#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_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_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_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
ITGB8	3696	hgsc.bcm.edu	37	7	20444382	20444382	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:20444382T>C	ENST00000222573.4	+	11	2503	c.1819T>C	c.(1819-1821)Tgt>Cgt	p.C607R	ITGB8_ENST00000537992.1_Missense_Mutation_p.C472R	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	607	Cysteine-rich tandem repeats.				cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						AAGAGGCACGTGTGTGTGTGG	0.557																																																	0			7											195.0	154.0	167.0					7																	20444382		2203	4300	6503	20410907	SO:0001583	missense	3696				CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"""Integrins"""	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.1819T>C	7.37:g.20444382T>C	ENSP00000222573:p.Cys607Arg	Somatic		Capture	Illumina HiSeq	Phase_I	20410907	A4D133|B4DHD4	Missense_Mutation	SNP	ENST00000222573.4	37	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.662441	0.88251	.	.	ENSG00000105855	ENST00000537992;ENST00000222573	D;D	0.97831	-4.56;-4.56	5.65	5.65	0.86999	EGF, extracellular (1);	0.000000	0.85682	D	0.000000	D	0.98868	0.9617	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99811	1.1041	10	0.87932	D	0	.	16.175	0.81844	0.0:0.0:0.0:1.0	.	607	P26012	ITB8_HUMAN	R	472;607	ENSP00000441561:C472R;ENSP00000222573:C607R	ENSP00000222573:C607R	C	+	1	0	ITGB8	20410907	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	7.336000	0.79245	2.274000	0.75844	0.528000	0.53228	TGT		ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214	
STK31	56164	hgsc.bcm.edu	37	7	23810668	23810668	+	Silent	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:23810668T>C	ENST00000355870.3	+	14	1877	c.1758T>C	c.(1756-1758)agT>agC	p.S586S	STK31_ENST00000428484.1_Silent_p.S563S|STK31_ENST00000433467.2_Silent_p.S586S|STK31_ENST00000405627.3_3'UTR|STK31_ENST00000354639.3_Silent_p.S563S	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	586						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						ATACATATAGTCAAGTACTGC	0.353																																																	0			7											176.0	177.0	176.0					7																	23810668		2203	4300	6503	23777193	SO:0001819	synonymous_variant	56164			AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1758T>C	7.37:g.23810668T>C		Somatic		Capture	Illumina HiSeq	Phase_I	23777193	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Silent	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																				STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
FKBP9	11328	hgsc.bcm.edu	37	7	33016063	33016063	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:33016063C>T	ENST00000242209.4	+	4	824	c.655C>T	c.(655-657)Cgc>Tgc	p.R219C	AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000489038.1_3'UTR|FKBP9_ENST00000538336.1_Missense_Mutation_p.R272C|FKBP9_ENST00000538443.1_Missense_Mutation_p.R81C	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	219	PPIase FKBP-type 2. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			GGGTGAGAAGCGCATCATCAC	0.483																																																	0			7											165.0	143.0	151.0					7																	33016063		2202	4286	6488	32982588	SO:0001583	missense	11328			AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"""EF-hand domain containing"""	3725	protein-coding gene	gene with protein product			"""FK506-binding protein 9 (63 kD)"""			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.655C>T	7.37:g.33016063C>T	ENSP00000242209:p.Arg219Cys	Somatic		Capture	Illumina HiSeq	Phase_I	32982588	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Missense_Mutation	SNP	ENST00000242209.4	37	CCDS5439.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.459301	0.84317	.	.	ENSG00000122642	ENST00000242209;ENST00000538336;ENST00000538443	D;D;D	0.87887	-2.31;-2.31;-2.31	4.73	4.73	0.59995	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.000000	0.85682	D	0.000000	D	0.94735	0.8301	M	0.89715	3.055	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95748	0.8789	10	0.72032	D	0.01	-14.008	18.074	0.89422	0.0:1.0:0.0:0.0	.	272;219;219	B7Z6H3;O95302;B3KQQ0	.;FKBP9_HUMAN;.	C	219;272;81	ENSP00000242209:R219C;ENSP00000439250:R272C;ENSP00000437504:R81C	ENSP00000242209:R219C	R	+	1	0	FKBP9	32982588	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	5.960000	0.70348	2.341000	0.79615	0.455000	0.32223	CGC		FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270	
BBS9	27241	hgsc.bcm.edu	37	7	33217166	33217166	+	Silent	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:33217166C>T	ENST00000242067.6	+	5	926	c.405C>T	c.(403-405)gcC>gcT	p.A135A	RNA5SP229_ENST00000410809.1_RNA|BBS9_ENST00000355070.2_Silent_p.A135A|BBS9_ENST00000425508.2_Silent_p.A90A|BBS9_ENST00000350941.3_Silent_p.A135A|BBS9_ENST00000354265.4_Silent_p.A135A|BBS9_ENST00000396127.2_Silent_p.A135A	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	135					cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			AGAGAACAGCCTGCAATATGA	0.333									Bardet-Biedl syndrome																																								0			7											166.0	156.0	159.0					7																	33217166		2203	4300	6503	33183691	SO:0001819	synonymous_variant	27241	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"""parathyroid hormone responsive B1 gene"""	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.405C>T	7.37:g.33217166C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33183691	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Silent	SNP	ENST00000242067.6	37	CCDS43566.1																																																																																				BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1		
MYO1G	64005	hgsc.bcm.edu	37	7	45011719	45011719	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:45011719G>A	ENST00000258787.7	-	6	860	c.724C>T	c.(724-726)Cac>Tac	p.H242Y		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	242	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						CTCACACTGTGCACAGTCATG	0.562																																																	0			7											267.0	207.0	227.0					7																	45011719		2203	4300	6503	44978244	SO:0001583	missense	64005			AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"""Myosins / Myosin superfamily : Class I"""	13880	protein-coding gene	gene with protein product	"""minor histocompatibility antigen HA-2"""	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.724C>T	7.37:g.45011719G>A	ENSP00000258787:p.His242Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	44978244	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	37	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	G	8.187	0.795222	0.16327	.	.	ENSG00000136286	ENST00000258787	D	0.87179	-2.22	2.8	2.8	0.32819	Myosin head, motor domain (2);	0.818686	0.10273	N	0.694573	T	0.76877	0.4049	L	0.29908	0.895	0.09310	N	1	B;B	0.24533	0.105;0.002	B;B	0.23150	0.044;0.003	T	0.61098	-0.7131	10	0.13108	T	0.6	.	7.1836	0.25786	0.0:0.0:0.7341:0.2658	.	242;242	B0I1T2-4;B0I1T2	.;MYO1G_HUMAN	Y	242	ENSP00000258787:H242Y	ENSP00000258787:H242Y	H	-	1	0	MYO1G	44978244	0.011000	0.17503	0.003000	0.11579	0.056000	0.15407	0.628000	0.24522	1.857000	0.53885	0.561000	0.74099	CAC		MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		
ZPBP	11055	hgsc.bcm.edu	37	7	50097724	50097724	+	Silent	SNP	A	A	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:50097724A>C	ENST00000046087.2	-	4	417	c.348T>G	c.(346-348)acT>acG	p.T116T	ZPBP_ENST00000419417.1_Silent_p.T115T|ZPBP_ENST00000491129.1_5'Flank	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	116					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					TTATTTGTGCAGTGCGGTTTT	0.353																																																	0			7											102.0	103.0	103.0					7																	50097724		2203	4300	6503	50068270	SO:0001819	synonymous_variant	11055			D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.348T>G	7.37:g.50097724A>C		Somatic		Capture	Illumina HiSeq	Phase_I	50068270	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Silent	SNP	ENST00000046087.2	37	CCDS5509.1																																																																																				ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009	
ACHE	43	hgsc.bcm.edu	37	7	100490108	100490108	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:100490108G>A	ENST00000412389.1	-	2	1555	c.1400C>T	c.(1399-1401)aCg>aTg	p.T467M	ACHE_ENST00000428317.1_Missense_Mutation_p.T467M|ACHE_ENST00000302913.4_Missense_Mutation_p.T467M|ACHE_ENST00000411582.1_Missense_Mutation_p.T467M|ACHE_ENST00000419336.2_Missense_Mutation_p.T379M|ACHE_ENST00000241069.5_Missense_Mutation_p.T467M|UFSP1_ENST00000388761.2_5'Flank			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	467					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	CCAGGAGAGCGTGGAAGCACG	0.652																																																	0			7											47.0	48.0	47.0					7																	100490108		2203	4300	6503	100328044	SO:0001583	missense	43				CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"""Blood group antigens"""	108	protein-coding gene	gene with protein product	"""Yt blood group"""	100740	"""acetylcholinesterase (YT blood group)"", ""acetylcholinesterase (Yt blood group)"", ""acetylcholinesterase"""	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1400C>T	7.37:g.100490108G>A	ENSP00000394976:p.Thr467Met	Somatic		Capture	Illumina HiSeq	Phase_I	100328044	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Missense_Mutation	SNP	ENST00000412389.1	37	CCDS5709.1	.	.	.	.	.	.	.	.	.	.	G	8.651	0.898262	0.17686	.	.	ENSG00000087085	ENST00000419336;ENST00000241069;ENST00000428317;ENST00000302913;ENST00000412389;ENST00000411582;ENST00000422451	T;T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29;-0.29	3.92	3.92	0.45320	Carboxylesterase, type B (1);	0.189628	0.42964	D	0.000636	T	0.67748	0.2926	L	0.31578	0.945	0.09310	N	1	D;D;D	0.89917	0.981;1.0;0.999	P;D;P	0.65773	0.665;0.938;0.873	T	0.57728	-0.7761	10	0.56958	D	0.05	.	9.095	0.36634	0.0:0.0:0.7812:0.2188	.	379;467;467	P22303-3;P22303-2;P22303	.;.;ACES_HUMAN	M	379;467;467;467;467;467;467	ENSP00000403474:T379M;ENSP00000241069:T467M;ENSP00000414858:T467M;ENSP00000303211:T467M;ENSP00000394976:T467M;ENSP00000404865:T467M	ENSP00000241069:T467M	T	-	2	0	ACHE	100328044	0.987000	0.35691	0.826000	0.32828	0.404000	0.30871	2.636000	0.46545	2.202000	0.70862	0.491000	0.48974	ACG		ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831	
CPED1	79974	hgsc.bcm.edu	37	7	120768470	120768470	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:120768470T>C	ENST00000310396.5	+	11	1804	c.1337T>C	c.(1336-1338)cTg>cCg	p.L446P	CPED1_ENST00000450913.2_Missense_Mutation_p.L446P|CPED1_ENST00000423795.1_Missense_Mutation_p.L226P	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	446						endoplasmic reticulum (GO:0005783)											AATCAGTGTCTGTCCTTAGAA	0.348																																																	0			7											90.0	91.0	91.0					7																	120768470		2203	4300	6503	120555706	SO:0001583	missense	79974				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.1337T>C	7.37:g.120768470T>C	ENSP00000309772:p.Leu446Pro	Somatic		Capture	Illumina HiSeq	Phase_I	120555706	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.565339	0.65651	.	.	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000423795;ENST00000443817	T;T;T;T;T	0.66099	1.11;-0.19;0.78;0.9;0.41	5.74	5.74	0.90152	.	0.268462	0.30850	N	0.008741	T	0.77605	0.4155	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.994;0.953	T	0.80165	-0.1496	10	0.87932	D	0	.	13.4072	0.60919	0.0:0.0:0.0:1.0	.	226;446;446	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	P	446;446;446;226;226	ENSP00000309772:L446P;ENSP00000398082:L446P;ENSP00000406122:L446P;ENSP00000415573:L226P;ENSP00000391952:L226P	ENSP00000309772:L446P	L	+	2	0	C7orf58	120555706	0.994000	0.37717	0.883000	0.34634	0.681000	0.39784	4.637000	0.61346	2.191000	0.70037	0.477000	0.44152	CTG		CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
KCP	375616	hgsc.bcm.edu	37	7	128517344	128517344	+	RNA	SNP	C	C	T	rs149314913	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:128517344C>T	ENST00000476647.2	-	0	4682							Q6ZWJ8	KCP_HUMAN	kielin/chordin-like protein							extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)	4						CACGAAGCCACGCTCCAGGGG	0.662													C|||	3	0.000599042	0.0023	0.0	5008	,	,		18194	0.0		0.0	False		,,,				2504	0.0																0			7											13.0	17.0	16.0					7																	128517344		690	1589	2279	128304580			375616			AK122706		7q32.3	2009-11-06	2009-02-18	2009-02-18	ENSG00000135253	ENSG00000135253			17585	protein-coding gene	gene with protein product	"""kielin"""	609344	"""cysteine rich BMP regulator 2 (chordin-like)"""	CRIM2		15793581	Standard	NM_001135914		Approved	FLJ33365, NET67	uc011kor.2	Q6ZWJ8	OTTHUMG00000158363		7.37:g.128517344C>T		Somatic		Capture	Illumina HiSeq	Phase_I	128304580	Q8NBE0	Missense_Mutation	SNP	ENST00000476647.2	37																																																																																					KCP-006	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000403051.1	NM_199349	
STRIP2	57464	hgsc.bcm.edu	37	7	129091565	129091565	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:129091565G>A	ENST00000249344.2	+	4	426	c.386G>A	c.(385-387)cGg>cAg	p.R129Q	STRIP2_ENST00000435494.2_Missense_Mutation_p.R129Q	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	129					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											AAGGTGGCCCGGGCTGTTCTC	0.562																																																	0			7											56.0	58.0	57.0					7																	129091565		2203	4300	6503	128878801	SO:0001583	missense	57464			AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"""FAR11 factor arrest 11 homolog B (yeast)"""		"""family with sequence similarity 40, member B"""	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.386G>A	7.37:g.129091565G>A	ENSP00000249344:p.Arg129Gln	Somatic		Capture	Illumina HiSeq	Phase_I	128878801	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	G	32	5.106905	0.94292	.	.	ENSG00000128578	ENST00000249344;ENST00000435494	T;T	0.55760	0.51;0.5	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	T	0.75744	0.3891	M	0.89287	3.02	0.80722	D	1	D;P	0.71674	0.998;0.938	D;P	0.76575	0.988;0.511	T	0.79734	-0.1679	10	0.48119	T	0.1	-15.4226	15.256	0.73585	0.0:0.0:1.0:0.0	.	129;129	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	Q	129	ENSP00000249344:R129Q;ENSP00000392393:R129Q	ENSP00000249344:R129Q	R	+	2	0	FAM40B	128878801	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.885000	0.92439	2.262000	0.75019	0.650000	0.86243	CGG		STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336	
SMARCD3	6604	hgsc.bcm.edu	37	7	150938678	150938678	+	Missense_Mutation	SNP	C	C	T	rs139896646		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr7:150938678C>T	ENST00000262188.8	-	8	1249	c.839G>A	c.(838-840)cGc>cAc	p.R280H	SMARCD3_ENST00000356800.2_Missense_Mutation_p.R267H|SMARCD3_ENST00000392811.2_Missense_Mutation_p.R267H|SMARCD3_ENST00000477169.1_5'Flank|RP4-548D19.3_ENST00000607902.1_RNA	NM_001003801.1	NP_001003801.1	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	280	SWIB.				cardiac right ventricle formation (GO:0003219)|cellular lipid metabolic process (GO:0044255)|chromatin remodeling (GO:0006338)|muscle cell differentiation (GO:0042692)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein binding (GO:0043393)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|secondary heart field specification (GO:0003139)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|receptor binding (GO:0005102)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(2)	15			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AATGGCTGAGCGGCTCTGTGT	0.562																																																	0			7						C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	37.0	33.0	35.0		839,800,800	5.5	1.0	7	dbSNP_134	35	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	SMARCD3	NM_001003801.1,NM_001003802.1,NM_003078.3	29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	280/484,267/471,267/471	150938678	1,13005	2203	4300	6503	150569611	SO:0001583	missense	6604			U66619	CCDS5924.1, CCDS34780.1	7q35-q36	2008-07-18			ENSG00000082014	ENSG00000082014			11108	protein-coding gene	gene with protein product	"""mammalian chromatin remodeling complex BRG1-associated factor 60C"", ""Swp73-like protein"", ""SWI/SNF complex 60 kDa subunit C"", ""60kDa BRG-1/Brm associated factor subunit c"""	601737				8804307, 9693044	Standard	NM_001003801		Approved	BAF60C, Rsc6p, CRACD3	uc003wjs.3	Q6STE5	OTTHUMG00000157431	ENST00000262188.8:c.839G>A	7.37:g.150938678C>T	ENSP00000262188:p.Arg280His	Somatic		Capture	Illumina HiSeq	Phase_I	150569611	D3DX10|Q2YD86|Q75MJ2|Q75MR8|Q92926|Q9BUH1	Missense_Mutation	SNP	ENST00000262188.8	37	CCDS34780.1	.	.	.	.	.	.	.	.	.	.	C	30	5.055819	0.93793	0.0	1.16E-4	ENSG00000082014	ENST00000262188;ENST00000392811;ENST00000356800;ENST00000347683	T;T;T	0.55588	0.51;0.52;0.52	5.48	5.48	0.80851	SWIB domain (1);SWIB/MDM2 domain (2);	0.000000	0.85682	D	0.000000	T	0.80082	0.4558	M	0.93594	3.435	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.989;0.993	D	0.85275	0.1058	10	0.87932	D	0	-12.7736	16.8808	0.86062	0.0:1.0:0.0:0.0	.	280;267;280	B7Z4U8;Q6STE5-2;Q6STE5	.;.;SMRD3_HUMAN	H	280;267;267;232	ENSP00000262188:R280H;ENSP00000376558:R267H;ENSP00000349254:R267H	ENSP00000262188:R280H	R	-	2	0	SMARCD3	150569611	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.572000	0.86782	0.655000	0.94253	CGC		SMARCD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348825.1	NM_001003801	
PTPRA	5786	hgsc.bcm.edu	37	20	3002012	3002012	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:3002012G>A	ENST00000216877.6	+	13	1472	c.1072G>A	c.(1072-1074)Gtg>Atg	p.V358M	PTPRA_ENST00000380393.3_Missense_Mutation_p.V367M|PTPRA_ENST00000358719.4_Missense_Mutation_p.V223M|PTPRA_ENST00000425918.2_Missense_Mutation_p.V378M|PTPRA_ENST00000399903.2_Missense_Mutation_p.V367M|PTPRA_ENST00000356147.3_Missense_Mutation_p.V358M|PTPRA_ENST00000318266.5_Missense_Mutation_p.V358M	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	367	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GAATATTCGGGTGTCTGTAGA	0.507																																																	0			20											204.0	164.0	177.0					20																	3002012		2203	4300	6503	2950012	SO:0001583	missense	5786				CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.1072G>A	20.37:g.3002012G>A	ENSP00000216877:p.Val358Met	Somatic		Capture	Illumina HiSeq	Phase_I	2950012	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Missense_Mutation	SNP	ENST00000216877.6	37	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.014943	0.93404	.	.	ENSG00000132670	ENST00000380393;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000425918;ENST00000318266;ENST00000356147	T;T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96;1.96	4.68	4.68	0.58851	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.146530	0.45126	U	0.000384	T	0.64450	0.2599	H	0.97983	4.12	0.80722	D	1	D;D;D	0.89917	1.0;0.995;1.0	D;D;D	0.83275	0.996;0.917;0.987	T	0.79801	-0.1650	10	0.87932	D	0	.	18.1483	0.89665	0.0:0.0:1.0:0.0	.	378;367;358	B7Z2A4;P18433;P18433-4	.;PTPRA_HUMAN;.	M	367;358;367;223;378;358;358	ENSP00000369756:V367M;ENSP00000216877:V358M;ENSP00000382787:V367M;ENSP00000351559:V223M;ENSP00000393553:V378M;ENSP00000314568:V358M;ENSP00000348468:V358M	ENSP00000216877:V358M	V	+	1	0	PTPRA	2950012	1.000000	0.71417	0.998000	0.56505	0.860000	0.49131	9.625000	0.98406	2.584000	0.87258	0.563000	0.77884	GTG		PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3		
HCK	3055	hgsc.bcm.edu	37	20	30681683	30681683	+	Silent	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:30681683C>T	ENST00000520553.1	+	11	1293	c.1047C>T	c.(1045-1047)gcC>gcT	p.A349A	HCK_ENST00000538448.1_Silent_p.A349A|HCK_ENST00000375852.2_Silent_p.A370A|HCK_ENST00000534862.1_Silent_p.A350A|HCK_ENST00000375862.2_Silent_p.A369A|HCK_ENST00000518730.1_Silent_p.A348A	NM_001172129.1|NM_001172130.1|NM_001172131.1|NM_002110.3	NP_001165600.1|NP_001165601.1|NP_001165602.1|NP_002101.2	P08631	HCK_HUMAN	HCK proto-oncogene, Src family tyrosine kinase	370	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|innate immune response-activating signal transduction (GO:0002758)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte degranulation (GO:0043299)|leukocyte migration involved in immune response (GO:0002522)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|regulation of inflammatory response (GO:0050727)|regulation of phagocytosis (GO:0050764)|regulation of podosome assembly (GO:0071801)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|respiratory burst after phagocytosis (GO:0045728)|viral process (GO:0016032)	caveola (GO:0005901)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(4)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)		Bosutinib(DB06616)	AAGGCATGGCCTTCATCGAGC	0.562																																																	0			20											153.0	104.0	120.0					20																	30681683		2203	4300	6503	30145344	SO:0001819	synonymous_variant	3055			AK026432	CCDS33460.1, CCDS54453.1, CCDS54455.1, CCDS54456.1	20q11-q12	2014-06-25	2014-06-25		ENSG00000101336	ENSG00000101336		"""SH2 domain containing"""	4840	protein-coding gene	gene with protein product		142370	"""hemopoietic cell kinase"""			3496523	Standard	NM_002110		Approved	JTK9	uc002wxh.3	P08631	OTTHUMG00000032204	ENST00000520553.1:c.1047C>T	20.37:g.30681683C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30145344	A8K1I1|B4DQB6|E1P5M2|Q29RX1|Q2VPE2|Q504R5|Q5T7K1|Q5T7K2|Q96CC0|Q9H5Y5|Q9NUA4|Q9UMJ5	Silent	SNP	ENST00000520553.1	37	CCDS54455.1																																																																																				HCK-006	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000375751.1		
ASXL1	171023	hgsc.bcm.edu	37	20	31022871	31022871	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:31022871A>G	ENST00000375687.4	+	13	2780	c.2356A>G	c.(2356-2358)Aga>Gga	p.R786G	ASXL1_ENST00000306058.5_Missense_Mutation_p.R781G	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	786					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.H782fs*8(1)|p.R786G(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						TCCGGATGTTAGAACTGAATG	0.552			"""F, N, Mis"""		"""MDS, CMML"""																																			Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	2	Substitution - Missense(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(2)	20											78.0	70.0	73.0					20																	31022871		2203	4300	6503	30486532	SO:0001583	missense	171023			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.2356A>G	20.37:g.31022871A>G	ENSP00000364839:p.Arg786Gly	Somatic		Capture	Illumina HiSeq	Phase_I	30486532	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.232443	0.58777	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.26373	1.74;1.74	5.17	4.05	0.47172	.	0.328852	0.37219	N	0.002188	T	0.44498	0.1296	M	0.72118	2.19	0.37189	D	0.903857	D;D	0.69078	0.997;0.991	P;P	0.61874	0.895;0.761	T	0.52503	-0.8567	10	0.49607	T	0.09	-14.8326	11.2115	0.48802	0.8466:0.1534:0.0:0.0	.	781;786	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	G	786;786;786;707;781	ENSP00000364839:R786G;ENSP00000305119:R781G	ENSP00000305119:R781G	R	+	1	2	ASXL1	30486532	0.991000	0.36638	0.845000	0.33349	0.881000	0.50899	2.875000	0.48491	1.064000	0.40671	0.533000	0.62120	AGA		ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338	
GSS	2937	hgsc.bcm.edu	37	20	33524779	33524779	+	Missense_Mutation	SNP	T	T	C	rs28938472		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:33524779T>C	ENST00000216951.2	-	7	754	c.656A>G	c.(655-657)gAc>gGc	p.D219G	GSS_ENST00000451957.2_Missense_Mutation_p.D108G|GSS_ENST00000541098.1_Missense_Mutation_p.D91G	NM_000178.2	NP_000169.1	P48637	GSHB_HUMAN	glutathione synthetase	219			D -> A (in GSS deficiency).|D -> G (in GSS deficiency; dbSNP:rs28938472). {ECO:0000269|PubMed:8896573}.		aging (GO:0007568)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|nervous system development (GO:0007399)|response to amino acid (GO:0043200)|response to cadmium ion (GO:0046686)|response to nutrient levels (GO:0031667)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|glutathione binding (GO:0043295)|glutathione synthase activity (GO:0004363)|glycine binding (GO:0016594)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(18;0.035)		Acetylcysteine(DB06151)|Glutathione(DB00143)|Glycine(DB00145)|L-Cysteine(DB00151)	GGCACGCTGGTCAAATATGTT	0.498																																																	0			20	GRCh37	CM960787|CM970698	GSS	M	rs28938472						158.0	140.0	146.0					20																	33524779		2203	4300	6503	32988440	SO:0001583	missense	5621				CCDS13245.1	20q11.2	1996-06-18			ENSG00000100983	ENSG00000100983	6.3.2.3		4624	protein-coding gene	gene with protein product		601002				8825653	Standard	NM_000178		Approved		uc002xbg.3	P48637	OTTHUMG00000032315	ENST00000216951.2:c.656A>G	20.37:g.33524779T>C	ENSP00000216951:p.Asp219Gly	Somatic		Capture	Illumina HiSeq	Phase_I	32988440	B2R697|B6F210|E1P5P9|Q4TTD9	Missense_Mutation	SNP	ENST00000216951.2	37	CCDS13245.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.994984	0.93167	.	.	ENSG00000100983	ENST00000216951;ENST00000541098;ENST00000451957	D;D;D	0.94723	-3.5;-3.5;-3.5	5.9	5.9	0.94986	PreATP-grasp-like fold (1);Glutathione synthase, substrate-binding, eukaryotic (2);	0.168662	0.64402	D	0.000006	D	0.97923	0.9317	M	0.93375	3.41	0.80722	A	1	D;D	0.76494	0.999;0.998	D;D	0.73380	0.98;0.975	D	0.98894	1.0774	9	0.72032	D	0.01	-25.3403	15.993	0.80220	0.0:0.0:0.0:1.0	rs28938472	108;219	B6F210;P48637	.;GSHB_HUMAN	G	219;91;108	ENSP00000216951:D219G;ENSP00000439744:D91G;ENSP00000407517:D108G	ENSP00000216951:D219G	D	-	2	0	GSS	32988440	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.309000	0.78937	2.248000	0.74166	0.459000	0.35465	GAC		GSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078821.2		
ELMO2	63916	hgsc.bcm.edu	37	20	44999993	44999993	+	Missense_Mutation	SNP	T	T	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:44999993T>A	ENST00000290246.6	-	19	1993	c.1799A>T	c.(1798-1800)aAa>aTa	p.K600I	ELMO2_ENST00000352077.2_Missense_Mutation_p.K598I|ELMO2_ENST00000454865.2_Missense_Mutation_p.K332I|ELMO2_ENST00000396391.1_Missense_Mutation_p.K600I|ELMO2_ENST00000372176.1_Missense_Mutation_p.K512I|ELMO2_ENST00000445496.2_Missense_Mutation_p.K417I|ELMO2_ENST00000439931.2_Missense_Mutation_p.K612I	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	600	PH.				apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				GAACCTACTTTTCTCCTGCAG	0.488																																																	0			20											101.0	99.0	100.0					20																	44999993		2203	4300	6503	44433400	SO:0001583	missense	63916			AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"""Engulfment and cell motility proteins"""	17233	protein-coding gene	gene with protein product		606421	"""engulfment and cell motility 2 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.1799A>T	20.37:g.44999993T>A	ENSP00000290246:p.Lys600Ile	Somatic		Capture	Illumina HiSeq	Phase_I	44433400	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Missense_Mutation	SNP	ENST00000290246.6	37	CCDS13398.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.673718	0.67928	.	.	ENSG00000062598	ENST00000290246;ENST00000372176;ENST00000452857;ENST00000396391;ENST00000439931;ENST00000445496;ENST00000454865;ENST00000352077	T;T;T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78	4.45	4.45	0.53987	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.68961	0.3058	M	0.85041	2.73	0.80722	D	1	P;D;D;B	0.62365	0.85;0.991;0.991;0.447	P;D;P;B	0.64595	0.666;0.927;0.903;0.365	T	0.75505	-0.3294	10	0.87932	D	0	-16.302	13.3564	0.60631	0.0:0.0:0.0:1.0	.	612;332;417;600	B4DRL5;B4DZ20;B7Z1S8;Q96JJ3	.;.;.;ELMO2_HUMAN	I	600;512;167;600;612;417;332;598	ENSP00000290246:K600I;ENSP00000361249:K512I;ENSP00000414329:K167I;ENSP00000379673:K600I;ENSP00000396519:K612I;ENSP00000409920:K417I;ENSP00000415641:K332I;ENSP00000326172:K598I	ENSP00000290246:K600I	K	-	2	0	ELMO2	44433400	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.825000	0.86693	2.000000	0.58554	0.533000	0.62120	AAA		ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086	
ELMO2	63916	hgsc.bcm.edu	37	20	45004386	45004386	+	Missense_Mutation	SNP	T	T	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr20:45004386T>G	ENST00000290246.6	-	12	1045	c.851A>C	c.(850-852)cAt>cCt	p.H284P	ELMO2_ENST00000352077.2_Missense_Mutation_p.H282P|ELMO2_ENST00000454865.2_Missense_Mutation_p.H16P|ELMO2_ENST00000396391.1_Missense_Mutation_p.H284P|ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000372176.1_Missense_Mutation_p.H196P|ELMO2_ENST00000445496.2_Missense_Mutation_p.H101P|ELMO2_ENST00000439931.2_Missense_Mutation_p.H296P	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	284					apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)	p.H284L(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				ATATAGCTGATGGGCCATCTC	0.502																																																	1	Substitution - Missense(1)	ovary(1)	20											128.0	113.0	118.0					20																	45004386		2203	4300	6503	44437793	SO:0001583	missense	63916			AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"""Engulfment and cell motility proteins"""	17233	protein-coding gene	gene with protein product		606421	"""engulfment and cell motility 2 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.851A>C	20.37:g.45004386T>G	ENSP00000290246:p.His284Pro	Somatic		Capture	Illumina HiSeq	Phase_I	44437793	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Missense_Mutation	SNP	ENST00000290246.6	37	CCDS13398.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.575878	0.86645	.	.	ENSG00000062598	ENST00000290246;ENST00000372176;ENST00000396391;ENST00000439931;ENST00000445496;ENST00000454865;ENST00000352077;ENST00000425546;ENST00000450812	T;T;T;T;T;T;T;T;T	0.38560	2.19;1.93;2.19;1.65;1.56;1.27;2.19;1.13;1.16	4.99	4.99	0.66335	Terpene synthase-like (1);	0.000000	0.85682	D	0.000000	T	0.66790	0.2825	M	0.82193	2.58	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.986;0.999;0.993;0.987;0.986	T	0.72730	-0.4205	10	0.87932	D	0	-17.0858	14.0317	0.64619	0.0:0.0:0.0:1.0	.	296;16;284;101;284	B4DRL5;B4DZ20;E9PBG2;B7Z1S8;Q96JJ3	.;.;.;.;ELMO2_HUMAN	P	284;196;284;296;101;16;282;72;284	ENSP00000290246:H284P;ENSP00000361249:H196P;ENSP00000379673:H284P;ENSP00000396519:H296P;ENSP00000409920:H101P;ENSP00000415641:H16P;ENSP00000326172:H282P;ENSP00000388962:H72P;ENSP00000416181:H284P	ENSP00000290246:H284P	H	-	2	0	ELMO2	44437793	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.868000	0.87116	2.096000	0.63516	0.454000	0.30748	CAT		ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086	
