#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
ANKRD19P	138649	broad.mit.edu	37	9	95646900	95646900	+	RNA	SNP	A	A	T			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr9:95646900A>T	ENST00000446878.1	+	0	434				ANKRD19P_ENST00000473204.1_RNA																							TGCTTTCACAACTGCAGAGGT	0.612																																						ENST00000446878.1																			0																																																			138649							g.chr9:95646900A>T																													9.37:g.95646900A>T						ANKRD19P_ENST00000473204.1_RNA								0	434	+									RNA	SNP	ENST00000446878.1	37																																																																																						0.612	RP11-526D8.7-006	PUTATIVE	basic	processed_transcript	pseudogene	OTTHUMT00000316907.1			7	130	0	0	0	1	0	7	130				
OR52D1	390066	broad.mit.edu	37	11	5510364	5510364	+	Missense_Mutation	SNP	T	T	A			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr11:5510364T>A	ENST00000322641.5	+	1	450	c.428T>A	c.(427-429)gTc>gAc	p.V143D	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	143					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AACCATGCTGTCATAGGCAGA	0.483																																						ENST00000322641.5																			0				central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22						c.(427-429)gTc>gAc		olfactory receptor, family 52, subfamily D, member 1							265.0	247.0	253.0					11																	5510364		2201	4297	6498	SO:0001583	missense	390066				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:5510364T>A	BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"""GPCR / Class A : Olfactory receptors"""	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.428T>A	11.37:g.5510364T>A	ENSP00000326232:p.Val143Asp					HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	p.V143D	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	1	450	+		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)	143					B9EGY9|Q6IFI6	Missense_Mutation	SNP	ENST00000322641.5	37	c.428T>A	CCDS31384.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.769300	0.49680	.	.	ENSG00000181609	ENST00000322641	T	0.39229	1.09	5.58	5.58	0.84498	GPCR, rhodopsin-like superfamily (1);	0.242522	0.30285	N	0.009964	T	0.55737	0.1939	M	0.89840	3.065	0.31530	N	0.661358	P	0.40302	0.712	P	0.47015	0.534	T	0.71206	-0.4661	10	0.87932	D	0	.	5.8667	0.18779	0.0:0.0822:0.1688:0.7491	.	143	Q9H346	O52D1_HUMAN	D	143	ENSP00000326232:V143D	ENSP00000326232:V143D	V	+	2	0	OR52D1	5466940	0.000000	0.05858	0.966000	0.40874	0.893000	0.52053	0.588000	0.23924	2.343000	0.79666	0.533000	0.62120	GTC		0.483	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163		6	113	0	0	0	1	0	6	113				
ZNF493	284443	broad.mit.edu	37	19	21606782	21606782	+	Missense_Mutation	SNP	A	A	G			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr19:21606782A>G	ENST00000355504.4	+	2	1203	c.937A>G	c.(937-939)Acc>Gcc	p.T313A	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.T441A	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	313					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T313A(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						ATGTGGCAAAACCTTTAGTGT	0.338																																						ENST00000392288.2																			1	Substitution - Missense(1)	p.T313A(1)	prostate(1)	central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						c.(1321-1323)Acc>Gcc		zinc finger protein 493							29.0	32.0	31.0					19																	21606782		2185	4280	6465	SO:0001583	missense	284443				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:21606782A>G	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.937A>G	19.37:g.21606782A>G	ENSP00000347691:p.Thr313Ala					CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000355504.4_Missense_Mutation_p.T313A	p.T441A	NM_001076678.2	NP_001070146.1	Q6ZR52	ZN493_HUMAN			4	1430	+			313					G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	c.1321A>G	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	0.001	-3.683025	0.00006	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.35421	1.31;1.31	1.03	-2.07	0.07276	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08802	0.0218	N	0.01824	-0.7	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.17198	-1.0377	9	0.02654	T	1	.	0.7425	0.00976	0.3856:0.1658:0.2821:0.1665	.	313;441	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	A	441;313	ENSP00000376110:T441A;ENSP00000347691:T313A	ENSP00000347691:T313A	T	+	1	0	ZNF493	21398622	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	-2.542000	0.00935	-1.612000	0.01579	-1.635000	0.00777	ACC		0.338	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		3	36	0	0	0	1	0	3	36				
