#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
ITM2A	9452	genome.wustl.edu	37	X	78618445	78618445	+	Missense_Mutation	SNP	A	A	C			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chrX:78618445A>C	ENST00000373298.2	-	3	578	c.435T>G	c.(433-435)ttT>ttG	p.F145L	ITM2A_ENST00000434584.2_Missense_Mutation_p.F101L|ITM2A_ENST00000469541.1_5'UTR	NM_004867.4	NP_004858.1	O43736	ITM2A_HUMAN	integral membrane protein 2A	145	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.					integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	18						CCACCTTTTCAAAGTCATGAA	0.388																																							0											0													70.0	63.0	65.0					X																	78618445		2203	4300	6503	SO:0001583	missense	0			BC034485	CCDS14444.1, CCDS55455.1	Xq13.3-q21.2	2012-10-10			ENSG00000078596	ENSG00000078596		"""BRICHOS domain containing"""	6173	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2A"""	300222				9892734, 8702637	Standard	NM_004867		Approved	BRICD2A, E25A	uc004edh.3	O43736	OTTHUMG00000021900	ENST00000373298.2:c.435T>G	X.37:g.78618445A>C	ENSP00000362395:p.Phe145Leu		B2R7X5|B4E062|Q6IBC9	Missense_Mutation	SNP	pfam_BRICHOS_dom,pfscan_BRICHOS_dom	p.F145L	ENST00000373298.2	37	c.435	CCDS14444.1	X	.	.	.	.	.	.	.	.	.	.	a	19.39	3.817777	0.71028	.	.	ENSG00000078596	ENST00000373298;ENST00000434584	D;D	0.84800	-1.9;-1.9	4.6	-0.558	0.11796	BRICHOS (2);	0.000000	0.85682	D	0.000000	D	0.89798	0.6819	M	0.81942	2.565	0.58432	D	0.999995	D;D	0.59357	0.985;0.977	D;P	0.68039	0.955;0.817	D	0.87505	0.2436	10	0.87932	D	0	-18.1639	8.8468	0.35174	0.5336:0.0:0.4664:0.0	.	101;145	B4E062;O43736	.;ITM2A_HUMAN	L	145;101	ENSP00000362395:F145L;ENSP00000415533:F101L	ENSP00000362395:F145L	F	-	3	2	ITM2A	78505101	0.995000	0.38212	0.995000	0.50966	0.862000	0.49288	0.346000	0.19997	-0.219000	0.10003	0.433000	0.28618	TTT	0	pfam_BRICHOS_dom,pfscan_BRICHOS_dom		0.388	ITM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ITM2A	protein_coding	OTTHUMT00000057329.1	34	113	0	0.00	0	0	A	NM_004867	0	0		78618445	-1	no_errors	ENST00000373298	ensembl	human	known	74_37	missense	31	92	24.39	16.36	10	18	SNP	0.998	C
SCNN1D	6339	genome.wustl.edu	37	1	1222276	1222276	+	Missense_Mutation	SNP	C	C	T	rs543238689		TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr1:1222276C>T	ENST00000338555.2	+	5	1692	c.548C>T	c.(547-549)cCc>cTc	p.P183L	SCNN1D_ENST00000379116.5_Missense_Mutation_p.P347L|SCNN1D_ENST00000325425.8_Missense_Mutation_p.P249L|SCNN1D_ENST00000400928.3_Missense_Mutation_p.P183L			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	183					ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	CGCCACGAGCCCCCCTTCCAC	0.657													C|||	1	0.000199681	0.0008	0.0	5008	,	,		13877	0.0		0.0	False		,,,				2504	0.0						0.9998,0.0001997											0													34.0	44.0	40.0					1																	1222276		2193	4294	6487	SO:0001583	missense	0			U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10601	protein-coding gene	gene with protein product		601328	"""sodium channel, nonvoltage-gated 1, delta"", ""sodium channel, non-voltage-gated 1, delta"""			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.548C>T	1.37:g.1222276C>T	ENSP00000339504:p.Pro183Leu		A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Missense_Mutation	SNP	pfam_Na+channel_ASC,prints_Na+channel_ASC,tigrfam_EnaC	p.P347L	ENST00000338555.2	37	c.1040		1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.746181	0.30955	.	.	ENSG00000162572	ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928	T;T;T;T	0.69685	-0.42;-0.37;-0.42;-0.37	4.38	-0.112	0.13572	.	2202.840000	0.00166	N	0.000000	T	0.68504	0.3008	L	0.52905	1.665	0.09310	N	1	P;P	0.48230	0.891;0.907	P;B	0.48677	0.586;0.444	T	0.55464	-0.8137	10	0.59425	D	0.04	.	6.0309	0.19679	0.0:0.5901:0.1384:0.2715	.	