#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
LRP1B	53353	genome.wustl.edu	37	2	141751564	141751564	+	Splice_Site	SNP	A	A	T			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr2:141751564A>T	ENST00000389484.3	-	16	3615	c.2644T>A	c.(2644-2646)Ttc>Atc	p.F882I	Y_RNA_ENST00000365022.1_RNA	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	882	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GAGAACATACAGCAGTTTACT	0.418										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)		0											0													108.0	104.0	106.0					2																	141751564		2203	4300	6503	SO:0001630	splice_region_variant	0			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2644+1T>A	2.37:g.141751564A>T			Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	pfam_LDrepeatLR_classA_rpt,pfam_LDLR_classB_rpt,pfam_EG-like_dom,superfamily_Growth_fac_rcpt_N_dom,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,smart_EG-like_dom,smart_EGF-like_Ca-bd_dom,smart_LDLR_classB_rpt,pfscan_EG-like_dom,pfscan_LDrepeatLR_classA_rpt,pfscan_LDLR_classB_rpt,prints_LDrepeatLR_classA_rpt	p.F882I	ENST00000389484.3	37	c.2644	CCDS2182.1	2	.	.	.	.	.	.	.	.	.	.	A	12.52	1.963994	0.34659	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.90844	-2.74	5.8	5.8	0.92144	.	0.224065	0.39020	U	0.001482	D	0.85031	0.5604	L	0.40543	1.245	0.46396	D	0.999028	B	0.17038	0.02	B	0.14023	0.01	T	0.79410	-0.1815	9	.	.	.	.	10.4879	0.44733	0.9278:0.0:0.0722:0.0	.	882	Q9NZR2	LRP1B_HUMAN	I	882;820	ENSP00000374135:F882I	.	F	-	1	0	LRP1B	141468034	1.000000	0.71417	1.000000	0.80357	0.512000	0.34134	3.004000	0.49513	2.203000	0.70933	0.460000	0.39030	TTC	0	superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,pfscan_LDrepeatLR_classA_rpt		0.418	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRP1B	protein_coding	OTTHUMT00000254736.2	54	264	0	0.00	0	0	A	NM_018557	0	0	Missense_Mutation	141751564	-1	no_errors	ENST00000389484	ensembl	human	known	74_37	missense	36	161	33.33	30.90	18	72	SNP	1	T
AGAP1	116987	genome.wustl.edu	37	2	236617824	236617824	+	Splice_Site	SNP	T	T	A			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr2:236617824T>A	ENST00000304032.8	+	2	745	c.165T>A	c.(163-165)gaT>gaA	p.D55E	AGAP1_ENST00000336665.5_Splice_Site_p.D55E|AGAP1_ENST00000409457.1_Splice_Site_p.D55E|AGAP1_ENST00000409538.1_Splice_Site_p.D320E	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	55					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						CTTTTTCAGATGCCTTCGTGA	0.532																																							0											0													209.0	188.0	195.0					2																	236617824		2203	4300	6503	SO:0001630	splice_region_variant	0			AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.164-1T>A	2.37:g.236617824T>A			B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	pfam_ArfGAP,pfam_MIRO-like,pfam_Small_GTPase,pfam_Ankyrin_rpt,pfam_Pleckstrin_homology,superfamily_P-loop_NTPase,superfamily_Ankyrin_rpt-contain_dom,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Pleckstrin_homology,smart_ArfGAP,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_Pleckstrin_homology,pfscan_ArfGAP,prints_ArfGAP,prints_Small_GTPase	p.D55E	ENST00000304032.8	37	c.165	CCDS33408.1	2	.	.	.	.	.	.	.	.	.	.	t	12.78	2.041667	0.35989	.	.	ENSG00000157985	ENST00000409457;ENST00000304032;ENST00000336665;ENST00000402604;ENST00000409538	D;T;T;D;T	0.90133	-2.07;-0.55;-0.54;-2.62;-0.64	3.88	2.72	0.32119	.	0.071163	0.53938	U	0.000059	D	0.92642	0.7662	M	0.61703	1.905	0.80722	D	1	D;P	0.76494	0.999;0.841	D;P	0.74023	0.982;0.785	D	0.89875	0.4026	10	0.33141	T	0.24	.	9.2437	0.37511	0.0:0.0871:0.0:0.9129	.	55;55	Q9UPQ3-2;Q9UPQ3	.;AGAP1_HUMAN	E	55;55;55;2;320	ENSP00000387174:D55E;ENSP00000307634:D55E;ENSP00000338378:D55E;ENSP00000385492:D2E;ENSP00000386897:D320E	ENSP00000307634:D55E	D	+	3	2	AGAP1	236282563	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	1.390000	0.34464	0.676000	0.31285	-0.383000	0.06682	GAT	0	NULL		0.532	AGAP1-001	KNOWN	basic|CCDS	protein_coding	AGAP1	protein_coding	OTTHUMT00000257076.2	110	221	0	0.00	0	0	T	NM_014914	0	0	Missense_Mutation	236617824	1	no_errors	ENST00000304032	ensembl	human	known	74_37	missense	84	171	10.64	4.44	10	8	SNP	1	A