COL11A1	1301	broad.mit.edu	37	1	103400017	103400017	+	Silent	SNP	T	T	G			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr1:103400017T>G	ENST00000370096.3	-	46	3900	c.3588A>C	c.(3586-3588)ccA>ccC	p.P1196P	COL11A1_ENST00000353414.4_Silent_p.P1157P|COL11A1_ENST00000358392.2_Silent_p.P1208P|COL11A1_ENST00000512756.1_Silent_p.P1080P	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1196	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GAAGACCTATTGGACCAGGAG	0.468																																						ENST00000358392.2																			0				NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258						c.(3622-3624)ccA>ccC		collagen, type XI, alpha 1							88.0	80.0	83.0					1																	103400017		2203	4300	6503	SO:0001819	synonymous_variant	1301				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging	g.chr1:103400017T>G	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3588A>C	1.37:g.103400017T>G						COL11A1_ENST00000353414.4_Silent_p.P1157P|COL11A1_ENST00000512756.1_Silent_p.P1080P|COL11A1_ENST00000370096.3_Silent_p.P1196P	p.P1208P	NM_080629.2	NP_542196.2	P12107	COBA1_HUMAN		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)	46	3941	-		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)	1196			Triple-helical region.		B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	37	c.3624A>C	CCDS778.1																																																																																				0.468	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		5	19	0	0	0	1	0	5	19				
WHSC1L1	54904	broad.mit.edu	37	8	38175553	38175553	+	Intron	SNP	G	G	T			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr8:38175553G>T	ENST00000317025.8	-	9	2373				WHSC1L1_ENST00000527502.1_Intron|WHSC1L1_ENST00000525081.1_5'UTR|WHSC1L1_ENST00000316985.3_Nonsense_Mutation_p.S620*|WHSC1L1_ENST00000433384.2_Intron	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1						histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			CCGGTCCGCCGACCCTGTGGA	0.557			T	NUP98	AML																																	ENST00000316985.3				Dom	yes		8	8p12	54904	T	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)			L	NUP98		AML		0				NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24						c.(1858-1860)tCg>tAg		Wolf-Hirschhorn syndrome candidate 1-like 1							65.0	61.0	63.0					8																	38175553		2203	4300	6503	SO:0001627	intron_variant	54904				cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding	g.chr8:38175553G>T	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.1855+859C>A	8.37:g.38175553G>T						WHSC1L1_ENST00000527502.1_Intron|WHSC1L1_ENST00000433384.2_Intron|WHSC1L1_ENST00000317025.8_Intron|WHSC1L1_ENST00000525081.1_5'UTR	p.S620*	NM_017778.2	NP_060248.2	Q9BZ95	NSD3_HUMAN	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)		10	2376	-	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	620					B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Nonsense_Mutation	SNP	ENST00000317025.8	37	c.1859C>A	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	G	41	8.572971	0.98868	.	.	ENSG00000147548	ENST00000316985	.	.	.	5.95	5.95	0.96441	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	15.8933	0.79318	0.0:0.0:1.0:0.0	.	.	.	.	X	620	.	ENSP00000313410:S620X	S	-	2	0	WHSC1L1	38294710	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	1.563000	0.36364	2.824000	0.97209	0.655000	0.94253	TCG		0.557	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		21	23	1	0	1.87028e-06	1	2.00882e-06	21	23				
CCDC40	55036	broad.mit.edu	37	17	78058656	78058656	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr17:78058656G>A	ENST00000397545.4	+	13	2131	c.2104G>A	c.(2104-2106)Gtg>Atg	p.V702M	CCDC40_ENST00000374877.3_Missense_Mutation_p.V702M	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	702					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			GGACCAGGACGTGAAGAAAGT	0.562																																						ENST00000397545.4																			0				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38						c.(2104-2106)Gtg>Atg		coiled-coil domain containing 40							60.0	63.0	62.0					17																	78058656		2130	4232	6362	SO:0001583	missense	55036				axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium|cytoplasm		g.chr17:78058656G>A	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.2104G>A	17.37:g.78058656G>A	ENSP00000380679:p.Val702Met					CCDC40_ENST00000374877.3_Missense_Mutation_p.V702M	p.V702M	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)		13	2131	+	all_neural(118;0.167)		702					A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Missense_Mutation	SNP	ENST00000397545.4	37	c.2104G>A	CCDS42395.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.919307	0.33908	.	.	ENSG00000141519	ENST00000374877;ENST00000397545	T;T	0.51817	0.69;0.7	5.35	4.38	0.52667	.	.	.	.	.	T	0.36110	0.0955	M	0.65975	2.015	0.26834	N	0.968518	P;P	0.42296	0.775;0.676	B;B	0.29353	0.079;0.101	T	0.40961	-0.9535	9	0.35671	T	0.21	-50.2482	5.0736	0.14618	0.29:0.0:0.71:0.0	.	702;485	Q4G0X9;Q4G0X9-3	CCD40_HUMAN;.	M	702	ENSP00000364011:V702M;ENSP00000380679:V702M	ENSP00000364011:V702M	V	+	1	0	CCDC40	75673251	0.986000	0.35501	0.969000	0.41365	0.309000	0.27889	1.459000	0.35234	2.487000	0.83934	0.655000	0.94253	GTG		0.562	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082		8	22	0	0	0	1	0	8	22				
