#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_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ADAM29	11086	hgsc.bcm.edu	37	4	175899075	175899076	+	Missense_Mutation	DNP	CA	CA	TG	rs140568401|rs61744599	byFrequency	TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr4:175899075_175899076CA>TG	ENST00000359240.3	+	5	3069_3070	c.2399_2400CA>TG	c.(2398-2400)aCA>aTG	p.T800M	ADAM29_ENST00000445694.1_Missense_Mutation_p.T800M|ADAM29_ENST00000404450.4_Missense_Mutation_p.T800M|ADAM29_ENST00000514159.1_Missense_Mutation_p.T800M|RP13-577H12.2_ENST00000507525.1_RNA	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	800	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CCTCCTGTGACACCCTCCCAGA	0.564																																					Ovarian(140;1727 1835 21805 25838 41440)												0																																										SO:0001583	missense	11086			AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	Exception_encountered	4.37:g.175899075_175899076delinsTG	ENSP00000352177:p.Thr800Met		Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation|Silent	SNP	ENST00000359240.3	37	CCDS3823.1																																																																																				0.564	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				
ADAM29	11086	hgsc.bcm.edu	37	4	175899079	175899079	+	Silent	SNP	C	C	T	rs151310201	byFrequency	TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr4:175899079C>T	ENST00000359240.3	+	5	3073	c.2403C>T	c.(2401-2403)ccC>ccT	p.P801P	ADAM29_ENST00000445694.1_Silent_p.P801P|ADAM29_ENST00000404450.4_Silent_p.P801P|ADAM29_ENST00000514159.1_Silent_p.P801P|RP13-577H12.2_ENST00000507525.1_RNA	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	801	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CTGTGACACCCTCCCAGAGGC	0.567																																					Ovarian(140;1727 1835 21805 25838 41440)												0													138.0	128.0	131.0					4																	175899079		2203	4300	6503	SO:0001819	synonymous_variant	11086			AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2403C>T	4.37:g.175899079C>T			Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Silent	SNP	ENST00000359240.3	37	CCDS3823.1																																																																																				0.567	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				
AHNAK2	113146	hgsc.bcm.edu	37	14	105418458	105418458	+	Frame_Shift_Del	DEL	C	C	-	rs578056159	byFrequency	TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr14:105418458delC	ENST00000333244.5	-	7	3449	c.3330delG	c.(3328-3330)ctgfs	p.L1110fs	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1110						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGGGGCTTTTCAGGTCCAGCT	0.632																																																	0										241,3393		2,237,1578	114.0	144.0	134.0			2.0	0.0	14	dbSNP_130	135	72,7796		0,72,3862	no	frameshift	AHNAK2	NM_138420.2		2,309,5440	A1A1,A1R,RR		0.9151,6.6318,2.7213			105418458	313,11189	1876	4113	5989	SO:0001589	frameshift_variant	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3330delG	14.37:g.105418458delC	ENSP00000353114:p.Leu1110fs		Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Frame_Shift_Del	DEL	ENST00000333244.5	37	CCDS45177.1																																																																																				0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1		NM_138420	
ANKRD27	84079	hgsc.bcm.edu;ucsc.edu	37	19	33149837	33149841	+	Frame_Shift_Del	DEL	CCACT	CCACT	-			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	CCACT	CCACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr19:33149837_33149841delCCACT	ENST00000306065.4	-	2	239_243	c.81_85delAGTGG	c.(79-87)aaagtggccfs	p.KVA27fs	ANKRD27_ENST00000587352.1_Frame_Shift_Del_p.KVA27fs	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	27					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					TGGATTTGGGCCACTTTGCTGCACA	0.507																																																	0																																										SO:0001589	frameshift_variant	84079			AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.81_85delAGTGG	19.37:g.33149837_33149841delCCACT	ENSP00000304292:p.Lys27fs		Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Frame_Shift_Del	DEL	ENST00000306065.4	37	CCDS32986.1																																																																																				0.507	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1		NM_032139	
ATP6V1B1	525	broad.mit.edu;ucsc.edu	37	2	71190307	71190307	+	Missense_Mutation	SNP	G	G	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr2:71190307G>C	ENST00000234396.4	+	10	998	c.925G>C	c.(925-927)Gag>Cag	p.E309Q	AC007040.11_ENST00000606025.1_Intron|RN7SL160P_ENST00000468558.2_RNA|ATP6V1B1_ENST00000412314.1_Missense_Mutation_p.E309Q	NM_001692.3	NP_001683.2	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	309					ATP hydrolysis coupled proton transport (GO:0015991)|ATP metabolic process (GO:0046034)|calcium ion homeostasis (GO:0055074)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|pH reduction (GO:0045851)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(1)	19						TGCTGCTAGAGAGGAGGTGCC	0.607																																																	0													82.0	88.0	86.0					2																	71190307		2203	4300	6503	SO:0001583	missense	525			AF107466	CCDS1912.1	2p13	2010-04-21	2008-07-31	2002-05-10	ENSG00000116039	ENSG00000116039	3.6.3.14	"""ATPases / V-type"""	853	protein-coding gene	gene with protein product	"""Renal tubular acidosis with deafness"""	192132	"""vacuolar proton pump 3"""	VPP3, ATP6B1		9916796, 2527371	Standard	XM_005264368		Approved	VATB, RTA1B, Vma2	uc002shj.3	P15313	OTTHUMG00000129711	ENST00000234396.4:c.925G>C	2.37:g.71190307G>C	ENSP00000234396:p.Glu309Gln		Q53FY0|Q6P4H6	Missense_Mutation	SNP	ENST00000234396.4	37	CCDS1912.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.943945	0.92593	.	.	ENSG00000116039	ENST00000234396;ENST00000483246;ENST00000412314	D;D	0.82255	-1.59;-1.59	4.99	4.99	0.66335	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.000000	0.64402	D	0.000001	D	0.92309	0.7560	M	0.92833	3.35	0.80722	D	1	P;D;D	0.64830	0.938;0.989;0.994	P;D;D	0.63381	0.813;0.914;0.914	D	0.93939	0.7221	10	0.87932	D	0	-1.2484	15.8116	0.78568	0.0:0.0:1.0:0.0	.	284;309;309	B4DWH7;C9JL73;P15313	.;.;VATB1_HUMAN	Q	309;284;309	ENSP00000234396:E309Q;ENSP00000388353:E309Q	ENSP00000234396:E309Q	E	+	1	0	ATP6V1B1	71043815	1.000000	0.71417	0.983000	0.44433	0.968000	0.65278	9.648000	0.98483	2.612000	0.88384	0.650000	0.86243	GAG		0.607	ATP6V1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251920.2		NM_001692	
BCL9L	283149	broad.mit.edu;ucsc.edu	37	11	118779364	118779364	+	Splice_Site	SNP	C	C	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr11:118779364C>T	ENST00000334801.3	-	2	991	c.27G>A	c.(25-27)agG>agA	p.R9R	BCL9L_ENST00000526143.1_5'UTR|MIR4492_ENST00000581627.1_RNA	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	9					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GGTGGGGTAACCTGGGAGGAG	0.597																																																	0													19.0	25.0	23.0					11																	118779364		1968	4121	6089	SO:0001630	splice_region_variant	283149			AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.27-1G>A	11.37:g.118779364C>T			A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	37	CCDS8403.1																																																																																				0.597	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1		NM_182557	Silent
TMEM254	80195	broad.mit.edu;ucsc.edu	37	10	81838462	81838462	+	Missense_Mutation	SNP	A	A	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr10:81838462A>C	ENST00000372281.3	+	1	37	c.7A>C	c.(7-9)Acg>Ccg	p.T3P	TMEM254-AS1_ENST00000412298.1_RNA|TMEM254-AS1_ENST00000432070.2_RNA|TMEM254_ENST00000372277.3_Missense_Mutation_p.T3P|TMEM254-AS1_ENST00000448729.2_RNA|TMEM254_ENST00000372275.1_Missense_Mutation_p.T3P|TMEM254_ENST00000372274.1_Missense_Mutation_p.T3P	NM_001270372.1|NM_025125.3	NP_001257301.1|NP_079401.2	Q8TBM7	TM254_HUMAN	transmembrane protein 254	3						integral component of membrane (GO:0016021)											AGCCATGGCTACGGCAGCCGG	0.677																																																	0													47.0	41.0	43.0					10																	81838462		2203	4298	6501	SO:0001583	missense	0			BC022252	CCDS7363.1, CCDS58086.1, CCDS58087.1, CCDS73157.1	10q23.1	2012-11-06	2012-11-06	2012-11-06	ENSG00000133678	ENSG00000133678			25804	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 57"""	C10orf57		14702039	Standard	NM_025125		Approved	FLJ13263, bA369J21.6	uc010qlw.3	Q8TBM7	OTTHUMG00000018602	ENST00000372281.3:c.7A>C	10.37:g.81838462A>C	ENSP00000361355:p.Thr3Pro		D3DWC8|Q53HP4|Q5JTC0|Q5JTC1|Q6IA45|Q9H8S6	Missense_Mutation	SNP	ENST00000372281.3	37	CCDS7363.1	.	.	.	.	.	.	.	.	.	.	A	12.15	1.851119	0.32699	.	.	ENSG00000133678	ENST00000372281;ENST00000372277;ENST00000372275;ENST00000372274	.	.	.	4.89	-8.2	0.01045	.	.	.	.	.	T	0.14141	0.0342	N	0.12182	0.205	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.20009	-1.0288	8	0.46703	T	0.11	.	2.1672	0.03840	0.2749:0.3951:0.138:0.192	.	3;3	Q5JTC0;Q8TBM7	.;CJ057_HUMAN	P	3	.	ENSP00000361348:T3P	T	+	1	0	C10orf57	81828442	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.076000	0.11412	-1.942000	0.01040	-3.448000	0.00036	ACG		0.677	TMEM254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049030.1		NM_025125	
