#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_classification	i_context	i_dataset	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_type
BPI	671	hgsc.bcm.edu	37	20	36936066	36936066	+	Silent	SNP	G	G	A			TCGA-36-1571-01	TCGA-36-1571-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr20:36936066G>A	ENST00000262865.4	+	2	329	c.240G>A	c.(238-240)ggG>ggA	p.G80G	CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	80					defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)	p.G80G(1)		kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				TTGGGAAGGGGCATTATAGCT	0.517																																																1	Substitution - coding silent(1)	ovary(1)	20											107.0	101.0	103.0					20																	36936066		2203	4300	6503	36369480	SO:0001819	synonymous_variant	671			J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"""BPI fold containing"""	1095	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 1"""	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.240G>A	20.37:g.36936066G>A		Somatic		Capture	SOLID	Phase_III	36369480	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Silent	SNP	ENST00000262865.4	37	CCDS13303.1	SNP	42	Baylor																																																																																				0.517	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725		Silent
CLCN7	1186	hgsc.bcm.edu	37	16	1515271	1515271	+	Silent	SNP	G	G	A			TCGA-36-1571-01	TCGA-36-1571-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr16:1515271G>A	ENST00000382745.4	-	2	815	c.210C>T	c.(208-210)gaC>gaT	p.D70D	CLCN7_ENST00000448525.1_Intron|CLCN7_ENST00000566812.1_5'Flank|CLCN7_ENST00000262318.8_Intron|LA16c-390E6.3_ENST00000563223.1_RNA	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	70					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.D70D(1)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				AACTCACCGGGTCCAAAAGTT	0.582																																																1	Substitution - coding silent(1)	ovary(1)	16											118.0	80.0	93.0					16																	1515271		2199	4300	6499	1455272	SO:0001819	synonymous_variant	1186			Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.210C>T	16.37:g.1515271G>A		Somatic		Capture	SOLID	Phase_III	1455272	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1	SNP	44	Baylor																																																																																				0.582	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		Silent
SLX4	84464	hgsc.bcm.edu	37	16	3652171	3652171	+	Nonsense_Mutation	SNP	G	G	A			TCGA-36-1571-01	TCGA-36-1571-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr16:3652171G>A	ENST00000294008.3	-	4	1538	c.898C>T	c.(898-900)Caa>Taa	p.Q300*		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	300	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						AGGTTCTTTTGACAAATCTGG	0.557								Direct reversal of damage																																								0			16											137.0	117.0	124.0					16																	3652171		2197	4300	6497	3592172	SO:0001587	stop_gained	84464			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.898C>T	16.37:g.3652171G>A	ENSP00000294008:p.Gln300*	Somatic		Capture	SOLID	Phase_III	3592172	Q69YT8|Q8TF15|Q96JP1	Nonsense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	SNP	45	Baylor	.	.	.	.	.	.	.	.	.	.	G	44	11.260293	0.99538	.	.	ENSG00000188827	ENST00000294008	.	.	.	5.83	5.83	0.93111	.	0.317230	0.34603	N	0.003832	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	18.6822	0.91549	0.0:0.0:1.0:0.0	.	.	.	.	X	300	.	ENSP00000294008:Q300X	Q	-	1	0	SLX4	3592172	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.674000	0.83992	2.769000	0.95229	0.655000	0.94253	CAA		0.557	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		Nonsense_Mutation