WARS2	10352	broad.mit.edu	37	1	119575971	119575971	+	Nonsense_Mutation	SNP	T	T	A			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr1:119575971T>A	ENST00000235521.4	-	6	672	c.646A>T	c.(646-648)Aag>Tag	p.K216*	WARS2_ENST00000369426.5_3'UTR|WARS2_ENST00000537870.1_Nonsense_Mutation_p.K122*	NM_015836.3|NM_201263.2	NP_056651.1|NP_957715.1	Q9UGM6	SYWM_HUMAN	tryptophanyl tRNA synthetase 2, mitochondrial	216					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)|vasculogenesis (GO:0001570)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(2)	15	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	GATTTTACCTTCTTCATGGAT	0.438																																						ENST00000235521.4																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(2)	15						c.(646-648)Aag>Tag		tryptophanyl tRNA synthetase 2, mitochondrial	L-Tryptophan(DB00150)						170.0	168.0	169.0					1																	119575971		2203	4300	6503	SO:0001587	stop_gained	10352				tryptophanyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|tryptophan-tRNA ligase activity	g.chr1:119575971T>A	BC021722	CCDS900.1, CCDS30817.1	1p12	2011-07-01	2007-02-23		ENSG00000116874	ENSG00000116874	6.1.1.2	"""Aminoacyl tRNA synthetases / Class I"""	12730	protein-coding gene	gene with protein product	"""tryptophan tRNA ligase 2, mitochondrial"""	604733				10072595, 10828066	Standard	NM_201263		Approved	TrpRS	uc001ehn.3	Q9UGM6	OTTHUMG00000012335	ENST00000235521.4:c.646A>T	1.37:g.119575971T>A	ENSP00000235521:p.Lys216*					WARS2_ENST00000537870.1_Nonsense_Mutation_p.K122*|WARS2_ENST00000369426.5_3'UTR	p.K216*	NM_015836.3|NM_201263.2	NP_056651.1|NP_957715.1	Q9UGM6	SYWM_HUMAN		Lung(183;0.0629)	6	672	-	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)	216					B1ALR1|B2R9D4|Q53FT4|Q5VUD2|Q86TQ0	Nonsense_Mutation	SNP	ENST00000235521.4	37	c.646A>T	CCDS900.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.823176	0.90873	.	.	ENSG00000116874	ENST00000235521;ENST00000537870	.	.	.	5.87	5.87	0.94306	.	0.132994	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	-21.9079	16.27	0.82612	0.0:0.0:0.0:1.0	.	.	.	.	X	216;122	.	ENSP00000235521:K216X	K	-	1	0	WARS2	119377494	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.456000	0.80751	2.248000	0.74166	0.533000	0.62120	AAG		0.438	WARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034362.1	NM_015836		17	94	0	0	0	1	0	17	94				
TRAF2	7186	broad.mit.edu	37	9	139804402	139804402	+	Missense_Mutation	SNP	T	T	G			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr9:139804402T>G	ENST00000247668.2	+	6	611	c.559T>G	c.(559-561)Tta>Gta	p.L187V	TRAF2_ENST00000536468.1_Missense_Mutation_p.L187V|TRAF2_ENST00000359662.3_Missense_Mutation_p.L239V|TRAF2_ENST00000482854.1_3'UTR	NM_021138.3	NP_066961.2	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	187					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein complex assembly (GO:0043623)|cellular response to nitric oxide (GO:0071732)|innate immune response (GO:0045087)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron death (GO:1901215)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|programmed necrotic cell death (GO:0097300)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein complex assembly (GO:0006461)|protein heterooligomerization (GO:0051291)|protein homotrimerization (GO:0070207)|protein K63-linked ubiquitination (GO:0070534)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of immunoglobulin secretion (GO:0051023)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|membrane raft (GO:0045121)|ubiquitin ligase complex (GO:0000151)	CD40 receptor binding (GO:0005174)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein phosphatase binding (GO:0019903)|signal transducer activity (GO:0004871)|sphingolipid binding (GO:0046625)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)		CAAGTTCCCCTTAACTTGTGA	0.627																																						ENST00000359662.3																			0				breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						c.(715-717)Tta>Gta		TNF receptor-associated factor 2							97.0	75.0	83.0					9																	139804402		2203	4300	6503	SO:0001583	missense	7186				activation of caspase activity|activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cellular protein complex assembly|induction of apoptosis by extracellular signals|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|protein autoubiquitination|protein homotrimerization|protein K63-linked ubiquitination|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane	CD40 receptor binding|enzyme binding|protein binding|signal transducer activity|sphingolipid binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr9:139804402T>G	U12597	CCDS7013.1	9q34	2013-01-09			ENSG00000127191	ENSG00000127191		"""RING-type (C3HC4) zinc fingers"""	12032	protein-coding gene	gene with protein product		601895				7639698	Standard	NM_021138		Approved	TRAP3	uc004cjv.3	Q12933	OTTHUMG00000020952	ENST00000247668.2:c.559T>G	9.37:g.139804402T>G	ENSP00000247668:p.Leu187Val					TRAF2_ENST00000247668.2_Missense_Mutation_p.L187V|TRAF2_ENST00000482854.1_3'UTR|TRAF2_ENST00000536468.1_Missense_Mutation_p.L187V	p.L239V			Q12933	TRAF2_HUMAN	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)	6	760	+	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	187	Missing (in Ref. 2; BAB70792).				