#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
FUT4	2526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	94278274	94278274	+	Silent	SNP	C	C	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr11:94278274C>T	ENST00000358752.2	+	1	1258	c.975C>T	c.(973-975)gaC>gaT	p.D325D	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_002033.3	NP_002024.1	P22083	FUT4_HUMAN	fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-specific)	325					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	cell periphery (GO:0071944)|cell surface (GO:0009986)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(2)|endometrium(2)|lung(1)|skin(2)|upper_aerodigestive_tract(1)	8		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CGGACTCGGACGTCTTTGTGC	0.647																																																0													27.0	32.0	30.0					11																	94278274		2193	4289	6482	SO:0001819	synonymous_variant	2526				CCDS8301.1	11q21	2013-02-26			ENSG00000196371	ENSG00000196371		"""CD molecules"", ""Fucosyltransferases"""	4015	protein-coding gene	gene with protein product	"""ELAM ligand fucosyltransferase"", ""galactoside 3-L-fucosyltransferase"""	104230		CD15, FCT3A, ELFT		1702034	Standard	NM_002033		Approved	FUC-TIV	uc001pez.3	P22083	OTTHUMG00000167795	ENST00000358752.2:c.975C>T	11.37:g.94278274C>T			B2RMS0	Silent	SNP	ENST00000358752.2	37	CCDS8301.1																																																																																				0.647	FUT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396327.2	NM_002033		26	64	26	64
TAS2R13	50838	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	11061883	11061883	+	Silent	SNP	C	C	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr12:11061883C>T	ENST00000390677.2	-	1	278	c.15G>A	c.(13-15)ctG>ctA	p.L5L	PRR4_ENST00000536668.1_Intron	NM_023920.2	NP_076409.1	Q9NYV9	T2R13_HUMAN	taste receptor, type 2, member 13	5					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						AGATACTCGGCAGGGCACTTT	0.383																																																0													33.0	33.0	33.0					12																	11061883		2201	4297	6498	SO:0001819	synonymous_variant	50838			AF227137	CCDS8635.1	12p13	2012-08-22			ENSG00000212128	ENSG00000212128		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14919	protein-coding gene	gene with protein product		604792				10761934, 10766242	Standard	NM_023920		Approved	T2R13, TRB3	uc001qzg.1	Q9NYV9		ENST00000390677.2:c.15G>A	12.37:g.11061883C>T			Q4G0I5|Q502V8|Q645X2	Silent	SNP	ENST00000390677.2	37	CCDS8635.1																																																																																				0.383	TAS2R13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400229.1			8	46	8	46
PRICKLE1	144165	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	42860093	42860093	+	Silent	SNP	T	T	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr12:42860093T>A	ENST00000455697.1	-	6	963	c.678A>T	c.(676-678)ggA>ggT	p.G226G	PRICKLE1_ENST00000548696.1_Silent_p.G226G|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000552240.1_Silent_p.G226G|PRICKLE1_ENST00000345127.3_Silent_p.G226G|PRICKLE1_ENST00000445766.2_Silent_p.G226G	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	226	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		ACCTCTGTCCTCCCAGGACCG	0.488																																																0													99.0	83.0	89.0					12																	42860093		2203	4300	6503	SO:0001819	synonymous_variant	144165			AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"""prickle-like 1 (Drosophila)"""			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.678A>T	12.37:g.42860093T>A			Q14C83|Q71QF8|Q96N00	Silent	SNP	ENST00000455697.1	37	CCDS8742.1																																																																																				0.488	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			12	86	12	86
GPR68	8111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	91700786	91700786	+	Silent	SNP	C	C	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr14:91700786C>T	ENST00000531499.2	-	2	948	c.609G>A	c.(607-609)gcG>gcA	p.A203A	GPR68_ENST00000529300.1_5'Flank|GPR68_ENST00000238699.3_Silent_p.A213A|GPR68_ENST00000535815.1_Silent_p.A203A			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	203					cellular response to pH (GO:0071467)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of osteoclast development (GO:2001206)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	8		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		CCTGGTAGGACGCCAGCAGCA	0.652																																																0													40.0	31.0	34.0					14																	91700786		2202	4300	6502	SO:0001819	synonymous_variant	8111			U48405	CCDS9894.1, CCDS9894.2	14q31	2012-08-21				ENSG00000119714		"""GPCR / Class A : Orphans"""	4519	protein-coding gene	gene with protein product		601404				8661159	Standard	NM_001177676		Approved	OGR1	uc001xzg.3	Q15743		ENST00000531499.2:c.609G>A	14.37:g.91700786C>T			Q13334|Q4VBB4|Q6IX34	Silent	SNP	ENST00000531499.2	37	CCDS9894.2																																																																																				0.652	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2			10	33	10	33
ITGAL	3683	hgsc.bcm.edu;broad.mit.edu	37	16	30485546	30485546	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr16:30485546C>T	ENST00000356798.6	+	2	271	c.91C>T	c.(91-93)Cgg>Tgg	p.R31W	ITGAL_ENST00000358164.5_Missense_Mutation_p.R31W|Y_RNA_ENST00000410769.1_RNA|ITGAL_ENST00000433423.2_Missense_Mutation_p.R31W|RP11-297C4.2_ENST00000569459.1_RNA|ITGAL_ENST00000454514.2_Missense_Mutation_p.R31W	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	31					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	CCTGGACGTGCGGGGCGCGCG	0.706																																					NSCLC(110;1462 1641 3311 33990 49495)											0													17.0	20.0	19.0					16																	30485546		2190	4281	6471	SO:0001583	missense	3683				CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"""CD molecules"", ""Integrins"""	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.91C>T	16.37:g.30485546C>T	ENSP00000349252:p.Arg31Trp		O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	37	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.874624	0.72180	.	.	ENSG00000005844	ENST00000356798;ENST00000358164;ENST00000454514;ENST00000433423	T;T;D;T	0.92299	-0.68;-0.68;-3.01;1.69	4.73	-2.77	0.05877	.	1.151710	0.06520	N	0.739556	D	0.89354	0.6691	M	0.76328	2.33	0.09310	N	1	B;B;D	0.63046	0.013;0.013;0.992	B;B;B	0.42386	0.003;0.002;0.386	T	0.80906	-0.1173	10	0.87932	D	0	.	3.7092	0.08413	0.4155:0.3454:0.0:0.2391	.	31;31;31	B4E021;Q96HB1;P20701	.;.;ITAL_HUMAN	W	31	ENSP00000349252:R31W;ENSP00000350886:R31W;ENSP00000408615:R31W;ENSP00000409377:R31W	ENSP00000349252:R31W	R	+	1	2	ITGAL	30393047	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-0.456000	0.06754	-0.193000	0.10415	0.467000	0.42956	CGG		0.706	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			7	16	7	16
