#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_Chromosome_hg18	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_End_position_hg18	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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_classification	i_context	i_dataset	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_type
ACOT12	134526	hgsc.bcm.edu	37	5	80641811	80641811	+	Nonsense_Mutation	SNP	C	C	T			TCGA-36-1574-01	TCGA-36-1574-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr5:80641811C>T	ENST00000307624.3	-	7	694	c.666G>A	c.(664-666)tgG>tgA	p.W222*	ACOT12_ENST00000508234.1_5'Flank	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	222	Acyl coenzyme A hydrolase 2.				acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)	p.W222*(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		AGGGATGAGCCCAACACAGGC	0.453																																																1	Substitution - Nonsense(1)	ovary(1)	5											62.0	58.0	60.0					5																	80641811		2203	4300	6503	80677567	SO:0001587	stop_gained	134526			AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"""Acyl CoA thioesterases"", ""StAR-related lipid transfer (START) domain containing"""	24436	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 15"""	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.666G>A	5.37:g.80641811C>T	ENSP00000303246:p.Trp222*	Somatic		Capture	SOLID	Phase_III	80677567	B3KVK9|Q5FWE9	Nonsense_Mutation	SNP	ENST00000307624.3	37	CCDS4055.1	SNP	22	Baylor	.	.	.	.	.	.	.	.	.	.	C	14.48	2.548424	0.45383	.	.	ENSG00000172497	ENST00000307624	.	.	.	5.95	-11.9	0.00025	.	1.569550	0.03369	N	0.198738	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-32.396	1.4595	0.02392	0.2328:0.113:0.211:0.4433	.	.	.	.	X	222	.	ENSP00000303246:W222X	W	-	3	0	ACOT12	80677567	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.364000	0.02590	-2.334000	0.00630	-0.334000	0.08254	TGG		0.453	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767		Nonsense_Mutation
CCR9	10803	hgsc.bcm.edu	37	3	45943063	45943063	+	Silent	SNP	C	C	T			TCGA-36-1574-01	TCGA-36-1574-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr3:45943063C>T	ENST00000357632.2	+	3	963	c.783C>T	c.(781-783)acC>acT	p.T261T	LZTFL1_ENST00000536047.1_Intron|Y_RNA_ENST00000364765.1_RNA|CCR9_ENST00000395963.2_Silent_p.T249T|LZTFL1_ENST00000539217.1_Intron|CCR9_ENST00000355983.2_Silent_p.T249T|CCR9_ENST00000422395.1_3'UTR	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	261					cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)	p.T261T(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		CTGTCCTGACCGTCTTTGTCT	0.473																																																1	Substitution - coding silent(1)	ovary(1)	3											216.0	176.0	189.0					3																	45943063		2203	4300	6503	45918067	SO:0001819	synonymous_variant	10803			AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.783C>T	3.37:g.45943063C>T		Somatic		Capture	SOLID	Phase_III	45918067	Q4VBM3|Q549E0|Q9UQQ6	Silent	SNP	ENST00000357632.2	37	CCDS2732.1	SNP	23	Baylor																																																																																				0.473	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2			Silent
EFEMP1	2202	hgsc.bcm.edu	37	2	56144830	56144831	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-36-1574-01	TCGA-36-1574-10	AG	AG	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr2:56144830_56144831delAG	ENST00000394555.2	-	4	921_922	c.486_487delCT	c.(484-489)ggctacfs	p.Y163fs	EFEMP1_ENST00000394554.1_Frame_Shift_Del_p.Y163fs|EFEMP1_ENST00000424836.2_Frame_Shift_Del_p.Y105fs|EFEMP1_ENST00000355426.3_Frame_Shift_Del_p.Y163fs	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	163					epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)	p.Y163fs*4(1)		NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CTTTGCTCGTAGCCTGCTGCAC	0.505																																					GBM(92;934 1319 7714 28760 40110)											1	Deletion - Frameshift(1)	ovary(1)	2																																								55998335	SO:0001589	frameshift_variant	2202			U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"""Fibulins"""	3218	protein-coding gene	gene with protein product	"""fibulin 3"""	601548	"""fibrillin-like"", ""EGF-containing fibulin-like extracellular matrix protein 1"""	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.486_487delCT	2.37:g.56144830_56144831delAG	ENSP00000378058:p.Tyr163fs	Somatic		Capture	SOLID	Phase_III	55998334	A8K3I4|B4DW75|D6W5D2|Q541U7	Frame_Shift_Del	DEL	ENST00000394555.2	37	CCDS1857.1	DEL	15	Baylor																																																																																				0.505	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2			Frame_Shift_Del