A8K107|B4DPJ7|Q7Z337|Q96NT2	Missense_Mutation	SNP	ENST00000247668.2	37	c.715T>G	CCDS7013.1	.	.	.	.	.	.	.	.	.	.	T	9.803	1.181084	0.21787	.	.	ENSG00000127191	ENST00000536468;ENST00000429509;ENST00000247668;ENST00000359662	T;T;T;T	0.25579	1.82;1.79;1.82;1.82	4.53	-8.64	0.00874	Zinc finger, TRAF-type (1);	0.117935	0.53938	N	0.000058	T	0.11707	0.0285	N	0.25992	0.78	0.23731	N	0.996991	B;P;B	0.41102	0.384;0.738;0.006	B;P;B	0.46299	0.389;0.511;0.012	T	0.40270	-0.9572	10	0.02654	T	1	-7.7789	5.6785	0.17761	0.1007:0.4801:0.2047:0.2145	.	176;239;187	Q12933-3;Q12933-2;Q12933	.;.;TRAF2_HUMAN	V	187;187;187;239	ENSP00000446414:L187V;ENSP00000406524:L187V;ENSP00000247668:L187V;ENSP00000352685:L239V	ENSP00000247668:L187V	L	+	1	2	TRAF2	138924223	0.000000	0.05858	0.038000	0.18304	0.430000	0.31655	-1.218000	0.02976	-1.783000	0.01274	-0.441000	0.05720	TTA		0.627	TRAF2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055166.1	NM_021138		13	14	0	0	0	1	0	13	14				
BMS1P20	96610	broad.mit.edu	37	22	22661272	22661272	+	RNA	SNP	C	C	T			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr22:22661272C>T	ENST00000426066.1	+	0	360					NR_027293.1				BMS1 pseudogene 20																		CTGGGATGTACGTCTGCGTTG	0.488																																						ENST00000426066.1																			0																																																			96610							g.chr22:22661272C>T			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22661272C>T								NR_027293.1						0	360	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.488	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			4	45	0	0	0	1	0	4	45				
LRRC7	57554	broad.mit.edu	37	1	70504190	70504190	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr1:70504190G>A	ENST00000035383.5	+	19	2599	c.2569G>A	c.(2569-2571)Gct>Act	p.A857T	LRRC7_ENST00000310961.5_Missense_Mutation_p.A862T|LRRC7_ENST00000415775.2_Missense_Mutation_p.A141T	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	857						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.A857T(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						AGACAGGACCGCTTTTCCTTC	0.468																																						ENST00000310961.5																			1	Substitution - Missense(1)	p.A857T(1)	endometrium(1)	breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						c.(2584-2586)Gct>Act		leucine rich repeat containing 7							80.0	89.0	86.0					1																	70504190		2203	4300	6503	SO:0001583	missense	57554					centrosome|focal adhesion|nucleolus	protein binding	g.chr1:70504190G>A		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2569G>A	1.37:g.70504190G>A	ENSP00000035383:p.Ala857Thr					LRRC7_ENST00000415775.2_Missense_Mutation_p.A141T|LRRC7_ENST00000035383.5_Missense_Mutation_p.A857T	p.A862T			Q96NW7	LRRC7_HUMAN			22	3002	+			857					Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	c.2584G>A	CCDS645.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.437615	0.83885	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.56275	0.47;0.57;1.68	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.62563	0.2438	L	0.53249	1.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.99	T	0.53258	-0.8464	10	0.28530	T	0.3	.	19.3033	0.94151	0.0:0.0:1.0:0.0	.	141;857;857	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	T	862;857;141;680	ENSP00000309245:A862T;ENSP00000035383:A857T;ENSP00000394867:A141T	ENSP00000035383:A857T	A	+	1	0	LRRC7	70276778	1.000000	0.71417	0.998000	0.56505	0.857000	0.48899	9.447000	0.97595	2.809000	0.96659	0.467000	0.42956	GCT		0.468	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		10	39	0	0	0	1	0	10	39				
PLXNA2	5362	broad.mit.edu	37	1	208212983	208212983	+	Missense_Mutation	SNP	T	T	C			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr1:208212983T>C	ENST00000367033.3	-	24	5240	c.4483A>G	c.(4483-4485)Atc>Gtc	p.I1495V		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1495					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TTGTACTCGATCTGCTGCCGG	0.582																																						ENST00000367033.3																			0				NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80						c.(4483-4485)Atc>Gtc		plexin A2							86.0	90.0	89.0					1																	208212983		2203	4300	6503	SO:0001583	missense	5362				axon guidance	integral to membrane|intracellular|plasma membrane		g.chr1:208212983T>C	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.4483A>G	1.37:g.208212983T>C	ENSP00000356000:p.Ile1495Val						p.I1495V	NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.199)	24	5240	-			1495					A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	c.4483A>G	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.165272	0.78339	.	.	ENSG00000076356	ENST00000367033	T	0.11169	2.8	5.51	5.51	0.81932	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.25344	0.0616	L	0.42632	1.34	0.80722	D	1	D	0.54772	0.968	D	0.71184	0.972	T	0.00571	-1.1665	10	0.38643	T	0.18	.	15.6604	0.77182	0.0:0.0:0.0:1.0	.	1495	O75051	PLXA2_HUMAN	V	1495	ENSP00000356000:I1495V	ENSP00000356000:I1495V	I	-	1	0	PLXNA2	206279606	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.016000	0.70798	2.095000	0.63458	0.528000	0.53228	ATC		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		10	49	0	0	0	1	0	10	49				
