#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_BAM_File	i_CAF	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_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_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_type	i_havana_transcript	i_normal_ref_reads	i_normal_ref_reads_val	i_normal_vaf	i_normal_vaf_val	i_normal_var_reads	i_normal_var_reads_val	i_reference	i_refseq_mrna_id	i_rsID	i_rsID_ref_var_alleles	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_ref_reads	i_tumor_ref_reads_val	i_tumor_vaf	i_tumor_vaf_val	i_tumor_var_reads	i_tumor_var_reads_val	i_type	i_ucsc_cons	i_variant
MT-ND5	4540	genome.wustl.edu	37	M	13753	13753	+	Missense_Mutation	SNP	T	T	C			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chrM:13753T>C	ENST00000361567.2	+	1	1417	c.1417T>C	c.(1417-1419)Tcc>Ccc	p.S473P	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TT_ENST00000387460.2_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	473					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						CTAACAACATTTCCCCCGCAT	0.483																																							0											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.1417T>C	M.37:g.13753T>C	ENSP00000354813:p.Ser473Pro		Q34773|Q8WCY3	Missense_Mutation	SNP	pfam_NADH_UbQ/plastoQ_OxRdtase,pfam_NADH_DH_su5_C,pfam_NADH_UbQ_OxRdtase_chain5/L_N,tigrfam_NADHpl_OxRdtase_5	p.S473P	ENST00000361567.2	37	c.1417		MT																																																																																			0	pfam_NADH_DH_su5_C,tigrfam_NADHpl_OxRdtase_5		0.483	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	MT-ND5	protein_coding		16	3	0	0.00	0	0	T	YP_003024036	0	0		13753	1	no_errors	ENST00000361567	ensembl	human	known	74_37	missense	2	1	80	83.33	8	5	SNP	NULL	C
COL11A1	1301	genome.wustl.edu	37	1	103540214	103540214	+	Missense_Mutation	SNP	G	G	A	rs199595073		TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr1:103540214G>A	ENST00000370096.3	-	4	923	c.611C>T	c.(610-612)aCg>aTg	p.T204M	COL11A1_ENST00000512756.1_Missense_Mutation_p.T204M|COL11A1_ENST00000353414.4_Missense_Mutation_p.T204M|COL11A1_ENST00000358392.2_Missense_Mutation_p.T204M	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	204	Laminin G-like.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TCCAAAAACCGTGATTCCATT	0.353													G|||	1	0.000199681	0.0	0.0	5008	,	,		18022	0.001		0.0	False		,,,				2504	0.0						0.9998,0.0001997											0													152.0	137.0	142.0					1																	103540214		2203	4300	6503	SO:0001583	missense	0			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.611C>T	1.37:g.103540214G>A	ENSP00000359114:p.Thr204Met		B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	pfam_Collagen,pfam_Fib_collagen_C,pfam_Laminin_G,superfamily_ConA-like_lec_gl_sf,superfamily_Fibrinogen_a/b/g_C_dom,smart_Laminin_G,smart_Fib_collagen_C	p.T204M	ENST00000370096.3	37	c.611	CCDS778.1	1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	13.02	2.112117	0.37242	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239;ENST00000447608	T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	5.73	3.85	0.44370	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);Laminin G, subdomain 2 (1);	0.105191	0.64402	N	0.000004	T	0.78892	0.4355	M	0.73598	2.24	0.44660	D	0.997641	D;D;B;B	0.67145	0.989;0.996;0.038;0.047	P;P;B;B	0.62491	0.903;0.844;0.015;0.031	T	0.78650	-0.2121	10	0.44086	T	0.13	.	9.0416	0.36321	0.2256:0.0:0.7744:0.0	.	