#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
ART3	419	hgsc.bcm.edu	37	4	77003060	77003060	+	Silent	SNP	C	C	T			TCGA-25-1634-01	TCGA-25-1634-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr4:77003060C>T	ENST00000355810.4	+	3	272	c.153C>T	c.(151-153)taC>taT	p.Y51Y	ART3_ENST00000513494.1_3'UTR|ART3_ENST00000349321.3_Silent_p.Y51Y|ART3_ENST00000341029.5_Silent_p.Y51Y	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	51					protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.Y51Y(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|stomach(1)	16			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			AAATTAAATACGTTCCCCAAC	0.413																																																1	Substitution - coding silent(1)	ovary(1)	4											116.0	116.0	116.0					4																	77003060		2203	4300	6503	77222084	SO:0001819	synonymous_variant	419			X95827	CCDS3575.1, CCDS47079.1, CCDS47080.1	4q21.1	2008-05-15			ENSG00000156219	ENSG00000156219			725	protein-coding gene	gene with protein product		603086				9119374	Standard	NM_001130017		Approved		uc003hjo.3	Q13508	OTTHUMG00000130110	ENST00000355810.4:c.153C>T	4.37:g.77003060C>T		Somatic		Capture	SOLID	Phase_III	77222084	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	Silent	SNP	ENST00000355810.4	37	CCDS47079.1	SNP	19	Baylor																																																																																				0.413	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252416.2	NM_001179		Silent
ATP13A4	84239	hgsc.bcm.edu	37	3	193125105	193125105	+	Silent	SNP	G	G	T			TCGA-25-1634-01	TCGA-25-1634-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr3:193125105G>T	ENST00000342695.4	-	29	3697	c.3375C>A	c.(3373-3375)gcC>gcA	p.A1125A	ATP13A4_ENST00000482964.1_5'UTR|ATP13A4_ENST00000400270.2_Silent_p.A141A|ATP13A4_ENST00000392443.3_Silent_p.A1106A	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1125						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.A1125A(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		CACTTACCTCGGCCACAAGGG	0.522																																																1	Substitution - coding silent(1)	ovary(1)	3											139.0	103.0	115.0					3																	193125105		2203	4300	6503	194607799	SO:0001819	synonymous_variant	84239			AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.3375C>A	3.37:g.193125105G>T		Somatic		Capture	SOLID	Phase_III	194607799	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2	SNP	39	Baylor																																																																																				0.522	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		Silent
CHRND	1144	hgsc.bcm.edu	37	2	233394757	233394757	+	Missense_Mutation	SNP	G	G	A	rs148869069	byFrequency	TCGA-25-1634-01	TCGA-25-1634-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr2:233394757G>A	ENST00000258385.3	+	7	760	c.728G>A	c.(727-729)cGc>cAc	p.R243H	CHRND_ENST00000543200.1_Missense_Mutation_p.R228H|CHRND_ENST00000457943.2_Intron|CHRND_ENST00000536614.1_Silent_p.P206P	NM_000751.2	NP_000742.1	Q07001	ACHD_HUMAN	cholinergic receptor, nicotinic, delta (muscle)	243					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|musculoskeletal movement (GO:0050881)|neuromuscular process (GO:0050905)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)	p.R243H(2)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)	34		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)	Galantamine(DB00674)	CTCATCATCCGCCGCAAGCCC	0.607																																																2	Substitution - Missense(2)	ovary(1)|prostate(1)	2						G	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	174.0	143.0	154.0		728	5.2	1.0	2	dbSNP_134	154	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CHRND	NM_000751.1	29	0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308	probably-damaging	243/518	233394757	4,13002	2203	4300	6503	233103001	SO:0001583	missense	1144			X55019	CCDS2494.1, CCDS58754.1	2q37.1	2012-02-11	2012-02-07		ENSG00000135902	ENSG00000135902		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1965	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, delta (muscle)"""	100720	"""cholinergic receptor, nicotinic, delta"""	ACHRD			Standard	NM_000751		Approved		uc002vsw.4	Q07001	OTTHUMG00000133261	ENST00000258385.3:c.728G>A	2.37:g.233394757G>A	ENSP00000258385:p.Arg243His	Somatic		Capture	SOLID	Phase_III	233103001	A8K661|B4DT92|Q52LH4	Missense_Mutation	SNP	ENST00000258385.3	37	CCDS2494.1	SNP	38	Baylor	.	.	.	.	.	.	.	.	.	.	G	23.3	4.393946	0.83011	6.81E-4	1.16E-4	ENSG00000135902	ENST00000543200;ENST00000258385	T;T	0.80738	-1.41;-1.41	5.18	5.18	0.71444	Neurotransmitter-gated ion-channel ligand-binding (3);	0.418674	0.24967	N	0.034174	D	0.88258	0.6388	M	0.86343	2.81	0.80722	D	1	D;D;D	0.65815	0.995;0.994;0.994	D;D;D	0.64144	0.918;0.922;0.922	D	0.88969	0.3399	10	0.87932	D	0	.	7.0628	0.25135	0.212:0.0:0.788:0.0	.	228;243;243	B4DT92;A8K661;Q07001	.;.;ACHD_HUMAN	H	228;243	ENSP00000438380:R228H;ENSP00000258385:R243H	ENSP00000258385:R243H	R	+	2	0	CHRND	233103001	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.558000	0.60789	2.605000	0.88082	0.655000	0.94253	CGC		0.607	CHRND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257038.2			Missense_Mutation
CIZ1	25792	hgsc.bcm.edu	37	9	130942745	130942745	+	Missense_Mutation	SNP	G	G	C			TCGA-25-1634-01	TCGA-25-1634-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr9:130942745G>C	ENST00000393608.1	-	7	942	c.740C>G	c.(739-741)cCt>cGt	p.P247R	CIZ1_ENST00000277465.4_Missense_Mutation_p.P247R|CIZ1_ENST00000372954.1_Missense_Mutation_p.P223R|CIZ1_ENST00000541172.1_Missense_Mutation_p.P146R|CIZ1_ENST00000538431.1_Missense_Mutation_p.P247R|CIZ1_ENST00000476727.2_5'UTR|CIZ1_ENST00000325721.8_Missense_Mutation_p.P218R|CIZ1_ENST00000372938.5_Missense_Mutation_p.P247R|CIZ1_ENST00000357558.5_Missense_Mutation_p.P247R|CIZ1_ENST00000372948.3_Missense_Mutation_p.P247R	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	247					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.P247R(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						CTCAGGCTCAGGTGCTGGAGT	0.577																																																1	Substitution - Missense(1)	ovary(1)	9											242.0	204.0	217.0					9																	130942745		2203	4300	6503	129982566	SO:0001583	missense	25792			AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.740C>G	9.37:g.130942745G>C	ENSP00000377232:p.Pro247Arg	Somatic		Capture	SOLID	Phase_III	129982566	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Missense_Mutation	SNP	ENST00000393608.1	37	CCDS6894.1	SNP	35	Baylor	.	.	.	.	.	.	.	.	.	.	G	13.32	2.202560	0.38905	.	.	ENSG00000148337	ENST00000372954;ENST00000393608;ENST00000538431;ENST00000357558;ENST00000325721;ENST00000537314;ENST00000541172;ENST00000277465;ENST00000372941;ENST00000372948;ENST00000372938;ENST00000415526;ENST00000324544	T;T;T;T;T;T;T;T;T;T;T	0.69306	1.12;1.27;1.26;1.43;1.29;0.81;1.43;1.1;1.27;1.88;-0.39	4.21	2.37	0.29283	.	0.162750	0.29715	N	0.011397	T	0.66557	0.2801	L	0.34521	1.04	0.09310	N	1	P;D;P;D;D;D;D;D	0.76494	0.917;0.997;0.95;0.999;0.997;0.993;0.971;0.997	P;D;P;D;D;P;P;D	0.69479	0.548;0.921;0.735;0.964;0.95;0.878;0.839;0.921	T	0.53739	-0.8396	10	0.40728	T	0.16	-0.9801	6.1225	0.20161	0.309:0.0:0.691:0.0	.	247;242;247;247;223;247;218;247	B7Z3U7;B4E0A3;F5H2X7;Q9ULV3-4;Q9ULV3-3;Q9ULV3;Q9ULV3-2;Q5SYW2	.;.;.;.;.;CIZ1_HUMAN;.;.	R	223;247;247;247;218;214;146;247;223;247;247;169;247	ENSP00000362045:P223R;ENSP00000377232:P247R;ENSP00000439244:P247R;ENSP00000350169:P247R;ENSP00000320374:P218R;ENSP00000445057:P146R;ENSP00000277465:P247R;ENSP00000362039:P247R;ENSP00000362029:P247R;ENSP00000398011:P169R;ENSP00000321780:P247R	ENSP00000277465:P247R	P	-	2	0	CIZ1	129982566	0.034000	0.19679	0.117000	0.21633	0.065000	0.16274	1.219000	0.32479	0.719000	0.32188	0.655000	0.94253	CCT		0.577	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		Missense_Mutation