DLX2	1746	hgsc.bcm.edu	37	2	172966865	172966865	+	Splice_Site	SNP	A	A	G			TCGA-36-1574-01	TCGA-36-1574-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr2:172966865A>G	ENST00000234198.4	-	1	762		c.e1+1		AC104801.1_ENST00000448117.1_lincRNA|DLX2_ENST00000466293.2_Splice_Site	NM_004405.3	NP_004396.1	Q07687	DLX2_HUMAN	distal-less homeobox 2						brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|cartilage development (GO:0051216)|cerebral cortex GABAergic interneuron fate commitment (GO:0021893)|embryonic cranial skeleton morphogenesis (GO:0048701)|hippocampus development (GO:0021766)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|subpallium development (GO:0021544)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded RNA binding (GO:0003727)	p.?(1)		endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.216)			CGTTATGCATACCAGGCTCGT	0.562																																					GBM(188;775 2993 11256 23072)											1	Unknown(1)	ovary(1)	2											124.0	117.0	120.0					2																	172966865		2203	4300	6503	172675111	SO:0001630	splice_region_variant	1746			U51003	CCDS2248.1	2q31.1	2011-06-20	2005-12-22		ENSG00000115844	ENSG00000115844		"""Homeoboxes / ANTP class : NKL subclass"""	2915	protein-coding gene	gene with protein product		126255	"""distal-less homeo box 2"""			1354641	Standard	NM_004405		Approved	TES-1	uc002uhn.3	Q07687	OTTHUMG00000132276	ENST00000234198.4:c.400+1T>C	2.37:g.172966865A>G		Somatic		Capture	SOLID	Phase_III	172675111	B4DMK4|B7ZA14	Splice_Site_SNP	SNP	ENST00000234198.4	37	CCDS2248.1	SNP	14	Baylor	.	.	.	.	.	.	.	.	.	.	A	19.80	3.894395	0.72639	.	.	ENSG00000115844	ENST00000234198;ENST00000466293	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0935	0.65006	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DLX2	172675111	1.000000	0.71417	0.866000	0.34008	0.891000	0.51852	6.618000	0.74214	1.799000	0.52666	0.454000	0.30748	.		0.562	DLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255368.3		Intron	Splice_Site_SNP
FIG4	9896	hgsc.bcm.edu	37	6	110087933	110087933	+	Splice_Site	SNP	T	T	G	rs539336245		TCGA-36-1574-01	TCGA-36-1574-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr6:110087933T>G	ENST00000230124.3	+	15	1709	c.1585T>G	c.(1585-1587)Tta>Gta	p.L529V	FIG4_ENST00000441478.2_Splice_Site_p.L252V	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	529	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)	p.L529V(1)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		TTTTTTTAGGTTATTTGAGGA	0.348																																																1	Substitution - Missense(1)	ovary(1)	6											127.0	120.0	123.0					6																	110087933		2203	4300	6503	110194626	SO:0001630	splice_region_variant	9896			D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"""KIAA0274"", ""FIG4 homolog (S. cerevisiae)"", ""FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"""	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.1584-1T>G	6.37:g.110087933T>G		Somatic		Capture	SOLID	Phase_III	110194626	Q53H49|Q5TCS6	Missense_Mutation	SNP	ENST00000230124.3	37	CCDS5078.1	SNP	60	Baylor	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.79|13.79	2.341796|2.341796	0.41498|0.41498	.|.	.|.	ENSG00000112367|ENSG00000112367	ENST00000441478;ENST00000230124|ENST00000415980	T;T|.	0.53423|.	1.92;0.62|.	5.3|5.3	2.97|2.97	0.34412|0.34412	Synaptojanin, N-terminal (1);|.	0.000000|.	0.64402|.	D|.	0.000012|.	T|T	0.28101|0.28101	0.0693|0.0693	N|N	0.25380|0.25380	0.74|0.74	0.49915|0.49915	D|D	0.999838|0.999838	D;P|.	0.67145|.	0.996;0.462|.	D;B|.	0.80764|.	0.994;0.288|.	T|T	0.05733|0.05733	-1.0867|-1.0867	10|5	0.30078|.	T|.	0.28|.	-13.5222|-13.5222	8.4565|8.4565	0.32901|0.32901	0.0:0.2571:0.0:0.7429|0.0:0.2571:0.0:0.7429	.|.	252;529|.	F5H8L9;Q92562|.	.;FIG4_HUMAN|.	V|G	252;529|1	ENSP00000399443:L252V;ENSP00000230124:L529V|.	ENSP00000230124:L529V|.	L|V	+|+	1|2	2|0	FIG4|FIG4	110194626|110194626	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.044000|2.044000	0.41241|0.41241	2.009000|2.009000	0.58944|0.58944	0.454000|0.454000	0.30748|0.30748	TTA|GTT		0.348	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845	Missense_Mutation	Missense_Mutation