CYTH2	9266	hgsc.bcm.edu	37	19	48977465	48977465	+	Missense_Mutation	SNP	G	G	A	rs141113238		TCGA-36-1571-01	TCGA-36-1571-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr19:48977465G>A	ENST00000452733.2	+	7	1050	c.574G>A	c.(574-576)Gtc>Atc	p.V192I	CYTH2_ENST00000427476.1_Missense_Mutation_p.V192I			Q99418	CYH2_HUMAN	cytohesin 2	192	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|inositol 1,4,5 trisphosphate binding (GO:0070679)|lipid binding (GO:0008289)	p.V192I(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						GTCCTTCGCCGTCATCATGCT	0.632																																																1	Substitution - Missense(1)	ovary(1)	19						G	ILE/VAL,ILE/VAL	0,4406		0,0,2203	123.0	97.0	106.0		574,574	4.1	1.0	19	dbSNP_134	106	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CYTH2	NM_004228.6,NM_017457.5	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	192/400,192/401	48977465	1,13005	2203	4300	6503	53669277	SO:0001583	missense	9266			X99753	CCDS12722.1	19q13.32	2014-05-02	2008-08-14	2008-08-14	ENSG00000105443	ENSG00000105443		"""Pleckstrin homology (PH) domain containing"""	9502	protein-coding gene	gene with protein product		602488	"""pleckstrin homology, Sec7 and coiled/coil domains 2 (cytohesin-2)"", ""pleckstrin homology, Sec7 and coiled-coil domains 2"""	PSCD2L, PSCD2		8706128, 8945478, 20525696	Standard	NM_004228		Approved	CTS18.1, Sec7p-L, ARNO, Sec7p-like, cytohesin-2	uc002pjj.4	Q99418	OTTHUMG00000150245	ENST00000452733.2:c.574G>A	19.37:g.48977465G>A	ENSP00000408236:p.Val192Ile	Somatic		Capture	SOLID	Phase_III	53669277	A8K8P0|Q8IXY9|Q92958	Missense_Mutation	SNP	ENST00000452733.2	37	CCDS12722.1	SNP	40	Baylor	.	.	.	.	.	.	.	.	.	.	G	5.642	0.303105	0.10678	0.0	1.16E-4	ENSG00000105443	ENST00000452733;ENST00000427476;ENST00000325139	T;T;T	0.43688	0.94;0.94;0.94	4.06	4.06	0.47325	.	0.064561	0.64402	D	0.000010	T	0.16471	0.0396	N	0.02266	-0.62	0.44547	D	0.997506	B	0.09022	0.002	B	0.06405	0.002	T	0.16364	-1.0405	10	0.02654	T	1	.	14.1425	0.65329	0.0:0.0:1.0:0.0	.	192	Q99418-2	.	I	192;192;214	ENSP00000408236:V192I;ENSP00000391648:V192I;ENSP00000314566:V214I	ENSP00000314566:V214I	V	+	1	0	CYTH2	53669277	1.000000	0.71417	0.969000	0.41365	0.840000	0.47671	3.470000	0.53100	2.268000	0.75426	0.561000	0.74099	GTC		0.632	CYTH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317060.1	NM_004228		Missense_Mutation
DNMT3B	1789	hgsc.bcm.edu	37	20	31383297	31383297	+	Missense_Mutation	SNP	C	C	G			TCGA-36-1571-01	TCGA-36-1571-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr20:31383297C>G	ENST00000328111.2	+	11	1530	c.1209C>G	c.(1207-1209)tgC>tgG	p.C403W	DNMT3B_ENST00000443239.3_Missense_Mutation_p.C341W|DNMT3B_ENST00000456297.2_Missense_Mutation_p.C307W|DNMT3B_ENST00000344505.4_Missense_Mutation_p.C383W|DNMT3B_ENST00000353855.2_Missense_Mutation_p.C383W|DNMT3B_ENST00000375623.4_Missense_Mutation_p.A293G|DNMT3B_ENST00000348286.2_Missense_Mutation_p.C383W|DNMT3B_ENST00000201963.3_Missense_Mutation_p.C395W	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	403					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)	p.C403W(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGACAAATTGCTATAACAACG	0.532																																																1	Substitution - Missense(1)	ovary(1)	20											110.0	126.0	121.0					20																	31383297		2203	4300	6503	30846958	SO:0001583	missense	1789				CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.1209C>G	20.37:g.31383297C>G	ENSP00000328547:p.Cys403Trp	Somatic		Capture	SOLID	Phase_III	30846958	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	37	CCDS13205.1	SNP	28	Baylor	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.71|16.71	3.197834|3.197834	0.58126|0.58126	.|.	.|.	ENSG00000088305|ENSG00000088305	ENST00000375623|ENST00000328111;ENST00000537219;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000201963	T|D;D;D;D;D;D;D	0.67865|0.96856	-0.29|-4.15;-4.15;-4.15;-4.15;-4.15;-4.15;-4.15	5.29|5.29	-3.11|-3.11	0.05299|0.05299	.|.	.|0.341423	.|0.35708	.|N	.|0.003029	D|D	0.94006|0.94006	0.8080|0.8080	L|L	0.40543|0.40543	1.245|1.245	0.25501|0.25501	N|N	0.987557|0.987557	.|P;P;P;P;P;P;P	.|0.47409	.|0.704;0.704;0.483;0.804;0.617;0.804;0.895	.|P;B;P;P;P;P;P	.|0.54460	.|0.497;0.353;0.447;0.753;0.482;0.753;0.502	D|D	0.88674|0.88674	0.3197|0.3197	7|10	0.62326|0.66056	D|D	0.03|0.02	-17.5743|-17.5743	6.6819|6.6819	0.23125|0.23125	0.0:0.3861:0.1245:0.4894|0.0:0.3861:0.1245:0.4894	.|.	.|307;341;102;395;383;383;403	.|E9PBF2;E7EN63;B3KM53;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.|.;.;.;.;.;.;DNM3B_HUMAN	G|W	293|403;469;383;383;341;307;383;395	ENSP00000364774:A293G|ENSP00000328547:C403W;ENSP00000313397:C383W;ENSP00000337764:C383W;ENSP00000403169:C341W;ENSP00000412305:C307W;ENSP00000345105:C383W;ENSP00000201963:C395W	ENSP00000364774:A293G|ENSP00000201963:C395W	A|C	+|+	2|3	0|2	DNMT3B|DNMT3B	30846958|30846958	0.002000|0.002000	0.14202|0.14202	0.837000|0.837000	0.33122|0.33122	0.655000|0.655000	0.38815|0.38815	-0.494000|-0.494000	0.06451|0.06451	-0.149000|-0.149000	0.11215|0.11215	0.650000|0.650000	0.86243|0.86243	GCT|TGC		0.532	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		Missense_Mutation
LRRK2	120892	hgsc.bcm.edu	37	12	40699634	40699634	+	Silent	SNP	C	C	G			TCGA-36-1571-01	TCGA-36-1571-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr12:40699634C>G	ENST00000298910.7	+	28	3883	c.3825C>G	c.(3823-3825)gtC>gtG	p.V1275V		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1275					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.V1275V(4)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CTCTGGATGTCAGTTACAACT	0.383																																																4	Substitution - coding silent(4)	ovary(2)|large_intestine(2)	12											90.0	88.0	89.0					12																	40699634		2203	4300	6503	38985901	SO:0001819	synonymous_variant	120892			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.3825C>G	12.37:g.40699634C>G		Somatic		Capture	SOLID	Phase_III	38985901	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1	SNP	29	Baylor																																																																																				0.383	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		Silent
