#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
LRRC42	115353	genome.wustl.edu	37	1	54432012	54432012	+	Missense_Mutation	SNP	C	C	A			TCGA-ZB-A963-01A-11D-A428-09	TCGA-ZB-A963-10A-01D-A42B-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	8597e4e5-c134-4dce-9b91-62ef0c573ebf	06601478-0cf9-430a-b343-8051ae4396d1	g.chr1:54432012C>A	ENST00000371370.3	+	8	1492	c.971C>A	c.(970-972)cCa>cAa	p.P324Q	LRRC42_ENST00000319223.4_Missense_Mutation_p.P324Q|LRRC42_ENST00000477905.1_3'UTR	NM_001256409.1	NP_001243338.1	Q9Y546	LRC42_HUMAN	leucine rich repeat containing 42	324										breast(2)|kidney(1)|large_intestine(1)|lung(5)	9						GCTGTGAAGCCACGGGAGACC	0.433																																							0											0													90.0	95.0	93.0					1																	54432012		2203	4300	6503	SO:0001583	missense	0			AK075201	CCDS585.1	1p33-p32.1	2014-02-12			ENSG00000116212	ENSG00000116212			28792	protein-coding gene	gene with protein product						12477932	Standard	NM_001256409		Approved	MGC8974	uc001cwj.2	Q9Y546	OTTHUMG00000008436	ENST00000371370.3:c.971C>A	1.37:g.54432012C>A	ENSP00000360421:p.Pro324Gln		D3DQ46|Q8N2Q8	Missense_Mutation	SNP	NULL	p.P324Q	ENST00000371370.3	37	c.971	CCDS585.1	1	.	.	.	.	.	.	.	.	.	.	C	7.698	0.692575	0.15039	.	.	ENSG00000116212	ENST00000371370;ENST00000319223	.	.	.	5.7	0.437	0.16555	.	0.489250	0.24150	N	0.041095	T	0.20536	0.0494	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.13019	-1.0525	9	0.25106	T	0.35	0.0851	5.1227	0.14869	0.2576:0.5365:0.0:0.2058	.	324	Q9Y546	LRC42_HUMAN	Q	324	.	ENSP00000318185:P324Q	P	+	2	0	LRRC42	54204600	0.389000	0.25205	0.012000	0.15200	0.417000	0.31264	0.792000	0.26929	-0.158000	0.11040	-0.136000	0.14681	CCA	0	NULL		0.433	LRRC42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	LRRC42	protein_coding	OTTHUMT00000023250.1	81	127	0	0.00	0	0	C	NM_052940	0	0		54432012	1	no_errors	ENST00000319223	ensembl	human	known	74_37	missense	42	85	12.24	10.53	6	10	SNP	0.016	A
LINC00487	400941	genome.wustl.edu	37	2	6876837	6876837	+	lincRNA	SNP	G	G	T			TCGA-ZB-A963-01A-11D-A428-09	TCGA-ZB-A963-10A-01D-A42B-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	8597e4e5-c134-4dce-9b91-62ef0c573ebf	06601478-0cf9-430a-b343-8051ae4396d1	g.chr2:6876837G>T	ENST00000382045.3	-	0	242					NR_038369.1				long intergenic non-protein coding RNA 487																		TGGTTGCCAGGCTCCTCTGCC	0.512																																							0											0																																												0					2p25.2	2012-10-12			ENSG00000205837	ENSG00000205837		"""Long non-coding RNAs"""	42947	non-coding RNA	RNA, long non-coding							Standard	NR_038369		Approved	FLJ42418	uc002qym.2		OTTHUMG00000151630		2.37:g.6876837G>T				RNA	SNP	0	NULL	ENST00000382045.3	37	NULL		2																																																																																			0	0		0.512	LINC00487-001	KNOWN	basic	lincRNA	LINC00487	lincRNA	OTTHUMT00000323346.2	63	186	0	0.00	0	0	G	NR_038369	0	0		6876837	-1	no_errors	ENST00000382045	ensembl	human	known	74_37	rna	42	133	8.7	8.90	4	13	SNP	0	T
