#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
ITIH5	80760	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	7679258	7679258	+	Silent	SNP	C	C	T			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr10:7679258C>T	ENST00000256861.6	-	5	663	c.585G>A	c.(583-585)gcG>gcA	p.A195A	ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397146.2_Silent_p.A195A|ITIH5_ENST00000446830.2_5'UTR|ITIH5_ENST00000397145.2_Silent_p.A195A	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	195					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						ATGCGATGCCCGCGCTCTCCA	0.657																																																0													71.0	72.0	72.0					10																	7679258		2203	4300	6503	SO:0001819	synonymous_variant	80760					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.585G>A	10.37:g.7679258C>T			Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	37																																																																																					0.657	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		61	128	61	128
TEAD1	7003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	12883803	12883803	+	Missense_Mutation	SNP	A	A	G			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr11:12883803A>G	ENST00000527575.1	+	3	322	c.209A>G	c.(208-210)aAt>aGt	p.N70S	TEAD1_ENST00000361905.4_Missense_Mutation_p.N55S|TEAD1_ENST00000527636.1_Missense_Mutation_p.N70S|TEAD1_ENST00000361985.2_Missense_Mutation_p.N70S|TEAD1_ENST00000334310.6_Missense_Mutation_p.N55S			P28347	TEAD1_HUMAN	TEA domain family member 1 (SV40 transcriptional enhancer factor)	70					gene expression (GO:0010467)|hippo signaling (GO:0035329)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)	17				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		TCAGGTAGGAATGAATTGATA	0.403																																																0													106.0	95.0	99.0					11																	12883803		2200	4294	6494	SO:0001583	missense	7003			X84839	CCDS7810.1, CCDS7810.2	11p15.4	2008-11-12				ENSG00000187079			11714	protein-coding gene	gene with protein product		189967	"""atrophia areata, peripapillary chorioretinal degeneration"""	TCF13, AA		1851669, 9889009, 15016762	Standard	NM_021961		Approved	TEF-1	uc021qdx.1	P28347		ENST00000527575.1:c.209A>G	11.37:g.12883803A>G	ENSP00000435977:p.Asn70Ser		A4FUP2|E7EV65	Missense_Mutation	SNP	ENST00000527575.1	37		.	.	.	.	.	.	.	.	.	.	A	24.8	4.568505	0.86439	.	.	ENSG00000187079	ENST00000361905;ENST00000527636;ENST00000527575;ENST00000334310;ENST00000361985	T;T;T;T;T	0.61627	0.09;0.09;0.09;0.09;0.09	5.79	5.79	0.91817	.	0.041690	0.85682	D	0.000000	T	0.81754	0.4889	H	0.94183	3.505	0.80722	D	1	D	0.59357	0.985	D	0.64687	0.928	D	0.86752	0.1961	10	0.66056	D	0.02	-13.2949	15.7943	0.78398	1.0:0.0:0.0:0.0	.	70	P28347	TEAD1_HUMAN	S	55;70;70;55;70	ENSP00000355332:N55S;ENSP00000435233:N70S;ENSP00000435977:N70S;ENSP00000334754:N55S;ENSP00000354588:N70S	ENSP00000334754:N55S	N	+	2	0	TEAD1	12840379	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.208000	0.71279	0.533000	0.62120	AAT		0.403	TEAD1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000386888.1	NM_021961		7	61	7	61
OR4C16	219428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	55339694	55339694	+	Missense_Mutation	SNP	C	C	T			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr11:55339694C>T	ENST00000314634.3	+	1	91	c.91C>T	c.(91-93)Cgt>Tgt	p.R31C		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	31						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				TATTTTTTTGCGTCTCTACTT	0.373																																																0													182.0	171.0	175.0					11																	55339694		2201	4296	6497	SO:0001583	missense	219428			AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.91C>T	11.37:g.55339694C>T	ENSP00000324913:p.Arg31Cys		Q6IEV8	Missense_Mutation	SNP	ENST00000314634.3	37	CCDS31502.1	.	.	.	.	.	.	.	.	.	.	C	9.601	1.128613	0.21041	.	.	ENSG00000181935	ENST00000314634	T	0.00438	7.42	4.98	-6.75	0.01738	.	2.239510	0.01631	N	0.023546	T	0.00109	0.0003	N	0.00677	-1.265	0.09310	N	1	B	0.25351	0.124	B	0.12837	0.008	T	0.49670	-0.8915	10	0.66056	D	0.02	.	2.689	0.05115	0.0976:0.2919:0.1926:0.418	.	31	Q8NGL9	OR4CG_HUMAN	C	31	ENSP00000324913:R31C	ENSP00000324913:R31C	R	+	1	0	OR4C16	55096270	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.079000	0.00082	-1.262000	0.02459	-2.709000	0.00134	CGT		0.373	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701		47	87	47	87
POU2AF1	5450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	111229622	111229622	+	Missense_Mutation	SNP	G	G	A			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr11:111229622G>A	ENST00000393067.3	-	2	552	c.38C>T	c.(37-39)cCa>cTa	p.P13L		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	13					humoral immune response (GO:0006959)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(2)|lung(2)	5		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		GGCCGGGGCTGGGGCTTGCTC	0.632			T	BCL6	NHL																																		Dom	yes		11	11q23.1	5450	"""POU domain, class 2, associating factor 1 (OBF1)"""		L	0													48.0	49.0	49.0					11																	111229622		2201	4297	6498	SO:0001583	missense	5450				CCDS31675.1	11q23.1	2011-06-01	2007-07-13			ENSG00000110777			9211	protein-coding gene	gene with protein product		601206	"""POU domain class 2, associating factor 1"""			8617501	Standard	NM_006235		Approved	OBF1	uc001plg.4	Q16633		ENST00000393067.3:c.38C>T	11.37:g.111229622G>A	ENSP00000376786:p.Pro13Leu		B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	37	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165888	0.78339	.	.	ENSG00000110777	ENST00000393067;ENST00000531398	T;T	0.32753	1.44;1.44	5.0	5.0	0.66597	.	0.238634	0.35936	N	0.002889	T	0.33990	0.0882	L	0.45581	1.43	0.49389	D	0.999781	P	0.48089	0.905	P	0.47941	0.562	T	0.03761	-1.1006	10	0.15499	T	0.54	-1.2837	16.0815	0.81007	0.0:0.0:1.0:0.0	.	13	Q16633	OBF1_HUMAN	L	13;15	ENSP00000376786:P13L;ENSP00000433527:P15L	ENSP00000376786:P13L	P	-	2	0	POU2AF1	110734832	0.999000	0.42202	0.973000	0.42090	0.656000	0.38851	3.990000	0.56965	2.331000	0.79229	0.305000	0.20034	CCA		0.632	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235		18	33	18	33