CSRNP1	64651	genome.wustl.edu	37	3	39186572	39186572	+	Missense_Mutation	SNP	C	C	G			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr3:39186572C>G	ENST00000273153.5	-	3	558	c.381G>C	c.(379-381)gaG>gaC	p.E127D	CSRNP1_ENST00000514182.1_Missense_Mutation_p.E127D	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	127					apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						CCTGCGCAAACTCAGCCAAAG	0.612																																							0											0													71.0	62.0	65.0					3																	39186572		2203	4300	6503	SO:0001583	missense	0			AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"""AXIN1 up-regulated 1"""	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.381G>C	3.37:g.39186572C>G	ENSP00000273153:p.Glu127Asp		Q69YY5	Missense_Mutation	SNP	prints_Cys/Ser-rich_nuc_prot	p.E127D	ENST00000273153.5	37	c.381	CCDS2682.1	3	.	.	.	.	.	.	.	.	.	.	C	18.94	3.729746	0.69074	.	.	ENSG00000144655	ENST00000273153;ENST00000514182	T;T	0.17528	2.27;2.27	5.14	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.41811	0.1175	M	0.73430	2.235	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.41088	-0.9528	10	0.72032	D	0.01	-26.2996	13.8913	0.63740	0.0:0.9261:0.0:0.0739	.	127	Q96S65	CSRN1_HUMAN	D	127	ENSP00000273153:E127D;ENSP00000422532:E127D	ENSP00000273153:E127D	E	-	3	2	CSRNP1	39161576	1.000000	0.71417	0.979000	0.43373	0.287000	0.27160	2.647000	0.46639	1.311000	0.45024	0.561000	0.74099	GAG	0	NULL		0.612	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSRNP1	protein_coding	OTTHUMT00000254061.1	40	43	0	0.00	0	0	C	NM_033027	0	0		39186572	-1	no_errors	ENST00000273153	ensembl	human	known	74_37	missense	19	29	45.71	17.14	16	6	SNP	1	G
STAG1	10274	genome.wustl.edu	37	3	136068118	136068118	+	Silent	SNP	T	T	C			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr3:136068118T>C	ENST00000383202.2	-	29	3409	c.3153A>G	c.(3151-3153)tcA>tcG	p.S1051S	STAG1_ENST00000536929.1_Silent_p.S635S|STAG1_ENST00000236698.5_Silent_p.S1051S|STAG1_ENST00000434713.2_Silent_p.S791S	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1051					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						CAGTGACTAATGAATTTCTAT	0.428																																							0											0													123.0	113.0	117.0					3																	136068118		2203	4300	6503	SO:0001819	synonymous_variant	0			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.3153A>G	3.37:g.136068118T>C			O00539|Q6P275	Silent	SNP	pfam_STAG,superfamily_ARM-type_fold	p.S1051	ENST00000383202.2	37	c.3153	CCDS3090.1	3																																																																																			0	NULL		0.428	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STAG1	protein_coding	OTTHUMT00000357366.1	64	264	0	0.38	0	1	T	NM_005862	0	0		136068118	-1	no_errors	ENST00000383202	ensembl	human	known	74_37	silent	51	191	37.04	24.71	30	63	SNP	0.112	C
TAS2R1	50834	genome.wustl.edu	37	5	9630072	9630072	+	Missense_Mutation	SNP	C	C	A			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr5:9630072C>A	ENST00000382492.2	-	1	391	c.73G>T	c.(73-75)Ggc>Tgc	p.G25C	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	25					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						ACAATGATGCCATTTGTGAAA	0.353																																							0											0													54.0	58.0	57.0					5																	9630072		2196	4299	6495	SO:0001583	missense	0			AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.73G>T	5.37:g.9630072C>A	ENSP00000371932:p.Gly25Cys		Q646G8	Missense_Mutation	SNP	pfam_TAS2_rcpt	p.G25C	ENST00000382492.2	37	c.73	CCDS3876.1	5	.	.	.	.	.	.	.	.	.	.	C	11.56	1.674523	0.29693	.	.	ENSG00000169777	ENST00000382492	T	0.38560	1.13	5.32	2.45	0.29901	.	0.347345	0.24848	N	0.035105	T	0.58708	0.2141	M	0.78049	2.395	0.37771	D	0.92666	D	0.89917	1.0	D	0.97110	1.0	T	0.59139	-0.7510	9	.	.	.	.	5.706	0.17909	0.154:0.667:0.0:0.179	.	25	Q9NYW7	TA2R1_HUMAN	C	25	ENSP00000371932:G25C	.	G	-	1	0	TAS2R1	9683072	0.785000	0.28726	0.041000	0.18516	0.037000	0.13140	1.136000	0.31467	0.327000	0.23409	-0.345000	0.07892	GGC	0	pfam_TAS2_rcpt		0.353	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TAS2R1	protein_coding	OTTHUMT00000206988.2	49	251	0	0.00	0	0	C		0	0		9630072	-1	no_errors	ENST00000382492	ensembl	human	known	74_37	missense	43	162	24.56	24.42	14	53	SNP	0.883	A
