#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_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	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_Description	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_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_AccessionNumbers	i_HGNC_CCDS IDs	i_HGNC_CCDSIDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_DateModified	i_HGNC_DateNameChanged	i_HGNC_DateSymbolChanged	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_EnsemblGeneID	i_HGNC_EnsemblIDsuppliedbyEnsembl	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_Genefamilydescription	i_HGNC_HGNC ID	i_HGNC_HGNCID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_LocusGroup	i_HGNC_LocusType	i_HGNC_Name Synonyms	i_HGNC_NameSynonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_OMIMIDsuppliedbyNCBI	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_PreviousNames	i_HGNC_PreviousSymbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_PubmedIDs	i_HGNC_Record Type	i_HGNC_RecordType	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_RefSeqsuppliedbyNCBI	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UCSCIDsuppliedbyUCSC	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_UniProtIDsuppliedbyUniProt	i_HGNC_VEGA IDs	i_HGNC_VEGAIDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	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_Region	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_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_folddegenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_hg18_pos1coor	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_init_n_lod	i_init_t_lod	i_n_alt_count	i_n_alt_count_full	i_n_ref_count	i_n_ref_count_full	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_lod_fstar	i_t_lod_fstar_full	i_t_ref_count_full	i_tumor_f_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	tumor_f
LINC00174	285908	broad.mit.edu	37	7	65842570	65842570	+	lincRNA	SNP	A	A	T			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr7:65842570A>T	ENST00000421767.1	-	0	3162					NR_026873.1				long intergenic non-protein coding RNA 174																		GGCTTATTTCAGGACGATTTG	0.557																																						ENST00000421767.1											0																	37.0	33.0	34.0					7																	65842570		2203	4300	6503			0						g.chr7:65842570A>T	AK091213	AK091213			7q11.21	2013-12-05	2013-12-05	2013-12-05	2013-12-05	2013-12-05	2013-12-05	ENSG00000179406	ENSG00000179406	ENSG00000179406	ENSG00000179406		"""Long non-coding RNAs"""	"""Long non-coding RNAs"""	27788	27788	non-coding RNA	RNA, long non-coding	non-coding RNA	RNA, long non-coding					"""non-protein coding RNA 174"""	NCRNA00174	"""non-protein coding RNA 174"""	NCRNA00174				Standard	Standard	NR_026873	NR_026873		Approved		uc003tux.4	uc003tux.4			OTTHUMG00000156590	OTTHUMG00000156590		7.37:g.65842570A>T					NR_026873.1						0	3162	-						RNA	SNP	ENST00000421767.1	37																																																																																											0.557	LINC00174-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000344721.1		10.694738	10	10	30	30	NR_026873		4	11.431434	11.431434	11	0.266667	0	0	0	1	0	4	11	0.266667
TMEM68	137695	broad.mit.edu	37	8	56675150	56675150	+	Intron	SNP	G	G	A			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr8:56675150G>A	ENST00000434581.2	-	3	525				TMEM68_ENST00000519784.1_Intron|TMEM68_ENST00000523073.1_Intron|TMEM68_ENST00000521229.1_Silent_p.C123C|TMEM68_ENST00000334667.2_Intron|TMEM68_ENST00000522576.1_Silent_p.C123C			Q96MH6	TMM68_HUMAN	transmembrane protein 68							integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			NS(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6			Epithelial(17;0.000361)|all cancers(17;0.00326)			TTCCAATGCAGCACACATGAA	0.403																																						ENST00000521229.1											0			NS(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6						c.(367-369)tgC>tgT	transmembrane protein 68						81.0	74.0	77.0					8																	56675150		2203	4300	6503	SO:0001627	intron_variant	137695				integral to membrane	acyltransferase activity	g.chr8:56675150G>A	AK056932	AK056932	CCDS6161.1, CCDS75740.1, CCDS75741.1, CCDS75742.1	CCDS6161.1, CCDS75740.1, CCDS75741.1, CCDS75742.1	8q12.1	2011-12-12			2011-12-12			ENSG00000167904	ENSG00000167904	ENSG00000167904	ENSG00000167904				26510	26510	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product										12477932	12477932	Standard	Standard	XM_005251150	XM_005251150		Approved	FLJ32370	uc003xsh.1	uc003xsh.1	Q96MH6	Q96MH6	OTTHUMG00000164293	OTTHUMG00000164293	ENST00000434581.2:c.325+43C>T	8.37:g.56675150G>A			TMEM68_ENST00000522576.1_Silent_p.C123C|TMEM68_ENST00000434581.2_Intron|TMEM68_ENST00000523073.1_Intron|TMEM68_ENST00000519784.1_Intron|TMEM68_ENST00000334667.2_Intron	p.C123C			Q96MH6	TMM68_HUMAN	Epithelial(17;0.000361)|all cancers(17;0.00326)		3	581	-			0		Q658X6|Q8WUD2	Silent	SNP	ENST00000434581.2	37	c.369C>T																																																																																										0.403	TMEM68-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000378137.1		-16.388383	6	6	71	71	NM_152417		4	8.117271	8.117271	102	0.037736	0	0	0	1	0	4	102	0.037736