A2ML1	144568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	8976368	8976368	+	Missense_Mutation	SNP	G	G	A			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr12:8976368G>A	ENST00000299698.7	+	3	479	c.299G>A	c.(298-300)gGa>gAa	p.G100E	A2ML1-AS1_ENST00000537288.1_RNA	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						CGGGTGTCGGGAGTTGGAAAT	0.527																																																0													103.0	104.0	104.0					12																	8976368		1883	4092	5975	SO:0001583	missense	144568			AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.299G>A	12.37:g.8976368G>A	ENSP00000299698:p.Gly100Glu			Missense_Mutation	SNP	ENST00000299698.7	37	CCDS8596.2	.	.	.	.	.	.	.	.	.	.	G	8.677	0.904292	0.17760	.	.	ENSG00000166535	ENST00000299698;ENST00000539161	T	0.34667	1.35	3.99	2.03	0.26663	.	0.354583	0.20631	N	0.088585	T	0.25791	0.0628	N	0.24115	0.695	0.18873	N	0.999988	P	0.37370	0.592	B	0.39562	0.303	T	0.13845	-1.0494	10	0.72032	D	0.01	.	10.0485	0.42201	0.0:0.4019:0.5981:0.0	.	100	A8K2U0	A2ML1_HUMAN	E	100	ENSP00000299698:G100E	ENSP00000299698:G100E	G	+	2	0	A2ML1	8867635	0.001000	0.12720	0.003000	0.11579	0.352000	0.29268	0.085000	0.14912	0.574000	0.29417	0.655000	0.94253	GGA		0.527	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		75	126	75	126
SPATA13	221178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	24858319	24858319	+	Missense_Mutation	SNP	C	C	G	rs367888214		TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr13:24858319C>G	ENST00000382095.4	+	4	743	c.336C>G	c.(334-336)aaC>aaG	p.N112K	SPATA13_ENST00000409126.1_Missense_Mutation_p.N34K|SPATA13_ENST00000424834.2_Missense_Mutation_p.N737K|SPATA13_ENST00000343003.6_Missense_Mutation_p.N56K|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.N615K|SPATA13_ENST00000399949.2_Missense_Mutation_p.N34K|SPATA13_ENST00000382108.3_Missense_Mutation_p.N737K	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	112	ABR (APC-binding region) domain.				cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		TGGATGACAACGgtagtgagg	0.493																																																0													78.0	67.0	70.0					13																	24858319		2203	4300	6503	SO:0001583	missense	221178			AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.336C>G	13.37:g.24858319C>G	ENSP00000371527:p.Asn112Lys		A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	37	CCDS9305.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	8.051|8.051	0.765954|0.765954	0.15983|0.15983	.|.	.|.	ENSG00000182957|ENSG00000182957	ENST00000382108;ENST00000382095;ENST00000434675;ENST00000438694;ENST00000399949;ENST00000409126;ENST00000343003;ENST00000454083|ENST00000424834	T;T;T;T;T;T;T|.	0.77229|.	-0.73;-0.4;-1.08;-0.44;-1.05;-0.46;-0.46|.	5.65|5.65	-9.98|-9.98	0.00438|0.00438	.|.	0.082034|.	0.85682|.	N|.	0.000000|.	T|T	0.54647|0.54647	0.1871|0.1871	L|L	0.55481|0.55481	1.735|1.735	0.22745|0.22745	N|N	0.998781|0.998781	D;B;D;B;B;B|.	0.57899|.	0.981;0.01;0.969;0.006;0.018;0.002|.	P;B;P;B;B;B|.	0.51974|.	0.625;0.01;0.686;0.023;0.007;0.004|.	T|T	0.60419|0.60419	-0.7267|-0.7267	10|5	0.06099|.	T|.	0.92|.	.|.	20.865|20.865	0.99795|0.99795	0.0:0.2172:0.0:0.7828|0.0:0.2172:0.0:0.7828	.|.	34;56;58;58;34;112|.	E9PFR9;Q96N96-3;Q96N96-5;Q96N96-4;Q96N96-2;Q96N96|.	.;.;.;.;.;SPT13_HUMAN|.	K|G	737;112;72;58;34;34;56;56|775	ENSP00000371542:N737K;ENSP00000371527:N112K;ENSP00000401605:N72K;ENSP00000382830:N34K;ENSP00000386471:N34K;ENSP00000343631:N56K;ENSP00000397498:N56K|.	ENSP00000343631:N56K|.	N|R	+|+	3|1	2|2	SPATA13|SPATA13	23756319|23756319	0.018000|0.018000	0.18449|0.18449	0.028000|0.028000	0.17463|0.17463	0.116000|0.116000	0.19942|0.19942	-1.365000|-1.365000	0.02587|0.02587	-2.529000|-2.529000	0.00492|0.00492	-2.133000|-2.133000	0.00342|0.00342	AAC|CGG		0.493	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		19	12	19	12
PLK1	5347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	23695207	23695207	+	Missense_Mutation	SNP	C	C	G			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr16:23695207C>G	ENST00000300093.4	+	5	944	c.833C>G	c.(832-834)gCc>gGc	p.A278G		NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	278	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		AACCCCGTGGCCGCCTCCCTC	0.557																																					Colon(12;240 564 27038 33155)											0													202.0	213.0	209.0					16																	23695207		2197	4300	6497	SO:0001583	missense	5347				CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"""polo-like kinase (Drosophila)"""	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.833C>G	16.37:g.23695207C>G	ENSP00000300093:p.Ala278Gly		Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	37	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.829805	0.91036	.	.	ENSG00000166851	ENST00000300093;ENST00000425844	T	0.67698	-0.28	5.32	5.32	0.75619	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.80597	0.4653	M	0.66378	2.025	0.80722	D	1	D	0.69078	0.997	D	0.77557	0.99	T	0.82250	-0.0550	10	0.87932	D	0	-16.4203	16.8404	0.85967	0.0:1.0:0.0:0.0	.	278	P53350	PLK1_HUMAN	G	278;181	ENSP00000300093:A278G	ENSP00000300093:A278G	A	+	2	0	PLK1	23602708	1.000000	0.71417	0.997000	0.53966	0.857000	0.48899	7.135000	0.77276	2.637000	0.89404	0.655000	0.94253	GCC		0.557	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		57	579	57	579
