#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
NCDN	23154	broad.mit.edu	37	1	36026232	36026232	+	Silent	SNP	G	G	T	rs139104373		TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr1:36026232G>T	ENST00000373243.2	+	3	863	c.480G>T	c.(478-480)acG>acT	p.T160T	NCDN_ENST00000459931.1_3'UTR|NCDN_ENST00000373253.3_Silent_p.T143T|NCDN_ENST00000356090.4_Silent_p.T160T	NM_014284.2	NP_055099.1	Q9UBB6	NCDN_HUMAN	neurochondrin	160					bone resorption (GO:0045453)|neuron projection development (GO:0031175)|regulation of neuronal synaptic plasticity (GO:0048168)	cytosol (GO:0005829)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AGTGCCTGACGGCTGTAGCAG	0.617																																						ENST00000373243.2																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16						c.(478-480)acG>acT		neurochondrin							73.0	75.0	74.0					1																	36026232		2203	4300	6503	SO:0001819	synonymous_variant	23154				neuron projection development	cytosol|dendrite|neuronal cell body		g.chr1:36026232G>T	AB011179	CCDS392.1, CCDS30672.1	1p34.3	2008-02-05			ENSG00000020129	ENSG00000020129			17597	protein-coding gene	gene with protein product		608458				15007648	Standard	NM_014284		Approved	NCDN-1, NCDN-2	uc001bza.3	Q9UBB6	OTTHUMG00000059204	ENST00000373243.2:c.480G>T	1.37:g.36026232G>T			Somatic				NCDN_ENST00000459931.1_3'UTR|NCDN_ENST00000356090.4_Silent_p.T160T|NCDN_ENST00000373253.3_Silent_p.T143T	p.T160T	NM_014284.2	NP_055099.1	WXS	Illumina GAIIx	Phase_I	Q9UBB6	NCDN_HUMAN			3	863	+		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)	160					D3DPR9|Q9UBY2|Q9Y4A6|Q9Y4D9	Silent	SNP	ENST00000373243.2	37	c.480G>T	CCDS392.1																																																																																				0.617	NCDN-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131298.1	NM_014284		4	78	4	78	---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103400616	103400616	+	Splice_Site	SNP	A	A	T			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr1:103400616A>T	ENST00000370096.3	-	45	3804	c.3492T>A	c.(3490-3492)gcT>gcA	p.A1164A	COL11A1_ENST00000353414.4_Splice_Site_p.A1125A|COL11A1_ENST00000512756.1_Splice_Site_p.A1048A|COL11A1_ENST00000358392.2_Splice_Site_p.A1176A	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1164	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GAATACTCACAGCAATTCCAG	0.428																																						ENST00000358392.2																			0				NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258						c.(3526-3528)gcT>gcA		collagen, type XI, alpha 1							38.0	40.0	39.0					1																	103400616		2203	4300	6503	SO:0001630	splice_region_variant	1301				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging	g.chr1:103400616A>T	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3492+1T>A	1.37:g.103400616A>T			Somatic				COL11A1_ENST00000353414.4_Splice_Site_p.A1125A|COL11A1_ENST00000370096.3_Splice_Site_p.A1164A|COL11A1_ENST00000512756.1_Splice_Site_p.A1048A	p.A1176A	NM_080629.2	NP_542196.2	WXS	Illumina GAIIx	Phase_I	P12107	COBA1_HUMAN		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)	45	3845	-		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)	1164			Triple-helical region.		B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Splice_Site	SNP	ENST00000370096.3	37	c.3528T>A	CCDS778.1																																																																																				0.428	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	Silent	3	31	3	31	---	---	---	---
