#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	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_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
NOP9	161424	broad.mit.edu	37	14	24774190	24774190	+	Silent	SNP	G	G	T			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr14:24774190G>T	ENST00000267425.3	+	10	1893	c.1800G>T	c.(1798-1800)gtG>gtT	p.V600V	NOP9_ENST00000396802.3_3'UTR	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	600							poly(A) RNA binding (GO:0044822)										GCCACCATGTGGCTCGAAATG	0.552																																						ENST00000267425.3																			0											c.(1798-1800)gtG>gtT		NOP9 nucleolar protein							62.0	57.0	59.0					14																	24774190		2203	4300	6503	SO:0001819	synonymous_variant	161424							g.chr14:24774190G>T		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.1800G>T	14.37:g.24774190G>T						NOP9_ENST00000396802.3_3'UTR	p.V600V	NM_174913.1	NP_777573.1					10	1893	+								A8MY76|Q8IVF0|Q8TBS6	Silent	SNP	ENST00000267425.3	37	c.1800G>T	CCDS9624.1																																																																																				0.552	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2			29	60	1	0	1.36615e-20	1	1.54434e-20	29	60				
CPSF3	51692	broad.mit.edu	37	2	9570993	9570993	+	Missense_Mutation	SNP	G	G	A			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr2:9570993G>A	ENST00000238112.3	+	4	531	c.325G>A	c.(325-327)Gat>Aat	p.D109N	CPSF3_ENST00000460593.1_Missense_Mutation_p.D72N	NM_016207.3	NP_057291.1	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3, 73kDa	109					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	5'-3' exonuclease activity (GO:0008409)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		GCTTCTTTCTGATTATGTCAA	0.348																																					Colon(194;1259 2048 3845 5218 19985)	ENST00000460593.1																			0				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						c.(214-216)Gat>Aat		cleavage and polyadenylation specific factor 3, 73kDa							94.0	99.0	98.0					2																	9570993		2203	4300	6503	SO:0001583	missense	51692				histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding	g.chr2:9570993G>A	AF171877	CCDS1664.1	2p25.1	2009-01-06	2002-08-29		ENSG00000119203	ENSG00000119203			2326	protein-coding gene	gene with protein product		606029	"""cleavage and polyadenylation specific factor 3, 73kD subunit"""			8929409	Standard	NM_016207		Approved	CPSF-73, CPSF73, YSH1	uc002qzo.2	Q9UKF6	OTTHUMG00000090415	ENST00000238112.3:c.325G>A	2.37:g.9570993G>A	ENSP00000238112:p.Asp109Asn					CPSF3_ENST00000238112.3_Missense_Mutation_p.D109N	p.D72N			Q9UKF6	CPSF3_HUMAN		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)	4	1352	+	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)	109					O14769|Q53RS2|Q96F36	Missense_Mutation	SNP	ENST00000238112.3	37	c.214G>A	CCDS1664.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.037056	0.93630	.	.	ENSG00000119203	ENST00000238112;ENST00000475482;ENST00000427001;ENST00000460593	T;T;T	0.60672	0.17;0.17;0.17	5.65	5.65	0.86999	Beta-lactamase-like (2);	0.000000	0.85682	D	0.000000	D	0.83608	0.5291	H	0.94698	3.57	0.80722	D	1	D;D	0.89917	1.0;0.981	D;D	0.77004	0.989;0.966	D	0.87595	0.2493	10	0.72032	D	0.01	-6.0454	19.7341	0.96195	0.0:0.0:1.0:0.0	.	109;109	E7ER23;Q9UKF6	.;CPSF3_HUMAN	N	109;72;109;72	ENSP00000238112:D109N;ENSP00000419744:D72N;ENSP00000418957:D72N	ENSP00000238112:D109N	D	+	1	0	CPSF3	9488444	1.000000	0.71417	0.998000	0.56505	0.922000	0.55478	9.759000	0.98931	2.672000	0.90937	0.650000	0.86243	GAT		0.348	CPSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206843.1	NM_016207		20	46	0	0	0	1	0	20	46				
ZPBP	11055	broad.mit.edu	37	7	50057890	50057890	+	Silent	SNP	T	T	C			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr7:50057890T>C	ENST00000046087.2	-	6	798	c.729A>G	c.(727-729)aaA>aaG	p.K243K	ZPBP_ENST00000491129.1_Intron|ZPBP_ENST00000419417.1_Silent_p.K242K	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	243					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					GCTTGGGTCCTTTTTCAGTGT	0.294																																						ENST00000046087.2																			0				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29						c.(727-729)aaA>aaG		zona pellucida binding protein							91.0	89.0	90.0					7																	50057890		2203	4300	6503	SO:0001819	synonymous_variant	11055				binding of sperm to zona pellucida	extracellular region		g.chr7:50057890T>C	D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.729A>G	7.37:g.50057890T>C						ZPBP_ENST00000419417.1_Silent_p.K242K|ZPBP_ENST00000491129.1_Intron	p.K243K	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN			6	798	-	Glioma(55;0.08)|all_neural(89;0.245)		243					A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Silent	SNP	ENST00000046087.2	37	c.729A>G	CCDS5509.1																																																																																				0.294	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009		3	55	0	0	0	1	0	3	55				
DCP1A	55802	broad.mit.edu	37	3	53381536	53381536	+	Silent	SNP	C	C	A			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr3:53381536C>A	ENST00000607628.1	-	1	118	c.9G>T	c.(7-9)gcG>gcT	p.A3A	DCP1A_ENST00000606822.1_Silent_p.A3A|DCP1A_ENST00000480258.1_5'UTR|DCP1A_ENST00000294241.6_Silent_p.A3A	NM_018403.5	NP_060873.4	Q9NPI6	DCP1A_HUMAN	decapping mRNA 1A	3					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)		CTCGACTCAGCGCCTCCATCT	0.617																																						ENST00000607628.1																			0				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						c.(7-9)gcG>gcT		decapping mRNA 1A							69.0	82.0	78.0					3																	53381536		2134	4261	6395	SO:0001819	synonymous_variant	55802				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus	hydrolase activity|protein binding	g.chr3:53381536C>A	AJ275986	CCDS74946.1	3p21.1	2013-05-02	2013-05-02		ENSG00000162290	ENSG00000272886			18714	protein-coding gene	gene with protein product		607010	"""DCP1 decapping enzyme homolog A (S. cerevisiae)"""				Standard	XM_005278360		Approved	HSA275986, SMIF, SMAD4IP1	uc021wzi.1	Q9NPI6	OTTHUMG00000158193	ENST00000607628.1:c.9G>T	3.37:g.53381536C>A						DCP1A_ENST00000480258.1_5'UTR|DCP1A_ENST00000606822.1_Silent_p.A3A|DCP1A_ENST00000294241.6_Silent_p.A3A	p.A3A	NM_018403.5	NP_060873.4	Q9NPI6	DCP1A_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)	1	118	-			3					B4DHN9|U3KQM8	Silent	SNP	ENST00000607628.1	37	c.9G>T																																																																																					0.617	DCP1A-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018403		4	109	1	0	0.000602214	1	0.000602214	4	109				
