#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
SULF1	23213	broad.mit.edu	37	8	70540461	70540461	+	Missense_Mutation	SNP	C	C	T			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr8:70540461C>T	ENST00000260128.4	+	18	2815	c.2098C>T	c.(2098-2100)Cac>Tac	p.H700Y	SULF1_ENST00000419716.3_Missense_Mutation_p.H700Y|SULF1_ENST00000458141.2_Missense_Mutation_p.H700Y|SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000402687.4_Missense_Mutation_p.H700Y	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	700					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			GAGCCATCTTCACCCATTCAA	0.428																																						ENST00000260128.4																			0				breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						c.(2098-2100)Cac>Tac		sulfatase 1							104.0	109.0	108.0					8																	70540461		2203	4300	6503	SO:0001583	missense	23213				apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding	g.chr8:70540461C>T	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2098C>T	8.37:g.70540461C>T	ENSP00000260128:p.His700Tyr					SULF1_ENST00000402687.4_Missense_Mutation_p.H700Y|SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000419716.3_Missense_Mutation_p.H700Y|SULF1_ENST00000458141.2_Missense_Mutation_p.H700Y	p.H700Y	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)		18	2815	+	Breast(64;0.0654)		700					Q86YV8|Q8NCA2|Q9UPS5	Missense_Mutation	SNP	ENST00000260128.4	37	c.2098C>T	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	C	19.46	3.831028	0.71258	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000402687;ENST00000419716	T;T;T;T	0.21734	1.99;1.99;1.99;1.99	5.14	5.14	0.70334	Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	T	0.30510	0.0767	M	0.79258	2.445	0.48395	D	0.99964	P	0.36330	0.548	B	0.36030	0.216	T	0.10776	-1.0615	10	0.33141	T	0.24	.	18.621	0.91321	0.0:1.0:0.0:0.0	.	700	Q8IWU6	SULF1_HUMAN	Y	700	ENSP00000403040:H700Y;ENSP00000260128:H700Y;ENSP00000385704:H700Y;ENSP00000390315:H700Y	ENSP00000260128:H700Y	H	+	1	0	SULF1	70703015	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	4.331000	0.59273	2.371000	0.80710	0.563000	0.77884	CAC		0.428	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		20	56	0	0	0	1	0	20	56				
CCBL2	56267	broad.mit.edu	37	1	89427800	89427800	+	Missense_Mutation	SNP	C	C	A			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr1:89427800C>A	ENST00000260508.4	-	6	819	c.482G>T	c.(481-483)tGc>tTc	p.C161F	CCBL2_ENST00000446900.2_5'UTR|CCBL2_ENST00000370485.2_3'UTR|CCBL2_ENST00000370491.3_Missense_Mutation_p.C127F	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	161					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	mitochondrion (GO:0005739)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|kynurenine-glyoxylate transaminase activity (GO:0047315)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|ovary(2)|skin(2)|soft_tissue(1)	18		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)		GGGCTCATAGCAGTCATAGAA	0.378																																						ENST00000260508.4																			0				endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|ovary(2)|skin(2)|soft_tissue(1)	18						c.(481-483)tGc>tTc		cysteine conjugate-beta lyase 2	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)						124.0	113.0	117.0					1																	89427800		2203	4300	6503	SO:0001583	missense	56267				biosynthetic process|kynurenine metabolic process|tryptophan catabolic process		cysteine-S-conjugate beta-lyase activity|kynurenine-glyoxylate transaminase activity|kynurenine-oxoglutarate transaminase activity|pyridoxal phosphate binding	g.chr1:89427800C>A	AF091090	CCDS30766.1, CCDS30767.1	1p22.2	2009-06-23			ENSG00000137944	ENSG00000137944			33238	protein-coding gene	gene with protein product		610656				16376499	Standard	NM_001008662		Approved	RBM1, RP11-82K18.3, KAT3	uc001dmp.2	Q6YP21	OTTHUMG00000010617	ENST00000260508.4:c.482G>T	1.37:g.89427800C>A	ENSP00000260508:p.Cys161Phe					CCBL2_ENST00000370485.2_3'UTR|CCBL2_ENST00000370491.3_Missense_Mutation_p.C127F|CCBL2_ENST00000446900.2_5'UTR	p.C161F	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN		all cancers(265;0.0117)|Epithelial(280;0.0341)	6	819	-		Lung NSC(277;0.123)	161					B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Missense_Mutation	SNP	ENST00000260508.4	37	c.482G>T	CCDS30766.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.718404	0.89205	.	.	ENSG00000137944	ENST00000370491;ENST00000260508;ENST00000370486	D;D;D	0.90197	-2.63;-2.63;-2.63	5.92	5.92	0.95590	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.96648	0.8906	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96719	0.9531	10	0.87932	D	0	-35.4141	20.2995	0.98608	0.0:1.0:0.0:0.0	.	161	Q6YP21	KAT3_HUMAN	F	127;161;161	ENSP00000359522:C127F;ENSP00000260508:C161F;ENSP00000359517:C161F	ENSP00000260508:C161F	C	-	2	0	CCBL2	89200388	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.176000	0.77643	2.799000	0.96334	0.655000	0.94253	TGC		0.378	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661		3	41	1	0	1	1	1	3	41				