LYST	1130	broad.mit.edu	37	1	235973754	235973754	+	Missense_Mutation	SNP	A	A	T			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr1:235973754A>T	ENST00000389794.3	-	5	538	c.364T>A	c.(364-366)Tta>Ata	p.L122I	LYST_ENST00000389793.2_Missense_Mutation_p.L122I|LYST_ENST00000536965.1_Missense_Mutation_p.L122I			Q99698	LYST_HUMAN	lysosomal trafficking regulator	122					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TCTAAATGTAATTTTTCCTGA	0.368																																						ENST00000389794.3																			0				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162						c.(364-366)Tta>Ata		lysosomal trafficking regulator							64.0	67.0	66.0					1																	235973754		2203	4300	6503	SO:0001583	missense	1130				defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding	g.chr1:235973754A>T	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.364T>A	1.37:g.235973754A>T	ENSP00000374444:p.Leu122Ile		Somatic				LYST_ENST00000536965.1_Missense_Mutation_p.L122I|LYST_ENST00000389793.2_Missense_Mutation_p.L122I	p.L122I			WXS	Illumina GAIIx	Phase_I	Q99698	LYST_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.000674)		5	538	-	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	122					O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	c.364T>A	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	A	7.564	0.665242	0.14710	.	.	ENSG00000143669	ENST00000389794;ENST00000389793;ENST00000536965	T;T;T	0.14144	2.53;2.53;2.53	5.8	0.71	0.18157	.	0.820902	0.11112	N	0.598400	T	0.09555	0.0235	L	0.44542	1.39	0.09310	N	1	P;B	0.43352	0.804;0.083	B;B	0.39706	0.307;0.02	T	0.21827	-1.0234	10	0.35671	T	0.21	.	0.9485	0.01371	0.4393:0.2214:0.1366:0.2027	.	122;122	Q99698-3;Q99698	.;LYST_HUMAN	I	122	ENSP00000374444:L122I;ENSP00000374443:L122I;ENSP00000438315:L122I	ENSP00000374443:L122I	L	-	1	2	LYST	234040377	0.030000	0.19436	0.998000	0.56505	0.983000	0.72400	0.618000	0.24373	0.466000	0.27193	0.460000	0.39030	TTA		0.368	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			28	61	28	61	---	---	---	---
PLXNB1	5364	broad.mit.edu	37	3	48463187	48463187	+	Missense_Mutation	SNP	C	C	A			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr3:48463187C>A	ENST00000358536.4	-	7	1818	c.1549G>T	c.(1549-1551)Ggc>Tgc	p.G517C	PLXNB1_ENST00000456774.1_Missense_Mutation_p.G517C|PLXNB1_ENST00000296440.6_Missense_Mutation_p.G517C|PLXNB1_ENST00000358459.4_Missense_Mutation_p.G517C|PLXNB1_ENST00000448774.2_Intron	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	517					axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GGGCCCTGGCCCCTCGAGCAC	0.612																																						ENST00000358536.4																			0				NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47						c.(1549-1551)Ggc>Tgc		plexin B1							49.0	49.0	49.0					3																	48463187		2203	4300	6503	SO:0001583	missense	5364				axon guidance|cell migration|intracellular signal transduction|regulation of cell shape|regulation of cytoskeleton organization|regulation of small GTPase mediated signal transduction|semaphorin-plexin signaling pathway	extracellular region|integral to plasma membrane|intracellular|semaphorin receptor complex	GTPase activator activity|semaphorin receptor activity|semaphorin receptor binding	g.chr3:48463187C>A	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"""Plexins"""	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.1549G>T	3.37:g.48463187C>A	ENSP00000351338:p.Gly517Cys		Somatic				PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Missense_Mutation_p.G517C|PLXNB1_ENST00000456774.1_Missense_Mutation_p.G517C|PLXNB1_ENST00000296440.6_Missense_Mutation_p.G517C	p.G517C	NM_002673.4	NP_002664.2	WXS	Illumina GAIIx	Phase_I	O43157	PLXB1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)	7	1818	-			517					A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	37	c.1549G>T	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.493936	0.84962	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774	T;T;T;T	0.18174	2.23;2.23;2.23;2.23	5.62	3.84	0.44239	.	0.485971	0.22272	N	0.062253	T	0.34832	0.0911	L	0.56769	1.78	0.80722	D	1	D;D	0.76494	0.98;0.999	P;D	0.71414	0.88;0.973	T	0.02860	-1.1101	10	0.62326	D	0.03	.	10.9572	0.47364	0.0:0.8506:0.0:0.1494	.	517;517	O43157;O43157-2	PLXB1_HUMAN;.	C	517	ENSP00000296440:G517C;ENSP00000351242:G517C;ENSP00000351338:G517C;ENSP00000414199:G517C	ENSP00000296440:G517C	G	-	1	0	PLXNB1	48438191	0.947000	0.32204	0.993000	0.49108	0.950000	0.60333	2.489000	0.45285	0.747000	0.32809	0.655000	0.94253	GGC		0.612	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		3	28	3	28	---	---	---	---