204;204;204;204	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	M	204;204;204;204;204;131	ENSP00000359114:T204M;ENSP00000351163:T204M;ENSP00000302551:T204M;ENSP00000426533:T204M;ENSP00000408640:T204M;ENSP00000410177:T131M	ENSP00000302551:T204M	T	-	2	0	COL11A1	103312802	0.997000	0.39634	0.643000	0.29450	0.998000	0.95712	2.497000	0.45354	0.750000	0.32877	0.650000	0.86243	ACG	0	pfam_Laminin_G,superfamily_ConA-like_lec_gl_sf,smart_Laminin_G		0.353	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	COL11A1	protein_coding	OTTHUMT00000029997.1	78	358	0	0.00	0	0	G	NM_080630	rs199595073	G->A		103540214	-1	no_errors	ENST00000358392	ensembl	human	known	74_37	missense	58	248	13.43	8.15	9	22	SNP	0.991	A
PKLR	5313	genome.wustl.edu	37	1	155265093	155265093	+	Splice_Site	SNP	C	C	T			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr1:155265093C>T	ENST00000342741.4	-	5	546	c.508G>A	c.(508-510)Ggt>Agt	p.G170S	PKLR_ENST00000392414.3_Splice_Site_p.G139S	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	170					ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	GACTCTGGACCCTAAGGAGGG	0.687																																							0											0													44.0	52.0	49.0					1																	155265093		2201	4298	6499	SO:0001630	splice_region_variant	0			BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.508-1G>A	1.37:g.155265093C>T			O75758|P11973	Missense_Mutation	SNP	pfam_Pyrv_Knase_brl,pfam_Pyrv_Knase_C,superfamily_Pyrv/PenolPyrv_Kinase-like_dom,superfamily_Pyrv_Knase_C,superfamily_Pyrv_Knase-like_insert_dom,prints_Pyr_Knase,tigrfam_Pyr_Knase	p.G170S	ENST00000342741.4	37	c.508	CCDS1109.1	1	.	.	.	.	.	.	.	.	.	.	C	11.43	1.636349	0.29068	.	.	ENSG00000143627	ENST00000423816;ENST00000392414;ENST00000342741;ENST00000271946	D;D	0.99751	-6.63;-6.63	4.05	4.05	0.47172	Pyruvate/Phosphoenolpyruvate kinase (1);Pyruvate kinase, beta-barrel insert domain (1);Pyruvate kinase-like, insert domain (1);Pyruvate kinase, barrel (1);	0.257566	0.38720	N	0.001582	D	0.97914	0.9314	L	0.28776	0.89	0.49687	D	0.999816	B;B	0.10296	0.003;0.003	B;B	0.19148	0.024;0.024	D	0.99965	1.1839	10	0.20519	T	0.43	-12.6638	14.0736	0.64874	0.0:1.0:0.0:0.0	.	170;161	P30613;B1AVT1	KPYR_HUMAN;.	S	195;139;170;84	ENSP00000376214:G139S;ENSP00000339933:G170S	ENSP00000271946:G84S	G	-	1	0	PKLR	153531717	1.000000	0.71417	0.955000	0.39395	0.060000	0.15804	4.348000	0.59379	2.251000	0.74343	0.289000	0.19496	GGT	0	pfam_Pyrv_Knase_brl,superfamily_Pyrv/PenolPyrv_Kinase-like_dom,superfamily_Pyrv_Knase-like_insert_dom,tigrfam_Pyr_Knase		0.687	PKLR-001	KNOWN	basic|CCDS	protein_coding	PKLR	protein_coding	OTTHUMT00000087407.2	74	57	1.33	0.00	1	0	C	NM_000298	0	0	Missense_Mutation	155265093	-1	no_errors	ENST00000342741	ensembl	human	known	74_37	missense	85	79	14.14	7.06	14	6	SNP	1	T
PCDHGB1	56104	genome.wustl.edu	37	5	140730598	140730598	+	Silent	SNP	C	C	T			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr5:140730598C>T	ENST00000523390.1	+	1	771	c.771C>T	c.(769-771)tcC>tcT	p.S257S	PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	257	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGGAACCTCCGTGCTGCGGG	0.507																																							0											0													99.0	106.0	104.0					5																	140730598		2034	4184	6218	SO:0001819	synonymous_variant	0			AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.771C>T	5.37:g.140730598C>T			Q3SY75|Q9Y5C8	Silent	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.S257	ENST00000523390.1	37	c.771	CCDS54923.1	5																																																																																			0	pfam_Cadherin,superfamily_Cadherin-like,pfscan_Cadherin,prints_Cadherin		0.507	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHGB1	protein_coding	OTTHUMT00000374740.1	44	240	0	0.00	0	0	C	NM_018922	0	0		140730598	1	no_errors	ENST00000523390	ensembl	human	known	74_37	silent	58	212	9.23	9.01	6	21	SNP	0	T