ALS2	57679	broad.mit.edu	37	2	202619377	202619377	+	Missense_Mutation	SNP	T	T	C			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr2:202619377T>C	ENST00000264276.6	-	6	1861	c.1489A>G	c.(1489-1491)Aga>Gga	p.R497G		NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	497					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						GCAGCCTTTCTTAAGAGCCTG	0.498																																						ENST00000264276.6																			0				NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						c.(1489-1491)Aga>Gga		amyotrophic lateral sclerosis 2 (juvenile)							71.0	71.0	71.0					2																	202619377		1875	4098	5973	SO:0001583	missense	57679				cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity	g.chr2:202619377T>C	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"""Rho guanine nucleotide exchange factors"""	443	protein-coding gene	gene with protein product	"""alsin"""	606352	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"""	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.1489A>G	2.37:g.202619377T>C	ENSP00000264276:p.Arg497Gly						p.R497G	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN			6	1861	-			497					Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	37	c.1489A>G	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	T	18.38	3.610966	0.66558	.	.	ENSG00000003393	ENST00000264276	T	0.59083	0.29	6.07	3.66	0.41972	.	0.000000	0.85682	D	0.000000	T	0.65101	0.2659	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.964;0.964	T	0.65780	-0.6085	10	0.56958	D	0.05	.	14.5777	0.68262	0.0:0.0:0.49:0.51	.	497;497;497	Q96Q42-3;Q6IQ41;Q96Q42	.;.;ALS2_HUMAN	G	497	ENSP00000264276:R497G	ENSP00000264276:R497G	R	-	1	2	ALS2	202327622	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.812000	0.38952	0.509000	0.28195	-0.313000	0.08912	AGA		0.498	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		11	50	0	0	0	1	0	11	50				
COL11A1	1301	broad.mit.edu	37	1	103400018	103400018	+	Missense_Mutation	SNP	G	G	T			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr1:103400018G>T	ENST00000370096.3	-	46	3899	c.3587C>A	c.(3586-3588)cCa>cAa	p.P1196Q	COL11A1_ENST00000353414.4_Missense_Mutation_p.P1157Q|COL11A1_ENST00000358392.2_Missense_Mutation_p.P1208Q|COL11A1_ENST00000512756.1_Missense_Mutation_p.P1080Q	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1196	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		AAGACCTATTGGACCAGGAGG	0.468																																						ENST00000358392.2																			0				NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258						c.(3622-3624)cCa>cAa		collagen, type XI, alpha 1							89.0	81.0	84.0					1																	103400018		2203	4300	6503	SO:0001583	missense	1301				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging	g.chr1:103400018G>T	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3587C>A	1.37:g.103400018G>T	ENSP00000359114:p.Pro1196Gln					COL11A1_ENST00000353414.4_Missense_Mutation_p.P1157Q|COL11A1_ENST00000512756.1_Missense_Mutation_p.P1080Q|COL11A1_ENST00000370096.3_Missense_Mutation_p.P1196Q	p.P1208Q	NM_080629.2	NP_542196.2	P12107	COBA1_HUMAN		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)	46	3940	-		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)	1196			Triple-helical region.		B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	c.3623C>A	CCDS778.1	.	.	.	.	.	.	.	.	.	.	G	18.87	3.715996	0.68844	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.96913	-4.17;-4.1;-4.17;-4.17	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.97798	0.9277	M	0.72576	2.205	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.989;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.996;0.981;0.999;0.997;0.998	D	0.98494	1.0611	10	0.87932	D	0	.	19.1416	0.93448	0.0:0.0:1.0:0.0	.	1080;1157;1208;1196;416	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	Q	1196;1208;1157;416;1080	ENSP00000359114:P1196Q;ENSP00000351163:P1208Q;ENSP00000302551:P1157Q;ENSP00000426533:P1080Q	ENSP00000302551:P1157Q	P	-	2	0	COL11A1	103172606	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	9.781000	0.99029	2.589000	0.87451	0.655000	0.94253	CCA		0.468	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		5	21	1	0	1.23904e-05	1	1.28329e-05	5	21				
