#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
EBF3	253738	hgsc.bcm.edu;broad.mit.edu	37	10	131671806	131671806	+	Missense_Mutation	SNP	T	T	G			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr10:131671806T>G	ENST00000355311.5	-	8	763	c.691A>C	c.(691-693)Aac>Cac	p.N231H	EBF3_ENST00000368648.3_Missense_Mutation_p.N231H			Q9H4W6	COE3_HUMAN	early B-cell factor 3	231					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		ACAAACATGTTGTCTGACACG	0.512																																																0													64.0	61.0	62.0					10																	131671806		2203	4300	6503	SO:0001583	missense	253738				CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.691A>C	10.37:g.131671806T>G	ENSP00000347463:p.Asn231His		A0AUY1|Q5T6H9|Q9H4W5	Missense_Mutation	SNP	ENST00000355311.5	37		.	.	.	.	.	.	.	.	.	.	T	24.2	4.500008	0.85176	.	.	ENSG00000108001	ENST00000355311;ENST00000368648	T;T	0.56776	0.44;0.5	4.87	4.87	0.63330	.	0.091794	0.64402	D	0.000001	T	0.74756	0.3758	M	0.85041	2.73	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.80134	-0.1509	10	0.87932	D	0	-20.9951	14.8159	0.70034	0.0:0.0:0.0:1.0	.	231	Q9H4W6-2	.	H	231	ENSP00000347463:N231H;ENSP00000357637:N231H	ENSP00000347463:N231H	N	-	1	0	EBF3	131561796	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.936000	0.87665	1.973000	0.57446	0.533000	0.62120	AAC		0.512	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		4	49	4	49
JAKMIP3	282973	hgsc.bcm.edu;broad.mit.edu	37	10	133967332	133967332	+	Splice_Site	SNP	G	G	T			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr10:133967332G>T	ENST00000298622.4	+	17	2274		c.e17+1		JAKMIP3_ENST00000477275.1_Splice_Site	NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3							Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		GAGCGAGAAGGTTGGTGGCAC	0.592																																																0													137.0	137.0	137.0					10																	133967332		2203	4300	6503	SO:0001630	splice_region_variant	282973			AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.2136+1G>T	10.37:g.133967332G>T			A6PW00|Q69YM6|Q6ZT29	Splice_Site	SNP	ENST00000298622.4	37	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.547593	0.86022	.	.	ENSG00000188385	ENST00000298622	.	.	.	4.76	4.76	0.60689	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7977	0.88578	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	JAKMIP3	133817322	1.000000	0.71417	0.994000	0.49952	0.926000	0.56050	9.251000	0.95483	2.185000	0.69588	0.585000	0.79938	.		0.592	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	Intron	12	194	12	194
MMP26	56547	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	5012621	5012621	+	Missense_Mutation	SNP	T	T	A			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr11:5012621T>A	ENST00000380390.1	+	5	706	c.490T>A	c.(490-492)Ttt>Att	p.F164I	MMP26_ENST00000300762.1_Missense_Mutation_p.F164I			Q9NRE1	MMP26_HUMAN	matrix metallopeptidase 26	164					collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(3)|stomach(1)	22		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191)	Marimastat(DB00786)	TGGTTGGCCCTTTGATGGGCC	0.463																																																0													283.0	273.0	276.0					11																	5012621		2201	4298	6499	SO:0001583	missense	56547			AF230354	CCDS7752.1	11p15	2008-07-18	2005-08-08		ENSG00000167346	ENSG00000167346	3.4.24.1		14249	protein-coding gene	gene with protein product	"""matrilysin 2"""	605470	"""matrix metalloproteinase 26"""			10801841, 10824119	Standard	NM_021801		Approved	endometase, MGC126590, MGC126592	uc001lzv.3	Q9NRE1	OTTHUMG00000066442	ENST00000380390.1:c.490T>A	11.37:g.5012621T>A	ENSP00000369753:p.Phe164Ile		Q3MJ78|Q9GZS2|Q9NR87	Missense_Mutation	SNP	ENST00000380390.1	37	CCDS7752.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.192603	0.78902	.	.	ENSG00000167346	ENST00000380390;ENST00000300762	T;T	0.37915	1.17;1.17	3.93	3.93	0.45458	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.41097	U	0.000952	T	0.62258	0.2413	M	0.86420	2.815	0.37385	D	0.912214	D	0.89917	1.0	D	0.97110	1.0	T	0.72481	-0.4280	10	0.87932	D	0	.	10.7633	0.46277	0.0:0.0:0.0:1.0	.	164	Q9NRE1	MMP26_HUMAN	I	164	ENSP00000369753:F164I;ENSP00000300762:F164I	ENSP00000300762:F164I	F	+	1	0	MMP26	4969197	1.000000	0.71417	0.818000	0.32626	0.800000	0.45204	5.494000	0.66905	1.415000	0.47037	0.533000	0.62120	TTT		0.463	MMP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142058.3	NM_021801		55	205	55	205
GALNT6	11226	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	51751986	51751986	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr12:51751986G>T	ENST00000543196.2	-	8	1633	c.1428C>A	c.(1426-1428)aaC>aaA	p.N476K	GALNT6_ENST00000356317.3_Missense_Mutation_p.N476K			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	476					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						ACCAGGAAAAGTTGTGACAGT	0.517																																																0													283.0	227.0	246.0					12																	51751986		2203	4300	6503	SO:0001583	missense	11226			Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"""Glycosyltransferase family 2 domain containing"""	4128	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 6"""	605148	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"""			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.1428C>A	12.37:g.51751986G>T	ENSP00000444171:p.Asn476Lys		Q8IYH4|Q9H6G2|Q9UIV5	Missense_Mutation	SNP	ENST00000543196.2	37	CCDS8813.1	.	.	.	.	.	.	.	.	.	.	g	15.05	2.718766	0.48622	.	.	ENSG00000139629	ENST00000543196;ENST00000356317;ENST00000546163	T;T	0.28895	1.59;1.59	4.0	4.0	0.46444	.	0.139109	0.64402	D	0.000005	T	0.29491	0.0735	M	0.62088	1.915	0.48975	D	0.999737	P	0.44260	0.83	B	0.39185	0.293	T	0.14671	-1.0464	10	0.66056	D	0.02	.	10.1076	0.42544	0.0988:0.0:0.9012:0.0	.	476	Q8NCL4	GALT6_HUMAN	K	476;476;457	ENSP00000444171:N476K;ENSP00000348668:N476K	ENSP00000348668:N476K	N	-	3	2	GALNT6	50038253	1.000000	0.71417	0.998000	0.56505	0.743000	0.42351	2.139000	0.42149	2.518000	0.84900	0.457000	0.33378	AAC		0.517	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		22	110	22	110