MKRN3	7681	hgsc.bcm.edu	37	15	23811187	23811187	+	Silent	SNP	G	G	A			TCGA-36-1571-01	TCGA-36-1571-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr15:23811187G>A	ENST00000314520.3	+	1	734	c.258G>A	c.(256-258)ccG>ccA	p.P86P	MKRN3_ENST00000568252.1_Silent_p.P86P|RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000564592.1_Silent_p.P86P	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	86					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.P86P(2)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		GGCCCAGTCCGTTGCCAAGCC	0.627																																																2	Substitution - coding silent(2)	ovary(1)|large_intestine(1)	15											39.0	38.0	38.0					15																	23811187		2203	4300	6503	21362280	SO:0001819	synonymous_variant	7681			U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"""RING-type (C3HC4) zinc fingers"""	7114	protein-coding gene	gene with protein product	"""zinc finger protein 127"""	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.258G>A	15.37:g.23811187G>A		Somatic		Capture	SOLID	Phase_III	21362280		Silent	SNP	ENST00000314520.3	37	CCDS10013.1	SNP	40	Baylor																																																																																				0.627	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664		Silent
NXT2	55916	hgsc.bcm.edu	37	X	108784760	108784760	+	Silent	SNP	T	T	C			TCGA-36-1571-01	TCGA-36-1571-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chrX:108784760T>C	ENST00000372106.1	+	3	290	c.159T>C	c.(157-159)gtT>gtC	p.V53V	NXT2_ENST00000372103.1_Silent_p.V25V|NXT2_ENST00000218004.1_Silent_p.V108V|NXT2_ENST00000372107.1_Silent_p.V25V	NM_001242617.1	NP_001229546.1	Q9NPJ8	NXT2_HUMAN	nuclear transport factor 2-like export factor 2	53	NTF2. {ECO:0000255|PROSITE- ProRule:PRU00137}.				mRNA transport (GO:0051028)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	6						GAAATGCTGTTTCAGGGCTGG	0.378																																																0			X											114.0	94.0	101.0					X																	108784760		2203	4300	6503	108671416	SO:0001819	synonymous_variant	55916			AF246127	CCDS14546.1, CCDS56605.1, CCDS56606.1	Xq22.3	2008-02-05			ENSG00000101888	ENSG00000101888			18151	protein-coding gene	gene with protein product		300320				11073998	Standard	NM_018698		Approved	P15-2	uc004eoe.2	Q9NPJ8	OTTHUMG00000022185	ENST00000372106.1:c.159T>C	X.37:g.108784760T>C		Somatic		Capture	SOLID	Phase_III	108671416	D3DUY1|Q0VAN8|Q5JYV5|Q5JYV6|Q5JYV7|Q9H8U0|Q9NQ64|Q9NRL7|Q9Y3M4|Q9Y3M5	Silent	SNP	ENST00000372106.1	37	CCDS56605.1	SNP	64	Baylor																																																																																				0.378	NXT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057886.1	NM_018698		Silent
PYGO1	26108	hgsc.bcm.edu	37	15	55841125	55841125	+	Missense_Mutation	SNP	G	G	A	rs147959519		TCGA-36-1571-01	TCGA-36-1571-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr15:55841125G>A	ENST00000302000.6	-	2	212	c.118C>T	c.(118-120)Cgc>Tgc	p.R40C	PYGO1_ENST00000563719.1_Missense_Mutation_p.R40C	NM_015617.1	NP_056432.1	Q9Y3Y4	PYGO1_HUMAN	pygopus family PHD finger 1	40					hematopoietic progenitor cell differentiation (GO:0002244)|kidney development (GO:0001822)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|spermatid nucleus differentiation (GO:0007289)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R40C(1)		endometrium(4)|kidney(2)|large_intestine(6)|lung(6)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	27				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		TTTGCCTTGCGCTTTTTCTTA	0.373																																																1	Substitution - Missense(1)	ovary(1)	15						G	CYS/ARG	1,4385	2.1+/-5.4	0,1,2192	157.0	153.0	155.0		118	4.2	1.0	15	dbSNP_134	155	0,8584		0,0,4292	no	missense	PYGO1	NM_015617.1	180	0,1,6484	AA,AG,GG		0.0,0.0228,0.0077	probably-damaging	40/420	55841125	1,12969	2193	4292	6485	53628417	SO:0001583	missense	26108			AF457207	CCDS10155.1	15q21.1	2013-10-09	2013-10-09		ENSG00000171016	ENSG00000171016		"""Zinc fingers, PHD-type"""	30256	protein-coding gene	gene with protein product		606902	"""pygopus homolog 1 (Drosophila)"""			11988739	Standard	NM_015617		Approved		uc002adf.1	Q9Y3Y4	OTTHUMG00000132009	ENST00000302000.6:c.118C>T	15.37:g.55841125G>A	ENSP00000302327:p.Arg40Cys	Somatic		Capture	SOLID	Phase_III	53628417	A7Y2D6	Missense_Mutation	SNP	ENST00000302000.6	37	CCDS10155.1	SNP	38	Baylor	.	