#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
SEMA5A	9037	broad.mit.edu	37	5	9066644	9066644	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr5:9066644G>A	ENST00000382496.5	-	17	2853	c.2188C>T	c.(2188-2190)Cga>Tga	p.R730*		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	730	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						CATGTGTATCGGAATCGTTGC	0.557																																						ENST00000382496.5																			0				biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						c.(2188-2190)Cga>Tga		sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A							158.0	147.0	151.0					5																	9066644		2203	4300	6503	SO:0001587	stop_gained	9037				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane		g.chr5:9066644G>A	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.2188C>T	5.37:g.9066644G>A	ENSP00000371936:p.Arg730*						p.R730*	NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN			17	2853	-			730			TSP type-1 4.		D3DTC6|O60408|Q1RLL9	Nonsense_Mutation	SNP	ENST00000382496.5	37	c.2188C>T	CCDS3875.1	.	.	.	.	.	.	.	.	.	.	G	44	10.876622	0.99482	.	.	ENSG00000112902	ENST00000382496	.	.	.	5.52	4.65	0.58169	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9373	0.64032	0.0:0.0:0.8468:0.1532	.	.	.	.	X	730	.	ENSP00000371936:R730X	R	-	1	2	SEMA5A	9119644	1.000000	0.71417	0.961000	0.40146	0.351000	0.29236	2.938000	0.48987	1.468000	0.48064	-0.230000	0.12252	CGA		0.557	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			26	767	0	0	0	1	0	26	767				
EPHA8	2046	broad.mit.edu	37	1	22923888	22923888	+	Missense_Mutation	SNP	G	G	A	rs371894783		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:22923888G>A	ENST00000166244.3	+	10	1921	c.1849G>A	c.(1849-1851)Gag>Aag	p.E617K		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	617	Mediates interaction with PIK3CG and required for endocytosis. {ECO:0000250}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CCACACCTACGAGGAGCCAGG	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		13338	0.0		0.0	False		,,,				2504	0.001					ENST00000166244.3																			0				breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61						c.(1849-1851)Gag>Aag		EPH receptor A8		G	LYS/GLU	0,4406		0,0,2203	63.0	78.0	73.0		1849	4.6	1.0	1		73	1,8599	1.2+/-3.3	0,1,4299	no	missense	EPHA8	NM_020526.3	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	617/1006	22923888	1,13005	2203	4300	6503	SO:0001583	missense	2046					integral to plasma membrane	ATP binding|ephrin receptor activity	g.chr1:22923888G>A	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.1849G>A	1.37:g.22923888G>A	ENSP00000166244:p.Glu617Lys						p.E617K	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)	10	1921	+		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)	617					Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	37	c.1849G>A	CCDS225.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.987973	0.74589	0.0	1.16E-4	ENSG00000070886	ENST00000166244	T	0.23754	1.89	4.63	4.63	0.57726	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.53094	0.1775	M	0.82716	2.605	0.80722	D	1	D	0.71674	0.998	D	0.65987	0.94	T	0.61407	-0.7069	10	0.87932	D	0	.	16.2101	0.82150	0.0:0.0:1.0:0.0	.	617	P29322	EPHA8_HUMAN	K	617	ENSP00000166244:E617K	ENSP00000166244:E617K	E	+	1	0	EPHA8	22796475	1.000000	0.71417	0.978000	0.43139	0.105000	0.19272	9.657000	0.98554	2.412000	0.81896	0.491000	0.48974	GAG		0.637	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		18	813	0	0	0	1	0	18	813				
APEH	327	broad.mit.edu	37	3	49723551	49723551	+	IGR	SNP	A	A	G	rs199957562		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:49723551A>G	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000449682.2_Missense_Mutation_p.M364T	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.M350T(3)		endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGCCGCGCGCATGCCGGGCCG	0.667																																						ENST00000449682.2																			3	Substitution - Missense(3)	p.M350T(3)	NS(2)|skin(1)	NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2)	41						c.(1090-1092)aTg>aCg		macrophage stimulating 1 (hepatocyte growth factor-like)							13.0	16.0	15.0					3																	49723551		2196	4289	6485	SO:0001628	intergenic_variant	4485				proteolysis	extracellular region	serine-type endopeptidase activity	g.chr3:49723551A>G	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723551A>G						MST1_ENST00000383728.3_3'UTR	p.M364T	NM_020998.3	NP_066278.3	P26927	HGFL_HUMAN		BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	9	1452	-			350					Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	c.1091T>C	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	A	15.79	2.937159	0.52972	.	.	ENSG00000173531	ENST00000449682	T	0.61510	0.1	5.4	4.17	0.49024	.	0.132069	0.34338	N	0.004055	T	0.35508	0.0934	N	0.04805	-0.155	0.80722	D	1	B	0.09022	0.002	B	0.17979	0.02	T	0.24083	-1.0170	10	0.51188	T	0.08	.	10.9733	0.47450	0.86:0.0:0.0:0.14	.	364	G3XAK1	.	T	364	ENSP00000414287:M364T	ENSP00000414287:M364T	M	-	2	0	MST1	49698555	1.000000	0.71417	0.995000	0.50966	0.875000	0.50365	7.395000	0.79876	2.042000	0.60477	0.533000	0.62120	ATG		0.667	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			5	117	0	0	0	1	0	5	117				
KRTAP4-11	653240	broad.mit.edu	37	17	39274087	39274087	+	Missense_Mutation	SNP	G	G	C	rs141357429		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:39274087G>C	ENST00000391413.2	-	1	519	c.481C>G	c.(481-483)Ctg>Gtg	p.L161V		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	161	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.L161V(1)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ACTGGACGCAGGcagcagcag	0.657																																						ENST00000391413.2																			1	Substitution - Missense(1)	p.L161V(1)	prostate(1)	endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33						c.(481-483)Ctg>Gtg		keratin associated protein 4-11							17.0	21.0	20.0					17																	39274087		692	1589	2281	SO:0001583	missense	653240					keratin filament		g.chr17:39274087G>C	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.481C>G	17.37:g.39274087G>C	ENSP00000375232:p.Leu161Val						p.L161V	NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	STAD - Stomach adenocarcinoma(17;0.000371)		1	519	-		Breast(137;0.000496)	161			27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	c.481C>G	CCDS45675.1	249	0.11401098901098901	67	0.13617886178861788	40	0.11049723756906077	104	0.18181818181818182	38	0.05013192612137203	.	1.347	-0.592411	0.03799	.	.	ENSG00000212721	ENST00000391413	T	0.00614	6.21	4.35	0.986	0.19784	.	.	.	.	.	T	0.00012	0.0000	L	0.31752	0.955	0.80722	P	0.0	B	0.30068	0.267	B	0.18871	0.023	T	0.19063	-1.0317	8	0.11794	T	0.64	.	5.8913	0.18915	0.1751:0.0:0.6569:0.168	.	161	Q9BYQ6	KR411_HUMAN	V	161	ENSP00000375232:L161V	ENSP00000375232:L161V	L	-	1	2	KRTAP4-11	36527613	0.671000	0.27521	0.912000	0.35992	0.970000	0.65996	0.971000	0.29396	0.348000	0.23949	0.609000	0.83330	CTG		0.657	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			8	79	0	0	0	1	0	8	79				
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:16918653C>T	ENST00000430580.2	-	6	853		c.e6+1			NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418																																						ENST00000430580.2																			0											c.e6+1		neuroblastoma breakpoint family, member 1																																				SO:0001630	splice_region_variant	55672					cytoplasm		g.chr1:16918653C>T	AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"""neuroblastoma breakpoint family"""	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.34+1G>A	1.37:g.16918653C>T								NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)	6	853	-								Q8N4E8|Q9C0H0	Splice_Site	SNP	ENST00000430580.2	37																																																																																						0.418	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940	Intron	21	317	0	0	0	1	0	21	317				
GRM6	2916	broad.mit.edu	37	5	178410024	178410024	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr5:178410024C>T	ENST00000517717.1	-	10	2361	c.2323G>A	c.(2323-2325)Gtg>Atg	p.V775M	GRM6_ENST00000231188.5_Missense_Mutation_p.V775M|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	775					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)	p.V775M(2)		NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		GTCTCGGGCACGCCACGGGCC	0.597																																						ENST00000231188.5																			2	Substitution - Missense(2)	p.V775M(2)	urinary_tract(1)|large_intestine(1)	NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55						c.(2323-2325)Gtg>Atg		glutamate receptor, metabotropic 6							131.0	107.0	115.0					5																	178410024		2203	4300	6503	SO:0001583	missense	2916				detection of visible light|visual perception	integral to plasma membrane		g.chr5:178410024C>T	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.2323G>A	5.37:g.178410024C>T	ENSP00000430767:p.Val775Met					GRM6_ENST00000517717.1_Missense_Mutation_p.V775M|RP11-281O15.4_ENST00000519491.1_RNA	p.V775M	NM_000843.3	NP_000834.2	O15303	GRM6_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)	9	2501	-	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	775						Missense_Mutation	SNP	ENST00000517717.1	37	c.2323G>A	CCDS4442.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.379871	0.61845	.	.	ENSG00000113262	ENST00000231188;ENST00000517717	D;D	0.89485	-2.52;-2.52	5.18	5.18	0.71444	GPCR, family 3, C-terminal (2);	.	.	.	.	D	0.94823	0.8328	M	0.84683	2.71	0.54753	D	0.999987	D;D	0.76494	0.999;0.998	D;D	0.77557	0.99;0.967	D	0.95314	0.8414	9	0.72032	D	0.01	.	16.5534	0.84478	0.0:1.0:0.0:0.0	.	775;69	O15303;Q5HYM4	GRM6_HUMAN;.	M	775	ENSP00000231188:V775M;ENSP00000430767:V775M	ENSP00000231188:V775M	V	-	1	0	GRM6	178342630	1.000000	0.71417	0.767000	0.31495	0.036000	0.12997	7.658000	0.83755	2.591000	0.87537	0.313000	0.20887	GTG		0.597	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2			10	368	0	0	0	1	0	10	368				
SP4	6671	broad.mit.edu	37	7	21516727	21516727	+	Missense_Mutation	SNP	T	T	C			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr7:21516727T>C	ENST00000222584.3	+	4	1927	c.1709T>C	c.(1708-1710)gTc>gCc	p.V570A		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	570					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						GGAGTAAAAGTCCAGCAAGCT	0.378																																						ENST00000222584.3																			0				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						c.(1708-1710)gTc>gCc		Sp4 transcription factor							74.0	68.0	70.0					7																	21516727		2203	4300	6503	SO:0001583	missense	6671				regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|transcription coactivator activity|zinc ion binding	g.chr7:21516727T>C		CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.1709T>C	7.37:g.21516727T>C	ENSP00000222584:p.Val570Ala						p.V570A	NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN			4	1927	+			570					O60402|Q32M52	Missense_Mutation	SNP	ENST00000222584.3	37	c.1709T>C	CCDS5373.1	.	.	.	.	.	.	.	.	.	.	T	17.25	3.341432	0.60963	.	.	ENSG00000105866	ENST00000222584;ENST00000432066	T	0.10099	2.91	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.26195	0.0639	L	0.49126	1.545	0.80722	D	1	D	0.58970	0.984	D	0.68192	0.956	T	0.01858	-1.1259	10	0.18276	T	0.48	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	570	Q02446	SP4_HUMAN	A	570;13	ENSP00000222584:V570A	ENSP00000222584:V570A	V	+	2	0	SP4	21483252	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.611000	0.82962	2.371000	0.80710	0.533000	0.62120	GTC		0.378	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		5	187	0	0	0	1	0	5	187				
ZNRD1-AS1	80862	broad.mit.edu	37	6	29977358	29977358	+	RNA	SNP	T	T	C			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr6:29977358T>C	ENST00000376797.3	-	0	731				ZNRD1-AS1_ENST00000444051.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		GATTTGTTCATGCCTTCCCTT	0.448																																						ENST00000376797.3																			0																																																			0							g.chr6:29977358T>C	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.29977358T>C						ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA								0	731	-									RNA	SNP	ENST00000376797.3	37																																																																																						0.448	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253083.1	NR_026751		18	242	0	0	0	1	0	18	242				
TRAPPC9	83696	broad.mit.edu	37	8	141461429	141461429	+	Missense_Mutation	SNP	G	G	A	rs142839408		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr8:141461429G>A	ENST00000438773.2	-	2	177	c.44C>T	c.(43-45)aCg>aTg	p.T15M	TRAPPC9_ENST00000389328.4_Missense_Mutation_p.T113M|TRAPPC9_ENST00000389327.3_Missense_Mutation_p.T15M	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	15					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						CACGAGCAGCGTCTGGTGGTC	0.537													G|||	1	0.000199681	0.0008	0.0	5008	,	,		22017	0.0		0.0	False		,,,				2504	0.0					ENST00000389328.4																			0				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						c.(337-339)aCg>aTg		trafficking protein particle complex 9		G	MET/THR,MET/THR	5,4395		0,5,2195	30.0	31.0	31.0		44,338	4.4	0.9	8	dbSNP_134	31	2,8594		0,2,4296	yes	missense,missense	TRAPPC9	NM_001160372.1,NM_031466.5	81,81	0,7,6491	AA,AG,GG		0.0233,0.1136,0.0539	probably-damaging,probably-damaging	15/1149,113/1247	141461429	7,12989	2200	4298	6498	SO:0001583	missense	83696				cell differentiation	endoplasmic reticulum|Golgi apparatus		g.chr8:141461429G>A	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.44C>T	8.37:g.141461429G>A	ENSP00000405060:p.Thr15Met					TRAPPC9_ENST00000438773.2_Missense_Mutation_p.T15M|TRAPPC9_ENST00000389327.3_Missense_Mutation_p.T15M	p.T113M	NM_031466.5	NP_113654.4	Q96Q05	TPPC9_HUMAN			2	352	-			15					Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	37	c.338C>T	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	G	19.95	3.921045	0.73213	0.001136	2.33E-4	ENSG00000167632	ENST00000389328;ENST00000389327;ENST00000438773	.	.	.	5.26	4.39	0.52855	.	0.046901	0.85682	D	0.000000	T	0.70369	0.3216	L	0.54323	1.7	0.44221	D	0.99705	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.987;0.967;0.967	T	0.71474	-0.4582	9	0.51188	T	0.08	.	13.9017	0.63809	0.0735:0.0:0.9265:0.0	.	15;15;113	Q96Q05;Q96Q05-3;Q96Q05-2	TPPC9_HUMAN;.;.	M	113;15;15	.	ENSP00000373978:T15M	T	-	2	0	TRAPPC9	141530611	1.000000	0.71417	0.924000	0.36721	0.956000	0.61745	9.640000	0.98453	1.210000	0.43336	0.650000	0.86243	ACG		0.537	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		9	191	0	0	0	1	0	9	191				
BBS1	582	broad.mit.edu	37	11	66283170	66283170	+	Silent	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:66283170G>A	ENST00000318312.7	+	6	537	c.486G>A	c.(484-486)acG>acA	p.T162T	BBS1_ENST00000393994.2_Silent_p.T162T|BBS1_ENST00000537537.1_Silent_p.T50T|BBS1_ENST00000455748.2_Intron|CTD-3074O7.11_ENST00000419755.3_Silent_p.T199T|BBS1_ENST00000529766.1_3'UTR	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	162					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						GCAGGGAGACGGCAGAGGAGC	0.617									Bardet-Biedl syndrome																												GBM(152;173 2612 9770 10137)	ENST00000419755.3																			0											c.(595-597)acG>acA									52.0	51.0	52.0					11																	66283170		2200	4295	6495	SO:0001819	synonymous_variant	0		Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome				g.chr11:66283170G>A	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.486G>A	11.37:g.66283170G>A						BBS1_ENST00000455748.2_Intron|BBS1_ENST00000537537.1_Silent_p.T50T|BBS1_ENST00000393994.2_Silent_p.T162T|BBS1_ENST00000318312.7_Silent_p.T162T|BBS1_ENST00000529766.1_3'UTR	p.T199T							6	675	+								Q32MM9|Q32MN0|Q96SN4	Silent	SNP	ENST00000318312.7	37	c.597G>A	CCDS8142.1																																																																																				0.617	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2			9	341	0	0	0	1	0	9	341				
POM121	9883	broad.mit.edu	37	7	72413896	72413896	+	Missense_Mutation	SNP	A	A	G	rs201049716		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr7:72413896A>G	ENST00000434423.2	+	11	3364	c.3364A>G	c.(3364-3366)Acc>Gcc	p.T1122A	POM121_ENST00000395270.1_Missense_Mutation_p.T857A|POM121_ENST00000257622.4_Missense_Mutation_p.T857A|POM121_ENST00000358357.3_Missense_Mutation_p.T857A|POM121_ENST00000446813.1_Missense_Mutation_p.T857A			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	1122	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.T857A(8)		NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				AGGCTCCAGCACCACCACCGG	0.637																																						ENST00000395270.1																			8	Substitution - Missense(8)	p.T857A(8)	lung(4)|kidney(4)	NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						c.(2569-2571)Acc>Gcc		POM121 transmembrane nucleoporin							32.0	30.0	30.0					7																	72413896		2201	4299	6500	SO:0001583	missense	9883				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore		g.chr7:72413896A>G	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.3364A>G	7.37:g.72413896A>G	ENSP00000405562:p.Thr1122Ala					POM121_ENST00000257622.4_Missense_Mutation_p.T857A|POM121_ENST00000358357.3_Missense_Mutation_p.T857A|POM121_ENST00000434423.2_Missense_Mutation_p.T1122A|POM121_ENST00000446813.1_Missense_Mutation_p.T857A	p.T857A	NM_001257190.1	NP_001244119.1	Q96HA1	P121A_HUMAN			14	3610	+		Lung NSC(55;0.163)	1122			Pore side (Potential).|Thr-rich.		A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37	c.2569A>G		56	0.02564102564102564	11	0.022357723577235773	14	0.03867403314917127	19	0.033216783216783216	12	0.0158311345646438	G	2.480	-0.319876	0.05386	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.05649	3.46;3.41;3.46;3.41;3.71	2.86	-2.18	0.07037	.	0.720175	0.11383	N	0.569582	T	0.00724	0.0024	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.42275	-0.9461	10	0.36615	T	0.2	.	4.8571	0.13564	0.1842:0.0:0.3666:0.4491	.	857;1122	A8MXF9;Q96HA1	.;P121A_HUMAN	A	857;857;857;857;1122	ENSP00000393020:T857A;ENSP00000257622:T857A;ENSP00000378687:T857A;ENSP00000351124:T857A;ENSP00000405562:T1122A	ENSP00000257622:T857A	T	+	1	0	POM121	72051832	0.360000	0.24964	0.406000	0.26421	0.004000	0.04260	0.000000	0.12993	-0.499000	0.06623	-2.511000	0.00188	ACC		0.637	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1			4	156	0	0	0	1	0	4	156				
FRMD7	90167	broad.mit.edu	37	X	131216469	131216469	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:131216469G>A	ENST00000298542.4	-	9	1002	c.827C>T	c.(826-828)gCt>gTt	p.A276V	FRMD7_ENST00000464296.1_Missense_Mutation_p.A261V|FRMD7_ENST00000370879.1_Missense_Mutation_p.A156V	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	276	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					CCTGAAGAAAGCATGGTATTC	0.468																																						ENST00000298542.4																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24						c.(826-828)gCt>gTt		FERM domain containing 7							220.0	208.0	212.0					X																	131216469		2203	4300	6503	SO:0001583	missense	90167				regulation of neuron projection development	cytoskeleton|growth cone|neuronal cell body	binding	g.chrX:131216469G>A	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.827C>T	X.37:g.131216469G>A	ENSP00000298542:p.Ala276Val					FRMD7_ENST00000464296.1_Missense_Mutation_p.A261V|FRMD7_ENST00000370879.1_Missense_Mutation_p.A156V	p.A276V	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN			9	1002	-	Acute lymphoblastic leukemia(192;0.000127)		276			FERM.		C0LLJ3|Q5JX99	Missense_Mutation	SNP	ENST00000298542.4	37	c.827C>T	CCDS35397.1	.	.	.	.	.	.	.	.	.	.	G	32	5.112065	0.94339	.	.	ENSG00000165694	ENST00000370879;ENST00000298542;ENST00000464296	D;D;D	0.87650	-2.28;-2.28;-2.28	5.2	5.2	0.72013	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.116646	0.56097	D	0.000024	D	0.94686	0.8286	M	0.90019	3.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.996	D	0.95702	0.8750	10	0.87932	D	0	.	16.9793	0.86323	0.0:0.0:1.0:0.0	.	261;276	Q6ZUT3-2;Q6ZUT3	.;FRMD7_HUMAN	V	156;276;261	ENSP00000359916:A156V;ENSP00000298542:A276V;ENSP00000417996:A261V	ENSP00000298542:A276V	A	-	2	0	FRMD7	131044150	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	9.813000	0.99286	2.305000	0.77605	0.544000	0.68410	GCT		0.468	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		41	1458	0	0	0	1	0	41	1458				
ZNF616	90317	broad.mit.edu	37	19	52619638	52619638	+	Missense_Mutation	SNP	T	T	C			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:52619638T>C	ENST00000600228.1	-	4	1040	c.779A>G	c.(778-780)cAa>cGa	p.Q260R	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	260					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)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		GTGACTCCTTTGGTGTCTTAC	0.383																																						ENST00000600228.1																			0				breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						c.(778-780)cAa>cGa		zinc finger protein 616							88.0	86.0	87.0					19																	52619638		2203	4300	6503	SO:0001583	missense	90317				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:52619638T>C	AK092266	CCDS33090.1	19q13.41	2013-01-08				ENSG00000204611		"""Zinc fingers, C2H2-type"", ""-"""	28062	protein-coding gene	gene with protein product							Standard	NM_178523		Approved	MGC45556	uc002pym.3	Q08AN1		ENST00000600228.1:c.779A>G	19.37:g.52619638T>C	ENSP00000471000:p.Gln260Arg					ZNF616_ENST00000330123.5_3'UTR	p.Q260R	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN		GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)	4	1040	-			260					B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	37	c.779A>G	CCDS33090.1	.	.	.	.	.	.	.	.	.	.	T	9.538	1.112700	0.20795	.	.	ENSG00000204611	ENST00000330123	.	.	.	0.954	-0.118	0.13547	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25457	0.0619	L	0.28344	0.845	0.09310	N	1	B	0.27594	0.182	B	0.28638	0.092	T	0.20874	-1.0262	8	0.35671	T	0.21	.	4.2259	0.10580	0.0:0.2336:0.0:0.7664	.	260	Q08AN1	ZN616_HUMAN	R	260	.	ENSP00000328722:Q260R	Q	-	2	0	ZNF616	57311450	0.000000	0.05858	0.004000	0.12327	0.858000	0.48976	-0.069000	0.11542	-0.101000	0.12219	0.254000	0.18369	CAA		0.383	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892		19	499	0	0	0	1	0	19	499				
CCDC87	55231	broad.mit.edu	37	11	66360267	66360267	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:66360267C>T	ENST00000333861.3	-	1	287	c.220G>A	c.(220-222)Gga>Aga	p.G74R	CCS_ENST00000310190.4_5'Flank|CCS_ENST00000533244.1_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	74					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						GGAGGCACTCCCGCTGCTATC	0.657											OREG0021111	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000333861.3																			0				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						c.(220-222)Gga>Aga		coiled-coil domain containing 87							29.0	30.0	30.0					11																	66360267		2200	4293	6493	SO:0001583	missense	55231							g.chr11:66360267C>T	BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.220G>A	11.37:g.66360267C>T	ENSP00000328487:p.Gly74Arg		OREG0021111	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1091		p.G74R	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN			1	287	-			74					Q8NE76	Missense_Mutation	SNP	ENST00000333861.3	37	c.220G>A	CCDS8145.1	.	.	.	.	.	.	.	.	.	.	G	4.935	0.173708	0.09391	.	.	ENSG00000182791	ENST00000333861	T	0.27890	1.64	5.39	2.33	0.28932	.	1.311630	0.05373	N	0.535892	T	0.08492	0.0211	N	0.00237	-1.79	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26950	-1.0088	10	0.11485	T	0.65	-0.9844	8.4993	0.33148	0.0872:0.4903:0.4226:0.0	.	74	Q9NVE4	CCD87_HUMAN	R	74	ENSP00000328487:G74R	ENSP00000328487:G74R	G	-	1	0	CCDC87	66116843	0.004000	0.15560	0.000000	0.03702	0.003000	0.03518	1.494000	0.35616	0.405000	0.25532	-0.120000	0.15030	GGA		0.657	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219		9	234	0	0	0	1	0	9	234				
PCDHGB4	8641	broad.mit.edu	37	5	140769030	140769030	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr5:140769030G>A	ENST00000519479.1	+	1	1579	c.1579G>A	c.(1579-1581)Gaa>Aaa	p.E527K	PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	527	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCGCCTTCGAACTCACACT	0.677																																						ENST00000519479.1																			0				endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37						c.(1579-1581)Gaa>Aaa									38.0	43.0	42.0					5																	140769030		2038	4188	6226	SO:0001583	missense	0							g.chr5:140769030G>A	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1579G>A	5.37:g.140769030G>A	ENSP00000428288:p.Glu527Lys					PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron	p.E527K	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	1579	+								O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	37	c.1579G>A	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	8.696	0.908490	0.17833	.	.	ENSG00000253953	ENST00000519479	T	0.54071	0.59	4.95	-1.96	0.07525	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.43831	0.1265	L	0.46947	1.48	0.09310	N	1	P;P	0.44478	0.836;0.697	B;B	0.38458	0.261;0.274	T	0.29336	-1.0015	9	0.33940	T	0.23	.	15.7771	0.78232	0.1245:0.6211:0.2544:0.0	.	527;527	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	K	527	ENSP00000428288:E527K	ENSP00000428288:E527K	E	+	1	0	PCDHGB4	140749214	0.000000	0.05858	0.688000	0.30117	0.248000	0.25809	-2.903000	0.00703	-1.088000	0.03077	-2.589000	0.00165	GAA		0.677	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		8	300	0	0	0	1	0	8	300				
OR10AG1	282770	broad.mit.edu	37	11	55735162	55735162	+	Silent	SNP	T	T	G			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:55735162T>G	ENST00000312345.2	-	1	828	c.778A>C	c.(778-780)Agg>Cgg	p.R260R		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					TTCCCCATCCTTTGAAACTGA	0.383																																						ENST00000312345.2																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40						c.(778-780)Agg>Cgg		olfactory receptor, family 10, subfamily AG, member 1							69.0	70.0	70.0					11																	55735162		2201	4296	6497	SO:0001819	synonymous_variant	282770				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55735162T>G	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.778A>C	11.37:g.55735162T>G							p.R260R	NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN			1	828	-	Esophageal squamous(21;0.0137)		260					B2RNH4|Q6IEU3	Silent	SNP	ENST00000312345.2	37	c.778A>C	CCDS31514.1																																																																																				0.383	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491		6	286	0	0	0	1	0	6	286				
UPF3A	65110	broad.mit.edu	37	13	115047559	115047559	+	Silent	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr13:115047559C>T	ENST00000375299.3	+	2	327	c.271C>T	c.(271-273)Ctg>Ttg	p.L91L	UPF3A_ENST00000351487.5_Silent_p.L91L	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	91	Required for interaction with UPF2.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleocytoplasmic transport (GO:0006913)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.L91L(8)		autonomic_ganglia(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	16	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		GCTGCGCCCGCTGCCAGCACA	0.731																																						ENST00000375299.3																			8	Substitution - coding silent(8)	p.L91L(8)	lung(2)|prostate(2)|kidney(2)|central_nervous_system(2)	autonomic_ganglia(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	16						c.(271-273)Ctg>Ttg		UPF3 regulator of nonsense transcripts homolog A (yeast)							4.0	4.0	4.0					13																	115047559		1902	3804	5706	SO:0001819	synonymous_variant	65110				mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding	g.chr13:115047559C>T	AF318575	CCDS9543.1, CCDS9544.1	13q34	2010-04-30			ENSG00000169062	ENSG00000169062			20332	protein-coding gene	gene with protein product		605530				11113196, 11163187	Standard	NM_023011		Approved	RENT3A, UPF3, HUPF3A	uc001vup.3	Q9H1J1	OTTHUMG00000017403	ENST00000375299.3:c.271C>T	13.37:g.115047559C>T						UPF3A_ENST00000351487.5_Silent_p.L91L	p.L91L	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)	2	327	+	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	91			Required for interaction with UPF2.		A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Silent	SNP	ENST00000375299.3	37	c.271C>T	CCDS9543.1																																																																																				0.731	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2			4	15	0	0	0	1	0	4	15				
MED14	9282	broad.mit.edu	37	X	40573077	40573077	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:40573077C>T	ENST00000324817.1	-	5	723	c.605G>A	c.(604-606)cGg>cAg	p.R202Q		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	202	Interaction with STAT2.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGTTACAAGCCGATGTCTAAG	0.383																																						ENST00000324817.1																			0				NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						c.(604-606)cGg>cAg		mediator complex subunit 14							171.0	158.0	162.0					X																	40573077		2203	4300	6503	SO:0001583	missense	9282				androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding	g.chrX:40573077C>T	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"""cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"""	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.605G>A	X.37:g.40573077C>T	ENSP00000323720:p.Arg202Gln						p.R202Q	NM_004229.3	NP_004220.2	O60244	MED14_HUMAN			5	723	-			202			Interaction with STAT2.		Q4KMR7|Q9UNB3	Missense_Mutation	SNP	ENST00000324817.1	37	c.605G>A	CCDS14254.1	.	.	.	.	.	.	.	.	.	.	C	36	5.665183	0.96745	.	.	ENSG00000180182	ENST00000324817	.	.	.	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.74756	0.3758	M	0.88105	2.93	0.80722	D	1	D	0.54397	0.966	P	0.47645	0.553	T	0.82108	-0.0620	9	0.72032	D	0.01	.	18.0658	0.89390	0.0:1.0:0.0:0.0	.	202	O60244	MED14_HUMAN	Q	202	.	ENSP00000323720:R202Q	R	-	2	0	MED14	40458021	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.400000	0.79949	2.290000	0.77057	0.544000	0.68410	CGG		0.383	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229		16	501	0	0	0	1	0	16	501				
APOB	338	broad.mit.edu	37	2	21251239	21251239	+	Missense_Mutation	SNP	T	T	C			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:21251239T>C	ENST00000233242.1	-	13	1916	c.1789A>G	c.(1789-1791)Att>Gtt	p.I597V	APOB_ENST00000399256.4_Missense_Mutation_p.I597V	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	597	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATATTGGCAATATGGGAAGCC	0.418																																						ENST00000233242.1																			0				NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305						c.(1789-1791)Att>Gtt		apolipoprotein B	Atorvastatin(DB01076)						99.0	101.0	101.0					2																	21251239		2203	4300	6503	SO:0001583	missense	338				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity	g.chr2:21251239T>C	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.1789A>G	2.37:g.21251239T>C	ENSP00000233242:p.Ile597Val					APOB_ENST00000399256.4_Missense_Mutation_p.I597V	p.I597V	NM_000384.2	NP_000375.2	P04114	APOB_HUMAN			13	1916	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		597			Vitellogenin.		O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	c.1789A>G	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.558392	0.45590	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.57436	0.4;0.4	5.69	3.17	0.36434	Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (2);	0.352961	0.27764	N	0.017944	T	0.47229	0.1434	L	0.56769	1.78	0.36909	D	0.890822	P	0.42908	0.793	B	0.38655	0.278	T	0.57757	-0.7756	10	0.42905	T	0.14	.	12.4341	0.55590	0.0:0.0:0.2866:0.7134	.	597	P04114	APOB_HUMAN	V	597	ENSP00000233242:I597V;ENSP00000382200:I597V	ENSP00000233242:I597V	I	-	1	0	APOB	21104744	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	0.596000	0.24044	1.098000	0.41479	0.533000	0.62120	ATT		0.418	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			20	399	0	0	0	1	0	20	399				
ZNF733P	643955	broad.mit.edu	37	7	62752443	62752443	+	RNA	SNP	G	G	C	rs372167638		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr7:62752443G>C	ENST00000331425.6	-	0	992					NR_003952.1				zinc finger protein 733, pseudogene																		CTTATGTCTAGTAAGGTTTGA	0.438																																						ENST00000331425.6																			0																																																			0							g.chr7:62752443G>C			7q11.21	2012-04-20	2012-04-20	2012-04-20	ENSG00000185037	ENSG00000185037			32473	pseudogene	pseudogene			"""zinc finger protein 733"""	ZNF733			Standard	NR_003952		Approved		uc011kdj.2		OTTHUMG00000156270		7.37:g.62752443G>C								NR_003952.1						0	992	-									RNA	SNP	ENST00000331425.6	37																																																																																						0.438	ZNF733P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000343679.1			6	150	0	0	0	1	0	6	150				
TUBB8P7	197331	broad.mit.edu	37	16	90162513	90162513	+	RNA	SNP	T	T	C			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr16:90162513T>C	ENST00000564451.1	+	0	1866				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7									p.N415N(2)									GCAACATGAATGACCTGGTGT	0.537																																						ENST00000567960.1																			2	Substitution - coding silent(2)	p.N415N(2)	prostate(1)|kidney(1)																																																0							g.chr16:90162513T>C			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162513T>C						TUBB8P7_ENST00000564451.1_RNA								0	1249	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.537	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		17	554	0	0	0	1	0	17	554				
FRG1B	284802	broad.mit.edu	37	20	29625971	29625971	+	Missense_Mutation	SNP	C	C	A	rs145033899		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr20:29625971C>A	ENST00000278882.3	+	5	595	c.215C>A	c.(214-216)cCa>cAa	p.P72Q	FRG1B_ENST00000439954.2_Missense_Mutation_p.P77Q|FRG1B_ENST00000358464.4_Missense_Mutation_p.P72Q			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	72										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						CAATGGGAACCAGTCTTTCAA	0.328																																						ENST00000278882.3																			0				endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(214-216)cCa>cAa																																						SO:0001583	missense	0							g.chr20:29625971C>A			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.215C>A	20.37:g.29625971C>A	ENSP00000278882:p.Pro72Gln					FRG1B_ENST00000358464.4_Missense_Mutation_p.P72Q|FRG1B_ENST00000439954.2_Missense_Mutation_p.P77Q	p.P72Q							5	595	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.215C>A		.	.	.	.	.	.	.	.	.	.	c	12.14	1.847531	0.32606	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.49720	0.77	1.68	1.68	0.24146	.	0.112402	0.64402	D	0.000009	T	0.63271	0.2497	.	.	.	0.49483	D	0.999795	D	0.63046	0.992	D	0.79784	0.993	T	0.65948	-0.6044	9	0.66056	D	0.02	.	9.3557	0.38164	0.0:1.0:0.0:0.0	.	77	F5H5R5	.	Q	72;77;72	ENSP00000408863:P77Q	ENSP00000278882:P72Q	P	+	2	0	FRG1B	28239632	1.000000	0.71417	1.000000	0.80357	0.229000	0.25112	6.442000	0.73443	1.250000	0.43966	0.184000	0.17185	CCA		0.328	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		14	497	1	0	2.35188e-11	1	2.47852e-11	14	497				
LINC00969	440993	broad.mit.edu	37	3	195395399	195395399	+	lincRNA	SNP	G	G	A	rs62287990	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:195395399G>A	ENST00000445430.1	+	0	806									long intergenic non-protein coding RNA 969																		GGCTACGGGCGCACCTACTTG	0.607																																						ENST00000445430.1																			0																																																			0							g.chr3:195395399G>A	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195395399G>A														0	806	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.607	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			22	226	0	0	0	1	0	22	226				
ZNF845	91664	broad.mit.edu	37	19	53856761	53856761	+	Missense_Mutation	SNP	T	T	C	rs528924232		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:53856761T>C	ENST00000595091.1	+	5	3052	c.2833T>C	c.(2833-2835)Tgt>Cgt	p.C945R	ZNF845_ENST00000458035.1_Missense_Mutation_p.C945R			Q96IR2	ZN845_HUMAN	zinc finger protein 845	945					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C945R(1)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						ACCTTACAAGTGTAATGAATG	0.348																																						ENST00000458035.1																			1	Substitution - Missense(1)	p.C945R(1)	kidney(1)	endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						c.(2833-2835)Tgt>Cgt		zinc finger protein 845							25.0	23.0	24.0					19																	53856761		692	1590	2282	SO:0001583	missense	91664				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:53856761T>C	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2833T>C	19.37:g.53856761T>C	ENSP00000470005:p.Cys945Arg					ZNF845_ENST00000595091.1_Missense_Mutation_p.C945R	p.C945R	NM_138374.1	NP_612383.1	Q96IR2	ZN845_HUMAN			4	2950	+			945						Missense_Mutation	SNP	ENST00000595091.1	37	c.2833T>C	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	T	7.922	0.738844	0.15642	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	D	0.85258	-1.96	2.04	0.921	0.19403	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94417	0.8204	H	0.99336	4.52	0.38301	D	0.942985	D	0.89917	1.0	D	0.91635	0.999	D	0.91222	0.5007	9	0.66056	D	0.02	.	6.1858	0.20495	0.2258:0.0:0.0:0.7742	.	945	Q96IR2	ZN845_HUMAN	R	945;861	ENSP00000388311:C945R	ENSP00000412086:C861R	C	+	1	0	ZNF845	58548573	1.000000	0.71417	0.080000	0.20451	0.053000	0.15095	4.520000	0.60524	0.031000	0.15407	-0.871000	0.02989	TGT		0.348	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		5	157	0	0	0	1	0	5	157				
TVP23C	201158	broad.mit.edu	37	17	15441469	15441469	+	Intron	SNP	C	C	T	rs568909748	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:15441469C>T	ENST00000225576.3	-	5	558				TVP23C_ENST00000428082.2_Splice_Site|TVP23C_ENST00000583206.1_5'Flank|TVP23C-CDRT4_ENST00000522212.2_Intron|TVP23C_ENST00000584811.1_Splice_Site|TVP23C_ENST00000438826.3_Splice_Site|TVP23C_ENST00000519970.1_Intron	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)							integral component of membrane (GO:0016021)											TCCAGTGTTCCGCAAAAGACA	0.393													c|||	3	0.000599042	0.0015	0.0	5008	,	,		17476	0.001		0.0	False		,,,				2504	0.0					ENST00000584811.1																			0											c.e7-2		trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)																																				SO:0001627	intron_variant	201158							g.chr17:15441469C>T	BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"""family with sequence similarity 18, member B2"""	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.462+7629G>A	17.37:g.15441469C>T						TVP23C-CDRT4_ENST00000522212.2_Intron|TVP23C_ENST00000428082.2_Splice_Site|TVP23C_ENST00000225576.3_Intron|TVP23C_ENST00000438826.3_Splice_Site|TVP23C_ENST00000519970.1_Intron								7	1815	-								Q3LIC7	Splice_Site	SNP	ENST00000225576.3	37		CCDS11170.1	.	.	.	.	.	.	.	.	.	.	c	13.58	2.280351	0.40294	.	.	ENSG00000175106	ENST00000438826	.	.	.	4.5	4.5	0.54988	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.0583	0.25111	0.0:0.1033:0.0:0.8967	.	.	.	.	.	-1	.	.	.	-	.	.	FAM18B2	15382194	1.000000	0.71417	0.996000	0.52242	0.698000	0.40448	1.919000	0.40015	0.852000	0.35287	-0.352000	0.07741	.		0.393	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2	NM_145301		12	394	0	0	0	1	0	12	394				
FREM2	341640	broad.mit.edu	37	13	39357268	39357268	+	Missense_Mutation	SNP	C	C	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr13:39357268C>A	ENST00000280481.7	+	5	5919	c.5703C>A	c.(5701-5703)ttC>ttA	p.F1901L		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1901	Calx-beta 2.				cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GTGAGCTGTTCATTCCCATCA	0.448																																						ENST00000280481.7																			0				NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148						c.(5701-5703)ttC>ttA		FRAS1 related extracellular matrix protein 2							211.0	196.0	201.0					13																	39357268		2203	4300	6503	SO:0001583	missense	341640				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding	g.chr13:39357268C>A	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.5703C>A	13.37:g.39357268C>A	ENSP00000280481:p.Phe1901Leu						p.F1901L	NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)	5	5919	+		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)	1901			Calx-beta 2.		Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	c.5703C>A	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	0.016	-1.513669	0.00975	.	.	ENSG00000150893	ENST00000280481	T	0.28454	1.61	5.84	3.09	0.35607	Na-Ca exchanger/integrin-beta4 (2);	0.154739	0.64402	N	0.000015	T	0.09555	0.0235	N	0.03177	-0.4	0.41029	D	0.985147	B	0.02656	0.0	B	0.09377	0.004	T	0.22487	-1.0215	10	0.05620	T	0.96	.	4.3073	0.10953	0.1488:0.4504:0.0:0.4008	.	1901	Q5SZK8	FREM2_HUMAN	L	1901	ENSP00000280481:F1901L	ENSP00000280481:F1901L	F	+	3	2	FREM2	38255268	0.416000	0.25424	0.826000	0.32828	0.043000	0.13939	-0.373000	0.07494	0.334000	0.23590	0.514000	0.50259	TTC		0.448	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		17	597	1	0	4.7546e-09	1	4.9347e-09	17	597				
CCDC60	160777	broad.mit.edu	37	12	119773039	119773039	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr12:119773039C>T	ENST00000327554.2	+	1	523	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W	CCDC60_ENST00000539847.1_Missense_Mutation_p.R20W|CCDC60_ENST00000546345.1_3'UTR|CCDC60_ENST00000536742.1_Missense_Mutation_p.R20W	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	20										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		GGGGGCTGTCCGGCCCTTTTA	0.502																																						ENST00000327554.2																			0				endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						c.(58-60)Cgg>Tgg		coiled-coil domain containing 60							69.0	77.0	74.0					12																	119773039		2203	4300	6503	SO:0001583	missense	160777							g.chr12:119773039C>T	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.58C>T	12.37:g.119773039C>T	ENSP00000333374:p.Arg20Trp					CCDC60_ENST00000546345.1_3'UTR|CCDC60_ENST00000536742.1_Missense_Mutation_p.R20W|CCDC60_ENST00000539847.1_Missense_Mutation_p.R20W	p.R20W	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN		BRCA - Breast invasive adenocarcinoma(302;0.207)	1	523	+	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)		20						Missense_Mutation	SNP	ENST00000327554.2	37	c.58C>T	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	C	6.197	0.404573	0.11754	.	.	ENSG00000183273	ENST00000536742;ENST00000327554;ENST00000539847	T;T;T	0.48836	0.8;1.83;0.95	4.42	-3.66	0.04489	.	1.591660	0.03532	N	0.222527	T	0.17492	0.0420	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09773	-1.0659	9	.	.	.	0.016	3.2878	0.06937	0.3849:0.3158:0.0:0.2993	.	20	Q8IWA6	CCD60_HUMAN	W	20	ENSP00000445505:R20W;ENSP00000333374:R20W;ENSP00000443403:R20W	.	R	+	1	2	CCDC60	118257422	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	-0.894000	0.04123	-0.330000	0.08514	-0.377000	0.06932	CGG		0.502	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		11	354	0	0	0	1	0	11	354				
PASD1	139135	broad.mit.edu	37	X	150840063	150840063	+	Missense_Mutation	SNP	C	C	T	rs201707889		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:150840063C>T	ENST00000370357.4	+	13	1494	c.1249C>T	c.(1249-1251)Cgc>Tgc	p.R417C		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	417						nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.R417C(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					AAACACATTACGCCACGTTGT	0.498																																						ENST00000370357.4																			1	Substitution - Missense(1)	p.R417C(1)	breast(1)	breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						c.(1249-1251)Cgc>Tgc		PAS domain containing 1		C	CYS/ARG	0,3835		0,0,1632,571	216.0	171.0	186.0		1249	-5.2	0.0	X		186	1,6727		0,1,2427,1872	yes	missense	PASD1	NM_173493.2	180	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	benign	417/774	150840063	1,10562	2203	4300	6503	SO:0001583	missense	139135					nucleus	signal transducer activity	g.chrX:150840063C>T	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.1249C>T	X.37:g.150840063C>T	ENSP00000359382:p.Arg417Cys						p.R417C	NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN			13	1494	+	Acute lymphoblastic leukemia(192;6.56e-05)		417					Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	37	c.1249C>T	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	C	3.252	-0.153046	0.06585	0.0	1.49E-4	ENSG00000166049	ENST00000370357	T	0.19250	2.16	3.29	-5.21	0.02815	.	.	.	.	.	T	0.07503	0.0189	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.23940	-1.0174	9	0.38643	T	0.18	-28.8384	1.7157	0.02901	0.1165:0.3389:0.2296:0.315	.	417	Q8IV76	PASD1_HUMAN	C	417	ENSP00000359382:R417C	ENSP00000359382:R417C	R	+	1	0	PASD1	150590719	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.494000	0.02296	-2.249000	0.00702	-2.831000	0.00106	CGC		0.498	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		12	806	0	0	0	1	0	12	806				
MLLT3	4300	broad.mit.edu	37	9	20414346	20414346	+	Silent	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr9:20414346G>A	ENST00000380338.4	-	5	784	c.498C>T	c.(496-498)agC>agT	p.S166S	MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S163S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	166	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S166S(4)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctactgctgctgctgc	0.527			T	MLL	ALL																																	ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		4	Substitution - coding silent(4)	p.S166S(4)	urinary_tract(2)|lung(1)|prostate(1)	central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66						c.(496-498)agC>agT		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							8.0	15.0	13.0					9																	20414346		1434	3114	4548	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414346G>A	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.498C>T	9.37:g.20414346G>A						MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S163S|MLLT3_ENST00000355930.6_5'UTR	p.S166S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN		GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)	5	784	-			166			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.498C>T	CCDS6494.1																																																																																				0.527	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		10	396	0	0	0	1	0	10	396				
DIP2C	22982	broad.mit.edu	37	10	395301	395301	+	Missense_Mutation	SNP	C	C	T	rs548883145		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr10:395301C>T	ENST00000280886.6	-	25	3166	c.3079G>A	c.(3079-3081)Ggc>Agc	p.G1027S		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1027						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		ACGTGGTCGCCGTCCTGAAGG	0.652																																						ENST00000280886.6																			0				breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81						c.(3079-3081)Ggc>Agc		DIP2 disco-interacting protein 2 homolog C (Drosophila)							96.0	70.0	79.0					10																	395301		2203	4300	6503	SO:0001583	missense	22982					nucleus	catalytic activity|transcription factor binding	g.chr10:395301C>T	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3079G>A	10.37:g.395301C>T	ENSP00000280886:p.Gly1027Ser						p.G1027S	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)	25	3166	-		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	1027					B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	37	c.3079G>A	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.501679	0.85176	.	.	ENSG00000151240	ENST00000280886	T	0.19532	2.14	5.18	5.18	0.71444	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.52451	0.1735	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59606	-0.7423	10	0.87932	D	0	-23.0966	18.7109	0.91656	0.0:1.0:0.0:0.0	.	1027	Q9Y2E4	DIP2C_HUMAN	S	1027	ENSP00000280886:G1027S	ENSP00000280886:G1027S	G	-	1	0	DIP2C	385301	1.000000	0.71417	0.421000	0.26609	0.302000	0.27658	7.811000	0.86092	2.409000	0.81822	0.563000	0.77884	GGC		0.652	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		5	175	0	0	0	1	0	5	175				