CENPE	1062	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	104080236	104080236	+	Missense_Mutation	SNP	A	A	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr4:104080236A>C	ENST00000265148.3	-	22	2621	c.2532T>G	c.(2530-2532)aaT>aaG	p.N844K	CENPE_ENST00000380026.3_Missense_Mutation_p.N819K	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	844					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CTATTTCCTGATTCATTCTCT	0.353																																																	0													94.0	91.0	92.0					4																	104080236		2203	4300	6503	SO:0001583	missense	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.2532T>G	4.37:g.104080236A>C	ENSP00000265148:p.Asn844Lys		A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	A	0.691	-0.794488	0.02862	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	T;T;T	0.75821	-0.97;-0.97;-0.97	5.03	-7.9	0.01169	.	.	.	.	.	T	0.34106	0.0886	N	0.02802	-0.49	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.43376	-0.9395	9	0.02654	T	1	.	1.7353	0.02941	0.1513:0.3857:0.2155:0.2474	.	819;844	Q02224-3;Q02224	.;CENPE_HUMAN	K	844;844;819;844	ENSP00000265148:N844K;ENSP00000369365:N819K;ENSP00000423981:N844K	ENSP00000265148:N844K	N	-	3	2	CENPE	104299685	0.004000	0.15560	0.000000	0.03702	0.876000	0.50452	-0.895000	0.04118	-0.912000	0.03837	-1.009000	0.02473	AAT		0.353	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				
COX19	90639	broad.mit.edu;ucsc.edu	37	7	1012903	1012903	+	Missense_Mutation	SNP	T	T	A			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr7:1012903T>A	ENST00000344111.3	-	2	197	c.108A>T	c.(106-108)aaA>aaT	p.K36N		NM_001031617.2	NP_001026788.1	Q49B96	COX19_HUMAN	cytochrome c oxidase assembly homolog 19 (S. cerevisiae)	36	CHCH.					cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)	5		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;2.15e-15)		ACTTCATGAATTTCTCTTTAA	0.353																																																	0													88.0	85.0	86.0					7																	1012903		2202	4299	6501	SO:0001583	missense	90639			AY957566	CCDS34582.1	7p22.3	2012-10-15	2012-10-15		ENSG00000240230	ENSG00000240230		"""Mitochondrial respiratory chain complex assembly factors"""	28074	protein-coding gene	gene with protein product		610429	"""COX19 cytochrome c oxidase assembly homolog (S. cerevisiae)"""			15596615, 16212937	Standard	NM_001031617		Approved	MGC104475	uc003sjp.1	Q49B96	OTTHUMG00000151476	ENST00000344111.3:c.108A>T	7.37:g.1012903T>A	ENSP00000342015:p.Lys36Asn		A4FTX0	Missense_Mutation	SNP	ENST00000344111.3	37	CCDS34582.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.090094	0.36855	.	.	ENSG00000240230	ENST00000344111	T	0.77098	-1.07	4.77	-3.75	0.04372	CHCH (1);	0.176921	0.31834	N	0.006993	T	0.65668	0.2713	.	.	.	0.33063	D	0.534301	P	0.38677	0.642	B	0.43225	0.412	T	0.66143	-0.5997	9	0.17832	T	0.49	-2.0081	11.4701	0.50264	0.0:0.4806:0.0:0.5194	.	36	Q49B96	COX19_HUMAN	N	36	ENSP00000342015:K36N	ENSP00000342015:K36N	K	-	3	2	COX19	979429	0.493000	0.26035	0.970000	0.41538	0.603000	0.37013	-0.488000	0.06497	-0.616000	0.05671	0.383000	0.25322	AAA		0.353	COX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322812.1		NM_001031617	
CTDSP2	10106	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	58220853	58220853	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr12:58220853C>T	ENST00000398073.2	-	4	583	c.280G>A	c.(280-282)Gtg>Atg	p.V94M	CTDSP2_ENST00000548823.1_Intron|MIR26A2_ENST00000385054.1_RNA|CTDSP2_ENST00000547701.1_De_novo_Start_InFrame	NM_005730.3	NP_005721.3	O14595	CTDS2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	94					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein dephosphorylation (GO:0006470)	nucleoplasm (GO:0005654)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(1)|prostate(2)	7	all_neural(12;0.00559)|Glioma(12;0.0143)|Melanoma(17;0.122)					TCCTCTGTCACCTCTGGGAGC	0.493																																																	0													92.0	90.0	90.0					12																	58220853		1959	4143	6102	SO:0001583	missense	10106			AF000152	CCDS41801.1	12q14.1	2012-06-14			ENSG00000175215	ENSG00000175215		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	17077	protein-coding gene	gene with protein product	"""conserved gene amplified in osteosarcoma"", ""nuclear LIM interactor-interacting factor 2"", ""NLI-interacting factor 2"", ""small CTD phosphatase 2"""	608711				9315096, 12721286	Standard	XM_005268556		Approved	OS4, SCP2, PSR2	uc001sqm.3	O14595	OTTHUMG00000170483	ENST00000398073.2:c.280G>A	12.37:g.58220853C>T	ENSP00000381148:p.Val94Met		A8K5H4|Q53ZR2|Q6NZY3|Q9UEX1	Missense_Mutation	SNP	ENST00000398073.2	37	CCDS41801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.25|16.25	3.070018|3.070018	0.55539|0.55539	.|.	.|.	ENSG00000175215|ENSG00000175215	ENST00000550144|ENST00000398073	.|T	.|0.18016	.|2.24	4.92|4.92	4.92|4.92	0.64577|0.64577	.|HAD-like domain (2);	.|0.061993	.|0.64402	.|D	.|0.000006	T|T	0.15998|0.15998	0.0385|0.0385	L|L	0.35288|0.35288	1.05|1.05	0.80722|0.80722	D|D	1|1	.|B	.|0.20368	.|0.044	.|B	.|0.15870	.|0.014	T|T	0.03000|0.03000	-1.1084|-1.1084	5|10	.|0.45353	.|T	.|0.12	-18.7958|-18.7958	17.3988|17.3988	0.87453|0.87453	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|94	.|O14595	.|CTDS2_HUMAN	D|M	63|94	.|ENSP00000381148:V94M	.|ENSP00000381148:V94M	G|V	-|-	2|1	0|0	CTDSP2|CTDSP2	56507120|56507120	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.816000|1.816000	0.38992|0.38992	2.717000|2.717000	0.92951|0.92951	0.563000|0.563000	0.77884|0.77884	GGT|GTG		0.493	CTDSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409353.1		NM_005730	
DDX1	1653	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	15758358	15758358	+	Missense_Mutation	SNP	G	G	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr2:15758358G>C	ENST00000381341.2	+	17	1559	c.1170G>C	c.(1168-1170)caG>caC	p.Q390H	DDX1_ENST00000233084.3_Missense_Mutation_p.Q390H			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	390	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Necessary for interaction with RELA.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		TGCACAATCAGATTCCTCAGG	0.308																																																	0													125.0	143.0	137.0					2																	15758358		2203	4299	6502	SO:0001583	missense	1653			X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"""DEAD-boxes"""	2734	protein-coding gene	gene with protein product		601257	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"""			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.1170G>C	2.37:g.15758358G>C	ENSP00000370745:p.Gln390His		B4DME8|B4DPN6	Missense_Mutation	SNP	ENST00000381341.2	37	CCDS1686.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.398233	0.42512	.	.	ENSG00000079785	ENST00000381341;ENST00000233084;ENST00000543614	T;T	0.16897	2.31;2.31	6.17	4.4	0.53042	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.11367	0.0277	N	0.16166	0.38	0.80722	D	1	B	0.23990	0.095	B	0.28139	0.086	T	0.11155	-1.0599	10	0.44086	T	0.13	-16.4651	10.8871	0.46972	0.2136:0.0:0.7864:0.0	.	390	Q92499	DDX1_HUMAN	H	390;390;374	ENSP00000370745:Q390H;ENSP00000233084:Q390H	ENSP00000233084:Q390H	Q	+	3	2	DDX1	15675809	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	2.118000	0.41949	0.957000	0.37930	-0.136000	0.14681	CAG		0.308	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2		NM_004939	
EDN1	1906	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	12292680	12292680	+	Silent	SNP	C	C	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr6:12292680C>T	ENST00000379375.5	+	2	438	c.171C>T	c.(169-171)tcC>tcT	p.S57S		NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN	endothelin 1	57					artery smooth muscle contraction (GO:0014824)|body fluid secretion (GO:0007589)|calcium-mediated signaling (GO:0019722)|cartilage development (GO:0051216)|cell growth (GO:0016049)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|dorsal/ventral pattern formation (GO:0009953)|epithelial fluid transport (GO:0042045)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose transport (GO:0015758)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|inositol phosphate-mediated signaling (GO:0048016)|leukocyte activation (GO:0045321)|maternal process involved in parturition (GO:0060137)|membrane depolarization (GO:0051899)|middle ear morphogenesis (GO:0042474)|multicellular organismal aging (GO:0010259)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of hormone secretion (GO:0046888)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|nitric oxide transport (GO:0030185)|patterning of blood vessels (GO:0001569)|peptide hormone secretion (GO:0030072)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase D-activating G-protein coupled receptor signaling pathway (GO:0031583)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of odontogenesis (GO:0042482)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of urine volume (GO:0035810)|prostaglandin biosynthetic process (GO:0001516)|protein kinase C deactivation (GO:0042313)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|respiratory gaseous exchange (GO:0007585)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to testosterone (GO:0033574)|rhythmic excitation (GO:0043179)|sensory perception of pain (GO:0019233)|superoxide anion generation (GO:0042554)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|endothelin A receptor binding (GO:0031707)|endothelin B receptor binding (GO:0031708)|hormone activity (GO:0005179)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)				CCTGCTCGTCCCTGATGGATA	0.582																																																	0													82.0	79.0	80.0					6																	12292680		2203	4300	6503	SO:0001819	synonymous_variant	1906			S56805	CCDS4522.1	6p24.1	2014-03-19			ENSG00000078401	ENSG00000078401		"""Endogenous ligands"""	3176	protein-coding gene	gene with protein product		131240					Standard	NM_001168319		Approved	ET1	uc003nae.4	P05305	OTTHUMG00000014266	ENST00000379375.5:c.171C>T	6.37:g.12292680C>T			Q96DA1	Silent	SNP	ENST00000379375.5	37	CCDS4522.1																																																																																				0.582	EDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039872.1		NM_001955	