COMMD3	23412	hgsc.bcm.edu	37	10	22605357	22605357	+	Missense_Mutation	SNP	C	C	T			TCGA-25-1634-01	TCGA-25-1634-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr10:22605357C>T	ENST00000376836.3	+	1	455	c.11C>T	c.(10-12)tCg>tTg	p.S4L	COMMD3-BMI1_ENST00000602390.1_Missense_Mutation_p.S4L	NM_012071.3	NP_036203.1	Q9UBI1	COMD3_HUMAN	COMM domain containing 3	4								p.S4L(1)		kidney(2)|lung(2)|ovary(1)	5						ATGGAGCTCTCGGAGTCTGTG	0.677																																																1	Substitution - Missense(1)	ovary(1)	10											55.0	35.0	42.0					10																	22605357		2100	4142	6242	22645363	SO:0001583	missense	23412			AY542159	CCDS7137.1	10p12.2	2012-09-20	2004-02-13	2004-02-18	ENSG00000148444	ENSG00000148444			23332	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 8"""	C10orf8		11042152, 15799966	Standard	NM_012071		Approved	BUP		Q9UBI1	OTTHUMG00000017806	ENST00000376836.3:c.11C>T	10.37:g.22605357C>T	ENSP00000366032:p.Ser4Leu	Somatic		Capture	SOLID	Phase_III	22645363	D3DRU7|Q5T8Y9	Missense_Mutation	SNP	ENST00000376836.3	37	CCDS7137.1	SNP	31	Baylor	.	.	.	.	.	.	.	.	.	.	C	22.1	4.246191	0.80024	.	.	ENSG00000148444	ENST00000376836;ENST00000376776;ENST00000376787	T	0.52057	0.68	4.78	3.87	0.44632	.	0.000000	0.64402	D	0.000001	T	0.65015	0.2651	M	0.73217	2.22	0.51767	D	0.999936	B;D	0.69078	0.086;0.997	B;D	0.70227	0.014;0.968	T	0.69300	-0.5181	10	0.87932	D	0	-11.2238	12.3524	0.55155	0.0:0.9161:0.0:0.0839	.	4;4	Q9UBI1;E9PC68	COMD3_HUMAN;.	L	4	ENSP00000366032:S4L	ENSP00000365968:S4L	S	+	2	0	COMMD3	22645363	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	6.390000	0.73204	1.382000	0.46385	-0.140000	0.14226	TCG		0.677	COMMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047159.1	NM_012071		Missense_Mutation
COPS5	10987	hgsc.bcm.edu	37	8	67974106	67974106	+	Silent	SNP	C	C	A			TCGA-25-1634-01	TCGA-25-1634-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr8:67974106C>A	ENST00000357849.4	-	1	446	c.126G>T	c.(124-126)gcG>gcT	p.A42A	CSPP1_ENST00000262210.5_5'Flank|COPS5_ENST00000519963.1_5'UTR|CSPP1_ENST00000412460.1_5'Flank|AC109335.1_ENST00000578628.1_RNA|COPS5_ENST00000517736.1_Intron	NM_006837.2	NP_006828.2	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5	42					cullin deneddylation (GO:0010388)|exosomal secretion (GO:1990182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein deneddylation (GO:0000338)|protein deubiquitination (GO:0016579)|regulation of cell cycle (GO:0051726)|regulation of JNK cascade (GO:0046328)|transcription from RNA polymerase II promoter (GO:0006366)|translation (GO:0006412)|translational initiation (GO:0006413)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 3 complex (GO:0005852)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|transcription coactivator activity (GO:0003713)|translation initiation factor activity (GO:0003743)|ubiquitin-specific protease activity (GO:0004843)	p.A42A(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(3)	14	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)			TCCAGGGCTTCGCCGCCAGGA	0.552																																																1	Substitution - coding silent(1)	ovary(1)	8											147.0	137.0	140.0					8																	67974106		2203	4300	6503	68136660	SO:0001819	synonymous_variant	10987			U65928	CCDS6198.1	8q13.1	2013-03-14	2013-03-14		ENSG00000121022	ENSG00000121022			2240	protein-coding gene	gene with protein product		604850	"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 5"", ""COP9 constitutive photomorphogenic homolog subunit 5 (Arabidopsis)"""			8837781, 9341143	Standard	NM_006837		Approved	JAB1, SGN5, MOV-34, CSN5	uc003xxe.3	Q92905	OTTHUMG00000164563	ENST00000357849.4:c.126G>T	8.37:g.67974106C>A		Somatic		Capture	SOLID	Phase_III	68136660	O15386|Q6AW95|Q86WQ4|Q9BQ17	Silent	SNP	ENST00000357849.4	37	CCDS6198.1	SNP	31	Baylor																																																																																				0.552	COPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379245.2			Silent
DHX30	22907	hgsc.bcm.edu	37	3	47888228	47888228	+	Missense_Mutation	SNP	G	G	A	rs36045705	byFrequency	TCGA-25-1634-01	TCGA-25-1634-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr3:47888228G>A	ENST00000445061.1	+	11	2073	c.1666G>A	c.(1666-1668)Gtc>Atc	p.V556I	DHX30_ENST00000446256.2_Missense_Mutation_p.V517I|MIR1226_ENST00000408658.1_RNA|DHX30_ENST00000457607.1_Missense_Mutation_p.V584I|DHX30_ENST00000348968.4_Missense_Mutation_p.V528I	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	556	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.V556I(1)		endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CGTGAGCCACGTCATCGTGGA	0.637																																																1	Substitution - Missense(1)	ovary(1)	3						G	ILE/VAL,ILE/VAL	8,4398	14.3+/-33.2	0,8,2195	57.0	48.0	51.0		1549,1666	4.8	0.6	3	dbSNP_126	51	0,8600		0,0,4300	yes	missense,missense	DHX30	NM_014966.3,NM_138615.2	29,29	0,8,6495	AA,AG,GG		0.0,0.1816,0.0615	benign,benign	517/1156,556/1195	47888228	8,12998	2203	4300	6503	47863232	SO:0001583	missense	22907			AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"""DEAH-boxes"""	16716	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 30"""	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.1666G>A	3.37:g.47888228G>A	ENSP00000405620:p.Val556Ile	Somatic		Capture	SOLID	Phase_III	47863232	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Missense_Mutation	SNP	ENST00000445061.1	37	CCDS2759.1	SNP	40	Baylor	.	.	.	.	.	.	.	.	.	.	G	16.63	3.177478	0.57692	0.001816	0.0	ENSG00000132153	ENST00000446256;ENST00000445061;ENST00000348968;ENST00000457607	T;T;T;T	0.04862	3.54;3.54;3.54;3.54	4.81	4.81	0.61882	DEAD-like helicase (2);DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.065701	0.64402	D	0.000011	T	0.04092	0.0114	N	0.11313	0.125	0.53688	D	0.999974	P;B	0.43788	0.817;0.174	B;B	0.40228	0.323;0.134	T	0.52555	-0.8560	10	0.46703	T	0.11	.	10.511	0.44862	0.0889:0.0:0.9111:0.0	rs36045705	556;517	Q7L2E3;Q7L2E3-3	DHX30_HUMAN;.	I	517;556;528;584	ENSP00000392601:V517I;ENSP00000405620:V556I;ENSP00000343442:V528I;ENSP00000394682:V584I	ENSP00000343442:V528I	V	+	1	0	DHX30	47863232	1.000000	0.71417	0.615000	0.29064	0.861000	0.49209	5.445000	0.66594	2.219000	0.72066	0.462000	0.41574	GTC		0.637	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		Missense_Mutation