RPTN	126638	broad.mit.edu	37	1	152128186	152128186	+	Silent	SNP	A	A	G			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr1:152128186A>G	ENST00000316073.3	-	3	1453	c.1389T>C	c.(1387-1389)taT>taC	p.Y463Y		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	463	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						CTGTCTGACCATAGTGGGAAC	0.512																																						ENST00000316073.3																			0				breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						c.(1387-1389)taT>taC		repetin							788.0	697.0	725.0					1																	152128186		1568	3582	5150	SO:0001819	synonymous_variant	126638					proteinaceous extracellular matrix	calcium ion binding	g.chr1:152128186A>G	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1389T>C	1.37:g.152128186A>G							p.Y463Y	NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN			3	1453	-			463			Gln-rich.		B7ZBZ3	Silent	SNP	ENST00000316073.3	37	c.1389T>C	CCDS41397.1																																																																																				0.512	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		6	788	0	0	0	1	0	6	788				
TBC1D3P5	440419	broad.mit.edu	37	17	25748637	25748637	+	RNA	SNP	C	C	A			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr17:25748637C>A	ENST00000586223.1	+	0	554					NR_033892.1				TBC1 domain family, member 3 pseudogene 5																		CTAACTCCAACATTCCTCATT	0.537																																						ENST00000586223.1																			0																																																			440419							g.chr17:25748637C>A			17q11.1	2014-03-20			ENSG00000266433	ENSG00000266433			43567	pseudogene	pseudogene							Standard	NR_033892		Approved		uc002gzg.3		OTTHUMG00000179156		17.37:g.25748637C>A								NR_033892.1						0	554	+									RNA	SNP	ENST00000586223.1	37																																																																																						0.537	TBC1D3P5-003	KNOWN	non_canonical_TEC|basic	processed_transcript	pseudogene	OTTHUMT00000451073.1	NR_033892		10	20	1	0	0.000442599	1	0.000540955	10	20				
ZNF407	55628	broad.mit.edu	37	18	72776115	72776115	+	Missense_Mutation	SNP	C	C	G			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr18:72776115C>G	ENST00000299687.5	+	8	6438	c.6438C>G	c.(6436-6438)atC>atG	p.I2146M		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	2146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CGCAGATCATCGTGACGGAGG	0.652																																						ENST00000299687.5																			0				central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67						c.(6436-6438)atC>atG		zinc finger protein 407							29.0	35.0	33.0					18																	72776115		2182	4289	6471	SO:0001583	missense	55628				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr18:72776115C>G	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.6438C>G	18.37:g.72776115C>G	ENSP00000299687:p.Ile2146Met						p.I2146M	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN		BRCA - Breast invasive adenocarcinoma(31;0.184)	8	6438	+		Esophageal squamous(42;0.131)|Prostate(75;0.173)	2146					B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	c.6438C>G	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.813811	0.50527	.	.	ENSG00000215421	ENST00000299687	T	0.19669	2.13	4.67	-5.06	0.02946	.	.	.	.	.	T	0.35711	0.0941	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.67688	-0.5606	9	0.87932	D	0	.	7.8148	0.29252	0.1121:0.2568:0.0:0.631	.	2146	Q9C0G0	ZN407_HUMAN	M	2146	ENSP00000299687:I2146M	ENSP00000299687:I2146M	I	+	3	3	ZNF407	70905103	0.229000	0.23729	0.621000	0.29145	0.953000	0.61014	-1.014000	0.03641	2.140000	0.66376	0.462000	0.41574	ATC		0.652	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		4	9	0	0	0	1	0	4	9				