EFHC2	80258	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	44132000	44132000	+	Missense_Mutation	SNP	T	T	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chrX:44132000T>C	ENST00000420999.1	-	3	397	c.314A>G	c.(313-315)tAc>tGc	p.Y105C		NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	105	DM10 1. {ECO:0000255|PROSITE- ProRule:PRU00665}.						calcium ion binding (GO:0005509)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						AGGGTAGAAGTAGATTTTATA	0.323																																																	0													146.0	125.0	132.0					X																	44132000		1876	4050	5926	SO:0001583	missense	80258			AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"""EF-hand domain containing"""	26233	protein-coding gene	gene with protein product		300817	"""mental retardation, X-linked 74"""	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.314A>G	X.37:g.44132000T>C	ENSP00000404232:p.Tyr105Cys		Q5JST8|Q68DK4|Q8NEI0|Q9H653	Missense_Mutation	SNP	ENST00000420999.1	37	CCDS55405.1	.	.	.	.	.	.	.	.	.	.	T	12.63	1.995581	0.35226	.	.	ENSG00000183690	ENST00000333807;ENST00000420999	T;T	0.44083	0.93;0.93	5.47	-0.36	0.12568	Uncharacterised domain DM10 (2);	0.072462	0.56097	N	0.000021	T	0.57051	0.2027	M	0.80508	2.5	0.53688	D	0.999976	D	0.89917	1.0	D	0.81914	0.995	T	0.54735	-0.8249	10	0.49607	T	0.09	-4.939	5.824	0.18544	0.3592:0.0711:0.0:0.5698	.	105	Q5JST6	EFHC2_HUMAN	C	105;133	ENSP00000333823:Y105C;ENSP00000404232:Y133C	ENSP00000333823:Y105C	Y	-	2	0	EFHC2	44016944	1.000000	0.71417	0.987000	0.45799	0.193000	0.23685	1.232000	0.32636	0.224000	0.20940	-0.424000	0.05967	TAC		0.323	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2		NM_025184	
FBXO18	84893	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	5951142	5951142	+	Missense_Mutation	SNP	G	G	A	rs201500988		TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr10:5951142G>A	ENST00000362091.4	+	5	1020	c.905G>A	c.(904-906)tGc>tAc	p.C302Y	FBXO18_ENST00000397269.3_5'UTR|FBXO18_ENST00000470089.1_3'UTR|FBXO18_ENST00000379999.5_Missense_Mutation_p.C353Y	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	302					DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)			NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						ACCACTAAGTGCTCTCCGAGT	0.577																																																	0													94.0	86.0	89.0					10																	5951142		2203	4300	6503	SO:0001583	missense	84893			AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"""F-boxes /  ""other"""""	13620	protein-coding gene	gene with protein product		607222	"""F-box only protein 18"""			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.905G>A	10.37:g.5951142G>A	ENSP00000355415:p.Cys302Tyr		Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Missense_Mutation	SNP	ENST00000362091.4	37	CCDS7072.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.928995	0.00493	.	.	ENSG00000134452	ENST00000362091;ENST00000544954;ENST00000379999;ENST00000379994	.	.	.	4.99	4.07	0.47477	.	0.613882	0.17575	N	0.169332	T	0.18341	0.0440	N	0.08118	0	0.29325	N	0.867086	B;B;B	0.10296	0.003;0.001;0.001	B;B;B	0.08055	0.003;0.001;0.001	T	0.16394	-1.0404	9	0.02654	T	1	-15.24	9.5415	0.39255	0.0848:0.1478:0.7674:0.0	.	353;302;228	Q8NFZ0-2;Q8NFZ0;Q2TAK1	.;FBX18_HUMAN;.	Y	302;39;353;39	.	ENSP00000355415:C302Y	C	+	2	0	FBXO18	5991148	0.754000	0.28360	0.996000	0.52242	0.073000	0.16967	1.563000	0.36364	2.478000	0.83669	0.561000	0.74099	TGC		0.577	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1		NM_032807	
FITM1	161247	broad.mit.edu	37	14	24600851	24600851	+	Missense_Mutation	SNP	G	G	A	rs139596139	byFrequency	TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr14:24600851G>A	ENST00000267426.5	+	1	368	c.79G>A	c.(79-81)Gtg>Atg	p.V27M	RP11-468E2.6_ENST00000558325.1_Missense_Mutation_p.G214D|FITM1_ENST00000559294.1_5'Flank	NM_203402.2	NP_981947.1	A5D6W6	FITM1_HUMAN	fat storage-inducing transmembrane protein 1	27					lipid particle organization (GO:0034389)|positive regulation of sequestering of triglyceride (GO:0010890)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						CCTGCTCAAGGTGCTGCTCTG	0.687																																																	0								G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	27.0	31.0	30.0		79	4.6	1.0	14	dbSNP_134	30	0,8600		0,0,4300	no	missense	FITM1	NM_203402.2	21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	27/293	24600851	1,13005	2203	4300	6503	SO:0001583	missense	161247				CCDS9611.1	14q12	2009-07-09			ENSG00000139914	ENSG00000139914			33714	protein-coding gene	gene with protein product	"""fat-inducing transcript 1"""	612028				18160536	Standard	NM_203402		Approved	FIT1	uc001wmf.2	A5D6W6	OTTHUMG00000133476	ENST00000267426.5:c.79G>A	14.37:g.24600851G>A	ENSP00000267426:p.Val27Met		Q8IUQ7	Missense_Mutation	SNP	ENST00000267426.5	37	CCDS9611.1	.	.	.	.	.	.	.	.	.	.	g	16.13	3.036399	0.54896	2.27E-4	0.0	ENSG00000139914	ENST00000267426	.	.	.	4.6	4.6	0.57074	.	0.539313	0.16094	N	0.229922	T	0.44685	0.1305	N	0.14661	0.345	0.80722	D	1	P	0.51240	0.943	P	0.49361	0.608	T	0.46162	-0.9211	9	0.54805	T	0.06	-1.6306	12.8056	0.57612	0.0:0.0:1.0:0.0	.	27	A5D6W6	FITM1_HUMAN	M	27	.	ENSP00000267426:V27M	V	+	1	0	FITM1	23670691	1.000000	0.71417	0.997000	0.53966	0.760000	0.43138	3.152000	0.50677	2.369000	0.80426	0.462000	0.41574	GTG		0.687	FITM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257366.1		NM_203402	
FLG	2312	broad.mit.edu;hgsc.bcm.edu	37	1	152280282	152280282	+	Missense_Mutation	SNP	G	G	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr1:152280282G>C	ENST00000368799.1	-	3	7115	c.7080C>G	c.(7078-7080)caC>caG	p.H2360Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2360	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGACCCTCGGTGTCCACTGT	0.587									Ichthyosis																																								0													60.0	77.0	71.0					1																	152280282		2171	4256	6427	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7080C>G	1.37:g.152280282G>C	ENSP00000357789:p.His2360Gln		Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	9.514	1.106505	0.20632	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.03860	3.78	3.71	-7.42	0.01388	.	.	.	.	.	T	0.01029	0.0034	L	0.46157	1.445	0.09310	N	1	B	0.34349	0.45	B	0.34138	0.176	T	0.41858	-0.9485	9	0.29301	T	0.29	.	1.0899	0.01661	0.3784:0.2725:0.2126:0.1365	.	2360	P20930	FILA_HUMAN	Q	2360;270	ENSP00000357789:H2360Q	ENSP00000271820:H270Q	H	-	3	2	FLG	150546906	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.888000	0.00173	-1.126000	0.02929	-0.690000	0.03725	CAC		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1		NM_002016	
GNL3L	54552	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	54577474	54577474	+	Missense_Mutation	SNP	G	G	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chrX:54577474G>C	ENST00000336470.4	+	10	993	c.854G>C	c.(853-855)gGa>gCa	p.G285A	GNL3L_ENST00000360845.2_Missense_Mutation_p.G285A	NM_019067.5	NP_061940.1	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)-like	285	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	30						GCTGTTCCTGGAATTACCAAG	0.547																																																	0													106.0	84.0	91.0					X																	54577474		2203	4300	6503	SO:0001583	missense	54552			AK001475	CCDS14360.1	Xp11.22	2010-03-17			ENSG00000130119	ENSG00000130119			25553	protein-coding gene	gene with protein product		300873				12477932	Standard	NM_019067		Approved	FLJ10613	uc004dth.2	Q9NVN8	OTTHUMG00000021629	ENST00000336470.4:c.854G>C	X.37:g.54577474G>C	ENSP00000338573:p.Gly285Ala			Missense_Mutation	SNP	ENST00000336470.4	37	CCDS14360.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934018	0.73442	.	.	ENSG00000130119	ENST00000336470;ENST00000360845	T;T	0.23754	1.89;1.89	4.62	4.62	0.57501	GTP-binding domain, HSR1-related (1);	0.000000	0.85682	D	0.000000	T	0.57917	0.2086	M	0.88241	2.94	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68081	-0.5503	10	0.87932	D	0	-12.9784	15.9815	0.80114	0.0:0.0:1.0:0.0	.	285	Q9NVN8	GNL3L_HUMAN	A	285	ENSP00000338573:G285A;ENSP00000354091:G285A	ENSP00000338573:G285A	G	+	2	0	GNL3L	54594199	1.000000	0.71417	0.941000	0.38009	0.558000	0.35554	9.005000	0.93587	2.223000	0.72356	0.429000	0.28392	GGA		0.547	GNL3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056805.1		NM_019067	
HSPD1	3329	broad.mit.edu;hgsc.bcm.edu	37	2	198362076	198362076	+	Missense_Mutation	SNP	T	T	G			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr2:198362076T>G	ENST00000388968.3	-	3	482	c.215A>C	c.(214-216)aAa>aCa	p.K72T	HSPE1_ENST00000409729.1_5'Flank|HSPD1_ENST00000345042.2_Missense_Mutation_p.K72T|HSPD1_ENST00000544407.1_Missense_Mutation_p.K72T|HSPE1_ENST00000233893.5_5'Flank	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	72					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			TTTTGTTACTTTGGGACTTCC	0.338																																																	0													71.0	70.0	70.0					2																	198362076		2203	4300	6503	SO:0001583	missense	3329			M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"""Heat Shock Proteins / Chaperonins"""	5261	protein-coding gene	gene with protein product		118190	"""heat shock 60kD protein 1 (chaperonin)"", ""spastic paraplegia 13 (autosomal dominant)"""	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.215A>C	2.37:g.198362076T>G	ENSP00000373620:p.Lys72Thr		B2R5M6|B7Z712|Q38L19|Q9UCR6	Missense_Mutation	SNP	ENST00000388968.3	37	CCDS33357.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.472900	0.84640	.	.	ENSG00000144381	ENST00000388968;ENST00000345042;ENST00000430176;ENST00000452200;ENST00000544407;ENST00000426480;ENST00000428204;ENST00000439605	T;T;T;T;T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17	4.24	4.24	0.50183	.	0.091610	0.85682	D	0.000000	D	0.83908	0.5356	L	0.52011	1.625	0.80722	D	1	D;D;D;D	0.67145	0.993;0.996;0.996;0.982	D;D;D;P	0.74674	0.911;0.984;0.984;0.864	D	0.85850	0.1403	10	0.87932	D	0	-25.0224	13.8498	0.63489	0.0:0.0:0.0:1.0	.	72;72;72;72	B7Z712;B7Z597;B3GQS7;P10809	.;.;.;CH60_HUMAN	T	72;72;72;72;72;114;72;72	ENSP00000373620:K72T;ENSP00000340019:K72T;ENSP00000393670:K72T;ENSP00000412717:K72T;ENSP00000441296:K72T;ENSP00000414446:K114T;ENSP00000396460:K72T;ENSP00000402478:K72T	ENSP00000340019:K72T	K	-	2	0	HSPD1	198070321	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.822000	0.86651	1.912000	0.55364	0.524000	0.50904	AAA		0.338	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2		NM_002156	