.	.	.	.	.	.	.	.	.	G	19.94	3.920050	0.73098	2.28E-4	0.0	ENSG00000171016	ENST00000302000;ENST00000401688	T	0.67698	-0.28	5.16	4.19	0.49359	.	0.229367	0.36234	N	0.002702	T	0.63873	0.2548	L	0.36672	1.1	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	P;P	0.50082	0.63;0.63	T	0.68383	-0.5423	10	0.72032	D	0.01	-7.5893	13.0829	0.59123	0.0:0.0:0.8409:0.1591	.	40;40	A7Y2D6;Q9Y3Y4	.;PYGO1_HUMAN	C	40	ENSP00000302327:R40C	ENSP00000302327:R40C	R	-	1	0	PYGO1	53628417	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.727000	0.61993	2.555000	0.86185	0.655000	0.94253	CGC		0.373	PYGO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254977.2	NM_015617		Missense_Mutation
SMARCB1	6598	hgsc.bcm.edu	37	22	24175888	24175888	+	Silent	SNP	G	G	A	rs117084604	byFrequency	TCGA-36-1571-01	TCGA-36-1571-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr22:24175888G>A	ENST00000263121.7	+	8	1312	c.1116G>A	c.(1114-1116)acG>acA	p.T372T	DERL3_ENST00000464023.1_5'Flank|SMARCB1_ENST00000407082.3_Silent_p.T326T|SMARCB1_ENST00000344921.6_Silent_p.T381T|SMARCB1_ENST00000407422.3_Silent_p.T363T	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	372					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.T372T(2)|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)				ACAGGAACACGAGGTACCCCT	0.627			"""D, N, F, S"""		malignant rhabdoid	malignant rhabdoid							G|||	5	0.000998403	0.0	0.0	5008	,	,		19506	0.005		0.0	False		,,,				2504	0.0					yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"""		M	5	Unknown(2)|Substitution - coding silent(2)|Deletion - In frame(1)	central_nervous_system(3)|ovary(1)|soft_tissue(1)	22						G	,	0,4406		0,0,2203	106.0	91.0	96.0		1089,1116	-5.1	1.0	22	dbSNP_132	96	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	SMARCB1	NM_001007468.1,NM_003073.3	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	363/377,372/386	24175888	2,13004	2203	4300	6503	22505888	SO:0001819	synonymous_variant	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.1116G>A	22.37:g.24175888G>A		Somatic		Capture	SOLID	Phase_III	22505888	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Silent	SNP	ENST00000263121.7	37	CCDS13817.1	SNP	37	Baylor																																																																																				0.627	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		Silent
STAC3	246329	hgsc.bcm.edu	37	12	57643044	57643044	+	Missense_Mutation	SNP	C	C	A			TCGA-36-1571-01	TCGA-36-1571-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr12:57643044C>A	ENST00000332782.2	-	3	315	c.114G>T	c.