T|T	0.61207|0.61207	-0.7109|-0.7109	5|10	.|0.20519	.|T	.|0.43	.|.	12.7049|12.7049	0.57056|0.57056	0.1343:0.0:0.8657:0.0|0.1343:0.0:0.8657:0.0	.|.	.|977;941;1012	.|Q8NDI1-2;Q8NDI1-3;Q8NDI1	.|.;.;EHBP1_HUMAN	N|I	171|941;941;1012;977;977	.|ENSP00000384143:V941I;ENSP00000403783:V941I;ENSP00000263991:V1012I;ENSP00000346482:V977I;ENSP00000385524:V977I	.|ENSP00000263991:V1012I	S|V	+|+	2|1	0|0	EHBP1|EHBP1	63074256|63074256	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.633000|5.633000	0.67825|0.67825	0.817000|0.817000	0.34445|0.34445	0.650000|0.650000	0.86243|0.86243	AGT|GTC		0.338	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		8	42	0	0	0	1	0	8	42				
CUX1	1523	broad.mit.edu	37	7	101559400	101559400	+	Silent	SNP	A	A	G			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr7:101559400A>G	ENST00000292535.7	+	2	74	c.36A>G	c.(34-36)gaA>gaG	p.E12E	CUX1_ENST00000437600.4_Silent_p.E23E|CUX1_ENST00000292538.4_Silent_p.E23E|CUX1_ENST00000546411.2_Silent_p.E12E|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000550008.2_Silent_p.E12E|CUX1_ENST00000556210.1_Silent_p.E12E|CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000547394.2_Silent_p.E23E|CUX1_ENST00000425244.2_Silent_p.E23E|CUX1_ENST00000360264.3_Silent_p.E23E|CUX1_ENST00000549414.2_Silent_p.E12E	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	12					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						AACAGAGAGAACTCGATGCCA	0.502																																						ENST00000360264.3																			0				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						c.(67-69)gaA>gaG		cut-like homeobox 1							147.0	143.0	144.0					7																	101559400		2203	4300	6503	SO:0001819	synonymous_variant	1523				negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr7:101559400A>G	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.36A>G	7.37:g.101559400A>G						CUX1_ENST00000546411.2_Silent_p.E12E|CUX1_ENST00000437600.4_Silent_p.E23E|CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000547394.2_Silent_p.E23E|CUX1_ENST00000292535.7_Silent_p.E12E|CUX1_ENST00000550008.2_Silent_p.E12E|CUX1_ENST00000292538.4_Silent_p.E23E|CUX1_ENST00000549414.2_Silent_p.E12E|CUX1_ENST00000425244.2_Silent_p.E23E|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000556210.1_Silent_p.E12E	p.E23E	NM_001202543.1	NP_001189472.1	P39880	CUX1_HUMAN			2	89	+			12					B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	37	c.69A>G	CCDS5721.1																																																																																				0.502	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		9	121	0	0	0	1	0	9	121				
HCN1	348980	broad.mit.edu	37	5	45695987	45695995	+	In_Frame_Del	DEL	CCGCCGCCA	CCGCCGCCA	-	rs483352934|rs56064803|rs55852304	byFrequency	TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr5:45695987_45695995delCCGCCGCCA	ENST00000303230.4	-	1	258_266	c.201_209delTGGCGGCGG	c.(199-210)ggtggcggcggc>ggc	p.67_70GGGG>G		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	67	Gly-rich.				apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.G72_G74delGGG(1)		NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						gccgccgccgccgccgccaccgccgccac	0.77														109	0.0217652	0.0703	0.0115	5008	,	,		5548	0.001		0.003	False		,,,				2504	0.0041					ENST00000303230.4																			1	Deletion - In frame(1)	p.G72_G74delGGG(1)	prostate(1)	NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						c.(199-210)ggc>gg		hyperpolarization activated cyclic nucleotide-gated potassium channel 1				62,378		27,8,185						4.2	1.0		dbSNP_129	4	100,1458		36,28,715	no	coding	HCN1	NM_021072.3		63,36,900	A1A1,A1R,RR		6.4185,14.0909,8.1081				162,1836				SO:0001651	inframe_deletion	348980					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity	g.chr5:45695987_45695995delCCGCCGCCA	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.201_209delTGGCGGCGG	5.37:g.45695996_45696004delCCGCCGCCA	ENSP00000307342:p.Gly70_Gly72del						p.GGGG71del	NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN			1	258_266	-			71			Gly-rich.			In_Frame_Del	DEL	ENST00000303230.4	37	c.201_209delTGGCGGCGG	CCDS3952.1																																																																																				0.770	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		6	7						6	7	---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88512304	88512305	+	Frame_Shift_Ins	INS	-	-	T	rs77980773		TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr12:88512304_88512305insT	ENST00000552810.1	-	17	2009_2010	c.1666_1667insA	c.