RCVRN	5957	broad.mit.edu	37	17	9808122	9808122	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:9808122C>T	ENST00000226193.5	-	1	816	c.376G>A	c.(376-378)Gtc>Atc	p.V126I		NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin	126	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of calcium ion transport (GO:0051924)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	dendrite (GO:0030425)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						CTGACCATGACGATCTCCAGC	0.642																																						ENST00000226193.5																			0				endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						c.(376-378)Gtc>Atc		recoverin							124.0	102.0	109.0					17																	9808122		2203	4300	6503	SO:0001583	missense	5957				visual perception		calcium ion binding|calcium sensitive guanylate cyclase activator activity	g.chr17:9808122C>T	BC001720	CCDS11151.1	17p13.1	2013-01-10		2006-09-26	ENSG00000109047	ENSG00000109047		"""EF-hand domain containing"""	9937	protein-coding gene	gene with protein product		179618		RCV1		1387789, 12507501, 1467959, 12789533	Standard	NM_002903		Approved		uc002gme.1	P35243	OTTHUMG00000130268	ENST00000226193.5:c.376G>A	17.37:g.9808122C>T	ENSP00000226193:p.Val126Ile						p.V126I	NM_002903.2	NP_002894.1	P35243	RECO_HUMAN			1	816	-			126			EF-hand 3.		Q53XL0	Missense_Mutation	SNP	ENST00000226193.5	37	c.376G>A	CCDS11151.1	.	.	.	.	.	.	.	.	.	.	C	8.226	0.803586	0.16467	.	.	ENSG00000109047	ENST00000226193	T	0.66280	-0.2	4.86	1.66	0.24008	EF-hand-like domain (1);	0.252761	0.39909	N	0.001225	T	0.41282	0.1152	N	0.21508	0.67	0.80722	D	1	B	0.11235	0.004	B	0.04013	0.001	T	0.11542	-1.0583	10	0.26408	T	0.33	.	7.0455	0.25042	0.0:0.6107:0.0:0.3893	.	126	P35243	RECO_HUMAN	I	126	ENSP00000226193:V126I	ENSP00000226193:V126I	V	-	1	0	RCVRN	9748847	0.052000	0.20516	0.997000	0.53966	0.306000	0.27790	0.015000	0.13355	0.554000	0.29061	0.655000	0.94253	GTC		0.642	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252600.2	NM_002903		17	451	0	0	0	1	0	17	451				
TGIF2LX	90316	broad.mit.edu	37	X	89177404	89177404	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:89177404G>A	ENST00000561129.2	+	1	450	c.320G>A	c.(319-321)cGc>cAc	p.R107H	TGIF2LX_ENST00000283891.5_Missense_Mutation_p.R107H			Q8IUE1	TF2LX_HUMAN	TGFB-induced factor homeobox 2-like, X-linked	107					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(29)|ovary(1)|skin(3)|urinary_tract(1)	40						GCTCGCAGACGCATTCTCCCG	0.493																																						ENST00000561129.2																			0				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(29)|ovary(1)|skin(3)|urinary_tract(1)	40						c.(319-321)cGc>cAc		TGFB-induced factor homeobox 2-like, X-linked							136.0	123.0	127.0					X																	89177404		2203	4300	6503	SO:0001583	missense	90316					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chrX:89177404G>A	AF497480	CCDS14459.1	Xq21.31	2014-05-14	2007-02-07		ENSG00000153779	ENSG00000153779		"""Homeoboxes / TALE class"""	18570	protein-coding gene	gene with protein product		300411	"""TGFB-induced factor 2-like, X-linked"""				Standard	NM_138960		Approved		uc004efe.3	Q8IUE1	OTTHUMG00000021954	ENST00000561129.2:c.320G>A	X.37:g.89177404G>A	ENSP00000453704:p.Arg107His					TGIF2LX_ENST00000283891.5_Missense_Mutation_p.R107H	p.R107H			Q8IUE1	TF2LX_HUMAN			1	450	+			107					Q5JRM9|Q8TD48	Missense_Mutation	SNP	ENST00000561129.2	37	c.320G>A	CCDS14459.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.041557	0.55003	.	.	ENSG00000153779	ENST00000283891	D	0.98617	-5.03	3.08	2.18	0.27775	Homeodomain-related (1);Homeobox (2);Homeobox KN domain (1);Homeodomain-like (1);	.	.	.	.	D	0.99245	0.9737	H	0.96048	3.76	0.18873	N	0.999989	D	0.76494	0.999	D	0.70227	0.968	D	0.95720	0.8765	8	.	.	.	-22.4853	8.1044	0.30877	0.1341:0.0:0.8659:0.0	.	107	Q8IUE1	TF2LX_HUMAN	H	107	ENSP00000355119:R107H	.	R	+	2	0	TGIF2LX	89064060	0.232000	0.23762	0.001000	0.08648	0.285000	0.27093	3.495000	0.53280	0.663000	0.31027	0.513000	0.50165	CGC		0.493	TGIF2LX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417911.2	NM_138960		20	859	0	0	0	1	0	20	859				
ZNF430	80264	broad.mit.edu	37	19	21239860	21239860	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:21239860C>T	ENST00000261560.5	+	5	927	c.746C>T	c.(745-747)aCt>aTt	p.T249I	AC012627.1_ENST00000578233.1_RNA	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	249					regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						TCAACCCTTACTAGACACAGA	0.348																																						ENST00000261560.5																			0				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						c.(745-747)aCt>aTt		zinc finger protein 430							53.0	58.0	57.0					19																	21239860		2203	4300	6503	SO:0001583	missense	80264				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:21239860C>T	AK023721	CCDS32978.1	19p12	2013-01-08				ENSG00000118620		"""Zinc fingers, C2H2-type"", ""-"""	20808	protein-coding gene	gene with protein product							Standard	NM_025189		Approved	FLJ13659	uc002npj.3	Q9H8G1		ENST00000261560.5:c.746C>T	19.37:g.21239860C>T	ENSP00000261560:p.Thr249Ile						p.T249I	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN			5	927	+			249					Q86V70	Missense_Mutation	SNP	ENST00000261560.5	37	c.746C>T	CCDS32978.1	.	.	.	.	.	.	.	.	.	.	.	3.684	-0.064825	0.07273	.	.	ENSG00000118620	ENST00000261560	T	0.33865	1.39	1.04	-0.123	0.13527	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.26195	0.0639	N	0.12471	0.22	0.09310	N	1	D;P	0.56968	0.978;0.723	P;B	0.53760	0.734;0.41	T	0.12915	-1.0529	9	0.38643	T	0.18	.	4.5907	0.12306	0.0:0.5789:0.0:0.4211	.	248;249	Q2NKJ9;Q9H8G1	.;ZN430_HUMAN	I	249	ENSP00000261560:T249I	ENSP00000261560:T249I	T	+	2	0	ZNF430	21031700	0.000000	0.05858	0.015000	0.15790	0.014000	0.08584	-3.561000	0.00430	0.452000	0.26830	0.455000	0.32223	ACT		0.348	ZNF430-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463539.1	NM_025189		9	289	0	0	0	1	0	9	289				
LOC440040	440040	broad.mit.edu	37	11	49831678	49831678	+	RNA	SNP	G	G	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:49831678G>T	ENST00000527477.1	+	0	1903																											TTCCTGGATTGTGAAGCTAGA	0.448																																						ENST00000527477.1																			0																																																			0							g.chr11:49831678G>T																													11.37:g.49831678G>T														0	1903	+									RNA	SNP	ENST00000527477.1	37																																																																																						0.448	RP11-707M1.1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000391378.2			22	555	1	0	8.10497e-08	1	8.34873e-08	22	555				
SEPT9	10801	broad.mit.edu	37	17	75398245	75398245	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:75398245C>T	ENST00000427177.1	+	3	307	c.181C>T	c.(181-183)Cag>Tag	p.Q61*	SEPT9_ENST00000423034.2_Nonsense_Mutation_p.Q54*|SEPT9_ENST00000585930.1_5'Flank|SEPT9_ENST00000427674.2_5'UTR|SEPT9_ENST00000329047.8_Nonsense_Mutation_p.Q43*|SEPT9_ENST00000590294.1_Nonsense_Mutation_p.Q43*|SEPT9_ENST00000592420.1_5'UTR|SEPT9_ENST00000591198.1_Nonsense_Mutation_p.Q42*|SEPT9_ENST00000431235.2_5'UTR|SEPT9_ENST00000588690.1_5'UTR|SEPT9_ENST00000449803.2_5'UTR	NM_001113491.1	NP_001106963.1	Q9UHD8	SEPT9_HUMAN	septin 9	61					cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|protein heterooligomerization (GO:0051291)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)	16			BRCA - Breast invasive adenocarcinoma(99;0.153)			CAGCTCCACCCAGAAATTCCA	0.627																																						ENST00000329047.8																			0				autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)	16						c.(127-129)Cag>Tag		septin 9							31.0	35.0	34.0					17																	75398245		1926	4138	6064	SO:0001587	stop_gained	10801				cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding	g.chr17:75398245C>T	AB023208	CCDS45790.1, CCDS45791.1, CCDS45792.1, CCDS45793.1, CCDS45794.1, CCDS45795.1, CCDS74166.1	17q25.3	2014-09-17	2005-01-11	2005-01-12	ENSG00000184640	ENSG00000184640		"""Septins"""	7323	protein-coding gene	gene with protein product	"""Ov/Br septin"""	604061	"""MLL septin-like fusion"""	MSF		10339604, 10485469	Standard	NM_006640		Approved	MSF1, KIAA0991, PNUTL4, AF17q25, SeptD1	uc002jts.4	Q9UHD8		ENST00000427177.1:c.181C>T	17.37:g.75398245C>T	ENSP00000391249:p.Gln61*					SEPT9_ENST00000427177.1_Nonsense_Mutation_p.Q61*|SEPT9_ENST00000588690.1_5'UTR|SEPT9_ENST00000590294.1_Nonsense_Mutation_p.Q43*|SEPT9_ENST00000427674.2_5'UTR|SEPT9_ENST00000423034.2_Nonsense_Mutation_p.Q54*|SEPT9_ENST00000431235.2_5'UTR|SEPT9_ENST00000592420.1_5'UTR|SEPT9_ENST00000591198.1_Nonsense_Mutation_p.Q42*|SEPT9_ENST00000449803.2_5'UTR	p.Q43*	NM_006640.4	NP_006631.2	Q9UHD8	SEPT9_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.153)		2	939	+			61					A8K2V3|B3KPM0|B4DTL9|B4E0N2|B4E274|B7Z654|Q96QF3|Q96QF4|Q96QF5|Q9HA04|Q9UG40|Q9Y5W4	Nonsense_Mutation	SNP	ENST00000427177.1	37	c.127C>T	CCDS45790.1	.	.	.	.	.	.	.	.	.	.	C	45	11.389194	0.99555	.	.	ENSG00000184640	ENST00000427177;ENST00000329047;ENST00000423034	.	.	.	4.89	4.89	0.63831	.	2.942800	0.01335	U	0.011366	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	17.0435	0.86496	0.0:1.0:0.0:0.0	.	.	.	.	X	61;43;54	.	ENSP00000329161:Q43X	Q	+	1	0	SEPT9	72909840	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.105000	0.57797	2.262000	0.75019	0.555000	0.69702	CAG		0.627	SEPT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436304.2	NM_006640		11	221	0	0	0	1	0	11	221				
TPTE2P6	374491	broad.mit.edu	37	13	25161438	25161438	+	RNA	SNP	T	T	A	rs3869320		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr13:25161438T>A	ENST00000453498.1	+	0	962				TPTE2P6_ENST00000440905.1_RNA																							CTCTTTATAATAAGATTCATT	0.378																																						ENST00000453498.1																			0																																																			0							g.chr13:25161438T>A																													13.37:g.25161438T>A														0	962	+									RNA	SNP	ENST00000453498.1	37																																																																																						0.378	RP11-556N21.1-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000044193.1			24	188	0	0	0	1	0	24	188				
USP32	84669	broad.mit.edu	37	17	58292024	58292024	+	Missense_Mutation	SNP	C	C	T	rs571048538	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:58292024C>T	ENST00000300896.4	-	17	2173	c.1979G>A	c.(1978-1980)cGc>cAc	p.R660H	USP32_ENST00000592339.1_Missense_Mutation_p.R330H	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	660					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			CTCTTTAATGCGCAGCCTTTG	0.408													C|||	3	0.000599042	0.0023	0.0	5008	,	,		19451	0.0		0.0	False		,,,				2504	0.0					ENST00000300896.4																			0				NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62						c.(1978-1980)cGc>cAc		ubiquitin specific peptidase 32							41.0	38.0	39.0					17																	58292024		2201	4295	6496	SO:0001583	missense	84669				protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity	g.chr17:58292024C>T	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"""Ubiquitin-specific peptidases"", ""EF-hand domain containing"""	19143	protein-coding gene	gene with protein product		607740	"""ubiquitin specific protease 32"""			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.1979G>A	17.37:g.58292024C>T	ENSP00000300896:p.Arg660His					USP32_ENST00000592339.1_Missense_Mutation_p.R330H	p.R660H	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)		17	2173	-	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		660					Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	c.1979G>A	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	C	35	5.530108	0.96446	.	.	ENSG00000170832	ENST00000300896	T	0.50001	0.76	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.46073	0.1374	L	0.48642	1.525	0.80722	D	1	P	0.50617	0.937	B	0.41440	0.357	T	0.49113	-0.8973	10	0.49607	T	0.09	.	19.155	0.93506	0.0:1.0:0.0:0.0	.	660	Q8NFA0	UBP32_HUMAN	H	660	ENSP00000300896:R660H	ENSP00000300896:R660H	R	-	2	0	USP32	55646806	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.717000	0.84732	2.539000	0.85634	0.650000	0.86243	CGC		0.408	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		7	369	0	0	0	1	0	7	369				
TGFBR1	7046	broad.mit.edu	37	9	101900288	101900288	+	Nonsense_Mutation	SNP	C	C	A	rs111854391		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr9:101900288C>A	ENST00000374994.4	+	4	839	c.722C>A	c.(721-723)tCg>tAg	p.S241*	TGFBR1_ENST00000552516.1_Nonsense_Mutation_p.S245*|TGFBR1_ENST00000550253.1_Nonsense_Mutation_p.S172*|TGFBR1_ENST00000374990.2_Nonsense_Mutation_p.S164*	NM_004612.2	NP_004603.1	P36897	TGFR1_HUMAN	transforming growth factor, beta receptor 1	241	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> L (in LDS1). {ECO:0000269|PubMed:16596670, ECO:0000269|PubMed:16791849}.		activation of MAPKK activity (GO:0000186)|angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|artery morphogenesis (GO:0048844)|blastocyst development (GO:0001824)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen fibril organization (GO:0030199)|embryonic cranial skeleton morphogenesis (GO:0048701)|endothelial cell migration (GO:0043542)|epithelial to mesenchymal transition (GO:0001837)|extracellular structure organization (GO:0043062)|germ cell migration (GO:0008354)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mesenchymal cell differentiation (GO:0048762)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|parathyroid gland development (GO:0060017)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of protein binding (GO:0043393)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|response to cholesterol (GO:0070723)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	endosome (GO:0005768)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)	p.S241L(2)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	27		Acute lymphoblastic leukemia(62;0.0559)				GAAGAACGTTCGTGGTTCCGT	0.418																																						ENST00000374994.4																			2	Substitution - Missense(2)	p.S241L(2)	large_intestine(2)	endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	27	GRCh37	CM061221	TGFBR1	M	rs111854391	c.(721-723)tCg>tAg		transforming growth factor, beta receptor 1							173.0	168.0	170.0					9																	101900288		2203	4300	6503	SO:0001587	stop_gained	7046				activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway		ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding	g.chr9:101900288C>A		CCDS6738.1, CCDS47998.1	9q22	2014-01-30	2008-07-31		ENSG00000106799	ENSG00000106799			11772	protein-coding gene	gene with protein product	"""activin A receptor type II-like kinase, 53kDa"""	190181	"""transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kD)"", ""multiple self-healing squamous epithelioma"""	MSSE, ESS1		1319842, 8530052, 21358634	Standard	NM_001130916		Approved	ALK-5, ACVRLK4	uc004azc.3	P36897	OTTHUMG00000020353	ENST00000374994.4:c.722C>A	9.37:g.101900288C>A	ENSP00000364133:p.Ser241*					TGFBR1_ENST00000374990.2_Nonsense_Mutation_p.S164*|TGFBR1_ENST00000552516.1_Nonsense_Mutation_p.S245*|TGFBR1_ENST00000550253.1_Nonsense_Mutation_p.S172*	p.S241*	NM_004612.2	NP_004603.1	P36897	TGFR1_HUMAN			4	839	+		Acute lymphoblastic leukemia(62;0.0559)	241		S -> L (in LDS1A).	Protein kinase.		Q6IR47|Q706C0|Q706C1	Nonsense_Mutation	SNP	ENST00000374994.4	37	c.722C>A	CCDS6738.1	.	.	.	.	.	.	.	.	.	.	C	36	5.794315	0.96952	.	.	ENSG00000106799	ENST00000374994;ENST00000540092;ENST00000374990;ENST00000552516;ENST00000549021;ENST00000550253	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3707	0.90406	0.0:1.0:0.0:0.0	.	.	.	.	X	241;241;164;245;95;172	.	.	S	+	2	0	TGFBR1	100940109	1.000000	0.71417	0.996000	0.52242	0.851000	0.48451	7.773000	0.85462	2.642000	0.89623	0.650000	0.86243	TCG		0.418	TGFBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053390.3			8	428	1	0	5.18039e-06	1	5.21848e-06	8	428				
RADIL	55698	broad.mit.edu	37	7	4917630	4917630	+	Silent	SNP	G	G	A	rs368969739		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr7:4917630G>A	ENST00000399583.3	-	2	328	c.141C>T	c.(139-141)ggC>ggT	p.G47G	RADIL_ENST00000536091.1_Silent_p.G47G	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	47					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CATCGCTGGCGCCCAGGCTGG	0.627																																						ENST00000399583.3																			0				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						c.(139-141)ggC>ggT		Ras association and DIL domains																																				SO:0001819	synonymous_variant	55698				cell adhesion|multicellular organismal development|signal transduction		protein binding	g.chr7:4917630G>A	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.141C>T	7.37:g.4917630G>A						RADIL_ENST00000536091.1_Silent_p.G47G	p.G47G	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)	2	328	-		Ovarian(82;0.0175)	47					A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	c.141C>T	CCDS43544.1																																																																																				0.627	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		5	106	0	0	0	1	0	5	106				
SPSB3	90864	broad.mit.edu	37	16	1828584	1828584	+	Silent	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr16:1828584G>A	ENST00000566339.1	-	3	486	c.156C>T	c.(154-156)taC>taT	p.Y52Y	SPSB3_ENST00000301717.4_Silent_p.Y52Y	NM_080861.3	NP_543137.2	Q6PJ21	SPSB3_HUMAN	splA/ryanodine receptor domain and SOCS box containing 3	52					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					endometrium(1)|kidney(4)|lung(3)|prostate(2)	10						GCAGCGTGGAGTACTCGGGGT	0.652																																						ENST00000566339.1																			0				endometrium(1)|kidney(4)|lung(3)|prostate(2)	10						c.(154-156)taC>taT		splA/ryanodine receptor domain and SOCS box containing 3							95.0	98.0	97.0					16																	1828584		2199	4300	6499	SO:0001819	synonymous_variant	90864				intracellular signal transduction			g.chr16:1828584G>A		CCDS32365.1	16p13.3	2008-02-05				ENSG00000162032			30629	protein-coding gene	gene with protein product		611659	"""chromosome 16 open reading frame 31"""	C16orf31		12076535	Standard	NM_080861		Approved	SSB-3	uc002cmu.3	Q6PJ21		ENST00000566339.1:c.156C>T	16.37:g.1828584G>A						SPSB3_ENST00000301717.4_Silent_p.Y52Y	p.Y52Y	NM_080861.3	NP_543137.2	Q6PJ21	SPSB3_HUMAN			3	486	-			52					D3DU78|Q49A96|Q86X18|Q8WXK5|Q96IE6|Q96RY2	Silent	SNP	ENST00000566339.1	37	c.156C>T	CCDS32365.1																																																																																				0.652	SPSB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433512.1	NM_080861		12	342	0	0	0	1	0	12	342				
LOC220729	220729	broad.mit.edu	37	3	197348739	197348739	+	RNA	SNP	G	G	C	rs371325185	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:197348739G>C	ENST00000418868.1	-	0	520					NR_003266.2																						TAATTTTCTAGCTGTGAAAGA	0.398													g|||	29	0.00579073	0.0008	0.0072	5008	,	,		22210	0.002		0.0109	False		,,,				2504	0.0102					ENST00000418868.1																			0																																																			0							g.chr3:197348739G>C																													3.37:g.197348739G>C								NR_003266.2						0	520	-									RNA	SNP	ENST00000418868.1	37																																																																																						0.398	AC024560.3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340283.1			11	600	0	0	0	1	0	11	600				
HAS2	3037	broad.mit.edu	37	8	122641537	122641537	+	Missense_Mutation	SNP	G	G	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr8:122641537G>T	ENST00000303924.4	-	2	581	c.44C>A	c.(43-45)aCc>aAc	p.T15N		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	15					atrioventricular canal development (GO:0036302)|bone morphogenesis (GO:0060349)|cellular response to fluid shear stress (GO:0071498)|cellular response to interleukin-1 (GO:0071347)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|endocardial cushion to mesenchymal transition (GO:0090500)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|hyaluronan biosynthetic process (GO:0030213)|kidney development (GO:0001822)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	hyaluronan synthase activity (GO:0050501)		HAS2/PLAG1(10)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(19)|ovary(5)|skin(1)	38	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)			AAAGAGTGTGGTTCCAATTAT	0.378																																						ENST00000303924.4																		HAS2/PLAG1(10)	0				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(19)|ovary(5)|skin(1)	38						c.(43-45)aCc>aAc		hyaluronan synthase 2							58.0	56.0	56.0					8																	122641537		2203	4299	6502	SO:0001583	missense	3037					integral to plasma membrane	hyaluronan synthase activity	g.chr8:122641537G>T	U54804	CCDS6335.1	8q24.12	2013-02-22			ENSG00000170961	ENSG00000170961	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4819	protein-coding gene	gene with protein product		601636				9169154	Standard	NM_005328		Approved		uc003yph.2	Q92819	OTTHUMG00000164953	ENST00000303924.4:c.44C>A	8.37:g.122641537G>T	ENSP00000306991:p.Thr15Asn						p.T15N	NM_005328.2	NP_005319.1	Q92819	HAS2_HUMAN	STAD - Stomach adenocarcinoma(47;0.00503)		2	581	-	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		15					Q32MM3	Missense_Mutation	SNP	ENST00000303924.4	37	c.44C>A	CCDS6335.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.369297	0.82463	.	.	ENSG00000170961	ENST00000303924;ENST00000443194	T	0.57107	0.42	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.70780	0.3263	M	0.79123	2.44	0.80722	D	1	D	0.56035	0.974	P	0.55615	0.78	T	0.69495	-0.5130	10	0.49607	T	0.09	-22.0036	20.8794	0.99867	0.0:0.0:1.0:0.0	.	15	Q92819	HAS2_HUMAN	N	15	ENSP00000306991:T15N	ENSP00000306991:T15N	T	-	2	0	HAS2	122710718	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.800000	0.99124	2.941000	0.99782	0.655000	0.94253	ACC		0.378	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328		8	327	1	0	1.06961e-07	1	1.09356e-07	8	327				
LRP5	4041	broad.mit.edu	37	11	68115353	68115353	+	Missense_Mutation	SNP	C	C	T	rs371690402		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:68115353C>T	ENST00000294304.7	+	2	236	c.130C>T	c.(130-132)Cgg>Tgg	p.R44W		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	44	Beta-propeller 1.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CCGGGACGTACGGCTGGTGGA	0.647																																						ENST00000294304.7																			0				autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						c.(130-132)Cgg>Tgg		low density lipoprotein receptor-related protein 5		C	TRP/ARG	0,4312		0,0,2156	37.0	39.0	38.0		130	2.2	1.0	11		38	1,8375		0,1,4187	no	missense	LRP5	NM_002335.2	101	0,1,6343	TT,TC,CC		0.0119,0.0,0.0079	probably-damaging	44/1616	68115353	1,12687	2156	4188	6344	SO:0001583	missense	4041				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity	g.chr11:68115353C>T	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.130C>T	11.37:g.68115353C>T	ENSP00000294304:p.Arg44Trp						p.R44W	NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN			2	236	+			44			Beta-propeller 1.		Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	37	c.130C>T	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.342253	0.41498	0.0	1.19E-4	ENSG00000162337	ENST00000294304	D	0.91792	-2.91	4.23	2.22	0.28083	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.38436	U	0.001695	D	0.96513	0.8862	H	0.95079	3.62	0.49483	D	0.999798	D	0.89917	1.0	D	0.97110	1.0	D	0.95702	0.8750	10	0.87932	D	0	.	8.5936	0.33701	0.2119:0.7033:0.0:0.0848	.	44	O75197	LRP5_HUMAN	W	44	ENSP00000294304:R44W	ENSP00000294304:R44W	R	+	1	2	LRP5	67871929	0.948000	0.32251	0.964000	0.40570	0.037000	0.13140	2.186000	0.42593	1.148000	0.42385	-0.215000	0.12644	CGG		0.647	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		13	383	0	0	0	1	0	13	383				
PCDHGB3	56102	broad.mit.edu	37	5	140751764	140751764	+	Silent	SNP	C	C	T	rs57763341	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr5:140751764C>T	ENST00000576222.1	+	1	1934	c.1803C>T	c.(1801-1803)aaC>aaT	p.N601N	PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	601	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGGATACAACGCCTGGCTGT	0.672													.|||	5	0.000998403	0.0	0.0	5008	,	,		16837	0.005		0.0	False		,,,				2504	0.0					ENST00000576222.1																			0				endometrium(1)|kidney(1)|lung(3)	5						c.(1801-1803)aaC>aaT				C	,,,,,,,,	0,4406		0,0,2203	58.0	67.0	64.0		,,,,,,,1803,1803	-4.6	0.2	5	dbSNP_129	64	1,8599		0,1,4299	no	intron,intron,intron,intron,intron,intron,intron,coding-synonymous,coding-synonymous	PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032097.1	,,,,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,,,,	,,,,,,,601/930,601/815	140751764	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	0							g.chr5:140751764C>T	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1803C>T	5.37:g.140751764C>T						PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron	p.N601N	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	1934	+								A7E229|Q9Y5C7	Silent	SNP	ENST00000576222.1	37	c.1803C>T	CCDS58980.1																																																																																				0.672	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		8	451	0	0	0	1	0	8	451				
EPHA8	2046	broad.mit.edu	37	1	22927844	22927844	+	Silent	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:22927844C>T	ENST00000166244.3	+	16	2853	c.2781C>T	c.(2779-2781)agC>agT	p.S927S		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	927					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GAGGGGGCAGCGGTGGCGGTG	0.692																																						ENST00000166244.3																			0				breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61						c.(2779-2781)agC>agT		EPH receptor A8							34.0	41.0	39.0					1																	22927844		2178	4228	6406	SO:0001819	synonymous_variant	2046					integral to plasma membrane	ATP binding|ephrin receptor activity	g.chr1:22927844C>T	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.2781C>T	1.37:g.22927844C>T							p.S927S	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)	16	2853	+		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)	927					Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	37	c.2781C>T	CCDS225.1																																																																																				0.692	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		10	437	0	0	0	1	0	10	437				
KCTD11	147040	broad.mit.edu	37	17	7256580	7256580	+	Missense_Mutation	SNP	C	C	T	rs35280612		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:7256580C>T	ENST00000333751.3	+	1	1373	c.319C>T	c.(319-321)Cgg>Tgg	p.R107W	RP11-542C16.1_ENST00000572417.1_RNA|TMEM95_ENST00000330767.4_5'Flank|TMEM95_ENST00000576060.1_5'Flank|TMEM95_ENST00000389982.4_5'Flank	NM_001002914.2	NP_001002914.1	Q693B1	KCD11_HUMAN	potassium channel tetramerization domain containing 11	107					cell cycle (GO:0007049)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)				kidney(1)|large_intestine(2)|lung(1)	4		Prostate(122;0.157)				CTCTGCTCGCCGGGGACCCCA	0.642																																						ENST00000333751.3																			0				kidney(1)|large_intestine(2)|lung(1)	4						c.(319-321)Cgg>Tgg		potassium channel tetramerization domain containing 11							55.0	50.0	52.0					17																	7256580		2203	4300	6503	SO:0001583	missense	147040				cell cycle|regulation of growth	voltage-gated potassium channel complex	voltage-gated potassium channel activity	g.chr17:7256580C>T	AK056227	CCDS32545.1	17p13.2	2013-06-20	2013-06-20	2003-11-26	ENSG00000213859	ENSG00000213859			21302	protein-coding gene	gene with protein product		609848	"""chromosome 17 open reading frame 36"", ""potassium channel tetramerisation domain containing 11"""	C17orf36		12186855, 21472142	Standard	NM_001002914		Approved	REN, KCASH1	uc002gge.4	Q693B1	OTTHUMG00000132061	ENST00000333751.3:c.319C>T	17.37:g.7256580C>T	ENSP00000328352:p.Arg107Trp					RP11-542C16.1_ENST00000572417.1_RNA	p.R107W	NM_001002914.2	NP_001002914.1	Q693B1	KCD11_HUMAN			1	1373	+		Prostate(122;0.157)	107					B3KPE0	Missense_Mutation	SNP	ENST00000333751.3	37	c.319C>T	CCDS32545.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.382499	0.61845	.	.	ENSG00000213859	ENST00000333751	T	0.71698	-0.59	5.38	-3.06	0.05379	.	0.158994	0.26979	U	0.021525	T	0.47002	0.1422	N	0.19112	0.55	0.09310	N	1	P	0.51537	0.946	B	0.33521	0.165	T	0.55471	-0.8136	10	0.72032	D	0.01	.	15.0564	0.71917	0.774:0.226:0.0:0.0	.	107	Q693B1	KCD11_HUMAN	W	107	ENSP00000328352:R107W	ENSP00000328352:R107W	R	+	1	2	KCTD11	7197304	0.646000	0.27295	0.873000	0.34254	0.874000	0.50279	0.512000	0.22755	-0.389000	0.07786	0.462000	0.41574	CGG		0.642	KCTD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255084.2	NM_001002914		11	299	0	0	0	1	0	11	299				
CA10	56934	broad.mit.edu	37	17	50008436	50008436	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:50008436G>A	ENST00000285273.4	-	4	1304	c.193C>T	c.(193-195)Cgg>Tgg	p.R65W	CA10_ENST00000570565.1_De_novo_Start_OutOfFrame|CA10_ENST00000451037.2_Missense_Mutation_p.R65W|CA10_ENST00000442502.2_Missense_Mutation_p.R65W|CA10_ENST00000340813.6_Missense_Mutation_p.R71W	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	65					brain development (GO:0007420)					cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	GGCGACTGCCGTTTCCCCACA	0.473																																						ENST00000570565.1																			0				cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41								carbonic anhydrase X							201.0	187.0	192.0					17																	50008436		2203	4300	6503	SO:0001583	missense	56934				brain development			g.chr17:50008436G>A	AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"""Carbonic anhydrases"""	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.193C>T	17.37:g.50008436G>A	ENSP00000285273:p.Arg65Trp					CA10_ENST00000442502.2_Missense_Mutation_p.R65W|CA10_ENST00000451037.2_Missense_Mutation_p.R65W|CA10_ENST00000340813.6_Missense_Mutation_p.R71W|CA10_ENST00000285273.4_Missense_Mutation_p.R65W				Q9NS85	CAH10_HUMAN	BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		0	210	-								B2R7J0|B4DGL6	Translation_Start_Site	SNP	ENST00000285273.4	37		CCDS32684.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.725381	0.89298	.	.	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813	T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53	5.93	4.93	0.64822	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.64402	D	0.000001	D	0.84875	0.5569	M	0.86502	2.82	0.46061	D	0.998844	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.988	D	0.86086	0.1547	9	.	.	.	.	13.5205	0.61566	0.0:0.0:0.6936:0.3064	.	65;71	Q9NS85;Q68D28	CAH10_HUMAN;.	W	65;65;65;71	ENSP00000390666:R65W;ENSP00000285273:R65W;ENSP00000405388:R65W;ENSP00000340363:R71W	.	R	-	1	2	CA10	47363435	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.008000	0.57103	2.826000	0.97356	0.655000	0.94253	CGG		0.473	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178		21	677	0	0	0	1	0	21	677				
ZNF561	93134	broad.mit.edu	37	19	9721440	9721440	+	Silent	SNP	G	G	A	rs532347484		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:9721440G>A	ENST00000302851.3	-	6	1260	c.897C>T	c.(895-897)caC>caT	p.H299H	ZNF561_ENST00000495503.1_5'Flank|ZNF561_ENST00000424629.1_Silent_p.H230H|ZNF561_ENST00000326044.5_3'UTR|ZNF561_ENST00000354661.4_Silent_p.H163H	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	299					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						GAATTTGAATGTGATCATTAA	0.373													G|||	1	0.000199681	0.0008	0.0	5008	,	,		22312	0.0		0.0	False		,,,				2504	0.0					ENST00000302851.3																			0				breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						c.(895-897)caC>caT		zinc finger protein 561							113.0	108.0	110.0					19																	9721440		2203	4300	6503	SO:0001819	synonymous_variant	93134				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:9721440G>A	AK074787	CCDS12216.2	19p13.2	2013-09-20			ENSG00000171469	ENSG00000171469		"""Zinc fingers, C2H2-type"", ""-"""	28684	protein-coding gene	gene with protein product						12477932	Standard	NM_152289		Approved	MGC45408	uc002mlu.3	Q8N587	OTTHUMG00000157054	ENST00000302851.3:c.897C>T	19.37:g.9721440G>A						ZNF561_ENST00000354661.4_Silent_p.H163H|ZNF561_ENST00000326044.5_3'UTR|ZNF561_ENST00000424629.1_Silent_p.H230H	p.H299H	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN			6	1260	-			299					B4E2Q8|Q6PJS0	Silent	SNP	ENST00000302851.3	37	c.897C>T	CCDS12216.2																																																																																				0.373	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289		25	646	0	0	0	1	0	25	646				
DCBLD2	131566	broad.mit.edu	37	3	98518461	98518461	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:98518461G>A	ENST00000326840.6	-	16	2445	c.2083C>T	c.(2083-2085)Cag>Tag	p.Q695*	DCBLD2_ENST00000326857.9_Nonsense_Mutation_p.Q709*	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	695					cell adhesion (GO:0007155)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell growth (GO:0030308)|wound healing (GO:0042060)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						GTGGAGGGCTGACCAACTGAA	0.527																																						ENST00000326840.6																			0				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						c.(2083-2085)Cag>Tag		discoidin, CUB and LCCL domain containing 2							154.0	156.0	156.0					3																	98518461		1954	4159	6113	SO:0001587	stop_gained	131566				cell adhesion|intracellular receptor mediated signaling pathway|negative regulation of cell growth|wound healing	cell surface|integral to plasma membrane		g.chr3:98518461G>A		CCDS46878.1	3q12.2	2006-04-12			ENSG00000057019	ENSG00000057019			24627	protein-coding gene	gene with protein product		608698				11447234	Standard	NM_080927		Approved	CLCP1, ESDN	uc003dtd.3	Q96PD2	OTTHUMG00000151985	ENST00000326840.6:c.2083C>T	3.37:g.98518461G>A	ENSP00000321573:p.Gln695*					DCBLD2_ENST00000326857.9_Nonsense_Mutation_p.Q709*	p.Q695*	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN			16	2445	-			695					B7WNL1|D3DN41|Q8N6M4|Q8TDX2	Nonsense_Mutation	SNP	ENST00000326840.6	37	c.2083C>T	CCDS46878.1	.	.	.	.	.	.	.	.	.	.	G	37	6.627228	0.97718	.	.	ENSG00000057019	ENST00000326840;ENST00000326857	.	.	.	5.65	2.79	0.32731	.	0.592892	0.15545	N	0.256738	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-6.2138	1.8248	0.03118	0.1818:0.169:0.4938:0.1554	.	.	.	.	X	695;709	.	ENSP00000321573:Q695X	Q	-	1	0	DCBLD2	100001151	0.025000	0.19082	0.703000	0.30354	0.563000	0.35712	1.076000	0.30729	1.393000	0.46605	0.655000	0.94253	CAG		0.527	DCBLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324675.2	NM_080927		13	462	0	0	0	1	0	13	462				
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:3427845C>T	ENST00000529482.1	+	0	962									tumor suppressing subtransferable candidate 2 pseudogene																		CTTCAAGTGGCAGGAGCAGAA	0.587																																						ENST00000529482.1																			0																																																			0							g.chr11:3427845C>T			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427845C>T														0	962	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			9	215	0	0	0	1	0	9	215				
CNGA3	1261	broad.mit.edu	37	2	99013339	99013339	+	Missense_Mutation	SNP	G	G	A	rs201782746		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:99013339G>A	ENST00000272602.2	+	7	1745	c.1706G>A	c.(1705-1707)cGc>cAc	p.R569H	CNGA3_ENST00000393504.1_Missense_Mutation_p.R569H|CNGA3_ENST00000436404.2_Missense_Mutation_p.R551H|CNGA3_ENST00000409937.1_Missense_Mutation_p.R573H			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	569			R -> H (in ACHM2). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:14757870}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						GCCAACATCCGCAGCATTGGC	0.582																																						ENST00000393504.1																			0				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49	GRCh37	CM014559	CNGA3	M		c.(1705-1707)cGc>cAc		cyclic nucleotide gated channel alpha 3		G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	114.0	110.0	111.0		1652,1706	5.4	1.0	2		111	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CNGA3	NM_001079878.1,NM_001298.2	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	551/677,569/695	99013339	1,13005	2203	4300	6503	SO:0001583	missense	1261				signal transduction|visual perception	integral to membrane	cGMP binding	g.chr2:99013339G>A	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.1706G>A	2.37:g.99013339G>A	ENSP00000272602:p.Arg569His					CNGA3_ENST00000272602.2_Missense_Mutation_p.R569H|CNGA3_ENST00000436404.2_Missense_Mutation_p.R551H|CNGA3_ENST00000409937.1_Missense_Mutation_p.R573H	p.R569H	NM_001298.2	NP_001289.1	Q16281	CNGA3_HUMAN			8	2123	+			569		R -> H (in ACHM2).			E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	37	c.1706G>A	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	G	19.46	3.832457	0.71258	0.0	1.16E-4	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.97161	-4.27;-4.27;-4.27;-4.27	5.42	5.42	0.78866	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.98833	0.9606	H	0.96208	3.785	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.988;0.988;0.991	D	0.98965	1.0799	10	0.87932	D	0	.	12.1196	0.53883	0.0815:0.0:0.9185:0.0	.	573;551;569	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	H	569;551;569;573	ENSP00000377140:R569H;ENSP00000410070:R551H;ENSP00000272602:R569H;ENSP00000386761:R573H	ENSP00000272602:R569H	R	+	2	0	CNGA3	98379771	0.987000	0.35691	1.000000	0.80357	0.697000	0.40408	4.514000	0.60482	2.826000	0.97356	0.563000	0.77884	CGC		0.582	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		31	679	0	0	0	1	0	31	679				
POM121L9P	29774	broad.mit.edu	37	22	24659809	24659809	+	RNA	SNP	G	G	A	rs376621154		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr22:24659809G>A	ENST00000414583.2	+	0	3334					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		CCCTATCTGCGCACCCGGAGG	0.612																																						ENST00000414583.2																			0																																																			0							g.chr22:24659809G>A	AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659809G>A								NR_003714.1						0	3334	+									RNA	SNP	ENST00000414583.2	37																																																																																						0.612	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1	NM_014549		4	26	0	0	0	1	0	4	26				
ITGB4	3691	broad.mit.edu	37	17	73748594	73748594	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:73748594G>A	ENST00000200181.3	+	32	4231	c.4044G>A	c.(4042-4044)atG>atA	p.M1348I	ITGB4_ENST00000449880.2_Missense_Mutation_p.M1348I|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000450894.3_Missense_Mutation_p.M1348I|ITGB4_ENST00000579662.1_Missense_Mutation_p.M1348I|ITGB4_ENST00000339591.3_Missense_Mutation_p.M1348I	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1348					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCTTCCTTATGTACAGCGATG	0.627																																						ENST00000200181.3																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43						c.(4042-4044)atG>atA		integrin, beta 4							116.0	111.0	112.0					17																	73748594		2203	4300	6503	SO:0001583	missense	3691				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity	g.chr17:73748594G>A		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.4044G>A	17.37:g.73748594G>A	ENSP00000200181:p.Met1348Ile					ITGB4_ENST00000449880.2_Missense_Mutation_p.M1348I|ITGB4_ENST00000579662.1_Missense_Mutation_p.M1348I|ITGB4_ENST00000339591.3_Missense_Mutation_p.M1348I|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000450894.3_Missense_Mutation_p.M1348I	p.M1348I	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		32	4231	+	all_cancers(13;1.5e-07)		1348					A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	c.4044G>A	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	14.88	2.667504	0.47677	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	T;T;T	0.75938	-0.98;-0.94;-0.94	4.31	4.31	0.51392	.	0.000000	0.85682	D	0.000000	T	0.80449	0.4625	L	0.36672	1.1	0.80722	D	1	D;D;D	0.69078	0.997;0.995;0.995	D;D;D	0.80764	0.994;0.987;0.987	T	0.81342	-0.0976	10	0.46703	T	0.11	.	16.9575	0.86263	0.0:0.0:1.0:0.0	.	1348;1348;1348	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	I	1348	ENSP00000200181:M1348I;ENSP00000344079:M1348I;ENSP00000400217:M1348I	ENSP00000200181:M1348I	M	+	3	0	ITGB4	71260189	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	9.571000	0.98176	2.207000	0.71202	0.561000	0.74099	ATG		0.627	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			18	571	0	0	0	1	0	18	571				
LINC00969	440993	broad.mit.edu	37	3	195395402	195395402	+	lincRNA	SNP	C	C	A	rs199554501	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:195395402C>A	ENST00000445430.1	+	0	809									long intergenic non-protein coding RNA 969																		TACGGGCGCACCTACTTGAGC	0.597																																						ENST00000445430.1																			0																																																			0							g.chr3:195395402C>A	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195395402C>A														0	809	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.597	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			20	231	1	0	2.24893e-16	1	2.46483e-16	20	231				
TFE3	7030	broad.mit.edu	37	X	48896768	48896768	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:48896768C>T	ENST00000315869.7	-	3	657	c.398G>A	c.(397-399)cGt>cAt	p.R133H	TFE3_ENST00000487451.1_5'UTR	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	133					humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)		NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						CTGTTCCCGACGCTCACGCCT	0.662			T	"""SFPQ, ASPSCR1, PRCC, NONO, CLTC"""	"""papillary renal, alveolar soft part sarcoma, renal"""																																	ENST00000315869.7				Dom	yes		X	Xp11.22	7030	T	transcription factor binding to IGHM enhancer 3			E	"""SFPQ, ASPSCR1, PRCC, NONO, CLTC"""		"""papillary renal, alveolar soft part sarcoma, renal"""	NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	0				central_nervous_system(1)	1						c.(397-399)cGt>cAt		transcription factor binding to IGHM enhancer 3							23.0	22.0	22.0					X																	48896768		2200	4295	6495	SO:0001583	missense	7030				humoral immune response|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding	g.chrX:48896768C>T	X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"""Basic helix-loop-helix proteins"""	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.398G>A	X.37:g.48896768C>T	ENSP00000314129:p.Arg133His					TFE3_ENST00000493583.1_5'UTR	p.R133H	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN			3	657	-			133					A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Missense_Mutation	SNP	ENST00000315869.7	37	c.398G>A	CCDS14315.3	.	.	.	.	.	.	.	.	.	.	C	15.44	2.834420	0.50951	.	.	ENSG00000068323	ENST00000315869	T	0.17370	2.28	5.36	4.49	0.54785	.	0.207799	0.40554	N	0.001077	T	0.12646	0.0307	L	0.52011	1.625	0.30557	N	0.764871	P	0.49783	0.928	B	0.35813	0.211	T	0.23797	-1.0178	10	0.72032	D	0.01	-7.8369	6.4239	0.21758	0.0:0.8025:0.0:0.1975	.	133	P19532	TFE3_HUMAN	H	133	ENSP00000314129:R133H	ENSP00000314129:R133H	R	-	2	0	TFE3	48783712	0.253000	0.23982	0.998000	0.56505	0.716000	0.41182	0.777000	0.26718	2.224000	0.72417	0.513000	0.50165	CGT		0.662	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521		4	85	0	0	0	1	0	4	85				
COX6A1	1337	broad.mit.edu	37	12	120876314	120876314	+	Missense_Mutation	SNP	T	T	G			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr12:120876314T>G	ENST00000229379.2	+	2	273	c.236T>G	c.(235-237)aTc>aGc	p.I79S	AL021546.6_ENST00000551806.1_Missense_Mutation_p.H55Q	NM_004373.3	NP_004364.2	P12074	CX6A1_HUMAN	cytochrome c oxidase subunit VIa polypeptide 1	79					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CATCTCCGCATCAGGACCAAG	0.557																																						ENST00000229379.2																			0											c.(235-237)aTc>aGc		cytochrome c oxidase subunit VIa polypeptide 1							121.0	105.0	110.0					12																	120876314		2203	4300	6503	SO:0001583	missense	1337				respiratory electron transport chain	mitochondrial respiratory chain complex IV	cytochrome-c oxidase activity	g.chr12:120876314T>G	X15341	CCDS9197.1	12q24	2011-07-04			ENSG00000111775	ENSG00000111775	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2277	protein-coding gene	gene with protein product		602072		COX6A		9284905	Standard	NM_004373		Approved		uc001tyf.2	P12074	OTTHUMG00000047791	ENST00000229379.2:c.236T>G	12.37:g.120876314T>G	ENSP00000229379:p.Ile79Ser					AL021546.6_ENST00000551806.1_Missense_Mutation_p.H55Q	p.I79S	NM_004373.3	NP_004364.2	P12074	CX6A1_HUMAN			2	273	+	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)		79					B2R500|O43714|Q32Q37	Missense_Mutation	SNP	ENST00000229379.2	37	c.236T>G	CCDS9197.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.2|27.2	4.807742|4.807742	0.90623|0.90623	.|.	.|.	ENSG00000111780|ENSG00000111775	ENST00000551806|ENST00000229379	.|.	.|.	.|.	5.13|5.13	5.13|5.13	0.70059|0.70059	.|Cytochrome c oxidase, subunit VIa, conserved site (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.79522|0.79522	0.4460|0.4460	M|M	0.83603|0.83603	2.65|2.65	0.80722|0.80722	D|D	1|1	.|D	.|0.55385	.|0.971	.|D	.|0.64877	.|0.93	T|T	0.83227|0.83227	-0.0065|-0.0065	5|9	.|0.87932	.|D	.|0	-22.4471|-22.4471	15.2512|15.2512	0.73549|0.73549	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|79	.|P12074	.|CX6A1_HUMAN	Q|S	55|79	.|.	.|ENSP00000229379:I79S	H|I	+|+	3|2	2|0	GATC|COX6A1	119360697|119360697	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	7.119000|7.119000	0.77145|0.77145	2.057000|2.057000	0.61298|0.61298	0.533000|0.533000	0.62120|0.62120	CAT|ATC		0.557	COX6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108984.3	NM_004373		10	582	0	0	0	1	0	10	582				
TBC1D25	4943	broad.mit.edu	37	X	48418156	48418156	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:48418156C>T	ENST00000376771.4	+	6	1201	c.860C>T	c.(859-861)aCg>aTg	p.T287M	TBC1D25_ENST00000537536.1_Missense_Mutation_p.T33M|snoU13_ENST00000459609.1_RNA	NM_002536.2	NP_002527.1	Q3MII6	TBC25_HUMAN	TBC1 domain family, member 25	287	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				autophagy (GO:0006914)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of autophagic vacuole maturation (GO:1901096)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4						ATCCGCAGCACGGTCCTCAAG	0.627																																						ENST00000376771.4																			0				large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4						c.(859-861)aCg>aTg		TBC1 domain family, member 25							51.0	44.0	46.0					X																	48418156		2202	4300	6502	SO:0001583	missense	4943					intracellular	Rab GTPase activator activity	g.chrX:48418156C>T	L08240	CCDS35242.1	Xp11.23	2014-01-28	2007-01-12	2007-01-12	ENSG00000068354	ENSG00000068354			8092	protein-coding gene	gene with protein product		311240	"""ornithine aminotransferase-like 1"""	OATL1		21383079	Standard	NM_002536		Approved		uc004dka.1	Q3MII6	OTTHUMG00000024123	ENST00000376771.4:c.860C>T	X.37:g.48418156C>T	ENSP00000365962:p.Thr287Met					TBC1D25_ENST00000427713.1_3'UTR|TBC1D25_ENST00000537536.1_Missense_Mutation_p.T33M|TBC1D25_ENST00000481090.1_3'UTR	p.T287M	NM_002536.2	NP_002527.1	Q3MII6	TBC25_HUMAN			6	1201	+			287			Rab-GAP TBC.		Q08AN9|Q3MII4|Q8TAR9	Missense_Mutation	SNP	ENST00000376771.4	37	c.860C>T	CCDS35242.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.272312	0.23221	.	.	ENSG00000068354	ENST00000376771;ENST00000537536	T;T	0.12361	2.69;2.69	5.89	4.95	0.65309	Rab-GAP/TBC domain (4);	0.053790	0.64402	D	0.000001	T	0.03178	0.0093	N	0.00765	-1.205	0.34569	D	0.713181	B;B;B	0.25441	0.126;0.023;0.013	B;B;B	0.14023	0.01;0.01;0.01	T	0.28996	-1.0026	10	0.02654	T	1	-2.3984	9.7287	0.40348	0.3521:0.6479:0.0:0.0	.	291;229;287	B4DF03;B4DGU3;Q3MII6	.;.;TBC25_HUMAN	M	287;33	ENSP00000365962:T287M;ENSP00000444091:T33M	ENSP00000365962:T287M	T	+	2	0	TBC1D25	48303100	0.998000	0.40836	0.967000	0.41034	0.807000	0.45602	3.928000	0.56506	2.499000	0.84300	0.529000	0.55759	ACG		0.627	TBC1D25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060764.2	NM_002536		7	191	0	0	0	1	0	7	191				
