#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_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_annotation_transcript	i_build	i_ccds_id	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_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_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
NUP98	4928	hgsc.bcm.edu;broad.mit.edu	37	11	3716782	3716782	+	Missense_Mutation	SNP	C	C	T	rs144659895	byFrequency	TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr11:3716782C>T	ENST00000324932.7	-	26	4484	c.4064G>A	c.(4063-4065)cGg>cAg	p.R1355Q	NUP98_ENST00000355260.3_Missense_Mutation_p.R1355Q|NUP98_ENST00000359171.4_Missense_Mutation_p.R1355Q|NUP98_ENST00000488828.1_5'UTR	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1372					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		GAGCAGCTCCCGGACTGACTG	0.473			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML								C|||	2	0.000399361	0.0	0.0	5008	,	,		16995	0.0		0.002	False		,,,				2504	0.0						Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	0								C	GLN/ARG,GLN/ARG	0,4402		0,0,2201	118.0	116.0	117.0		4064,4064	4.3	1.0	11	dbSNP_134	117	8,8588	6.4+/-24.3	0,8,4290	yes	missense,missense	NUP98	NM_016320.4,NM_139132.3	43,43	0,8,6491	TT,TC,CC		0.0931,0.0,0.0615	probably-damaging,probably-damaging	1355/1801,1355/1727	3716782	8,12990	2201	4298	6499	SO:0001583	missense	4928			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.4064G>A	11.37:g.3716782C>T	ENSP00000316032:p.Arg1355Gln		Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	22.5	4.304812	0.81247	0.0	9.31E-4	ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260	.	.	.	5.25	4.33	0.51752	.	0.059710	0.64402	N	0.000002	T	0.52041	0.1710	M	0.74881	2.28	0.44018	D	0.996739	P;B;P	0.42039	0.769;0.316;0.641	B;B;B	0.30029	0.08;0.04;0.11	T	0.59204	-0.7498	9	0.48119	T	0.1	-9.6206	13.1234	0.59340	0.0:0.9225:0.0:0.0775	.	1355;1355;1269	P52948-2;P52948-5;P52948-6	.;.;.	Q	1355	.	ENSP00000316032:R1355Q	R	-	2	0	NUP98	3673358	0.997000	0.39634	1.000000	0.80357	0.880000	0.50808	4.468000	0.60162	1.350000	0.45770	0.558000	0.71614	CGG		0.473	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		9	149	9	149
ENTPD5	957	hgsc.bcm.edu;broad.mit.edu	37	14	74442654	74442654	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr14:74442654T>C	ENST00000334696.6	-	10	1026	c.707A>G	c.(706-708)aAg>aGg	p.K236R	ENTPD5_ENST00000557325.1_Missense_Mutation_p.K236R	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	236					'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		TGTATAGAGCTTATAAGTGCT	0.378																																																0													97.0	94.0	95.0					14																	74442654		2203	4300	6503	SO:0001583	missense	957			AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"""proto-oncogene CPH"""	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.707A>G	14.37:g.74442654T>C	ENSP00000335246:p.Lys236Arg		A1L4C5|Q96RX0	Missense_Mutation	SNP	ENST00000334696.6	37	CCDS9825.1	.	.	.	.	.	.	.	.	.	.	T	15.16	2.750869	0.49257	.	.	ENSG00000187097	ENST00000557325;ENST00000334696	T;T	0.12569	2.67;2.67	5.53	5.53	0.82687	.	0.226087	0.45867	D	0.000332	T	0.07593	0.0191	N	0.16066	0.365	0.80722	D	1	B;B	0.22800	0.075;0.061	B;B	0.19666	0.026;0.015	T	0.32771	-0.9894	10	0.12430	T	0.62	-15.9412	10.1855	0.42995	0.0:0.0734:0.0:0.9266	.	236;236	O75356;G3V4I0	ENTP5_HUMAN;.	R	236	ENSP00000451810:K236R;ENSP00000335246:K236R	ENSP00000335246:K236R	K	-	2	0	ENTPD5	73512407	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.300000	0.65721	2.324000	0.78689	0.533000	0.62120	AAG		0.378	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249		10	132	10	132