STAB2	55576	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	104099417	104099417	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr12:104099417A>G	ENST00000388887.2	+	37	4112	c.3908A>G	c.(3907-3909)gAg>gGg	p.E1303G		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CAGGGTAATGAGAAGAGGAGA	0.428																																																0													127.0	109.0	115.0					12																	104099417		2203	4300	6503	SO:0001583	missense	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.3908A>G	12.37:g.104099417A>G	ENSP00000373539:p.Glu1303Gly			Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	A	14.94	2.685408	0.47991	.	.	ENSG00000136011	ENST00000388887	T	0.64438	-0.1	5.76	5.76	0.90799	Growth factor, receptor (1);	0.614265	0.17467	N	0.173216	T	0.50650	0.1628	N	0.25031	0.7	0.38744	D	0.953956	P	0.46706	0.883	B	0.44224	0.444	T	0.50338	-0.8840	10	0.24483	T	0.36	.	12.3036	0.54889	0.8734:0.0:0.0:0.1266	.	1303	Q8WWQ8	STAB2_HUMAN	G	1303	ENSP00000373539:E1303G	ENSP00000373539:E1303G	E	+	2	0	STAB2	102623547	1.000000	0.71417	0.821000	0.32701	0.019000	0.09904	3.161000	0.50747	2.209000	0.71365	0.533000	0.62120	GAG		0.428	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			8	33	8	33
PCDH20	64881	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	61987072	61987072	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr13:61987072C>T	ENST00000409186.1	-	5	3265	c.1160G>A	c.(1159-1161)gGa>gAa	p.G387E	PCDH20_ENST00000409204.4_Missense_Mutation_p.G387E			Q8N6Y1	PCD20_HUMAN	protocadherin 20	387	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		AACACTTCCTCCAATCTTACT	0.398																																																0													100.0	97.0	98.0					13																	61987072		2203	4300	6503	SO:0001583	missense	64881			AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"""Cadherins / Protocadherins : Non-clustered"""	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.1160G>A	13.37:g.61987072C>T	ENSP00000386653:p.Gly387Glu		A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	37	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	C	6.387	0.439475	0.12104	.	.	ENSG00000197991	ENST00000409204;ENST00000409186;ENST00000358674	T;T	0.48201	0.82;0.82	5.91	5.06	0.68205	.	0.097560	0.45867	D	0.000327	T	0.31199	0.0789	N	0.16743	0.435	0.34264	D	0.68021	B	0.30146	0.27	B	0.31812	0.136	T	0.45160	-0.9280	10	0.87932	D	0	.	8.0351	0.30488	0.0:0.7614:0.0:0.2386	.	387	A8K1K9	.	E	387;387;133	ENSP00000387250:G387E;ENSP00000386653:G387E	ENSP00000351500:G133E	G	-	2	0	PCDH20	60885073	0.994000	0.37717	0.940000	0.37924	0.178000	0.23041	2.649000	0.46656	2.813000	0.96785	0.655000	0.94253	GGA		0.398	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		8	110	8	110
MYCBP2	23077	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	77862494	77862494	+	Missense_Mutation	SNP	A	A	T			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr13:77862494A>T	ENST00000544440.2	-	3	299	c.282T>A	c.(280-282)aaT>aaA	p.N94K	MYCBP2_ENST00000357337.6_Missense_Mutation_p.N94K|MYCBP2_ENST00000407578.2_Missense_Mutation_p.N132K|MYCBP2_ENST00000360084.5_5'UTR					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TGATTACTGTATTCTCTAAGT	0.323																																																0													88.0	89.0	89.0					13																	77862494		2203	4300	6503	SO:0001583	missense	23077			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.282T>A	13.37:g.77862494A>T	ENSP00000444596:p.Asn94Lys			Missense_Mutation	SNP	ENST00000544440.2	37		.	.	.	.	.	.	.	.	.	.	A	14.02	2.411716	0.42817	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.27402	1.68;1.67;1.68	5.87	2.19	0.27852	.	0.126066	0.56097	D	0.000034	T	0.17534	0.0421	N	0.22421	0.69	0.27113	N	0.96233	B	0.20052	0.041	B	0.14023	0.01	T	0.21965	-1.0230	10	0.19590	T	0.45	.	9.3528	0.38149	0.7407:0.0:0.2593:0.0	.	94	O75592	MYCB2_HUMAN	K	94;132;94	ENSP00000349892:N94K;ENSP00000384288:N132K;ENSP00000444596:N94K	ENSP00000349892:N94K	N	-	3	2	MYCBP2	76760495	1.000000	0.71417	0.987000	0.45799	0.983000	0.72400	2.378000	0.44309	0.153000	0.19213	0.482000	0.46254	AAT		0.323	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		7	40	7	40
CIITA	4261	hgsc.bcm.edu;broad.mit.edu	37	16	11002910	11002910	+	Silent	SNP	G	G	A	rs148091568	byFrequency	TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr16:11002910G>A	ENST00000324288.8	+	12	2815	c.2682G>A	c.(2680-2682)gcG>gcA	p.A894A	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Silent_p.A310A	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	894					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)	p.A894A(1)		central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						ACACGGTGGCGCTGTGGGAGT	0.602			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								G|||	5	0.000998403	0.0008	0.0014	5008	,	,		19642	0.003		0.0	False		,,,				2504	0.0						Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	1	Substitution - coding silent(1)	endometrium(1)						G		6,4388	11.4+/-27.6	0,6,2191	60.0	45.0	50.0		2682	3.9	0.8	16	dbSNP_134	50	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	CIITA	NM_000246.3		0,8,6489	AA,AG,GG		0.0233,0.1365,0.0616		894/1131	11002910	8,12986	2197	4300	6497	SO:0001819	synonymous_variant	4261			U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2682G>A	16.37:g.11002910G>A			A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																				0.602	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		7	59	7	59