TLR9	54106	broad.mit.edu	37	3	52255986	52255986	+	Silent	SNP	G	G	A	rs562283382		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:52255986G>A	ENST00000360658.2	-	2	2979	c.2346C>T	c.(2344-2346)ccC>ccT	p.P782P	TLR9_ENST00000494383.1_Missense_Mutation_p.R936W|TLR9_ENST00000597542.1_Silent_p.P806P	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	782					defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	TGGGCAGACCGGGCACGGCAG	0.647													A|||	1	0.000199681	0.0	0.0	5008	,	,		17726	0.0		0.0	False		,,,				2504	0.001					ENST00000494383.1																			0				endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30						c.(2806-2808)Cgg>Tgg		toll-like receptor 9	Chloroquine(DB00608)						17.0	20.0	19.0					3																	52255986		2200	4291	6491	SO:0001819	synonymous_variant	54106				defense response to bacterium|fibroblast growth factor receptor signaling pathway|I-kappaB phosphorylation|inflammatory response|innate immune response|insulin receptor signaling pathway|maintenance of gastrointestinal epithelium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-beta production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|response to molecule of bacterial origin	apical plasma membrane|basolateral plasma membrane|early phagosome|endoplasmic reticulum membrane|endosome membrane|extracellular region|integral to membrane|lysosome	interleukin-1 receptor binding|siRNA binding|transmembrane receptor activity	g.chr3:52255986G>A	AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"""CD molecules"""	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.2346C>T	3.37:g.52255986G>A						TLR9_ENST00000360658.2_Silent_p.P782P|TLR9_ENST00000597542.1_Silent_p.P806P	p.R936W			Q9NR96	TLR9_HUMAN		BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	5	2805	-			0			TIR.		B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	37	c.2806C>T	CCDS2848.1	.	.	.	.	.	.	.	.	.	.	A	4.348	0.064092	0.08388	.	.	ENSG00000173366	ENST00000494383	.	.	.	5.14	-10.3	0.00346	.	.	.	.	.	T	0.33440	0.0863	.	.	.	0.54753	D	0.999986	.	.	.	.	.	.	T	0.40403	-0.9565	4	.	.	.	.	2.3241	0.04218	0.4323:0.1532:0.2706:0.1439	.	.	.	.	W	936	.	.	R	-	1	2	RP11-330H6.5	52231026	0.000000	0.05858	0.004000	0.12327	0.786000	0.44442	-5.459000	0.00120	-2.475000	0.00527	-0.521000	0.04368	CGG		0.647	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1			8	187	0	0	0	1	0	8	187				
TCN1	6947	broad.mit.edu	37	11	59629067	59629067	+	Silent	SNP	G	G	A	rs185999138	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:59629067G>A	ENST00000257264.3	-	4	593	c.489C>T	c.(487-489)acC>acT	p.T163T	TCN1_ENST00000532419.1_5'UTR	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	163	Globular N-terminal alpha domain.				cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAACTTCGGCGGTTGAGTAGT	0.448													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18199	0.001		0.0	False		,,,				2504	0.0					ENST00000257264.3																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29						c.(487-489)acC>acT		transcobalamin I (vitamin B12 binding protein, R binder family)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)						120.0	119.0	119.0					11																	59629067		2201	4295	6496	SO:0001819	synonymous_variant	6947				cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular region	cobalamin binding	g.chr11:59629067G>A	J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827			11652	protein-coding gene	gene with protein product	"""haptocorin"", ""haptocorrin"""	189905					Standard	NM_001062		Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.489C>T	11.37:g.59629067G>A						TCN1_ENST00000532419.1_5'UTR	p.T163T	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN			4	593	-		all_epithelial(135;0.198)	163					A8KAC5|Q8WV77	Silent	SNP	ENST00000257264.3	37	c.489C>T	CCDS7978.1																																																																																				0.448	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062		12	576	0	0	0	1	0	12	576				
SLC6A7	6534	broad.mit.edu	37	5	149576606	149576606	+	Splice_Site	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr5:149576606C>T	ENST00000230671.2	+	4	722	c.351C>T	c.(349-351)ggC>ggT	p.G117G	SLC6A7_ENST00000524041.1_Splice_Site_p.G117G	NM_014228.3	NP_055043.2	Q99884	SC6A7_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 7	117					proline transport (GO:0015824)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)|stomach(1)	16		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	CCACACCAGGCGCCGGCGCAG	0.637																																						ENST00000230671.2																			0				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)|stomach(1)	16						c.e4-1		solute carrier family 6 (neurotransmitter transporter), member 7	L-Proline(DB00172)						62.0	59.0	60.0					5																	149576606		2203	4300	6503	SO:0001630	splice_region_variant	6534					integral to plasma membrane|membrane fraction	neurotransmitter:sodium symporter activity|proline:sodium symporter activity	g.chr5:149576606C>T	S80071	CCDS4305.1	5q32	2013-07-19	2013-07-19		ENSG00000011083	ENSG00000011083		"""Solute carriers"""	11054	protein-coding gene	gene with protein product	"""brain-specific L-proline transporter"", ""sodium-dependent proline transporter"""	606205	"""solute carrier family 6 (neurotransmitter transporter, L-proline), member 7"""			7651355	Standard	NM_014228		Approved	PROT	uc003lrr.3	Q99884	OTTHUMG00000130046	ENST00000230671.2:c.350-1C>T	5.37:g.149576606C>T						SLC6A7_ENST00000524041.1_Splice_Site_p.G117_splice	p.G117_splice	NM_014228.3	NP_055043.2	Q99884	SC6A7_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		4	722	+		all_hematologic(541;0.224)	117					Q0VG81|Q52LU6	Splice_Site	SNP	ENST00000230671.2	37	c.349_splice	CCDS4305.1																																																																																				0.637	SLC6A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252325.1	NM_014228	Silent	5	133	0	0	0	1	0	5	133				
FRG1B	284802	broad.mit.edu	37	20	29625885	29625885	+	Missense_Mutation	SNP	A	A	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr20:29625885A>T	ENST00000278882.3	+	5	509	c.129A>T	c.(127-129)aaA>aaT	p.K43N	FRG1B_ENST00000439954.2_Missense_Mutation_p.K48N|FRG1B_ENST00000358464.4_Missense_Mutation_p.K43N			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	43								p.K43N(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TCGCCCTGAAATCTGGCTATG	0.353																																						ENST00000278882.3																			2	Substitution - Missense(2)	p.K43N(2)	prostate(2)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(127-129)aaA>aaT																																						SO:0001583	missense	0							g.chr20:29625885A>T			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.129A>T	20.37:g.29625885A>T	ENSP00000278882:p.Lys43Asn					FRG1B_ENST00000358464.4_Missense_Mutation_p.K43N|FRG1B_ENST00000439954.2_Missense_Mutation_p.K48N	p.K43N							5	509	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.129A>T		.	.	.	.	.	.	.	.	.	.	a	10.23	1.292024	0.23564	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.62364	0.03	1.68	1.68	0.24146	.	0.000000	0.85682	D	0.000000	T	0.74145	0.3678	.	.	.	0.48762	D	0.999701	D	0.71674	0.998	D	0.79784	0.993	T	0.74598	-0.3612	9	0.87932	D	0	.	7.3757	0.26827	1.0:0.0:0.0:0.0	.	48	F5H5R5	.	N	43;48;43	ENSP00000408863:K48N	ENSP00000278882:K43N	K	+	3	2	FRG1B	28239546	1.000000	0.71417	1.000000	0.80357	0.064000	0.16182	0.595000	0.24029	1.028000	0.39785	0.155000	0.16302	AAA		0.353	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		9	523	0	0	0	1	0	9	523				
POM121L9P	29774	broad.mit.edu	37	22	24659813	24659813	+	RNA	SNP	C	C	T	rs368832816		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr22:24659813C>T	ENST00000414583.2	+	0	3338					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		ATCTGCGCACCCGGAGGTGGG	0.607																																						ENST00000414583.2																			0																																																			0							g.chr22:24659813C>T	AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659813C>T								NR_003714.1						0	3338	+									RNA	SNP	ENST00000414583.2	37																																																																																						0.607	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1	NM_014549		5	27	0	0	0	1	0	5	27				
DGKH	160851	broad.mit.edu	37	13	42774011	42774011	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr13:42774011C>T	ENST00000337343.4	+	20	2480	c.2459C>T	c.(2458-2460)tCg>tTg	p.S820L	DGKH_ENST00000379274.2_Missense_Mutation_p.S684L|DGKH_ENST00000540693.1_Missense_Mutation_p.S820L|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000261491.5_Missense_Mutation_p.S820L|DGKH_ENST00000538674.1_Missense_Mutation_p.S575L|DGKH_ENST00000536612.1_Missense_Mutation_p.S684L	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	820					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TTACAGAGATCGTACAAGAAT	0.333																																						ENST00000379274.2																			0				breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						c.(2050-2052)tCg>tTg		diacylglycerol kinase, eta							54.0	59.0	57.0					13																	42774011		2203	4300	6503	SO:0001583	missense	160851				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding	g.chr13:42774011C>T	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.2459C>T	13.37:g.42774011C>T	ENSP00000337572:p.Ser820Leu					DGKH_ENST00000337343.4_Missense_Mutation_p.S820L|DGKH_ENST00000261491.4_Missense_Mutation_p.S820L|DGKH_ENST00000536612.1_Missense_Mutation_p.S684L|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000540693.1_Missense_Mutation_p.S820L|DGKH_ENST00000538674.1_Missense_Mutation_p.S575L	p.S684L			Q86XP1	DGKH_HUMAN		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)	20	2480	+		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)	820					A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	c.2051C>T	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.184618	0.78677	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612;ENST00000538674	T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93	5.69	5.69	0.88448	Diacylglycerol kinase, accessory domain (2);	0.059562	0.64402	D	0.000004	T	0.49304	0.1549	M	0.75615	2.305	0.58432	D	0.999998	P;P;P;P	0.46952	0.874;0.644;0.887;0.824	B;B;B;B	0.40375	0.3;0.22;0.22;0.327	T	0.58869	-0.7560	10	0.87932	D	0	.	19.8013	0.96509	0.0:1.0:0.0:0.0	.	575;684;820;820	F5GYP2;Q86XP1-3;Q86XP1-2;Q86XP1	.;.;.;DGKH_HUMAN	L	820;820;820;684;684;575	ENSP00000440823:S820L;ENSP00000337572:S820L;ENSP00000261491:S820L;ENSP00000368576:S684L;ENSP00000445114:S684L;ENSP00000441308:S575L	ENSP00000261491:S820L	S	+	2	0	DGKH	41672011	1.000000	0.71417	0.963000	0.40424	0.825000	0.46686	7.818000	0.86416	2.670000	0.90874	0.591000	0.81541	TCG		0.333	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		6	161	0	0	0	1	0	6	161				
SLC7A3	84889	broad.mit.edu	37	X	70146745	70146745	+	Missense_Mutation	SNP	T	T	C			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:70146745T>C	ENST00000374299.3	-	9	1577	c.1433A>G	c.(1432-1434)tAt>tGt	p.Y478C	SLC7A3_ENST00000298085.4_Missense_Mutation_p.Y478C			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	478					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GGAACAAACATAGACAATTTG	0.488																																						ENST00000374299.3																			0				breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31						c.(1432-1434)tAt>tGt		solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)						90.0	79.0	83.0					X																	70146745		2203	4300	6503	SO:0001583	missense	84889				cellular nitrogen compound metabolic process	integral to membrane|plasma membrane		g.chrX:70146745T>C	AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"""Solute carriers"""	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.1433A>G	X.37:g.70146745T>C	ENSP00000363417:p.Tyr478Cys					SLC7A3_ENST00000298085.4_Missense_Mutation_p.Y478C	p.Y478C			Q8WY07	CTR3_HUMAN			9	1577	-	Renal(35;0.156)		478					D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Missense_Mutation	SNP	ENST00000374299.3	37	c.1433A>G	CCDS14404.1	.	.	.	.	.	.	.	.	.	.	T	13.07	2.126783	0.37533	.	.	ENSG00000165349	ENST00000374299;ENST00000298085	D;D	0.88431	-2.38;-2.38	5.31	5.31	0.75309	.	0.111999	0.64402	D	0.000006	D	0.89626	0.6769	M	0.86028	2.79	0.52099	D	0.999945	B	0.26081	0.141	B	0.25759	0.063	D	0.88089	0.2812	10	0.51188	T	0.08	.	13.061	0.59008	0.0:0.0:0.0:1.0	.	478	Q8WY07	CTR3_HUMAN	C	478	ENSP00000363417:Y478C;ENSP00000298085:Y478C	ENSP00000298085:Y478C	Y	-	2	0	SLC7A3	70063470	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.912000	0.69948	1.968000	0.57251	0.430000	0.28490	TAT		0.488	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803		7	208	0	0	0	1	0	7	208				
POTEC	388468	broad.mit.edu	37	18	14513764	14513764	+	Missense_Mutation	SNP	C	C	T	rs201788045		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr18:14513764C>T	ENST00000358970.5	-	10	1429	c.1430G>A	c.(1429-1431)cGg>cAg	p.R477Q		NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	477								p.R477Q(12)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						AAGTTGTTTCCGGGTATCATT	0.358																																						ENST00000358970.5																			12	Substitution - Missense(12)	p.R477Q(12)	endometrium(4)|kidney(3)|urinary_tract(2)|prostate(2)|soft_tissue(1)	NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						c.(1429-1431)cGg>cAg		POTE ankyrin domain family, member C							13.0	9.0	10.0					18																	14513764		683	1543	2226	SO:0001583	missense	388468							g.chr18:14513764C>T	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.1430G>A	18.37:g.14513764C>T	ENSP00000351856:p.Arg477Gln						p.R477Q	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN			10	1429	-			477						Missense_Mutation	SNP	ENST00000358970.5	37	c.1430G>A	CCDS45835.1	492	0.22527472527472528	61	0.12398373983739837	82	0.2265193370165746	187	0.3269230769230769	162	0.21372031662269128	c	0.001	-3.539655	0.00009	.	.	ENSG00000183206	ENST00000358970	T	0.20881	2.04	1.34	0.0657	0.14358	.	.	.	.	.	T	0.00012	0.0000	N	0.00116	-2.08	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42430	-0.9452	9	0.06757	T	0.87	.	3.4153	0.07373	0.0:0.2473:0.0:0.7527	.	477	B2RU33	POTEC_HUMAN	Q	477	ENSP00000351856:R477Q	ENSP00000351856:R477Q	R	-	2	0	POTEC	14503764	0.885000	0.30320	0.063000	0.19743	0.005000	0.04900	1.581000	0.36558	0.005000	0.14708	-1.615000	0.00797	CGG		0.358	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		10	236	0	0	0	1	0	10	236				
ZNF845	91664	broad.mit.edu	37	19	53856730	53856730	+	Silent	SNP	G	G	A	rs201351032	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:53856730G>A	ENST00000595091.1	+	5	3021	c.2802G>A	c.(2800-2802)aaG>aaA	p.K934K	ZNF845_ENST00000458035.1_Silent_p.K934K			Q96IR2	ZN845_HUMAN	zinc finger protein 845	934					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K934K(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						TAATTCATAAGACAATTCATA	0.368													.|||	271	0.0541134	0.0507	0.0576	5008	,	,		22260	0.0456		0.0924	False		,,,				2504	0.0256					ENST00000458035.1																			3	Substitution - coding silent(3)	p.K934K(3)	kidney(3)	endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						c.(2800-2802)aaG>aaA		zinc finger protein 845																																				SO:0001819	synonymous_variant	91664				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:53856730G>A	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2802G>A	19.37:g.53856730G>A						ZNF845_ENST00000595091.1_Silent_p.K934K	p.K934K	NM_138374.1	NP_612383.1	Q96IR2	ZN845_HUMAN			4	2919	+			934						Silent	SNP	ENST00000595091.1	37	c.2802G>A	CCDS46170.1																																																																																				0.368	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		6	166	0	0	0	1	0	6	166				
NCOA3	8202	broad.mit.edu	37	20	46279860	46279860	+	Silent	SNP	G	G	A	rs151060280	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr20:46279860G>A	ENST00000371998.3	+	20	3977	c.3786G>A	c.(3784-3786)caG>caA	p.Q1262Q	NCOA3_ENST00000341724.6_Silent_p.Q1188Q|NCOA3_ENST00000372004.3_Silent_p.Q1258Q|NCOA3_ENST00000371997.3_Silent_p.Q1253Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1262	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q1262Q(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						agcagcagcagcagcaacagc	0.567																																						ENST00000372004.3																			1	Substitution - coding silent(1)	p.Q1262Q(1)	endometrium(1)	breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						c.(3772-3774)caG>caA		nuclear receptor coactivator 3		G	,,,	10,4396	11.4+/-27.6	1,8,2194	53.0	58.0	56.0		3783,3759,3774,3786	-0.1	0.1	20	dbSNP_134	56	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	1,20,6482	AA,AG,GG		0.1395,0.227,0.1692	,,,	1261/1424,1253/1416,1258/1421,1262/1425	46279860	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	8202				androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding	g.chr20:46279860G>A	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3786G>A	20.37:g.46279860G>A						NCOA3_ENST00000371998.3_Silent_p.Q1262Q|NCOA3_ENST00000371997.3_Silent_p.Q1253Q|NCOA3_ENST00000341724.6_Silent_p.Q1188Q	p.Q1258Q	NM_001174087.1|NM_001174088.1|NM_006534.3|NM_181659.2	NP_001167558.1|NP_001167559.1|NP_006525.2|NP_858045.1	Q9Y6Q9	NCOA3_HUMAN			20	3990	+			1262			Acetyltransferase.|Poly-Gln.		A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	c.3774G>A	CCDS13407.1																																																																																				0.567	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		10	335	0	0	0	1	0	10	335				
CACNB1	782	broad.mit.edu	37	17	37339981	37339981	+	Silent	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:37339981C>T	ENST00000394303.3	-	11	1242	c.1035G>A	c.(1033-1035)aaG>aaA	p.K345K	CACNB1_ENST00000582877.1_5'Flank|CACNB1_ENST00000394310.3_Silent_p.K345K|CACNB1_ENST00000344140.5_Silent_p.K390K	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit	345					axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.K390N(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GAGAGGTGATCTTGATGTAAA	0.567																																					Esophageal Squamous(5;100 366 38393 41452 45827)	ENST00000394303.3																			1	Substitution - Missense(1)	p.K390N(1)	ovary(1)	breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16						c.(1033-1035)aaG>aaA		calcium channel, voltage-dependent, beta 1 subunit	Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Verapamil(DB00661)						40.0	33.0	35.0					17																	37339981		2203	4299	6502	SO:0001819	synonymous_variant	782				axon guidance	voltage-gated calcium channel complex		g.chr17:37339981C>T		CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"""Calcium channel subunits"""	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.1035G>A	17.37:g.37339981C>T						CACNB1_ENST00000394310.3_Silent_p.K345K|CACNB1_ENST00000344140.5_Silent_p.K390K	p.K345K	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN			11	1242	-			345					A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Silent	SNP	ENST00000394303.3	37	c.1035G>A	CCDS42311.1																																																																																				0.567	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256945.3			4	65	0	0	0	1	0	4	65				
APEH	327	broad.mit.edu	37	3	49723545	49723545	+	IGR	SNP	G	G	A	rs4052562		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:49723545G>A	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000449682.2_Missense_Mutation_p.A366V	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GCAAAAGGCCGCGCGCATGCC	0.667																																						ENST00000449682.2																			0				NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2)	41						c.(1096-1098)gCg>gTg		macrophage stimulating 1 (hepatocyte growth factor-like)							13.0	16.0	15.0					3																	49723545		2196	4290	6486	SO:0001628	intergenic_variant	4485				proteolysis	extracellular region	serine-type endopeptidase activity	g.chr3:49723545G>A	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723545G>A						MST1_ENST00000383728.3_3'UTR	p.A366V	NM_020998.3	NP_066278.3	P26927	HGFL_HUMAN		BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	9	1458	-			352					Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	c.1097C>T	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	A	6.330	0.429012	0.11987	.	.	ENSG00000173531	ENST00000449682	T	0.61510	0.1	5.4	2.9	0.33743	.	0.872863	0.09498	N	0.793992	T	0.22322	0.0538	N	0.01048	-1.04	0.58432	D	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.34129	-0.9841	10	0.02654	T	1	.	6.4095	0.21682	0.7107:0.0:0.0698:0.2196	rs4052562	366	G3XAK1	.	V	366	ENSP00000414287:A366V	ENSP00000414287:A366V	A	-	2	0	MST1	49698549	1.000000	0.71417	0.233000	0.24025	0.897000	0.52465	4.372000	0.59530	0.016000	0.14998	-0.254000	0.11334	GCG		0.667	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			5	115	0	0	0	1	0	5	115				
TBC1D3P2	440452	broad.mit.edu	37	17	60342280	60342280	+	RNA	SNP	C	C	T	rs80012429	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:60342280C>T	ENST00000581291.1	-	0	1873									TBC1 domain family, member 3 pseudogene 2											breast(2)|kidney(1)|lung(2)	5						TTAATACATTCTCATAAGTTT	0.488													.|||	1114	0.222444	0.1596	0.2277	5008	,	,		1867	0.244		0.2455	False		,,,				2504	0.2577					ENST00000581291.1																			0				breast(2)|kidney(1)|lung(2)	5																																														0							g.chr17:60342280C>T			17q23.2	2009-05-14				ENSG00000188755			27783	pseudogene	pseudogene							Standard	NR_027486		Approved		uc002izq.2				17.37:g.60342280C>T														0	1873	-									RNA	SNP	ENST00000581291.1	37																																																																																						0.488	TBC1D3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445021.1	NR_027486		13	383	0	0	0	1	0	13	383				
LOC220729	220729	broad.mit.edu	37	3	197348646	197348646	+	RNA	SNP	T	T	C	rs377377382		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:197348646T>C	ENST00000418868.1	-	0	613					NR_003266.2																						TGGGCCTGCCTGCCCTTTCCA	0.532																																						ENST00000418868.1																			0																																																			0							g.chr3:197348646T>C																													3.37:g.197348646T>C								NR_003266.2						0	613	-									RNA	SNP	ENST00000418868.1	37																																																																																						0.532	AC024560.3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340283.1			16	495	0	0	0	1	0	16	495				
TRPM6	140803	broad.mit.edu	37	9	77386696	77386696	+	Silent	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr9:77386696G>A	ENST00000360774.1	-	25	3696	c.3459C>T	c.(3457-3459)tgC>tgT	p.C1153C	TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000361255.3_Silent_p.C1148C|TRPM6_ENST00000449912.2_Silent_p.C1148C|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Silent_p.C1153C|TRPM6_ENST00000451710.3_Silent_p.C1153C	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1153					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						ATTTTTCCACGCACTGCTCCT	0.358																																						ENST00000451710.3																			0				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						c.(3457-3459)tgC>tgT		transient receptor potential cation channel, subfamily M, member 6							116.0	105.0	109.0					9																	77386696		2203	4300	6503	SO:0001819	synonymous_variant	140803				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr9:77386696G>A	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.3459C>T	9.37:g.77386696G>A						TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Silent_p.C1148C|TRPM6_ENST00000376864.4_Silent_p.C1153C|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000360774.1_Silent_p.C1153C|TRPM6_ENST00000361255.3_Silent_p.C1148C	p.C1153C			Q9BX84	TRPM6_HUMAN			25	3696	-			1153					Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	c.3459C>T	CCDS6647.1																																																																																				0.358	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		10	213	0	0	0	1	0	10	213				
CHD5	26038	broad.mit.edu	37	1	6202252	6202252	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:6202252C>T	ENST00000262450.3	-	15	2471	c.2372G>A	c.(2371-2373)cGg>cAg	p.R791Q	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		CTCGTTCTCCCGAATCACCGA	0.557																																						ENST00000262450.3																			0				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16						c.(2371-2373)cGg>cAg		chromodomain helicase DNA binding protein 5							153.0	144.0	147.0					1																	6202252		2203	4300	6503	SO:0001583	missense	26038				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding	g.chr1:6202252C>T	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2372G>A	1.37:g.6202252C>T	ENSP00000262450:p.Arg791Gln					CHD5_ENST00000378021.1_5'UTR	p.R791Q	NM_015557.2	NP_056372.1	Q8TDI0	CHD5_HUMAN		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)	15	2471	-	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)	791			Helicase ATP-binding.		A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	c.2372G>A	CCDS57.1	.	.	.	.	.	.	.	.	.	.	C	32	5.152028	0.94645	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000536802;ENST00000538279	D	0.93712	-3.27	4.07	4.07	0.47477	DEAD-like helicase (2);SNF2-related (1);	0.076633	0.49305	D	0.000151	D	0.95475	0.8530	L	0.56769	1.78	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	D	0.94752	0.7928	10	0.35671	T	0.21	-22.1812	16.6218	0.84932	0.0:1.0:0.0:0.0	.	791	Q8TDI0	CHD5_HUMAN	Q	791;307;199;199	ENSP00000262450:R791Q	ENSP00000262450:R791Q	R	-	2	0	CHD5	6124839	1.000000	0.71417	0.996000	0.52242	0.952000	0.60782	7.693000	0.84214	1.977000	0.57605	0.561000	0.74099	CGG		0.557	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		24	823	0	0	0	1	0	24	823				
PPAPDC3	84814	broad.mit.edu	37	9	134165668	134165668	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr9:134165668G>A	ENST00000372264.3	+	1	588	c.284G>A	c.(283-285)cGg>cAg	p.R95Q	PPAPDC3_ENST00000372261.1_Missense_Mutation_p.R95Q	NM_032728.3	NP_116117.3	Q8NBV4	PPAC3_HUMAN	phosphatidic acid phosphatase type 2 domain containing 3	95					negative regulation of myotube differentiation (GO:0010832)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	hydrolase activity (GO:0016787)			breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	16	all_hematologic(7;0.0119)			OV - Ovarian serous cystadenocarcinoma(145;1.22e-05)|Epithelial(140;0.000173)		ATGTCCAAGCGGCTGGGGGTG	0.652																																						ENST00000372264.3																			0				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	16						c.(283-285)cGg>cAg		phosphatidic acid phosphatase type 2 domain containing 3							73.0	74.0	73.0					9																	134165668		2203	4300	6503	SO:0001583	missense	84814					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	hydrolase activity	g.chr9:134165668G>A	AK027568	CCDS6942.1	9q34.2-q34.3	2008-02-26	2005-07-15	2005-07-15	ENSG00000160539	ENSG00000160539			28174	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 67"""	C9orf67		12958361	Standard	NM_032728		Approved	MGC12921, FLJ14662, NET39	uc004cal.2	Q8NBV4	OTTHUMG00000020822	ENST00000372264.3:c.284G>A	9.37:g.134165668G>A	ENSP00000361338:p.Arg95Gln					PPAPDC3_ENST00000372261.1_Missense_Mutation_p.R95Q	p.R95Q	NM_032728.3	NP_116117.3	Q8NBV4	PPAC3_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;1.22e-05)|Epithelial(140;0.000173)	1	588	+	all_hematologic(7;0.0119)		95					Q5T6P0|Q96SS7|Q9BRC3	Missense_Mutation	SNP	ENST00000372264.3	37	c.284G>A	CCDS6942.1	.	.	.	.	.	.	.	.	.	.	G	37	6.011501	0.97200	.	.	ENSG00000160539	ENST00000372264;ENST00000372261	T;T	0.50548	1.8;0.74	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.68961	0.3058	M	0.71581	2.175	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	T	0.70174	-0.4944	10	0.62326	D	0.03	-40.1758	18.802	0.92022	0.0:0.0:1.0:0.0	.	95	Q8NBV4	PPAC3_HUMAN	Q	95	ENSP00000361338:R95Q;ENSP00000361335:R95Q	ENSP00000361335:R95Q	R	+	2	0	PPAPDC3	133155489	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.608000	0.82898	2.682000	0.91365	0.561000	0.74099	CGG		0.652	PPAPDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054724.1	NM_032728		11	533	0	0	0	1	0	11	533				
DCAF12L2	340578	broad.mit.edu	37	X	125299285	125299285	+	Missense_Mutation	SNP	G	G	C	rs199739505		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:125299285G>C	ENST00000360028.2	-	1	649	c.623C>G	c.(622-624)gCt>gGt	p.A208G	DCAF12L2_ENST00000538699.1_Missense_Mutation_p.A208G			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	208										NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						GCCGCTCACAGCTACGGTGTC	0.647																																						ENST00000538699.1																			0				NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						c.(622-624)gCt>gGt		DDB1 and CUL4 associated factor 12-like 2							45.0	48.0	47.0					X																	125299285		2203	4299	6502	SO:0001583	missense	340578							g.chrX:125299285G>C	AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"""WD repeat domain containing"""	32950	protein-coding gene	gene with protein product			"""WD repeat domain 40C"""	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.623C>G	X.37:g.125299285G>C	ENSP00000353128:p.Ala208Gly					DCAF12L2_ENST00000360028.2_Missense_Mutation_p.A208G	p.A208G	NM_001013628.2	NP_001013650.1	Q5VW00	DC122_HUMAN			2	703	-			208					B2RN42	Missense_Mutation	SNP	ENST00000360028.2	37	c.623C>G	CCDS43991.1	.	.	.	.	.	.	.	.	.	.	G	11.11	1.543243	0.27563	.	.	ENSG00000198354	ENST00000538699;ENST00000360028	T;T	0.60171	0.21;0.21	3.87	0.855	0.19013	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.817806	0.10000	N	0.728605	T	0.56702	0.2003	L	0.51422	1.61	0.30815	N	0.738405	P	0.44659	0.84	P	0.48552	0.581	T	0.57717	-0.7763	10	0.87932	D	0	.	6.7549	0.23507	0.4053:0.0:0.5947:0.0	.	208	Q5VW00	DC122_HUMAN	G	208	ENSP00000441489:A208G;ENSP00000353128:A208G	ENSP00000353128:A208G	A	-	2	0	DCAF12L2	125126966	0.998000	0.40836	0.002000	0.10522	0.010000	0.07245	2.707000	0.47143	0.042000	0.15717	0.544000	0.68410	GCT		0.647	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628		10	360	0	0	0	1	0	10	360				
APEH	327	broad.mit.edu	37	3	49723542	49723542	+	IGR	SNP	G	G	C	rs2087732		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:49723542G>C	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000449682.2_Missense_Mutation_p.A367G	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GTAGCAAAAGGCCGCGCGCAT	0.672																																						ENST00000449682.2																			0				NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2)	41						c.(1099-1101)gCc>gGc		macrophage stimulating 1 (hepatocyte growth factor-like)							13.0	16.0	15.0					3																	49723542		2194	4290	6484	SO:0001628	intergenic_variant	4485				proteolysis	extracellular region	serine-type endopeptidase activity	g.chr3:49723542G>C	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723542G>C						MST1_ENST00000383728.3_3'UTR	p.A367G	NM_020998.3	NP_066278.3	P26927	HGFL_HUMAN		BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	9	1461	-			353					Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	c.1100C>G	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.511278	0.44660	.	.	ENSG00000173531	ENST00000449682	T	0.61980	0.06	5.4	5.4	0.78164	.	0.000000	0.42172	D	0.000758	T	0.49508	0.1561	N	0.14661	0.345	0.80722	D	1	B	0.24368	0.102	B	0.33254	0.16	T	0.42699	-0.9436	10	0.12103	T	0.63	.	18.7813	0.91933	0.0:0.0:1.0:0.0	rs2087732;rs4052587	367	G3XAK1	.	G	367	ENSP00000414287:A367G	ENSP00000414287:A367G	A	-	2	0	MST1	49698546	1.000000	0.71417	0.998000	0.56505	0.965000	0.64279	6.615000	0.74201	2.526000	0.85167	0.655000	0.94253	GCC		0.672	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			5	114	0	0	0	1	0	5	114				
DRD5	1816	broad.mit.edu	37	4	9784785	9784785	+	Missense_Mutation	SNP	T	T	G			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr4:9784785T>G	ENST00000304374.2	+	1	1528	c.1132T>G	c.(1132-1134)Ttc>Gtc	p.F378V		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	378					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)	p.F378V(4)		NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	GTGCAGCCACTTCTGCTCCCG	0.562																																						ENST00000304374.2																			4	Substitution - Missense(4)	p.F378V(4)	skin(2)|NS(1)|endometrium(1)	NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57						c.(1132-1134)Ttc>Gtc		dopamine receptor D5	Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)						63.0	55.0	57.0					4																	9784785		2203	4300	6503	SO:0001583	missense	0				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane		g.chr4:9784785T>G	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.1132T>G	4.37:g.9784785T>G	ENSP00000306129:p.Phe378Val						p.F378V	NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN			1	1528	+			378					B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	c.1132T>G	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	t	1.422	-0.572511	0.03882	.	.	ENSG00000169676	ENST00000304374	T	0.36878	1.23	4.73	-0.492	0.12041	.	1.972870	0.02341	N	0.074845	T	0.21103	0.0508	N	0.17474	0.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10109	-1.0644	10	0.16420	T	0.52	.	4.5978	0.12338	0.0:0.3044:0.1738:0.5218	.	378	P21918	DRD5_HUMAN	V	378	ENSP00000306129:F378V	ENSP00000306129:F378V	F	+	1	0	DRD5	9393883	0.067000	0.21026	0.022000	0.16811	0.197000	0.23852	0.558000	0.23469	-0.022000	0.13986	-2.216000	0.00297	TTC		0.562	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			8	314	0	0	0	1	0	8	314				
HMCN1	83872	broad.mit.edu	37	1	186057376	186057376	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:186057376C>T	ENST00000271588.4	+	62	9774	c.9545C>T	c.(9544-9546)aCg>aTg	p.T3182M	HMCN1_ENST00000367492.2_Missense_Mutation_p.T3182M	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3182	Ig-like C2-type 30.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CCACCTCCCACGATAGCATGG	0.443																																						ENST00000271588.4																			0				NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						c.(9544-9546)aCg>aTg		hemicentin 1							95.0	83.0	87.0					1																	186057376		2203	4300	6503	SO:0001583	missense	83872				response to stimulus|visual perception	basement membrane	calcium ion binding	g.chr1:186057376C>T	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.9545C>T	1.37:g.186057376C>T	ENSP00000271588:p.Thr3182Met					HMCN1_ENST00000367492.2_Missense_Mutation_p.T3182M	p.T3182M	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN			62	9774	+			3182			Ig-like C2-type 30.		A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	c.9545C>T	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.535093	0.27475	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.68479	-0.33;-0.33	5.63	-1.85	0.07784	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.735216	0.13487	N	0.384223	T	0.62925	0.2468	M	0.78456	2.415	0.09310	N	1	B	0.27791	0.189	B	0.24155	0.051	T	0.54234	-0.8324	10	0.48119	T	0.1	.	11.2133	0.48813	0.0:0.5779:0.0:0.4221	.	3182	Q96RW7	HMCN1_HUMAN	M	3182	ENSP00000271588:T3182M;ENSP00000356462:T3182M	ENSP00000271588:T3182M	T	+	2	0	HMCN1	184323999	0.002000	0.14202	0.000000	0.03702	0.741000	0.42261	0.371000	0.20450	-0.692000	0.05128	-0.471000	0.05019	ACG		0.443	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		7	228	0	0	0	1	0	7	228				
ZNF208	7757	broad.mit.edu	37	19	22171675	22171675	+	Missense_Mutation	SNP	A	A	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:22171675A>T	ENST00000397126.4	-	2	188	c.40T>A	c.(40-42)Tct>Act	p.S14T	ZNF208_ENST00000601773.1_Missense_Mutation_p.S14T|ZNF208_ENST00000597040.1_5'UTR|ZNF208_ENST00000599916.1_Missense_Mutation_p.S14T	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	14	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TCCTCCAGAGAGAATTCTATG	0.403																																						ENST00000397126.4																			0				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113						c.(40-42)Tct>Act		zinc finger protein 208							121.0	131.0	128.0					19																	22171675		2203	4300	6503	SO:0001583	missense	7757							g.chr19:22171675A>T	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.40T>A	19.37:g.22171675A>T	ENSP00000380315:p.Ser14Thr					ZNF208_ENST00000597040.1_5'UTR|ZNF208_ENST00000601773.1_Missense_Mutation_p.S14T|ZNF208_ENST00000599916.1_Missense_Mutation_p.S14T	p.S14T	NM_007153.3	NP_009084.2					2	188	-		all_lung(12;0.0961)|Lung NSC(12;0.103)							Missense_Mutation	SNP	ENST00000397126.4	37	c.40T>A	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	A	3.819	-0.038200	0.07497	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.01484	4.84	1.32	-0.168	0.13343	Krueppel-associated box (4);	.	.	.	.	T	0.02304	0.0071	.	.	.	0.09310	N	1	D;P	0.63046	0.992;0.876	P;P	0.60012	0.867;0.652	T	0.27640	-1.0068	8	0.07175	T	0.84	.	3.607	0.08046	0.3597:0.0:0.0:0.6403	.	14;14	O43345;F8WEA0	ZN208_HUMAN;.	T	14	ENSP00000380315:S14T	ENSP00000380315:S14T	S	-	1	0	ZNF208	21963515	0.002000	0.14202	0.009000	0.14445	0.641000	0.38312	-0.021000	0.12504	-0.610000	0.05716	0.234000	0.17832	TCT		0.403	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		16	748	0	0	0	1	0	16	748				
SERPINB11	89778	broad.mit.edu	37	18	61377522	61377522	+	RNA	SNP	C	C	T	rs375026731		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr18:61377522C>T	ENST00000382749.5	+	0	340				SERPINB11_ENST00000489748.1_RNA|SERPINB11_ENST00000536691.1_RNA|SERPINB11_ENST00000538847.1_RNA|SERPINB11_ENST00000544088.1_RNA			Q96P15	SPB11_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene)						negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|kidney(1)|lung(3)	6		Esophageal squamous(42;0.129)				TTCTTTTCTTCGCTGAGTCTG	0.428																																					Ovarian(27;496 784 5942 8975 23930)	ENST00000544088.1																			0				breast(1)|cervix(1)|kidney(1)|lung(3)	6								serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene)		C	LEU/SER	1,3831		0,1,1915	126.0	117.0	120.0		95	4.3	0.1	18		120	0,8290		0,0,4145	no	missense	SERPINB11	NM_080475.2	145	0,1,6060	TT,TC,CC		0.0,0.0261,0.0082	benign	32/393	61377522	1,12121	1916	4145	6061			89778				regulation of proteolysis	cytoplasm	serine-type endopeptidase inhibitor activity	g.chr18:61377522C>T			18q21.33	2014-02-18	2009-01-22		ENSG00000206072	ENSG00000206072		"""Serine (or cysteine) peptidase inhibitors"""	14221	protein-coding gene	gene with protein product		615682	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 11"", ""serpin peptidase inhibitor, clade B (ovalbumin), member 11"""			17562709, 24172014	Standard	XM_006722569		Approved	EPIPIN	uc002ljk.4	Q96P15	OTTHUMG00000060404		18.37:g.61377522C>T						SERPINB11_ENST00000489748.1_RNA|SERPINB11_ENST00000538847.1_RNA|SERPINB11_ENST00000536691.1_RNA|SERPINB11_ENST00000382749.5_RNA		NM_080475.2	NP_536723.2	Q96P15	SPB11_HUMAN			0	157	+		Esophageal squamous(42;0.129)						A8K9R0|Q5Q120|Q5Q121|Q5Q122|Q5Q123|Q6ISD3|Q96P13|Q96P14	RNA	SNP	ENST00000382749.5	37			.	.	.	.	.	.	.	.	.	.	C	9.959	1.222256	0.22457	2.61E-4	0.0	ENSG00000206072	ENST00000544088;ENST00000538847	D;D	0.82526	-1.62;-1.62	5.14	4.27	0.50696	Serpin domain (3);	0.266677	0.26734	N	0.022770	T	0.73329	0.3573	L	0.28649	0.875	0.80722	D	1	B;B	0.31611	0.098;0.331	B;B	0.28385	0.033;0.089	T	0.73920	-0.3830	10	0.87932	D	0	.	11.7438	0.51809	0.0:0.9128:0.0:0.0872	.	32;32	F5GY69;Q96P15	.;SPB11_HUMAN	L	32	ENSP00000441497:S32L;ENSP00000440795:S32L	ENSP00000421854:S32L	S	+	2	0	SERPINB11	59528502	0.717000	0.27966	0.110000	0.21437	0.034000	0.12701	3.569000	0.53827	1.284000	0.44531	0.655000	0.94253	TCG		0.428	SERPINB11-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000207392.3	NM_080475		6	170	0	0	0	1	0	6	170				
AJAP1	55966	broad.mit.edu	37	1	4772583	4772585	+	In_Frame_Del	DEL	CCA	CCA	-	rs141981296	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:4772583_4772585delCCA	ENST00000378191.4	+	2	1034_1036	c.653_655delCCA	c.(652-657)gccacc>gcc	p.T225del	AJAP1_ENST00000378190.3_In_Frame_Del_p.T225del	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	225	Thr-rich.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T225_A226insT(1)		endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		ACTGTGGccgccaccaccaccac	0.635																																						ENST00000378191.4																			1	Insertion - In frame(1)	p.T225_A226insT(1)	large_intestine(1)	endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24						c.(652-657)gcc>g		adherens junctions associated protein 1																																				SO:0001651	inframe_deletion	55966				cell adhesion	adherens junction|apical plasma membrane|basolateral plasma membrane|integral to membrane		g.chr1:4772583_4772585delCCA	AF175409	CCDS54.1	1p36.32	2008-02-05	2008-01-08		ENSG00000196581	ENSG00000196581			30801	protein-coding gene	gene with protein product	"""transmembrane protein SHREW1"""	610972				14595118	Standard	NM_001042478		Approved	SHREW1, SHREW-1, MOT8	uc001aln.3	Q9UKB5	OTTHUMG00000000645	ENST00000378191.4:c.653_655delCCA	1.37:g.4772592_4772594delCCA	ENSP00000367433:p.Thr225del					AJAP1_ENST00000378190.3_In_Frame_Del_p.AT218del	p.AT218del	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)	2	1034_1036	+	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)	218			Thr-rich.		Q9Y229	In_Frame_Del	DEL	ENST00000378191.4	37	c.653_655delCCA	CCDS54.1																																																																																				0.635	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836		8	159						8	159	---	---	---	---
ACTL8	81569	broad.mit.edu	37	1	18152849	18152850	+	Frame_Shift_Ins	INS	-	-	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:18152849_18152850insA	ENST00000375406.1	+	3	1152_1153	c.936_937insA	c.(937-939)aggfs	p.R313fs		NM_030812.2	NP_110439.2	Q9H568	ACTL8_HUMAN	actin-like 8	313					epithelial cell differentiation (GO:0030855)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	28		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00186)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;6.43e-06)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.00652)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)		AGCGCCTGTTCAGGGAGCTGAT	0.619											OREG0013157	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000375406.1																			0				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	28						c.(934-939)ttgggafs		actin-like 8																																				SO:0001589	frameshift_variant	81569					cytoplasm|cytoskeleton		g.chr1:18152849_18152850insA	AK057339	CCDS183.1	1p36.2-p35	2009-03-25			ENSG00000117148	ENSG00000117148			24018	protein-coding gene	gene with protein product	"""cancer/testis antigen 57"""						Standard	NM_030812		Approved	CT57	uc001bat.3	Q9H568	OTTHUMG00000002512	ENST00000375406.1:c.937dupA	1.37:g.18152850_18152850dupA	ENSP00000364555:p.Arg313fs		OREG0013157	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	723		p.LG312fs	NM_030812.2	NP_110439.2	Q9H568	ACTL8_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;6.43e-06)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.00652)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	3	1152_1153	+		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00186)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)	312					Q13104|Q96M75	Frame_Shift_Ins	INS	ENST00000375406.1	37	c.936_937insA	CCDS183.1																																																																																				0.619	ACTL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007143.1	NM_030812		12	510						12	510	---	---	---	---
TMCO2	127391	broad.mit.edu	37	1	40713708	40713709	+	Frame_Shift_Del	DEL	TC	TC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:40713708_40713709delTC	ENST00000372766.3	+	1	136_137	c.43_44delTC	c.(43-45)tctfs	p.S15fs	TMCO2_ENST00000468258.1_Intron	NM_001008740.3	NP_001008740.1	Q7Z6W1	TMCO2_HUMAN	transmembrane and coiled-coil domains 2	15						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(1)|ovary(1)	6	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			CCTCTTAGAGTCTCTCTCTCTC	0.406																																						ENST00000372766.3																			0				kidney(1)|large_intestine(3)|lung(1)|ovary(1)	6						c.(43-45)tfs		transmembrane and coiled-coil domains 2																																				SO:0001589	frameshift_variant	127391					integral to membrane		g.chr1:40713708_40713709delTC	AL050341	CCDS30684.1	1p34.2	2014-02-12			ENSG00000188800	ENSG00000188800			23312	protein-coding gene	gene with protein product							Standard	NM_001008740		Approved	dJ39G22.2	uc001cfe.2	Q7Z6W1	OTTHUMG00000005764	ENST00000372766.3:c.43_44delTC	1.37:g.40713718_40713719delTC	ENSP00000361852:p.Ser15fs					TMCO2_ENST00000468258.1_Intron	p.S15fs	NM_001008740.3	NP_001008740.1	Q7Z6W1	TMCO2_HUMAN	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)		1	136_137	+	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	15						Frame_Shift_Del	DEL	ENST00000372766.3	37	c.43_44delTC	CCDS30684.1																																																																																				0.406	TMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015769.1	NM_001008740		10	1067						10	1067	---	---	---	---
IPP	3652	broad.mit.edu	37	1	46184897	46184898	+	Frame_Shift_Del	DEL	AC	AC	-	rs144663569		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:46184897_46184898delAC	ENST00000396478.3	-	6	1265_1266	c.1163_1164delGT	c.(1162-1164)tgtfs	p.C388fs		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	388						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					TAGCCCCATAACACACACACAC	0.347																																						ENST00000396478.3																			0				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20						c.(1162-1164)tfs		intracisternal A particle-promoted polypeptide																																				SO:0001589	frameshift_variant	3652					actin cytoskeleton|cytoplasm	actin binding	g.chr1:46184897_46184898delAC	BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"""Kelch-like"", ""BTB/POZ domain containing"""	6108	protein-coding gene	gene with protein product	"""kelch-like family member 27"""	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.1163_1164delGT	1.37:g.46184907_46184908delAC	ENSP00000379739:p.Cys388fs						p.C388fs	NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN			6	1265_1266	-	Acute lymphoblastic leukemia(166;0.155)		388					A2A6V4|D3DQ11|Q8N5C3	Frame_Shift_Del	DEL	ENST00000396478.3	37	c.1163_1164delGT	CCDS30702.1																																																																																				0.347	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		14	371						14	371	---	---	---	---
CYP4Z2P	163720	broad.mit.edu	37	1	47310359	47310360	+	RNA	INS	-	-	T	rs372212671		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:47310359_47310360insT	ENST00000505841.1	-	0	1269					NR_002788.2		Q8N1L4	CP4Z2_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 2, pseudogene							integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)										CAAAAACAAAACCCTAGATATT	0.421																																						ENST00000505841.1																			0																																																			0							g.chr1:47310359_47310360insT	AY262057		1p33	2013-07-25	2013-05-03		ENSG00000154198	ENSG00000154198		"""Cytochrome P450s"""	24426	pseudogene	pseudogene						15059886	Standard	NR_002788		Approved	FLJ40054	uc031pmm.1	Q8N1L4	OTTHUMG00000008024		1.37:g.47310359_47310360insT								NR_002788.2						0	1269	-								Q66ZJ5	RNA	INS	ENST00000505841.1	37																																																																																						0.421	CYP4Z2P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000361094.1	NR_002788		7	44						7	44	---	---	---	---
LRRIQ3	127255	broad.mit.edu	37	1	74575212	74575213	+	Frame_Shift_Ins	INS	-	-	T	rs375424853		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:74575212_74575213insT	ENST00000395089.1	-	4	731_732	c.732_733insA	c.(730-735)aaacagfs	p.Q245fs	LRRIQ3_ENST00000354431.4_Frame_Shift_Ins_p.Q245fs|LRRIQ3_ENST00000370909.2_Frame_Shift_Ins_p.Q137fs|LRRIQ3_ENST00000468759.1_5'UTR			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	245				QQEKII -> TAGKNY (in Ref. 1; BAD18621). {ECO:0000305}.						NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						TTTTCCTGCTGTTTTTTTTTGT	0.327																																						ENST00000354431.4																			0				NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						c.(730-735)aaagcafs		leucine-rich repeats and IQ motif containing 3																																				SO:0001589	frameshift_variant	127255							g.chr1:74575212_74575213insT	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"""leucine rich repeat containing 44"""	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.733dupA	1.37:g.74575221_74575221dupT	ENSP00000378524:p.Gln245fs					LRRIQ3_ENST00000468759.1_5'UTR|LRRIQ3_ENST00000395089.1_Frame_Shift_Ins_p.A245fs|LRRIQ3_ENST00000370909.2_Frame_Shift_Ins_p.A137fs	p.A245fs	NM_001105659.1	NP_001099129.1	A6PVS8	LRIQ3_HUMAN			5	923_924	-			245	QQEKII -> TAGKNY (in Ref. 1; BAD18621).				A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Frame_Shift_Ins	INS	ENST00000395089.1	37	c.732_733insA	CCDS41350.1																																																																																				0.327	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		18	359						18	359	---	---	---	---