PKD1	5310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	2139950	2139950	+	Silent	SNP	G	G	A	rs148433208	byFrequency	TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr16:2139950G>A	ENST00000262304.4	-	46	12898	c.12690C>T	c.(12688-12690)aaC>aaT	p.N4230N	PKD1_ENST00000423118.1_Silent_p.N4229N|MIR1225_ENST00000408729.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	4230					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CTGTGGCCTGGTTGAGTCGGT	0.687													G|||	3	0.000599042	0.0023	0.0	5008	,	,		14851	0.0		0.0	False		,,,				2504	0.0															0								G	,	10,4376	15.5+/-35.6	0,10,2183	35.0	33.0	33.0		12687,12690	2.8	1.0	16	dbSNP_134	33	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	0,10,6479	AA,AG,GG		0.0,0.228,0.0771	,	4229/4303,4230/4304	2139950	10,12968	2193	4296	6489	SO:0001819	synonymous_variant	5310			L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.12690C>T	16.37:g.2139950G>A			Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																				0.687	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			4	24	4	24
CCDC181	57821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	169394121	169394121	+	Silent	SNP	G	G	A	rs199771563		TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr1:169394121G>A	ENST00000367806.3	-	2	197	c.45C>T	c.(43-45)taC>taT	p.Y15Y	CCDC181_ENST00000367805.3_Silent_p.Y15Y|CCDC181_ENST00000491570.1_5'UTR|CCDC181_ENST00000545005.1_Silent_p.Y15Y	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	15						nucleus (GO:0005634)											AGTCATCTTCGTATTCTTCAC	0.289													G|||	1	0.000199681	0.0	0.0	5008	,	,		16372	0.001		0.0	False		,,,				2504	0.0															0													152.0	144.0	147.0					1																	169394121		2202	4297	6499	SO:0001819	synonymous_variant	57821			AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 114"""	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.45C>T	1.37:g.169394121G>A			O60780|Q53FD5|Q5TID9|Q8TC48	Silent	SNP	ENST00000367806.3	37																																																																																					0.289	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179		13	68	13	68
CLDN14	23562	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	37833827	37833827	+	Nonsense_Mutation	SNP	C	C	T	rs371100799		TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr21:37833827C>T	ENST00000399137.1	-	3	1033	c.167G>A	c.(166-168)tGg>tAg	p.W56*	CLDN14_ENST00000399135.1_Nonsense_Mutation_p.W56*|CLDN14_ENST00000399136.1_Nonsense_Mutation_p.W56*|CLDN14_ENST00000399139.1_Nonsense_Mutation_p.W56*|AP000695.6_ENST00000429588.1_RNA|CLDN14_ENST00000342108.2_Nonsense_Mutation_p.W56*|AP000695.4_ENST00000454980.1_RNA|AP000695.4_ENST00000428667.1_RNA	NM_144492.2	NP_652763.1	O95500	CLD14_HUMAN	claudin 14	56					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein complex assembly (GO:0006461)|tight junction assembly (GO:0070830)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|lung(5)|skin(1)	7						TGTGCTGTGCCACACACACTC	0.637																																																0								C	stop/TRP,stop/TRP,stop/TRP,stop/TRP,stop/TRP	1,4405		0,1,2202	58.0	39.0	45.0		167,167,167,167,167	5.5	1.0	21		45	0,8600		0,0,4300	no	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	CLDN14	NM_001146077.1,NM_001146078.1,NM_001146079.1,NM_012130.2,NM_144492.2	,,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,,	56/240,56/240,56/240,56/240,56/240	37833827	1,13005	2203	4300	6503	SO:0001587	stop_gained	23562			AJ132445	CCDS13645.1	21q22.3	2008-07-31			ENSG00000159261	ENSG00000159261		"""Claudins"""	2035	protein-coding gene	gene with protein product		605608		DFNB29		11163249	Standard	NM_144492		Approved		uc002yvk.2	O95500	OTTHUMG00000086638	ENST00000399137.1:c.167G>A	21.37:g.37833827C>T	ENSP00000382090:p.Trp56*			Nonsense_Mutation	SNP	ENST00000399137.1	37	CCDS13645.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.592285	0.86953	2.27E-4	0.0	ENSG00000159261	ENST00000399139;ENST00000399137;ENST00000399135;ENST00000399136;ENST00000342108	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	.	19.4085	0.94658	0.0:1.0:0.0:0.0	.	.	.	.	X	56	.	ENSP00000339292:W56X	W	-	2	0	CLDN14	36755697	1.000000	0.71417	1.000000	0.80357	0.065000	0.16274	2.573000	0.46007	2.576000	0.86940	0.561000	0.74099	TGG		0.637	CLDN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194697.1	NM_144492		6	44	6	44