SECISBP2	79048	broad.mit.edu	37	9	91972365	91972365	+	Missense_Mutation	SNP	C	C	T			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr9:91972365C>T	ENST00000375807.3	+	15	2224	c.2153C>T	c.(2152-2154)gCc>gTc	p.A718V	SECISBP2_ENST00000339901.4_Missense_Mutation_p.A645V|SECISBP2_ENST00000534113.2_Missense_Mutation_p.A650V	NM_001282688.1|NM_001282690.1|NM_024077.3	NP_001269617.1|NP_001269619.1|NP_076982.3	Q96T21	SEBP2_HUMAN	SECIS binding protein 2	718					translation (GO:0006412)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(3)|skin(2)	32						ATTGATTATGCCTGTGAGCAG	0.468																																						ENST00000375807.3																			0				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(3)|skin(2)	32						c.(2152-2154)gCc>gTc		SECIS binding protein 2							301.0	274.0	283.0					9																	91972365		2203	4300	6503	SO:0001583	missense	79048				translation	nucleus	mRNA 3'-UTR binding	g.chr9:91972365C>T	AF380995	CCDS6683.1, CCDS65076.1, CCDS65077.1	9q22	2008-02-05			ENSG00000187742	ENSG00000187742			30972	protein-coding gene	gene with protein product		607693				11230166	Standard	XM_005252193		Approved		uc004aqj.1	Q96T21	OTTHUMG00000020182	ENST00000375807.3:c.2153C>T	9.37:g.91972365C>T	ENSP00000364965:p.Ala718Val					SECISBP2_ENST00000339901.4_Missense_Mutation_p.A645V|SECISBP2_ENST00000534113.2_Missense_Mutation_p.A650V	p.A718V	NM_024077.3	NP_076982.3	Q96T21	SEBP2_HUMAN			15	2224	+			718					F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Missense_Mutation	SNP	ENST00000375807.3	37	c.2153C>T	CCDS6683.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354685	0.82243	.	.	ENSG00000187742	ENST00000375807;ENST00000395669;ENST00000339901;ENST00000534113	T;T;T	0.80824	-1.42;-1.42;-1.42	4.54	4.54	0.55810	Ribosomal protein L7Ae/L30e/S12e/Gadd45 (1);	0.123631	0.64402	D	0.000019	D	0.89726	0.6798	M	0.78049	2.395	0.37452	D	0.914843	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	D	0.92402	0.5930	10	0.72032	D	0.01	-15.9529	17.8153	0.88630	0.0:1.0:0.0:0.0	.	725;645;718	Q59H19;Q96T21-2;Q96T21	.;.;SEBP2_HUMAN	V	718;724;645;650	ENSP00000364965:A718V;ENSP00000364959:A645V;ENSP00000436650:A650V	ENSP00000364959:A645V	A	+	2	0	SECISBP2	91162185	1.000000	0.71417	0.998000	0.56505	0.957000	0.61999	3.825000	0.55730	2.511000	0.84671	0.561000	0.74099	GCC		0.468	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077		4	202	0	0	0	1	0	4	202				
TUBB8P7	197331	broad.mit.edu	37	16	90161618	90161618	+	RNA	SNP	C	C	T	rs13338202	byFrequency	TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr16:90161618C>T	ENST00000564451.1	+	0	971				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7									p.D118D(2)									CAGTGATGGACGTTGTCAGAA	0.607													.|||	94	0.01877	0.0469	0.0173	5008	,	,		18765	0.0		0.0169	False		,,,				2504	0.0031					ENST00000567960.1																			2	Substitution - coding silent(2)	p.D118D(2)	kidney(2)																																																197331							g.chr16:90161618C>T			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90161618C>T						TUBB8P7_ENST00000564451.1_RNA								0	354	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.607	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		4	30	0	0	0	1	0	4	30				
PRPF8	10594	broad.mit.edu	37	17	1577856	1577856	+	Missense_Mutation	SNP	T	T	C			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr17:1577856T>C	ENST00000572621.1	-	20	3444	c.3179A>G	c.(3178-3180)gAg>gGg	p.E1060G	PRPF8_ENST00000304992.6_Missense_Mutation_p.E1060G			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	1060	Reverse transcriptase homology domain.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CCCAGCCATCTCACTGGCCCG	0.517																																						ENST00000572621.1																			0				NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77						c.(3178-3180)gAg>gGg		pre-mRNA processing factor 8							150.0	145.0	147.0					17																	1577856		2203	4300	6503	SO:0001583	missense	10594					catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding	g.chr17:1577856T>C	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.3179A>G	17.37:g.1577856T>C	ENSP00000460348:p.Glu1060Gly					PRPF8_ENST00000304992.6_Missense_Mutation_p.E1060G	p.E1060G			Q6P2Q9	PRP8_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)	20	3444	-			1060					O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	37	c.3179A>G	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.708336	0.89018	.	.	ENSG00000174231	ENST00000304992	D	0.83075	-1.68	5.25	5.25	0.73442	RNA recognition motif, spliceosomal PrP8 (1);	0.000000	0.85682	D	0.000000	D	0.91975	0.7458	M	0.92555	3.32	0.80722	D	1	P	0.51791	0.948	P	0.59012	0.85	D	0.93853	0.7147	10	0.87932	D	0	.	15.3304	0.74203	0.0:0.0:0.0:1.0	.	1060	Q6P2Q9	PRP8_HUMAN	G	1060	ENSP00000304350:E1060G	ENSP00000304350:E1060G	E	-	2	0	PRPF8	1524606	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.868000	0.87116	2.212000	0.71576	0.260000	0.18958	GAG		0.517	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			9	109	0	0	0	1	0	9	109				