IL1RL2	8808	hgsc.bcm.edu	37	2	102818085	102818085	+	Missense_Mutation	SNP	G	G	A			TCGA-36-1574-01	TCGA-36-1574-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr2:102818085G>A	ENST00000264257.2	+	5	685	c.559G>A	c.(559-561)Gca>Aca	p.A187T	IL1RL2_ENST00000481806.1_3'UTR|IL1RL2_ENST00000539491.1_Missense_Mutation_p.A187T|IL1RL2_ENST00000441515.2_Missense_Mutation_p.A70T	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	187	Ig-like C2-type 2.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)	p.A187T(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						CAATGTCTCGGCAGAGGACAG	0.433																																																1	Substitution - Missense(1)	ovary(1)	2											131.0	114.0	120.0					2																	102818085		2203	4300	6503	102184517	SO:0001583	missense	8808			U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.559G>A	2.37:g.102818085G>A	ENSP00000264257:p.Ala187Thr	Somatic		Capture	SOLID	Phase_III	102184517	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	37	CCDS2056.1	SNP	42	Baylor	.	.	.	.	.	.	.	.	.	.	G	10.55	1.381003	0.24944	.	.	ENSG00000115598	ENST00000264257;ENST00000441515;ENST00000539491	T;T;T	0.14516	2.5;3.94;2.5	4.81	2.72	0.32119	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.910742	0.09490	N	0.795006	T	0.10078	0.0247	L	0.38531	1.155	0.09310	N	1	B;B	0.24258	0.059;0.1	B;B	0.25405	0.017;0.06	T	0.43491	-0.9388	10	0.09843	T	0.71	.	6.4763	0.22037	0.2618:0.0:0.7382:0.0	.	70;187	A4FU63;Q9HB29	.;ILRL2_HUMAN	T	187;70;187	ENSP00000264257:A187T;ENSP00000413348:A70T;ENSP00000442184:A187T	ENSP00000264257:A187T	A	+	1	0	IL1RL2	102184517	0.000000	0.05858	0.000000	0.03702	0.099000	0.18886	0.176000	0.16782	0.563000	0.29222	0.462000	0.41574	GCA		0.433	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		Missense_Mutation
LAMB2	3913	hgsc.bcm.edu	37	3	49169731	49169731	+	Silent	SNP	C	C	A			TCGA-36-1574-01	TCGA-36-1574-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr3:49169731C>A	ENST00000418109.1	-	4	521	c.357G>T	c.(355-357)cgG>cgT	p.R119R	LAMB2_ENST00000305544.4_Silent_p.R119R	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	119	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.R119R(1)		NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AGGCTGCCCGCCGCTGTGGTG	0.582																																																1	Substitution - coding silent(1)	ovary(1)	3											67.0	72.0	71.0					3																	49169731		2203	4300	6503	49144735	SO:0001819	synonymous_variant	3913				CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.357G>T	3.37:g.49169731C>A		Somatic		Capture	SOLID	Phase_III	49144735	Q16321	Silent	SNP	ENST00000418109.1	37	CCDS2789.1	SNP	26	Baylor																																																																																				0.582	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		Silent
MACF1	23499	hgsc.bcm.edu	37	1	39853297	39853297	+	Missense_Mutation	SNP	A	A	G			TCGA-36-1574-01	TCGA-36-1574-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr1:39853297A>G	ENST00000372915.3	+	57	14885	c.14798A>G	c.(14797-14799)gAg>gGg	p.E4933G	MACF1_ENST00000539005.1_Missense_Mutation_p.E2845G|MACF1_ENST00000361689.2_Missense_Mutation_p.E2866G|MACF1_ENST00000289893.4_Missense_Mutation_p.E3368G|MACF1_ENST00000567887.1_Missense_Mutation_p.E4965G|MACF1_ENST00000545844.1_Missense_Mutation_p.E2866G|MACF1_ENST00000564288.1_Missense_Mutation_p.E4928G|MACF1_ENST00000317713.7_Missense_Mutation_p.E2866G			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4933					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.E2866G(1)|p.E3368G(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AAGATGTCTGAGTTGCGAGTC	0.478																																																2	Substitution - Missense(2)	ovary(2)	1											62.0	60.0	61.0					1																	39853297		2203	4300	6503	39625884	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.14798A>G	1.37:g.39853297A>G	ENSP00000362006:p.Glu4933Gly	Somatic		Capture	SOLID	Phase_III	39625884	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		SNP	11	Baylor	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.76|11.76	1.733321|1.733321	0.30684|0.30684	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.53206|.	