GRAMD1A	57655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	35504508	35504508	+	Silent	SNP	C	C	T			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr19:35504508C>T	ENST00000317991.5	+	9	975	c.783C>T	c.(781-783)gaC>gaT	p.D261D	CTD-2527I21.14_ENST00000605640.1_RNA|GRAMD1A_ENST00000599564.1_Silent_p.D348D|GRAMD1A_ENST00000504615.2_Silent_p.D27D|GRAMD1A_ENST00000411896.2_Silent_p.D254D	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	261						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GGGCAGCTGACCGCAGCCAGG	0.662																																																0													24.0	29.0	27.0					19																	35504508		2113	4218	6331	SO:0001819	synonymous_variant	57655			AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"""KIAA1533"""	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.783C>T	19.37:g.35504508C>T			A6NKY7|Q8NC77|Q9P1Z5	Silent	SNP	ENST00000317991.5	37	CCDS42546.1																																																																																				0.662	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		26	25	26	25
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	42791828	42791828	+	Nonsense_Mutation	SNP	G	G	A			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr19:42791828G>A	ENST00000575354.2	+	5	754	c.714G>A	c.(712-714)tgG>tgA	p.W238*	CIC_ENST00000160740.3_Nonsense_Mutation_p.W238*|CIC_ENST00000572681.2_Nonsense_Mutation_p.W1147*	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	238					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				GCGAGTGGTGGTATGCCCTGG	0.617			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0													82.0	75.0	77.0					19																	42791828		2203	4300	6503	SO:0001587	stop_gained	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.714G>A	19.37:g.42791828G>A	ENSP00000458663:p.Trp238*		Q7LGI1|Q9UEG5|Q9Y6T1	Nonsense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	G	41	8.802137	0.98960	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.39	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-8.5755	14.5138	0.67807	0.0:0.0:1.0:0.0	.	.	.	.	X	238	.	ENSP00000160740:W238X	W	+	3	0	CIC	47483668	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.261000	0.95576	2.284000	0.76573	0.555000	0.69702	TGG		0.617	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			37	54	37	54
CIC	23152	hgsc.bcm.edu;broad.mit.edu	37	19	42796879	42796879	+	Nonsense_Mutation	SNP	C	C	T			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr19:42796879C>T	ENST00000575354.2	+	14	3377	c.3337C>T	c.(3337-3339)Cag>Tag	p.Q1113*	CIC_ENST00000160740.3_Nonsense_Mutation_p.Q1112*|CIC_ENST00000572681.2_Nonsense_Mutation_p.Q2021*	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1113	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CCAGCCATCCCAGGCCCCCCC	0.682			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0													45.0	54.0	51.0					19																	42796879		2203	4299	6502	SO:0001587	stop_gained	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.3337C>T	19.37:g.42796879C>T	ENSP00000458663:p.Gln1113*		Q7LGI1|Q9UEG5|Q9Y6T1	Nonsense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.442044	0.83993	.	.	ENSG00000079432	ENST00000160740	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.67	13.7474	0.62883	0.0:1.0:0.0:0.0	.	.	.	.	X	1113	.	ENSP00000160740:Q1113X	Q	+	1	0	CIC	47488719	1.000000	0.71417	0.995000	0.50966	0.676000	0.39594	3.621000	0.54210	2.635000	0.89317	0.484000	0.47621	CAG		0.682	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			6	85	6	85
HRNR	388697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	152191766	152191766	+	Missense_Mutation	SNP	C	C	T	rs368316243		TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr1:152191766C>T	ENST00000368801.2	-	3	2414	c.2339G>A	c.(2338-2340)cGa>cAa	p.R780Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	780					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGACCCATGTCGGACACGGCT	0.602																																																0								C	GLN/ARG	0,4406		0,0,2203	72.0	76.0	75.0		2339	-6.1	0.0	1		75	2,8598		0,2,4298	no	missense	HRNR	NM_001009931.1	43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	780/2851	152191766	2,13004	2203	4300	6503	SO:0001583	missense	388697			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.2339G>A	1.37:g.152191766C>T	ENSP00000357791:p.Arg780Gln		Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	8.654	0.898922	0.17686	0.0	2.33E-4	ENSG00000197915	ENST00000368801	T	0.04654	3.58	3.06	-6.13	0.02118	.	.	.	.	.	T	0.00695	0.0023	N	0.17082	0.46	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.47586	-0.9106	9	0.24483	T	0.36	.	5.4697	0.16662	0.0:0.1723:0.4738:0.3539	.	780	Q86YZ3	HORN_HUMAN	Q	780	ENSP00000357791:R780Q	ENSP00000357791:R780Q	R	-	2	0	HRNR	150458390	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.585000	0.05794	-1.585000	0.01634	-1.628000	0.00784	CGA		0.602	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		38	85	38	85