PPM1F	9647	hgsc.bcm.edu	37	22	22277784	22277784	+	Missense_Mutation	SNP	G	G	A	rs144940091		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr22:22277784G>A	ENST00000263212.5	-	8	1151	c.1046C>T	c.(1045-1047)aCg>aTg	p.T349M	PPM1F_ENST00000407142.1_Missense_Mutation_p.T181M|PPM1F_ENST00000538191.1_Missense_Mutation_p.T245M	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	349					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		CTCGGAGCCCGTCAGCGCCCG	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		16544	0.001		0.0	False		,,,				2504	0.0																0			22											45.0	49.0	48.0					22																	22277784		2203	4300	6503	20607784	SO:0001583	missense	9647			D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19388	protein-coding gene	gene with protein product	"""partner of PIX 2"", ""Ca(2+)/calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1F (PP2C domain containing)"""			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.1046C>T	22.37:g.22277784G>A	ENSP00000263212:p.Thr349Met	Somatic		Capture	Illumina HiSeq	Phase_I	20607784	A8K6G3|B7Z2C3|Q96PM2	Missense_Mutation	SNP	ENST00000263212.5	37	CCDS13796.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	14.49	2.550561	0.45383	.	.	ENSG00000100034	ENST00000263212;ENST00000407142;ENST00000406981;ENST00000538191	T;T;T	0.11277	2.79;2.79;2.79	5.23	4.17	0.49024	Protein phosphatase 2C-like (5);	0.847094	0.10581	N	0.657927	T	0.32645	0.0836	M	0.71036	2.16	0.09310	N	1	D;D	0.89917	1.0;0.998	D;D	0.70716	0.97;0.967	T	0.06075	-1.0847	10	0.52906	T	0.07	-13.385	14.5396	0.67984	0.0:0.2704:0.7296:0.0	.	245;349	B7Z2C3;P49593	.;PPM1F_HUMAN	M	349;181;181;245	ENSP00000263212:T349M;ENSP00000384930:T181M;ENSP00000439915:T245M	ENSP00000263212:T349M	T	-	2	0	PPM1F	20607784	0.002000	0.14202	0.741000	0.31004	0.264000	0.26372	0.610000	0.24253	2.721000	0.93114	0.655000	0.94253	ACG		PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634	
EP300	2033	hgsc.bcm.edu	37	22	41569717	41569717	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr22:41569717A>G	ENST00000263253.7	+	29	5927	c.4708A>G	c.(4708-4710)Aaa>Gaa	p.K1570E	RP1-85F18.5_ENST00000420537.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1570	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CAACAAGAAGAAACCCGGGAT	0.448			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																															Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	0			22											152.0	160.0	157.0					22																	41569717		2203	4300	6503	39899663	SO:0001583	missense	2033	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.4708A>G	22.37:g.41569717A>G	ENSP00000263253:p.Lys1570Glu	Somatic		Capture	Illumina HiSeq	Phase_I	39899663	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.356564	0.82243	.	.	ENSG00000100393	ENST00000263253	D	0.92911	-3.13	5.52	5.52	0.82312	.	0.000000	0.48767	D	0.000171	D	0.95868	0.8655	M	0.79475	2.455	0.47862	D	0.999533	D	0.76494	0.999	D	0.83275	0.996	D	0.96248	0.9181	10	0.66056	D	0.02	-13.6072	15.643	0.77020	1.0:0.0:0.0:0.0	.	1570	Q09472	EP300_HUMAN	E	1570	ENSP00000263253:K1570E	ENSP00000263253:K1570E	K	+	1	0	EP300	39899663	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.237000	0.95368	2.094000	0.63399	0.533000	0.62120	AAA		EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
SMC1B	27127	hgsc.bcm.edu	37	22	45789613	45789613	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr22:45789613A>G	ENST00000357450.4	-	9	1445	c.1446T>C	c.(1444-1446)agT>agC	p.S482S	SMC1B_ENST00000404354.3_Silent_p.S482S	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	482					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TCTGCAATTCACTTCTAATAA	0.373																																																	0			22											121.0	108.0	112.0					22																	45789613		1838	4085	5923	44168277	SO:0001819	synonymous_variant	27127			AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.1446T>C	22.37:g.45789613A>G		Somatic		Capture	Illumina HiSeq	Phase_I	44168277	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																				SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50664611	50664611	+	Silent	SNP	C	C	T	rs142499686	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr22:50664611C>T	ENST00000248846.5	-	9	1805	c.1701G>A	c.(1699-1701)ttG>ttA	p.L567L	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_Silent_p.L567L			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	567			L -> S (in dbSNP:rs4838865). {ECO:0000269|PubMed:11694571}.		G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GTGTCCAGTACAACTTATCTA	0.577													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		15444	0.0		0.001	False		,,,				2504	0.0																0			22						C		3,4403	2.1+/-5.4	0,3,2200	213.0	198.0	203.0		1701	-8.5	0.0	22	dbSNP_134	203	13,8587	6.4+/-24.3	0,13,4287	no	coding-synonymous	TUBGCP6	NM_020461.3		0,16,6487	TT,TC,CC		0.1512,0.0681,0.123		567/1820	50664611	16,12990	2203	4300	6503	49006738	SO:0001819	synonymous_variant	85378			AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.1701G>A	22.37:g.50664611C>T		Somatic		Capture	Illumina HiSeq	Phase_I	49006738	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																				TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
SLC39A2	29986	hgsc.bcm.edu	37	14	21469413	21469413	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:21469413A>G	ENST00000298681.4	+	4	762	c.605A>G	c.(604-606)cAt>cGt	p.H202R	SLC39A2_ENST00000554422.1_3'UTR|RP11-84C10.4_ENST00000557335.1_RNA	NM_014579.3	NP_055394.2	Q9NP94	S39A2_HUMAN	solute carrier family 39 (zinc transporter), member 2	202					transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	14	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0187)		GTCCTGGCTCATAAGGGGCTT	0.527																																																	0			14											140.0	117.0	125.0					14																	21469413		2203	4300	6503	20539253	SO:0001583	missense	29986			AF186081	CCDS9563.1, CCDS58303.1	14q11.1	2013-05-22			ENSG00000165794	ENSG00000165794		"""Solute carriers"""	17127	protein-coding gene	gene with protein product		612166				10681536, 7751801	Standard	NM_014579		Approved	ZIP2	uc001vyr.3	Q9NP94	OTTHUMG00000029616	ENST00000298681.4:c.605A>G	14.37:g.21469413A>G	ENSP00000298681:p.His202Arg	Somatic		Capture	Illumina HiSeq	Phase_I	20539253	B2RC76|G3V5X2|Q4QQJ1|Q4V9S4|Q96JT6|Q9UD20	Missense_Mutation	SNP	ENST00000298681.4	37	CCDS9563.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.121291	0.77436	.	.	ENSG00000165794	ENST00000298681	T	0.74421	-0.84	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.88987	0.6587	M	0.92970	3.365	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91420	0.5158	10	0.87932	D	0	-9.9851	13.9183	0.63914	1.0:0.0:0.0:0.0	.	202	Q9NP94	S39A2_HUMAN	R	202	ENSP00000298681:H202R	ENSP00000298681:H202R	H	+	2	0	SLC39A2	20539253	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	8.483000	0.90442	2.170000	0.68504	0.533000	0.62120	CAT		SLC39A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073829.2	NM_014579	
CHD8	57680	hgsc.bcm.edu	37	14	21875078	21875078	+	Missense_Mutation	SNP	A	A	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:21875078A>T	ENST00000557364.1	-	14	3107	c.2844T>A	c.(2842-2844)gaT>gaA	p.D948E	CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Missense_Mutation_p.D669E|CHD8_ENST00000399982.2_Missense_Mutation_p.D948E			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	948	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		GATGGGCTTCATCAATGATAA	0.453																																																	0			14											96.0	87.0	90.0					14																	21875078		1968	4155	6123	20944918	SO:0001583	missense	57680			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.2844T>A	14.37:g.21875078A>T	ENSP00000451601:p.Asp948Glu	Somatic		Capture	Illumina HiSeq	Phase_I	20944918	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	37	CCDS53885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.4|22.4	4.279095|4.279095	0.80692|0.80692	.|.	.|.	ENSG00000100888|ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364|ENST00000555935	D;D;D|.	0.99857|.	-7.22;-7.22;-7.22|.	5.41|5.41	5.41|5.41	0.78517|0.78517	DEAD-like helicase (2);SNF2-related (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.89005|.	0.6592|.	H|H	0.99659|0.99659	4.685|4.685	0.58432|0.58432	D|D	0.999992|0.999992	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|.	0.91663|.	0.5344|.	10|.	0.87932|.	D|.	0|.	-23.4087|-23.4087	9.5|9.5	0.39011|0.39011	0.9185:0.0:0.0815:0.0|0.9185:0.0:0.0815:0.0	.|.	948;669|.	Q9HCK8;Q9HCK8-2|.	CHD8_HUMAN;.|.	E|R	669;948;668;948|174	ENSP00000406288:D669E;ENSP00000382863:D948E;ENSP00000451601:D948E|.	ENSP00000262707:D668E|.	D|X	-|-	3|1	2|0	CHD8|CHD8	20944918|20944918	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	0.807000|0.807000	0.27140|0.27140	2.272000|2.272000	0.75746|0.75746	0.459000|0.459000	0.35465|0.35465	GAT|TGA		CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
HECTD1	25831	hgsc.bcm.edu	37	14	31578715	31578715	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:31578715A>G	ENST00000399332.1	-	36	6856	c.6368T>C	c.(6367-6369)tTt>tCt	p.F2123S	HECTD1_ENST00000553700.1_Missense_Mutation_p.F2123S	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2123					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)	p.F2123Y(1)		breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		ACCAACTCGAAACTCTCCAGG	0.473																																																	1	Substitution - Missense(1)	ovary(1)	14											107.0	109.0	108.0					14																	31578715		2051	4207	6258	30648466	SO:0001583	missense	25831			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.6368T>C	14.37:g.31578715A>G	ENSP00000382269:p.Phe2123Ser	Somatic		Capture	Illumina HiSeq	Phase_I	30648466	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	29.3|29.3	4.996740|4.996740	0.93167|0.93167	.|.	.|.	ENSG00000092148|ENSG00000092148	ENST00000554882|ENST00000553700;ENST00000261312;ENST00000399332	T|T;T	0.11930|0.14516	2.73|2.5;2.5	5.73|5.73	5.73|5.73	0.89815|0.89815	.|HECT (1);	0.000000|0.000000	0.85682|0.85682	U|U	0.000000|0.000000	T|T	0.31420|0.31420	0.0796|0.0796	L|L	0.58925|0.58925	1.835|1.835	0.80722|0.80722	D|D	1|1	.|D	.|0.54601	.|0.967	.|D	.|0.63033	.|0.91	T|T	0.01001|0.01001	-1.1485|-1.1485	7|10	.|0.31617	.|T	.|0.26	-13.3026|-13.3026	16.0096|16.0096	0.80391|0.80391	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|2123	.|Q9ULT8	.|HECD1_HUMAN	L|S	489|2123;2125;2123	ENSP00000451260:F489L|ENSP00000450697:F2123S;ENSP00000382269:F2123S	.|ENSP00000261312:F2125S	F|F	-|-	1|2	0|0	HECTD1|HECTD1	30648466|30648466	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	8.678000|8.678000	0.91211|0.91211	2.184000|2.184000	0.69523|0.69523	0.477000|0.477000	0.44152|0.44152	TTC|TTT		HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
RALGAPA1	253959	hgsc.bcm.edu	37	14	36039877	36039877	+	Missense_Mutation	SNP	G	G	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:36039877G>T	ENST00000389698.3	-	38	6314	c.5924C>A	c.(5923-5925)aCa>aAa	p.T1975K	RALGAPA1_ENST00000307138.6_Missense_Mutation_p.T1975K|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.T1988K|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.T2022K	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1975	Minimal domain that binds to TCF3/E12. {ECO:0000250}.|Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.T1975R(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						ATTTATAGCTGTTGCTCTAAC	0.363																																																	1	Substitution - Missense(1)	breast(1)	14											55.0	51.0	52.0					14																	36039877		2203	4297	6500	35109628	SO:0001583	missense	0			AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.5924C>A	14.37:g.36039877G>T	ENSP00000374348:p.Thr1975Lys	Somatic		Capture	Illumina HiSeq	Phase_I	35109628	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.308097|5.308097	0.95629|0.95629	.|.	.|.	ENSG00000174373|ENSG00000174373	ENST00000554573|ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000554259;ENST00000382366;ENST00000553892	.|D;D;D;D;D;D	.|0.92699	.|-3.09;-3.09;-3.09;-3.09;-3.09;-3.09	5.96|5.96	5.96|5.96	0.96718|0.96718	.|Rap/ran-GAP (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.96037|0.96037	0.8709|0.8709	M|M	0.70903|0.70903	2.155|2.155	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|0.997;1.0;0.994;0.999	D|D	0.95744|0.95744	0.8786|0.8786	5|10	.|0.87932	.|D	.|0	-16.1049|-16.1049	20.4008|20.4008	0.98991|0.98991	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2022;1988;1975;1975	.|Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.|.;.;.;RGPA1_HUMAN	K|K	258|1975;1975;1975;2022;613;1988;2022	.|ENSP00000374348:T1975K;ENSP00000302647:T1975K;ENSP00000258840:T2022K;ENSP00000451133:T613K;ENSP00000371803:T1988K;ENSP00000451877:T2022K	.|ENSP00000258840:T2022K	Q|T	-|-	1|2	0|0	RALGAPA1|RALGAPA1	35109628|35109628	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.869000|9.869000	0.99810|0.99810	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	CAG|ACA		RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	
SMEK1	55671	hgsc.bcm.edu	37	14	91931635	91931635	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:91931635T>C	ENST00000554943.1	-	11	1904	c.1789A>G	c.(1789-1791)Atg>Gtg	p.M597V	SMEK1_ENST00000555462.1_Missense_Mutation_p.M358V|SMEK1_ENST00000337238.4_Missense_Mutation_p.M584V|SMEK1_ENST00000554684.1_Missense_Mutation_p.M584V|SMEK1_ENST00000555718.1_5'UTR|SMEK1_ENST00000428424.2_Missense_Mutation_p.M358V			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	597					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		GCAGAGTTCATCAGATTGTAG	0.299																																																	0			14											94.0	97.0	96.0					14																	91931635		2203	4300	6503	91001388	SO:0001583	missense	55671			AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"""KIAA2010"""	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.1789A>G	14.37:g.91931635T>C	ENSP00000450883:p.Met597Val	Somatic		Capture	Illumina HiSeq	Phase_I	91001388	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Missense_Mutation	SNP	ENST00000554943.1	37		.	.	.	.	.	.	.	.	.	.	T	11.41	1.629466	0.28978	.	.	ENSG00000100796	ENST00000554684;ENST00000337238;ENST00000428424;ENST00000554943;ENST00000555462;ENST00000554390	T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25	6.17	5.02	0.67125	Armadillo-type fold (1);	0.033652	0.85682	D	0.000000	T	0.25791	0.0628	N	0.19112	0.55	0.54753	D	0.999988	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.11329	0.006;0.0;0.001	T	0.02758	-1.1114	10	0.45353	T	0.12	-18.5462	12.8957	0.58098	0.1219:0.0:0.0:0.8781	.	358;597;584	Q6IN85-4;Q6IN85;Q6IN85-2	.;P4R3A_HUMAN;.	V	584;584;358;597;358;584	ENSP00000450864:M584V;ENSP00000337125:M584V;ENSP00000392704:M358V;ENSP00000450883:M597V;ENSP00000450891:M358V;ENSP00000452596:M584V	ENSP00000337125:M584V	M	-	1	0	SMEK1	91001388	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	3.307000	0.51888	1.129000	0.42072	-0.336000	0.08194	ATG		SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560	
SERPINA6	866	hgsc.bcm.edu	37	14	94780730	94780730	+	Missense_Mutation	SNP	G	G	A	rs199699199		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr14:94780730G>A	ENST00000341584.3	-	2	402	c.256C>T	c.(256-258)Cgg>Tgg	p.R86W		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	86					glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	AGCTGGGCCCGTGTGTGGCCA	0.557													G|||	1	0.000199681	0.0	0.0	5008	,	,		20254	0.0		0.0	False		,,,				2504	0.001																0			14						G	TRP/ARG	0,4406		0,0,2203	57.0	59.0	59.0		256	1.7	0.0	14		59	1,8599	1.2+/-3.3	0,1,4299	no	missense	SERPINA6	NM_001756.3	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	86/406	94780730	1,13005	2203	4300	6503	93850483	SO:0001583	missense	866			J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"""Serine (or cysteine) peptidase inhibitors"""	1540	protein-coding gene	gene with protein product	"""corticosteroid binding globulin"", ""transcortin"""	122500	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"""	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.256C>T	14.37:g.94780730G>A	ENSP00000342850:p.Arg86Trp	Somatic		Capture	Illumina HiSeq	Phase_I	93850483	A8K456|Q7Z2Q9	Missense_Mutation	SNP	ENST00000341584.3	37	CCDS9924.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.947664	0.34377	0.0	1.16E-4	ENSG00000170099	ENST00000341584;ENST00000557225	D;D	0.85258	-1.96;-1.96	4.7	1.68	0.24146	Serpin domain (3);	1.892330	0.02844	N	0.128250	D	0.85978	0.5823	M	0.84219	2.685	0.09310	N	1	B	0.32829	0.386	B	0.33799	0.17	T	0.65886	-0.6059	10	0.59425	D	0.04	.	4.2057	0.10488	0.0757:0.1416:0.4896:0.2931	.	86	P08185	CBG_HUMAN	W	86	ENSP00000342850:R86W;ENSP00000452018:R86W	ENSP00000342850:R86W	R	-	1	2	SERPINA6	93850483	0.235000	0.23794	0.000000	0.03702	0.166000	0.22503	2.993000	0.49425	0.153000	0.19213	-0.309000	0.09137	CGG		SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756	
BRD4	23476	hgsc.bcm.edu	37	19	15379766	15379766	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:15379766A>G	ENST00000263377.2	-	3	594	c.373T>C	c.(373-375)Tgt>Cgt	p.C125R	BRD4_ENST00000360016.5_Missense_Mutation_p.C125R|BRD4_ENST00000371835.4_Missense_Mutation_p.C125R	NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	125	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			TCCTGGATACATTCCTGAGCA	0.443			T	C15orf55	lethal midline carcinoma of young people																																			Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	0			19											170.0	153.0	159.0					19																	15379766		2203	4300	6503	15240766	SO:0001583	missense	23476			Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"""chromosome-associated protein"""	608749	"""bromodomain-containing 4"""			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.373T>C	19.37:g.15379766A>G	ENSP00000263377:p.Cys125Arg	Somatic		Capture	Illumina HiSeq	Phase_I	15240766	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	37	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314965	0.81358	.	.	ENSG00000141867	ENST00000263377;ENST00000371835;ENST00000360016	T;T;T	0.28895	1.59;1.59;1.59	5.25	5.25	0.73442	Bromodomain (6);Bromodomain, conserved site (1);	0.000000	0.64402	D	0.000003	T	0.61739	0.2371	M	0.89095	3.005	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.999	T	0.70142	-0.4953	10	0.87932	D	0	-6.8729	14.1422	0.65327	1.0:0.0:0.0:0.0	.	125;125;125	Q4G0X8;O60885-2;O60885	.;.;BRD4_HUMAN	R	125	ENSP00000263377:C125R;ENSP00000360901:C125R;ENSP00000353112:C125R	ENSP00000263377:C125R	C	-	1	0	BRD4	15240766	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.287000	0.95975	1.987000	0.57996	0.533000	0.62120	TGT		BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243	
ZNF91	7644	hgsc.bcm.edu	37	19	23545420	23545420	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:23545420G>A	ENST00000300619.7	-	4	566	c.361C>T	c.(361-363)Cag>Tag	p.Q121*	ZNF91_ENST00000397082.2_Nonsense_Mutation_p.Q89*|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	121					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.Q121K(1)					all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TTTCTTAACTGTAAATTCTCA	0.358																																																	1	Substitution - Missense(1)	ovary(1)	19											66.0	69.0	68.0					19																	23545420		2122	4266	6388	23337260	SO:0001587	stop_gained	7644			M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.361C>T	19.37:g.23545420G>A	ENSP00000300619:p.Gln121*	Somatic		Capture	Illumina HiSeq	Phase_I	23337260	A8K5E1|B7Z6G6	Nonsense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.496023	0.26774	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	.	.	.	0.987	-1.05	0.10036	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	3.3973	0.07311	0.0:0.0:0.5482:0.4518	.	.	.	.	X	121;89	.	ENSP00000300619:Q121X	Q	-	1	0	ZNF91	23337260	0.001000	0.12720	0.007000	0.13788	0.597000	0.36814	-0.381000	0.07417	0.436000	0.26393	0.174000	0.16983	CAG		ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
HPN	3249	hgsc.bcm.edu	37	19	35556185	35556185	+	Silent	SNP	C	C	T	rs199890888	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:35556185C>T	ENST00000262626.2	+	10	1668	c.843C>T	c.(841-843)gcC>gcT	p.A281A	HPN_ENST00000597419.1_Silent_p.A123A|HPN-AS1_ENST00000392227.2_RNA|HPN_ENST00000392226.1_Silent_p.A281A	NM_182983.2	NP_892028.1	P05981	HEPS_HUMAN	hepsin	281	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				basement membrane disassembly (GO:0034769)|cholesterol homeostasis (GO:0042632)|cochlea morphogenesis (GO:0090103)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|epithelium development (GO:0060429)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pilomotor reflex (GO:0097195)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|positive regulation of gene expression (GO:0010628)|positive regulation of hepatocyte proliferation (GO:2000347)|positive regulation of plasminogen activation (GO:0010756)|positive regulation of thyroid hormone generation (GO:2000611)|potassium ion transmembrane transport (GO:0071805)|proteolysis (GO:0006508)|regulation of cell shape (GO:0008360)|response to thyroid hormone (GO:0097066)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	19	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	TCCCAGCTGCCGGCCAGGCCC	0.612													C|||	3	0.000599042	0.0	0.0	5008	,	,		19083	0.003		0.0	False		,,,				2504	0.0																0			19											79.0	65.0	70.0					19																	35556185		2203	4300	6503	40248025	SO:0001819	synonymous_variant	3249				CCDS32993.1	19q13.12	2013-04-25	2008-12-08		ENSG00000105707	ENSG00000105707		"""Serine peptidases / Transmembrane"""	5155	protein-coding gene	gene with protein product	"""transmembrane protease, serine 1"""	142440				2835076	Standard	NM_182983		Approved	TMPRSS1	uc002nxq.2	P05981	OTTHUMG00000182474	ENST00000262626.2:c.843C>T	19.37:g.35556185C>T		Somatic		Capture	Illumina HiSeq	Phase_I	40248025	B2RDS4	Silent	SNP	ENST00000262626.2	37	CCDS32993.1																																																																																				HPN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461573.1	NM_002151	
FCGBP	8857	hgsc.bcm.edu	37	19	40368416	40368416	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:40368416A>G	ENST00000221347.6	-	28	12939	c.12932T>C	c.(12931-12933)gTc>gCc	p.V4311A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4311						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			ACCCATGCAGACGTCCAGAAC	0.622																																																	0			19											136.0	139.0	138.0					19																	40368416		2203	4297	6500	45060256	SO:0001583	missense	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12932T>C	19.37:g.40368416A>G	ENSP00000221347:p.Val4311Ala	Somatic		Capture	Illumina HiSeq	Phase_I	45060256	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	A	12.37	1.916642	0.33815	.	.	ENSG00000090920	ENST00000221347	T	0.77098	-1.07	4.08	4.08	0.47627	Uncharacterised domain, cysteine-rich (2);	0.260617	0.31167	U	0.008139	T	0.64182	0.2575	L	0.39692	1.235	0.23802	N	0.996805	B	0.29085	0.232	B	0.27076	0.076	T	0.50389	-0.8834	10	0.02654	T	1	.	12.4404	0.55621	1.0:0.0:0.0:0.0	.	4311	Q9Y6R7	FCGBP_HUMAN	A	4311	ENSP00000221347:V4311A	ENSP00000221347:V4311A	V	-	2	0	FCGBP	45060256	0.005000	0.15991	0.997000	0.53966	0.708000	0.40852	2.418000	0.44662	1.848000	0.53677	0.254000	0.18369	GTC		FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZNF224	7767	hgsc.bcm.edu	37	19	44612142	44612142	+	Missense_Mutation	SNP	C	C	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:44612142C>G	ENST00000336976.6	+	6	2083	c.1829C>G	c.(1828-1830)aCt>aGt	p.T610S	AC084219.4_ENST00000592946.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	610					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19		Prostate(69;0.0435)				TGGTCCTCAACTCGTCTGACC	0.448																																																	0			19											82.0	83.0	83.0					19																	44612142		2203	4300	6503	49303982	SO:0001583	missense	7767			AF187990	CCDS33046.1	19q13.2	2013-01-08	2004-02-13			ENSG00000267680		"""Zinc fingers, C2H2-type"", ""-"""	13017	protein-coding gene	gene with protein product		194555	"""zinc finger protein 255"", ""zinc finger protein 27"""	ZNF255, ZNF27			Standard	NM_013398		Approved	BMZF-2, KOX22	uc002oyh.2	Q9NZL3		ENST00000336976.6:c.1829C>G	19.37:g.44612142C>G	ENSP00000337368:p.Thr610Ser	Somatic		Capture	Illumina HiSeq	Phase_I	49303982	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Missense_Mutation	SNP	ENST00000336976.6	37	CCDS33046.1	.	.	.	.	.	.	.	.	.	.	c	0.010	-1.756597	0.00657	.	.	ENSG00000186019	ENST00000336976	T	0.59502	0.26	2.37	-1.82	0.07857	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19127	0.0459	N	0.01134	-0.995	0.09310	N	1	B	0.16802	0.019	B	0.17433	0.018	T	0.29640	-1.0005	9	0.02654	T	1	.	5.8389	0.18623	0.5975:0.2882:0.1143:0.0	.	610	Q9NZL3	ZN224_HUMAN	S	610	ENSP00000337368:T610S	ENSP00000337368:T610S	T	+	2	0	ZNF224	49303982	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.251000	0.08818	-0.485000	0.06754	0.591000	0.81541	ACT		ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398	
ZNF112	7771	hgsc.bcm.edu	37	19	44831652	44831652	+	Silent	SNP	T	T	C	rs192670888		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:44831652T>C	ENST00000337401.4	-	5	2764	c.2676A>G	c.(2674-2676)gaA>gaG	p.E892E	ZNF112_ENST00000536500.1_Silent_p.E909E|ZNF112_ENST00000354340.4_Silent_p.E886E	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	892					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TACCATAGTCTTCGCTTTTAT	0.388													T|||	1	0.000199681	0.0	0.0	5008	,	,		17680	0.001		0.0	False		,,,				2504	0.0																0			19											72.0	68.0	69.0					19																	44831652		2203	4299	6502	49523492	SO:0001819	synonymous_variant	7771			AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"""Zinc fingers, C2H2-type"""	12892	protein-coding gene	gene with protein product		603994	"""zinc finger protein 112 homolog (mouse)"", ""zinc finger protein 228"""	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.2676A>G	19.37:g.44831652T>C		Somatic		Capture	Illumina HiSeq	Phase_I	49523492	A4FU53|Q9HCA7	Silent	SNP	ENST00000337401.4	37	CCDS54276.1																																																																																				ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380	
TRPM4	54795	hgsc.bcm.edu	37	19	49703897	49703897	+	Silent	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:49703897C>T	ENST00000252826.5	+	19	2934	c.2808C>T	c.(2806-2808)ttC>ttT	p.F936F	TRPM4_ENST00000427978.2_Silent_p.F791F|TRPM4_ENST00000355712.5_Silent_p.F582F	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	936					calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		TCCTCTTCTTCCTCGGCGTGT	0.602																																																	0			19											54.0	51.0	52.0					19																	49703897		2203	4300	6503	54395709	SO:0001819	synonymous_variant	54795			AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.2808C>T	19.37:g.49703897C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54395709	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Silent	SNP	ENST00000252826.5	37	CCDS33073.1																																																																																				TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636	
DNAAF3	352909	hgsc.bcm.edu	37	19	55673654	55673654	+	Silent	SNP	T	T	C	rs3848618	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:55673654T>C	ENST00000524407.2	-	5	360	c.327A>G	c.(325-327)cgA>cgG	p.R109R	CTD-2587H24.5_ENST00000591665.1_RNA|DNAAF3_ENST00000587789.2_5'Flank|DNAAF3_ENST00000391720.4_Silent_p.R156R|CTD-2587H24.4_ENST00000587871.1_5'Flank|DNAAF3_ENST00000455045.1_Silent_p.R55R|DNAAF3_ENST00000527223.2_Silent_p.R177R			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	109					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											AGGTCTCGCTTCGCTCTACGG	0.577													c|||	643	0.128395	0.0688	0.2651	5008	,	,		12792	0.2024		0.0169	False		,,,				2504	0.1503																0			19						C		111,3373		2,107,1633	11.0	13.0	13.0		468	-4.6	0.1	19	dbSNP_108	13	158,7134		0,158,3488	yes	coding-synonymous	C19orf51	NM_178837.3		2,265,5121	CC,CT,TT		2.1668,3.186,2.4963		156/589	55673654	269,10507	1742	3646	5388	60365466	SO:0001819	synonymous_variant	352909			AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"""chromosome 19 open reading frame 51"", ""ciliary dyskinesia, primary 2"""	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.327A>G	19.37:g.55673654T>C		Somatic		Capture	Illumina HiSeq	Phase_I	60365466	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Silent	SNP	ENST00000524407.2	37	CCDS59422.1																																																																																				DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837	
PEG3	5178	hgsc.bcm.edu	37	19	57328029	57328029	+	Missense_Mutation	SNP	C	C	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:57328029C>A	ENST00000326441.9	-	10	2144	c.1781G>T	c.(1780-1782)cGt>cTt	p.R594L	ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.R594L|PEG3_ENST00000593695.1_Missense_Mutation_p.R468L|PEG3_ENST00000598410.1_Missense_Mutation_p.R470L	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	594			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R594H(1)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		ttcatgttcacgctcatTATC	0.453																																																	1	Substitution - Missense(1)	large_intestine(1)	19											107.0	83.0	91.0					19																	57328029		2203	4300	6503	62019841	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.1781G>T	19.37:g.57328029C>A	ENSP00000326581:p.Arg594Leu	Somatic		Capture	Illumina HiSeq	Phase_I	62019841	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	9.368	1.069879	0.20147	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.03358	3.96;3.96	1.94	1.94	0.25998	.	0.173402	0.28171	N	0.016329	T	0.03608	0.0103	L	0.46157	1.445	.	.	.	B;B;P	0.38827	0.247;0.247;0.649	B;B;B	0.34489	0.065;0.065;0.184	T	0.15292	-1.0442	9	0.66056	D	0.02	.	7.4011	0.26965	0.0:1.0:0.0:0.0	.	470;594;529	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	L	594	ENSP00000326581:R594L;ENSP00000403051:R594L	ENSP00000326581:R594L	R	-	2	0	ZIM2	62019841	0.002000	0.14202	0.004000	0.12327	0.404000	0.30871	0.388000	0.20735	1.397000	0.46682	0.650000	0.86243	CGT		PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		
NCOA2	10499	hgsc.bcm.edu	37	8	71053502	71053502	+	Missense_Mutation	SNP	C	C	T	rs560768671		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr8:71053502C>T	ENST00000452400.2	-	14	3126	c.2945G>A	c.(2944-2946)cGg>cAg	p.R982Q	NCOA2_ENST00000267974.4_Missense_Mutation_p.R70Q	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	982					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TGCTGGGTTCCGAATCATACC	0.572			T	"""RUNXBP2, HEY1"""	"""AML, Chondrosarcoma"""								C|||	1	0.000199681	0.0	0.0	5008	,	,		16562	0.001		0.0	False		,,,				2504	0.0							Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	0			8											61.0	66.0	65.0					8																	71053502		2064	4215	6279	71216056	SO:0001583	missense	10499			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.2945G>A	8.37:g.71053502C>T	ENSP00000399968:p.Arg982Gln	Somatic		Capture	Illumina HiSeq	Phase_I	71216056	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.01|17.01	3.278609|3.278609	0.59758|0.59758	.|.	.|.	ENSG00000140396|ENSG00000140396	ENST00000518363|ENST00000452400;ENST00000267974	.|T;T	.|0.07021	.|4.81;3.23	6.05|6.05	6.05|6.05	0.98169|0.98169	.|.	.|0.187477	.|0.46442	.|D	.|0.000290	T|T	0.26882|0.26882	0.0658|0.0658	L|L	0.60455|0.60455	1.87|1.87	0.48288|0.48288	D|D	0.999622|0.999622	.|D;D	.|0.89917	.|1.0;0.991	.|D;B	.|0.70227	.|0.968;0.405	T|T	0.00059|0.00059	-1.2166|-1.2166	5|10	.|0.28530	.|T	.|0.3	.|.	20.6013|20.6013	0.99457|0.99457	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|70;982	.|F8WAJ2;Q15596	.|.;NCOA2_HUMAN	R|Q	83|982;70	.|ENSP00000399968:R982Q;ENSP00000267974:R70Q	.|ENSP00000267974:R70Q	G|R	-|-	1|2	0|0	NCOA2|NCOA2	71216056|71216056	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.927000|0.927000	0.56198|0.56198	2.930000|2.930000	0.48924|0.48924	2.878000|2.878000	0.98634|0.98634	0.650000|0.650000	0.86243|0.86243	GGA|CGG		NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1		