LILRP2	79166	broad.mit.edu	37	19	55221501	55221501	+	RNA	SNP	C	C	G			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr19:55221501C>G	ENST00000413439.1	+	0	1281									leukocyte immunoglobulin-like receptor pseudogene 2																		CAGCCCCAGGCTGGGCTCTCC	0.632																																					Ovarian(107;788 1543 20399 31552 46707)												0																																												79166			AF072100		19q13.4	2010-02-17			ENSG00000240258	ENSG00000170858		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"""	15497	pseudogene	pseudogene						10941842	Standard	NR_003061		Approved	ILT10, CD85m	uc002qgs.1		OTTHUMG00000065886		19.37:g.55221501C>G				RNA	SNP	ENST00000413439.1	37																																																																																					0.632	LILRP2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000141240.2		NM_024317	
RP6-206I17.1	0	broad.mit.edu	37	1	143663875	143663875	+	lincRNA	SNP	G	G	T	rs373397451	byFrequency	TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr1:143663875G>T	ENST00000445753.1	-	0	531																											CCCCGACACAGACCTGAACCG	0.632													.|||	793	0.158347	0.4062	0.0504	5008	,	,		8835	0.12		0.0408	False		,,,				2504	0.0603																0																																												100286793																															1.37:g.143663875G>T				RNA	SNP	ENST00000445753.1	37																																																																																					0.632	RP6-206I17.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037956.1			
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr11:3427845C>T	ENST00000529482.1	+	0	962									tumor suppressing subtransferable candidate 2 pseudogene																		CTTCAAGTGGCAGGAGCAGAA	0.587																																																	0																																												650368					11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427845C>T				RNA	SNP	ENST00000529482.1	37																																																																																					0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			
TSSC2	650368	broad.mit.edu	37	11	3427885	3427885	+	RNA	SNP	A	A	G			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr11:3427885A>G	ENST00000529482.1	+	0	1002									tumor suppressing subtransferable candidate 2 pseudogene																		AGCTTCACAGATCCACCGCTG	0.587																																																	0																																												650368					11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427885A>G				RNA	SNP	ENST00000529482.1	37																																																																																					0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			
BMS1P20	96610	broad.mit.edu	37	22	22661517	22661517	+	RNA	SNP	G	G	A	rs574597848	byFrequency	TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr22:22661517G>A	ENST00000426066.1	+	0	407					NR_027293.1				BMS1 pseudogene 20																		CTCAAGTCCCGAGATCCAATC	0.463													.|||	3	0.000599042	0.0	0.0	5008	,	,		21550	0.003		0.0	False		,,,				2504	0.0																0																																												96610					22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22661517G>A				RNA	SNP	ENST00000426066.1	37																																																																																					0.463	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			
MIR429	554210	broad.mit.edu;ucsc.edu	37	1	1104459	1104459	+	lincRNA	SNP	A	A	G			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr1:1104459A>G	ENST00000606993.1	+	0	0				MIR429_ENST00000362106.1_RNA|MIR200A_ENST00000384875.1_RNA|MIR200B_ENST00000384997.1_RNA																							AAAACCGTCCATCCGCTGCCT	0.622																																																	0													43.0	49.0	47.0					1																	1104459		1567	3582	5149			554210																															1.37:g.1104459A>G				RNA	SNP	ENST00000606993.1	37																																																																																					0.622	RP11-465B22.8-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470776.1			
MAGI3	260425	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	114184768	114184768	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr1:114184768G>T	ENST00000307546.9	+	10	1671	c.1596G>T	c.(1594-1596)aaG>aaT	p.K532N	MAGI3_ENST00000369615.1_Missense_Mutation_p.K532N|MAGI3_ENST00000369617.4_Missense_Mutation_p.K557N|MAGI3_ENST00000369611.4_Missense_Mutation_p.K532N	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	557					apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGGATTTTAAGCCAGGAGCAA	0.468																																																	0													129.0	127.0	128.0					1																	114184768		2203	4300	6503	SO:0001583	missense	260425			AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.1596G>T	1.37:g.114184768G>T	ENSP00000304604:p.Lys532Asn		Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Missense_Mutation	SNP	ENST00000307546.9	37	CCDS44196.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.162102	0.38217	.	.	ENSG00000081026	ENST00000369617;ENST00000307546;ENST00000369615;ENST00000369611	T;T;T;T	0.16073	2.52;2.37;2.51;2.51	5.6	2.18	0.27775	.	0.178001	0.64402	D	0.000011	T	0.07593	0.0191	L	0.40543	1.245	0.35191	D	0.773379	P;B;B	0.47106	0.89;0.261;0.23	P;B;B	0.46796	0.527;0.076;0.098	T	0.11817	-1.0572	10	0.52906	T	0.07	-9.7537	5.3932	0.16255	0.572:0.0:0.428:0.0	.	532;532;557	Q5TCQ9-4;Q5TCQ9-3;Q5TCQ9-2	.;.;.	N	557;532;532;532	ENSP00000358630:K557N;ENSP00000304604:K532N;ENSP00000358628:K532N;ENSP00000358624:K532N	ENSP00000304604:K532N	K	+	3	2	MAGI3	113986291	0.973000	0.33851	0.994000	0.49952	0.992000	0.81027	1.712000	0.37940	0.815000	0.34398	0.650000	0.86243	AAG		0.468	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1		NM_152900	
MUC4	4585	hgsc.bcm.edu	37	3	195508343	195508343	+	Missense_Mutation	SNP	A	A	T	rs555793435|rs396680		TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr3:195508343A>T	ENST00000463781.3	-	2	10567	c.10108T>A	c.(10108-10110)Tcc>Acc	p.S3370T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3370T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TCACCTGTGGAAGCTGAGGAA	0.587																																																	0													36.0	31.0	33.0					3																	195508343		686	1582	2268	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10108T>A	3.37:g.195508343A>T	ENSP00000417498:p.Ser3370Thr		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	a	3.051	-0.195478	0.06259	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.38401	1.29;1.14	0.423	-0.846	0.10734	.	.	.	.	.	T	0.15046	0.0363	N	0.19112	0.55	0.09310	N	1	P	0.38110	0.618	B	0.25759	0.063	T	0.13818	-1.0495	8	.	.	.	.	4.4467	0.11600	0.3383:0.0:0.6617:0.0	.	3242	E7ESK3	.	T	3370	ENSP00000417498:S3370T;ENSP00000420243:S3370T	.	S	-	1	0	MUC4	196993122	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	-2.391000	0.01057	-0.409000	0.07553	0.076000	0.15429	TCC		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195510011	195510011	+	Missense_Mutation	SNP	C	C	T	rs28375716		TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr3:195510011C>T	ENST00000463781.3	-	2	8899	c.8440G>A	c.(8440-8442)Gcc>Acc	p.A2814T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2814T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGAGGTGGCGTGACCTGTG	0.587																																																	0													70.0	44.0	52.0					3																	195510011		685	1518	2203	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8440G>A	3.37:g.195510011C>T	ENSP00000417498:p.Ala2814Thr		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	8.082	0.772585	0.16051	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34472	1.37;1.36	.	.	.	.	.	.	.	.	T	0.23330	0.0564	N	0.19112	0.55	0.09310	N	0.999993	D	0.53312	0.959	P	0.45971	0.499	T	0.13575	-1.0504	7	.	.	.	.	5.8178	0.18506	0.0:0.999:0.0:0.001	.	2686	E7ESK3	.	T	2814	ENSP00000417498:A2814T;ENSP00000420243:A2814T	.	A	-	1	0	MUC4	196994790	0.001000	0.12720	0.022000	0.16811	0.020000	0.10135	-2.830000	0.00744	-0.000000	0.14550	0.000000	0.15137	GCC		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC6	4588	hgsc.bcm.edu	37	11	1018089	1018089	+	Frame_Shift_Del	DEL	G	G	-	rs368342230		TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr11:1018089delG	ENST00000421673.2	-	31	4762	c.4712delC	c.(4711-4713)ccafs	p.P1572fs		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1572	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGTGAAGGGTGGTGGTGGCCT	0.577																																																	0													258.0	266.0	263.0					11																	1018089		2180	4263	6443	SO:0001589	frameshift_variant	4588			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4712delC	11.37:g.1018089delG	ENSP00000406861:p.Pro1572fs		O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Frame_Shift_Del	DEL	ENST00000421673.2	37	CCDS44513.1																																																																																				0.577	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2		XM_290540	