CNKSR3	154043	genome.wustl.edu	37	6	154763352	154763352	+	Missense_Mutation	SNP	T	T	C			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr6:154763352T>C	ENST00000607772.1	-	3	833	c.289A>G	c.(289-291)Aat>Gat	p.N97D	CNKSR3_ENST00000479339.1_Missense_Mutation_p.N17D	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	97	CRIC. {ECO:0000255|PROSITE- ProRule:PRU00621}.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		CTTATGTAATTCTGTAAATTG	0.463																																							0											0													91.0	98.0	95.0					6																	154763352		2203	4300	6503	SO:0001583	missense	0			AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"""Sterile alpha motif (SAM) domain containing"""	23034	protein-coding gene	gene with protein product			"""membrane associated guanylate kinase interacting protein-like 1"""	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.289A>G	6.37:g.154763352T>C	ENSP00000475915:p.Asn97Asp		Q5SGD5|Q96N65	Missense_Mutation	SNP	pfam_CNKSR2,pfam_CRIC_domain_Chordata,pfam_SAM_type1,pfam_SAM_2,pfam_PDZ,superfamily_SAM/pointed,superfamily_PDZ,smart_SAM,smart_PDZ,pfscan_PDZ,pfscan_SAM	p.N97D	ENST00000607772.1	37	c.289	CCDS5246.1	6	.	.	.	.	.	.	.	.	.	.	T	18.73	3.686069	0.68157	.	.	ENSG00000153721	ENST00000367213;ENST00000479339	T;T	0.50813	1.38;0.73	5.57	5.57	0.84162	CRIC domain (1);CRIC domain, Chordata (1);	0.273852	0.41605	D	0.000853	T	0.32645	0.0836	L	0.53249	1.67	0.34104	D	0.662199	P	0.38677	0.642	B	0.36808	0.233	T	0.44636	-0.9315	10	0.56958	D	0.05	.	16.023	0.80512	0.0:0.0:0.0:1.0	.	97	Q6P9H4	CNKR3_HUMAN	D	97;17	ENSP00000356182:N97D;ENSP00000418975:N17D	ENSP00000356182:N97D	N	-	1	0	CNKSR3	154805044	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.926000	0.70070	2.244000	0.73946	0.533000	0.62120	AAT	0	pfam_CRIC_domain_Chordata		0.463	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CNKSR3	protein_coding	OTTHUMT00000042792.2	69	204	0	0.00	0	0	T	NM_173515	0	0		154763352	-1	no_errors	ENST00000607772	ensembl	human	known	74_37	missense	100	208	10.71	11.49	12	27	SNP	1	C
PEG10	23089	genome.wustl.edu	37	7	94293816	94293816	+	Silent	SNP	G	G	A			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr7:94293816G>A	ENST00000482108.1	+	2	1427	c.948G>A	c.(946-948)tcG>tcA	p.S316S	PEG10_ENST00000488574.1_Silent_p.S316S	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10	316					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			CAAAGTCTTCGCCGGCGGGAA	0.547																																							0											0													15.0	19.0	18.0					7																	94293816		1900	4084	5984	SO:0001819	synonymous_variant	0			AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265			14005	protein-coding gene	gene with protein product		609810				11318613, 15716091, 16093683	Standard	NM_001172437		Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	ENST00000482108.1:c.948G>A	7.37:g.94293816G>A			Q96A68|Q9UPV1	Silent	SNP	pfam_Retrotrans_gag_dom,superfamily_Znf_CCHC,pfscan_Znf_CCHC	p.S316	ENST00000482108.1	37	c.948	CCDS55126.1	7																																																																																			0	superfamily_Znf_CCHC		0.547	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PEG10	protein_coding	OTTHUMT00000340751.1	66	113	0	0.00	0	0	G	NM_015068	0	0		94293816	1	no_errors	ENST00000482108	ensembl	human	known	74_37	silent	69	102	10.39	6.42	8	7	SNP	0.972	A