0.63;0.63;0.63;0.63;0.63;0.63|.	6.17|6.17	5.06|5.06	0.68205|0.68205	.|.	0.269982|.	0.32015|.	N|.	0.006705|.	T|.	0.53867|.	0.1823|.	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	B;B;B|.	0.13145|.	0.0;0.007;0.005|.	B;B;B|.	0.17979|.	0.007;0.017;0.02|.	T|.	0.49826|.	-0.8898|.	10|.	0.34782|.	T|.	0.22|.	.|.	11.8368|11.8368	0.52330|0.52330	0.9327:0.0:0.0673:0.0|0.9327:0.0:0.0673:0.0	.|.	4933;2866;2810|.	Q9UPN3;F8W8Q1;Q9UPN3-3|.	MACF1_HUMAN;.;.|.	G|W	2866;4933;2866;2866;2845;3368|1978	ENSP00000439537:E2866G;ENSP00000362006:E4933G;ENSP00000354573:E2866G;ENSP00000313438:E2866G;ENSP00000444364:E2845G;ENSP00000289893:E3368G|.	ENSP00000289893:E3368G|.	E|X	+|+	2|3	0|0	MACF1|MACF1	39625884|39625884	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.998000|0.998000	0.95712|0.95712	5.173000|5.173000	0.65010|0.65010	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	GAG|TGA		0.478	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		Missense_Mutation
MANBA	4126	hgsc.bcm.edu	37	4	103645120	103645120	+	Missense_Mutation	SNP	A	A	G			TCGA-36-1574-01	TCGA-36-1574-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr4:103645120A>G	ENST00000226578.4	-	3	376	c.277T>C	c.(277-279)Tgg>Cgg	p.W93R	MANBA_ENST00000505239.1_Missense_Mutation_p.W93R	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	93					cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)	p.W93R(1)		cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		ACTTTTTGCCATTTGCTAAAA	0.279																																																1	Substitution - Missense(1)	ovary(1)	4											39.0	40.0	39.0					4																	103645120		2201	4296	6497	103864166	SO:0001583	missense	4126				CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.277T>C	4.37:g.103645120A>G	ENSP00000226578:p.Trp93Arg	Somatic		Capture	SOLID	Phase_III	103864166	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	SNP	8	Baylor	.	.	.	.	.	.	.	.	.	.	A	9.727	1.161149	0.21538	.	.	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.71698	-0.59;0.54	5.03	3.81	0.43845	Galactose-binding domain-like (1);Glycoside hydrolase, family 2, N-terminal (1);	0.364959	0.32401	N	0.006145	T	0.53400	0.1794	N	0.25201	0.72	0.29386	N	0.862966	B;B	0.10296	0.003;0.0	B;B	0.11329	0.001;0.006	T	0.42766	-0.9432	10	0.18710	T	0.47	-5.0045	10.9409	0.47273	0.8594:0.0:0.0:0.1406	.	93;93	E9PFW2;O00462	.;MANBA_HUMAN	R	93	ENSP00000226578:W93R;ENSP00000427322:W93R	ENSP00000226578:W93R	W	-	1	0	MANBA	103864166	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	2.736000	0.47385	0.830000	0.34757	0.477000	0.44152	TGG		0.279	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2			Missense_Mutation
NRCAM	4897	hgsc.bcm.edu	37	7	107824879	107824879	+	Missense_Mutation	SNP	A	A	G			TCGA-36-1574-01	TCGA-36-1574-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr7:107824879A>G	ENST00000425651.2	-	18	2214	c.2215T>C	c.(2215-2217)Tat>Cat	p.Y739H	NRCAM_ENST00000413765.2_Missense_Mutation_p.Y720H|NRCAM_ENST00000379028.3_Missense_Mutation_p.Y739H|NRCAM_ENST00000379024.4_Missense_Mutation_p.Y720H|NRCAM_ENST00000351718.4_Missense_Mutation_p.Y723H|NRCAM_ENST00000379022.4_Missense_Mutation_p.Y739H	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	739	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)	p.Y723H(1)		breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						TTCGTCAAATACTGCTCAGAC	0.498																																																1	Substitution - Missense(1)	ovary(1)	7											81.0	72.0	75.0					7																	107824879		2203	4300	6503	107612115	SO:0001583	missense	4897				CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.2215T>C	7.37:g.107824879A>G	ENSP00000401244:p.Tyr739His	Somatic		Capture	SOLID	Phase_III	107612115	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	SNP	14	Baylor	.	.	.	.	.	.	.	.	.	.	A	11.83	1.755242	0.31046	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022;ENST00000445979	T;T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59;0.59	5.46	5.46	0.80206	Fibronectin, type III (2);	0.058395	0.64402	D	0.000001	T	0.65439	0.2691	L	0.59436	1.845	0.80722	D	1	D;B;D;B;B	0.61697	0.957;0.008;0.99;0.008;0.063	P;B;P;B;B	0.62435	0.894;0.068;0.902;0.084;0.048	T	0.62334	-0.6876	10	0.27082	T	0.32	.	