SEC16B	89866	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	177936856	177936856	+	Silent	SNP	G	G	A			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr1:177936856G>A	ENST00000308284.6	-	2	350	c.261C>T	c.(259-261)gaC>gaT	p.D87D	RP4-798P15.3_ENST00000354921.3_RNA|SEC16B_ENST00000464631.2_Silent_p.D87D	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	87	Required for endoplasmic reticulum localization.				COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CTTCGTAATAGTCAACTCCAG	0.517																																																0													74.0	77.0	76.0					1																	177936856		2023	4188	6211	SO:0001819	synonymous_variant	89866			AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.261C>T	1.37:g.177936856G>A			A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																				0.517	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		9	68	9	68
NLRP3	114548	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	247588165	247588165	+	Missense_Mutation	SNP	G	G	A			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr1:247588165G>A	ENST00000336119.3	+	3	2166	c.1420G>A	c.(1420-1422)Gca>Aca	p.A474T	NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000366496.2_Missense_Mutation_p.A474T|NLRP3_ENST00000366497.2_Missense_Mutation_p.A474T|NLRP3_ENST00000391827.2_Missense_Mutation_p.A474T|NLRP3_ENST00000348069.2_Missense_Mutation_p.A474T|NLRP3_ENST00000391828.3_Missense_Mutation_p.A474T	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	474	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CTCTTTGGCTGCAGATGGAAT	0.582																																																0													27.0	28.0	28.0					1																	247588165		2203	4300	6503	SO:0001583	missense	114548			AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1420G>A	1.37:g.247588165G>A	ENSP00000337383:p.Ala474Thr		B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	37	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.966543	0.53507	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	D;D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	4.17	4.17	0.49024	NACHT nucleoside triphosphatase (1);	0.000000	0.52532	D	0.000063	D	0.91958	0.7453	M	0.85197	2.74	0.40143	D	0.976858	D;D;D;D;P	0.89917	0.979;0.998;1.0;0.987;0.866	P;D;D;D;P	0.91635	0.78;0.98;0.999;0.966;0.766	D	0.91980	0.5594	10	0.48119	T	0.1	.	12.2773	0.54744	0.0:0.0:1.0:0.0	.	474;474;474;474;474	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	T	474	ENSP00000375704:A474T;ENSP00000355453:A474T;ENSP00000337383:A474T;ENSP00000294752:A474T;ENSP00000355452:A474T;ENSP00000375703:A474T	ENSP00000337383:A474T	A	+	1	0	NLRP3	245654788	0.998000	0.40836	0.236000	0.24074	0.087000	0.18053	4.494000	0.60347	2.612000	0.88384	0.655000	0.94253	GCA		0.582	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		11	30	11	30
HADHA	3030	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	26426943	26426943	+	Missense_Mutation	SNP	T	T	A			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr2:26426943T>A	ENST00000380649.3	-	12	1337	c.1208A>T	c.(1207-1209)cAa>cTa	p.Q403L		NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	403					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTGAACACTTGTTGCTGTCC	0.483																																																0													350.0	328.0	336.0					2																	26426943		2203	4300	6503	SO:0001583	missense	3030			D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"""gastrin-binding protein"", ""long-chain-3-hydroxyacyl-CoA dehydrogenase"", ""long-chain 2-enoyl-CoA hydratase"", ""mitochondrial trifunctional protein, alpha subunit"""	600890	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"""			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.1208A>T	2.37:g.26426943T>A	ENSP00000370023:p.Gln403Leu		B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000380649.3	37	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.328462	0.81690	.	.	ENSG00000084754	ENST00000380649	T	0.76578	-1.03	4.86	4.86	0.63082	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.81446	0.4824	L	0.49256	1.55	0.80722	D	1	P;P	0.52316	0.952;0.952	P;P	0.58620	0.842;0.842	T	0.79405	-0.1817	10	0.30078	T	0.28	-18.266	13.5831	0.61915	0.0:0.0:0.0:1.0	.	403;403	E9KL44;P40939	.;ECHA_HUMAN	L	403	ENSP00000370023:Q403L	ENSP00000370023:Q403L	Q	-	2	0	HADHA	26280447	1.000000	0.71417	0.971000	0.41717	0.923000	0.55619	8.005000	0.88553	1.940000	0.56252	0.459000	0.35465	CAA		0.483	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		166	359	166	359
