#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
MARK1	4139	genome.wustl.edu	37	1	220808856	220808856	+	Missense_Mutation	SNP	C	C	T			TCGA-XM-A8RD-01A-11D-A423-09	TCGA-XM-A8RD-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	6dcf015f-75c3-4cb1-a7d2-4c3834265d30	63c446d7-2dd1-4181-bfb9-005d3d96416b	g.chr1:220808856C>T	ENST00000366917.4	+	12	1527	c.1261C>T	c.(1261-1263)Cgt>Tgt	p.R421C	MARK1_ENST00000366918.4_Missense_Mutation_p.R399C|MARK1_ENST00000402574.1_Missense_Mutation_p.R286C					MAP/microtubule affinity-regulating kinase 1											central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		GAAGCAGCGGCGTTTCAGTGA	0.463																																							0											0													73.0	69.0	70.0					1																	220808856		2203	4300	6503	SO:0001583	missense	0			AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.1261C>T	1.37:g.220808856C>T	ENSP00000355884:p.Arg421Cys			Missense_Mutation	SNP	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_KA1_dom,superfamily_Kinase-like_dom,superfamily_KA1/Ssp2_C,superfamily_UBA-like,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_UBA/transl_elong_EF1B_N_euk,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_UBA/transl_elong_EF1B_N_euk,pfscan_Prot_kinase_dom	p.R421C	ENST00000366917.4	37	c.1261	CCDS31029.2	1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.414215	0.83449	.	.	ENSG00000116141	ENST00000402574;ENST00000366918;ENST00000366917	T;T;T	0.79247	-1.14;-1.0;-1.25	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.89022	0.6597	M	0.84773	2.715	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.972;0.998;0.985;0.998	D	0.90036	0.4138	10	0.87932	D	0	.	15.0828	0.72127	0.1417:0.8583:0.0:0.0	.	421;286;421;399	B4DIB3;Q9P0L2-2;Q9P0L2;Q9P0L2-3	.;.;MARK1_HUMAN;.	C	286;399;421	ENSP00000386017:R286C;ENSP00000355885:R399C;ENSP00000355884:R421C	ENSP00000355884:R421C	R	+	1	0	MARK1	218875479	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.707000	0.61852	2.813000	0.96785	0.561000	0.74099	CGT	0	NULL		0.463	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	MARK1	protein_coding	OTTHUMT00000090899.1	35	147	0	0.00	0	0	C		0	0		220808856	1	no_errors	ENST00000366917	ensembl	human	known	74_37	missense	20	127	13.04	20.13	3	32	SNP	1	T
PIK3R1	5295	genome.wustl.edu	37	5	67588086	67588086	+	Splice_Site	SNP	G	G	A			TCGA-XM-A8RD-01A-11D-A423-09	TCGA-XM-A8RD-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	6dcf015f-75c3-4cb1-a7d2-4c3834265d30	63c446d7-2dd1-4181-bfb9-005d3d96416b	g.chr5:67588086G>A	ENST00000521381.1	+	8	1532		c.e8-1		PIK3R1_ENST00000274335.5_Splice_Site|PIK3R1_ENST00000320694.8_Splice_Site|PIK3R1_ENST00000523872.1_5'Flank|PIK3R1_ENST00000396611.1_Splice_Site|PIK3R1_ENST00000336483.5_Splice_Site|PIK3R1_ENST00000521657.1_Splice_Site	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)						B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.?(2)|p.0?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TTCATCTGCAGCACTGCCTCC	0.343			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																													0		Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	3	Unknown(2)|Whole gene deletion(1)	large_intestine(1)|lung(1)|ovary(1)											141.0	130.0	134.0					5																	67588086		2203	4300	6503	SO:0001630	splice_region_variant	0			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.917-1G>A	5.37:g.67588086G>A			B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Splice_Site	SNP	0	e7-1	ENST00000521381.1	37	c.917-1	CCDS3993.1	5	.	