15.5468	0.76108	1.0:0.0:0.0:0.0	.	739;720;720;723;739	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	H	739;739;720;739;723;720;739;739;723	ENSP00000368314:Y739H;ENSP00000407858:Y720H;ENSP00000325269:Y723H;ENSP00000368310:Y720H;ENSP00000401244:Y739H;ENSP00000368308:Y739H	ENSP00000325269:Y723H	Y	-	1	0	NRCAM	107612115	1.000000	0.71417	0.299000	0.25016	0.416000	0.31233	9.268000	0.95675	2.061000	0.61500	0.482000	0.46254	TAT		0.498	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		Missense_Mutation
NSMAF	8439	hgsc.bcm.edu	37	8	59508179	59508179	+	Missense_Mutation	SNP	G	G	A			TCGA-36-1574-01	TCGA-36-1574-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr8:59508179G>A	ENST00000038176.3	-	22	2044	c.1832C>T	c.(1831-1833)aCa>aTa	p.T611I	NSMAF_ENST00000427130.2_Missense_Mutation_p.T642I	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	611					ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)	p.T611I(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				CCAGGCCAGTGTTTTGCTTTC	0.408																																																1	Substitution - Missense(1)	ovary(1)	8											193.0	176.0	182.0					8																	59508179		2203	4300	6503	59670733	SO:0001583	missense	8439			X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"""WD repeat domain containing"""	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.1832C>T	8.37:g.59508179G>A	ENSP00000038176:p.Thr611Ile	Somatic		Capture	SOLID	Phase_III	59670733	B4DFB0|E9PCH0|Q8IW26	Missense_Mutation	SNP	ENST00000038176.3	37	CCDS6173.1	SNP	48	Baylor	.	.	.	.	.	.	.	.	.	.	G	11.97	1.798472	0.31777	.	.	ENSG00000035681	ENST00000038176;ENST00000427130	T;T	0.53857	0.61;0.6	5.95	4.11	0.48088	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.263058	0.43919	D	0.000510	T	0.38852	0.1056	L	0.36672	1.1	0.09310	N	1	B;B	0.25235	0.098;0.121	B;B	0.26770	0.073;0.021	T	0.22138	-1.0225	9	.	.	.	.	7.3945	0.26929	0.066:0.1241:0.6808:0.129	.	642;611	Q92636-2;Q92636	.;FAN_HUMAN	I	611;642	ENSP00000038176:T611I;ENSP00000411012:T642I	.	T	-	2	0	NSMAF	59670733	0.697000	0.27767	0.202000	0.23494	0.731000	0.41821	0.985000	0.29578	0.798000	0.33994	0.650000	0.86243	ACA		0.408	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		Missense_Mutation
PASK	23178	hgsc.bcm.edu	37	2	242046885	242046885	+	Nonsense_Mutation	SNP	G	G	A			TCGA-36-1574-01	TCGA-36-1574-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr2:242046885G>A	ENST00000405260.1	-	17	4395	c.3697C>T	c.(3697-3699)Cag>Tag	p.Q1233*	PASK_ENST00000544142.1_Nonsense_Mutation_p.Q1047*|PASK_ENST00000539818.1_Nonsense_Mutation_p.Q1017*|PASK_ENST00000358649.4_Nonsense_Mutation_p.Q1240*|PASK_ENST00000475666.1_5'UTR|PASK_ENST00000234040.4_Nonsense_Mutation_p.Q1233*	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	1233	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.Q1233*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GGGACTGGCTGCAGCAGCCCA	0.532																																																1	Substitution - Nonsense(1)	ovary(1)	2											132.0	129.0	130.0					2																	242046885		2203	4300	6503	241695558	SO:0001587	stop_gained	23178			U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.3697C>T	2.37:g.242046885G>A	ENSP00000384016:p.Gln1233*	Somatic		Capture	SOLID	Phase_III	241695558	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Nonsense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	SNP	46	Baylor	.	.	.	.	.	.	.	.	.	.	G	47	13.599208	0.99752	.	.	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818	.	.	.	5.05	5.05	0.67936	.	0.390556	0.21919	N	0.067184	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	.	18.4158	0.90570	0.0:0.0:1.0:0.0	.	.	.	.	X	1233;1047;1233;1240;1017	.	ENSP00000234040:Q1233X	Q	-	1	0	PASK	241695558	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.804000	0.85993	2.338000	0.79540	0.655000	0.94253	CAG		0.532	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		Nonsense_Mutation