RNF180	285671	genome.wustl.edu	37	5	63510131	63510131	+	Silent	SNP	T	T	C			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr5:63510131T>C	ENST00000389100.4	+	4	1050	c.978T>C	c.(976-978)acT>acC	p.T326T	RNF180_ENST00000296615.6_Silent_p.T326T|RNF180_ENST00000381081.2_Intron	NM_001113561.1	NP_001107033.1	Q86T96	RN180_HUMAN	ring finger protein 180	326	Interaction with ZIC2. {ECO:0000250}.				adult behavior (GO:0030534)|norepinephrine metabolic process (GO:0042415)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|regulation of catalytic activity (GO:0050790)|serotonin metabolic process (GO:0042428)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	20		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)		ATACTAATACTAACAATCTGA	0.517																																							0											0													69.0	72.0	71.0					5																	63510131		2203	4300	6503	SO:0001819	synonymous_variant	0			AK090756	CCDS34169.1, CCDS47219.1	5q12.3	2013-01-09			ENSG00000164197	ENSG00000164197		"""RING-type (C3HC4) zinc fingers"""	27752	protein-coding gene	gene with protein product							Standard	NM_178532		Approved		uc003jti.3	Q86T96	OTTHUMG00000162278	ENST00000389100.4:c.978T>C	5.37:g.63510131T>C			Q0JSU3|Q495A8|Q8NBD1	Silent	SNP	pfam_Znf_C3HC4_RING-type,smart_Znf_RING,pfscan_Znf_RING	p.T326	ENST00000389100.4	37	c.978	CCDS47219.1	5																																																																																			0	NULL		0.517	RNF180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RNF180	protein_coding	OTTHUMT00000368394.1	52	189	0	0.00	0	0	T	NM_178532	0	0		63510131	1	no_errors	ENST00000389100	ensembl	human	known	74_37	silent	42	202	10.64	7.76	5	17	SNP	0.003	C
REV3L	5980	genome.wustl.edu	37	6	111710309	111710309	+	Splice_Site	SNP	C	C	T			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr6:111710309C>T	ENST00000358835.3	-	8	1316	c.862G>A	c.(862-864)Gat>Aat	p.D288N	REV3L_ENST00000368802.3_Splice_Site_p.D288N|REV3L_ENST00000435970.1_Splice_Site_p.D210N|REV3L_ENST00000368805.1_Splice_Site_p.D288N			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	288					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		AGGTTTATACCTTGTGACTCA	0.353								DNA polymerases (catalytic subunits)																															0											0													191.0	166.0	174.0					6																	111710309		2203	4300	6503	SO:0001630	splice_region_variant	0			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.862+1G>A	6.37:g.111710309C>T			O43214|Q5TC33	Missense_Mutation	SNP	pfam_DNA-dir_DNA_pol_B_multi_dom,pfam_DNA-dir_DNA_pol_B_exonuc,superfamily_RNaseH-like_dom,smart_DNA-dir_DNA_pol_B,prints_DNA-dir_DNA_pol_B	p.D288N	ENST00000358835.3	37	c.862	CCDS5091.2	6	.	.	.	.	.	.	.	.	.	.	C	35	5.428957	0.96131	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.38887	1.11;1.11;1.11;1.11	5.48	5.48	0.80851	Ribonuclease H-like (1);	0.245896	0.34750	N	0.003703	T	0.54224	0.1845	L	0.54323	1.7	0.51012	D	0.999909	D	0.89917	1.0	D	0.80764	0.994	T	0.45279	-0.9272	9	.	.	.	.	19.7082	0.96082	0.0:1.0:0.0:0.0	.	288	O60673	DPOLZ_HUMAN	N	288;288;288;210	ENSP00000357792:D288N;ENSP00000357795:D288N;ENSP00000351697:D288N;ENSP00000402003:D210N	.	D	-	1	0	REV3L	111817002	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	5.207000	0.65197	2.718000	0.92993	0.655000	0.94253	GAT	0	superfamily_RNaseH-like_dom		0.353	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	REV3L	protein_coding	OTTHUMT00000043695.1	61	333	0	0.00	0	0	C	NM_002912	0	0	Missense_Mutation	111710309	-1	no_errors	ENST00000358835	ensembl	human	known	74_37	missense	52	247	17.46	28.94	11	101	SNP	1	T
L3MBTL3	84456	genome.wustl.edu	37	6	130374131	130374131	+	Nonsense_Mutation	SNP	G	G	T			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr6:130374131G>T	ENST00000529410.1	+	9	1056	c.577G>T	c.(577-579)Gaa>Taa	p.E193*	L3MBTL3_ENST00000533560.1_Nonsense_Mutation_p.E168*|L3MBTL3_ENST00000361794.2_Nonsense_Mutation_p.E193*|L3MBTL3_ENST00000368136.2_Nonsense_Mutation_p.E193*|L3MBTL3_ENST00000526019.1_Nonsense_Mutation_p.E168*|L3MBTL3_ENST00000368139.2_Nonsense_Mutation_p.E168*			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	193					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		GAGAGATGATGAAATGGTGAG	0.468																																							0											0													75.0	63.0	67.0					6																	130374131		2203	4300	6503	SO:0001587	stop_gained	0			AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"""Sterile alpha motif (SAM) domain containing"""	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.577G>T	6.37:g.130374131G>T	ENSP00000431962:p.Glu193*		Q4VXE1|Q5VUM9|Q6P9B5	Nonsense_Mutation	SNP	pfam_Mbt,pfam_SAM_type1,pfam_SAM_2,superfamily_SAM/pointed,smart_Mbt,smart_SAM,pfscan_Mbt,pfscan_SAM	p.E193*	ENST00000529410.1	37	c.577	CCDS34537.1	6	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155727	0.78114	.	