RBM47	54502	broad.mit.edu	37	4	40440487	40440487	+	Missense_Mutation	SNP	G	G	A			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr4:40440487G>A	ENST00000381793.2	-	3	820	c.424C>T	c.(424-426)Ctc>Ttc	p.L142F	RBM47_ENST00000514014.1_Missense_Mutation_p.L104F|RBM47_ENST00000515809.1_Intron|RBM47_ENST00000295971.7_Missense_Mutation_p.L142F|RBM47_ENST00000381795.6_Missense_Mutation_p.L142F|RBM47_ENST00000319592.4_Missense_Mutation_p.L142F			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	142	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						CACACGCCGAGCAGGCGGCCC	0.622																																						ENST00000319592.4																			0				breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						c.(424-426)Ctc>Ttc		RNA binding motif protein 47							43.0	38.0	39.0					4																	40440487		2203	4300	6503	SO:0001583	missense	54502					nucleus	nucleotide binding|RNA binding	g.chr4:40440487G>A	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"""RNA binding motif (RRM) containing"""	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.424C>T	4.37:g.40440487G>A	ENSP00000371212:p.Leu142Phe					RBM47_ENST00000515809.1_Intron|RBM47_ENST00000381795.6_Missense_Mutation_p.L142F|RBM47_ENST00000381793.2_Missense_Mutation_p.L142F|RBM47_ENST00000514014.1_Missense_Mutation_p.L104F|RBM47_ENST00000295971.7_Missense_Mutation_p.L142F	p.L142F			A0AV96	RBM47_HUMAN			4	1133	-			142			RRM 1.		A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Missense_Mutation	SNP	ENST00000381793.2	37	c.424C>T	CCDS43223.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.414495	0.42817	.	.	ENSG00000163694	ENST00000319592;ENST00000381793;ENST00000381795;ENST00000295971;ENST00000514014;ENST00000515053;ENST00000513473;ENST00000505414	T;T;T;T;T;T;T;T	0.57107	2.97;0.42;2.97;0.42;0.42;2.97;0.42;0.42	5.78	5.78	0.91487	RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.76709	0.4025	M	0.92219	3.285	0.80722	D	1	D;D	0.76494	0.999;0.996	D;D	0.80764	0.994;0.969	T	0.81239	-0.1023	10	0.87932	D	0	-21.5585	10.4174	0.44329	0.1444:0.0:0.8556:0.0	.	142;142	A0AV96-2;A0AV96	.;RBM47_HUMAN	F	142;142;142;142;104;142;142;142	ENSP00000320108:L142F;ENSP00000371212:L142F;ENSP00000371214:L142F;ENSP00000295971:L142F;ENSP00000423243:L104F;ENSP00000422564:L142F;ENSP00000421589:L142F;ENSP00000423527:L142F	ENSP00000295971:L142F	L	-	1	0	RBM47	40135244	1.000000	0.71417	0.999000	0.59377	0.095000	0.18619	4.255000	0.58804	2.740000	0.93945	0.313000	0.20887	CTC		0.622	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027		3	63	0	0	0	1	0	3	63				
CHST2	9435	broad.mit.edu	37	3	142841171	142841171	+	Missense_Mutation	SNP	G	G	A			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr3:142841171G>A	ENST00000309575.3	+	2	2897	c.1513G>A	c.(1513-1515)Gtc>Atc	p.V505I		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	505					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						GCCCATGGCCGTCCTGGGCTA	0.607																																						ENST00000309575.3																			0				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						c.(1513-1515)Gtc>Atc		carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2							40.0	44.0	42.0					3																	142841171		2203	4300	6503	SO:0001583	missense	9435				inflammatory response|multicellular organismal development|N-acetylglucosamine metabolic process|sulfur compound metabolic process	integral to membrane|intrinsic to Golgi membrane|trans-Golgi network	N-acetylglucosamine 6-O-sulfotransferase activity	g.chr3:142841171G>A	BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"""Sulfotransferases, membrane-bound"""	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.1513G>A	3.37:g.142841171G>A	ENSP00000307911:p.Val505Ile						p.V505I	NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN			2	2897	+			505					D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	37	c.1513G>A	CCDS3129.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.469872	0.26423	.	.	ENSG00000175040	ENST00000309575	D	0.96104	-3.91	4.74	4.74	0.60224	.	0.170535	0.38492	N	0.001674	D	0.88912	0.6566	N	0.21194	0.64	0.28804	N	0.898624	B	0.20671	0.047	B	0.17979	0.02	T	0.79019	-0.1974	10	0.36615	T	0.2	-15.204	5.2101	0.15312	0.1725:0.1952:0.6322:0.0	.	505	Q9Y4C5	CHST2_HUMAN	I	505	ENSP00000307911:V505I	ENSP00000307911:V505I	V	+	1	0	CHST2	144323861	0.980000	0.34600	0.704000	0.30370	0.938000	0.57974	1.893000	0.39758	2.443000	0.82685	0.609000	0.83330	GTC		0.607	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		4	93	0	0	0	1	0	4	93				
CASZ1	54897	broad.mit.edu	37	1	10714607	10714607	+	Missense_Mutation	SNP	C	C	T			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr1:10714607C>T	ENST00000377022.3	-	10	2024	c.1707G>A	c.(1705-1707)atG>atA	p.M569I	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Missense_Mutation_p.M569I	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	569					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		TCTCGTGGGTCATCACGTCAG	0.597																																						ENST00000377022.3																			0				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54						c.(1705-1707)atG>atA		castor zinc finger 1							251.0	227.0	236.0					1																	10714607		2203	4300	6503	SO:0001583	missense	54897				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding	g.chr1:10714607C>T	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.1707G>A	1.37:g.10714607C>T	ENSP00000366221:p.Met569Ile					CASZ1_ENST00000344008.5_Missense_Mutation_p.M569I	p.M569I	NM_001079843.1	NP_001073312.1	Q86V15	CASZ1_HUMAN	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)	10	2024	-	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	569					Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	c.1707G>A	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.280048	0.80692	.	.	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.97	4.97	0.65823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.64000	0.2559	N	0.22421	0.69	0.54753	D	0.999989	B;P;P	0.46952	0.335;0.669;0.887	B;B;P	0.62184	0.188;0.259;0.899	T	0.66126	-0.6001	9	0.49607	T	0.09	-28.3319	18.6257	0.91336	0.0:1.0:0.0:0.0	.	593;569;569	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	I	569	.	ENSP00000339445:M569I	M	-	3	0	CASZ1	10637194	1.000000	0.71417	1.000000	0.80357	0.630000	0.37929	7.424000	0.80242	2.478000	0.83669	0.561000	0.74099	ATG		0.597	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		6	286	0	0	0	1	0	6	286				