EGFR	1956	hgsc.bcm.edu	37	7	55259452	55259452	+	Missense_Mutation	SNP	A	A	T			TCGA-25-1634-01	TCGA-25-1634-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr7:55259452A>T	ENST00000275493.2	+	21	2687	c.2510A>T	c.(2509-2511)gAc>gTc	p.D837V	EGFR_ENST00000454757.2_Missense_Mutation_p.D784V|EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Missense_Mutation_p.D792V	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	837	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.D837G(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GTGCACCGCGACCTGGCAGCC	0.537		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	1	Substitution - Missense(1)	lung(1)	7											115.0	100.0	105.0					7																	55259452		2203	4300	6503	55226946	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2510A>T	7.37:g.55259452A>T	ENSP00000275493:p.Asp837Val	Somatic		Capture	SOLID	Phase_III	55226946	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	SNP	10	Baylor	.	.	.	.	.	.	.	.	.	.	A	27.9	4.870612	0.91587	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000454757	T;T;T	0.80909	-1.43;-1.43;-1.43	5.82	5.82	0.92795	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94466	0.8219	H	0.99454	4.575	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.977;0.999	D	0.96734	0.9541	10	0.87932	D	0	.	15.0046	0.71501	1.0:0.0:0.0:0.0	.	792;837	Q504U8;P00533	.;EGFR_HUMAN	V	792;707;837;784	ENSP00000415559:D792V;ENSP00000275493:D837V;ENSP00000395243:D784V	ENSP00000275493:D837V	D	+	2	0	EGFR	55226946	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.184000	0.94893	2.221000	0.72209	0.528000	0.53228	GAC		0.537	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		Missense_Mutation
EIF3E	3646	hgsc.bcm.edu	37	8	109215225	109215225	+	Frame_Shift_Del	DEL	T	T	-			TCGA-25-1634-01	TCGA-25-1634-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr8:109215225delT	ENST00000220849.5	-	12	1348	c.1286delA	c.(1285-1287)aatfs	p.N429fs	EIF3E_ENST00000519517.1_5'Flank|EIF3E_ENST00000519030.1_Frame_Shift_Del_p.N336fs	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E									p.N429fs*>17(1)	EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			TGACCTGCTATTCTGATTAAG	0.383																																					GBM(15;360 410 8460 34179 52246)											1	Deletion - Frameshift(1)	ovary(1)	8											161.0	145.0	150.0					8																	109215225		2203	4300	6503	109284401	SO:0001589	frameshift_variant	3646			U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"""eukaryotic translation initiation factor 3, subunit 6 48kDa"""	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.1286delA	8.37:g.109215225delT	ENSP00000220849:p.Asn429fs	Somatic		Capture	SOLID	Phase_III	109284401		Indel	Indel	ENST00000220849.5	37	CCDS6308.1	Indel	52	Baylor																																																																																				0.383	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		Indel
FERD3L	222894	hgsc.bcm.edu	37	7	19184746	19184747	+	In_Frame_Ins	INS	-	-	TCT	rs34966908|rs199985178|rs71017023	byFrequency	TCGA-25-1634-01	TCGA-25-1634-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr7:19184746_19184747insTCT	ENST00000275461.3	-	1	297_298	c.239_240insAGA	c.(238-240)gag>gaAGAg	p.80_80E>EE	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	80	Poly-Glu.				cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E81_R82insE(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						ttccgcgctcctcttcctcctc	0.624														836	0.166933	0.0446	0.1643	5008	,	,		17679	0.1587		0.2654	False		,,,				2504	0.2413															1	Insertion - In frame(1)	ovary(1)	7								307,0,3957		13,0,281,0,0,1838						0.6	0.7		dbSNP_134	60	2211,1,6042		291,0,1629,0,1,2206	no	codingComplex	FERD3L	NM_152898.2		304,0,1910,0,1,4044	A1A1,A1A2,A1R,A2A2,A2R,RR		26.7991,7.1998,20.123				2518,1,9999				19151272	SO:0001652	inframe_insertion	222894			AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"""Basic helix-loop-helix proteins"""	16660	protein-coding gene	gene with protein product			"""Fer3-like (Drosophila)"""			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.237_239dupAGA	7.37:g.19184747_19184749dupTCT	ENSP00000275461:p.Glu81dup	Somatic		Capture	SOLID	Phase_III	19151271	Q495K0	In_Frame_Ins	INS	ENST00000275461.3	37	CCDS5368.1	INS	24	Baylor																																																																																				0.624	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1			In_Frame_Ins
GBP5	115362	hgsc.bcm.edu	37	1	89730613	89730613	+	Missense_Mutation	SNP	A	A	T			TCGA-25-1634-01	TCGA-25-1634-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr1:89730613A>T	ENST00000370459.3	-	7	1032	c.905T>A	c.(904-906)aTc>aAc	p.I302N	GBP5_ENST00000471171.1_5'Flank|GBP5_ENST00000343435.5_Missense_Mutation_p.I302N|RP4-620F22.2_ENST00000437128.1_RNA			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	302	GTPase domain (Globular). {ECO:0000250}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.I302N(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		CCCACTGCTGATGGCATTGAC	0.448																																																1	Substitution - Missense(1)	ovary(1)	1											92.0	82.0	85.0					1																	89730613		2203	4300	6503	89503201	SO:0001583	missense	115362			AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.905T>A	1.37:g.89730613A>T	ENSP00000359488:p.Ile302Asn	Somatic		Capture	SOLID	Phase_III	89503201	B2RCE1|Q86TM5	Missense_Mutation	SNP	ENST00000370459.3	37	CCDS722.1	SNP	12	Baylor	.	.	.	.	.	.	.	.	.	.	A	15.82	2.945332	0.53079	.	.	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	T;T;T	0.05447	3.44;3.44;3.44	4.96	4.96	0.65561	Guanylate-binding protein, C-terminal (3);	0.052522	0.64402	D	0.000001	T	0.23014	0.0556	M	0.90977	3.165	0.38353	D	0.944394	D	0.89917	1.0	D	0.97110	1.0	T	0.10405	-1.0631	10	0.87932	D	0	-20.5671	12.9668	0.58488	1.0:0.0:0.0:0.0	.	302	Q96PP8	GBP5_HUMAN	N	302	ENSP00000340396:I302N;ENSP00000359488:I302N;ENSP00000403010:I302N	ENSP00000340396:I302N	I	-	2	0	GBP5	89503201	1.000000	0.71417	0.990000	0.47175	0.018000	0.09664	6.397000	0.73239	2.227000	0.72691	0.454000	0.30748	ATC		0.448	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942		Missense_Mutation
GDPD5	81544	hgsc.bcm.edu	37	11	75188687	75188687	+	Missense_Mutation	SNP	G	G	A			TCGA-25-1634-01	TCGA-25-1634-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr11:75188687G>A	ENST00000336898.3	-	3	931	c.94C>T	c.(94-96)Cgc>Tgc	p.R32C	GDPD5_ENST00000376282.3_Missense_Mutation_p.R32C|GDPD5_ENST00000529721.1_Missense_Mutation_p.R32C|GDPD5_ENST00000533784.1_Missense_Mutation_p.R32C|GDPD5_ENST00000443276.2_Missense_Mutation_p.R32C	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	32					cerebral cortex neuron differentiation (GO:0021895)|glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)|negative regulation of Notch signaling pathway (GO:0045746)|neuron projection development (GO:0031175)|positive regulation of neuron differentiation (GO:0045666)|regulation of timing of cell differentiation (GO:0048505)|spinal cord motor neuron differentiation (GO:0021522)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)	p.R32C(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|skin(2)	20						TCATGGGAGCGCTGGTAGCGC	0.637																																																1	Substitution - Missense(1)	ovary(1)	11											46.0	41.0	43.0					11																	75188687		2200	4293	6493	74866335	SO:0001583	missense	81544			AF318377	CCDS8238.1	11q13.4-q13.5	2011-01-25				ENSG00000158555			28804	protein-coding gene	gene with protein product		609632				18667693, 17275818	Standard	NM_030792		Approved	PP1665, GDE2	uc001owp.4	Q8WTR4		ENST00000336898.3:c.94C>T	11.37:g.75188687G>A	ENSP00000337972:p.Arg32Cys	Somatic		Capture	SOLID	Phase_III	74866335	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Missense_Mutation	SNP	ENST00000336898.3	37	CCDS8238.1	SNP	38	Baylor	.	.	.	.	.	.	.	.	.	.	G	21.3	4.129490	0.77549	.	.	ENSG00000158555	ENST00000533784;ENST00000529721;ENST00000336898;ENST00000376282;ENST00000443276;ENST00000532435	T;T;T;T;T	0.34859	2.07;1.34;1.34;2.07;1.34	4.88	2.83	0.33086	.	0.124090	0.53938	D	0.000055	T	0.56062	0.1960	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;P	0.87578	0.998;0.84	T	0.60606	-0.7230	10	0.87932	D	0	-24.3836	11.467	0.50246	0.0:0.0:0.6762:0.3238	.	32;32	Q8WTR4-2;Q8WTR4	.;GDPD5_HUMAN	C	32	ENSP00000437049:R32C;ENSP00000433214:R32C;ENSP00000337972:R32C;ENSP00000365459:R32C;ENSP00000396535:R32C	ENSP00000337972:R32C	R	-	1	0	GDPD5	74866335	1.000000	0.71417	0.959000	0.39883	0.982000	0.71751	6.176000	0.71955	1.155000	0.42497	0.655000	0.94253	CGC		0.637	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792		Missense_Mutation