183;347	P51172;A6NNF7	SCNND_HUMAN;.	L	214;347;183;249;183	ENSP00000368411:P347L;ENSP00000339504:P183L;ENSP00000321594:P249L;ENSP00000383717:P183L	ENSP00000321594:P249L	P	+	2	0	SCNN1D	1212139	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.525000	0.06214	0.282000	0.22254	0.313000	0.20887	CCC	0	pfam_Na+channel_ASC,tigrfam_EnaC		0.657	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	SCNN1D	protein_coding	OTTHUMT00000005802.2	43	132	0	0.00	0	0	C	NM_002978	rs543238689	C->T		1222276	1	no_errors	ENST00000379116	ensembl	human	known	74_37	missense	28	96	24.32	12.73	9	14	SNP	0	T
SENP6	26054	genome.wustl.edu	37	6	76343306	76343306	+	Silent	SNP	C	C	A			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr6:76343306C>A	ENST00000447266.2	+	4	695	c.217C>A	c.(217-219)Cga>Aga	p.R73R	SENP6_ENST00000370010.2_Silent_p.R73R|SENP6_ENST00000370014.3_Silent_p.R73R|SENP6_ENST00000327284.8_Silent_p.R73R	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	73					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				GTTAAATCGTCGATCTGAAAT	0.299																																							0											0													80.0	78.0	78.0					6																	76343306		1811	4066	5877	SO:0001819	synonymous_variant	0				CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.217C>A	6.37:g.76343306C>A			A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Silent	SNP	pfam_Peptidase_C48,pfscan_Peptidase_C48	p.R73	ENST00000447266.2	37	c.217	CCDS47454.1	6																																																																																			0	NULL		0.299	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SENP6	protein_coding	OTTHUMT00000041272.2	118	276	0	0.36	0	1	C	NM_015571	0	0		76343306	1	no_errors	ENST00000370014	ensembl	human	known	74_37	silent	79	236	7.06	10.27	6	27	SNP	0.996	A
GTF2I	2969	genome.wustl.edu	37	7	74146970	74146970	+	Missense_Mutation	SNP	T	T	A			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr7:74146970T>A	ENST00000324896.4	+	15	1660	c.1271T>A	c.(1270-1272)cTt>cAt	p.L424H	GTF2I_ENST00000353920.4_Missense_Mutation_p.L404H|GTF2I_ENST00000346152.4_Missense_Mutation_p.L403H|GTF2I_ENST00000416070.1_Missense_Mutation_p.L383H	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	390	164	0	0.00	0	0	T	NM_032999	0	0		74146970	1	no_errors	ENST00000324896	ensembl	human	known	74_37	missense	272	129	10.23	12.84	31	19	SNP	1	A
B4GALNT1	2583	genome.wustl.edu	37	12	58019923	58019923	+	3'UTR	SNP	C	C	T			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr12:58019923C>T	ENST00000341156.4	-	0	2790				SLC26A10_ENST00000379218.2_3'UTR|SLC26A10_ENST00000490243.1_3'UTR	NM_001478.3	NP_001469.1	Q00973	B4GN1_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 1						carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|ganglioside biosynthetic process (GO:0001574)|glycosphingolipid metabolic process (GO:0006687)|lipid glycosylation (GO:0030259)|lipid storage (GO:0019915)|protein glycosylation (GO:0006486)|spermatogenesis (GO:0007283)	integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|plasma membrane (GO:0005886)	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity (GO:0003947)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|urinary_tract(1)	20	Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			AAGCTGAGAGCTTTGGAATCC	0.483																																							0											0																																										SO:0001624	3_prime_UTR_variant	0			M83651	CCDS8950.1, CCDS61170.1, CCDS61171.1	12q13.3	2013-09-11	2006-01-08	2006-01-08	ENSG00000135454	ENSG00000135454	2.4.1.92	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	4117	protein-coding gene	gene with protein product	"""GD2 synthase, GM2 synthase"""	601873	"""UDP-N-acetyl-alpha-D-galactosamine:(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase (GalNAc-T)"", ""UDP-Gal:betaGlcNAc beta-1,4-N-acetylgalactosaminyltransferase transferase 1"", ""spastic paraplegia 26"""	GALGT, SPG26		1601877, 23746551	Standard	NM_001478		Approved	beta1-4GalNAc-T	uc001spg.2	Q00973	OTTHUMG00000170190	ENST00000341156.4:c.