.	.	.	.	.	.	.	.	.	G	19.41	3.822180	0.71028	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000523807;ENST00000522084;ENST00000320694;ENST00000336483	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.115	0.93334	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PIK3R1	67623842	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.601000	0.98297	2.822000	0.97130	0.563000	0.77884	.	0	0		0.343	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIK3R1	protein_coding	OTTHUMT00000254013.2	118	287	0	0.00	0	0	G	NM_181504	0	0	Intron	67588086	1	no_errors	ENST00000396611	ensembl	human	known	74_37	splice_site	75	244	7.41	12.86	6	36	SNP	1	A
ZNF658	26149	genome.wustl.edu	37	9	40774255	40774255	+	Missense_Mutation	SNP	A	A	C			TCGA-XM-A8RD-01A-11D-A423-09	TCGA-XM-A8RD-10A-01D-A426-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	6dcf015f-75c3-4cb1-a7d2-4c3834265d30	63c446d7-2dd1-4181-bfb9-005d3d96416b	g.chr9:40774255A>C	ENST00000602553.1	-	5	1314	c.1020T>G	c.(1018-1020)caT>caG	p.H340Q	ZNF658_ENST00000441795.1_Missense_Mutation_p.H338Q|ZNF658_ENST00000377626.3_Missense_Mutation_p.H340Q			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	340					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GATGTACTATATGGGCTGAGC	0.388																																							0											0													64.0	67.0	66.0					9																	40774255		2198	4279	6477	SO:0001583	missense	0			AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"""Zinc fingers, C2H2-type"", ""-"""	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.1020T>G	9.37:g.40774255A>C	ENSP00000473484:p.His340Gln		Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.H340Q	ENST00000602553.1	37	c.1020	CCDS35023.1	9	.	.	.	.	.	.	.	.	.	.	a	8.979	0.974927	0.18736	.	.	ENSG00000196409	ENST00000441795;ENST00000377626	T;T	0.14893	2.47;2.47	1.65	0.457	0.16661	.	.	.	.	.	T	0.08714	0.0216	N	0.24115	0.695	0.09310	N	1	P;B	0.35821	0.523;0.182	B;B	0.26864	0.074;0.019	T	0.24119	-1.0169	9	0.72032	D	0.01	.	4.9493	0.14006	0.8178:0.0:0.1822:0.0	.	340;340	Q5TYW1-2;Q5TYW1	.;ZN658_HUMAN	Q	338;340	ENSP00000408462:H338Q;ENSP00000366853:H340Q	ENSP00000366853:H340Q	H	-	3	2	ZNF658	40764255	0.000000	0.05858	0.000000	0.03702	0.338000	0.28826	-1.358000	0.02604	0.125000	0.18397	0.315000	0.21342	CAT	0	NULL		0.388	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF658	protein_coding	OTTHUMT00000467800.1	109	106	0.91	1.85	1	2	A	NM_033160	0	0		40774255	-1	no_errors	ENST00000377626	ensembl	human	known	74_37	missense	82	90	9.89	5.26	9	5	SNP	0.003	C
PRKRIR	5612	genome.wustl.edu	37	11	76062107	76062107	+	Missense_Mutation	SNP	C	C	T	rs34345847	byFrequency	TCGA-XM-A8RD-01A-11D-A423-09	TCGA-XM-A8RD-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	6dcf015f-75c3-4cb1-a7d2-4c3834265d30	63c446d7-2dd1-4181-bfb9-005d3d96416b	g.chr11:76062107C>T	ENST00000260045.3	-	5	2192	c.2087G>A	c.