#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_ ensembl_gene_id	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_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_GMAF	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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_dbSNP	i_default_gene_name	i_deletion_substructures	i_domain	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_name	i_gene_name_source	i_gene_type	i_havana_transcript	i_n_alt_count	i_n_alt_count_full	i_n_alt_count_val	i_n_ref_count	i_n_ref_count_full	i_n_ref_count_val	i_normal_vaf	i_normal_vaf_val	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_t_alt_count_full	i_t_alt_count_val	i_t_ref_count_full	i_t_ref_count_val	i_tier	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_vaf	i_tumor_vaf_val	i_type	i_ucsc_cons	i_variant	t_alt_count	t_ref_count
ETV5	2119	genome.wustl.edu	37	3	185823280	185823280	+	Missense_Mutation	SNP	A	A	G			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr3:185823280A>G	ENST00000306376.5	-	4	385	c.139T>C	c.(139-141)Ttt>Ctt	p.F47L	DGKG_ENST00000447054.1_5'Flank|ETV5_ENST00000434744.1_Missense_Mutation_p.F47L|ETV5_ENST00000537818.1_Missense_Mutation_p.F89L	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	47					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			AGATCCTGAAATAGCTCTGAA	0.403			T	"""TMPRSS2, SCL45A3"""	Prostate								ENSG00000244405																												Dom	yes		3	3q28	2119	ets variant gene 5		E	0													76.0	82.0	80.0					3																	185823280		2203	4300	6503	SO:0001583	missense	0			-	BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"""ets-related molecule"""	601600	"""ets variant gene 5 (ets-related molecule)"""			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.139T>C	3.37:g.185823280A>G	ENSP00000306894:p.Phe47Leu		A6NH46|B7Z7D7|Q6IBN5	Missense_Mutation	SNP	pfam_ETS_PEA3_N,pfam_Ets_dom,smart_Ets_dom,pfscan_Ets_dom,prints_Ets_dom	p.F89L	ENST00000306376.5	37	c.265	CCDS33906.1	3	.	.	.	.	.	.	.	.	.	.	A	22.7	4.328041	0.81690	.	.	ENSG00000244405	ENST00000306376;ENST00000434744;ENST00000537818;ENST00000440773;ENST00000421809;ENST00000413301;ENST00000422039	T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.35	5.35	0.76521	PEA3-type ETS-domain transcription factor, N-terminal (1);	0.052176	0.85682	D	0.000000	T	0.69133	0.3077	M	0.81112	2.525	0.51482	D	0.999927	D;D	0.69078	0.997;0.979	D;D	0.77004	0.989;0.982	T	0.73994	-0.3807	10	0.87932	D	0	.	13.1469	0.59467	1.0:0.0:0.0:0.0	.	47;89	P41161;B7Z7D7	ETV5_HUMAN;.	L	47;47;89;47;47;47;47	ENSP00000306894:F47L;ENSP00000413755:F47L;ENSP00000441737:F89L;ENSP00000389707:F47L;ENSP00000412171:F47L;ENSP00000405157:F47L;ENSP00000388737:F47L	ENSP00000306894:F47L	F	-	1	0	ETV5	187305974	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	8.226000	0.89785	2.147000	0.66899	0.379000	0.24179	TTT	-	ETV5	-	pfam_ETS_PEA3_N		0.403	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ETV5	HGNC	protein_coding	OTTHUMT00000344947.1	0	0	0	36	36	101	0.00	0.00	A	NM_004454		185823280	-1	11	17	39	87	tier1	no_errors	ENST00000537818	ensembl	human	known	74_37	missense	22.00	16.35	SNP	1.000	G	11	39