*604G>A	12.37:g.58019923C>T			B4DE26|Q8N636	RNA	SNP	0	NULL	ENST00000341156.4	37	NULL	CCDS8950.1	12																																																																																			0	0		0.483	B4GALNT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC26A10	protein_coding	OTTHUMT00000407853.1	37	290	0	0.00	0	0	C	NM_001478	0	0		58019923	1	no_errors	ENST00000483647	ensembl	human	known	74_37	rna	25	186	13.79	14.68	4	32	SNP	0	T
SETD1A	9739	genome.wustl.edu	37	16	30972682	30972682	+	Missense_Mutation	SNP	G	G	T			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr16:30972682G>T	ENST00000262519.8	+	4	1027	c.341G>T	c.(340-342)tGc>tTc	p.C114F		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	114	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						AAGGATATGTGCCGTAAGTAC	0.567																																							0											0													133.0	104.0	114.0					16																	30972682		2197	4300	6497	SO:0001583	missense	0			AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.341G>T	16.37:g.30972682G>T	ENSP00000262519:p.Cys114Phe		A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	pfam_COMPASS_Set1_N-SET,pfam_SET_dom,pfam_RRM_dom,smart_RRM_dom,smart_SET_dom,smart_Post-SET_dom,pfscan_SET_dom,pfscan_Post-SET_dom,pfscan_RRM_dom	p.C114F	ENST00000262519.8	37	c.341	CCDS32435.1	16	.	.	.	.	.	.	.	.	.	.	G	18.61	3.661593	0.67700	.	.	ENSG00000099381	ENST00000262519;ENST00000452917	T;T	0.15487	2.42;2.42	5.36	5.36	0.76844	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.33556	0.0867	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.01532	-1.1331	10	0.41790	T	0.15	.	17.8447	0.88727	0.0:0.0:1.0:0.0	.	114	O15047	SET1A_HUMAN	F	114	ENSP00000262519:C114F;ENSP00000391408:C114F	ENSP00000262519:C114F	C	+	2	0	SETD1A	30880183	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.869000	0.99810	2.517000	0.84864	0.591000	0.81541	TGC	0	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom		0.567	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SETD1A	protein_coding	OTTHUMT00000318244.2	45	176	0	0.56	0	1	G	NM_014712	0	0		30972682	1	no_errors	ENST00000262519	ensembl	human	known	74_37	missense	41	154	8.89	7.23	4	12	SNP	1	T
ZNF177	7730	genome.wustl.edu	37	19	9489731	9489731	+	Missense_Mutation	SNP	A	A	G			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr19:9489731A>G	ENST00000589262.1	+	3	193	c.127A>G	c.(127-129)Atg>Gtg	p.M43V	ZNF177_ENST00000605471.1_3'UTR|ZNF177_ENST00000446085.4_Missense_Mutation_p.M43V|ZNF177_ENST00000343499.4_Missense_Mutation_p.M43V|ZNF177_ENST00000602856.1_Missense_Mutation_p.M43V|ZNF177_ENST00000434737.2_Missense_Mutation_p.M43V|ZNF177_ENST00000602738.1_Missense_Mutation_p.M43V|ZNF177_ENST00000541595.2_Missense_Mutation_p.M43V|ZNF177_ENST00000590616.1_Missense_Mutation_p.M43V	NM_001172651.1	NP_001166122.1	Q13360	ZN177_HUMAN	zinc finger protein 177	43	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.M43L(2)		breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|stomach(2)	13						CAAAGATGTGATGCTGGAGAA	0.428																																							0											2	Substitution - Missense(2)	prostate(2)											109.0	98.0	101.0					19																	9489731		2203	4300	6503	SO:0001583	missense	0			U37263, BC012012	CCDS12212.1, CCDS54214.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	12966	protein-coding gene	gene with protein product		601276					Standard	NM_003451		Approved		uc021uon.1	Q13360		ENST00000589262.1:c.127A>G	19.37:g.9489731A>G	ENSP00000468531:p.Met43Val		B4DY57|E9PDG0|I3L0I4|Q96ER2	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.M43V	ENST00000589262.1	37	c.127	CCDS54214.1	19	.	