DNAH6	1768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	84784902	84784902	+	Nonsense_Mutation	SNP	T	T	G			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr2:84784902T>G	ENST00000237449.6	+	10	1654	c.1646T>G	c.(1645-1647)tTa>tGa	p.L549*	DNAH6_ENST00000398278.2_Nonsense_Mutation_p.L549*|DNAH6_ENST00000389394.3_Nonsense_Mutation_p.L549*			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	549	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						AACACTGTGTTATCAGTTCCT	0.343																																																0													153.0	143.0	147.0					2																	84784902		2203	4300	6503	SO:0001587	stop_gained	1768			U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.1646T>G	2.37:g.84784902T>G	ENSP00000237449:p.Leu549*		A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Nonsense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	T	34	5.382346	0.95967	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	.	.	.	5.22	5.22	0.72569	.	0.000000	0.36740	N	0.002440	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	.	14.0916	0.64995	0.0:0.0:0.0:1.0	.	.	.	.	X	549	.	ENSP00000237449:L549X	L	+	2	0	DNAH6	84638413	1.000000	0.71417	0.994000	0.49952	0.345000	0.29048	5.100000	0.64560	1.969000	0.57287	0.533000	0.62120	TTA		0.343	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		46	118	46	118
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			21	51	21	51
EPHA4	2043	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	222301821	222301821	+	Missense_Mutation	SNP	G	G	T			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr2:222301821G>T	ENST00000281821.2	-	12	2137	c.2096C>A	c.(2095-2097)aCa>aAa	p.T699K	EPHA4_ENST00000392071.4_Missense_Mutation_p.T648K|EPHA4_ENST00000409938.1_Missense_Mutation_p.T699K|EPHA4_ENST00000409854.1_Missense_Mutation_p.T699K	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	699	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		CATGTACTCTGTTATGATCAT	0.378																																																0													106.0	108.0	108.0					2																	222301821		2203	4300	6503	SO:0001583	missense	2043			L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3388	protein-coding gene	gene with protein product		602188	"""EphA4"""	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.2096C>A	2.37:g.222301821G>T	ENSP00000281821:p.Thr699Lys		A8K2P1|B2R601|B7Z6Q8|Q2M380	Missense_Mutation	SNP	ENST00000281821.2	37	CCDS2447.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.706135	0.89018	.	.	ENSG00000116106	ENST00000281821;ENST00000409854;ENST00000409938;ENST00000392071	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	6.03	6.03	0.97812	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84835	0.5560	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86822	0.2005	10	0.87932	D	0	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	699	P54764	EPHA4_HUMAN	K	699;699;699;648	ENSP00000281821:T699K;ENSP00000386276:T699K;ENSP00000386829:T699K;ENSP00000375923:T648K	ENSP00000281821:T699K	T	-	2	0	EPHA4	222010065	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.004000	0.88535	2.854000	0.98071	0.655000	0.94253	ACA		0.378	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			36	61	36	61
PIK3CA	5290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	178917478	178917478	+	Splice_Site	SNP	G	G	A			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr3:178917478G>A	ENST00000263967.3	+	3	510	c.353G>A	c.(352-354)gGt>gAt	p.G118D		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	118			G -> D (in CWS5). {ECO:0000269|PubMed:23246288}.		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.G118D(26)		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)	TTTATTAAAGGTTTTGCTATC	0.338		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"""	26	Substitution - Missense(26)	endometrium(11)|breast(4)|large_intestine(3)|central_nervous_system(3)|lung(3)|prostate(2)											93.0	87.0	89.0					3																	178917478		1809	4071	5880	SO:0001630	splice_region_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.353-1G>A	3.37:g.178917478G>A			Q14CW1|Q99762	Splice_Site	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.954561	0.53293	.	.	ENSG00000121879	ENST00000263967	T	0.46451	0.87	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.58722	0.2142	M	0.63843	1.955	0.80722	D	1	D	0.61080	0.989	P	0.56398	0.797	T	0.53823	-0.8384	9	.	.	.	.	20.1236	0.97970	0.0:0.0:1.0:0.0	.	118	P42336	PK3CA_HUMAN	D	118	ENSP00000263967:G118D	.	G	+	2	0	PIK3CA	180400172	1.000000	0.71417	1.000000	0.80357	0.017000	0.09413	9.471000	0.97696	2.746000	0.94184	0.563000	0.77884	GGT		0.338	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		Missense_Mutation	33	42	33	42
TSSK1B	83942	hgsc.bcm.edu;broad.mit.edu	37	5	112770050	112770050	+	Missense_Mutation	SNP	G	G	A	rs139028259		TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr5:112770050G>A	ENST00000390666.3	-	1	678	c.487C>T	c.(487-489)Cgg>Tgg	p.R163W	MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000383058.4_RNA|CTD-2201G3.1_ENST00000510381.2_RNA|CTD-2201G3.1_ENST00000416046.2_RNA	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	163	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		CTGTCATCCCGCAGGCAGCGC	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		20963	0.0		0.001	False		,,,				2504	0.0															0								G	,TRP/ARG	0,4404		0,0,2202	79.0	75.0	76.0		,487	0.2	0.9	5	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	yes	intron,missense	MCC,TSSK1B	NM_001085377.1,NM_032028.3	,101	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,probably-damaging	,163/368	112770050	1,13003	2202	4300	6502	SO:0001583	missense	83942			AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"""serine/threonine kinase 22D (spermiogenesis associated)"", ""testis-specific serine kinase 1"""	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.487C>T	5.37:g.112770050G>A	ENSP00000375081:p.Arg163Trp		B2R8D9	Missense_Mutation	SNP	ENST00000390666.3	37	CCDS4112.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	7.254	0.603871	0.14002	0.0	1.16E-4	ENSG00000212122	ENST00000390666	T	0.25414	1.8	1.24	0.19	0.15125	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.32055	U	0.006643	T	0.34193	0.0889	L	0.46157	1.445	0.09310	N	1	D	0.76494	0.999	D	0.69479	0.964	T	0.14839	-1.0458	10	0.44086	T	0.13	.	6.1779	0.20455	0.0:0.0:0.7032:0.2967	.	163	Q9BXA7	TSSK1_HUMAN	W	163	ENSP00000375081:R163W	ENSP00000375081:R163W	R	-	1	2	TSSK1B	112797949	0.000000	0.05858	0.903000	0.35520	0.224000	0.24922	0.233000	0.17911	-0.435000	0.07264	-0.823000	0.03104	CGG		0.577	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028		4	68	4	68