DPM1	8813	broad.mit.edu	37	20	49551759	49551759	+	Silent	SNP	A	A	G			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr20:49551759A>G	ENST00000371588.5	-	9	719	c.693T>C	c.(691-693)ttT>ttC	p.F231F	DPM1_ENST00000371582.4_Silent_p.F258F|DPM1_ENST00000371583.5_Silent_p.F226F|RP5-914P20.5_ENST00000558899.2_RNA|DPM1_ENST00000466152.1_5'UTR	NM_003859.1	NP_003850.1	O60762	DPM1_HUMAN	dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit	231					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|dolichol metabolic process (GO:0019348)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose metabolic process (GO:0019673)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|protein mannosylation (GO:0035268)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked mannosylation (GO:0035269)	dolichol-phosphate-mannose synthase complex (GO:0033185)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nucleus (GO:0005634)	alcohol binding (GO:0043178)|dolichyl-phosphate beta-D-mannosyltransferase activity (GO:0004582)|dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannose binding (GO:0005537)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	7						CACGATCCACAAATGATATTG	0.318																																						ENST00000371582.4																			0				endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	7						c.(772-774)ttT>ttC		dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit							74.0	83.0	80.0					20																	49551759		2201	4294	6495	SO:0001819	synonymous_variant	8813				C-terminal protein lipidation|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|protein N-linked glycosylation via asparagine|protein O-linked mannosylation	dolichol-phosphate-mannose synthase complex|endoplasmic reticulum membrane|membrane fraction	dolichyl-phosphate beta-D-mannosyltransferase activity|dolichyl-phosphate-mannose-protein mannosyltransferase activity|protein binding	g.chr20:49551759A>G	AF007875	CCDS13434.1	20q13.1	2013-02-26			ENSG00000000419	ENSG00000000419	2.4.1.83	"""Glycosyltransferase family 2 domain containing"""	3005	protein-coding gene	gene with protein product	"""DPM synthase complex, catalytic subunit"""	603503				9223280, 9535917	Standard	NM_003859		Approved	MPDS, CDGIE	uc002xvw.1	O60762	OTTHUMG00000032742	ENST00000371588.5:c.693T>C	20.37:g.49551759A>G						DPM1_ENST00000466152.1_5'UTR|DPM1_ENST00000371583.5_Silent_p.F226F|DPM1_ENST00000371588.5_Silent_p.F231F|RP5-914P20.5_ENST00000558899.2_RNA	p.F258F			O60762	DPM1_HUMAN			10	805	-			231					O15157|Q6IB78|Q96HK0	Silent	SNP	ENST00000371588.5	37	c.774T>C	CCDS13434.1	.	.	.	.	.	.	.	.	.	.	A	1.087	-0.665324	0.03428	.	.	ENSG00000000419	ENST00000371584	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	T	0.71256	0.3318	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70615	-0.4823	4	.	.	.	-18.8742	15.1194	0.72429	1.0:0.0:0.0:0.0	.	.	.	.	R	266	.	.	C	-	1	0	DPM1	48985166	1.000000	0.71417	1.000000	0.80357	0.185000	0.23345	6.760000	0.74939	2.050000	0.60909	0.374000	0.22700	TGT		0.318	DPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079716.1	NM_003859		36	95	0	0	0	1	0	36	95				
RET	5979	broad.mit.edu	37	10	43617416	43617416	+	Missense_Mutation	SNP	T	T	C	rs74799832		TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr10:43617416T>C	ENST00000355710.3	+	16	2985	c.2753T>C	c.