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577022	7577022	+	Nonsense_Mutation	SNP	G	G	A	rs121913344		TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr17:7577022G>A	ENST00000269305.4	-	8	1105	c.916C>T	c.(916-918)Cga>Tga	p.R306*	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Nonsense_Mutation_p.R306*|TP53_ENST00000455263.2_Nonsense_Mutation_p.R306*|TP53_ENST00000445888.2_Nonsense_Mutation_p.R306*|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Nonsense_Mutation_p.R306*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	306	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		R -> P (in LFS; germline mutation and in a sporadic cancer; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R306*(133)|p.0?(8)|p.?(3)|p.R306fs*39(2)|p.K305fs*1(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGCTTACCTCGCTTAGTGCTC	0.562	R306*(HCC1937_BREAST)|R306*(JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(MFE296_ENDOMETRIUM)|R306*(MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(RCM1_LARGE_INTESTINE)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	147	Substitution - Nonsense(133)|Whole gene deletion(8)|Unknown(3)|Deletion - Frameshift(2)|Insertion - Frameshift(1)	large_intestine(39)|breast(21)|upper_aerodigestive_tract(15)|ovary(11)|central_nervous_system(10)|oesophagus(10)|stomach(8)|lung(8)|endometrium(6)|bone(4)|pancreas(3)|haematopoietic_and_lymphoid_tissue(3)|biliary_tract(3)|kidney(2)|NS(2)|urinary_tract(1)|liver(1)	GRCh37	CM971506	TP53	M	rs121913344						120.0	106.0	110.0					17																	7577022		2203	4300	6503	SO:0001587	stop_gained	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.916C>T	17.37:g.7577022G>A	ENSP00000269305:p.Arg306*		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782988	0.90282	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.26	3.21	0.36854	.	1.348720	0.05032	N	0.474808	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4785	0.44678	0.0:0.0:0.6334:0.3666	.	.	.	.	X	306;306;306;306;306;295;174	.	ENSP00000269305:R306X	R	-	1	2	TP53	7517747	1.000000	0.71417	0.970000	0.41538	0.345000	0.29048	2.280000	0.43443	0.735000	0.32537	0.561000	0.74099	CGA		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		32	75	32	75
MYOCD	93649	hgsc.bcm.edu;broad.mit.edu	37	17	12655919	12655919	+	Silent	SNP	T	T	A			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr17:12655919T>A	ENST00000343344.4	+	10	1314	c.1314T>A	c.(1312-1314)tcT>tcA	p.S438S	MYOCD_ENST00000425538.1_Silent_p.S438S|AC005358.1_ENST00000609971.1_Silent_p.S342S|MYOCD_ENST00000395988.1_3'UTR			Q8IZQ8	MYCD_HUMAN	myocardin	438	Ser-rich.				cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		CTTCCTCTTCTACCAGTGCCC	0.582																																																0													138.0	121.0	127.0					17																	12655919		2203	4300	6503	SO:0001819	synonymous_variant	93649			AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.1314T>A	17.37:g.12655919T>A			Q5UBU5|Q8N7Q1	Silent	SNP	ENST00000343344.4	37	CCDS11163.1																																																																																				0.582	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604		10	137	10	137
ASXL3	80816	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	31323665	31323665	+	Missense_Mutation	SNP	A	A	G	rs548915343		TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr18:31323665A>G	ENST00000269197.5	+	12	3853	c.3853A>G	c.(3853-3855)Atc>Gtc	p.I1285V		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1285	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						GTTAAAAACCATCCAGGGAAC	0.408																																																0													84.0	81.0	82.0					18																	31323665		1905	4119	6024	SO:0001583	missense	80816			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.3853A>G	18.37:g.31323665A>G	ENSP00000269197:p.Ile1285Val		Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.041698	0.35989	.	.	ENSG00000141431	ENST00000269197	T	0.17213	2.29	5.92	4.76	0.60689	.	.	.	.	.	T	0.14098	0.0341	L	0.29908	0.895	0.32105	N	0.590129	B	0.06786	0.001	B	0.06405	0.002	T	0.05354	-1.0890	9	0.44086	T	0.13	.	12.0109	0.53286	0.9326:0.0:0.0674:0.0	.	1285	Q9C0F0	ASXL3_HUMAN	V	1285	ENSP00000269197:I1285V	ENSP00000269197:I1285V	I	+	1	0	ASXL3	29577663	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.593000	0.46180	1.062000	0.40625	0.533000	0.62120	ATC		0.408	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			17	70	17	70
MUC16	94025	hgsc.bcm.edu;broad.mit.edu	37	19	9069935	9069935	+	Silent	SNP	G	G	T			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr19:9069935G>T	ENST00000397910.4	-	3	17714	c.17511C>A	c.(17509-17511)ccC>ccA	p.P5837P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5839	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGGAGATGTAGGGTGACATTT	0.473																																																0													212.0	199.0	203.0					19																	9069935		1953	4134	6087	SO:0001819	synonymous_variant	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.17511C>A	19.37:g.9069935G>T			Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		11	125	11	125
BCAM	4059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	45322041	45322041	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr19:45322041C>T	ENST00000270233.6	+	10	1260	c.1238C>T	c.(1237-1239)tCt>tTt	p.S413F	BCAM_ENST00000589651.1_Missense_Mutation_p.S413F	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	413	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)	p.S413F(1)		central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				TCGCTCAGTTCTATCACCTTC	0.627																																																1	Substitution - Missense(1)	upper_aerodigestive_tract(1)											131.0	113.0	119.0					19																	45322041		2203	4300	6503	SO:0001583	missense	4059			X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6722	protein-coding gene	gene with protein product		612773	"""Lutheran blood group (Auberger b antigen included)"", ""basal cell adhesion molecule (Lu and Au blood groups)"""	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1238C>T	19.37:g.45322041C>T	ENSP00000270233:p.Ser413Phe		A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	.	.	.	.	.	.	.	.	.	.	.	17.84	3.487291	0.63962	.	.	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.11277	2.79;2.79	4.6	-2.5	0.06384	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.15089	0.0364	M	0.85373	2.75	0.09310	N	1	B	0.12013	0.005	B	0.12837	0.008	T	0.36986	-0.9725	9	0.72032	D	0.01	0.346	7.1033	0.25351	0.5514:0.3606:0.0:0.088	.	413	P50895	BCAM_HUMAN	F	413	ENSP00000270233:S413F;ENSP00000375817:S413F	ENSP00000270233:S413F	S	+	2	0	BCAM	50013881	0.000000	0.05858	0.000000	0.03702	0.347000	0.29111	0.144000	0.16135	-0.122000	0.11766	0.491000	0.48974	TCT		0.627	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581		23	147	23	147