MED1	5469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	37565972	37565972	+	Silent	SNP	T	T	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr17:37565972T>A	ENST00000300651.6	-	17	2725	c.2502A>T	c.(2500-2502)ccA>ccT	p.P834P	MED1_ENST00000394287.3_Intron	NM_004774.3	NP_004765.2	O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		GATCAGTGTATGGATTTTCAT	0.433										HNSCC(31;0.082)																											Pancreas(21;279 768 2492 4877 24026)											0													62.0	64.0	63.0					17																	37565972		2203	4300	6503	SO:0001819	synonymous_variant	5469			L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"""PPAR binding protein"""	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000300651.6:c.2502A>T	17.37:g.37565972T>A			B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Silent	SNP	ENST00000300651.6	37	CCDS11336.1																																																																																				0.433	MED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256943.3	NM_004774		20	86	20	86
SMURF2	64750	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	62574689	62574689	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr17:62574689T>C	ENST00000262435.9	-	9	965	c.778A>G	c.(778-780)Agg>Ggg	p.R260G	SMURF2_ENST00000578200.1_Intron	NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	260	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				BMP signaling pathway (GO:0030509)|gene expression (GO:0010467)|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)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|SMAD binding (GO:0046332)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(4)	22	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			TGCGTTGTCCTCTGTTCTGTA	0.373																																																0													123.0	103.0	110.0					17																	62574689		2203	4300	6503	SO:0001583	missense	64750			AF301463	CCDS32707.1	17q22-q23	2012-10-05			ENSG00000108854	ENSG00000108854			16809	protein-coding gene	gene with protein product		605532				11016919	Standard	XM_005257585		Approved		uc002jep.1	Q9HAU4	OTTHUMG00000179189	ENST00000262435.9:c.778A>G	17.37:g.62574689T>C	ENSP00000262435:p.Arg260Gly		Q52LL1|Q9H260	Missense_Mutation	SNP	ENST00000262435.9	37	CCDS32707.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.954901	0.34471	.	.	ENSG00000108854	ENST00000262435	D	0.83914	-1.78	5.63	5.63	0.86233	WW/Rsp5/WWP (5);	0.000000	0.85682	D	0.000000	D	0.91355	0.7273	M	0.80028	2.48	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92471	0.5985	10	0.87932	D	0	.	16.1339	0.81465	0.0:0.0:0.0:1.0	.	260	Q9HAU4	SMUF2_HUMAN	G	260	ENSP00000262435:R260G	ENSP00000262435:R260G	R	-	1	2	SMURF2	60005151	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.543000	0.53633	2.271000	0.75665	0.533000	0.62120	AGG		0.373	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445227.1	NM_022739		16	29	16	29
TCEB3	6924	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	24080638	24080638	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr1:24080638G>A	ENST00000418390.2	+	6	1935	c.1664G>A	c.(1663-1665)aGa>aAa	p.R555K	TCEB3_ENST00000609199.1_Missense_Mutation_p.R529K	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	555	Activation domain. {ECO:0000250}.				gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		ACTGGGCGCAGAATGAATTCC	0.448																																																0													130.0	117.0	121.0					1																	24080638		2203	4300	6503	SO:0001583	missense	6924			L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"""transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"""			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.1664G>A	1.37:g.24080638G>A	ENSP00000395574:p.Arg555Lys		B2R7Q8|Q8IXH1	Missense_Mutation	SNP	ENST00000418390.2	37	CCDS239.2	.	.	.	.	.	.	.	.	.	.	G	36	5.843942	0.97016	.	.	ENSG00000011007	ENST00000418390	T	0.10192	2.9	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000005	T	0.38825	0.1055	M	0.80982	2.52	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.16276	-1.0408	10	0.87932	D	0	-22.1753	19.854	0.96750	0.0:0.0:1.0:0.0	.	555	Q14241	ELOA1_HUMAN	K	555	ENSP00000395574:R555K	ENSP00000395574:R555K	R	+	2	0	TCEB3	23953225	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	9.835000	0.99442	2.699000	0.92147	0.462000	0.41574	AGA		0.448	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198		45	8	45	8
ZNF683	257101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	26691295	26691295	+	Missense_Mutation	SNP	C	C	T	rs144078461|rs372936882	byFrequency	TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr1:26691295C>T	ENST00000436292.1	-	4	862	c.742G>A	c.(742-744)Gct>Act	p.A248T	ZNF683_ENST00000403843.1_Missense_Mutation_p.A248T|ZNF683_ENST00000349618.3_Missense_Mutation_p.A248T|ZNF683_ENST00000374204.1_Missense_Mutation_p.A248T			Q8IZ20	ZN683_HUMAN	zinc finger protein 683	248					natural killer cell differentiation (GO:0001779)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L228_W235delLGHPSARW(1)|p.L243_W250delLGHPSARW(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	15		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		TCCCACCGAGCGCTGGGGTGC	0.642																																																2	Deletion - In frame(2)	large_intestine(2)											33.0	44.0	40.0					1																	26691295		1996	4267	6263	SO:0001583	missense	257101			BC029505	CCDS279.2	1p36.11	2013-01-08			ENSG00000176083	ENSG00000176083		"""Zinc fingers, C2H2-type"""	28495	protein-coding gene	gene with protein product	"""hypothetical protein MGC33414"""					12477932	Standard	NM_173574		Approved	MGC33414	uc009vsj.1	Q8IZ20	OTTHUMG00000003521	ENST00000436292.1:c.742G>A	1.37:g.26691295C>T	ENSP00000388792:p.Ala248Thr		Q5T141|Q5T146|Q5T147|Q5T149|Q8NEN4	Missense_Mutation	SNP	ENST00000436292.1	37		.	