MUC6	4588	hgsc.bcm.edu	37	11	1018093	1018094	+	Frame_Shift_Ins	INS	-	-	T	rs376177791|rs372288551		TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr11:1018093_1018094insT	ENST00000421673.2	-	31	4757_4758	c.4707_4708insA	c.(4705-4710)ccaccafs	p.P1570fs		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1570	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AAGGGTGGTGGTGGCCTGCTGC	0.574																																																	0																																										SO:0001589	frameshift_variant	4588			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4708dupA	11.37:g.1018094_1018094dupT	ENSP00000406861:p.Pro1570fs		O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Frame_Shift_Ins	INS	ENST00000421673.2	37	CCDS44513.1																																																																																				0.574	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2		XM_290540	
MUC6	4588	hgsc.bcm.edu	37	11	1018168	1018170	+	In_Frame_Del	DEL	TCG	TCG	-	rs111749447|rs77647814	byFrequency	TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	TCG	TCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr11:1018168_1018170delTCG	ENST00000421673.2	-	31	4681_4683	c.4631_4633delCGA	c.(4630-4635)acgatt>att	p.T1544del		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1544	Pro-rich.|Thr-rich.			T -> S (in Ref. 2; AAQ82434). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TTGGGAGTAATCGTGGTAGTAGA	0.557																																																	0																																										SO:0001651	inframe_deletion	4588			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4631_4633delCGA	11.37:g.1018168_1018170delTCG	ENSP00000406861:p.Thr1544del		O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	In_Frame_Del	DEL	ENST00000421673.2	37	CCDS44513.1																																																																																				0.557	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2		XM_290540	
NTRK3	4916	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	88476307	88476307	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr15:88476307C>T	ENST00000360948.2	-	15	1986	c.1825G>A	c.(1825-1827)Gat>Aat	p.D609N	NTRK3_ENST00000558676.1_Missense_Mutation_p.D601N|NTRK3_ENST00000557856.1_Missense_Mutation_p.D601N|NTRK3_ENST00000542733.2_Missense_Mutation_p.D511N|NTRK3_ENST00000355254.2_Missense_Mutation_p.D609N|NTRK3_ENST00000394480.2_Missense_Mutation_p.D609N|NTRK3_ENST00000357724.2_Missense_Mutation_p.D601N	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	609	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			GGGTCCCCATCGCCGCACACT	0.552			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)																														Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	0													80.0	70.0	74.0					15																	88476307		2201	4299	6500	SO:0001583	missense	4916			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1825G>A	15.37:g.88476307C>T	ENSP00000354207:p.Asp609Asn		B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.470816	0.84533	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000343782	D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62	5.49	5.49	0.81192	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84561	0.5499	N	0.16656	0.425	0.80722	D	1	D;D;D;D;P	0.89917	0.999;1.0;0.999;0.999;0.954	D;D;D;D;P	0.76575	0.965;0.988;0.983;0.94;0.59	D	0.84294	0.0501	10	0.33940	T	0.23	.	18.3583	0.90365	0.0:1.0:0.0:0.0	.	511;601;601;609;609	B7Z7U4;E9PG56;B7Z4C5;Q16288-3;Q16288	.;.;.;.;NTRK3_HUMAN	N	609;609;601;609;511;105	ENSP00000377990:D609N;ENSP00000354207:D609N;ENSP00000350356:D601N;ENSP00000347397:D609N;ENSP00000437773:D511N	ENSP00000342792:D105N	D	-	1	0	NTRK3	86277311	1.000000	0.71417	0.524000	0.27887	0.539000	0.34962	7.636000	0.83301	2.574000	0.86865	0.650000	0.86243	GAT		0.552	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52651357	52651357	+	Missense_Mutation	SNP	T	T	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr3:52651357T>C	ENST00000296302.7	-	14	1740	c.1739A>G	c.(1738-1740)tAt>tGt	p.Y580C	PBRM1_ENST00000337303.4_Missense_Mutation_p.Y580C|PBRM1_ENST00000409767.1_Missense_Mutation_p.Y595C|PBRM1_ENST00000409057.1_Missense_Mutation_p.Y580C|PBRM1_ENST00000409114.3_Missense_Mutation_p.Y595C|PBRM1_ENST00000394830.3_Missense_Mutation_p.Y580C|PBRM1_ENST00000410007.1_Missense_Mutation_p.Y580C|PBRM1_ENST00000356770.4_Missense_Mutation_p.Y548C			Q86U86	PB1_HUMAN	polybromo 1	580	Bromo 4. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTCACCAGCATATTTGTCATT	0.433			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	0													121.0	112.0	115.0					3																	52651357		2203	4300	6503	SO:0001583	missense	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1739A>G	3.37:g.52651357T>C	ENSP00000296302:p.Tyr580Cys		A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	T	22.8	4.339655	0.81911	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	T;T;T;T;T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	5.84	5.84	0.93424	Bromodomain (5);Bromodomain, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.87958	0.6309	H	0.98833	4.345	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;0.999;1.0;0.999;1.0;1.0;0.999;0.999	D	0.92807	0.6261	10	0.87932	D	0	-16.5987	16.2167	0.82231	0.0:0.0:0.0:1.0	.	580;580;580;580;595;595;580;548;580	Q86U86-9;Q86U86-6;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;.;PB1_HUMAN;.;.	C	548;580;580;580;580;580;595;595;580;539	ENSP00000349213:Y548C;ENSP00000378307:Y580C;ENSP00000296302:Y580C;ENSP00000338302:Y580C;ENSP00000386593:Y580C;ENSP00000386529:Y580C;ENSP00000386643:Y595C;ENSP00000386601:Y595C;ENSP00000387775:Y580C;ENSP00000397662:Y539C	ENSP00000296302:Y580C	Y	-	2	0	PBRM1	52626397	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.231000	0.72958	0.533000	0.62120	TAT		0.433	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PCDHB10	56126	broad.mit.edu	37	5	140574170	140574175	+	In_Frame_Del	DEL	AGGCCG	AGGCCG	-	rs58244182|rs140613424|rs140393827	byFrequency	TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	AGGCCG	AGGCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr5:140574170_140574175delAGGCCG	ENST00000239446.4	+	1	2229_2234	c.2045_2050delAGGCCG	c.(2044-2052)caggccgag>cag	p.AE683del		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	683					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCCCAGGCCCAGGCCGAGGCCGACTT	0.704														2124	0.424121	0.4372	0.4971	5008	,	,		11585	0.5347		0.3658	False		,,,				2504	0.3006																0										851,2755		246,359,1198						2.2	0.0		dbSNP_129	38	1442,5672		362,718,2477	no	coding	PCDHB10	NM_018930.3		608,1077,3675	A1A1,A1R,RR		20.2699,23.5996,21.3899				2293,8427				SO:0001651	inframe_deletion	56126			AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.2045_2050delAGGCCG	5.37:g.140574176_140574181delAGGCCG	ENSP00000239446:p.Ala683_Glu684del		Q96T99	In_Frame_Del	DEL	ENST00000239446.4	37	CCDS4252.1																																																																																				0.704	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1		NM_018930	
PCDHB3	56132	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	140480794	140480794	+	Silent	SNP	C	C	T	rs374383309		TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr5:140480794C>T	ENST00000231130.2	+	1	561	c.561C>T	c.(559-561)gaC>gaT	p.D187D	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	187	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTCGTAGGGACGGAAGGAAGT	0.562																																																	0								C		0,4406		0,0,2203	82.0	80.0	81.0		561	-2.8	0.3	5		81	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PCDHB3	NM_018937.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		187/797	140480794	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"""Cadherins / Protocadherins : Clustered"""	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.561C>T	5.37:g.140480794C>T			B2R8P2	Silent	SNP	ENST00000231130.2	37	CCDS4245.1																																																																																				0.562	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2		NM_018937	
PCNA	5111	hgsc.bcm.edu;ucsc.edu	37	20	5098236	5098236	+	Missense_Mutation	SNP	A	A	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr20:5098236A>C	ENST00000379160.3	-	5	704	c.462T>G	c.(460-462)atT>atG	p.I154M	PCNA_ENST00000379143.5_Missense_Mutation_p.I154M	NM_002592.2	NP_002583.1	P12004	PCNA_HUMAN	proliferating cell nuclear antigen	154					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|epithelial cell differentiation (GO:0030855)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|leading strand elongation (GO:0006272)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of deoxyribonuclease activity (GO:0032077)|regulation of DNA replication (GO:0006275)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cadmium ion (GO:0046686)|response to lipid (GO:0033993)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)|translesion synthesis (GO:0019985)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|nuclear replication fork (GO:0043596)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA complex (GO:0043626)|PCNA-p21 complex (GO:0070557)	dinucleotide insertion or deletion binding (GO:0032139)|DNA polymerase binding (GO:0070182)|DNA polymerase processivity factor activity (GO:0030337)|identical protein binding (GO:0042802)|MutLalpha complex binding (GO:0032405)|purine-specific mismatch base pair DNA N-glycosylase activity (GO:0000701)|receptor tyrosine kinase binding (GO:0030971)			endometrium(2)|kidney(1)|large_intestine(4)|lung(2)	9						CAGCATCTCCAATATGGCTGA	0.378								DNA polymerases (catalytic subunits)																																									0													107.0	105.0	106.0					20																	5098236		2203	4300	6503	SO:0001583	missense	5111			J04718	CCDS13087.1	20p13-p12.3	2013-09-19			ENSG00000132646	ENSG00000132646			8729	protein-coding gene	gene with protein product		176740				2565339	Standard	NM_002592		Approved		uc002wlp.3	P12004	OTTHUMG00000031798	ENST00000379160.3:c.462T>G	20.37:g.5098236A>C	ENSP00000368458:p.Ile154Met		B2R897|D3DW02	Missense_Mutation	SNP	ENST00000379160.3	37	CCDS13087.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.730790	0.48939	.	.	ENSG00000132646	ENST00000379143;ENST00000379160	.	.	.	5.24	1.78	0.24846	Proliferating cell nuclear antigen, PCNA, C-terminal (1);	0.043989	0.85682	D	0.000000	T	0.62600	0.2441	L	0.49778	1.585	0.54753	D	0.999981	B	0.26318	0.146	P	0.44394	0.448	T	0.56631	-0.7947	9	0.37606	T	0.19	-13.4523	8.0325	0.30474	0.7554:0.0:0.2446:0.0	.	154	P12004	PCNA_HUMAN	M	154	.	ENSP00000368438:I154M	I	-	3	3	PCNA	5046236	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	1.368000	0.34216	0.327000	0.23409	0.379000	0.24179	ATT		0.378	PCNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077852.2			