MLLT3	4300	broad.mit.edu	37	9	20414346	20414346	+	Silent	SNP	G	G	A			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr9:20414346G>A	ENST00000380338.4	-	5	784	c.498C>T	c.(496-498)agC>agT	p.S166S	MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S163S|MLLT3_ENST00000475957.1_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	166	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S166S(4)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctactgctgctgctgc	0.527			T	MLL	ALL																																	ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		4	Substitution - coding silent(4)	p.S166S(4)	urinary_tract(2)|lung(1)|prostate(1)	central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66						c.(496-498)agC>agT		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							8.0	15.0	13.0					9																	20414346		1434	3114	4548	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414346G>A	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.498C>T	9.37:g.20414346G>A						MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S163S|MLLT3_ENST00000355930.6_5'UTR	p.S166S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN		GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)	5	784	-			166			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.498C>T	CCDS6494.1																																																																																				0.527	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		3	13	0	0	0	1	0	3	13				
GOT1L1	137362	broad.mit.edu	37	8	37795175	37795175	+	Silent	SNP	G	G	A			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr8:37795175G>A	ENST00000307599.4	-	3	489	c.390C>T	c.(388-390)taC>taT	p.Y130Y	GOT1L1_ENST00000518826.1_5'Flank	NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	glutamic-oxaloacetic transaminase 1-like 1	130					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)	cytoplasm (GO:0005737)	pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1)	14	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)			AAGAGATGATGTAAACTATAC	0.498																																						ENST00000307599.4																			0				central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1)	14						c.(388-390)taC>taT		glutamic-oxaloacetic transaminase 1-like 1							62.0	63.0	63.0					8																	37795175		2000	4173	6173	SO:0001819	synonymous_variant	137362				biosynthetic process|cellular amino acid metabolic process	cytoplasm	pyridoxal phosphate binding|transaminase activity	g.chr8:37795175G>A	BC029504	CCDS47839.1	8p12	2005-09-22			ENSG00000169154	ENSG00000169154			28487	protein-coding gene	gene with protein product						12477932	Standard	NM_152413		Approved	MGC33309	uc011lbj.1	Q8NHS2	OTTHUMG00000164027	ENST00000307599.4:c.390C>T	8.37:g.37795175G>A							p.Y130Y	NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	LUSC - Lung squamous cell carcinoma(8;1.37e-11)		3	489	-	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	130					A8MWL4	Silent	SNP	ENST00000307599.4	37	c.390C>T	CCDS47839.1																																																																																				0.498	GOT1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376823.1	NM_152413		10	14	0	0	0	1	0	10	14				
PGM5	5239	broad.mit.edu	37	9	70999448	70999448	+	Missense_Mutation	SNP	A	A	G			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr9:70999448A>G	ENST00000396396.1	+	3	788	c.559A>G	c.(559-561)Aaa>Gaa	p.K187E	PGM5_ENST00000396392.1_Missense_Mutation_p.K187E|PGM5_ENST00000604870.2_3'UTR	NM_021965.3	NP_068800.2	Q15124	PGM5_HUMAN	phosphoglucomutase 5	187					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)	cell-cell adherens junction (GO:0005913)|costamere (GO:0043034)|cytoplasmic side of plasma membrane (GO:0009898)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|sarcolemma (GO:0042383)|spot adherens junction (GO:0005914)|stress fiber (GO:0001725)|Z disc (GO:0030018)	intramolecular transferase activity, phosphotransferases (GO:0016868)|magnesium ion binding (GO:0000287)|structural molecule activity (GO:0005198)			endometrium(5)|kidney(1)|large_intestine(5)|liver(2)|lung(15)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	34						AAACAAATTCAAACCATTCAG	0.378																																						ENST00000396396.1																			0				endometrium(5)|kidney(1)|large_intestine(5)|liver(2)|lung(15)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	34						c.(559-561)Aaa>Gaa		phosphoglucomutase 5							60.0	59.0	60.0					9																	70999448		2203	4299	6502	SO:0001583	missense	5239				cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity	g.chr9:70999448A>G	L40933	CCDS6622.2	9q13	2008-02-05			ENSG00000154330	ENSG00000154330			8908	protein-coding gene	gene with protein product	"""phosphoglucomutase-related protein"""	600981				8586438, 8631316	Standard	NM_021965		Approved	PGMRP	uc004agr.3	Q15124	OTTHUMG00000019966	ENST00000396396.1:c.559A>G	9.37:g.70999448A>G	ENSP00000379678:p.Lys187Glu					PGM5_ENST00000396392.1_Missense_Mutation_p.K187E|PGM5_ENST00000604870.2_3'UTR	p.K187E	NM_021965.3	NP_068800.2	Q15124	PGM5_HUMAN			3	788	+			187					B1AM46|B4DLQ6|Q5VYV3|Q8N527|Q9UDH4	Missense_Mutation	SNP	ENST00000396396.1	37	c.559A>G	CCDS6622.2	.	.	.	.	.	.	.	.	.	.	.	14.18	2.458050	0.43634	.	.	ENSG00000154330	ENST00000396396;ENST00000396392	T;T	0.62941	-0.01;-0.01	4.36	4.36	0.52297	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);	0.054741	0.64402	U	0.000001	T	0.48589	0.1508	L	0.27053	0.805	0.50171	D	0.999856	B	0.10296	0.003	B	0.06405	0.002	T	0.45026	-0.9289	10	0.42905	T	0.14	.	12.8119	0.57645	1.0:0.0:0.0:0.0	.	187	Q15124	PGM5_HUMAN	E	187	ENSP00000379678:K187E;ENSP00000379674:K187E	ENSP00000379674:K187E	K	+	1	0	PGM5	70189268	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.105000	0.77031	1.712000	0.51347	0.467000	0.42956	AAA		0.378	PGM5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052548.2	NM_021965		27	49	0	0	0	1	0	27	49				