GPRC6A	222545	hgsc.bcm.edu	37	6	117130582	117130582	+	Silent	SNP	A	A	G			TCGA-25-1634-01	TCGA-25-1634-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr6:117130582A>G	ENST00000310357.3	-	2	414	c.393T>C	c.(391-393)tgT>tgC	p.C131C	GPRC6A_ENST00000368549.3_Silent_p.C131C|GPRC6A_ENST00000530250.1_Silent_p.C131C	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	131					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.C131C(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TGGAATAGTCACACTTAAACT	0.428																																																1	Substitution - coding silent(1)	ovary(1)	6											100.0	94.0	96.0					6																	117130582		2203	4300	6503	117237275	SO:0001819	synonymous_variant	222545			AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.393T>C	6.37:g.117130582A>G		Somatic		Capture	SOLID	Phase_III	117237275	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1	SNP	6	Baylor																																																																																				0.428	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			Silent
GPRIN2	9721	hgsc.bcm.edu	37	10	46999863	46999863	+	Missense_Mutation	SNP	C	C	G	rs4445576	byFrequency	TCGA-25-1634-01	TCGA-25-1634-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr10:46999863C>G	ENST00000374317.1	+	3	1256	c.983C>G	c.(982-984)tCc>tGc	p.S328C	GPRIN2_ENST00000374314.4_Missense_Mutation_p.S328C	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	328			S -> C (in dbSNP:rs4445576).							breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						GCAGAGGCATCCCCGCTGTCA	0.652													C|||	825	0.164736	0.1021	0.3285	5008	,	,		36299	0.004		0.3042	False		,,,				2504	0.1554															0			10						C	CYS/SER	471,3935		0,471,1732	56.0	59.0	58.0		983	3.2	0.0	10	dbSNP_111	58	2030,6570		1,2028,2271	yes	missense	GPRIN2	NM_014696.3	112	1,2499,4003	GG,GC,CC		23.6047,10.69,19.2296	probably-damaging	328/459	46999863	2501,10505	2203	4300	6503	46419869	SO:0001583	missense	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.983C>G	10.37:g.46999863C>G	ENSP00000363436:p.Ser328Cys	Somatic		Capture	SOLID	Phase_III	46419869	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	SNP	30	Baylor	386	0.17673992673992675	56	0.11382113821138211	102	0.281767955801105	0	0.0	228	0.3007915567282322	C	11.15	1.553761	0.27739	0.1069	0.236047	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.03889	3.77;3.77	3.15	3.15	0.36227	.	0.474723	0.15845	N	0.241802	T	0.00012	0.0000	L	0.51422	1.61	0.09310	N	1	D	0.65815	0.995	P	0.55824	0.785	T	0.47959	-0.9076	10	0.54805	T	0.06	.	12.1335	0.53957	0.0:1.0:0.0:0.0	rs4445576	328	O60269	GRIN2_HUMAN	C	328	ENSP00000363436:S328C;ENSP00000363433:S328C	ENSP00000363433:S328C	S	+	2	0	GPRIN2	46419869	.	.	0.005000	0.12908	0.392000	0.30506	.	.	1.788000	0.52465	0.313000	0.20887	TCC		0.652	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		Missense_Mutation
GSN	2934	hgsc.bcm.edu	37	9	124094799	124094799	+	Missense_Mutation	SNP	T	T	C			TCGA-25-1634-01	TCGA-25-1634-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr9:124094799T>C	ENST00000373818.4	+	17	2336	c.2267T>C	c.(2266-2268)tTt>tCt	p.F756S	GSN_ENST00000436847.1_Missense_Mutation_p.F716S|GSN_ENST00000373808.2_Missense_Mutation_p.F705S|GSN_ENST00000449733.1_Missense_Mutation_p.F705S|GSN_ENST00000412819.1_Missense_Mutation_p.F705S|GSN_ENST00000341272.2_Missense_Mutation_p.F705S|GSN_ENST00000545652.1_Missense_Mutation_p.F713S|GSN_ENST00000394353.2_Missense_Mutation_p.F716S|GSN_ENST00000373823.3_Missense_Mutation_p.F705S|GSN_ENST00000373806.1_Missense_Mutation_p.F181S	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	756	Actin-binding, Ca-sensitive. {ECO:0000255}.				actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)	p.F705S(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						CCTCCCTCCTTTGTGGGCTGG	0.627											OREG0019445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	ovary(1)	9											155.0	129.0	138.0					9																	124094799		2203	4300	6503	123134620	SO:0001583	missense	2934			X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"""amyloidosis, Finnish type"""	137350	"""gelsolin (amyloidosis, Finnish type)"""			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.2267T>C	9.37:g.124094799T>C	ENSP00000362924:p.Phe756Ser	Somatic	1531	Capture	SOLID	Phase_III	123134620	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Missense_Mutation	SNP	ENST00000373818.4	37	CCDS6828.1	SNP	64	Baylor	.	.	.	.	.	.	.	.	.	.	T	26.5	4.747856	0.89663	.	.	ENSG00000148180	ENST00000373823;ENST00000436847;ENST00000394353;ENST00000449733;ENST00000412819;ENST00000341272;ENST00000373808;ENST00000394352;ENST00000456109;ENST00000545652;ENST00000373818;ENST00000373806;ENST00000373805	T;T;T;T;T;T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02	6.07	6.07	0.98685	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	D	0.87128	0.6100	H	0.98155	4.16	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	D	0.91713	0.5383	10	0.87932	D	0	-17.5025	15.8218	0.78654	0.0:0.0:0.0:1.0	.	729;713;716;756	B7Z9A0;F5H1A8;B7Z373;P06396	.;.;.;GELS_HUMAN	S	705;716;716;705;705;705;705;689;679;713;756;181;162	ENSP00000362929:F705S;ENSP00000411293:F716S;ENSP00000377882:F716S;ENSP00000409358:F705S;ENSP00000416586:F705S;ENSP00000340888:F705S;ENSP00000362914:F705S;ENSP00000445823:F713S;ENSP00000362924:F756S;ENSP00000362912:F181S	ENSP00000340888:F705S	F	+	2	0	GSN	123134620	1.000000	0.71417	0.846000	0.33378	0.685000	0.39939	7.559000	0.82265	2.326000	0.78906	0.533000	0.62120	TTT		0.627	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177		Missense_Mutation
INHBA	3624	hgsc.bcm.edu	37	7	41729297	41729297	+	Frame_Shift_Del	DEL	A	A	-			TCGA-25-1634-01	TCGA-25-1634-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr7:41729297delA	ENST00000242208.4	-	3	1478	c.1232delT	c.(1231-1233)atcfs	p.I411fs	INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Frame_Shift_Del_p.I411fs|AC005027.3_ENST00000416150.1_RNA	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	411					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GTCCTTTTTGATGATGTTTTG	0.512										TSP Lung(11;0.080)																																						0			7											114.0	99.0	104.0					7																	41729297		2203	4300	6503	41695822	SO:0001589	frameshift_variant	3624				CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"""Endogenous ligands"""	6066	protein-coding gene	gene with protein product		147290	"""inhibin, beta A (activin A, activin AB alpha polypeptide)"""			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.1232delT	7.37:g.41729297delA	ENSP00000242208:p.Ile411fs	Somatic		Capture	SOLID	Phase_III	41695822	Q14599	Frame_Shift_Del	DEL	ENST00000242208.4	37	CCDS5464.1	DEL	12	Baylor																																																																																				0.512	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			Frame_Shift_Del