PLEKHA8	84725	hgsc.bcm.edu	37	7	30094902	30094902	+	Missense_Mutation	SNP	G	G	T			TCGA-36-1574-01	TCGA-36-1574-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr7:30094902G>T	ENST00000449726.1	+	9	1333	c.983G>T	c.(982-984)aGt>aTt	p.S328I	PLEKHA8_ENST00000258679.7_Missense_Mutation_p.S328I|PLEKHA8_ENST00000396257.2_Missense_Mutation_p.S328I|PLEKHA8_ENST00000396259.1_Missense_Mutation_p.S328I	NM_001197027.1	NP_001183956.1	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	328	Glycolipid transfer protein homology domain.				ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)	p.S328I(1)		breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						CTGGAAGACAGTGGCATTCCC	0.393																																																1	Substitution - Missense(1)	ovary(1)	7											216.0	182.0	193.0					7																	30094902		2203	4300	6503	30061427	SO:0001583	missense	84725			BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086		"""Pleckstrin homology (PH) domain containing"""	30037	protein-coding gene	gene with protein product		608639				11001876	Standard	NM_001197027		Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000449726.1:c.983G>T	7.37:g.30094902G>T	ENSP00000397947:p.Ser328Ile	Somatic		Capture	SOLID	Phase_III	30061427	B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	Missense_Mutation	SNP	ENST00000449726.1	37	CCDS56473.1	SNP	36	Baylor	.	.	.	.	.	.	.	.	.	.	G	21.8	4.207241	0.79127	.	.	ENSG00000106086	ENST00000258679;ENST00000449726;ENST00000396257;ENST00000396259;ENST00000440706	.	.	.	5.93	5.93	0.95920	Glycolipid transfer protein domain (2);	0.181679	0.52532	D	0.000063	T	0.67439	0.2893	L	0.50333	1.59	0.37064	D	0.898196	D;D;B;D	0.55800	0.958;0.966;0.429;0.973	P;P;B;P	0.61275	0.748;0.837;0.421;0.886	T	0.70988	-0.4722	9	0.49607	T	0.09	-22.506	13.2015	0.59772	0.0765:0.0:0.9235:0.0	.	328;328;328;328	Q96JA3-2;Q96JA3;Q96JA3-3;B4DH00	.;PKHA8_HUMAN;.;.	I	328;328;328;328;354	.	ENSP00000258679:S328I	S	+	2	0	PLEKHA8	30061427	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.330000	0.52068	2.814000	0.96858	0.591000	0.81541	AGT		0.393	PLEKHA8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032639		Missense_Mutation
SCGN	10590	hgsc.bcm.edu	37	6	25665246	25665246	+	Missense_Mutation	SNP	G	G	A	rs182880487		TCGA-36-1574-01	TCGA-36-1574-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr6:25665246G>A	ENST00000377961.2	+	4	490	c.322G>A	c.(322-324)Gtg>Atg	p.V108M	SCGN_ENST00000334979.6_3'UTR	NM_006998.3	NP_008929.2	O76038	SEGN_HUMAN	secretagogin, EF-hand calcium binding protein	108	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)	p.V108M(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GGACAGCAGCGTGGAGTTTAT	0.488													G|||	1	0.000199681	0.0008	0.0	5008	,	,		22560	0.0		0.0	False		,,,				2504	0.0															1	Substitution - Missense(1)	ovary(1)	6											117.0	107.0	111.0					6																	25665246		2203	4300	6503	25773225	SO:0001583	missense	10590			BC000336	CCDS4561.1	6p22.3-p22.1	2013-01-10			ENSG00000079689	ENSG00000079689		"""EF-hand domain containing"""	16941	protein-coding gene	gene with protein product	"""calbindin-like"""	609202				10811645	Standard	NM_006998		Approved	SECRET, DJ501N12.8, SEGN, CALBL	uc003nfb.3	O76038	OTTHUMG00000014409	ENST00000377961.2:c.322G>A	6.37:g.25665246G>A	ENSP00000367197:p.Val108Met	Somatic		Capture	SOLID	Phase_III	25773225	A8K0B2|Q5VV44|Q96QV7|Q9UJF6	Missense_Mutation	SNP	ENST00000377961.2	37	CCDS4561.1	SNP	40	Baylor	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	14.28	2.487350	0.44249	.	.	ENSG00000079689	ENST00000377961	T	0.09630	2.96	5.09	5.09	0.68999	EF-hand-like domain (1);	0.056322	0.64402	D	0.000001	T	0.28200	0.0696	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	P	0.61940	0.896	T	0.13872	-1.0493	10	0.56958	D	0.05	.	17.2839	0.87136	0.0:0.0:1.0:0.0	.	108	O76038	SEGN_HUMAN	M	108	ENSP00000367197:V108M	ENSP00000367197:V108M	V	+	1	0	SCGN	25773225	1.000000	0.71417	0.997000	0.53966	0.114000	0.19823	5.395000	0.66291	2.343000	0.79666	0.585000	0.79938	GTG		0.488	SCGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040067.1			Missense_Mutation