(112-114)aaG>aaT	p.K38N	STAC3_ENST00000554578.1_De_novo_Start_OutOfFrame|STAC3_ENST00000546246.2_Intron	NM_145064.1	NP_659501.1	Q96MF2	STAC3_HUMAN	SH3 and cysteine rich domain 3	38					intracellular signal transduction (GO:0035556)|neuromuscular synaptic transmission (GO:0007274)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)		identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.K38N(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(2)|skin(1)	18						GTTCCATCTCCTTTGTCCCTG	0.537																																																1	Substitution - Missense(1)	ovary(1)	12											67.0	64.0	65.0					12																	57643044		2203	4300	6503	55929311	SO:0001583	missense	246329			AK057013	CCDS8936.1, CCDS66405.1, CCDS66406.1	12q13.3	2014-08-12			ENSG00000185482	ENSG00000185482			28423	protein-coding gene	gene with protein product		615521				12477932	Standard	NM_001286257		Approved	MGC2793	uc009zpl.2	Q96MF2	OTTHUMG00000171271	ENST00000332782.2:c.114G>T	12.37:g.57643044C>A	ENSP00000329200:p.Lys38Asn	Somatic		Capture	SOLID	Phase_III	55929311	B4DUK9|Q96HU5	Missense_Mutation	SNP	ENST00000332782.2	37	CCDS8936.1	SNP	24	Baylor	.	.	.	.	.	.	.	.	.	.	C	10.59	1.392486	0.25118	.	.	ENSG00000185482	ENST00000332782;ENST00000553489	D;D	0.95035	-1.61;-3.59	5.58	-0.585	0.11698	.	0.275866	0.26418	N	0.024496	D	0.83059	0.5172	N	0.14661	0.345	0.80722	D	1	B	0.14438	0.01	B	0.12156	0.007	T	0.64668	-0.6353	10	0.16420	T	0.52	-0.9746	2.6156	0.04902	0.1172:0.5008:0.1138:0.2682	.	38	Q96MF2	STAC3_HUMAN	N	38	ENSP00000329200:K38N;ENSP00000452299:K38N	ENSP00000329200:K38N	K	-	3	2	STAC3	55929311	0.997000	0.39634	0.935000	0.37517	0.167000	0.22549	0.380000	0.20602	-0.305000	0.08831	-0.137000	0.14449	AAG		0.537	STAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412724.2	NM_145064		Missense_Mutation
TMEM182	130827	hgsc.bcm.edu	37	2	103414359	103414359	+	Silent	SNP	G	G	A	rs373489178		TCGA-36-1571-01	TCGA-36-1571-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr2:103414359G>A	ENST00000412401.2	+	4	574	c.369G>A	c.(367-369)ggG>ggA	p.G123G	TMEM182_ENST00000486293.1_3'UTR|TMEM182_ENST00000409173.1_Silent_p.G80G|TMEM182_ENST00000409528.1_Silent_p.G27G	NM_144632.3	NP_653233.3	Q6ZP80	TM182_HUMAN	transmembrane protein 182	123						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)	11						TGCTCCTGGGGGTAGTTGCTG	0.488																																																0			2											117.0	118.0	118.0					2																	103414359		2203	4300	6503	102780791	SO:0001819	synonymous_variant	130827			AK054856	CCDS2064.1	2q12.1	2009-08-25			ENSG00000170417	ENSG00000170417			26391	protein-coding gene	gene with protein product						12477932	Standard	NM_144632		Approved	FLJ30294	uc010fjb.3	Q6ZP80	OTTHUMG00000130779	ENST00000412401.2:c.369G>A	2.37:g.103414359G>A		Somatic		Capture	SOLID	Phase_III	102780791	C9JML7|Q3B7B8|Q53TT9|Q6GMU0|Q8WW45|Q96NR4	Silent	SNP	ENST00000412401.2	37	CCDS2064.1	SNP	43	Baylor																																																																																				0.488	TMEM182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253293.1	NM_144632		Silent
TP53	7157	hgsc.bcm.edu	37	17	7574018	7574018	+	Missense_Mutation	SNP	G	G	A	rs587782529		TCGA-36-1571-01	TCGA-36-1571-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr17:7574018G>A	ENST00000269305.4	-	10	1198	c.1009C>T	c.(1009-1011)Cgc>Tgc	p.R337C	TP53_ENST00000455263.2_3'UTR|TP53_ENST00000359597.4_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.R337C|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_3'UTR	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	337	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:9452042}.|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:11481490}.|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R337C(18)|p.0?(8)|p.R337fs*8(2)|p.R337G(1)|p.?