.	.	.	.	.	.	.	.	.	A	11.71	1.720931	0.30503	.	.	ENSG00000188629	ENST00000541595;ENST00000446085;ENST00000343499;ENST00000434737	T;T;T;T	0.03065	4.06;4.06;4.06;4.06	2.74	2.74	0.32292	Krueppel-associated box (4);	.	.	.	.	T	0.22166	0.0534	H	0.95079	3.62	0.23916	N	0.996479	D	0.53885	0.963	D	0.67231	0.95	T	0.32851	-0.9891	8	0.87932	D	0	.	7.3506	0.26689	1.0:0.0:0.0:0.0	.	43	Q13360	ZN177_HUMAN	V	43	ENSP00000445323:M43V;ENSP00000413568:M43V;ENSP00000341497:M43V;ENSP00000415070:M43V	ENSP00000341497:M43V	M	+	1	0	ZNF177	9350731	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.495000	0.60353	1.509000	0.48786	0.383000	0.25322	ATG	0	pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,pfscan_Krueppel-associated_box		0.428	ZNF177-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZNF177	protein_coding	OTTHUMT00000449028.1	64	296	0	0.00	0	0	A	NM_003451	0	0		9489731	1	no_errors	ENST00000434737	ensembl	human	known	74_37	missense	41	219	24.07	9.88	13	24	SNP	1	G
ZNF222	7673	genome.wustl.edu	37	19	44529568	44529568	+	5'UTR	SNP	C	C	G	rs571210898	byFrequency	TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr19:44529568C>G	ENST00000187879.8	+	0	54				ZNF222_ENST00000587846.1_5'UTR|ZNF222_ENST00000391960.3_5'UTR|AC067968.3_ENST00000592583.1_lincRNA|ZNF222_ENST00000590160.1_3'UTR|ZNF223_ENST00000591793.1_5'UTR	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222						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(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				GTCTCCTTTCCTTGGGGCTCG	0.547																																							0											0													29.0	27.0	28.0					19																	44529568		692	1591	2283	SO:0001623	5_prime_UTR_variant	0			AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"""Zinc fingers, C2H2-type"", ""-"""	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.-109C>G	19.37:g.44529568C>G			G5E9B9|Q8N6G7|Q9P1U5	RNA	SNP	0	NULL	ENST00000187879.8	37	NULL	CCDS33045.1	19																																																																																			0	0		0.547	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	ZNF222	protein_coding	OTTHUMT00000460465.2	36	175	0	0.00	0	0	C		0	0		44529568	1	no_errors	ENST00000590160	ensembl	human	known	74_37	rna	39	126	9.3	9.35	4	13	SNP	0	G
SCO2	9997	genome.wustl.edu	37	22	50962528	50962528	+	Missense_Mutation	SNP	G	G	A			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr22:50962528G>A	ENST00000543927.1	-	2	519	c.313C>T	c.(313-315)Cac>Tac	p.H105Y	SCO2_ENST00000252785.3_Missense_Mutation_p.H105Y|CTA-384D8.36_ENST00000608319.1_RNA|SCO2_ENST00000535425.1_Missense_Mutation_p.H105Y|SCO2_ENST00000395693.3_Missense_Mutation_p.H105Y	NM_001169109.1	NP_001162580.1	O43819	SCO2_HUMAN	SCO2 cytochrome c oxidase assembly protein	105	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|eye development (GO:0001654)|in utero embryonic development (GO:0001701)|muscle system process (GO:0003012)|oxidation-reduction process (GO:0055114)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			endometrium(1)|lung(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TCCAGCAGGTGGAAGTCGCCC	0.652																																							0											0													29.0	32.0	31.0					22																	50962528		2203	4300	6503	SO:0001583	missense	0			AL021683	CCDS14095.1	22q13.33	2014-01-30	2012-10-15		ENSG00000130489	ENSG00000130489		"""Mitochondrial respiratory chain complex assembly factors"""	10604	protein-coding gene	gene with protein product		604272	"""SCO (cytochrome oxidase deficient, yeast) homolog 2"", ""SCO cytochrome oxidase deficient homolog 2 (yeast)"", ""myopia 6"""	MYP6		10218584, 16091356, 23643385	Standard	NM_005138		Approved	SCO1L	uc003bma.3	O43819	OTTHUMG00000150251	ENST00000543927.1:c.313C>T	22.37:g.50962528G>A	ENSP00000444433:p.His105Tyr		Q3T1B5|Q9UK87	Missense_Mutation	SNP	pfam_SCO1/SenC,superfamily_Thioredoxin-like_fold,pirsf_Synth_of_cyt-c-oxidase_Sco1/2	p.H105Y	ENST00000543927.1	37	c.313	CCDS14095.1	22	.	