.	.	.	.	.	.	.	.	.	C	1.905	-0.452032	0.04540	.	.	ENSG00000176083	ENST00000403843;ENST00000436292;ENST00000374204;ENST00000349618;ENST00000455900;ENST00000451801	T;T;T;T;T;T	0.19394	3.01;3.01;2.98;2.98;2.15;2.16	4.74	-9.48	0.00591	.	1.566820	0.03789	N	0.262592	T	0.08447	0.0210	N	0.17082	0.46	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.22277	-1.0221	10	0.19147	T	0.46	-5.0E-4	0.9764	0.01426	0.1715:0.2424:0.2243:0.3618	.	248;248	Q8IZ20-2;Q8IZ20	.;ZN683_HUMAN	T	248;248;248;248;256;248	ENSP00000384782:A248T;ENSP00000388792:A248T;ENSP00000363320:A248T;ENSP00000344095:A248T;ENSP00000411289:A256T;ENSP00000411290:A248T	ENSP00000344095:A248T	A	-	1	0	ZNF683	26563882	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.393000	0.02521	-3.454000	0.00160	-2.069000	0.00389	GCT		0.642	ZNF683-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009794.2	NM_173574		56	7	56	7
ARID4B	51742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	235345098	235345098	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr1:235345098T>C	ENST00000264183.3	-	20	3633	c.3136A>G	c.(3136-3138)Aca>Gca	p.T1046A	ARID4B_ENST00000366603.2_Missense_Mutation_p.T1046A|ARID4B_ENST00000349213.3_Missense_Mutation_p.T960A|ARID4B_ENST00000494543.1_5'UTR	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	1046					histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TCTGATACTGTTACAGAAGAC	0.473																																																0													103.0	89.0	94.0					1																	235345098		2203	4300	6503	SO:0001583	missense	51742			AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.3136A>G	1.37:g.235345098T>C	ENSP00000264183:p.Thr1046Ala		A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Missense_Mutation	SNP	ENST00000264183.3	37	CCDS31061.1	.	.	.	.	.	.	.	.	.	.	T	3.856	-0.030776	0.07543	.	.	ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183	T;T;T	0.21543	2.0;2.0;2.0	4.92	3.78	0.43462	.	0.426958	0.24022	N	0.042279	T	0.08626	0.0214	N	0.03115	-0.41	0.18873	N	0.999983	B;B;B;B	0.12013	0.001;0.001;0.005;0.0	B;B;B;B	0.12156	0.004;0.003;0.007;0.001	T	0.20338	-1.0278	10	0.49607	T	0.09	-12.911	5.7446	0.18112	0.2614:0.0741:0.0:0.6645	.	727;1046;960;1046	Q4LE39-4;Q4LE39-3;Q4LE39-2;Q4LE39	.;.;.;ARI4B_HUMAN	A	1046;960;1046;1046	ENSP00000264184:T960A;ENSP00000355562:T1046A;ENSP00000264183:T1046A	ENSP00000264183:T1046A	T	-	1	0	ARID4B	233411721	0.213000	0.23551	0.397000	0.26308	0.980000	0.70556	0.429000	0.21412	0.873000	0.35799	0.477000	0.44152	ACA		0.473	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		35	28	35	28
TPO	7173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	1491722	1491722	+	Missense_Mutation	SNP	C	C	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr2:1491722C>A	ENST00000345913.4	+	10	1818	c.1727C>A	c.(1726-1728)gCg>gAg	p.A576E	TPO_ENST00000346956.3_Missense_Mutation_p.A576E|TPO_ENST00000349624.3_Missense_Mutation_p.A403E|TPO_ENST00000329066.4_Missense_Mutation_p.A576E|TPO_ENST00000382201.3_Intron|TPO_ENST00000497517.2_Intron|TPO_ENST00000337415.3_Missense_Mutation_p.A576E|TPO_ENST00000382198.1_Missense_Mutation_p.A403E	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	576					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)	p.A576E(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TTGGATCTGGCGTCCATCAAC	0.592																																																1	Substitution - Missense(1)	ovary(1)											116.0	103.0	107.0					2																	1491722		2203	4300	6503	SO:0001583	missense	7173				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.1727C>A	2.37:g.1491722C>A	ENSP00000318820:p.Ala576Glu		P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.824933	0.90955	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57;-0.57;-0.57;-0.57	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	D	0.89301	0.6676	H	0.96111	3.77	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.79784	0.98;0.991;0.993	D	0.93095	0.6503	10	0.87932	D	0	-23.2278	17.8262	0.88666	0.0:1.0:0.0:0.0	.	576;403;576	P07202-4;P07202-5;P07202	.;.;PERT_HUMAN	E	576;576;576;403;576;403;505	ENSP00000337263:A576E;ENSP00000318820:A576E;ENSP00000263886:A576E;ENSP00000332044:A403E;ENSP00000329869:A576E;ENSP00000371633:A403E;ENSP00000405788:A505E	ENSP00000329869:A576E	A	+	2	0	TPO	1470729	0.998000	0.40836	0.922000	0.36590	0.923000	0.55619	3.799000	0.55529	2.191000	0.70037	0.591000	0.81541	GCG		0.592	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		59	74	59	74
MBD5	55777	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	149227787	149227787	+	Missense_Mutation	SNP	G	G	A	rs377604964		TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr2:149227787G>A	ENST00000407073.1	+	9	3272	c.2275G>A	c.(2275-2277)Gtg>Atg	p.V759M	MBD5_ENST00000404807.1_Missense_Mutation_p.V759M	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	759					glucose homeostasis (GO:0042593)|nervous system development (GO:0007399)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|regulation of multicellular organism growth (GO:0040014)|single-organism behavior (GO:0044708)	chromocenter (GO:0010369)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(16)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	62				BRCA - Breast invasive adenocarcinoma(221;0.0569)		AGGGGAAGCCGTGCACTGCCA	0.448																																																0								G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	117.0	108.0	111.0		2275	2.2	1.0	2		111	2,8598	2.2+/-6.3	0,2,4298	no	missense	MBD5	NM_018328.4	21	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	benign	759/1495	149227787	3,13003	2203	4300	6503	SO:0001583	missense	55777			AB040894	CCDS33302.1	2q23.2	2009-04-17			ENSG00000204406	ENSG00000204406			20444	protein-coding gene	gene with protein product		611472				12529184	Standard	NM_018328		Approved	FLJ11113, KIAA1461	uc002twm.4	Q9P267	OTTHUMG00000150440	ENST00000407073.1:c.2275G>A	2.37:g.149227787G>A	ENSP00000386049:p.Val759Met		A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	37	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	G	0.055	-1.238426	0.01493	2.27E-4	2.33E-4	ENSG00000204406	ENST00000407073;ENST00000404807	T;T	0.46063	0.9;0.88	4.96	2.2	0.27929	.	0.333204	0.25132	N	0.032887	T	0.16685	0.0401	N	0.04508	-0.205	0.31434	N	0.672803	B;B	0.14805	0.001;0.011	B;B	0.09377	0.0;0.004	T	0.06058	-1.0848	10	0.34782	T	0.22	-0.1977	3.7052	0.08398	0.3658:0.1814:0.4529:0.0	.	759;759	Q9P267-2;Q9P267	.;MBD5_HUMAN	M	759	ENSP00000386049:V759M;ENSP00000384672:V759M	ENSP00000384672:V759M	V	+	1	0	MBD5	148944257	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.878000	0.28126	0.812000	0.34326	0.655000	0.94253	GTG		0.448	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			52	61	52	61