MYCBP	26292	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	39330370	39330370	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr1:39330370G>A	ENST00000397572.2	-	5	1083	c.284C>T	c.(283-285)cCa>cTa	p.P95L	GJA9_ENST00000454994.2_3'UTR|RP5-864K19.4_ENST00000433671.2_RNA|MYCBP_ENST00000489803.1_5'UTR|RP5-864K19.4_ENST00000456813.1_RNA	NM_012333.4	NP_036465.2	Q99417	MYCBP_HUMAN	MYC binding protein	95					regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(1)|skin(1)	3	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)				CTCCTGAGGTGGTTCATACTG	0.328																																					Esophageal Squamous(155;912 1855 21572 25911 44247)											0													76.0	71.0	73.0					1																	39330370		2203	4300	6503	SO:0001583	missense	26292			AB007191	CCDS431.1	1p33-p32.2	2013-07-09	2013-07-09		ENSG00000214114	ENSG00000214114			7554	protein-coding gene	gene with protein product	"""associate of myc-1"""	606535	"""c-myc binding protein"""			9797456	Standard	NM_012333		Approved	AMY-1	uc001ccs.3	Q99417	OTTHUMG00000000484	ENST00000397572.2:c.284C>T	1.37:g.39330370G>A	ENSP00000380702:p.Pro95Leu		B2R4N0|Q5TA64|Q96HE2	Missense_Mutation	SNP	ENST00000397572.2	37	CCDS431.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.531931	0.45073	.	.	ENSG00000214114	ENST00000397572	.	.	.	5.51	5.51	0.81932	.	0.138665	0.48767	U	0.000169	T	0.54615	0.1869	L	0.29908	0.895	0.80722	D	1	B	0.19073	0.033	B	0.23018	0.043	T	0.52888	-0.8515	9	0.66056	D	0.02	0.7227	17.5956	0.88011	0.0:0.0:1.0:0.0	.	95	Q99417	MYCBP_HUMAN	L	95	.	ENSP00000380702:P95L	P	-	2	0	MYCBP	39102957	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.033000	0.64146	2.577000	0.86979	0.563000	0.77884	CCA		0.328	MYCBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001209.1	NM_012333		13	53	13	53
SMC1B	27127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	45779410	45779410	+	Silent	SNP	G	G	A			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr22:45779410G>A	ENST00000357450.4	-	12	1994	c.1995C>T	c.(1993-1995)tgC>tgT	p.C665C	SMC1B_ENST00000404354.3_Silent_p.C665C	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	665	Flexible hinge.				meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TCTCATCCCAGCATCTAGCCT	0.343																																																0													175.0	158.0	163.0					22																	45779410		1823	4080	5903	SO:0001819	synonymous_variant	27127			AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.1995C>T	22.37:g.45779410G>A			A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																				0.343	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		9	45	9	45
SCN1A	6323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	166897764	166897764	+	Missense_Mutation	SNP	T	T	A			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr2:166897764T>A	ENST00000303395.4	-	13	2391	c.2392A>T	c.(2392-2394)Aat>Tat	p.N798Y	AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.N787Y|SCN1A_ENST00000409050.1_Missense_Mutation_p.N770Y|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000423058.2_Missense_Mutation_p.N798Y			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	798					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GTAAGCACATTATTGAAATGG	0.363																																																0													80.0	72.0	75.0					2																	166897764		2203	4300	6503	SO:0001583	missense	6323			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.2392A>T	2.37:g.166897764T>A	ENSP00000303540:p.Asn798Tyr		E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	T	1.021	-0.684857	0.03328	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97378	-4.36;-4.36;-4.36;-4.36	5.39	-2.09	0.07232	.	0.345579	0.28166	N	0.016360	D	0.93703	0.7988	L	0.55481	1.735	0.28406	N	0.918406	B;B;B	0.14805	0.005;0.011;0.0	B;B;B	0.17722	0.019;0.014;0.001	D	0.87483	0.2422	10	0.62326	D	0.03	.	8.5615	0.33514	0.0:0.167:0.5378:0.2951	.	787;770;798	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	Y	798;798;787;770	ENSP00000407030:N798Y;ENSP00000303540:N798Y;ENSP00000364554:N787Y;ENSP00000386312:N770Y	ENSP00000303540:N798Y	N	-	1	0	SCN1A	166606010	0.002000	0.14202	0.926000	0.36857	0.871000	0.50021	-0.571000	0.05889	-0.251000	0.09542	-0.438000	0.05819	AAT		0.363	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		18	64	18	64
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	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			11	56	11	56
TRANK1	9881	hgsc.bcm.edu;broad.mit.edu	37	3	36875229	36875229	+	Silent	SNP	A	A	G			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr3:36875229A>G	ENST00000429976.2	-	21	5960	c.5713T>C	c.(5713-5715)Tta>Cta	p.L1905L	TRANK1_ENST00000428977.2_Silent_p.L1355L|TRANK1_ENST00000301807.6_Silent_p.L1355L	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1905							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						GCTTCTGCTAAGCGTTTCCGA	0.512																																																0													118.0	117.0	117.0					3																	36875229		1968	4159	6127	SO:0001819	synonymous_variant	9881			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.5713T>C	3.37:g.36875229A>G			Q8N8K0	Silent	SNP	ENST00000429976.2	37	CCDS46789.2																																																																																				0.512	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		8	116	8	116