.	ENSG00000198945	ENST00000529410;ENST00000533560;ENST00000361794;ENST00000368139;ENST00000526019;ENST00000368136	.	.	.	5.0	5.0	0.66597	.	1.129670	0.06539	N	0.742821	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	16.4241	0.83808	0.0:0.0:1.0:0.0	.	.	.	.	X	193;168;193;168;168;193	.	ENSP00000354526:E193X	E	+	1	0	L3MBTL3	130415824	1.000000	0.71417	1.000000	0.80357	0.685000	0.39939	6.148000	0.71788	2.488000	0.83962	0.462000	0.41574	GAA	0	NULL		0.468	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	L3MBTL3	protein_coding	OTTHUMT00000042195.2	23	125	0	0.00	0	0	G	XM_027074	0	0		130374131	1	no_errors	ENST00000361794	ensembl	human	known	74_37	nonsense	44	106	10.2	5.36	5	6	SNP	1	T
GTF2I	2969	genome.wustl.edu	37	7	74146970	74146970	+	Missense_Mutation	SNP	T	T	A			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	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_ENST00000353920.4_Missense_Mutation_p.L404H|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	300	149	0	0.00	0	0	T	NM_032999	0	0		74146970	1	no_errors	ENST00000324896	ensembl	human	known	74_37	missense	281	75	28.68	35.59	113	42	SNP	1	A
CSMD1	64478	genome.wustl.edu	37	8	2832146	2832146	+	Splice_Site	SNP	G	G	A			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr8:2832146G>A	ENST00000520002.1	-	57	9125	c.8570C>T	c.(8569-8571)gCt>gTt	p.A2857V	CSMD1_ENST00000400186.3_Splice_Site_p.A2799V|CSMD1_ENST00000542608.1_Splice_Site_p.A2798V|CSMD1_ENST00000602557.1_Splice_Site_p.A2857V|CSMD1_ENST00000537824.1_Splice_Site_p.A2856V|CSMD1_ENST00000602723.1_Splice_Site_p.A2799V			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2857	Sushi 20. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ACACGATATAGCTTCAGAAAA	0.478																																							0											0													28.0	30.0	29.0					8																	2832146		1916	4115	6031	SO:0001630	splice_region_variant	0					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.8570-1C>T	8.37:g.2832146G>A			Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	pfam_CUB_dom,pfam_Sushi_SCR_CCP,superfamily_CUB_dom,superfamily_Sushi_SCR_CCP,smart_CUB_dom,smart_Sushi_SCR_CCP,pfscan_CUB_dom,pfscan_Sushi_SCR_CCP	p.A2857V	ENST00000520002.1	37	c.8570		8	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.624371	0.00820	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	5.81	0.559	0.17272	Complement control module (2);Sushi/SCR/CCP (1);	0.399644	0.25256	N	0.031991	T	0.17450	0.0419	L	0.41632	1.29	0.80722	D	1	B;B;B	0.09022	0.002;0.0;0.002	B;B;B	0.15052	0.003;0.004;0.012	T	0.15009	-1.0452	10	0.14252	T	0.57	.	10.1733	0.42924	0.3541:0.0:0.6459:0.0	.	2857;2857;2798	E5RIG2;Q96PZ7;F5H2I8	.;CSMD1_HUMAN;.	V	2799;2857;2718;2856;2798	ENSP00000383047:A2799V;ENSP00000430733:A2857V;ENSP00000441462:A2856V;ENSP00000446243:A2798V	ENSP00000320445:A2718V	A	-	2	0	CSMD1	2819553	0.856000	0.29760	0.009000	0.14445	0.036000	0.12997	1.241000	0.32743	-0.191000	0.10448	-0.136000	0.14681	GCT	0	superfamily_Sushi_SCR_CCP,pfscan_Sushi_SCR_CCP		0.478	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	CSMD1	protein_coding	OTTHUMT00000374500.2	51	225	0	0.00	0	0	G	NM_033225	0	0	Missense_Mutation	2832146	-1	no_errors	ENST00000520002	ensembl	human	known	74_37	missense	39	213	13.33	7.39	6	17	SNP	0.142	A