CNBD1	168975	hgsc.bcm.edu	37	8	87878745	87878745	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr8:87878745G>A	ENST00000518476.1	+	1	73	c.22G>A	c.(22-24)Gca>Aca	p.A8T		NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	8										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						TTCTCTTCCAGCAGCTATTTT	0.453																																																	0			8											103.0	95.0	98.0					8																	87878745		1960	4162	6122	87947861	SO:0001583	missense	168975			AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.22G>A	8.37:g.87878745G>A	ENSP00000430073:p.Ala8Thr	Somatic		Capture	Illumina HiSeq	Phase_I	87947861		Missense_Mutation	SNP	ENST00000518476.1	37	CCDS55259.1	.	.	.	.	.	.	.	.	.	.	G	2.246	-0.372694	0.05034	.	.	ENSG00000176571	ENST00000518476	T	0.18174	2.23	4.78	-1.86	0.07760	.	1.752230	0.03492	N	0.216755	T	0.07954	0.0199	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.25916	-1.0118	10	0.23302	T	0.38	.	3.4266	0.07413	0.2651:0.0:0.2918:0.4431	.	8	Q8NA66	CNBD1_HUMAN	T	8	ENSP00000430073:A8T	ENSP00000430073:A8T	A	+	1	0	CNBD1	87947861	0.000000	0.05858	0.000000	0.03702	0.931000	0.56810	-0.464000	0.06688	-0.517000	0.06461	0.563000	0.77884	GCA		CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538	
MMP16	4325	hgsc.bcm.edu	37	8	89128918	89128918	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr8:89128918T>C	ENST00000286614.6	-	6	1182	c.901A>G	c.(901-903)Aga>Gga	p.R301G	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	301					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R301*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	GGTAGAGGTCTTGTAGGTGGA	0.512																																																	1	Substitution - Nonsense(1)	ovary(1)	8											198.0	205.0	202.0					8																	89128918		2203	4300	6503	89198034	SO:0001583	missense	4325			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"""matrix metalloproteinase 16 (membrane-inserted)"", ""chromosome 8 open reading frame 57"""	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.901A>G	8.37:g.89128918T>C	ENSP00000286614:p.Arg301Gly	Somatic		Capture	Illumina HiSeq	Phase_I	89198034	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	37	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	T	13.63	2.294493	0.40594	.	.	ENSG00000156103	ENST00000286614	T	0.16897	2.31	5.79	3.32	0.38043	.	0.154467	0.52532	D	0.000077	T	0.17365	0.0417	M	0.62723	1.935	0.44380	D	0.997288	B;B	0.12013	0.005;0.0	B;B	0.15052	0.012;0.001	T	0.06144	-1.0843	10	0.11794	T	0.64	.	12.6824	0.56928	0.0:0.0:0.2603:0.7397	.	301;301	P51512-2;P51512	.;MMP16_HUMAN	G	301	ENSP00000286614:R301G	ENSP00000286614:R301G	R	-	1	2	MMP16	89198034	1.000000	0.71417	0.974000	0.42286	0.998000	0.95712	2.488000	0.45276	0.412000	0.25729	0.455000	0.32223	AGA		MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941	
PTCHD2	57540	hgsc.bcm.edu	37	1	11561557	11561557	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:11561557C>T	ENST00000294484.6	+	2	646	c.508C>T	c.(508-510)Cga>Tga	p.R170*	PTCHD2_ENST00000389575.3_Nonsense_Mutation_p.R170*	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	170					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GCAAGCCTCCCGAGCCCCCCG	0.682																																																	0			1											12.0	15.0	14.0					1																	11561557		1893	4089	5982	11484144	SO:0001587	stop_gained	57540			AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.508C>T	1.37:g.11561557C>T	ENSP00000294484:p.Arg170*	Somatic		Capture	Illumina HiSeq	Phase_I	11484144	Q5VTU9|Q9UJD6	Nonsense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.981249	0.53827	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	.	.	.	5.53	-3.03	0.05429	.	0.429524	0.22945	N	0.053731	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.4	13.1682	0.59583	0.2811:0.6473:0.0716:0.0	.	.	.	.	X	170	.	ENSP00000294484:R170X	R	+	1	2	PTCHD2	11484144	0.063000	0.20901	0.010000	0.14722	0.072000	0.16883	-0.093000	0.11111	-0.258000	0.09446	-0.410000	0.06199	CGA		PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
CATSPER4	378807	hgsc.bcm.edu	37	1	26527920	26527920	+	Silent	SNP	G	G	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:26527920G>T	ENST00000456354.2	+	9	1342	c.1275G>T	c.(1273-1275)acG>acT	p.T425T		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	425					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.T425T(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		GCTCGTCGACGAGCGGGTCGT	0.577																																																	1	Substitution - coding silent(1)	ovary(1)	1											102.0	92.0	95.0					1																	26527920		2203	4300	6503	26400507	SO:0001819	synonymous_variant	378807			BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.1275G>T	1.37:g.26527920G>T		Somatic		Capture	Illumina HiSeq	Phase_I	26400507	A1A4W6|Q5VY71	Silent	SNP	ENST00000456354.2	37	CCDS30645.1																																																																																				CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
FAM167B	84734	hgsc.bcm.edu	37	1	32713034	32713034	+	Silent	SNP	G	G	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:32713034G>C	ENST00000373582.3	+	1	201	c.12G>C	c.(10-12)ggG>ggC	p.G4G		NM_032648.2	NP_116037.2	Q9BTA0	F167B_HUMAN	family with sequence similarity 167, member B	4										endometrium(1)|large_intestine(1)|lung(1)|ovary(2)	5						TGTCCCTGGGGCTACTGAAAT	0.587																																																	0			1											60.0	67.0	65.0					1																	32713034		2048	4202	6250	32485621	SO:0001819	synonymous_variant	84734			BC004269	CCDS358.2	1p35.1	2010-08-27	2008-06-11	2008-06-11	ENSG00000183615	ENSG00000183615			28133	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 90"""	C1orf90		12477932	Standard	NM_032648		Approved	MGC10820	uc001buw.3	Q9BTA0	OTTHUMG00000007462	ENST00000373582.3:c.12G>C	1.37:g.32713034G>C		Somatic		Capture	Illumina HiSeq	Phase_I	32485621	Q5TDH6	Silent	SNP	ENST00000373582.3	37	CCDS358.2																																																																																				FAM167B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019615.2	NM_032648	
CLSPN	63967	hgsc.bcm.edu	37	1	36209097	36209097	+	Missense_Mutation	SNP	A	A	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:36209097A>T	ENST00000318121.3	-	17	3058	c.3001T>A	c.(3001-3003)Ttt>Att	p.F1001I	CLSPN_ENST00000520551.1_Missense_Mutation_p.F948I|CLSPN_ENST00000373220.3_Missense_Mutation_p.F937I|CLSPN_ENST00000251195.5_Missense_Mutation_p.F1001I|RP11-435D7.3_ENST00000373226.2_RNA	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	1001					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ACAAGCCGAAAGTCTCCAAAT	0.378																																																	0			1											165.0	157.0	160.0					1																	36209097		2203	4300	6503	35981684	SO:0001583	missense	63967			AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"""claspin homolog (Xenopus laevis)"""			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.3001T>A	1.37:g.36209097A>T	ENSP00000312995:p.Phe1001Ile	Somatic		Capture	Illumina HiSeq	Phase_I	35981684	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.110652	0.56398	.	.	ENSG00000092853	ENST00000251195;ENST00000318121;ENST00000373220;ENST00000520551	T;T;T;T	0.25912	1.77;1.78;1.82;1.82	5.29	5.29	0.74685	.	0.060670	0.64402	D	0.000004	T	0.48132	0.1483	M	0.66939	2.045	0.40289	D	0.978487	D;P	0.67145	0.996;0.797	D;P	0.77557	0.99;0.615	T	0.44772	-0.9306	10	0.38643	T	0.18	-12.6596	14.3462	0.66665	1.0:0.0:0.0:0.0	.	937;1001	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	I	1001;1001;937;948	ENSP00000251195:F1001I;ENSP00000312995:F1001I;ENSP00000362317:F937I;ENSP00000428848:F948I	ENSP00000251195:F1001I	F	-	1	0	CLSPN	35981684	1.000000	0.71417	0.997000	0.53966	0.188000	0.23474	5.232000	0.65332	2.125000	0.65367	0.459000	0.35465	TTT		CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111	
MROH7	374977	hgsc.bcm.edu	37	1	55144987	55144987	+	Missense_Mutation	SNP	G	G	A	rs554316180		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:55144987G>A	ENST00000421030.2	+	12	2386	c.2101G>A	c.(2101-2103)Gcc>Acc	p.A701T	MROH7_ENST00000409996.1_Missense_Mutation_p.A269T|MROH7_ENST00000339553.5_Missense_Mutation_p.A701T|MROH7_ENST00000454855.2_Missense_Mutation_p.A219T|MROH7_ENST00000395690.2_Missense_Mutation_p.A701T|MROH7_ENST00000545244.1_Missense_Mutation_p.A269T|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.A701T	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	701						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GCTGCTGGCCGCCCTGGAAGG	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		18498	0.001		0.0	False		,,,				2504	0.0																0			1											71.0	78.0	76.0					1																	55144987		1921	4127	6048	54917575	SO:0001583	missense	374977			AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"""maestro heat-like repeat containing"""	24802	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 175"", ""HEAT repeat containing 8"""	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.2101G>A	1.37:g.55144987G>A	ENSP00000396622:p.Ala701Thr	Somatic		Capture	Illumina HiSeq	Phase_I	54917575	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	G	12.32	1.902147	0.33628	.	.	ENSG00000184313	ENST00000421030;ENST00000545244;ENST00000414867;ENST00000339553;ENST00000409996;ENST00000454855;ENST00000395690	T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4	4.88	3.95	0.45737	.	0.000000	0.47093	D	0.000243	T	0.41236	0.1150	L	0.33485	1.01	0.32843	D	0.505581	D;D;D	0.89917	0.999;1.0;0.997	D;D;P	0.71414	0.95;0.973;0.67	T	0.42882	-0.9425	10	0.22706	T	0.39	-6.3043	8.1381	0.31067	0.1075:0.0:0.8925:0.0	.	701;701;269	F8W8P2;Q68CQ1;F5H7R4	.;HEAT8_HUMAN;.	T	701;269;730;701;269;219;701	ENSP00000396622:A701T;ENSP00000442333:A269T;ENSP00000343211:A701T;ENSP00000387048:A269T;ENSP00000401130:A219T;ENSP00000379044:A701T	ENSP00000343211:A701T	A	+	1	0	HEATR8	54917575	0.974000	0.33945	0.992000	0.48379	0.751000	0.42716	2.215000	0.42862	2.250000	0.74265	0.557000	0.71058	GCC		MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
AGL	178	hgsc.bcm.edu	37	1	100349686	100349686	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:100349686A>G	ENST00000294724.4	+	18	2797	c.2319A>G	c.(2317-2319)gaA>gaG	p.E773E	AGL_ENST00000361915.3_Silent_p.E773E|AGL_ENST00000361522.4_Silent_p.E756E|AGL_ENST00000370163.3_Silent_p.E773E|AGL_ENST00000370165.3_Silent_p.E773E|AGL_ENST00000370161.2_Silent_p.E757E|AGL_ENST00000361302.3_Silent_p.E757E	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	773					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		GCAAAATTGAAGAAGTAGTTC	0.303																																																	0			1											78.0	83.0	81.0					1																	100349686		2203	4297	6500	100122274	SO:0001819	synonymous_variant	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.2319A>G	1.37:g.100349686A>G		Somatic		Capture	Illumina HiSeq	Phase_I	100122274	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	37	CCDS759.1																																																																																				AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
FAM102B	284611	hgsc.bcm.edu	37	1	109154825	109154825	+	Missense_Mutation	SNP	C	C	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:109154825C>A	ENST00000370035.3	+	4	654	c.314C>A	c.(313-315)gCa>gAa	p.A105E	FAM102B_ENST00000405454.1_Missense_Mutation_p.A105E	NM_001010883.2	NP_001010883.2	Q5T8I3	F102B_HUMAN	family with sequence similarity 102, member B	105										autonomic_ganglia(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	5		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)		CTAAACCTGGCAGAGTTTGCT	0.368																																																	0			1											104.0	104.0	104.0					1																	109154825		2203	4300	6503	108956348	SO:0001583	missense	284611			CR749397	CCDS30786.2	1p13.3	2012-11-05			ENSG00000162636	ENSG00000162636			27637	protein-coding gene	gene with protein product	"""sym-3 homolog B (C. elegans)"""						Standard	NM_001010883		Approved	DKFZp779B126, SYM-3B	uc010ouy.2	Q5T8I3	OTTHUMG00000010967	ENST00000370035.3:c.314C>A	1.37:g.109154825C>A	ENSP00000359052:p.Ala105Glu	Somatic		Capture	Illumina HiSeq	Phase_I	108956348	A1L1A1|B0QZ46|B0QZ47|Q68DH7	Missense_Mutation	SNP	ENST00000370035.3	37	CCDS30786.2	.	.	.	.	.	.	.	.	.	.	C	24.8	4.572444	0.86542	.	.	ENSG00000162636	ENST00000370035;ENST00000405454;ENST00000437902	T;T	0.56275	0.47;0.47	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.52289	0.1725	M	0.87827	2.91	0.80722	D	1	P	0.43231	0.801	B	0.38378	0.272	T	0.67181	-0.5735	10	0.72032	D	0.01	-18.1451	19.0387	0.92989	0.0:1.0:0.0:0.0	.	105	Q5T8I3	F102B_HUMAN	E	105	ENSP00000359052:A105E;ENSP00000386084:A105E	ENSP00000359052:A105E	A	+	2	0	FAM102B	108956348	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.805000	0.86005	2.500000	0.84329	0.655000	0.94253	GCA		FAM102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030188.3	NM_001010883	
MPZ	4359	hgsc.bcm.edu	37	1	161276238	161276238	+	Silent	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:161276238C>T	ENST00000533357.1	-	4	531	c.465G>A	c.(463-465)ggG>ggA	p.G155G	MPZ_ENST00000360451.6_Silent_p.G165G|MPZ_ENST00000336559.4_Silent_p.G155G|MPZ_ENST00000526189.1_5'UTR|MPZ_ENST00000491222.2_5'UTR	NM_000530.6	NP_000521.2	P25189	MYP0_HUMAN	myelin protein zero	155					cell death (GO:0008219)|cell-cell junction maintenance (GO:0045217)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	10	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)	Breast(1374;0.181)	BRCA - Breast invasive adenocarcinoma(70;0.00376)			CCAGAACGACCCCGTACCTAG	0.592																																																	0			1											116.0	104.0	108.0					1																	161276238		2203	4300	6503	159542862	SO:0001819	synonymous_variant	4359			BC006491	CCDS1229.1, CCDS1229.2	1q22	2014-09-17	2008-08-01		ENSG00000158887	ENSG00000158887		"""Immunoglobulin superfamily / V-set domain containing"""	7225	protein-coding gene	gene with protein product		159440	"""Charcot-Marie-Tooth neuropathy 1B"""	CMT1, CMT1B		7693129	Standard	NM_000530		Approved	HMSNIB	uc001gaf.4	P25189	OTTHUMG00000034341	ENST00000533357.1:c.465G>A	1.37:g.161276238C>T		Somatic		Capture	Illumina HiSeq	Phase_I	159542862	Q16072|Q5VTH4|Q92677|Q9BR67	Silent	SNP	ENST00000533357.1	37	CCDS1229.2																																																																																				MPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082987.2	NM_000530	
KIF21B	23046	hgsc.bcm.edu	37	1	200972808	200972808	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:200972808T>C	ENST00000422435.2	-	8	1434	c.1118A>G	c.(1117-1119)aAg>aGg	p.K373R	KIF21B_ENST00000360529.5_Missense_Mutation_p.K373R|KIF21B_ENST00000461742.2_Missense_Mutation_p.K373R|KIF21B_ENST00000332129.2_Missense_Mutation_p.K373R	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	373					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CACTACCACCTTGTTCTTGAT	0.542																																																	0			1											193.0	148.0	163.0					1																	200972808		2203	4300	6503	199239431	SO:0001583	missense	23046			BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.1118A>G	1.37:g.200972808T>C	ENSP00000411831:p.Lys373Arg	Somatic		Capture	Illumina HiSeq	Phase_I	199239431	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	t	16.77	3.215667	0.58452	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73	5.19	5.19	0.71726	Kinesin, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.71358	0.3330	L	0.52573	1.65	0.52501	D	0.999952	D;D;B;D	0.56746	0.961;0.961;0.006;0.977	P;P;B;P	0.51974	0.489;0.489;0.005;0.686	T	0.73132	-0.4079	10	0.52906	T	0.07	.	9.5798	0.39481	0.0:0.0786:0.0:0.9214	.	373;373;373;373	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	R	373	ENSP00000328494:K373R;ENSP00000353724:K373R;ENSP00000433808:K373R;ENSP00000411831:K373R	ENSP00000328494:K373R	K	-	2	0	KIF21B	199239431	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.128000	0.64733	1.959000	0.56917	0.524000	0.50904	AAG		KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
KCNH1	3756	hgsc.bcm.edu	37	1	210977424	210977424	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:210977424A>G	ENST00000271751.4	-	8	1574	c.1547T>C	c.(1546-1548)cTc>cCc	p.L516P	KCNH1_ENST00000367007.4_Missense_Mutation_p.L489P			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	516					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)	p.L516P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		AACACTGTTGAGCATCTCATG	0.478																																																	1	Substitution - Missense(1)	ovary(1)	1											161.0	147.0	152.0					1																	210977424		2203	4300	6503	209044047	SO:0001583	missense	3756			AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.1547T>C	1.37:g.210977424A>G	ENSP00000271751:p.Leu516Pro	Somatic		Capture	Illumina HiSeq	Phase_I	209044047	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.414958	0.83449	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.97256	-4.31;-4.31	5.6	5.6	0.85130	Cyclic nucleotide-binding-like (1);	0.060386	0.64402	D	0.000003	D	0.98226	0.9413	M	0.78801	2.425	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.69824	0.966;0.954	D	0.99323	1.0907	10	0.87932	D	0	.	15.7772	0.78232	1.0:0.0:0.0:0.0	.	489;516	Q14CL3;O95259	.;KCNH1_HUMAN	P	516;489	ENSP00000271751:L516P;ENSP00000355974:L489P	ENSP00000271751:L516P	L	-	2	0	KCNH1	209044047	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.982000	0.93471	2.137000	0.66172	0.418000	0.28097	CTC		KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238	
OR2W5	441932	hgsc.bcm.edu	37	1	247655202	247655202	+	RNA	SNP	G	G	A	rs118113848	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:247655202G>A	ENST00000522351.1	+	0	833							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R258L(1)|p.R258H(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			CATCATCTACGTGTACCTGAA	0.532													G|||	4	0.000798722	0.0	0.0	5008	,	,		17476	0.004		0.0	False		,,,				2504	0.0																2	Substitution - Missense(2)	lung(1)|endometrium(1)	1						G	HIS/ARG	0,4406		0,0,2203	132.0	115.0	121.0		773	-1.0	1.0	1	dbSNP_132	121	2,8598	2.2+/-6.3	0,2,4298	no	missense	OR2W5	NM_001004698.2	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	258/321	247655202	2,13004	2203	4300	6503	245721825			441932					1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"""GPCR / Class A : Olfactory receptors"""	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		1.37:g.247655202G>A		Somatic		Capture	Illumina HiSeq	Phase_I	245721825	B9EH85	Missense_Mutation	SNP	ENST00000522351.1	37																																																																																					OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698	
UBQLNL	143630	hgsc.bcm.edu	37	11	5536733	5536733	+	Silent	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:5536733T>C	ENST00000380184.1	-	1	1202	c.939A>G	c.(937-939)ccA>ccG	p.P313P	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	313	Poly-Pro.									endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		GTGATGGTGGTGGAGGTGGGG	0.498																																																	0			11											180.0	159.0	166.0					11																	5536733		2201	4297	6498	5493309	SO:0001819	synonymous_variant	143630			AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.939A>G	11.37:g.5536733T>C		Somatic		Capture	Illumina HiSeq	Phase_I	5493309	Q6ZRU1|Q96EK3|Q96MB0	Silent	SNP	ENST00000380184.1	37	CCDS31385.1																																																																																				UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
PTPMT1	114971	hgsc.bcm.edu	37	11	47593119	47593119	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:47593119T>C	ENST00000326674.9	+	4	566	c.544T>C	c.(544-546)Ttc>Ctc	p.F182L	PTPMT1_ENST00000534775.1_3'UTR|PTPMT1_ENST00000527079.2_3'UTR|PTPMT1_ENST00000426530.2_3'UTR|PTPMT1_ENST00000326656.8_Missense_Mutation_p.F118L|NDUFS3_ENST00000533507.1_3'UTR	NM_175732.2	NP_783859.1	Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1	182	Tyrosine-protein phosphatase.				cardiolipin biosynthetic process (GO:0032049)|glycerophospholipid biosynthetic process (GO:0046474)|inositol phosphate dephosphorylation (GO:0046855)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylglycerophosphatase activity (GO:0008962)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	6						TCTTAAAGAGTTCCACAAGCA	0.478																																																	0			11											122.0	113.0	116.0					11																	47593119		1901	4129	6030	47549695	SO:0001583	missense	114971			BC014048	CCDS41643.1, CCDS44593.1	11p11.2	2011-06-09			ENSG00000110536	ENSG00000110536	3.1.3.36	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	26965	protein-coding gene	gene with protein product		609538				12477932	Standard	NM_175732		Approved	PLIP, DUSP23, MOSP	uc001nfs.4	Q8WUK0	OTTHUMG00000166892	ENST00000326674.9:c.544T>C	11.37:g.47593119T>C	ENSP00000325958:p.Phe182Leu	Somatic		Capture	Illumina HiSeq	Phase_I	47549695	E9PAT8|Q7Z557|Q96CR2|Q9BXV8	Missense_Mutation	SNP	ENST00000326674.9	37	CCDS41643.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.940835	0.92526	.	.	ENSG00000110536	ENST00000326656;ENST00000326674	T;T	0.61274	1.82;0.12	5.93	5.93	0.95920	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.075144	0.53938	U	0.000046	T	0.70482	0.3229	M	0.63428	1.95	0.49130	D	0.999757	D;D	0.69078	0.995;0.997	P;P	0.61800	0.894;0.865	T	0.71603	-0.4543	10	0.49607	T	0.09	-8.3213	14.6096	0.68507	0.0:0.0:0.0:1.0	.	118;182	Q8WUK0-2;Q8WUK0	.;PTPM1_HUMAN	L	118;182	ENSP00000325882:F118L;ENSP00000325958:F182L	ENSP00000325882:F118L	F	+	1	0	PTPMT1	47549695	1.000000	0.71417	1.000000	0.80357	0.658000	0.38924	6.376000	0.73141	2.271000	0.75665	0.533000	0.62120	TTC		PTPMT1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391746.1	XM_374879	
OR5AN1	390195	hgsc.bcm.edu	37	11	59132242	59132242	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:59132242T>C	ENST00000313940.2	+	1	358	c.311T>C	c.(310-312)aTc>aCc	p.I104T		NM_001004729.1	NP_001004729.1	Q8NGI8	O5AN1_HUMAN	olfactory receptor, family 5, subfamily AN, member 1	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	21						CAGTACTTTATCTTTTCAACG	0.433																																																	0			11											204.0	187.0	193.0					11																	59132242		2201	4295	6496	58888818	SO:0001583	missense	390195			AB065806	CCDS31559.1	11q12.1	2012-08-09			ENSG00000176495	ENSG00000176495		"""GPCR / Class A : Olfactory receptors"""	15255	protein-coding gene	gene with protein product		615702					Standard	NM_001004729		Approved		uc010rks.2	Q8NGI8	OTTHUMG00000167337	ENST00000313940.2:c.311T>C	11.37:g.59132242T>C	ENSP00000320302:p.Ile104Thr	Somatic		Capture	Illumina HiSeq	Phase_I	58888818	B9EIS2|Q6IEV4	Missense_Mutation	SNP	ENST00000313940.2	37	CCDS31559.1	.	.	.	.	.	.	.	.	.	.	T	5.152	0.213567	0.09757	.	.	ENSG00000176495	ENST00000313940	T	0.00397	7.57	4.42	4.42	0.53409	GPCR, rhodopsin-like superfamily (1);	0.722427	0.12385	N	0.473539	T	0.00300	0.0009	L	0.37750	1.13	0.09310	N	1	P	0.37914	0.611	B	0.33750	0.169	T	0.56432	-0.7980	10	0.87932	D	0	-4.2895	12.7707	0.57419	0.0:0.0:0.0:1.0	.	104	Q8NGI8	O5AN1_HUMAN	T	104	ENSP00000320302:I104T	ENSP00000320302:I104T	I	+	2	0	OR5AN1	58888818	0.277000	0.24220	0.035000	0.18076	0.033000	0.12548	3.149000	0.50655	1.745000	0.51790	0.533000	0.62120	ATC		OR5AN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394231.1	NM_001004729	
ATG2A	23130	hgsc.bcm.edu	37	11	64677563	64677563	+	Silent	SNP	G	G	C	rs200504454		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:64677563G>C	ENST00000377264.3	-	13	1924	c.1812C>G	c.(1810-1812)gcC>gcG	p.A604A	ATG2A_ENST00000421419.2_Silent_p.A604A	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	604					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						GCAGTAGGGCGGCCAGCCGGT	0.731																																																	0			11											14.0	19.0	18.0					11																	64677563		2188	4277	6465	64434139	SO:0001819	synonymous_variant	23130				CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.1812C>G	11.37:g.64677563G>C		Somatic		Capture	Illumina HiSeq	Phase_I	64434139	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Silent	SNP	ENST00000377264.3	37	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	G	0.251	-1.006815	0.02112	.	.	ENSG00000110046	ENST00000418259	.	.	.	4.64	-2.16	0.07080	.	.	.	.	.	T	0.22126	0.0533	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.30794	-0.9966	4	.	.	.	.	4.9991	0.14255	0.5313:0.2878:0.1808:0.0	.	.	.	.	G	406	.	.	R	-	1	0	ATG2A	64434139	0.001000	0.12720	0.289000	0.24876	0.084000	0.17831	-0.350000	0.07721	-0.149000	0.11215	-1.195000	0.01675	CGC		ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
ZW10	9183	hgsc.bcm.edu	37	11	113608342	113608342	+	Silent	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:113608342T>C	ENST00000200135.3	-	14	2112	c.1968A>G	c.(1966-1968)ttA>ttG	p.L656L		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	656					ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		CTGTATTGAGTAAAGTCCCCA	0.438																																																	0			11											156.0	144.0	148.0					11																	113608342		2201	4296	6497	113113552	SO:0001819	synonymous_variant	9183			U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"""ZW10 (Drosophila) homolog, centromere/kinetochore protein"", ""ZW10, kinetochore associated, homolog (Drosophila)"""			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.1968A>G	11.37:g.113608342T>C		Somatic		Capture	Illumina HiSeq	Phase_I	113113552	A1A528	Silent	SNP	ENST00000200135.3	37	CCDS8363.1																																																																																				ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724	
ROBO3	64221	hgsc.bcm.edu	37	11	124740592	124740592	+	Missense_Mutation	SNP	G	G	A	rs373820994		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:124740592G>A	ENST00000397801.1	+	6	1193	c.1001G>A	c.(1000-1002)cGc>cAc	p.R334H	ROBO3_ENST00000538940.1_Missense_Mutation_p.R312H	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	334	Ig-like C2-type 3.				axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		AGTGTGGGCCGCGCTGAAGCA	0.582																																																	0			11						G	HIS/ARG	0,4288		0,0,2144	47.0	52.0	50.0		1001	3.3	0.8	11		50	2,8514		0,2,4256	no	missense	ROBO3	NM_022370.3	29	0,2,6400	AA,AG,GG		0.0235,0.0,0.0156	probably-damaging	334/1387	124740592	2,12802	2144	4258	6402	124245802	SO:0001583	missense	64221			AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13433	protein-coding gene	gene with protein product		608630	"""roundabout (axon guidance receptor, Drosophila) homolog 3"", ""horizontal gaze palsy with progressive scoliosis"""	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.1001G>A	11.37:g.124740592G>A	ENSP00000380903:p.Arg334His	Somatic		Capture	Illumina HiSeq	Phase_I	124245802		Missense_Mutation	SNP	ENST00000397801.1	37	CCDS44755.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.403699	0.62288	0.0	2.35E-4	ENSG00000154134	ENST00000397801;ENST00000538940	T;T	0.67523	-0.27;-0.27	4.21	3.29	0.37713	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.35646	N	0.003061	T	0.68979	0.3060	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.68926	-0.5280	10	0.62326	D	0.03	.	7.2509	0.26148	0.2777:0.0:0.7223:0.0	.	334	Q96MS0	ROBO3_HUMAN	H	334;312	ENSP00000380903:R334H;ENSP00000441797:R312H	ENSP00000380903:R334H	R	+	2	0	ROBO3	124245802	1.000000	0.71417	0.810000	0.32431	0.801000	0.45260	3.958000	0.56737	1.110000	0.41699	0.462000	0.41574	CGC		ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663	
ETS1	2113	hgsc.bcm.edu	37	11	128332291	128332291	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr11:128332291C>T	ENST00000319397.6	-	8	1600	c.1291G>A	c.(1291-1293)Gcc>Acc	p.A431T	ETS1_ENST00000526145.2_Missense_Mutation_p.A344T|ETS1_ENST00000345075.4_Missense_Mutation_p.A344T|ETS1_ENST00000531611.1_3'UTR|ETS1_ENST00000392668.4_Missense_Mutation_p.A475T|ETS1_ENST00000535549.1_Missense_Mutation_p.A215T	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	431					angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		TCCAGCATGGCGTGCAGCTCC	0.587																																																	0			11											105.0	90.0	95.0					11																	128332291		2201	4297	6498	127837501	SO:0001583	missense	2113				CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"""Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1"", ""ets protein"""	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.1291G>A	11.37:g.128332291C>T	ENSP00000324578:p.Ala431Thr	Somatic		Capture	Illumina HiSeq	Phase_I	127837501	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Missense_Mutation	SNP	ENST00000319397.6	37	CCDS8475.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190611	0.78789	.	.	ENSG00000134954	ENST00000345075;ENST00000535549;ENST00000392668;ENST00000319397;ENST00000526145	T;T;T;T;T	0.13901	2.55;2.55;2.55;2.55;2.55	5.96	5.96	0.96718	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.10809	0.0264	L	0.28344	0.845	0.80722	D	1	P;B;P	0.46395	0.877;0.165;0.569	B;B;B	0.32864	0.154;0.015;0.041	T	0.05273	-1.0895	10	0.45353	T	0.12	.	20.4082	0.99013	0.0:1.0:0.0:0.0	.	431;215;475	P14921;F5GYX9;Q6N087	ETS1_HUMAN;.;.	T	344;215;475;431;344	ENSP00000340485:A344T;ENSP00000441430:A215T;ENSP00000376436:A475T;ENSP00000324578:A431T;ENSP00000433500:A344T	ENSP00000324578:A431T	A	-	1	0	ETS1	127837501	1.000000	0.71417	0.994000	0.49952	0.888000	0.51559	5.782000	0.68973	2.814000	0.96858	0.655000	0.94253	GCC		ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238	
ERVFRD-1	405754	hgsc.bcm.edu	37	6	11105463	11105463	+	Silent	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:11105463T>C	ENST00000472091.1	-	2	456	c.81A>G	c.(79-81)aaA>aaG	p.K27K	SMIM13_ENST00000416247.2_Intron|ERVFRD-1_ENST00000542862.1_Silent_p.K27K	NM_207582.2	NP_997465.1	P60508	SYCY2_HUMAN	endogenous retrovirus group FRD, member 1	27					syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(4)|stomach(1)	15						GTTGCTGAGCTTTTTCCAATA	0.507																																																	0			6											61.0	61.0	61.0					6																	11105463		2203	4300	6503	11213449	SO:0001819	synonymous_variant	0			AK075092, AK123938, AY358244	CCDS4519.1	6p24.2	2014-05-02			ENSG00000244476	ENSG00000244476			33823	other	endogenous retrovirus		610524				12970426, 14557543, 15476554, 21542922	Standard	NM_207582		Approved	HERV-W/FRD, HERV-FRD, envFRD, ERVFRDE1, syncytin-2	uc003mzt.3	P60508	OTTHUMG00000159193	ENST00000472091.1:c.81A>G	6.37:g.11105463T>C		Somatic		Capture	Illumina HiSeq	Phase_I	11213449		Silent	SNP	ENST00000472091.1	37	CCDS4519.1																																																																																				ERVFRD-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353776.1	NM_207582	