PIPSL	266971	broad.mit.edu	37	10	95720827	95720827	+	RNA	SNP	C	C	A			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr10:95720827C>A	ENST00000480546.1	-	0	470					NR_002319.2		A2A3N6	PIPSL_HUMAN	PIP5K1A and PSMD4-like, pseudogene							cytoplasm (GO:0005737)	phosphatidylinositol phosphate kinase activity (GO:0016307)										AGAGGGAATACAAGTAATCAT	0.498																																																	0																																												266971			BC068549		10q23.33	2010-10-27	2010-10-27	2007-07-06	ENSG00000180764	ENSG00000180764		"""Proteasome (prosome, macropain) subunits"""	23733	pseudogene	pseudogene			"""proteasome (prosome, macropain) 26S subunit, non-ATPase, 4, pseudogene 2"", ""phosphatidylinositol-4-phosphate 5-kinase, type I-like 1"", ""PIP5K1A and PSMD4-like"""	PSMD4P2, PIP5K1L1		16344562	Standard	NR_002319		Approved	PIP5K1A-PSMD4, PIP5K1P3	uc009xuj.2	A2A3N6	OTTHUMG00000137480		10.37:g.95720827C>A			Q6NUK8	Missense_Mutation	SNP	ENST00000480546.1	37																																																																																					0.498	PIPSL-002	PUTATIVE	basic	processed_transcript	pseudogene	OTTHUMT00000351483.1		NR_002319	
POTEA	340441	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	43147724	43147724	+	RNA	SNP	C	C	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr8:43147724C>T	ENST00000522175.2	+	0	99							Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A											breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(27)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CTGCTGCTTCCCCTGCTGCAG	0.587																																																	0													51.0	55.0	53.0					8																	43147724		2202	4300	6502			340441			AY462869		8p11.1	2013-01-11	2008-11-26	2008-11-26	ENSG00000188877	ENSG00000188877		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33893	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 3"""	608915	"""ANKRD26-like family A, member 1"""	A26A1			Standard	NM_001002920		Approved	POTE8, POTE-8, CT104.3	uc003xpz.1	Q6S8J7	OTTHUMG00000164111		8.37:g.43147724C>T			A6ND17|A6ND71|Q6S8J6	Missense_Mutation	SNP	ENST00000522175.2	37																																																																																					0.587	POTEA-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000383492.1		NM_001002920	
RAB39B	116442	broad.mit.edu	37	X	154490260	154490260	+	Missense_Mutation	SNP	G	G	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chrX:154490260G>C	ENST00000369454.3	-	2	770	c.470C>G	c.(469-471)gCc>gGc	p.A157G		NM_171998.2	NP_741995.1	Q96DA2	RB39B_HUMAN	RAB39B, member RAS oncogene family	157					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|synapse organization (GO:0050808)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTP binding (GO:0005525)|myosin V binding (GO:0031489)			breast(1)|central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(12)	19	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CACATTAATGGCATCTCGGGC	0.512																																																	0													108.0	86.0	94.0					X																	154490260		2203	4300	6503	SO:0001583	missense	116442			AY052478	CCDS14766.1	Xq28	2014-01-31			ENSG00000155961	ENSG00000155961		"""RAB, member RAS oncogene"""	16499	protein-coding gene	gene with protein product		300774	"""mental retardation, X-linked 72"""	MRX72		12438742, 20159109	Standard	NM_171998		Approved		uc004fne.3	Q96DA2	OTTHUMG00000022659	ENST00000369454.3:c.470C>G	X.37:g.154490260G>C	ENSP00000358466:p.Ala157Gly		Q5JT79|Q8NEX3	Missense_Mutation	SNP	ENST00000369454.3	37	CCDS14766.1	.	.	.	.	.	.	.	.	.	.	G	11.31	1.600095	0.28534	.	.	ENSG00000155961	ENST00000369454	T	0.74842	-0.88	5.17	5.17	0.71159	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.36880	0.0983	N	0.00095	-2.16	0.58432	D	0.999994	B	0.13594	0.008	B	0.19666	0.026	T	0.48151	-0.9060	10	0.21014	T	0.42	.	15.2574	0.73596	0.0:0.0:1.0:0.0	.	157	Q96DA2	RB39B_HUMAN	G	157	ENSP00000358466:A157G	ENSP00000358466:A157G	A	-	2	0	RAB39B	154143454	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.387000	0.97232	2.280000	0.76307	0.513000	0.50165	GCC		0.512	RAB39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058792.1		NM_171998	
RELA	5970	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	65426222	65426222	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr11:65426222C>T	ENST00000406246.3	-	7	892	c.631G>A	c.(631-633)Gag>Aag	p.E211K	RELA_ENST00000308639.9_Missense_Mutation_p.E208K|RELA_ENST00000525693.1_Missense_Mutation_p.E211K	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	211	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|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 distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|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 factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						AGGAAGATCTCATCCCCACCG	0.567																																																	0													140.0	120.0	127.0					11																	65426222		2201	4297	6498	SO:0001583	missense	5970			Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"""	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.631G>A	11.37:g.65426222C>T	ENSP00000384273:p.Glu211Lys		Q6GTV1|Q6SLK1	Missense_Mutation	SNP	ENST00000406246.3	37	CCDS31609.1	.	.	.	.	.	.	.	.	.	.	C	34	5.370256	0.95900	.	.	ENSG00000173039	ENST00000406246;ENST00000525693;ENST00000308639;ENST00000426617;ENST00000545816;ENST00000532999;ENST00000534558;ENST00000527749	T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16	5.13	5.13	0.70059	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.70692	0.3253	H	0.94886	3.595	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	0.982;0.999;0.999;0.999;1.0;0.989	P;D;D;D;D;P	0.91635	0.822;0.989;0.989;0.975;0.999;0.798	T	0.80200	-0.1481	10	0.87932	D	0	-21.9559	16.0771	0.80976	0.0:1.0:0.0:0.0	.	211;198;208;211;222;211	Q04206-3;Q04206-2;Q04206-4;Q04206;B4E082;Q2TAM5	.;.;.;TF65_HUMAN;.;.	K	211;211;208;211;222;222;202;180	ENSP00000384273:E211K;ENSP00000432537:E211K;ENSP00000311508:E208K;ENSP00000433526:E222K;ENSP00000434372:E202K;ENSP00000436545:E180K	ENSP00000311508:E208K	E	-	1	0	RELA	65182798	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.634000	0.83273	2.387000	0.81309	0.655000	0.94253	GAG		0.567	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2		NM_021975	
RHBDL1	9028	hgsc.bcm.edu;ucsc.edu	37	16	726989	726990	+	Frame_Shift_Ins	INS	-	-	AA			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr16:726989_726990insAA	ENST00000219551.2	+	3	667_668	c.640_641insAA	c.(640-642)tacfs	p.Y214fs	LA16c-313D11.9_ENST00000571933.1_RNA|RHBDL1_ENST00000352681.3_Frame_Shift_Ins_p.Y149fs|LA16c-313D11.9_ENST00000567091.1_RNA			O75783	RHBL1_HUMAN	rhomboid, veinlet-like 1 (Drosophila)	214					signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(1)|lung(4)|urinary_tract(3)	9		Hepatocellular(780;0.0218)				GTTCCTGTGTTACGGGGCCCGC	0.688																																																	0																																										SO:0001589	frameshift_variant	9028			Y17108	CCDS61779.1	16p13.3	2008-02-05	2001-11-28	2003-04-11	ENSG00000103269	ENSG00000103269			10007	protein-coding gene	gene with protein product		603264	"""rhomboid (veinlet, Drosophila)-like"""	RHBDL		9662444	Standard	NM_001278720		Approved	RRP	uc002cis.1	O75783	OTTHUMG00000121141	Exception_encountered	16.37:g.726989_726990insAA	ENSP00000219551:p.Tyr214fs		A2IDC0|A2IDC1|Q0VAX4|Q9NQ85	Frame_Shift_Del	INS	ENST00000219551.2	37	CCDS10418.1																																																																																				0.688	RHBDL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241619.1		NM_003961	
S1PR2	9294	broad.mit.edu;hgsc.bcm.edu	37	19	10334693	10334693	+	Missense_Mutation	SNP	G	G	A			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr19:10334693G>A	ENST00000590320.1	-	2	999	c.889C>T	c.(889-891)Cgg>Tgg	p.R297W	CTD-2369P2.2_ENST00000317726.4_lincRNA	NM_004230.3	NP_004221.3	O95136	S1PR2_HUMAN	sphingosine-1-phosphate receptor 2	297					activation of MAPK activity (GO:0000187)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of endothelial barrier (GO:1903142)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						AGCACCTCCCGCCGCAGGTCC	0.692																																					Pancreas(194;229 3020 15179 45747)												0													27.0	30.0	29.0					19																	10334693		2200	4297	6497	SO:0001583	missense	9294			AF034780	CCDS12229.1	19q13	2013-03-13	2008-04-30	2008-04-30	ENSG00000267534	ENSG00000267534		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	3169	protein-coding gene	gene with protein product		605111	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 5"""	EDG5		8087418, 8878560	Standard	NM_004230		Approved	Gpcr13, H218, AGR16	uc002mnl.2	O95136	OTTHUMG00000180399	ENST00000590320.1:c.889C>T	19.37:g.10334693G>A	ENSP00000466933:p.Arg297Trp		Q86UN8	Missense_Mutation	SNP	ENST00000590320.1	37	CCDS12229.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.863378	0.51482	.	.	ENSG00000175898	ENST00000317726	.	.	.	5.49	-1.58	0.08479	.	0.306404	0.29466	N	0.012065	T	0.30198	0.0757	N	0.24115	0.695	0.37685	D	0.923613	D	0.61697	0.99	B	0.43623	0.425	T	0.35301	-0.9794	9	0.87932	D	0	.	9.3075	0.37885	0.0:0.2083:0.2543:0.5374	.	297	O95136	S1PR2_HUMAN	W	297	.	ENSP00000322049:R297W	R	-	1	2	S1PR2	10195693	0.000000	0.05858	0.995000	0.50966	0.967000	0.64934	0.272000	0.18644	0.221000	0.20879	0.556000	0.70494	CGG		0.692	S1PR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451194.1		NM_004230	
