#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_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_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_Description	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_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_AccessionNumbers	i_HGNC_CCDS IDs	i_HGNC_CCDSIDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_DateModified	i_HGNC_DateNameChanged	i_HGNC_DateSymbolChanged	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_EnsemblGeneID	i_HGNC_EnsemblIDsuppliedbyEnsembl	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_Genefamilydescription	i_HGNC_HGNC ID	i_HGNC_HGNCID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_LocusGroup	i_HGNC_LocusType	i_HGNC_Name Synonyms	i_HGNC_NameSynonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_OMIMIDsuppliedbyNCBI	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_PreviousNames	i_HGNC_PreviousSymbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_PubmedIDs	i_HGNC_Record Type	i_HGNC_RecordType	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_RefSeqsuppliedbyNCBI	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UCSCIDsuppliedbyUCSC	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_UniProtIDsuppliedbyUniProt	i_HGNC_VEGA IDs	i_HGNC_VEGAIDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Region	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_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_folddegenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_hg18_pos1coor	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_init_n_lod	i_init_t_lod	i_n_alt_count	i_n_alt_count_full	i_n_ref_count	i_n_ref_count_full	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_lod_fstar	i_t_lod_fstar_full	i_t_ref_count_full	i_tumor_f_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	tumor_f
LRP1B	53353	broad.mit.edu	37	2	141201962	141201962	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr2:141201962G>A	ENST00000389484.3	-	65	11202	c.10231C>T	c.(10231-10233)Cca>Tca	p.P3411S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3411	LDL-receptor class A 23. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AAGTTTACTGGGATACATTTC	0.393										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)	ENST00000389484.3											0			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606						c.(10231-10233)Cca>Tca	low density lipoprotein receptor-related protein 1B						203.0	189.0	194.0					2																	141201962		2203	4300	6503	SO:0001583	missense	53353			protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding	g.chr2:141201962G>A	AF176832	AF176832	CCDS2182.1	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702	ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	"""Low density lipoprotein receptors"""	6693	6693	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	"""LRP-deleted in tumors"""	608766	608766						10766186	10766186	Standard	Standard	NM_018557	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	uc002tvj.1	Q9NZR2	Q9NZR2	OTTHUMG00000131799	OTTHUMG00000131799	ENST00000389484.3:c.10231C>T	2.37:g.141201962G>A	ENSP00000374135:p.Pro3411Ser			p.P3411S	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	65	11202	-		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)	3411	LDL-receptor class A 23.	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	c.10231C>T	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.866382	0.91511	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.95554	-3.74	5.42	5.42	0.78866	5.42	5.42	0.78866	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	U	0.000000	D	0.96231	0.8771	L	0.37800	1.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94538	0.7742	10	0.25751	T	0.34	.	19.4095	0.94665	0.0:0.0:1.0:0.0	.	3411	Q9NZR2	LRP1B_HUMAN	S	3411;3349	ENSP00000374135:P3411S	ENSP00000374135:P3411S	P	-	1	0	0	LRP1B	140918432	140918432	1.000000	0.71417	0.998000	0.56505	0.873000	0.50193	9.601000	0.98297	2.817000	0.96982	0.563000	0.77884	CCA		0.393	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2		183.430693	7	7	109	109	NM_018557		58	184.13217	184.132170	79	0.423358	0	0	0	1	0	58	79	0.423358
CSNK1A1P1	161635	broad.mit.edu	37	15	37109490	37109490	+	RNA	SNP	C	C	T			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr15:37109490C>T	ENST00000430593.3	-	0	733					NR_027320.1				casein kinase 1, alpha 1 pseudogene 1																		GATCAGGGTCCTGAAAAGAAT	0.473																																						ENST00000430593.3											0																																																0						g.chr15:37109490C>T	BC028192	BC028192			15q13.3	2010-09-21	2010-07-20	2010-07-20	2010-09-21	2010-07-20	2010-07-20		ENSG00000223518		ENSG00000223518				30446	30446	pseudogene	pseudogene	pseudogene	pseudogene					"""casein kinase 1, alpha 1 pseudogene"""	CSNK1A1P	"""casein kinase 1, alpha 1 pseudogene"""	CSNK1A1P				Standard	Standard	NR_027320	NR_027320		Approved		uc001zjg.4	uc001zjg.4						15.37:g.37109490C>T					NR_027320.1						0	733	-						RNA	SNP	ENST00000430593.3	37																																																																																											0.473	CSNK1A1P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000419759.1		22.389637	-2	-2	49	49	NR_027320		8	23.391509	23.391509	19	0.296296	0	0	0	1	0	8	19	0.296296