HYDIN	54768	genome.wustl.edu	37	16	70841824	70841824	+	Missense_Mutation	SNP	C	C	T	rs199657414		TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr16:70841824C>T	ENST00000393567.2	-	86	15175	c.15025G>A	c.(15025-15027)Gca>Aca	p.A5009T		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	5009					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TCTCCACCTGCGAGCGATGAT	0.582													ENSG00000157423																																					0													87.0	91.0	90.0					16																	70841824		2000	4170	6170	SO:0001583	missense	0			-	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.15025G>A	16.37:g.70841824C>T	ENSP00000377197:p.Ala5009Thr		A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	superfamily_P-loop_NTPase,superfamily_PapD-like	p.A5009T	ENST00000393567.2	37	c.15025	CCDS59269.1	16	.	.	.	.	.	.	.	.	.	.	C	3.757	-0.050399	0.07407	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00792	5.69	6.17	-7.19	0.01500	.	1.715750	0.04730	N	0.420971	T	0.00412	0.0013	N	0.04090	-0.28	0.09310	N	1	B	0.21688	0.059	B	0.15870	0.014	T	0.48352	-0.9043	10	0.14252	T	0.57	.	4.1725	0.10336	0.1094:0.4365:0.1801:0.274	.	5008	F8WD23	.	T	5009;5008	ENSP00000377197:A5009T	ENSP00000313052:A5008T	A	-	1	0	HYDIN	69399325	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.186000	0.03070	-1.845000	0.01176	-0.140000	0.14226	GCA	rs199657414	HYDIN	-	NULL		0.582	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	HYDIN	HGNC	protein_coding	OTTHUMT00000398624.3	0	0	0	42	42	102	0.00	0.00	C			70841824	-1	11	21	68	96	tier1	no_errors	ENST00000393567	ensembl	human	putative	74_37	missense	13.92	17.95	SNP	0.000	T	11	68
KDM5B	10765	genome.wustl.edu	37	1	202709871	202709871	+	Silent	SNP	G	G	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr1:202709871G>A	ENST00000367265.3	-	20	4179	c.3015C>T	c.(3013-3015)ccC>ccT	p.P1005P	KDM5B_ENST00000367264.2_Silent_p.P1041P	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1005					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						CCGCACCATTGGGCAGATATG	0.453													ENSG00000117139																																					0													80.0	82.0	82.0					1																	202709871		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.3015C>T	1.37:g.202709871G>A			O95811|Q15752|Q9Y3Q5	Silent	SNP	pfam_Lys_sp_deMease_like_dom,pfam_JmjC_dom,pfam_Znf_PHD-finger,pfam_ARID/BRIGHT_D-bd,pfam_Znf_C5HC2,pfam_TF_JmjN,superfamily_ARID/BRIGHT_D-bd,superfamily_Znf_FYVE_PHD,smart_TF_JmjN,smart_ARID/BRIGHT_D-bd,smart_Znf_PHD,smart_JmjC_dom,pfscan_TF_JmjN,pfscan_JmjC_dom,pfscan_Znf_PHD-finger,pfscan_ARID/BRIGHT_D-bd	p.P1041	ENST00000367265.3	37	c.3123	CCDS30974.1	1																																																																																			-	KDM5B	-	pfam_Lys_sp_deMease_like_dom		0.453	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KDM5B	HGNC	protein_coding	OTTHUMT00000099184.2	0	0	0	42	42	73	0.00	0.00	G	NM_006618		202709871	-1	4	9	29	69	tier1	no_errors	ENST00000367264	ensembl	human	known	74_37	silent	12.12	11.54	SNP	1.000	A	4	29
NYAP2	57624	genome.wustl.edu	37	2	226516263	226516263	+	Silent	SNP	G	G	A	rs374009602		TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr2:226516263G>A	ENST00000272907.6	+	6	2357	c.1944G>A	c.