WDR63	126820	broad.mit.edu	37	1	85547084	85547084	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:85547084delA	ENST00000294664.6	+	4	451	c.271delA	c.(271-273)aaafs	p.K92fs	WDR63_ENST00000370596.1_Frame_Shift_Del_p.K92fs|WDR63_ENST00000326813.8_Frame_Shift_Del_p.K92fs	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	92										NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		CCACCCAGTCAAAAAAATTGT	0.383																																						ENST00000294664.6																			0				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36						c.(271-273)aafs		WD repeat domain 63							82.0	83.0	83.0					1																	85547084		2202	4300	6502	SO:0001589	frameshift_variant	126820							g.chr1:85547084delA		CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"""WD repeat domain containing"""	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.271delA	1.37:g.85547084delA	ENSP00000294664:p.Lys92fs					WDR63_ENST00000326813.8_Frame_Shift_Del_p.K92fs|WDR63_ENST00000370596.1_Frame_Shift_Del_p.K92fs	p.K92fs	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN		all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)	4	451	+			92					A8K988|Q96L72|Q96NU4	Frame_Shift_Del	DEL	ENST00000294664.6	37	c.271delA	CCDS702.1																																																																																				0.383	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172		9	534						9	534	---	---	---	---
BRDT	676	broad.mit.edu	37	1	92447228	92447230	+	In_Frame_Del	DEL	AGC	AGC	-	rs375773077		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:92447228_92447230delAGC	ENST00000362005.3	+	13	2336_2338	c.1918_1920delAGC	c.(1918-1920)agcdel	p.S648del	BRDT_ENST00000394530.3_In_Frame_Del_p.S602del|BRDT_ENST00000399546.2_In_Frame_Del_p.S648del|BRDT_ENST00000402388.1_In_Frame_Del_p.S648del|BRDT_ENST00000370389.2_In_Frame_Del_p.S575del	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	648	Ser-rich.				cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		ACTGAGTGAGagcagcagcagca	0.419																																						ENST00000370389.2																			0				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56						c.(1699-1701)del		bromodomain, testis-specific																																				SO:0001651	inframe_deletion	676				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity	g.chr1:92447228_92447230delAGC	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.1918_1920delAGC	1.37:g.92447237_92447239delAGC	ENSP00000354568:p.Ser648del					BRDT_ENST00000399546.2_In_Frame_Del_p.S648del|BRDT_ENST00000362005.3_In_Frame_Del_p.S648del|BRDT_ENST00000402388.1_In_Frame_Del_p.S648del|BRDT_ENST00000394530.3_In_Frame_Del_p.S602del	p.S575del	NM_001242810.1	NP_001229739.1	Q58F21	BRDT_HUMAN		all cancers(265;0.0228)|Epithelial(280;0.133)	12	2623_2625	+		all_lung(203;0.00531)|Lung NSC(277;0.0194)	648					A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	In_Frame_Del	DEL	ENST00000362005.3	37	c.1699_1701delAGC	CCDS735.1																																																																																				0.419	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189		10	465						10	465	---	---	---	---
SRGAP2-AS1	100873165	broad.mit.edu	37	1	121137698	121137699	+	lincRNA	INS	-	-	TT	rs57730437|rs371916849		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:121137698_121137699insTT	ENST00000417218.1	+	0	0				RP11-343N15.1_ENST00000437515.1_lincRNA																							CTACTTACATCTTTTTGTCTTT	0.441																																						ENST00000437515.1																			0																																																			0							g.chr1:121137698_121137699insTT																													1.37:g.121137701_121137702dupTT														0	329	-									RNA	INS	ENST00000417218.1	37																																																																																						0.441	AL592494.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000036739.1			18	115						18	115	---	---	---	---
LOC101927209	101927209	broad.mit.edu	37	1	142716575	142716578	+	lincRNA	DEL	AAAC	AAAC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:142716575_142716578delAAAC	ENST00000610091.1	-	0	418																											catctcagaaaaacaaacaaacaa	0.422																																						ENST00000595144.1																			0																																																			0							g.chr1:142716575_142716578delAAAC																													1.37:g.142716583_142716586delAAAC														0	418	-									RNA	DEL	ENST00000610091.1	37																																																																																						0.422	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			9	347						9	347	---	---	---	---
LOC101927209	101927209	broad.mit.edu	37	1	142720897	142720898	+	lincRNA	INS	-	-	A	rs112730110|rs374883772	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:142720897_142720898insA	ENST00000610091.1	-	0	204_205																											GCTCTTCCTCTAAGCCACTGGT	0.277													|||unknown(NO_COVERAGE)	2342	0.467652	0.2436	0.7118	5008	,	,		10169	0.4038		0.666	False		,,,				2504	0.4591					ENST00000595144.1																			0																																																			0							g.chr1:142720897_142720898insA																													1.37:g.142720899_142720899dupA														0	204_205	-									RNA	INS	ENST00000610091.1	37																																																																																						0.277	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			16	124						16	124	---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145311123	145311123	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:145311123delA	ENST00000369339.3	+	10	1262	c.1009delA	c.(1009-1011)aaafs	p.K338fs	NBPF10_ENST00000342960.5_Frame_Shift_Del_p.K609fs|NBPF10_ENST00000369338.1_Frame_Shift_Del_p.K338fs|RP11-458D21.5_ENST00000468030.1_3'UTR			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	609						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GGATCAAGTGAAAAAGGAGGA	0.448																																						ENST00000342960.5																			0				NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73						c.(1822-1824)aafs		neuroblastoma breakpoint family, member 10							115.0	100.0	104.0					1																	145311123		692	1590	2282	SO:0001589	frameshift_variant	100132406							g.chr1:145311123delA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.1009delA	1.37:g.145311123delA	ENSP00000358345:p.Lys338fs					NBPF10_ENST00000369338.1_Frame_Shift_Del_p.K338fs|NBPF10_ENST00000369339.2_Frame_Shift_Del_p.K338fs|RP11-458D21.5_ENST00000468030.1_3'UTR	p.K609fs	NM_001039703.4	NP_001034792.4	A6NDV3	A6NDV3_HUMAN		Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	13	1857	+	all_hematologic(923;0.032)		609					Q5RHC0|Q9NWN6	Frame_Shift_Del	DEL	ENST00000369339.3	37	c.1822delA																																																																																					0.448	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703		7	2504						7	2504	---	---	---	---
HFE2	148738	broad.mit.edu	37	1	145415369	145415371	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:145415369_145415371delGAG	ENST00000336751.5	+	3	426_428	c.188_190delGAG	c.(187-192)cgagga>cga	p.G69del	HFE2_ENST00000357836.5_5'UTR|HFE2_ENST00000475797.1_Intron|HFE2_ENST00000497365.1_Intron	NM_213653.3	NP_998818.1	Q6ZVN8	RGMC_HUMAN	hemochromatosis type 2 (juvenile)	69	Poly-Gly.			G -> GG (in Ref. 3; ABC40718). {ECO:0000305}.	axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|iron ion homeostasis (GO:0055072)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	14	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGAGCACTTCGAGGAGGAGGAGG	0.626																																						ENST00000336751.5																			0				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	14						c.(187-192)cga>c		hemochromatosis type 2 (juvenile)			,,,	49,31,4178		2,0,45,10,11,2061					,,,	2.7	0.0			51	5,73,8160		0,0,5,23,27,4064	no	codingComplex,intron,intron,utr-5	HFE2	NM_213653.3,NM_213652.3,NM_202004.3,NM_145277.4	,,,	2,0,50,33,38,6125	A1A1,A1A2,A1R,A2A2,A2R,RR		0.9468,1.8788,1.2644	,,,	,,,		54,104,12338				SO:0001651	inframe_deletion	148738				axon guidance	anchored to membrane		g.chr1:145415369_145415371delGAG	AY372521	CCDS72877.1, CCDS72878.1, CCDS72879.1	1q21.2	2014-06-26			ENSG00000168509	ENSG00000168509			4887	protein-coding gene	gene with protein product	"""repulsive guidance molecule c"""	608374				10205270, 14647275	Standard	NM_213653		Approved	JH, HFE2A, RGMC, HJV, hemojuvelin, haemojuvelin	uc001eni.2	Q6ZVN8	OTTHUMG00000013748	ENST00000336751.5:c.188_190delGAG	1.37:g.145415378_145415380delGAG	ENSP00000337014:p.Gly69del					HFE2_ENST00000475797.1_Intron|HFE2_ENST00000357836.5_5'UTR|HFE2_ENST00000497365.1_Intron	p.RG63del	NM_213653.3	NP_998818.1	Q6ZVN8	RGMC_HUMAN			3	426_428	+	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		63					B1ALI7|Q2PQ63|Q6IMF6|Q8NAH2|Q8WVJ5	In_Frame_Del	DEL	ENST00000336751.5	37	c.188_190delGAG	CCDS910.1																																																																																				0.626	HFE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038527.1	NM_145277		7	343						7	343	---	---	---	---
ADAMTSL4	54507	broad.mit.edu	37	1	150530506	150530506	+	Frame_Shift_Del	DEL	G	G	-	rs149280379		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:150530506delG	ENST00000369038.2	+	12	2464	c.2263delG	c.(2263-2265)gggfs	p.G758fs	ADAMTSL4_ENST00000369039.5_Frame_Shift_Del_p.G781fs|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000369041.5_Frame_Shift_Del_p.G758fs|ADAMTSL4_ENST00000271643.4_Frame_Shift_Del_p.G758fs			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	758	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GCAGGAATTTGGGGGGGGTGG	0.692																																						ENST00000271643.4																			0				breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32						c.(2263-2265)ggfs		ADAMTS-like 4							41.0	49.0	46.0					1																	150530506		2147	4195	6342	SO:0001589	frameshift_variant	54507				apoptosis|positive regulation of apoptosis		metalloendopeptidase activity|protease binding	g.chr1:150530506delG	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"""thrombospondin repeat containing 1"""	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.2263delG	1.37:g.150530506delG	ENSP00000358034:p.Gly758fs					ADAMTSL4_ENST00000369039.5_Frame_Shift_Del_p.G781fs|ADAMTSL4_ENST00000369038.2_Frame_Shift_Del_p.G758fs|ADAMTSL4_ENST00000369041.5_Frame_Shift_Del_p.G758fs	p.G758fs	NM_019032.4	NP_061905.2	Q6UY14	ATL4_HUMAN	UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		14	2499	+	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		758			TSP type-1 2.		B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Frame_Shift_Del	DEL	ENST00000369038.2	37	c.2263delG	CCDS955.1																																																																																				0.692	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		8	655						8	655	---	---	---	---
RASAL2	9462	broad.mit.edu	37	1	178412040	178412041	+	Frame_Shift_Ins	INS	-	-	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:178412040_178412041insA	ENST00000462775.1	+	6	839_840	c.714_715insA	c.(715-717)aaafs	p.K239fs	RASAL2_ENST00000448150.3_Frame_Shift_Ins_p.K369fs|RASAL2_ENST00000367649.3_Frame_Shift_Ins_p.K387fs	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	239	C2.|Poly-Lys.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						TGGAAAAAAAGAAAAAAAAGGA	0.406																																						ENST00000448150.3																			0				biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						c.(1102-1107)aaaaaafs		RAS protein activator like 2																																				SO:0001589	frameshift_variant	9462				negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity	g.chr1:178412040_178412041insA	AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"""Pleckstrin homology (PH) domain containing"""	9874	protein-coding gene	gene with protein product	"""Ras GTPase activating protein-like"", ""Ras protein activator like 1"""	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.722dupA	1.37:g.178412048_178412048dupA	ENSP00000420558:p.Lys239fs					RASAL2_ENST00000462775.1_Frame_Shift_Ins_p.KK238fs|RASAL2_ENST00000367649.3_Frame_Shift_Ins_p.KK386fs	p.KK368fs	NM_170692.2	NP_733793.2	Q9UJF2	NGAP_HUMAN			8	1922_1923	+			238			Ras-GAP.		F8W755|O95174|Q2TB22|Q5TFU9	Frame_Shift_Ins	INS	ENST00000462775.1	37	c.1104_1105insA	CCDS1322.1																																																																																				0.406	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692		7	455						7	455	---	---	---	---
PRG4	10216	broad.mit.edu	37	1	186281436	186281436	+	Missense_Mutation	SNP	T	T	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:186281436T>A	ENST00000445192.2	+	11	3968	c.3923T>A	c.(3922-3924)aTa>aAa	p.I1308K	PRG4_ENST00000367486.3_Missense_Mutation_p.I1265K|PRG4_ENST00000367483.4_Missense_Mutation_p.I1267K|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367484.3_Missense_Mutation_p.I837K|PRG4_ENST00000367485.4_Missense_Mutation_p.I1215K|TPR_ENST00000367478.4_3'UTR	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1308					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						GAACGTGCTATAGGACCTTCT	0.418																																						ENST00000445192.2																			0				NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						c.(3922-3924)aTa>aAa		proteoglycan 4							144.0	143.0	143.0					1																	186281436		2203	4300	6503	SO:0001583	missense	10216				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity	g.chr1:186281436T>A	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.3923T>A	1.37:g.186281436T>A	ENSP00000399679:p.Ile1308Lys					PRG4_ENST00000367484.3_Missense_Mutation_p.I837K|PRG4_ENST00000367485.4_Missense_Mutation_p.I1215K|PRG4_ENST00000367483.4_Missense_Mutation_p.I1267K|PRG4_ENST00000367486.3_Missense_Mutation_p.I1265K	p.I1308K	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN			11	3968	+			1308					Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	c.3923T>A	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	T	11.11	1.543642	0.27563	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.07688	3.17;3.29;3.27;3.18;3.27	5.48	1.86	0.25419	Hemopexin/matrixin (1);	0.514144	0.16080	N	0.230549	T	0.15652	0.0377	L	0.47716	1.5	0.09310	N	1	D;D;D;D	0.71674	0.988;0.988;0.998;0.988	P;P;P;P	0.62014	0.851;0.851;0.897;0.851	T	0.08534	-1.0717	10	0.87932	D	0	-2.0141	5.7754	0.18277	0.0:0.1475:0.1412:0.7113	.	1174;1215;1308;1267	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	K	1265;837;1267;1215;1308	ENSP00000356456:I1265K;ENSP00000356454:I837K;ENSP00000356453:I1267K;ENSP00000356455:I1215K;ENSP00000399679:I1308K	ENSP00000356453:I1267K	I	+	2	0	PRG4	184548059	0.007000	0.16637	0.001000	0.08648	0.291000	0.27294	1.709000	0.37909	0.121000	0.18284	0.477000	0.44152	ATA		0.418	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		20	674	0	0	0	1	0	20	674				
GPR37L1	9283	broad.mit.edu	37	1	202097525	202097527	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:202097525_202097527delCTG	ENST00000367282.5	+	2	1393_1395	c.1287_1289delCTG	c.(1285-1290)gactgc>gac	p.C436del		NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN	G protein-coupled receptor 37 like 1	436	Cys-rich.				negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						CCTTCCTGGActgctgctgctgc	0.626																																						ENST00000367282.4																			0				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						c.(1285-1290)gac>ga		G protein-coupled receptor 37 like 1				2,128,4136		0,0,2,9,110,2012						3.1	1.0			46	5,240,8007		0,0,5,10,220,3891	no	codingComplex	GPR37L1	NM_004767.3		0,0,7,19,330,5903	A1A1,A1A2,A1R,A2A2,A2R,RR		2.969,3.0474,2.9957				7,368,12143				SO:0001651	inframe_deletion	9283					integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding	g.chr1:202097525_202097527delCTG	AJ310210	CCDS1420.1	1q32	2012-08-21	2006-02-15		ENSG00000170075	ENSG00000170075		"""GPCR / Class A : Orphans"""	14923	protein-coding gene	gene with protein product						9539149	Standard	NM_004767		Approved	ETBR-LP-2	uc001gxj.3	O60883	OTTHUMG00000035924	ENST00000367282.5:c.1287_1289delCTG	1.37:g.202097534_202097536delCTG	ENSP00000356251:p.Cys436del						p.DC429del	NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN			2	1393_1395	+			429			Cys-rich.		B2R7M9|Q5SXP7|Q86VP7	In_Frame_Del	DEL	ENST00000367282.5	37	c.1287_1289delCTG	CCDS1420.1																																																																																				0.626	GPR37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087496.2	NM_004767		7	195						7	195	---	---	---	---
PTPN14	5784	broad.mit.edu	37	1	214557049	214557051	+	In_Frame_Del	DEL	CCT	CCT	-	rs143136196|rs376331360|rs189081489|rs539310988	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:214557049_214557051delCCT	ENST00000366956.5	-	13	2341_2343	c.2147_2149delAGG	c.(2146-2151)gaggct>gct	p.E716del	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	716	Poly-Glu.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)	p.E716delE(1)		NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GATTCTGGAGCCTCCTCCTCCTC	0.626																																					Colon(92;557 1424 24372 34121 40073)	ENST00000366956.5																			1	Deletion - In frame(1)	p.E716delE(1)	liver(1)	NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						c.(2146-2151)gct>g		protein tyrosine phosphatase, non-receptor type 14																																				SO:0001651	inframe_deletion	5784				lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding	g.chr1:214557049_214557051delCCT	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.2147_2149delAGG	1.37:g.214557058_214557060delCCT	ENSP00000355923:p.Glu716del					PTPN14_ENST00000543945.1_3'UTR	p.EA716del	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)	13	2341_2343	-			716			Poly-Glu.		Q5VSI0	In_Frame_Del	DEL	ENST00000366956.5	37	c.2147_2149delAGG	CCDS1514.1																																																																																				0.626	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		18	329						18	329	---	---	---	---
OR2T2	401992	broad.mit.edu	37	1	248616705	248616711	+	Frame_Shift_Del	DEL	TGCTGCG	TGCTGCG	-	rs199823862|rs372931983		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr1:248616705_248616711delTGCTGCG	ENST00000342927.3	+	1	629_635	c.607_613delTGCTGCG	c.(607-615)tgctgcgtgfs	p.CCV203fs		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GATGTATGCCTGCTGCGTGCTGATGCT	0.527																																						ENST00000342927.3																			0				cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37						c.(607-615)tgfs		olfactory receptor, family 2, subfamily T, member 2				51,3755		2,47,1854						-2.5	0.6			76	261,7371		12,237,3567	no	frameshift	OR2T2	NM_001004136.1		14,284,5421	A1A1,A1R,RR		3.4198,1.34,2.7277				312,11126				SO:0001589	frameshift_variant	401992				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248616705_248616711delTGCTGCG	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.607_613delTGCTGCG	1.37:g.248616705_248616711delTGCTGCG	ENSP00000343062:p.Cys203fs						p.CCV203fs	NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		1	629_635	+	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		203					B2RNM1|B9EH01	Frame_Shift_Del	DEL	ENST00000342927.3	37	c.607_613delTGCTGCG	CCDS31116.1																																																																																				0.527	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136		9	503						9	503	---	---	---	---
ALK	238	broad.mit.edu	37	2	29451793	29451794	+	Frame_Shift_Ins	INS	-	-	C	rs75861155		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:29451793_29451794insC	ENST00000389048.3	-	16	3677_3678	c.2771_2772insG	c.(2770-2772)ggtfs	p.G924fs	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	924	Gly-rich.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	ACCCCCCTCCACCCCCTCCGAA	0.594			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													ENST00000389048.3			yes	Dom	yes	Familial neuroblastoma	2	2p23	238	"""T, Mis, A"""	anaplastic lymphoma kinase (Ki-1)			"""L, E, M"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	neuroblastoma	"""ALCL, NSCLC, Neuroblastoma"""	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	0				NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340						c.(2770-2772)gggfs		anaplastic lymphoma receptor tyrosine kinase	Adenosine triphosphate(DB00171)																																			SO:0001589	frameshift_variant	238	Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	g.chr2:29451793_29451794insC	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.2772dupG	2.37:g.29451798_29451798dupC	ENSP00000373700:p.Gly924fs					ALK_ENST00000431873.1_Intron	p.G924fs	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN			16	3677_3678	-	Acute lymphoblastic leukemia(172;0.155)		924			Gly-rich.		Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Frame_Shift_Ins	INS	ENST00000389048.3	37	c.2771_2772insG	CCDS33172.1																																																																																				0.594	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		9	278						9	278	---	---	---	---
RTN4	57142	broad.mit.edu	37	2	55253745	55253746	+	Frame_Shift_Ins	INS	-	-	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:55253745_55253746insT	ENST00000337526.6	-	3	1732_1733	c.1489_1490insA	c.(1489-1491)atafs	p.I497fs	RTN4_ENST00000317610.7_Intron|RTN4_ENST00000357376.3_Frame_Shift_Ins_p.I291fs|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000394611.2_Frame_Shift_Ins_p.I291fs|RTN4_ENST00000354474.6_Frame_Shift_Ins_p.I265fs|RTN4_ENST00000405240.1_Frame_Shift_Ins_p.I291fs|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000404909.1_Frame_Shift_Ins_p.I291fs	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	497					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						CTTTTCTTCTATTTTTTTTTCA	0.381																																						ENST00000337526.6																			0				NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						c.(1489-1491)agafs		reticulon 4																																				SO:0001589	frameshift_variant	57142				apoptosis|axonal fasciculation|cerebral cortex radial glia guided migration|endoplasmic reticulum tubular network organization|negative regulation of anti-apoptosis|negative regulation of axon extension|nerve growth factor receptor signaling pathway|regulation of apoptosis|regulation of branching morphogenesis of a nerve|regulation of cell migration	integral to endoplasmic reticulum membrane|nuclear envelope|plasma membrane	protein binding	g.chr2:55253745_55253746insT	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.1490dupA	2.37:g.55253754_55253754dupT	ENSP00000337838:p.Ile497fs					RTN4_ENST00000394611.2_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357376.3_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000354474.6_Frame_Shift_Ins_p.R265fs|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000404909.1_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000405240.1_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000317610.7_Intron	p.R497fs	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN			3	1732_1733	-			497					O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Frame_Shift_Ins	INS	ENST00000337526.6	37	c.1489_1490insA	CCDS42684.1																																																																																				0.381	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			16	568						16	568	---	---	---	---
MOGS	7841	broad.mit.edu	37	2	74690035	74690035	+	Frame_Shift_Del	DEL	G	G	-	rs184209905	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:74690035delG	ENST00000233616.4	-	4	1043	c.881delC	c.(880-882)cctfs	p.P294fs	MOGS_ENST00000535045.1_3'UTR|MOGS_ENST00000409065.1_3'UTR|MOGS_ENST00000462443.1_5'UTR|MOGS_ENST00000452063.2_Frame_Shift_Del_p.P188fs	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	294					cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						GTAGCGTTCAGGGGGGGCCCC	0.587																																						ENST00000233616.4																			0				cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						c.(880-882)ctfs		mannosyl-oligosaccharide glucosidase							113.0	121.0	118.0					2																	74690035		1954	4148	6102	SO:0001589	frameshift_variant	7841				oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane|membrane fraction	mannosyl-oligosaccharide glucosidase activity	g.chr2:74690035delG	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"""glucosidase I"", ""processing A-glucosidase I"""	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.881delC	2.37:g.74690035delG	ENSP00000233616:p.Pro294fs					MOGS_ENST00000409065.1_3'UTR|MOGS_ENST00000452063.2_Frame_Shift_Del_p.P188fs|MOGS_ENST00000462443.1_5'UTR|MOGS_ENST00000535045.1_3'UTR	p.P294fs	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN			4	1043	-			294					A8K938|F5H6D0|Q17RN9|Q8TCT5	Frame_Shift_Del	DEL	ENST00000233616.4	37	c.881delC	CCDS42700.1																																																																																				0.587	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302		7	1284						7	1284	---	---	---	---
LOXL3	84695	broad.mit.edu	37	2	74763923	74763924	+	Frame_Shift_Ins	INS	-	-	C			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:74763923_74763924insC	ENST00000264094.3	-	5	895_896	c.824_825insG	c.(823-825)ggcfs	p.G275fs	LOXL3_ENST00000409986.1_Intron|LOXL3_ENST00000393937.2_Intron|LOXL3_ENST00000484369.1_5'Flank|LOXL3_ENST00000409249.1_Frame_Shift_Ins_p.G275fs|LOXL3_ENST00000409549.1_Frame_Shift_Ins_p.G275fs	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	275	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)	p.A277fs*57(1)		endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						CCACTGCAGGGCCCCCCCCAGG	0.649																																						ENST00000264094.3																			1	Insertion - Frameshift(1)	p.A277fs*57(1)	large_intestine(1)	endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						c.(823-825)gccfs		lysyl oxidase-like 3																																				SO:0001589	frameshift_variant	84695					extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity	g.chr2:74763923_74763924insC	AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.825dupG	2.37:g.74763931_74763931dupC	ENSP00000264094:p.Gly275fs					LOXL3_ENST00000409986.1_Intron|LOXL3_ENST00000409249.1_Frame_Shift_Ins_p.A275fs|LOXL3_ENST00000409549.1_Frame_Shift_Ins_p.A275fs|LOXL3_ENST00000393937.2_Intron	p.A275fs	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN			5	895_896	-			275			SRCR 2.		D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Frame_Shift_Ins	INS	ENST00000264094.3	37	c.824_825insG	CCDS1953.1																																																																																				0.649	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		7	518						7	518	---	---	---	---
IGKV1D-8	28904	broad.mit.edu	37	2	90259860	90259861	+	RNA	INS	-	-	C			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:90259860_90259861insC	ENST00000471857.1	+	0	236									immunoglobulin kappa variable 1D-8																		AATTTACTCAGCCAATGTGCTC	0.48																																						ENST00000471857.1																			0																																																			0							g.chr2:90259860_90259861insC	Z00008		2p11.2	2012-02-08			ENSG00000239819	ENSG00000239819		"""Immunoglobulins / IGK locus"""	5759	other	immunoglobulin gene							Standard	NG_000833		Approved				OTTHUMG00000151570		2.37:g.90259862_90259862dupC														0	236	+									RNA	INS	ENST00000471857.1	37																																																																																						0.480	IGKV1D-8-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000323145.2	NG_000833		9	722						9	722	---	---	---	---
ANKRD20A8P	729171	broad.mit.edu	37	2	95513688	95513689	+	RNA	INS	-	-	TA			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:95513688_95513689insTA	ENST00000432432.2	-	0	850				RNU6-1320P_ENST00000390838.1_RNA	NR_040113.1		Q5CZ79	AN20B_HUMAN	ankyrin repeat domain 20 family, member A8, pseudogene																		CTCACCTAATGTATAAGATGGA	0.327																																						ENST00000432432.2																			0																																																			0							g.chr2:95513688_95513689insTA			2q11.1	2011-09-16	2010-12-15	2010-12-15	ENSG00000229089	ENSG00000229089			23666	pseudogene	pseudogene			"""ankyrin repeat domain 20B"""	ANKRD20B			Standard	NR_003366		Approved		uc010fhq.2	Q5CZ79	OTTHUMG00000155138		2.37:g.95513691_95513692dupTA								NR_040113.1						0	850	-								A6NC18	RNA	INS	ENST00000432432.2	37																																																																																						0.327	ANKRD20A8P-002	KNOWN	not_best_in_genome_evidence|basic	processed_transcript	pseudogene	OTTHUMT00000451404.1			18	605						18	605	---	---	---	---
ERMN	57471	broad.mit.edu	37	2	158178062	158178064	+	In_Frame_Del	DEL	ATC	ATC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:158178062_158178064delATC	ENST00000410096.1	-	3	865_867	c.574_576delGAT	c.(574-576)gatdel	p.D192del	ERMN_ENST00000535935.1_In_Frame_Del_p.D86del|ERMN_ENST00000397283.2_In_Frame_Del_p.D205del|ERMN_ENST00000420719.2_In_Frame_Del_p.D172del	NM_020711.1	NP_065762.1	Q8TAM6	ERMIN_HUMAN	ermin, ERM-like protein	192	Poly-Asp.				actin filament organization (GO:0007015)|morphogenesis of a branching structure (GO:0001763)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|internode region of axon (GO:0033269)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|paranode region of axon (GO:0033270)				endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12						tattgcaattatcatcatcatca	0.365																																						ENST00000410096.1																			0				endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12						c.(574-576)del		ermin, ERM-like protein																																				SO:0001651	inframe_deletion	57471					cytoplasm|cytoskeleton		g.chr2:158178062_158178064delATC	AB033015	CCDS42764.1, CCDS46431.1	2q24	2008-02-05	2008-01-15	2008-01-15	ENSG00000136541	ENSG00000136541			29208	protein-coding gene	gene with protein product	"""juxtanodin"", ""ermin"""	610072	"""KIAA1189"""	KIAA1189		16051705, 16421295	Standard	NM_020711		Approved	JN, ERMIN	uc002tzi.3	Q8TAM6	OTTHUMG00000153843	ENST00000410096.1:c.574_576delGAT	2.37:g.158178071_158178073delATC	ENSP00000387047:p.Asp192del					ERMN_ENST00000397283.2_In_Frame_Del_p.D205del|ERMN_ENST00000535935.1_In_Frame_Del_p.D86del|ERMN_ENST00000420719.2_In_Frame_Del_p.D172del	p.D192del	NM_020711.1	NP_065762.1	Q8TAM6	ERMIN_HUMAN			3	865_867	-			192			Poly-Asp.		B4DKA6|Q9ULN1	In_Frame_Del	DEL	ENST00000410096.1	37	c.574_576delGAT	CCDS46431.1																																																																																				0.365	ERMN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332659.1	NM_001009959		8	700						8	700	---	---	---	---
HIBCH	26275	broad.mit.edu	37	2	191161629	191161629	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:191161629delT	ENST00000359678.5	-	3	423	c.129delA	c.(127-129)aaafs	p.K43fs	HIBCH_ENST00000392332.3_Frame_Shift_Del_p.K43fs	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	43					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			CCGTGCAACCTTTTTTTTCCA	0.353																																						ENST00000392332.3																			0				NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13						c.(127-129)aafs		3-hydroxyisobutyryl-CoA hydrolase							116.0	104.0	108.0					2																	191161629		2203	4300	6503	SO:0001589	frameshift_variant	26275				branched chain family amino acid catabolic process	mitochondrial matrix	3-hydroxyisobutyryl-CoA hydrolase activity|protein binding	g.chr2:191161629delT	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"""3-hydroxyisobutyryl-Coenzyme A hydrolase"""			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.129delA	2.37:g.191161629delT	ENSP00000352706:p.Lys43fs					HIBCH_ENST00000359678.5_Frame_Shift_Del_p.K43fs	p.K43fs			Q6NVY1	HIBCH_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)		3	268	-			43					D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Frame_Shift_Del	DEL	ENST00000359678.5	37	c.129delA	CCDS2304.1																																																																																				0.353	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1			8	284						8	284	---	---	---	---
ALS2CR11	151254	broad.mit.edu	37	2	202352352	202352352	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:202352352delT	ENST00000286195.3	-	15	1899	c.1855delA	c.(1855-1857)attfs	p.I619fs	ALS2CR11_ENST00000439802.1_3'UTR|ALS2CR11_ENST00000482942.1_5'Flank|ALS2CR11_ENST00000439140.1_Frame_Shift_Del_p.I1816fs	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	619										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						CCTCTTTTAATTTTTTTTGGC	0.323																																						ENST00000439140.1																			0				NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						c.(5446-5448)ttfs		amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11							97.0	96.0	96.0					2																	202352352		2203	4300	6503	SO:0001589	frameshift_variant	151254							g.chr2:202352352delT	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.1855delA	2.37:g.202352352delT	ENSP00000286195:p.Ile619fs					ALS2CR11_ENST00000286195.3_Frame_Shift_Del_p.I619fs|ALS2CR11_ENST00000439802.1_3'UTR	p.I1816fs	NM_001168221.1	NP_001161693.1	Q53TS8	AL2SA_HUMAN			16	5490	-			619					C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Frame_Shift_Del	DEL	ENST00000286195.3	37	c.5446delA	CCDS2349.1																																																																																				0.323	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525		9	470						9	470	---	---	---	---
CYP20A1	57404	broad.mit.edu	37	2	204150380	204150380	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:204150380delA	ENST00000356079.4	+	9	1019	c.896delA	c.(895-897)caafs	p.Q299fs	CYP20A1_ENST00000461371.1_3'UTR|CYP20A1_ENST00000429815.2_Frame_Shift_Del_p.Q307fs	NM_177538.2	NP_803882.1	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A, polypeptide 1	299						integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	11						GAAGAAGTTCAAAAAAAATTA	0.348																																						ENST00000356079.4																			0				cervix(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	11						c.(895-897)cafs		cytochrome P450, family 20, subfamily A, polypeptide 1							65.0	72.0	70.0					2																	204150380		2203	4292	6495	SO:0001589	frameshift_variant	57404					integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	g.chr2:204150380delA	AK021770	CCDS2357.1	2q33	2008-02-05			ENSG00000119004	ENSG00000119004		"""Cytochrome P450s"""	20576	protein-coding gene	gene with protein product							Standard	NM_177538		Approved	CYP-M	uc002uzv.4	Q6UW02	OTTHUMG00000132854	ENST00000356079.4:c.896delA	2.37:g.204150380delA	ENSP00000348380:p.Gln299fs					CYP20A1_ENST00000461371.1_3'UTR|CYP20A1_ENST00000429815.2_Frame_Shift_Del_p.Q307fs	p.Q299fs	NM_177538.2	NP_803882.1	Q6UW02	CP20A_HUMAN			9	1019	+			299					Q4ZG61|Q8N4Q8|Q8WWA9|Q9HC04	Frame_Shift_Del	DEL	ENST00000356079.4	37	c.896delA	CCDS2357.1																																																																																				0.348	CYP20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256328.3	NM_020674		8	492						8	492	---	---	---	---
IRS1	3667	broad.mit.edu	37	2	227660808	227660810	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:227660808_227660810delGCT	ENST00000305123.5	-	1	3665_3667	c.2645_2647delAGC	c.(2644-2649)cagccc>ccc	p.Q882del	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	882	Poly-Gln.				cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		TGCAGCAAGGgctgctgctgctg	0.626																																						ENST00000305123.4																			0				autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69						c.(2644-2649)ccc>c		insulin receptor substrate 1																																				SO:0001651	inframe_deletion	3667				fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity	g.chr2:227660808_227660810delGCT		CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"""Pleckstrin homology (PH) domain containing"""	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.2645_2647delAGC	2.37:g.227660817_227660819delGCT	ENSP00000304895:p.Gln882del						p.QP882del	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)	1	3665_3667	-		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)	882			Poly-Gln.			In_Frame_Del	DEL	ENST00000305123.5	37	c.2645_2647delAGC	CCDS2463.1																																																																																				0.626	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		10	374						10	374	---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233785144	233785146	+	In_Frame_Del	DEL	CTC	CTC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr2:233785144_233785146delCTC	ENST00000264051.3	-	5	954_956	c.676_678delGAG	c.(676-678)gagdel	p.E226del	NGEF_ENST00000373552.4_In_Frame_Del_p.E134del|NGEF_ENST00000409079.1_In_Frame_Del_p.E134del	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	226	Poly-Glu.|Regulatory region; modulates activity toward RHOA, RAC1 and CDC42. {ECO:0000250}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		GGCTGGCCGGctcctcctcctcc	0.586																																						ENST00000264051.3																			0				central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35						c.(676-678)del		neuronal guanine nucleotide exchange factor																																				SO:0001651	inframe_deletion	25791				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity	g.chr2:233785144_233785146delCTC	AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"""Rho guanine nucleotide exchange factors"""	7807	protein-coding gene	gene with protein product	"""ephexin"""	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.676_678delGAG	2.37:g.233785153_233785155delCTC	ENSP00000264051:p.Glu226del					NGEF_ENST00000409079.1_In_Frame_Del_p.E134del|NGEF_ENST00000373552.4_In_Frame_Del_p.E134del	p.E226del	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)	5	954_956	-		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)	226			Poly-Glu.|Regulatory region; modulates activity toward RHOA, RAC1 and CDC42 (By similarity).		B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	In_Frame_Del	DEL	ENST00000264051.3	37	c.676_678delGAG	CCDS2500.1																																																																																				0.586	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799		7	388						7	388	---	---	---	---
PDCD6IP	10015	broad.mit.edu	37	3	33866811	33866811	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:33866811delT	ENST00000307296.3	+	5	972	c.595delT	c.(595-597)tttfs	p.F200fs	PDCD6IP_ENST00000457054.2_Frame_Shift_Del_p.F200fs			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	200	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.|Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						TCAAGAAGTATTTTTTTTAAA	0.368																																						ENST00000307296.3																			0				central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						c.(595-597)ttfs		programmed cell death 6 interacting protein							94.0	101.0	99.0					3																	33866811		2203	4300	6503	SO:0001589	frameshift_variant	10015				apoptosis|cell cycle|cell division|interspecies interaction between organisms|protein transport	cytosol|melanosome|microtubule organizing center	calcium-dependent protein binding	g.chr3:33866811delT	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"""ALG-2 interacting protein X"""	608074	"""programmed cell death 6-interacting protein"""			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.595delT	3.37:g.33866811delT	ENSP00000307387:p.Phe200fs					PDCD6IP_ENST00000457054.2_Frame_Shift_Del_p.F200fs	p.F200fs			Q8WUM4	PDC6I_HUMAN			5	972	+			200			BRO1.|Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9.		C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Frame_Shift_Del	DEL	ENST00000307296.3	37	c.595delT	CCDS2660.1																																																																																				0.368	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			7	584						7	584	---	---	---	---
QRICH1	54870	broad.mit.edu	37	3	49094314	49094316	+	In_Frame_Del	DEL	TGC	TGC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:49094314_49094316delTGC	ENST00000395443.2	-	3	1789_1791	c.1317_1319delGCA	c.(1315-1320)cagcaa>caa	p.439_440QQ>Q	QRICH1_ENST00000479449.1_5'UTR|QRICH1_ENST00000424300.1_In_Frame_Del_p.439_440QQ>Q|QRICH1_ENST00000357496.2_In_Frame_Del_p.439_440QQ>Q	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	439	Gln-rich.					nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		AACTTGGAgttgctgctgctgct	0.562																																						ENST00000395443.2																			0				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25						c.(1315-1320)caa>ca		glutamine-rich 1																																				SO:0001651	inframe_deletion	54870							g.chr3:49094314_49094316delTGC		CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.1317_1319delGCA	3.37:g.49094323_49094325delTGC	ENSP00000378830:p.Gln440del					QRICH1_ENST00000357496.2_In_Frame_Del_p.QQ439del|QRICH1_ENST00000424300.1_In_Frame_Del_p.QQ439del|QRICH1_ENST00000479449.1_5'UTR	p.QQ439del	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	3	1789_1791	-			439			Gln-rich.		Q4G0F7|Q7L621|Q8TEA5	In_Frame_Del	DEL	ENST00000395443.2	37	c.1317_1319delGCA	CCDS2787.1																																																																																				0.562	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		7	411						7	411	---	---	---	---
UBA7	7318	broad.mit.edu	37	3	49841761	49841763	+	IGR	DEL	GAG	GAG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:49841761_49841763delGAG	ENST00000333486.3	-	0	3299				FAM212A_ENST00000333323.4_In_Frame_Del_p.E73del|MIR5193_ENST00000584510.1_RNA	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7						cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		ggaggaggaagaggaggaggagg	0.626																																						ENST00000333323.4																			0											c.(205-207)del		family with sequence similarity 212, member A																																				SO:0001628	intergenic_variant	389119							g.chr3:49841761_49841763delGAG	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"""Ubiquitin-like modifier activating enzymes"""	12471	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)"", ""UBA7, ubiquitin-activating enzyme E1"""	191325	"""ubiquitin-activating enzyme E1-like"""	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267		3.37:g.49841770_49841772delGAG							p.E73del	NM_203370.1	NP_976248.1	Q96EL1	CC054_HUMAN			2	338_340	+			71					Q9BRB2	In_Frame_Del	DEL	ENST00000333486.3	37	c.205_207delGAG	CCDS2805.1																																																																																				0.626	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		7	335						7	335	---	---	---	---
OR5H8	79289	broad.mit.edu	37	3	98031434	98031434	+	lincRNA	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:98031434delA	ENST00000508616.1	+	0	149				OR5H8P_ENST00000394191.2_RNA																							TTACAATCTTAAAAAAAAAAG	0.333																																						ENST00000508616.1																			0																																																			0							g.chr3:98031434delA																													3.37:g.98031434delA						OR5H8P_ENST00000394191.2_RNA								0	149	+									RNA	DEL	ENST00000508616.1	37																																																																																						0.333	RP11-325B23.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000359282.1			9	155						9	155	---	---	---	---
IL12A-AS1	101928376	broad.mit.edu	37	3	159819452	159819453	+	RNA	DEL	AG	AG	-	rs368102646		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:159819452_159819453delAG	ENST00000497452.1	-	0	517									IL12A antisense RNA 1																		GGCTGCTGGCAGAGAGAGAGGA	0.465																																						ENST00000497452.1																			0																																																			0							g.chr3:159819452_159819453delAG	AK097161		3q25.33	2013-09-02			ENSG00000244040	ENSG00000244040		"""Long non-coding RNAs"""	49094	non-coding RNA	RNA, long non-coding							Standard	NR_108088		Approved				OTTHUMG00000158951		3.37:g.159819460_159819461delAG														0	517	-									RNA	DEL	ENST00000497452.1	37																																																																																						0.465	IL12A-AS1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000352647.1			7	1118						7	1118	---	---	---	---
EIF4G1	1981	broad.mit.edu	37	3	184039744	184039746	+	In_Frame_Del	DEL	GAA	GAA	-	rs530167757	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:184039744_184039746delGAA	ENST00000346169.2	+	10	1643_1645	c.1372_1374delGAA	c.(1372-1374)gaadel	p.E465del	EIF4G1_ENST00000382330.3_In_Frame_Del_p.E472del|EIF4G1_ENST00000427845.1_In_Frame_Del_p.E378del|EIF4G1_ENST00000435046.2_In_Frame_Del_p.E269del|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000319274.6_In_Frame_Del_p.E465del|EIF4G1_ENST00000441154.1_In_Frame_Del_p.E301del|EIF4G1_ENST00000434061.2_In_Frame_Del_p.E269del|EIF4G1_ENST00000342981.4_In_Frame_Del_p.E465del|EIF4G1_ENST00000414031.1_In_Frame_Del_p.E425del|EIF4G1_ENST00000352767.3_In_Frame_Del_p.E472del|EIF4G1_ENST00000424196.1_In_Frame_Del_p.E472del|EIF4G1_ENST00000411531.1_In_Frame_Del_p.E425del|EIF4G1_ENST00000392537.2_In_Frame_Del_p.E378del|EIF4G1_ENST00000350481.5_In_Frame_Del_p.E301del	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	465	Poly-Glu.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGAGGAAATGgaagaagaagaag	0.562																																						ENST00000342981.4																			0				central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75						c.(1372-1374)del		eukaryotic translation initiation factor 4 gamma, 1																																				SO:0001651	inframe_deletion	1981				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity	g.chr3:184039744_184039746delGAA	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1372_1374delGAA	3.37:g.184039753_184039755delGAA	ENSP00000316879:p.Glu465del					EIF4G1_ENST00000434061.2_In_Frame_Del_p.E269del|EIF4G1_ENST00000427845.1_In_Frame_Del_p.E378del|EIF4G1_ENST00000424196.1_In_Frame_Del_p.E472del|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000350481.5_In_Frame_Del_p.E301del|EIF4G1_ENST00000319274.6_In_Frame_Del_p.E465del|EIF4G1_ENST00000392537.2_In_Frame_Del_p.E378del|EIF4G1_ENST00000435046.2_In_Frame_Del_p.E269del|EIF4G1_ENST00000352767.3_In_Frame_Del_p.E472del|EIF4G1_ENST00000411531.1_In_Frame_Del_p.E425del|EIF4G1_ENST00000382330.3_In_Frame_Del_p.E472del|EIF4G1_ENST00000414031.1_In_Frame_Del_p.E425del|EIF4G1_ENST00000441154.1_In_Frame_Del_p.E301del|EIF4G1_ENST00000346169.2_In_Frame_Del_p.E465del	p.E465del	NM_182917.4	NP_886553.3	Q04637	IF4G1_HUMAN	Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		9	1786_1788	+	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		465			Poly-Glu.		D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	In_Frame_Del	DEL	ENST00000346169.2	37	c.1372_1374delGAA	CCDS3259.1																																																																																				0.562	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		7	519						7	519	---	---	---	---
TMEM41A	90407	broad.mit.edu	37	3	185212517	185212518	+	Frame_Shift_Ins	INS	-	-	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:185212517_185212518insA	ENST00000421852.1	-	4	562_563	c.467_468insT	c.(466-468)ttcfs	p.F156fs	TMEM41A_ENST00000475480.1_5'UTR|TMEM41A_ENST00000296254.3_Intron	NM_080652.3	NP_542383.1	Q96HV5	TM41A_HUMAN	transmembrane protein 41A	156						integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)|skin(1)	4	all_cancers(143;7.78e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			AAAACAATAAGAAAAAAAACAA	0.446																																						ENST00000421852.1																			0				large_intestine(1)|lung(2)|skin(1)	4						c.(466-468)tttfs		transmembrane protein 41A				0,4266		0,0,2133						1.0	0.8			116	1,8253		0,1,4126	no	frameshift	TMEM41A	NM_080652.3		0,1,6259	A1A1,A1R,RR		0.0121,0.0,0.0080				1,12519				SO:0001589	frameshift_variant	90407					integral to membrane		g.chr3:185212517_185212518insA	BC019884	CCDS3271.1	3q27.2	2006-04-12			ENSG00000163900	ENSG00000163900			30544	protein-coding gene	gene with protein product						12975309	Standard	NM_080652		Approved	MGC15397	uc003fpj.2	Q96HV5	OTTHUMG00000156660	ENST00000421852.1:c.468dupT	3.37:g.185212525_185212525dupA	ENSP00000406885:p.Phe156fs					TMEM41A_ENST00000296254.3_Intron|TMEM41A_ENST00000475480.1_5'UTR	p.F156fs	NM_080652.3	NP_542383.1	Q96HV5	TM41A_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)		4	562_563	-	all_cancers(143;7.78e-11)|Ovarian(172;0.0339)		156					A8K4B3|D3DNU2|Q6ZMJ0	Frame_Shift_Ins	INS	ENST00000421852.1	37	c.467_468insT	CCDS3271.1																																																																																				0.446	TMEM41A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345174.1	NM_080652		8	813						8	813	---	---	---	---