PTCH1	5727	genome.wustl.edu	37	9	98241284	98241284	+	Missense_Mutation	SNP	C	C	T			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr9:98241284C>T	ENST00000331920.6	-	8	1512	c.1213G>A	c.(1213-1215)Gag>Aag	p.E405K	PTCH1_ENST00000548379.1_5'Flank|PTCH1_ENST00000375274.2_Missense_Mutation_p.E404K|PTCH1_ENST00000429896.2_Missense_Mutation_p.E254K|PTCH1_ENST00000418258.1_Missense_Mutation_p.E254K|PTCH1_ENST00000421141.1_Missense_Mutation_p.E254K|PTCH1_ENST00000430669.2_Missense_Mutation_p.E339K|PTCH1_ENST00000437951.1_Missense_Mutation_p.E339K	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	405					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GGGTTTACCTCCACATATGTC	0.458																																							0											0													131.0	107.0	115.0					9																	98241284		2203	4300	6503	SO:0001583	missense	0			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1213G>A	9.37:g.98241284C>T	ENSP00000332353:p.Glu405Lys		A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	pfam_Patched,pfscan_SSD,tigrfam_TM_rcpt_patched	p.E405K	ENST00000331920.6	37	c.1213	CCDS6714.1	9	.	.	.	.	.	.	.	.	.	.	C	17.79	3.476229	0.63737	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274;ENST00000375271	D;D;D;D;D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89;-2.89;-2.89;-2.89;-2.56	5.65	5.65	0.86999	.	0.048312	0.85682	D	0.000000	D	0.88566	0.6471	L	0.40543	1.245	0.58432	D	0.999995	B;B;B;B	0.33807	0.426;0.097;0.046;0.1	B;B;B;B	0.36845	0.234;0.06;0.037;0.1	D	0.85036	0.0920	10	0.22706	T	0.39	-32.7334	14.7871	0.69810	0.0:0.7423:0.2577:0.0	.	254;339;404;405	Q13635-4;Q13635-3;Q13635-2;Q13635	.;.;.;PTC1_HUMAN	K	405;339;254;254;339;254;404;122	ENSP00000332353:E405K;ENSP00000389744:E339K;ENSP00000399981:E254K;ENSP00000396135:E254K;ENSP00000410287:E339K;ENSP00000414823:E254K;ENSP00000364423:E404K;ENSP00000364420:E122K	ENSP00000332353:E405K	E	-	1	0	PTCH1	97281105	1.000000	0.71417	1.000000	0.80357	0.255000	0.26057	4.389000	0.59639	2.941000	0.99782	0.655000	0.94253	GAG	0	pfam_Patched,tigrfam_TM_rcpt_patched		0.458	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTCH1	protein_coding	OTTHUMT00000053229.2	87	215	0	0.00	0	0	C	NM_000264	0	0		98241284	-1	no_errors	ENST00000331920	ensembl	human	known	74_37	missense	89	155	11.88	8.28	12	14	SNP	1	T
ZDHHC6	64429	genome.wustl.edu	37	10	114204970	114204970	+	Silent	SNP	G	G	A	rs367934020		TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr10:114204970G>A	ENST00000369405.3	-	2	648	c.225C>T	c.(223-225)gcC>gcT	p.A75A	ZDHHC6_ENST00000369404.3_Silent_p.A75A|VTI1A_ENST00000432306.1_5'Flank|VTI1A_ENST00000393077.2_5'Flank	NM_022494.1	NP_071939.1	Q9H6R6	ZDHC6_HUMAN	zinc finger, DHHC-type containing 6	75					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Colorectal(252;0.198)		Epithelial(162;0.0291)|all cancers(201;0.117)		CGACAAACATGGCATTGAAGT	0.388																																							0											0								G		0,4406		0,0,2203	78.0	70.0	73.0		225	3.2	1.0	10		73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZDHHC6	NM_022494.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		75/414	114204970	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	0			AK025605	CCDS7574.1	10q26.11	2008-05-02			ENSG00000023041	ENSG00000023041		"""Zinc fingers, DHHC-type"""	19160	protein-coding gene	gene with protein product							Standard	NM_022494		Approved	ZNF376, FLJ21952	uc001kzv.3	Q9H6R6	OTTHUMG00000019062	ENST00000369405.3:c.225C>T	10.37:g.114204970G>A			D3DRB6|Q53G45|Q96IV7|Q9H605	Silent	SNP	pfam_Znf_DHHC_palmitoyltrfase,pfam_SH3_2,superfamily_SH3_domain,pfscan_Znf_DHHC_palmitoyltrfase	p.A75	ENST00000369405.3	37	c.225	CCDS7574.1	10																																																																																			0	NULL		0.388	ZDHHC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZDHHC6	protein_coding	OTTHUMT00000050393.1	37	326	0	0.31	0	1	G	NM_022494	rs367934020	G->A		114204970	-1	no_errors	ENST00000369405	ensembl	human	known	74_37	silent	35	198	16.67	30.53	7	87	SNP	1	A
FRY	10129	genome.wustl.edu	37	13	32821485	32821485	+	Missense_Mutation	SNP	A	A	G			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr13:32821485A>G	ENST00000380250.3	+	48	7350	c.6854A>G	c.(6853-6855)aAt>aGt	p.N2285S		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2285						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GAAGCTCTGAATATCTTGAAG	0.373																																							0											0													123.0	115.0	117.0					13																	32821485		1835	4092	5927	SO:0001583	missense	0			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.6854A>G	13.37:g.32821485A>G	ENSP00000369600:p.Asn2285Ser		Q9Y3N6	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.N2285S	ENST00000380250.3	37	c.6854	CCDS41875.1	13	.	.	.	.	.	.	.	.	.	.	A	20.8	4.055678	0.75960	.	.	ENSG00000073910	ENST00000380250	T	0.22336	1.96	5.16	3.98	0.46160	.	0.090165	0.64402	D	0.000001	T	0.38453	0.1041	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.24548	-1.0157	10	0.12766	T	0.61	.	10.5755	0.45225	0.924:0.0:0.076:0.0	.	2285	Q5TBA9	FRY_HUMAN	S	2285	ENSP00000369600:N2285S	ENSP00000369600:N2285S	N	+	2	0	FRY	31719485	1.000000	0.71417	0.902000	0.35471	0.971000	0.66376	7.528000	0.81941	0.812000	0.34326	0.533000	0.62120	AAT	0	superfamily_ARM-type_fold		0.373	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FRY	protein_coding	OTTHUMT00000044405.1	52	312	0	0.00	0	0	A	NM_023037	0	0		32821485	1	no_errors	ENST00000380250	ensembl	human	known	74_37	missense	74	230	9.76	8.37	8	21	SNP	1	G