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_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			27	54	27	54
FAM124B	79843	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	225266211	225266211	+	Missense_Mutation	SNP	G	G	A	rs181816086		TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr2:225266211G>A	ENST00000409685.3	-	1	540	c.275C>T	c.(274-276)tCg>tTg	p.S92L	FAM124B_ENST00000389874.3_Missense_Mutation_p.S92L|FAM124B_ENST00000243806.2_Missense_Mutation_p.S92L	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	92										endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		CTGCCATGGCGAATGCTGGAG	0.582													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18416	0.0		0.0	False		,,,				2504	0.0															0													60.0	56.0	57.0					2																	225266211		2203	4300	6503	SO:0001583	missense	79843			AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.275C>T	2.37:g.225266211G>A	ENSP00000386895:p.Ser92Leu		A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	37	CCDS46527.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	14.33	2.502052	0.44455	.	.	ENSG00000124019	ENST00000389874;ENST00000409685;ENST00000243806	T;T;T	0.44881	0.91;0.91;0.91	5.69	4.81	0.61882	.	0.273838	0.41938	D	0.000784	T	0.27798	0.0684	N	0.22421	0.69	0.25126	N	0.990606	P;P	0.47106	0.89;0.89	B;B	0.34418	0.182;0.088	T	0.15780	-1.0425	10	0.72032	D	0.01	-1.9118	15.3105	0.74028	0.0:0.1794:0.8206:0.0	.	92;92	Q9H5Z6;Q9H5Z6-2	F124B_HUMAN;.	L	92	ENSP00000374524:S92L;ENSP00000386895:S92L;ENSP00000243806:S92L	ENSP00000243806:S92L	S	-	2	0	FAM124B	224974455	1.000000	0.71417	0.152000	0.22495	0.155000	0.21991	7.377000	0.79668	1.399000	0.46721	0.655000	0.94253	TCG		0.582	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785		31	37	31	37
COL7A1	1294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	48609570	48609570	+	Missense_Mutation	SNP	C	C	T	rs201011691		TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr3:48609570C>T	ENST00000328333.8	-	90	7120	c.7013G>A	c.(7012-7014)cGa>cAa	p.R2338Q	COL7A1_ENST00000454817.1_Missense_Mutation_p.R2306Q	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2338	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.R2338Q(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTTCTCGCCTCGCGGCCCTGG	0.612													C|||	1	0.000199681	0.0	0.0	5008	,	,		17445	0.0		0.001	False		,,,				2504	0.0															1	Substitution - Missense(1)	urinary_tract(1)											38.0	33.0	35.0					3																	48609570		2203	4300	6503	SO:0001583	missense	1294			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.7013G>A	3.37:g.48609570C>T	ENSP00000332371:p.Arg2338Gln		Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.23	1.875940	0.33162	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	D;D	0.93307	-3.2;-3.2	6.07	6.07	0.98685	.	0.000000	0.42821	D	0.000651	D	0.91287	0.7253	N	0.16201	0.385	0.09310	N	1	D	0.76494	0.999	P	0.61275	0.886	D	0.83377	0.0010	10	0.22109	T	0.4	.	12.4372	0.55606	0.0:0.9178:0.0:0.0822	.	2338	Q02388	CO7A1_HUMAN	Q	2338;2306	ENSP00000332371:R2338Q;ENSP00000412569:R2306Q	ENSP00000332371:R2338Q	R	-	2	0	COL7A1	48584574	0.000000	0.05858	0.908000	0.35775	0.637000	0.38172	0.365000	0.20348	2.884000	0.98904	0.655000	0.94253	CGA		0.612	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		27	30	27	30
GABRA4	2557	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	46979112	46979112	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr4:46979112C>T	ENST00000264318.3	-	5	1525	c.543G>A	c.(541-543)atG>atA	p.M181I		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	181					central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	CATGACCATCCATGGGAAAAT	0.333																																					Ovarian(6;283 369 8234 12290 33402)											0													57.0	55.0	56.0					4																	46979112		2203	4300	6503	SO:0001583	missense	2557				CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4078	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 4"""	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.543G>A	4.37:g.46979112C>T	ENSP00000264318:p.Met181Ile		Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	.	.	.	.	.	.	.	.	.	.	C	33	5.270244	0.95429	.	.	ENSG00000109158	ENST00000264318	T	0.79454	-1.27	5.31	5.31	0.75309	Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.91603	0.7347	H	0.94658	3.565	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.93493	0.6837	10	0.87932	D	0	.	18.1472	0.89661	0.0:1.0:0.0:0.0	.	181	P48169	GBRA4_HUMAN	I	181	ENSP00000264318:M181I	ENSP00000264318:M181I	M	-	3	0	GABRA4	46673869	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.651000	0.83577	2.755000	0.94549	0.650000	0.86243	ATG		0.333	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			9	41	9	41
CLOCK	9575	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	56301648	56301648	+	Silent	SNP	T	T	C			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr4:56301648T>C	ENST00000309964.4	-	22	2725	c.2475A>G	c.(2473-2475)caA>caG	p.Q825Q	CLOCK_ENST00000381322.1_Silent_p.Q825Q|CLOCK_ENST00000513440.1_Silent_p.Q825Q	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	825	Interaction with NR3C1. {ECO:0000250|UniProtKB:O08785}.|Poly-Gln.				cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|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 (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			GTTGCTGCTGTTGCTGAGACT	0.527																																																0													272.0	228.0	243.0					4																	56301648		2203	4300	6503	SO:0001819	synonymous_variant	9575			AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	2082	protein-coding gene	gene with protein product		601851	"""clock (mouse) homolog"", ""clock homolog (mouse)"""			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.2475A>G	4.37:g.56301648T>C			A0AV01|A2I2N9|O14516|Q9UIT8	Silent	SNP	ENST00000309964.4	37	CCDS3500.1																																																																																				0.527	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898		56	84	56	84