LINC00969	440993	broad.mit.edu	37	3	195400918	195400919	+	lincRNA	INS	-	-	T	rs55992531|rs397933710		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:195400918_195400919insT	ENST00000445430.1	+	0	1454									long intergenic non-protein coding RNA 969																		AGTCttttttctttttttttga	0.525																																						ENST00000445430.1																			0																																																			0							g.chr3:195400918_195400919insT	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195400927_195400927dupT														0	1454	+									RNA	INS	ENST00000445430.1	37																																																																																						0.525	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			21	65						21	65	---	---	---	---
SDHAP1	255812	broad.mit.edu	37	3	195713385	195713386	+	RNA	INS	-	-	T	rs199843390		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr3:195713385_195713386insT	ENST00000427841.1	-	0	176					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		AAAGCATGAACTTACGGAATCT	0.401																																					Ovarian(67;1158 1227 12109 20189 43170)	ENST00000427841.1																			0																																																			0							g.chr3:195713385_195713386insT	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195713387_195713387dupT								NR_003264.2						0	176	-									RNA	INS	ENST00000427841.1	37																																																																																						0.401	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			28	54						28	54	---	---	---	---
PROM1	8842	broad.mit.edu	37	4	15995680	15995680	+	Frame_Shift_Del	DEL	T	T	-	rs376676164		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr4:15995680delT	ENST00000510224.1	-	16	1945	c.1697delA	c.(1696-1698)aatfs	p.N566fs	PROM1_ENST00000543373.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000540805.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000539194.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000505450.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000447510.2_Frame_Shift_Del_p.N566fs|PROM1_ENST00000508167.1_Frame_Shift_Del_p.N557fs			O43490	PROM1_HUMAN	prominin 1	566					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						AGTGCCTCTATTTTTTTTGCA	0.428																																						ENST00000505450.1																			0				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						c.(1669-1671)atfs		prominin 1							189.0	187.0	188.0					4																	15995680		1901	4120	6021	SO:0001589	frameshift_variant	8842				camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding	g.chr4:15995680delT	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"""CD molecules"""	9454	protein-coding gene	gene with protein product		604365	"""prominin (mouse)-like 1"", ""macular dystrophy, retinal 2"", ""Stargardt disease 4 (autosomal dominant)"""	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.1697delA	4.37:g.15995680delT	ENSP00000426809:p.Asn566fs					PROM1_ENST00000543373.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000508167.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000539194.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000510224.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000447510.2_Frame_Shift_Del_p.N566fs|PROM1_ENST00000540805.1_Frame_Shift_Del_p.N566fs	p.N557fs	NM_001145848.1	NP_001139320.1	O43490	PROM1_HUMAN			15	2282	-			566					Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Frame_Shift_Del	DEL	ENST00000510224.1	37	c.1670delA	CCDS47029.1																																																																																				0.428	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		7	453						7	453	---	---	---	---
RPL9	6133	broad.mit.edu	37	4	39462464	39462464	+	5'Flank	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr4:39462464delA	ENST00000449470.2	-	0	0				LIAS_ENST00000513731.1_Frame_Shift_Del_p.K36fs|RPL9_ENST00000295955.9_5'Flank|LIAS_ENST00000261434.3_Frame_Shift_Del_p.K36fs|LIAS_ENST00000515061.1_3'UTR|LIAS_ENST00000340169.2_Frame_Shift_Del_p.K36fs|LIAS_ENST00000381846.1_Frame_Shift_Del_p.K36fs	NM_001024921.2	NP_001020092.1	P32969	RL9_HUMAN	ribosomal protein L9						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribosome (GO:0005840)	RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)	p.K36fs*31(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|skin(1)	8						CTTGCCAGATAAAAAAAAGGA	0.393																																						ENST00000261434.3																			1	Deletion - Frameshift(1)	p.K36fs*31(1)	large_intestine(1)	breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(2)|ovary(2)	12						c.(100-102)aafs		lipoic acid synthetase	Lipoic Acid(DB00166)						107.0	120.0	115.0					4																	39462464		2203	4300	6503	SO:0001631	upstream_gene_variant	11019				inflammatory response|response to lipopolysaccharide|response to oxidative stress	mitochondrion	4 iron, 4 sulfur cluster binding|lipoate synthase activity|metal ion binding	g.chr4:39462464delA	D14531	CCDS3452.1	4p13	2011-04-06			ENSG00000163682	ENSG00000163682		"""L ribosomal proteins"""	10369	protein-coding gene	gene with protein product		603686				8597601, 8415001	Standard	XM_005262661		Approved	L9	uc021sso.1	P32969	OTTHUMG00000099367		4.37:g.39462464delA	Exception_encountered					LIAS_ENST00000340169.2_Frame_Shift_Del_p.K36fs|LIAS_ENST00000515061.1_3'UTR|LIAS_ENST00000513731.1_Frame_Shift_Del_p.K36fs|LIAS_ENST00000381846.1_Frame_Shift_Del_p.K36fs	p.K36fs	NM_006859.2	NP_006850.2	O43766	LIAS_HUMAN			2	218	+			36						Frame_Shift_Del	DEL	ENST00000449470.2	37	c.100delA	CCDS3452.1																																																																																				0.393	RPL9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361018.1			7	884						7	884	---	---	---	---
GABRG1	2565	broad.mit.edu	37	4	46060358	46060358	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr4:46060358delA	ENST00000295452.4	-	7	959	c.792delT	c.(790-792)tttfs	p.F264fs		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	264					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.F264fs*3(1)		breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGCTCAGGTCAAAAAAAATTG	0.294																																						ENST00000295452.4																			1	Deletion - Frameshift(1)	p.F264fs*3(1)	large_intestine(1)	breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						c.(790-792)ttfs		gamma-aminobutyric acid (GABA) A receptor, gamma 1							94.0	97.0	96.0					4																	46060358		2203	4300	6503	SO:0001589	frameshift_variant	2565				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity	g.chr4:46060358delA	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4086	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma"""	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.792delT	4.37:g.46060358delA	ENSP00000295452:p.Phe264fs						p.F264fs	NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN		Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	7	959	-			264					Q5H9T8	Frame_Shift_Del	DEL	ENST00000295452.4	37	c.792delT	CCDS3470.1																																																																																				0.294	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536		7	327						7	327	---	---	---	---
CLOCK	9575	broad.mit.edu	37	4	56336954	56336954	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr4:56336954delA	ENST00000309964.4	-	7	618	c.368delT	c.(367-369)ttafs	p.L123fs	CLOCK_ENST00000513440.1_Frame_Shift_Del_p.L123fs|CLOCK_ENST00000381322.1_Frame_Shift_Del_p.L123fs	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	123	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.L123fs*1(2)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			CATGATTGCTAAAAAAAAACC	0.289																																						ENST00000309964.4																			2	Deletion - Frameshift(2)	p.L123fs*1(2)	ovary(1)|lung(1)	breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						c.(367-369)tafs		clock circadian regulator							88.0	93.0	92.0					4																	56336954		2201	4298	6499	SO:0001589	frameshift_variant	9575				circadian rhythm|photoperiodism|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|transcription factor complex	DNA binding|histone acetyltransferase activity|sequence-specific DNA binding transcription factor activity|signal transducer activity	g.chr4:56336954delA	AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	2082	protein-coding gene	gene with protein product		601851	"""clock (mouse) homolog"", ""clock homolog (mouse)"""			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.368delT	4.37:g.56336954delA	ENSP00000308741:p.Leu123fs					CLOCK_ENST00000381322.1_Frame_Shift_Del_p.L123fs|CLOCK_ENST00000513440.1_Frame_Shift_Del_p.L123fs	p.L123fs	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)		7	618	-	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		123			PAS 1.		A0AV01|A2I2N9|O14516|Q9UIT8	Frame_Shift_Del	DEL	ENST00000309964.4	37	c.368delT	CCDS3500.1																																																																																				0.289	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898		9	398						9	398	---	---	---	---
AASDH	132949	broad.mit.edu	37	4	57220269	57220269	+	Frame_Shift_Del	DEL	A	A	-	rs148777026		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr4:57220269delA	ENST00000205214.6	-	8	1499	c.1319delT	c.(1318-1320)ttgfs	p.L440fs	AASDH_ENST00000513376.1_Frame_Shift_Del_p.L340fs|AASDH_ENST00000510762.1_5'Flank|AASDH_ENST00000434343.2_Intron|AASDH_ENST00000502617.1_Frame_Shift_Del_p.L440fs|AASDH_ENST00000451613.1_Frame_Shift_Del_p.L440fs|AASDH_ENST00000602986.1_Frame_Shift_Del_p.L287fs	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	440					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)	p.?(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TTTTCGTCCCAAAAAAAAAAT	0.363																																						ENST00000205214.6																			1	Unknown(1)	p.?(1)	skin(1)	endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40						c.(1318-1320)tgfs		aminoadipate-semialdehyde dehydrogenase																																				SO:0001589	frameshift_variant	132949				fatty acid metabolic process		acid-thiol ligase activity|acyl carrier activity|ATP binding|cofactor binding	g.chr4:57220269delA	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.1319delT	4.37:g.57220269delA	ENSP00000205214:p.Leu440fs					AASDH_ENST00000502617.1_Frame_Shift_Del_p.L440fs|AASDH_ENST00000451613.1_Frame_Shift_Del_p.L440fs|AASDH_ENST00000434343.2_Intron|AASDH_ENST00000602986.1_Frame_Shift_Del_p.L287fs|AASDH_ENST00000513376.1_Frame_Shift_Del_p.L340fs	p.L440fs	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN			8	1499	-	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)	440					A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Frame_Shift_Del	DEL	ENST00000205214.6	37	c.1319delT	CCDS3504.1																																																																																				0.363	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		24	387						24	387	---	---	---	---
UTP3	57050	broad.mit.edu	37	4	71554620	71554622	+	In_Frame_Del	DEL	GAG	GAG	-	rs369776055		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr4:71554620_71554622delGAG	ENST00000254803.2	+	1	425_427	c.226_228delGAG	c.(226-228)gagdel	p.E81del		NM_020368.2	NP_065101.1	Q9NQZ2	SAS10_HUMAN	UTP3, small subunit (SSU) processome component, homolog (S. cerevisiae)	81	Glu-rich.				brain development (GO:0007420)|chromatin modification (GO:0016568)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(4)	18			Lung(101;0.235)			ggaggatggcgaggaggaggagg	0.567																																						ENST00000254803.2																			0				endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(4)	18						c.(226-228)del		UTP3, small subunit (SSU) processome component, homolog (S. cerevisiae)																																				SO:0001651	inframe_deletion	57050				brain development|chromatin modification|gene silencing	nucleolus		g.chr4:71554620_71554622delGAG	AL136590	CCDS3546.1	4q13.3	2008-02-05			ENSG00000132467	ENSG00000132467			24477	protein-coding gene	gene with protein product	"""disrupter of silencing 10"""	611614				12477932	Standard	NM_020368		Approved	FLJ23256, DKFZp761F222, SAS10, CRLZ1	uc003hfo.3	Q9NQZ2	OTTHUMG00000129911	ENST00000254803.2:c.226_228delGAG	4.37:g.71554629_71554631delGAG	ENSP00000254803:p.Glu81del						p.E81del	NM_020368.2	NP_065101.1	Q9NQZ2	SAS10_HUMAN	Lung(101;0.235)		1	425_427	+			81			Glu-rich.		Q6FI82	In_Frame_Del	DEL	ENST00000254803.2	37	c.226_228delGAG	CCDS3546.1																																																																																				0.567	UTP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252163.2	NM_020368		7	201						7	201	---	---	---	---
CDKL2	8999	broad.mit.edu	37	4	76539579	76539580	+	Frame_Shift_Ins	INS	-	-	T	rs533914363		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr4:76539579_76539580insT	ENST00000429927.2	-	3	925_926	c.222_223insA	c.(220-225)aaacgafs	p.R75fs	CDKL2_ENST00000307465.4_Frame_Shift_Ins_p.R75fs	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	75	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			AGGTACCATCGTTTTTTTTTCT	0.322																																						ENST00000429927.2																			0				breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22						c.(220-225)aagatgfs		cyclin-dependent kinase-like 2 (CDC2-related kinase)																																				SO:0001589	frameshift_variant	8999				sex differentiation|signal transduction	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity	g.chr4:76539579_76539580insT	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"""Cyclin-dependent kinases"""	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.223dupA	4.37:g.76539588_76539588dupT	ENSP00000412365:p.Arg75fs					CDKL2_ENST00000307465.4_Frame_Shift_Ins_p.M75fs	p.M75fs	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)		3	925_926	-			75			Protein kinase.		B2R695	Frame_Shift_Ins	INS	ENST00000429927.2	37	c.222_223insA	CCDS3570.1																																																																																				0.322	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		14	316						14	316	---	---	---	---
PAPD7	11044	broad.mit.edu	37	5	6755013	6755014	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr5:6755013_6755014delAC	ENST00000230859.6	+	13	1713_1714	c.1584_1585delAC	c.(1582-1587)aaacacfs	p.H529fs		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	759					double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)			cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						GGAGGAAAAAACACACACACAC	0.653																																					NSCLC(7;212 333 5667 23379 46547)	ENST00000230859.6																			0				cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						c.(1582-1587)aaacfs		PAP associated domain containing 7																																				SO:0001589	frameshift_variant	11044				cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion	nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding	g.chr5:6755013_6755014delAC	AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"""topoisomerase-related function protein 4-1"", ""polymerase (DNA-directed) sigma"", ""DNA polymerase kappa"", ""TUTase5"""	605198	"""polymerase (DNA directed) sigma"""	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.1584_1585delAC	5.37:g.6755023_6755024delAC	ENSP00000230859:p.His529fs						p.KH528fs	NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN			13	1713_1714	+			528					A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Frame_Shift_Del	DEL	ENST00000230859.6	37	c.1584_1585delAC	CCDS3871.1																																																																																				0.653	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		7	215						7	215	---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32789822	32789823	+	3'UTR	DEL	GT	GT	-	rs370388563		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr5:32789822_32789823delGT	ENST00000265074.8	+	0	5340_5341				AC026703.1_ENST00000326958.1_Frame_Shift_Del_p.C106fs	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	CTGATTTTGGGTGTGTGTGTGT	0.421																																						ENST00000326958.1																			0											c.(313-318)gggtfs																																						SO:0001624	3_prime_UTR_variant	0							g.chr5:32789822_32789823delGT		CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"""guanylate cyclase C"""	108962	"""chromosome 5 open reading frame 23"", ""atrionatriuretic peptide receptor C"", ""natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)"", ""natriuretic peptide receptor C"""	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.*3372GT>-	5.37:g.32789832_32789833delGT						NPR3_ENST00000265074.8_3'UTR	p.GC105fs							1	878_879	+								A2RRD1|B4DT84|E7EPG9	Frame_Shift_Del	DEL	ENST00000265074.8	37	c.315_316delGT	CCDS56357.1																																																																																				0.421	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908		8	467						8	467	---	---	---	---
MSH3	4437	broad.mit.edu	37	5	79970914	79970915	+	Frame_Shift_Ins	INS	-	-	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr5:79970914_79970915insA	ENST00000265081.6	+	7	1220_1221	c.1140_1141insA	c.(1141-1143)aaafs	p.K381fs		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	381					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		ATGTTAGGGACAAAAAAAAGGG	0.347								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)	ENST00000265081.6																			0				NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						c.(1138-1143)gaaaaafs	Mismatch excision repair (MMR)	mutS homolog 3																																				SO:0001589	frameshift_variant	4437				maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding	g.chr5:79970914_79970915insA	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.1148dupA	5.37:g.79970922_79970922dupA	ENSP00000265081:p.Lys381fs						p.EK380fs	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)	7	1220_1221	+		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)	380					A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Frame_Shift_Ins	INS	ENST00000265081.6	37	c.1140_1141insA	CCDS34195.1																																																																																				0.347	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		10	764						10	764	---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130815368	130815369	+	Frame_Shift_Ins	INS	-	-	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr5:130815368_130815369insT	ENST00000509018.1	-	16	2123_2124	c.1918_1919insA	c.(1918-1920)agtfs	p.S640fs	RAPGEF6_ENST00000507093.1_Frame_Shift_Ins_p.S640fs|RAPGEF6_ENST00000308008.6_Frame_Shift_Ins_p.S640fs|CTC-432M15.3_ENST00000514667.1_Frame_Shift_Ins_p.S690fs|RAPGEF6_ENST00000512052.1_Frame_Shift_Ins_p.S355fs|RAPGEF6_ENST00000510071.1_Frame_Shift_Ins_p.S640fs|RAPGEF6_ENST00000296859.6_Frame_Shift_Ins_p.S640fs|RAPGEF6_ENST00000307984.5_Frame_Shift_Ins_p.S640fs	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	640					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		ATGGCGATTACTTTTTTTTTCA	0.366																																					Melanoma(168;435 1955 13113 13877 23213)	ENST00000509018.1																			0				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31						c.(1918-1920)taafs		Rap guanine nucleotide exchange factor (GEF) 6																																				SO:0001589	frameshift_variant	51735				Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding	g.chr5:130815368_130815369insT	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.1919dupA	5.37:g.130815377_130815377dupT	ENSP00000421684:p.Ser640fs					RAPGEF6_ENST00000307984.5_Frame_Shift_Ins_p.*640fs|FNIP1_ENST00000514667.1_Frame_Shift_Ins_p.*690fs|RAPGEF6_ENST00000512052.1_Frame_Shift_Ins_p.*355fs|RAPGEF6_ENST00000296859.6_Frame_Shift_Ins_p.*640fs|RAPGEF6_ENST00000308008.6_Frame_Shift_Ins_p.*640fs|RAPGEF6_ENST00000510071.1_Frame_Shift_Ins_p.*640fs|RAPGEF6_ENST00000507093.1_Frame_Shift_Ins_p.*640fs	p.*640fs	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)	16	2123_2124	-			640					A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Frame_Shift_Ins	INS	ENST00000509018.1	37	c.1918_1919insA	CCDS34225.1																																																																																				0.366	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		10	650						10	650	---	---	---	---
DND1	373863	broad.mit.edu	37	5	140052285	140052285	+	Frame_Shift_Del	DEL	T	T	-	rs375722663	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr5:140052285delT	ENST00000542735.1	-	3	392	c.349delA	c.(349-351)acgfs	p.T117fs		NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	117	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)	p.T117fs*24(1)		central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGTGCAGCGTGGCGATGGCG	0.682													T|T|-|deletion	29	0.00579073	0.0	0.0173	5008	,	,		10844	0.002		0.0139	False		,,,				2504	0.001					ENST00000542735.1																			1	Deletion - Frameshift(1)	p.T117fs*24(1)	central_nervous_system(1)	central_nervous_system(1)|prostate(4)	5						c.(349-351)cgfs		DND microRNA-mediated repression inhibitor 1							6.0	7.0	6.0					5																	140052285		2084	4099	6183	SO:0001589	frameshift_variant	373863				multicellular organismal development|negative regulation of gene silencing by miRNA	cytoplasm|nucleus	AU-rich element binding|nucleotide binding	g.chr5:140052285delT	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.349delA	5.37:g.140052285delT	ENSP00000445366:p.Thr117fs						p.T117fs	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		3	392	-			117			RRM 1.			Frame_Shift_Del	DEL	ENST00000542735.1	37	c.349delA	CCDS4236.1																																																																																				0.682	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249		7	56						7	56	---	---	---	---
HMMR	3161	broad.mit.edu	37	5	162917425	162917426	+	Frame_Shift_Ins	INS	-	-	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr5:162917425_162917426insA	ENST00000358715.3	+	17	2025_2026	c.1989_1990insA	c.(1990-1992)aaafs	p.K664fs	HMMR_ENST00000393915.4_Frame_Shift_Ins_p.K665fs|RP11-80G7.1_ENST00000521666.1_RNA|RP11-80G7.1_ENST00000514724.2_RNA|HMMR_ENST00000353866.3_Frame_Shift_Ins_p.K649fs|HMMR_ENST00000432118.2_Frame_Shift_Ins_p.K578fs			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	664	Hyaluronic acid-binding. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	GTCAGCTTGCTAAAAAAAAACA	0.307																																						ENST00000416990.2																			0				cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23						c.(1645-1650)gcaaaafs		hyaluronan-mediated motility receptor (RHAMM)																																				SO:0001589	frameshift_variant	3161					cell surface|cytoplasm	hyaluronic acid binding	g.chr5:162917425_162917426insA	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"""CD molecules"""	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.1998dupA	5.37:g.162917434_162917434dupA	ENSP00000351554:p.Lys664fs					HMMR_ENST00000393915.4_Frame_Shift_Ins_p.AK664fs|HMMR_ENST00000432118.2_Frame_Shift_Ins_p.AK577fs|RP11-80G7.1_ENST00000521666.1_RNA|HMMR_ENST00000358715.3_Frame_Shift_Ins_p.AK663fs|RP11-80G7.1_ENST00000514724.2_RNA|HMMR_ENST00000353866.3_Frame_Shift_Ins_p.AK648fs	p.AK549fs			O75330	HMMR_HUMAN	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	17	2144_2145	+	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	663					A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Frame_Shift_Ins	INS	ENST00000358715.3	37	c.1647_1648insA	CCDS4362.1																																																																																				0.307	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484		7	329						7	329	---	---	---	---
RIOK1	83732	broad.mit.edu	37	6	7393450	7393452	+	In_Frame_Del	DEL	GAC	GAC	-	rs2274212|rs368069269	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr6:7393450_7393452delGAC	ENST00000379834.2	+	2	697_699	c.190_192delGAC	c.(190-192)gacdel	p.D69del		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	69							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.D57G(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					ggagggttatgacgatgatgatg	0.433																																						ENST00000379834.2																			1	Substitution - Missense(1)	p.D57G(1)	large_intestine(1)	cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19						c.(190-192)del		RIO kinase 1																																				SO:0001651	inframe_deletion	83732						ATP binding|protein serine/threonine kinase activity	g.chr6:7393450_7393452delGAC	BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"""RIO kinase 1 (yeast)"""				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.190_192delGAC	6.37:g.7393450_7393452delGAC	ENSP00000369162:p.Asp69del						p.D69del	NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN			2	697_699	+	Ovarian(93;0.0418)		69					B2RB28|Q8NDC8|Q96NV9	In_Frame_Del	DEL	ENST00000379834.2	37	c.190_192delGAC	CCDS4500.1																																																																																				0.433	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2	NM_031480		10	361						10	361	---	---	---	---
ZNRD1-AS1	80862	broad.mit.edu	37	6	29977389	29977393	+	RNA	DEL	CTTCT	CTTCT	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr6:29977389_29977393delCTTCT	ENST00000376797.3	-	0	731				ZNRD1-AS1_ENST00000444051.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		AGAACCCTGACTTCTCTTTCTGCAA	0.488																																						ENST00000376797.3																			0																																																			0							g.chr6:29977389_29977393delCTTCT	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.29977389_29977393delCTTCT						HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA								0	731	-									RNA	DEL	ENST00000376797.3	37																																																																																						0.488	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253083.1	NR_026751		10	147						10	147	---	---	---	---
DAXX	1616	broad.mit.edu	37	6	33287898	33287900	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr6:33287898_33287900delTCC	ENST00000374542.5	-	5	1557_1559	c.1353_1355delGGA	c.(1351-1356)gaggaa>gaa	p.451_452EE>E	DAXX_ENST00000414083.2_In_Frame_Del_p.376_377EE>E|DAXX_ENST00000477162.1_5'UTR|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000266000.6_In_Frame_Del_p.451_452EE>E|ZBTB22_ENST00000431845.2_5'Flank	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	451	Asp/Glu-rich (acidic).|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.E451E(2)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						ctcttcttcttcctcctcctcct	0.552			"""Mis, F, N"""		Pancreatic neuroendocrine tumors. Paediatric GBM																																	ENST00000374542.5				Rec	yes		6	6p21.3	1616	"""Mis, F, N"""	death-domain associated protein			E			Pancreatic neuroendocrine tumors. Paediatric GBM		2	Substitution - coding silent(2)	p.E451E(2)	prostate(1)|kidney(1)	breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						c.(1351-1356)gaa>ga		death-domain associated protein																																				SO:0001651	inframe_deletion	1616				activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent	chromosome, centromeric region|cytosol|nucleolus|PML body	androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding	g.chr6:33287898_33287900delTCC	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"""death-associated protein 6"""			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1353_1355delGGA	6.37:g.33287907_33287909delTCC	ENSP00000363668:p.Glu457del					DAXX_ENST00000477162.1_5'UTR|DAXX_ENST00000266000.6_In_Frame_Del_p.EE455del|DAXX_ENST00000414083.2_In_Frame_Del_p.EE380del	p.EE455del	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN			5	1557_1559	-			455			Asp/Glu-rich (acidic).|Necessary for interaction with USP7.		B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	In_Frame_Del	DEL	ENST00000374542.5	37	c.1353_1355delGGA	CCDS4776.1																																																																																				0.552	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			9	279						9	279	---	---	---	---
TRERF1	55809	broad.mit.edu	37	6	42196333	42196333	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr6:42196333delT	ENST00000372922.4	-	18	3915	c.3353delA	c.(3352-3354)aagfs	p.K1118fs	TRERF1_ENST00000340840.2_Frame_Shift_Del_p.K1047fs|TRERF1_ENST00000354325.2_Frame_Shift_Del_p.K1035fs|TRERF1_ENST00000372917.4_Frame_Shift_Del_p.K1047fs|TRERF1_ENST00000541110.1_Frame_Shift_Del_p.K1138fs	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	1118	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CTTCTGAGCCTTTTGCCTCTG	0.542																																						ENST00000541110.1																			0				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45						c.(3412-3414)agfs		transcriptional regulating factor 1							245.0	274.0	264.0					6																	42196333		2203	4300	6503	SO:0001589	frameshift_variant	55809				cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding	g.chr6:42196333delT	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.3353delA	6.37:g.42196333delT	ENSP00000362013:p.Lys1118fs					TRERF1_ENST00000372922.4_Frame_Shift_Del_p.K1118fs|TRERF1_ENST00000354325.2_Frame_Shift_Del_p.K1035fs|TRERF1_ENST00000372917.4_Frame_Shift_Del_p.K1047fs|TRERF1_ENST00000340840.2_Frame_Shift_Del_p.K1047fs	p.K1138fs			Q96PN7	TREF1_HUMAN	Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)		18	3981	-	Colorectal(47;0.196)		1118			Interacts with CREBBP.		Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Frame_Shift_Del	DEL	ENST00000372922.4	37	c.3413delA	CCDS4867.1																																																																																				0.542	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		7	2879						7	2879	---	---	---	---
TDRD6	221400	broad.mit.edu	37	6	46660414	46660415	+	Frame_Shift_Ins	INS	-	-	A	rs145334816		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr6:46660414_46660415insA	ENST00000316081.6	+	1	4549_4550	c.4549_4550insA	c.(4549-4551)gaafs	p.E1517fs	TDRD6_ENST00000544460.1_Frame_Shift_Ins_p.E1517fs	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1517					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			GTATAATCCAGAAAAAAAAATG	0.351																																						ENST00000544460.1																			0				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						c.(4549-4551)aaafs		tudor domain containing 6																																				SO:0001589	frameshift_variant	221400				cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding	g.chr6:46660414_46660415insA	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.4558dupA	6.37:g.46660423_46660423dupA	ENSP00000346065:p.Glu1517fs					TDRD6_ENST00000316081.6_Frame_Shift_Ins_p.K1517fs	p.K1517fs	NM_001168359.1	NP_001161831.1	O60522	TDRD6_HUMAN	Lung(136;0.192)		1	4803_4804	+			1517					B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Frame_Shift_Ins	INS	ENST00000316081.6	37	c.4549_4550insA	CCDS34470.1																																																																																				0.351	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		10	385						10	385	---	---	---	---
DDX43	55510	broad.mit.edu	37	6	74124410	74124413	+	Splice_Site	DEL	GTAA	GTAA	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr6:74124410_74124413delGTAA	ENST00000370336.4	+	14	1903		c.e14+1		MB21D1_ENST00000370318.1_Intron	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43						ATP catabolic process (GO:0006200)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						GAAGAGCAGGGTAAGTAAGCTTAG	0.402																																						ENST00000370336.4																			0				NS(1)|breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						c.e14+1		DEAD (Asp-Glu-Ala-Asp) box polypeptide 43																																				SO:0001630	splice_region_variant	55510					intracellular	ATP binding|ATP-dependent RNA helicase activity|RNA binding	g.chr6:74124410_74124413delGTAA		CCDS4977.1	6q13	2014-01-21			ENSG00000080007	ENSG00000080007		"""DEAD-boxes"""	18677	protein-coding gene	gene with protein product	"""cancer/testis antigen 13"""	606286				10919659	Standard	NM_018665		Approved	HAGE, DKFZp434H2114, CT13	uc003pgw.3	Q9NXZ2	OTTHUMG00000015033	ENST00000370336.4:c.1745+1GTAA>-	6.37:g.74124414_74124417delGTAA						MB21D1_ENST00000370318.1_Intron		NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN			14	1903	+								B4E0C8|Q6NXR1	Splice_Site	DEL	ENST00000370336.4	37		CCDS4977.1																																																																																				0.402	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665	Intron	14	430						14	430	---	---	---	---
GABRR1	2569	broad.mit.edu	37	6	89891719	89891721	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr6:89891719_89891721delAAG	ENST00000454853.2	-	8	962_964	c.852_854delCTT	c.(850-855)ttcttg>ttg	p.F284del	GABRR1_ENST00000369451.3_In_Frame_Del_p.F197del|GABRR1_ENST00000435811.1_In_Frame_Del_p.F267del	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	284					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	AGTTTGGAGCAAGAAGAAGAAGA	0.522																																						ENST00000435811.1																			0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35						c.(799-804)ttg>tt		gamma-aminobutyric acid (GABA) A receptor, rho 1	Picrotoxin(DB00466)																																			SO:0001651	inframe_deletion	2569				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity	g.chr6:89891719_89891721delAAG		CCDS5019.2, CCDS59028.1, CCDS59029.1	6q15	2012-06-22	2012-02-03		ENSG00000146276	ENSG00000146276		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4090	protein-coding gene	gene with protein product	"""GABA(A) receptor, rho 1"""	137161	"""gamma-aminobutyric acid (GABA) receptor, rho 1"""			1849271, 1315307	Standard	NM_002042		Approved		uc003pna.2	P24046	OTTHUMG00000015195	ENST00000454853.2:c.852_854delCTT	6.37:g.89891728_89891730delAAG	ENSP00000412673:p.Phe284del					GABRR1_ENST00000369451.3_In_Frame_Del_p.FL197del|GABRR1_ENST00000454853.2_In_Frame_Del_p.FL284del	p.FL267del	NM_001256703.1	NP_001243632.1	P24046	GBRR1_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.00917)	7	1255_1257	-		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)	284					A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	In_Frame_Del	DEL	ENST00000454853.2	37	c.801_803delCTT	CCDS5019.2																																																																																				0.522	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2			7	468						7	468	---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146264834	146264836	+	In_Frame_Del	DEL	ATC	ATC	-	rs561556028		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr6:146264834_146264836delATC	ENST00000367505.2	-	9	1945_1947	c.1681_1683delGAT	c.(1681-1683)gatdel	p.D561del	SHPRH_ENST00000438092.2_In_Frame_Del_p.D561del|SHPRH_ENST00000367503.3_In_Frame_Del_p.D561del|SHPRH_ENST00000275233.7_In_Frame_Del_p.D561del			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	561					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		AATAGTAAGGATCATCATCATCA	0.36																																						ENST00000367503.3																			0				breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79						c.(1681-1683)del		SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase																																				SO:0001651	inframe_deletion	257218				DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding	g.chr6:146264834_146264836delATC	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.1681_1683delGAT	6.37:g.146264843_146264845delATC	ENSP00000356475:p.Asp561del					SHPRH_ENST00000438092.2_In_Frame_Del_p.D561del|SHPRH_ENST00000367505.2_In_Frame_Del_p.D561del|SHPRH_ENST00000275233.7_In_Frame_Del_p.D561del	p.D561del	NM_001042683.2	NP_001036148.2	Q149N8	SHPRH_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)	9	2079_2081	-		Ovarian(120;0.0365)	561					Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	In_Frame_Del	DEL	ENST00000367505.2	37	c.1681_1683delGAT	CCDS43513.2																																																																																				0.360	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		7	662						7	662	---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152539540	152539540	+	Splice_Site	DEL	T	T	-	rs35128811		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr6:152539540delT	ENST00000367255.5	-	121	22646		c.e121-2		SYNE1_ENST00000265368.4_Splice_Site|SYNE1_ENST00000448038.1_Splice_Site|SYNE1_ENST00000356820.4_Splice_Site|SYNE1_ENST00000341594.5_Splice_Site|SYNE1_ENST00000423061.1_Splice_Site	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AACTCCAGCCTTTTTTTCCAC	0.343										HNSCC(10;0.0054)																												ENST00000367255.5																			0				NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524						c.e121-2		spectrin repeat containing, nuclear envelope 1							125.0	136.0	132.0					6																	152539540		2203	4300	6503	SO:0001630	splice_region_variant	23345				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding	g.chr6:152539540delT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.22045-2A>-	6.37:g.152539540delT		HNSCC(10;0.0054)				SYNE1_ENST00000423061.1_Splice_Site|SYNE1_ENST00000356820.4_Splice_Site|SYNE1_ENST00000448038.1_Splice_Site|SYNE1_ENST00000265368.4_Splice_Site|SYNE1_ENST00000341594.5_Splice_Site		NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)	121	22646	-		Ovarian(120;0.0955)						E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Splice_Site	DEL	ENST00000367255.5	37		CCDS5236.2																																																																																				0.343	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	Intron	8	1288						8	1288	---	---	---	---
INHBA	3624	broad.mit.edu	37	7	41729741	41729743	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr7:41729741_41729743delTTC	ENST00000242208.4	-	3	1032_1034	c.786_788delGAA	c.(784-789)aagaaa>aaa	p.262_263KK>K	INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_In_Frame_Del_p.262_263KK>K|AC005027.3_ENST00000416150.1_RNA	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	262					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						ctcctcttctttcttcttcttct	0.581										TSP Lung(11;0.080)																												ENST00000242208.4																			0				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						c.(784-789)aaa>aa		inhibin, beta A																																				SO:0001651	inframe_deletion	3624				cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity	g.chr7:41729741_41729743delTTC		CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"""Endogenous ligands"""	6066	protein-coding gene	gene with protein product		147290	"""inhibin, beta A (activin A, activin AB alpha polypeptide)"""			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.786_788delGAA	7.37:g.41729750_41729752delTTC	ENSP00000242208:p.Lys263del	TSP Lung(11;0.080)				INHBA_ENST00000464515.1_5'UTR|AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000442711.1_In_Frame_Del_p.KK262del	p.KK262del	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN			3	1032_1034	-			262					Q14599	In_Frame_Del	DEL	ENST00000242208.4	37	c.786_788delGAA	CCDS5464.1																																																																																				0.581	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1			10	274						10	274	---	---	---	---
OGDH	4967	broad.mit.edu	37	7	44684936	44684936	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr7:44684936delT	ENST00000222673.5	+	3	275	c.233delT	c.(232-234)attfs	p.I78fs	OGDH_ENST00000449767.1_Frame_Shift_Del_p.I78fs|OGDH_ENST00000543843.1_Frame_Shift_Del_p.I18fs|OGDH_ENST00000443864.2_Frame_Shift_Del_p.I78fs|OGDH_ENST00000444676.1_Frame_Shift_Del_p.I78fs|OGDH_ENST00000447398.1_Frame_Shift_Del_p.I78fs|OGDH_ENST00000439616.2_Intron	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	78					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.R81fs*19(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	TCATGGGACATTTTTTTTCGC	0.577																																						ENST00000222673.5																			1	Deletion - Frameshift(1)	p.R81fs*19(1)	breast(1)	breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36						c.(232-234)atfs		oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	NADH(DB00157)						127.0	121.0	123.0					7																	44684936		2203	4300	6503	SO:0001589	frameshift_variant	4967				glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding	g.chr7:44684936delT	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.233delT	7.37:g.44684936delT	ENSP00000222673:p.Ile78fs					OGDH_ENST00000443864.2_Frame_Shift_Del_p.I78fs|OGDH_ENST00000444676.1_Frame_Shift_Del_p.I78fs|OGDH_ENST00000439616.2_Intron|OGDH_ENST00000543843.1_Frame_Shift_Del_p.I18fs|OGDH_ENST00000447398.1_Frame_Shift_Del_p.I78fs|OGDH_ENST00000449767.1_Frame_Shift_Del_p.I78fs	p.I78fs	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN			3	275	+			78					B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Frame_Shift_Del	DEL	ENST00000222673.5	37	c.233delT	CCDS34627.1																																																																																				0.577	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			16	958						16	958	---	---	---	---
CCT6P1	643253	broad.mit.edu	37	7	65222951	65222951	+	RNA	DEL	T	T	-	rs564902644	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr7:65222951delT	ENST00000442266.1	+	0	561				SNORA22_ENST00000383907.1_RNA|SNORA15_ENST00000384058.1_RNA					chaperonin containing TCP1, subunit 6 (zeta) pseudogene 1																		TTTCTGTAACTTTTTTTTTTT	0.323													|||unknown(NO_COVERAGE)	42	0.00838658	0.0159	0.0014	5008	,	,		17660	0.004		0.005	False		,,,				2504	0.0112					ENST00000442266.1																			0																																																			0							g.chr7:65222951delT	BC052238, BC073761		7q11.21	2010-06-29	2008-09-22	2008-09-22	ENSG00000228409	ENSG00000228409			33094	pseudogene	pseudogene			"""chaperonin containing TCP1, subunit 6A (zeta 1) pseudogene 1"""	CCT6AP1			Standard	NR_003110		Approved		uc003tug.3		OTTHUMG00000156733		7.37:g.65222951delT														0	561	+									RNA	DEL	ENST00000442266.1	37																																																																																						0.323	CCT6P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345507.1	NR_003110		8	61						8	61	---	---	---	---
CYP51A1	1595	broad.mit.edu	37	7	91752494	91752494	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr7:91752494delT	ENST00000003100.8	-	7	1191	c.1026delA	c.(1024-1026)aaafs	p.K342fs	CYP51A1_ENST00000450723.1_Frame_Shift_Del_p.K237fs|LRRD1_ENST00000422722.1_5'UTR	NM_000786.3	NP_000777.1	Q16850	CP51A_HUMAN	cytochrome P450, family 51, subfamily A, polypeptide 1	336					cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via 24,25-dihydrolanosterol (GO:0033488)|demethylation (GO:0070988)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|sterol 14-demethylase activity (GO:0008398)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	10	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Itraconazole(DB01167)|Ketoconazole(DB01026)|Sertaconazole(DB01153)|Tioconazole(DB01007)	CTAAATAACATTTTTTTTGAA	0.398																																					GBM(70;1100 1190 11592 25836 51397)	ENST00000003100.8																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	10						c.(1024-1026)aafs		cytochrome P450, family 51, subfamily A, polypeptide 1	Fluconazole(DB00196)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Miconazole(DB01110)|Terconazole(DB00251)						119.0	123.0	121.0					7																	91752494		2203	4300	6503	SO:0001589	frameshift_variant	1595				cholesterol biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|sterol 14-demethylase activity	g.chr7:91752494delT	U51685	CCDS5623.1, CCDS55123.1	7q21.2	2012-10-10	2003-02-14	2003-02-28	ENSG00000001630	ENSG00000001630		"""Cytochrome P450s"""	2649	protein-coding gene	gene with protein product		601637	"""cytochrome P450, 51 (lanosterol 14-alpha-demethylase)"""	CYP51		8975714	Standard	NM_000786		Approved	CP51, CYPL1, P450L1, LDM, P450-14DM	uc003ulm.4	Q16850	OTTHUMG00000131131	ENST00000003100.8:c.1026delA	7.37:g.91752494delT	ENSP00000003100:p.Lys342fs					CYP51A1_ENST00000450723.1_Frame_Shift_Del_p.K237fs|LRRD1_ENST00000422722.1_5'UTR	p.K342fs	NM_000786.3	NP_000777.1	Q16850	CP51A_HUMAN	STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		7	1191	-	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		336					A4D1F8|B2RAI4|B4DJ55|O00770|O00772|Q16784|Q8N1A8|Q99868	Frame_Shift_Del	DEL	ENST00000003100.8	37	c.1026delA	CCDS5623.1																																																																																				0.398	CYP51A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253812.4			7	852						7	852	---	---	---	---
RBM33	155435	broad.mit.edu	37	7	155531073	155531074	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr7:155531073_155531074delCA	ENST00000401878.3	+	11	1911_1912	c.1713_1714delCA	c.(1711-1716)cccacafs	p.T572fs		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	572	Pro-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		CGTTTCTGCCCACACACACACA	0.53																																						ENST00000401878.3																			0				breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27						c.(1711-1716)cccafs		RNA binding motif protein 33																																				SO:0001589	frameshift_variant	155435						nucleotide binding|RNA binding	g.chr7:155531073_155531074delCA	AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"""RNA binding motif (RRM) containing"""	27223	protein-coding gene	gene with protein product			"""proline rich 8"""	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.1713_1714delCA	7.37:g.155531083_155531084delCA	ENSP00000384160:p.Thr572fs						p.PT571fs	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)	11	1911_1912	+	all_neural(206;0.101)	all_hematologic(28;0.0592)	571			Pro-rich.		A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Frame_Shift_Del	DEL	ENST00000401878.3	37	c.1713_1714delCA	CCDS5941.2																																																																																				0.530	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		7	325						7	325	---	---	---	---
USP17L2	377630	broad.mit.edu	37	8	11994579	11994580	+	IGR	DEL	TG	TG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr8:11994579_11994580delTG	ENST00000333796.3	-	0	1910				FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2						apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						TGTTCgtgtttgtgtgtgtgtg	0.505																																						ENST00000434078.2																			0																																																	SO:0001628	intergenic_variant	0							g.chr8:11994579_11994580delTG	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"""deubiquitinating enzyme 3"""	610186	"""ubiquitin specific peptidase 17-like 2"""				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295		8.37:g.11994589_11994590delTG								NR_027425.1						0	608	+									RNA	DEL	ENST00000333796.3	37		CCDS43713.1																																																																																				0.505	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402		8	171						8	171	---	---	---	---