PLK4	10733	genome.wustl.edu	37	4	128811126	128811126	+	Missense_Mutation	SNP	C	C	T	rs373445088		TCGA-ZB-A963-01A-11D-A428-09	TCGA-ZB-A963-10A-01D-A42B-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	8597e4e5-c134-4dce-9b91-62ef0c573ebf	06601478-0cf9-430a-b343-8051ae4396d1	g.chr4:128811126C>T	ENST00000270861.5	+	7	1839	c.1565C>T	c.(1564-1566)aCa>aTa	p.T522I	PLK4_ENST00000507249.1_Missense_Mutation_p.T488I|PLK4_ENST00000513090.1_Missense_Mutation_p.T490I|RNU6-583P_ENST00000516012.1_RNA|PLK4_ENST00000514379.1_Missense_Mutation_p.T481I|PLK4_ENST00000515069.1_Intron	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	522					centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						TGGACTGATACAAAAGTCAAA	0.388																																					Colon(135;508 1718 19061 31832 42879)		0											0													78.0	75.0	76.0					4																	128811126		2203	4300	6503	SO:0001583	missense	0			Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"""serine/threonine kinase 18"", ""polo-like kinase 4 (Drosophila)"""	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.1565C>T	4.37:g.128811126C>T	ENSP00000270861:p.Thr522Ile		B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_POLO_box_duplicated_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_POLO_box_duplicated_dom,pfscan_Prot_kinase_dom	p.T522I	ENST00000270861.5	37	c.1565	CCDS3735.1	4	.	.	.	.	.	.	.	.	.	.	C	0.233	-1.019594	0.02078	.	.	ENSG00000142731	ENST00000270861;ENST00000513090;ENST00000507249;ENST00000514379	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	4.22	-8.45	0.00946	.	1.115780	0.06583	N	0.750670	T	0.12475	0.0303	N	0.19112	0.55	0.09310	N	1	B;B	0.22003	0.063;0.0	B;B	0.17979	0.02;0.001	T	0.12734	-1.0536	10	0.07813	T	0.8	2.2691	4.3688	0.11237	0.1518:0.0779:0.3777:0.3926	.	490;522	O00444-2;O00444	.;PLK4_HUMAN	I	522;490;488;481	ENSP00000270861:T522I;ENSP00000427554:T490I;ENSP00000423412:T488I;ENSP00000423582:T481I	ENSP00000270861:T522I	T	+	2	0	PLK4	129030576	0.000000	0.05858	0.000000	0.03702	0.260000	0.26232	-2.646000	0.00860	-3.799000	0.00105	-1.434000	0.01081	ACA	0	NULL		0.388	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLK4	protein_coding	OTTHUMT00000257095.3	61	231	0	0.00	0	0	C		0	0		128811126	1	no_errors	ENST00000270861	ensembl	human	known	74_37	missense	46	163	9.8	11.41	5	21	SNP	0	T
ZNF727	442319	genome.wustl.edu	37	7	63538269	63538269	+	Missense_Mutation	SNP	A	A	T			TCGA-ZB-A963-01A-11D-A428-09	TCGA-ZB-A963-10A-01D-A42B-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	8597e4e5-c134-4dce-9b91-62ef0c573ebf	06601478-0cf9-430a-b343-8051ae4396d1	g.chr7:63538269A>T	ENST00000550760.3	+	4	1021	c.842A>T	c.(841-843)gAg>gTg	p.E281V	RP11-3N2.13_ENST00000445978.1_RNA	NM_001159522.1	NP_001152994.1	A8MUV8	ZN727_HUMAN	zinc finger protein 727	281					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|skin(1)|stomach(1)|urinary_tract(1)	8						CATACTGGAGAGAAACCCTAC	0.383																																							0											0													27.0	33.0	31.0					7																	63538269		692	1591	2283	SO:0001583	missense	0					7q11.21	2014-09-09	2014-09-09	2014-09-09	ENSG00000214652	ENSG00000214652		"""Zinc fingers, C2H2-type"", ""-"""	22785	pseudogene	pseudogene			"""zinc finger protein 727, pseudogene"""	ZNF727P			Standard	NM_001159522		Approved		uc011kdm.2	A8MUV8	OTTHUMG00000156536	ENST00000550760.3:c.842A>T	7.37:g.63538269A>T	ENSP00000447987:p.Glu281Val			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.E281V	ENST00000550760.3	37	c.842	CCDS55113.1	7	.	.	.	.	.	.	.	.	.	.	A	17.20	3.327980	0.60743	.	.	ENSG00000257482	ENST00000550760	T	0.26810	1.71	0.859	0.859	0.19036	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.34658	0.0905	L	0.41415	1.275	0.27352	N	0.956214	D	0.71674	0.998	D	0.81914	0.995	T	0.13415	-1.0510	8	.	