PAQR9	344838	broad.mit.edu	37	3	142681313	142681313	+	Missense_Mutation	SNP	A	A	C			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr3:142681313A>C	ENST00000340634.3	-	1	865	c.866T>G	c.(865-867)tTc>tGc	p.F289C	RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA|RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	289						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						CACGTTGAAGAAGGCGGCCAC	0.587																																						ENST00000340634.3																			0				endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						c.(865-867)tTc>tGc		progestin and adipoQ receptor family member IX							58.0	60.0	59.0					3																	142681313		2203	4300	6503	SO:0001583	missense	344838					integral to membrane	receptor activity	g.chr3:142681313A>C	AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.866T>G	3.37:g.142681313A>C	ENSP00000341564:p.Phe289Cys		Somatic					p.F289C	NM_198504.2	NP_940906.1	WXS	Illumina GAIIx	Phase_I	Q6ZVX9	PAQR9_HUMAN			1	865	-			289					Q147T6	Missense_Mutation	SNP	ENST00000340634.3	37	c.866T>G	CCDS3128.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.119695	0.77323	.	.	ENSG00000188582	ENST00000340634	T	0.31510	1.49	5.63	5.63	0.86233	.	0.152878	0.46145	D	0.000320	T	0.57460	0.2055	M	0.77103	2.36	0.45946	D	0.998776	D	0.89917	1.0	D	0.77557	0.99	T	0.60860	-0.7179	10	0.54805	T	0.06	-27.1099	15.87	0.79108	1.0:0.0:0.0:0.0	.	289	Q6ZVX9	PAQR9_HUMAN	C	289	ENSP00000341564:F289C	ENSP00000341564:F289C	F	-	2	0	PAQR9	144164003	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.424000	0.80242	2.145000	0.66743	0.533000	0.62120	TTC		0.587	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504		7	45	7	45	---	---	---	---
GPR125	166647	broad.mit.edu	37	4	22415404	22415404	+	Missense_Mutation	SNP	G	G	C			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr4:22415404G>C	ENST00000334304.5	-	13	2112	c.1843C>G	c.(1843-1845)Cct>Gct	p.P615A	GPR125_ENST00000282943.5_Intron	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	615					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				AAAAGGGAAGGAGGAAGCTGA	0.348																																						ENST00000334304.5																			0				breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56						c.(1843-1845)Cct>Gct		G protein-coupled receptor 125							61.0	62.0	62.0					4																	22415404		2203	4300	6503	SO:0001583	missense	166647				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity	g.chr4:22415404G>C	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"""	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.1843C>G	4.37:g.22415404G>C	ENSP00000334952:p.Pro615Ala		Somatic				GPR125_ENST00000282943.5_Intron	p.P615A	NM_145290.3	NP_660333.2	WXS	Illumina GAIIx	Phase_I	Q8IWK6	GP125_HUMAN			13	2112	-		Breast(46;0.198)	615					Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	37	c.1843C>G	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	G	11.93	1.786273	0.31593	.	.	ENSG00000152990	ENST00000334304	T	0.53206	0.63	5.82	3.1	0.35709	.	0.441295	0.27482	N	0.019166	T	0.26774	0.0655	N	0.20483	0.58	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.05305	-1.0893	10	0.17369	T	0.5	-35.6758	6.2048	0.20595	0.2166:0.268:0.5153:0.0	.	615	Q8IWK6	GP125_HUMAN	A	615	ENSP00000334952:P615A	ENSP00000334952:P615A	P	-	1	0	GPR125	22024502	0.930000	0.31532	0.490000	0.27465	0.996000	0.88848	1.485000	0.35519	0.343000	0.23821	0.650000	0.86243	CCT		0.348	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			11	41	11	41	---	---	---	---