S1PR2	9294	broad.mit.edu	37	19	10335160	10335160	+	Missense_Mutation	SNP	C	C	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr19:10335160C>T	ENST00000590320.1	-	2	532	c.422G>A	c.(421-423)gGc>gAc	p.G141D	CTD-2369P2.2_ENST00000317726.4_lincRNA	NM_004230.3	NP_004221.3	O95136	S1PR2_HUMAN	sphingosine-1-phosphate receptor 2	141					activation of MAPK activity (GO:0000187)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of endothelial barrier (GO:1903142)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						CTTGTCGCTGCCATACAGCTT	0.642																																					Pancreas(194;229 3020 15179 45747)												0													51.0	48.0	49.0					19																	10335160		2203	4300	6503	SO:0001583	missense	9294			AF034780	CCDS12229.1	19q13	2013-03-13	2008-04-30	2008-04-30	ENSG00000267534	ENSG00000267534		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	3169	protein-coding gene	gene with protein product		605111	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 5"""	EDG5		8087418, 8878560	Standard	NM_004230		Approved	Gpcr13, H218, AGR16	uc002mnl.2	O95136	OTTHUMG00000180399	ENST00000590320.1:c.422G>A	19.37:g.10335160C>T	ENSP00000466933:p.Gly141Asp		Q86UN8	Missense_Mutation	SNP	ENST00000590320.1	37	CCDS12229.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374970	0.61735	.	.	ENSG00000175898	ENST00000317726	.	.	.	5.46	5.46	0.80206	GPCR, rhodopsin-like superfamily (1);	0.059475	0.64402	D	0.000003	T	0.64360	0.2591	L	0.39020	1.185	0.58432	D	0.999998	D	0.71674	0.998	D	0.66847	0.947	T	0.55958	-0.8058	9	0.09338	T	0.73	.	18.0738	0.89421	0.0:1.0:0.0:0.0	.	141	O95136	S1PR2_HUMAN	D	141	.	ENSP00000322049:G141D	G	-	2	0	S1PR2	10196160	0.987000	0.35691	1.000000	0.80357	0.837000	0.47467	3.311000	0.51919	2.557000	0.86248	0.586000	0.80456	GGC		0.642	S1PR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451194.1		NM_004230	
SBNO1	55206	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	123800154	123800154	+	Missense_Mutation	SNP	A	A	G			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr12:123800154A>G	ENST00000602398.1	-	22	3116	c.2989T>C	c.(2989-2991)Tct>Cct	p.S997P	SBNO1_ENST00000267176.4_Missense_Mutation_p.S996P|SBNO1_ENST00000602750.1_Missense_Mutation_p.S996P|SBNO1_ENST00000420886.2_Missense_Mutation_p.S997P			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	997			S -> C (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		GCCAGTTCAGATATCAGAAAG	0.388																																																	0													156.0	145.0	149.0					12																	123800154		2203	4300	6503	SO:0001583	missense	55206			AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.2989T>C	12.37:g.123800154A>G	ENSP00000473665:p.Ser997Pro		Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.798499	0.90538	.	.	ENSG00000139697	ENST00000420886;ENST00000267176	T;T	0.76448	-1.02;-1.02	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.88459	0.6442	M	0.80616	2.505	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.996	D	0.89268	0.3602	10	0.54805	T	0.06	-20.63	16.0789	0.80985	1.0:0.0:0.0:0.0	.	997;996	A3KN83;A3KN83-2	SBNO1_HUMAN;.	P	997;996	ENSP00000387361:S997P;ENSP00000267176:S996P	ENSP00000267176:S996P	S	-	1	0	SBNO1	122366107	1.000000	0.71417	0.999000	0.59377	0.923000	0.55619	9.339000	0.96797	2.192000	0.70111	0.460000	0.39030	TCT		0.388	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1		NM_018183	
SSPO	23145	hgsc.bcm.edu	37	7	149515189	149515189	+	RNA	DEL	A	A	-	rs60594151	byFrequency	TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr7:149515189delA	ENST00000378016.2	+	0	11577							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GACCTCGAGTAACTGCCCCAG	0.667													A|AA|A|insertion	1839	0.367212	0.4402	0.3473	5008	,	,		16407	0.4206		0.2942	False		,,,				2504	0.3027																0										1497,2307		384,729,789	5.0	7.0	6.0			1.8	0.2	7	dbSNP_132	8	2537,5339		482,1573,1883	no	frameshift	SSPO	NM_198455.2		866,2302,2672	A1A1,A1R,RR		32.2118,39.3533,34.5377			149515189	4034,7646	1638	3723	5361			23145			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149515189delA			Q76B61	Frame_Shift_Del	DEL	ENST00000378016.2	37																																																																																					0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				
STAMBPL1	57559	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	90682964	90682964	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr10:90682964G>T	ENST00000371926.3	+	11	2252	c.1294G>T	c.(1294-1296)Gtg>Ttg	p.V432L	STAMBPL1_ENST00000371922.1_Missense_Mutation_p.V266L|STAMBPL1_ENST00000371927.3_Intron|STAMBPL1_ENST00000371924.1_Missense_Mutation_p.V432L	NM_020799.3	NP_065850.1	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1	432						membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(2)|endometrium(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(1)	11		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		AAAAATAATTGTGTTGGATCT	0.348																																																	0													107.0	102.0	104.0					10																	90682964		2203	4300	6503	SO:0001583	missense	57559			AB037794	CCDS7391.1	10q23.32	2006-11-08			ENSG00000138134	ENSG00000138134			24105	protein-coding gene	gene with protein product	"""associated molecule with the SH3 domain of STAM (AMSH) like protein"", ""associated molecule with the SH3 domain of STAM (AMSH) - Family Protein"""	612352				12810066, 12943674	Standard	NM_020799		Approved	AMSH-LP, KIAA1373, AMSH-FP, FLJ31524, ALMalpha, bA399O19.2	uc001kfk.4	Q96FJ0	OTTHUMG00000018702	ENST00000371926.3:c.1294G>T	10.37:g.90682964G>T	ENSP00000360994:p.Val432Leu		B3KPA7|Q5T9N4|Q5T9N9|Q7Z420|Q9P2H4	Missense_Mutation	SNP	ENST00000371926.3	37	CCDS7391.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.383736	0.42308	.	.	ENSG00000138134	ENST00000371926;ENST00000371924;ENST00000371922	T;T;T	0.26660	1.72;1.72;1.79	5.54	1.24	0.21308	.	.	.	.	.	T	0.17619	0.0423	L	0.35793	1.09	0.46416	D	0.999038	B	0.02656	0.0	B	0.01281	0.0	T	0.05435	-1.0885	9	0.42905	T	0.14	.	6.8567	0.24044	0.2352:0.1258:0.6389:0.0	.	432	Q96FJ0	STALP_HUMAN	L	432;432;266	ENSP00000360994:V432L;ENSP00000360992:V432L;ENSP00000360990:V266L	ENSP00000360990:V266L	V	+	1	0	STAMBPL1	90672944	0.934000	0.31675	0.728000	0.30774	0.988000	0.76386	1.356000	0.34079	0.344000	0.23847	0.591000	0.81541	GTG		0.348	STAMBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049283.1		NM_020799	
SURF4	6836	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	136234216	136234216	+	Missense_Mutation	SNP	G	G	A			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr9:136234216G>A	ENST00000371989.3	-	2	283	c.154C>T	c.(154-156)Cgc>Tgc	p.R52C	SURF4_ENST00000485435.2_Missense_Mutation_p.R52C|SURF4_ENST00000545297.1_Missense_Mutation_p.R52C|SURF4_ENST00000467910.1_5'UTR|SURF4_ENST00000371991.3_Missense_Mutation_p.R52C	NM_001280788.1|NM_001280790.1|NM_001280791.1|NM_033161.2	NP_001267717.1|NP_001267719.1|NP_001267720.1|NP_149351.1	O15260	SURF4_HUMAN	surfeit 4	52					Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(5)	8				OV - Ovarian serous cystadenocarcinoma(145;5.32e-07)|Epithelial(140;4.56e-06)|all cancers(34;4.25e-05)		ATGTAGTCGCGCTGCTCGCTC	0.612																																																	0													122.0	97.0	105.0					9																	136234216		2203	4300	6503	SO:0001583	missense	6836				CCDS6968.1, CCDS65177.1, CCDS65178.1, CCDS75929.1	9q33-q34	2008-07-21			ENSG00000148248	ENSG00000148248			11476	protein-coding gene	gene with protein product	"""surfeit locus protein 4"", ""surface 4 integral membrane protein"""	185660				8499913, 7540914	Standard	NM_033161		Approved	ERV29, FLJ22993, MGC102753	uc004cdj.3	O15260	OTTHUMG00000020868	ENST00000371989.3:c.154C>T	9.37:g.136234216G>A	ENSP00000361057:p.Arg52Cys		B7Z6A4|O60923|Q5T8U6|Q9UNZ0|Q9UNZ1	Missense_Mutation	SNP	ENST00000371989.3	37	CCDS6968.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.882755	0.51908	.	.	ENSG00000148248	ENST00000371989;ENST00000485435;ENST00000545297;ENST00000541390;ENST00000371991	.	.	.	4.97	3.99	0.46301	.	0.000000	0.85682	D	0.000000	T	0.50205	0.1602	M	0.64997	1.995	0.80722	D	1	P;B;B;B	0.35507	0.506;0.075;0.198;0.075	B;B;B;B	0.31495	0.131;0.035;0.056;0.035	T	0.56517	-0.7966	9	0.52906	T	0.07	-15.6935	9.8925	0.41298	0.0:0.0:0.5842:0.4158	.	52;43;52;52	B7Z6A4;B7Z7A8;O15260-2;O15260	.;.;.;SURF4_HUMAN	C	52;52;52;43;52	.	ENSP00000361057:R52C	R	-	1	0	SURF4	135224037	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	2.538000	0.45710	2.290000	0.77057	0.655000	0.94253	CGC		0.612	SURF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054886.1		NM_033161	