HIST1H4J	8363	hgsc.bcm.edu	37	6	27792188	27792188	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:27792188C>T	ENST00000355057.1	+	1	305	c.286C>T	c.(286-288)Cgc>Tgc	p.R96C		NM_021968.3	NP_068803.1	P62805	H4_HUMAN	histone cluster 1, H4j	96					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			lung(2)|ovary(1)|pancreas(1)	4						GCGCCAGGGCCGCACCCTCTA	0.577																																																	0			6											26.0	28.0	27.0					6																	27792188		2200	4289	6489	27900167	SO:0001583	missense	8363			J00188	CCDS4630.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197238	ENSG00000197238		"""Histones / Replication-dependent"""	4785	protein-coding gene	gene with protein product		602826	"""H4 histone family, member E"", ""histone 1, H4j"""	H4FE		6265100, 9439656, 12408966	Standard	NM_021968		Approved	H4/e, H4F2iv	uc003njp.3	P62805	OTTHUMG00000014487	ENST00000355057.1:c.286C>T	6.37:g.27792188C>T	ENSP00000347168:p.Arg96Cys	Somatic		Capture	Illumina HiSeq	Phase_I	27900167	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000355057.1	37	CCDS4630.1	.	.	.	.	.	.	.	.	.	.	.	19.42	3.823247	0.71143	.	.	ENSG00000197238	ENST00000355057	.	.	.	3.93	3.93	0.45458	.	0.000000	0.64402	U	0.000001	T	0.66982	0.2845	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.72427	-0.4297	6	0.72032	D	0.01	.	13.9744	0.64262	0.0:1.0:0.0:0.0	.	.	.	.	C	96	.	ENSP00000347168:R96C	R	+	1	0	HIST1H4J	27900167	1.000000	0.71417	0.970000	0.41538	0.346000	0.29079	7.340000	0.79292	2.134000	0.65973	0.585000	0.79938	CGC		HIST1H4J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040155.1	NM_021968	
HCP5	10866	hgsc.bcm.edu	37	6	31431174	31431174	+	RNA	SNP	G	G	A	rs182110306	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:31431174G>A	ENST00000414046.2	+	0	246					NR_040662.1		Q6MZN7	HCP5_HUMAN	HLA complex P5 (non-protein coding)						defense response (GO:0006952)					urinary_tract(1)	1						AGGCAGAAATGATCTCATTTT	0.448													g|||	13	0.00259585	0.0091	0.0014	5008	,	,		20023	0.0		0.0	False		,,,				2504	0.0																0			6							ASN/ASP	16,1368		0,16,676	49.0	51.0	50.0		91	0.1	0.3	6		50	0,3182		0,0,1591	no	missense	HCP5	NM_006674.3	23	0,16,2267	AA,AG,GG		0.0,1.1561,0.3504		31/43	31431174	16,4550	692	1591	2283	31539153			360158			D88650		6p21.3	2012-10-16	2011-08-02		ENSG00000206337	ENSG00000206337		"""Long non-coding RNAs"""	21659	non-coding RNA	RNA, long non-coding		604676	"""HLA complex P5"""			8462994, 10199916	Standard	NR_040662		Approved	D6S2650E, P5-1	uc003ntl.3	Q6MZN7	OTTHUMG00000031282		6.37:g.31431174G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31539153	Q04490	Missense_Mutation	SNP	ENST00000414046.2	37																																																																																					HCP5-001	KNOWN	basic	sense_overlapping	sense_overlapping	OTTHUMT00000076614.4	NR_040662	
ITPR3	3710	hgsc.bcm.edu	37	6	33657928	33657928	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:33657928A>G	ENST00000374316.5	+	52	8045	c.6985A>G	c.(6985-6987)Acc>Gcc	p.T2329A	ITPR3_ENST00000605930.1_Missense_Mutation_p.T2329A			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2329					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	CTACATCCTGACCAGTGTCCT	0.597																																																	0			6											120.0	96.0	104.0					6																	33657928		2203	4300	6503	33765906	SO:0001583	missense	3710			D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.6985A>G	6.37:g.33657928A>G	ENSP00000363435:p.Thr2329Ala	Somatic		Capture	Illumina HiSeq	Phase_I	33765906	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.728936	0.89390	.	.	ENSG00000096433	ENST00000374316	D	0.98362	-4.89	5.18	5.18	0.71444	Ion transport (1);	0.051258	0.85682	D	0.000000	D	0.98040	0.9354	L	0.52266	1.64	0.54753	D	0.999984	P;D	0.63046	0.67;0.992	B;D	0.67231	0.403;0.95	D	0.99833	1.1055	10	0.87932	D	0	-20.3344	15.0372	0.71757	1.0:0.0:0.0:0.0	.	2329;1999	Q14573;Q59ES2	ITPR3_HUMAN;.	A	2329	ENSP00000363435:T2329A	ENSP00000363435:T2329A	T	+	1	0	ITPR3	33765906	1.000000	0.71417	0.964000	0.40570	0.980000	0.70556	9.339000	0.96797	1.976000	0.57569	0.379000	0.24179	ACC		ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
TTK	7272	hgsc.bcm.edu	37	6	80745121	80745121	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:80745121A>G	ENST00000369798.2	+	16	2022	c.1911A>G	c.(1909-1911)acA>acG	p.T637T	TTK_ENST00000509894.1_Silent_p.T636T|TTK_ENST00000230510.3_Silent_p.T636T	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	637	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		CAGTTCACACAATCCATCAAC	0.299																																																	0			6											86.0	83.0	84.0					6																	80745121		2203	4300	6503	80801840	SO:0001819	synonymous_variant	7272				CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"""cancer/testis antigen 96"", ""monopolar spindle 1 kinase"""	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.1911A>G	6.37:g.80745121A>G		Somatic		Capture	Illumina HiSeq	Phase_I	80801840	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Silent	SNP	ENST00000369798.2	37	CCDS4993.1																																																																																				TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2		
RARS2	57038	hgsc.bcm.edu	37	6	88255345	88255345	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:88255345C>T	ENST00000369536.5	-	7	569	c.524G>A	c.(523-525)gGc>gAc	p.G175D		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	175					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		AAACTGCATGCCCCAATCGCC	0.299																																																	0			6											124.0	131.0	129.0					6																	88255345		2203	4298	6501	88312064	SO:0001583	missense	57038			AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	21406	protein-coding gene	gene with protein product	"""arginine tRNA ligase 2, mitochondrial (putative)"""	611524	"""arginyl-tRNA synthetase-like"""	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.524G>A	6.37:g.88255345C>T	ENSP00000358549:p.Gly175Asp	Somatic		Capture	Illumina HiSeq	Phase_I	88312064	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.6|26.6	4.752906|4.752906	0.89753|0.89753	.|.	.|.	ENSG00000146282|ENSG00000146282	ENST00000451155|ENST00000369536;ENST00000369523	.|D	.|0.83992	.|-1.79	6.17|6.17	6.17|6.17	0.99709|0.99709	.|Arginyl-tRNA synthetase, class Ia, core (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94689|0.94689	0.8287|0.8287	H|H	0.97707|0.97707	4.06|4.06	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.95512|0.95512	0.8587|0.8587	5|10	.|0.87932	.|D	.|0	.|.	19.6509|19.6509	0.95805|0.95805	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|175	.|Q5T160	.|SYRM_HUMAN	T|D	203|175;202	.|ENSP00000358549:G175D	.|ENSP00000358536:G202D	A|G	-|-	1|2	0|0	RARS2|RARS2	88312064|88312064	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.389000|6.389000	0.73199|0.73199	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GCA|GGC		RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
ACAT2	39	hgsc.bcm.edu	37	6	160197202	160197202	+	Missense_Mutation	SNP	G	G	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:160197202G>C	ENST00000367048.4	+	6	2415	c.655G>C	c.(655-657)Gat>Cat	p.D219H	ACAT2_ENST00000472052.1_3'UTR|ACAT2_ENST00000541436.1_Missense_Mutation_p.D248H	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	219					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		AGTTAAAACAGATGAGTTTCC	0.448																																																	0			6											121.0	115.0	117.0					6																	160197202		2203	4300	6503	160117192	SO:0001583	missense	8435			AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"""acetoacetyl Coenzyme A thiolase"""	100678	"""acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)"", ""acetyl-Coenzyme A acetyltransferase 2"""			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.655G>C	6.37:g.160197202G>C	ENSP00000356015:p.Asp219His	Somatic		Capture	Illumina HiSeq	Phase_I	160117192	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Missense_Mutation	SNP	ENST00000367048.4	37	CCDS5268.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.557648	0.86231	.	.	ENSG00000120437	ENST00000367048;ENST00000541436	D;D	0.95342	-3.68;-3.68	5.94	5.08	0.68730	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	D	0.98457	0.9486	H	0.99156	4.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99552	1.0966	10	0.87932	D	0	-0.0876	15.0966	0.72238	0.0676:0.0:0.9324:0.0	.	248;219	B7Z233;Q9BWD1	.;THIC_HUMAN	H	219;248	ENSP00000356015:D219H;ENSP00000437850:D248H	ENSP00000356015:D219H	D	+	1	0	ACAT2	160117192	1.000000	0.71417	0.981000	0.43875	0.993000	0.82548	9.397000	0.97276	1.527000	0.49086	0.561000	0.74099	GAT		ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891	
TP53	7157	hgsc.bcm.edu	37	17	7577532	7577532	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:7577532G>A	ENST00000269305.4	-	7	938	c.749C>T	c.(748-750)cCc>cTc	p.P250L	TP53_ENST00000413465.2_Missense_Mutation_p.P250L|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.P250L|TP53_ENST00000445888.2_Missense_Mutation_p.P250L|TP53_ENST00000420246.2_Missense_Mutation_p.P250L|TP53_ENST00000455263.2_Missense_Mutation_p.P250L	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	250	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> Q (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.P250L(45)|p.0?(8)|p.?(5)|p.P250H(4)|p.P250F(3)|p.P250N(2)|p.M246_P250delMNRRP(2)|p.P250_L252delPIL(2)|p.P250Q(2)|p.R248_P250delRRP(1)|p.P250_T253delPILT(1)|p.N247_P250delNRRP(1)|p.R249_P250delRP(1)|p.R249_T256delRPILTIIT(1)|p.I251fs*94(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGTGAGGATGGGCCTCCGGTT	0.577		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	80	Substitution - Missense(56)|Deletion - In frame(10)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(1)	large_intestine(14)|lung(10)|breast(10)|upper_aerodigestive_tract(5)|biliary_tract(5)|skin(5)|ovary(5)|stomach(4)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|oesophagus(3)|liver(2)|urinary_tract(1)|eye(1)|peritoneum(1)|pancreas(1)|thyroid(1)	17	GRCh37	CM973401	TP53	M							154.0	112.0	126.0					17																	7577532		2203	4300	6503	7518257	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.749C>T	17.37:g.7577532G>A	ENSP00000269305:p.Pro250Leu	Somatic		Capture	Illumina HiSeq	Phase_I	7518257	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504438	0.85176	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99885	-7.5;-7.5;-7.5;-7.5;-7.5;-7.5;-7.5	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99898	0.9951	M	0.91406	3.205	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.996;0.998;0.998;1.0	D	0.96045	0.9027	10	0.87932	D	0	-1.5308	15.3618	0.74483	0.0:0.0:1.0:0.0	.	250;250;250;250;250	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	L	250;250;250;250;250;250;239;118	ENSP00000410739:P250L;ENSP00000352610:P250L;ENSP00000269305:P250L;ENSP00000398846:P250L;ENSP00000391127:P250L;ENSP00000391478:P250L;ENSP00000425104:P118L	ENSP00000269305:P250L	P	-	2	0	TP53	7518257	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	9.601000	0.98297	2.564000	0.86499	0.462000	0.41574	CCC		TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
TP53	7157	hgsc.bcm.edu	37	17	7579393	7579393	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:7579393A>G	ENST00000269305.4	-	4	483	c.294T>C	c.(292-294)ccT>ccC	p.P98P	TP53_ENST00000413465.2_Silent_p.P98P|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Silent_p.P98P|TP53_ENST00000445888.2_Silent_p.P98P|TP53_ENST00000420246.2_Silent_p.P98P|TP53_ENST00000455263.2_Silent_p.P98P	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	98	Interaction with WWOX.		P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.S99fs*48(3)|p.S99fs*23(3)|p.Q100fs*37(3)|p.G59fs*23(3)|p.V73fs*9(1)|p.W91fs*13(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTTTCTGGGAAGGGACAGAAG	0.642		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	24	Deletion - Frameshift(16)|Whole gene deletion(8)	bone(4)|upper_aerodigestive_tract(3)|large_intestine(3)|central_nervous_system(3)|ovary(3)|lung(2)|pancreas(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|liver(1)	17											50.0	52.0	51.0					17																	7579393		2203	4300	6503	7520118	SO:0001819	synonymous_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.294T>C	17.37:g.7579393A>G		Somatic		Capture	Illumina HiSeq	Phase_I	7520118	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	37	CCDS11118.1																																																																																				TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
NF1	4763	hgsc.bcm.edu	37	17	29496930	29496930	+	Silent	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:29496930T>C	ENST00000358273.4	+	5	884	c.501T>C	c.(499-501)tgT>tgC	p.C167C	NF1_ENST00000356175.3_Silent_p.C167C|NF1_ENST00000431387.4_Silent_p.C167C	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	167					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.C167*(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TAACTGTTTGTTCAGAAGACA	0.323			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																													yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	13	Whole gene deletion(8)|Unknown(4)|Substitution - Nonsense(1)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)|thyroid(1)	17											92.0	91.0	91.0					17																	29496930		2203	4300	6503	26521056	SO:0001819	synonymous_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.501T>C	17.37:g.29496930T>C		Somatic		Capture	Illumina HiSeq	Phase_I	26521056	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
PGAP3	93210	hgsc.bcm.edu	37	17	37844108	37844108	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:37844108G>A	ENST00000300658.4	-	1	252	c.160C>T	c.(160-162)Cca>Tca	p.P54S	ERBB2_ENST00000406381.2_5'Flank|ERBB2_ENST00000578199.1_5'Flank|PGAP3_ENST00000429199.2_Missense_Mutation_p.P54S|PGAP3_ENST00000579146.1_Missense_Mutation_p.P54S|ERBB2_ENST00000584601.1_5'Flank|PGAP3_ENST00000378011.4_Missense_Mutation_p.P54S	NM_033419.3	NP_219487.3	Q96FM1	PGAP3_HUMAN	post-GPI attachment to proteins 3	54					GPI anchor biosynthetic process (GO:0006506)|GPI anchor metabolic process (GO:0006505)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12						ATGTAGATTGGCTGGCGGGAG	0.642																																																	0			17											21.0	20.0	20.0					17																	37844108		2202	4297	6499	35097634	SO:0001583	missense	93210			AB088396	CCDS32641.1	17q21.2	2009-06-02	2009-06-02	2009-06-02		ENSG00000161395			23719	protein-coding gene	gene with protein product	"""post-GPI attachment to proteins 3"""	611801	"""per1-like domain containing 1"""	PERLD1		15010812, 17021251, 17314402	Standard	NM_001291728		Approved	MGC9753, CAB2, PP1498, PER1	uc002hsj.3	Q96FM1		ENST00000300658.4:c.160C>T	17.37:g.37844108G>A	ENSP00000300658:p.Pro54Ser	Somatic		Capture	Illumina HiSeq	Phase_I	35097634	B4DGK7|Q86Z03|Q8NBJ8	Missense_Mutation	SNP	ENST00000300658.4	37	CCDS32641.1	.	.	.	.	.	.	.	.	.	.	G	35	5.415179	0.96092	.	.	ENSG00000161395	ENST00000300658;ENST00000378011;ENST00000429199	.	.	.	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.77565	0.4149	M	0.72576	2.205	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.993;0.996	T	0.76005	-0.3117	9	0.34782	T	0.22	-9.3794	16.7954	0.85600	0.0:0.0:1.0:0.0	.	54;54;54	B4DGK7;Q96FM1-2;Q96FM1	.;.;PGAP3_HUMAN	S	54	.	ENSP00000300658:P54S	P	-	1	0	PGAP3	35097634	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.622000	0.74233	2.519000	0.84933	0.561000	0.74099	CCA		PGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444825.2	NM_033419	
BRCA1	672	hgsc.bcm.edu	37	17	41244523	41244523	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:41244523A>G	ENST00000357654.3	-	10	3143	c.3025T>C	c.(3025-3027)Tca>Cca	p.S1009P	BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000354071.3_Missense_Mutation_p.S1009P|BRCA1_ENST00000346315.3_Missense_Mutation_p.S1009P|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.S1009P|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.S713P|BRCA1_ENST00000493795.1_Missense_Mutation_p.S962P	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1009					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CTTTCAGGTGACATTGAATGT	0.348			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																													yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	0			17											109.0	108.0	108.0					17																	41244523		2203	4300	6503	38498049	SO:0001583	missense	672	Familial Cancer Database		U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.3025T>C	17.37:g.41244523A>G	ENSP00000350283:p.Ser1009Pro	Somatic		Capture	Illumina HiSeq	Phase_I	38498049	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	A	9.406	1.079152	0.20227	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21;-1.21;-1.21	4.61	3.51	0.40186	.	0.000000	0.41938	D	0.000792	D	0.87144	0.6104	M	0.85373	2.75	0.09310	N	1	D;D;D;D;P;D	0.89917	0.997;0.999;0.995;0.999;0.927;1.0	D;D;D;D;P;D	0.78314	0.916;0.946;0.929;0.979;0.677;0.991	T	0.78565	-0.2155	10	0.66056	D	0.02	.	9.5687	0.39414	0.8434:0.0:0.0:0.1566	.	1009;968;1009;1009;1009;1009	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	P	1009;1009;1009;1009;713;1009;962	ENSP00000350283:S1009P;ENSP00000326002:S1009P;ENSP00000246907:S1009P;ENSP00000310938:S713P;ENSP00000418960:S1009P;ENSP00000418775:S962P	ENSP00000310938:S713P	S	-	1	0	BRCA1	38498049	0.858000	0.29795	0.039000	0.18376	0.013000	0.08279	5.359000	0.66074	0.874000	0.35823	-0.341000	0.08007	TCA		BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
TEX14	56155	hgsc.bcm.edu	37	17	56676693	56676693	+	Silent	SNP	C	C	T	rs142675831		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:56676693C>T	ENST00000240361.8	-	14	2116	c.2031G>A	c.(2029-2031)gcG>gcA	p.A677A	TEX14_ENST00000389934.3_Silent_p.A671A|TEX14_ENST00000349033.5_Silent_p.A671A			Q8IWB6	TEX14_HUMAN	testis expressed 14	677					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.A671A(1)|p.A677A(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CAAAACAACACGCCTCTCTCT	0.493																																																	2	Substitution - coding silent(2)	endometrium(2)	17						C	,,	1,4405	2.1+/-5.4	0,1,2202	146.0	140.0	142.0		2031,2013,2013	-10.5	0.0	17	dbSNP_134	142	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	677/1498,671/1452,671/1492	56676693	1,13005	2203	4300	6503	54031692	SO:0001819	synonymous_variant	56155			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2031G>A	17.37:g.56676693C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54031692	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Silent	SNP	ENST00000240361.8	37	CCDS56042.1																																																																																				TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
CSH1	1442	hgsc.bcm.edu	37	17	61972614	61972614	+	Intron	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:61972614G>A	ENST00000316193.8	-	5	598				CSH1_ENST00000453363.3_Intron|CSH1_ENST00000329882.8_Silent_p.S225S	NM_001317.5	NP_001308.1	P0DML2	CSH1_HUMAN	chorionic somatomammotropin hormone 1 (placental lactogen)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						GAGGCCAAGCGCTTGGGCACT	0.542									Russell-Silver syndrome																																								0			17											68.0	69.0	69.0					17																	61972614		2192	4297	6489	59326346	SO:0001627	intron_variant	1442	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	J00118	CCDS11649.1	17q22-q24	2008-07-18				ENSG00000136488			2440	protein-coding gene	gene with protein product	"""chorionic somatomammotropin A"", ""placental lactogen"", ""choriomammotropin"""	150200				6208192	Standard	NM_001317		Approved	hCS-A, CSA, PL, CSMT, FLJ75407	uc002jcs.2	P0DML2		ENST00000316193.8:c.457-35C>T	17.37:g.61972614G>A		Somatic		Capture	Illumina HiSeq	Phase_I	59326346	P01243|Q0VDB1|Q14407	Silent	SNP	ENST00000316193.8	37	CCDS11649.1																																																																																				CSH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416040.1	NM_001317	
PGS1	9489	hgsc.bcm.edu	37	17	76423179	76423179	+	IGR	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:76423179A>G	ENST00000262764.6	+	0	2201				DNAH17_ENST00000585328.1_Missense_Mutation_p.V4195A|DNAH17_ENST00000389840.5_Missense_Mutation_p.V4223A|DNAH17_ENST00000586052.1_5'UTR	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			GTCGTCCAGCACGGCCTTCAC	0.587																																					Esophageal Squamous(45;182 1126 10685 43198)												0			17											31.0	25.0	27.0					17																	76423179		2199	4288	6487	73934774	SO:0001628	intergenic_variant	8632				CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8			17.37:g.76423179A>G		Somatic		Capture	Illumina HiSeq	Phase_I	73934774	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Missense_Mutation	SNP	ENST00000262764.6	37	CCDS42391.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.150332	0.57151	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.09630	2.96	4.99	4.99	0.66335	.	0.130940	0.34200	N	0.004162	T	0.17023	0.0409	M	0.73372	2.23	0.46609	D	0.999127	B	0.14438	0.01	B	0.22152	0.038	T	0.01869	-1.1257	10	0.59425	D	0.04	.	14.6892	0.69072	1.0:0.0:0.0:0.0	.	4195	E7EUM8	.	A	4195;4223	ENSP00000374490:V4223A	ENSP00000300671:V4195A	V	-	2	0	DNAH17	73934774	0.870000	0.30015	0.997000	0.53966	0.504000	0.33889	5.278000	0.65592	1.880000	0.54463	0.533000	0.62120	GTG		PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419	
RUNX1	861	hgsc.bcm.edu	37	21	36171606	36171606	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr21:36171606C>T	ENST00000344691.4	-	5	2455	c.878G>A	c.(877-879)cGa>cAa	p.R293Q	RUNX1_ENST00000399240.1_Missense_Mutation_p.R229Q|RUNX1_ENST00000437180.1_Missense_Mutation_p.R320Q|RUNX1_ENST00000300305.3_Missense_Mutation_p.R320Q|RUNX1_ENST00000325074.5_Missense_Mutation_p.R308Q	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	293	Interaction with KAT6A.|Pro/Ser/Thr-rich.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R320fs*165(1)		breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						ACTTGAGAGTCGACTGGAAAG	0.522			T	"""RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"""	"""AML, preB- ALL, T-ALL"""																																			Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	1	Complex - frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	21											140.0	130.0	133.0					21																	36171606		2203	4300	6503	35093476	SO:0001583	missense	861			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"""aml1 oncogene"""	151385	"""acute myeloid leukemia 1"""	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.878G>A	21.37:g.36171606C>T	ENSP00000340690:p.Arg293Gln	Somatic		Capture	Illumina HiSeq	Phase_I	35093476	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Missense_Mutation	SNP	ENST00000344691.4	37	CCDS42922.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.536667	0.65085	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000431176;ENST00000399245	D;D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78;-2.78	5.78	5.78	0.91487	.	0.143790	0.47455	D	0.000221	D	0.93953	0.8064	L	0.51422	1.61	0.80722	D	1	B;B;P;B;D	0.69078	0.026;0.218;0.535;0.048;0.997	B;B;B;B;D	0.70227	0.003;0.016;0.049;0.008;0.968	D	0.93421	0.6777	10	0.51188	T	0.08	-9.4081	19.6065	0.95583	0.0:1.0:0.0:0.0	.	296;188;320;308;293	C9JK12;Q01196-11;Q01196-8;Q01196-10;Q01196	.;.;.;.;RUNX1_HUMAN	Q	293;320;320;308;229;54;296	ENSP00000340690:R293Q;ENSP00000300305:R320Q;ENSP00000409227:R320Q;ENSP00000319459:R308Q;ENSP00000382184:R229Q	ENSP00000300305:R320Q	R	-	2	0	RUNX1	35093476	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.581000	0.74045	2.731000	0.93534	0.650000	0.86243	CGA		RUNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194230.1		
CNOT1	23019	hgsc.bcm.edu	37	16	58622786	58622786	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr16:58622786C>T	ENST00000317147.5	-	3	459	c.127G>A	c.(127-129)Gca>Aca	p.A43T	CNOT1_ENST00000569240.1_Missense_Mutation_p.A43T|CNOT1_ENST00000441024.2_Missense_Mutation_p.A43T	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	43					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		TGCCTGTCTGCCTCAGGACCG	0.373																																																	0			16											73.0	62.0	66.0					16																	58622786		2198	4299	6497	57180287	SO:0001583	missense	23019			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.127G>A	16.37:g.58622786C>T	ENSP00000320949:p.Ala43Thr	Somatic		Capture	Illumina HiSeq	Phase_I	57180287	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	C	37	6.045014	0.97231	.	.	ENSG00000125107	ENST00000317147;ENST00000394200;ENST00000441024	T;T	0.23147	1.92;1.92	5.95	5.95	0.96441	.	0.108239	0.64402	D	0.000007	T	0.51244	0.1663	M	0.64404	1.975	0.80722	D	1	D;P;D	0.71674	0.998;0.956;0.997	D;P;D	0.78314	0.991;0.651;0.935	T	0.29243	-1.0018	9	.	.	.	.	20.458	0.99154	0.0:1.0:0.0:0.0	.	43;43;43	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	T	43	ENSP00000320949:A43T;ENSP00000413113:A43T	.	A	-	1	0	CNOT1	57180287	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.835000	0.97688	0.650000	0.86243	GCA		CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
CHST9	83539	hgsc.bcm.edu	37	18	24496363	24496363	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr18:24496363T>C	ENST00000284224.8	-	6	1469	c.1192A>G	c.(1192-1194)Agg>Ggg	p.R398G	AQP4-AS1_ENST00000582605.1_RNA|AQP4-AS1_ENST00000568797.1_RNA|CHST9_ENST00000580774.1_3'UTR|AQP4-AS1_ENST00000579964.1_RNA|CHST9_ENST00000581714.1_Missense_Mutation_p.R398G|AQP4-AS1_ENST00000578701.1_RNA	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	398					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					GAAGAGTGCCTATCCTTAAAG	0.368																																																	0			18											155.0	142.0	146.0					18																	24496363		1839	4091	5930	22750361	SO:0001583	missense	83539			AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"""Sulfotransferases, membrane-bound"""	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.1192A>G	18.37:g.24496363T>C	ENSP00000284224:p.Arg398Gly	Somatic		Capture	Illumina HiSeq	Phase_I	22750361	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	37	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.610254	0.46527	.	.	ENSG00000154080	ENST00000284224	T	0.73681	-0.77	6.07	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.74191	0.3684	L	0.35542	1.07	0.80722	D	1	B	0.29162	0.235	P	0.45343	0.477	T	0.71111	-0.4687	10	0.38643	T	0.18	-25.1503	13.5852	0.61926	0.0:0.0:0.1297:0.8703	.	398	Q7L1S5	CHST9_HUMAN	G	398	ENSP00000284224:R398G	ENSP00000284224:R398G	R	-	1	2	CHST9	22750361	1.000000	0.71417	0.960000	0.40013	0.976000	0.68499	3.206000	0.51098	1.100000	0.41517	0.533000	0.62120	AGG		CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422	
KCNH8	131096	hgsc.bcm.edu	37	3	19436739	19436739	+	Silent	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:19436739G>A	ENST00000328405.2	+	7	1379	c.1113G>A	c.(1111-1113)gcG>gcA	p.A371A	KCNH8_ENST00000537696.1_Silent_p.A12A|KCNH8_ENST00000475063.1_3'UTR	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	371					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						ACTGGATGGCGTGTATCTGGT	0.453																																					NSCLC(124;1625 1765 8018 24930 42026)												0			3											170.0	146.0	154.0					3																	19436739		2203	4300	6503	19411743	SO:0001819	synonymous_variant	131096			AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.1113G>A	3.37:g.19436739G>A		Somatic		Capture	Illumina HiSeq	Phase_I	19411743	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	37	CCDS2632.1																																																																																				KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633	
BAP1	8314	hgsc.bcm.edu	37	3	52436805	52436805	+	Missense_Mutation	SNP	T	T	C	rs372282516		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:52436805T>C	ENST00000460680.1	-	15	2444	c.1973A>G	c.(1972-1974)aAg>aGg	p.K658R	BAP1_ENST00000296288.5_Missense_Mutation_p.K640R	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CTTGAACTTCTTCCTCTTCTC	0.547			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															GBM(101;493 1458 7992 21037 25532)			Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	0			3						T	ARG/LYS	0,4406		0,0,2203	234.0	218.0	224.0		1973	4.8	1.0	3		224	1,8599	1.2+/-3.3	0,1,4299	no	missense	BAP1	NM_004656.2	26	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	658/730	52436805	1,13005	2203	4300	6503	52411845	SO:0001583	missense	9223			AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1973A>G	3.37:g.52436805T>C	ENSP00000417132:p.Lys658Arg	Somatic		Capture	Illumina HiSeq	Phase_I	52411845	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	37	CCDS2853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.15|16.15	3.042685|3.042685	0.55003|0.55003	0.0|0.0	1.16E-4|1.16E-4	ENSG00000163930|ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000478368|ENST00000469613	T;T;T|.	0.48522|.	0.81;0.81;0.81|.	5.94|5.94	4.78|4.78	0.61160|0.61160	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.54481|0.54481	0.1861|0.1861	L|L	0.36672|0.36672	1.1|1.1	0.58432|0.58432	D|D	0.999998|0.999998	B|.	0.29531|.	0.247|.	B|.	0.31191|.	0.125|.	T|T	0.49113|0.49113	-0.8973|-0.8973	10|5	0.54805|.	T|.	0.06|.	.|.	11.7594|11.7594	0.51894|0.51894	0.0:0.0693:0.0:0.9307|0.0:0.0693:0.0:0.9307	.|.	658|.	Q92560|.	BAP1_HUMAN|.	R|G	658;640;182|58	ENSP00000417132:K658R;ENSP00000296288:K640R;ENSP00000420647:K182R|.	ENSP00000296288:K640R|.	K|R	-|-	2|1	0|2	BAP1|BAP1	52411845|52411845	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	6.182000|6.182000	0.71995|0.71995	1.065000|1.065000	0.40693|0.40693	0.533000|0.533000	0.62120|0.62120	AAG|AGA		BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		
CHDH	55349	hgsc.bcm.edu	37	3	53857360	53857360	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:53857360C>T	ENST00000315251.6	-	3	1113	c.676G>A	c.(676-678)Ggc>Agc	p.G226S		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	226					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	TCCATCCAGCCGAAGCCCTCC	0.602																																																	0			3											42.0	43.0	42.0					3																	53857360		2203	4300	6503	53832400	SO:0001583	missense	55349			AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.676G>A	3.37:g.53857360C>T	ENSP00000319851:p.Gly226Ser	Somatic		Capture	Illumina HiSeq	Phase_I	53832400	Q9NY17	Missense_Mutation	SNP	ENST00000315251.6	37	CCDS2873.1	.	.	.	.	.	.	.	.	.	.	C	36	5.605073	0.96626	.	.	ENSG00000016391	ENST00000315251	T	0.42900	0.96	5.72	5.72	0.89469	Glucose-methanol-choline oxidoreductase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.56470	0.1987	L	0.38838	1.175	0.80722	D	1	D	0.89917	1.0	D	0.65987	0.94	T	0.56625	-0.7948	10	0.66056	D	0.02	-37.0968	19.8824	0.96903	0.0:1.0:0.0:0.0	.	226	Q8NE62	CHDH_HUMAN	S	226	ENSP00000319851:G226S	ENSP00000319851:G226S	G	-	1	0	CHDH	53832400	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.414000	0.80117	2.702000	0.92279	0.557000	0.71058	GGC		CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