PCDHB1	29930	broad.mit.edu	37	5	140432292	140432292	+	Nonsense_Mutation	SNP	G	G	T			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr5:140432292G>T	ENST00000306549.3	+	1	1314	c.1237G>T	c.(1237-1239)Gag>Tag	p.E413*		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	413	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTTGGATCGGGAGGAGGTCTC	0.458																																						ENST00000306549.3																			0				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53						c.(1237-1239)Gag>Tag									102.0	100.0	101.0					5																	140432292		2203	4300	6503	SO:0001587	stop_gained	29930				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:140432292G>T	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"""Cadherins / Protocadherins : Clustered"""	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.1237G>T	5.37:g.140432292G>T	ENSP00000307234:p.Glu413*		Somatic					p.E413*	NM_013340.2	NP_037472.2	WXS	Illumina GAIIx	Phase_I	Q9Y5F3	PCDB1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		1	1314	+			413			Cadherin 4.		Q2M257	Nonsense_Mutation	SNP	ENST00000306549.3	37	c.1237G>T	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	G	36	5.888550	0.97068	.	.	ENSG00000171815	ENST00000306549	.	.	.	6.03	6.03	0.97812	.	0.000000	0.48286	D	0.000199	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.177	0.98182	0.0:0.0:1.0:0.0	.	.	.	.	X	413	.	ENSP00000307234:E413X	E	+	1	0	PCDHB1	140412476	1.000000	0.71417	0.977000	0.42913	0.996000	0.88848	9.768000	0.98965	2.854000	0.98071	0.655000	0.94253	GAG		0.458	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		29	104	29	104	---	---	---	---
SND1	27044	broad.mit.edu	37	7	127343360	127343360	+	Missense_Mutation	SNP	G	G	T			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr7:127343360G>T	ENST00000354725.3	+	7	1017	c.823G>T	c.(823-825)Ggt>Tgt	p.G275C		NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	275	TNase-like 2. {ECO:0000255|PROSITE- ProRule:PRU00272}.				gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)			central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						GAACATTCTGGGTACCATCCT	0.488																																						ENST00000354725.3																			0				central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						c.(823-825)Ggt>Tgt		staphylococcal nuclease and tudor domain containing 1							73.0	66.0	69.0					7																	127343360		2203	4300	6503	SO:0001583	missense	27044				gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity	g.chr7:127343360G>T		CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"""Tudor domain containing"""	30646	protein-coding gene	gene with protein product	"""p100 EBNA2 co-activator"", ""Tudor-SN"""	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.823G>T	7.37:g.127343360G>T	ENSP00000346762:p.Gly275Cys		Somatic					p.G275C	NM_014390.2	NP_055205.2	WXS	Illumina GAIIx	Phase_I	Q7KZF4	SND1_HUMAN			7	1017	+			275			TNase-like 2.		Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	37	c.823G>T	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	G	31	5.065047	0.93898	.	.	ENSG00000197157	ENST00000354725;ENST00000438400	T	0.34667	1.35	6.07	6.07	0.98685	Staphylococcal nuclease (SNase-like) (4);Staphylococcal nuclease (SNase-like), OB-fold (1);	0.045277	0.85682	D	0.000000	T	0.67933	0.2946	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.71341	-0.4622	10	0.59425	D	0.04	-14.8565	18.1531	0.89682	0.0:0.0:1.0:0.0	.	275	Q7KZF4	SND1_HUMAN	C	275;265	ENSP00000346762:G275C	ENSP00000346762:G275C	G	+	1	0	SND1	127130596	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.523000	0.98034	2.885000	0.99019	0.655000	0.94253	GGT		0.488	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390		7	35	7	35	---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139144959	139144959	+	Silent	SNP	C	C	A			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr8:139144959C>A	ENST00000395297.1	-	20	4268	c.4098G>T	c.