NEFL	4747	broad.mit.edu	37	8	24811843	24811843	+	RNA	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr8:24811843delA	ENST00000221169.5	-	0	1639				CTD-2168K21.2_ENST00000607735.1_RNA			P07196	NFL_HUMAN	neurofilament, light polypeptide						anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|intermediate filament organization (GO:0045109)|locomotion (GO:0040011)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron apoptotic process (GO:0043524)|neurofilament bundle assembly (GO:0033693)|neuromuscular process controlling balance (GO:0050885)|neuron projection morphogenesis (GO:0048812)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of axonogenesis (GO:0050772)|protein polymerization (GO:0051258)|regulation of axon diameter (GO:0031133)|response to corticosterone (GO:0051412)|response to peptide hormone (GO:0043434)|response to toxic substance (GO:0009636)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|neurofilament (GO:0005883)	identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|protein C-terminus binding (GO:0008022)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)	21		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		AAAATAAAACAAAAAAAAAAT	0.328																																						ENST00000221169.5																			0				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)	21								neurofilament, light polypeptide				13,77,3392		0,0,13,0,77,1651	83.0	77.0	79.0			-0.0	0.0	8		84	21,171,7606		1,0,19,1,169,3709	no	intron	NEFL	NM_006158.3		1,0,32,1,246,5360	A1A1,A1A2,A1R,A2A2,A2R,RR		2.4622,2.5847,2.5			24811843	34,248,10998	1807	4067	5874			4747				anterograde axon cargo transport|axon transport of mitochondrion|neurofilament bundle assembly|retrograde axon cargo transport|synaptic transmission	cytosol|neurofilament	identical protein binding|protein C-terminus binding|structural constituent of cytoskeleton	g.chr8:24811843delA		CCDS75712.1	8p21.2	2014-09-17	2008-09-19		ENSG00000104725	ENSG00000277586		"""Intermediate filaments type IV"""	7739	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 110"""	162280	"""neurofilament, light polypeptide 68kDa"""			17620486, 3145240	Standard	NM_006158		Approved	NFL, CMT1F, CMT2E, NF68, PPP1R110	uc003xee.4	P07196	OTTHUMG00000134284		8.37:g.24811843delA										P07196	NFL_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)	0	1639	-		Ovarian(32;0.00965)|Prostate(55;0.157)						B9ZVN2|Q16154|Q8IU72	RNA	DEL	ENST00000221169.5	37																																																																																						0.328	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158		12	249						12	249	---	---	---	---
TEX15	56154	broad.mit.edu	37	8	30695491	30695491	+	Frame_Shift_Del	DEL	T	T	-	rs571456178		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr8:30695491delT	ENST00000256246.2	-	3	7234	c.7160delA	c.(7159-7161)aagfs	p.K2387fs		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	2387					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		CATTTCAACCTTTTTTGGCGT	0.388																																						ENST00000256246.2																			0				NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138						c.(7159-7161)agfs		testis expressed 15							183.0	183.0	183.0					8																	30695491		2203	4300	6503	SO:0001589	frameshift_variant	56154							g.chr8:30695491delT	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.7160delA	8.37:g.30695491delT	ENSP00000256246:p.Lys2387fs						p.K2387fs	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN		KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)	3	7234	-			2387						Frame_Shift_Del	DEL	ENST00000256246.2	37	c.7160delA	CCDS6080.1																																																																																				0.388	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			8	1009						8	1009	---	---	---	---
WRN	7486	broad.mit.edu	37	8	30945377	30945379	+	In_Frame_Del	DEL	AAG	AAG	-	rs555283914	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr8:30945377_30945379delAAG	ENST00000298139.5	+	12	1766_1768	c.1517_1519delAAG	c.(1516-1521)aaagaa>aaa	p.E510del		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	510	Poly-Glu.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		CTTCCTACTAaagaagaagaaga	0.36			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome					3	0.000599042	0.0	0.0	5008	,	,		22085	0.001		0.001	False		,,,				2504	0.001				Ovarian(18;161 598 2706 14834 27543)	ENST00000298139.5			yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	"""Mis, N, F, S"""	Werner syndrome (RECQL2)			"""L, E, M, O"""		"""osteosarcoma, meningioma, others"""			0				central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60						c.(1516-1521)aaa>a	Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome, RecQ helicase-like																																				SO:0001651	inframe_deletion	7486	Werner syndrome	Familial Cancer Database	WS, Adult Progeria	base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding	g.chr8:30945377_30945379delAAG		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.1517_1519delAAG	8.37:g.30945386_30945388delAAG	ENSP00000298139:p.Glu510del						p.KE506del	NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)	12	1766_1768	+		Breast(100;0.195)	506					A1KYY9	In_Frame_Del	DEL	ENST00000298139.5	37	c.1517_1519delAAG	CCDS6082.1																																																																																				0.360	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			9	406						9	406	---	---	---	---
PCMTD1	115294	broad.mit.edu	37	8	52733063	52733063	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr8:52733063delT	ENST00000360540.5	-	7	1328	c.922delA	c.(922-924)atgfs	p.M308fs	PCMTD1_ENST00000544451.1_Frame_Shift_Del_p.M232fs|PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000522514.1_Frame_Shift_Del_p.M308fs	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	308						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				tcctcttccattttttcatcc	0.373																																						ENST00000360540.5																			0				NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37						c.(922-924)tgfs		protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1							102.0	88.0	92.0					8																	52733063		2203	4300	6503	SO:0001589	frameshift_variant	115294					cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity	g.chr8:52733063delT		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.922delA	8.37:g.52733063delT	ENSP00000353739:p.Met308fs					PCMTD1_ENST00000544451.1_Frame_Shift_Del_p.M232fs|PCMTD1_ENST00000522514.1_Frame_Shift_Del_p.M308fs|PCMTD1_ENST00000519559.1_5'UTR	p.M308fs	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN			7	1328	-		Lung NSC(129;0.0795)|all_lung(136;0.144)	308					Q96FK9	Frame_Shift_Del	DEL	ENST00000360540.5	37	c.922delA	CCDS6148.1																																																																																				0.373	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937		21	482						21	482	---	---	---	---
TOX	9760	broad.mit.edu	37	8	59750796	59750798	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr8:59750796_59750798delCTT	ENST00000361421.1	-	5	986_988	c.766_768delAAG	c.(766-768)aagdel	p.K256del		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	256						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				CATTGGGATCCTTCTTCTTCTTC	0.453																																					Pancreas(161;610 1969 17913 21374 22725)	ENST00000361421.1																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33						c.(766-768)del		thymocyte selection-associated high mobility group box																																				SO:0001651	inframe_deletion	9760					nucleus	DNA binding	g.chr8:59750796_59750798delCTT		CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.766_768delAAG	8.37:g.59750805_59750807delCTT	ENSP00000354842:p.Lys256del						p.K256del	NM_014729.2	NP_055544.1	O94900	TOX_HUMAN			5	986_988	-		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)	256					Q96AV5	In_Frame_Del	DEL	ENST00000361421.1	37	c.766_768delAAG	CCDS34897.1																																																																																				0.453	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		8	676						8	676	---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81733713	81733713	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr8:81733713delT	ENST00000327835.3	-	2	348	c.117delA	c.(115-117)aaafs	p.K39fs		NM_001033723.2	NP_001028895.1	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	39							metal ion binding (GO:0046872)			lung(9)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			TCCGGCTGGCTTTTTTGGTGT	0.428																																						ENST00000327835.3																			0				lung(9)|skin(1)|upper_aerodigestive_tract(1)	11						c.(115-117)aafs		zinc finger protein 704							329.0	308.0	315.0					8																	81733713		2203	4300	6503	SO:0001589	frameshift_variant	619279					intracellular	zinc ion binding	g.chr8:81733713delT	AK131274	CCDS34913.1	8q21.13	2008-05-02			ENSG00000164684	ENSG00000164684			32291	protein-coding gene	gene with protein product							Standard	NM_001033723		Approved	FLJ16218, Gig1	uc003yby.2	Q6ZNC4	OTTHUMG00000164733	ENST00000327835.3:c.117delA	8.37:g.81733713delT	ENSP00000331462:p.Lys39fs						p.K39fs	NM_001033723.2	NP_001028895.1	Q6ZNC4	ZN704_HUMAN	BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)		2	348	-	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		39					B2RNE6|B9EGW6	Frame_Shift_Del	DEL	ENST00000327835.3	37	c.117delA	CCDS34913.1																																																																																				0.428	ZNF704-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379964.2	NM_001033723		7	1622						7	1622	---	---	---	---
FOXE1	2304	broad.mit.edu	37	9	100616701	100616706	+	In_Frame_Del	DEL	GCCGCC	GCCGCC	-	rs371516340|rs565664344|rs71369530	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr9:100616701_100616706delGCCGCC	ENST00000375123.3	+	1	1166_1171	c.505_510delGCCGCC	c.(505-510)gccgccdel	p.AA177del		NM_004473.3	NP_004464.2	O00358	FOXE1_HUMAN	forkhead box E1 (thyroid transcription factor 2)	177	Ala-rich.|Poly-Ala.				anatomical structure morphogenesis (GO:0009653)|cell migration (GO:0016477)|embryonic organ morphogenesis (GO:0048562)|hair follicle morphogenesis (GO:0031069)|hard palate development (GO:0060022)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pharynx development (GO:0060465)|positive regulation of transcription, DNA-templated (GO:0045893)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5		Acute lymphoblastic leukemia(62;0.158)				Ggctgccgcagccgccgccgccgccg	0.767																																						ENST00000375123.3																			0				central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5						c.(505-510)del		forkhead box E1 (thyroid transcription factor 2)																																				SO:0001651	inframe_deletion	2304				cell migration|embryonic organ morphogenesis|hair follicle morphogenesis|hard palate development|lens morphogenesis in camera-type eye|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|peripheral nervous system development|pharynx development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|soft palate development|thymus development|thyroid gland development|thyroid hormone generation	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding	g.chr9:100616701_100616706delGCCGCC	U89995	CCDS35078.1	9q22	2008-09-05			ENSG00000178919	ENSG00000178919		"""Forkhead boxes"""	3806	protein-coding gene	gene with protein product		602617	"""forkhead box E2"""	FKHL15, TITF2, FOXE2		9169137, 9697705	Standard	NM_004473		Approved	TTF-2, HFKH4	uc004axu.3	O00358	OTTHUMG00000020333	ENST00000375123.3:c.505_510delGCCGCC	9.37:g.100616707_100616712delGCCGCC	ENSP00000364265:p.Ala177_Ala178del						p.AA177del	NM_004473.3	NP_004464.2	O00358	FOXE1_HUMAN			1	1166_1171	+		Acute lymphoblastic leukemia(62;0.158)	177			Ala-rich.|Poly-Ala.		O75765|Q5T109|Q99526	In_Frame_Del	DEL	ENST00000375123.3	37	c.505_510delGCCGCC	CCDS35078.1																																																																																				0.767	FOXE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053341.1			15	53						15	53	---	---	---	---
ZNF518A	9849	broad.mit.edu	37	10	97918855	97918856	+	RNA	INS	-	-	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr10:97918855_97918856insA	ENST00000534948.1	+	0	3633_3634							Q6AHZ1	Z518A_HUMAN	zinc finger protein 518A						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)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		AAATTCAGAACAAAAAAAAACT	0.347																																						ENST00000534948.1																			0				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24								zinc finger protein 518A																																						9849				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr10:97918855_97918856insA	AB002333	CCDS73170.1	10q23.33	2012-08-08	2007-12-07	2007-12-07	ENSG00000177853	ENSG00000177853		"""Zinc fingers, C2H2-type"""	29009	protein-coding gene	gene with protein product			"""zinc finger protein 518"""	ZNF518		9205841	Standard	NM_014803		Approved	KIAA0335	uc001klp.3	Q6AHZ1	OTTHUMG00000018828		10.37:g.97918864_97918864dupA										Q6AHZ1	Z518A_HUMAN		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)	0	3633_3634	+		Colorectal(252;0.0815)						A0PJI5|O15044|Q32MP4	RNA	INS	ENST00000534948.1	37																																																																																						0.347	ZNF518A-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014803		7	235						7	235	---	---	---	---
TM9SF3	56889	broad.mit.edu	37	10	98336475	98336475	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr10:98336475delT	ENST00000371142.4	-	2	430	c.214delA	c.(214-216)agtfs	p.S72fs		NM_020123.3	NP_064508.3	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3	72						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)	15		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)		TGACTGATACTTTTTTTTGAC	0.363																																						ENST00000371142.4																			0				breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)	15						c.(214-216)gtfs		transmembrane 9 superfamily member 3							146.0	145.0	145.0					10																	98336475		2203	4300	6503	SO:0001589	frameshift_variant	56889					integral to membrane	binding	g.chr10:98336475delT	AF160213, AF269150	CCDS7450.1	10q24.2	2006-04-12			ENSG00000077147	ENSG00000077147			21529	protein-coding gene	gene with protein product						11530251, 11595169	Standard	NM_020123		Approved	SMBP	uc001kmm.4	Q9HD45	OTTHUMG00000018834	ENST00000371142.4:c.214delA	10.37:g.98336475delT	ENSP00000360184:p.Ser72fs						p.S72fs	NM_020123.3	NP_064508.3	Q9HD45	TM9S3_HUMAN		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)	2	430	-		Colorectal(252;0.158)	72					Q5TB57|Q6UWE7|Q9NWL8|Q9P0G9|Q9UHW8	Frame_Shift_Del	DEL	ENST00000371142.4	37	c.214delA	CCDS7450.1																																																																																				0.363	TM9SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049610.2	NM_020123		11	735						11	735	---	---	---	---
NOLC1	9221	broad.mit.edu	37	10	103919000	103919002	+	In_Frame_Del	DEL	AGC	AGC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr10:103919000_103919002delAGC	ENST00000605788.1	+	6	893_895	c.658_660delAGC	c.(658-660)agcdel	p.S227del	NOLC1_ENST00000405356.1_In_Frame_Del_p.S227del|NOLC1_ENST00000488254.2_In_Frame_Del_p.S228del|NOLC1_ENST00000603742.1_5'UTR	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	227	11 X 12 AA approximate repeats of an acidic serine cluster.|Interacts with RPA194.				cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		tagcagcagtagcagcagcagca	0.517																																						ENST00000405356.1																			0				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31						c.(658-660)del		nucleolar and coiled-body phosphoprotein 1																																				SO:0001651	inframe_deletion	9221				mitosis|rRNA processing	cytoplasm|nucleolus	ATP binding|GTP binding|protein binding	g.chr10:103919000_103919002delAGC	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.658_660delAGC	10.37:g.103919009_103919011delAGC	ENSP00000474710:p.Ser227del					NOLC1_ENST00000605788.1_In_Frame_Del_p.S227del|NOLC1_ENST00000488254.2_In_Frame_Del_p.S228del|NOLC1_ENST00000603742.1_5'UTR	p.S227del			Q14978	NOLC1_HUMAN		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)	6	893_895	+		Colorectal(252;0.122)	227			11 X 12 AA approximate repeats of an acidic serine cluster.|Interacts with RPA194.		Q15030|Q5VV70|Q9BUV3	In_Frame_Del	DEL	ENST00000605788.1	37	c.658_660delAGC	CCDS7530.1																																																																																				0.517	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		11	1010						11	1010	---	---	---	---
NT5C2	22978	broad.mit.edu	37	10	104849436	104849438	+	In_Frame_Del	DEL	TCC	TCC	-	rs537259520	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr10:104849436_104849438delTCC	ENST00000404739.3	-	17	1700_1702	c.1677_1679delGGA	c.(1675-1680)gaggaa>gaa	p.559_560EE>E	NT5C2_ENST00000343289.5_In_Frame_Del_p.559_560EE>E|NT5C2_ENST00000369857.4_5'UTR|CNNM2_ENST00000369878.4_3'UTR|NT5C2_ENST00000423468.2_In_Frame_Del_p.530_531EE>E			P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	559	Asp/Glu-rich (acidic).				cell death (GO:0008219)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|nucleobase-containing small molecule metabolic process (GO:0055086)|phosphorylation (GO:0016310)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleoside phosphotransferase activity (GO:0050146)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|urinary_tract(1)	16		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	tccttattcttcctcctcctcct	0.502														3	0.000599042	0.0008	0.0	5008	,	,		18489	0.0		0.001	False		,,,				2504	0.001					ENST00000343289.5																			0				cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|urinary_tract(1)	16						c.(1675-1680)gaa>ga		5'-nucleotidase, cytosolic II	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)																																			SO:0001651	inframe_deletion	22978				purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding	g.chr10:104849436_104849438delTCC	D38524	CCDS7544.1	10q24.32	2014-03-03	2002-04-18	2002-04-19	ENSG00000076685	ENSG00000076685			8022	protein-coding gene	gene with protein product	"""purine 5' nucleotidase"""	600417	"""5'-nucleotidase (purine), cytosolic type B"""	NT5B		7999131, 24482476	Standard	NM_012229		Approved	PNT5, GMP, cN-II, SPG65	uc001kwq.3	P49902	OTTHUMG00000018981	ENST00000404739.3:c.1677_1679delGGA	10.37:g.104849445_104849447delTCC	ENSP00000383960:p.Glu561del					NT5C2_ENST00000423468.2_In_Frame_Del_p.EE530del|NT5C2_ENST00000369857.4_5'UTR|NT5C2_ENST00000404739.3_In_Frame_Del_p.EE559del	p.EE559del	NM_001134373.2|NM_012229.4	NP_001127845.1|NP_036361.1	P49902	5NTC_HUMAN		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	18	1764_1766	-		all_hematologic(284;0.176)|Colorectal(252;0.178)	559			Asp/Glu-rich (acidic).		B7Z382|D3DR91|Q5JUV5	In_Frame_Del	DEL	ENST00000404739.3	37	c.1677_1679delGGA	CCDS7544.1																																																																																				0.502	NT5C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050121.1	NM_012229		7	177						7	177	---	---	---	---
AFAP1L2	84632	broad.mit.edu	37	10	116062107	116062107	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr10:116062107delT	ENST00000304129.4	-	12	1450	c.1421delA	c.(1420-1422)aacfs	p.N474fs	AFAP1L2_ENST00000491814.1_5'Flank|AFAP1L2_ENST00000369271.3_Frame_Shift_Del_p.N474fs|AFAP1L2_ENST00000545353.1_Frame_Shift_Del_p.N527fs			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	474					inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		CAAGAGAGAGTTTTTGGCCGC	0.547																																						ENST00000369271.3																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21						c.(1420-1422)acfs		actin filament associated protein 1-like 2							154.0	171.0	165.0					10																	116062107		2203	4300	6503	SO:0001589	frameshift_variant	84632				inflammatory response|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of transcription, DNA-dependent|regulation of interleukin-6 production|regulation of mitotic cell cycle	cytoplasm	protein tyrosine kinase activator activity|SH2 domain binding|SH3 domain binding	g.chr10:116062107delT	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"""Pleckstrin homology (PH) domain containing"""	25901	protein-coding gene	gene with protein product		612420	"""KIAA1914"""	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.1421delA	10.37:g.116062107delT	ENSP00000303042:p.Asn474fs					AFAP1L2_ENST00000545353.1_Frame_Shift_Del_p.N527fs|AFAP1L2_ENST00000304129.4_Frame_Shift_Del_p.N474fs	p.N474fs	NM_001001936.1|NM_032550.2	NP_001001936.1|NP_115939.1	Q8N4X5	AF1L2_HUMAN		Epithelial(162;0.0219)|all cancers(201;0.0561)	12	1721	-		Colorectal(252;0.175)|Breast(234;0.231)	474					A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Frame_Shift_Del	DEL	ENST00000304129.4	37	c.1421delA	CCDS31286.1																																																																																				0.547	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550		7	1101						7	1101	---	---	---	---
CPXM2	119587	broad.mit.edu	37	10	125528165	125528167	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr10:125528165_125528167delCAG	ENST00000241305.3	-	9	1328_1330	c.1174_1176delCTG	c.(1174-1176)ctgdel	p.L392del	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	392	Poly-Leu.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		CGAACTGCACCAGCAGCAGCAGC	0.626																																						ENST00000241305.3																			0				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47						c.(1174-1176)del		carboxypeptidase X (M14 family), member 2																																				SO:0001651	inframe_deletion	119587				cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding	g.chr10:125528165_125528167delCAG	AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase"""					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.1174_1176delCTG	10.37:g.125528174_125528176delCAG	ENSP00000241305:p.Leu392del					CPXM2_ENST00000368854.3_5'UTR	p.L392del	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)	9	1328_1330	-		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)	392			Poly-Leu.		B4E3Q2	In_Frame_Del	DEL	ENST00000241305.3	37	c.1174_1176delCTG	CCDS7637.1																																																																																				0.626	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		13	861						13	861	---	---	---	---
TSPAN4	7106	broad.mit.edu	37	11	864443	864445	+	In_Frame_Del	DEL	CTG	CTG	-	rs61867552	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:864443_864445delCTG	ENST00000397404.1	+	5	521_523	c.262_264delCTG	c.(262-264)ctgdel	p.L92del	TSPAN4_ENST00000525201.1_In_Frame_Del_p.L28del|TSPAN4_ENST00000397408.1_In_Frame_Del_p.L92del|TSPAN4_ENST00000397411.2_In_Frame_Del_p.L92del|TSPAN4_ENST00000397396.1_In_Frame_Del_p.L28del|TSPAN4_ENST00000397406.1_In_Frame_Del_p.L92del|TSPAN4_ENST00000409531.1_In_Frame_Del_p.L111del|TSPAN4_ENST00000346501.4_In_Frame_Del_p.L92del|TSPAN4_ENST00000409543.2_In_Frame_Del_p.L92del|TSPAN4_ENST00000397397.2_In_Frame_Del_p.L92del	NM_001025237.1	NP_001020408.1	O14817	TSN4_HUMAN	tetraspanin 4	92					protein complex assembly (GO:0006461)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	antigen binding (GO:0003823)|integrin binding (GO:0005178)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)	3		all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)		all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ACAGTTCTTCCTGCTGCTGCTGC	0.65																																						ENST00000397404.1																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)	3						c.(262-264)del		tetraspanin 4																																				SO:0001651	inframe_deletion	0				protein complex assembly	integral to plasma membrane		g.chr11:864443_864445delCTG	AF022813	CCDS7721.1, CCDS41589.1	11p15.5	2013-02-14	2005-03-21	2005-03-21	ENSG00000214063	ENSG00000214063		"""Tetraspanins"""	11859	protein-coding gene	gene with protein product		602644	"""transmembrane 4 superfamily member 7"""	TM4SF7		9360996	Standard	XM_005253102		Approved	NAG-2, TSPAN-4, TETRASPAN	uc001lsf.1	O14817	OTTHUMG00000133305	ENST00000397404.1:c.262_264delCTG	11.37:g.864452_864454delCTG	ENSP00000380553:p.Leu92del					TSPAN4_ENST00000525201.1_In_Frame_Del_p.L28del|TSPAN4_ENST00000409543.2_In_Frame_Del_p.L92del|TSPAN4_ENST00000397397.2_In_Frame_Del_p.L92del|TSPAN4_ENST00000397408.1_In_Frame_Del_p.L92del|TSPAN4_ENST00000346501.4_In_Frame_Del_p.L92del|TSPAN4_ENST00000409531.1_In_Frame_Del_p.L111del|TSPAN4_ENST00000397406.1_In_Frame_Del_p.L92del|TSPAN4_ENST00000397396.1_In_Frame_Del_p.L28del|TSPAN4_ENST00000397411.2_In_Frame_Del_p.L92del	p.L92del	NM_001025237.1	NP_001020408.1	O14817	TSN4_HUMAN		all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	5	521_523	+		all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	92					Q6IAP6	In_Frame_Del	DEL	ENST00000397404.1	37	c.262_264delCTG	CCDS7721.1																																																																																				0.650	TSPAN4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257102.2			11	606						11	606	---	---	---	---
TSSC2	650368	broad.mit.edu	37	11	3424761	3424761	+	RNA	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:3424761delA	ENST00000529482.1	+	0	845									tumor suppressing subtransferable candidate 2 pseudogene																		gtctgtcaggaaaaaaaaaaa	0.413																																						ENST00000529482.1																			0																																																			0							g.chr11:3424761delA			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3424761delA														0	845	+									RNA	DEL	ENST00000529482.1	37																																																																																						0.413	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			17	134						17	134	---	---	---	---
SLC22A9	114571	broad.mit.edu	37	11	63149668	63149669	+	Frame_Shift_Ins	INS	-	-	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:63149668_63149669insA	ENST00000279178.3	+	6	1241_1242	c.992_993insA	c.(991-996)gcacaafs	p.Q332fs	SLC22A9_ENST00000310969.4_3'UTR	NM_080866.2	NP_543142.2	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion transporter), member 9	332					hormone transport (GO:0009914)|short-chain fatty acid import (GO:0015913)|sodium-independent organic anion transport (GO:0043252)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	anion:anion antiporter activity (GO:0015301)|short-chain fatty acid uptake transporter activity (GO:0015636)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	18						CTGGAGGCAGCACAAAAAAAAA	0.406																																						ENST00000279178.3																			0				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	18						c.(991-993)gcafs		solute carrier family 22 (organic anion transporter), member 9																																				SO:0001589	frameshift_variant	114571				transmembrane transport	integral to membrane		g.chr11:63149668_63149669insA	AP001880	CCDS8043.1	11q12.3	2014-05-20	2008-01-11		ENSG00000149742	ENSG00000149742		"""Solute carriers"""	16261	protein-coding gene	gene with protein product		607579				11327718, 17393504	Standard	NM_080866		Approved	OAT4, FLJ23666, UST3, OAT7	uc001nww.3	Q8IVM8	OTTHUMG00000167805	ENST00000279178.3:c.993dupA	11.37:g.63149669_63149669dupA	ENSP00000279178:p.Gln332fs					SLC22A9_ENST00000310969.4_3'UTR	p.A331fs	NM_080866.2	NP_543142.2	Q8IVM8	S22A9_HUMAN			6	1241_1242	+			331					A0AVB7|A4PB24|Q8TCC8|Q8TEC0|Q8WYN7	Frame_Shift_Ins	INS	ENST00000279178.3	37	c.992_993insA	CCDS8043.1																																																																																				0.406	SLC22A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396371.1	NM_080866		8	766						8	766	---	---	---	---
VEGFB	7423	broad.mit.edu	37	11	64004663	64004663	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:64004663delA	ENST00000309422.2	+	5	675	c.379delA	c.(379-381)aaafs	p.K129fs	RP11-783K16.14_ENST00000539963.1_RNA|RP11-783K16.14_ENST00000534988.1_RNA|VEGFB_ENST00000426086.2_Frame_Shift_Del_p.K129fs	NM_001243733.1|NM_003377.4	NP_001230662.1|NP_003368.1	P49765	VEGFB_HUMAN	vascular endothelial growth factor B	129					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|coronary vasculature development (GO:0060976)|induction of positive chemotaxis (GO:0050930)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular wound healing (GO:0035470)|protein O-linked glycosylation (GO:0006493)|response to drug (GO:0042493)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|heparin binding (GO:0008201)|vascular endothelial growth factor receptor 1 binding (GO:0043183)	p.K129fs*5(2)		endometrium(2)|large_intestine(2)|prostate(1)|stomach(1)	6					Aflibercept(DB08885)	TTTCAGACCTAAAAAAAAGGA	0.473																																						ENST00000309422.2																			2	Deletion - Frameshift(2)	p.K129fs*5(2)	large_intestine(2)	endometrium(2)|large_intestine(2)|prostate(1)|stomach(1)	6						c.(379-381)aafs		vascular endothelial growth factor B							137.0	121.0	126.0					11																	64004663		2201	4297	6498	SO:0001589	frameshift_variant	7423				anti-apoptosis|induction of positive chemotaxis|negative regulation of gene expression|negative regulation of neuron apoptosis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of endothelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of mast cell chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of vascular endothelial growth factor receptor signaling pathway|positive regulation of vascular wound healing|vascular endothelial growth factor receptor signaling pathway	extracellular region|extracellular space|membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity|heparin binding|vascular endothelial growth factor receptor 1 binding	g.chr11:64004663delA	BC008818	CCDS8062.1, CCDS58144.1	11q13	2005-09-29				ENSG00000173511			12681	protein-coding gene	gene with protein product		601398		VRF		8637916, 8919691	Standard	NM_001243733		Approved	VEGFL	uc001nyw.3	P49765		ENST00000309422.2:c.379delA	11.37:g.64004663delA	ENSP00000311127:p.Lys129fs					VEGFB_ENST00000426086.2_Frame_Shift_Del_p.K129fs	p.K129fs	NM_001243733.1|NM_003377.4	NP_001230662.1|NP_003368.1	P49765	VEGFB_HUMAN			5	675	+			129					Q16528	Frame_Shift_Del	DEL	ENST00000309422.2	37	c.379delA	CCDS8062.1																																																																																				0.473	VEGFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396393.2	NM_003377		8	611						8	611	---	---	---	---
PVRL1	5818	broad.mit.edu	37	11	119535678	119535680	+	In_Frame_Del	DEL	CCT	CCT	-	rs539461545|rs375181781|rs369523216		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr11:119535678_119535680delCCT	ENST00000264025.3	-	6	1861_1863	c.1331_1333delAGG	c.(1330-1335)gagggc>ggc	p.E444del	PVRL1_ENST00000341398.2_Intron	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	444	Poly-Glu.				adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)	p.E444fs*>73(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		CCTCCACCGCcctcctcctcctc	0.66																																						ENST00000264025.3																			1	Deletion - Frameshift(1)	p.E444fs*>73(1)	kidney(1)	breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						c.(1330-1335)ggc>g		poliovirus receptor-related 1 (herpesvirus entry mediator C)																																				SO:0001651	inframe_deletion	5818				adherens junction organization|cell junction assembly|entry of virus into host cell|heterophilic cell-cell adhesion|homophilic cell adhesion|immune response	cell-cell adherens junction|extracellular region|integral to membrane	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity	g.chr11:119535678_119535680delCCT	X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9706	protein-coding gene	gene with protein product	"""nectin"""	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000264025.3:c.1331_1333delAGG	11.37:g.119535687_119535689delCCT	ENSP00000264025:p.Glu444del					PVRL1_ENST00000341398.2_Intron	p.EG444del	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)	6	1861_1863	-		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	444			Poly-Glu.		O75465|Q2M3D3|Q9HBE6|Q9HBW2	In_Frame_Del	DEL	ENST00000264025.3	37	c.1331_1333delAGG	CCDS8426.1																																																																																				0.660	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1			10	203						10	203	---	---	---	---
SCAF11	9169	broad.mit.edu	37	12	46320707	46320708	+	Frame_Shift_Del	DEL	TC	TC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr12:46320707_46320708delTC	ENST00000369367.3	-	11	3009_3010	c.2776_2777delGA	c.(2776-2778)gaafs	p.E926fs	SCAF11_ENST00000419565.2_Frame_Shift_Del_p.E926fs|SCAF11_ENST00000465950.1_Frame_Shift_Del_p.E611fs|SCAF11_ENST00000549162.1_Frame_Shift_Del_p.E734fs|SCAF11_ENST00000550629.1_5'Flank	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	926	Arg-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						GGTTCTCCTTTCTCTCTCTCTC	0.446																																						ENST00000465950.1																			0				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						c.(1831-1833)afs		SR-related CTD-associated factor 11																																				SO:0001589	frameshift_variant	9169				spliceosome assembly	nucleus	protein binding|zinc ion binding	g.chr12:46320707_46320708delTC	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.2776_2777delGA	12.37:g.46320717_46320718delTC	ENSP00000358374:p.Glu926fs					SCAF11_ENST00000419565.2_Frame_Shift_Del_p.E926fs|SCAF11_ENST00000369367.3_Frame_Shift_Del_p.E926fs|SCAF11_ENST00000549162.1_Frame_Shift_Del_p.E734fs	p.E611fs			Q99590	SCAFB_HUMAN			1	3040_3041	-			926					A6NEU9|A6NLW5|Q8IW59	Frame_Shift_Del	DEL	ENST00000369367.3	37	c.1831_1832delGA	CCDS8748.2																																																																																				0.446	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		7	912						7	912	---	---	---	---
CBX5	23468	broad.mit.edu	37	12	54645832	54645832	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr12:54645832delT	ENST00000439541.2	-	3	442	c.317delA	c.(316-318)aagfs	p.K106fs	CBX5_ENST00000209875.4_Frame_Shift_Del_p.K106fs|CBX5_ENST00000550411.1_Frame_Shift_Del_p.K106fs	NM_001127321.1	NP_001120793.1	P45973	CBX5_HUMAN	chromobox homolog 5	106					blood coagulation (GO:0007596)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	chromocenter (GO:0010369)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear heterochromatin (GO:0005720)|nuclear pericentric heterochromatin (GO:0031618)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|protein binding, bridging (GO:0030674)|repressing transcription factor binding (GO:0070491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	8						TACCTCTCTCTTTTTTTTAGA	0.323																																					Colon(153;588 2459 18334 48613)	ENST00000209875.4																			0				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	8						c.(316-318)agfs		chromobox homolog 5							142.0	148.0	146.0					12																	54645832		2203	4300	6503	SO:0001589	frameshift_variant	23468				blood coagulation|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|nuclear centromeric heterochromatin|nuclear envelope|nucleolus|transcriptional repressor complex	methylated histone residue binding|protein binding, bridging|repressing transcription factor binding	g.chr12:54645832delT	U26311	CCDS8875.1	12q13.13	2010-07-06	2010-06-24		ENSG00000094916	ENSG00000094916			1555	protein-coding gene	gene with protein product	"""HP1 alpha homolog (Drosophila)"""	604478	"""chromobox homolog 5 (Drosophila HP1 alpha)"", ""chromobox homolog 5 (HP1 alpha homolog, Drosophila)"""			8663349	Standard	NM_012117		Approved	HP1Hs-alpha, HP1, HP1-ALPHA	uc001sfj.4	P45973		ENST00000439541.2:c.317delA	12.37:g.54645832delT	ENSP00000401009:p.Lys106fs					CBX5_ENST00000439541.2_Frame_Shift_Del_p.K106fs|CBX5_ENST00000550411.1_Frame_Shift_Del_p.K106fs	p.K106fs	NM_012117.2	NP_036249.1	P45973	CBX5_HUMAN			3	453	-			106					B2R8T9	Frame_Shift_Del	DEL	ENST00000439541.2	37	c.317delA	CCDS8875.1																																																																																				0.323	CBX5-004	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000405468.1	NM_012117		9	1042						9	1042	---	---	---	---
ARHGEF25	115557	broad.mit.edu	37	12	58010623	58010623	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr12:58010623delA	ENST00000286494.4	+	15	2149	c.1689delA	c.(1687-1689)ccafs	p.P563fs	AC025165.8_ENST00000593846.1_RNA|AC025165.8_ENST00000356672.3_RNA|ARHGEF25_ENST00000477314.1_3'UTR|ARHGEF25_ENST00000333972.7_Frame_Shift_Del_p.P602fs|AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000610219.1_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	563						cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						CTCCAACTCCAAAAACCCCTC	0.537																																						ENST00000286494.4																			0				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						c.(1687-1689)ccfs		Rho guanine nucleotide exchange factor (GEF) 25							106.0	119.0	115.0					12																	58010623		2203	4300	6503	SO:0001589	frameshift_variant	115557				regulation of Rho protein signal transduction	cytosol|plasma membrane|sarcomere	Rho guanyl-nucleotide exchange factor activity	g.chr12:58010623delA		CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"""Rho guanine nucleotide exchange factors"""	30275	protein-coding gene	gene with protein product	"""RAC/CDC42 exchange factor"""	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1689delA	12.37:g.58010623delA	ENSP00000286494:p.Pro563fs					ARHGEF25_ENST00000333972.7_Frame_Shift_Del_p.P602fs|AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000356672.3_RNA|AC025165.8_ENST00000593846.1_RNA|ARHGEF25_ENST00000477314.1_3'UTR	p.P563fs	NM_182947.3	NP_891992.2	Q86VW2	ARHGP_HUMAN			15	2149	+			563					A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Frame_Shift_Del	DEL	ENST00000286494.4	37	c.1689delA	CCDS8947.1																																																																																				0.537	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483		7	1032						7	1032	---	---	---	---
TMTC3	160418	broad.mit.edu	37	12	88566417	88566417	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr12:88566417delT	ENST00000266712.6	+	8	1314	c.1094delT	c.(1093-1095)cttfs	p.L365fs		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	365					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						GCATCGAACCTTTTTTTTCCA	0.313																																						ENST00000266712.6																			0				NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						c.(1093-1095)ctfs		transmembrane and tetratricopeptide repeat containing 3				18,4246		6,6,2120	135.0	127.0	130.0			5.5	1.0	12		131	19,8235		6,7,4114	no	frameshift	TMTC3	NM_181783.3		12,13,6234	A1A1,A1R,RR		0.2302,0.4221,0.2956			88566417	37,12481	2203	4299	6502	SO:0001589	frameshift_variant	160418					integral to membrane	binding	g.chr12:88566417delT		CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"""Tetratricopeptide (TTC) repeat domain containing"""	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.1094delT	12.37:g.88566417delT	ENSP00000266712:p.Leu365fs						p.L365fs	NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN			8	1314	+			365					Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Frame_Shift_Del	DEL	ENST00000266712.6	37	c.1094delT	CCDS9032.1																																																																																				0.313	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406421.1	NM_181783		9	659						9	659	---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101680157	101680157	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr12:101680157delT	ENST00000261637.4	+	5	559	c.385delT	c.(385-387)tttfs	p.F130fs		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	130					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CTTTCCAGAGTTTTTTTTGAC	0.398																																						ENST00000261637.4																			0				NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						c.(385-387)ttfs		UTP20, small subunit (SSU) processome component, homolog (yeast)							226.0	224.0	224.0					12																	101680157		2203	4300	6503	SO:0001589	frameshift_variant	27340				endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding	g.chr12:101680157delT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.385delT	12.37:g.101680157delT	ENSP00000261637:p.Phe130fs						p.F130fs	NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN			5	559	+			130					Q9H3H4	Frame_Shift_Del	DEL	ENST00000261637.4	37	c.385delT	CCDS9081.1																																																																																				0.398	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		7	1386						7	1386	---	---	---	---
TPTE2P2	644623	broad.mit.edu	37	13	52796688	52796688	+	RNA	DEL	C	C	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr13:52796688delC	ENST00000451298.1	-	0	1229				TPTE2P2_ENST00000606973.1_RNA																							cgctattgctccccacccatc	0.537																																						ENST00000451298.1																			0																																																			0							g.chr13:52796688delC																													13.37:g.52796688delC						RP11-64P12.8_ENST00000606031.1_RNA								0	1229	-									RNA	DEL	ENST00000451298.1	37																																																																																						0.537	RP11-248G5.8-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000471093.1			7	97						7	97	---	---	---	---
LOC102723968	102723968	broad.mit.edu	37	13	64407210	64407211	+	lincRNA	INS	-	-	TACTGTCAG			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr13:64407210_64407211insTACTGTCAG	ENST00000607822.1	-	0	2159																											AGACCTTTATATAATTGCCAAA	0.366																																						ENST00000607822.1																			0																																																			0							g.chr13:64407210_64407211insTACTGTCAG																													13.37:g.64407210_64407211insTACTGTCAG														0	2159	-									RNA	INS	ENST00000607822.1	37																																																																																						0.366	RP11-394A14.2-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000471084.1			9	674						9	674	---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	108518687	108518689	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr13:108518687_108518689delCTG	ENST00000375915.2	-	1	394_396	c.256_258delCAG	c.(256-258)cagdel	p.Q86del		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	86	Poly-Gln.					integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						gccgctgcctctgctgctgctgc	0.719																																						ENST00000375915.2																			0				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						c.(256-258)del		family with sequence similarity 155, member A																																				SO:0001651	inframe_deletion	728215					integral to membrane	binding	g.chr13:108518687_108518689delCTG	L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.256_258delCAG	13.37:g.108518696_108518698delCTG	ENSP00000365080:p.Gln86del						p.Q86del	NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN			1	394_396	-			86			Poly-Gln.		B2RUV1|B7Z334	In_Frame_Del	DEL	ENST00000375915.2	37	c.256_258delCAG	CCDS32006.1																																																																																				0.719	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045736.2	NM_001080396		27	250						27	250	---	---	---	---
IL25	64806	broad.mit.edu	37	14	23845057	23845058	+	Frame_Shift_Del	DEL	TG	TG	-	rs569851542		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr14:23845057_23845058delTG	ENST00000329715.2	+	2	760_761	c.502_503delTG	c.(502-504)tgtfs	p.C168fs	CMTM5_ENST00000555731.1_5'Flank|IL25_ENST00000397242.2_Frame_Shift_Del_p.C152fs|CMTM5_ENST00000359320.3_5'Flank|CMTM5_ENST00000397227.3_5'Flank|CMTM5_ENST00000382809.2_5'Flank|CMTM5_ENST00000342473.4_5'Flank|CMTM5_ENST00000339180.4_5'Flank	NM_022789.3	NP_073626.1	Q9H293	IL25_HUMAN	interleukin 25	168					eosinophil differentiation (GO:0030222)|inflammatory response to antigenic stimulus (GO:0002437)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to fungus (GO:0009620)|response to nematode (GO:0009624)	extracellular space (GO:0005615)	interleukin-17E receptor binding (GO:0030380)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9	all_cancers(95;2e-05)			GBM - Glioblastoma multiforme(265;0.00665)|READ - Rectum adenocarcinoma(4;0.0276)|Colorectal(4;0.0396)		TTCCTTAGCTTGTGTGTGTGTG	0.604																																						ENST00000329715.2																			0				NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9						c.(502-504)tfs		interleukin 25																																				SO:0001589	frameshift_variant	0				inflammatory response	extracellular space|membrane	cytokine activity|interleukin-17E receptor binding	g.chr14:23845057_23845058delTG	AF305200	CCDS9597.1, CCDS45086.1	14q11.2	2008-01-07	2006-05-17	2006-05-17	ENSG00000166090	ENSG00000166090		"""Interleukins and interleukin receptors"""	13765	protein-coding gene	gene with protein product		605658	"""interleukin 17E"""	IL17E		11058597, 11754819	Standard	NM_172314		Approved	IL-25, IL-17E	uc001wjq.3	Q9H293	OTTHUMG00000028749	ENST00000329715.2:c.502_503delTG	14.37:g.23845067_23845068delTG	ENSP00000328111:p.Cys168fs					IL25_ENST00000397242.2_Frame_Shift_Del_p.C152fs	p.C168fs	NM_022789.3	NP_073626.1	Q9H293	IL25_HUMAN		GBM - Glioblastoma multiforme(265;0.00665)|READ - Rectum adenocarcinoma(4;0.0276)|Colorectal(4;0.0396)	2	760_761	+	all_cancers(95;2e-05)		168					Q2M3F0|Q8IZV3|Q8WXB0	Frame_Shift_Del	DEL	ENST00000329715.2	37	c.502_503delTG	CCDS9597.1																																																																																				0.604	IL25-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071789.2			13	652						13	652	---	---	---	---
SNORA11	677799	broad.mit.edu	37	14	70270922	70270922	+	RNA	DEL	T	T	-	rs566317626		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr14:70270922delT	ENST00000408133.1	-	0	126									small nucleolar RNA, H/ACA box 11																		ATGGATTCTCTTTTTTTTTTT	0.353																																						ENST00000408133.1																			0																																																			0							g.chr14:70270922delT	AM055729		Xp11.21	2013-09-05			ENSG00000221716	ENSG00000221716		"""ncRNAs / Small nucleolar RNAs : H/ACA box containing"""	32599	non-coding RNA	RNA, small nucleolar	"""small nucleolar RNA, H/ACA box 11A"""	300662				16361266, 16381836	Standard	NR_002953		Approved	U107, SNORA11A	uc021ptl.1				14.37:g.70270922delT														0	126	-									RNA	DEL	ENST00000408133.1	37																																																																																						0.353	SNORA11.1-201	NOVEL	basic	snoRNA	snoRNA		NR_002953		9	57						9	57	---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73572607	73572608	+	Frame_Shift_Del	DEL	AG	AG	-	rs150988201		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr14:73572607_73572608delAG	ENST00000261973.7	+	11	1480_1481	c.1195_1196delAG	c.(1195-1197)agafs	p.R399fs	RBM25_ENST00000527432.1_Frame_Shift_Del_p.R399fs	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	399	Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		agagcgggaaagagagagagag	0.446																																						ENST00000261973.7																			0				breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31						c.(1195-1197)afs		RNA binding motif protein 25																																				SO:0001589	frameshift_variant	58517				apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding	g.chr14:73572607_73572608delAG	BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"""RNA binding motif (RRM) containing"""	23244	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 94"""	612427	"""RNA-binding region (RNP1, RRM) containing 7"""	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.1195_1196delAG	14.37:g.73572617_73572618delAG	ENSP00000261973:p.Arg399fs					RBM25_ENST00000527432.1_Frame_Shift_Del_p.R399fs	p.R399fs	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)	11	1480_1481	+			399			Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.		A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Frame_Shift_Del	DEL	ENST00000261973.7	37	c.1195_1196delAG	CCDS32113.1																																																																																				0.446	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330		15	191						15	191	---	---	---	---
ELMSAN1	91748	broad.mit.edu	37	14	74205954	74205956	+	In_Frame_Del	DEL	TGC	TGC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr14:74205954_74205956delTGC	ENST00000286523.5	-	2	1538_1540	c.756_758delGCA	c.(754-759)cagcaa>caa	p.252_253QQ>Q	ELMSAN1_ENST00000394071.2_In_Frame_Del_p.252_253QQ>Q|ELMSAN1_ENST00000486739.1_5'Flank	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	252	Gln-rich.|Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										ctgctgtggttgctgctgctgct	0.645																																						ENST00000286523.5																			0											c.(754-759)caa>ca		ELM2 and Myb/SANT-like domain containing 1																																				SO:0001651	inframe_deletion	91748							g.chr14:74205954_74205956delTGC	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 117"", ""chromosome 14 open reading frame 43"""	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.756_758delGCA	14.37:g.74205963_74205965delTGC	ENSP00000286523:p.Gln253del					ELMSAN1_ENST00000394071.2_In_Frame_Del_p.QQ252del	p.QQ252del	NM_194278.3	NP_919254.2					2	1538_1540	-								Q6PK13|Q6PK59|Q6ZS23	In_Frame_Del	DEL	ENST00000286523.5	37	c.756_758delGCA	CCDS9819.1																																																																																				0.645	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		7	193						7	193	---	---	---	---