(1942-1944)tcG>tcA	p.S648S		NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	648					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												TACCATCATCGTTAGCCAATC	0.502													ENSG00000144460																																					0								G		1,4227		0,1,2113	242.0	244.0	243.0		1944	4.8	1.0	2		243	0,8462		0,0,4231	no	coding-synonymous	KIAA1486	NM_020864.1		0,1,6344	AA,AG,GG		0.0,0.0237,0.0079		648/654	226516263	1,12689	2114	4231	6345	SO:0001819	synonymous_variant	0			-	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1944G>A	2.37:g.226516263G>A			A2RRN4|Q96NL2	Silent	SNP	NULL	p.S648	ENST00000272907.6	37	c.1944	CCDS46529.1	2																																																																																			-	NYAP2	-	NULL		0.502	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NYAP2	HGNC	protein_coding	OTTHUMT00000331258.1	0	0	0	44	44	96	0.00	0.00	G	NM_020864		226516263	+1	10	24	44	75	tier1	no_errors	ENST00000272907	ensembl	human	known	74_37	silent	18.52	24.24	SNP	1.000	A	10	44
ARHGEF9	23229	genome.wustl.edu	37	X	62898428	62898429	+	Frame_Shift_Ins	INS	-	-	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chrX:62898428_62898429insA	ENST00000253401.6	-	5	1385_1386	c.585_586insT	c.(583-588)tctgagfs	p.E196fs	ARHGEF9_ENST00000374872.1_Frame_Shift_Ins_p.E175fs|ARHGEF9_ENST00000433323.2_5'Flank|ARHGEF9_ENST00000495564.1_5'UTR|ARHGEF9_ENST00000374878.1_Frame_Shift_Ins_p.E194fs|ARHGEF9_ENST00000374870.4_Frame_Shift_Ins_p.E94fs|ARHGEF9_ENST00000437457.2_Frame_Shift_Ins_p.E143fs	NM_015185.2	NP_056000.1	O43307	ARHG9_HUMAN	Cdc42 guanine nucleotide exchange factor (GEF) 9	196	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|ion transmembrane transport (GO:0034220)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|skin(1)	35						TTACAATACTCAGAGTATATCC	0.455													ENSG00000131089																																					0																																										SO:0001589	frameshift_variant	0				AB007884	CCDS35315.1, CCDS55429.1, CCDS55430.1	Xq11.1	2013-01-10			ENSG00000131089	ENSG00000131089		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14561	protein-coding gene	gene with protein product	"""collybistin"""	300429				10559246, 9455477	Standard	NM_015185		Approved	KIAA0424, PEM-2	uc011mot.2	O43307	OTTHUMG00000021700	ENST00000253401.6:c.586dupT	X.37:g.62898429_62898429dupA	ENSP00000253401:p.Glu196fs		A8K1S8|B4DHC7|F8W7P8|Q5JSL6	Frame_Shift_Ins	INS	pfam_DH-domain,pfam_SH3_2,pfam_SH3_domain,pfam_Pleckstrin_homology,superfamily_DH-domain,superfamily_SH3_domain,smart_SH3_domain,smart_DH-domain,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_SH3_domain,pfscan_DH-domain	p.E195fs	ENST00000253401.6	37	c.586_585	CCDS35315.1	X																																																																																				ARHGEF9	-	pfam_DH-domain,superfamily_DH-domain,smart_DH-domain,pfscan_DH-domain		0.455	ARHGEF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARHGEF9	HGNC	protein_coding	OTTHUMT00000056937.1	0	0	0	25	25	44	0.00	0.00	-			62898429	-1	9	15	21	16	tier1	no_errors	ENST00000253401	ensembl	human	known	74_37	frame_shift_ins	30.00	48.39	INS	1.000:0.981	A	9	21
CGN	57530	genome.wustl.edu	37	1	151503079	151503079	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr1:151503079G>T	ENST00000271636.7	+	13	2561	c.2428G>T	c.(2428-2430)Gcc>Tcc	p.A810S	SNORA44_ENST00000517031.1_RNA	NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	804	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCGGGGGCTGGCCCGCCTGGG	0.697													ENSG00000143375																																					0													16.0	18.0	17.0					1																	151503079		2197	4290	6487	SO:0001583	missense	0			-	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.2428G>T	1.37:g.151503079G>T	ENSP00000271636:p.Ala810Ser		A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	pfam_Myosin_tail	p.A810S	ENST00000271636.7	37	c.2428	CCDS999.1	1	.	