.	.	.	.	.	.	.	.	.	G	7.880	0.730125	0.15507	.	.	ENSG00000130489	ENST00000395693;ENST00000543927;ENST00000535425;ENST00000252785;ENST00000439934;ENST00000423348	D;D;D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38;-3.38;-3.38	4.95	-1.78	0.07957	Thioredoxin-like fold (3);	0.495228	0.20813	N	0.085218	D	0.88804	0.6536	L	0.39898	1.24	0.27699	N	0.945847	B	0.29955	0.263	B	0.38194	0.267	T	0.82182	-0.0584	10	0.72032	D	0.01	-14.4871	6.8349	0.23931	0.2273:0.0:0.3611:0.4116	.	105	O43819	SCO2_HUMAN	Y	105	ENSP00000379046:H105Y;ENSP00000444433:H105Y;ENSP00000444242:H105Y;ENSP00000252785:H105Y;ENSP00000415642:H105Y;ENSP00000403570:H105Y	ENSP00000252785:H105Y	H	-	1	0	SCO2	49309394	0.000000	0.05858	0.311000	0.25182	0.095000	0.18619	-1.227000	0.02950	-0.246000	0.09611	-1.461000	0.01025	CAC	0	pfam_SCO1/SenC,superfamily_Thioredoxin-like_fold,pirsf_Synth_of_cyt-c-oxidase_Sco1/2		0.652	SCO2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	SCO2	protein_coding	OTTHUMT00000317091.1	28	98	0	0.00	0	0	G	NM_005138	0	0		50962528	-1	no_errors	ENST00000252785	ensembl	human	known	74_37	missense	14	80	12.5	11.11	2	10	SNP	0.903	A
TYMP	1890	genome.wustl.edu	37	22	50968040	50968040	+	Silent	SNP	G	G	C			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr22:50968040G>C	ENST00000252029.3	-	2	261	c.99C>G	c.(97-99)ccC>ccG	p.P33P	TYMP_ENST00000395681.1_Silent_p.P33P|TYMP_ENST00000395678.3_Silent_p.P33P|TYMP_ENST00000395680.1_Silent_p.P33P	NM_001113755.2|NM_001113756.2|NM_001257988.1|NM_001257989.1|NM_001953.4	NP_001107227.1|NP_001107228.1|NP_001244917.1|NP_001244918.1|NP_001944.1	P19971	TYPH_HUMAN	thymidine phosphorylase	33					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)|DNA replication (GO:0006260)|mitochondrial genome maintenance (GO:0000002)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphorylase activity (GO:0004645)|platelet-derived growth factor receptor binding (GO:0005161)|pyrimidine-nucleoside phosphorylase activity (GO:0016154)|thymidine phosphorylase activity (GO:0009032)|transferase activity, transferring pentosyl groups (GO:0016763)			large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Cidofovir(DB00369)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Trifluridine(DB00432)	GGAGCTGCTTGGGCTCTGGCG	0.692																																							0											0													22.0	25.0	24.0					22																	50968040		2203	4298	6501	SO:0001819	synonymous_variant	0			M63193	CCDS14096.1, CCDS58811.1	22q13	2014-09-17	2008-01-21	2008-01-21	ENSG00000025708	ENSG00000025708	2.4.2.4		3148	protein-coding gene	gene with protein product	"""gliostatin"""	131222	"""endothelial cell growth factor 1 (platelet-derived)"""	MNGIE, ECGF1		1590793, 11733540	Standard	NM_001113755		Approved		uc003bme.5	P19971	OTTHUMG00000150249	ENST00000252029.3:c.99C>G	22.37:g.50968040G>C			A8MW15|H9KVA0|Q13390|Q8WVB7	Silent	SNP	pfam_Glycosyl_Trfase_fam3,pfam_Glycosyl_Trfase_fam3_N_dom,pfam_PYNP_C,superfamily_Glycosyl_Trfase_fam3,superfamily_PYNP_C,superfamily_Glycosyl_Trfase_fam3_N_dom,smart_PYNP_C,pirsf_Pyrmidine_PPase,tigrfam_Pyrmidine_PPas_bac/euk	p.P33	ENST00000252029.3	37	c.99	CCDS14096.1	22																																																																																			0	superfamily_Glycosyl_Trfase_fam3_N_dom,pirsf_Pyrmidine_PPase		0.692	TYMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	TYMP	protein_coding	OTTHUMT00000317081.1	93	91	0	1.09	0	1	G	NM_001953	0	0		50968040	-1	no_errors	ENST00000252029	ensembl	human	known	74_37	silent	45	71	8.16	10.00	4	8	SNP	0	C