NR3C1	2908	broad.mit.edu	37	5	142780179	142780179	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr5:142780179G>A	ENST00000343796.2	-	2	1219	c.226C>T	c.(226-228)Cca>Tca	p.P76S	NR3C1_ENST00000231509.3_Missense_Mutation_p.P76S|NR3C1_ENST00000394466.2_Missense_Mutation_p.P76S|NR3C1_ENST00000503201.1_Missense_Mutation_p.P76S|NR3C1_ENST00000394464.2_Missense_Mutation_p.P76S|NR3C1_ENST00000424646.2_Missense_Mutation_p.P76S|NR3C1_ENST00000504572.1_Missense_Mutation_p.P76S|NR3C1_ENST00000416954.2_Intron|NR3C1_ENST00000415690.2_Missense_Mutation_p.P76S	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	76	Modulating.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	GACAGATCTGGCTGCTGCGCA	0.493																																						ENST00000343796.2											0			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35						c.(226-228)Cca>Tca	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)						132.0	145.0	140.0					5																	142780179		2203	4300	6503	SO:0001583	missense	2908			chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter	mitochondrial matrix|nucleoplasm	glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding	g.chr5:142780179G>A	X03225	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580	ENSG00000113580	ENSG00000113580		"""Nuclear hormone receptors"""	"""Nuclear hormone receptors"""	7978	7978	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			138040	138040	"""nuclear receptor subfamily 3, group C, member 1"""	GRL	"""nuclear receptor subfamily 3, group C, member 1"""	GRL		2867473	2867473	Standard	Standard	NM_001204258	NM_001204258		Approved	GR	uc003lnb.3	uc003lnb.3	P04150	P04150	OTTHUMG00000129677	OTTHUMG00000129677	ENST00000343796.2:c.226C>T	5.37:g.142780179G>A	ENSP00000343205:p.Pro76Ser		NR3C1_ENST00000394466.2_Missense_Mutation_p.P76S|NR3C1_ENST00000416954.2_Intron|NR3C1_ENST00000394464.2_Missense_Mutation_p.P76S|NR3C1_ENST00000504572.1_Missense_Mutation_p.P76S|NR3C1_ENST00000424646.2_Missense_Mutation_p.P76S|NR3C1_ENST00000503201.1_Missense_Mutation_p.P76S|NR3C1_ENST00000231509.3_Missense_Mutation_p.P76S|NR3C1_ENST00000415690.2_Missense_Mutation_p.P76S	p.P76S	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		2	1219	-		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	76	Modulating.	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Missense_Mutation	SNP	ENST00000343796.2	37	c.226C>T	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.705615	0.68615	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000361001;ENST00000415690;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000503201;ENST00000510170;ENST00000508760;ENST00000502892;ENST00000514699;ENST00000502500	T;T;T;T;T;T;T;T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51	4.84	4.84	0.62591	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.49864	0.1582	M	0.80746	2.51	0.80722	D	1	P;B;P	0.48998	0.918;0.201;0.756	P;B;P	0.50708	0.648;0.26;0.524	T	0.57225	-0.7848	10	0.54805	T	0.06	.	18.3334	0.90279	0.0:0.0:1.0:0.0	.	76;76;76	E5KQF5;P04150;E5KQF6	.;GCR_HUMAN;.	S	76	ENSP00000377977:P76S;ENSP00000343205:P76S;ENSP00000387672:P76S;ENSP00000405282:P76S;ENSP00000422518:P76S;ENSP00000377979:P76S;ENSP00000231509:P76S;ENSP00000427672:P76S;ENSP00000424747:P76S;ENSP00000425313:P76S;ENSP00000420856:P76S;ENSP00000426478:P76S;ENSP00000425374:P76S	ENSP00000231509:P76S	P	-	1	0	0	NR3C1	142760372	142760372	1.000000	0.71417	0.999000	0.59377	0.898000	0.52572	6.173000	0.71937	2.400000	0.81607	0.561000	0.74099	CCA		0.493	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1		154.332149	-45	-45	170	170			50	155.058844	155.058844	70	0.416667	0	0	0	1	0	50	70	0.416667