KLF6	1316	hgsc.bcm.edu	37	10	3824281	3824281	+	Silent	SNP	T	T	C			TCGA-25-1634-01	TCGA-25-1634-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr10:3824281T>C	ENST00000497571.1	-	2	488	c.228A>G	c.(226-228)gaA>gaG	p.E76E	KLF6_ENST00000173785.4_5'Flank|KLF6_ENST00000469435.1_Silent_p.E76E|KLF6_ENST00000542957.1_Silent_p.E76E	NM_001160124.1|NM_001300.5	NP_001153596.1|NP_001291.3	Q99612	KLF6_HUMAN	Kruppel-like factor 6	76					B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				Colorectal(1;0.238)		TCAGTTCGGATTCCTCCTTTT	0.478											OREG0019980	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0			10											126.0	135.0	131.0					10																	3824281		2203	4300	6503	3814281	SO:0001819	synonymous_variant	1316			U51869	CCDS7060.1, CCDS53490.1	10p15	2013-01-08	2004-11-29	2004-12-01	ENSG00000067082	ENSG00000067082		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	2235	protein-coding gene	gene with protein product	"""GC-rich binding factor"""	602053	"""core promoter element binding protein"""	BCD1, ST12, COPEB		9503030, 9685731	Standard	NM_001300		Approved	CPBP, GBF, Zf9, PAC1	uc001iha.3	Q99612	OTTHUMG00000017567	ENST00000497571.1:c.228A>G	10.37:g.3824281T>C		Somatic	614	Capture	SOLID	Phase_III	3814281	B2RE86|B4DDN0|D3DRR1|F5H3M5|Q5VUT7|Q5VUT8|Q9BT79	Silent	SNP	ENST00000497571.1	37	CCDS7060.1	SNP	52	Baylor	.	.	.	.	.	.	.	.	.	.	T	4.719	0.133786	0.09032	.	.	ENSG00000067082	ENST00000322510	.	.	.	4.91	-1.91	0.07641	.	.	.	.	.	T	0.25232	0.0613	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29212	-1.0019	5	0.05620	T	0.96	.	7.1151	0.25412	0.2188:0.0:0.489:0.2922	.	.	.	.	S	75	.	ENSP00000324925:N75S	N	-	2	0	KLF6	3814281	0.569000	0.26643	0.041000	0.18516	0.846000	0.48090	-0.037000	0.12164	-0.677000	0.05231	-0.396000	0.06452	AAT		0.478	KLF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046495.1			Silent
L3MBTL1	26013	hgsc.bcm.edu	37	20	42168808	42168808	+	Missense_Mutation	SNP	G	G	A			TCGA-25-1634-01	TCGA-25-1634-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr20:42168808G>A	ENST00000427442.2	+	20	2284	c.2125G>A	c.(2125-2127)Gtg>Atg	p.V709M	L3MBTL1_ENST00000373135.3_Missense_Mutation_p.V641M|L3MBTL1_ENST00000418998.1_Missense_Mutation_p.V709M|L3MBTL1_ENST00000444063.1_Missense_Mutation_p.V641M|L3MBTL1_ENST00000373134.1_Missense_Mutation_p.V646M			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	641	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.V641M(1)		breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						GCCCGATGTCGTGCACCAGTC	0.622																																																1	Substitution - Missense(1)	ovary(1)	20											92.0	66.0	74.0					20																	42168808		2203	4300	6503	41602222	SO:0001583	missense	26013			U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"""Zinc fingers, C2HC-type containing"", ""Sterile alpha motif (SAM) domain containing"""	15905	protein-coding gene	gene with protein product	"""lethal (3) malignant brain tumor l(3)"""	608802	"""l(3)mbt (Drosophila)-like"", ""l(3)mbt-like (Drosophila)"""	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.2125G>A	20.37:g.42168808G>A	ENSP00000402107:p.Val709Met	Somatic		Capture	SOLID	Phase_III	41602222	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Missense_Mutation	SNP	ENST00000427442.2	37	CCDS46602.2	SNP	40	Baylor	.	.	.	.	.	.	.	.	.	.	G	8.168	0.791089	0.16258	.	.	ENSG00000185513	ENST00000427442;ENST00000418998;ENST00000373135;ENST00000444063;ENST00000373134;ENST00000422861;ENST00000373133	T;T;T;T;T;T	0.23754	2.18;2.18;2.14;2.17;2.11;1.89	5.55	-1.96	0.07525	.	0.779472	0.12225	N	0.487976	T	0.10337	0.0253	N	0.05510	-0.035	0.09310	N	1	B;B;B;B;B	0.22211	0.02;0.045;0.066;0.04;0.013	B;B;B;B;B	0.19946	0.01;0.027;0.014;0.019;0.016	T	0.33292	-0.9874	10	0.23302	T	0.38	.	6.9344	0.24459	0.4785:0.1242:0.3974:0.0	.	709;293;29;641;641	Q9Y468-5;Q9Y468-3;Q6ZWF5;Q9Y468-2;Q9Y468-1	.;.;.;.;.	M	709;709;641;641;646;427;293	ENSP00000402107:V709M;ENSP00000398516:V709M;ENSP00000362227:V641M;ENSP00000403316:V641M;ENSP00000362226:V646M;ENSP00000410139:V427M	ENSP00000362225:V293M	V	+	1	0	L3MBTL1	41602222	0.843000	0.29541	0.020000	0.16555	0.178000	0.23041	1.461000	0.35255	-0.316000	0.08690	-0.150000	0.13652	GTG		0.622	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		Missense_Mutation
MCM4	4173	hgsc.bcm.edu	37	8	48882466	48882466	+	Missense_Mutation	SNP	G	G	A	rs376187463		TCGA-25-1634-01	TCGA-25-1634-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr8:48882466G>A	ENST00000262105.2	+	10	1492	c.1283G>A	c.(1282-1284)cGt>cAt	p.R428H	MCM4_ENST00000518680.1_3'UTR|MCM4_ENST00000523944.1_Missense_Mutation_p.R428H	NM_005914.3	NP_005905.2	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	428					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)	p.R428H(1)		biliary_tract(1)|breast(1)|endometrium(7)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	44		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				GATGCAAAACGTCTGCATGGC	0.418																																																1	Substitution - Missense(1)	ovary(1)	8						G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	164.0	152.0	156.0		1283,1283	4.4	1.0	8		156	0,8600		0,0,4300	no	missense,missense	MCM4	NM_005914.3,NM_182746.2	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	428/864,428/864	48882466	1,13005	2203	4300	6503	49045019	SO:0001583	missense	4173				CCDS6143.1	8q12-q13	2008-02-05	2007-04-04		ENSG00000104738	ENSG00000104738			6947	protein-coding gene	gene with protein product		602638	"""MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)"""	CDC21		7601140	Standard	NM_005914		Approved	CDC54, hCdc21, P1-Cdc21, MGC33310	uc003xql.2	P33991	OTTHUMG00000164205	ENST00000262105.2:c.1283G>A	8.37:g.48882466G>A	ENSP00000262105:p.Arg428His	Somatic		Capture	SOLID	Phase_III	49045019	Q8NEH1|Q99658	Missense_Mutation	SNP	ENST00000262105.2	37	CCDS6143.1	SNP	40	Baylor	.	.	.	.	.	.	.	.	.	.	G	19.38	3.815788	0.70912	2.27E-4	0.0	ENSG00000104738	ENST00000523944;ENST00000262105;ENST00000396826;ENST00000429229;ENST00000520637	T;T;T	0.09350	3.95;3.95;2.99	6.17	4.38	0.52667	.	0.044223	0.85682	D	0.000000	T	0.34513	0.0900	M	0.83223	2.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71414	0.973;0.973	T	0.28202	-1.0051	10	0.87932	D	0	-16.7133	13.5326	0.61631	0.1275:0.0:0.8725:0.0	.	428;428	B3KMX0;P33991	.;MCM4_HUMAN	H	428;428;415;388;146	ENSP00000430194:R428H;ENSP00000262105:R428H;ENSP00000427875:R146H	ENSP00000262105:R428H	R	+	2	0	MCM4	49045019	1.000000	0.71417	0.986000	0.45419	0.944000	0.59088	7.554000	0.82212	1.636000	0.50526	0.655000	0.94253	CGT		0.418	MCM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377791.1	NM_005914		Missense_Mutation