KAT6A	7994	genome.wustl.edu	37	8	41791074	41791074	+	Missense_Mutation	SNP	C	C	T			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr8:41791074C>T	ENST00000396930.3	-	18	5207	c.4664G>A	c.(4663-4665)aGc>aAc	p.S1555N	KAT6A_ENST00000265713.2_Missense_Mutation_p.S1555N|KAT6A_ENST00000406337.1_Missense_Mutation_p.S1555N	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1555	Interaction with PML.|Interaction with RUNX1-2.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GCTCTCAATGCTGCCCAGGTC	0.567																																							0											0													92.0	82.0	85.0					8																	41791074		2203	4300	6503	SO:0001583	missense	0			U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.4664G>A	8.37:g.41791074C>T	ENSP00000380136:p.Ser1555Asn		Q76L81	Missense_Mutation	SNP	pfam_MOZ_SAS,pfam_Znf_PHD-finger,superfamily_Acyl_CoA_acyltransferase,superfamily_Znf_FYVE_PHD,smart_Histone_H1/H5_H15,smart_Znf_PHD,pfscan_Znf_PHD-finger	p.S1555N	ENST00000396930.3	37	c.4664	CCDS6124.1	8	.	.	.	.	.	.	.	.	.	.	C	15.31	2.797084	0.50208	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.69435	-0.4;-0.4;-0.4	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.75700	0.3885	L	0.34521	1.04	0.58432	D	0.999999	D	0.71674	0.998	D	0.81914	0.995	T	0.74948	-0.3490	10	0.48119	T	0.1	-18.983	20.0051	0.97433	0.0:1.0:0.0:0.0	.	1555	Q92794	KAT6A_HUMAN	N	1555	ENSP00000265713:S1555N;ENSP00000385888:S1555N;ENSP00000380136:S1555N	ENSP00000265713:S1555N	S	-	2	0	KAT6A	41910231	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.445000	0.80570	2.799000	0.96334	0.650000	0.86243	AGC	0	NULL		0.567	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KAT6A	protein_coding	OTTHUMT00000318163.1	32	107	0	0.00	0	0	C	NM_006766	0	0		41791074	-1	no_errors	ENST00000265713	ensembl	human	known	74_37	missense	44	98	8.33	6.67	4	7	SNP	1	T
NRAP	4892	genome.wustl.edu	37	10	115374703	115374703	+	Silent	SNP	C	C	T	rs372300454		TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr10:115374703C>T	ENST00000359988.3	-	28	3325	c.3081G>A	c.(3079-3081)acG>acA	p.T1027T	NRAP_ENST00000360478.3_Silent_p.T992T|NRAP_ENST00000369358.4_Silent_p.T1035T|NRAP_ENST00000369360.3_Silent_p.T1000T	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CCTTATAACGCGTCTGTCGGG	0.473																																							0											0								T	,	1,4405	2.1+/-5.4	0,1,2202	144.0	129.0	134.0		2976,3081	-10.7	0.0	10		134	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	992/1696,1027/1731	115374703	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	0				CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3081G>A	10.37:g.115374703C>T				Silent	SNP	pfam_Nebulin_35r-motif,pfam_Znf_LIM,smart_Znf_LIM,smart_Nebulin_35r-motif,pfscan_Znf_LIM,pfscan_Nebulin_35r-motif,prints_Nebulin	p.T1035	ENST00000359988.3	37	c.3105	CCDS7579.1	10																																																																																			0	smart_Nebulin_35r-motif,pfscan_Nebulin_35r-motif		0.473	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NRAP	protein_coding	OTTHUMT00000050425.2	52	171	0	0.00	0	0	C	NM_006175	rs372300454	C->T		115374703	-1	no_errors	ENST00000369358	ensembl	human	known	74_37	silent	58	142	15.94	8.39	11	13	SNP	0.001	T