MEGF8	1954	broad.mit.edu	37	19	42857739	42857739	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr19:42857739G>A	ENST00000251268.6	+	21	3673	c.3673G>A	c.(3673-3675)Gac>Aac	p.D1225N	MEGF8_ENST00000334370.4_Missense_Mutation_p.D1158N	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1225	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				TGGCCACTGCGACAACCTCAG	0.692																																						ENST00000334370.4											0			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						c.(3472-3474)Gac>Aac	multiple EGF-like-domains 8						13.0	12.0	12.0					19																	42857739		2197	4282	6479	SO:0001583	missense	1954				integral to membrane	calcium ion binding|structural molecule activity	g.chr19:42857739G>A	AB011541	AB011541	CCDS12604.2, CCDS62693.1	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429	ENSG00000105429	ENSG00000105429				3233	3233	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	"""HBV pre s2 binding protein 1"""	604267	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	9693030	Standard	Standard	NM_001410	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	uc002otm.5	Q7Z7M0	Q7Z7M0	OTTHUMG00000150342	OTTHUMG00000150342	ENST00000251268.6:c.3673G>A	19.37:g.42857739G>A	ENSP00000251268:p.Asp1225Asn		MEGF8_ENST00000251268.6_Missense_Mutation_p.D1225N	p.D1158N	NM_001410.2	NP_001401.2	Q7Z7M0	MEGF8_HUMAN			20	4107	+		Prostate(69;0.00682)	1225		A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	37	c.3472G>A		.	.	.	.	.	.	.	.	.	.	G	15.97	2.989551	0.53934	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.62941	-0.01;-0.01	5.47	4.37	0.52481	5.47	4.37	0.52481	EGF-like, laminin (3);	0.065812	0.64402	D	0.000011	T	0.62307	0.2417	L	0.37850	1.14	0.80722	D	1	D;D	0.67145	0.996;0.987	P;P	0.58331	0.837;0.597	T	0.54221	-0.8326	10	0.11182	T	0.66	-36.3793	13.4243	0.61015	0.0:0.1588:0.8412:0.0	.	1225;1158	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	N	1158;1225	ENSP00000334219:D1158N;ENSP00000251268:D1225N	ENSP00000251268:D1225N	D	+	1	0	0	MEGF8	47549579	47549579	0.999000	0.42202	0.998000	0.56505	0.976000	0.68499	3.172000	0.50832	2.580000	0.87095	0.561000	0.74099	GAC		0.692	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1		9.725300	6	6	13	13	NM_001410		3	9.7253	9.725300	3	0.500000	0	0	0	1	0	3	3	0.5
PRKD1	5587	broad.mit.edu	37	14	30108044	30108044	+	Nonsense_Mutation	SNP	G	G	A			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr14:30108044G>A	ENST00000331968.5	-	5	992	c.763C>T	c.(763-765)Cga>Tga	p.R255*	PRKD1_ENST00000551644.1_5'UTR|PRKD1_ENST00000415220.2_Nonsense_Mutation_p.R263*	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	255					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		TGAATTGGTCGTCCAATGTAT	0.418																																						ENST00000331968.5											0			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78						c.(763-765)Cga>Tga	protein kinase D1						98.0	97.0	97.0					14																	30108044		2203	4300	6503	SO:0001587	stop_gained	5587			cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity	g.chr14:30108044G>A			CCDS9637.1	CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	"""Pleckstrin homology (PH) domain containing"""	9407	9407	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			605435	605435	"""protein kinase C, mu"""	PRKCM	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	8119958, 10965134	Standard	Standard	NM_002742	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	uc001wqh.3	Q15139	Q15139	OTTHUMG00000140203	OTTHUMG00000140203	ENST00000331968.5:c.763C>T	14.37:g.30108044G>A	ENSP00000333568:p.Arg255*		PRKD1_ENST00000551644.1_5'UTR|PRKD1_ENST00000415220.2_Nonsense_Mutation_p.R263*	p.R255*	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)	5	992	-	Hepatocellular(127;0.0604)		255		A6NL64|B2RAF6	Nonsense_Mutation	SNP	ENST00000331968.5	37	c.763C>T	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	G	37	6.102455	0.97286	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	.	.	.	5.45	3.54	0.40534	5.45	3.54	0.40534	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.9893	14.728	0.69360	0.0:0.0:0.7502:0.2498	.	.	.	.	X	255;263	.	ENSP00000333568:R255X	R	-	1	2	2	PRKD1	29177795	29177795	1.000000	0.71417	0.987000	0.45799	0.862000	0.49288	3.985000	0.56930	0.712000	0.32039	0.650000	0.86243	CGA		0.418	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2		69.802672	2	2	105	105	NM_002742		23	70.063508	70.063508	31	0.425926	0	0	0	1	0	23	31	0.425926
FBXL13	222235	broad.mit.edu	37	7	102669190	102669190	+	Nonsense_Mutation	SNP	C	C	T			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr7:102669190C>T	ENST00000313221.4	-	4	500	c.74G>A	c.(73-75)tGg>tAg	p.W25*	FBXL13_ENST00000393772.2_Nonsense_Mutation_p.W25*|FBXL13_ENST00000379308.3_Nonsense_Mutation_p.W25*|RP11-645N11.3_ENST00000447336.1_RNA|FBXL13_ENST00000436908.1_Nonsense_Mutation_p.W25*|FBXL13_ENST00000379306.3_Nonsense_Mutation_p.W25*|FBXL13_ENST00000379305.3_Nonsense_Mutation_p.W25*|FBXL13_ENST00000455112.2_Nonsense_Mutation_p.W25*|FBXL13_ENST00000456695.1_Nonsense_Mutation_p.W25*|FBXL13_ENST00000471074.1_Intron	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	25										NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						TATGTCTCTCCAAGTGCTGCA	0.318																																						ENST00000393772.2											0			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						c.