ITM2A	9452	genome.wustl.edu	37	X	78618440	78618440	+	Splice_Site	DEL	T	T	-	rs36103089		TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chrX:78618440delT	ENST00000373298.2	-	3	583	c.440delA	c.(439-441)aag>ag	p.K147fs	ITM2A_ENST00000434584.2_Splice_Site_p.K103fs|ITM2A_ENST00000469541.1_5'UTR	NM_004867.4	NP_004858.1	O43736	ITM2A_HUMAN	integral membrane protein 2A	147	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.					integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	18						GAAGCCCACCTTTTCAAAGTC	0.383																																							0											0													67.0	61.0	63.0					X																	78618440		2203	4299	6502	SO:0001630	splice_region_variant	0			BC034485	CCDS14444.1, CCDS55455.1	Xq13.3-q21.2	2012-10-10			ENSG00000078596	ENSG00000078596		"""BRICHOS domain containing"""	6173	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2A"""	300222				9892734, 8702637	Standard	NM_004867		Approved	BRICD2A, E25A	uc004edh.3	O43736	OTTHUMG00000021900	ENST00000373298.2:c.441+1A>-	X.37:g.78618440delT			B2R7X5|B4E062|Q6IBC9	Frame_Shift_Del	DEL	pfam_BRICHOS_dom,pfscan_BRICHOS_dom	p.K147fs	ENST00000373298.2	37	c.440	CCDS14444.1	X																																																																																			0	pfam_BRICHOS_dom,pfscan_BRICHOS_dom		0.383	ITM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ITM2A	protein_coding	OTTHUMT00000057329.1	33	109	0	0.00	0	0	T	NM_004867	rs36103089	CT->C	Frame_Shift_Del	78618440	-1	no_errors	ENST00000373298	ensembl	human	known	74_37	frame_shift_del	33	90	21.43	16.67	9	18	DEL	1	0
TRAK1	22906	genome.wustl.edu	37	3	42251577	42251578	+	Intron	INS	-	-	GGAGGA	rs10634555|rs35624871		TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	-	-	-	GGAGGA	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr3:42251577_42251578insGGAGGA	ENST00000327628.5	+	14	2363				TRAK1_ENST00000487159.1_Intron|TRAK1_ENST00000396175.1_Intron|TRAK1_ENST00000341421.3_In_Frame_Ins_p.639_640insEE	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1						endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.E640delE(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						CCAGCGGCCACggaggaggagg	0.629																																					GBM(44;195 884 22595 31865 41850)		0											1	Deletion - In frame(1)	kidney(1)																																								SO:0001627	intron_variant	0				CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1963+100->GGAGGA	3.37:g.42251578_42251583dupGGAGGA			E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	In_Frame_Ins	INS	pfam_HAP1_N,pfam_Traffickng_kinesin-bd_prot_dom	p.634in_frame_insEE	ENST00000327628.5	37	c.1889_1890	CCDS43072.1	3																																																																																			0	NULL		0.629	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	TRAK1	protein_coding	OTTHUMT00000343413.1	14	6	0	0.00	0	0	0	NM_014965	0	0		42251578	1	no_errors	ENST00000341421	ensembl	human	known	74_37	in_frame_ins	12	3	14.29	40.00	2	2	INS	0.010:0.044	GGAGGA
MUC12	10071	genome.wustl.edu	37	7	100641735	100641735	+	Missense_Mutation	SNP	A	A	G			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr7:100641735A>G	ENST00000379442.3	+	5	8320	c.8320A>G	c.(8320-8322)Aca>Gca	p.T2774A	MUC12_ENST00000536621.1_Missense_Mutation_p.T2631A			Q9UKN1	MUC12_HUMAN	mucin 12, cell surface associated	2774	28 X 19 AA approximate tandem repeats of E-E-S-X-X-X-H-X-X-P-X-X-T-X-T-X-X-X-P.