(4096-4098)gtG>gtT	p.V1366V		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1366										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GGGCGTGGAACACGTTGTGTC	0.532										HNSCC(54;0.14)																												ENST00000395297.1																			0				NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238						c.(4096-4098)gtG>gtT		family with sequence similarity 135, member B							250.0	258.0	256.0					8																	139144959		1986	4167	6153	SO:0001819	synonymous_variant	51059							g.chr8:139144959C>A	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.4098G>T	8.37:g.139144959C>A		HNSCC(54;0.14)	Somatic					p.V1366V	NM_015912.3	NP_056996.2	WXS	Illumina GAIIx	Phase_I	Q49AJ0	F135B_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.0805)		20	4268	-	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		1366					B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	c.4098G>T	CCDS6375.2																																																																																				0.532	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		10	275	10	275	---	---	---	---
RAB38	23682	broad.mit.edu	37	11	87847227	87847227	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr11:87847227C>T	ENST00000243662.6	-	3	647	c.565G>A	c.(565-567)Gag>Aag	p.E189K	RP11-164N3.3_ENST00000528458.1_RNA	NM_022337.2	NP_071732.1	P57729	RAB38_HUMAN	RAB38, member RAS oncogene family	189					endosome to melanosome transport (GO:0035646)|GTP catabolic process (GO:0006184)|melanosome organization (GO:0032438)|phagosome acidification (GO:0090383)|platelet dense granule organization (GO:0060155)|protein localization to membrane (GO:0072657)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|early endosome (GO:0005769)|melanosome (GO:0042470)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	AP-1 adaptor complex binding (GO:0035650)|AP-3 adaptor complex binding (GO:0035651)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)|protein complex binding (GO:0032403)			large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				ACGTCCGGCTCAATAGACTCC	0.463																																						ENST00000243662.6																			0				large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11						c.(565-567)Gag>Aag		RAB38, member RAS oncogene family							156.0	147.0	150.0					11																	87847227		2201	4299	6500	SO:0001583	missense	23682				protein transport|small GTPase mediated signal transduction	melanosome|plasma membrane	GTP binding|GTPase activity	g.chr11:87847227C>T	AF235022	CCDS8281.1	11q14	2008-05-14			ENSG00000123892	ENSG00000123892		"""RAB, member RAS oncogene"""	9776	protein-coding gene	gene with protein product		606281				10910072	Standard	NM_022337		Approved	NY-MEL-1	uc001pcj.2	P57729	OTTHUMG00000167288	ENST00000243662.6:c.565G>A	11.37:g.87847227C>T	ENSP00000243662:p.Glu189Lys		Somatic				RP11-164N3.3_ENST00000528458.1_RNA	p.E189K	NM_022337.2	NP_071732.1	WXS	Illumina GAIIx	Phase_I	P57729	RAB38_HUMAN			3	647	-		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)	189					Q53XK7	Missense_Mutation	SNP	ENST00000243662.6	37	c.565G>A	CCDS8281.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.523283	0.44866	.	.	ENSG00000123892	ENST00000243662	T	0.79454	-1.27	5.47	4.55	0.56014	.	0.120176	0.56097	D	0.000026	T	0.63570	0.2522	N	0.19112	0.55	0.38868	D	0.956638	B	0.25850	0.136	B	0.24006	0.05	T	0.60321	-0.7286	9	.	.	.	-0.3678	14.3992	0.67031	0.0:0.8411:0.1589:0.0	.	189	P57729	RAB38_HUMAN	K	189	ENSP00000243662:E189K	.	E	-	1	0	RAB38	87486875	0.993000	0.37304	0.528000	0.27938	0.755000	0.42902	3.123000	0.50453	1.414000	0.47017	0.650000	0.86243	GAG		0.463	RAB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394015.2			12	104	12	104	---	---	---	---