NPFFR2	10886	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	72994632	72994632	+	Silent	SNP	A	A	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr4:72994632A>T	ENST00000308744.6	+	2	728	c.630A>T	c.(628-630)atA>atT	p.I210I	NPFFR2_ENST00000344413.5_Intron|NPFFR2_ENST00000395999.1_Silent_p.I111I|NPFFR2_ENST00000358749.3_Silent_p.I108I	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	210					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			ACAATATTATAGCAGGTATGT	0.368																																																0													92.0	89.0	90.0					4																	72994632		2203	4300	6503	SO:0001819	synonymous_variant	10886			AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"""GPCR / Class A :  Neuropeptide receptors : FF/AF"", ""GPCR / Class A : RF amide peptide receptors"""	4525	protein-coding gene	gene with protein product	"""neuropeptide FF 2"""	607449	"""G protein-coupled receptor 74"""	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.630A>T	4.37:g.72994632A>T			Q96RV1|Q9NR49	Silent	SNP	ENST00000308744.6	37	CCDS3551.1																																																																																				0.368	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885		42	57	42	57
MARCH6	10299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	10426541	10426541	+	Missense_Mutation	SNP	A	A	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr5:10426541A>T	ENST00000274140.5	+	24	2545	c.2413A>T	c.(2413-2415)Att>Ttt	p.I805F	MARCH6_ENST00000449913.2_Missense_Mutation_p.I757F|MARCH6_ENST00000510792.1_Missense_Mutation_p.I503F|MARCH6_ENST00000503788.1_Missense_Mutation_p.I700F	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase	805					protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						CCTTCACTATATTGTTCGTAA	0.403																																																0													430.0	367.0	388.0					5																	10426541		2203	4300	6503	SO:0001583	missense	10299			AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	30550	protein-coding gene	gene with protein product		613297	"""membrane-associated ring finger (C3HC4) 6"""			14722266	Standard	NM_001270660		Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.2413A>T	5.37:g.10426541A>T	ENSP00000274140:p.Ile805Phe		A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	Missense_Mutation	SNP	ENST00000274140.5	37	CCDS34135.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.092126	0.76756	.	.	ENSG00000145495	ENST00000449913;ENST00000503788;ENST00000274140;ENST00000510792	T;T;T;T	0.43688	1.94;0.95;1.94;0.94	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.58977	0.2160	L	0.57536	1.79	0.80722	D	1	P;D;D;D	0.67145	0.674;0.99;0.996;0.987	B;P;P;P	0.62298	0.363;0.67;0.9;0.571	T	0.61138	-0.7123	10	0.62326	D	0.03	-20.5014	16.1485	0.81594	1.0:0.0:0.0:0.0	.	700;757;385;805	B4DKJ2;B4DT33;B2RBJ1;O60337	.;.;.;MARH6_HUMAN	F	757;700;805;503	ENSP00000414643:I757F;ENSP00000425930:I700F;ENSP00000274140:I805F;ENSP00000424512:I503F	ENSP00000274140:I805F	I	+	1	0	MARCH6	10479541	1.000000	0.71417	0.973000	0.42090	0.972000	0.66771	6.902000	0.75699	2.281000	0.76405	0.533000	0.62120	ATT		0.403	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366919.2	NM_005885		19	171	19	171
ZNF618	114991	hgsc.bcm.edu;broad.mit.edu	37	9	116811917	116811917	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr9:116811917G>A	ENST00000374126.5	+	15	2434	c.2335G>A	c.(2335-2337)Ggc>Agc	p.G779S	ZNF618_ENST00000470105.1_3'UTR|ZNF618_ENST00000288466.7_Missense_Mutation_p.G686S			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	779					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(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						CAACGACGCAGGCACTGTCAG	0.627																																																0													49.0	53.0	52.0					9																	116811917		2153	4253	6406	SO:0001583	missense	114991			BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.2335G>A	9.37:g.116811917G>A	ENSP00000363241:p.Gly779Ser		B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Missense_Mutation	SNP	ENST00000374126.5	37		.	.	.	.	.	.	.	.	.	.	G	19.88	3.909914	0.72983	.	.	ENSG00000157657	ENST00000374126;ENST00000288466	T;T	0.22134	1.97;1.97	5.24	4.34	0.51931	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.46600	0.1401	.	.	.	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.994;0.998;1.0	T	0.49952	-0.8884	9	0.62326	D	0.03	-29.2413	12.9532	0.58413	0.0782:0.0:0.9218:0.0	.	746;779;686	B9EG82;Q5T7W0;Q5T7W0-2	.;ZN618_HUMAN;.	S	779;686	ENSP00000363241:G779S;ENSP00000288466:G686S	ENSP00000288466:G686S	G	+	1	0	ZNF618	115851738	1.000000	0.71417	0.999000	0.59377	0.948000	0.59901	7.515000	0.81761	1.348000	0.45733	0.561000	0.74099	GGC		0.627	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983		12	127	12	127
PRSS3P2	154754	broad.mit.edu;ucsc.edu	37	7	142481317	142481317	+	RNA	SNP	G	G	A	rs201986742		TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr7:142481317G>A	ENST00000603901.1	+	0	391					NR_001296.3		Q8NHM4	TRY6_HUMAN	protease, serine, 3 pseudogene 2						endothelial cell migration (GO:0043542)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)										TCTGCCCACTGCCCCTCCAGC	0.547																																																0													144.0	105.0	117.0					7																	142481317		689	1515	2204			154754					7q34	2012-03-06			ENSG00000250606	ENSG00000275896			43788	pseudogene	pseudogene	"""trypsinogen C"""						Standard	NR_001296		Approved	TRY6	uc011ksq.2	Q8NHM4	OTTHUMG00000158904		7.37:g.142481317G>A				RNA	SNP	ENST00000603901.1	37																																																																																					0.547	PRSS3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470000.1	NR_001296		7	36	7	36