.	.	.	5.4662	0.16644	1.0:0.0:0.0:0.0	.	281	A8MUV8	ZN727_HUMAN	V	281	ENSP00000447987:E281V	.	E	+	2	0	ZNF727	63175704	1.000000	0.71417	0.631000	0.29282	0.609000	0.37215	6.100000	0.71473	0.175000	0.19841	0.172000	0.16884	GAG	0	pfscan_Znf_C2H2		0.383	ZNF727-201	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF727	protein_coding		81	122	0	0.00	0	0	A	NM_001159522	0	0		63538269	1	no_errors	ENST00000550760	ensembl	human	known	74_37	missense	46	118	11.54	6.35	6	8	SNP	1	T
GTF2I	2969	genome.wustl.edu	37	7	74146970	74146970	+	Missense_Mutation	SNP	T	T	A			TCGA-ZB-A963-01A-11D-A428-09	TCGA-ZB-A963-10A-01D-A42B-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	8597e4e5-c134-4dce-9b91-62ef0c573ebf	06601478-0cf9-430a-b343-8051ae4396d1	g.chr7:74146970T>A	ENST00000324896.4	+	15	1660	c.1271T>A	c.(1270-1272)cTt>cAt	p.L424H	GTF2I_ENST00000346152.4_Missense_Mutation_p.L403H|GTF2I_ENST00000416070.1_Missense_Mutation_p.L383H|GTF2I_ENST00000353920.4_Missense_Mutation_p.L404H	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	424					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						AGGATATTACTTGCAAAGGAA	0.378																																							0											0													13.0	13.0	13.0					7																	74146970		1741	3768	5509	SO:0001583	missense	0			U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"""General transcription factors"""	4659	protein-coding gene	gene with protein product		601679	"""general transcription factor II, i"""	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.1271T>A	7.37:g.74146970T>A	ENSP00000322542:p.Leu424His		O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Missense_Mutation	SNP	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I	p.L424H	ENST00000324896.4	37	c.1271	CCDS5573.1	7	.	.	.	.	.	.	.	.	.	.	T	18.18	3.565904	0.65651	.	.	ENSG00000077809	ENST00000324896;ENST00000539339;ENST00000353920;ENST00000346152;ENST00000416070	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	4.72	4.72	0.59763	.	0.110120	0.39544	N	0.001322	T	0.37019	0.0988	N	0.14661	0.345	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;0.999	D;D;P;D;D	0.74348	0.983;0.979;0.874;0.971;0.963	T	0.36089	-0.9762	10	0.56958	D	0.05	-16.5588	13.3771	0.60745	0.0:0.0:0.0:1.0	.	402;383;404;403;424	Q499G6;P78347-2;P78347-3;P78347-4;P78347	.;.;.;.;GTF2I_HUMAN	H	424;419;404;403;383	ENSP00000322542:L424H;ENSP00000322671:L404H;ENSP00000322599:L403H;ENSP00000387651:L383H	ENSP00000322542:L424H	L	+	2	0	GTF2I	73784906	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	5.342000	0.65970	1.753000	0.51906	0.477000	0.44152	CTT	0	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I		0.378	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GTF2I	protein_coding	OTTHUMT00000252708.1	468	133	0	0.00	0	0	T	NM_032999	0	0		74146970	1	no_errors	ENST00000324896	ensembl	human	known	74_37	missense	287	98	9.46	4.85	30	5	SNP	1	A