RAPGEF6	51735	broad.mit.edu	37	5	130769300	130769300	+	Missense_Mutation	SNP	T	T	A			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr5:130769300T>A	ENST00000509018.1	-	25	4002	c.3797A>T	c.(3796-3798)cAt>cTt	p.H1266L	RAPGEF6_ENST00000307984.5_Missense_Mutation_p.H1279L|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.H1274L|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.H1316L|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.H1274L	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1266	Ser-rich.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		AATCTCACTATGGCTGGAGTC	0.448																																					Melanoma(168;435 1955 13113 13877 23213)	ENST00000509018.1																			0				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31						c.(3796-3798)cAt>cTt		Rap guanine nucleotide exchange factor (GEF) 6							116.0	106.0	109.0					5																	130769300		2203	4300	6503	SO:0001583	missense	51735				Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding	g.chr5:130769300T>A	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3797A>T	5.37:g.130769300T>A	ENSP00000421684:p.His1266Leu					RAPGEF6_ENST00000507093.1_Missense_Mutation_p.H1274L|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.H1274L|FNIP1_ENST00000514667.1_Missense_Mutation_p.H1316L|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.H1279L	p.H1266L	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)	25	4002	-			1266			Ser-rich.		A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	37	c.3797A>T	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	T	31	5.086001	0.94100	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000514667	T;T;T;T;T	0.29142	1.68;1.58;1.59;1.68;1.78	5.83	5.83	0.93111	.	0.140369	0.64402	D	0.000005	T	0.52725	0.1752	M	0.68952	2.095	0.80722	D	1	D;P;P;D;P	0.60160	0.978;0.599;0.599;0.987;0.599	P;B;B;P;B	0.62813	0.809;0.284;0.284;0.907;0.284	T	0.55231	-0.8173	10	0.72032	D	0.01	.	16.2141	0.82191	0.0:0.0:0.0:1.0	.	1274;1274;1316;1279;1266	A3KN82;B7ZML2;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;RPGF6_HUMAN	L	1266;1279;1274;1274;1279;1316	ENSP00000421684:H1266L;ENSP00000309298:H1279L;ENSP00000426081:H1274L;ENSP00000296859:H1274L;ENSP00000426948:H1316L	ENSP00000426948:H1316L	H	-	2	0	RAPGEF6;FNIP1	130797199	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.160000	0.77495	2.224000	0.72417	0.528000	0.53228	CAT		0.448	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		32	62	0	0	0	1	0	32	62				
CDR2	1039	broad.mit.edu	37	16	22448704	22448704	+	5'Flank	SNP	G	G	A	rs185302570		TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr16:22448704G>A	ENST00000569045.1	-	0	0				RRN3P3_ENST00000551766.1_RNA			Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2, 62kDa							cytoplasm (GO:0005737)				endometrium(3)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(48;0.0188)		GCTTGGCCATGTCGTGTCGGG	0.716																																						ENST00000551766.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr16:22448704G>A	M63256	CCDS32404.1	16p13.1-p12	2008-02-05	2002-08-29			ENSG00000140743			1799	protein-coding gene	gene with protein product	"""Yo paraneoplastic antigen"""	117340	"""cerebellar degeneration-related protein (62kD)"""			2014264	Standard	NM_001802		Approved	CDR62, Yo	uc002dkn.3	Q01850			16.37:g.22448704G>A	Exception_encountered							NR_027460.1						0	332	-								A8K8A8|Q13977	RNA	SNP	ENST00000569045.1	37																																																																																						0.716	CDR2-006	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000430087.1			4	9	0	0	0	1	0	4	9				
TRHDE	29953	broad.mit.edu	37	12	73012793	73012793	+	Missense_Mutation	SNP	G	G	A			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr12:73012793G>A	ENST00000261180.4	+	13	2405	c.2309G>A	c.(2308-2310)cGc>cAc	p.R770H		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	770					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						TTACTGGACCGCATGGAAAAC	0.333																																						ENST00000261180.4																			0				NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						c.(2308-2310)cGc>cAc		thyrotropin-releasing hormone degrading enzyme							43.0	46.0	45.0					12																	73012793		2200	4300	6500	SO:0001583	missense	29953				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding	g.chr12:73012793G>A	AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"""pyroglutamyl-peptidase II"", ""pyroglutamyl aminopeptidase II"", ""TRH-specific aminopeptidase"""	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.2309G>A	12.37:g.73012793G>A	ENSP00000261180:p.Arg770His						p.R770H	NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN			13	2405	+			770					A5PL19|Q6UWJ4	Missense_Mutation	SNP	ENST00000261180.4	37	c.2309G>A	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.957892	0.73902	.	.	ENSG00000072657	ENST00000261180	T	0.05580	3.42	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.25606	0.0623	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00035	-1.2260	10	0.35671	T	0.21	.	20.3626	0.98863	0.0:0.0:1.0:0.0	.	770	Q9UKU6	TRHDE_HUMAN	H	770	ENSP00000261180:R770H	ENSP00000261180:R770H	R	+	2	0	TRHDE	71299060	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.055000	0.93873	2.885000	0.99019	0.655000	0.94253	CGC		0.333	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381		3	68	0	0	0	1	0	3	68				
MUC13	56667	broad.mit.edu	37	3	124629312	124629312	+	Silent	SNP	G	G	T			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr3:124629312G>T	ENST00000311075.3	-	10	1322	c.1284C>A	c.(1282-1284)atC>atA	p.I428I		NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	429					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						CAATGCCAGCGATGGTGCCCA	0.403																																						ENST00000311075.3																			0				breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						c.(1282-1284)atC>atA		mucin 13, cell surface associated							82.0	77.0	78.0					3																	124629312		2203	4300	6503	SO:0001819	synonymous_variant	56667					extracellular region|integral to membrane|plasma membrane		g.chr3:124629312G>T	AF286113		3q21.2	2007-01-17	2006-03-14		ENSG00000173702	ENSG00000173702		"""Mucins"""	7511	protein-coding gene	gene with protein product		612181	"""down-regulated in colon cancer 1"", ""mucin 13, epithelial transmembrane"""	DRCC1		11278439	Standard	NM_033049		Approved		uc003ehq.2	Q9H3R2	OTTHUMG00000159484	ENST00000311075.3:c.1284C>A	3.37:g.124629312G>T							p.I428I	NM_033049.3	NP_149038.3	Q9H3R2	MUC13_HUMAN			10	1322	-			428					Q6UWD9|Q9NXT5	Silent	SNP	ENST00000311075.3	37	c.1284C>A																																																																																					0.403	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049		22	103	1	0	2.47511e-08	1	2.68137e-08	22	103				