NKX3-2	579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	13543758	13543758	+	Silent	SNP	G	G	C			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr4:13543758G>C	ENST00000382438.5	-	2	1496	c.861C>G	c.(859-861)cgC>cgG	p.R287R		NM_001189.3	NP_001180.1	P78367	NKX32_HUMAN	NK3 homeobox 2	287					determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|intestinal epithelial cell development (GO:0060576)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|organ formation (GO:0048645)|pancreas development (GO:0031016)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|spleen development (GO:0048536)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(1)|lung(4)|prostate(1)	7						TCTGGTCGTCGCGCACCAGCA	0.647																																																0													34.0	31.0	32.0					4																	13543758		2202	4300	6502	SO:0001819	synonymous_variant	579			AF009801	CCDS3410.1	4p16.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000109705	ENSG00000109705		"""Homeoboxes / ANTP class : NKL subclass"""	951	protein-coding gene	gene with protein product		602183	"""bagpipe homeobox homolog 1 (Drosophila)"""	BAPX1		9344671	Standard	NM_001189		Approved	NKX3B, NKX3.2	uc003gmx.2	P78367	OTTHUMG00000090657	ENST00000382438.5:c.861C>G	4.37:g.13543758G>C			Q2M2I7	Silent	SNP	ENST00000382438.5	37	CCDS3410.1																																																																																				0.647	NKX3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207317.3			8	21	8	21
RBPJ	3516	hgsc.bcm.edu;broad.mit.edu	37	4	26432517	26432517	+	Missense_Mutation	SNP	A	A	G	rs1064404		TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr4:26432517A>G	ENST00000361572.6	+	11	1585	c.1391A>G	c.(1390-1392)aAt>aGt	p.N464S	RBPJ_ENST00000342320.4_Missense_Mutation_p.N450S|RBPJ_ENST00000504907.1_3'UTR|RBPJ_ENST00000348160.4_Missense_Mutation_p.N451S|RBPJ_ENST00000355476.3_Missense_Mutation_p.N450S|RBPJ_ENST00000342295.1_Missense_Mutation_p.N464S|RBPJ_ENST00000345843.3_Missense_Mutation_p.N449S|RBPJ_ENST00000507561.1_Missense_Mutation_p.N429S			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	464					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				CTTCGAGCCAATTCAAGCCAG	0.498																																																0													63.0	64.0	64.0					4																	26432517		2203	4300	6503	SO:0001583	missense	3516			L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"""suppressor of hairless homolog (Drosophila)"""	147183	"""recombining binding protein suppressor of hairless (Drosophila)"""	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.1391A>G	4.37:g.26432517A>G	ENSP00000354528:p.Asn464Ser		B4DY22|Q5XKH9|Q6P1N3	Missense_Mutation	SNP	ENST00000361572.6	37	CCDS3437.1	.	.	.	.	.	.	.	.	.	.	A	6.874	0.530669	0.13127	.	.	ENSG00000168214	ENST00000345843;ENST00000342295;ENST00000361572;ENST00000348160;ENST00000355476;ENST00000507561;ENST00000342320	T;T;T;T;T;T;T	0.33216	1.43;1.43;1.43;1.43;1.42;1.43;1.42	5.31	0.12	0.14691	.	0.356314	0.35378	N	0.003257	T	0.12008	0.0292	N	0.08118	0	0.30364	N	0.783538	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.001;0.0	T	0.34378	-0.9831	10	0.09843	T	0.71	-5.5964	9.144	0.36921	0.7197:0.0:0.2803:0.0	rs1064404;rs1064404	451;450;449;464	B4DY22;Q06330-6;Q06330-4;Q06330	.;.;.;SUH_HUMAN	S	449;464;464;451;450;429;450	ENSP00000305815:N449S;ENSP00000345206:N464S;ENSP00000354528:N464S;ENSP00000339699:N451S;ENSP00000347659:N450S;ENSP00000423907:N429S;ENSP00000340124:N450S	ENSP00000345206:N464S	N	+	2	0	RBPJ	26041615	0.150000	0.22732	0.137000	0.22149	0.996000	0.88848	0.769000	0.26604	-0.179000	0.10654	0.533000	0.62120	AAT		0.498	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		8	89	8	89
FAT4	79633	hgsc.bcm.edu;broad.mit.edu	37	4	126239282	126239282	+	Silent	SNP	C	C	G			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr4:126239282C>G	ENST00000394329.3	+	1	1729	c.1716C>G	c.(1714-1716)ctC>ctG	p.L572L		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	572	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TAGTAACTCTCCTAGATGTGA	0.498											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													51.0	53.0	53.0					4																	126239282		1954	4156	6110	SO:0001819	synonymous_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.1716C>G	4.37:g.126239282C>G		1548	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.498	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		6	60	6	60
DCLK2	166614	hgsc.bcm.edu;broad.mit.edu	37	4	151153981	151153981	+	Splice_Site	SNP	G	G	A			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr4:151153981G>A	ENST00000296550.7	+	10	2320		c.e10+1		DCLK2_ENST00000302176.8_Splice_Site|DCLK2_ENST00000506325.1_Splice_Site	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2						intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					GAATCTCTTGGTATGTCATCC	0.438																																					GBM(195;186 2215 13375 16801 37459)											0													222.0	194.0	203.0					4																	151153981		2203	4300	6503	SO:0001630	splice_region_variant	166614			BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390			19002	protein-coding gene	gene with protein product		613166	"""doublecortin and CaM kinase-like 2"""	DCAMKL2		12477932	Standard	NM_001040260		Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000296550.7:c.1566+1G>A	4.37:g.151153981G>A			C9J5Q9|Q59GC8|Q8N399	Splice_Site	SNP	ENST00000296550.7	37	CCDS34076.1	.	.	.	.	.	.	.	.	.	.	G	33	5.206723	0.95033	.	.	ENSG00000170390	ENST00000296550;ENST00000506325;ENST00000302176	.	.	.	6.02	6.02	0.97574	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DCLK2	151373431	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.729000	0.98795	2.865000	0.98341	0.655000	0.94253	.		0.438	DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	NM_001040260	Intron	9	119	9	119