TMEM225	338661	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	123753906	123753906	+	Missense_Mutation	SNP	G	G	A			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr11:123753906G>A	ENST00000375026.2	-	4	833	c.617C>T	c.(616-618)gCa>gTa	p.A206V		NM_001013743.1	NP_001013765.1	Q6GV28	TM225_HUMAN	transmembrane protein 225	206					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	28						CACAGTGTGTGCACGGACAAT	0.393																																																	0													182.0	166.0	172.0					11																	123753906		2202	4299	6501	SO:0001583	missense	338661			AY634366	CCDS31697.1	11q24.1	2014-06-13			ENSG00000204300	ENSG00000204300			32390	protein-coding gene	gene with protein product	"""PMP22 claudin domain containing"", ""protein phosphatase 1, regulatory subunit 154"""						Standard	XM_006718832		Approved	PMP22CD, PPP1R154	uc001pzi.3	Q6GV28	OTTHUMG00000165959	ENST00000375026.2:c.617C>T	11.37:g.123753906G>A	ENSP00000364166:p.Ala206Val			Missense_Mutation	SNP	ENST00000375026.2	37	CCDS31697.1	.	.	.	.	.	.	.	.	.	.	G	0.050	-1.252446	0.01469	.	.	ENSG00000204300	ENST00000375026	T	0.27720	1.65	3.64	-7.29	0.01451	.	6.550700	0.00166	N	0.000000	T	0.08626	0.0214	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26744	-1.0094	10	0.02654	T	1	1.9283	1.9353	0.03335	0.1819:0.1301:0.4305:0.2575	.	206	Q6GV28	TM225_HUMAN	V	206	ENSP00000364166:A206V	ENSP00000364166:A206V	A	-	2	0	TMEM225	123259116	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.150000	0.01290	-2.112000	0.00835	-0.794000	0.03295	GCA		0.393	TMEM225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387260.1		NM_001013743	
TP53BP2	7159	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	223994599	223994599	+	Silent	SNP	T	T	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr1:223994599T>C	ENST00000343537.7	-	5	714	c.423A>G	c.(421-423)gcA>gcG	p.A141A	TP53BP2_ENST00000391878.2_Silent_p.A12A	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	135	Gln-rich.				cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		GCTGGCGAGATGCCATTTCCT	0.418																																																	0													159.0	152.0	154.0					1																	223994599		2203	4300	6503	SO:0001819	synonymous_variant	7159			U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	12000	protein-coding gene	gene with protein product		602143	"""tumor protein p53-binding protein, 2"""			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.423A>G	1.37:g.223994599T>C			B4DG66|Q12892|Q86X75|Q96KQ3	Silent	SNP	ENST00000343537.7	37	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.952535	0.34471	.	.	ENSG00000143514	ENST00000494100	.	.	.	5.13	-5.62	0.02481	.	.	.	.	.	T	0.37544	0.1007	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36089	-0.9762	4	.	.	.	.	2.3145	0.04195	0.1093:0.3236:0.2256:0.3415	.	.	.	.	V	75	.	.	I	-	1	0	TP53BP2	222061222	0.000000	0.05858	0.871000	0.34182	0.998000	0.95712	-3.523000	0.00442	-1.341000	0.02225	0.460000	0.39030	ATC		0.418	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3		NM_001031685, NM_005426	
VCAN	1462	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	82815685	82815685	+	Missense_Mutation	SNP	G	G	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr5:82815685G>T	ENST00000265077.3	+	7	2125	c.1560G>T	c.(1558-1560)ttG>ttT	p.L520F	VCAN_ENST00000342785.4_Missense_Mutation_p.L520F|VCAN_ENST00000512590.2_Missense_Mutation_p.L472F|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	520	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AAACACCATTGGTAACTGCAA	0.393																																																	0													127.0	127.0	127.0					5																	82815685		2203	4300	6503	SO:0001583	missense	1462			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.1560G>T	5.37:g.82815685G>T	ENSP00000265077:p.Leu520Phe		P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	1.743	-0.491296	0.04322	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	D;D;D	0.86097	-1.96;-2.05;-2.07	5.77	-5.1	0.02911	.	1.309370	0.04890	N	0.449399	T	0.53786	0.1818	N	0.01576	-0.805	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.55088	-0.8195	10	0.07813	T	0.8	.	0.9228	0.01318	0.1928:0.1859:0.313:0.3082	.	520;520	P13611-3;P13611	.;CSPG2_HUMAN	F	520;520;472	ENSP00000265077:L520F;ENSP00000342768:L520F;ENSP00000425959:L472F	ENSP00000265077:L520F	L	+	3	2	VCAN	82851441	0.000000	0.05858	0.000000	0.03702	0.534000	0.34807	-0.559000	0.05971	-0.427000	0.07350	-1.112000	0.02068	TTG		0.393	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3		NM_004385	
VHL	7428	hgsc.bcm.edu;ucsc.edu	37	3	10191557	10191558	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr3:10191557_10191558insT	ENST00000256474.2	+	3	1390_1391	c.550_551insT	c.(550-552)ctcfs	p.L184fs	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Frame_Shift_Ins_p.L143fs	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	184			L -> P (in VHLD; type I). {ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829911}.|L -> R (in VHLD; type I). {ECO:0000269|PubMed:8956040}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L184P(6)|p.L184R(1)|p.Y185fs*14(1)|p.S183*(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CGTCAGGTCGCTCTACGAAGAT	0.515		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	9	Substitution - Missense(7)|Deletion - Frameshift(2)	kidney(9)	GRCh37	CM042503|CM941389|CM961440	VHL	M																																				SO:0001589	frameshift_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.551dupT	3.37:g.10191558_10191558dupT	ENSP00000256474:p.Leu184fs		B2RE45|Q13599|Q6PDA9	Frame_Shift_Ins	INS	ENST00000256474.2	37	CCDS2597.1																																																																																				0.515	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
ZEB1	6935	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	31799802	31799805	+	Splice_Site	DEL	AAGT	AAGT	-			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr10:31799802_31799805delAAGT	ENST00000320985.10	+	5	793_794	c.683_684delAAGT	c.(682-684)caa>c	p.Q228fs	ZEB1_ENST00000446923.2_Splice_Site_p.Q212fs|ZEB1_ENST00000559858.1_3'UTR|ZEB1_ENST00000542815.3_Splice_Site_p.Q161fs|ZEB1_ENST00000361642.5_Splice_Site_p.Q229fs|ZEB1_ENST00000560721.2_Splice_Site_p.Q208fs			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	228					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				GGAAGAGATCAAGTAAGTGCAATG	0.368																																					Ovarian(40;423 959 14296 36701 49589)												0																																										SO:0001630	splice_region_variant	6935			AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	11642	protein-coding gene	gene with protein product		189909	"""transcription factor 8 (represses interleukin 2 expression)"", ""posterior polymorphous corneal dystrophy 3"""	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.684+1AAGT>-	10.37:g.31799806_31799809delAAGT			B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	In_Frame_Del	DEL	ENST00000320985.10	37	CCDS7169.1																																																																																				0.368	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2		NM_030751	Frame_Shift_Del
ZNF383	163087	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	37733520	37733520	+	Missense_Mutation	SNP	G	G	C			TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr19:37733520G>C	ENST00000589413.1	+	8	965	c.382G>C	c.(382-384)Gca>Cca	p.A128P	ZNF383_ENST00000352998.3_Missense_Mutation_p.A128P|ZNF383_ENST00000590503.1_Missense_Mutation_p.A128P			Q8NA42	ZN383_HUMAN	zinc finger protein 383	128					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)	15			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAGCCACCTTGCAAAACAACT	0.383																																																	0													108.0	119.0	115.0					19																	37733520		2203	4299	6502	SO:0001583	missense	163087			AY438646	CCDS12501.1	19q13.13	2013-01-08				ENSG00000188283		"""Zinc fingers, C2H2-type"", ""-"""	18609	protein-coding gene	gene with protein product							Standard	NM_152604		Approved	FLJ35863	uc002ofu.1	Q8NA42		ENST00000589413.1:c.382G>C	19.37:g.37733520G>C	ENSP00000464871:p.Ala128Pro		Q6X2C7	Missense_Mutation	SNP	ENST00000589413.1	37	CCDS12501.1	.	.	.	.	.	.	.	.	.	.	G	7.613	0.675156	0.14841	.	.	ENSG00000188283	ENST00000352998	T	0.06768	3.26	3.3	0.966	0.19667	.	1.326770	0.05810	N	0.613885	T	0.04407	0.0121	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.43261	-0.9402	10	0.32370	T	0.25	.	7.1864	0.25801	0.0:0.1886:0.6169:0.1945	.	128	Q8NA42	ZN383_HUMAN	P	128	ENSP00000340132:A128P	ENSP00000340132:A128P	A	+	1	0	ZNF383	42425360	0.987000	0.35691	0.176000	0.23000	0.830000	0.47004	0.119000	0.15626	0.190000	0.20209	-0.311000	0.09066	GCA		0.383	ZNF383-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458141.1		NM_152604	
ZNF785	146540	hgsc.bcm.edu	37	16	30594709	30594718	+	Frame_Shift_Del	DEL	TTTTTGTTTT	TTTTTGTTTT	-	rs535168451		TCGA-B8-4148-01A-02D-1386-10	TCGA-B8-4148-10A-01D-1251-10	TTTTTGTTTT	TTTTTGTTTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	fe752e2b-e694-4fa9-99d6-46d5bff9e8cf	8dd6ee40-2fae-4cac-a322-ef15761ad2c7	g.chr16:30594709_30594718delTTTTTGTTTT	ENST00000395216.2	-	3	540_549	c.381_390delAAAACAAAAA	c.(379-390)ccaaaacaaaaafs	p.PKQK127fs	RP11-146F11.5_ENST00000563540.1_RNA|ZNF785_ENST00000470110.1_Frame_Shift_Del_p.PKQK112fs|AC002310.7_ENST00000492040.1_RNA|AC002310.7_ENST00000486926.1_RNA	NM_152458.6	NP_689671.2	A8K8V0	ZN785_HUMAN	zinc finger protein 785	127					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	9						GCGCCACCTCTTTTTGTTTTGGACACTTCT	0.533																																																	0										1,0,4263		0,0,1,0,0,2131						2.4	0.0			94	0,5,8249		0,0,0,0,5,4122	no	codingComplex	ZNF785	NM_152458.6		0,0,1,0,5,6253	A1A1,A1A2,A1R,A2A2,A2R,RR		0.0606,0.0235,0.0479				1,5,12512				SO:0001589	frameshift_variant	146540			BC040642	CCDS10685.1	16p11.2	2013-01-08			ENSG00000197162	ENSG00000197162		"""Zinc fingers, C2H2-type"", ""-"""	26496	protein-coding gene	gene with protein product						10493829	Standard	NM_152458		Approved	FLJ32130	uc002dyu.3	A8K8V0	OTTHUMG00000132398	ENST00000395216.2:c.381_390delAAAACAAAAA	16.37:g.30594709_30594718delTTTTTGTTTT	ENSP00000378642:p.Pro127fs		O75701|Q8IW91|Q8WV14|Q96MN0	Frame_Shift_Del	DEL	ENST00000395216.2	37	CCDS10685.1																																																																																				0.533	ZNF785-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255529.2		NM_152458	