NRG1	3084	genome.wustl.edu	37	8	32607058	32607058	+	Intron	SNP	G	G	A			TCGA-ZB-A963-01A-11D-A428-09	TCGA-ZB-A963-10A-01D-A42B-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	8597e4e5-c134-4dce-9b91-62ef0c573ebf	06601478-0cf9-430a-b343-8051ae4396d1	g.chr8:32607058G>A	ENST00000405005.3	+	8	700				NRG1_ENST00000287842.3_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000287845.5_Intron|NRG1_ENST00000539990.1_Intron|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000521670.1_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000523681.1_3'UTR			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TCTTTTTTTTGTCAACTTTCT	0.383																																							0											0													107.0	107.0	107.0					8																	32607058		2203	4300	6503	SO:0001627	intron_variant	0			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.701-4832G>A	8.37:g.32607058G>A			A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	RNA	SNP	0	NULL	ENST00000405005.3	37	NULL	CCDS6085.1	8																																																																																			0	0		0.383	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	NRG1	protein_coding	OTTHUMT00000472504.1	49	239	0	0.41	0	1	G		0	0		32607058	1	no_errors	ENST00000523681	ensembl	human	known	74_37	rna	28	154	17.65	15.14	6	28	SNP	1	A
USP2	9099	genome.wustl.edu	37	11	119230314	119230314	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ZB-A963-01A-11D-A428-09	TCGA-ZB-A963-10A-01D-A42B-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	8597e4e5-c134-4dce-9b91-62ef0c573ebf	06601478-0cf9-430a-b343-8051ae4396d1	g.chr11:119230314G>T	ENST00000260187.2	-	4	1176	c.882C>A	c.(880-882)taC>taA	p.Y294*	USP2_ENST00000525735.1_Nonsense_Mutation_p.Y85*|USP2_ENST00000455332.2_Nonsense_Mutation_p.Y51*	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	294	USP.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		TCTGGAGGCAGTAATCTCTCA	0.572																																							0											0													97.0	84.0	88.0					11																	119230314		2199	4295	6494	SO:0001587	stop_gained	0			AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.882C>A	11.37:g.119230314G>T	ENSP00000260187:p.Tyr294*		B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Nonsense_Mutation	SNP	pfam_Peptidase_C19/C67,pfscan_Peptidase_C19/C67	p.Y294*	ENST00000260187.2	37	c.882	CCDS8422.1	11	.	.	.	.	.	.	.	.	.	.	G	35	5.468652	0.96274	.	.	ENSG00000036672	ENST00000455332;ENST00000260187;ENST00000392808;ENST00000525735	.	.	.	5.28	-3.32	0.04973	.	0.123193	0.56097	D	0.000026	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.5471	11.7854	0.52039	0.5107:0.0:0.4893:0.0	.	.	.	.	X	51;294;41;85	.	ENSP00000260187:Y294X	Y	-	3	2	USP2	118735524	1.000000	0.71417	0.976000	0.42696	0.991000	0.79684	0.843000	0.27640	-0.498000	0.06632	-0.302000	0.09304	TAC	0	pfam_Peptidase_C19/C67,pfscan_Peptidase_C19/C67		0.572	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	USP2	protein_coding	OTTHUMT00000388361.2	26	152	0	0.00	0	0	G	NM_171997	0	0		119230314	-1	no_errors	ENST00000260187	ensembl	human	known	74_37	nonsense	28	117	12.5	10.69	4	14	SNP	0.999	T
CD163L1	283316	genome.wustl.edu	37	12	7510020	7510020	+	Missense_Mutation	SNP	C	C	T			TCGA-ZB-A963-01A-11D-A428-09	TCGA-ZB-A963-10A-01D-A42B-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	8597e4e5-c134-4dce-9b91-62ef0c573ebf	06601478-0cf9-430a-b343-8051ae4396d1	g.chr12:7510020C>T	ENST00000313599.3	-	19	4399	c.4342G>A	c.