TACC3	10460	hgsc.bcm.edu	37	4	1730307	1730308	+	Frame_Shift_Ins	INS	-	-	C	rs201356524		TCGA-36-1574-01	TCGA-36-1574-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr4:1730307_1730308insC	ENST00000313288.4	+	4	1284_1285	c.1178_1179insC	c.(1177-1182)gaccccfs	p.DP393fs		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	393					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.M396fs*17(1)		central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			GCAGGAGAGGACCCCCCCATGC	0.609																																					Ovarian(120;482 2294 11894 35824)											1	Insertion - Frameshift(1)	ovary(1)	4																																								1700106	SO:0001589	frameshift_variant	10460			AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.1185dupC	4.37:g.1730314_1730314dupC	ENSP00000326550:p.Asp393fs	Somatic		Capture	SOLID	Phase_III	1700105	Q2NKK4|Q3KQS5|Q9UMQ1	Frame_Shift_Ins	INS	ENST00000313288.4	37	CCDS3352.1	INS	10	Baylor																																																																																				0.609	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2			Frame_Shift_Ins
TG	7038	hgsc.bcm.edu	37	8	134034374	134034374	+	Missense_Mutation	SNP	G	G	A			TCGA-36-1574-01	TCGA-36-1574-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr8:134034374G>A	ENST00000220616.4	+	40	7055	c.7015G>A	c.(7015-7017)Gtc>Atc	p.V2339I	TG_ENST00000519543.1_Missense_Mutation_p.V472I|TG_ENST00000377869.1_Missense_Mutation_p.V2282I|TG_ENST00000542445.1_Missense_Mutation_p.V709I	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2339					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.V2339I(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CCGAGTGGGTGTCTTCGGCTT	0.607																																																1	Substitution - Missense(1)	ovary(1)	8											152.0	138.0	143.0					8																	134034374		2203	4300	6503	134103556	SO:0001583	missense	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.7015G>A	8.37:g.134034374G>A	ENSP00000220616:p.Val2339Ile	Somatic		Capture	SOLID	Phase_III	134103556	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	SNP	48	Baylor	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.99|11.99	1.804726|1.804726	0.31961|0.31961	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000519178;ENST00000518108|ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	.|T;T;T;T	.|0.57907	.|0.37;0.37;0.37;0.37	5.93|5.93	-3.33|-3.33	0.04958|0.04958	.|Carboxylesterase, type B (1);	.|0.707010	.|0.13621	.|N	.|0.374441	T|T	0.29945|0.29945	0.0749|0.0749	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.22480	.|0.039;0.009;0.07	.|B;B;B	.|0.25140	.|0.032;0.023;0.058	T|T	0.17531|0.17531	-1.0366|-1.0366	5|10	.|0.36615	.|T	.|0.2	.|.	8.509|8.509	0.33206|0.33206	0.4812:0.1028:0.416:0.0|0.4812:0.1028:0.416:0.0	.|.	.|472;709;2339	.|E7EVM0;F5GWW5;P01266	.|.;.;THYG_HUMAN	Y|I	794;134|2282;1145;2339;709;472	.|ENSP00000367100:V2282I;ENSP00000220616:V2339I;ENSP00000441693:V709I;ENSP00000430430:V472I	.|ENSP00000220616:V2339I	C|V	+|+	2|1	0|0	TG|TG	134103556|134103556	0.348000|0.348000	0.24861|0.24861	0.228000|0.228000	0.23943|0.23943	0.974000|0.974000	0.67602|0.67602	0.642000|0.642000	0.24735|0.24735	-0.574000|-0.574000	0.05990|0.05990	0.561000|0.561000	0.74099|0.74099	TGT|GTC		0.607	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		Missense_Mutation
TMEM18	129787	hgsc.bcm.edu	37	2	672847	672847	+	Missense_Mutation	SNP	C	C	A			TCGA-36-1574-01	TCGA-36-1574-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr2:672847C>A	ENST00000281017.3	-	3	287	c.194G>T	c.(193-195)tGt>tTt	p.C65F	TMEM18_ENST00000355654.2_Missense_Mutation_p.C52F|TMEM18_ENST00000405941.3_Missense_Mutation_p.C68F	NM_152834.2	NP_690047.2	Q96B42	TMM18_HUMAN	transmembrane protein 18	65					cell migration (GO:0016477)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)	p.C65F(1)		endometrium(1)|large_intestine(1)|lung(7)|ovary(1)	10	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;5.27e-05)|all_epithelial(98;2.11e-06)|Ovarian(717;0.0253)		all cancers(51;1.95e-21)|Epithelial(75;9.47e-21)|OV - Ovarian serous cystadenocarcinoma(76;8.15e-18)|GBM - Glioblastoma multiforme(21;0.0285)		GTATTCAGCACAGTAGACTAA	0.478																																																1	Substitution - Missense(1)	ovary(1)	2											62.0	64.0	63.0					2																	672847		2203	4300	6503	662847	SO:0001583	missense	129787			AL137269	CCDS33141.1	2p25.3	2008-02-05			ENSG00000151353	ENSG00000151353			25257	protein-coding gene	gene with protein product		613220				12477932	Standard	NM_152834		Approved	DKFZp434C1714	uc002qwl.3	Q96B42	OTTHUMG00000151381	ENST00000281017.3:c.194G>T	2.37:g.672847C>A	ENSP00000281017:p.Cys65Phe	Somatic		Capture	SOLID	Phase_III	662847	D6W4X9|Q8N5H2|Q9NTH3	Missense_Mutation	SNP	ENST00000281017.3	37	CCDS33141.1	SNP	17	Baylor	.	