(1666-1668)attfs	p.I556fs	CEP290_ENST00000397838.3_5'UTR|CEP290_ENST00000309041.7_Frame_Shift_Ins_p.I558fs	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	556					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)		p.I558fs*20(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						CATTTGACGAATTTTTTTTTTC	0.312																																						ENST00000552810.1																			1	Insertion - Frameshift(1)	p.I558fs*20(1)	central_nervous_system(1)	breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73	GRCh37	CD073590	CEP290	D	rs77980773	c.(1666-1668)tcgfs		centrosomal protein 290kDa																																				SO:0001589	frameshift_variant	80184				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding	g.chr12:88512304_88512305insT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.1667dupA	12.37:g.88512314_88512314dupT	ENSP00000448012:p.Ile556fs					CEP290_ENST00000397838.3_5'UTR|CEP290_ENST00000309041.7_Frame_Shift_Ins_p.S558fs	p.S556fs	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN			17	2009_2010	-			556					Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Frame_Shift_Ins	INS	ENST00000552810.1	37	c.1666_1667insA	CCDS55858.1																																																																																				0.312	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		2	4						2	4	---	---	---	---
SEZ6L2	26470	broad.mit.edu	37	16	29908335	29908335	+	Frame_Shift_Del	DEL	C	C	-			TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr16:29908335delC	ENST00000308713.5	-	3	846	c.319delG	c.(319-321)gtcfs	p.V107fs	SEZ6L2_ENST00000537485.1_Frame_Shift_Del_p.V63fs|SEZ6L2_ENST00000346932.5_Frame_Shift_Del_p.V107fs|SEZ6L2_ENST00000350527.3_Intron|SEZ6L2_ENST00000562159.1_5'UTR	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	107	Pro-rich.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TTAGGGGTGACGGCTGTTGTC	0.736																																						ENST00000308713.5																			0				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						c.(319-321)tcfs		seizure related 6 homolog (mouse)-like 2							6.0	9.0	8.0					16																	29908335		2166	4248	6414	SO:0001589	frameshift_variant	26470					endoplasmic reticulum membrane|integral to membrane|plasma membrane		g.chr16:29908335delC	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"""type I transmembrane receptor (seizure related protein)"""					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.319delG	16.37:g.29908335delC	ENSP00000312550:p.Val107fs					SEZ6L2_ENST00000537485.1_Frame_Shift_Del_p.V63fs|SEZ6L2_ENST00000350527.3_Intron|SEZ6L2_ENST00000346932.5_Frame_Shift_Del_p.V107fs|SEZ6L2_ENST00000562159.1_5'UTR	p.V107fs	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN			3	846	-			107			Pro-rich.		B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Frame_Shift_Del	DEL	ENST00000308713.5	37	c.319delG	CCDS10659.1																																																																																				0.736	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		2	4						2	4	---	---	---	---
ARFGAP3	26286	broad.mit.edu	37	22	43213780	43213780	+	Frame_Shift_Del	DEL	T	T	-	rs552164906		TCGA-SR-A6MV-01A-11D-A35I-08	TCGA-SR-A6MV-10D-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b60e6543-bc1d-4fb9-9149-548b39eb42fd	4180fbb4-7ea0-44cd-bb1e-b0899579ad93	g.chr22:43213780delT	ENST00000263245.5	-	10	1115	c.896delA	c.(895-897)aatfs	p.N299fs	ARFGAP3_ENST00000437119.2_Frame_Shift_Del_p.N255fs|ARFGAP3_ENST00000429508.2_Frame_Shift_Del_p.N227fs	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	299					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						TGAGTCAACATTTTTTTTGCC	0.363																																					GBM(58;544 1030 21460 27159 48838)	ENST00000263245.5																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						c.(895-897)atfs		ADP-ribosylation factor GTPase activating protein 3							317.0	285.0	296.0					22																	43213780		2203	4300	6503	SO:0001589	frameshift_variant	26286				intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding	g.chr22:43213780delT	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"""ADP-ribosylation factor GTPase activating proteins"""	661	protein-coding gene	gene with protein product		612439	"""ADP-ribosylation factor GTPase activating protein 1"""	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.896delA	22.37:g.43213780delT	ENSP00000263245:p.Asn299fs					ARFGAP3_ENST00000437119.2_Frame_Shift_Del_p.N255fs|ARFGAP3_ENST00000429508.2_Frame_Shift_Del_p.N227fs	p.N299fs	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN			10	1115	-			299					E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Frame_Shift_Del	DEL	ENST00000263245.5	37	c.896delA	CCDS14042.1																																																																																				0.363	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570		7	130						7	130	---	---	---	---