FAM111B	374393	genome.wustl.edu	37	11	58893330	58893330	+	Missense_Mutation	SNP	T	T	C			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr11:58893330T>C	ENST00000343597.3	+	4	1951	c.1760T>C	c.(1759-1761)aTa>aCa	p.I587T	FAM111B_ENST00000529618.1_Missense_Mutation_p.I557T|FAM111B_ENST00000411426.1_Missense_Mutation_p.I557T	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	587							catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						ATCAAGAAAATAGATGGTTGT	0.393																																							0											0													115.0	102.0	106.0					11																	58893330		2201	4295	6496	SO:0001583	missense	0			BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.1760T>C	11.37:g.58893330T>C	ENSP00000341565:p.Ile587Thr		B4E2G2|Q6P661	Missense_Mutation	SNP	superfamily_Trypsin-like_Pept_dom	p.I587T	ENST00000343597.3	37	c.1760	CCDS7972.1	11	.	.	.	.	.	.	.	.	.	.	T	10.91	1.484747	0.26598	.	.	ENSG00000189057	ENST00000411426;ENST00000529618;ENST00000343597	T;T;T	0.34667	1.36;1.36;1.35	4.62	0.103	0.14526	Peptidase cysteine/serine, trypsin-like (1);	0.326315	0.26715	N	0.022872	T	0.25232	0.0613	L	0.49256	1.55	0.09310	N	1	B	0.24920	0.114	B	0.23150	0.044	T	0.28933	-1.0028	10	0.12430	T	0.62	.	8.1769	0.31287	0.0:0.4396:0.0:0.5604	.	587	Q6SJ93	F111B_HUMAN	T	557;557;587	ENSP00000393855:I557T;ENSP00000432875:I557T;ENSP00000341565:I587T	ENSP00000341565:I587T	I	+	2	0	FAM111B	58649906	0.007000	0.16637	0.001000	0.08648	0.005000	0.04900	-0.299000	0.08254	-0.148000	0.11234	-0.297000	0.09499	ATA	0	superfamily_Trypsin-like_Pept_dom		0.393	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM111B	protein_coding	OTTHUMT00000393974.1	59	242	0	0.00	0	0	T	NM_198947	0	0		58893330	1	no_errors	ENST00000343597	ensembl	human	known	74_37	missense	56	236	12.5	10.61	8	28	SNP	0.013	C
TIMELESS	8914	genome.wustl.edu	37	12	56817404	56817404	+	Nonsense_Mutation	SNP	G	G	T			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr12:56817404G>T	ENST00000553532.1	-	17	2204	c.2054C>A	c.(2053-2055)tCg>tAg	p.S685*	TIMELESS_ENST00000229201.4_Nonsense_Mutation_p.S684*|TIMELESS_ENST00000554616.1_Intron					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						TTCTTTCTCCGACACCTGGAC	0.552																																							0											0													71.0	63.0	65.0					12																	56817404		2203	4300	6503	SO:0001587	stop_gained	0			AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.2054C>A	12.37:g.56817404G>T	ENSP00000450607:p.Ser685*			Nonsense_Mutation	SNP	pfam_TIMELESS_C,pfam_Timeless	p.S685*	ENST00000553532.1	37	c.2054	CCDS8918.1	12	.	.	.	.	.	.	.	.	.	.	G	40	8.384536	0.98786	.	.	ENSG00000111602	ENST00000229201;ENST00000553532	.	.	.	5.61	3.74	0.42951	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.5821	12.6738	0.56882	0.1471:0.0:0.8529:0.0	.	.	.	.	X	684;685	.	ENSP00000229201:S685X	S	-	2	0	TIMELESS	55103671	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	4.479000	0.60236	1.510000	0.48803	0.561000	0.74099	TCG	0	NULL		0.552	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TIMELESS	protein_coding	OTTHUMT00000409771.1	23	154	0	0.00	0	0	G	NM_003920	0	0		56817404	-1	no_errors	ENST00000553532	ensembl	human	known	74_37	nonsense	32	165	8.57	10.33	3	19	SNP	0.969	T
CCDC43	124808	genome.wustl.edu	37	17	42756399	42756399	+	Missense_Mutation	SNP	T	T	C			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr17:42756399T>C	ENST00000315286.8	-	5	508	c.500A>G	c.(499-501)aAc>aGc	p.N167S	CCDC43_ENST00000457422.2_Silent_p.K147K|C17orf104_ENST00000588805.1_3'UTR|CCDC43_ENST00000588210.1_Missense_Mutation_p.N170S|RP11-1072C15.4_ENST00000591628.1_RNA	NM_144609.2	NP_653210.2	Q96MW1	CCD43_HUMAN	coiled-coil domain containing 43	167										lung(2)	2		Prostate(33;0.0322)				CACATTGGTGTTTCGGAACAG	0.488																																							0											0													101.0	100.0	100.0					17																	42756399		2031	4200	6231	SO:0001583	missense	0			AK056357	CCDS45704.1, CCDS45705.1	17q21.31	2005-12-16							26472	protein-coding gene	gene with protein product						12477932	Standard	NM_001099225		Approved	FLJ31795	uc002ihc.2	Q96MW1		ENST00000315286.8:c.500A>G	17.37:g.42756399T>C	ENSP00000323782:p.Asn167Ser		C9JVK9	Missense_Mutation	SNP	NULL	p.N167S	ENST00000315286.8	37	c.500	CCDS45704.1	17	.	