ACAD10	80724	broad.mit.edu	37	12	112153743	112153743	+	Silent	SNP	C	C	T	rs112990162	byFrequency	TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr12:112153743C>T	ENST00000313698.4	+	7	1124	c.969C>T	c.(967-969)gcC>gcT	p.A323A	ACAD10_ENST00000455480.2_Silent_p.A354A|ACAD10_ENST00000392636.2_5'UTR|ACAD10_ENST00000413681.3_3'UTR|ACAD10_ENST00000549590.1_Silent_p.A323A	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	323						mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						TTCCATCTGCCCATGCCATAG	0.517																																						ENST00000455480.2																			0				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						c.(1060-1062)gcC>gcT		acyl-CoA dehydrogenase family, member 10							154.0	156.0	155.0					12																	112153743		2203	4300	6503	SO:0001819	synonymous_variant	80724						acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups	g.chr12:112153743C>T	AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271			21597	protein-coding gene	gene with protein product		611181	"""acyl-Coenzyme A dehydrogenase family, member 10"""			15560374	Standard	NM_025247		Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.969C>T	12.37:g.112153743C>T			Somatic				ACAD10_ENST00000413681.3_3'UTR|ACAD10_ENST00000392636.2_5'UTR|ACAD10_ENST00000549590.1_Silent_p.A323A|ACAD10_ENST00000313698.4_Silent_p.A323A	p.A354A	NM_001136538.1	NP_001130010.1	WXS	Illumina GAIIx	Phase_I	Q6JQN1	ACD10_HUMAN			8	1239	+			323					G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Silent	SNP	ENST00000313698.4	37	c.1062C>T	CCDS31903.1																																																																																				0.517	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		6	132	6	132	---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9061807	9061807	+	Missense_Mutation	SNP	C	C	G			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr19:9061807C>G	ENST00000397910.4	-	3	25842	c.25639G>C	c.(25639-25641)Gtg>Ctg	p.V8547L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8549	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGCCATGGCACATCTCCAGGA	0.498																																						ENST00000397910.4																			0				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						c.(25639-25641)Gtg>Ctg		mucin 16, cell surface associated							65.0	65.0	65.0					19																	9061807		1973	4150	6123	SO:0001583	missense	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9061807C>G	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.25639G>C	19.37:g.9061807C>G	ENSP00000381008:p.Val8547Leu		Somatic					p.V8547L	NM_024690.2	NP_078966.2	WXS	Illumina GAIIx	Phase_I	Q8WXI7	MUC16_HUMAN			3	25842	-			8549			Ser-rich.|Thr-rich.		Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	c.25639G>C	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	6.986	0.552046	0.13374	.	.	ENSG00000181143	ENST00000397910	T	0.19250	2.16	3.05	-2.52	0.06346	.	.	.	.	.	T	0.11580	0.0282	N	0.19112	0.55	.	.	.	B	0.24576	0.106	B	0.26517	0.07	T	0.30446	-0.9978	8	0.87932	D	0	.	4.6467	0.12575	0.0:0.316:0.4281:0.2558	.	8547	B5ME49	.	L	8547	ENSP00000381008:V8547L	ENSP00000381008:V8547L	V	-	1	0	MUC16	8922807	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.067000	0.11579	-0.337000	0.08426	0.450000	0.29827	GTG		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		7	29	7	29	---	---	---	---