SMARCB1	6598	broad.mit.edu;ucsc.edu	37	22	24176338	24176338	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr22:24176338C>T	ENST00000263121.7	+	9	1325	c.1129C>T	c.(1129-1131)Cgt>Tgt	p.R377C	SMARCB1_ENST00000407422.3_Missense_Mutation_p.R368C|SMARCB1_ENST00000407082.3_Missense_Mutation_p.R331C|SMARCB1_ENST00000344921.6_Missense_Mutation_p.R386C|DERL3_ENST00000464023.1_5'Flank	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	377			R -> H (in MRD15). {ECO:0000269|PubMed:22426308}.		ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				GCGGATGAGGCGTCTTGCCAA	0.647			"""D, N, F, S"""		malignant rhabdoid	malignant rhabdoid																																yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"""		M	3	Unknown(2)|Deletion - In frame(1)	central_nervous_system(3)											35.0	27.0	30.0					22																	24176338		2194	4298	6492	SO:0001583	missense	6598			U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"""sucrose nonfermenting, yeast, homolog-like 1"", ""integrase interactor 1"", ""malignant rhabdoid tumor suppressor"", ""protein phosphatase 1, regulatory subunit 144"""	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.1129C>T	22.37:g.24176338C>T	ENSP00000263121:p.Arg377Cys		O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Missense_Mutation	SNP	ENST00000263121.7	37	CCDS13817.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.021178	0.54576	.	.	ENSG00000099956	ENST00000344921;ENST00000263121;ENST00000407422;ENST00000407082	D;D;D;D	0.97731	-4.43;-4.51;-4.46;-4.3	5.07	4.05	0.47172	.	0.000000	0.85682	D	0.000000	D	0.98223	0.9412	M	0.75777	2.31	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;P;P	0.66084	0.941;0.751;0.875	D	0.98789	1.0735	10	0.87932	D	0	-2.1511	12.9974	0.58654	0.0:0.9214:0.0:0.0786	.	386;368;377	G5E975;Q17S11;Q12824	.;.;SNF5_HUMAN	C	386;377;368;331	ENSP00000340883:R386C;ENSP00000263121:R377C;ENSP00000383984:R368C;ENSP00000385226:R331C	ENSP00000263121:R377C	R	+	1	0	SMARCB1	22506338	1.000000	0.71417	1.000000	0.80357	0.125000	0.20455	5.759000	0.68785	1.293000	0.44690	-0.284000	0.09977	CGT		0.647	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		3	9	3	9
PRSS3P2	154754	broad.mit.edu;ucsc.edu	37	7	142481316	142481316	+	RNA	SNP	T	T	C	rs201020184		TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr7:142481316T>C	ENST00000603901.1	+	0	390					NR_001296.3		Q8NHM4	TRY6_HUMAN	protease, serine, 3 pseudogene 2						endothelial cell migration (GO:0043542)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)										CTCTGCCCACTGCCCCTCCAG	0.547																																																0													146.0	106.0	119.0					7																	142481316		689	1515	2204			154754					7q34	2012-03-06			ENSG00000250606	ENSG00000275896			43788	pseudogene	pseudogene	"""trypsinogen C"""						Standard	NR_001296		Approved	TRY6	uc011ksq.2	Q8NHM4	OTTHUMG00000158904		7.37:g.142481316T>C				RNA	SNP	ENST00000603901.1	37																																																																																					0.547	PRSS3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470000.1	NR_001296		7	36	7	36
UBA7	7318	broad.mit.edu;ucsc.edu	37	3	49848836	49848836	+	Missense_Mutation	SNP	C	C	T	rs12486358	byFrequency	TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr3:49848836C>T	ENST00000333486.3	-	9	1150	c.992G>A	c.(991-993)cGg>cAg	p.R331Q	UBA7_ENST00000494212.1_5'Flank	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	331	2 approximate repeats.				cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		ttccTCTGTCCGCTTCAGTGG	0.602																																																0													108.0	82.0	91.0					3																	49848836		2203	4300	6503	SO:0001583	missense	7318			BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"""Ubiquitin-like modifier activating enzymes"""	12471	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)"", ""UBA7, ubiquitin-activating enzyme E1"""	191325	"""ubiquitin-activating enzyme E1-like"""	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267	ENST00000333486.3:c.992G>A	3.37:g.49848836C>T	ENSP00000333266:p.Arg331Gln		Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	37	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	C	4.743	0.138237	0.09083	.	.	ENSG00000182179	ENST00000333486	T	0.28895	1.59	5.36	2.62	0.31277	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.827450	0.11496	N	0.558212	T	0.12518	0.0304	N	0.04787	-0.16	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.36138	-0.9760	10	0.11794	T	0.64	-6.9979	5.4915	0.16779	0.0:0.6626:0.1635:0.1739	rs12486358;rs52827209;rs12486358	331	P41226	UBA7_HUMAN	Q	331	ENSP00000333266:R331Q	ENSP00000333266:R331Q	R	-	2	0	UBA7	49823840	0.063000	0.20901	0.010000	0.14722	0.373000	0.29922	1.338000	0.33873	0.405000	0.25532	-0.215000	0.12644	CGG		0.602	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		4	34	4	34
CIC	23152	broad.mit.edu;ucsc.edu	37	19	42796331	42796331	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr19:42796331C>T	ENST00000575354.2	+	12	3020	c.2980C>T	c.(2980-2982)Cag>Tag	p.Q994*	CIC_ENST00000572681.2_Nonsense_Mutation_p.Q1903*|CIC_ENST00000160740.3_Nonsense_Mutation_p.Q994*	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	994	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.Q994*(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CTCTCAGCCTCAGAAGGTCCT	0.662			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	1	Substitution - Nonsense(1)	central_nervous_system(1)											49.0	57.0	54.0					19																	42796331		2203	4299	6502	SO:0001587	stop_gained	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.2980C>T	19.37:g.42796331C>T	ENSP00000458663:p.Gln994*		Q7LGI1|Q9UEG5|Q9Y6T1	Nonsense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.293305	0.60086	.	.	ENSG00000079432	ENST00000160740	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-14.9252	16.1439	0.81551	0.0:1.0:0.0:0.0	.	.	.	.	X	994	.	ENSP00000160740:Q994X	Q	+	1	0	CIC	47488171	0.999000	0.42202	1.000000	0.80357	0.360000	0.29518	5.065000	0.64344	2.686000	0.91538	0.561000	0.74099	CAG		0.662	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			24	38	24	38