CD163	9332	broad.mit.edu	37	12	7651662	7651662	+	Missense_Mutation	SNP	A	A	T			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr12:7651662A>T	ENST00000359156.4	-	4	782	c.580T>A	c.(580-582)Tct>Act	p.S194T	CD163_ENST00000396620.3_Missense_Mutation_p.S194T|CD163_ENST00000432237.2_Missense_Mutation_p.S194T|CD163_ENST00000541972.1_Missense_Mutation_p.S182T	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	194	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	CAAATGACAGATGCATGATCT	0.423																																						ENST00000359156.4																			0				breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76						c.(580-582)Tct>Act		CD163 molecule							278.0	254.0	262.0					12																	7651662		2203	4300	6503	SO:0001583	missense	9332				acute-phase response	extracellular region|integral to plasma membrane	protein binding|scavenger receptor activity	g.chr12:7651662A>T	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"""CD molecules"""	1631	protein-coding gene	gene with protein product		605545	"""CD163 antigen"""			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.580T>A	12.37:g.7651662A>T	ENSP00000352071:p.Ser194Thr					CD163_ENST00000432237.2_Missense_Mutation_p.S194T|CD163_ENST00000396620.3_Missense_Mutation_p.S194T|CD163_ENST00000541972.1_Missense_Mutation_p.S182T	p.S194T	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN			4	782	-			194			SRCR 2.		C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Missense_Mutation	SNP	ENST00000359156.4	37	c.580T>A	CCDS8578.1	.	.	.	.	.	.	.	.	.	.	A	8.121	0.780967	0.16120	.	.	ENSG00000177575	ENST00000359156;ENST00000541972;ENST00000396620;ENST00000432237	T;T;T;T	0.36157	1.27;1.27;1.27;1.27	5.16	-1.19	0.09585	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.945300	0.08849	N	0.884681	T	0.19967	0.0480	N	0.21373	0.66	0.23204	N	0.998124	B;B;B	0.29378	0.153;0.002;0.243	B;B;B	0.27262	0.078;0.005;0.078	T	0.26360	-1.0105	10	0.23891	T	0.37	.	5.609	0.17394	0.2865:0.4357:0.0:0.2778	.	194;194;194	C9JHR8;Q86VB7-3;Q86VB7	.;.;C163A_HUMAN	T	194;182;194;194	ENSP00000352071:S194T;ENSP00000444071:S182T;ENSP00000379863:S194T;ENSP00000403885:S194T	ENSP00000352071:S194T	S	-	1	0	CD163	7542929	0.000000	0.05858	0.751000	0.31187	0.305000	0.27757	-0.409000	0.07160	0.013000	0.14918	0.528000	0.53228	TCT		0.423	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		8	160	0	0	0	1	0	8	160				
PCDHGA6	56109	broad.mit.edu	37	5	140753701	140753701	+	Silent	SNP	C	C	A			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr5:140753701C>A	ENST00000517434.1	+	1	51	c.51C>A	c.(49-51)ctC>ctA	p.L17L	PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	17					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTGCTCCTCACGCTCCTGG	0.597																																						ENST00000517434.1																			0				breast(1)|large_intestine(1)	2						c.(49-51)ctC>ctA									14.0	17.0	16.0					5																	140753701		1997	4186	6183	SO:0001819	synonymous_variant	56109							g.chr5:140753701C>A	AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"""Cadherins / Protocadherins : Clustered"""	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.51C>A	5.37:g.140753701C>A						PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	p.L17L	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	51	+								A6H8K7|B2RN55|Q9Y5D1	Silent	SNP	ENST00000517434.1	37	c.51C>A	CCDS54926.1																																																																																				0.597	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		3	17	1	0	0.004672	1	0.004672	3	17				
MLLT3	4300	broad.mit.edu	37	9	20414340	20414340	+	Silent	SNP	G	G	A			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr9:20414340G>A	ENST00000380338.4	-	5	790	c.504C>T	c.(502-504)agC>agT	p.S168S	MLLT3_ENST00000429426.2_Silent_p.S165S|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	168	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.S168S(5)		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)		tgctgctgctgctactgctgc	0.537			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		5	Substitution - coding silent(5)	p.S168S(5)	lung(2)|urinary_tract(1)|endometrium(1)|kidney(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.(502-504)agC>agT		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							9.0	16.0	13.0					9																	20414340		1646	3412	5058	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414340G>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.504C>T	9.37:g.20414340G>A						MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S165S|MLLT3_ENST00000475957.1_5'UTR	p.S168S	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	790	-			168			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.504C>T	CCDS6494.1																																																																																				0.537	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		4	61	0	0	0	1	0	4	61				