SLC12A1	6557	genome.wustl.edu	37	15	48594991	48594991	+	Missense_Mutation	SNP	A	A	G			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr15:48594991A>G	ENST00000558405.1	+	26	3223	c.3209A>G	c.(3208-3210)tAt>tGt	p.Y1070C	SLC12A1_ENST00000396577.3_Missense_Mutation_p.Y1070C|SLC12A1_ENST00000380993.3_Missense_Mutation_p.Y1070C			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	1070					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	GATTTGTTGTATATGGCTTGG	0.353																																							0											0			GRCh37	CM081798	SLC12A1	M							103.0	105.0	104.0					15																	48594991		2198	4297	6495	SO:0001583	missense	0				CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.3209A>G	15.37:g.48594991A>G	ENSP00000453409:p.Tyr1070Cys		A8JYA2|E9PDW4	Missense_Mutation	SNP	pfam_AA-permease/SLC12A_dom,pfam_AA_permease_N,prints_Na/K/Cl_cotranspt2,prints_Na/K/Cl_cotranspt,tigrfam_Na/K/Cl_cotransptS	p.Y1070C	ENST00000558405.1	37	c.3209	CCDS10129.2	15	.	.	.	.	.	.	.	.	.	.	A	20.4	3.991283	0.74703	.	.	ENSG00000074803	ENST00000380993;ENST00000396577	D;D	0.96232	-3.95;-3.94	5.86	4.73	0.59995	.	0.000000	0.85682	D	0.000000	D	0.98623	0.9539	H	0.96239	3.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98914	1.0781	10	0.87932	D	0	.	12.4074	0.55447	0.8738:0.0:0.0:0.1262	.	1070;1070	E9PDW4;Q13621	.;S12A1_HUMAN	C	1070	ENSP00000370381:Y1070C;ENSP00000379822:Y1070C	ENSP00000370381:Y1070C	Y	+	2	0	SLC12A1	46382283	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.176000	0.94839	1.128000	0.42052	0.528000	0.53228	TAT	0	tigrfam_Na/K/Cl_cotransptS		0.353	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SLC12A1	protein_coding	OTTHUMT00000417131.1	155	291	0	0.00	0	0	A		0	0		48594991	1	no_errors	ENST00000380993	ensembl	human	known	74_37	missense	186	296	7.46	4.82	15	15	SNP	1	G
EPG5	57724	genome.wustl.edu	37	18	43437954	43437954	+	Missense_Mutation	SNP	C	C	T			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr18:43437954C>T	ENST00000282041.5	-	42	7340	c.7306G>A	c.(7306-7308)Gac>Aac	p.D2436N	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	2436					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						AGGACGGAGTCATTCTGCTCT	0.557																																							0											0													69.0	72.0	71.0					18																	43437954		1938	4146	6084	SO:0001583	missense	0			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.7306G>A	18.37:g.43437954C>T	ENSP00000282041:p.Asp2436Asn		A2BDF3|Q9H8C8	Missense_Mutation	SNP	NULL	p.D2436N	ENST00000282041.5	37	c.7306	CCDS11926.2	18	.	.	.	.	.	.	.	.	.	.	C	29.3	4.991985	0.93167	.	.	ENSG00000152223	ENST00000282041;ENST00000540322;ENST00000308403	T	0.10005	2.92	5.64	5.64	0.86602	.	.	.	.	.	T	0.18676	0.0448	L	0.53249	1.67	0.58432	D	0.999999	P	0.42692	0.787	B	0.43658	0.426	T	0.00262	-1.1867	9	0.62326	D	0.03	-4.4313	19.6884	0.95987	0.0:1.0:0.0:0.0	.	2436	Q9HCE0	EPG5_HUMAN	N	2436;364;1311	ENSP00000282041:D2436N	ENSP00000282041:D2436N	D	-	1	0	EPG5	41691952	1.000000	0.71417	0.658000	0.29665	0.981000	0.71138	5.666000	0.68059	2.658000	0.90341	0.561000	0.74099	GAC	0	NULL		0.557	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPG5	protein_coding	OTTHUMT00000445081.1	41	111	0	0.00	0	0	C	NM_020964	0	0		43437954	-1	no_errors	ENST00000282041	ensembl	human	known	74_37	missense	37	87	13.95	7.45	6	7	SNP	0.998	T