SBF1	6305	hgsc.bcm.edu;broad.mit.edu	37	22	50898008	50898008	+	Silent	SNP	G	G	A	rs374190021		TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr22:50898008G>A	ENST00000390679.3	-	27	3763	c.3579C>T	c.(3577-3579)ccC>ccT	p.P1193P	SBF1_ENST00000476293.1_5'Flank|SBF1_ENST00000348911.6_Silent_p.P1194P|SBF1_ENST00000380817.3_Silent_p.P1193P			O95248	MTMR5_HUMAN	SET binding factor 1	1193	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|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)		AGCAGACCACGGGGAAGCGGT	0.677																																																0								G		5,4221		0,5,2108	19.0	22.0	21.0		3579	-9.4	0.9	22		21	3,8431		0,3,4214	no	coding-synonymous	SBF1	NM_002972.2		0,8,6322	AA,AG,GG		0.0356,0.1183,0.0632		1193/1894	50898008	8,12652	2113	4217	6330	SO:0001819	synonymous_variant	6305			U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	10542	protein-coding gene	gene with protein product	"""myotubularin related 5"", ""DENN/MADD domain containing 7A"""	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.3579C>T	22.37:g.50898008G>A			A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37																																																																																					0.677	SBF1-201	KNOWN	basic	protein_coding	protein_coding				4	49	4	49
HSPD1	3329	hgsc.bcm.edu;broad.mit.edu	37	2	198352636	198352636	+	Silent	SNP	A	A	T			TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr2:198352636A>T	ENST00000388968.3	-	11	1782	c.1515T>A	c.(1513-1515)gcT>gcA	p.A505A	HSPD1_ENST00000345042.2_Silent_p.A505A	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	505					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			CTCCAGCCATAGCATCATAAC	0.348																																																0													75.0	74.0	74.0					2																	198352636		2203	4300	6503	SO:0001819	synonymous_variant	3329			M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"""Heat Shock Proteins / Chaperonins"""	5261	protein-coding gene	gene with protein product		118190	"""heat shock 60kD protein 1 (chaperonin)"", ""spastic paraplegia 13 (autosomal dominant)"""	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.1515T>A	2.37:g.198352636A>T			B2R5M6|B7Z712|Q38L19|Q9UCR6	Silent	SNP	ENST00000388968.3	37	CCDS33357.1																																																																																				0.348	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156		5	85	5	85
PLCL1	5334	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	198950679	198950679	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr2:198950679C>T	ENST00000428675.1	+	2	2836	c.2438C>T	c.(2437-2439)aCg>aTg	p.T813M	PLCL1_ENST00000437704.2_Missense_Mutation_p.T715M	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	813	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.T715M(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	GGGCAATATACGATACCATTT	0.443																																																1	Substitution - Missense(1)	prostate(1)											203.0	185.0	191.0					2																	198950679		2203	4300	6503	SO:0001583	missense	5334			D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"""phospholipase C related, but catalytically inactive protein"", ""protein phosphatase 1, regulatory subunit 127"""	600597	"""phospholipase C, epsilon"""	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.2438C>T	2.37:g.198950679C>T	ENSP00000402861:p.Thr813Met		Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	37	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	C	17.05	3.291111	0.59976	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.14766	2.48;2.48	5.5	5.5	0.81552	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.170853	0.41712	D	0.000836	T	0.53126	0.1777	H	0.95187	3.635	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	T	0.66677	-0.5863	9	.	