PCDHAC1	56135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	140306487	140306487	+	Missense_Mutation	SNP	T	T	C			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr5:140306487T>C	ENST00000253807.2	+	1	10	c.10T>C	c.(10-12)Tgt>Cgt	p.C4R	PCDHA13_ENST00000289272.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHAC1_ENST00000409700.3_Missense_Mutation_p.C4R|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	4					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(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATGGTGGGCTGTGGGGTGGC	0.647																																																0													128.0	152.0	144.0					5																	140306487		2203	4300	6503	SO:0001583	missense	56135			AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.10T>C	5.37:g.140306487T>C	ENSP00000253807:p.Cys4Arg		Q9Y5F5|Q9Y5I5	Missense_Mutation	SNP	ENST00000253807.2	37	CCDS4241.1	.	.	.	.	.	.	.	.	.	.	T	10.59	1.393946	0.25205	.	.	ENSG00000248383	ENST00000409700;ENST00000253807	T;T	0.51325	0.73;0.71	5.51	4.33	0.51752	.	.	.	.	.	T	0.29093	0.0723	N	0.12182	0.205	0.38391	D	0.945395	B;B	0.20164	0.042;0.001	B;B	0.22601	0.04;0.0	T	0.08932	-1.0698	9	0.22109	T	0.4	.	11.4535	0.50167	0.0:0.0:0.1506:0.8494	.	4;4	Q9H158;Q9H158-2	PCDC1_HUMAN;.	R	4	ENSP00000386356:C4R;ENSP00000253807:C4R	ENSP00000253807:C4R	C	+	1	0	PCDHAC1	140286671	0.994000	0.37717	0.995000	0.50966	0.218000	0.24690	1.671000	0.37513	0.897000	0.36392	0.459000	0.35465	TGT		0.647	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		15	66	15	66
UTRN	7402	hgsc.bcm.edu;broad.mit.edu	37	6	144835787	144835787	+	Splice_Site	SNP	G	G	T	rs201062311		TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr6:144835787G>T	ENST00000367545.3	+	36	5075	c.5075G>T	c.(5074-5076)cGt>cTt	p.R1692L		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1692	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TATAATTAGCGTTTAGTATCT	0.388																																																0													110.0	112.0	111.0					6																	144835787		2203	4300	6503	SO:0001630	splice_region_variant	7402			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.5074-1G>T	6.37:g.144835787G>T			Q5SYY1|Q5SZ57|Q9UJ40	Splice_Site	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782084	0.90282	.	.	ENSG00000152818	ENST00000367545	T	0.50548	0.74	5.34	5.34	0.76211	.	0.000000	0.49916	D	0.000127	T	0.64649	0.2617	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65915	-0.6052	10	0.59425	D	0.04	.	19.3965	0.94608	0.0:0.0:1.0:0.0	.	1692	P46939	UTRO_HUMAN	L	1692	ENSP00000356515:R1692L	ENSP00000356515:R1692L	R	+	2	0	UTRN	144877480	1.000000	0.71417	0.984000	0.44739	0.940000	0.58332	7.572000	0.82409	2.664000	0.90586	0.655000	0.94253	CGT		0.388	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		Missense_Mutation	11	117	11	117
PSPH	5723	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	56084931	56084931	+	Missense_Mutation	SNP	A	A	C			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr7:56084931A>C	ENST00000395471.3	-	6	1222	c.417T>G	c.(415-417)ttT>ttG	p.F139L	PSPH_ENST00000459834.1_Intron|PSPH_ENST00000275605.3_Missense_Mutation_p.F139L			P78330	SERB_HUMAN	phosphoserine phosphatase	139					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TCTTACCGTTAAAGTAGAATT	0.383																																																0													102.0	81.0	88.0					7																	56084931		2203	4300	6503	SO:0001583	missense	5723			Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.417T>G	7.37:g.56084931A>C	ENSP00000378854:p.Phe139Leu		B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	A	9.099	1.003578	0.19121	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626	D;D;D	0.83673	-1.75;-1.75;-1.75	4.85	-5.11	0.02901	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.71542	0.3352	L	0.48935	1.535	0.48452	D	0.999657	B;B	0.18610	0.029;0.007	B;B	0.18263	0.021;0.021	T	0.55692	-0.8101	10	0.11485	T	0.65	-11.5252	14.6984	0.69139	0.4629:0.0:0.5371:0.0	.	139;139	Q53EY1;P78330	.;SERB_HUMAN	L	139	ENSP00000275605:F139L;ENSP00000378854:F139L;ENSP00000398653:F139L	ENSP00000275605:F139L	F	-	3	2	PSPH	56052425	0.523000	0.26274	0.980000	0.43619	0.774000	0.43823	-0.111000	0.10807	-0.710000	0.05001	-0.457000	0.05445	TTT		0.383	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577		40	33	40	33