CEACAM5	1048	genome.wustl.edu	37	19	42222112	42222112	+	Missense_Mutation	SNP	C	C	A			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr19:42222112C>A	ENST00000221992.6	+	6	1417	c.1303C>A	c.(1303-1305)Ctc>Atc	p.L435I	CEA_ENST00000598976.1_Intron|CEACAM5_ENST00000398599.4_Missense_Mutation_p.L434I|CEACAM5_ENST00000405816.1_Missense_Mutation_p.L435I	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	435	Ig-like 5.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		GAACCTCAGCCTCTCCTGCCA	0.527																																							0											0													120.0	102.0	108.0					19																	42222112		2203	4300	6503	SO:0001583	missense	0			M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.1303C>A	19.37:g.42222112C>A	ENSP00000221992:p.Leu435Ile		H9KVA7	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Ig_V-set,pfam_Immunoglobulin,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like_dom	p.L435I	ENST00000221992.6	37	c.1303	CCDS12584.1	19	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.83|12.83	2.055460|2.055460	0.36277|0.36277	.|.	.|.	ENSG00000105388|ENSG00000105388	ENST00000221992;ENST00000405816;ENST00000378181|ENST00000398599	D;D|.	0.82167|.	-1.58;-1.58|.	2.39|2.39	2.39|2.39	0.29439|0.29439	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.60792|0.60792	0.2296|0.2296	M|M	0.85777|0.85777	2.775|2.775	0.09310|0.09310	N|N	1|1	D;P|.	0.54397|.	0.966;0.801|.	D;P|.	0.69479|.	0.964;0.713|.	T|T	0.52697|0.52697	-0.8541|-0.8541	9|5	0.36615|.	T|.	0.2|.	.|.	8.4077|8.4077	0.32625|0.32625	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	435;435|.	P06731;Q53G30|.	CEAM5_HUMAN;.|.	I|H	435;435;153|430	ENSP00000221992:L435I;ENSP00000385072:L435I|.	ENSP00000221992:L435I|.	L|P	+|+	1|2	0|0	CEACAM5|CEACAM5	46913952|46913952	0.071000|0.071000	0.21146|0.21146	0.329000|0.329000	0.25429|0.25429	0.076000|0.076000	0.17211|0.17211	0.849000|0.849000	0.27723|0.27723	1.668000|1.668000	0.50843|0.50843	0.531000|0.531000	0.56144|0.56144	CTC|CCT	0	pfam_Ig_I-set,pfam_Immunoglobulin,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like_dom		0.527	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CEACAM5	protein_coding	OTTHUMT00000321132.2	76	50	0	0.00	0	0	C	NM_004363	0	0		42222112	1	no_errors	ENST00000221992	ensembl	human	known	74_37	missense	66	41	9.59	6.82	7	3	SNP	0.359	A
SCP2D1	140856	genome.wustl.edu	37	20	18794489	18794489	+	Silent	SNP	G	G	A			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr20:18794489G>A	ENST00000377428.2	+	1	120	c.30G>A	c.(28-30)aaG>aaA	p.K10K	C20orf78_ENST00000463425.1_5'Flank|C20orf78_ENST00000278779.4_Intron	NM_178483.2	NP_848578.1	Q9UJQ7	SCP2D_HUMAN	SCP2 sterol-binding domain containing 1	10																	ATCAACCCAAGATCAAAGCAG	0.517																																							0											0													116.0	110.0	112.0					20																	18794489		2203	4300	6503	SO:0001819	synonymous_variant	0			AL035563	CCDS13139.1	20p11.23	2012-10-29	2012-10-29	2012-10-29	ENSG00000132631	ENSG00000132631			16211	protein-coding gene	gene with protein product	"""sterol carrier protein 2-like protein"""		"""chromosome 20 open reading frame 79"""	C20orf79		16501878	Standard	NM_178483		Approved	dJ1068E13.2, HSD22	uc002wrk.3	Q9UJQ7	OTTHUMG00000031983	ENST00000377428.2:c.30G>A	20.37:g.18794489G>A			Q548A4	Silent	SNP	pfam_SCP2_sterol-bd_dom,superfamily_SCP2_sterol-bd_dom	p.K10	ENST00000377428.2	37	c.30	CCDS13139.1	20																																																																																			0	NULL		0.517	SCP2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SCP2D1	protein_coding	OTTHUMT00000078193.1	34	153	0	0.00	0	0	G	NM_178483	0	0		18794489	1	no_errors	ENST00000377428	ensembl	human	known	74_37	silent	28	131	15.15	8.39	5	12	SNP	0.999	A
MKNK1	8569	genome.wustl.edu	37	1	47028358	47028358	+	Missense_Mutation	SNP	C	C	T			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr1:47028358C>T	ENST00000371946.4	-	11	1089	c.926G>A	c.(925-927)tGt>tAt	p.C309Y	MKNK1_ENST00000428112.2_Missense_Mutation_p.C268Y|MKNK1_ENST00000371945.4_Missense_Mutation_p.C268Y|MKNK1_ENST00000341183.5_Missense_Mutation_p.C268Y|MKNK1-AS1_ENST00000602433.1_RNA|MKNK1_ENST00000371944.4_Missense_Mutation_p.C173Y	NM_003684.5	NP_003675.2	Q9BUB5	MKNK1_HUMAN	MAP kinase interacting serine/threonine kinase 1	309	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fibroblast growth factor receptor signaling pathway (GO:0008543)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|response to salt stress (GO:0009651)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	13	Acute lymphoblastic leukemia(166;0.155)					GTCCCAGCCACAGTCGGCCCC	0.652																																							0											0													27.0	24.0	25.0					1																	47028358		2199	4282	6481	SO:0001583	missense	0			AB000409	CCDS538.1, CCDS30705.1, CCDS44134.1	1p33	2008-02-05			ENSG00000079277	ENSG00000079277			7110	protein-coding gene	gene with protein product		606724				9155018	Standard	NM_003684		Approved	MNK1	uc001cqb.4	Q9BUB5	OTTHUMG00000007983	ENST00000371946.4:c.926G>A	1.37:g.47028358C>T	ENSP00000361014:p.Cys309Tyr		D3DQ20|D3DQ21|O00312|Q5TC06|Q5TC07|Q6V0N6	Missense_Mutation	SNP	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom	p.C309Y	ENST00000371946.4	37	c.926	CCDS538.1	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.1|28.1	4.886926|4.886926	0.91814|0.91814	.