(73-75)tGg>tAg	F-box and leucine-rich repeat protein 13						79.0	71.0	74.0					7																	102669190		2203	4300	6503	SO:0001587	stop_gained	222235						g.chr7:102669190C>T	BC031285	BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			2014-07-18			ENSG00000161040	ENSG00000161040	ENSG00000161040	ENSG00000161040		"""F-boxes / Leucine-rich repeats"""	"""F-boxes / Leucine-rich repeats"""	21658	21658	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			609080	609080								Standard	Standard	NM_145032	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	uc003vaq.2	Q8NEE6	Q8NEE6	OTTHUMG00000157224	OTTHUMG00000157224	ENST00000313221.4:c.74G>A	7.37:g.102669190C>T	ENSP00000321927:p.Trp25*		FBXL13_ENST00000379305.3_Nonsense_Mutation_p.W25*|FBXL13_ENST00000313221.4_Nonsense_Mutation_p.W25*|FBXL13_ENST00000455112.2_Nonsense_Mutation_p.W25*|FBXL13_ENST00000471074.1_Intron|FBXL13_ENST00000379308.3_Nonsense_Mutation_p.W25*|FBXL13_ENST00000456695.1_Nonsense_Mutation_p.W25*|FBXL13_ENST00000436908.1_Nonsense_Mutation_p.W25*|FBXL13_ENST00000379306.3_Nonsense_Mutation_p.W25*	p.W25*			Q8NEE6	FXL13_HUMAN			4	500	-			25		C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Nonsense_Mutation	SNP	ENST00000313221.4	37	c.74G>A	CCDS5726.1	.	.	.	.	.	.	.	.	.	.	C	37	6.582179	0.97680	.	.	ENSG00000161040	ENST00000393772;ENST00000379308;ENST00000379306;ENST00000379305;ENST00000436908;ENST00000313221;ENST00000456695;ENST00000455112;ENST00000440067	.	.	.	3.94	3.94	0.45596	3.94	3.94	0.45596	.	0.000000	0.64402	D	0.000019	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7814	0.52018	0.0:1.0:0.0:0.0	.	.	.	.	X	25;25;25;25;25;25;25;25;115	.	ENSP00000321927:W25X	W	-	2	0	0	FBXL13	102456426	102456426	0.998000	0.40836	0.922000	0.36590	0.575000	0.36095	2.871000	0.48459	2.489000	0.83994	0.460000	0.39030	TGG		0.318	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1		2.466144	-19	-19	75	75	NM_145032		4	9.631055	9.631055	39	0.093023	0	0	0	1	0	4	39	0.093023
EXD1	161829	broad.mit.edu	37	15	41501729	41501729	+	Silent	SNP	T	T	C	rs370262959		TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr15:41501729T>C	ENST00000314992.5	-	5	520	c.330A>G	c.(328-330)gtA>gtG	p.V110V	EXD1_ENST00000458580.2_Silent_p.V168V	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	110	3'-5' exonuclease.						3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						CATGGCGACATACATTCGCTC	0.378																																						ENST00000314992.5											0			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						c.(328-330)gtA>gtG	exonuclease 3'-5' domain containing 1	T		0,4406		0,0,2203	68.0	62.0	64.0		330	1.8	1.0	15		64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EXD1	NM_152596.2		0,1,6502	CC,CT,TT		0.0116,0.0,0.0077		110/515	41501729	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	161829			nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding	g.chr15:41501729T>C	BC030628	BC030628	CCDS10072.1, CCDS66738.1	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997	ENSG00000178997	ENSG00000178997				28507	28507	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product					"""exonuclease 3'-5' domain-like 1"""	EXDL1	"""exonuclease 3'-5' domain-like 1"""	EXDL1		12477932	12477932	Standard	Standard	NM_001286441	NM_001286441		Approved	MGC33637	uc001znk.3	uc001znk.3	Q8NHP7	Q8NHP7	OTTHUMG00000130232	OTTHUMG00000130232	ENST00000314992.5:c.330A>G	15.37:g.41501729T>C			EXD1_ENST00000458580.2_Silent_p.V168V	p.V110V	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN			5	520	-			110	3'-5' exonuclease.	A8K909|B7Z839|Q6ZW94	Silent	SNP	ENST00000314992.5	37	c.330A>G	CCDS10072.1																																																																																									0.378	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2		32.881280	2	2	53	53	NM_152596		12	35.605128	35.605128	36	0.250000	0	0	0	1	0	12	36	0.25
CHST2	9435	broad.mit.edu	37	3	142840445	142840445	+	Missense_Mutation	SNP	C	C	T			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr3:142840445C>T	ENST00000309575.3	+	2	2171	c.787C>T	c.(787-789)Ctc>Ttc	p.L263F		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	263					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						CTCGTCACCACTCTGCCCCGC	0.672																																						ENST00000309575.3											0			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						c.