.	.	.	.	.	.	.	.	.	G	2.292	-0.362207	0.05103	.	.	ENSG00000143375	ENST00000271636	T	0.62639	0.01	4.99	-1.44	0.08856	.	0.484241	0.24659	N	0.036643	T	0.09423	0.0232	N	0.03608	-0.345	0.09310	N	1	B	0.13594	0.008	B	0.06405	0.002	T	0.37056	-0.9722	10	0.07813	T	0.8	-0.0757	5.3336	0.15945	0.4638:0.0:0.4026:0.1336	.	804	Q9P2M7	CING_HUMAN	S	810	ENSP00000271636:A810S	ENSP00000271636:A810S	A	+	1	0	CGN	149769703	0.002000	0.14202	0.875000	0.34327	0.967000	0.64934	-0.052000	0.11865	-0.175000	0.10725	-0.259000	0.10710	GCC	-	CGN	-	NULL		0.697	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CGN	HGNC	protein_coding	OTTHUMT00000034900.3	0	0	0	35	35	9	0.00	0.00	G	NM_020770		151503079	+1	4	0	22	4	tier1	no_errors	ENST00000271636	ensembl	human	known	74_37	missense	15.38	0.00	SNP	0.001	T	4	22
SCG3	29106	genome.wustl.edu	37	15	51987959	51987960	+	Intron	INS	-	-	A	rs78233272|rs370571693		TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr15:51987959_51987960insA	ENST00000220478.3	+	8	1271				SCG3_ENST00000542355.2_Intron|RP11-313P18.2_ENST00000559918.1_lincRNA	NM_013243.3	NP_037375.2	Q8WXD2	SCG3_HUMAN	secretogranin III						blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				all cancers(107;0.00488)		cctcgtctttgaaaaaaaaaaa	0.401													ENSG00000259241																																					0																																										SO:0001627	intron_variant	0				AF078851	CCDS10142.1, CCDS53947.1	15q21.2	2013-09-23			ENSG00000104112	ENSG00000104112			13707	protein-coding gene	gene with protein product		611796				2053134, 8825061	Standard	NM_013243		Approved	SGIII, FLJ90833	uc002abh.3	Q8WXD2	OTTHUMG00000131748	ENST00000220478.3:c.869-112->A	15.37:g.51987970_51987970dupA			A8K2B0|B3KQP6|B4DK99|F5H3R8|Q96C83|Q96GE8|Q9Y6G7	R	INS	-	NULL	ENST00000220478.3	37	NULL	CCDS10142.1	15																																																																																				RP11-313P18.2	-	-		0.401	SCG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000259241	Clone_based_vega_gene	protein_coding	OTTHUMT00000254670.2	0	0	0	15	15	1	0.00	0.00	-	NM_013243		51987960	-1	4	0	14	0	tier1	no_errors	ENST00000559918	ensembl	human	known	74_37	rna	22.22	0.00	INS	0.003:0.006	A	4	14
LRBA	987	genome.wustl.edu	37	4	151186065	151186069	+	3'UTR	DEL	AACAA	AACAA	-	rs113745272|rs9307874|rs75691255	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	AACAA	AACAA					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr4:151186065_151186069delAACAA	ENST00000357115.3	-	0	9640_9644				LRBA_ENST00000535741.1_3'UTR|LRBA_ENST00000510413.1_3'UTR|LRBA_ENST00000503716.1_5'UTR	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing							cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					GGGGTGCCCCAACAAAACAACAGTG	0.459													ENSG00000198589		2931	0.585264	0.3865	0.6974	5008	,	,		16738	0.4762		0.6501	False		,,,				2504	0.82																0																																										SO:0001624	3_prime_UTR_variant	0				AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.*809TTGTT>-	4.37:g.151186070_151186074delAACAA			Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	R	DEL	-	NULL	ENST00000357115.3	37	NULL	CCDS3773.1	4																																																																																				LRBA	-	-		0.459	LRBA-002	KNOWN	basic|CCDS	protein_coding	LRBA	HGNC	protein_coding	OTTHUMT00000364939.1	0	0	0	4	4	4	0.00	0.00	AACAA			151186069	-1	0	0	9	9	tier1	no_errors	ENST00000503716	ensembl	human	known	74_37	rna	0.00	0.00	DEL	0.005:0.005:0.005:0.005:0.004	-	0	9