(2752-2754)aTg>aCg	p.M918T	RET_ENST00000340058.5_Missense_Mutation_p.M918T	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	918	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		M -> T (in MEN2B and MTC; sporadic form; somatic mutation; also found in a patient with renal agenesis; dbSNP:rs74799832). {ECO:0000269|PubMed:18252215, ECO:0000269|PubMed:7906417, ECO:0000269|PubMed:7906866, ECO:0000269|PubMed:7911697, ECO:0000269|PubMed:8595427, ECO:0000269|PubMed:8807338}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.M918T(247)	CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	GTTAAATGGATGGCAATTGAA	0.443		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	ENST00000355710.3		1	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	"""T, Mis, N, F"""	ret proto-oncogene	yes	Hirschsprung disease	"""E, O"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	CCDC6/RET(4)|KIF5B/RET(79)	247	Substitution - Missense(247)	p.M918T(247)	thyroid(231)|adrenal_gland(16)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607	GRCh37	CM941246	RET	M	rs74799832	c.(2752-2754)aTg>aCg		ret proto-oncogene	Sunitinib(DB01268)						262.0	244.0	250.0					10																	43617416		2203	4300	6503	SO:0001583	missense	5979	Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	homophilic cell adhesion|positive regulation of metanephric glomerulus development|positive regulation of transcription, DNA-dependent|posterior midgut development	integral to membrane	ATP binding|calcium ion binding|transmembrane receptor protein tyrosine kinase activity	g.chr10:43617416T>C	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2753T>C	10.37:g.43617416T>C	ENSP00000347942:p.Met918Thr					RET_ENST00000340058.5_Missense_Mutation_p.M918T	p.M918T	NM_020975.4	NP_066124.1	P07949	RET_HUMAN			16	2985	+		Ovarian(717;0.0423)	918		M -> T (in RADYS, MEN2B and MTC; sporadic form; somatic mutation).	Protein kinase.		A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	c.2753T>C	CCDS7200.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.427864	0.83667	.	.	ENSG00000165731	ENST00000355710;ENST00000340058	D;D	0.90504	-2.68;-2.68	5.43	5.43	0.79202	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.93719	0.7993	L	0.52126	1.63	0.80722	A	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.94557	0.7759	9	0.87932	D	0	.	15.7766	0.78224	0.0:0.0:0.0:1.0	.	664;918;918	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	T	918	ENSP00000347942:M918T;ENSP00000344798:M918T	ENSP00000344798:M918T	M	+	2	0	RET	42937422	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.986000	0.88173	2.198000	0.70561	0.533000	0.62120	ATG		0.443	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		35	81	0	0	0	1	0	35	81				
TUBBP5	643224	broad.mit.edu	37	9	141070687	141070687	+	RNA	SNP	C	C	T	rs199688784	byFrequency	TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr9:141070687C>T	ENST00000503395.1	+	0	1462									tubulin, beta pseudogene 5																		ACAACTGGGCCAAGGGACGCT	0.577																																						ENST00000503395.1																			0																																																			643224							g.chr9:141070687C>T	AF355123		9q34.3	2012-03-06	2005-11-15		ENSG00000159247	ENSG00000159247			23674	pseudogene	pseudogene			"""tubulin, beta polypeptide pseudogene 5"""			11731935	Standard	NR_027156		Approved		uc010ncq.3		OTTHUMG00000021001		9.37:g.141070687C>T														0	1462	+									RNA	SNP	ENST00000503395.1	37																																																																																						0.577	TUBBP5-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373087.1	NR_027156		4	9	0	0	0	1	0	4	9				
HEXDC	284004	broad.mit.edu	37	17	80400118	80400118	+	Missense_Mutation	SNP	C	C	A			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr17:80400118C>A	ENST00000327949.9	+	12	1330	c.1319C>A	c.(1318-1320)cCg>cAg	p.P440Q	HEXDC_ENST00000337014.6_Silent_p.R470R|HEXDC_ENST00000577944.1_Silent_p.P442P			Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	440					carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	beta-N-acetylhexosaminidase activity (GO:0004563)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			GCTTTCTACCCGGATGCCGTG	0.667																																						ENST00000327949.9																			0				breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16						c.(1318-1320)cCg>cAg		hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing							23.0	26.0	25.0					17																	80400118		2091	4212	6303	SO:0001583	missense	284004				carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding	g.chr17:80400118C>A	AK074405	CCDS42402.1	17q25.3	2011-12-19			ENSG00000169660	ENSG00000169660			26307	protein-coding gene	gene with protein product						12477932	Standard	NM_173620		Approved	FLJ23825	uc002kev.4	Q8WVB3		ENST00000327949.9:c.1319C>A	17.37:g.80400118C>A	ENSP00000332634:p.Pro440Gln					HEXDC_ENST00000577944.1_Silent_p.P442P|HEXDC_ENST00000337014.6_Silent_p.R470R	p.P440Q			Q8WVB3	HEXDC_HUMAN	OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)		12	1330	+	Breast(20;0.00106)|all_neural(118;0.0804)		440					B7UUP6|Q8IYN4|Q8TE81	Missense_Mutation	SNP	ENST00000327949.9	37	c.1319C>A		.	