MLH3	27030	broad.mit.edu	37	14	75514603	75514604	+	Frame_Shift_Ins	INS	-	-	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr14:75514603_75514604insT	ENST00000556740.1	-	1	1790_1791	c.1755_1756insA	c.(1753-1758)aaagaafs	p.E586fs	MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000556257.1_Frame_Shift_Ins_p.E586fs|MLH3_ENST00000355774.2_Frame_Shift_Ins_p.E586fs|MLH3_ENST00000238662.7_Frame_Shift_Ins_p.E586fs|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000380968.2_5'UTR			Q9UHC1	MLH3_HUMAN	mutL homolog 3	586					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)	p.A577_S588delAQTEKEKKKESS(2)|p.E586*(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TTGCTAGATTCTTTTTTTTTCT	0.356								Mismatch excision repair (MMR)																														ENST00000355774.2																			3	Deletion - In frame(2)|Substitution - Nonsense(1)	p.A577_S588delAQTEKEKKKESS(2)|p.E586*(1)	breast(2)|large_intestine(1)	breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44						c.(1753-1758)aaaatcfs	Mismatch excision repair (MMR)	mutL homolog 3																																				SO:0001589	frameshift_variant	27030				mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding	g.chr14:75514603_75514604insT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"""mutL (E. coli) homolog 3"", ""mutL homolog 3 (E. coli)"""			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.1756dupA	14.37:g.75514612_75514612dupT	ENSP00000452316:p.Glu586fs					MLH3_ENST00000238662.7_Frame_Shift_Ins_p.I586fs|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000556740.1_Frame_Shift_Ins_p.I586fs|MLH3_ENST00000556257.1_Frame_Shift_Ins_p.I586fs	p.I586fs	NM_001040108.1	NP_001035197.1	Q9UHC1	MLH3_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.00688)	2	1970_1971	-			586					P49751|Q56DK9|Q9P292|Q9UHC0	Frame_Shift_Ins	INS	ENST00000556740.1	37	c.1755_1756insA	CCDS32123.1																																																																																				0.356	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		11	591						11	591	---	---	---	---
BTBD7	55727	broad.mit.edu	37	14	93712186	93712188	+	In_Frame_Del	DEL	TGC	TGC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr14:93712186_93712188delTGC	ENST00000334746.5	-	10	2873_2875	c.2566_2568delGCA	c.(2566-2568)gcadel	p.A856del	BTBD7_ENST00000393170.2_In_Frame_Del_p.A430del|BTBD7_ENST00000554565.1_In_Frame_Del_p.A505del	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	856	Poly-Ala.				multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		GCTTCTCAGAtgctgctgctgct	0.537																																						ENST00000334746.5																			0				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35						c.(2566-2568)del		BTB (POZ) domain containing 7																																				SO:0001651	inframe_deletion	55727							g.chr14:93712186_93712188delTGC	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"""BTB/POZ domain containing"""	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.2566_2568delGCA	14.37:g.93712195_93712197delTGC	ENSP00000335615:p.Ala856del					BTBD7_ENST00000554565.1_In_Frame_Del_p.A505del|BTBD7_ENST00000393170.2_In_Frame_Del_p.A430del	p.A856del	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)	10	2873_2875	-		all_cancers(154;0.08)	856			Poly-Ala.		A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	In_Frame_Del	DEL	ENST00000334746.5	37	c.2566_2568delGCA	CCDS32146.1																																																																																				0.537	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		7	280						7	280	---	---	---	---
DDX24	57062	broad.mit.edu	37	14	94545821	94545823	+	In_Frame_Del	DEL	CCT	CCT	-	rs371331758		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr14:94545821_94545823delCCT	ENST00000330836.5	-	2	397_399	c.266_268delAGG	c.(265-270)gaggga>gga	p.E89del	IFI27L1_ENST00000553664.1_5'Flank|DDX24_ENST00000544005.1_Intron|IFI27L1_ENST00000556381.1_5'Flank|IFI27L1_ENST00000557218.1_5'Flank|IFI27L1_ENST00000557066.1_5'Flank|IFI27L1_ENST00000555523.1_5'Flank|IFI27L1_ENST00000554544.1_5'Flank|DDX24_ENST00000555054.1_In_Frame_Del_p.E46del|IFI27L1_ENST00000393115.3_5'Flank	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	89	Poly-Glu.				RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		CTAGACTTTCCCTCCTCCTCCTC	0.443																																						ENST00000330836.5																			0				cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23						c.(265-270)gga>g		DEAD (Asp-Glu-Ala-Asp) box helicase 24																																				SO:0001651	inframe_deletion	57062				RNA metabolic process	cytoplasm|nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding	g.chr14:94545821_94545823delCCT	AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"""DEAD-boxes"""	13266	protein-coding gene	gene with protein product		606181	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"""			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.266_268delAGG	14.37:g.94545830_94545832delCCT	ENSP00000328690:p.Glu89del					DDX24_ENST00000544005.1_Intron|DDX24_ENST00000555054.1_In_Frame_Del_p.EG46del	p.EG89del	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)	2	397_399	-		all_cancers(154;0.12)	89			Poly-Glu.		E7EMJ4|Q4V9L5	In_Frame_Del	DEL	ENST00000330836.5	37	c.266_268delAGG	CCDS9918.1																																																																																				0.443	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		9	840						9	840	---	---	---	---
DYNC1H1	1778	broad.mit.edu	37	14	102445788	102445788	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr14:102445788delT	ENST00000360184.4	+	3	641	c.477delT	c.(475-477)cctfs	p.P159fs		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	159	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						CAGTGGCTCCTTTTTTTAAGT	0.408																																						ENST00000360184.4																			0				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						c.(475-477)ccfs		dynein, cytoplasmic 1, heavy chain 1							107.0	108.0	108.0					14																	102445788		2203	4300	6503	SO:0001589	frameshift_variant	1778				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding	g.chr14:102445788delT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.477delT	14.37:g.102445788delT	ENSP00000348965:p.Pro159fs						p.P159fs	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN			3	641	+			159			Stem (By similarity).		B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Frame_Shift_Del	DEL	ENST00000360184.4	37	c.477delT	CCDS9966.1																																																																																				0.408	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		7	760						7	760	---	---	---	---
EIF2AK4	440275	broad.mit.edu	37	15	40282508	40282508	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr15:40282508delT	ENST00000263791.5	+	16	2604	c.2561delT	c.(2560-2562)attfs	p.I854fs	EIF2AK4_ENST00000382727.2_Frame_Shift_Del_p.I826fs	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	854	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		CCTGTCAACATTTTTTTGGAT	0.358																																						ENST00000263791.5																			0				NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40						c.(2560-2562)atfs		eukaryotic translation initiation factor 2 alpha kinase 4							233.0	220.0	224.0					15																	40282508		1840	4082	5922	SO:0001589	frameshift_variant	440275				translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity	g.chr15:40282508delT	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.2561delT	15.37:g.40282508delT	ENSP00000263791:p.Ile854fs					EIF2AK4_ENST00000382727.2_Frame_Shift_Del_p.I826fs	p.I854fs	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)	16	2604	+		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)	854			Protein kinase 2.		C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Frame_Shift_Del	DEL	ENST00000263791.5	37	c.2561delT	CCDS42016.1																																																																																				0.358	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			7	1120						7	1120	---	---	---	---
ZNF106	64397	broad.mit.edu	37	15	42742957	42742957	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr15:42742957delA	ENST00000263805.4	-	2	1770	c.1444delT	c.(1444-1446)tccfs	p.S482fs	ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	482					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TCTCCAGGGGAAAAAAAATTT	0.393																																						ENST00000263805.4																			0											c.(1444-1446)ccfs		zinc finger protein 106							208.0	205.0	206.0					15																	42742957		2203	4299	6502	SO:0001589	frameshift_variant	64397							g.chr15:42742957delA	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"""Zinc fingers, C2H2-type"""	12886	protein-coding gene	gene with protein product	"""SH3-domain binding protein 3"""		"""zinc finger protein 106 homolog (mouse)"""	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.1444delT	15.37:g.42742957delA	ENSP00000263805:p.Ser482fs					ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_Intron	p.S482fs	NM_022473.1	NP_071918.1					2	1770	-								B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Frame_Shift_Del	DEL	ENST00000263805.4	37	c.1444delT	CCDS32208.1																																																																																				0.393	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		15	1294						15	1294	---	---	---	---
SLTM	79811	broad.mit.edu	37	15	59182525	59182526	+	Frame_Shift_Del	DEL	TC	TC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr15:59182525_59182526delTC	ENST00000380516.2	-	15	2120_2121	c.2033_2034delGA	c.(2032-2034)agafs	p.R678fs	AC025918.2_ENST00000452467.1_RNA|SLTM_ENST00000536328.1_Frame_Shift_Del_p.R247fs	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	678	Arg/Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CGCGTTCCATTCTCTCTCTCTC	0.431																																						ENST00000380516.2																			0				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						c.(2032-2034)afs		SAFB-like, transcription modulator																																				SO:0001589	frameshift_variant	79811				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding	g.chr15:59182525_59182526delTC	BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"""RNA binding motif (RRM) containing"""	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.2033_2034delGA	15.37:g.59182535_59182536delTC	ENSP00000369887:p.Arg678fs					SLTM_ENST00000536328.1_Frame_Shift_Del_p.R247fs|AC025918.2_ENST00000452467.1_RNA	p.R678fs	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN			15	2120_2121	-			678			Arg/Glu-rich.		A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Frame_Shift_Del	DEL	ENST00000380516.2	37	c.2033_2034delGA	CCDS10168.2																																																																																				0.431	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755		12	876						12	876	---	---	---	---
ADAMTS7	11173	broad.mit.edu	37	15	79058183	79058184	+	Frame_Shift_Ins	INS	-	-	TGGGTCC			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr15:79058183_79058184insTGGGTCC	ENST00000388820.4	-	19	4279_4280	c.4069_4070insGGACCCA	c.(4069-4071)aagfs	p.K1357fs	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1357					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						AGGCTGACCCTTGGGTCCTGGG	0.653																																						ENST00000388820.4																			0				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						c.(4069-4071)gggfs		ADAM metallopeptidase with thrombospondin type 1 motif, 7				119,2525		11,97,1214						-5.9	0.0			8	119,5765		2,115,2825	no	frameshift	ADAMTS7	NM_014272.3		13,212,4039	A1A1,A1R,RR		2.0224,4.5008,2.7908				238,8290				SO:0001589	frameshift_variant	11173				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding	g.chr15:79058183_79058184insTGGGTCC	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.4063_4069dupGGACCCA	15.37:g.79058184_79058190dupTGGGTCC	ENSP00000373472:p.Lys1357fs						p.-1357fs	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN			19	4279_4280	-								Q14F51|Q6P7J9	Frame_Shift_Ins	INS	ENST00000388820.4	37	c.4069_4070insGGACCCA	CCDS32303.1																																																																																				0.653	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		12	130						12	130	---	---	---	---
CSPG4P5	114817	broad.mit.edu	37	15	84958415	84958426	+	RNA	DEL	CGAGGACATTGG	CGAGGACATTGG	-	rs535146949|rs548644616|rs373234755	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr15:84958415_84958426delCGAGGACATTGG	ENST00000558801.1	-	0	6303_6314									DNM1 pseudogene 51																		TCGGGCACCACGAGGACATTGGTGAGGACAGG	0.557														177	0.0353435	0.0015	0.0403	5008	,	,		20334	0.0198		0.0905	False		,,,				2504	0.0368					ENST00000558801.1																			0																																																			0							g.chr15:84958415_84958426delCGAGGACATTGG			15q25.2	2013-05-16			ENSG00000259297	ENSG00000235370			48500	pseudogene	pseudogene							Standard			Approved				OTTHUMG00000172438		15.37:g.84958415_84958426delCGAGGACATTGG														0	6303_6314	-									RNA	DEL	ENST00000558801.1	37																																																																																						0.557	DNM1P51-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000471721.1			10	57						10	57	---	---	---	---
IL32	9235	broad.mit.edu	37	16	3119304	3119305	+	Frame_Shift_Ins	INS	-	-	G	rs398100042|rs2981599		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr16:3119304_3119305insG	ENST00000534507.1	+	6	864_865	c.653_654insG	c.(652-657)gacaagfs	p.DK218fs	IL32_ENST00000530538.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000552936.1_Frame_Shift_Ins_p.DK196fs|IL32_ENST00000529550.1_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000444393.3_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000525643.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000549213.1_Frame_Shift_Ins_p.DK115fs|IL32_ENST00000548476.1_Frame_Shift_Ins_p.DK218fs|IL32_ENST00000548246.1_Frame_Shift_Ins_p.DK132fs|IL32_ENST00000533097.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000551122.1_Frame_Shift_Ins_p.DK115fs|IL32_ENST00000396887.3_Frame_Shift_Ins_p.DK115fs|IL32_ENST00000526464.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000551513.1_Frame_Shift_Ins_p.DK209fs|IL32_ENST00000008180.9_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000529699.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000325568.5_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000530890.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000440815.3_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000552356.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000396890.2_Frame_Shift_Ins_p.DK218fs|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000528163.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000382213.3_Frame_Shift_Ins_p.DK163fs|IL32_ENST00000531965.1_Frame_Shift_Ins_p.DK162fs|IL32_ENST00000552664.1_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000548652.1_Frame_Shift_Ins_p.DK163fs			P24001	IL32_HUMAN	interleukin 32	218					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CCACGGGGGGACAAGGAGGAGC	0.574																																						ENST00000525643.2																			0				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						c.(514-516)gaafs		interleukin 32																																				SO:0001589	frameshift_variant	9235				cell adhesion|defense response|immune response	extracellular space	cytokine activity	g.chr16:3119304_3119305insG	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	Exception_encountered	16.37:g.3119304_3119305insG	ENSP00000431775:p.Asp218fs					IL32_ENST00000529699.1_Frame_Shift_Ins_p.E152fs|IL32_ENST00000396890.2_Frame_Shift_Ins_p.E218fs|IL32_ENST00000530538.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000382213.3_Frame_Shift_Ins_p.E163fs|IL32_ENST00000552936.1_Frame_Shift_Ins_p.E196fs|IL32_ENST00000551513.1_Frame_Shift_Ins_p.E209fs|IL32_ENST00000444393.3_Frame_Shift_Ins_p.E172fs|IL32_ENST00000548246.1_Frame_Shift_Ins_p.E132fs|IL32_ENST00000440815.3_Frame_Shift_Ins_p.E172fs|IL32_ENST00000552356.1_Frame_Shift_Ins_p.E152fs|IL32_ENST00000531965.1_Frame_Shift_Ins_p.E162fs|IL32_ENST00000396887.3_Frame_Shift_Ins_p.E115fs|IL32_ENST00000549213.1_Frame_Shift_Ins_p.E115fs|IL32_ENST00000528163.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000526464.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000534507.1_Frame_Shift_Ins_p.E218fs|IL32_ENST00000548476.1_Frame_Shift_Ins_p.E218fs|IL32_ENST00000008180.9_Frame_Shift_Ins_p.E152fs|IL32_ENST00000548652.1_Frame_Shift_Ins_p.E163fs|IL32_ENST00000325568.5_Frame_Shift_Ins_p.E172fs|IL32_ENST00000533097.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000552664.1_Frame_Shift_Ins_p.E172fs|IL32_ENST00000530890.1_Frame_Shift_Ins_p.E152fs|IL32_ENST00000529550.1_Frame_Shift_Ins_p.E172fs|IL32_ENST00000551122.1_Frame_Shift_Ins_p.E115fs	p.E172fs			P24001	IL32_HUMAN			7	847_848	+			218					A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Frame_Shift_Ins	INS	ENST00000534507.1	37	c.515_516insG																																																																																					0.574	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221		20	1048						20	1048	---	---	---	---
NTAN1	123803	broad.mit.edu	37	16	15131930	15131931	+	Frame_Shift_Ins	INS	-	-	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr16:15131930_15131931insT	ENST00000287706.3	-	10	982_983	c.890_891insA	c.(889-891)aatfs	p.N297fs	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	297					adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						AGCCATCTTCATTTTTTTTGTA	0.386																																						ENST00000287706.3																			0				endometrium(1)|large_intestine(4)|lung(3)	8						c.(889-891)agafs		N-terminal asparagine amidase																																				SO:0001589	frameshift_variant	123803					cytoplasm		g.chr16:15131930_15131931insT	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.891dupA	16.37:g.15131938_15131938dupT	ENSP00000287706:p.Asn297fs					PDXDC1_ENST00000535621.2_Intron	p.R297fs	NM_173474.2	NP_775745.1	Q96AB6	NTAN1_HUMAN			10	982_983	-			297					Q7Z4Z0	Frame_Shift_Ins	INS	ENST00000287706.3	37	c.890_891insA	CCDS10558.1																																																																																				0.386	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474		8	662						8	662	---	---	---	---
TNRC6A	27327	broad.mit.edu	37	16	24807240	24807240	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr16:24807240delA	ENST00000395799.3	+	9	3670	c.3541delA	c.(3541-3543)aaafs	p.K1182fs	TNRC6A_ENST00000315183.7_Frame_Shift_Del_p.K1182fs	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1182	Sufficient for interaction with AGO1 and AGO4.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		TCTGAGTGGCAAAAAAAGGAG	0.398																																						ENST00000395799.3																			0				breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64						c.(3541-3543)aafs		trinucleotide repeat containing 6A							243.0	224.0	231.0					16																	24807240		2197	4300	6497	SO:0001589	frameshift_variant	27327				negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|micro-ribonucleoprotein complex	nucleotide binding|RNA binding	g.chr16:24807240delA	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.3541delA	16.37:g.24807240delA	ENSP00000379144:p.Lys1182fs					TNRC6A_ENST00000315183.7_Frame_Shift_Del_p.K1182fs	p.K1182fs	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN		GBM - Glioblastoma multiforme(48;0.0394)	9	3670	+			1182			Sufficient for interaction with EIF2C1 and EIF2C4.		C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Frame_Shift_Del	DEL	ENST00000395799.3	37	c.3541delA	CCDS10624.2																																																																																				0.398	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		9	1014						9	1014	---	---	---	---
SLC5A11	115584	broad.mit.edu	37	16	24921737	24921739	+	In_Frame_Del	DEL	CAG	CAG	-	rs140499762		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr16:24921737_24921739delCAG	ENST00000347898.3	+	15	2383_2385	c.1761_1763delCAG	c.(1759-1764)gccagc>gcc	p.S592del	SLC5A11_ENST00000565769.1_In_Frame_Del_p.S528del|SLC5A11_ENST00000545376.1_In_Frame_Del_p.S522del|SLC5A11_ENST00000568579.1_In_Frame_Del_p.S522del|SLC5A11_ENST00000449109.2_In_Frame_Del_p.S436del|SLC5A11_ENST00000569071.1_In_Frame_Del_p.S436del|SLC5A11_ENST00000567758.1_In_Frame_Del_p.S557del|SLC5A11_ENST00000539472.1_In_Frame_Del_p.S528del|SLC5A11_ENST00000424767.2_In_Frame_Del_p.S557del	NM_052944.3	NP_443176.2			solute carrier family 5 (sodium/inositol cotransporter), member 11											endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		TGCCAGAGGCCAGCAGCAGCAGC	0.542																																						ENST00000347898.3																			0				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49						c.(1759-1764)gcc>gc		solute carrier family 5 (sodium/inositol cotransporter), member 11				0,59,4205		0,0,0,0,59,2073						2.3	0.0		dbSNP_134	91	12,151,8089		0,0,12,0,151,3963	no	codingComplex	SLC5A11	NM_052944.2		0,0,12,0,210,6036	A1A1,A1A2,A1R,A2A2,A2R,RR		1.9753,1.3837,1.7737				12,210,12294				SO:0001651	inframe_deletion	115584				apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity	g.chr16:24921737_24921739delCAG	AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"""Solute carriers"""	23091	protein-coding gene	gene with protein product		610238	"""solute carrier family 5 (sodium/glucose cotransporter), member 11"""			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000347898.3:c.1761_1763delCAG	16.37:g.24921746_24921748delCAG	ENSP00000289932:p.Ser592del					SLC5A11_ENST00000567758.1_In_Frame_Del_p.AS552del|SLC5A11_ENST00000545376.1_In_Frame_Del_p.AS517del|SLC5A11_ENST00000539472.1_In_Frame_Del_p.AS523del|SLC5A11_ENST00000424767.2_In_Frame_Del_p.AS552del|SLC5A11_ENST00000565769.1_In_Frame_Del_p.AS523del|SLC5A11_ENST00000449109.2_In_Frame_Del_p.AS431del|SLC5A11_ENST00000568579.1_In_Frame_Del_p.AS517del|SLC5A11_ENST00000569071.1_In_Frame_Del_p.AS431del	p.AS587del	NM_052944.3	NP_443176.2	Q8WWX8	SC5AB_HUMAN		GBM - Glioblastoma multiforme(48;0.0365)	15	2383_2385	+			587						In_Frame_Del	DEL	ENST00000347898.3	37	c.1761_1763delCAG	CCDS10625.1																																																																																				0.542	SLC5A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214091.3	NM_052944		7	368						7	368	---	---	---	---
IL4R	3566	broad.mit.edu	37	16	27373787	27373789	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr16:27373787_27373789delGAG	ENST00000395762.2	+	11	1373_1375	c.1114_1116delGAG	c.(1114-1116)gagdel	p.E376del	IL4R_ENST00000543915.2_In_Frame_Del_p.E376del|IL4R_ENST00000380922.3_In_Frame_Del_p.E361del|IL4R_ENST00000170630.2_In_Frame_Del_p.E376del|IL4R_ENST00000565915.1_3'UTR	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	376	Poly-Glu.				defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						GGTGGAGTGTGAGGAGGAGGAGG	0.591																																						ENST00000395762.2																			0				breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						c.(1114-1116)del		interleukin 4 receptor																																				SO:0001651	inframe_deletion	3566				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity	g.chr16:27373787_27373789delGAG	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1114_1116delGAG	16.37:g.27373796_27373798delGAG	ENSP00000379111:p.Glu376del					IL4R_ENST00000565915.1_3'UTR|IL4R_ENST00000543915.2_In_Frame_Del_p.E376del|IL4R_ENST00000380922.3_In_Frame_Del_p.E361del|IL4R_ENST00000170630.2_In_Frame_Del_p.E376del	p.E376del	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN			11	1373_1375	+			376			Poly-Glu.		B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	In_Frame_Del	DEL	ENST00000395762.2	37	c.1114_1116delGAG	CCDS10629.1																																																																																				0.591	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4			9	353						9	353	---	---	---	---
CTB-134H23.3	0	broad.mit.edu	37	16	29113498	29113498	+	RNA	DEL	T	T	-	rs11366120	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr16:29113498delT	ENST00000562618.1	-	0	1840				RRN3P2_ENST00000564580.1_RNA																							AGGAGGTGGAttttttttttc	0.542													|||unknown(NO_COVERAGE)	2145	0.428315	0.5507	0.4856	5008	,	,		13214	0.248		0.4334	False		,,,				2504	0.4029					ENST00000564580.1																			0																																																			0							g.chr16:29113498delT																													16.37:g.29113498delT														0	1360	+									RNA	DEL	ENST00000562618.1	37																																																																																						0.542	CTB-134H23.3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000433241.1			10	138						10	138	---	---	---	---
NPIPB15	440348	broad.mit.edu	37	16	74425400	74425402	+	In_Frame_Del	DEL	CAA	CAA	-	rs370078939		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr16:74425400_74425402delCAA	ENST00000429990.1	+	7	850_852	c.754_756delCAA	c.(754-756)caadel	p.Q253del				A6NHN6	NPB15_HUMAN	nuclear pore complex interacting protein family, member B15	253	Pro-rich.					extracellular region (GO:0005576)											TCCTCCAACTCAACAACATTCTA	0.517																																						ENST00000429990.1																			0											c.(754-756)del		nuclear pore complex interacting protein family, member B15																																				SO:0001651	inframe_deletion	440348							g.chr16:74425400_74425402delCAA	BC160029		16q22.3	2013-06-11	2013-06-11	2013-06-11	ENSG00000196436	ENSG00000196436			34409	protein-coding gene	gene with protein product			"""nuclear pore complex interacting protein-like 2"""	NPIPL2			Standard	XM_005256273		Approved	LOC440348	uc010vmt.1	A6NHN6	OTTHUMG00000156916	ENST00000429990.1:c.754_756delCAA	16.37:g.74425403_74425405delCAA	ENSP00000411140:p.Gln253del						p.Q253del							7	850_852	+								C9J9U8	In_Frame_Del	DEL	ENST00000429990.1	37	c.754_756delCAA																																																																																					0.517	NPIPB15-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346597.2	NM_001018059		8	574						8	574	---	---	---	---
PELP1	27043	broad.mit.edu	37	17	4608074	4608075	+	5'Flank	DEL	GT	GT	-	rs367809718		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:4608074_4608075delGT	ENST00000574876.1	-	0	0				PELP1_ENST00000301396.4_5'Flank|PELP1_ENST00000269230.7_5'Flank|RP11-314A20.2_ENST00000497885.1_RNA|PELP1_ENST00000572293.1_5'Flank|PELP1_ENST00000436683.2_5'Flank|PELP1_ENST00000570823.1_5'Flank			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1						cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						AATCAGTAACGTGTGTGTGTGT	0.515																																						ENST00000497885.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr17:4608074_4608075delGT		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8			17.37:g.4608084_4608085delGT	Exception_encountered							NR_103482.1						0	141	+								O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	RNA	DEL	ENST00000574876.1	37		CCDS58503.1																																																																																				0.515	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		9	80						9	80	---	---	---	---
CAMTA2	23125	broad.mit.edu	37	17	4889561	4889562	+	5'UTR	INS	-	-	G	rs200275454|rs201093195		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:4889561_4889562insG	ENST00000348066.3	-	0	79_80				RP5-1050D4.4_ENST00000575985.1_RNA|CAMTA2_ENST00000358183.4_5'UTR|CAMTA2_ENST00000571831.1_5'Flank|CAMTA2_ENST00000361571.5_Frame_Shift_Ins_p.R9fs|RP5-1050D4.5_ENST00000574260.1_RNA|CAMTA2_ENST00000414043.3_Frame_Shift_Ins_p.R9fs|CAMTA2_ENST00000572543.1_5'UTR|CAMTA2_ENST00000381311.5_Intron	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2						cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						CCTGAGGGGCCGGGGGGAGGGG	0.579																																						ENST00000361571.5																			0				breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						c.(25-27)gccfs		calmodulin binding transcription activator 2																																				SO:0001623	5_prime_UTR_variant	23125				cardiac muscle hypertrophy in response to stress|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	calmodulin binding|chromatin binding|histone deacetylase binding|transcription factor binding	g.chr17:4889561_4889562insG	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.-45->C	17.37:g.4889567_4889567dupG						CAMTA2_ENST00000414043.3_Frame_Shift_Ins_p.A9fs|CAMTA2_ENST00000381311.5_Intron|CAMTA2_ENST00000348066.3_5'UTR|CAMTA2_ENST00000358183.4_5'UTR|CAMTA2_ENST00000572543.1_5'UTR	p.A9fs	NM_001171168.1	NP_001164639.1	O94983	CMTA2_HUMAN			2	436_437	-			474					B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Frame_Shift_Ins	INS	ENST00000348066.3	37	c.25_26insC	CCDS11063.1																																																																																				0.579	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099		12	105						12	105	---	---	---	---
AC005863.1	0	broad.mit.edu	37	17	14673542	14673543	+	lincRNA	INS	-	-	T			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:14673542_14673543insT	ENST00000379640.1	-	0	354_355																											GCTGGTCCCAGTTTTTTTTTCT	0.45																																						ENST00000379640.1																			0																	4,4260		0,4,2128						0.2	0.0			65	15,8239		0,15,4112	no	intergenic				0,19,6240	A1A1,A1R,RR		0.1817,0.0938,0.1518				19,12499						0							g.chr17:14673542_14673543insT																													17.37:g.14673551_14673551dupT														0	354_355	-									RNA	INS	ENST00000379640.1	37																																																																																						0.450	AC005863.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000130001.1			7	258						7	258	---	---	---	---
NUFIP2	57532	broad.mit.edu	37	17	27620990	27620992	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:27620990_27620992delGCT	ENST00000225388.4	-	1	144_146	c.86_88delAGC	c.(85-90)cagccg>ccg	p.Q29del	NUFIP2_ENST00000579665.1_In_Frame_Del_p.Q29del	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein interacting protein 2	29	His-rich.					cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			tggtggtgcggctgctgctgctg	0.591																																						ENST00000225388.4																			0				breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24						c.(85-90)ccg>c		nuclear fragile X mental retardation protein interacting protein 2																																				SO:0001651	inframe_deletion	57532					nucleus|polysomal ribosome	protein binding|RNA binding	g.chr17:27620990_27620992delGCT	AB037742	CCDS32600.1	17q11.1	2006-03-01				ENSG00000108256			17634	protein-coding gene	gene with protein product		609356				12837692, 16407062	Standard	NM_020772		Approved	KIAA1321, MGC117262, PIG1, 182-FIP, FIP-82, 82-FIP	uc002hdy.4	Q7Z417		ENST00000225388.4:c.86_88delAGC	17.37:g.27620999_27621001delGCT	ENSP00000225388:p.Gln29del					NUFIP2_ENST00000579665.1_In_Frame_Del_p.QP29del	p.QP29del	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)		1	144_146	-			29			His-rich.		A1L3A6|Q9P2M5	In_Frame_Del	DEL	ENST00000225388.4	37	c.86_88delAGC	CCDS32600.1																																																																																				0.591	NUFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447015.2	NM_020772		11	413						11	413	---	---	---	---
ZNF207	7756	broad.mit.edu	37	17	30677314	30677316	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:30677314_30677316delAAG	ENST00000321233.6	+	1	164_166	c.10_12delAAG	c.(10-12)aagdel	p.K7del	ZNF207_ENST00000342555.6_5'UTR|MIR632_ENST00000385193.1_RNA|ZNF207_ENST00000341711.6_In_Frame_Del_p.K7del|ZNF207_ENST00000394673.2_In_Frame_Del_p.K7del|RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000577908.1_In_Frame_Del_p.K7del|ZNF207_ENST00000394670.4_In_Frame_Del_p.K7del	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	7	Microtubule-binding region.				attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			TATGGGTCGCAAGAAGAAGAAGC	0.542																																						ENST00000394670.4																			0				breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10						c.(10-12)del		zinc finger protein 207																																				SO:0001651	inframe_deletion	7756					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr17:30677314_30677316delAAG	AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"""Zinc fingers, C2H2-type"""	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.10_12delAAG	17.37:g.30677323_30677325delAAG	ENSP00000322777:p.Lys7del					ZNF207_ENST00000321233.6_In_Frame_Del_p.K7del|RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000577908.1_In_Frame_Del_p.K7del|ZNF207_ENST00000394673.2_In_Frame_Del_p.K7del|ZNF207_ENST00000342555.6_5'UTR|ZNF207_ENST00000341711.6_In_Frame_Del_p.K7del	p.K7del	NM_001098507.1	NP_001091977.1	O43670	ZN207_HUMAN	BRCA - Breast invasive adenocarcinoma(9;0.239)		1	179_181	+		Breast(31;0.116)|Ovarian(249;0.182)	7					A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	In_Frame_Del	DEL	ENST00000321233.6	37	c.10_12delAAG	CCDS11271.1																																																																																				0.542	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2			9	1099						9	1099	---	---	---	---
WIPF2	147179	broad.mit.edu	37	17	38421174	38421176	+	In_Frame_Del	DEL	CTC	CTC	-	rs151273872	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:38421174_38421176delCTC	ENST00000323571.4	+	5	986_988	c.746_748delCTC	c.(745-750)gctcct>gct	p.P254del	WIPF2_ENST00000536600.1_Intron|WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000394103.3_Intron|WIPF2_ENST00000583130.1_In_Frame_Del_p.P254del|WIPF2_ENST00000585043.1_In_Frame_Del_p.P254del	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	254	Poly-Pro.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						CAGTCTCTGGCTCCTCCTCCTCC	0.596										HNSCC(43;0.11)																												ENST00000323571.4																			0				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						c.(745-750)gct>g		WAS/WASL interacting protein family, member 2																																				SO:0001651	inframe_deletion	147179					cytoplasm|cytoskeleton	actin binding	g.chr17:38421174_38421176delCTC	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.746_748delCTC	17.37:g.38421183_38421185delCTC	ENSP00000320924:p.Pro254del	HNSCC(43;0.11)				WIPF2_ENST00000536600.1_Intron|WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000394103.3_Intron|WIPF2_ENST00000585043.1_In_Frame_Del_p.AP249del|WIPF2_ENST00000583130.1_In_Frame_Del_p.AP249del	p.AP249del	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN			5	986_988	+			249					A8K0L3|Q658J8|Q71RE1|Q8TE44	In_Frame_Del	DEL	ENST00000323571.4	37	c.746_748delCTC	CCDS11364.1																																																																																				0.596	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264		7	1194						7	1194	---	---	---	---
CCDC103	388389	broad.mit.edu	37	17	42980014	42980015	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:42980014_42980015delAG	ENST00000417826.2	+	4	653_654	c.558_559delAG	c.(556-561)gcagagfs	p.E187fs	FAM187A_ENST00000412523.2_Intron|FAM187A_ENST00000331733.4_5'UTR|AC015936.3_ENST00000441312.1_RNA|EFTUD2_ENST00000426333.2_5'Flank|CCDC103_ENST00000410006.2_Frame_Shift_Del_p.E187fs	NM_001258399.1|NM_213607.2	NP_001245328.1|NP_998772.1	Q8IW40	CC103_HUMAN	coiled-coil domain containing 103	187					axonemal dynein complex assembly (GO:0070286)|cell projection organization (GO:0030030)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|outer dynein arm assembly (GO:0036158)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)	protein homodimerization activity (GO:0042803)	p.E187K(1)		endometrium(1)|kidney(1)|large_intestine(3)|prostate(1)|skin(1)	7		Prostate(33;0.109)				TGAGCCGGGCAGAGAGAGAGAG	0.644																																						ENST00000417826.2																			1	Substitution - Missense(1)	p.E187K(1)	large_intestine(1)	endometrium(1)|kidney(1)|large_intestine(3)|prostate(1)|skin(1)	7						c.(556-561)gcagfs		coiled-coil domain containing 103																																				SO:0001589	frameshift_variant	388389							g.chr17:42980014_42980015delAG	AK023156	CCDS11490.1, CCDS58554.1	17q21.31	2013-02-22			ENSG00000167131	ENSG00000167131			32700	protein-coding gene	gene with protein product		614677				22581229	Standard	NM_213607		Approved	FLJ13094, FLJ34211, PR46b, CILD17	uc031ray.1	Q8IW40	OTTHUMG00000154264	ENST00000417826.2:c.558_559delAG	17.37:g.42980024_42980025delAG	ENSP00000391692:p.Glu187fs					FAM187A_ENST00000331733.4_5'UTR|CCDC103_ENST00000410006.2_Frame_Shift_Del_p.AE186fs|FAM187A_ENST00000412523.2_Intron	p.AE186fs	NM_001258399.1|NM_213607.2	NP_001245328.1|NP_998772.1	Q8IW40	CC103_HUMAN			4	653_654	+		Prostate(33;0.109)	186					A8K145|B8ZZU0	Frame_Shift_Del	DEL	ENST00000417826.2	37	c.558_559delAG	CCDS11490.1																																																																																				0.644	CCDC103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334578.1	NM_213607		7	280						7	280	---	---	---	---
CDC27	996	broad.mit.edu	37	17	45219612	45219612	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:45219612delA	ENST00000066544.3	-	11	1454	c.1361delT	c.(1360-1362)ctafs	p.L454fs	CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs|CDC27_ENST00000527547.1_Frame_Shift_Del_p.L454fs|CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	454					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TGCTTTTTGTAGATTAAAGGC	0.308																																						ENST00000066544.3																			0				NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						c.(1360-1362)cafs		cell division cycle 27							30.0	30.0	30.0					17																	45219612		2201	4295	6496	SO:0001589	frameshift_variant	996				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding	g.chr17:45219612delA	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1361delT	17.37:g.45219612delA	ENSP00000066544:p.Leu454fs					CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs|CDC27_ENST00000527547.1_Frame_Shift_Del_p.L454fs|CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs	p.L454fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN			11	1454	-			454					G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	37	c.1361delT	CCDS11509.1																																																																																				0.308	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			24	203						24	203	---	---	---	---
BZRAP1	9256	broad.mit.edu	37	17	56386383	56386384	+	Frame_Shift_Ins	INS	-	-	T	rs373235874		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:56386383_56386384insT	ENST00000343736.4	-	22	4412_4413	c.4249_4250insA	c.(4249-4251)agcfs	p.S1417fs	BZRAP1_ENST00000268893.6_Frame_Shift_Ins_p.S1357fs|BZRAP1_ENST00000355701.3_Frame_Shift_Ins_p.S1417fs			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1417						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCGCCTGCGGCTTGGGGGCTTC	0.653																																						ENST00000355701.3																			0				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						c.(4249-4251)ccgfs		benzodiazapine receptor (peripheral) associated protein 1																																				SO:0001589	frameshift_variant	9256					mitochondrion	benzodiazepine receptor binding	g.chr17:56386383_56386384insT	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4250dupA	17.37:g.56386385_56386385dupT	ENSP00000345824:p.Ser1417fs					BZRAP1_ENST00000343736.4_Frame_Shift_Ins_p.P1417fs|BZRAP1_ENST00000268893.6_Frame_Shift_Ins_p.P1357fs	p.P1417fs	NM_001261835.1|NM_004758.3	NP_001248764.1|NP_004749.2	O95153	RIMB1_HUMAN			22	5119_5120	-	Medulloblastoma(34;0.127)|all_neural(34;0.237)		1417					O75111|Q8N5W3	Frame_Shift_Ins	INS	ENST00000343736.4	37	c.4249_4250insA	CCDS11605.1																																																																																				0.653	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		161	767						161	767	---	---	---	---
BZRAP1	9256	broad.mit.edu	37	17	56387404	56387406	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:56387404_56387406delTCC	ENST00000343736.4	-	21	3976_3978	c.3813_3815delGGA	c.(3811-3816)gaggaa>gaa	p.1271_1272EE>E	BZRAP1_ENST00000268893.6_In_Frame_Del_p.1211_1212EE>E|BZRAP1_ENST00000355701.3_In_Frame_Del_p.1271_1272EE>E			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1271	Poly-Glu.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CAGctcctcttcctcctcctcct	0.586																																						ENST00000355701.3																			0				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						c.(3811-3816)gaa>ga		benzodiazapine receptor (peripheral) associated protein 1			,	10,0,4254		4,0,2,0,0,2126					,	-7.0	0.1			91	24,2,8228		10,0,4,0,2,4111	no	codingComplex,codingComplex	BZRAP1	NM_024418.1,NM_004758.2	,	14,0,6,0,2,6237	A1A1,A1A2,A1R,A2A2,A2R,RR		0.315,0.2345,0.2876	,	,		34,2,12482				SO:0001651	inframe_deletion	9256					mitochondrion	benzodiazepine receptor binding	g.chr17:56387404_56387406delTCC	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.3813_3815delGGA	17.37:g.56387413_56387415delTCC	ENSP00000345824:p.Glu1274del					BZRAP1_ENST00000343736.4_In_Frame_Del_p.EE1273del|BZRAP1_ENST00000268893.6_In_Frame_Del_p.EE1213del	p.EE1273del	NM_001261835.1|NM_004758.3	NP_001248764.1|NP_004749.2	O95153	RIMB1_HUMAN			21	4683_4685	-	Medulloblastoma(34;0.127)|all_neural(34;0.237)		1273			Poly-Glu.		O75111|Q8N5W3	In_Frame_Del	DEL	ENST00000343736.4	37	c.3813_3815delGGA	CCDS11605.1																																																																																				0.586	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		7	378						7	378	---	---	---	---
ITGB4	3691	broad.mit.edu	37	17	73732157	73732158	+	Frame_Shift_Del	DEL	GT	GT	-	rs121912463		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr17:73732157_73732158delGT	ENST00000200181.3	+	14	1870_1871	c.1683_1684delGT	c.(1681-1686)cagtgtfs	p.C562fs	ITGB4_ENST00000449880.2_Frame_Shift_Del_p.C562fs|ITGB4_ENST00000450894.3_Frame_Shift_Del_p.C562fs|ITGB4_ENST00000579662.1_Frame_Shift_Del_p.C562fs|ITGB4_ENST00000339591.3_Frame_Shift_Del_p.C562fs|ITGB4_ENST00000584558.1_3'UTR	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	562	Cysteine-rich tandem repeats.		C -> R (in EB-PA; mild form). {ECO:0000269|PubMed:9792864}.		amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCATGGGCCAGTGTGTGTGTGA	0.604																																						ENST00000200181.3																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	GRCh37	CM981091	ITGB4	M	rs121912463	c.(1681-1686)cagtfs		integrin, beta 4																																				SO:0001589	frameshift_variant	3691				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity	g.chr17:73732157_73732158delGT		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.1683_1684delGT	17.37:g.73732165_73732166delGT	ENSP00000200181:p.Cys562fs					ITGB4_ENST00000339591.3_Frame_Shift_Del_p.QC561fs|ITGB4_ENST00000449880.2_Frame_Shift_Del_p.QC561fs|ITGB4_ENST00000450894.3_Frame_Shift_Del_p.QC561fs|ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000579662.1_Frame_Shift_Del_p.QC561fs	p.QC561fs	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		14	1870_1871	+	all_cancers(13;1.5e-07)		561			Cysteine-rich tandem repeats.		A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Frame_Shift_Del	DEL	ENST00000200181.3	37	c.1683_1684delGT	CCDS11727.1																																																																																				0.604	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			10	905						10	905	---	---	---	---
OSBPL1A	114876	broad.mit.edu	37	18	21745096	21745097	+	Frame_Shift_Ins	INS	-	-	T	rs370244500		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr18:21745096_21745097insT	ENST00000319481.3	-	27	2888_2889	c.2682_2683insA	c.(2680-2685)aaacgafs	p.R895fs	OSBPL1A_ENST00000357041.4_Frame_Shift_Ins_p.R513fs|OSBPL1A_ENST00000399443.3_Frame_Shift_Ins_p.R382fs|RP11-799B12.4_ENST00000583267.1_lincRNA	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	895					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					TCCTCAAGTCGTTTTTTTTCTT	0.46																																						ENST00000319481.3																			0				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36						c.(2680-2685)aagactfs		oxysterol binding protein-like 1A																																				SO:0001589	frameshift_variant	114876				cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding	g.chr18:21745096_21745097insT	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"""Oxysterol binding proteins"", ""Ankyrin repeat domain containing"""	16398	protein-coding gene	gene with protein product		606730	"""oxysterol binding protein-like 1B"""	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.2683dupA	18.37:g.21745104_21745104dupT	ENSP00000320291:p.Arg895fs					OSBPL1A_ENST00000399443.3_Frame_Shift_Ins_p.T382fs|OSBPL1A_ENST00000357041.4_Frame_Shift_Ins_p.T513fs	p.T895fs	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN			27	2888_2889	-	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)		895					B7Z7D3|Q9BZF5|Q9NW87	Frame_Shift_Ins	INS	ENST00000319481.3	37	c.2682_2683insA	CCDS11884.1																																																																																				0.460	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		9	1003						9	1003	---	---	---	---
ZNF563	147837	broad.mit.edu	37	19	12430217	12430217	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:12430217delA	ENST00000293725.5	-	4	827	c.622delT	c.(622-624)tggfs	p.W208fs	ZNF563_ENST00000595977.1_Intron	NM_145276.2	NP_660319.1	Q8TA94	ZN563_HUMAN	zinc finger protein 563	208					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						AAACTGGGCCAAAAAAAAGCT	0.393																																					GBM(39;623 795 5132 29510 31476)	ENST00000293725.5																			0				breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						c.(622-624)ggfs		zinc finger protein 563							124.0	126.0	126.0					19																	12430217		2203	4300	6503	SO:0001589	frameshift_variant	147837				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:12430217delA	BC022523	CCDS12270.1	19p13.2	2013-09-20			ENSG00000188868	ENSG00000188868		"""Zinc fingers, C2H2-type"", ""-"""	30498	protein-coding gene	gene with protein product							Standard	NM_145276		Approved	FLJ34797	uc002mtp.3	Q8TA94	OTTHUMG00000156413	ENST00000293725.5:c.622delT	19.37:g.12430217delA	ENSP00000293725:p.Trp208fs					ZNF563_ENST00000595977.1_Intron	p.W208fs	NM_145276.2	NP_660319.1	Q8TA94	ZN563_HUMAN			4	827	-			208					B2R9E7|Q8NAT7	Frame_Shift_Del	DEL	ENST00000293725.5	37	c.622delT	CCDS12270.1																																																																																				0.393	ZNF563-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344114.1	NM_145276		10	860						10	860	---	---	---	---
COMP	1311	broad.mit.edu	37	19	18895747	18895748	+	Frame_Shift_Ins	INS	-	-	C	rs200802161	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:18895747_18895748insC	ENST00000222271.2	-	16	1916_1917	c.1872_1873insG	c.(1870-1875)gcgaacfs	p.N625fs	COMP_ENST00000542601.2_Frame_Shift_Ins_p.N592fs|COMP_ENST00000425807.1_Frame_Shift_Ins_p.N572fs	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	625	Mediates cell survival and induction of the IAP family of survival proteins.|TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CGGAAGGGGTTCGCCTGCCAAT	0.604																																						ENST00000542601.2																			0				breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						c.(1771-1776)gcacccfs		cartilage oligomeric matrix protein																																				SO:0001589	frameshift_variant	1311				anti-apoptosis|apoptosis|cell adhesion|limb development	extracellular space|proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent|heparan sulfate proteoglycan binding|heparin binding	g.chr19:18895747_18895748insC	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"""thrombospondin-5"""	600310	"""cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"""	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1873dupG	19.37:g.18895748_18895748dupC	ENSP00000222271:p.Asn625fs					COMP_ENST00000425807.1_Frame_Shift_Ins_p.P572fs|COMP_ENST00000222271.2_Frame_Shift_Ins_p.P625fs	p.P592fs			P49747	COMP_HUMAN			15	2162_2163	-			625			Mediates cell survival and induction of the IAP family of survival proteins.|TSP C-terminal.		B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Frame_Shift_Ins	INS	ENST00000222271.2	37	c.1773_1774insG	CCDS12385.1																																																																																				0.604	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095		7	325						7	325	---	---	---	---