RTTN	25914	ucsc.edu	37	18	67776945	67776945	+	Missense_Mutation	SNP	G	G	A	rs369864357		TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr18:67776945G>A	ENST00000255674.6	-	28	3978	c.3692C>T	c.(3691-3693)tCg>tTg	p.S1231L	RTTN_ENST00000437017.1_Missense_Mutation_p.S1231L|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1231					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				AAGAAGTTCCGAGCATTTCCT	0.438																																																	0												G	LEU/SER	1,3743		0,1,1871	43.0	43.0	43.0		3692	-0.5	0.7	18		43	0,8208		0,0,4104	no	missense	RTTN	NM_173630.3	145	0,1,5975	AA,AG,GG		0.0,0.0267,0.0084	benign	1231/2227	67776945	1,11951	1872	4104	5976	SO:0001583	missense	25914							AL117635	AL117635	CCDS42443.1	CCDS42443.1	18q22.1	2008-08-01			2008-08-01				ENSG00000176225		ENSG00000176225				18654	18654	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			610436	610436						11900971	11900971	Standard	Standard	NM_173630	NM_173630		Approved	DKFZP434G145	uc002lkp.2	uc002lkp.2	Q86VV8	Q86VV8			ENST00000255674.6:c.3692C>T	18.37:g.67776945G>A	ENSP00000255674:p.Ser1231Leu																	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37		CCDS42443.1	.	.	.	.	.	.	.	.	.	.	G	2.235	-0.375116	0.05034	2.67E-4	0.0	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.68479	-0.33;-0.33	5.08	-0.495	0.12030	5.08	-0.495	0.12030	.	0.291643	0.29362	N	0.012375	T	0.17534	0.0421	N	0.00128	-2.045	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40421	-0.9564	10	0.02654	T	1	.	5.6031	0.17365	0.6496:0.133:0.2174:0.0	.	1231	Q86VV8	RTTN_HUMAN	L	1231	ENSP00000255674:S1231L;ENSP00000399520:S1231L	ENSP00000255674:S1231L	S	-	2	0	0	RTTN	65927925	65927925	0.872000	0.30054	0.700000	0.30305	0.943000	0.58893	1.381000	0.34362	-0.264000	0.09365	-0.440000	0.05779	TCG		0.438	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1			-17	-17	28	28	NM_173630		4			32							4	32	
LMLN	89782	broad.mit.edu	37	3	197710814	197710814	+	Splice_Site	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr3:197710814G>A	ENST00000330198.4	+	7	751	c.729G>A	c.(727-729)agG>agA	p.R243R	LMLN_ENST00000420910.2_Splice_Site_p.R243R|LMLN_ENST00000482695.1_Splice_Site_p.R191R|LMLN_ENST00000332636.5_Splice_Site_p.R191R	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	243					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		GTTTTGACAGGCCAATAGCAG	0.368																																						ENST00000330198.4											0			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						c.(727-729)agG>agA	leishmanolysin-like (metallopeptidase M8 family)						127.0	113.0	118.0					3																	197710814		2203	4300	6503	SO:0001630	splice_region_variant	89782			cell adhesion|cell division|mitosis|proteolysis	cytoplasm|membrane	metalloendopeptidase activity|zinc ion binding	g.chr3:197710814G>A	AJ312398	AJ312398	CCDS3332.1, CCDS46988.1	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			2008-02-04			ENSG00000185621	ENSG00000185621	ENSG00000185621	ENSG00000185621	3.4.24.36			15991	15991	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			609380	609380								Standard	Standard	NM_033029	NM_033029		Approved	Gp63, Msp	uc010iar.3	uc010iar.3	Q96KR4	Q96KR4	OTTHUMG00000155375	OTTHUMG00000155375	ENST00000330198.4:c.729-1G>A	3.37:g.197710814G>A			LMLN_ENST00000482695.1_Splice_Site_p.R191R|LMLN_ENST00000420910.2_Splice_Site_p.R243R|LMLN_ENST00000332636.5_Splice_Site_p.R191R	p.R243R	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)	7	751	+	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	243		B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Splice_Site	SNP	ENST00000330198.4	37	c.729G>A	CCDS3332.1																																																																																									0.368	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1		-6.125926	11	11	77	77	NM_033029	Silent	3	6.483899	6.483899	56	0.050847	0	0	0	1	0	3	56	0.050847