.	.	.	.	.	.	.	.	.	C	8.425	0.847282	0.17034	.	.	ENSG00000169660	ENST00000327949	T	0.29655	1.56	5.4	5.4	0.78164	.	.	.	.	.	T	0.29716	0.0742	.	.	.	0.31883	N	0.618202	D	0.53619	0.961	P	0.46718	0.525	T	0.16571	-1.0398	8	0.25751	T	0.34	-4.7649	11.0339	0.47789	0.1431:0.7187:0.1382:0.0	.	440	Q8WVB3	HEXDC_HUMAN	Q	440	ENSP00000332634:P440Q	ENSP00000332634:P440Q	P	+	2	0	HEXDC	77993407	0.182000	0.23173	0.949000	0.38748	0.235000	0.25334	0.964000	0.29306	2.532000	0.85374	0.561000	0.74099	CCG		0.667	HEXDC-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000443513.1	NM_173620		5	17	1	0	0.184627	1	0.193419	5	17				
PRSS3P2	154754	broad.mit.edu	37	7	142482229	142482229	+	RNA	SNP	T	T	A			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr7:142482229T>A	ENST00000603901.1	+	0	609					NR_001296.3		Q8NHM4	TRY6_HUMAN	protease, serine, 3 pseudogene 2						endothelial cell migration (GO:0043542)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.P203P(1)									CTGGTGGCCCTGTGGTCTGCA	0.493																																						ENST00000603901.1																			1	Substitution - coding silent(1)	p.P203P(1)	prostate(1)																																																154754							g.chr7:142482229T>A			7q34	2012-03-06			ENSG00000250606	ENSG00000275896			43788	pseudogene	pseudogene	"""trypsinogen C"""						Standard	NR_001296		Approved	TRY6	uc011ksq.2	Q8NHM4	OTTHUMG00000158904		7.37:g.142482229T>A								NR_001296.3						0	609	+									RNA	SNP	ENST00000603901.1	37																																																																																						0.493	PRSS3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470000.1	NR_001296		3	36	0	0	0	1	0	3	36				
CACNA1S	779	broad.mit.edu	37	1	201029810	201029810	+	Silent	SNP	G	G	T	rs140294191		TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr1:201029810G>T	ENST00000362061.3	-	26	3616	c.3390C>A	c.(3388-3390)ctC>ctA	p.L1130L	CACNA1S_ENST00000367338.3_Silent_p.L1130L	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1130					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AGATGGTGTTGAGCATGATGA	0.527																																						ENST00000362061.3																			0				NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102						c.(3388-3390)ctC>ctA		calcium channel, voltage-dependent, L type, alpha 1S subunit	Magnesium Sulfate(DB00653)|Verapamil(DB00661)						214.0	199.0	204.0					1																	201029810		2203	4300	6503	SO:0001819	synonymous_variant	779				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity	g.chr1:201029810G>T	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.3390C>A	1.37:g.201029810G>T						CACNA1S_ENST00000367338.3_Silent_p.L1130L	p.L1130L	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN			26	3616	-			1130					A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	c.3390C>A	CCDS1407.1																																																																																				0.527	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		6	132	1	0	0.0215528	1	0.023708	6	132				
BBS2	583	broad.mit.edu	37	16	56545120	56545120	+	Missense_Mutation	SNP	T	T	C	rs144680278	byFrequency	TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr16:56545120T>C	ENST00000245157.5	-	3	842	c.422A>G	c.(421-423)aAt>aGt	p.N141S	BBS2_ENST00000561951.1_5'UTR|BBS2_ENST00000568104.1_Missense_Mutation_p.N141S	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	141					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						CAGAGCACAATTGCCACCAAT	0.398									Bardet-Biedl syndrome				T|||	2	0.000399361	0.0	0.0	5008	,	,		18807	0.002		0.0	False		,,,				2504	0.0					ENST00000245157.5																			0				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						c.(421-423)aAt>aGt		Bardet-Biedl syndrome 2							126.0	109.0	115.0					16																	56545120		2198	4300	6498	SO:0001583	missense	583	Bardet-Biedl syndrome	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding	g.chr16:56545120T>C	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.422A>G	16.37:g.56545120T>C	ENSP00000245157:p.Asn141Ser					BBS2_ENST00000568104.1_Missense_Mutation_p.N141S|BBS2_ENST00000561951.1_5'UTR	p.N141S	NM_031885.3	NP_114091.3	Q9BXC9	BBS2_HUMAN			3	842	-			141					Q96CM0|Q96SN9	Missense_Mutation	SNP	ENST00000245157.5	37	c.422A>G	CCDS32451.