MYH15	22989	hgsc.bcm.edu	37	3	108224571	108224571	+	Splice_Site	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:108224571T>C	ENST00000273353.3	-	3	310	c.254A>G	c.(253-255)gAg>gGg	p.E85G		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	85						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TTTCTTTACCTCTCCATCTGC	0.333																																																	0			3											189.0	174.0	179.0					3																	108224571		1861	4108	5969	109707261	SO:0001630	splice_region_variant	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.255+1A>G	3.37:g.108224571T>C		Somatic		Capture	Illumina HiSeq	Phase_I	109707261		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	T	8.102	0.776942	0.16120	.	.	ENSG00000144821	ENST00000273353	D	0.81739	-1.53	3.54	2.4	0.29515	Myosin, N-terminal, SH3-like (1);	.	.	.	.	T	0.77785	0.4182	M	0.64997	1.995	0.24112	N	0.995834	B	0.20671	0.047	B	0.30316	0.114	T	0.70299	-0.4910	9	0.72032	D	0.01	.	7.6036	0.28089	0.0:0.1913:0.0:0.8087	.	85	Q9Y2K3	MYH15_HUMAN	G	85	ENSP00000273353:E85G	ENSP00000273353:E85G	E	-	2	0	MYH15	109707261	0.995000	0.38212	0.987000	0.45799	0.116000	0.19942	0.330000	0.19715	0.739000	0.32628	0.533000	0.62120	GAG		MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	Missense_Mutation
CFAP44	55779	hgsc.bcm.edu	37	3	113085054	113085054	+	Missense_Mutation	SNP	C	C	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:113085054C>A	ENST00000295868.2	-	19	2709	c.2547G>T	c.(2545-2547)tgG>tgT	p.W849C	WDR52_ENST00000393845.2_Missense_Mutation_p.W849C	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						TATTGAAGTGCCAGTAGTCCA	0.353																																																	0			3											99.0	91.0	94.0					3																	113085054		2203	4300	6503	114567744	SO:0001583	missense	55779																														ENST00000295868.2:c.2547G>T	3.37:g.113085054C>A	ENSP00000295868:p.Trp849Cys	Somatic		Capture	Illumina HiSeq	Phase_I	114567744		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.575070	0.65878	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.17054	2.3;2.3	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.45135	0.1327	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.24225	-1.0166	8	.	.	.	.	17.733	0.88384	0.0:1.0:0.0:0.0	.	849;849	Q96MT7;Q96MT7-2	WDR52_HUMAN;.	C	849	ENSP00000377428:W849C;ENSP00000295868:W849C	.	W	-	3	0	WDR52	114567744	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	5.523000	0.67099	2.793000	0.96121	0.650000	0.86243	TGG		WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
RNF13	11342	hgsc.bcm.edu	37	3	149613280	149613280	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:149613280A>G	ENST00000344229.3	+	6	1044	c.342A>G	c.(340-342)gcA>gcG	p.A114A	RNF13_ENST00000392894.3_Silent_p.A114A|RNF13_ENST00000361785.6_5'UTR	NM_007282.4	NP_009213.1	O43567	RNF13_HUMAN	ring finger protein 13	114	PA.				protein autoubiquitination (GO:0051865)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	11		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			CACAGAGAGCAGGATACAAGG	0.343																																																	0			3											134.0	113.0	120.0					3																	149613280		2203	4300	6503	151095970	SO:0001819	synonymous_variant	11342			AF037204	CCDS3146.1	3q25.1	2013-01-09			ENSG00000082996	ENSG00000082996		"""RING-type (C3HC4) zinc fingers"""	10057	protein-coding gene	gene with protein product		609247					Standard	NM_183381		Approved	RZF	uc003exp.4	O43567	OTTHUMG00000150338	ENST00000344229.3:c.342A>G	3.37:g.149613280A>G		Somatic		Capture	Illumina HiSeq	Phase_I	151095970	A6NC87|B3KR12|Q05D66|Q6IBJ9	Silent	SNP	ENST00000344229.3	37	CCDS3146.1																																																																																				RNF13-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356876.1	NM_183384	
LRRC31	79782	hgsc.bcm.edu	37	3	169566000	169566000	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:169566000T>C	ENST00000316428.5	-	8	1292	c.1235A>G	c.(1234-1236)aAg>aGg	p.K412R	LRRC31_ENST00000264676.5_Missense_Mutation_p.K356R|LRRC31_ENST00000523069.1_Missense_Mutation_p.K412R	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	412				K -> E (in Ref. 3; BAB15589). {ECO:0000305}.						cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			CAGAAGCAGCTTCAAGTTGCC	0.473																																																	0			3											78.0	79.0	79.0					3																	169566000		2001	4181	6182	171048694	SO:0001583	missense	79782			AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248			26261	protein-coding gene	gene with protein product						12975309	Standard	NM_001277127		Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.1235A>G	3.37:g.169566000T>C	ENSP00000325978:p.Lys412Arg	Somatic		Capture	Illumina HiSeq	Phase_I	171048694	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	Missense_Mutation	SNP	ENST00000316428.5	37	CCDS43167.1	.	.	.	.	.	.	.	.	.	.	T	5.250	0.231496	0.09969	.	.	ENSG00000114248	ENST00000316428;ENST00000264676;ENST00000523069	T;T;T	0.53857	0.6;0.6;0.6	4.61	2.16	0.27623	.	0.504809	0.22750	N	0.056084	T	0.49253	0.1546	M	0.75264	2.295	0.21147	N	0.999774	P;B	0.42692	0.787;0.083	B;B	0.41988	0.372;0.022	T	0.36986	-0.9725	10	0.27785	T	0.31	-5.4006	7.1729	0.25728	0.0:0.0775:0.1471:0.7754	.	356;412	Q6UY01-2;Q6UY01	.;LRC31_HUMAN	R	412;356;412	ENSP00000325978:K412R;ENSP00000264676:K356R;ENSP00000429145:K412R	ENSP00000264676:K356R	K	-	2	0	LRRC31	171048694	1.000000	0.71417	0.825000	0.32803	0.015000	0.08874	1.899000	0.39818	0.155000	0.19261	-0.313000	0.08912	AAG		LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378699.1	NM_024727	
PIK3CA	5290	hgsc.bcm.edu	37	3	178942591	178942591	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:178942591A>G	ENST00000263967.3	+	16	2555	c.2398A>G	c.(2398-2400)Atc>Gtc	p.I800V		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	800	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CAATGAGATCATCTTTAAAAA	0.363		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	0			3											144.0	134.0	137.0					3																	178942591		1857	4094	5951	180425285	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2398A>G	3.37:g.178942591A>G	ENSP00000263967:p.Ile800Val	Somatic		Capture	Illumina HiSeq	Phase_I	180425285	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.471237	0.84533	.	.	ENSG00000121879	ENST00000263967	T	0.77750	-1.12	5.39	5.39	0.77823	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.88500	0.6453	M	0.87827	2.91	0.80722	D	1	D	0.67145	0.996	D	0.63381	0.914	D	0.90685	0.4608	10	0.87932	D	0	-10.5967	15.7036	0.77560	1.0:0.0:0.0:0.0	.	800	P42336	PK3CA_HUMAN	V	800	ENSP00000263967:I800V	ENSP00000263967:I800V	I	+	1	0	PIK3CA	180425285	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.807000	0.91935	2.173000	0.68751	0.460000	0.39030	ATC		PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
PIK3CA	5290	hgsc.bcm.edu	37	3	178951978	178951978	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:178951978A>G	ENST00000263967.3	+	21	3190	c.3033A>G	c.(3031-3033)ccA>ccG	p.P1011P	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1011	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.P1011P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CTGGAATGCCAGAACTACAAT	0.383		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1	Substitution - coding silent(1)	large_intestine(1)	3											111.0	99.0	102.0					3																	178951978		1882	4110	5992	180434672	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3033A>G	3.37:g.178951978A>G		Somatic		Capture	Illumina HiSeq	Phase_I	180434672	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
PIK3CA	5290	hgsc.bcm.edu	37	3	178951998	178951998	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:178951998A>G	ENST00000263967.3	+	21	3210	c.3053A>G	c.(3052-3054)gAc>gGc	p.D1018G	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1018	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCTTTTGATGACATTGCATAC	0.398		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	0			3											107.0	95.0	99.0					3																	178951998		1877	4118	5995	180434692	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3053A>G	3.37:g.178951998A>G	ENSP00000263967:p.Asp1018Gly	Somatic		Capture	Illumina HiSeq	Phase_I	180434692	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	18.89	3.718873	0.68844	.	.	ENSG00000121879	ENST00000263967	D	0.82167	-1.58	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.91998	0.7465	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.93021	0.6440	10	0.87932	D	0	-20.7568	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1018	P42336	PK3CA_HUMAN	G	1018	ENSP00000263967:D1018G	ENSP00000263967:D1018G	D	+	2	0	PIK3CA	180434692	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.798000	0.91888	2.333000	0.79357	0.482000	0.46254	GAC		PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
PIK3CA	5290	hgsc.bcm.edu	37	3	178952036	178952036	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:178952036A>G	ENST00000263967.3	+	21	3248	c.3091A>G	c.(3091-3093)Act>Gct	p.T1031A	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1031	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CTTAGATAAAACTGAGCAAGA	0.378		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	0			3											93.0	82.0	86.0					3																	178952036		1872	4117	5989	180434730	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3091A>G	3.37:g.178952036A>G	ENSP00000263967:p.Thr1031Ala	Somatic		Capture	Illumina HiSeq	Phase_I	180434730	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	12.16	1.855179	0.32791	.	.	ENSG00000121879	ENST00000263967	D	0.81739	-1.53	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.258350	0.36972	N	0.002317	D	0.84611	0.5510	M	0.88181	2.935	0.58432	D	0.999999	B	0.18013	0.025	B	0.18561	0.022	T	0.82585	-0.0384	10	0.72032	D	0.01	-20.0073	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1031	P42336	PK3CA_HUMAN	A	1031	ENSP00000263967:T1031A	ENSP00000263967:T1031A	T	+	1	0	PIK3CA	180434730	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.555000	0.45854	2.333000	0.79357	0.482000	0.46254	ACT		PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
FGF12	2257	hgsc.bcm.edu	37	3	192078255	192078255	+	Missense_Mutation	SNP	C	C	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:192078255C>A	ENST00000454309.2	-	2	1097	c.272G>T	c.(271-273)gGt>gTt	p.G91V	FGF12_ENST00000450716.1_Missense_Mutation_p.G29V|FGF12_ENST00000430714.1_Intron|FGF12_ENST00000264730.3_Missense_Mutation_p.G29V|FGF12_ENST00000445105.2_Missense_Mutation_p.G29V	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12	91					adult locomotory behavior (GO:0008344)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell-cell signaling (GO:0007267)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|JNK cascade (GO:0007254)|negative regulation of cation channel activity (GO:2001258)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|regulation of membrane depolarization (GO:0003254)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)			endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		ATCAATGGTACCATCTGGGTG	0.408																																																	0			3											175.0	150.0	158.0					3																	192078255		2203	4300	6503	193560949	SO:0001583	missense	2257			U66197	CCDS3301.1, CCDS46983.1	3q28	2008-07-18			ENSG00000114279	ENSG00000114279			3668	protein-coding gene	gene with protein product	"""fibroblast growth factor 12B"", ""fibroblast growth factor homologous factor 1"", ""myocyte-activating factor"", ""fibroblast growth factor FGF-12b"""	601513		FGF12B		8790420, 9345906	Standard	NM_021032		Approved	FHF1	uc003fsx.3	P61328	OTTHUMG00000156132	ENST00000454309.2:c.272G>T	3.37:g.192078255C>A	ENSP00000413496:p.Gly91Val	Somatic		Capture	Illumina HiSeq	Phase_I	193560949	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Missense_Mutation	SNP	ENST00000454309.2	37	CCDS3301.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.558103	0.86231	.	.	ENSG00000114279	ENST00000264730;ENST00000392454;ENST00000445105;ENST00000454309;ENST00000450716;ENST00000448795;ENST00000418610	D;D;D;D;D;D	0.90261	-2.64;-2.64;-2.64;-2.64;-2.64;-2.64	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.97084	0.9047	H	0.96301	3.8	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.83275	0.967;0.996	D	0.98117	1.0423	10	0.87932	D	0	.	18.4573	0.90725	0.0:1.0:0.0:0.0	.	29;91	P61328-2;P61328	.;FGF12_HUMAN	V	29;29;29;91;29;5;29	ENSP00000264730:G29V;ENSP00000393686:G29V;ENSP00000413496:G91V;ENSP00000397635:G29V;ENSP00000412904:G5V;ENSP00000395517:G29V	ENSP00000264730:G29V	G	-	2	0	FGF12	193560949	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.398000	0.79919	2.613000	0.88420	0.591000	0.81541	GGT		FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032	
CD163L1	283316	hgsc.bcm.edu	37	12	7585297	7585297	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:7585297T>C	ENST00000313599.3	-	4	538	c.481A>G	c.(481-483)Aac>Gac	p.N161D	CD163L1_ENST00000416109.2_Missense_Mutation_p.N171D|CD163L1_ENST00000396630.1_Missense_Mutation_p.N161D			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	161	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						CAGGAGTTGTTTCCATCCACT	0.438																																																	0			12											87.0	82.0	84.0					12																	7585297		2203	4300	6503	7476564	SO:0001583	missense	283316			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.481A>G	12.37:g.7585297T>C	ENSP00000315945:p.Asn161Asp	Somatic		Capture	Illumina HiSeq	Phase_I	7476564	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	T	1.449	-0.565630	0.03910	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630	T;T;T	0.35048	1.33;1.33;1.33	2.22	-2.95	0.05564	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.14399	0.0348	N	0.03903	-0.33	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.30765	-0.9967	9	0.20519	T	0.43	.	9.9234	0.41478	0.0:0.7101:0.0:0.2899	.	171;161	E7EVK4;Q9NR16	.;C163B_HUMAN	D	161;171;161	ENSP00000315945:N161D;ENSP00000393474:N171D;ENSP00000379871:N161D	ENSP00000315945:N161D	N	-	1	0	CD163L1	7476564	0.000000	0.05858	0.002000	0.10522	0.228000	0.25075	-1.924000	0.01565	-0.836000	0.04229	0.460000	0.39030	AAC		CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
PLCZ1	89869	hgsc.bcm.edu	37	12	18836250	18836250	+	Missense_Mutation	SNP	G	G	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:18836250G>T	ENST00000538330.1	-	11	1477	c.1096C>A	c.(1096-1098)Cgt>Agt	p.R366S	PLCZ1_ENST00000534932.1_Missense_Mutation_p.R65S|PLCZ1_ENST00000435379.1_Missense_Mutation_p.R389S|PLCZ1_ENST00000539875.1_Missense_Mutation_p.R391S|PLCZ1_ENST00000541695.1_3'UTR|PLCZ1_ENST00000447925.2_Missense_Mutation_p.R582S|PLCZ1_ENST00000266505.7_Missense_Mutation_p.R584S					phospholipase C, zeta 1									p.R584C(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					AGAGGAATACGACGATAACCT	0.383																																																	1	Substitution - Missense(1)	lung(1)	12											107.0	98.0	101.0					12																	18836250		2203	4300	6503	18727517	SO:0001583	missense	89869			AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"""EF-hand domain containing"""	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000538330.1:c.1096C>A	12.37:g.18836250G>T	ENSP00000445880:p.Arg366Ser	Somatic		Capture	Illumina HiSeq	Phase_I	18727517		Missense_Mutation	SNP	ENST00000538330.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.26|12.26	1.885022|1.885022	0.33255|0.33255	.|.	.|.	ENSG00000139151|ENSG00000139151	ENST00000534932;ENST00000538330;ENST00000266505;ENST00000447925;ENST00000435379;ENST00000539875|ENST00000536023	T;T;T;T;T;T|.	0.12984|.	2.63;2.63;2.63;2.63;2.63;2.63|.	5.34|5.34	4.39|4.39	0.52855|0.52855	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);|.	0.308722|.	0.33515|.	N|.	0.004826|.	T|.	0.31765|.	0.0807|.	N|N	0.04090|0.04090	-0.28|-0.28	0.54753|0.54753	D|D	0.999981|0.999981	B;B|.	0.32128|.	0.304;0.357|.	B;B|.	0.28709|.	0.069;0.093|.	T|.	0.10894|.	-1.0610|.	10|.	0.87932|.	D|.	0|.	.|.	10.3184|10.3184	0.43751|0.43751	0.0:0.0:0.7906:0.2094|0.0:0.0:0.7906:0.2094	.|.	584;366|.	Q86YW0;Q8N7S5|.	PLCZ1_HUMAN;.|.	S|X	65;366;584;582;389;391|76	ENSP00000438826:R65S;ENSP00000445880:R366S;ENSP00000266505:R584S;ENSP00000402358:R582S;ENSP00000400504:R389S;ENSP00000445026:R391S|.	ENSP00000266505:R584S|.	R|S	-|-	1|2	0|0	PLCZ1|PLCZ1	18727517|18727517	0.531000|0.531000	0.26338|0.26338	0.997000|0.997000	0.53966|0.53966	0.382000|0.382000	0.30200|0.30200	3.279000|3.279000	0.51670|0.51670	2.776000|2.776000	0.95493|0.95493	0.655000|0.655000	0.94253|0.94253	CGT|TCG		PLCZ1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000401666.3	NM_033123	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43846451	43846451	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:43846451C>T	ENST00000389420.3	-	13	1807	c.1808G>A	c.(1807-1809)cGa>cAa	p.R603Q	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.R603Q	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	603	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ATTACATGATCGAAATTTCAT	0.398																																																	0			12											78.0	67.0	70.0					12																	43846451		2203	4300	6503	42132718	SO:0001583	missense	80070			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1808G>A	12.37:g.43846451C>T	ENSP00000374071:p.Arg603Gln	Somatic		Capture	Illumina HiSeq	Phase_I	42132718	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	C	35	5.437596	0.96168	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.49720	0.77;0.77	4.85	4.85	0.62838	.	0.000000	0.43416	D	0.000561	T	0.55481	0.1923	N	0.20685	0.6	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.57900	-0.7731	10	0.44086	T	0.13	.	18.851	0.92230	0.0:1.0:0.0:0.0	.	603	P59510	ATS20_HUMAN	Q	603	ENSP00000374071:R603Q;ENSP00000448341:R603Q	ENSP00000374068:R603Q	R	-	2	0	ADAMTS20	42132718	0.998000	0.40836	0.995000	0.50966	0.998000	0.95712	3.766000	0.55280	2.624000	0.88883	0.563000	0.77884	CGA		ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
ARID2	196528	hgsc.bcm.edu	37	12	46245966	46245966	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:46245966A>G	ENST00000334344.6	+	15	4232	c.4060A>G	c.(4060-4062)Aga>Gga	p.R1354G	ARID2_ENST00000422737.1_Missense_Mutation_p.R1205G|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000444670.1_Missense_Mutation_p.R964G	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1354					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		AAGTGATTTGAGAAAACCGCT	0.348			"""N, S, F"""		hepatocellular carcinoma																																			Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	0			12											65.0	64.0	64.0					12																	46245966		2203	4300	6503	44532233	SO:0001583	missense	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4060A>G	12.37:g.46245966A>G	ENSP00000335044:p.Arg1354Gly	Somatic		Capture	Illumina HiSeq	Phase_I	44532233	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	A	12.55	1.971335	0.34754	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670	T	0.33654	1.4	6.07	6.07	0.98685	.	0.040149	0.85682	D	0.000000	T	0.24392	0.0591	N	0.08118	0	0.80722	D	1	B;B;B	0.16802	0.019;0.019;0.011	B;B;B	0.18561	0.022;0.022;0.005	T	0.06499	-1.0823	10	0.87932	D	0	-5.9255	16.6288	0.85011	1.0:0.0:0.0:0.0	.	1354;964;1354	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	G	1354;471;471;1205;964	ENSP00000335044:R1354G	ENSP00000335044:R1354G	R	+	1	2	ARID2	44532233	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.690000	0.91272	2.326000	0.78906	0.533000	0.62120	AGA		ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	
LIMA1	51474	hgsc.bcm.edu	37	12	50571248	50571248	+	Missense_Mutation	SNP	C	C	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:50571248C>G	ENST00000341247.4	-	11	2028	c.1879G>C	c.(1879-1881)Ggt>Cgt	p.G627R	LIMA1_ENST00000552823.1_Missense_Mutation_p.G467R|LIMA1_ENST00000547825.1_Missense_Mutation_p.G325R|LIMA1_ENST00000552783.1_Missense_Mutation_p.G468R|LIMA1_ENST00000394943.3_Missense_Mutation_p.G628R|LIMA1_ENST00000552491.1_Missense_Mutation_p.G324R|LIMA1_ENST00000552909.1_Missense_Mutation_p.G466R	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	627					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						ACTCTTCCACCCACAGACTCT	0.458																																																	0			12											268.0	276.0	274.0					12																	50571248		2203	4300	6503	48857515	SO:0001583	missense	51474			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1879G>C	12.37:g.50571248C>G	ENSP00000340184:p.Gly627Arg	Somatic		Capture	Illumina HiSeq	Phase_I	48857515	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	1.775	-0.483428	0.04383	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;T;T;D;T;T;T	0.83837	-1.03;-1.03;-1.35;-1.77;-1.03;-1.36;-1.35	5.7	5.7	0.88788	.	0.810925	0.11593	N	0.548543	T	0.79941	0.4533	L	0.57536	1.79	0.09310	N	1	B;B;B	0.18610	0.013;0.013;0.029	B;B;B	0.18871	0.008;0.008;0.023	T	0.65146	-0.6239	10	0.26408	T	0.33	.	11.2795	0.49186	0.0:0.89:0.0:0.11	.	637;627;466	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	R	324;325;467;628;627;468;466;546	ENSP00000448463:G324R;ENSP00000448706:G325R;ENSP00000450266:G467R;ENSP00000378400:G628R;ENSP00000340184:G627R;ENSP00000448779:G468R;ENSP00000450087:G466R	ENSP00000340184:G627R	G	-	1	0	LIMA1	48857515	0.006000	0.16342	0.021000	0.16686	0.118000	0.20060	2.081000	0.41596	2.850000	0.98022	0.650000	0.86243	GGT		LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357	
LIMA1	51474	hgsc.bcm.edu	37	12	50642509	50642509	+	Missense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:50642509C>T	ENST00000341247.4	-	2	175	c.26G>A	c.(25-27)cGg>cAg	p.R9Q	LIMA1_ENST00000394943.3_Missense_Mutation_p.R9Q	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	9					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						GGTCCATTGCCGTCTATTAAA	0.388																																																	0			12											170.0	151.0	158.0					12																	50642509		2203	4300	6503	48928776	SO:0001583	missense	51474			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.26G>A	12.37:g.50642509C>T	ENSP00000340184:p.Arg9Gln	Somatic		Capture	Illumina HiSeq	Phase_I	48928776	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.361317	0.41801	.	.	ENSG00000050405	ENST00000394943;ENST00000341247;ENST00000551691;ENST00000550592	D;T	0.85411	-1.98;-1.24	4.7	2.86	0.33363	.	0.276630	0.33670	N	0.004665	T	0.70422	0.3222	N	0.21583	0.68	0.80722	D	1	B;B	0.30193	0.07;0.272	B;B	0.16289	0.003;0.015	T	0.62779	-0.6782	10	0.29301	T	0.29	-6.9825	8.9102	0.35548	0.0:0.8158:0.0:0.1842	.	18;9	Q59FE8;Q9UHB6	.;LIMA1_HUMAN	Q	9	ENSP00000378400:R9Q;ENSP00000340184:R9Q	ENSP00000340184:R9Q	R	-	2	0	LIMA1	48928776	0.987000	0.35691	0.999000	0.59377	0.979000	0.70002	0.530000	0.23036	0.659000	0.30945	0.655000	0.94253	CGG		LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357	
MUCL1	118430	hgsc.bcm.edu	37	12	55250571	55250571	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:55250571G>A	ENST00000308796.6	+	3	164	c.118G>A	c.(118-120)Gaa>Aaa	p.E40K	MUCL1_ENST00000547990.1_3'UTR|MUCL1_ENST00000546809.1_Missense_Mutation_p.E35K	NM_058173.2	NP_477521.1	Q96DR8	MUCL1_HUMAN	mucin-like 1	40	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|membrane (GO:0016020)				breast(1)|kidney(1)|lung(1)	3						tgctgatgatgaagcccctga	0.502																																																	0			12											103.0	81.0	88.0					12																	55250571		2203	4300	6503	53536838	SO:0001583	missense	118430			AF414087	CCDS8885.1	12q13.2	2007-07-02							30588	protein-coding gene	gene with protein product	"""small breast epithelial mucin"""	610857				12019145	Standard	NM_058173		Approved	SBEM	uc001sgk.3	Q96DR8		ENST00000308796.6:c.118G>A	12.37:g.55250571G>A	ENSP00000311364:p.Glu40Lys	Somatic		Capture	Illumina HiSeq	Phase_I	53536838	Q0VG95|Q32ZB5	Missense_Mutation	SNP	ENST00000308796.6	37	CCDS8885.1	.	.	.	.	.	.	.	.	.	.	G	5.182	0.219210	0.09863	.	.	ENSG00000172551	ENST00000546809;ENST00000308796	.	.	.	2.09	-1.68	0.08212	.	9.544620	0.01122	U	0.005800	T	0.30947	0.0781	.	.	.	0.09310	N	1	P	0.46020	0.871	B	0.41036	0.346	T	0.33007	-0.9885	8	0.87932	D	0	.	5.6198	0.17451	0.5843:0.0:0.4157:0.0	.	40	Q96DR8	MUCL1_HUMAN	K	35;40	.	ENSP00000311364:E40K	E	+	1	0	MUCL1	53536838	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.066000	0.01385	-0.446000	0.07149	0.561000	0.74099	GAA		MUCL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406062.1	NM_058173	
PPFIA2	8499	hgsc.bcm.edu	37	12	81799572	81799572	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:81799572A>G	ENST00000549396.1	-	8	916	c.756T>C	c.(754-756)caT>caC	p.H252H	PPFIA2_ENST00000333447.7_Silent_p.H234H|PPFIA2_ENST00000549325.1_Silent_p.H234H|RP11-315E17.1_ENST00000546936.1_RNA|PPFIA2_ENST00000550359.2_Silent_p.H99H|PPFIA2_ENST00000443686.3_Silent_p.H153H|PPFIA2_ENST00000548586.1_Silent_p.H252H|PPFIA2_ENST00000407050.4_Silent_p.H178H|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000550584.2_Silent_p.H252H|PPFIA2_ENST00000552948.1_Silent_p.H252H	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	252	Glu-rich.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						ATACCTTCTCATGGACTTTCT	0.373																																																	0			12											101.0	93.0	96.0					12																	81799572		1914	4120	6034	80323703	SO:0001819	synonymous_variant	8499			AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9246	protein-coding gene	gene with protein product	"""Liprin-alpha2"""	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.756T>C	12.37:g.81799572A>G		Somatic		Capture	Illumina HiSeq	Phase_I	80323703	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Silent	SNP	ENST00000549396.1	37	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	A	8.862	0.947074	0.18356	.	.	ENSG00000139220	ENST00000548790	.	.	.	5.15	3.99	0.46301	.	.	.	.	.	T	0.59142	0.2172	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55121	-0.8190	4	.	.	.	-16.3209	9.0926	0.36621	0.905:0.0:0.095:0.0	.	.	.	.	T	70	.	.	M	-	2	0	PPFIA2	80323703	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.882000	0.48546	0.899000	0.36444	0.455000	0.32223	ATG		PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1		
CEP290	80184	hgsc.bcm.edu	37	12	88465168	88465168	+	Missense_Mutation	SNP	C	C	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:88465168C>A	ENST00000552810.1	-	43	6257	c.5914G>T	c.(5914-5916)Gat>Tat	p.D1972Y	CEP290_ENST00000397838.3_Missense_Mutation_p.D1032Y|CEP290_ENST00000547691.2_Missense_Mutation_p.D1032Y|CEP290_ENST00000309041.7_Missense_Mutation_p.D1974Y	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1972					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						AAAACCTGATCAACAGTCATG	0.323																																																	0			12											142.0	127.0	132.0					12																	88465168		1811	4077	5888	86989299	SO:0001583	missense	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5914G>T	12.37:g.88465168C>A	ENSP00000448012:p.Asp1972Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	86989299	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	C	19.49	3.836618	0.71373	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	T;T;T;T	0.70399	0.16;-0.48;-0.48;0.16	5.23	4.28	0.50868	.	0.042775	0.85682	D	0.000000	T	0.80783	0.4689	M	0.70595	2.14	0.54753	D	0.999989	D	0.63880	0.993	P	0.62740	0.906	T	0.82518	-0.0417	10	0.66056	D	0.02	.	12.9114	0.58182	0.0:0.914:0.0:0.086	.	1972	O15078	CE290_HUMAN	Y	1032;1972;1974;1032	ENSP00000446905:D1032Y;ENSP00000448012:D1972Y;ENSP00000308021:D1974Y;ENSP00000380938:D1032Y	ENSP00000308021:D1974Y	D	-	1	0	CEP290	86989299	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.174000	0.65015	1.208000	0.43306	0.484000	0.47621	GAT		CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
MYBPC1	4604	hgsc.bcm.edu	37	12	102043144	102043144	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:102043144G>A	ENST00000550270.1	+	13	1228	c.1228G>A	c.(1228-1230)Gct>Act	p.A410T	MYBPC1_ENST00000536007.1_Missense_Mutation_p.A391T|MYBPC1_ENST00000549145.1_Missense_Mutation_p.A423T|MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000547405.1_Missense_Mutation_p.A384T|RP11-755O11.2_ENST00000552081.1_RNA|MYBPC1_ENST00000452455.2_Missense_Mutation_p.A410T|MYBPC1_ENST00000545503.2_Missense_Mutation_p.A410T|MYBPC1_ENST00000541119.1_Missense_Mutation_p.A398T|MYBPC1_ENST00000547509.1_Missense_Mutation_p.A396T|MYBPC1_ENST00000551300.1_Missense_Mutation_p.A311T|MYBPC1_ENST00000361466.2_Missense_Mutation_p.A435T|MYBPC1_ENST00000361685.2_Missense_Mutation_p.A435T|MYBPC1_ENST00000392934.3_Missense_Mutation_p.A397T|MYBPC1_ENST00000553190.1_Missense_Mutation_p.A410T|MYBPC1_ENST00000441232.1_Missense_Mutation_p.A410T|RP11-755O11.2_ENST00000547027.1_RNA|MYBPC1_ENST00000360610.2_Missense_Mutation_p.A410T			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	410	Ig-like C2-type 3.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						AAAGGCTGATGCTGCAGAATA	0.398																																																	0			12											191.0	174.0	179.0					12																	102043144		2203	4300	6503	100567275	SO:0001583	missense	4604				CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7549	protein-coding gene	gene with protein product		160794	"""myosin-binding protein C, slow-type"""			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.1228G>A	12.37:g.102043144G>A	ENSP00000449702:p.Ala410Thr	Somatic		Capture	Illumina HiSeq	Phase_I	100567275	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	37	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	G	3.297	-0.143683	0.06627	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000540770;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.98	0.805	0.18703	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.660490	0.03710	N	0.250087	T	0.49304	0.1549	N	0.20807	0.61	0.09310	N	0.999995	B;B;B;B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B;B;B	0.09377	0.004;0.0;0.001;0.0;0.001;0.002;0.0;0.001;0.001;0.0;0.0	T	0.21280	-1.0250	10	0.14252	T	0.57	.	6.831	0.23911	0.493:0.0:0.0626:0.4444	.	391;398;410;410;397;384;410;410;435;435;423	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2;F8VZY0	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.;.	T	384;410;410;410;397;396;435;423;410;435;410;391;398;435;311;410	ENSP00000448175:A384T;ENSP00000400908:A410T;ENSP00000388989:A410T;ENSP00000353822:A410T;ENSP00000376665:A397T;ENSP00000447362:A396T;ENSP00000354845:A435T;ENSP00000447660:A423T;ENSP00000447900:A410T;ENSP00000440034:A410T;ENSP00000446128:A391T;ENSP00000442847:A398T;ENSP00000354849:A435T;ENSP00000447116:A311T;ENSP00000449702:A410T	ENSP00000353822:A410T	A	+	1	0	MYBPC1	100567275	0.604000	0.26932	0.015000	0.15790	0.010000	0.07245	2.207000	0.42788	-0.095000	0.12351	-1.619000	0.00793	GCT		MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
SLC24A5	283652	hgsc.bcm.edu	37	15	48431257	48431257	+	Silent	SNP	C	C	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr15:48431257C>G	ENST00000341459.3	+	7	1036	c.963C>G	c.(961-963)acC>acG	p.T321T	SLC24A5_ENST00000449382.2_Silent_p.T261T	NM_205850.2	NP_995322.1	Q71RS6	NCKX5_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 5	321					ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|negative regulation of melanin biosynthetic process (GO:0048022)|response to stimulus (GO:0050896)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|skin(1)|upper_aerodigestive_tract(1)	27		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		TTTTTCTAACCACACCAGATT	0.338																																																	0			15											70.0	70.0	70.0					15																	48431257		2197	4292	6489	46218549	SO:0001819	synonymous_variant	283652			AF348468	CCDS10128.1	15q21.1	2014-01-28	2013-07-18		ENSG00000188467	ENSG00000188467		"""Solute carriers"""	20611	protein-coding gene	gene with protein product	"""oculocutaneous albinism 6 (autosomal recessive)"""	609802	"""solute carrier family 24, member 5"""			23364476	Standard	XM_005254308		Approved	JSX, OCA6	uc001zwe.3	Q71RS6	OTTHUMG00000131494	ENST00000341459.3:c.963C>G	15.37:g.48431257C>G		Somatic		Capture	Illumina HiSeq	Phase_I	46218549	A5X8Z8|A5X8Z9|Q14CT4|Q6DKH3	Silent	SNP	ENST00000341459.3	37	CCDS10128.1																																																																																				SLC24A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254340.2	NM_205850	