.	.	.	.	.	.	.	.	.	C	0.888	-0.726472	0.03158	.	.	ENSG00000151353	ENST00000281017;ENST00000355654;ENST00000405941	.	.	.	5.12	4.19	0.49359	.	0.187999	0.56097	D	0.000023	T	0.43144	0.1234	L	0.29908	0.895	0.38158	D	0.938945	B	0.18461	0.028	B	0.17433	0.018	T	0.36890	-0.9729	9	0.23302	T	0.38	-4.0E-4	12.1844	0.54229	0.0:0.8273:0.1727:0.0	.	65	Q96B42	TMM18_HUMAN	F	65;52;68	.	ENSP00000281017:C65F	C	-	2	0	TMEM18	662847	0.732000	0.28121	0.843000	0.33291	0.086000	0.17979	1.288000	0.33296	2.556000	0.86216	0.555000	0.69702	TGT		0.478	TMEM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322427.1	NM_152834		Missense_Mutation
VCAN	1462	hgsc.bcm.edu	37	5	82816305	82816305	+	Missense_Mutation	SNP	C	C	T	rs199694481		TCGA-36-1574-01	TCGA-36-1574-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr5:82816305C>T	ENST00000265077.3	+	7	2745	c.2180C>T	c.(2179-2181)tCt>tTt	p.S727F	VCAN_ENST00000342785.4_Missense_Mutation_p.S727F|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000512590.2_Missense_Mutation_p.S679F|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	727	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.S727F(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	ATGAAACTCTCTACATCTCTC	0.368													C|||	1	0.000199681	0.0	0.0	5008	,	,		19358	0.0		0.001	False		,,,				2504	0.0															1	Substitution - Missense(1)	ovary(1)	5											71.0	73.0	72.0					5																	82816305		2203	4300	6503	82852061	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.2180C>T	5.37:g.82816305C>T	ENSP00000265077:p.Ser727Phe	Somatic		Capture	SOLID	Phase_III	82852061	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	SNP	32	Baylor	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.359	-0.940600	0.02322	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.29917	1.55;1.55;1.55	5.36	3.55	0.40652	.	0.364135	0.23821	N	0.044228	T	0.27063	0.0663	L	0.50333	1.59	0.09310	N	1	B;B	0.15473	0.009;0.013	B;B	0.19148	0.008;0.024	T	0.13335	-1.0513	10	0.51188	T	0.08	.	9.7155	0.40272	0.0:0.8541:0.0:0.1459	.	727;727	P13611-3;P13611	.;CSPG2_HUMAN	F	727;727;679	ENSP00000265077:S727F;ENSP00000342768:S727F;ENSP00000425959:S679F	ENSP00000265077:S727F	S	+	2	0	VCAN	82852061	0.000000	0.05858	0.052000	0.19188	0.003000	0.03518	-0.448000	0.06820	2.516000	0.84829	0.655000	0.94253	TCT		0.368	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		Missense_Mutation
ZBTB5	9925	hgsc.bcm.edu	37	9	37442044	37442044	+	Missense_Mutation	SNP	C	C	T			TCGA-36-1574-01	TCGA-36-1574-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1574-01	TCGA-36-1574-10	g.chr9:37442044C>T	ENST00000307750.4	-	2	693	c.505G>A	c.(505-507)Gcc>Acc	p.A169T		NM_014872.2	NP_055687.1	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A169T(1)		NS(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		CTCATGGGGGCTGGCTGCTCC	0.612																																																1	Substitution - Missense(1)	ovary(1)	9											53.0	53.0	53.0					9																	37442044		2203	4298	6501	37432044	SO:0001583	missense	9925			AB002352	CCDS6610.1	9p13.1	2013-01-09			ENSG00000168795	ENSG00000168795		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	23836	protein-coding gene	gene with protein product						9205841	Standard	NM_014872		Approved	KIAA0354	uc003zzx.3	O15062	OTTHUMG00000019918	ENST00000307750.4:c.505G>A	9.37:g.37442044C>T	ENSP00000307604:p.Ala169Thr	Somatic		Capture	SOLID	Phase_III	37432044		Missense_Mutation	SNP	ENST00000307750.4	37	CCDS6610.1	SNP	28	Baylor	.	.	.	.	.	.	.	.	.	.	C	8.678	0.904337	0.17760	.	.	ENSG00000168795	ENST00000307750	T	0.08458	3.09	5.54	3.57	0.40892	.	0.267397	0.29459	N	0.012084	T	0.03739	0.0106	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42932	-0.9422	10	0.19147	T	0.46	.	7.2223	0.25994	0.0:0.6639:0.0:0.3361	.	169	O15062	ZBTB5_HUMAN	T	169	ENSP00000307604:A169T	ENSP00000307604:A169T	A	-	1	0	ZBTB5	37432044	.	.	0.869000	0.34112	0.932000	0.56968	.	.	1.571000	0.49722	0.655000	0.94253	GCC		0.612	ZBTB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052462.1	NM_014872		Missense_Mutation