EWSR1	2130	broad.mit.edu	37	22	29674050	29674050	+	Nonsense_Mutation	SNP	C	C	G			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr22:29674050C>G	ENST00000397938.2	+	5	577	c.258C>G	c.(256-258)taC>taG	p.Y86*	EWSR1_ENST00000331029.7_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000332035.6_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000333395.6_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000332050.6_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000406548.1_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000414183.2_Nonsense_Mutation_p.Y92*	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN	EWS RNA-binding protein 1	86	31 X approximate tandem repeats.|EAD (Gln/Pro/Thr-rich).				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		EWSR1/ATF1(347)|EWSR1/POU5F1(10)|EWSR1/PBX1(3)|EWSR1/DDIT3(45)|EWSR1/FEV(11)|EWSR1/CREB1(44)|EWSR1/SMARCA5(2)|EWSR1/ETV4(6)|EWSR1/ERG(178)|EWSR1/ZNF384(4)|EWSR1/ETV1(7)|EWSR1/FLI1(2569)|EWSR1/NR4A3(146)|EWSR1/SP3(3)|EWSR1/PATZ1(2)|EWSR1/WT1(234)|EWSR1/NFATC2(9)	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CCCAGGCATACAGCCAGCCTG	0.527			T	"""FLI1, ERG, ZNF278, NR4A3, FEV, ATF1, ETV1, ETV4, WT1, ZNF384, CREB1, POU5F1,  PBX1"""	"""Ewing sarcoma,  desmoplastic small round cell tumor , ALL, clear cell sarcoma, sarcoma, myoepithelioma"""																																	ENST00000397938.2		Dom	yes		22	22q12	2130	Ewing sarcoma breakpoint region 1 (EWS)		"""L, M"""	0			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						c.(256-258)taC>taG	EWS RNA-binding protein 1						35.0	36.0	35.0					22																	29674050		2203	4300	6503	SO:0001587	stop_gained	2130			regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	calmodulin binding|nucleotide binding|RNA binding|zinc ion binding	g.chr22:29674050C>G			CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	CCDS13851.1, CCDS13852.1, CCDS13852.2, CCDS54512.1, CCDS54513.1, CCDS54514.1	22q12.2	2013-05-24	2013-05-24		2013-05-24	2013-05-24		ENSG00000182944	ENSG00000182944	ENSG00000182944	ENSG00000182944		"""RNA binding motif (RRM) containing"""	"""RNA binding motif (RRM) containing"""	3508	3508	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			133450	133450	"""Ewing sarcoma breakpoint region 1"""		"""Ewing sarcoma breakpoint region 1"""			1522903	1522903	Standard	Standard	NM_005243	NM_005243		Approved	EWS	uc003aev.3	uc003aev.3	Q01844	Q01844	OTTHUMG00000151107	OTTHUMG00000151107	ENST00000397938.2:c.258C>G	22.37:g.29674050C>G	ENSP00000381031:p.Tyr86*		EWSR1_ENST00000414183.2_Nonsense_Mutation_p.Y92*|EWSR1_ENST00000331029.7_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000332050.6_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000406548.1_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000332035.6_Nonsense_Mutation_p.Y86*|EWSR1_ENST00000333395.6_Nonsense_Mutation_p.Y86*	p.Y86*	NM_001163285.1|NM_001163286.1|NM_005243.3|NM_013986.3	NP_001156757.1|NP_001156758.1|NP_005234.1|NP_053733.2	Q01844	EWS_HUMAN			5	577	+			86	31 X approximate tandem repeats.|EAD (Gln/Pro/Thr-rich).	B0QYK1|Q5THL0|Q92635|Q96FE8|Q96MN4|Q96MX4|Q9BWA2	Nonsense_Mutation	SNP	ENST00000397938.2	37	c.258C>G	CCDS13851.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466621	0.63625	.	.	ENSG00000182944	ENST00000332050;ENST00000397938;ENST00000436425;ENST00000447973;ENST00000406548;ENST00000437155;ENST00000331029;ENST00000414183;ENST00000333395;ENST00000455726;ENST00000332035	.	.	.	5.31	2.09	0.27110	5.31	2.09	0.27110	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3611	0.32359	0.0:0.6285:0.0:0.3715	.	.	.	.	X	86;86;93;92;86;87;86;92;86;86;86	.	ENSP00000330516:Y86X	Y	+	3	2	2	EWSR1	28004050	28004050	0.968000	0.33430	0.998000	0.56505	0.992000	0.81027	0.039000	0.13884	0.325000	0.23359	-0.142000	0.14014	TAC		0.527	EWSR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321345.1		38.527190	17	17	42	42	NM_005243		11	38.57069	38.570690	9	0.550000	0	0	0	1	0	11	9	0.55
GNAQ	2776	broad.mit.edu	37	9	80409488	80409488	+	Missense_Mutation	SNP	T	T	A	rs121913492		TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr9:80409488T>A	ENST00000286548.4	-	5	848	c.626A>T	c.(625-627)cAa>cTa	p.Q209L	GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7L	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	209			Q -> L (found in blue naevi and uveal melanoma samples; somatic mutation; constitutive activation).		action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.Q209L(87)|p.Q209P(64)|p.Q209Y(1)|p.Q209R(1)		NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						CTCTGACCTTTGGCCCCCTAC	0.348			Mis		uveal melanoma																																	ENST00000286548.4		Dom	yes		9	9q21	2776	"""guanine nucleotide binding protein (G protein), q polypeptide"""		E	153	Substitution - Missense(153)	eye(99)|skin(43)|meninges(10)|NS(1)	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						c.(625-627)cAa>cTa	guanine nucleotide binding protein (G protein), q polypeptide						108.0	105.0	106.0					9																	80409488		2203	4300	6503	SO:0001583	missense	2776			activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	g.chr9:80409488T>A			CCDS6658.1	CCDS6658.1	9q21	2010-03-17			2010-03-17			ENSG00000156052	ENSG00000156052	ENSG00000156052	ENSG00000156052				4390	4390	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			600998	600998						8825633	8825633	Standard	Standard	NM_002072	NM_002072		Approved	G-ALPHA-q, GAQ	uc004akw.3	uc004akw.3	P50148	P50148	OTTHUMG00000020059	OTTHUMG00000020059	ENST00000286548.4:c.626A>T	9.37:g.80409488T>A	ENSP00000286548:p.Gln209Leu		GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7L	p.Q209L	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN			5	848	-			209		O15108|Q13462|Q6NT27|Q92471|Q9BZB9	Missense_Mutation	SNP	ENST00000286548.4	37	c.626A>T	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.985495	0.93044	.	