CRHBP	1393	hgsc.bcm.edu;broad.mit.edu	37	5	76259212	76259212	+	Silent	SNP	G	G	A			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr5:76259212G>A	ENST00000274368.4	+	6	1160	c.738G>A	c.(736-738)ctG>ctA	p.L246L	CRHBP_ENST00000514258.1_3'UTR	NM_001882.3	NP_001873.2	P24387	CRHBP_HUMAN	corticotropin releasing hormone binding protein	246					behavioral response to ethanol (GO:0048149)|cellular response to calcium ion (GO:0071277)|cellular response to cAMP (GO:0071320)|cellular response to cocaine (GO:0071314)|cellular response to drug (GO:0035690)|cellular response to estradiol stimulus (GO:0071392)|cellular response to estrogen stimulus (GO:0071391)|cellular response to gonadotropin-releasing hormone (GO:0097211)|cellular response to potassium ion (GO:0035865)|cellular response to stress (GO:0033554)|cellular response to tumor necrosis factor (GO:0071356)|female pregnancy (GO:0007565)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|inflammatory response (GO:0006954)|learning or memory (GO:0007611)|maternal aggressive behavior (GO:0002125)|negative regulation of corticotropin secretion (GO:0051460)|negative regulation of corticotropin-releasing hormone receptor activity (GO:1900011)|regulated secretory pathway (GO:0045055)|regulation of corticotropin secretion (GO:0051459)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|synaptic transmission, dopaminergic (GO:0001963)	axon terminus (GO:0043679)|dendrite (GO:0030425)|dense core granule (GO:0031045)|extracellular space (GO:0005615)|intracellular (GO:0005622)|microtubule (GO:0005874)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|perikaryon (GO:0043204)|secondary lysosome (GO:0005767)|secretory granule (GO:0030141)|varicosity (GO:0043196)	corticotropin-releasing hormone binding (GO:0051424)|peptide binding (GO:0042277)			kidney(3)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	16		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)		TTGTGGAGCTGCTGGGAGGAA	0.458																																																0													173.0	175.0	175.0					5																	76259212		2203	4300	6503	SO:0001819	synonymous_variant	1393			X58022	CCDS4034.1	5q	2008-07-18	2001-11-28		ENSG00000145708	ENSG00000145708			2356	protein-coding gene	gene with protein product		122559	"""corticotropin releasing hormone-binding protein"""			8198617	Standard	NM_001882		Approved	CRF-BP, CRFBP	uc003ker.3	P24387	OTTHUMG00000102133	ENST00000274368.4:c.738G>A	5.37:g.76259212G>A			Q53F32|Q6FHT5	Silent	SNP	ENST00000274368.4	37	CCDS4034.1																																																																																				0.458	CRHBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219972.2	NM_001882		9	113	9	113
PCDHB3	56132	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	140480508	140480508	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr5:140480508G>A	ENST00000231130.2	+	1	275	c.275G>A	c.(274-276)cGg>cAg	p.R92Q	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	92	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AAATTGGACCGGGAGGAGCTA	0.483																																																0													84.0	90.0	88.0					5																	140480508		2203	4300	6503	SO:0001583	missense	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"""Cadherins / Protocadherins : Clustered"""	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.275G>A	5.37:g.140480508G>A	ENSP00000231130:p.Arg92Gln		B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.404657	0.83230	.	.	ENSG00000113205	ENST00000231130	T	0.53206	0.63	4.7	4.7	0.59300	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.82403	0.5029	H	0.99286	4.5	0.35609	D	0.808506	D	0.89917	1.0	D	0.97110	1.0	D	0.92863	0.6307	9	0.87932	D	0	.	17.6382	0.88129	0.0:0.0:1.0:0.0	.	92	Q9Y5E6	PCDB3_HUMAN	Q	92	ENSP00000231130:R92Q	ENSP00000231130:R92Q	R	+	2	0	PCDHB3	140460692	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	9.394000	0.97261	2.305000	0.77605	0.655000	0.94253	CGG		0.483	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		11	115	11	115
CRISP1	167	hgsc.bcm.edu;broad.mit.edu	37	6	49814258	49814258	+	Missense_Mutation	SNP	T	T	C	rs185407783		TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr6:49814258T>C	ENST00000335847.4	-	5	511	c.410A>G	c.(409-411)gAc>gGc	p.D137G	CRISP1_ENST00000355791.2_Missense_Mutation_p.D137G|CRISP1_ENST00000536021.1_Missense_Mutation_p.D137G|CRISP1_ENST00000507853.1_Missense_Mutation_p.D137G|CRISP1_ENST00000505118.1_Missense_Mutation_p.D137G|CRISP1_ENST00000329411.5_Missense_Mutation_p.D137G	NM_001131.2	NP_001122.2	P54107	CRIS1_HUMAN	cysteine-rich secretory protein 1	137	SCP.				binding of sperm to zona pellucida (GO:0007339)|fusion of sperm to egg plasma membrane (GO:0007342)|regulation of acrosome reaction (GO:0060046)	extracellular space (GO:0005615)|nucleus (GO:0005634)	calcium channel regulator activity (GO:0005246)			endometrium(1)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0358)					AGTAGTTATGTCATCATCCGT	0.403																																																0													433.0	341.0	372.0					6																	49814258		2203	4300	6503	SO:0001583	missense	167			D38451	CCDS4931.1, CCDS4932.1	6p21.2-p21.1	2008-02-05	2003-09-03	2003-09-05	ENSG00000124812	ENSG00000124812			304	protein-coding gene	gene with protein product		601193	"""acidic epididymal glycoprotein-like 1"""	AEGL1		8838800	Standard	NM_001131		Approved	CRISP-1, ARP, HUMARP, HSCRISP1D, HSCRISP1G	uc003ozw.2	P54107	OTTHUMG00000014827	ENST00000335847.4:c.410A>G	6.37:g.49814258T>C	ENSP00000338276:p.Asp137Gly		B5BU98|O00698|Q13248|Q14082|Q96SF6	Missense_Mutation	SNP	ENST00000335847.4	37	CCDS4931.1	.	.	.	.	.	.	.	.	.	.	T	3.323	-0.138241	0.06669	.	.	ENSG00000124812	ENST00000507853;ENST00000335847;ENST00000355791;ENST00000329411;ENST00000505118;ENST00000536021	T;T;T;T;T;T	0.08193	3.12;3.12;3.12;3.12;3.12;3.12	5.35	-10.7	0.00240	CAP domain (3);	1.042900	0.07610	N	0.925165	T	0.00666	0.0022	N	0.05259	-0.085	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.45160	-0.9280	9	.	.	.	.	4.7286	0.12954	0.2499:0.4711:0.0922:0.1868	.	137;137	P54107-2;P54107	.;CRIS1_HUMAN	G	137	ENSP00000425020:D137G;ENSP00000338276:D137G;ENSP00000348044:D137G;ENSP00000331317:D137G;ENSP00000427589:D137G;ENSP00000441798:D137G	.	D	-	2	0	CRISP1	49922217	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.218000	0.02976	-2.433000	0.00555	-1.054000	0.02325	GAC		0.403	CRISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040875.2	NM_001131		7	87	7	87