|Ser-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|regulation of cell growth (GO:0001558)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)				breast(6)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)|stomach(13)	25						TGGAGAATCTACAACCTCACG	0.517																																							0											0													1.0	1.0	1.0					7																	100641735		229	583	812	SO:0001583	missense	0			AF147790, AF147791	CCDS55139.1	7q22	2007-01-17	2006-03-14		ENSG00000205277	ENSG00000205277		"""Mucins"""	7510	protein-coding gene	gene with protein product		604609	"""mucin 11"""	MUC11		10463611	Standard	NM_001164462		Approved		uc003uxo.3	Q9UKN1	OTTHUMG00000157042	ENST00000379442.3:c.8320A>G	7.37:g.100641735A>G	ENSP00000368755:p.Thr2774Ala		A6ND38|F5GWV9|Q9UKN0	Missense_Mutation	SNP	pfam_SEA_dom	p.T2631A	ENST00000379442.3	37	c.7891		7	.	.	.	.	.	.	.	.	.	.	a	7.566	0.665810	0.14710	.	.	ENSG00000205277	ENST00000379442;ENST00000536621	T;T	0.11063	2.81;2.81	0.704	0.704	0.18121	.	.	.	.	.	T	0.04907	0.0132	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.45789	-0.9237	6	0.20519	T	0.43	.	.	.	.	.	.	.	.	A	2774;2631	ENSP00000368755:T2774A;ENSP00000441929:T2631A	ENSP00000368755:T2774A	T	+	1	0	MUC12	100428455	0.002000	0.14202	0.006000	0.13384	0.061000	0.15899	0.396000	0.20867	0.558000	0.29135	0.145000	0.16022	ACA	0	NULL		0.517	MUC12-001	NOVEL	basic|appris_candidate_longest	protein_coding	MUC12	protein_coding	OTTHUMT00000347234.1	9	6	0	0.00	0	0	A	XM_379904	0	0		100641735	1	no_errors	ENST00000536621	ensembl	human	known	74_37	missense	7	3	41.67	0.00	5	0	SNP	0.006	G
ZNF532	55205	genome.wustl.edu	37	18	56651490	56651490	+	Missense_Mutation	SNP	C	C	T			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr18:56651490C>T	ENST00000336078.4	+	11	4474	c.3698C>T	c.(3697-3699)cCa>cTa	p.P1233L	ZNF532_ENST00000591083.1_Missense_Mutation_p.P1233L|ZNF532_ENST00000591808.1_Missense_Mutation_p.P1233L|ZNF532_ENST00000588956.1_3'UTR|ZNF532_ENST00000591230.1_Missense_Mutation_p.P1233L|ZNF532_ENST00000589288.1_Missense_Mutation_p.P1233L	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	1233					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						GAACCTCAGCCAGTGTCCAAG	0.547																																							0											0													34.0	35.0	35.0					18																	56651490		2202	4288	6490	SO:0001583	missense	0			AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"""Zinc fingers, C2H2-type"""	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.3698C>T	18.37:g.56651490C>T	ENSP00000338217:p.Pro1233Leu		Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.P1233L	ENST00000336078.4	37	c.3698	CCDS11969.1	18	.	.	.	.	.	.	.	.	.	.	c	17.98	3.521725	0.64747	.	.	ENSG00000074657	ENST00000336078	T	0.01527	4.8	5.83	5.83	0.93111	.	0.108849	0.64402	D	0.000007	T	0.03178	0.0093	N	0.11427	0.14	0.53688	D	0.999972	P;D	0.65815	0.937;0.995	P;P	0.54590	0.585;0.756	T	0.68784	-0.5317	10	0.41790	T	0.15	-3.5668	19.7233	0.96151	0.0:1.0:0.0:0.0	.	1233;1233	B3KXW2;Q9HCE3	.;ZN532_HUMAN	L	1233	ENSP00000338217:P1233L	ENSP00000338217:P1233L	P	+	2	0	ZNF532	54802470	1.000000	0.71417	0.967000	0.41034	0.860000	0.49131	4.793000	0.62474	2.766000	0.95052	0.556000	0.70494	CCA	0	NULL		0.547	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF532	protein_coding	OTTHUMT00000256130.1	63	0	0	0.00	0	0	C	NM_018181	0	0		56651490	1	no_errors	ENST00000336078	ensembl	human	known	74_37	missense	53	0	7.02	0.00	4	0	SNP	0.998	T
FOXE3	2301	genome.wustl.edu	37	1	47882166	47882168	+	In_Frame_Del	DEL	GGC	GGC	-			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	GGC	GGC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr1:47882166_47882168delGGC	ENST00000335071.2	+	1	423_425	c.179_181delGGC	c.