(1)|p.I332fs*5(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATCTCGAAGCGCTCACGCCCA	0.522		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	31	Substitution - Missense(19)|Whole gene deletion(8)|Deletion - Frameshift(3)|Unknown(1)	central_nervous_system(6)|large_intestine(5)|ovary(4)|bone(4)|breast(3)|haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|stomach(1)|liver(1)|peritoneum(1)|lung(1)|kidney(1)	17	GRCh37	CM981929	TP53	M							56.0	44.0	48.0					17																	7574018		2203	4300	6503	7514743	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.1009C>T	17.37:g.7574018G>A	ENSP00000269305:p.Arg337Cys	Somatic		Capture	SOLID	Phase_III	7514743	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	SNP	38	Baylor	.	.	.	.	.	.	.	.	.	.	G	9.719	1.159246	0.21454	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	D;D	0.95205	-3.64;-3.64	5.43	3.38	0.38709	p53, tetramerisation domain (3);	0.000000	0.85682	D	0.000000	D	0.94321	0.8175	M	0.82323	2.585	0.48341	D	0.999635	P	0.39940	0.696	B	0.40940	0.344	D	0.93083	0.6493	10	0.87932	D	0	-7.3279	12.447	0.55657	0.0:0.0:0.6947:0.3053	.	337	P04637	P53_HUMAN	C	337;337;326	ENSP00000269305:R337C;ENSP00000391478:R337C	ENSP00000269305:R337C	R	-	1	0	TP53	7514743	0.558000	0.26554	0.006000	0.13384	0.274000	0.26718	1.012000	0.29924	0.615000	0.30124	0.561000	0.74099	CGC		0.522	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		Missense_Mutation
TRAF5	7188	hgsc.bcm.edu	37	1	211533308	211533308	+	Missense_Mutation	SNP	C	C	G			TCGA-36-1571-01	TCGA-36-1571-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr1:211533308C>G	ENST00000261464.5	+	5	487	c.433C>G	c.(433-435)Cgg>Ggg	p.R145G	TRAF5_ENST00000462410.1_3'UTR|TRAF5_ENST00000427925.2_Intron|TRAF5_ENST00000367004.3_Missense_Mutation_p.R145G|TRAF5_ENST00000336184.2_Missense_Mutation_p.R145G	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	145					apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R145G(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		TGAGAAGTGCCGGGAGCCAGT	0.478																																																1	Substitution - Missense(1)	ovary(1)	1											130.0	123.0	126.0					1																	211533308		2203	4300	6503	209599931	SO:0001583	missense	7188			AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"""RING-type (C3HC4) zinc fingers"""	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	ENST00000261464.5:c.433C>G	1.37:g.211533308C>G	ENSP00000261464:p.Arg145Gly	Somatic		Capture	SOLID	Phase_III	209599931	B4DIS9|B4E0A2|Q6FHY1	Missense_Mutation	SNP	ENST00000261464.5	37	CCDS1497.1	SNP	23	Baylor	.	.	.	.	.	.	.	.	.	.	C	3.891	-0.023899	0.07634	.	.	ENSG00000082512	ENST00000336184;ENST00000261464;ENST00000367004	T;T;T	0.22134	1.97;1.97;1.97	4.97	2.02	0.26589	Zinc finger, TRAF-type (1);TRAF-like (1);Seven In Absentia Homolog-type (1);	2.490430	0.01085	N	0.005073	T	0.09555	0.0235	N	0.01522	-0.82	0.21527	N	0.99965	B;B	0.22683	0.044;0.073	B;B	0.28232	0.087;0.08	T	0.30822	-0.9965	10	0.17832	T	0.49	-19.8123	6.432	0.21803	0.0:0.5934:0.1269:0.2796	.	156;145	B4E0A2;O00463	.;TRAF5_HUMAN	G	145	ENSP00000336825:R145G;ENSP00000261464:R145G;ENSP00000355971:R145G	ENSP00000261464:R145G	R	+	1	2	TRAF5	209599931	0.040000	0.19996	0.012000	0.15200	0.044000	0.14063	0.443000	0.21644	0.135000	0.18707	-0.218000	0.12543	CGG		0.478	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619		Missense_Mutation