VHL	7428	broad.mit.edu	37	3	10188286	10188286	+	Missense_Mutation	SNP	C	C	G			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr3:10188286C>G	ENST00000256474.2	+	2	1269	c.429C>G	c.(427-429)gaC>gaG	p.D143E	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	143	Involved in binding to CCT complex.		D -> E (in VHLD; type II). {ECO:0000269|PubMed:8825918}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.G144fs*14(4)|p.D143E(2)|p.D143fs*16(2)|p.V142fs*30(1)|p.Q145fs*30(1)|p.D143fs*29(1)|p.N141fs*30(1)|p.S139fs*12(1)|p.G144fs*19(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TCAATGTTGACGGACAGCCTA	0.423		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													ENST00000256474.2		1	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	"""D, Mis, N, F, S"""	von Hippel-Lindau syndrome gene			"""E, M, O"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""		14	Deletion - Frameshift(11)|Substitution - Missense(2)|Insertion - Frameshift(1)	p.G144fs*14(4)|p.D143E(2)|p.D143fs*16(2)|p.V142fs*30(1)|p.Q145fs*30(1)|p.D143fs*29(1)|p.N141fs*30(1)|p.S139fs*12(1)|p.G144fs*19(1)	kidney(13)|adrenal_gland(1)	adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769	GRCh37	CD951875	VHL	D		c.(427-429)gaC>gaG		von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase							219.0	202.0	208.0					3																	10188286		2203	4300	6503	SO:0001583	missense	7428	von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	g.chr3:10188286C>G	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.429C>G	3.37:g.10188286C>G	ENSP00000256474:p.Asp143Glu					VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	p.D143E	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN		Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)	2	1269	+			143		D -> E (in VHLD; type II).	Involved in binding to CCT complex.		B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	c.429C>G	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	12.49	1.952917	0.34471	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99823	-6.95	5.07	-2.72	0.05968	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.344265	0.32719	N	0.005731	D	0.98235	0.9416	N	0.19112	0.55	0.80722	D	1	B	0.17268	0.021	B	0.17979	0.02	D	0.93621	0.6948	10	0.20519	T	0.43	0.1775	11.0594	0.47938	0.0:0.5225:0.0:0.4775	.	143	P40337	VHL_HUMAN	E	143;61	ENSP00000256474:D143E	ENSP00000256474:D143E	D	+	3	2	VHL	10163286	0.996000	0.38824	0.987000	0.45799	0.861000	0.49209	0.102000	0.15272	-0.425000	0.07371	-0.471000	0.05019	GAC		0.423	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		59	59	0	0	0	1	0	59	59				
PIK3C2A	5286	broad.mit.edu	37	11	17111301	17111301	+	Missense_Mutation	SNP	G	G	A	rs201133316		TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr11:17111301G>A	ENST00000265970.7	-	32	5044	c.5045C>T	c.(5044-5046)gCg>gTg	p.A1682V	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.A1302V	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1682					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						GTATGTTGCCGCAGTCAGCTG	0.428																																						ENST00000265970.7																			0				central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						c.(5044-5046)gCg>gTg		phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	Phosphatidylserine(DB00144)						142.0	132.0	136.0					11																	17111301		2200	4294	6494	SO:0001583	missense	5286				cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling	clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity	g.chr11:17111301G>A	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"""phosphoinositide-3-kinase, class 2, alpha polypeptide"""			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.5045C>T	11.37:g.17111301G>A	ENSP00000265970:p.Ala1682Val					PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.A1302V	p.A1682V	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN			32	5044	-			1682					B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	c.5045C>T	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.811506	0.70797	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.64803	-0.12;0.3	5.58	5.58	0.84498	.	0.099306	0.64402	D	0.000001	T	0.55114	0.1900	L	0.50333	1.59	0.54753	D	0.999989	D	0.56521	0.976	B	0.38655	0.278	T	0.62909	-0.6754	10	0.62326	D	0.03	-16.2899	14.7582	0.69583	0.0:0.0:0.8555:0.1445	.	1682	O00443	P3C2A_HUMAN	V	1682;1302	ENSP00000265970:A1682V;ENSP00000438687:A1302V	ENSP00000265970:A1682V	A	-	2	0	PIK3C2A	17067877	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.390000	0.79816	2.794000	0.96219	0.655000	0.94253	GCG		0.428	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		3	64	0	0	0	1	0	3	64				
POTEA	340441	broad.mit.edu	37	8	43155495	43155496	+	RNA	INS	-	-	G	rs201380174	byFrequency	TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr8:43155495_43155496insG	ENST00000522175.2	+	0	590							Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A											breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(27)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TTCCAAGGGAAGAGCAGTGTGT	0.386													gg|G|GG|deletion	308	0.0615016	0.1936	0.0187	5008	,	,		6538	0.0		0.0199	False		,,,				2504	0.0194					ENST00000522175.2																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(27)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46								POTE ankyrin domain family, member A																																						340441							g.chr8:43155495_43155496insG	AY462869		8p11.1	2013-01-11	2008-11-26	2008-11-26	ENSG00000188877	ENSG00000188877		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33893	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 3"""	608915	"""ANKRD26-like family A, member 1"""	A26A1			Standard	NM_001002920		Approved	POTE8, POTE-8, CT104.3	uc003xpz.1	Q6S8J7	OTTHUMG00000164111		8.37:g.43155496_43155496dupG										Q6S8J7	POTEA_HUMAN			0	590	+								A6ND17|A6ND71|Q6S8J6	RNA	INS	ENST00000522175.2	37																																																																																						0.386	POTEA-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000383492.1	NM_001002920		4	3						4	3	---	---	---	---