.	ENSG00000156052	ENST00000286548;ENST00000397476	D;D	0.91237	-2.81;-2.81	5.69	5.69	0.88448	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97573	0.9205	H	0.99347	4.525	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99402	1.0928	10	0.87932	D	0	.	15.9502	0.79827	0.0:0.0:0.0:1.0	.	209	P50148	GNAQ_HUMAN	L	209;7	ENSP00000286548:Q209L;ENSP00000443197:Q7L	ENSP00000286548:Q209L	Q	-	2	0	0	GNAQ	79599308	79599308	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.040000	0.89188	2.167000	0.68274	0.460000	0.39030	CAA		0.348	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1		145.834004	-7	-7	105	105	NM_002072		46	146.411989	146.411989	63	0.422018	0	0	0	1	0	46	63	0.422018
SYTL3	94120	broad.mit.edu	37	6	159181693	159181693	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr6:159181693G>A	ENST00000297239.9	+	14	1524	c.1330G>A	c.(1330-1332)Gtt>Att	p.V444I	SYTL3_ENST00000360448.3_Missense_Mutation_p.V376I|SYTL3_ENST00000367081.3_Missense_Mutation_p.V170I			Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	444					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	calcium-dependent phospholipid binding (GO:0005544)			endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|urinary_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		CGAAGACAGCGTTCCTCAGAG	0.557																																						ENST00000297239.9											0			endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|urinary_tract(1)	20						c.(1330-1332)Gtt>Att	synaptotagmin-like 3						123.0	114.0	117.0					6																	159181693		2203	4300	6503	SO:0001583	missense	94120			intracellular protein transport	endomembrane system|membrane	Rab GTPase binding	g.chr6:159181693G>A	AK055750	AK055750	CCDS34563.1, CCDS56458.1	CCDS34563.1, CCDS56458.1	6q25.3	2008-07-04			2008-07-04			ENSG00000164674	ENSG00000164674	ENSG00000164674	ENSG00000164674				15587	15587	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product										11773082	11773082	Standard	Standard	NM_001242384	NM_001242384		Approved	SLP3, exophilin-6	uc003qrp.3	uc003qrp.3	Q4VX76	Q4VX76	OTTHUMG00000015916	OTTHUMG00000015916	ENST00000297239.9:c.1330G>A	6.37:g.159181693G>A	ENSP00000297239:p.Val444Ile		SYTL3_ENST00000360448.3_Missense_Mutation_p.V376I|SYTL3_ENST00000367081.3_Missense_Mutation_p.V170I	p.V444I			Q4VX76	SYTL3_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)	14	1524	+		Breast(66;0.000776)|Ovarian(120;0.0303)	444		Q496J4|Q496J6|Q5U3B9	Missense_Mutation	SNP	ENST00000297239.9	37	c.1330G>A	CCDS56458.1	.	.	.	.	.	.	.	.	.	.	G	7.930	0.740384	0.15642	.	.	ENSG00000164674	ENST00000360448;ENST00000543689;ENST00000297239;ENST00000367081	T;T;T	0.63096	2.15;2.14;-0.02	4.3	-8.0	0.01126	4.3	-8.0	0.01126	.	2.784810	0.01180	N	0.007074	T	0.11452	0.0279	N	0.08118	0	0.09310	N	1	B;B;B	0.12630	0.006;0.0;0.005	B;B;B	0.09377	0.003;0.001;0.004	T	0.06144	-1.0843	10	0.15066	T	0.55	.	3.4759	0.07585	0.3914:0.3776:0.1257:0.1053	.	170;444;376	F8W7H4;Q4VX76;Q4VX76-2	.;SYTL3_HUMAN;.	I	376;444;444;170	ENSP00000353631:V376I;ENSP00000297239:V444I;ENSP00000356048:V170I	ENSP00000297239:V444I	V	+	1	0	0	SYTL3	159101681	159101681	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.851000	0.00732	-1.958000	0.01019	-0.119000	0.15052	GTT		0.557	SYTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042876.1		137.898842	-24	-24	90	90			41	140.36428	140.364280	16	0.719298	0	0	0	1	0	41	16	0.719298
PITRM1	10531	broad.mit.edu	37	10	3191920	3191920	+	Silent	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr10:3191920G>A	ENST00000224949.4	-	16	1798	c.1764C>T	c.(1762-1764)tgC>tgT	p.C588C	PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380994.1_Silent_p.C146C|PITRM1_ENST00000451104.2_Silent_p.C556C|PITRM1_ENST00000464395.1_5'Flank|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380989.2_Silent_p.C588C			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	588					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TGGGCTGGGCGCAGTACTGAA	0.473																																						ENST00000380989.2											0			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						c.(1762-1764)tgC>tgT	pitrilysin metallopeptidase 1						110.0	113.0	112.0					10																	3191920		1889	4123	6012	SO:0001819	synonymous_variant	10531			proteolysis		metalloendopeptidase activity|zinc ion binding	g.chr10:3191920G>A	AB029027	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959	ENSG00000107959	ENSG00000107959				17663	17663	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""PreP peptidasome"""	"""PreP peptidasome"""			"""pitrilysin metalloproteinase 1"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	1036083, 10470851, 16849325	Standard	Standard	NM_014889	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	uc009xhv.2	Q5JRX3	Q5JRX3	OTTHUMG00000017557	OTTHUMG00000017557	ENST00000224949.4:c.1764C>T	10.37:g.3191920G>A			PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000451104.2_Silent_p.C556C|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380994.1_Silent_p.C146C|PITRM1_ENST00000224949.4_Silent_p.C588C	p.C588C	NM_001242307.1|NM_014889.3	NP_001229236.1|NP_055704.2	E7ES23	E7ES23_HUMAN			16	1802	-			556		B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent	SNP	ENST00000224949.4	37	c.1764C>T	CCDS59208.1																																																																																									0.473	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		-18.695429	-9	-9	103	103			4	7.805297	7.805297	109	0.035398	0	0	0	1	0	4	109	0.035398