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	T	22.4	4.289858	0.80914	.	.	ENSG00000125124	ENST00000245157	D	0.84873	-1.91	5.9	5.9	0.94986	WD40 repeat-like-containing domain (1);	0.081471	0.85682	D	0.000000	D	0.92267	0.7547	M	0.78456	2.415	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.92489	0.5999	10	0.52906	T	0.07	-25.8089	16.3294	0.83004	0.0:0.0:0.0:1.0	.	141;141	A8K0N9;Q9BXC9	.;BBS2_HUMAN	S	141	ENSP00000245157:N141S	ENSP00000245157:N141S	N	-	2	0	BBS2	55102621	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.066000	0.71185	2.259000	0.74868	0.523000	0.50628	AAT		0.398	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		5	90	0	0	0	1	0	5	90				
LRRC37A4P	55073	broad.mit.edu	37	17	43587569	43587569	+	RNA	SNP	G	G	C	rs202189074		TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr17:43587569G>C	ENST00000579913.1	-	0	1444				RP11-798G7.5_ENST00000253803.2_RNA	NR_002940.2				leucine rich repeat containing 37, member A4, pseudogene																		aactccgtctgaaaagaaaag	0.443																																						ENST00000253803.2																			0																																																			100294341							g.chr17:43587569G>C	AK000982		17q21.31	2014-04-01	2012-03-07	2012-03-07	ENSG00000214425	ENSG00000214425			25479	pseudogene	pseudogene			"""leucine rich repeat containing 37, member A4 (pseudogene)"""	LRRC37A4			Standard	NR_002940		Approved	FLJ10120	uc031rhd.1		OTTHUMG00000179212		17.37:g.43587569G>C						LRRC37A4P_ENST00000579913.1_RNA								0	267	+									RNA	SNP	ENST00000579913.1	37																																																																																						0.443	LRRC37A4P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445300.1	NR_002940		3	26	0	0	0	1	0	3	26				
LRRC37A4P	55073	broad.mit.edu	37	17	43587576	43587576	+	RNA	SNP	A	A	G	rs2684618	byFrequency	TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr17:43587576A>G	ENST00000579913.1	-	0	1444				RP11-798G7.5_ENST00000253803.2_RNA	NR_002940.2				leucine rich repeat containing 37, member A4, pseudogene																		tctgaaaagaaaagaaaaaaa	0.428													A|||	308	0.0615016	0.0204	0.0548	5008	,	,		16882	0.0685		0.1113	False		,,,				2504	0.0634					ENST00000253803.2																			0																																																			100294341							g.chr17:43587576A>G	AK000982		17q21.31	2014-04-01	2012-03-07	2012-03-07	ENSG00000214425	ENSG00000214425			25479	pseudogene	pseudogene			"""leucine rich repeat containing 37, member A4 (pseudogene)"""	LRRC37A4			Standard	NR_002940		Approved	FLJ10120	uc031rhd.1		OTTHUMG00000179212		17.37:g.43587576A>G						LRRC37A4P_ENST00000579913.1_RNA								0	267	+									RNA	SNP	ENST00000579913.1	37																																																																																						0.428	LRRC37A4P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445300.1	NR_002940		3	33	0	0	0	1	0	3	33				
MUC6	4588	broad.mit.edu	37	11	1031058	1031059	+	Splice_Site	INS	-	-	G	rs71464128	byFrequency	TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr11:1031058_1031059insG	ENST00000421673.2	-	6	625		c.e6-2			NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming						cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGAACTTGCCTGGGGTGCAGAA	0.703													GGGGG|GGGG|GGGGG|deletion	644	0.128594	0.348	0.0879	5008	,	,		7216	0.002		0.0895	False		,,,				2504	0.0317					ENST00000421673.2																			0				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						c.e6-2		mucin 6, oligomeric mucus/gel-forming				1070,2502		189,692,905						2.3	0.8		dbSNP_130	29	606,7194		45,516,3339	no	splice-3	MUC6	NM_005961.2		234,1208,4244	A1A1,A1R,RR		7.7692,29.9552,14.738				1676,9696				SO:0001630	splice_region_variant	4588				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent	g.chr11:1031058_1031059insG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.575-2->C	11.37:g.1031062_1031062dupG								NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	6	625	-		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)						O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Splice_Site	INS	ENST00000421673.2	37		CCDS44513.1																																																																																				0.703	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	Intron	5	5						5	5	---	---	---	---