TINAG	27283	hgsc.bcm.edu;broad.mit.edu	37	6	54254705	54254705	+	Silent	SNP	G	G	A			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr6:54254705G>A	ENST00000259782.4	+	11	1509	c.1413G>A	c.(1411-1413)acG>acA	p.T471T		NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	471					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			GCCAACTGACGAGTTCTGATG	0.408																																																0													126.0	124.0	125.0					6																	54254705		2203	4300	6503	SO:0001819	synonymous_variant	27283			AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.1413G>A	6.37:g.54254705G>A			Q5T467|Q9UJW1|Q9ULZ4	Silent	SNP	ENST00000259782.4	37	CCDS4955.1																																																																																				0.408	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		9	129	9	129
MUC17	140453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	100679992	100679992	+	Missense_Mutation	SNP	G	G	T	rs148096926	byFrequency	TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr7:100679992G>T	ENST00000306151.4	+	3	5359	c.5295G>T	c.(5293-5295)gaG>gaT	p.E1765D		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1765	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCAGTTCTGAGGCTAGCACCC	0.502																																																0													290.0	303.0	299.0					7																	100679992		2203	4300	6503	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5295G>T	7.37:g.100679992G>T	ENSP00000302716:p.Glu1765Asp		O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	1.171	-0.640978	0.03557	.	.	ENSG00000169876	ENST00000306151	T	0.01998	4.51	0.824	-1.65	0.08291	.	.	.	.	.	T	0.01353	0.0044	L	0.27053	0.805	0.09310	N	1	P	0.50156	0.932	B	0.38954	0.286	T	0.45673	-0.9245	9	0.13108	T	0.6	.	4.0827	0.09934	0.5284:0.0:0.4716:0.0	.	1765	Q685J3	MUC17_HUMAN	D	1765	ENSP00000302716:E1765D	ENSP00000302716:E1765D	E	+	3	2	MUC17	100466712	0.000000	0.05858	0.003000	0.11579	0.022000	0.10575	-1.344000	0.02639	-0.647000	0.05444	-1.368000	0.01194	GAG		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		88	449	88	449
GAPVD1	26130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	128094894	128094894	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr9:128094894A>G	ENST00000495955.1	+	15	2704	c.2414A>G	c.(2413-2415)gAt>gGt	p.D805G	GAPVD1_ENST00000297933.6_Missense_Mutation_p.D805G|GAPVD1_ENST00000312123.9_Missense_Mutation_p.D784G|GAPVD1_ENST00000470056.1_Missense_Mutation_p.D805G|GAPVD1_ENST00000394083.2_Missense_Mutation_p.D784G|GAPVD1_ENST00000394104.2_Missense_Mutation_p.D805G|GAPVD1_ENST00000265956.4_Missense_Mutation_p.D805G|GAPVD1_ENST00000394105.2_Missense_Mutation_p.D805G			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	805					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CCAGACATGGATGAAATAACT	0.448																																																0													88.0	88.0	88.0					9																	128094894		2203	4300	6503	SO:0001583	missense	26130				CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.2414A>G	9.37:g.128094894A>G	ENSP00000419063:p.Asp805Gly		A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.31|19.31	3.802522|3.802522	0.70682|0.70682	.|.	.|.	ENSG00000165219|ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000467750;ENST00000297933;ENST00000312123|ENST00000431329	T;T;T;T;T;T;T;T;T|.	0.14266|.	2.52;2.52;2.52;2.52;2.52;2.52;2.52;2.52;2.52|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	0.049381|.	0.85682|.	D|.	0.000000|.	T|T	0.48205|0.48205	0.1487|0.1487	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	D|D	0.999994|0.999994	B;B;B;B;B;P|.	0.39480|.	0.135;0.083;0.135;0.135;0.135;0.675|.	B;B;B;B;B;B|.	0.41813|.	0.157;0.075;0.101;0.101;0.101;0.367|.	T|T	0.45673|0.45673	-0.9245|-0.9245	10|5	0.40728|.	T|.	0.16|.	.|.	15.148|15.148	0.72674|0.72674	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	805;805;805;784;805;805|.	Q14C86-5;Q14C86;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6|.	.;GAPD1_HUMAN;.;.;.;.|.	G|V	805;805;805;805;784;805;805;805;784|668	ENSP00000419767:D805G;ENSP00000377665:D805G;ENSP00000377664:D805G;ENSP00000265956:D805G;ENSP00000377645:D784G;ENSP00000419063:D805G;ENSP00000418747:D805G;ENSP00000297933:D805G;ENSP00000309582:D784G|.	ENSP00000265956:D805G|.	D|M	+|+	2|1	0|0	GAPVD1|GAPVD1	127134715|127134715	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	9.339000|9.339000	0.96797|0.96797	2.182000|2.182000	0.69389|0.69389	0.459000|0.459000	0.35465|0.35465	GAT|ATG		0.448	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			15	61	15	61
NCOA2	10499	broad.mit.edu;ucsc.edu	37	8	71044226	71044226	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr8:71044226C>T	ENST00000452400.2	-	16	3351	c.3170G>A	c.(3169-3171)gGc>gAc	p.G1057D	NCOA2_ENST00000267974.4_Missense_Mutation_p.G145D	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	1057					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TGGAGAACTGCCAAATGGCTG	0.453			T	"""RUNXBP2, HEY1"""	"""AML, Chondrosarcoma"""																																		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	0													49.0	48.0	49.0					8																	71044226		1948	4154	6102	SO:0001583	missense	10499			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.3170G>A	8.37:g.71044226C>T	ENSP00000399968:p.Gly1057Asp		Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.83|17.83	3.486411|3.486411	0.63962|0.63962	.|.	.|.	ENSG00000140396|ENSG00000140396	ENST00000518363|ENST00000452400;ENST00000267974	.|T;T	.|0.06849	.|4.79;3.25	5.81|5.81	4.01|4.01	0.46588|0.46588	.|.	.|0.409870	.|0.28488	.|N	.|0.015180	T|T	0.21631|0.21631	0.0521|0.0521	M|M	0.66939|0.66939	2.045|2.045	0.49915|0.49915	D|D	0.999839|0.999839	.|D;D	.|0.65815	.|0.995;0.968	.|P;P	.|0.60609	.|0.877;0.587	T|T	0.00356|0.00356	-1.1793|-1.1793	5|10	.|0.44086	.|T	.|0.13	.|.	11.601|11.601	0.51003|0.51003	0.0:0.8076:0.1254:0.067|0.0:0.8076:0.1254:0.067	.|.	.|145;1057	.|F8WAJ2;Q15596	.|.;NCOA2_HUMAN	T|D	158|1057;145	.|ENSP00000399968:G1057D;ENSP00000267974:G145D	.|ENSP00000267974:G145D	A|G	-|-	1|2	0|0	NCOA2|NCOA2	71206780|71206780	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.689000|0.689000	0.40095|0.40095	3.817000|3.817000	0.55668|0.55668	0.802000|0.802000	0.34089|0.34089	0.655000|0.655000	0.94253|0.94253	GCA|GGC		0.453	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			3	26	3	26