DMD	1756	hgsc.bcm.edu	37	X	32827653	32827653	+	Silent	SNP	G	G	A	rs138335295		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chrX:32827653G>A	ENST00000357033.4	-	7	812	c.606C>T	c.(604-606)atC>atT	p.I202I	DMD_ENST00000288447.4_Silent_p.I194I|DMD_ENST00000378677.2_Silent_p.I198I	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	202	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GATATCTGGCGATGTTGAATG	0.408																																																	0			X						G	,,,,	1,3832		0,1,1630,571	189.0	140.0	157.0		582,606,237,594,237	-10.2	0.4	X	dbSNP_134	157	0,6728		0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	,,,,	0,1,4058,2443	AA,AG,GG,G		0.0,0.0261,0.0095	,,,,	194/3678,202/3686,79/3563,198/3682,79/3563	32827653	1,10560	2202	4300	6502	32737574	SO:0001819	synonymous_variant	1756			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.606C>T	X.37:g.32827653G>A		Somatic		Capture	Illumina HiSeq	Phase_I	32737574	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																				DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
PAK3	5063	hgsc.bcm.edu	37	X	110366490	110366490	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chrX:110366490A>G	ENST00000372010.1	+	5	601	c.159A>G	c.(157-159)ccA>ccG	p.P53P	PAK3_ENST00000446737.1_Silent_p.P53P|PAK3_ENST00000262836.4_Silent_p.P53P|PAK3_ENST00000518291.1_Silent_p.P53P|PAK3_ENST00000417227.1_Silent_p.P53P|PAK3_ENST00000372007.5_Silent_p.P53P|PAK3_ENST00000425146.1_Silent_p.P53P|PAK3_ENST00000519681.1_Silent_p.P53P|PAK3_ENST00000360648.4_Silent_p.P53P			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	53					activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						CTATCTTCCCAGGAGGAGGGG	0.448										TSP Lung(19;0.15)																																							0			X											74.0	73.0	73.0					X																	110366490		2203	4300	6503	110253146	SO:0001819	synonymous_variant	8874			AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"""mental retardation, X-linked 47"", ""p21 (CDKN1A)-activated kinase 3"""	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.159A>G	X.37:g.110366490A>G		Somatic		Capture	Illumina HiSeq	Phase_I	110253146	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Silent	SNP	ENST00000372010.1	37	CCDS48153.1																																																																																				PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578	
PRR32	100130613	hgsc.bcm.edu	37	X	125954937	125954937	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chrX:125954937A>G	ENST00000371125.3	+	2	396	c.316A>G	c.(316-318)Aca>Gca	p.T106A		NM_001122716.1	NP_001116188.1	B1ATL7	PRR32_HUMAN		106																	GTCCCTAGCAACAGCAGAAGT	0.552																																																	0			X											45.0	35.0	38.0					X																	125954937		692	1591	2283	125782618	SO:0001583	missense	100130613																														ENST00000371125.3:c.316A>G	X.37:g.125954937A>G	ENSP00000360166:p.Thr106Ala	Somatic		Capture	Illumina HiSeq	Phase_I	125782618		Missense_Mutation	SNP	ENST00000371125.3	37	CCDS48163.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.819720	0.50633	.	.	ENSG00000183631	ENST00000371125	T	0.43294	0.95	4.01	4.01	0.46588	.	0.000000	0.34725	N	0.003721	T	0.45816	0.1361	L	0.34521	1.04	0.31088	N	0.711173	D	0.65815	0.995	P	0.60886	0.88	T	0.51521	-0.8695	10	0.87932	D	0	-14.4197	8.4065	0.32619	1.0:0.0:0.0:0.0	.	106	B1ATL7	CX064_HUMAN	A	106	ENSP00000360166:T106A	ENSP00000360166:T106A	T	+	1	0	CXorf64	125782618	1.000000	0.71417	1.000000	0.80357	0.514000	0.34195	3.057000	0.49931	1.804000	0.52760	0.481000	0.45027	ACA		CXorf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058188.1		
ATP11C	286410	hgsc.bcm.edu	37	X	138832229	138832229	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chrX:138832229T>C	ENST00000327569.3	-	24	2890	c.2792A>G	c.(2791-2793)cAg>cGg	p.Q931R	ATP11C_ENST00000370557.1_Missense_Mutation_p.Q925R|ATP11C_ENST00000370543.1_Missense_Mutation_p.Q931R|ATP11C_ENST00000359686.2_Missense_Mutation_p.Q931R|ATP11C_ENST00000460773.1_5'UTR|ATP11C_ENST00000361648.2_Missense_Mutation_p.Q931R	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	931			Q -> P (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.Q931P(1)		breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					GTTGATGTGCTGTTCCAGTAG	0.383																																																	1	Substitution - Missense(1)	large_intestine(1)	X											215.0	182.0	193.0					X																	138832229		2203	4300	6503	138659895	SO:0001583	missense	286410			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"""ATPases / P-type"""	13554	protein-coding gene	gene with protein product		300516	"""ATPase, Class VI, type 11C"""			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.2792A>G	X.37:g.138832229T>C	ENSP00000332756:p.Gln931Arg	Somatic		Capture	Illumina HiSeq	Phase_I	138659895	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.479344	0.84747	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	D;D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35;-2.35	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	D	0.93213	0.7838	M	0.67397	2.05	0.58432	D	0.999996	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.87578	0.998;0.995;0.998	D	0.92283	0.5835	10	0.33940	T	0.23	.	14.3858	0.66942	0.0:0.0:0.0:1.0	.	931;931;931	Q8NB49-3;Q8NB49;Q8NB49-2	.;AT11C_HUMAN;.	R	925;931;931;931;931	ENSP00000359588:Q925R;ENSP00000355165:Q931R;ENSP00000332756:Q931R;ENSP00000359574:Q931R;ENSP00000352715:Q931R	ENSP00000332756:Q931R	Q	-	2	0	ATP11C	138659895	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	7.698000	0.84413	1.996000	0.58369	0.481000	0.45027	CAG		ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694	
CCKAR	886	hgsc.bcm.edu	37	4	26483526	26483526	+	Missense_Mutation	SNP	C	C	T	rs115488558		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:26483526C>T	ENST00000295589.3	-	5	1215	c.1021G>A	c.(1021-1023)Gcc>Acc	p.A341T		NM_000730.2	NP_000721.1	P32238	CCKAR_HUMAN	cholecystokinin A receptor	341					axonogenesis (GO:0007409)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|feeding behavior (GO:0007631)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cholecystokinin receptor activity (GO:0004951)			NS(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|pancreas(1)|skin(1)	29		Breast(46;0.0503)			Ceruletide(DB00403)	TCTGCGGAGGCGGTGTCGTAG	0.587																																																	0			4						C	THR/ALA	2,4404	4.2+/-10.8	0,2,2201	103.0	93.0	97.0		1021	3.5	0.6	4	dbSNP_132	97	0,8600		0,0,4300	yes	missense	CCKAR	NM_000730.2	58	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	341/429	26483526	2,13004	2203	4300	6503	26092624	SO:0001583	missense	886			L19315	CCDS3438.1	4p15.2	2013-09-20			ENSG00000163394	ENSG00000163394		"""GPCR / Class A : Cholecystokinin receptors"""	1570	protein-coding gene	gene with protein product		118444					Standard	NM_000730		Approved		uc003gse.1	P32238	OTTHUMG00000128567	ENST00000295589.3:c.1021G>A	4.37:g.26483526C>T	ENSP00000295589:p.Ala341Thr	Somatic		Capture	Illumina HiSeq	Phase_I	26092624	B2R9Z5	Missense_Mutation	SNP	ENST00000295589.3	37	CCDS3438.1	.	.	.	.	.	.	.	.	.	.	C	6.814	0.519356	0.13005	4.54E-4	0.0	ENSG00000163394	ENST00000295589	T	0.71579	-0.58	5.29	3.46	0.39613	GPCR, rhodopsin-like superfamily (1);	0.399005	0.27691	N	0.018255	T	0.51534	0.1680	N	0.21545	0.675	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.26121	-1.0112	10	0.12766	T	0.61	.	10.3464	0.43909	0.0:0.791:0.1351:0.0739	.	341	P32238	CCKAR_HUMAN	T	341	ENSP00000295589:A341T	ENSP00000295589:A341T	A	-	1	0	CCKAR	26092624	0.000000	0.05858	0.556000	0.28293	0.564000	0.35744	0.084000	0.14891	1.234000	0.43709	0.563000	0.77884	GCC		CCKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250418.2		
KIT	3815	hgsc.bcm.edu	37	4	55599348	55599348	+	Missense_Mutation	SNP	T	T	C	rs121913524		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:55599348T>C	ENST00000288135.5	+	17	2571	c.2474T>C	c.(2473-2475)gTt>gCt	p.V825A		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	825	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V825A(27)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AATTATGTGGTTAAAGGAAAC	0.373		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																														yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	27	Substitution - Missense(27)	haematopoietic_and_lymphoid_tissue(27)	4											150.0	153.0	152.0					4																	55599348		2203	4300	6503	55294105	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2474T>C	4.37:g.55599348T>C	ENSP00000288135:p.Val825Ala	Somatic		Capture	Illumina HiSeq	Phase_I	55294105	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.521679	0.85600	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.82255	-1.59;-1.59	5.47	5.47	0.80525	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.51477	D	0.000093	D	0.84529	0.5492	N	0.16478	0.41	0.80722	D	1	P;D	0.76494	0.945;0.999	P;D	0.87578	0.815;0.998	D	0.87077	0.2163	10	0.62326	D	0.03	.	15.5485	0.76129	0.0:0.0:0.0:1.0	.	821;825	P10721-2;P10721	.;KIT_HUMAN	A	825;821	ENSP00000288135:V825A;ENSP00000390987:V821A	ENSP00000288135:V825A	V	+	2	0	KIT	55294105	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.130000	0.71663	2.084000	0.62774	0.477000	0.44152	GTT		KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
RASGEF1B	153020	hgsc.bcm.edu	37	4	82355042	82355042	+	Missense_Mutation	SNP	G	G	C	rs201599232		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:82355042G>C	ENST00000264400.2	-	12	1427	c.1276C>G	c.(1276-1278)Cgg>Ggg	p.R426G	RASGEF1B_ENST00000335927.7_Missense_Mutation_p.R384G|RASGEF1B_ENST00000509081.1_Missense_Mutation_p.R425G	NM_152545.1	NP_689758.1	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	426	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			endometrium(2)|kidney(5)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	26						AAGATCTTCCGGTCCCTCTCA	0.413																																																	0			4						G	GLY/ARG	0,4406		0,0,2203	211.0	187.0	196.0		1276	5.1	1.0	4		196	1,8599	1.2+/-3.3	0,1,4299	no	missense	RASGEF1B	NM_152545.1	125	0,1,6502	CC,CG,GG		0.0116,0.0,0.0077	possibly-damaging	426/474	82355042	1,13005	2203	4300	6503	82574066	SO:0001583	missense	153020			AK056257	CCDS34022.1, CCDS75151.1, CCDS75152.1	4q21.21	2013-09-24				ENSG00000138670			24881	protein-coding gene	gene with protein product		614532				12488504	Standard	XM_005262776		Approved	GPIG4, FLJ31695	uc003hmi.1	Q0VAM2		ENST00000264400.2:c.1276C>G	4.37:g.82355042G>C	ENSP00000264400:p.Arg426Gly	Somatic		Capture	Illumina HiSeq	Phase_I	82574066	Q0VAM1|Q4W5L7|Q4W5M3|Q96MY8	Missense_Mutation	SNP	ENST00000264400.2	37	CCDS34022.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.403906	0.62288	0.0	1.16E-4	ENSG00000138670	ENST00000509081;ENST00000264400;ENST00000335927	T;T;T	0.31510	1.49;1.49;1.49	5.05	5.05	0.67936	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.43077	0.1231	M	0.75615	2.305	0.80722	D	1	B;B;B	0.29627	0.252;0.252;0.25	B;B;B	0.36608	0.229;0.229;0.115	T	0.44590	-0.9318	10	0.59425	D	0.04	.	18.1775	0.89766	0.0:0.0:1.0:0.0	.	384;425;426	Q0VAM2-2;Q0VAM2-3;Q0VAM2	.;.;RGF1B_HUMAN	G	425;426;384	ENSP00000425393:R425G;ENSP00000264400:R426G;ENSP00000338437:R384G	ENSP00000264400:R426G	R	-	1	2	RASGEF1B	82574066	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.230000	0.58632	2.640000	0.89533	0.585000	0.79938	CGG		RASGEF1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362830.1	NM_152545	
NFKB1	4790	hgsc.bcm.edu	37	4	103459065	103459065	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:103459065A>G	ENST00000505458.1	+	5	484	c.207A>G	c.(205-207)ctA>ctG	p.L69L	NFKB1_ENST00000394820.4_Silent_p.L69L|NFKB1_ENST00000226574.4_Silent_p.L70L			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	69	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.L70L(1)		biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	ATGGTGGACTACCTGGTGCCT	0.393																																																	1	Substitution - coding silent(1)	ovary(1)	4											162.0	153.0	156.0					4																	103459065		2203	4300	6503	103678093	SO:0001819	synonymous_variant	4790			M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"""Ankyrin repeat domain containing"""	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.207A>G	4.37:g.103459065A>G		Somatic		Capture	Illumina HiSeq	Phase_I	103678093	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	ENST00000505458.1	37	CCDS54783.1																																																																																				NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1		
PDGFC	56034	hgsc.bcm.edu	37	4	157732157	157732157	+	Silent	SNP	T	T	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:157732157T>A	ENST00000502773.1	-	3	817	c.327A>T	c.(325-327)gtA>gtT	p.V109V	PDGFC_ENST00000422544.2_Silent_p.V109V|PDGFC_ENST00000541126.1_5'UTR|PDGFC_ENST00000542208.1_5'UTR	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	109	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		CCTCAACTTCTACAAAATCAT	0.383																																																	0			4											63.0	60.0	61.0					4																	157732157		2203	4299	6502	157951607	SO:0001819	synonymous_variant	56034			AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431			8801	protein-coding gene	gene with protein product		608452				10858496, 10858548	Standard	NM_016205		Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.327A>T	4.37:g.157732157T>A		Somatic		Capture	Illumina HiSeq	Phase_I	157951607	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Silent	SNP	ENST00000502773.1	37	CCDS3795.1																																																																																				PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1		
APOB	338	hgsc.bcm.edu	37	2	21230730	21230730	+	Missense_Mutation	SNP	C	C	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:21230730C>A	ENST00000233242.1	-	26	9137	c.9010G>T	c.(9010-9012)Gct>Tct	p.A3004S		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3004					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATGCCTTTAGCAGTTAGAACA	0.408																																																	0			2											71.0	75.0	74.0					2																	21230730		2203	4300	6503	21084235	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.9010G>T	2.37:g.21230730C>A	ENSP00000233242:p.Ala3004Ser	Somatic		Capture	Illumina HiSeq	Phase_I	21084235	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.349945	0.41599	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00848	5.62	5.87	5.87	0.94306	.	0.207969	0.33670	N	0.004662	T	0.04003	0.0112	M	0.68317	2.08	0.53688	D	0.999977	D	0.69078	0.997	P	0.60789	0.879	T	0.33471	-0.9867	10	0.62326	D	0.03	.	14.3787	0.66897	0.0:0.9298:0.0:0.0702	.	3004	P04114	APOB_HUMAN	S	3004	ENSP00000233242:A3004S	ENSP00000233242:A3004S	A	-	1	0	APOB	21084235	0.049000	0.20398	0.083000	0.20561	0.647000	0.38526	1.505000	0.35736	2.780000	0.95670	0.655000	0.94253	GCT		APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
MSH2	4436	hgsc.bcm.edu	37	2	47639567	47639567	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:47639567A>G	ENST00000233146.2	+	4	883	c.660A>G	c.(658-660)ggA>ggG	p.G220G	MSH2_ENST00000406134.1_Silent_p.G220G|MSH2_ENST00000543555.1_Silent_p.G154G	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	220					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTCAAAGAGGAGGAATTCTGA	0.313			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																														yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	2											47.0	48.0	48.0					2																	47639567		2203	4300	6503	47493071	SO:0001819	synonymous_variant	4436	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.660A>G	2.37:g.47639567A>G		Somatic		Capture	Illumina HiSeq	Phase_I	47493071	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																				MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
GTF2A1L	11036	hgsc.bcm.edu	37	2	48848421	48848421	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:48848421C>A	ENST00000403751.3	+	3	276	c.239C>A	c.(238-240)tCg>tAg	p.S80*	STON1-GTF2A1L_ENST00000394754.1_Nonsense_Mutation_p.S784*|GTF2A1L_ENST00000430487.2_Nonsense_Mutation_p.S46*|STON1-GTF2A1L_ENST00000309827.2_Nonsense_Mutation_p.S784*|STON1-GTF2A1L_ENST00000402114.2_Nonsense_Mutation_p.S784*|STON1-GTF2A1L_ENST00000394751.3_Nonsense_Mutation_p.S784*|GTF2A1L_ENST00000468326.1_3'UTR|STON1-GTF2A1L_ENST00000405008.1_Nonsense_Mutation_p.S784*	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	80					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ACATTGCAATCGTCAACAGGT	0.383																																																	0			2											75.0	75.0	75.0					2																	48848421		2203	4300	6503	48701925	SO:0001587	stop_gained	11036			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"""TFIIA alpha/beta like factor"""	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.239C>A	2.37:g.48848421C>A	ENSP00000384597:p.Ser80*	Somatic		Capture	Illumina HiSeq	Phase_I	48701925	B4DY14|Q53FD9|Q5D050	Nonsense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	C	36	5.771749	0.96922	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000448460;ENST00000437125;ENST00000430487;ENST00000403751	.	.	.	3.59	3.59	0.41128	.	0.480024	0.20172	N	0.097715	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	10.8977	0.47031	0.0:0.8087:0.1913:0.0	.	.	.	.	X	784;784;784;784;784;79;46;80;46;80	.	ENSP00000384597:S80X	S	+	2	0	STON1-GTF2A1L;GTF2A1L	48701925	0.974000	0.33945	0.679000	0.29978	0.362000	0.29581	2.179000	0.42528	1.997000	0.58415	0.563000	0.77884	TCG		GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872	
THSD7B	80731	hgsc.bcm.edu	37	2	138208522	138208522	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:138208522C>T	ENST00000409968.1	+	15	3245	c.3067C>T	c.(3067-3069)Cga>Tga	p.R1023*	THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000272643.3_Nonsense_Mutation_p.R1023*|THSD7B_ENST00000413152.2_Nonsense_Mutation_p.R992*			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	1023	TSP type-1 13. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.R1023*(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		AGTGAGAATTCGATCCAAATG	0.408																																																	1	Substitution - Nonsense(1)	skin(1)	2											93.0	88.0	90.0					2																	138208522		1866	4110	5976	137924992	SO:0001587	stop_gained	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.3067C>T	2.37:g.138208522C>T	ENSP00000387145:p.Arg1023*	Somatic		Capture	Illumina HiSeq	Phase_I	137924992		Nonsense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	C	43	10.496149	0.99416	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	.	.	.	5.87	4.05	0.47172	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7785	0.69749	0.4926:0.5074:0.0:0.0	.	.	.	.	X	1023;1023;992	.	ENSP00000272643:R1023X	R	+	1	2	THSD7B	137924992	0.980000	0.34600	1.000000	0.80357	0.998000	0.95712	0.841000	0.27613	0.795000	0.33922	0.655000	0.94253	CGA		THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9	
ORC4	5000	hgsc.bcm.edu	37	2	148730337	148730337	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:148730337T>C	ENST00000392857.5	-	4	303	c.196A>G	c.(196-198)Atc>Gtc	p.I66V	ORC4_ENST00000540442.1_5'UTR|ORC4_ENST00000535373.1_Missense_Mutation_p.I66V|ORC4_ENST00000264169.2_Missense_Mutation_p.I66V|ORC4_ENST00000542387.1_5'UTR|ORC4_ENST00000392858.1_Missense_Mutation_p.I66V|ORC4_ENST00000536575.1_Intron	NM_001190879.2|NM_001190882.2|NM_002552.4|NM_181741.3	NP_001177808.1|NP_001177811.1|NP_002543.2|NP_859525.1	O43929	ORC4_HUMAN	origin recognition complex, subunit 4	66					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)	p.I66F(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	14						CGGGGTCCGATAATAAGGACA	0.333																																																	1	Substitution - Missense(1)	ovary(1)	2											69.0	72.0	71.0					2																	148730337		2203	4300	6503	148446807	SO:0001583	missense	5000			AF022108	CCDS2187.1, CCDS54404.1, CCDS54405.1	2q22-q23	2010-10-12	2010-10-12	2010-10-12	ENSG00000115947	ENSG00000115947		"""ATPases / AAA-type"""	8490	protein-coding gene	gene with protein product		603056	"""origin recognition complex, subunit 4 (yeast homolog)-like"", ""origin recognition complex, subunit 4-like (yeast)"", ""origin recognition complex, subunit 4-like (S. cerevisiae)"", ""origin recognition complex, subunit 4 homolog (S. cerevisiae)"""	ORC4L		9353276, 9691185	Standard	NM_181742		Approved	HsORC4, Orc4p	uc002twk.3	O43929	OTTHUMG00000131849	ENST00000392857.5:c.196A>G	2.37:g.148730337T>C	ENSP00000376597:p.Ile66Val	Somatic		Capture	Illumina HiSeq	Phase_I	148446807	B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42	Missense_Mutation	SNP	ENST00000392857.5	37	CCDS2187.1	.	.	.	.	.	.	.	.	.	.	T	12.20	1.865607	0.32977	.	.	ENSG00000115947	ENST00000264169;ENST00000535373;ENST00000392858;ENST00000392857;ENST00000416719;ENST00000457954;ENST00000440042	T;T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34;1.34	5.88	1.01	0.19927	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.112463	0.64402	N	0.000006	T	0.18173	0.0436	N	0.14661	0.345	0.80722	D	1	B;B;B	0.10296	0.002;0.003;0.002	B;B;B	0.16722	0.006;0.016;0.004	T	0.09707	-1.0662	10	0.16896	T	0.51	-8.4926	8.9634	0.35860	0.0:0.2852:0.0:0.7148	.	66;66;66	B7Z2M4;A8K7H4;O43929	.;.;ORC4_HUMAN	V	66	ENSP00000264169:I66V;ENSP00000441953:I66V;ENSP00000376598:I66V;ENSP00000376597:I66V;ENSP00000413939:I66V;ENSP00000391484:I66V;ENSP00000403105:I66V	ENSP00000264169:I66V	I	-	1	0	ORC4	148446807	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	1.753000	0.38359	-0.049000	0.13379	0.533000	0.62120	ATC		ORC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254797.3	NM_181742	
HAT1	8520	hgsc.bcm.edu	37	2	172844219	172844219	+	Silent	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:172844219C>T	ENST00000264108.4	+	10	1071	c.1035C>T	c.(1033-1035)gcC>gcT	p.A345A	SLC25A12_ENST00000472748.1_Intron|HAT1_ENST00000392584.1_Silent_p.A260A	NM_003642.3	NP_003633.1	O14929	HAT1_HUMAN	histone acetyltransferase 1	345					chromatin organization (GO:0006325)|chromatin silencing at telomere (GO:0006348)|DNA packaging (GO:0006323)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4 acetylation (GO:0043967)|internal protein amino acid acetylation (GO:0006475)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	H4 histone acetyltransferase activity (GO:0010485)|histone acetyltransferase activity (GO:0004402)	p.A345A(1)		breast(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|prostate(1)	19			OV - Ovarian serous cystadenocarcinoma(117;0.216)			TGAGTGATGCCGAACAATACA	0.348																																																	1	Substitution - coding silent(1)	lung(1)	2											131.0	132.0	132.0					2																	172844219		2203	4300	6503	172552465	SO:0001819	synonymous_variant	8520			AF030424	CCDS2245.1	2q31.2-q33.1	2011-07-01			ENSG00000128708	ENSG00000128708	2.3.1.48	"""Chromatin-modifying enzymes / K-acetyltransferases"""	4821	protein-coding gene	gene with protein product		603053				9427644	Standard	NM_003642		Approved	KAT1	uc002uhi.3	O14929	OTTHUMG00000132282	ENST00000264108.4:c.1035C>T	2.37:g.172844219C>T		Somatic		Capture	Illumina HiSeq	Phase_I	172552465	Q49A44|Q53QF0|Q53SU4|Q6P594|Q8WWB9	Silent	SNP	ENST00000264108.4	37	CCDS2245.1																																																																																				HAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255377.1	NM_003642	
TTN	7273	hgsc.bcm.edu	37	2	179635038	179635038	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:179635038A>G	ENST00000591111.1	-	36	8614	c.8390T>C	c.(8389-8391)aTc>aCc	p.I2797T	TTN_ENST00000589042.1_Missense_Mutation_p.I2797T|TTN_ENST00000342992.6_Missense_Mutation_p.I2797T|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.I2797T|TTN_ENST00000359218.5_Missense_Mutation_p.I2751T|TTN_ENST00000460472.2_Missense_Mutation_p.I2751T|TTN_ENST00000342175.6_Missense_Mutation_p.I2751T|TTN-AS1_ENST00000584485.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13125					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTTTAATGATCTTGACAGC	0.393																																																	0			2											98.0	96.0	97.0					2																	179635038		2203	4300	6503	179343283	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.8390T>C	2.37:g.179635038A>G	ENSP00000465570:p.Ile2797Thr	Somatic		Capture	Illumina HiSeq	Phase_I	179343283	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	13.82	2.349759	0.41599	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54;-0.54	6.06	6.06	0.98353	Immunoglobulin I-set (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.87208	0.6120	M	0.91459	3.21	0.36185	D	0.849692	D;D;D;D;D	0.76494	0.978;0.978;0.978;0.989;0.999	P;P;P;D;D	0.69479	0.871;0.871;0.871;0.927;0.964	D	0.92372	0.5906	9	0.87932	D	0	.	16.6154	0.84909	1.0:0.0:0.0:0.0	.	2751;2751;2751;2797;2797	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	T	2797;2751;2751;2751;2751;2797	ENSP00000343764:I2797T;ENSP00000434586:I2751T;ENSP00000340554:I2751T;ENSP00000352154:I2751T;ENSP00000354117:I2797T	ENSP00000340554:I2751T	I	-	2	0	TTN	179343283	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.927000	0.92846	2.315000	0.78130	0.533000	0.62120	ATC		TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ACSL3	2181	hgsc.bcm.edu	37	2	223786008	223786008	+	Silent	SNP	T	T	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:223786008T>A	ENST00000357430.3	+	8	1347	c.816T>A	c.(814-816)ccT>ccA	p.P272P	ACSL3_ENST00000392066.3_Silent_p.P272P|AC097461.4_ENST00000446709.1_RNA	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	272					brain development (GO:0007420)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty acid import (GO:0044539)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)|positive regulation of phosphatidylcholine biosynthetic process (GO:2001247)|positive regulation of secretion (GO:0051047)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)|skin(2)	22		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)	AAAACCAACCTCATAGCAAAC	0.358			T	ETV1	prostate																																			Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	0			2											141.0	137.0	138.0					2																	223786008		2203	4300	6503	223494252	SO:0001819	synonymous_variant	2181			D89053	CCDS2455.1	2q34-q35	2008-02-05	2004-02-19	2004-02-20	ENSG00000123983	ENSG00000123983		"""Acyl-CoA synthetase family"""	3570	protein-coding gene	gene with protein product		602371	"""fatty-acid-Coenzyme A ligase, long-chain 3"""	FACL3			Standard	NM_004457		Approved	ACS3, PRO2194	uc002vnj.3	O95573	OTTHUMG00000133160	ENST00000357430.3:c.816T>A	2.37:g.223786008T>A		Somatic		Capture	Illumina HiSeq	Phase_I	223494252	Q60I92|Q8IUM9	Silent	SNP	ENST00000357430.3	37	CCDS2455.1																																																																																				ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457	
SCAI	286205	hgsc.bcm.edu	37	9	127733651	127733651	+	Silent	SNP	G	G	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr9:127733651G>T	ENST00000336505.6	-	17	1730	c.1672C>A	c.(1672-1674)Cgg>Agg	p.R558R	SCAI_ENST00000373549.4_Silent_p.R581R	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	558					negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						TTGCCTACCCGAAAAATCTTG	0.313																																																	0			9											93.0	85.0	87.0					9																	127733651		1822	4081	5903	126773472	SO:0001819	synonymous_variant	0			AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 126"""	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.1672C>A	9.37:g.127733651G>T		Somatic		Capture	Illumina HiSeq	Phase_I	126773472	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Silent	SNP	ENST00000336505.6	37	CCDS48017.1																																																																																				SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690	
PSPC1	55269	hgsc.bcm.edu	37	13	20325440	20325440	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr13:20325440T>C	ENST00000338910.4	-	4	1097	c.938A>G	c.(937-939)cAt>cGt	p.H313R		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	313	Sufficient for paraspeckles localization.|Sufficient for perinucleolar caps localization and interaction with NONO.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		TTGGTGTTCATGCCTAGCTGC	0.398																																																	0			13											287.0	264.0	272.0					13																	20325440		1928	4127	6055	19223440	SO:0001583	missense	55269			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"""RNA binding motif (RRM) containing"""	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.938A>G	13.37:g.20325440T>C	ENSP00000343966:p.His313Arg	Somatic		Capture	Illumina HiSeq	Phase_I	19223440	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Missense_Mutation	SNP	ENST00000338910.4	37	CCDS41870.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.313494	0.60414	.	.	ENSG00000121390	ENST00000338910;ENST00000422828	T	0.16073	2.37	4.83	4.83	0.62350	.	0.112999	0.64402	D	0.000011	T	0.21347	0.0514	M	0.66297	2.02	0.53688	D	0.999977	P	0.45672	0.864	B	0.39299	0.296	T	0.04307	-1.0961	10	0.51188	T	0.08	-18.8568	14.705	0.69183	0.0:0.0:0.0:1.0	.	313	Q8WXF1	PSPC1_HUMAN	R	313;253	ENSP00000343966:H313R	ENSP00000343966:H313R	H	-	2	0	PSPC1	19223440	1.000000	0.71417	0.998000	0.56505	0.888000	0.51559	7.988000	0.88194	1.943000	0.56356	0.454000	0.30748	CAT		PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2		
COG6	57511	hgsc.bcm.edu	37	13	40297568	40297568	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr13:40297568A>G	ENST00000455146.3	+	16	1733	c.1683A>G	c.(1681-1683)aaA>aaG	p.K561K	COG6_ENST00000416691.1_Silent_p.K561K	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	561					glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		AGCAACATAAACCTGAACAGG	0.398																																																	0			13											99.0	90.0	93.0					13																	40297568		2203	4299	6502	39195568	SO:0001819	synonymous_variant	57511			AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"""Components of oligomeric golgi complex"""	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.1683A>G	13.37:g.40297568A>G		Somatic		Capture	Illumina HiSeq	Phase_I	39195568	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Silent	SNP	ENST00000455146.3	37	CCDS9370.1																																																																																				COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3		