|.	.|.	ENSG00000079277|ENSG00000079277	ENST00000371946;ENST00000371945;ENST00000371944;ENST00000341183;ENST00000428112|ENST00000524749	T;T;T;T;T|.	0.19105|.	2.17;2.17;2.17;2.17;2.17|.	5.42|5.42	5.42|5.42	0.78866|0.78866	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67505|0.67505	0.2900|0.2900	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D|.	0.87578|.	0.998;0.998;0.997;0.994;0.996;0.997|.	T|T	0.62053|0.62053	-0.6935|-0.6935	10|5	0.87932|.	D|.	0|.	.|.	18.3905|18.3905	0.90481|0.90481	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	173;173;268;268;268;309|.	B4DQK5;Q7Z319;A8K341;Q9BUB5-3;Q9BUB5-2;Q9BUB5|.	.;.;.;.;.;MKNK1_HUMAN|.	Y|M	309;268;173;268;268|61	ENSP00000361014:C309Y;ENSP00000361013:C268Y;ENSP00000361012:C173Y;ENSP00000339573:C268Y;ENSP00000411135:C268Y|.	ENSP00000339573:C268Y|.	C|V	-|-	2|1	0|0	MKNK1|MKNK1	46800945|46800945	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.879000|0.879000	0.50718|0.50718	7.651000|7.651000	0.83577|0.83577	2.826000|2.826000	0.97356|0.97356	0.563000|0.563000	0.77884|0.77884	TGT|GTG	0	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom		0.652	MKNK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MKNK1	protein_coding	OTTHUMT00000021897.2	36	12	0	0.00	0	0	C	NM_003684	0	0		47028358	-1	no_errors	ENST00000371946	ensembl	human	known	74_37	missense	63	8	7.35	0.00	5	0	SNP	1	T
GSC	145258	genome.wustl.edu	37	14	95236123	95236123	+	Missense_Mutation	SNP	C	C	A			TCGA-X7-A8D8-01A-11D-A423-09	TCGA-X7-A8D8-10A-01D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	1659418d-2e29-4aeb-9e15-f1d2ddc6e778	e03ab0b1-b597-4490-b50c-43d1928ceb64	g.chr14:95236123C>A	ENST00000238558.3	-	1	439	c.230G>T	c.(229-231)cGc>cTc	p.R77L		NM_173849.2	NP_776248.1	P56915	GSC_HUMAN	goosecoid homeobox	77					dorsal/ventral neural tube patterning (GO:0021904)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|gastrulation (GO:0007369)|middle ear morphogenesis (GO:0042474)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell fate specification (GO:0014036)|signal transduction involved in regulation of gene expression (GO:0023019)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)			skin(1)	1		all_cancers(154;0.0896)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.202)|Epithelial(152;0.239)		GTAGCCGAGGCGGGAGCCGCT	0.786																																					Pancreas(105;2165 2186 4892 18008)		0											0													1.0	1.0	1.0					14																	95236123		211	469	680	SO:0001583	missense	0				CCDS9930.1	14q32.13	2011-06-20	2007-07-11			ENSG00000133937		"""Homeoboxes / PRD class"""	4612	protein-coding gene	gene with protein product		138890				7916327	Standard	NM_173849		Approved		uc001ydu.3	P56915		ENST00000238558.3:c.230G>T	14.37:g.95236123C>A	ENSP00000238558:p.Arg77Leu		Q86YR1	Missense_Mutation	SNP	pfam_Homeobox_dom,superfamily_Homeodomain-like,smart_Homeobox_dom,pfscan_Homeobox_dom	p.R77L	ENST00000238558.3	37	c.230	CCDS9930.1	14	.	.	.	.	.	.	.	.	.	.	C	14.83	2.653905	0.47362	.	.	ENSG00000133937	ENST00000238558	D	0.92149	-2.98	4.6	2.63	0.31362	.	0.127670	0.47455	D	0.000233	D	0.83912	0.5357	L	0.29908	0.895	0.52501	D	0.999957	P	0.38827	0.649	B	0.34489	0.184	T	0.80621	-0.1301	10	0.42905	T	0.14	-15.25	8.5539	0.33469	0.1518:0.7671:0.0:0.0811	.	77	P56915	GSC_HUMAN	L	77	ENSP00000238558:R77L	ENSP00000238558:R77L	R	-	2	0	GSC	94305876	1.000000	0.71417	0.998000	0.56505	0.432000	0.31715	4.439000	0.59968	0.931000	0.37242	0.491000	0.48974	CGC	0	NULL		0.786	GSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GSC	protein_coding	OTTHUMT00000410746.1	10	6	0	0.00	0	0	C		0	0		95236123	-1	no_errors	ENST00000238558	ensembl	human	known	74_37	missense	8	1	38.46	0.00	5	0	SNP	1	A