NUP188	23511	broad.mit.edu	37	9	131760467	131760467	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr9:131760467G>A	ENST00000372577.2	+	31	3410	c.3389G>A	c.(3388-3390)cGc>cAc	p.R1130H		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1130					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						GTGGTGCGTCGCCAGCTCTTT	0.438																																						ENST00000372577.2											0			breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						c.(3388-3390)cGc>cAc	nucleoporin 188kDa						203.0	205.0	204.0					9																	131760467		2203	4300	6503	SO:0001583	missense	23511			carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding	g.chr9:131760467G>A	D79991	D79991	CCDS35156.1	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319	ENSG00000095319	ENSG00000095319				17859	17859	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			615587	615587	"""KIAA0169"""	KIAA0169	"""KIAA0169"""	KIAA0169		11029043	11029043	Standard	Standard	NM_015354	NM_015354		Approved		uc004bws.2	uc004bws.2	Q5SRE5	Q5SRE5	OTTHUMG00000020768	OTTHUMG00000020768	ENST00000372577.2:c.3389G>A	9.37:g.131760467G>A	ENSP00000361658:p.Arg1130His			p.R1130H	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN			31	3410	+			1130		Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	37	c.3389G>A	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	G	9.043	0.990052	0.18966	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.31510	1.49	5.67	2.86	0.33363	5.67	2.86	0.33363	.	0.257998	0.39544	N	0.001326	T	0.20740	0.0499	L	0.36672	1.1	0.30026	N	0.813911	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.22347	-1.0219	10	0.15499	T	0.54	-2.5035	9.5606	0.39366	0.3138:0.0:0.6862:0.0	.	463;1130	E9PET9;Q5SRE5	.;NU188_HUMAN	H	1019;1130	ENSP00000361658:R1130H	ENSP00000349125:R1019H	R	+	2	0	0	NUP188	130800288	130800288	0.998000	0.40836	1.000000	0.80357	0.579000	0.36224	0.717000	0.25851	0.349000	0.23975	-1.149000	0.01842	CGC		0.438	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		-84.332469	-94	-94	278	278			5	7.001185	7.001185	336	0.014663	0	0	0	1	0	5	336	0.014663
ACVRL1	94	broad.mit.edu	37	12	52309036	52309036	+	Missense_Mutation	SNP	G	G	A	rs377201195		TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr12:52309036G>A	ENST00000388922.4	+	7	1083	c.800G>A	c.(799-801)cGc>cAc	p.R267H	ACVRL1_ENST00000550683.1_Missense_Mutation_p.R281H|ACVRL1_ENST00000419526.2_Missense_Mutation_p.R93H	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	267	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|artery development (GO:0060840)|blood circulation (GO:0008015)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|blood vessel maturation (GO:0001955)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|cellular response to transforming growth factor beta stimulus (GO:0071560)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of focal adhesion assembly (GO:0051895)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of blood pressure (GO:0008217)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of DNA replication (GO:0006275)|regulation of endothelial cell proliferation (GO:0001936)|regulation of transcription, DNA-templated (GO:0006355)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|venous blood vessel development (GO:0060841)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	ATGACCTCCCGCAACTCGAGC	0.617																																						ENST00000550683.1											0			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20						c.