(787-789)Ctc>Ttc	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2						20.0	24.0	23.0					3																	142840445		2201	4299	6500	SO:0001583	missense	9435			inflammatory response|multicellular organismal development|N-acetylglucosamine metabolic process|sulfur compound metabolic process	integral to membrane|intrinsic to Golgi membrane|trans-Golgi network	N-acetylglucosamine 6-O-sulfotransferase activity	g.chr3:142840445C>T	BC042160	BC042160	CCDS3129.1	CCDS3129.1	3q24	2007-03-14			2007-03-14			ENSG00000175040	ENSG00000175040	ENSG00000175040	ENSG00000175040		"""Sulfotransferases, membrane-bound"""	"""Sulfotransferases, membrane-bound"""	1970	1970	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			603798	603798						10049591	10049591	Standard	Standard	NM_004267	NM_004267		Approved	C6ST	uc003evm.3	uc003evm.3	Q9Y4C5	Q9Y4C5	OTTHUMG00000159351	OTTHUMG00000159351	ENST00000309575.3:c.787C>T	3.37:g.142840445C>T	ENSP00000307911:p.Leu263Phe			p.L263F	NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN			2	2171	+			263		D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	37	c.787C>T	CCDS3129.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.415669	0.42817	.	.	ENSG00000175040	ENST00000309575	D	0.96459	-4.02	4.17	4.17	0.49024	4.17	4.17	0.49024	Sulfotransferase domain (1);	0.000000	0.56097	U	0.000026	D	0.96291	0.8790	L	0.36672	1.1	0.58432	D	0.999996	D	0.76494	0.999	D	0.79784	0.993	D	0.94391	0.7614	10	0.14656	T	0.56	-16.2734	16.6656	0.85252	0.0:1.0:0.0:0.0	.	263	Q9Y4C5	CHST2_HUMAN	F	263	ENSP00000307911:L263F	ENSP00000307911:L263F	L	+	1	0	0	CHST2	144323135	144323135	1.000000	0.71417	0.771000	0.31576	0.403000	0.30841	4.781000	0.62389	2.152000	0.67230	0.407000	0.27541	CTC		0.672	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1		25.904978	-11	-11	13	13	NM_004267		8	26.741604	26.741604	2	0.800000	0	0	0	1	0	8	2	0.8
ARMC9	80210	ucsc.edu	37	2	232135739	232135739	+	Silent	SNP	G	G	A			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr2:232135739G>A	ENST00000349938.4	+	13	1358	c.1164G>A	c.(1162-1164)cgG>cgA	p.R388R	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	388						extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		ACGTGGTGCGGCAGTACATGG	0.483																																																	0																	110.0	90.0	97.0					2																	232135739		2203	4300	6503	SO:0001819	synonymous_variant	80210							BC004514	BC004514	CCDS2484.1, CCDS74666.1	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			2013-02-14			ENSG00000135931	ENSG00000135931	ENSG00000135931	ENSG00000135931		"""Armadillo repeat containing"""	"""Armadillo repeat containing"""	20730	20730	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product										11347906	11347906	Standard	Standard	NM_025139	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	uc031rrs.1	Q7Z3E5	Q7Z3E5	OTTHUMG00000133229	OTTHUMG00000133229	ENST00000349938.4:c.1164G>A	2.37:g.232135739G>A																		Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Silent	SNP	ENST00000349938.4	37		CCDS2484.1	.	.	.	.	.	.	.	.	.	.	G	9.289	1.050194	0.19827	.	.	ENSG00000135931	ENST00000424740	.	.	.	4.56	-5.45	0.02616	4.56	-5.45	0.02616	.	.	.	.	.	T	0.39759	0.1090	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38693	-0.9649	4	.	.	.	-17.8376	4.1663	0.10308	0.2993:0.4623:0.1412:0.0973	.	.	.	.	D	91	.	.	G	+	2	0	0	ARMC9	231843983	231843983	0.021000	0.18746	0.809000	0.32408	0.843000	0.47879	-0.908000	0.04063	-1.087000	0.03081	-0.769000	0.03391	GGC		0.483	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3			-5	-5	50	50	NM_025139		4			37							4	37	
SYNE1	23345	broad.mit.edu	37	6	152763338	152763338	+	Nonsense_Mutation	SNP	G	G	A			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr6:152763338G>A	ENST00000367255.5	-	31	4481	c.3880C>T	c.(3880-3882)Cag>Tag	p.Q1294*	SYNE1_ENST00000265368.4_Nonsense_Mutation_p.Q1294*|SYNE1_ENST00000367253.4_Nonsense_Mutation_p.Q1294*|SYNE1_ENST00000423061.1_Nonsense_Mutation_p.Q1301*|SYNE1_ENST00000448038.1_Nonsense_Mutation_p.Q1301*|SYNE1_ENST00000367248.3_Nonsense_Mutation_p.Q1284*|SYNE1_ENST00000413186.2_Nonsense_Mutation_p.Q1294*|SYNE1_ENST00000341594.5_Nonsense_Mutation_p.Q1360*	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1294					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GCGATCTGCTGCTGCACATCT	0.542										HNSCC(10;0.0054)																												ENST00000367255.5											0			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524						c.