PKN3	29941	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	131479035	131479035	+	Missense_Mutation	SNP	C	C	G			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr9:131479035C>G	ENST00000291906.4	+	16	2211	c.1818C>G	c.(1816-1818)tgC>tgG	p.C606W	PKN3_ENST00000485301.1_3'UTR	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	606	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						GCCTGTACTGCGAGAAGCGGA	0.602																																																0													138.0	117.0	124.0					9																	131479035		2203	4300	6503	SO:0001583	missense	29941			AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.1818C>G	9.37:g.131479035C>G	ENSP00000291906:p.Cys606Trp		Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	37	CCDS6908.1	.	.	.	.	.	.	.	.	.	.	C	16.38	3.107824	0.56291	.	.	ENSG00000160447	ENST00000291906	T	0.24151	1.87	5.44	-3.5	0.04710	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.34948	0.0915	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.23476	-1.0187	9	0.87932	D	0	.	11.1236	0.48304	0.0:0.4356:0.0:0.5644	.	606	Q6P5Z2	PKN3_HUMAN	W	606	ENSP00000291906:C606W	ENSP00000291906:C606W	C	+	3	2	PKN3	130518856	0.888000	0.30383	0.966000	0.40874	0.960000	0.62799	-0.103000	0.10940	-0.776000	0.04578	-1.202000	0.01658	TGC		0.602	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		18	171	18	171
GPR15	2838	broad.mit.edu;ucsc.edu	37	3	98251295	98251295	+	Missense_Mutation	SNP	G	G	A	rs202120393		TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr3:98251295G>A	ENST00000284311.3	+	1	553	c.418G>A	c.(418-420)Gta>Ata	p.V140I		NM_005290.1	NP_005281.1	P49685	GPR15_HUMAN	G protein-coupled receptor 15	140					G-protein coupled receptor signaling pathway (GO:0007186)|T cell migration (GO:0072678)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Lung NSC(201;7.93e-06)|all_neural(597;0.00172)|Hepatocellular(537;0.00825)|Myeloproliferative disorder(1037;0.0255)		Lung(72;0.246)		GTGGCCAGTCGTATCCAGGAA	0.522																																																0													80.0	66.0	71.0					3																	98251295		2203	4300	6503	SO:0001583	missense	2838				CCDS2931.1	3q11.2-q13.1	2014-01-30			ENSG00000154165	ENSG00000154165		"""GPCR / Class A : Orphans"""	4469	protein-coding gene	gene with protein product		601166				8838812	Standard	NM_005290		Approved		uc011bgy.3	P49685	OTTHUMG00000160017	ENST00000284311.3:c.418G>A	3.37:g.98251295G>A	ENSP00000284311:p.Val140Ile		Q3MIL4|Q6ISN6	Missense_Mutation	SNP	ENST00000284311.3	37	CCDS2931.1	.	.	.	.	.	.	.	.	.	.	G	2.976	-0.211319	0.06140	.	.	ENSG00000154165	ENST00000284311	T	0.36878	1.23	4.83	-2.46	0.06461	GPCR, rhodopsin-like superfamily (1);	1.635800	0.03796	N	0.263582	T	0.15262	0.0368	N	0.05078	-0.115	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.08597	-1.0714	10	0.21540	T	0.41	2.8908	1.992	0.03448	0.4205:0.1212:0.3281:0.1303	.	140	P49685	GPR15_HUMAN	I	140	ENSP00000284311:V140I	ENSP00000284311:V140I	V	+	1	0	GPR15	99733985	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-1.149000	0.03182	-0.636000	0.05524	0.591000	0.81541	GTA		0.522	GPR15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358907.1			8	64	8	64
CEP63	80254	broad.mit.edu;ucsc.edu	37	3	134277174	134277174	+	Missense_Mutation	SNP	A	A	T			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr3:134277174A>T	ENST00000337090.3	+	13	1831	c.1658A>T	c.(1657-1659)aAg>aTg	p.K553M	CEP63_ENST00000513612.2_Missense_Mutation_p.K553M|CEP63_ENST00000606977.1_Missense_Mutation_p.K553M|CEP63_ENST00000354446.3_Intron|CEP63_ENST00000383229.3_Intron|CEP63_ENST00000332047.5_Intron			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	553					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						ACTGAGTTCAAGAATACAGAG	0.289																																																0													43.0	44.0	44.0					3																	134277174		2202	4299	6501	SO:0001583	missense	80254			AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.1658A>T	3.37:g.134277174A>T	ENSP00000336524:p.Lys553Met		D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	37	CCDS3086.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.27|16.27	3.075842|3.075842	0.55646|0.55646	.|.	.|.	ENSG00000182923|ENSG00000182923	ENST00000337090;ENST00000513612|ENST00000504929	T;T|.	0.21543|.	2.0;2.0|.	4.76|4.76	3.6|3.6	0.41247|0.41247	.|.	0.489229|.	0.21946|.	N|.	0.066813|.	T|.	0.54398|.	0.1856|.	L|L	0.57536|0.57536	1.79|1.79	0.32759|0.32759	N|N	0.505415|0.505415	D|.	0.69078|.	0.997|.	D|.	0.63192|.	0.912|.	T|.	0.62077|.	-0.6930|.	10|.	0.48119|.	T|.	0.1|.	-16.0171|-16.0171	8.3171|8.3171	0.32106|0.32106	0.9076:0.0:0.0924:0.0|0.9076:0.0:0.0924:0.0	.|.	553|.	Q96MT8|.	CEP63_HUMAN|.	M|X	553|242	ENSP00000336524:K553M;ENSP00000426129:K553M|.	ENSP00000336524:K553M|.	K|R	+|+	2|1	0|2	CEP63|CEP63	135759864|135759864	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	2.455000|2.455000	0.44988|0.44988	0.965000|0.965000	0.38133|0.38133	0.383000|0.383000	0.25322|0.25322	AAG|AGA		0.289	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180		9	36	9	36
USP8	9101	broad.mit.edu;ucsc.edu	37	15	50769066	50769066	+	Silent	SNP	G	G	C			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr15:50769066G>C	ENST00000396444.3	+	9	1208	c.870G>C	c.(868-870)ctG>ctC	p.L290L	USP8_ENST00000307179.4_Silent_p.L290L|USP8_ENST00000433963.1_Silent_p.L290L|USP8_ENST00000425032.3_Silent_p.L213L	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	290	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		AAACTGTCCTGCGCAATGAGC	0.393																																																0													107.0	102.0	104.0					15																	50769066		2196	4294	6490	SO:0001819	synonymous_variant	9101			D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"""Ubiquitin-specific peptidases"""	12631	protein-coding gene	gene with protein product		603158	"""ubiquitin specific protease 8"""			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.870G>C	15.37:g.50769066G>C			B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Silent	SNP	ENST00000396444.3	37	CCDS10137.1																																																																																				0.393	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154		30	70	30	70