.	.	.	19.5916	0.95514	0.0:1.0:0.0:0.0	.	813;739	Q15111;B4DYZ4	PLCL1_HUMAN;.	M	813;715	ENSP00000402861:T813M;ENSP00000414138:T715M	.	T	+	2	0	PLCL1	198658924	1.000000	0.71417	0.224000	0.23877	0.930000	0.56654	7.641000	0.83368	2.861000	0.98227	0.655000	0.94253	ACG		0.443	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		15	129	15	129
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			16	113	16	113
ZBTB20	26137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	114070191	114070191	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr3:114070191G>C	ENST00000474710.1	-	4	912	c.734C>G	c.(733-735)tCg>tGg	p.S245W	ZBTB20_ENST00000481632.1_Missense_Mutation_p.S172W|ZBTB20_ENST00000357258.3_Missense_Mutation_p.S172W|ZBTB20-AS1_ENST00000475939.1_RNA|ZBTB20_ENST00000462705.1_Missense_Mutation_p.S172W|ZBTB20_ENST00000393785.2_Missense_Mutation_p.S172W|ZBTB20-AS1_ENST00000467304.1_RNA|ZBTB20-AS1_ENST00000496219.1_RNA|ZBTB20_ENST00000471418.1_Missense_Mutation_p.S172W|ZBTB20_ENST00000464560.1_Missense_Mutation_p.S172W	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	245						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		GTAGAGTGCCGAGTAGATCCT	0.672																																					NSCLC(69;748 1344 9802 11203 30933)											0													86.0	77.0	80.0					3																	114070191		2203	4300	6503	SO:0001583	missense	26137			AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13503	protein-coding gene	gene with protein product		606025	"""zinc finger protein 288"""	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.734C>G	3.37:g.114070191G>C	ENSP00000419153:p.Ser245Trp		Q63HP6|Q8N6R5|Q9Y410	Missense_Mutation	SNP	ENST00000474710.1	37	CCDS54626.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.647945	0.67358	.	.	ENSG00000181722	ENST00000462705;ENST00000393785;ENST00000481632;ENST00000471418;ENST00000474710;ENST00000357258;ENST00000464560	T;T;T;T;T;T;T	0.11277	2.82;2.82;2.82;2.82;2.79;2.82;2.82	5.52	5.52	0.82312	.	0.062557	0.64402	D	0.000003	T	0.20577	0.0495	N	0.24115	0.695	0.80722	D	1	D	0.71674	0.998	P	0.61658	0.892	T	0.00875	-1.1531	10	0.87932	D	0	.	19.6361	0.95733	0.0:0.0:1.0:0.0	.	245	Q9HC78	ZBT20_HUMAN	W	172;172;172;172;245;172;172	ENSP00000420324:S172W;ENSP00000377375:S172W;ENSP00000418092:S172W;ENSP00000419902:S172W;ENSP00000419153:S245W;ENSP00000349803:S172W;ENSP00000417307:S172W	ENSP00000349803:S172W	S	-	2	0	ZBTB20	115552881	1.000000	0.71417	0.989000	0.46669	0.949000	0.60115	9.017000	0.93651	2.878000	0.98634	0.650000	0.86243	TCG		0.672	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		14	121	14	121
MAN2B2	23324	hgsc.bcm.edu;broad.mit.edu	37	4	6599987	6599987	+	Silent	SNP	G	G	A	rs373027055		TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr4:6599987G>A	ENST00000285599.3	+	9	1347	c.1311G>A	c.(1309-1311)acG>acA	p.T437T	MAN2B2_ENST00000504248.1_Silent_p.T386T	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	437					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						TGTACGCAACGCACCTGGCCT	0.632																																																0								G		4,4402	8.1+/-20.4	0,4,2199	93.0	81.0	85.0		1311	3.0	1.0	4		85	0,8600		0,0,4300	no	coding-synonymous	MAN2B2	NM_015274.1		0,4,6499	AA,AG,GG		0.0,0.0908,0.0308		437/1010	6599987	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	23324			BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.1311G>A	4.37:g.6599987G>A			Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	37	CCDS33951.1	.	.	.	.	.	.	.	.	.	.	G	3.333	-0.136334	0.06711	9.08E-4	0.0	ENSG00000013288	ENST00000505907	.	.	.	4.86	2.95	0.34219	.	.	.	.	.	T	0.44808	0.1311	.	.	.	0.44985	D	0.998	.	.	.	.	.	.	T	0.34601	-0.9822	4	.	.	.	-16.8918	2.5046	0.04642	0.1978:0.1547:0.5072:0.1404	.	.	.	.	H	436	.	.	R	+	2	0	MAN2B2	6650888	0.779000	0.28652	0.969000	0.41365	0.334000	0.28698	0.094000	0.15107	0.987000	0.38709	0.655000	0.94253	CGC		0.632	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		6	103	6	103