(2086-2088)cGg>cAg	p.R696Q	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	696					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						ATTTTCATACCGCTCATTCTC	0.393																																							0											0													76.0	72.0	73.0					11																	76062107		2200	4291	6491	SO:0001583	missense	0			AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"""THAP (C2CH-type zinc finger) domain containing"""	9440	protein-coding gene	gene with protein product	"""THAP domain containing 12"""	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.2087G>A	11.37:g.76062107C>T	ENSP00000260045:p.Arg696Gln		A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	pfam_Znf_C2CH,pfam_HATC_dom_C,superfamily_RNaseH-like_dom,smart_Znf_C2CH,pfscan_Znf_C2CH	p.R696Q	ENST00000260045.3	37	c.2087	CCDS8243.1	11	.	.	.	.	.	.	.	.	.	.	C	10.29	1.309319	0.23821	.	.	ENSG00000137492	ENST00000529901;ENST00000260045	T;T	0.36340	1.26;1.26	5.44	4.51	0.55191	HAT dimerisation (1);Ribonuclease H-like (1);	0.372411	0.29080	N	0.013205	T	0.35480	0.0933	M	0.75884	2.315	0.29867	N	0.827114	B	0.20887	0.049	B	0.15052	0.012	T	0.39313	-0.9620	10	0.51188	T	0.08	.	6.5111	0.22222	0.0:0.7019:0.1818:0.1164	rs34345847	696	O43422	P52K_HUMAN	Q	521;696	ENSP00000436249:R521Q;ENSP00000260045:R696Q	ENSP00000260045:R696Q	R	-	2	0	PRKRIR	75739755	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	2.247000	0.43151	1.456000	0.47831	0.644000	0.83932	CGG	0	pfam_HATC_dom_C,superfamily_RNaseH-like_dom		0.393	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRKRIR	protein_coding	OTTHUMT00000383188.1	116	115	0	1.71	0	2	C	NM_004705	rs34345847	C->T		76062107	-1	no_errors	ENST00000260045	ensembl	human	known	74_37	missense	88	75	11.11	7.41	11	6	SNP	0.979	T
MVP	9961	genome.wustl.edu	37	16	29848216	29848216	+	Silent	SNP	C	C	T			TCGA-XM-A8RD-01A-11D-A423-09	TCGA-XM-A8RD-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	6dcf015f-75c3-4cb1-a7d2-4c3834265d30	63c446d7-2dd1-4181-bfb9-005d3d96416b	g.chr16:29848216C>T	ENST00000357402.5	+	7	984	c.846C>T	c.(844-846)tgC>tgT	p.C282C	MVP_ENST00000395353.1_Silent_p.C282C|MVP_ENST00000452209.2_Missense_Mutation_p.R97C	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	282					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)	p.C282*(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						ACAACTACTGCGTGATTCTCG	0.637																																							0											1	Substitution - Nonsense(1)	cervix(1)											71.0	55.0	61.0					16																	29848216		2197	4300	6497	SO:0001819	synonymous_variant	0			X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"""lung resistance-related protein"""	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.846C>T	16.37:g.29848216C>T			Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	NULL	p.R97C	ENST00000357402.5	37	c.289	CCDS10656.1	16	.	.	.	.	.	.	.	.	.	.	C	11.63	1.695005	0.30052	.	.	ENSG00000013364	ENST00000452209	T	0.64991	-0.13	5.58	2.13	0.27403	.	.	.	.	.	T	0.59609	0.2206	.	.	.	0.35797	D	0.82283	.	.	.	.	.	.	T	0.60737	-0.7204	5	.	.	.	-12.8557	7.8448	0.29419	0.0:0.2477:0.0:0.7523	.	.	.	.	C	97	ENSP00000387916:R97C	.	R	+	1	0	MVP	29755717	0.999000	0.42202	1.000000	0.80357	0.943000	0.58893	0.476000	0.22180	0.401000	0.25424	-0.487000	0.04747	CGT	0	NULL		0.637	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MVP	protein_coding	OTTHUMT00000109711.3	55	104	1.79	0.95	1	1	C	NM_005115	0	0		29848216	1	no_errors	ENST00000452209	ensembl	human	known	74_37	missense	70	103	7.79	8.04	6	9	SNP	1	T