SPTBN4	57731	broad.mit.edu	37	19	41078060	41078060	+	Silent	SNP	T	T	C			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr19:41078060T>C	ENST00000352632.3	+	34	7541	c.7455T>C	c.(7453-7455)gcT>gcC	p.A2485A	SPTBN4_ENST00000392025.1_Silent_p.A1228A|SPTBN4_ENST00000593816.1_3'UTR|SPTBN4_ENST00000598249.1_Silent_p.A2485A			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	2485	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCGAGGTGGCTAGTGACTACA	0.607																																						ENST00000352632.3																			0				breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73						c.(7453-7455)gcT>gcC		spectrin, beta, non-erythrocytic 4							77.0	82.0	80.0					19																	41078060		2203	4300	6503	SO:0001819	synonymous_variant	57731				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton	g.chr19:41078060T>C	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"""Pleckstrin homology (PH) domain containing"""	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.7455T>C	19.37:g.41078060T>C			Somatic				SPTBN4_ENST00000593816.1_3'UTR|SPTBN4_ENST00000392025.1_Silent_p.A1228A|SPTBN4_ENST00000598249.1_Silent_p.A2485A	p.A2485A			WXS	Illumina GAIIx	Phase_I	Q9H254	SPTN4_HUMAN	Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)		34	7541	+			2485			PH.		E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	37	c.7455T>C	CCDS12559.1																																																																																				0.607	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			6	121	6	121	---	---	---	---
SIM2	6493	broad.mit.edu	37	21	38098585	38098585	+	Missense_Mutation	SNP	A	A	G			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chr21:38098585A>G	ENST00000290399.6	+	6	1322	c.709A>G	c.(709-711)Agc>Ggc	p.S237G	SIM2_ENST00000430056.3_Missense_Mutation_p.S237G	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	237	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						GTTCAGGGCCAGCCTTGACCT	0.582																																						ENST00000290399.6																			0				breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						c.(709-711)Agc>Ggc		single-minded family bHLH transcription factor 2							86.0	62.0	71.0					21																	38098585		2203	4300	6503	SO:0001583	missense	6493				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity	g.chr21:38098585A>G		CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"""Basic helix-loop-helix proteins"""	10883	protein-coding gene	gene with protein product	"""transcription factor SIM2"""	600892	"""single-minded (Drosophila) homolog 2"", ""single-minded homolog 2 (Drosophila)"""	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.709A>G	21.37:g.38098585A>G	ENSP00000290399:p.Ser237Gly		Somatic				SIM2_ENST00000430056.3_Missense_Mutation_p.S237G	p.S237G	NM_005069.3	NP_005060.1	WXS	Illumina GAIIx	Phase_I	Q14190	SIM2_HUMAN			6	1322	+			237			PAS 2.		O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Missense_Mutation	SNP	ENST00000290399.6	37	c.709A>G	CCDS13646.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.8|21.8	4.200838|4.200838	0.79015|0.79015	.|.	.|.	ENSG00000159263|ENSG00000159263	ENST00000431229|ENST00000290399;ENST00000430056	.|T;T	.|0.79554	.|-1.28;-1.28	5.44|5.44	5.44|5.44	0.79542|0.79542	.|PAS (2);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.90287|0.90287	0.6962|0.6962	M|M	0.87328|0.87328	2.875|2.875	0.46376|0.46376	D|D	0.99901|0.99901	.|D;D	.|0.69078	.|0.997;0.997	.|D;D	.|0.65684	.|0.936;0.937	D|D	0.92076|0.92076	0.5668|0.5668	5|10	.|0.87932	.|D	.|0	.|.	15.804|15.804	0.78477|0.78477	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|237;237	.|Q14190;Q14190-2	.|SIM2_HUMAN;.	R|G	174|237	.|ENSP00000290399:S237G;ENSP00000404176:S237G	.|ENSP00000290399:S237G	Q|S	+|+	2|1	0|0	SIM2|SIM2	37020455|37020455	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.732000|8.732000	0.91534|0.91534	2.193000|2.193000	0.70182|0.70182	0.533000|0.533000	0.62120|0.62120	CAG|AGC		0.582	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586		4	26	4	26	---	---	---	---