MYH10	4628	hgsc.bcm.edu	37	17	8415793	8415793	+	Frame_Shift_Del	DEL	C	C	-			TCGA-25-1634-01	TCGA-25-1634-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr17:8415793delC	ENST00000269243.4	-	22	2973	c.2835delG	c.(2833-2835)aagfs	p.K947fs	MYH10_ENST00000360416.3_Frame_Shift_Del_p.K978fs|MYH10_ENST00000396239.1_Frame_Shift_Del_p.K968fs|RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000379980.4_Frame_Shift_Del_p.K963fs	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	947					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						GCATTTTTTTCTTTTCATTTT	0.323																																																0			17											48.0	49.0	48.0					17																	8415793		2203	4299	6502	8356518	SO:0001589	frameshift_variant	4628			M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2835delG	17.37:g.8415793delC	ENSP00000269243:p.Lys947fs	Somatic		Capture	SOLID	Phase_III	8356518	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Frame_Shift_Del	DEL	ENST00000269243.4	37	CCDS11144.1	DEL	32	Baylor																																																																																				0.323	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			Frame_Shift_Del
NBPF14	25832	hgsc.bcm.edu	37	1	148009509	148009509	+	Missense_Mutation	SNP	C	C	T	rs143363070	byFrequency	TCGA-25-1634-01	TCGA-25-1634-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr1:148009509C>T	ENST00000369219.1	-	16	1814	c.1798G>A	c.(1798-1800)Ggg>Agg	p.G600R				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	600	NBPF 7. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.G600R(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					AACAGCTCCCCGCTGAGCCTG	0.463													-|||	151	0.0301518	0.0938	0.013	5008	,	,		57917	0.003		0.007	False		,,,				2504	0.0082															1	Substitution - Missense(1)	ovary(1)	1																																								146476133	SO:0001583	missense	25832			AK092351		1q21.1	2013-01-17			ENSG00000122497			"""neuroblastoma breakpoint family"""	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.1798G>A	1.37:g.148009509C>T	ENSP00000358221:p.Gly600Arg	Somatic		Capture	SOLID	Phase_III	146476133	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	37		SNP	23	Baylor	.	.	.	.	.	.	.	.	.	.	N	0.003	-2.577581	0.00131	.	.	ENSG00000122497	ENST00000369219;ENST00000434489	T	0.04156	3.69	.	.	.	DUF1220 (2);	.	.	.	.	T	0.00300	0.0009	N	0.00339	-1.615	0.09310	N	1	.	.	.	.	.	.	T	0.44097	-0.9350	4	0.02654	T	1	.	.	.	.	.	600	Q5TI25	NBPFE_HUMAN	R	600;190	ENSP00000358221:G600R	ENSP00000358221:G600R	G	-	1	0	NBPF14	146476133	0.988000	0.35896	.	.	.	.	-1.256000	0.02869	.	.	.	.	GGG		0.463	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383		Missense_Mutation
NUF2	83540	hgsc.bcm.edu	37	1	163310216	163310216	+	Splice_Site	SNP	G	G	C			TCGA-25-1634-01	TCGA-25-1634-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr1:163310216G>C	ENST00000271452.3	+	9	948	c.669G>C	c.(667-669)ttG>ttC	p.L223F	NUF2_ENST00000524800.1_Splice_Site_p.L223F|NUF2_ENST00000367900.3_Splice_Site_p.L223F	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	223	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)		p.L223F(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					CCAAGCGTTTGGTAAACATCT	0.333																																																1	Substitution - Missense(1)	ovary(1)	1											96.0	104.0	101.0					1																	163310216		2202	4300	6502	161576840	SO:0001630	splice_region_variant	83540			BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"""cancer/testis antigen 106"""	611772	"""cell division cycle associated 1"", ""NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"""	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.669+1G>C	1.37:g.163310216G>C		Somatic		Capture	SOLID	Phase_III	161576840	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	37	CCDS1245.1	SNP	47	Baylor	.	.	.	.	.	.	.	.	.	.	G	10.61	1.397825	0.25205	.	.	ENSG00000143228	ENST00000524800;ENST00000367900;ENST00000271452	T;T;T	0.37235	1.21;1.21;1.21	4.77	2.87	0.33458	.	0.073983	0.56097	D	0.000028	T	0.30510	0.0767	L	0.55481	1.735	.	.	.	D;D	0.69078	0.997;0.997	P;P	0.59643	0.861;0.861	T	0.20739	-1.0266	9	0.62326	D	0.03	-2.1981	5.8041	0.18430	0.0984:0.0:0.71:0.1917	.	223;223	E9PQC4;Q9BZD4	.;NUF2_HUMAN	F	223	ENSP00000436888:L223F;ENSP00000356875:L223F;ENSP00000271452:L223F	ENSP00000271452:L223F	L	+	3	2	NUF2	161576840	1.000000	0.71417	0.998000	0.56505	0.907000	0.53573	1.794000	0.38774	0.704000	0.31869	0.655000	0.94253	TTG		0.333	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697	Missense_Mutation	Missense_Mutation
PNPLA8	50640	hgsc.bcm.edu	37	7	108154999	108154999	+	Missense_Mutation	SNP	A	A	C	rs113406943		TCGA-25-1634-01	TCGA-25-1634-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr7:108154999A>C	ENST00000422087.1	-	4	1343	c.937T>G	c.(937-939)Tta>Gta	p.L313V	PNPLA8_ENST00000426128.2_Missense_Mutation_p.L313V|PNPLA8_ENST00000436062.1_Missense_Mutation_p.L313V|PNPLA8_ENST00000483879.1_Intron|PNPLA8_ENST00000453144.1_Missense_Mutation_p.L213V|PNPLA8_ENST00000388728.5_Missense_Mutation_p.L313V|PNPLA8_ENST00000257694.8_Missense_Mutation_p.L313V	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	313					arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)			breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						TCATACTTTAATTTGGGGACA	0.403																																																0			7											115.0	116.0	116.0					7																	108154999		2203	4300	6503	107942235	SO:0001583	missense	50640			AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"""Patatin-like phospholipase domain containing"""	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.937T>G	7.37:g.108154999A>C	ENSP00000410804:p.Leu313Val	Somatic		Capture	SOLID	Phase_III	107942235	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Missense_Mutation	SNP	ENST00000422087.1	37	CCDS34733.1	SNP	4	Baylor	.	.	.	.	.	.	.	.	.	.	A	13.31	2.200138	0.38905	.	.	ENSG00000135241	ENST00000426128;ENST00000257694;ENST00000388728;ENST00000422087;ENST00000453144;ENST00000436062;ENST00000453085	T;T;T;T;D;T;D	0.98381	2.28;2.28;2.28;2.28;-4.9;2.28;-4.9	4.5	3.26	0.37387	.	0.216156	0.40144	N	0.001180	D	0.95648	0.8585	M	0.62723	1.935	0.38992	D	0.959171	P	0.38300	0.626	B	0.32465	0.146	D	0.93273	0.6653	10	0.40728	T	0.16	.	7.567	0.27885	0.821:0.0:0.179:0.0	.	313	Q9NP80	PLPL8_HUMAN	V	313;313;313;313;213;313;213	ENSP00000394988:L313V;ENSP00000257694:L313V;ENSP00000373380:L313V;ENSP00000410804:L313V;ENSP00000387789:L213V;ENSP00000406779:L313V;ENSP00000402274:L213V	ENSP00000257694:L313V	L	-	1	2	PNPLA8	107942235	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.203000	0.51075	0.792000	0.33850	0.482000	0.46254	TTA		0.403	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723		Missense_Mutation