RB1	5925	hgsc.bcm.edu	37	13	48881429	48881429	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr13:48881429G>T	ENST00000267163.4	+	2	289	c.151G>T	c.(151-153)Gaa>Taa	p.E51*		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	51					androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(3)|p.E51*(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TGAGTTTGAAGAAACAGAAGA	0.313		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																													yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	19	Whole gene deletion(15)|Unknown(3)|Substitution - Nonsense(1)	bone(10)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|eye(1)|soft_tissue(1)|central_nervous_system(1)|endometrium(1)|stomach(1)	13											115.0	114.0	114.0					13																	48881429		2203	4298	6501	47779430	SO:0001587	stop_gained	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.151G>T	13.37:g.48881429G>T	ENSP00000267163:p.Glu51*	Somatic		Capture	Illumina HiSeq	Phase_I	47779430	A8K5E3|P78499|Q5VW46|Q8IZL4	Nonsense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	36	5.888494	0.97068	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	4.74	3.88	0.44766	.	0.591344	0.18246	N	0.147093	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	9.591	0.39545	0.101:0.0:0.899:0.0	.	.	.	.	X	30;51	.	ENSP00000267163:E51X	E	+	1	0	RB1	47779430	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	3.074000	0.50065	1.077000	0.40990	0.650000	0.86243	GAA		RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
RB1	5925	hgsc.bcm.edu	37	13	49033838	49033838	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr13:49033838T>C	ENST00000267163.4	+	20	2113	c.1975T>C	c.(1975-1977)Tat>Cat	p.Y659H		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	659	Domain B.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(11)|p.Y659H(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TCGGCTAGCCTATCTCCGGCT	0.378		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																													yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	27	Whole gene deletion(15)|Unknown(11)|Substitution - Missense(1)	bone(10)|haematopoietic_and_lymphoid_tissue(5)|breast(5)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|lung(1)|liver(1)	13											73.0	78.0	77.0					13																	49033838		2203	4300	6503	47931839	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1975T>C	13.37:g.49033838T>C	ENSP00000267163:p.Tyr659His	Somatic		Capture	Illumina HiSeq	Phase_I	47931839	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.019440	0.75275	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.90900	-2.75	5.79	5.79	0.91817	Retinoblastoma-associated protein, B-box (1);Cyclin-like (2);	0.000000	0.85682	D	0.000000	D	0.95401	0.8507	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95880	0.8898	10	0.87932	D	0	.	16.1338	0.81465	0.0:0.0:0.0:1.0	.	659	P06400	RB_HUMAN	H	638;659	ENSP00000267163:Y659H	ENSP00000267163:Y659H	Y	+	1	0	RB1	47931839	1.000000	0.71417	0.926000	0.36857	0.782000	0.44232	7.698000	0.84413	2.216000	0.71823	0.528000	0.53228	TAT		RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
CYSLTR2	57105	hgsc.bcm.edu	37	13	49281933	49281933	+	Missense_Mutation	SNP	A	A	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr13:49281933A>T	ENST00000282018.3	+	1	983	c.980A>T	c.(979-981)aAg>aTg	p.K327M		NM_020377.2	NP_065110.1	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	327					immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell death (GO:0010942)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteinyl leukotriene receptor activity (GO:0001631)|leukotriene receptor activity (GO:0004974)			endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)	CATCCACAGAAGGCAAAGACA	0.443																																																	0			13											77.0	71.0	73.0					13																	49281933		2203	4300	6503	48179934	SO:0001583	missense	57105			AB038269	CCDS9412.1	13q14.2	2012-08-10			ENSG00000152207	ENSG00000152207		"""GPCR / Class A : Leukotriene receptors"""	18274	protein-coding gene	gene with protein product		605666				10913337, 1085123	Standard	NM_020377		Approved	CysLT(2), CYSLT2R	uc001vck.2	Q9NS75	OTTHUMG00000016906	ENST00000282018.3:c.980A>T	13.37:g.49281933A>T	ENSP00000282018:p.Lys327Met	Somatic		Capture	Illumina HiSeq	Phase_I	48179934	Q9HCQ2	Missense_Mutation	SNP	ENST00000282018.3	37	CCDS9412.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.021314	0.54576	.	.	ENSG00000152207	ENST00000282018	T	0.38560	1.13	5.51	3.03	0.35002	.	3.293900	0.01734	U	0.029019	T	0.22936	0.0554	N	0.08118	0	0.09310	N	1	P	0.35077	0.483	B	0.21546	0.035	T	0.20538	-1.0272	10	0.39692	T	0.17	.	6.4304	0.21794	0.776:0.0:0.0771:0.1468	.	327	Q9NS75	CLTR2_HUMAN	M	327	ENSP00000282018:K327M	ENSP00000282018:K327M	K	+	2	0	CYSLTR2	48179934	0.001000	0.12720	0.001000	0.08648	0.055000	0.15305	0.423000	0.21313	0.368000	0.24481	0.533000	0.62120	AAG		CYSLTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044894.1		
PFKFB3	5209	hgsc.bcm.edu	37	10	6264905	6264905	+	Missense_Mutation	SNP	G	G	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:6264905G>C	ENST00000379775.4	+	11	1501	c.1171G>C	c.(1171-1173)Gtc>Ctc	p.V391L	PFKFB3_ENST00000360521.2_Missense_Mutation_p.V391L|PFKFB3_ENST00000379785.1_Missense_Mutation_p.V391L|PFKFB3_ENST00000540253.1_Missense_Mutation_p.V405L|PFKFB3_ENST00000317350.4_Missense_Mutation_p.V391L|PFKFB3_ENST00000379782.3_Missense_Mutation_p.V391L|PFKFB3_ENST00000536985.1_Intron|PFKFB3_ENST00000379789.4_Missense_Mutation_p.V371L	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	391	Fructose-2,6-bisphosphatase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						CCACCAGGCCGTCCTGCGCTG	0.647																																																	0			10											67.0	50.0	56.0					10																	6264905		2203	4300	6503	6304911	SO:0001583	missense	5209				CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.1171G>C	10.37:g.6264905G>C	ENSP00000369100:p.Val391Leu	Somatic		Capture	Illumina HiSeq	Phase_I	6304911	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Missense_Mutation	SNP	ENST00000379775.4	37	CCDS7078.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.6|27.6	4.846500|4.846500	0.91277|0.91277	.|.	.|.	ENSG00000170525|ENSG00000170525	ENST00000450232|ENST00000379789;ENST00000379784;ENST00000540253;ENST00000317350;ENST00000379785;ENST00000379782;ENST00000360521;ENST00000379775;ENST00000358499	.|T;T;T;T;T;T;T	.|0.73258	.|-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73	5.21|5.21	5.21|5.21	0.72293|0.72293	.|Histidine phosphatase superfamily, clade-1 (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.87935|0.87935	0.6303|0.6303	M|M	0.91612|0.91612	3.225|3.225	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;0.996;1.0;0.997	.|D;D;D;D	.|0.87578	.|0.998;0.985;0.98;0.988	D|D	0.90643|0.90643	0.4576|0.4576	5|10	.|0.87932	.|D	.|0	0.0715|0.0715	18.7523|18.7523	0.91820|0.91820	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|405;391;391;371	.|B7Z955;Q16875-2;Q16875;Q5VX15	.|.;.;F263_HUMAN;.	P|L	71|371;117;405;391;391;391;391;391;391	.|ENSP00000369115:V371L;ENSP00000446384:V405L;ENSP00000369105:V391L;ENSP00000369111:V391L;ENSP00000369108:V391L;ENSP00000353712:V391L;ENSP00000369100:V391L	.|ENSP00000369105:V391L	R|V	+|+	2|1	0|0	PFKFB3|PFKFB3	6304911|6304911	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.734000|0.734000	0.41952|0.41952	9.469000|9.469000	0.97679|0.97679	2.431000|2.431000	0.82371|0.82371	0.462000|0.462000	0.41574|0.41574	CGT|GTC		PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1		
NMT2	9397	hgsc.bcm.edu	37	10	15175312	15175312	+	Missense_Mutation	SNP	G	G	A	rs540952796		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:15175312G>A	ENST00000378165.4	-	4	522	c.442C>T	c.(442-444)Cgc>Tgc	p.R148C	NMT2_ENST00000540259.1_De_novo_Start_OutOfFrame|NMT2_ENST00000535341.1_Missense_Mutation_p.R135C|RPP38_ENST00000451677.1_Intron|NMT2_ENST00000378150.1_Missense_Mutation_p.R135C	NM_004808.2	NP_004799.1	O60551	NMT2_HUMAN	N-myristoyltransferase 2	148					intracellular transport of virus (GO:0075733)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(3)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(3)	21						GGTTCTTGGCGTACGTTGTCT	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		19974	0.0		0.0	False		,,,				2504	0.001				Melanoma(117;1345 1645 4130 12688 30625)												0			10											168.0	165.0	166.0					10																	15175312		2203	4300	6503	15215318	SO:0001583	missense	9397			AF043325	CCDS7109.1	10p13	2006-07-11			ENSG00000152465	ENSG00000152465			7858	protein-coding gene	gene with protein product		603801				9506952	Standard	NM_004808		Approved		uc001inz.1	O60551	OTTHUMG00000017723	ENST00000378165.4:c.442C>T	10.37:g.15175312G>A	ENSP00000367407:p.Arg148Cys	Somatic		Capture	Illumina HiSeq	Phase_I	15215318	B0YJ49|Q53Y38|Q5VUC8|Q9BRB4	Missense_Mutation	SNP	ENST00000378165.4	37	CCDS7109.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.324475	0.81580	.	.	ENSG00000152465	ENST00000378165;ENST00000378150;ENST00000378143;ENST00000535341	T	0.50277	0.75	5.81	5.81	0.92471	Acyl-CoA N-acyltransferase (2);Myristoyl-CoA:protein N-myristoyltransferase, N-terminal (1);	0.050733	0.85682	D	0.000000	T	0.69744	0.3145	H	0.95365	3.66	0.80722	D	1	P;P;P	0.51537	0.909;0.946;0.909	B;P;B	0.46510	0.381;0.519;0.381	T	0.80600	-0.1310	10	0.87932	D	0	-15.6528	20.0726	0.97729	0.0:0.0:1.0:0.0	.	148;135;148	B2RCF3;Q5VUC6;O60551	.;.;NMT2_HUMAN	C	148;135;179;135	ENSP00000367407:R148C	ENSP00000367385:R179C	R	-	1	0	NMT2	15215318	1.000000	0.71417	0.254000	0.24359	0.941000	0.58515	5.165000	0.64959	2.738000	0.93877	0.655000	0.94253	CGC		NMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046958.2	NM_004808	
MRC1	4360	hgsc.bcm.edu	37	10	17865239	17865239	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:17865239A>G	ENST00000331429.2	+	2	331	c.228A>G	c.(226-228)ggA>ggG	p.G76G	MRC1L1_ENST00000457317.1_Silent_p.G76G																breast(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TATGCCTGGGAGTGCCATCAA	0.453																																																	0			10											165.0	166.0	166.0					10																	17865239		2033	3971	6004	17905245	SO:0001819	synonymous_variant	414308																														ENST00000331429.2:c.228A>G	10.37:g.17865239A>G		Somatic		Capture	Illumina HiSeq	Phase_I	17905245		Silent	SNP	ENST00000331429.2	37																																																																																					MRC1L1-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047054.1		
PTEN	5728	hgsc.bcm.edu	37	10	89624305	89624305	+	Splice_Site	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:89624305T>C	ENST00000371953.3	+	1	1436	c.79T>C	c.(79-81)Tat>Cat	p.Y27H	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	27	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		Y -> S (loss of phosphatase activity towards Ins(1,3,4,5)P4).		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(13)|p.Y27D(2)|p.Y27N(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		AGACTTGACCTGTATCCATTT	0.463		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	53	Whole gene deletion(37)|Unknown(13)|Substitution - Missense(3)	prostate(14)|central_nervous_system(10)|skin(7)|lung(6)|ovary(3)|breast(3)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|kidney(1)	10											155.0	148.0	150.0					10																	89624305		2203	4300	6503	89614285	SO:0001630	splice_region_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.79+1T>C	10.37:g.89624305T>C		Somatic		Capture	Illumina HiSeq	Phase_I	89614285	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.821122	0.90873	.	.	ENSG00000171862	ENST00000371953	D	0.98762	-5.12	5.28	5.28	0.74379	Phosphatase tensin type (1);	0.071107	0.64402	D	0.000018	D	0.99064	0.9679	H	0.96691	3.865	0.80722	D	1	P	0.45396	0.857	P	0.48524	0.58	D	0.99246	1.0886	9	.	.	.	-0.7134	14.1807	0.65572	0.0:0.0:0.0:1.0	.	27	P60484	PTEN_HUMAN	H	27	ENSP00000361021:Y27H	.	Y	+	1	0	PTEN	89614285	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.216000	0.77974	1.996000	0.58369	0.459000	0.35465	TAT		PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	Missense_Mutation
PTEN	5728	hgsc.bcm.edu	37	10	89720776	89720776	+	Silent	SNP	A	A	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:89720776A>C	ENST00000371953.3	+	8	2284	c.927A>C	c.(925-927)gcA>gcC	p.A309A	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	309	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.W274_F341del(1)|p.R308fs*7(1)|p.A309A(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TAGAGCGTGCAGATAATGACA	0.343		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	52	Whole gene deletion(37)|Deletion - Frameshift(10)|Deletion - In frame(2)|Unknown(2)|Substitution - coding silent(1)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)|endometrium(1)|liver(1)	10											106.0	103.0	104.0					10																	89720776		2203	4299	6502	89710756	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.927A>C	10.37:g.89720776A>C		Somatic		Capture	Illumina HiSeq	Phase_I	89710756	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
PSD	5662	hgsc.bcm.edu	37	10	104173750	104173750	+	Silent	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:104173750C>T	ENST00000020673.5	-	5	1855	c.1329G>A	c.(1327-1329)gaG>gaA	p.E443E	PSD_ENST00000406432.1_Silent_p.E443E|PSD_ENST00000492902.2_5'Flank	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	443	Pro-rich.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		GGGGAGGCAGCTCAAAGGTGA	0.657																																																	0			10											51.0	64.0	59.0					10																	104173750		2203	4300	6503	104163740	SO:0001819	synonymous_variant	79176			X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"""Pleckstrin homology (PH) domain containing"""	9507	protein-coding gene	gene with protein product		602327	"""pleckstrin and Sec7 domain protein"""			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.1329G>A	10.37:g.104173750C>T		Somatic		Capture	Illumina HiSeq	Phase_I	104163740	B1AKX7|D3DR87|Q15673|Q8IVG0	Silent	SNP	ENST00000020673.5	37	CCDS31272.1																																																																																				PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2		
TCF7L2	6934	hgsc.bcm.edu	37	10	114925643	114925643	+	Missense_Mutation	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:114925643A>G	ENST00000355995.4	+	15	2279	c.1772A>G	c.(1771-1773)cAg>cGg	p.Q591R	TCF7L2_ENST00000538897.1_3'UTR|TCF7L2_ENST00000542695.1_Missense_Mutation_p.Q307R|TCF7L2_ENST00000369386.1_3'UTR|TCF7L2_ENST00000543371.1_Missense_Mutation_p.Q574R|TCF7L2_ENST00000545257.1_Missense_Mutation_p.Q591R|TCF7L2_ENST00000466338.1_3'UTR|TCF7L2_ENST00000369397.4_Missense_Mutation_p.Q568R|TCF7L2_ENST00000536810.1_Missense_Mutation_p.Q574R|TCF7L2_ENST00000355717.4_3'UTR			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	591					blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		TCAATTGCACAGCCGTCGACT	0.642			T	VTI1A	colorectal																																			Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	0			10											40.0	47.0	45.0					10																	114925643		2203	4300	6503	114915633	SO:0001583	missense	6934			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1772A>G	10.37:g.114925643A>G	ENSP00000348274:p.Gln591Arg	Somatic		Capture	Illumina HiSeq	Phase_I	114915633	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Missense_Mutation	SNP	ENST00000355995.4	37		.	.	.	.	.	.	.	.	.	.	A	11.40	1.627388	0.28978	.	.	ENSG00000148737	ENST00000355995;ENST00000545257;ENST00000543371;ENST00000536810;ENST00000369397;ENST00000542695	D;D;D;D;D;D	0.98437	-4.91;-4.91;-4.89;-4.93;-4.92;-4.91	5.08	5.08	0.68730	.	0.677027	0.14027	N	0.346395	D	0.97238	0.9097	N	0.16478	0.41	0.41169	D	0.986151	P;B;D;B;B;B;B	0.56521	0.936;0.323;0.976;0.003;0.003;0.002;0.001	P;B;D;B;B;B;B	0.66351	0.885;0.363;0.943;0.002;0.002;0.004;0.002	D	0.95385	0.8476	10	0.19590	T	0.45	-14.2705	14.8505	0.70292	1.0:0.0:0.0:0.0	.	591;462;506;551;551;574;568	Q9NQB0;C6ZRK4;C6ZRJ6;C6ZRJ8;C6ZRK5;Q9NQB0-7;Q6FHW4	TF7L2_HUMAN;.;.;.;.;.;.	R	591;591;574;574;568;307	ENSP00000348274:Q591R;ENSP00000440547:Q591R;ENSP00000444972:Q574R;ENSP00000446238:Q574R;ENSP00000358404:Q568R;ENSP00000443883:Q307R	ENSP00000348274:Q591R	Q	+	2	0	TCF7L2	114915633	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	4.516000	0.60496	1.902000	0.55061	0.460000	0.39030	CAG		TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756	
SEC23IP	11196	hgsc.bcm.edu	37	10	121685736	121685736	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:121685736A>G	ENST00000369075.3	+	13	2382	c.2310A>G	c.(2308-2310)ggA>ggG	p.G770G	SEC23IP_ENST00000543134.1_Silent_p.G559G	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	770					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		TTGGCGCCGGACAGGTGAGTT	0.398																																																	0			10											135.0	138.0	137.0					10																	121685736		2203	4300	6503	121675726	SO:0001819	synonymous_variant	11196			AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"""Sterile alpha motif (SAM) domain containing"""	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.2310A>G	10.37:g.121685736A>G		Somatic		Capture	Illumina HiSeq	Phase_I	121675726	D3DRD2|Q8IXH5|Q9BUK5	Silent	SNP	ENST00000369075.3	37	CCDS7618.1																																																																																				SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1		
CDH18	1016	hgsc.bcm.edu	37	5	19721514	19721514	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:19721514A>G	ENST00000507958.1	-	7	1575	c.585T>C	c.(583-585)gcT>gcC	p.A195A	CDH18_ENST00000506372.1_Silent_p.A195A|CDH18_ENST00000511273.1_Silent_p.A195A|CDH18_ENST00000502796.1_Silent_p.A195A|CDH18_ENST00000274170.4_Silent_p.A195A|CDH18_ENST00000382275.1_Silent_p.A195A			Q13634	CAD18_HUMAN	cadherin 18, type 2	195	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					AAACCACCCGAGCGCTGTTTC	0.468																																																	0			5											153.0	136.0	142.0					5																	19721514		2203	4300	6503	19757271	SO:0001819	synonymous_variant	1016			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"""Cadherins / Major cadherins"""	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.585T>C	5.37:g.19721514A>G		Somatic		Capture	Illumina HiSeq	Phase_I	19757271	A8K0I2|B4DHG6|Q8N5Z2	Silent	SNP	ENST00000507958.1	37	CCDS3889.1																																																																																				CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934	
RAB3C	115827	hgsc.bcm.edu	37	5	58147071	58147071	+	Missense_Mutation	SNP	G	G	A	rs199850819		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:58147071G>A	ENST00000282878.4	+	5	746	c.577G>A	c.(577-579)Gac>Aac	p.D193N	CTD-2176I21.2_ENST00000510198.1_RNA	NM_138453.2	NP_612462.1	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family	193					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)	21		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		TATCATCTGCGACAAAATGTC	0.468																																																	0			5											138.0	123.0	128.0					5																	58147071		2203	4300	6503	58182828	SO:0001583	missense	115827			AY026936	CCDS3976.1	5q13	2008-02-05			ENSG00000152932	ENSG00000152932		"""RAB, member RAS oncogene"""	30269	protein-coding gene	gene with protein product		612829				12296628	Standard	NM_138453		Approved		uc003jrp.3	Q96E17	OTTHUMG00000097053	ENST00000282878.4:c.577G>A	5.37:g.58147071G>A	ENSP00000282878:p.Asp193Asn	Somatic		Capture	Illumina HiSeq	Phase_I	58182828		Missense_Mutation	SNP	ENST00000282878.4	37	CCDS3976.1	.	.	.	.	.	.	.	.	.	.	G	18.99	3.739560	0.69304	.	.	ENSG00000152932	ENST00000282878	T	0.79352	-1.26	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000005	T	0.67429	0.2892	N	0.17838	0.53	0.80722	D	1	B	0.12630	0.006	B	0.12837	0.008	T	0.60026	-0.7343	10	0.19590	T	0.45	-21.3131	20.3539	0.98825	0.0:0.0:1.0:0.0	.	193	Q96E17	RAB3C_HUMAN	N	193	ENSP00000282878:D193N	ENSP00000282878:D193N	D	+	1	0	RAB3C	58182828	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	9.860000	0.99555	2.826000	0.97356	0.655000	0.94253	GAC		RAB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214156.2	NM_138453	
IQGAP2	10788	hgsc.bcm.edu	37	5	75996931	75996931	+	Silent	SNP	A	A	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:75996931A>G	ENST00000274364.6	+	34	4695	c.4398A>G	c.(4396-4398)ggA>ggG	p.G1466G	IQGAP2_ENST00000502745.1_Silent_p.G962G|IQGAP2_ENST00000396234.3_Silent_p.G962G|CTD-2384B11.2_ENST00000507514.1_RNA|IQGAP2_ENST00000379730.3_Silent_p.G968G	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1466					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AACTAGATGGAAAAGGAGAAC	0.423																																																	0			5											96.0	94.0	95.0					5																	75996931		2203	4300	6503	76032687	SO:0001819	synonymous_variant	10788			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.4398A>G	5.37:g.75996931A>G		Somatic		Capture	Illumina HiSeq	Phase_I	76032687	A8K4V1|B7Z8A4|J3KR91	Silent	SNP	ENST00000274364.6	37	CCDS34188.1																																																																																				IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
KIAA0825	285600	hgsc.bcm.edu	37	5	93732091	93732091	+	Missense_Mutation	SNP	T	T	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:93732091T>G	ENST00000513200.3	-	16	3083	c.3011A>C	c.(3010-3012)aAa>aCa	p.K1004T	KIAA0825_ENST00000427991.2_Missense_Mutation_p.K1004T	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	1004										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TTCAACAAATTTTTTTGACAT	0.373																																																	0			5											34.0	29.0	31.0					5																	93732091		692	1590	2282	93757847	SO:0001583	missense	285600			BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 36"""	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.3011A>C	5.37:g.93732091T>G	ENSP00000424618:p.Lys1004Thr	Somatic		Capture	Illumina HiSeq	Phase_I	93757847	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000513200.3	37		.	.	.	.	.	.	.	.	.	.	T	9.646	1.140237	0.21205	.	.	ENSG00000185261	ENST00000513200;ENST00000427991	T;T	0.46819	0.86;0.86	5.34	4.18	0.49190	.	.	.	.	.	T	0.28499	0.0705	N	0.14661	0.345	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.05517	-1.0880	9	0.41790	T	0.15	.	7.6659	0.28430	0.0:0.0735:0.1405:0.786	.	1004;1004	Q8IV33;C9J0Q2	K0825_HUMAN;.	T	1004	ENSP00000424618:K1004T;ENSP00000400288:K1004T	ENSP00000400288:K1004T	K	-	2	0	KIAA0825	93757847	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	2.024000	0.41049	0.886000	0.36113	-0.371000	0.07208	AAA		KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665	
APC	324	hgsc.bcm.edu	37	5	112174880	112174880	+	Missense_Mutation	SNP	T	T	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:112174880T>C	ENST00000457016.1	+	16	3969	c.3589T>C	c.(3589-3591)Ttc>Ctc	p.F1197L	APC_ENST00000257430.4_Missense_Mutation_p.F1197L|APC_ENST00000508376.2_Missense_Mutation_p.F1197L|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1197	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.		F -> S (in gastric cancer).		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GTCATTTTCATTCTCAAAGAG	0.363		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	5											84.0	88.0	87.0					5																	112174880		2202	4300	6502	112202779	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3589T>C	5.37:g.112174880T>C	ENSP00000413133:p.Phe1197Leu	Somatic		Capture	Illumina HiSeq	Phase_I	112202779	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	10.83	1.461227	0.26248	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D	0.89552	-2.31;-2.31;-2.31;-2.53	5.91	5.91	0.95273	.	0.231571	0.45867	D	0.000324	D	0.82568	0.5065	L	0.27053	0.805	0.34995	D	0.755371	B;B	0.26318	0.146;0.146	B;B	0.24974	0.057;0.057	T	0.82452	-0.0450	9	.	.	.	-12.8334	16.0187	0.80464	0.0:0.0:0.0:1.0	.	1199;1197	Q4LE70;P25054	.;APC_HUMAN	L	1197	ENSP00000413133:F1197L;ENSP00000257430:F1197L;ENSP00000427089:F1197L;ENSP00000423828:F1197L	.	F	+	1	0	APC	112202779	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.476000	0.66793	2.261000	0.74972	0.533000	0.62120	TTC		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175358	112175358	+	Nonsense_Mutation	SNP	C	C	G			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:112175358C>G	ENST00000457016.1	+	16	4447	c.4067C>G	c.(4066-4068)tCa>tGa	p.S1356*	APC_ENST00000257430.4_Nonsense_Mutation_p.S1356*|APC_ENST00000508376.2_Nonsense_Mutation_p.S1356*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1356	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1356*(11)|p.G1357fs*13(2)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAATTTTCTTCAGGAGCGAAA	0.473		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	15	Substitution - Nonsense(11)|Deletion - Frameshift(3)|Unknown(1)	large_intestine(13)|soft_tissue(1)|skin(1)	5											62.0	64.0	63.0					5																	112175358		2202	4300	6502	112203257	SO:0001587	stop_gained	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4067C>G	5.37:g.112175358C>G	ENSP00000413133:p.Ser1356*	Somatic		Capture	Illumina HiSeq	Phase_I	112203257	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	9.058983	0.99051	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.141330	0.49916	D	0.000133	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.6466	20.4898	0.99202	0.0:1.0:0.0:0.0	.	.	.	.	X	1356	.	.	S	+	2	0	APC	112203257	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	TCA		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
LVRN	206338	hgsc.bcm.edu	37	5	115346463	115346463	+	Missense_Mutation	SNP	G	G	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:115346463G>T	ENST00000357872.4	+	14	2243	c.2119G>T	c.(2119-2121)Gca>Tca	p.A707S		NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		707						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A707T(1)									GATTGAAACAGCACTTGAGTT	0.343																																																	1	Substitution - Missense(1)	central_nervous_system(1)	5											123.0	122.0	122.0					5																	115346463		2201	4300	6501	115374362	SO:0001583	missense	0																														ENST00000357872.4:c.2119G>T	5.37:g.115346463G>T	ENSP00000350541:p.Ala707Ser	Somatic		Capture	Illumina HiSeq	Phase_I	115374362	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.764795	0.90020	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.05925	3.37	6.03	6.03	0.97812	.	0.158255	0.44285	D	0.000469	T	0.33323	0.0859	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.04593	-1.0940	10	0.56958	D	0.05	.	19.3283	0.94273	0.0:0.0:1.0:0.0	.	707	Q6Q4G3	AMPQ_HUMAN	S	707;696	ENSP00000350541:A707S	ENSP00000350541:A707S	A	+	1	0	AC010282.1	115374362	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	6.003000	0.70701	2.861000	0.98227	0.655000	0.94253	GCA		AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
DMXL1	1657	hgsc.bcm.edu	37	5	118469391	118469391	+	Missense_Mutation	SNP	G	G	A			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:118469391G>A	ENST00000311085.8	+	12	1852	c.1772G>A	c.(1771-1773)aGt>aAt	p.S591N	DMXL1_ENST00000539542.1_Missense_Mutation_p.S591N	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	591										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		TTAAAATTAAGTATTTTTACG	0.378																																																	0			5											80.0	80.0	80.0					5																	118469391		2202	4300	6502	118497290	SO:0001583	missense	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.1772G>A	5.37:g.118469391G>A	ENSP00000309690:p.Ser591Asn	Somatic		Capture	Illumina HiSeq	Phase_I	118497290		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	G	13.17	2.157150	0.38119	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.16324	2.97;2.35	5.43	5.43	0.79202	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.10852	0.0265	N	0.12182	0.205	0.58432	D	0.999999	B;B	0.34226	0.443;0.139	B;B	0.29077	0.098;0.045	T	0.23940	-1.0174	9	.	.	.	-16.2905	19.2239	0.93810	0.0:0.0:1.0:0.0	.	591;591	F5H269;Q9Y485	.;DMXL1_HUMAN	N	591	ENSP00000309690:S591N;ENSP00000439479:S591N	.	S	+	2	0	DMXL1	118497290	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.431000	0.73395	2.562000	0.86427	0.591000	0.81541	AGT		DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
PPIC	5480	hgsc.bcm.edu	37	5	122361521	122361521	+	Silent	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:122361521C>T	ENST00000306442.4	-	4	583	c.468G>A	c.(466-468)ttG>ttA	p.L156L		NM_000943.4	NP_000934.1	P45877	PPIC_HUMAN	peptidylprolyl isomerase C (cyclophilin C)	156	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	6		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)	GTTTGCCGTCCAACCAGGTGG	0.438																																					Ovarian(99;690 1502 20765 45543 49568)												0			5											84.0	72.0	76.0					5																	122361521		2203	4300	6503	122389420	SO:0001819	synonymous_variant	5480			S71018	CCDS4133.1	5q23.2	2008-02-05			ENSG00000168938	ENSG00000168938	5.2.1.8		9256	protein-coding gene	gene with protein product		123842				1383094, 8031755	Standard	NM_000943		Approved	CYPC	uc003kth.3	P45877	OTTHUMG00000128921	ENST00000306442.4:c.468G>A	5.37:g.122361521C>T		Somatic		Capture	Illumina HiSeq	Phase_I	122389420	A4LBB5	Silent	SNP	ENST00000306442.4	37	CCDS4133.1																																																																																				PPIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250898.2	NM_000943	
CHSY3	337876	hgsc.bcm.edu	37	5	129243804	129243804	+	Silent	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:129243804C>T	ENST00000305031.4	+	2	1195	c.837C>T	c.(835-837)aaC>aaT	p.N279N	CTC-575N7.1_ENST00000515569.1_RNA|CTC-575N7.1_ENST00000503616.1_RNA|CHSY3_ENST00000507545.1_3'UTR	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	279					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		GATCGCTAAACAGCAGTAAGC	0.423																																																	0			5											75.0	77.0	77.0					5																	129243804		2203	4300	6503	129271703	SO:0001819	synonymous_variant	337876			AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.837C>T	5.37:g.129243804C>T		Somatic		Capture	Illumina HiSeq	Phase_I	129271703	B2RP97|Q76L22|Q86Y52	Silent	SNP	ENST00000305031.4	37	CCDS34223.1																																																																																				CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856	
PCDHB12	56124	hgsc.bcm.edu	37	5	140588820	140588820	+	Missense_Mutation	SNP	C	C	T	rs143200514		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:140588820C>T	ENST00000239450.2	+	1	530	c.341C>T	c.(340-342)aCg>aTg	p.T114M	PCDHB12_ENST00000541609.1_Intron	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	114	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AAAAACCCCACGCAGTTTTTA	0.448																																																	0			5											90.0	100.0	97.0					5																	140588820		2203	4300	6503	140569004	SO:0001583	missense	56124			AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.341C>T	5.37:g.140588820C>T	ENSP00000239450:p.Thr114Met	Somatic		Capture	Illumina HiSeq	Phase_I	140569004	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	C	1.592	-0.528831	0.04112	.	.	ENSG00000120328	ENST00000239450	T	0.51574	0.7	4.25	3.09	0.35607	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.20941	0.0504	N	0.05078	-0.115	0.27767	N	0.94361	P	0.43973	0.823	B	0.32677	0.15	T	0.03306	-1.1050	9	0.31617	T	0.26	.	8.7747	0.34753	0.0:0.0954:0.0:0.9046	.	114	Q9Y5F1	PCDBC_HUMAN	M	114	ENSP00000239450:T114M	ENSP00000239450:T114M	T	+	2	0	PCDHB12	140569004	0.247000	0.23920	0.001000	0.08648	0.084000	0.17831	3.399000	0.52586	0.619000	0.30197	-0.367000	0.07326	ACG		PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