(841-843)cGc>cAc	activin A receptor type II-like 1	G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	64.0	55.0	58.0		800,800	5.4	1.0	12		58	0,8600		0,0,4300	no	missense,missense	ACVRL1	NM_000020.2,NM_001077401.1	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	267/504,267/504	52309036	1,13005	2203	4300	6503	SO:0001583	missense	94			blood vessel endothelial cell proliferation involved in sprouting angiogenesis|blood vessel maturation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of endothelial cell migration|negative regulation of focal adhesion assembly|positive regulation of BMP signaling pathway|positive regulation of transcription, DNA-dependent|regulation of blood pressure|regulation of blood vessel endothelial cell migration|regulation of DNA replication|regulation of endothelial cell proliferation|transforming growth factor beta receptor signaling pathway|wound healing, spreading of epidermal cells	cell surface|integral to plasma membrane	activin binding|activin receptor activity, type I|ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity	g.chr12:52309036G>A	L17075	L17075	CCDS31804.1	CCDS31804.1	12q13.13	2014-09-17			2014-09-17			ENSG00000139567	ENSG00000139567	ENSG00000139567	ENSG00000139567				175	175	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			601284	601284		ACVRLK1, ORW2		ACVRLK1, ORW2		8397373, 8640225	8397373, 8640225	Standard	Standard	NM_000020	NM_000020		Approved	HHT2, ALK1, HHT	uc001rzk.3	uc001rzk.3	P37023	P37023	OTTHUMG00000169507	OTTHUMG00000169507	ENST00000388922.4:c.800G>A	12.37:g.52309036G>A	ENSP00000373574:p.Arg267His		ACVRL1_ENST00000419526.2_Missense_Mutation_p.R93H|ACVRL1_ENST00000388922.4_Missense_Mutation_p.R267H	p.R281H	NM_001077401.1	NP_001070869.1	P37023	ACVL1_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.0991)	6	943	+			267	Protein kinase.	A6NGA8	Missense_Mutation	SNP	ENST00000388922.4	37	c.842G>A	CCDS31804.1	.	.	.	.	.	.	.	.	.	.	G	19.63	3.863696	0.71949	2.27E-4	0.0	ENSG00000139567	ENST00000388922;ENST00000267008;ENST00000550683;ENST00000548659;ENST00000419526	D;D;D	0.93426	-3.22;-3.22;-3.22	5.44	5.44	0.79542	5.44	5.44	0.79542	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.45126	D	0.000385	D	0.94935	0.8362	L	0.36672	1.1	0.54753	D	0.999988	B;D	0.89917	0.212;1.0	B;D	0.74674	0.024;0.984	D	0.94983	0.8127	10	0.59425	D	0.04	.	19.055	0.93059	0.0:0.0:1.0:0.0	.	93;267	E7EN07;P37023	.;ACVL1_HUMAN	H	267;267;281;93;93	ENSP00000373574:R267H;ENSP00000447884:R281H;ENSP00000392492:R93H	ENSP00000267008:R267H	R	+	2	0	0	ACVRL1	50595303	50595303	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.461000	0.53035	2.824000	0.97209	0.655000	0.94253	CGC		0.617	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2		3.715687	-4	-4	45	45			3	7.250615	7.250615	22	0.120000	0	0	0	1	0	3	22	0.12
SERPINB4	6318	broad.mit.edu	37	18	61305232	61305232	+	Silent	SNP	C	C	T			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr18:61305232C>T	ENST00000341074.5	-	8	1009	c.894G>A	c.(892-894)acG>acA	p.T298T	SERPINB4_ENST00000356424.6_Silent_p.T246T	NM_002974.2	NP_002965.1	P48594	SPB4_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 4	298					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42						TGGTTCTCAACGTGTCCTTGA	0.453																																						ENST00000341074.5											0			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42						c.(892-894)acG>acA	serpin peptidase inhibitor, clade B (ovalbumin), member 4						185.0	160.0	168.0					18																	61305232		2203	4300	6503	SO:0001819	synonymous_variant	6318						g.chr18:61305232C>T	X89015	X89015	CCDS11986.1	CCDS11986.1	18q21.33	2014-02-18	2005-08-18		2014-02-18	2005-08-18		ENSG00000206073	ENSG00000206073	ENSG00000206073	ENSG00000206073		"""Serine (or cysteine) peptidase inhibitors"""	"""Serine (or cysteine) peptidase inhibitors"""	10570	10570	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""squamous cell carcinoma antigen 2"""	"""squamous cell carcinoma antigen 2"""	600518	600518	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"""	SCCA2	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"""	SCCA2		7724531, 14630915, 24172014	7724531, 14630915, 24172014	Standard	Standard	NM_175041	NM_175041		Approved	PI11, LEUPIN, SCCA-2, SCCA1			P48594	P48594	OTTHUMG00000060405	OTTHUMG00000060405	ENST00000341074.5:c.894G>A	18.37:g.61305232C>T			SERPINB4_ENST00000356424.6_Silent_p.T246T	p.T298T	NM_002974.2	NP_002965.1					8	1009	-					A8K847	Silent	SNP	ENST00000341074.5	37	c.894G>A	CCDS11986.1	.	.	.	.	.	.	.	.	.	.	C	5.939	0.357213	0.11239	.	.	ENSG00000206073	ENST00000413673	.	.	.	4.51	-9.03	0.00737	4.51	-9.03	0.00737	.	.	.	.	.	T	0.16514	0.0397	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.14699	-1.0463	4	.	.	.	.	3.1776	0.06573	0.1342:0.1224:0.239:0.5045	.	.	.	.	H	279	.	.	R	-	2	0	0	SERPINB4	59456212	59456212	0.000000	0.05858	0.000000	0.03702	0.222000	0.24845	-4.287000	0.00259	-2.264000	0.00689	-0.192000	0.12808	CGT		0.453	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2		66.299786	-11	-11	71	71	NM_175041		23	68.520153	68.520153	50	0.315068	0	0	0	1	0	23	50	0.315068