HEBP1	50865	broad.mit.edu	37	12	13154653	13154653	+	5'Flank	DEL	G	G	-			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr12:13154653delG	ENST00000014930.4	-	0	0				HEBP1_ENST00000536942.1_5'Flank|RP11-377D9.3_ENST00000543321.1_lincRNA	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1						circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		CTCCGGCCGCGGGGAGCAAAT	0.682																																						ENST00000543321.1																			0																																																	SO:0001631	upstream_gene_variant	93164							g.chr12:13154653delG	AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"""Endogenous ligands"""	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771		12.37:g.13154653delG	Exception_encountered					HTR7P1_ENST00000535469.1_RNA								0	31	+								A8K1G2|Q9Y5Z5	RNA	DEL	ENST00000014930.4	37		CCDS31749.1																																																																																				0.682	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1			2	4						2	4	---	---	---	---
DNM1P47	100216544	broad.mit.edu	37	15	102299886	102299887	+	RNA	INS	-	-	G	rs199996275	byFrequency	TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr15:102299886_102299887insG	ENST00000561463.1	+	0	7932_7933									DNM1 pseudogene 47																		AACCTGTACTCGCGTCGGAACC	0.589													|||unknown(NO_COVERAGE)	758	0.151358	0.2511	0.1167	5008	,	,		74102	0.0595		0.163	False		,,,				2504	0.1237					ENST00000561463.1																			0																																																			100216544							g.chr15:102299886_102299887insG	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102299887_102299887dupG														0	7932_7933	+									RNA	INS	ENST00000561463.1	37																																																																																						0.589	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149		3	4						3	4	---	---	---	---
SCARNA6	677772	broad.mit.edu	37	16	21598984	21598985	+	RNA	INS	-	-	T			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr16:21598984_21598985insT	ENST00000516989.1	+	0	37_38									small Cajal body-specific RNA 6																		ccagcagcCCATTTTTTTTTTC	0.366																																						ENST00000516989.1																			0																																																			677772							g.chr16:21598984_21598985insT	AY077738		2q37.1	2013-09-05			ENSG00000251791	ENSG00000251791		"""ncRNAs / Small nucleolar RNAs : Small cajal body-specific"""	32562	non-coding RNA	RNA, small nucleolar		615641				12032087	Standard	NR_003006		Approved	U88	uc002vuf.1				16.37:g.21598994_21598994dupT														0	37_38	+									RNA	INS	ENST00000516989.1	37																																																																																						0.366	SCARNA6.1-201	NOVEL	basic	snoRNA	snoRNA		NR_003006		2	4						2	4	---	---	---	---
HSPA12B	116835	broad.mit.edu	37	20	3732491	3732491	+	Frame_Shift_Del	DEL	C	C	-			TCGA-WB-A819-01A-11D-A35I-08	TCGA-WB-A819-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41c1bfb8-9744-4af4-a1f8-462abc9004a4	f6cc1cf9-c3e3-4b5a-8265-401390550102	g.chr20:3732491delC	ENST00000254963.2	+	13	1884	c.1739delC	c.(1738-1740)gccfs	p.A580fs	HSPA12B_ENST00000542646.1_Frame_Shift_Del_p.A414fs	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	580							ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						TTCGTGGCCGCCGAGCAGTCG	0.716																																						ENST00000254963.2																			0				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						c.(1738-1740)gcfs		heat shock 70kD protein 12B							3.0	4.0	3.0					20																	3732491		1848	3642	5490	SO:0001589	frameshift_variant	116835						ATP binding	g.chr20:3732491delC	AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"""Heat shock proteins / HSP70"""	16193	protein-coding gene	gene with protein product		610702	"""chromosome 20 open reading frame 60"""	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.1739delC	20.37:g.3732491delC	ENSP00000254963:p.Ala580fs					HSPA12B_ENST00000542646.1_Frame_Shift_Del_p.A414fs	p.A580fs	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN			13	1884	+			580					D3DVX7|Q2TAK3|Q9BR52	Frame_Shift_Del	DEL	ENST00000254963.2	37	c.1739delC	CCDS13061.1																																																																																				0.716	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077756.2	NM_052970		2	4						2	4	---	---	---	---