(4342-4344)Gcc>Acc	p.A1448T	CD163L1_ENST00000416109.2_Missense_Mutation_p.A1458T|CD163L1_ENST00000396630.1_Missense_Mutation_p.A1416T			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1448						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						GCTTCAGAGGCAGGAAGAACT	0.428																																							0											0													99.0	93.0	95.0					12																	7510020		2203	4300	6503	SO:0001583	missense	0			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.4342G>A	12.37:g.7510020C>T	ENSP00000315945:p.Ala1448Thr		B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	pfam_SRCR,superfamily_Srcr_rcpt-rel,smart_Srcr_rcpt-rel,pfscan_SRCR,prints_SRCR	p.A1448T	ENST00000313599.3	37	c.4342	CCDS8577.1	12	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.900|9.900	1.206600|1.206600	0.22205|0.22205	.|.	.|.	ENSG00000177675|ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630|ENST00000539726	T;T;T|.	0.02280|.	4.89;4.89;4.36|.	1.07|1.07	0.0724|0.0724	0.14386|0.14386	.|.	.|.	.|.	.|.	.|.	T|T	0.15046|0.15046	0.0363|0.0363	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	0.999999|0.999999	P;D|.	0.53885|.	0.895;0.963|.	B;B|.	0.41036|.	0.264;0.346|.	T|T	0.26916|0.26916	-1.0089|-1.0089	9|5	0.27785|.	T|.	0.31|.	.|.	4.1752|4.1752	0.10348|0.10348	0.3998:0.6002:0.0:0.0|0.3998:0.6002:0.0:0.0	.|.	1458;1448|.	E7EVK4;Q9NR16|.	.;C163B_HUMAN|.	T|Y	1448;1458;1416|103	ENSP00000315945:A1448T;ENSP00000393474:A1458T;ENSP00000379871:A1416T|.	ENSP00000315945:A1448T|.	A|C	-|-	1|2	0|0	CD163L1|CD163L1	7401287|7401287	0.331000|0.331000	0.24713|0.24713	0.335000|0.335000	0.25508|0.25508	0.265000|0.265000	0.26407|0.26407	-0.250000|-0.250000	0.08830|0.08830	0.008000|0.008000	0.14787|0.14787	-0.335000|-0.335000	0.08231|0.08231	GCC|TGC	0	NULL		0.428	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	CD163L1	protein_coding	OTTHUMT00000399329.1	80	223	0	0.00	0	0	C	NM_174941	0	0		7510020	-1	no_errors	ENST00000313599	ensembl	human	known	74_37	missense	44	160	10.2	8.52	5	15	SNP	0.459	T
KDM2A	22992	genome.wustl.edu	37	11	67018081	67018081	+	Silent	SNP	G	G	A			TCGA-ZB-A963-01A-11D-A428-09	TCGA-ZB-A963-10A-01D-A42B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	8597e4e5-c134-4dce-9b91-62ef0c573ebf	06601478-0cf9-430a-b343-8051ae4396d1	g.chr11:67018081G>A	ENST00000529006.2	+	17	3026	c.2580G>A	c.(2578-2580)gaG>gaA	p.E860E	KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000308783.5_Silent_p.E318E|KDM2A_ENST00000530342.1_Silent_p.E421E|KDM2A_ENST00000398645.2_Intron	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	860					histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						aggaggaagaggaggaggagg	0.657																																							0											0													23.0	27.0	26.0					11																	67018081		2111	4226	6337	SO:0001819	synonymous_variant	0			BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13606	protein-coding gene	gene with protein product	"""F-box protein FBL11"", ""jumonji C domain-containing histone demethylase 1A"""	605657	"""F-box and leucine-rich repeat protein 11"""	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.2580G>A	11.37:g.67018081G>A			D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Silent	SNP	pfam_Znf_CXXC,pfam_F-box_dom,pfam_JmjC_dom,superfamily_Znf_FYVE_PHD,smart_JmjC_dom,smart_Znf_PHD,smart_Leu-rich_rpt_Cys-con_subtyp,pfscan_JmjC_dom,pfscan_Znf_PHD-finger,pfscan_Znf_CXXC	p.E860	ENST00000529006.2	37	c.2580	CCDS44657.1	11																																																																																			0	NULL		0.657	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	KDM2A	protein_coding	OTTHUMT00000393140.2	16	8	0	0.00	0	0	G	NM_012308	0	0		67018081	1	no_errors	ENST00000529006	ensembl	human	known	74_37	silent	11	5	26.67	0.00	4	0	SNP	0.994	A