WDR47	22911	broad.mit.edu	37	1	109553777	109553777	+	Silent	SNP	G	G	C			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr1:109553777G>C	ENST00000369962.3	-	5	1113	c.891C>G	c.(889-891)tcC>tcG	p.S297S	WDR47_ENST00000357672.3_Silent_p.S269S|WDR47_ENST00000361054.3_Silent_p.S269S|WDR47_ENST00000400794.3_Silent_p.S304S|WDR47_ENST00000369965.4_Silent_p.S297S			O94967	WDR47_HUMAN	WD repeat domain 47	297					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		TTCTCATTGGGGATGATGGAT	0.428																																						ENST00000357672.3											0			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20						c.(805-807)tcC>tcG	WD repeat domain 47						267.0	284.0	278.0					1																	109553777		2203	4296	6499	SO:0001819	synonymous_variant	22911						g.chr1:109553777G>C	AB020700	AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			2013-01-09			ENSG00000085433	ENSG00000085433	ENSG00000085433	ENSG00000085433		"""WD repeat domain containing"""	"""WD repeat domain containing"""	29141	29141	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			615734	615734						10048485	10048485	Standard	Standard	NM_014969	NM_014969		Approved	KIAA0893	uc001dwl.3	uc001dwl.3	O94967	O94967	OTTHUMG00000011734	OTTHUMG00000011734	ENST00000369962.3:c.891C>G	1.37:g.109553777G>C			WDR47_ENST00000400794.3_Silent_p.S304S|WDR47_ENST00000369965.4_Silent_p.S297S|WDR47_ENST00000361054.3_Silent_p.S269S|WDR47_ENST00000369962.3_Silent_p.S297S	p.S269S			O94967	WDR47_HUMAN		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)	4	1182	-		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)	297		A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	Silent	SNP	ENST00000369962.3	37	c.807C>G	CCDS44187.1																																																																																									0.428	WDR47-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032414.2		375.126026	-32	-32	277	277	NM_014969		127	379.091558	379.091558	204	0.383686	0	0	0	1	0	127	204	0.383686
PAMR1	25891	broad.mit.edu	37	11	35513670	35513670	+	Frame_Shift_Del	DEL	C	C	-			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr11:35513670delC	ENST00000378880.2	-	3	747	c.302delG	c.(301-303)ggtfs	p.G101fs	PAMR1_ENST00000532848.1_Frame_Shift_Del_p.G61fs|PAMR1_ENST00000378878.3_Frame_Shift_Del_p.G101fs|PAMR1_ENST00000278360.3_Frame_Shift_Del_p.G101fs|PAMR1_ENST00000534803.1_5'UTR	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	101						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						ATCCAAGGTACCCCCCCATGA	0.517																																						ENST00000378880.2											0			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						c.(301-303)ggtfs	peptidase domain containing associated with muscle regeneration 1						201.0	193.0	196.0					11																	35513670		2202	4298	6500	SO:0001589	frameshift_variant	25891			proteolysis	extracellular region	serine-type endopeptidase activity	g.chr11:35513670delC			CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			2009-09-30			ENSG00000149090	ENSG00000149090	ENSG00000149090	ENSG00000149090				24554	24554	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""regeneration-associated muscle protease"""	"""regeneration-associated muscle protease"""								15111323	15111323	Standard	Standard	NM_001282675	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	uc001mwf.3	Q6UXH9	Q6UXH9	OTTHUMG00000166328	OTTHUMG00000166328	ENST00000378880.2:c.302delG	11.37:g.35513670delC	ENSP00000368158:p.Gly101fs		PAMR1_ENST00000532848.1_Frame_Shift_Del_p.G61fs|PAMR1_ENST00000534803.1_5'UTR|PAMR1_ENST00000278360.3_Frame_Shift_Del_p.G101fs|PAMR1_ENST00000378878.3_Frame_Shift_Del_p.G101fs	p.G101fs	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN			3	747	-			101		A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Frame_Shift_Del	DEL	ENST00000378880.2	37	c.302delG	CCDS31460.1																																																																																									0.517	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	.	.	-43	-43	191	191	NM_015430		7			286	0.02						7	286	0.02
ZNF473	25888	broad.mit.edu	37	19	50549632	50549632	+	Frame_Shift_Del	DEL	C	C	-			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr19:50549632delC	ENST00000595661.1	+	6	2427	c.1932delC	c.(1930-1932)cacfs	p.H644fs	CTD-2126E3.3_ENST00000599914.1_RNA|ZNF473_ENST00000601364.1_Intron|ZNF473_ENST00000270617.3_Frame_Shift_Del_p.H644fs|CTD-2126E3.3_ENST00000599410.1_RNA|ZNF473_ENST00000445728.3_Frame_Shift_Del_p.H632fs|ZNF473_ENST00000391821.2_Frame_Shift_Del_p.H644fs			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	644					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		CAAAGGAGCACCCTTTTAAAT	0.453																																						ENST00000595661.1											0			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						c.(1930-1932)cacfs	zinc finger protein 473						78.0	73.0	75.0					19																	50549632		2203	4300	6503	SO:0001589	frameshift_variant	25888			histone mRNA 3'-end processing|regulation of transcription, DNA-dependent|termination of RNA polymerase II transcription	Cajal body	DNA binding|protein binding|zinc ion binding	g.chr19:50549632delC	AB032967	AB032967	CCDS33077.1	CCDS33077.1	19q13.33	2013-01-08			2013-01-08								"""Zinc fingers, C2H2-type"", ""-"""	"""Zinc fingers, C2H2-type"", ""-"""	23239	23239	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product										11782445	11782445	Standard	Standard	NM_015428	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	uc002prn.3	Q8WTR7	Q8WTR7			ENST00000595661.1:c.1932delC	19.37:g.50549632delC	ENSP00000472808:p.His644fs		ZNF473_ENST00000601364.1_Intron|CTD-2126E3.3_ENST00000599914.1_RNA|ZNF473_ENST00000391821.2_Frame_Shift_Del_p.H644fs|ZNF473_ENST00000270617.3_Frame_Shift_Del_p.H644fs|CTD-2126E3.3_ENST00000599410.1_RNA|ZNF473_ENST00000445728.3_Frame_Shift_Del_p.H632fs	p.H644fs			Q8WTR7	ZN473_HUMAN		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)	6	2427	+		all_neural(266;0.0459)|Ovarian(192;0.0728)	644		A8K8T7|Q9ULS9|Q9Y4Q7	Frame_Shift_Del	DEL	ENST00000595661.1	37	c.1932delC	CCDS33077.1																																																																																									0.453	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	.	