(178-183)gggcgg>ggg	p.R65del		NM_012186.2	NP_036318.1	Q13461	FOXE3_HUMAN	forkhead box E3	65	Poly-Arg.				camera-type eye development (GO:0043010)|cell development (GO:0048468)|positive regulation of epithelial cell proliferation (GO:0050679)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(3)|prostate(1)|upper_aerodigestive_tract(1)	5				READ - Rectum adenocarcinoma(2;0.0908)		cccggcccggggcggcggcggcg	0.823																																							0											0										4,216		2,0,108						2.6	0.0			1	26,1088		7,12,538	no	coding	FOXE3	NM_012186.2		9,12,646	A1A1,A1R,RR		2.3339,1.8182,2.2489				30,1304				SO:0001651	inframe_deletion	0			AF275722	CCDS550.1	1p32	2008-02-05			ENSG00000186790	ENSG00000186790		"""Forkhead boxes"""	3808	protein-coding gene	gene with protein product		601094		FKHL12		8825632	Standard	NM_012186		Approved	FREAC8	uc001crk.3	Q13461	OTTHUMG00000007954	ENST00000335071.2:c.179_181delGGC	1.37:g.47882175_47882177delGGC	ENSP00000334472:p.Arg65del		Q5SVY9|Q9NQV9	In_Frame_Del	DEL	pfam_TF_fork_head,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head	p.R64in_frame_del	ENST00000335071.2	37	c.179_181	CCDS550.1	1																																																																																			0	NULL		0.823	FOXE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOXE3	protein_coding	OTTHUMT00000021836.1	8	0	0	0.00	0	0	GGC	NM_012186	0	0		47882168	1	no_errors	ENST00000335071	ensembl	human	known	74_37	in_frame_del	4	0	33.33	0.00	2	0	DEL	0.991:0.856:0.786	0
NKPD1	284353	genome.wustl.edu	37	19	45655769	45655771	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	CTG	CTG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr19:45655769_45655771delCTG	ENST00000438936.2	-	3	1469_1471	c.1258_1260delCAG	c.(1258-1260)cagdel	p.Q420del	AC005757.7_ENST00000589594.1_lincRNA|NKPD1_ENST00000429338.1_In_Frame_Del_p.Q420del|NKPD1_ENST00000589776.1_In_Frame_Del_p.Q420del|NKPD1_ENST00000317951.4_In_Frame_Del_p.Q642del			Q17RQ9	NKPD1_HUMAN	NTPase, KAP family P-loop domain containing 1	420	Poly-Gln.					integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|prostate(2)|urinary_tract(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)		CAAAGTCCCCCTGCTGCTGCTGC	0.704																																							0											0										80,72,3002		15,0,50,16,40,1456						2.5	0.9			7	8,143,6913		1,0,6,18,107,3400	no	codingComplex	NKPD1	NM_198478.3		16,0,56,34,147,4856	A1A1,A1A2,A1R,A2A2,A2R,RR		2.1376,4.8193,2.9654				88,215,9915				SO:0001651	inframe_deletion	0			AK090919		19q13.32	2012-07-02		2012-07-02	ENSG00000179846	ENSG00000179846			24739	protein-coding gene	gene with protein product						14702039	Standard	NM_198478		Approved	FLJ33600	uc010xxi.2	Q17RQ9	OTTHUMG00000160521	ENST00000438936.2:c.1258_1260delCAG	19.37:g.45655778_45655780delCTG	ENSP00000401739:p.Gln420del		B7ZLG6|D6RH15|Q8N2A2	In_Frame_Del	DEL	pfam_KAP_NTPase	p.Q642in_frame_del	ENST00000438936.2	37	c.1926_1924		19																																																																																			0	NULL		0.704	NKPD1-001	KNOWN	basic	protein_coding	NKPD1	protein_coding	OTTHUMT00000360950.2	35	28	0	0.00	0	0	CTG	NM_198478	0	0		45655771	-1	no_errors	ENST00000317951	ensembl	human	known	74_37	in_frame_del	17	10	10.53	0.00	2	0	DEL	0.910:0.925:0.950	0
BMS1P20	96610	genome.wustl.edu	37	22	22661172	22661173	+	RNA	INS	-	-	C	rs377142963|rs7410785|rs60559515	byFrequency	TCGA-ZB-A96A-01A-11D-A428-09	TCGA-ZB-A96A-10A-01D-A42B-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a646c617-55f7-49ec-9a1a-a5bd4f8d147a	b7627666-1ce3-43b3-b2b7-42ae973cd6ad	g.chr22:22661172_22661173insC	ENST00000426066.1	+	0	264_265					NR_027293.1				BMS1 pseudogene 20																		CATACAGGTTTTCCCCCCCCAC	0.411																																							0											0																																												0					22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22661172_22661173insC				RNA	INS	0	NULL	ENST00000426066.1	37	NULL		22																																																																																			0	0		0.411	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	BMS1P20	processed_transcript	OTTHUMT00000473090.1	135	0	0	0.00	0	0	0		0	0		22661173	1	no_errors	ENST00000426066	ensembl	human	known	74_37	rna	114	0	7.32	0.00	9	0	INS	0.640:0.833	C