.	.	.	.	.	.	.	.	.	T	27.4	4.823705	0.90873	.	.	ENSG00000180329	ENST00000315286	.	.	.	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.80798	0.4692	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83131	-0.0113	8	0.87932	D	0	-30.2785	16.4675	0.84087	0.0:0.0:0.0:1.0	.	167	Q96MW1	CCD43_HUMAN	S	167	.	ENSP00000323782:N167S	N	-	2	0	CCDC43	40111925	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.097000	0.76967	2.367000	0.80283	0.528000	0.53228	AAC	0	NULL		0.488	CCDC43-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	CCDC43	protein_coding	OTTHUMT00000457812.1	47	287	0	0.00	0	0	T	NM_144609	0	0		42756399	-1	no_errors	ENST00000315286	ensembl	human	known	74_37	missense	50	276	13.79	7.33	8	22	SNP	1	C
LGALS3BP	3959	genome.wustl.edu	37	17	76969290	76969290	+	Missense_Mutation	SNP	G	G	C			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr17:76969290G>C	ENST00000262776.3	-	5	699	c.391C>G	c.(391-393)Cac>Gac	p.H131D	LGALS3BP_ENST00000585407.1_Missense_Mutation_p.H131D|LGALS3BP_ENST00000591778.1_Intron	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	131					cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(5)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			TCCAGGGTGTGGGTGCTCCTG	0.622																																					GBM(89;1105 1755 18102 21513)		0											0													8.0	8.0	8.0					17																	76969290		2188	4285	6473	SO:0001583	missense	0			L13210	CCDS11759.1	17q25	2014-07-09				ENSG00000108679		"""BTB/POZ domain containing"", ""Endogenous ligands"""	6564	protein-coding gene	gene with protein product	"""L3 antigen"", ""Mac-2-binding protein"", ""serum protein 90K"", ""transport and golgi organization 10 homolog B (Drosophila)"""	600626				7698018, 8034587, 8390986	Standard	NM_005567		Approved	MAC-2-BP, 90K, BTBD17B, TANGO10B, M2BP, gp90, CyCAP	uc002jwh.3	Q08380		ENST00000262776.3:c.391C>G	17.37:g.76969290G>C	ENSP00000262776:p.His131Asp		Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Missense_Mutation	SNP	pfam_SRCR,pfam_BACK,superfamily_Srcr_rcpt-rel,superfamily_BTB/POZ_fold,smart_Srcr_rcpt-rel,smart_BACK,pfscan_BTB/POZ-like,pfscan_SRCR,prints_SRCR	p.H131D	ENST00000262776.3	37	c.391	CCDS11759.1	17	.	.	.	.	.	.	.	.	.	.	G	11.30	1.598096	0.28445	.	.	ENSG00000108679	ENST00000262776;ENST00000536190	T	0.46063	0.88	2.9	-2.14	0.07123	BTB/POZ fold (1);Speract/scavenger receptor-related (1);	0.470871	0.15928	N	0.237813	T	0.27967	0.0689	L	0.43152	1.355	0.22858	N	0.998647	B	0.11235	0.004	B	0.06405	0.002	T	0.16305	-1.0407	10	0.29301	T	0.29	.	6.99	0.24750	0.493:0.0:0.507:0.0	.	131	Q08380	LG3BP_HUMAN	D	131;119	ENSP00000262776:H131D	ENSP00000262776:H131D	H	-	1	0	LGALS3BP	74480885	0.212000	0.23540	0.022000	0.16811	0.181000	0.23173	0.521000	0.22893	-0.428000	0.07339	0.561000	0.74099	CAC	0	superfamily_Srcr_rcpt-rel,superfamily_BTB/POZ_fold		0.622	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LGALS3BP	protein_coding	OTTHUMT00000437785.3	37	103	0	0.00	0	0	G	NM_005567	0	0		76969290	-1	no_errors	ENST00000262776	ensembl	human	known	74_37	missense	37	104	11.9	8.77	5	10	SNP	0.039	C