.	-10	-10	46	46	XM_046390		25			47	0.35						25	47	0.35
BAP1	8314	broad.mit.edu	37	3	52438542	52438542	+	Nonsense_Mutation	SNP	G	G	A			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr3:52438542G>A	ENST00000460680.1	-	12	1648	c.1177C>T	c.(1177-1179)Cag>Tag	p.Q393*	BAP1_ENST00000296288.5_Nonsense_Mutation_p.Q375*	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TCTGAGTACTGCTGGGGTGGG	0.572			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															GBM(101;493 1458 7992 21037 25532)	ENST00000460680.1		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	0			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180						c.(1177-1179)Cag>Tag	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)						117.0	89.0	99.0					3																	52438542		2203	4300	6503	SO:0001587	stop_gained	8314			anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	g.chr3:52438542G>A	AF045581	AF045581	CCDS2853.1	CCDS2853.1	3p21.31-p21.2	2014-09-17			2014-09-17			ENSG00000163930	ENSG00000163930	ENSG00000163930	ENSG00000163930				950	950	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			603089	603089						9528852	9528852	Standard	Standard	NM_004656	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	uc003ddx.4	Q92560	Q92560	OTTHUMG00000158392	OTTHUMG00000158392	ENST00000460680.1:c.1177C>T	3:g.52438542G>A	ENSP00000417132:p.Gln393*		BAP1_ENST00000296288.5_Nonsense_Mutation_p.Q375*	p.Q393*	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN		BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	12	1648	-			0		B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Nonsense_Mutation	SNP	ENST00000460680.1		c.1177C>T	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	38	6.723555	0.97788	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	.	.	.	5.54	5.54	0.83059	5.54	5.54	0.83059	.	0.124915	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	17.6638	0.88198	0.0:0.0:1.0:0.0	.	.	.	.	X	393;375	.	ENSP00000296288:Q375X	Q	-	1	0	0	BAP1	52413582	52413582	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.512000	0.81728	2.603000	0.88011	0.655000	0.94253	CAG		0.572	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	8.120000e+00	1.635000e+01	2	2	28	28			4			2	6.670000e-01						4	2	0.667
BAP1	8314	broad.mit.edu	37	3	52438543	52438548	+	In_Frame_Del	DEL	CTGGGG	CTGGGG	-			TCGA-V4-A9EL-01A-11D-A39W-08	TCGA-V4-A9EL-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6bf15a15-4a35-4e55-9c10-770fdff09fad	9dc7146a-1ee2-431a-a6b8-b8e9f16417c7	g.chr3:52438543_52438548delCTGGGG	ENST00000460680.1	-	12	1642_1647	c.1171_1176delCCCCAG	c.(1171-1176)ccccagdel	p.PQ391del	BAP1_ENST00000296288.5_In_Frame_Del_p.PQ373del	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CTGAGTACTGCTGGGGTGGGCGGACT	0.578			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															GBM(101;493 1458 7992 21037 25532)	ENST00000460680.1		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	0			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180						c.(1171-1176)ccccagdel	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)																																			SO:0001651	inframe_deletion	8314			anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	g.chr3:52438543_52438548delCTGGGG	AF045581	AF045581	CCDS2853.1	CCDS2853.1	3p21.31-p21.2	2014-09-17			2014-09-17			ENSG00000163930	ENSG00000163930	ENSG00000163930	ENSG00000163930				950	950	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			603089	603089						9528852	9528852	Standard	Standard	NM_004656	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	uc003ddx.4	Q92560	Q92560	OTTHUMG00000158392	OTTHUMG00000158392	ENST00000460680.1:c.1171_1176delCCCCAG	3:g.52438543_52438548delCTGGGG	ENSP00000417132:p.Pro391_Gln392del		BAP1_ENST00000296288.5_In_Frame_Del_p.PQ373del	p.PQ391del	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN		BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	12	1642_1647	-			0		B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	In_Frame_Del	DEL	ENST00000460680.1		c.1171_1176delCCCCAG	CCDS2853.1																																																																																									0.578	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	8.110000e+00	1.634000e+01	1	1	27	27			4			2	6.670000e-01						4	2	0.667