TH	7054	broad.mit.edu;ucsc.edu	37	11	2190969	2190969	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr11:2190969C>T	ENST00000381178.1	-	3	334	c.316G>A	c.(316-318)Gag>Aag	p.E106K	TH_ENST00000333684.5_Missense_Mutation_p.E79K|TH_ENST00000352909.3_Missense_Mutation_p.E75K|TH_ENST00000381175.1_Missense_Mutation_p.E102K	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	106					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CCCTCCTTCTCCTCAAAGGCC	0.692																																																0													41.0	43.0	42.0					11																	2190969		2202	4299	6501	SO:0001583	missense	7054			X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.316G>A	11.37:g.2190969C>T	ENSP00000370571:p.Glu106Lys		B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Missense_Mutation	SNP	ENST00000381178.1	37	CCDS7731.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.125047	0.77436	.	.	ENSG00000180176	ENST00000381178;ENST00000381175;ENST00000352909;ENST00000333684	D;D;D;D	0.98362	-4.89;-4.89;-4.89;-4.89	3.06	2.08	0.27032	.	0.130022	0.49916	D	0.000127	D	0.96140	0.8742	M	0.69823	2.125	0.47245	D	0.999363	P;P;P;B;B;B	0.41041	0.736;0.455;0.455;0.078;0.047;0.135	B;B;B;B;B;B	0.33196	0.159;0.102;0.102;0.099;0.03;0.067	D	0.93907	0.7193	10	0.72032	D	0.01	.	10.9263	0.47193	0.0:0.8073:0.1927:0.0	.	79;79;75;75;106;102	B7ZL73;Q0PWM2;Q0PWM3;P07101-3;P07101;P07101-2	.;.;.;.;TY3H_HUMAN;.	K	106;102;75;79	ENSP00000370571:E106K;ENSP00000370567:E102K;ENSP00000325951:E75K;ENSP00000328814:E79K	ENSP00000328814:E79K	E	-	1	0	TH	2147545	1.000000	0.71417	0.002000	0.10522	0.707000	0.40811	5.259000	0.65485	0.572000	0.29383	0.491000	0.48974	GAG		0.692	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360		6	54	6	54
DDX52	11056	broad.mit.edu;ucsc.edu	37	17	35974371	35974371	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr17:35974371C>G	ENST00000349699.2	-	15	1813	c.1770G>C	c.(1768-1770)aaG>aaC	p.K590N	DDX52_ENST00000394367.3_Missense_Mutation_p.K482N|RP11-697E22.1_ENST00000591689.1_RNA	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	590	Lys-rich.					membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				CTACTTTCTTCTTGCTGTTCT	0.323																																																0													93.0	86.0	88.0					17																	35974371		2201	4300	6501	SO:0001583	missense	11056			AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.1770G>C	17.37:g.35974371C>G	ENSP00000268854:p.Lys590Asn		Q86YG1|Q8N213|Q9NVE0|Q9Y482	Missense_Mutation	SNP	ENST00000349699.2	37	CCDS11323.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348810	0.41599	.	.	ENSG00000141141	ENST00000349699;ENST00000394367	T;T	0.15603	2.41;2.43	5.6	2.4	0.29515	.	1.819250	0.02473	N	0.087707	T	0.20659	0.0497	L	0.55834	1.745	0.36411	D	0.863719	B	0.13594	0.008	B	0.09377	0.004	T	0.10451	-1.0629	10	0.41790	T	0.15	.	7.9099	0.29785	0.0:0.6085:0.3079:0.0836	.	590	Q9Y2R4	DDX52_HUMAN	N	590;482	ENSP00000268854:K590N;ENSP00000377893:K482N	ENSP00000268854:K590N	K	-	3	2	DDX52	33048484	1.000000	0.71417	0.955000	0.39395	0.900000	0.52787	1.318000	0.33643	0.357000	0.24183	0.655000	0.94253	AAG		0.323	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300		5	28	5	28
BEST1	7439	broad.mit.edu;ucsc.edu	37	11	61724345	61724345	+	Silent	SNP	T	T	C			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr11:61724345T>C	ENST00000378043.4	+	5	1154	c.511T>C	c.(511-513)Ttg>Ctg	p.L171L	BEST1_ENST00000378042.3_Silent_p.L111L|BEST1_ENST00000534553.1_Intron|BEST1_ENST00000449131.2_Silent_p.L111L|BEST1_ENST00000526988.1_Silent_p.L65L|BEST1_ENST00000435278.2_Silent_p.L171L|BEST1_ENST00000301774.9_Intron	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	171					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						ACACAAGCAGTTGGAGAAACT	0.577																																																0													194.0	192.0	193.0					11																	61724345		2202	4299	6501	SO:0001819	synonymous_variant	7439			AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.511T>C	11.37:g.61724345T>C			A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																				0.577	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183		30	279	30	279
AGBL1	123624	broad.mit.edu;ucsc.edu	37	15	86838484	86838484	+	Splice_Site	SNP	A	A	C			TCGA-HT-8106-01A-11D-2395-08	TCGA-HT-8106-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eda36bc8-66a9-4901-95f4-d98528290e84	dfb6bde7-00dc-4892-a8e2-a111cff05939	g.chr15:86838484A>C	ENST00000441037.2	+	16	2177		c.e16-1		AGBL1_ENST00000421325.2_Splice_Site|AGBL1-AS1_ENST00000564487.1_RNA|AGBL1_ENST00000389298.3_Splice_Site|AGBL1-AS1_ENST00000566878.1_RNA	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						TTTCTGCTCCAGACTCATCTT	0.398																																																0													46.0	46.0	46.0					15																	86838484		1877	4104	5981	SO:0001630	splice_region_variant	123624			AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2083-1A>C	15.37:g.86838484A>C			A1A4X5|A6NJH6|C9JHL5	Splice_Site	SNP	ENST00000441037.2	37	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	A	12.12	1.842447	0.32513	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5211	0.61568	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AGBL1	84639488	1.000000	0.71417	0.985000	0.45067	0.180000	0.23129	7.213000	0.77950	2.133000	0.65898	0.528000	0.53228	.		0.398	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	Intron	4	27	4	27