BCL11A	53335	broad.mit.edu	37	2	60688216	60688216	+	Missense_Mutation	SNP	C	C	T			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr2:60688216C>T	ENST00000335712.6	-	4	2058	c.1831G>A	c.(1831-1833)Gag>Aag	p.E611K	BCL11A_ENST00000356842.4_Missense_Mutation_p.E611K|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000537768.1_Missense_Mutation_p.E280K|BCL11A_ENST00000538214.1_Missense_Mutation_p.E577K|BCL11A_ENST00000358510.4_Missense_Mutation_p.E577K|BCL11A_ENST00000477659.1_5'UTR	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	611					B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|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)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			GAGGCCGACTCGCCCGGGGAG	0.662			T	IGH@	B-CLL																																	ENST00000335712.6				Dom	yes		2	2p13	53335	T	B-cell CLL/lymphoma 11A			L	IGH@		B-CLL		0				NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59						c.(1831-1833)Gag>Aag		B-cell CLL/lymphoma 11A (zinc finger protein)							13.0	17.0	15.0					2																	60688216		2139	4227	6366	SO:0001583	missense	53335				negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding	g.chr2:60688216C>T	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"""Zinc fingers, C2H2-type"""	13221	protein-coding gene	gene with protein product		606557	"""ecotropic viral integration site 9"""	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.1831G>A	2.37:g.60688216C>T	ENSP00000338774:p.Glu611Lys					BCL11A_ENST00000358510.4_Missense_Mutation_p.E577K|BCL11A_ENST00000356842.4_Missense_Mutation_p.E611K|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000538214.1_Missense_Mutation_p.E577K|BCL11A_ENST00000537768.1_Missense_Mutation_p.E280K|BCL11A_ENST00000477659.1_5'UTR	p.E611K	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)		4	2058	-			611					D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Missense_Mutation	SNP	ENST00000335712.6	37	c.1831G>A	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.110620	0.56398	.	.	ENSG00000119866	ENST00000356842;ENST00000378117;ENST00000538214;ENST00000537768;ENST00000335712;ENST00000358510	T;T;T;T;T	0.09630	2.96;3.23;3.13;3.25;3.18	6.17	6.17	0.99709	.	0.329559	0.31809	N	0.007030	T	0.25494	0.0620	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D	0.67145	0.996;0.993;0.988;0.979;0.994	P;B;P;B;P	0.56788	0.806;0.439;0.548;0.342;0.738	T	0.00699	-1.1604	10	0.15952	T	0.53	-3.0403	20.8794	0.99867	0.0:1.0:0.0:0.0	.	577;280;577;611;611	F5H2Y4;B4DT16;Q9H165-6;Q9H165;D9YZV9	.;.;.;BC11A_HUMAN;.	K	611;636;577;280;611;577	ENSP00000349300:E611K;ENSP00000438303:E577K;ENSP00000443712:E280K;ENSP00000338774:E611K;ENSP00000351307:E577K	ENSP00000338774:E611K	E	-	1	0	BCL11A	60541720	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.813000	0.86123	2.941000	0.99782	0.655000	0.94253	GAG		0.662	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893		16	29	0	0	0	1	0	16	29				
BMP2K	55589	broad.mit.edu	37	4	79792085	79792085	+	Missense_Mutation	SNP	G	G	C	rs376418550	byFrequency	TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr4:79792085G>C	ENST00000335016.5	+	11	1546	c.1380G>C	c.(1378-1380)caG>caC	p.Q460H	BMP2K_ENST00000502871.1_Missense_Mutation_p.Q460H	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	460	Gln/His-rich.				regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)	p.Q460H(3)		NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						ATCCTCACcagcagcagcagc	0.577																																						ENST00000335016.5																			3	Substitution - Missense(3)	p.Q460H(3)	endometrium(2)|prostate(1)	NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						c.(1378-1380)caG>caC		BMP2 inducible kinase							40.0	45.0	44.0					4																	79792085		2203	4300	6503	SO:0001583	missense	55589					nucleus	ATP binding|protein serine/threonine kinase activity	g.chr4:79792085G>C	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.1380G>C	4.37:g.79792085G>C	ENSP00000334836:p.Gln460His					BMP2K_ENST00000502871.1_Missense_Mutation_p.Q460H	p.Q460H	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN			11	1546	+			460			Gln/His-rich.		O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	37	c.1380G>C	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.089|8.089	0.774118|0.774118	0.16051|0.16051	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000502613|ENST00000502871;ENST00000335016;ENST00000264889	.|T;T	.|0.74002	.|0.79;-0.8	5.12|5.12	2.26|2.26	0.28386|0.28386	.|.	.|1.238260	.|0.06146	.|N	.|0.673324	T|T	0.57504|0.57504	0.2058|0.2058	N|N	0.15975|0.15975	0.35|0.35	0.30181|0.30181	N|N	0.800383|0.800383	.|B;B	.|0.06786	.|0.001;0.0	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.51803|0.51803	-0.8659|-0.8659	5|10	.|0.42905	.|T	.|0.14	0.0809|0.0809	5.9141|5.9141	0.19045|0.19045	0.0722:0.2493:0.5501:0.1284|0.0722:0.2493:0.5501:0.1284	.|.	.|460;460	.|Q9NSY1;Q4W5H2	.|BMP2K_HUMAN;.	P|H	153|460;460;474	.|ENSP00000421768:Q460H;ENSP00000334836:Q460H	.|ENSP00000264889:Q474H	A|Q	+|+	1|3	0|2	BMP2K|BMP2K	80011109|80011109	0.996000|0.996000	0.38824|0.38824	0.995000|0.995000	0.50966|0.50966	0.181000|0.181000	0.23173|0.23173	0.092000|0.092000	0.15066|0.15066	0.524000|0.524000	0.28502|0.28502	0.460000|0.460000	0.39030|0.39030	GCA|CAG		0.577	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		3	67	0	0	0	1	0	3	67				