KRTAP4-3	85290	genome.wustl.edu	37	17	39324104	39324104	+	Silent	SNP	A	A	G	rs368619075		TCGA-XM-A8RD-01A-11D-A423-09	TCGA-XM-A8RD-10A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	6dcf015f-75c3-4cb1-a7d2-4c3834265d30	63c446d7-2dd1-4181-bfb9-005d3d96416b	g.chr17:39324104A>G	ENST00000391356.2	-	1	320	c.321T>C	c.(319-321)tcT>tcC	p.S107S		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	107	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].		Missing (in allele KAP3-v2). {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.S107S(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			TGCAGCAACTAGAAATGCAGC	0.597																																							0											1	Substitution - coding silent(1)	large_intestine(1)											18.0	23.0	21.0					17																	39324104		2109	4252	6361	SO:0001819	synonymous_variant	0			AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.321T>C	17.37:g.39324104A>G				Silent	SNP	pfam_Keratin-assoc	p.S107	ENST00000391356.2	37	c.321	CCDS42331.1	17																																																																																			0	NULL		0.597	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRTAP4-3	protein_coding	OTTHUMT00000257784.1	87	15	1.14	0.00	1	0	A		rs368619075	A->G		39324104	-1	no_errors	ENST00000391356	ensembl	human	known	74_37	silent	91	24	7.14	7.69	7	2	SNP	0.009	G
MT-ND2	4536	genome.wustl.edu	37	M	2778	2778	+	5'Flank	SNP	T	T	C			TCGA-XM-A8RD-01A-11D-A423-09	TCGA-XM-A8RD-10A-01D-A426-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	6dcf015f-75c3-4cb1-a7d2-4c3834265d30	63c446d7-2dd1-4181-bfb9-005d3d96416b	g.chrM:2778T>C	ENST00000361453.3	+	0	0				MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-ND1_ENST00000361390.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TA_ENST00000387392.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TF_ENST00000387314.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TQ_ENST00000387372.1_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		552	2	0.18	0.00	1	0	T	YP_003024027	0	0		2778	1	no_errors	ENST00000387347	ensembl	human	known	74_37	rna	122	0	38.07	0.00	75	0	SNP	NULL	C
SPDYE2B	100310812	genome.wustl.edu	37	7	102294058	102294058	+	Silent	SNP	G	G	A			TCGA-XM-A8RD-01A-11D-A423-09	TCGA-XM-A8RD-10A-01D-A426-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	6dcf015f-75c3-4cb1-a7d2-4c3834265d30	63c446d7-2dd1-4181-bfb9-005d3d96416b	g.chr7:102294058G>A	ENST00000507450.1	+	3	795	c.321G>A	c.(319-321)aaG>aaA	p.K107K	SPDYE2B_ENST00000455020.2_5'Flank|POLR2J2_ENST00000333432.6_Intron|POLR2J2_ENST00000591000.1_Intron|SPDYE2B_ENST00000436228.2_Silent_p.K107K|POLR2J2_ENST00000476151.1_Intron	NM_001166339.1	NP_001159811.1	A6NHP3	SPE2B_HUMAN	speedy/RINGO cell cycle regulator family member E2B	107																	TGAAGCTGAAGCAACAGCGAG	0.557																																							0											0																																										SO:0001819	synonymous_variant	0				CCDS59507.1	7q22.1	2013-05-08			ENSG00000173678	ENSG00000173678		"""Speedy homologs"""	48334	protein-coding gene	gene with protein product							Standard	NM_001166339		Approved			A6NHP3	OTTHUMG00000158393	ENST00000507450.1:c.321G>A	7.37:g.102294058G>A			D6RBN0	Silent	SNP	pfam_Cell_cycle_regulatory_Spy1	p.K107	ENST00000507450.1	37	c.321	CCDS59507.1	7																																																																																			0	NULL		0.557	SPDYE2B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	SPDYE2B	protein_coding	OTTHUMT00000350899.3	25	0	0	0.00	0	0	G		0	0		102294058	1	no_errors	ENST00000436228	ensembl	human	known	74_37	silent	23	0	17.86	0.00	5	0	SNP	0.067	A