UBQLN3	50613	hgsc.bcm.edu	37	11	5528898	5528898	+	Missense_Mutation	SNP	G	G	C			TCGA-36-1571-01	TCGA-36-1571-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chr11:5528898G>C	ENST00000311659.4	-	2	2038	c.1891C>G	c.(1891-1893)Cgt>Ggt	p.R631G	HBG2_ENST00000380252.1_5'Flank|HBE1_ENST00000380237.1_5'Flank|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	631	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.							p.R631G(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGGCTTCACGATTCAGAAAG	0.522																																					Ovarian(72;684 1260 12332 41642 52180)											1	Substitution - Missense(1)	ovary(1)	11											77.0	79.0	79.0					11																	5528898		2201	4297	6498	5485474	SO:0001583	missense	50613			AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"""Ubiquilin family"""	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.1891C>G	11.37:g.5528898G>C	ENSP00000347997:p.Arg631Gly	Somatic		Capture	SOLID	Phase_III	5485474	Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	37	CCDS7758.1	SNP	37	Baylor	.	.	.	.	.	.	.	.	.	.	G	12.03	1.814352	0.32053	.	.	ENSG00000175520	ENST00000311659	T	0.21932	1.98	5.14	3.22	0.36961	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.596206	0.15026	N	0.284721	T	0.28300	0.0699	M	0.84846	2.72	0.27814	N	0.942043	B	0.28971	0.229	B	0.29942	0.109	T	0.18650	-1.0330	10	0.46703	T	0.11	0.1964	7.9766	0.30159	0.0844:0.0:0.7557:0.1599	.	631	Q9H347	UBQL3_HUMAN	G	631	ENSP00000347997:R631G	ENSP00000347997:R631G	R	-	1	0	UBQLN3	5485474	1.000000	0.71417	0.694000	0.30210	0.964000	0.63967	3.460000	0.53028	0.826000	0.34661	0.655000	0.94253	CGT		0.522	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		Missense_Mutation
USP11	8237	hgsc.bcm.edu	37	X	47098492	47098492	+	Missense_Mutation	SNP	A	A	G			TCGA-36-1571-01	TCGA-36-1571-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	Unknown	.	.	Illumina GAIIx	TCGA-36-1571-01	TCGA-36-1571-10	g.chrX:47098492A>G	ENST00000218348.3	+	2	329	c.329A>G	c.(328-330)tAt>tGt	p.Y110C	USP11_ENST00000377107.2_Missense_Mutation_p.Y67C	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	110	DUSP. {ECO:0000255|PROSITE- ProRule:PRU00613}.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)	p.Y110C(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						AAGCACTGGTATAAGCAGTGG	0.542																																																1	Substitution - Missense(1)	ovary(1)	X											71.0	49.0	56.0					X																	47098492		2203	4300	6503	46983436	SO:0001583	missense	8237			U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"""Ubiquitin-specific peptidases"""	12609	protein-coding gene	gene with protein product		300050	"""ubiquitin specific protease 11"""			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.329A>G	X.37:g.47098492A>G	ENSP00000218348:p.Tyr110Cys	Somatic		Capture	SOLID	Phase_III	46983436	B2RTX1|Q8IUG6|Q9BWE1	Missense_Mutation	SNP	ENST00000218348.3	37	CCDS14277.1	SNP	16	Baylor	.	.	.	.	.	.	.	.	.	.	A	17.69	3.450940	0.63290	.	.	ENSG00000102226	ENST00000377107;ENST00000218348	T;T	0.23950	1.88;1.88	5.95	5.95	0.96441	Peptidase C19, ubiquitin-specific peptidase, DUSP domain (3);	0.076031	0.53938	D	0.000046	T	0.49762	0.1576	M	0.79258	2.445	0.47308	D	0.999385	D	0.89917	1.0	D	0.79784	0.993	T	0.54807	-0.8238	10	0.87932	D	0	-18.2344	9.6192	0.39710	0.8419:0.0:0.0:0.1581	.	110	P51784	UBP11_HUMAN	C	67;110	ENSP00000366311:Y67C;ENSP00000218348:Y110C	ENSP00000218348:Y110C	Y	+	2	0	USP11	46983436	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.567000	0.36407	1.999000	0.58509	0.486000	0.48141	TAT		0.542	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651		Missense_Mutation