SSX5	6758	broad.mit.edu	37	X	48054447	48054447	+	Intron	SNP	G	G	A			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chrX:48054447G>A	ENST00000376923.1	-	2	69				SSX5_ENST00000311798.1_Missense_Mutation_p.A63V|SSX5_ENST00000347757.1_Intron			O60225	SSX5_HUMAN	synovial sarcoma, X breakpoint 5						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|skin(1)	18						ACCTACCCTAGCTTCTCCCCT	0.537																																						ENST00000311798.1																			0				endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|skin(1)	18						c.(187-189)gCt>gTt		synovial sarcoma, X breakpoint 5							61.0	53.0	55.0					X																	48054447		2203	4299	6502	SO:0001627	intron_variant	6758				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding	g.chrX:48054447G>A	BC016640	CCDS14288.1, CCDS14289.1	Xp11.23	2008-02-05			ENSG00000165583	ENSG00000165583			11339	protein-coding gene	gene with protein product		300327					Standard	NM_021015		Approved		uc004diz.1	O60225	OTTHUMG00000021471	ENST00000376923.1:c.70-157C>T	X.37:g.48054447G>A			Somatic				SSX5_ENST00000347757.1_Intron|SSX5_ENST00000376923.1_Intron	p.A63V	NM_021015.3	NP_066295.3	WXS	Illumina GAIIx	Phase_I	O60225	SSX5_HUMAN			3	240	-			23			KRAB-related.		Q5JQ59|Q5JQ60|Q96AW3	Missense_Mutation	SNP	ENST00000376923.1	37	c.188C>T	CCDS14289.1	.	.	.	.	.	.	.	.	.	.	N	12.54	1.968378	0.34754	.	.	ENSG00000165583	ENST00000311798	T	0.00784	5.7	1.51	-0.735	0.11137	.	.	.	.	.	T	0.01870	0.0059	.	.	.	0.09310	N	1	D	0.76494	0.999	D	0.80764	0.994	T	0.49103	-0.8974	8	0.33141	T	0.24	.	2.809	0.05435	0.2328:0.3441:0.4231:0.0	.	63	O60225-2	.	V	63	ENSP00000312415:A63V	ENSP00000312415:A63V	A	-	2	0	SSX5	47939391	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	0.431000	0.21444	-0.319000	0.08652	0.171000	0.16805	GCT		0.537	SSX5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056466.1	NM_021015		6	15	6	15	---	---	---	---
HCFC1	3054	broad.mit.edu	37	X	153216820	153216820	+	Missense_Mutation	SNP	T	T	C			TCGA-KK-A7AV-01A-11D-A32B-08	TCGA-KK-A7AV-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7f3b9e81-6a08-4d69-9cfa-8a6b2debb441	ac932a61-4c1c-4987-96e1-97364aca3e20	g.chrX:153216820T>C	ENST00000310441.7	-	22	6464	c.5498A>G	c.(5497-5499)gAt>gGt	p.D1833G	HCFC1_ENST00000354233.3_Missense_Mutation_p.D1764G|HCFC1_ENST00000369984.4_Missense_Mutation_p.D1878G	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	1833	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GACAGCATCATCTGGTGGCAG	0.542																																						ENST00000310441.7																			0				NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						c.(5497-5499)gAt>gGt		host cell factor C1 (VP16-accessory protein)							221.0	224.0	223.0					X																	153216820		2114	4213	6327	SO:0001583	missense	3054				cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity	g.chrX:153216820T>C		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.5498A>G	X.37:g.153216820T>C	ENSP00000309555:p.Asp1833Gly		Somatic				HCFC1_ENST00000369984.4_Missense_Mutation_p.D1878G|HCFC1_ENST00000354233.3_Missense_Mutation_p.D1764G	p.D1833G	NM_005334.2	NP_005325.2	WXS	Illumina GAIIx	Phase_I	P51610	HCFC1_HUMAN			22	6464	-	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)		1833					Q6P4G5	Missense_Mutation	SNP	ENST00000310441.7	37	c.5498A>G	CCDS44020.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.032183	0.75504	.	.	ENSG00000172534	ENST00000310441;ENST00000369984;ENST00000354233	T;T;T	0.53423	0.62;0.62;0.62	5.66	5.66	0.87406	Fibronectin, type III (1);	0.044852	0.85682	D	0.000000	T	0.51584	0.1683	M	0.69823	2.125	0.49389	D	0.999788	B	0.32968	0.392	B	0.36289	0.221	T	0.55952	-0.8059	10	0.66056	D	0.02	.	13.8755	0.63651	0.0:0.0:0.0:1.0	.	1833	P51610	HCFC1_HUMAN	G	1833;1878;1764	ENSP00000309555:D1833G;ENSP00000359001:D1878G;ENSP00000346174:D1764G	ENSP00000309555:D1833G	D	-	2	0	HCFC1	152870014	1.000000	0.71417	0.868000	0.34077	0.968000	0.65278	3.890000	0.56220	1.921000	0.55644	0.427000	0.28365	GAT		0.542	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334		5	128	5	128	---	---	---	---