TRIM36	55521	broad.mit.edu	37	5	114482788	114482788	+	Missense_Mutation	SNP	G	G	T			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr5:114482788G>T	ENST00000282369.3	-	3	723	c.602C>A	c.(601-603)cCa>cAa	p.P201Q	TRIM36_ENST00000514154.1_Missense_Mutation_p.P46Q|TRIM36_ENST00000515104.1_5'UTR|TRIM36-IT1_ENST00000503723.1_RNA|TRIM36_ENST00000513154.1_Missense_Mutation_p.P189Q	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	201					acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		GTTAGTAGTTGGACCAACATA	0.328																																						ENST00000513154.1																			0				breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37						c.(565-567)cCa>cAa		tripartite motif containing 36							81.0	82.0	81.0					5																	114482788		2202	4300	6502	SO:0001583	missense	55521					acrosomal vesicle|cytoskeleton	ligase activity|zinc ion binding	g.chr5:114482788G>T	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16280	protein-coding gene	gene with protein product	"""zinc-binding protein Rbcc728"", ""tripartite motif protein 36"", ""RING finger protein 98"""	609317	"""tripartite motif-containing 36"""			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.602C>A	5.37:g.114482788G>T	ENSP00000282369:p.Pro201Gln					TRIM36_ENST00000282369.3_Missense_Mutation_p.P201Q|TRIM36_ENST00000514154.1_Missense_Mutation_p.P46Q|TRIM36_ENST00000515104.1_5'UTR	p.P189Q			Q9NQ86	TRI36_HUMAN		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)	3	892	-		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)	201					A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	37	c.566C>A	CCDS4115.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.536008	0.85812	.	.	ENSG00000152503	ENST00000282369;ENST00000513154;ENST00000514154	D;D;T	0.87571	-2.27;-2.27;-0.53	5.49	5.49	0.81192	.	0.196250	0.56097	D	0.000035	D	0.94647	0.8274	M	0.90309	3.105	0.80722	D	1	D;D	0.67145	0.993;0.996	P;D	0.65684	0.843;0.937	D	0.95351	0.8447	10	0.87932	D	0	.	19.3708	0.94484	0.0:0.0:1.0:0.0	.	189;201	E9PFI8;Q9NQ86	.;TRI36_HUMAN	Q	201;189;46	ENSP00000282369:P201Q;ENSP00000423934:P189Q;ENSP00000424259:P46Q	ENSP00000282369:P201Q	P	-	2	0	TRIM36	114510687	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	9.338000	0.96553	2.571000	0.86741	0.467000	0.42956	CCA		0.328	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		15	29	1	0	3.27435e-08	1	3.40533e-08	15	29				
MAP3K9	4293	broad.mit.edu	37	14	71275776	71275776	+	Missense_Mutation	SNP	T	T	G	rs397840789|rs201322413		TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr14:71275776T>G	ENST00000554752.2	-	1	112	c.113A>C	c.(112-114)gAg>gCg	p.E38A	MAP3K9_ENST00000555993.2_Missense_Mutation_p.E38A|MAP3K9_ENST00000381250.4_Missense_Mutation_p.E38A|RP6-65G23.3_ENST00000557691.1_lincRNA	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	38	Ala-rich.|Poly-Glu.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.E38delE(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		CGCCGCCGcctcctcctcctc	0.776																																					GBM(114;411 1587 13539 28235 50070)	ENST00000554752.2																			1	Deletion - In frame(1)	p.E38delE(1)	ovary(1)	breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46						c.(112-114)gAg>gCg		mitogen-activated protein kinase kinase kinase 9							3.0	4.0	4.0					14																	71275776		1664	3359	5023	SO:0001583	missense	4293				activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity	g.chr14:71275776T>G	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.113A>C	14.37:g.71275776T>G	ENSP00000451612:p.Glu38Ala					MAP3K9_ENST00000555993.2_Missense_Mutation_p.E38A|MAP3K9_ENST00000381250.4_Missense_Mutation_p.E38A	p.E38A			P80192	M3K9_HUMAN		all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)	1	112	-			38			Ala-rich.|Poly-Glu.		A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Missense_Mutation	SNP	ENST00000554752.2	37	c.113A>C		.	.	.	.	.	.	.	.	.	.	T	10.15	1.272242	0.23221	.	.	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000381250	T;T	0.74209	-0.82;-0.81	3.07	-0.248	0.13015	.	1.098320	0.07227	N	0.861903	T	0.54415	0.1857	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.13548	-1.0505	10	0.23302	T	0.38	.	11.6179	0.51099	0.0:0.0:0.4494:0.5506	.	38;38	P80192;P80192-4	M3K9_HUMAN;.	A	38	ENSP00000451612:E38A;ENSP00000370649:E38A	ENSP00000005198:E38A	E	-	2	0	MAP3K9	70345529	0.912000	0.30974	0.992000	0.48379	0.724000	0.41520	1.143000	0.31553	-0.577000	0.05967	-1.313000	0.01306	GAG		0.776	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2			2	3	0	0	0	1	0	2	3				
TENM1	10178	broad.mit.edu	37	X	123556255	123556255	+	Silent	SNP	G	G	C	rs369708233		TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chrX:123556255G>C	ENST00000371130.3	-	23	4380	c.4317C>G	c.(4315-4317)ctC>ctG	p.L1439L	STAG2_ENST00000469481.1_3'UTR|TENM1_ENST00000422452.2_Silent_p.L1446L	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1439					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CAGCTATGAAGAGCAGCCCGC	0.537																																						ENST00000422452.2																			0											c.(4336-4338)ctC>ctG		teneurin transmembrane protein 1		G	,,	1,3834		0,0,1,1632,570	158.0	120.0	133.0		4338,4335,4317	3.8	1.0	X		133	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	,,	0,0,1,4060,2442	CC,CG,C,GG,G		0.0,0.0261,0.0095	,,	1446/2733,1445/2732,1439/2726	123556255	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	10178							g.chrX:123556255G>C	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.4317C>G	X.37:g.123556255G>C						STAG2_ENST00000469481.1_3'UTR|TENM1_ENST00000371130.3_Silent_p.L1439L	p.L1446L	NM_001163278.1|NM_001163279.1	NP_001156750.1|NP_001156751.1					24	4401	-								B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	c.4338C>G	CCDS14609.1																																																																																				0.537	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		6	209	0	0	0	1	0	6	209				