ARAP3	64411	hgsc.bcm.edu	37	5	141051195	141051195	+	Missense_Mutation	SNP	C	C	T	rs149532200	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:141051195C>T	ENST00000239440.4	-	12	1861	c.1796G>A	c.(1795-1797)cGt>cAt	p.R599H	ARAP3_ENST00000508305.1_Missense_Mutation_p.R521H|ARAP3_ENST00000513878.1_Missense_Mutation_p.R261H	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	599	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						GAGACCCAGACGGTACTTTCG	0.637																																																	0			5						C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	37.0	37.0	37.0		1796	2.5	0.9	5	dbSNP_134	37	2,8598	2.2+/-6.3	0,2,4298	no	missense	ARAP3	NM_022481.5	29	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	possibly-damaging	599/1545	141051195	3,13003	2203	4300	6503	141031379	SO:0001583	missense	64411			AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.1796G>A	5.37:g.141051195C>T	ENSP00000239440:p.Arg599His	Somatic		Capture	Illumina HiSeq	Phase_I	141031379	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.985377	0.74474	2.27E-4	2.33E-4	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.44083	0.93;0.93;0.93	3.44	2.55	0.30701	.	0.211226	0.31335	U	0.007827	T	0.47857	0.1468	L	0.33485	1.01	0.24492	N	0.9943	P;D;D	0.89917	0.694;1.0;0.99	B;D;P	0.69824	0.14;0.966;0.751	T	0.29150	-1.0021	10	0.51188	T	0.08	.	9.4582	0.38767	0.0:0.8891:0.0:0.1109	.	261;521;599	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	H	521;599;261	ENSP00000421826:R521H;ENSP00000239440:R599H;ENSP00000421468:R261H	ENSP00000239440:R599H	R	-	2	0	ARAP3	141031379	0.994000	0.37717	0.886000	0.34754	0.955000	0.61496	3.085000	0.50151	0.618000	0.30179	0.563000	0.77884	CGT		ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
KCTD16	57528	hgsc.bcm.edu	37	5	143586926	143586926	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:143586926C>T	ENST00000507359.3	+	2	1740	c.649C>T	c.(649-651)Cga>Tga	p.R217*	KCTD16_ENST00000512467.1_Nonsense_Mutation_p.R217*	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	217					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)		p.R217G(1)		large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			AGACCCTGATCGAGCCCCAGA	0.453																																																	1	Substitution - Missense(1)	large_intestine(1)	5											60.0	65.0	63.0					5																	143586926		2203	4300	6503	143567119	SO:0001587	stop_gained	57528			AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"""potassium channel tetramerisation domain containing 16"""			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.649C>T	5.37:g.143586926C>T	ENSP00000426548:p.Arg217*	Somatic		Capture	Illumina HiSeq	Phase_I	143567119	Q9P2M9	Nonsense_Mutation	SNP	ENST00000507359.3	37	CCDS34260.1	.	.	.	.	.	.	.	.	.	.	C	47	13.333572	0.99735	.	.	ENSG00000183775	ENST00000512467;ENST00000507359	.	.	.	5.69	2.85	0.33270	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.719	0.77694	0.6228:0.3772:0.0:0.0	.	.	.	.	X	217	.	ENSP00000426548:R217X	R	+	1	2	KCTD16	143567119	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	1.417000	0.34770	0.298000	0.22638	0.561000	0.74099	CGA		KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368	
ERGIC1	57222	hgsc.bcm.edu	37	5	172324048	172324048	+	Silent	SNP	G	G	T	rs543897451		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr5:172324048G>T	ENST00000393784.3	+	3	265	c.126G>T	c.(124-126)tcG>tcT	p.S42S	ERGIC1_ENST00000519860.1_3'UTR|ERGIC1_ENST00000523291.1_Silent_p.S42S	NM_001031711.2	NP_001026881.1	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	42					ER to Golgi vesicle-mediated transport (GO:0006888)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.S42S(1)		endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)	9	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCTTCCTCTCGGAGCTCACCG	0.512																																																	1	Substitution - coding silent(1)	ovary(1)	5											255.0	195.0	215.0					5																	172324048		2203	4300	6503	172256654	SO:0001819	synonymous_variant	57222			AF267855	CCDS34292.1	5q35.1	2009-11-06			ENSG00000113719	ENSG00000113719			29205	protein-coding gene	gene with protein product						10574461, 15308636	Standard	NM_001031711		Approved	ERGIC32, ERGIC-32, KIAA1181, NET24	uc003mbw.4	Q969X5	OTTHUMG00000130520	ENST00000393784.3:c.126G>T	5.37:g.172324048G>T		Somatic		Capture	Illumina HiSeq	Phase_I	172256654	Q9H0L0|Q9H2J2|Q9ULN9	Silent	SNP	ENST00000393784.3	37	CCDS34292.1																																																																																				ERGIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252938.3	NM_020462	
PUM1	9698	hgsc.bcm.edu	37	1	31426559	31426559	+	Splice_Site	SNP	A	A	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:31426559A>C	ENST00000257075.5	-	15	2685		c.e15+1		PUM1_ENST00000424085.2_Splice_Site|PUM1_ENST00000440538.2_Splice_Site|PUM1_ENST00000373742.2_Splice_Site|PUM1_ENST00000426105.2_Splice_Site|PUM1_ENST00000373747.3_Splice_Site|PUM1_ENST00000423018.2_Splice_Site|PUM1_ENST00000373741.4_Splice_Site	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1						membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		CCAAGTACTCACCTGGACCCA	0.413																																																	0			1											106.0	116.0	112.0					1																	31426559		2203	4300	6503	31199146	SO:0001630	splice_region_variant	9698			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"""pumilio (Drosophila) homolog 1"", ""pumilio homolog 1 (Drosophila)"""				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.2591+1T>G	1.37:g.31426559A>C		Somatic		Capture	Illumina HiSeq	Phase_I	31199146	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Splice_Site	SNP	ENST00000257075.5	37	CCDS338.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.028601	0.75390	.	.	ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000525843;ENST00000426105;ENST00000498419;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742;ENST00000529846;ENST00000525997	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7636	0.78106	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PUM1	31199146	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	9.339000	0.96797	2.210000	0.71456	0.533000	0.62120	.		PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		Intron
LOR	4014	hgsc.bcm.edu	37	1	153233488	153233489	+	In_Frame_Ins	INS	-	-	GGCGGT	rs150026164	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:153233488_153233489insGGCGGT	ENST00000368742.3	+	2	120_121	c.63_64insGGCGGT	c.(64-66)ggc>GGCGGTggc	p.22_22G>GGG		NM_000427.2	NP_000418.2	P23490	LORI_HUMAN	loricrin	22					keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein binding, bridging (GO:0030674)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.G22S(1)		lung(2)	2	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGACCTCTggcggcggtggcgg	0.673														971	0.19389	0.3812	0.1542	5008	,	,		8118	0.0685		0.2326	False		,,,				2504	0.0583																1	Substitution - Missense(1)	lung(1)	1								1372,2418		364,644,887						1.9	0.9		dbSNP_130	14	1619,5813		315,989,2412	no	coding	LOR	NM_000427.2		679,1633,3299	A1A1,A1R,RR		21.7842,36.2005,26.653				2991,8231				151500113	SO:0001652	inframe_insertion	4014			M61120	CCDS30870.1	1q21	2008-02-05			ENSG00000203782	ENSG00000203782			6663	protein-coding gene	gene with protein product		152445				2007607, 1355480	Standard	NM_000427		Approved		uc001fbm.3	P23490	OTTHUMG00000013938	ENST00000368742.3:c.70_75dupGGCGGT	1.37:g.153233489_153233494dupGGCGGT	ENSP00000357731:p.GlyGly28dup	Somatic		Capture	Illumina HiSeq	Phase_I	151500112	Q5T869|Q5XKF8	In_Frame_Ins	INS	ENST00000368742.3	37	CCDS30870.1																																																																																				LOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039107.1	NM_000427	
FMN2	56776	hgsc.bcm.edu	37	1	240371056	240371121	+	In_Frame_Del	DEL	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	-	rs139764401|rs71646825|rs557827551|rs537036439|rs71646826|rs141912031|rs202207586|rs71646890|rs11586155|rs71646889|rs71646891|rs71646887|rs375298881|rs71646827|rs373490785	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	CCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr1:240371056_240371121delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	ENST00000319653.9	+	5	3174_3239	c.2944_3009delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	c.(2944-3009)cccggagcgggcataccccctcctcccccacttcccggagcgggcataccccctccgcccccacttdel	p.PGAGIPPPPPLPGAGIPPPPPL1070del		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1070	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.P1131T(2)|p.P1143P(1)|p.G1128A(1)|p.G1128G(1)|p.P1134L(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ACCCCCTCTACCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTTCCCGGAGCGG	0.714																																																	6	Substitution - Missense(4)|Substitution - coding silent(2)	lung(3)|prostate(1)|ovary(1)|large_intestine(1)	1																																								238437744	SO:0001651	inframe_deletion	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2944_3009delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	1.37:g.240371056_240371121delCCCGGAGCGGGCATACCCCCTCCTCCCCCACTTCCCGGAGCGGGCATACCCCCTCCGCCCCCACTT	ENSP00000318884:p.Pro1070_Leu1091del	Somatic		Capture	Illumina HiSeq	Phase_I	238437679	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	In_Frame_Del	DEL	ENST00000319653.9	37	CCDS31069.2																																																																																				FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
SPATA3	130560	hgsc.bcm.edu	37	2	231861033	231861059	+	In_Frame_Del	DEL	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA	-	rs13005918|rs72362780	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:231861033_231861059delCAGCAGCCTAGCCCTGAATCCACACCA	ENST00000452881.1	+	1	193_219	c.85_111delCAGCAGCCTAGCCCTGAATCCACACCA	c.(85-111)cagcagcctagccctgaatccacaccadel	p.QQPSPESTP47del	SPATA3_ENST00000433428.2_In_Frame_Del_p.QQPSPESTP47del|AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000455816.1_In_Frame_Del_p.QQPSPESTP47del|SPATA3_ENST00000424440.1_In_Frame_Del_p.QQPSPESTP47del			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	47			Missing.							endometrium(2)|lung(1)	3						TTCCACCTCTCAGCAGCCTAGCCCTGAATCCACACCACAGCAGCCTA	0.564																																																	0			2								924,1842		222,480,681						-8.0	0.0		dbSNP_130	187	2754,2350		871,1012,669	no	coding	SPATA3	NM_139073.3		1093,1492,1350	A1A1,A1R,RR		46.0423,33.4056,46.7344				3678,4192				231569303	SO:0001651	inframe_deletion	130560			AY032925	CCDS2481.1	2q37.1	2008-02-05			ENSG00000173699	ENSG00000173699			17884	protein-coding gene	gene with protein product							Standard	NM_139073		Approved	TSARG1	uc010zmd.2	Q8NHX4	OTTHUMG00000133221	ENST00000452881.1:c.85_111delCAGCAGCCTAGCCCTGAATCCACACCA	2.37:g.231861033_231861059delCAGCAGCCTAGCCCTGAATCCACACCA	ENSP00000388895:p.Gln47_Pro55del	Somatic		Capture	Illumina HiSeq	Phase_I	231569277	Q86WX5|Q8N9Y6	In_Frame_Del	DEL	ENST00000452881.1	37	CCDS2481.1																																																																																				SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
AQP12A	375318	hgsc.bcm.edu	37	2	241631786	241631786	+	Frame_Shift_Del	DEL	G	G	-	rs369196482		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr2:241631786delG	ENST00000337801.4	+	2	488	c.419delG	c.(418-420)agcfs	p.S141fs	AQP12A_ENST00000429564.1_Frame_Shift_Del_p.S153fs|AC011298.2_ENST00000407635.2_lincRNA	NM_198998.2	NP_945349.1	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	141						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(3)|large_intestine(2)|lung(7)	14		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		CAGAGCTGCAGCTCGGCCCTG	0.692																																																	0			2								36,3516		5,26,1745	5.0	8.0	7.0			2.5	1.0	2		7	36,7602		2,32,3785	no	frameshift	AQP12A	NM_198998.1		7,58,5530	A1A1,A1R,RR		0.4713,1.0135,0.6434			241631786	72,11118	1936	4133	6069	241280459	SO:0001589	frameshift_variant	375318			AB040748		2q37.3	2013-06-03	2005-05-26	2005-05-26	ENSG00000184945	ENSG00000184945		"""Ion channels / Aquaporins"""	19941	protein-coding gene	gene with protein product		609789	"""aquaporin 12"""	AQP12			Standard	NM_198998		Approved		uc002vzu.3	Q8IXF9	OTTHUMG00000183906	ENST00000337801.4:c.419delG	2.37:g.241631786delG	ENSP00000337144:p.Ser141fs	Somatic		Capture	Illumina HiSeq	Phase_I	241280459		Frame_Shift_Del	DEL	ENST00000337801.4	37																																																																																					AQP12A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257185.2	NM_198998	
MUC4	4585	hgsc.bcm.edu	37	3	195514998	195515045	+	In_Frame_Del	DEL	GGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA	GGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA	-	rs200518052|rs538504516|rs199975352|rs200763050|rs552771790|rs570974278|rs368837663|rs201206859|rs199883835|rs78683709|rs201451131|rs76196931	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	GGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA	GGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr3:195514998_195515045delGGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA	ENST00000463781.3	-	2	3865_3912	c.3406_3453delTCTCTTCCTGTCACCGACACTTCCTCAGTATCCACAGGTCACACCACC	c.(3406-3453)tctcttcctgtcaccgacacttcctcagtatccacaggtcacaccaccdel	p.SLPVTDTSSVSTGHTT1136del	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.SLPVTDTSSVSTGHTT1136del|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	603					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T1142S(3)|p.V1145A(2)|p.P1138L(1)|p.H1149H(1)|p.T1142T(1)|p.T1150A(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CATGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGAGGTGGCGTGA	0.569																																																	9	Substitution - Missense(7)|Substitution - coding silent(2)	endometrium(4)|stomach(2)|skin(2)|kidney(1)	3							,,	1034,2304		279,476,914					,,	-1.1	0.0			8	2849,3303		990,869,1217	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	1269,1345,2131	A1A1,A1R,RR		46.3101,30.9766,40.9168	,,	,,		3883,5607				196999440	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3406_3453delTCTCTTCCTGTCACCGACACTTCCTCAGTATCCACAGGTCACACCACC	3.37:g.195514998_195515045delGGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA	ENSP00000417498:p.Ser1136_Thr1151del	Somatic		Capture	Illumina HiSeq	Phase_I	196999393	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FBXW7	55294	hgsc.bcm.edu	37	4	153258991	153258995	+	Frame_Shift_Del	DEL	TGGGG	TGGGG	-			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	TGGGG	TGGGG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr4:153258991_153258995delTGGGG	ENST00000281708.4	-	5	2049_2053	c.820_824delCCCCA	c.(820-825)ccccagfs	p.PQ274fs	FBXW7_ENST00000263981.5_Frame_Shift_Del_p.PQ194fs|RP11-461L13.2_ENST00000605147.1_RNA|FBXW7_ENST00000603548.1_Frame_Shift_Del_p.PQ274fs|FBXW7_ENST00000393956.3_Frame_Shift_Del_p.PQ98fs|FBXW7_ENST00000296555.5_Frame_Shift_Del_p.PQ156fs|FBXW7_ENST00000603841.1_Frame_Shift_Del_p.PQ274fs	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	274					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TCGTTGAAACTGGGGTTCTATCACT	0.361			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	4																																								153478445	SO:0001589	frameshift_variant	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.820_824delCCCCA	4.37:g.153258991_153258995delTGGGG	ENSP00000281708:p.Pro274fs	Somatic		Capture	Illumina HiSeq	Phase_I	153478441	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Frame_Shift_Del	DEL	ENST00000281708.4	37	CCDS3777.1																																																																																				FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376831	168376832	+	lincRNA	DEL	GT	GT	-	rs78125251|rs142011748		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	GT	GT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr6:168376831_168376832delGT	ENST00000538528.1	-	0	787_788																											TCCCCCTGCAGTGTGTGTGTGG	0.599																																																	0			6																																								168119681			100128124																															6.37:g.168376839_168376840delGT		Somatic		Capture	Illumina HiSeq	Phase_I	168119680		Frame_Shift_Del	DEL	ENST00000538528.1	37																																																																																					RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
GPRIN2	9721	hgsc.bcm.edu	37	10	46999591	46999592	+	In_Frame_Ins	INS	-	-	ATGAGGGAG	rs112620425	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr10:46999591_46999592insATGAGGGAG	ENST00000374317.1	+	3	984_985	c.711_712insATGAGGGAG	c.(712-714)atg>ATGAGGGAGatg	p.238_238M>MREM	GPRIN2_ENST00000374314.4_In_Frame_Ins_p.238_238M>MREM	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	238								p.G237_M238insMRE(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TACTCTGTGGCATGAGGGAGGT	0.629														2399	0.479034	0.4697	0.4856	5008	,	,		38874	0.4782		0.4761	False		,,,				2504	0.4908																1	Insertion - In frame(1)	breast(1)	10								2080,27,2157		11,3,2055,0,24,39						0.9	0.0		dbSNP_130	49	3974,98,4180		16,7,3935,0,91,77	no	codingComplex	GPRIN2	NM_014696.3		27,10,5990,0,115,116	A1A1,A1A2,A1R,A2A2,A2R,RR		49.3456,49.4137,49.3688				6054,125,6337				46419598	SO:0001652	inframe_insertion	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.712_720dupATGAGGGAG	10.37:g.46999592_46999600dupATGAGGGAG	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	46419597	Q5SVF0	In_Frame_Ins	INS	ENST00000374317.1	37	CCDS31192.1																																																																																				GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
PRB4	5545	hgsc.bcm.edu	37	12	11461534	11461596	+	In_Frame_Del	DEL	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	-	rs11054244|rs59021567|rs11054243|rs551775057|rs12303607|rs199532199|rs148027029|rs71057722|rs59189129|rs536297617	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:11461534_11461596delCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	ENST00000535904.1	-	3	354_416	c.321_383delAAACCAGTCCCAAGGTACCCCACCTCCTCCAGGAAAGCCAGAAAGACCACCCCCACAAGGAGG	c.(319-384)ggaaaccagtcccaaggtaccccacctcctccaggaaagccagaaagaccacccccacaaggaggc>ggc	p.107_128GNQSQGTPPPPGKPERPPPQGG>G	PRB4_ENST00000279575.1_In_Frame_Del_p.107_128GNQSQGTPPPPGKPERPPPQGG>G|PRB4_ENST00000445719.2_Splice_Site_p.107_112GNQSQG>G			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	128	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.		Missing (in allele M and allele S).	SR -> RP (in Ref. 7; CAA30542). {ECO:0000305}.		extracellular region (GO:0005576)		p.P115L(1)|p.G118E(1)|p.P117T(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						GGACTGGTTGCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTTCCTCCTTGTG	0.605										HNSCC(22;0.051)																																							3	Substitution - Missense(3)	lung(1)|kidney(1)|skin(1)	12																																								11352863	SO:0001651	inframe_deletion	5545				CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.321_383delAAACCAGTCCCAAGGTACCCCACCTCCTCCAGGAAAGCCAGAAAGACCACCCCCACAAGGAGG	12.37:g.11461534_11461596delCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	ENSP00000442834:p.Gly107_Gly127del	Somatic		Capture	Illumina HiSeq	Phase_I	11352801	A1L439|O00600|P02813|P10161|P10162|P81489	In_Frame_Del	DEL	ENST00000535904.1	37	CCDS8641.1																																																																																				PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723	
KRT4	3851	hgsc.bcm.edu	37	12	53207602	53207603	+	Frame_Shift_Ins	INS	-	-	G	rs7135148|rs71092788		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr12:53207602_53207603insG	ENST00000551956.1	-	1	732_733	c.240_241insC	c.(238-243)tttggcfs	p.G81fs	KRT4_ENST00000458244.2_Frame_Shift_Ins_p.G61fs|KRT4_ENST00000293774.4_Frame_Shift_Ins_p.G155fs			P19013	K2C4_HUMAN	keratin 4	81	Gly-rich.|Head.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CCACCAGTGCCAAAGCCTCCAG	0.599																																					Pancreas(190;284 2995 41444 45903)												0			12																																								51493870	SO:0001589	frameshift_variant	3851				CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.240_241insC	12.37:g.53207602_53207603insG	ENSP00000448220:p.Gly81fs	Somatic		Capture	Illumina HiSeq	Phase_I	51493869	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Frame_Shift_Ins	INS	ENST00000551956.1	37	CCDS41787.2																																																																																				KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
Unknown	0	hgsc.bcm.edu	37	Unknown	0	0	+	IGR	DEL	AACCCCGAGGCCCTCAAGGGCTTCCACCCT	AACCCCGAGGCCCTCAAGGGCTTCCACCCT	-			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	AACCCCGAGGCCCTCAAGGGCTTCCACCCT	AACCCCGAGGCCCTCAAGGGCTTCCACCCT					Unknown	Invalid:failed_liftOver	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chrUnknown:0delAACCCCGAGGCCCTCAAGGGCTTCCACCCT								None (None upstream) : None (None downstream)																								0																																																	0			17																																								263631	SO:0001628	intergenic_variant	400566																															Unknown.37:g.0delAACCCCGAGGCCCTCAAGGGCTTCCACCCT		Somatic		Capture	Illumina HiSeq	Phase_I	263602		Frame_Shift_Del	DEL		37																																																																																				0								
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383323	39383334	+	In_Frame_Del	DEL	CTGCTGCCAGCC	CTGCTGCCAGCC	-	rs201521857|rs542786200	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	CTGCTGCCAGCC	CTGCTGCCAGCC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr17:39383323_39383334delCTGCTGCCAGCC	ENST00000377721.3	+	1	424_435	c.417_428delCTGCTGCCAGCC	c.(415-429)aactgctgccagccc>aac	p.CCQP140del	KRTAP9-2_ENST00000455970.2_In_Frame_Del_p.CCQP124del	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	140	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GTGGCTCCAACTGCTGCCAGCCCTGCTGCCGC	0.613														133	0.0265575	0.0038	0.0519	5008	,	,		19177	0.0		0.0646	False		,,,				2504	0.0276																0			17																																								36636860	SO:0001651	inframe_deletion	83899			AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.417_428delCTGCTGCCAGCC	17.37:g.39383323_39383334delCTGCTGCCAGCC	ENSP00000366950:p.Cys140_Pro143del	Somatic		Capture	Illumina HiSeq	Phase_I	36636849	Q17RK8|Q2TB15|Q6ISF6	In_Frame_Del	DEL	ENST00000377721.3	37	CCDS32651.1																																																																																				KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
ZNF516	9658	hgsc.bcm.edu	37	18	74090958	74090958	+	Frame_Shift_Del	DEL	G	G	-	rs398079646|rs398033573|rs56087742		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr18:74090958delG	ENST00000443185.2	-	5	3428	c.3111delC	c.(3109-3111)cccfs	p.P1037fs	ZNF516_ENST00000524431.2_5'UTR|RP11-504I13.3_ENST00000583287.1_RNA	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	1037					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		AGTGTAGGACGGGGGGGCGCC	0.652													GGGGGG|GGGGGGG|GGGGGG|insertion	5008	1.0	1.0	1.0	5008	,	,		13278	1.0		1.0	False		,,,				2504	1.0																0			18								3517,17		1755,7,5	7.0	7.0	7.0			-0.6	0.0	18	dbSNP_131	33	7701,27		3846,9,9	no	frameshift	ZNF516	NM_014643.3		5601,16,14	A1A1,A1R,RR		0.3494,0.481,0.3907			74090958	11218,44	1730	3829	5559	72219946	SO:0001589	frameshift_variant	9658			D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.3111delC	18.37:g.74090958delG	ENSP00000394757:p.Pro1037fs	Somatic		Capture	Illumina HiSeq	Phase_I	72219946		Frame_Shift_Del	DEL	ENST00000443185.2	37																																																																																					ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
UHRF1	29128	hgsc.bcm.edu	37	19	4954679	4954680	+	RNA	INS	-	-	C	rs397767650|rs55946225	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:4954679_4954680insC	ENST00000592666.1	+	0	2551_2552							Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains 1						cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|histone monoubiquitination (GO:0010390)|histone ubiquitination (GO:0016574)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autoubiquitination (GO:0051865)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|replication fork (GO:0005657)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|hemi-methylated DNA-binding (GO:0044729)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(2)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		CCCGAGCAGGGCGGGTCCCCGC	0.683																																																	0			19							,	3444,10		1720,4,3					,	-6.1	0.0		dbSNP_131	9	7668,10		3830,8,1	no	frameshift,frameshift	UHRF1	NM_013282.3,NM_001048201.1	,	5550,12,4	A1A1,A1R,RR		0.1302,0.2895,0.1797	,	,		11112,20				4905680			29128			AF129507	CCDS74262.1, CCDS74263.1	19p13.3	2012-04-20	2008-08-14		ENSG00000034063	ENSG00000276043		"""RING-type (C3HC4) zinc fingers"""	12556	protein-coding gene	gene with protein product		607990				10646863	Standard	NM_001048201		Approved	ICBP90, Np95, FLJ21925, RNF106	uc002mbo.3	Q96T88			19.37:g.4954680_4954680dupC		Somatic		Capture	Illumina HiSeq	Phase_I	4905679	A0JBR2|A8K024|B2RBA9|Q2HIX7|Q8J022|Q9H6S6|Q9P115|Q9P1U7	Frame_Shift_Ins	INS	ENST00000592666.1	37																																																																																					UHRF1-006	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000450444.1	NM_001048201	
LILRB4	11006	hgsc.bcm.edu	37	19	55179244	55179244	+	Splice_Site	DEL	G	G	-	rs571881532|rs386810941	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:55179244delG	ENST00000391736.1	+	13	1515	c.1200delG	c.(1198-1200)gag>ga	p.E400fs	LILRB4_ENST00000391734.3_Intron|LILRB4_ENST00000391733.3_Splice_Site_p.E401fs|LILRB4_ENST00000270452.2_Splice_Site_p.E400fs|LILRB4_ENST00000430952.2_Splice_Site_p.E399fs	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	400					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		TGGACACTGAGGTGAGTCCTT	0.617													?|GG|G|unsure	97	0.019369	0.0461	0.0144	5008	,	,		16664	0.002		0.0169	False		,,,				2504	0.0072																0			19							,	175,4085		12,151,1967	99.0	93.0	95.0		,	1.0	0.0	19		95	101,8151		5,91,4030	no	frameshift-near-splice,frameshift-near-splice	LILRB4	NM_006847.3,NM_001081438.1	,	17,242,5997	A1A1,A1R,RR		1.2239,4.108,2.2059	,	,	55179244	276,12236	2193	4296	6489	59871056	SO:0001630	splice_region_variant	11006			U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1200+1G>-	19.37:g.55179244delG		Somatic		Capture	Illumina HiSeq	Phase_I	59871056	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Frame_Shift_Del	DEL	ENST00000391736.1	37	CCDS12902.1																																																																																				LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		Frame_Shift_Del
ZNF814	730051	hgsc.bcm.edu	37	19	58385869	58385870	+	In_Frame_Ins	INS	-	-	ATA	rs199684163|rs10687775|rs55789144|rs66767659	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr19:58385869_58385870insATA	ENST00000435989.2	-	3	1122_1123	c.888_889insTAT	c.(886-891)catgaa>catTATgaa	p.296_297HE>HYE	ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	296				H -> HY (in Ref. 1; BAH13293 and 3; EAW72539). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TCTCCACATTCATGTTTTTTTT	0.361														2541	0.507388	0.4463	0.5072	5008	,	,		7847	0.5774		0.5199	False		,,,				2504	0.5051																0			19																																								63077682	SO:0001652	inframe_insertion	730051				CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.888_889insTAT	19.37:g.58385869_58385870insATA	ENSP00000410545:p.His296_Glu297insTyr	Somatic		Capture	Illumina HiSeq	Phase_I	63077681	A6NF35	In_Frame_Ins	INS	ENST00000435989.2	37	CCDS46212.1																																																																																				ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
Unknown	0	hgsc.bcm.edu	37	Unknown	0	0	+	IGR	INS	-	-	C			TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	-	-					Unknown	Invalid:failed_liftOver	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chrUnknown:0_0insC								None (None upstream) : None (None downstream)																								0																																																	0			20																																								55400100	SO:0001628	intergenic_variant	55544																															Unknown.37:g.0_0insC		Somatic		Capture	Illumina HiSeq	Phase_I	55400099		Frame_Shift_Ins	INS		37																																																																																				0								
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020656	46020670	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-	rs36208679|rs60739860|rs373191083		TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chr21:46020656_46020670delCTGCTGCGCCCCCAG	ENST00000380102.2	+	1	160_174	c.135_149delCTGCTGCGCCCCCAG	c.(133-150)ccctgctgcgcccccagc>ccc	p.CCAPS46del	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	46	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S50_P54delSCCAP(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GCGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCC	0.698																																																	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	21							,	2258,1042		849,560,241					,	-0.7	1.0		dbSNP_126	22	6001,1123		2605,791,166	no	coding,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	,	3454,1351,407	A1A1,A1R,RR		15.7636,31.5758,20.7694	,	,		8259,2165				44845098	SO:0001651	inframe_deletion	386675			AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.135_149delCTGCTGCGCCCCCAG	21.37:g.46020656_46020670delCTGCTGCGCCCCCAG	ENSP00000369445:p.Cys46_Ser50del	Somatic		Capture	Illumina HiSeq	Phase_I	44845084	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	37																																																																																					KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
VCX2	51480	hgsc.bcm.edu	37	X	8138165	8138168	+	Frame_Shift_Del	DEL	CCTC	CCTC	-	rs1058237|rs144469326	byFrequency	TCGA-CI-6619-01B-11D-1826-10	TCGA-CI-6619-10A-01D-1826-10	CCTC	CCTC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	a59609de-b5d4-4648-9e25-92a0fd2d76fe	1994071a-1627-4370-83dc-eb33cbf06fdd	g.chrX:8138165_8138168delCCTC	ENST00000317103.4	-	3	631_634	c.325_328delGAGG	c.(325-330)gaggtgfs	p.EV109fs		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	109	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.									endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GGTTCTTCCACCTCGCTCTCCTGA	0.642																																																	0			X																																								8098168	SO:0001589	frameshift_variant	51480			AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.325_328delGAGG	X.37:g.8138165_8138168delCCTC	ENSP00000321309:p.Glu109fs	Somatic		Capture	Illumina HiSeq	Phase_I	8098165	A3KPB6|Q4V9T2|Q9P0H5	Frame_Shift_Del	DEL	ENST00000317103.4	37	CCDS35200.1																																																																																				VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378	