MT-CO1	4512	genome.wustl.edu	37	M	6733	6733	+	Missense_Mutation	SNP	T	T	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chrM:6733T>A	ENST00000361624.2	+	1	830	c.830T>A	c.(829-831)aTg>aAg	p.M277K	MT-ATP8_ENST00000361851.1_5'Flank|MT-TQ_ENST00000387372.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TM_ENST00000387377.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	277					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						GGTCTGAGCTATGATATCAAT	0.393													ENSG00000198804																																					0																																										SO:0001583	missense	0			-			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.830T>A	M.37:g.6733T>A	ENSP00000354499:p.Met277Lys		Q34770	Missense_Mutation	SNP	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom,prints_Cyt_c_Oxase_su1	p.M277K	ENST00000361624.2	37	c.830		MT																																																																																			-	MT-CO1	-	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom		0.393	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	MT-CO1	HGNC	protein_coding		0	0	0	153	153	2	0.00	0.00	T	YP_003024028		6733	+1	2	0	13	0	tier1	no_errors	ENST00000361624	ensembl	human	known	74_37	missense	13.33	0.00	SNP	NULL	A	2	13
MT-ND5	4540	genome.wustl.edu	37	M	12684	12684	+	Silent	SNP	G	G	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chrM:12684G>A	ENST00000361567.2	+	1	348	c.348G>A	c.(346-348)caG>caA	p.Q116Q	MT-TR_ENST00000387439.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	116					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						AACATTAATCAGTTCTTCAAA	0.368													ENSG00000198786																																					0																																										SO:0001819	synonymous_variant	0			-			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.348G>A	M.37:g.12684G>A			Q34773|Q8WCY3	Silent	SNP	pfam_DH_UbQ/plastoQ_OxRdtase,pfam_DH_DH_su5_C,pfam_DH_UbQ_OxRdtase_chain5/L_N,tigrfam_DHpl_OxRdtase_5	p.Q116	ENST00000361567.2	37	c.348		MT																																																																																			rs28410409	MT-ND5	-	pfam_DH_UbQ_OxRdtase_chain5/L_N,tigrfam_DHpl_OxRdtase_5		0.368	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	MT-ND5	HGNC	protein_coding		0	0	0	188	188	1	0.00	0.00	G	YP_003024036		12684	+1	6	0	25	1	tier1	no_errors	ENST00000361567	ensembl	human	known	74_37	silent	19.35	0.00	SNP	NULL	A	6	25
MT-ND5	4540	genome.wustl.edu	37	M	12705	12705	+	Silent	SNP	C	C	T			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chrM:12705C>T	ENST00000361567.2	+	1	369	c.369C>T	c.(367-369)atC>atT	p.I123I	MT-TR_ENST00000387439.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	123					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TATCTACTCATTTTCCTAATT	0.373													ENSG00000198786																																					0																																										SO:0001819	synonymous_variant	0			-			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.369C>T	M.37:g.12705C>T			Q34773|Q8WCY3	Silent	SNP	pfam_DH_UbQ/plastoQ_OxRdtase,pfam_DH_DH_su5_C,pfam_DH_UbQ_OxRdtase_chain5/L_N,tigrfam_DHpl_OxRdtase_5	p.I123	ENST00000361567.2	37	c.369		MT																																																																																			rs2854122	MT-ND5	-	pfam_DH_UbQ_OxRdtase_chain5/L_N,tigrfam_DHpl_OxRdtase_5		0.373	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	MT-ND5	HGNC	protein_coding		0	0	0	178	178	1	0.00	0.00	C	YP_003024036		12705	+1	5	0	19	2	tier1	no_errors	ENST00000361567	ensembl	human	known	74_37	silent	20.83	0.00	SNP	NULL	T	5	19