RBL2	5934	hgsc.bcm.edu	37	16	53498216	53498216	+	Missense_Mutation	SNP	C	C	G			TCGA-25-1634-01	TCGA-25-1634-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr16:53498216C>G	ENST00000262133.6	+	12	1776	c.1639C>G	c.(1639-1641)Cct>Gct	p.P547A	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Missense_Mutation_p.P331A	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	547	Domain A.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)	p.P547A(1)		breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TTATAAGCCTCCTGGGAATTT	0.338																																																1	Substitution - Missense(1)	ovary(1)	16											90.0	94.0	93.0					16																	53498216		2198	4300	6498	52055717	SO:0001583	missense	5934			X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.1639C>G	16.37:g.53498216C>G	ENSP00000262133:p.Pro547Ala	Somatic		Capture	SOLID	Phase_III	52055717	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	37	CCDS10748.1	SNP	30	Baylor	.	.	.	.	.	.	.	.	.	.	C	17.68	3.450140	0.63290	.	.	ENSG00000103479	ENST00000262133;ENST00000544405;ENST00000379935;ENST00000544545	D;D;D	0.86562	-2.14;-2.14;-2.14	5.86	5.86	0.93980	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	0.050790	0.85682	D	0.000000	D	0.85881	0.5800	L	0.49455	1.56	0.47621	D	0.999475	B;B;B;B	0.25048	0.046;0.091;0.02;0.117	B;B;B;B	0.32022	0.066;0.139;0.081;0.103	T	0.82116	-0.0616	10	0.44086	T	0.13	-15.6206	16.4446	0.83913	0.0:0.8689:0.1311:0.0	.	331;547;257;547	B7Z913;Q8NE70;E9PG04;Q08999	.;.;.;RBL2_HUMAN	A	547;473;257;331	ENSP00000262133:P547A;ENSP00000443744:P473A;ENSP00000444685:P331A	ENSP00000262133:P547A	P	+	1	0	RBL2	52055717	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.855000	0.69510	2.776000	0.95493	0.650000	0.86243	CCT		0.338	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		Missense_Mutation
RBM25	58517	hgsc.bcm.edu	37	14	73576088	73576088	+	Missense_Mutation	SNP	A	A	G			TCGA-25-1634-01	TCGA-25-1634-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr14:73576088A>G	ENST00000261973.7	+	14	1865	c.1580A>G	c.(1579-1581)aAg>aGg	p.K527R	RBM25_ENST00000527432.1_Missense_Mutation_p.K527R|RBM25_ENST00000532483.1_3'UTR	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	527	Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K527R(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		GATAGAGAAAAGGAAATGGAA	0.438																																																1	Substitution - Missense(1)	ovary(1)	14											120.0	124.0	123.0					14																	73576088		2203	4300	6503	72645841	SO:0001583	missense	58517			BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"""RNA binding motif (RRM) containing"""	23244	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 94"""	612427	"""RNA-binding region (RNP1, RRM) containing 7"""	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.1580A>G	14.37:g.73576088A>G	ENSP00000261973:p.Lys527Arg	Somatic		Capture	SOLID	Phase_III	72645841	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Missense_Mutation	SNP	ENST00000261973.7	37	CCDS32113.1	SNP	3	Baylor	.	.	.	.	.	.	.	.	.	.	A	17.68	3.449694	0.63290	.	.	ENSG00000119707	ENST00000261973;ENST00000527432	T;T	0.10860	2.83;2.83	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.15349	0.0370	N	0.17379	0.485	0.80722	D	1	P	0.52842	0.956	P	0.62184	0.899	T	0.16837	-1.0389	10	0.08599	T	0.76	.	16.4608	0.84044	1.0:0.0:0.0:0.0	.	527	P49756	RBM25_HUMAN	R	527	ENSP00000261973:K527R;ENSP00000431150:K527R	ENSP00000261973:K527R	K	+	2	0	RBM25	72645841	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.141000	0.94612	2.288000	0.76882	0.533000	0.62120	AAG		0.438	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330		Missense_Mutation
RPS6KC1	26750	hgsc.bcm.edu	37	1	213403885	213403885	+	Nonsense_Mutation	SNP	A	A	T			TCGA-25-1634-01	TCGA-25-1634-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr1:213403885A>T	ENST00000366960.3	+	9	1240	c.1090A>T	c.(1090-1092)Aaa>Taa	p.K364*	RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543354.1_Nonsense_Mutation_p.K67*|RPS6KC1_ENST00000366959.3_Nonsense_Mutation_p.K352*|RPS6KC1_ENST00000543470.1_Nonsense_Mutation_p.K152*	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	364	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)	p.K364*(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		TTTCATTTTAAAAGTAAGTAA	0.378																																																1	Substitution - Nonsense(1)	ovary(1)	1											52.0	55.0	54.0					1																	213403885		2202	4299	6501	211470508	SO:0001587	stop_gained	26750			AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.1090A>T	1.37:g.213403885A>T	ENSP00000355927:p.Lys364*	Somatic		Capture	SOLID	Phase_III	211470508	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Nonsense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	SNP	1	Baylor	.	.	.	.	.	.	.	.	.	.	A	39	7.467476	0.98302	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.9574	15.5705	0.76330	1.0:0.0:0.0:0.0	.	.	.	.	X	152;364;352;67	.	ENSP00000355926:K352X	K	+	1	0	RPS6KC1	211470508	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.960000	0.87893	2.141000	0.66446	0.459000	0.35465	AAA		0.378	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		Nonsense_Mutation
SCLT1	132320	hgsc.bcm.edu	37	4	129960215	129960215	+	Missense_Mutation	SNP	C	C	G	rs370155503		TCGA-25-1634-01	TCGA-25-1634-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr4:129960215C>G	ENST00000281142.5	-	5	774	c.271G>C	c.(271-273)Gtc>Ctc	p.V91L	SCLT1_ENST00000503215.1_Missense_Mutation_p.V68L|SCLT1_ENST00000434680.1_Missense_Mutation_p.V91L|SCLT1_ENST00000506368.1_Missense_Mutation_p.V91L|SCLT1_ENST00000439369.2_Missense_Mutation_p.V91L	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	91					cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)	p.V91L(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						TCCTTGATGACATTTTCAAGT	0.284																																																1	Substitution - Missense(1)	ovary(1)	4											55.0	53.0	53.0					4																	129960215		2199	4297	6496	130179665	SO:0001583	missense	132320			AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.271G>C	4.37:g.129960215C>G	ENSP00000281142:p.Val91Leu	Somatic		Capture	SOLID	Phase_III	130179665	A4QN04|Q0VAH2|Q6P2M4	Missense_Mutation	SNP	ENST00000281142.5	37	CCDS3740.1	SNP	17	Baylor	.	.	.	.	.	.	.	.	.	.	C	19.03	3.748637	0.69533	.	.	ENSG00000151466	ENST00000281142;ENST00000434680;ENST00000439369;ENST00000503215;ENST00000506368	T;T;T	0.09911	2.93;2.93;2.93	4.83	3.97	0.46021	.	0.129487	0.50627	D	0.000115	T	0.15219	0.0367	L	0.34521	1.04	0.41655	D	0.989157	P;P;D;P	0.56521	0.732;0.851;0.976;0.732	B;P;P;B	0.56398	0.26;0.546;0.797;0.26	T	0.01242	-1.1408	9	.	.	.	-7.3179	10.7144	0.46005	0.0:0.9074:0.0:0.0926	.	91;91;91;91	Q96NL6-3;D6RBA6;Q96NL6-2;Q96NL6	.;.;.;SCLT1_HUMAN	L	91;91;91;68;91	ENSP00000281142:V91L;ENSP00000401539:V91L;ENSP00000424029:V68L	.	V	-	1	0	SCLT1	130179665	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.928000	0.28831	2.498000	0.84270	0.655000	0.94253	GTC		0.284	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643		Missense_Mutation
SMOC2	64094	hgsc.bcm.edu	37	6	169008908	169008908	+	Frame_Shift_Del	DEL	G	G	-			TCGA-25-1634-01	TCGA-25-1634-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr6:169008908delG	ENST00000356284.2	+	9	1116	c.896delG	c.(895-897)cgcfs	p.R299fs	SMOC2_ENST00000354536.5_Frame_Shift_Del_p.R310fs	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	299					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		TACAAGGGCCGCCAGCTACAA	0.592																																																0			6											26.0	25.0	25.0					6																	169008908		2201	4297	6498	168750833	SO:0001589	frameshift_variant	64094			AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562		"""EF-hand domain containing"""	20323	protein-coding gene	gene with protein product		607223				12031507	Standard	NM_022138		Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.896delG	6.37:g.169008908delG	ENSP00000348630:p.Arg299fs	Somatic		Capture	SOLID	Phase_III	168750833	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	Frame_Shift_Del	DEL	ENST00000356284.2	37	CCDS55076.1	DEL	38	Baylor																																																																																				0.592	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043201.1			Frame_Shift_Del