TRIM46	80128	broad.mit.edu	37	1	155147749	155147749	+	Intron	SNP	G	G	A			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr1:155147749G>A	ENST00000334634.4	+	2	63				TRIM46_ENST00000543729.1_Intron|TRIM46_ENST00000545012.1_Intron|KRTCAP2_ENST00000490672.1_5'Flank|TRIM46_ENST00000392451.2_Intron|TRIM46_ENST00000368383.3_Intron|TRIM46_ENST00000368382.1_Intron|RP11-201K10.3_ENST00000473363.2_Intron|TRIM46_ENST00000368385.4_Intron|TRIM46_ENST00000468878.1_Splice_Site|KRTCAP2_ENST00000295682.4_5'Flank	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46							intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			AAAGCTGCAGGTAGCTTGTCT	0.582																																						ENST00000468878.1																			0				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29						c.e2+1		tripartite motif containing 46																																				SO:0001627	intron_variant	80128					intracellular	zinc ion binding	g.chr1:155147749G>A		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19019	protein-coding gene	gene with protein product		600986	"""tripartite motif-containing 46"""				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.64-113G>A	1.37:g.155147749G>A						TRIM46_ENST00000545012.1_Intron|TRIM46_ENST00000543729.1_Intron|TRIM46_ENST00000334634.4_Intron|TRIM46_ENST00000368382.1_Intron|TRIM46_ENST00000392451.2_Intron|TRIM46_ENST00000368383.3_Intron|TRIM46_ENST00000368385.4_Intron		NR_046327.1|NR_046329.1		Q7Z4K8	TRI46_HUMAN	Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		2	302	+	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)							A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Splice_Site	SNP	ENST00000334634.4	37		CCDS1097.1																																																																																				0.582	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058		3	47	0	0	0	1	0	3	47				
COL4A5	1287	broad.mit.edu	37	X	107812034	107812034	+	Missense_Mutation	SNP	G	G	A	rs104886046		TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chrX:107812034G>A	ENST00000361603.2	+	6	611	c.367G>A	c.(367-369)Gga>Aga	p.G123R	COL4A5_ENST00000328300.6_Missense_Mutation_p.G123R	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	123	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						AGGTATTCCCGGATGCAATGG	0.383									Alport syndrome with Diffuse Leiomyomatosis																													ENST00000328300.6																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						c.(367-369)Gga>Aga		collagen, type IV, alpha 5							89.0	84.0	85.0					X																	107812034		2203	4300	6503	SO:0001583	missense	1287	Alport syndrome with Diffuse Leiomyomatosis	Familial Cancer Database		axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding	g.chrX:107812034G>A	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.367G>A	X.37:g.107812034G>A	ENSP00000354505:p.Gly123Arg					COL4A5_ENST00000361603.2_Missense_Mutation_p.G123R	p.G123R	NM_033380.2	NP_203699.1	P29400	CO4A5_HUMAN			6	611	+			123			Triple-helical region.		Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	c.367G>A	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	18.94	3.729193	0.69074	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.99186	-5.53;-5.53	4.89	4.89	0.63831	.	0.062950	0.64402	D	0.000006	D	0.99597	0.9854	H	0.97874	4.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97575	1.0107	10	0.87932	D	0	.	17.3152	0.87221	0.0:0.0:1.0:0.0	.	123;123	E7EVY4;P29400	.;CO4A5_HUMAN	R	123	ENSP00000331902:G123R;ENSP00000354505:G123R	ENSP00000331902:G123R	G	+	1	0	COL4A5	107698690	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	8.860000	0.92272	2.270000	0.75569	0.600000	0.82982	GGA		0.383	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			55	104	0	0	0	1	0	55	104				
LOC728730	728730	broad.mit.edu	37	2	39791858	39791860	+	RNA	DEL	TGC	TGC	-			TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr2:39791858_39791860delTGC	ENST00000449569.1	+	0	538				AC007246.3_ENST00000425775.1_RNA|AC007246.3_ENST00000446698.1_RNA|AC007246.3_ENST00000451547.1_RNA|AC007246.3_ENST00000438649.1_RNA|AC007246.3_ENST00000422128.1_RNA|AC007246.3_ENST00000426083.1_RNA|AC007246.3_ENST00000415640.1_RNA	NR_037875.1																						tatagaagggtgctgctgctgct	0.601																																						ENST00000449569.1																			0																																																			0							g.chr2:39791858_39791860delTGC																													2.37:g.39791867_39791869delTGC						AC007246.3_ENST00000422128.1_RNA|AC007246.3_ENST00000451547.1_RNA|AC007246.3_ENST00000415640.1_RNA|AC007246.3_ENST00000438649.1_RNA|AC007246.3_ENST00000425775.1_RNA|AC007246.3_ENST00000426083.1_RNA|AC007246.3_ENST00000446698.1_RNA		NR_037875.1						0	538	+									RNA	DEL	ENST00000449569.1	37																																																																																						0.601	AC007246.3-002	KNOWN	basic	antisense	antisense	OTTHUMT00000325723.1			4	3						4	3	---	---	---	---
SFRP1	6422	broad.mit.edu	37	8	41166638	41166640	+	In_Frame_Del	DEL	GCT	GCT	-	rs3055861|rs3832595	byFrequency	TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr8:41166638_41166640delGCT	ENST00000220772.3	-	1	376_378	c.39_41delAGC	c.(37-42)gcagcc>gcc	p.13_14AA>A	SFRP1_ENST00000379845.3_5'Flank	NM_003012.4	NP_003003.3	Q8N474	SFRP1_HUMAN	secreted frizzled-related protein 1	13				Missing (in Ref. 1 and 3). {ECO:0000305}.	bone trabecula formation (GO:0060346)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to BMP stimulus (GO:0071773)|cellular response to estradiol stimulus (GO:0071392)|cellular response to estrogen stimulus (GO:0071391)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to prostaglandin E stimulus (GO:0071380)|cellular response to starvation (GO:0009267)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vitamin D (GO:0071305)|cellular response to X-ray (GO:0071481)|convergent extension involved in somitogenesis (GO:0090246)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral axis specification (GO:0009950)|female gonad development (GO:0008585)|gonad development (GO:0008406)|hematopoietic progenitor cell differentiation (GO:0002244)|hematopoietic stem cell differentiation (GO:0060218)|male gonad development (GO:0008584)|menstrual cycle phase (GO:0022601)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of bone remodeling (GO:0046851)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000080)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000054)|neural crest cell fate commitment (GO:0014034)|neural tube closure (GO:0001843)|osteoblast differentiation (GO:0001649)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of non-canonical Wnt signaling pathway (GO:2000052)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|proteolysis (GO:0006508)|regulation of angiogenesis (GO:0045765)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell cycle process (GO:0010564)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|somatic stem cell maintenance (GO:0035019)|stromal-epithelial cell signaling involved in prostate gland development (GO:0044345)|ureteric bud development (GO:0001657)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cysteine-type endopeptidase activity (GO:0004197)|drug binding (GO:0008144)|frizzled binding (GO:0005109)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|central_nervous_system(1)|large_intestine(2)|liver(1)|lung(1)|skin(1)	7	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)			CACGCCCAGGGCTGCCCCGCGGC	0.764														1558	0.311102	0.0401	0.389	5008	,	,		9448	0.4038		0.3956	False		,,,				2504	0.4397					ENST00000220772.3																			0				breast(1)|central_nervous_system(1)|large_intestine(2)|liver(1)|lung(1)|skin(1)	7						c.