ZFC3H1	196441	broad.mit.edu	37	12	72030395	72030395	+	Frame_Shift_Del	DEL	G	G	-			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr12:72030395delG	ENST00000378743.3	-	9	2333	c.1975delC	c.(1975-1977)ctgfs	p.L659fs	SNORA17_ENST00000391159.1_RNA	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	659					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						GAATTGTTCAGAACTGGAGGT	0.383																																						ENST00000378743.3																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						c.(1975-1977)tgfs		zinc finger, C3H1-type containing							164.0	153.0	157.0					12																	72030395		1901	4124	6025	SO:0001589	frameshift_variant	196441				RNA processing	intracellular	metal ion binding	g.chr12:72030395delG	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.1975delC	12.37:g.72030395delG	ENSP00000368017:p.Leu659fs						p.L659fs	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN			9	2333	-			659					Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Frame_Shift_Del	DEL	ENST00000378743.3	37	c.1975delC	CCDS41813.1																																																																																				0.383	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		22	56						22	56	---	---	---	---
MBD3L5	284428	broad.mit.edu	37	19	7032331	7032332	+	Frame_Shift_Ins	INS	-	-	A			TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr19:7032331_7032332insA	ENST00000329753.5	+	2	87_88	c.53_54insA	c.(52-57)ctcaaafs	p.K19fs		NM_001136507.1	NP_001129979.1	A6NJ08	MB3L5_HUMAN	methyl-CpG binding domain protein 3-like 5	19																	AAGGGGAAGCTCAAAAGAAACA	0.485																																						ENST00000329753.5																			0											c.(52-54)caafs		methyl-CpG binding domain protein 3-like 5																																				SO:0001589	frameshift_variant	284428							g.chr19:7032331_7032332insA		CCDS45942.1	19p13.2	2014-04-01			ENSG00000237247	ENSG00000237247			37204	protein-coding gene	gene with protein product							Standard	NM_001136507		Approved		uc010xjl.2	A6NJ08	OTTHUMG00000181973	Exception_encountered	19.37:g.7032331_7032332insA	ENSP00000331435:p.Lys19fs						p.Q18fs	NM_001136507.1	NP_001129979.1	A6NJ08	MB3L5_HUMAN			2	87_88	+			18						Frame_Shift_Ins	INS	ENST00000329753.5	37	c.53_54insA	CCDS45942.1																																																																																				0.485	MBD3L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458497.1	NM_001136507		2	4						2	4	---	---	---	---
MAP3K10	4294	broad.mit.edu	37	19	40719906	40719917	+	In_Frame_Del	DEL	CCCTCCCCACCA	CCCTCCCCACCA	-	rs533682595	byFrequency	TCGA-QR-A70N-01A-12D-A35D-08	TCGA-QR-A70N-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffd4f038-8b57-4f33-b442-576ad662a41e	7a4b6abb-dee6-4d5d-9c6b-39fe7c7c4f60	g.chr19:40719906_40719917delCCCTCCCCACCA	ENST00000253055.3	+	9	2608_2619	c.2320_2331delCCCTCCCCACCA	c.(2320-2331)ccctccccaccadel	p.PSPP778del		NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	778					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						ACCGGccgcgccctccccaccaccctccccgc	0.717														14	0.00279553	0.0106	0.0	5008	,	,		5371	0.0		0.0	False		,,,				2504	0.0					ENST00000253055.3																			0				NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						c.(2320-2331)del		mitogen-activated protein kinase kinase kinase 10				44,3676		10,24,1826						0.6	1.0			6	23,7333		11,1,3666	no	coding	MAP3K10	NM_002446.3		21,25,5492	A1A1,A1R,RR		0.3127,1.1828,0.6049				67,11009				SO:0001651	inframe_deletion	4294				activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway	cytoplasm	ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity	g.chr19:40719906_40719917delCCCTCCCCACCA	X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6849	protein-coding gene	gene with protein product	"""MKN28 kinase"", ""mixed lineage kinase 2"", ""MKN28 derived nonreceptor_type serine/threonine kinase"""	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.2320_2331delCCCTCCCCACCA	19.37:g.40719906_40719917delCCCTCCCCACCA	ENSP00000253055:p.Pro778_Pro781del						p.PSPP778del	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN			9	2608_2619	+			778					Q12761|Q14871	In_Frame_Del	DEL	ENST00000253055.3	37	c.2320_2331delCCCTCCCCACCA	CCDS12549.1																																																																																				0.717	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446		7	5						7	5	---	---	---	---