TBX3	6926	hgsc.bcm.edu	37	12	115115428	115115428	+	Frame_Shift_Del	DEL	C	C	-			TCGA-25-1634-01	TCGA-25-1634-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr12:115115428delC	ENST00000257566.3	-	5	1287	c.898delG	c.(898-900)gcafs	p.A300fs	TBX3_ENST00000349155.2_Frame_Shift_Del_p.A280fs	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	300					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A300fs*23(1)		breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		AAACCTTTTGCAAAAGGGTTG	0.353																																																1	Deletion - Frameshift(1)	ovary(1)	12											90.0	87.0	88.0					12																	115115428		2203	4300	6503	113599811	SO:0001589	frameshift_variant	6926			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.898delG	12.37:g.115115428delC	ENSP00000257566:p.Ala300fs	Somatic		Capture	SOLID	Phase_III	113599811	Q8TB20|Q9UKF8	Frame_Shift_Del	DEL	ENST00000257566.3	37	CCDS9176.1	DEL	25	Baylor																																																																																				0.353	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		Frame_Shift_Del
U2AF2	11338	hgsc.bcm.edu	37	19	56179887	56179887	+	Missense_Mutation	SNP	G	G	A			TCGA-25-1634-01	TCGA-25-1634-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr19:56179887G>A	ENST00000308924.4	+	8	797	c.757G>A	c.(757-759)Gtg>Atg	p.V253M	CTD-2537I9.12_ENST00000589456.1_RNA|CTD-2537I9.12_ENST00000585940.1_RNA|CTD-2537I9.13_ENST00000592252.1_RNA|U2AF2_ENST00000590551.1_Missense_Mutation_p.V89M|U2AF2_ENST00000450554.2_Missense_Mutation_p.V253M			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	253					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.V253M(1)		biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		TGTGTCCACTGTGGTCCCCGA	0.567																																																1	Substitution - Missense(1)	ovary(1)	19											118.0	105.0	109.0					19																	56179887		2203	4300	6503	60871699	SO:0001583	missense	11338			BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"""RNA binding motif (RRM) containing"""	23156	protein-coding gene	gene with protein product	"""U2 small nuclear ribonucleoprotein auxiliary factor (65kD)"", ""splicing factor U2AF 65 kD subunit"", ""U2 snRNP auxiliary factor large subunit"""	191318	"""U2 (RNU2) small nuclear RNA auxiliary factor 2"""			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.757G>A	19.37:g.56179887G>A	ENSP00000307863:p.Val253Met	Somatic		Capture	SOLID	Phase_III	60871699	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	37	CCDS12933.1	SNP	48	Baylor	.	.	.	.	.	.	.	.	.	.	G	16.28	3.079306	0.55753	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	T;T	0.74842	-0.88;1.26	3.72	3.72	0.42706	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.64402	D	0.000001	T	0.75635	0.3876	M	0.83384	2.64	0.80722	D	1	B;B	0.29301	0.173;0.241	B;B	0.28385	0.089;0.078	T	0.78254	-0.2275	10	0.46703	T	0.11	-26.2581	14.8266	0.70117	0.0:0.0:1.0:0.0	.	253;253	P26368;P26368-2	U2AF2_HUMAN;.	M	253	ENSP00000307863:V253M;ENSP00000388475:V253M	ENSP00000307863:V253M	V	+	1	0	U2AF2	60871699	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.867000	0.92314	2.102000	0.63906	0.655000	0.94253	GTG		0.567	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		Missense_Mutation
WDFY3	23001	hgsc.bcm.edu	37	4	85717847	85717847	+	Missense_Mutation	SNP	T	T	A			TCGA-25-1634-01	TCGA-25-1634-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr4:85717847T>A	ENST00000295888.4	-	19	3401	c.2994A>T	c.(2992-2994)gaA>gaT	p.E998D	WDFY3_ENST00000322366.6_Missense_Mutation_p.E998D	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	998					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.E998D(1)		breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AATGGTTATCTTCATGTAAGC	0.438																																																1	Substitution - Missense(1)	ovary(1)	4											128.0	123.0	125.0					4																	85717847		2203	4300	6503	85936871	SO:0001583	missense	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.2994A>T	4.37:g.85717847T>A	ENSP00000295888:p.Glu998Asp	Somatic		Capture	SOLID	Phase_III	85936871	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	SNP	56	Baylor	.	.	.	.	.	.	.	.	.	.	T	15.47	2.844468	0.51164	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.64438	-0.1;-0.09	5.63	5.63	0.86233	.	0.044471	0.85682	D	0.000000	T	0.41119	0.1145	N	0.08118	0	0.58432	D	0.999999	B	0.06786	0.001	B	0.08055	0.003	T	0.30592	-0.9973	10	0.30854	T	0.27	.	11.9902	0.53171	0.0:0.0695:0.0:0.9305	.	998	Q8IZQ1	WDFY3_HUMAN	D	998	ENSP00000318466:E998D;ENSP00000295888:E998D	ENSP00000295888:E998D	E	-	3	2	WDFY3	85936871	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.281000	0.43452	2.268000	0.75426	0.455000	0.32223	GAA		0.438	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		Missense_Mutation
ZNF286A	57335	hgsc.bcm.edu	37	17	15611544	15611544	+	Missense_Mutation	SNP	C	C	T			TCGA-25-1634-01	TCGA-25-1634-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-25-1634-01	TCGA-25-1634-10	g.chr17:15611544C>T	ENST00000464847.2	+	4	870	c.317C>T	c.(316-318)cCc>cTc	p.P106L	ZNF286A_ENST00000395893.2_Missense_Mutation_p.P106L|ZNF286A_ENST00000395894.2_Missense_Mutation_p.P106L|ZNF286A_ENST00000472486.1_Missense_Mutation_p.P96L|ZNF286A_ENST00000583566.1_Missense_Mutation_p.P106L|ZNF286A_ENST00000421016.1_Missense_Mutation_p.P106L|ZNF286A_ENST00000580259.1_3'UTR|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000585194.1_Missense_Mutation_p.P106L|ZNF286A_ENST00000581529.1_3'UTR|ZNF286A_ENST00000593105.1_Missense_Mutation_p.P96L|ZNF286A_ENST00000413242.2_Missense_Mutation_p.P106L			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	106	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P106L(2)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		AGAAAAGCCCCCAAAAGCAGC	0.403																																																2	Substitution - Missense(2)	ovary(1)|central_nervous_system(1)	17											57.0	58.0	57.0					17																	15611544		2203	4300	6503	15552269	SO:0001583	missense	57335			AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"""Zinc fingers, C2H2-type"", ""-"""	13501	protein-coding gene	gene with protein product			"""zinc finger protein 286"""	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.317C>T	17.37:g.15611544C>T	ENSP00000464218:p.Pro106Leu	Somatic		Capture	SOLID	Phase_III	15552269	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	SNP	22	Baylor	.	.	.	.	.	.	.	.	.	.	c	11.26	1.587257	0.28268	.	.	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894;ENST00000395893	T;T;T;T	0.08282	3.47;3.11;5.43;5.59	4.85	3.84	0.44239	Krueppel-associated box (1);	30.442900	0.00744	N	0.001035	T	0.06280	0.0162	N	0.10685	0.025	0.09310	N	1	B	0.27498	0.18	B	0.21546	0.035	T	0.31696	-0.9934	10	0.27785	T	0.31	-0.0869	10.6557	0.45673	0.2079:0.7921:0.0:0.0	.	106	Q9HBT8	Z286A_HUMAN	L	106;96;106;106	ENSP00000397163:P106L;ENSP00000408168:P96L;ENSP00000379231:P106L;ENSP00000379230:P106L	ENSP00000435872:P106L	P	+	2	0	ZNF286A	15552269	0.000000	0.05858	0.003000	0.11579	0.188000	0.23474	0.417000	0.21214	1.321000	0.45227	0.563000	0.77884	CCC		0.403	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652		Missense_Mutation