FLG	2312	broad.mit.edu;ucsc.edu	37	1	152286155	152286155	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr1:152286155C>T	ENST00000368799.1	-	3	1242	c.1207G>A	c.(1207-1209)Ggg>Agg	p.G403R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	403	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAAGCTTGCCCGCGCCCAGTG	0.562									Ichthyosis																																							0													240.0	244.0	243.0					1																	152286155		2203	4300	6503	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1207G>A	1.37:g.152286155C>T	ENSP00000357789:p.Gly403Arg		Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	11.65	1.702544	0.30232	.	.	ENSG00000143631	ENST00000368799	T	0.04015	3.73	4.17	0.0271	0.14153	.	.	.	.	.	T	0.03915	0.0110	L	0.41824	1.3	0.09310	N	1	D	0.69078	0.997	D	0.73708	0.981	T	0.35025	-0.9805	9	0.46703	T	0.11	.	3.9384	0.09316	0.0:0.5099:0.1784:0.3117	.	403	P20930	FILA_HUMAN	R	403	ENSP00000357789:G403R	ENSP00000357789:G403R	G	-	1	0	FLG	150552779	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.689000	0.05144	-0.081000	0.12662	0.499000	0.49734	GGG		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		117	511	117	511
SYCP2L	221711	broad.mit.edu;hgsc.bcm.edu	37	6	10955433	10955436	+	Frame_Shift_Del	DEL	AAGA	AAGA	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr6:10955433_10955436delAAGA	ENST00000283141.6	+	24	2335_2338	c.2039_2042delAAGA	c.(2038-2043)gaagaafs	p.EE680fs		NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	680						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			TCAATAACAGAAGAAAGAGAGTTG	0.451											OREG0017189	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0																																										SO:0001589	frameshift_variant	221711			AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 177"""	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.2039_2042delAAGA	6.37:g.10955437_10955440delAAGA	ENSP00000283141:p.Glu680fs	668	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Frame_Shift_Del	DEL	ENST00000283141.6	37	CCDS43423.1																																																																																				0.451	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		27	100	27	100
PRPF18	8559	broad.mit.edu;hgsc.bcm.edu	37	10	13655742	13655744	+	Splice_Site	DEL	TTC	TTC	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr10:13655742_13655744delTTC	ENST00000378572.3	+	7	741_743	c.581_583delTTC	c.(580-585)tttctt>ttt	p.L196del		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	196					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)			central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						TTTCAACAGTTTCTTCTTGGCGT	0.429																																																0																																										SO:0001630	splice_region_variant	8559			U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"""PRP18 pre-mRNA processing factor 18 homolog (yeast)"", ""PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"""			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.580-1TTC>-	10.37:g.13655745_13655747delTTC			Q5T9P9|Q9BUI9	In_Frame_Del	DEL	ENST00000378572.3	37	CCDS7100.1																																																																																				0.429	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1		In_Frame_Del	16	71	16	71
NCAM1	4684	broad.mit.edu;hgsc.bcm.edu	37	11	113126648	113126649	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr11:113126648_113126649delCT	ENST00000533760.1	+	15	2093_2094	c.1494_1495delCT	c.(1492-1497)aactctfs	p.S499fs	NCAM1_ENST00000316851.7_Frame_Shift_Del_p.S617fs|NCAM1_ENST00000397957.4_3'UTR	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	627	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		AGGATGGAAACTCTATTAAAGT	0.5																																																0																																										SO:0001589	frameshift_variant	4684				CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.1494_1495delCT	11.37:g.113126650_113126651delCT	ENSP00000473281:p.Ser499fs		A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	37																																																																																					0.500	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		12	17	12	17
ZMYM2	7750	broad.mit.edu;hgsc.bcm.edu	37	13	20577051	20577052	+	Frame_Shift_Del	DEL	TT	TT	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr13:20577051_20577052delTT	ENST00000382874.2	+	5	1099_1100	c.909_910delTT	c.(907-912)tctttafs	p.L304fs	ZMYM2_ENST00000382881.3_Frame_Shift_Del_p.L217fs|ZMYM2_ENST00000382869.3_Frame_Shift_Del_p.L304fs|ZMYM2_ENST00000382871.2_Frame_Shift_Del_p.L304fs|ZMYM2_ENST00000382883.3_5'Flank	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	304				L -> V (in Ref. 4; CAB66556). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		GGGTGGACTCTTTATCACCAGT	0.421																																																0																																										SO:0001589	frameshift_variant	7750			AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"""Zinc fingers, MYM type"""	12989	protein-coding gene	gene with protein product		602221	"""zinc finger protein 198"""	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.909_910delTT	13.37:g.20577051_20577052delTT	ENSP00000372327:p.Leu304fs		A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Frame_Shift_Del	DEL	ENST00000382874.2	37	CCDS45016.1																																																																																				0.421	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		100	108	100	108
TCF12	6938	broad.mit.edu;hgsc.bcm.edu	37	15	57526268	57526269	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr15:57526268_57526269delCA	ENST00000267811.5	+	12	1302_1303	c.998_999delCA	c.(997-999)tcafs	p.S333fs	TCF12_ENST00000333725.5_Frame_Shift_Del_p.S333fs|TCF12_ENST00000438423.2_Frame_Shift_Del_p.S333fs|TCF12_ENST00000452095.2_Frame_Shift_Del_p.S329fs|TCF12_ENST00000537840.1_Frame_Shift_Del_p.S97fs|TCF12_ENST00000543579.1_Frame_Shift_Del_p.S163fs|TCF12_ENST00000560764.1_3'UTR|TCF12_ENST00000343827.3_Frame_Shift_Del_p.S163fs|TCF12_ENST00000557843.1_Frame_Shift_Del_p.S333fs	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	333					immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		GCTGGAAGCTCACAGACAGGTG	0.356			T	TEC	extraskeletal myxoid chondrosarcoma																																		Dom	yes		15	15q21	6938	"""transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"""		M	0																																										SO:0001589	frameshift_variant	6938			BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"""Basic helix-loop-helix proteins"""	11623	protein-coding gene	gene with protein product	"""helix-loop-helix transcription factor 4"""	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.998_999delCA	15.37:g.57526270_57526271delCA	ENSP00000267811:p.Ser333fs		Q7Z3D9|Q86TC1|Q86VM2	Frame_Shift_Del	DEL	ENST00000267811.5	37	CCDS10159.1																																																																																				0.356	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		15	59	15	59