GPS1	2873	genome.wustl.edu	37	17	80012657	80012657	+	Missense_Mutation	SNP	G	G	A	rs149095451		TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr17:80012657G>A	ENST00000306823.6	+	4	615	c.592G>A	c.(592-594)Gtc>Atc	p.V198I	GPS1_ENST00000320548.4_Missense_Mutation_p.V178I|GPS1_ENST00000578552.1_Missense_Mutation_p.V194I|GPS1_ENST00000392358.2_Missense_Mutation_p.V234I|GPS1_ENST00000355130.2_Missense_Mutation_p.V234I			Q13098	CSN1_HUMAN	G protein pathway suppressor 1	198					cell cycle (GO:0007049)|cullin deneddylation (GO:0010388)|inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)			breast(1)|central_nervous_system(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|skin(2)	13	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			CGCCAAACACGTCATCAACAT	0.662													.|||	1	0.000199681	0.0	0.0	5008	,	,		16114	0.001		0.0	False		,,,				2504	0.0						0.9998,0.0001997											0								G	ILE/VAL,ILE/VAL	0,4404		0,0,2202	52.0	48.0	49.0		592,700	4.7	1.0	17	dbSNP_134	49	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	GPS1	NM_004127.4,NM_212492.1	29,29	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	198/492,234/528	80012657	2,13002	2202	4300	6502	SO:0001583	missense	0				CCDS11800.1, CCDS32774.1	17q25.3	2013-03-14				ENSG00000169727			4549	protein-coding gene	gene with protein product	"""COP9 signalosome subunit 1"""	601934				9535219	Standard	NM_212492		Approved	COPS1, CSN1	uc002kdl.1	Q13098		ENST00000306823.6:c.592G>A	17.37:g.80012657G>A	ENSP00000302873:p.Val198Ile		Q8NA10|Q9BWL1	Missense_Mutation	SNP	pfam_26S_proteasome_reg_su-Rpn7,pfam_PCI_dom,smart_PCI_dom	p.V234I	ENST00000306823.6	37	c.700	CCDS32774.1	17	.	.	.	.	.	.	.	.	.	.	G	16.11	3.029683	0.54790	0.0	2.33E-4	ENSG00000169727	ENST00000392358;ENST00000320548;ENST00000306823;ENST00000355130;ENST00000392357	T;T;T	0.75477	-0.77;-0.94;-0.77	4.65	4.65	0.58169	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.57301	0.2044	N	0.17631	0.505	0.80722	D	1	B;B;B;B;B;B	0.27229	0.024;0.007;0.172;0.019;0.023;0.005	B;B;B;B;B;B	0.23275	0.023;0.01;0.045;0.02;0.026;0.006	T	0.57075	-0.7873	10	0.05721	T	0.95	-53.6521	17.5075	0.87750	0.0:0.0:1.0:0.0	.	190;234;183;194;198;234	B4DND6;A8K070;Q13098-6;Q13098-5;Q13098;Q13098-7	.;.;.;.;CSN1_HUMAN;.	I	234;184;198;234;119	ENSP00000376167:V234I;ENSP00000302873:V198I;ENSP00000347251:V234I	ENSP00000302873:V198I	V	+	1	0	GPS1	77605946	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.098000	0.94202	2.150000	0.67090	0.491000	0.48974	GTC	0	pfam_26S_proteasome_reg_su-Rpn7		0.662	GPS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GPS1	protein_coding	OTTHUMT00000442176.1	36	134	0	0.00	0	0	G	NM_212492	rs149095451	G->A		80012657	1	no_errors	ENST00000355130	ensembl	human	known	74_37	missense	32	129	13.51	11.64	5	17	SNP	1	A
GATAD2A	54815	genome.wustl.edu	37	19	19613159	19613159	+	Missense_Mutation	SNP	G	G	T			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr19:19613159G>T	ENST00000360315.3	+	11	1907	c.1595G>T	c.(1594-1596)cGg>cTg	p.R532L	GATAD2A_ENST00000252577.5_Missense_Mutation_p.R507L|GATAD2A_ENST00000404158.1_Missense_Mutation_p.R533L|GATAD2A_ENST00000537887.1_Missense_Mutation_p.R161L|GATAD2A_ENST00000429563.2_Missense_Mutation_p.R335L|GATAD2A_ENST00000358713.3_Missense_Mutation_p.R532L	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	532					anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						CAGCTGTCCCGGGGTTCGGCC	0.657																																							0											0													47.0	50.0	49.0					19																	19613159		2202	4300	6502	SO:0001583	missense	0			AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"""GATA zinc finger domain containing"""	29989	protein-coding gene	gene with protein product	"""p66 alpha"""	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.1595G>T	19.37:g.19613159G>T	ENSP00000353463:p.Arg532Leu		B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Missense_Mutation	SNP	pfam_Znf_GATA,pfscan_Znf_GATA	p.R532L	ENST00000360315.3	37	c.1595	CCDS12402.2	19	.	