(3880-3882)Cag>Tag	spectrin repeat containing, nuclear envelope 1						81.0	71.0	74.0					6																	152763338		2203	4300	6503	SO:0001587	stop_gained	23345			cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding	g.chr6:152763338G>A	AB018339	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			2014-09-17			ENSG00000131018	ENSG00000131018	ENSG00000131018	ENSG00000131018				17089	17089	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	608441	"""chromosome 6 open reading frame 98"""	C6orf98	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	9872452, 10878022	Standard	Standard	NM_182961	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	uc003qou.4	Q8NF91	Q8NF91	OTTHUMG00000015841	OTTHUMG00000015841	ENST00000367255.5:c.3880C>T	6.37:g.152763338G>A	ENSP00000356224:p.Gln1294*		SYNE1_ENST00000341594.5_Nonsense_Mutation_p.Q1360*|SYNE1_ENST00000448038.1_Nonsense_Mutation_p.Q1301*|SYNE1_ENST00000265368.4_Nonsense_Mutation_p.Q1294*|SYNE1_ENST00000423061.1_Nonsense_Mutation_p.Q1301*|SYNE1_ENST00000367253.4_Nonsense_Mutation_p.Q1294*|SYNE1_ENST00000367248.3_Nonsense_Mutation_p.Q1284*|SYNE1_ENST00000413186.2_Nonsense_Mutation_p.Q1294*	p.Q1294*	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)	31	4481	-		Ovarian(120;0.0955)	1294		E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Nonsense_Mutation	SNP	ENST00000367255.5	37	c.3880C>T	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	43	10.124505	0.99342	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186	.	.	.	5.41	2.39	0.29439	5.41	2.39	0.29439	.	0.237208	0.29551	N	0.011825	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	13.1528	0.59498	0.0:0.314:0.5746:0.1115	.	.	.	.	X	1294;1301;1294;1301;1360;1294;1284;1294	.	ENSP00000265368:Q1294X	Q	-	1	0	0	SYNE1	152805031	152805031	1.000000	0.71417	1.000000	0.80357	0.369000	0.29798	1.698000	0.37794	0.710000	0.31997	0.650000	0.86243	CAG		0.542	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2		42.544245	-10	-10	77	77	NM_182961		17	45.557482	45.557482	46	0.269841	0	0	0	1	0	17	46	0.269841
GNA11	2767	broad.mit.edu	37	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	AC005262.2_ENST00000585980.1_RNA|AC005262.3_ENST00000587701.1_RNA|GNA11_ENST00000586180.1_3'UTR	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	209					action potential (GO:0001508)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cellular response to pH (GO:0071467)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|regulation of melanocyte differentiation (GO:0045634)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.Q209L(80)|p.Q209P(2)		endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)		GTGGGGGGCCAGCGGTCGGAG	0.612			Mis		uveal melanoma																																	ENST00000078429.4		Dom	yes		19	19p13.3	2767	"""guanine nucleotide binding protein (G protein), alpha 11 (Gq class)"""		E	82	Substitution - Missense(82)	eye(69)|skin(8)|meninges(5)	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161						c.(625-627)cAg>cTg	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)						104.0	89.0	94.0					19																	3118942		2203	4300	6503	SO:0001583	missense	2767			activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	g.chr19:3118942A>T	AF493900	AF493900	CCDS12103.1	CCDS12103.1	19p13.3	2014-02-04			2014-02-04			ENSG00000088256	ENSG00000088256	ENSG00000088256	ENSG00000088256				4379	4379	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			139313	139313	"""hypocalciuric hypercalcemia 2"""	HHC2	"""hypocalciuric hypercalcemia 2"""	HHC2		1302014, 23802516	1302014, 23802516	Standard	Standard	NM_002067	NM_002067		Approved	FBH, FBH2, FHH2	uc002lxd.3	uc002lxd.3	P29992	P29992	OTTHUMG00000180631	OTTHUMG00000180631	ENST00000078429.4:c.626A>T	19.37:g.3118942A>T	ENSP00000078429:p.Gln209Leu		GNA11_ENST00000586180.1_3'UTR|AC005262.3_ENST00000587701.1_RNA	p.Q209L	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	5	868	+		Hepatocellular(1079;0.137)	209		O15109|Q14350|Q6IB00	Missense_Mutation	SNP	ENST00000078429.4	37	c.626A>T	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.718086	0.48622	.	.	ENSG00000088256	ENST00000078429	D	0.91237	-2.81	3.26	3.26	0.37387	3.26	3.26	0.37387	.	0.000000	0.64402	U	0.000006	D	0.96950	0.9004	H	0.99357	4.53	0.80722	D	1	D	0.59767	0.986	D	0.68483	0.958	D	0.96823	0.9605	10	0.87932	D	0	.	10.7338	0.46113	1.0:0.0:0.0:0.0	.	209	P29992	GNA11_HUMAN	L	209	ENSP00000078429:Q209L	ENSP00000078429:Q209L	Q	+	2	0	0	GNA11	3069942	3069942	1.000000	0.71417	0.438000	0.26821	0.027000	0.11550	9.104000	0.94239	1.256000	0.44068	0.379000	0.24179	CAG		0.612	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2		23.462308	3	3	84	84	NM_002067		9	24.684178	24.684178	22	0.290323	0	0	0	1	0	9	22	0.290323