TCF12	6938	broad.mit.edu;hgsc.bcm.edu	37	15	57565414	57565416	+	In_Frame_Del	DEL	TCA	TCA	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr15:57565414_57565416delTCA	ENST00000267811.5	+	18	2164_2166	c.1860_1862delTCA	c.(1858-1863)cttcat>ctt	p.H621del	TCF12_ENST00000333725.5_In_Frame_Del_p.H645del|TCF12_ENST00000559703.1_In_Frame_Del_p.H278del|TCF12_ENST00000438423.2_In_Frame_Del_p.H645del|TCF12_ENST00000452095.2_In_Frame_Del_p.H641del|TCF12_ENST00000537840.1_In_Frame_Del_p.H385del|TCF12_ENST00000543579.1_In_Frame_Del_p.H475del|TCF12_ENST00000559710.1_In_Frame_Del_p.H255del|TCF12_ENST00000343827.3_In_Frame_Del_p.H451del|TCF12_ENST00000557843.1_In_Frame_Del_p.H621del	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	621	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		TCCTTATTCTTCATCAAGCCGTG	0.448			T	TEC	extraskeletal myxoid chondrosarcoma																																		Dom	yes		15	15q21	6938	"""transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"""		M	0																																										SO:0001651	inframe_deletion	6938			BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"""Basic helix-loop-helix proteins"""	11623	protein-coding gene	gene with protein product	"""helix-loop-helix transcription factor 4"""	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.1860_1862delTCA	15.37:g.57565417_57565419delTCA	ENSP00000267811:p.His621del		Q7Z3D9|Q86TC1|Q86VM2	In_Frame_Del	DEL	ENST00000267811.5	37	CCDS10159.1																																																																																				0.448	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		39	20	39	20
ZNF689	115509	broad.mit.edu;hgsc.bcm.edu	37	16	30616099	30616101	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr16:30616099_30616101delGAG	ENST00000287461.3	-	3	1324_1326	c.987_989delCTC	c.(985-990)tcctct>tct	p.329_330SS>S	ZNF689_ENST00000566673.1_5'UTR|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	329					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			GACCAGGCGAGAGGAGGAGGAGA	0.7																																																0																																										SO:0001651	inframe_deletion	115509			BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"""Zinc fingers, C2H2-type"", ""-"""	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.987_989delCTC	16.37:g.30616108_30616110delGAG	ENSP00000287461:p.Ser330del		Q658J5	In_Frame_Del	DEL	ENST00000287461.3	37	CCDS10686.1																																																																																				0.700	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447		14	38	14	38
CEP89	84902	broad.mit.edu;hgsc.bcm.edu	37	19	33392289	33392292	+	Frame_Shift_Del	DEL	CTTT	CTTT	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr19:33392289_33392292delCTTT	ENST00000305768.5	-	15	1680_1683	c.1592_1595delAAAG	c.(1591-1596)gaaaggfs	p.ER531fs		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	531					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CATCTCAGCCCTTTCTTTCTCTTC	0.451																																																0																																										SO:0001589	frameshift_variant	84902			AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.1592_1595delAAAG	19.37:g.33392293_33392296delCTTT	ENSP00000306105:p.Glu531fs		B9EGA6|Q8N5J8	Frame_Shift_Del	DEL	ENST00000305768.5	37	CCDS32987.1																																																																																				0.451	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		27	66	27	66
CIC	23152	broad.mit.edu;hgsc.bcm.edu	37	19	42796905	42796906	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr19:42796905_42796906delTG	ENST00000575354.2	+	14	3403_3404	c.3363_3364delTG	c.(3361-3366)actgtgfs	p.V1122fs	CIC_ENST00000572681.2_Frame_Shift_Del_p.V2030fs|CIC_ENST00000160740.3_Frame_Shift_Del_p.V1121fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1122	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				TGGTCTACACTGTGGCCACCAG	0.668			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0																																										SO:0001589	frameshift_variant	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.3363_3364delTG	19.37:g.42796907_42796908delTG	ENSP00000458663:p.Val1122fs		Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																				0.668	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			19	79	19	79
NOTCH1	4851	broad.mit.edu	37	9	139412381	139412381	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr9:139412381G>A	ENST00000277541.6	-	8	1339	c.1264C>T	c.(1264-1266)Ccc>Tcc	p.P422S	MIR4673_ENST00000584777.1_RNA	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	422	EGF-like 11; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P422S(2)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TGCTCGCAGGGGTTGGCACCT	0.667			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																													Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	2	Substitution - Missense(2)	upper_aerodigestive_tract(2)											31.0	35.0	34.0					9																	139412381		2190	4285	6475	SO:0001583	missense	4851			AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.1264C>T	9.37:g.139412381G>A	ENSP00000277541:p.Pro422Ser		Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516376	0.85495	.	.	ENSG00000148400	ENST00000277541	D	0.96041	-3.89	4.69	4.69	0.59074	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.97337	0.9129	M	0.83852	2.665	0.80722	D	1	P	0.50710	0.938	P	0.59643	0.861	D	0.97827	1.0260	10	0.56958	D	0.05	.	16.5828	0.84718	0.0:0.0:1.0:0.0	.	422	P46531	NOTC1_HUMAN	S	422	ENSP00000277541:P422S	ENSP00000277541:P422S	P	-	1	0	NOTCH1	138532202	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.635000	0.98437	2.161000	0.67846	0.462000	0.41574	CCC		0.667	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		5	67	5	67