MT-ND5	4540	genome.wustl.edu	37	M	13177	13177	+	Missense_Mutation	SNP	G	G	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chrM:13177G>A	ENST00000361567.2	+	1	841	c.841G>A	c.(841-843)Ggc>Agc	p.G281S	MT-TR_ENST00000387439.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TP_ENST00000387461.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	281					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CACTATGCTTAGGCGCTATCA	0.448													ENSG00000198786																																					0																																										SO:0001583	missense	0			-			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.841G>A	M.37:g.13177G>A	ENSP00000354813:p.Gly281Ser		Q34773|Q8WCY3	Missense_Mutation	SNP	pfam_DH_UbQ/plastoQ_OxRdtase,pfam_DH_DH_su5_C,pfam_DH_UbQ_OxRdtase_chain5/L_N,tigrfam_DHpl_OxRdtase_5	p.G281S	ENST00000361567.2	37	c.841		MT																																																																																			-	MT-ND5	-	pfam_DH_UbQ/plastoQ_OxRdtase,tigrfam_DHpl_OxRdtase_5		0.448	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	MT-ND5	HGNC	protein_coding		0	0	0	216	216	0	0.00	0.00	G	YP_003024036		13177	+1	6	0	20	0	tier1	no_errors	ENST00000361567	ensembl	human	known	74_37	missense	23.08	0.00	SNP	NULL	A	6	20
PPP2R2B	5521	genome.wustl.edu	37	5	146258290	146258291	+	5'UTR	INS	-	-	GCTGCTGCT	rs142461655|rs57408722|rs10591869	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr5:146258290_146258291insGCTGCTGCT	ENST00000453001.1	-	0	166_167				PPP2R2B_ENST00000394411.4_5'UTR|PPP2R2B_ENST00000530902.1_5'UTR|PPP2R2B_ENST00000394413.3_5'Flank|PPP2R2B_ENST00000394410.2_Intron|PPP2R2B_ENST00000336640.6_Intron|PPP2R2B_ENST00000394414.1_Intron|PPP2R2B_ENST00000508545.2_Intron|PPP2R2B_ENST00000504198.1_Intron|PPP2R2B_ENST00000356826.3_Intron|PPP2R2B_ENST00000394409.3_Intron			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta						apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCGCACTCGCAgctgctgctgc	0.718													ENSG00000156475		1222	0.24401	0.2375	0.2262	5008	,	,		13292	0.3562		0.1421	False		,,,				2504	0.2546																0																																										SO:0001623	5_prime_UTR_variant	0				M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9305	protein-coding gene	gene with protein product	"""PP2A subunit B isoform beta"""	604325	"""spinocerebellar ataxia 12"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"""	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000453001.1:c.-152->AGCAGCAGC	5.37:g.146258291_146258299dupGCTGCTGCT			A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	R	INS	-	NULL	ENST00000453001.1	37	NULL	CCDS4284.1	5																																																																																				PPP2R2B	-	-		0.718	PPP2R2B-204	KNOWN	basic|appris_principal|CCDS	protein_coding	PPP2R2B	HGNC	protein_coding	OTTHUMT00000388939.2	0	0	0	0	0	0	0.00	0.00	-	NM_181678		146258291	-1	0	0	3	3	tier1	no_errors	ENST00000530902	ensembl	human	known	74_37	rna	0.00	0.00	INS	0.975:0.996	GCTGCTGCT	0	3