HIRA	7290	broad.mit.edu	37	22	19343354	19343354	+	Silent	SNP	C	C	T			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr22:19343354C>T	ENST00000263208.5	-	21	2746	c.2490G>A	c.(2488-2490)acG>acA	p.T830T	HIRA_ENST00000541063.1_Silent_p.T786T|HIRA_ENST00000546308.1_Intron|HIRA_ENST00000340170.4_Silent_p.T623T	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	830	Interaction with histone H4.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					TTCCATGCTGCGTCAGCAAGA	0.478																																						ENST00000263208.5											0			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37						c.(2488-2490)acG>acA	histone cell cycle regulator						165.0	114.0	131.0					22																	19343354		2203	4300	6503	SO:0001819	synonymous_variant	7290			chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity	g.chr22:19343354C>T	X75296	X75296	CCDS13759.1	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084	ENSG00000100084	ENSG00000100084		"""WD repeat domain containing"""	"""WD repeat domain containing"""	4916	4916	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""DiGeorge critical region gene 1"""	"""DiGeorge critical region gene 1"""	600237	600237	"""HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)"", ""HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"""	TUPLE1	"""HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)"", ""HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"""	TUPLE1		8111380, 7633437, 9731536	8111380, 7633437, 9731536	Standard	Standard	NM_003325	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	uc002zpf.1	P54198	P54198	OTTHUMG00000150134	OTTHUMG00000150134	ENST00000263208.5:c.2490G>A	22.37:g.19343354C>T			HIRA_ENST00000340170.4_Silent_p.T623T|HIRA_ENST00000541063.1_Silent_p.T786T|HIRA_ENST00000546308.1_Intron	p.T830T	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN			21	2746	-	Colorectal(54;0.0993)		830	Interaction with histone H4.	Q05BU9|Q8IXN2	Silent	SNP	ENST00000263208.5	37	c.2490G>A	CCDS13759.1																																																																																									0.478	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2		23.591709	10	10	51	51	NM_003325		8	24.311082	24.311082	17	0.320000	0	0	0	1	0	8	17	0.32
H2AFZ	3015	broad.mit.edu	37	4	100870470	100870470	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr4:100870470G>A	ENST00000296417.5	-	3	372	c.155C>T	c.(154-156)gCt>gTt	p.A52V	RP11-15B17.1_ENST00000501976.2_RNA|RP11-15B17.1_ENST00000507494.1_RNA|H2AFZ_ENST00000529158.1_5'UTR|DNAJB14_ENST00000471738.1_5'Flank|RP11-15B17.1_ENST00000514624.1_RNA|DNAJB14_ENST00000442697.2_5'Flank	NM_002106.3	NP_002097.1	P0C0S5	H2AZ_HUMAN	H2A histone family, member Z	52					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular vesicular exosome (GO:0070062)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|nucleosomal DNA binding (GO:0031492)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|endometrium(3)|lung(1)	5				OV - Ovarian serous cystadenocarcinoma(123;2.32e-08)		GCTGTACACAGCGGCAGTCGC	0.542											OREG0016271	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000296417.5											0			breast(1)|endometrium(3)|lung(1)	5						c.(154-156)gCt>gTt	H2A histone family, member Z						53.0	51.0	51.0					4																	100870470		2203	4300	6503	SO:0001583	missense	3015			nucleosome assembly	nucleosome|nucleus	DNA binding	g.chr4:100870470G>A	X52317	X52317	CCDS3654.1	CCDS3654.1	4q23	2011-01-27			2011-01-27			ENSG00000164032	ENSG00000164032	ENSG00000164032	ENSG00000164032		"""Histones / Replication-independent"""	"""Histones / Replication-independent"""	4741	4741	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			142763	142763		H2AZ		H2AZ		1697587	1697587	Standard	Standard	XM_005262971	XM_005262971		Approved	H2A.Z	uc003hvo.1	uc003hvo.1	P0C0S5	P0C0S5	OTTHUMG00000131048	OTTHUMG00000131048	ENST00000296417.5:c.155C>T	4.37:g.100870470G>A	ENSP00000296417:p.Ala52Val	1354	H2AFZ_ENST00000529158.1_5'UTR	p.A52V	NM_002106.3	NP_002097.1	P0C0S5	H2AZ_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;2.32e-08)	3	372	-			52		B2RD56|P17317|Q6I9U0	Missense_Mutation	SNP	ENST00000296417.5	37	c.155C>T	CCDS3654.1	.	.	.	.	.	.	.	.	.	.	G	29.4	4.999941	0.93227	.	.	ENSG00000164032	ENST00000296417	T	0.65178	-0.14	3.75	3.75	0.43078	3.75	3.75	0.43078	Histone-fold (2);Histone core (1);Histone H2A (2);	0.000000	0.85682	D	0.000000	T	0.75317	0.3833	M	0.78637	2.42	0.80722	D	1	D	0.67145	0.996	P	0.58077	0.832	T	0.81028	-0.1118	10	0.72032	D	0.01	.	15.7657	0.78126	0.0:0.0:1.0:0.0	.	52	P0C0S5	H2AZ_HUMAN	V	52	ENSP00000296417:A52V	ENSP00000296417:A52V	A	-	2	0	0	H2AFZ	101089493	101089493	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	6.839000	0.75364	1.925000	0.55765	0.650000	0.86243	GCT		0.542	H2AFZ-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000253695.1		38.163812	14	14	55	55	NM_002106		13	38.885025	38.885025	24	0.351351	0	0	0	1	0	13	24	0.351351