.	.	.	.	.	.	.	.	.	G	18.56	3.651110	0.67472	.	.	ENSG00000167491	ENST00000360315;ENST00000252577;ENST00000537887;ENST00000404158;ENST00000358713;ENST00000429563	T;T;T;T	0.50001	1.36;1.31;1.36;0.76	5.23	5.23	0.72850	.	0.054549	0.85682	D	0.000000	T	0.64260	0.2582	M	0.68952	2.095	0.50813	D	0.999899	P;D;D	0.69078	0.945;0.997;0.994	B;P;P	0.60286	0.445;0.872;0.554	T	0.65261	-0.6211	10	0.48119	T	0.1	-13.9582	17.4151	0.87497	0.0:0.0:1.0:0.0	.	335;552;532	B4DKZ7;B5MC40;Q86YP4	.;.;P66A_HUMAN	L	532;507;161;552;532;335	ENSP00000353463:R532L;ENSP00000252577:R507L;ENSP00000351552:R532L;ENSP00000388416:R335L	ENSP00000252577:R507L	R	+	2	0	GATAD2A	19474159	1.000000	0.71417	0.994000	0.49952	0.557000	0.35523	6.342000	0.72982	2.452000	0.82932	0.585000	0.79938	CGG	0	NULL		0.657	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	GATAD2A	protein_coding	OTTHUMT00000326671.4	49	44	0	0.00	0	0	G	NM_017660	0	0		19613159	1	no_errors	ENST00000358713	ensembl	human	known	74_37	missense	61	76	7.58	8.43	5	7	SNP	1	T
MT-ND2	4536	genome.wustl.edu	37	M	2778	2778	+	5'Flank	SNP	T	T	C			TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chrM:2778T>C	ENST00000361453.3	+	0	0				MT-TM_ENST00000387377.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-TF_ENST00000387314.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-ND1_ENST00000361390.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TA_ENST00000387392.1_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|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(2)|lung(1)	3						CAAACCCACAGGTCCTAAACT	0.473																																							0											0																																										SO:0001631	upstream_gene_variant	0					mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891			M.37:g.2778T>C	Exception_encountered		Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	RNA	SNP	0	NULL	ENST00000361453.3	37	NULL		MT																																																																																			0	0		0.473	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	MT-RNR2	protein_coding		400	0	0.25	0.00	1	0	T	YP_003024027	0	0		2778	1	no_errors	ENST00000387347	ensembl	human	known	74_37	rna	299	0	13.83	0.00	48	0	SNP	NULL	C
DNM1P47	100216544	genome.wustl.edu	37	15	102304673	102304673	+	RNA	SNP	T	T	C	rs200623579	byFrequency	TCGA-XU-A92Y-01A-11D-A423-09	TCGA-XU-A92Y-10A-01D-A426-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	d5cdc7f7-9e87-45b5-a91b-4a2cfa9fd9e8	52477ee5-459e-424e-9f5a-7d9aa1216d21	g.chr15:102304673T>C	ENST00000561463.1	+	0	12719									DNM1 pseudogene 47																		GGCACAGCGGTGCGACGAGAT	0.617																																							0											0																																												0			AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102304673T>C				RNA	SNP	0	NULL	ENST00000561463.1	37	NULL		15																																																																																			0	0		0.617	DNM1P47-001	KNOWN	basic	processed_transcript	DNM1P47	pseudogene	OTTHUMT00000417589.1	21	3	0	0.00	0	0	T	NG_009149	rs200623579	T->C		102304673	1	no_errors	ENST00000561463	ensembl	human	known	74_37	rna	15	1	21.05	0.00	4	0	SNP	0.999	C