CDH12	1010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	21975457	21975457	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr5:21975457T>C	ENST00000382254.1	-	6	1355	c.269A>G	c.(268-270)aAa>aGa	p.K90R	CDH12_ENST00000522262.1_Missense_Mutation_p.K90R|CDH12_ENST00000504376.2_Missense_Mutation_p.K90R	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	90	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						GAGGGTGTATTTCACAGTGCC	0.463										HNSCC(59;0.17)																																						0													67.0	68.0	67.0					5																	21975457		2046	3890	5936	SO:0001583	missense	1010			L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"""Cadherins / Major cadherins"""	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.269A>G	5.37:g.21975457T>C	ENSP00000371689:p.Lys90Arg		B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	37	CCDS3890.1	.	.	.	.	.	.	.	.	.	.	T	15.17	2.754923	0.49362	.	.	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.50277	0.75;0.75;0.75	5.16	5.16	0.70880	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.36963	0.0986	N	0.17800	0.525	0.46222	D	0.998933	B;B	0.30033	0.026;0.266	B;B	0.36418	0.044;0.224	T	0.34378	-0.9831	10	0.56958	D	0.05	.	11.6254	0.51142	0.0:0.0:0.1486:0.8514	.	90;90	B7Z2U6;P55289	.;CAD12_HUMAN	R	90	ENSP00000423577:K90R;ENSP00000371689:K90R;ENSP00000428786:K90R	ENSP00000371689:K90R	K	-	2	0	CDH12	22011214	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	5.824000	0.69279	1.954000	0.56735	0.397000	0.26171	AAA		0.463	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		18	169	18	169
AHR	196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	17379139	17379139	+	Missense_Mutation	SNP	A	A	T			TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr7:17379139A>T	ENST00000242057.4	+	10	2333	c.1690A>T	c.(1690-1692)Aat>Tat	p.N564Y	AHR_ENST00000492120.1_3'UTR	NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	564					apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	ATTTTTCAGAAATGATTTTTC	0.353																																																0													56.0	64.0	61.0					7																	17379139		2203	4299	6502	SO:0001583	missense	196			L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"""Basic helix-loop-helix proteins"""	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.1690A>T	7.37:g.17379139A>T	ENSP00000242057:p.Asn564Tyr		A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	37	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.308494	0.40895	.	.	ENSG00000106546	ENST00000242057	T	0.24538	1.85	6.02	-2.33	0.06724	.	0.550751	0.19833	N	0.105055	T	0.18045	0.0433	L	0.48362	1.52	0.09310	N	1	B	0.34103	0.437	B	0.35859	0.212	T	0.13415	-1.0510	10	0.72032	D	0.01	.	4.5288	0.11995	0.5462:0.0:0.2422:0.2116	.	564	P35869	AHR_HUMAN	Y	564	ENSP00000242057:N564Y	ENSP00000242057:N564Y	N	+	1	0	AHR	17345664	0.009000	0.17119	0.349000	0.25694	0.923000	0.55619	0.341000	0.19909	-0.375000	0.07955	0.528000	0.53228	AAT		0.353	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		33	115	33	115