SH2D5	400745	broad.mit.edu	37	1	21051092	21051092	+	Frame_Shift_Del	DEL	G	G	-			TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr1:21051092delG	ENST00000444387.2	-	6	824	c.427delC	c.(427-429)cagfs	p.Q143fs	SH2D5_ENST00000375031.1_Frame_Shift_Del_p.Q59fs|SH2D5_ENST00000460804.1_5'UTR	NM_001103161.1	NP_001096631.1	Q6ZV89	SH2D5_HUMAN	SH2 domain containing 5	143										lung(4)|prostate(1)|upper_aerodigestive_tract(1)	6		Colorectal(325;3.46e-05)|all_lung(284;5.32e-05)|Lung NSC(340;5.51e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|GBM - Glioblastoma multiforme(114;0.000465)|Kidney(64;0.000476)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(64;0.00634)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TAAGCCAGCTGGAAAGAGCGG	0.657																																						ENST00000375031.1											0			lung(4)|prostate(1)|upper_aerodigestive_tract(1)	6						c.(175-177)cagfs	SH2 domain containing 5						13.0	16.0	15.0					1																	21051092		2019	4183	6202	SO:0001589	frameshift_variant	400745						g.chr1:21051092delG	AK124869, AK123236	AK124869, AK123236	CCDS41280.1, CCDS44080.1	CCDS41280.1, CCDS44080.1	1p36.12	2008-02-05			2008-02-05			ENSG00000189410	ENSG00000189410	ENSG00000189410	ENSG00000189410				28819	28819	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product												Standard	Standard	NM_001103161	NM_001103161		Approved		uc009vpy.1	uc009vpy.1	Q6ZV89	Q6ZV89	OTTHUMG00000002620	OTTHUMG00000002620	ENST00000444387.2:c.427delC	1.37:g.21051092delG	ENSP00000406026:p.Gln143fs		SH2D5_ENST00000444387.2_Frame_Shift_Del_p.Q143fs|SH2D5_ENST00000460804.1_5'UTR	p.Q59fs	NM_001103160.1	NP_001096630.1	Q6ZV89	SH2D5_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|GBM - Glioblastoma multiforme(114;0.000465)|Kidney(64;0.000476)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(64;0.00634)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)	5	799	-		Colorectal(325;3.46e-05)|all_lung(284;5.32e-05)|Lung NSC(340;5.51e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)	59		B7Z3W3|Q5SSJ2	Frame_Shift_Del	DEL	ENST00000444387.2	37	c.175delC	CCDS44080.1																																																																																									0.657	SH2D5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007455.2	.	.	2	2	6	6	XM_375698		2			4	0.33						2	4	0.33
BAP1	8314	broad.mit.edu	37	3	52440322	52440363	+	In_Frame_Del	DEL	TGGCCTCATACTTGATCCTGCGGTCGGGCACCACTGCCATCA	TGGCCTCATACTTGATCCTGCGGTCGGGCACCACTGCCATCA	-	rs367867008|rs138180791		TCGA-V4-A9EV-01A-11D-A39W-08	TCGA-V4-A9EV-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71f74e00-8749-4728-be0c-8daf403005be	91f22713-25ca-4cf0-8c3e-ded4ea72d224	g.chr3:52440322_52440363delTGGCCTCATACTTGATCCTGCGGTCGGGCACCACTGCCATCA	ENST00000460680.1	-	9	1160_1201	c.689_730delTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCA	c.(688-732)ctgatggcagtggtgcccgaccgcaggatcaagtatgaggccagg>cgg	p.LMAVVPDRRIKYEA230del	BAP1_ENST00000296288.5_Splice_Site_p.DGSGAR221del	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.V234fs*15(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		ACATGCAGCCTGGCCTCATACTTGATCCTGCGGTCGGGCACCACTGCCATCAGGTTGAAGCG	0.628			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															GBM(101;493 1458 7992 21037 25532)	ENST00000460680.1		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	1	Deletion - Frameshift(1)	pleura(1)	NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180						c.(688-732)ctgatggcagtggtgcccgaccgcaggatcaagtatgaggccagg>cgg	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)																																			SO:0001651	inframe_deletion	8314			anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	g.chr3:52440322_52440363delTGGCCTCATACTTGATCCTGCGGTCGGGCACCACTGCCATCA	AF045581	AF045581	CCDS2853.1	CCDS2853.1	3p21.31-p21.2	2014-09-17			2014-09-17			ENSG00000163930	ENSG00000163930	ENSG00000163930	ENSG00000163930				950	950	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			603089	603089						9528852	9528852	Standard	Standard	NM_004656	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	uc003ddx.4	Q92560	Q92560	OTTHUMG00000158392	OTTHUMG00000158392	ENST00000460680.1:c.689_730delTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCA	3:g.52440322_52440363delTGGCCTCATACTTGATCCTGCGGTCGGGCACCACTGCCATCA	ENSP00000417132:p.Leu230_Ala243del		BAP1_ENST00000296288.5_Splice_Site_p.DGSGAR221del	p.LMAVVPDRRIKYEA230del	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN		BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	9	1160_1201	-			0		B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	In_Frame_Del	DEL	ENST00000460680.1		c.689_730delTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCA	CCDS2853.1																																																																																									0.628	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	1.980000e+01	2.555000e+01	-10	-10	34	34			7			15	3.480000e-01						7	15	0.348