(37-42)gcc>gc		secreted frizzled-related protein 1				337,0,3741		45,0,247,0,0,1747						1.6	0.3		dbSNP_107	8	2693,2,5163		669,0,1355,0,2,1903	no	codingComplex	SFRP1	NM_003012.4		714,0,1602,0,2,3650	A1A1,A1A2,A1R,A2A2,A2R,RR		34.2963,8.2639,25.4021				3030,2,8904				SO:0001651	inframe_deletion	6422				brain development|canonical Wnt receptor signaling pathway|cellular response to BMP stimulus|cellular response to estradiol stimulus|cellular response to fibroblast growth factor stimulus|cellular response to heparin|cellular response to hypoxia|cellular response to interleukin-1|cellular response to prostaglandin E stimulus|cellular response to starvation|cellular response to transforming growth factor beta stimulus|cellular response to tumor necrosis factor|cellular response to vitamin D|DNA fragmentation involved in apoptotic nuclear change|dorsal/ventral axis specification|hemopoietic progenitor cell differentiation|hemopoietic stem cell differentiation|menstrual cycle phase|negative regulation of androgen receptor signaling pathway|negative regulation of B cell differentiation|negative regulation of bone remodeling|negative regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cysteine-type endopeptidase activity|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast apoptosis|negative regulation of fibroblast proliferation|negative regulation of insulin secretion|negative regulation of ossification|negative regulation of osteoblast proliferation|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|osteoblast differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell growth|positive regulation of epithelial cell proliferation|positive regulation of fat cell differentiation|positive regulation of fibroblast apoptosis|positive regulation of focal adhesion assembly|positive regulation of non-canonical Wnt receptor signaling pathway|positive regulation of Rac GTPase activity|positive regulation of smoothened signaling pathway|positive regulation of stress fiber assembly|positive regulation of transcription, DNA-dependent|regulation of angiogenesis|regulation of cell cycle process|response to drug|response to organic cyclic compound|vasculature development	cell surface|cytosol|extracellular space|plasma membrane|proteinaceous extracellular matrix	cysteine-type endopeptidase activity|drug binding|frizzled binding|heparin binding|identical protein binding|PDZ domain binding|Wnt receptor activity|Wnt-protein binding	g.chr8:41166638_41166640delGCT	AF017987	CCDS34886.1	8p11.21	2006-12-15			ENSG00000104332	ENSG00000104332		"""Secreted frizzled-related proteins"""	10776	protein-coding gene	gene with protein product		604156				9391078, 9192640	Standard	NM_003012		Approved	SARP2, FRP, FRP-1	uc003xnt.3	Q8N474	OTTHUMG00000164074	ENST00000220772.3:c.39_41delAGC	8.37:g.41166638_41166640delGCT	ENSP00000220772:p.Ala14del						p.AA13del	NM_003012.4	NP_003003.3	Q8N474	SFRP1_HUMAN	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)		1	376_378	-	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	13					O00546|O14779	In_Frame_Del	DEL	ENST00000220772.3	37	c.39_41delAGC	CCDS34886.1																																																																																				0.764	SFRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377132.1	NM_003012		5	1						5	1	---	---	---	---
HPN-AS1	100128675	broad.mit.edu	37	19	35596483	35596500	+	5'Flank	DEL	CACCATCACCATCATCAT	CACCATCACCATCATCAT	-	rs374271888|rs143642353|rs142820274|rs371694256|rs150197593	byFrequency	TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr19:35596483_35596500delCACCATCACCATCATCAT	ENST00000313865.6	+	0	0				HPN-AS1_ENST00000392227.2_RNA																							tcaccatcaccaccatcaccatcatcatcaccaccacc	0.477																																						ENST00000392227.2																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr19:35596483_35596500delCACCATCACCATCATCAT																													19.37:g.35596483_35596500delCACCATCACCATCATCAT	Exception_encountered							NR_024562.1						0	76	-									RNA	DEL	ENST00000313865.6	37																																																																																						0.477	AC020907.1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				6	4						6	4	---	---	---	---
BCAS1	8537	broad.mit.edu	37	20	52557949	52557950	+	IGR	INS	-	-	TT	rs72548465|rs201903487|rs141488543|rs2870294		TCGA-E3-A3E0-01A-11D-A20C-08	TCGA-E3-A3E0-10A-01D-A20C-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc913911-8fc0-4cd6-8ba0-ebdb9cc664d1	6928cbfc-6138-441b-bc97-62a73788ef08	g.chr20:52557949_52557950insTT	ENST00000395961.3	-	0	3303				AC005220.3_ENST00000450473.1_RNA	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			gtgtgtgtgtgtgtgtgtgcgc	0.5																																						ENST00000450473.1																			0																	194,519,1821		59,6,70,144,225,763						1.3	0.0		dbSNP_101	4	657,726,3403		150,19,338,195,317,1374	no	intergenic				209,25,408,339,542,2137	A1A1,A1A2,A1R,A2A2,A2R,RR		28.8968,28.1373,28.6339				851,1245,5224				SO:0001628	intergenic_variant	0							g.chr20:52557949_52557950insTT	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772		20.37:g.52557949_52557950insTT														0	550	+								A0AVG5|Q68CZ3	RNA	INS	ENST00000395961.3	37		CCDS13444.1																																																																																				0.500	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657		5	2						5	2	---	---	---	---