ZNF425	155054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	148801044	148801044	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr7:148801044C>T	ENST00000378061.2	-	4	2051	c.1919G>A	c.(1918-1920)tGt>tAt	p.C640Y		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	640					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			GCACATCACACAAGAGAATGG	0.537																																																0													151.0	141.0	145.0					7																	148801044		2203	4300	6503	SO:0001583	missense	155054			AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"""Zinc fingers, C2H2-type"", ""-"""	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.1919G>A	7.37:g.148801044C>T	ENSP00000367300:p.Cys640Tyr		B3KPM1|Q08AG3	Missense_Mutation	SNP	ENST00000378061.2	37	CCDS34773.1	.	.	.	.	.	.	.	.	.	.	C	17.22	3.333071	0.60853	.	.	ENSG00000204947	ENST00000378061	D	0.85088	-1.94	3.16	3.16	0.36331	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93697	0.7986	H	0.94582	3.555	0.40544	D	0.981051	D	0.89917	1.0	D	0.97110	1.0	D	0.94998	0.8140	9	0.87932	D	0	.	12.1153	0.53861	0.0:1.0:0.0:0.0	.	640	Q6IV72	ZN425_HUMAN	Y	640	ENSP00000367300:C640Y	ENSP00000367300:C640Y	C	-	2	0	ZNF425	148431977	1.000000	0.71417	0.012000	0.15200	0.044000	0.14063	6.358000	0.73055	1.766000	0.52107	0.655000	0.94253	TGT		0.537	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		18	202	18	202
P2RX1	5023	broad.mit.edu;ucsc.edu	37	17	3801122	3801122	+	Missense_Mutation	SNP	T	T	C	rs34617528	byFrequency	TCGA-HT-7881-01A-11D-2395-08	TCGA-HT-7881-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cc49bdb9-54e2-4a0d-9896-cbc1dfb32e26	dc36499d-6903-4254-bbcd-e9dbc544951f	g.chr17:3801122T>C	ENST00000225538.3	-	12	1460	c.1186A>G	c.(1186-1188)Atg>Gtg	p.M396V		NM_002558.2	NP_002549.1	P51575	P2RX1_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 1	396			M -> V (in dbSNP:rs34617528).		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ceramide biosynthetic process (GO:0046513)|insemination (GO:0007320)|ion transport (GO:0006811)|neuronal action potential (GO:0019228)|platelet activation (GO:0030168)|positive regulation of ion transport (GO:0043270)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of vascular smooth muscle contraction (GO:0003056)|response to ATP (GO:0033198)|serotonin secretion by platelet (GO:0002554)|signal transduction (GO:0007165)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|vasoconstriction (GO:0042310)	external side of cell outer membrane (GO:0031240)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	13				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		GATGTCCTCATGTTCTCCTGC	0.647													T|||	38	0.00758786	0.0287	0.0	5008	,	,		7004	0.0		0.0	False		,,,				2504	0.0															0								T	VAL/MET	96,4310	78.8+/-117.2	3,90,2110	85.0	75.0	78.0		1186	0.9	1.0	17	dbSNP_126	78	2,8598	1.2+/-3.3	0,2,4298	yes	missense	P2RX1	NM_002558.2	21	3,92,6408	CC,CT,TT		0.0233,2.1788,0.7535	benign	396/400	3801122	98,12908	2203	4300	6503	SO:0001583	missense	5023			X83688	CCDS11040.1	17p13.3	2012-01-17				ENSG00000108405		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8533	protein-coding gene	gene with protein product		600845				8834001	Standard	NM_002558		Approved	P2X1	uc002fww.3	P51575		ENST00000225538.3:c.1186A>G	17.37:g.3801122T>C	ENSP00000225538:p.Met396Val		Q9UK84	Missense_Mutation	SNP	ENST00000225538.3	37	CCDS11040.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	T	7.222	0.597515	0.13875	0.021788	2.33E-4	ENSG00000108405	ENST00000225538	T	0.03951	3.75	4.74	0.921	0.19403	.	0.153918	0.42420	D	0.000701	T	0.01661	0.0053	L	0.36672	1.1	0.29771	N	0.834759	B	0.06786	0.001	B	0.06405	0.002	T	0.25745	-1.0123	10	0.37606	T	0.19	-24.6451	5.1163	0.14836	0.0:0.0967:0.3566:0.5467	rs34617528	396	P51575	P2RX1_HUMAN	V	396	ENSP00000225538:M396V	ENSP00000225538:M396V	M	-	1	0	P2RX1	3747871	1.000000	0.71417	1.000000	0.80357	0.181000	0.23173	0.566000	0.23593	0.350000	0.24002	-0.707000	0.03653	ATG		0.647	P2RX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438391.1	NM_002558		4	32	4	32