NACA2	342538	broad.mit.edu;ucsc.edu	37	17	59668211	59668211	+	Missense_Mutation	SNP	C	C	T			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr17:59668211C>T	ENST00000521764.1	-	1	352	c.331G>A	c.(331-333)Gtc>Atc	p.V111I		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	111	NAC-A/B. {ECO:0000255|PROSITE- ProRule:PRU00507}.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					CTCTTGTAGACGTCCAGTTTT	0.443																																																0													181.0	180.0	180.0					17																	59668211		2203	4300	6503	SO:0001583	missense	342538			BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"""alpha-NAC protein"""	609274	"""nascent-polypeptide-associated complex alpha polypeptide-like"""	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.331G>A	17.37:g.59668211C>T	ENSP00000427802:p.Val111Ile		Q2VIR9	Missense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.040939	0.55003	.	.	ENSG00000253506	ENST00000521764	T	0.65732	-0.17	0.753	0.753	0.18404	Nascent polypeptide-associated complex NAC (2);	0.000000	0.64402	U	0.000010	T	0.75133	0.3808	M	0.83603	2.65	0.48762	D	0.999704	D	0.89917	1.0	D	0.91635	0.999	T	0.73898	-0.3837	9	.	.	.	.	7.3227	0.26536	0.0:1.0:0.0:0.0	.	111	Q9H009	NACA2_HUMAN	I	111	ENSP00000427802:V111I	.	V	-	1	0	NACA2	57022993	1.000000	0.71417	0.314000	0.25224	0.041000	0.13682	5.234000	0.65343	0.702000	0.31825	0.411000	0.27672	GTC		0.443	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290		80	202	80	202
ZFX	7543	broad.mit.edu;hgsc.bcm.edu	37	X	24229107	24229109	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chrX:24229107_24229109delAAG	ENST00000379177.1	+	11	2459_2461	c.2032_2034delAAG	c.(2032-2034)aagdel	p.K679del	ZFX_ENST00000540034.1_In_Frame_Del_p.K718del|ZFX_ENST00000304543.5_In_Frame_Del_p.K679del|ZFX_ENST00000338565.3_In_Frame_Del_p.K629del|ZFX_ENST00000379188.3_In_Frame_Del_p.K679del|ZFX_ENST00000539115.1_In_Frame_Del_p.K450del	NM_001178085.1|NM_003410.3	NP_001171556.1|NP_003401.2	P17010	ZFX_HUMAN	zinc finger protein, X-linked	679					death (GO:0016265)|fertilization (GO:0009566)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|parental behavior (GO:0060746)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|prostate(1)	24						TTCAGAACTCAAGAAACACGTGG	0.424																																					Esophageal Squamous(20;306 562 7346 32868 37983)											0																																										SO:0001651	inframe_deletion	7543				CCDS14211.1, CCDS55390.1	Xp22.1-p21.3	2013-01-08			ENSG00000005889	ENSG00000005889		"""Zinc fingers, C2H2-type"""	12869	protein-coding gene	gene with protein product		314980					Standard	NM_003410		Approved	ZNF926	uc022bua.1	P17010	OTTHUMG00000021264	ENST00000379177.1:c.2032_2034delAAG	X.37:g.24229107_24229109delAAG	ENSP00000368475:p.Lys679del		B9EG97|O43668|Q8WYJ8	In_Frame_Del	DEL	ENST00000379177.1	37	CCDS14211.1																																																																																				0.424	ZFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056084.1	NM_003410		15	52	15	52
NOTCH1	4851	broad.mit.edu	37	9	139412283	139412285	+	In_Frame_Del	DEL	GTT	GTT	-	rs373152976		TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr9:139412283_139412285delGTT	ENST00000277541.6	-	8	1435_1437	c.1360_1362delAAC	c.(1360-1362)aacdel	p.N454del	MIR4673_ENST00000584777.1_RNA	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	454	EGF-like 12; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N454delN(2)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		AGACGCACTCGTTGACGTCGATC	0.66			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																													Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	2	Deletion - In frame(2)	central_nervous_system(2)																																								SO:0001651	inframe_deletion	4851			AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.1360_1362delAAC	9.37:g.139412283_139412285delGTT	ENSP00000277541:p.Asn454del		Q59ED8|Q5SXM3	In_Frame_Del	DEL	ENST00000277541.6	37	CCDS43905.1																																																																																				0.660	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		13	113	13	113
CIC	23152	broad.mit.edu	37	19	42795615	42795615	+	Frame_Shift_Del	DEL	A	A	-			TCGA-P5-A5F0-01A-11D-A289-08	TCGA-P5-A5F0-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1edcbd6b-d64f-453b-8e9e-c1fbf6d99cf4	a5d89ce8-081f-4b72-993d-47b28b7bf6e3	g.chr19:42795615delA	ENST00000575354.2	+	10	2735	c.2695delA	c.(2695-2697)aaafs	p.K899fs	CIC_ENST00000160740.3_Frame_Shift_Del_p.K899fs|CIC_ENST00000572681.2_Frame_Shift_Del_p.K1808fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	899	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CCCACCCCCCAAAGGTGAGAC	0.617			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0													53.0	54.0	54.0					19																	42795615		2174	4270	6444	SO:0001589	frameshift_variant	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.2695delA	19.37:g.42795615delA	ENSP00000458663:p.Lys899fs		Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																				0.617	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			18	120	18	120