SUGP2	10147	broad.mit.edu	37	19	19136394	19136394	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:19136394delT	ENST00000601879.1	-	3	1060	c.763delA	c.(763-765)atafs	p.I255fs	SUGP2_ENST00000452918.2_Frame_Shift_Del_p.I255fs|SUGP2_ENST00000600377.1_Frame_Shift_Del_p.I269fs|SUGP2_ENST00000337018.6_Frame_Shift_Del_p.I255fs|SUGP2_ENST00000456085.2_Intron|SUGP2_ENST00000598202.1_5'UTR			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	255					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						ACGGTGGGTATTTTTTTTGTG	0.502																																						ENST00000601879.1																			0				NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						c.(763-765)tafs		SURP and G patch domain containing 2							168.0	156.0	160.0					19																	19136394		2203	4300	6503	SO:0001589	frameshift_variant	10147				mRNA processing|RNA splicing	nucleus	RNA binding	g.chr19:19136394delT	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"""G patch domain containing"""	18641	protein-coding gene	gene with protein product		607993	"""splicing factor, arginine/serine-rich 14"""	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.763delA	19.37:g.19136394delT	ENSP00000472286:p.Ile255fs					SUGP2_ENST00000600377.1_Frame_Shift_Del_p.I269fs|SUGP2_ENST00000598202.1_5'UTR|SUGP2_ENST00000456085.2_Intron|SUGP2_ENST00000337018.6_Frame_Shift_Del_p.I255fs|SUGP2_ENST00000452918.2_Frame_Shift_Del_p.I255fs	p.I255fs			Q8IX01	SUGP2_HUMAN			3	1060	-			255					C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Frame_Shift_Del	DEL	ENST00000601879.1	37	c.763delA	CCDS12392.1																																																																																				0.502	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		14	682						14	682	---	---	---	---
FFAR2	2867	broad.mit.edu	37	19	35940788	35940790	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:35940788_35940790delCTG	ENST00000599180.2	+	2	252_254	c.172_174delCTG	c.(172-174)ctgdel	p.L62del	FFAR2_ENST00000601590.1_Intron|FFAR2_ENST00000246549.2_In_Frame_Del_p.L62del			O15552	FFAR2_HUMAN	free fatty acid receptor 2	62					cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to fatty acid (GO:0071398)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipid storage (GO:0019915)|mucosal immune response (GO:0002385)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of interleukin-8 secretion (GO:2000484)|regulation of acute inflammatory response (GO:0002673)|regulation of peptide hormone secretion (GO:0090276)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CGACCTCCTCCTGCTGCTGCTGC	0.645																																					GBM(40;139 809 9833 23358 48736)	ENST00000599180.1																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22						c.(172-174)del		free fatty acid receptor 2																																				SO:0001651	inframe_deletion	2867					integral to plasma membrane	G-protein coupled receptor activity|lipid binding	g.chr19:35940788_35940790delCTG	AF024690	CCDS12461.1	19q13.1	2012-08-08	2006-02-15	2006-02-15		ENSG00000126262		"""GPCR / Class A : Fatty acid receptors"""	4501	protein-coding gene	gene with protein product		603823	"""G protein-coupled receptor 43"""	GPR43		9344866	Standard	NM_005306		Approved	FFA2R	uc010eea.3	O15552		ENST00000599180.2:c.172_174delCTG	19.37:g.35940797_35940799delCTG	ENSP00000473159:p.Leu62del					FFAR2_ENST00000246549.2_In_Frame_Del_p.L62del|FFAR2_ENST00000601590.1_Intron	p.L62del			O15552	FFAR2_HUMAN	LUSC - Lung squamous cell carcinoma(66;0.0724)		2	252_254	+	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		62					B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	In_Frame_Del	DEL	ENST00000599180.2	37	c.172_174delCTG	CCDS12461.1																																																																																				0.645	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	NM_005306		8	268						8	268	---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36583666	36583668	+	In_Frame_Del	DEL	GCA	GCA	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:36583666_36583668delGCA	ENST00000270301.7	+	19	2286_2288	c.2286_2288delGCA	c.(2284-2289)cggcag>cgg	p.Q766del	WDR62_ENST00000401500.2_In_Frame_Del_p.Q766del			O43379	WDR62_HUMAN	WD repeat domain 62	766					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TTGACCACCGGCAGCAGCAGCAG	0.616																																						ENST00000401500.2																			0				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43						c.(2284-2289)cgg>cg		WD repeat domain 62																																				SO:0001651	inframe_deletion	284403				cerebral cortex development	nucleus		g.chr19:36583666_36583668delGCA	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.2286_2288delGCA	19.37:g.36583675_36583677delGCA	ENSP00000270301:p.Gln766del					WDR62_ENST00000270301.7_In_Frame_Del_p.RQ762del	p.RQ762del	NM_001083961.1|NM_173636.4	NP_001077430.1|NP_775907.4	O43379	WDR62_HUMAN	LUSC - Lung squamous cell carcinoma(66;0.06)		19	2321_2323	+	Esophageal squamous(110;0.162)		762					Q63HP9|Q659D7|Q8NBF7|Q96AD9	In_Frame_Del	DEL	ENST00000270301.7	37	c.2286_2288delGCA	CCDS33001.1																																																																																				0.616	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671		8	740						8	740	---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38948159	38948160	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:38948159_38948160delTG	ENST00000359596.3	+	17	1814_1815	c.1814_1815delTG	c.(1813-1815)ctgfs	p.L605fs	RYR1_ENST00000360985.3_Frame_Shift_Del_p.L605fs|RYR1_ENST00000355481.4_Frame_Shift_Del_p.L605fs			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	605	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTATGCTCCCTGTGTGTGTGTA	0.53																																						ENST00000355481.4																			0				NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285						c.(1813-1815)cfs		ryanodine receptor 1 (skeletal)	Dantrolene(DB01219)																																			SO:0001589	frameshift_variant	6261				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr19:38948159_38948160delTG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.1814_1815delTG	19.37:g.38948167_38948168delTG	ENSP00000352608:p.Leu605fs					RYR1_ENST00000359596.3_Frame_Shift_Del_p.L605fs|RYR1_ENST00000360985.3_Frame_Shift_Del_p.L605fs	p.L605fs	NM_000540.2|NM_001042723.1	NP_000531.2|NP_001036188.1	P21817	RYR1_HUMAN	Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		17	1945_1946	+	all_cancers(60;7.91e-06)		605			B30.2/SPRY 1.		Q16314|Q16368|Q9NPK1|Q9P1U4	Frame_Shift_Del	DEL	ENST00000359596.3	37	c.1814_1815delTG	CCDS33011.1																																																																																				0.530	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			8	1104						8	1104	---	---	---	---
LIPE-AS1	100996307	broad.mit.edu	37	19	43136362	43136363	+	RNA	DEL	TG	TG	-	rs142080128		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:43136362_43136363delTG	ENST00000594688.1	+	0	1450				LIPE-AS1_ENST00000594624.2_RNA	NR_073179.1				LIPE antisense RNA 1																		TGAGTATGTATGTGTGTGTGTG	0.505																																						ENST00000594688.1																			0																																																			0							g.chr19:43136362_43136363delTG	AK096849, BM974950		19q13.2	2013-05-21			ENSG00000213904	ENSG00000213904		"""Long non-coding RNAs"""	48589	non-coding RNA	RNA, long non-coding							Standard	NR_073179		Approved				OTTHUMG00000182815		19.37:g.43136372_43136373delTG						LIPE-AS1_ENST00000594624.2_RNA		NR_073179.1						0	1450	+									RNA	DEL	ENST00000594688.1	37																																																																																						0.505	LIPE-AS1-004	KNOWN	basic	antisense	antisense	OTTHUMT00000464099.1	NR_073179		7	151						7	151	---	---	---	---
FLT3LG	2323	broad.mit.edu	37	19	49978960	49978962	+	In_Frame_Del	DEL	CTG	CTG	-	rs372504451		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:49978960_49978962delCTG	ENST00000594009.1	+	2	125_127	c.46_48delCTG	c.(46-48)ctgdel	p.L20del	FLT3LG_ENST00000344019.3_In_Frame_Del_p.L20del|FLT3LG_ENST00000595510.1_5'UTR|FLT3LG_ENST00000597551.1_In_Frame_Del_p.L20del|FLT3LG_ENST00000596435.1_In_Frame_Del_p.L20del|FLT3LG_ENST00000204637.2_5'UTR|FLT3LG_ENST00000600429.1_In_Frame_Del_p.L20del|CTD-3148I10.15_ENST00000595815.1_RNA|CTD-3148I10.9_ENST00000599536.1_Intron	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand	20					embryonic hemopoiesis (GO:0035162)|lymphocyte differentiation (GO:0030098)|positive regulation of cell proliferation (GO:0008284)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|membrane (GO:0016020)	receptor binding (GO:0005102)			large_intestine(2)|lung(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	10		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		CTATCTCCTCCTGCTGCTGCTGC	0.621																																						ENST00000594009.1																			0				large_intestine(2)|lung(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	10						c.(46-48)del		fms-related tyrosine kinase 3 ligand																																				SO:0001651	inframe_deletion	0				positive regulation of cell proliferation|signal transduction	extracellular space|integral to membrane|plasma membrane|soluble fraction	cytokine activity	g.chr19:49978960_49978962delCTG	U04806	CCDS12767.1, CCDS62753.1	19q13.3	2014-01-30				ENSG00000090554		"""Endogenous ligands"""	3766	protein-coding gene	gene with protein product		600007				8145851, 7824267	Standard	NM_001204502		Approved		uc010yau.2	P49771		ENST00000594009.1:c.46_48delCTG	19.37:g.49978969_49978971delCTG	ENSP00000469613:p.Leu20del					FLT3LG_ENST00000595510.1_5'UTR|FLT3LG_ENST00000204637.2_5'UTR|FLT3LG_ENST00000595815.1_3'UTR|FLT3LG_ENST00000597551.1_In_Frame_Del_p.L20del|FLT3LG_ENST00000344019.3_In_Frame_Del_p.L20del|CTD-3148I10.9_ENST00000599536.1_Intron|FLT3LG_ENST00000600429.1_In_Frame_Del_p.L20del|FLT3LG_ENST00000596435.1_In_Frame_Del_p.L20del	p.L20del	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)	2	125_127	+		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)	20					A0AVC2|B9EGH2|Q05C96	In_Frame_Del	DEL	ENST00000594009.1	37	c.46_48delCTG	CCDS12767.1																																																																																				0.621	FLT3LG-007	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465305.1			7	311						7	311	---	---	---	---
SIGLEC9	27180	broad.mit.edu	37	19	51628233	51628235	+	Start_Codon_Del	DEL	TGC	TGC	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:51628233_51628235delTGC	ENST00000250360.3	+	0	69_71				SIGLEC9_ENST00000440804.3_Start_Codon_Del	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9						cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		ACCCCAGACATGCTGCTGCTGCT	0.611																																						ENST00000440804.3																			0				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45								sialic acid binding Ig-like lectin 9																																				SO:0001582	initiator_codon_variant	27180				cell adhesion|cell surface receptor linked signaling pathway	integral to plasma membrane	sugar binding	g.chr19:51628233_51628235delTGC	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336			19.37:g.51628242_51628244delTGC						SIGLEC9_ENST00000250360.3_Start_Codon_Del		NM_001198558.1	NP_001185487.1	Q9Y336	SIGL9_HUMAN		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)	0	69_71	+		all_neural(266;0.0529)						Q6GTU4|Q9BYI9	Translation_Start_Site	DEL	ENST00000250360.3	37		CCDS12825.1																																																																																				0.611	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		8	184						8	184	---	---	---	---
SIGLEC8	27181	broad.mit.edu	37	19	51961617	51961619	+	In_Frame_Del	DEL	GCA	GCA	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr19:51961617_51961619delGCA	ENST00000321424.3	-	1	89_91	c.23_25delTGC	c.(22-27)ctgccc>ccc	p.L8del	SIGLEC8_ENST00000340550.5_In_Frame_Del_p.L8del|SIGLEC8_ENST00000430817.1_In_Frame_Del_p.L8del|SIGLEC8_ENST00000597352.1_5'Flank	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	8					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CAGagcaggggcagcagcagcag	0.596																																						ENST00000321424.3																			0				NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50						c.(22-27)ccc>c		sialic acid binding Ig-like lectin 8																																				SO:0001651	inframe_deletion	27181				cell adhesion	integral to membrane	sugar binding|transmembrane receptor activity	g.chr19:51961617_51961619delGCA	AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.23_25delTGC	19.37:g.51961626_51961628delGCA	ENSP00000321077:p.Leu8del					SIGLEC8_ENST00000340550.5_In_Frame_Del_p.LP8del|SIGLEC8_ENST00000430817.1_In_Frame_Del_p.LP8del	p.LP8del	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)	1	89_91	-		all_neural(266;0.0199)	8					Q7Z728	In_Frame_Del	DEL	ENST00000321424.3	37	c.23_25delTGC	CCDS33086.1																																																																																				0.596	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442		11	434						11	434	---	---	---	---
SYNDIG1	79953	broad.mit.edu	37	20	24524183	24524185	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr20:24524183_24524185delGGA	ENST00000376862.3	+	2	1083_1085	c.450_452delGGA	c.(448-453)gtggag>gtg	p.E155del		NM_024893.1	NP_079169.1	Q9H7V2	SYNG1_HUMAN	synapse differentiation inducing 1	155	Poly-Glu.				intracellular protein transport (GO:0006886)|positive regulation of synapse assembly (GO:0051965)|response to biotic stimulus (GO:0009607)|synaptic vesicle clustering (GO:0097091)	cell body (GO:0044297)|cell junction (GO:0030054)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	glutamate receptor binding (GO:0035254)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(1)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	24						CCTACGATGTGGAGGAGGAGGAG	0.547																																						ENST00000376862.3																			0				breast(2)|endometrium(1)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	24						c.(448-453)gtg>gt		synapse differentiation inducing 1																																				SO:0001651	inframe_deletion	79953				response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane		g.chr20:24524183_24524185delGGA	AK024282	CCDS13164.1	20p11.21	2011-06-30	2011-06-30	2011-06-30	ENSG00000101463	ENSG00000101463			15885	protein-coding gene	gene with protein product	"""interferon induced transmembrane protein domain containing 5"", ""synapse differentiation induced gene 1"""	614311	"""chromosome 20 open reading frame 39"", ""transmembrane protein 90B"""	C20orf39, TMEM90B		20152115	Standard	NM_024893		Approved	FLJ14220, IFITMD5, SynDIG1	uc002wtw.1	Q9H7V2	OTTHUMG00000032104	ENST00000376862.3:c.450_452delGGA	20.37:g.24524192_24524194delGGA	ENSP00000366058:p.Glu155del						p.VE150del	NM_024893.1	NP_079169.1	Q9H7V2	SYNG1_HUMAN			2	1083_1085	+			150					Q6IA30|Q9H514	In_Frame_Del	DEL	ENST00000376862.3	37	c.450_452delGGA	CCDS13164.1																																																																																				0.547	SYNDIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078376.1	NM_024893		7	828						7	828	---	---	---	---
ZNF337	26152	broad.mit.edu	37	20	25657231	25657232	+	Frame_Shift_Del	DEL	TG	TG	-	rs200386201		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr20:25657231_25657232delTG	ENST00000376436.1	-	4	1231_1232	c.692_693delCA	c.(691-693)acafs	p.T231fs	ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000428254.1_RNA|RP4-694B14.5_ENST00000455791.1_RNA|RP4-694B14.5_ENST00000421829.1_RNA|ZNF337_ENST00000538750.1_Frame_Shift_Del_p.T199fs|RP4-694B14.5_ENST00000414393.1_RNA|ZNF337_ENST00000252979.5_Frame_Shift_Del_p.T231fs|RP4-694B14.5_ENST00000439498.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	231					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						ACTTCTCTCCTGTGTGTGTGTT	0.51																																						ENST00000376436.1																			0				breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						c.(691-693)afs		zinc finger protein 337																																				SO:0001589	frameshift_variant	26152							g.chr20:25657231_25657232delTG		CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"""Zinc fingers, C2H2-type"", ""-"""	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.692_693delCA	20.37:g.25657239_25657240delTG	ENSP00000365619:p.Thr231fs					RP4-694B14.5_ENST00000414393.1_RNA|ZNF337_ENST00000538750.1_Frame_Shift_Del_p.T199fs|RP4-694B14.5_ENST00000439498.1_RNA|RP4-694B14.5_ENST00000455791.1_RNA|ZNF337_ENST00000252979.5_Frame_Shift_Del_p.T231fs	p.T231fs							4	1231_1232	-								B4DSM2|Q9Y3Y5	Frame_Shift_Del	DEL	ENST00000376436.1	37	c.692_693delCA	CCDS13174.1																																																																																				0.510	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1			10	506						10	506	---	---	---	---
NCOA6	23054	broad.mit.edu	37	20	33330968	33330970	+	In_Frame_Del	DEL	TGC	TGC	-	rs140426729	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr20:33330968_33330970delTGC	ENST00000374796.2	-	12	5660_5662	c.3090_3092delGCA	c.(3088-3093)cagcaa>caa	p.1030_1031QQ>Q	NCOA6_ENST00000359003.2_In_Frame_Del_p.1030_1031QQ>Q			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1030	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						CATCATTtgttgctgctgctgct	0.576																																						ENST00000374796.2																			0				NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						c.(3088-3093)caa>ca		nuclear receptor coactivator 6																																				SO:0001651	inframe_deletion	23054				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding	g.chr20:33330968_33330970delTGC	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.3090_3092delGCA	20.37:g.33330977_33330979delTGC	ENSP00000363929:p.Gln1032del					NCOA6_ENST00000359003.2_In_Frame_Del_p.QQ1030del	p.QQ1030del			Q14686	NCOA6_HUMAN			12	5660_5662	-			1030			CREBBP-binding region.|Gln-rich.|NCOA1-binding region.		A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	In_Frame_Del	DEL	ENST00000374796.2	37	c.3090_3092delGCA	CCDS13241.1																																																																																				0.576	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		9	506						9	506	---	---	---	---
DDX27	55661	broad.mit.edu	37	20	47858504	47858504	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr20:47858504delA	ENST00000371764.4	+	17	2074	c.2065delA	c.(2065-2067)aaafs	p.K691fs	ZNFX1_ENST00000469991.1_Intron|DDX27_ENST00000484427.1_3'UTR|ZNFX1_ENST00000371754.4_Intron	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	691						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.K691fs*4(3)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GAAGGATGCCAAAAAAAAGGG	0.488																																						ENST00000371764.4																			3	Deletion - Frameshift(3)	p.K691fs*4(3)	large_intestine(2)|ovary(1)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45						c.(2065-2067)aafs		DEAD (Asp-Glu-Ala-Asp) box polypeptide 27							67.0	72.0	70.0					20																	47858504		2203	4300	6503	SO:0001589	frameshift_variant	55661					nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding	g.chr20:47858504delA	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"""DEAD-boxes"""	15837	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"""				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.2065delA	20.37:g.47858504delA	ENSP00000360828:p.Lys691fs					ZNFX1_ENST00000371754.4_Intron|DDX27_ENST00000484427.1_3'UTR|ZNFX1_ENST00000469991.1_Intron	p.K691fs	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		17	2074	+			691					A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Frame_Shift_Del	DEL	ENST00000371764.4	37	c.2065delA	CCDS13416.1																																																																																				0.488	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1			8	466						8	466	---	---	---	---
SYCP2	10388	broad.mit.edu	37	20	58490593	58490593	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr20:58490593delT	ENST00000357552.3	-	9	751	c.526delA	c.(526-528)atgfs	p.M176fs	SYCP2_ENST00000371001.2_Frame_Shift_Del_p.M176fs			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	176					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			ATAGCATTCATTTTTTTTATA	0.289																																						ENST00000357552.3																			0				NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						c.(526-528)tgfs		synaptonemal complex protein 2							75.0	82.0	80.0					20																	58490593		2200	4289	6489	SO:0001589	frameshift_variant	10388				cell division|meiotic prophase I|synaptonemal complex assembly		DNA binding	g.chr20:58490593delT	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.526delA	20.37:g.58490593delT	ENSP00000350162:p.Met176fs					SYCP2_ENST00000371001.2_Frame_Shift_Del_p.M176fs	p.M176fs			Q9BX26	SYCP2_HUMAN	BRCA - Breast invasive adenocarcinoma(7;1.19e-09)		9	751	-	all_lung(29;0.00344)		176					A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Frame_Shift_Del	DEL	ENST00000357552.3	37	c.526delA	CCDS13482.1																																																																																				0.289	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		9	364						9	364	---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10944697	10944697	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr21:10944697delA	ENST00000361285.4	-	11	866	c.537delT	c.(535-537)tttfs	p.F179fs	TPTE_ENST00000298232.7_Frame_Shift_Del_p.F161fs|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Frame_Shift_Del_p.F141fs	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	179					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ACTTAATGTCAAAAAAAATGT	0.299																																						ENST00000298232.7																			0				NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130						c.(481-483)ttfs		transmembrane phosphatase with tensin homology							157.0	168.0	164.0					21																	10944697		2203	4300	6503	SO:0001589	frameshift_variant	7179				signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	g.chr21:10944697delA	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.537delT	21.37:g.10944697delA	ENSP00000355208:p.Phe179fs					TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000361285.4_Frame_Shift_Del_p.F179fs|TPTE_ENST00000342420.5_Frame_Shift_Del_p.F141fs	p.F161fs	NM_199259.2	NP_954868.1	P56180	TPTE_HUMAN	Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	10	850	-			179					B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Frame_Shift_Del	DEL	ENST00000361285.4	37	c.483delT	CCDS13560.2																																																																																				0.299	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			25	1044						25	1044	---	---	---	---
MIR99AHG	388815	broad.mit.edu	37	21	17443416	17443417	+	lincRNA	DEL	TG	TG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr21:17443416_17443417delTG	ENST00000458468.1	+	0	27					NR_027790.1																						TTTTTCTTTTTGTGTGTGTGTG	0.431																																						ENST00000458468.1																			0																																																			0							g.chr21:17443416_17443417delTG																													21.37:g.17443426_17443427delTG								NR_027790.1						0	27	+									RNA	DEL	ENST00000458468.1	37																																																																																						0.431	LINC00478-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000158029.1			8	849						8	849	---	---	---	---
COL18A1	80781	broad.mit.edu	37	21	46897721	46897721	+	Frame_Shift_Del	DEL	G	G	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr21:46897721delG	ENST00000359759.4	+	7	2329	c.2308delG	c.(2308-2310)ggcfs	p.G770fs	COL18A1_ENST00000400337.2_Frame_Shift_Del_p.G355fs|COL18A1_ENST00000355480.5_Frame_Shift_Del_p.G535fs			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	770	Triple-helical region 1 (COL1).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		TGGCCGGGCAGGCCCCCCAGG	0.706																																						ENST00000359759.4																			0				breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						c.(2308-2310)gcfs		collagen, type XVIII, alpha 1							8.0	11.0	10.0					21																	46897721		1784	3950	5734	SO:0001589	frameshift_variant	80781				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding	g.chr21:46897721delG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2308delG	21.37:g.46897721delG	ENSP00000352798:p.Gly770fs					COL18A1_ENST00000355480.5_Frame_Shift_Del_p.G535fs|COL18A1_ENST00000400337.2_Frame_Shift_Del_p.G355fs	p.G770fs			P39060	COIA1_HUMAN		Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)	7	2329	+			770			Triple-helical region 1 (COL1).		A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Frame_Shift_Del	DEL	ENST00000359759.4	37	c.2308delG																																																																																					0.706	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			2	4						2	4	---	---	---	---
MED15	51586	broad.mit.edu	37	22	20918916	20918918	+	In_Frame_Del	DEL	CAG	CAG	-	rs374794651		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr22:20918916_20918918delCAG	ENST00000263205.7	+	6	700_702	c.631_633delCAG	c.(631-633)cagdel	p.Q218del	MED15_ENST00000406969.1_In_Frame_Del_p.Q192del|MED15_ENST00000292733.7_In_Frame_Del_p.Q218del|MED15_ENST00000382974.2_In_Frame_Del_p.Q147del|MED15_ENST00000542773.1_In_Frame_Del_p.Q23del|MED15_ENST00000541476.1_In_Frame_Del_p.Q192del|MED15_ENST00000425759.2_In_Frame_Del_p.Q107del	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	218	Poly-Gln.			Missing (in Ref. 4; CAG30423). {ECO:0000305}.	gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			gcagcagctccagcagcagcagc	0.567											OREG0026319	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000263205.7																			0				central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25						c.(631-633)del		mediator complex subunit 15																																				SO:0001651	inframe_deletion	51586				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding	g.chr22:20918916_20918918delCAG	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.631_633delCAG	22.37:g.20918925_20918927delCAG	ENSP00000263205:p.Gln218del		OREG0026319	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	744	MED15_ENST00000292733.7_In_Frame_Del_p.Q218del|MED15_ENST00000382974.2_In_Frame_Del_p.Q147del|MED15_ENST00000406969.1_In_Frame_Del_p.Q192del|MED15_ENST00000425759.2_In_Frame_Del_p.Q107del|MED15_ENST00000542773.1_In_Frame_Del_p.Q23del|MED15_ENST00000541476.1_In_Frame_Del_p.Q192del	p.Q218del	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)		6	700_702	+	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	218	Missing (in Ref. 4; CAG30423).		Poly-Gln.		D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	In_Frame_Del	DEL	ENST00000263205.7	37	c.631_633delCAG	CCDS33602.1																																																																																				0.567	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889		9	142						9	142	---	---	---	---
MED15	51586	broad.mit.edu	37	22	20920814	20920816	+	In_Frame_Del	DEL	CAG	CAG	-	rs67182670|rs535773989	byFrequency	TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr22:20920814_20920816delCAG	ENST00000263205.7	+	7	820_822	c.751_753delCAG	c.(751-753)cagdel	p.Q262del	MED15_ENST00000406969.1_In_Frame_Del_p.Q236del|MED15_ENST00000292733.7_In_Frame_Del_p.Q262del|MED15_ENST00000382974.2_In_Frame_Del_p.Q191del|MED15_ENST00000478831.1_3'UTR|MED15_ENST00000542773.1_In_Frame_Del_p.Q67del|MED15_ENST00000541476.1_In_Frame_Del_p.Q236del|MED15_ENST00000425759.2_In_Frame_Del_p.Q151del	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	262	Poly-Gln.		Missing.	Missing (in Ref. 3; BAB85034). {ECO:0000305}.	gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.Q250_Q251insQ(4)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			acaacagcaacagcagcagcagc	0.591																																						ENST00000263205.7																			4	Insertion - In frame(4)	p.Q250_Q251insQ(4)	ovary(2)|large_intestine(2)	central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25						c.(751-753)del		mediator complex subunit 15																																				SO:0001651	inframe_deletion	51586				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding	g.chr22:20920814_20920816delCAG	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.751_753delCAG	22.37:g.20920823_20920825delCAG	ENSP00000263205:p.Gln262del					MED15_ENST00000478831.1_3'UTR|MED15_ENST00000292733.7_In_Frame_Del_p.Q262del|MED15_ENST00000382974.2_In_Frame_Del_p.Q191del|MED15_ENST00000406969.1_In_Frame_Del_p.Q236del|MED15_ENST00000425759.2_In_Frame_Del_p.Q151del|MED15_ENST00000542773.1_In_Frame_Del_p.Q67del|MED15_ENST00000541476.1_In_Frame_Del_p.Q236del	p.Q262del	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)		7	820_822	+	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	262	Missing (in Ref. 3; BAB85034).	Missing.	Poly-Gln.		D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	In_Frame_Del	DEL	ENST00000263205.7	37	c.751_753delCAG	CCDS33602.1																																																																																				0.591	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889		41	314						41	314	---	---	---	---
ZNRF3	84133	broad.mit.edu	37	22	29445819	29445821	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr22:29445819_29445821delCAG	ENST00000544604.2	+	8	1825_1827	c.1650_1652delCAG	c.(1648-1653)gacagc>gac	p.S557del	ZNRF3_ENST00000402174.1_In_Frame_Del_p.S457del|ZNRF3_ENST00000406323.3_In_Frame_Del_p.S457del|ZNRF3_ENST00000332811.4_In_Frame_Del_p.S457del	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	557					canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						CAGgcagcgacagcagcagcagc	0.66																																						ENST00000544604.2																			0				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						c.(1648-1653)gac>ga		zinc and ring finger 3			,	78,3554		2,74,1740					,	5.4	1.0			16	199,7043		14,171,3436	no	coding,coding	ZNRF3	NM_032173.3,NM_001206998.1	,	16,245,5176	A1A1,A1R,RR		2.7479,2.1476,2.5474	,	,		277,10597				SO:0001651	inframe_deletion	84133					integral to membrane	zinc ion binding	g.chr22:29445819_29445821delCAG	AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579		"""RING-type (C3HC4) zinc fingers"""	18126	protein-coding gene	gene with protein product		612062				10574461	Standard	NM_032173		Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.1650_1652delCAG	22.37:g.29445828_29445830delCAG	ENSP00000443824:p.Ser557del					ZNRF3_ENST00000402174.1_In_Frame_Del_p.DS450del|ZNRF3_ENST00000332811.4_In_Frame_Del_p.DS450del|ZNRF3_ENST00000406323.3_In_Frame_Del_p.DS450del	p.DS550del	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN			8	1825_1827	+			550					B3KU18|Q6ICH1|Q6NTF8|Q8WU18	In_Frame_Del	DEL	ENST00000544604.2	37	c.1650_1652delCAG	CCDS56225.1																																																																																				0.660	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		10	251						10	251	---	---	---	---
SH3BP1	23616	broad.mit.edu	37	22	38039752	38039754	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr22:38039752_38039754delAGG	ENST00000357436.4	+	7	888_890	c.575_577delAGG	c.(574-579)aaggag>aag	p.E197del	SH3BP1_ENST00000599616.1_In_Frame_Del_p.E133del|SH3BP1_ENST00000442465.2_In_Frame_Del_p.E197del|SH3BP1_ENST00000336738.5_In_Frame_Del_p.E197del|Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000495174.1_3'UTR	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	197	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					GAGACGCTGAAGGAGGAGGAGGA	0.606											OREG0026546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000599616.1																			0				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						c.(382-387)aag>a		SH3-domain binding protein 1				1,4261		0,1,2130						5.1	1.0			112	1,8253		0,1,4126	no	coding	SH3BP1	NM_018957.3		0,2,6256	A1A1,A1R,RR		0.0121,0.0235,0.016				2,12514				SO:0001651	inframe_deletion	23616				signal transduction	cytoplasm	GTPase activator activity|SH3 domain binding	g.chr22:38039752_38039754delAGG		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"""Rho GTPase activating proteins"""	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.575_577delAGG	22.37:g.38039761_38039763delAGG	ENSP00000350018:p.Glu197del		OREG0026546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	875	SH3BP1_ENST00000495174.1_3'UTR|Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000336738.5_In_Frame_Del_p.KE192del|SH3BP1_ENST00000357436.4_In_Frame_Del_p.KE192del|SH3BP1_ENST00000442465.2_In_Frame_Del_p.KE192del	p.KE128del			Q9Y3L3	3BP1_HUMAN			5	383_385	+	Melanoma(58;0.0574)		192			BAR.		Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	In_Frame_Del	DEL	ENST00000357436.4	37	c.383_385delAGG	CCDS13952.2																																																																																				0.606	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957		7	475						7	475	---	---	---	---
SREBF2	6721	broad.mit.edu	37	22	42262949	42262951	+	In_Frame_Del	DEL	GCA	GCA	-	rs143615881		TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chr22:42262949_42262951delGCA	ENST00000361204.4	+	2	369_371	c.203_205delGCA	c.(202-207)ggcagc>ggc	p.S74del		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	74	Gly/Pro/Ser-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						ggcagcagtggcagcagcagcag	0.567																																						ENST00000361204.4																			0				NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						c.(202-207)ggc>g		sterol regulatory element binding transcription factor 2																																				SO:0001651	inframe_deletion	6721				cholesterol metabolic process	ER to Golgi transport vesicle membrane|Golgi membrane|nucleus|SREBP-SCAP-Insig complex	protein C-terminus binding	g.chr22:42262949_42262951delGCA	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.203_205delGCA	22.37:g.42262958_42262960delGCA	ENSP00000354476:p.Ser74del						p.GS68del	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN			2	369_371	+			68			Gly/Pro/Ser-rich.		Q05BD5|Q6GTH7|Q86V36|Q9UH04	In_Frame_Del	DEL	ENST00000361204.4	37	c.203_205delGCA	CCDS14023.1																																																																																				0.567	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		16	527						16	527	---	---	---	---
SH3KBP1	30011	broad.mit.edu	37	X	19764546	19764549	+	Frame_Shift_Del	DEL	TCTT	TCTT	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:19764546_19764549delTCTT	ENST00000397821.3	-	3	463_466	c.173_176delAAGA	c.(172-177)aaagagfs	p.KE58fs	SH3KBP1_ENST00000379697.3_Frame_Shift_Del_p.KE58fs|SH3KBP1_ENST00000379698.4_Frame_Shift_Del_p.KE21fs	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	58	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						TTTCTTCATCTCTTTCTTTATTTC	0.402																																						ENST00000397821.3																			0				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						c.(172-177)agfs		SH3-domain kinase binding protein 1																																				SO:0001589	frameshift_variant	30011				apoptosis|cell-cell signaling|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytoplasmic vesicle membrane|cytoskeleton|cytosol|focal adhesion|nucleus|synapse|synaptosome	SH3 domain binding	g.chrX:19764546_19764549delTCTT	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.173_176delAAGA	X.37:g.19764550_19764553delTCTT	ENSP00000380921:p.Lys58fs					SH3KBP1_ENST00000379698.4_Frame_Shift_Del_p.KE21fs|SH3KBP1_ENST00000379697.3_Frame_Shift_Del_p.KE58fs	p.KE58fs	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN			3	463_466	-			58			SH3 1.		B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Frame_Shift_Del	DEL	ENST00000397821.3	37	c.173_176delAAGA	CCDS14193.1																																																																																				0.402	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892		22	919						22	919	---	---	---	---
MED12	9968	broad.mit.edu	37	X	70360648	70360650	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:70360648_70360650delCAG	ENST00000374080.3	+	42	6240_6242	c.6208_6210delCAG	c.(6208-6210)cagdel	p.Q2076del	MED12_ENST00000374102.1_In_Frame_Del_p.Q2075del|AL590764.1_ENST00000579622.1_RNA|MED12_ENST00000333646.6_In_Frame_Del_p.Q2079del			Q93074	MED12_HUMAN	mediator complex subunit 12	2076	Gln-rich.				androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					gcaacagcaacagcagcagcagc	0.621			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																															ENST00000333646.6				Dom	yes		X	Xq13	9968	"""M, S"""	mediator complex subunit 12	Yes	Opitz-Kaveggia Syndrome	M			uterine leiomyoma		0				breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420						c.(6217-6219)del		mediator complex subunit 12				7,109,3423		0,0,6,1,1,78,29,1439,461						2.6	0.4			23	29,192,5891		2,0,16,9,2,98,90,2148,1481	no	codingComplex	MED12	NM_005120.2		2,0,22,10,3,176,119,3587,1942	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		3.6158,3.2778,3.4919				36,301,9314				SO:0001651	inframe_deletion	9968				androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding	g.chrX:70360648_70360650delCAG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.6208_6210delCAG	X.37:g.70360657_70360659delCAG	ENSP00000363193:p.Gln2076del					MED12_ENST00000374080.3_In_Frame_Del_p.Q2076del|MED12_ENST00000478889.1_3'UTR|MED12_ENST00000374102.1_In_Frame_Del_p.Q2075del	p.Q2079del	NM_005120.2	NP_005111.2	Q93074	MED12_HUMAN			42	6416_6418	+	Renal(35;0.156)		2076			Gln-rich.		O15410|O75557|Q9UHV6|Q9UND7	In_Frame_Del	DEL	ENST00000374080.3	37	c.6217_6219delCAG	CCDS43970.1																																																																																				0.621	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		9	367						9	367	---	---	---	---
MED12	9968	broad.mit.edu	37	X	70360680	70360682	+	In_Frame_Del	DEL	GCA	GCA	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:70360680_70360682delGCA	ENST00000374080.3	+	42	6272_6274	c.6240_6242delGCA	c.(6238-6243)cggcag>cgg	p.Q2086del	MED12_ENST00000374102.1_In_Frame_Del_p.Q2085del|AL590764.1_ENST00000579622.1_RNA|MED12_ENST00000333646.6_In_Frame_Del_p.Q2089del			Q93074	MED12_HUMAN	mediator complex subunit 12	2086	Gln-rich.				androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					accacatccggcagcagcagcag	0.586			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																															ENST00000333646.6				Dom	yes		X	Xq13	9968	"""M, S"""	mediator complex subunit 12	Yes	Opitz-Kaveggia Syndrome	M			uterine leiomyoma		0				breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420						c.(6247-6252)cgg>cg		mediator complex subunit 12																																				SO:0001651	inframe_deletion	9968				androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding	g.chrX:70360680_70360682delGCA	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.6240_6242delGCA	X.37:g.70360689_70360691delGCA	ENSP00000363193:p.Gln2086del					MED12_ENST00000374080.3_In_Frame_Del_p.RQ2080del|MED12_ENST00000374102.1_In_Frame_Del_p.RQ2079del	p.RQ2083del	NM_005120.2	NP_005111.2	Q93074	MED12_HUMAN			42	6448_6450	+	Renal(35;0.156)		2080			Gln-rich.		O15410|O75557|Q9UHV6|Q9UND7	In_Frame_Del	DEL	ENST00000374080.3	37	c.6249_6251delGCA	CCDS43970.1																																																																																				0.586	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		11	334						11	334	---	---	---	---
XIST	7503	broad.mit.edu	37	X	73072090	73072091	+	lincRNA	INS	-	-	A			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:73072090_73072091insA	ENST00000429829.1	-	0	497_498					NR_001564.2				X inactive specific transcript (non-protein coding)																		ATGGGCTAAGGAAAAAAAAATA	0.465																																						ENST00000429829.1																			0																																																			0							g.chrX:73072090_73072091insA	M97168		Xq13.2	2013-12-18	2013-02-07		ENSG00000229807	ENSG00000229807		"""Long non-coding RNAs"", ""-"""	12810	non-coding RNA	RNA, long non-coding	"""long intergenic non-protein coding RNA 1"""	314670	"""X (inactive)-specific transcript"", ""X (inactive)-specific transcript (non-protein coding)"""	DXS399E		1985261, 2034279	Standard	NR_001564		Approved	NCRNA00001, DXS1089, swd66, LINC00001	uc004ebm.2		OTTHUMG00000021839		X.37:g.73072099_73072099dupA								NR_001564.2						0	497_498	-									RNA	INS	ENST00000429829.1	37																																																																																						0.465	XIST-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000057239.1	NR_001564		7	127						7	127	---	---	---	---
ATRX	546	broad.mit.edu	37	X	76778785	76778787	+	In_Frame_Del	DEL	TCT	TCT	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:76778785_76778787delTCT	ENST00000373344.5	-	31	7006_7008	c.6792_6794delAGA	c.(6790-6795)gaagag>gag	p.2264_2265EE>E	ATRX_ENST00000395603.3_In_Frame_Del_p.2226_2227EE>E|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2264	Interaction with MECP2.|Poly-Glu.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TTCAGTCAACTCTTCTTCTTCTT	0.369			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															ENST00000373344.5				Rec	yes		X	Xq21.1	546	"""Mis, F, N"""	alpha thalassemia/mental retardation syndrome X-linked	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E			"""Pancreatic neuroendocrine tumors, paediatric GBM"""		0				bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						c.(6790-6795)gag>ga		alpha thalassemia/mental retardation syndrome X-linked	Phosphatidylserine(DB00144)																																			SO:0001651	inframe_deletion	546				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	g.chrX:76778785_76778787delTCT	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.6792_6794delAGA	X.37:g.76778794_76778796delTCT	ENSP00000362441:p.Glu2265del					ATRX_ENST00000395603.3_In_Frame_Del_p.EE2226del|ATRX_ENST00000480283.1_5'UTR	p.EE2264del	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN			31	7006_7008	-			2264			Poly-Glu.		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	In_Frame_Del	DEL	ENST00000373344.5	37	c.6792_6794delAGA	CCDS14434.1																																																																																				0.369	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		10	1185						10	1185	---	---	---	---
IRS4	8471	broad.mit.edu	37	X	107977802	107977803	+	Frame_Shift_Ins	INS	-	-	C			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:107977802_107977803insC	ENST00000372129.2	-	1	1848_1849	c.1772_1773insG	c.(1771-1773)ggcfs	p.G591fs	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	591					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						CTGAGCCTTTGCCCCCCCCAGA	0.545																																						ENST00000372129.2																			0				NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						c.(1771-1773)gaafs		insulin receptor substrate 4				32,3681		0,19,13,1569,524						4.0	0.4			181	25,6453		0,7,18,2347,1752	no	frameshift	IRS4	NM_003604.2		0,26,31,3916,2276	A1A1,A1R,A1,RR,R		0.3859,0.8618,0.5593				57,10134				SO:0001589	frameshift_variant	8471					plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity	g.chrX:107977802_107977803insC	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1773dupG	X.37:g.107977810_107977810dupC	ENSP00000361202:p.Gly591fs						p.E591fs	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN			1	1848_1849	-			591						Frame_Shift_Ins	INS	ENST00000372129.2	37	c.1772_1773insG	CCDS14544.1																																																																																				0.545	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		17	1685						17	1685	---	---	---	---
GUCY2F	2986	broad.mit.edu	37	X	108619355	108619355	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:108619355delT	ENST00000218006.2	-	18	3483	c.3192delA	c.(3190-3192)aaafs	p.K1064fs		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	1064					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						TCATGAAGCCTTTTTTCCCAA	0.418																																						ENST00000218006.2																			0				breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						c.(3190-3192)aafs		guanylate cyclase 2F, retinal							171.0	156.0	161.0					X																	108619355		2203	4300	6503	SO:0001589	frameshift_variant	2986				intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity	g.chrX:108619355delT	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"""guanylate cyclase 2D-like, membrane (retina-specific)"""	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.3192delA	X.37:g.108619355delT	ENSP00000218006:p.Lys1064fs						p.K1064fs	NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN			18	3483	-			1064					Q9UJF1	Frame_Shift_Del	DEL	ENST00000218006.2	37	c.3192delA	CCDS14545.1																																																																																				0.418	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522		8	1325						8	1325	---	---	---	---
HTATSF1	27336	broad.mit.edu	37	X	135585048	135585050	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:135585048_135585050delAAG	ENST00000218364.4	+	5	856_858	c.682_684delAAG	c.(682-684)aagdel	p.K232del	HTATSF1_ENST00000535601.1_In_Frame_Del_p.K232del	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	232	Poly-Lys.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					TGATGCCTCAAAGAAGAAGAAGA	0.335																																						ENST00000535601.1																			0				NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30						c.(682-684)del		HIV-1 Tat specific factor 1																																				SO:0001651	inframe_deletion	27336				regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|viral genome replication	nucleus	nucleotide binding|protein binding|RNA binding	g.chrX:135585048_135585050delAAG	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"""RNA binding motif (RRM) containing"""	5276	protein-coding gene	gene with protein product		300346	"""HIV TAT specific factor 1"""			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.682_684delAAG	X.37:g.135585057_135585059delAAG	ENSP00000218364:p.Lys232del					HTATSF1_ENST00000218364.4_In_Frame_Del_p.K232del	p.K232del	NM_001163280.1	NP_001156752.1	O43719	HTSF1_HUMAN			6	1104_1106	+	Acute lymphoblastic leukemia(192;0.000127)		232			Poly-Lys.		D3DWG9|Q59G06|Q99730	In_Frame_Del	DEL	ENST00000218364.4	37	c.682_684delAAG	CCDS14657.1																																																																																				0.335	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		9	627						9	627	---	---	---	---
CD99L2	83692	broad.mit.edu	37	X	149984524	149984526	+	In_Frame_Del	DEL	GTG	GTG	-			TCGA-FB-A4P5-01A-11D-A26I-08	TCGA-FB-A4P5-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3c284834-b0e8-490a-a7c7-e7b880122282	e9984562-78e0-444d-92ca-64a3135fb628	g.chrX:149984524_149984526delGTG	ENST00000370377.3	-	3	273_275	c.156_158delCAC	c.(154-159)accaca>aca	p.52_53TT>T	CD99L2_ENST00000346693.4_5'UTR|CD99L2_ENST00000437787.2_In_Frame_Del_p.52_53TT>T|CD99L2_ENST00000466436.1_Intron|CD99L2_ENST00000355149.3_Intron	NM_001242614.1|NM_031462.3	NP_001229543.1|NP_113650.2	Q8TCZ2	C99L2_HUMAN	CD99 molecule-like 2	52	Poly-Thr.				cell adhesion (GO:0007155)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					CCTATTGGTTGTGGTGGTGGTGG	0.552																																						ENST00000370377.3																			0				endometrium(4)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	23						c.(154-159)aca>ac		CD99 molecule-like 2																																				SO:0001651	inframe_deletion	83692				cell adhesion	cell junction|integral to membrane		g.chrX:149984524_149984526delGTG	BC030536	CCDS14697.1, CCDS14698.1, CCDS35427.1, CCDS55527.1, CCDS76044.1	Xq28	2007-12-04	2006-03-28	2003-02-14	ENSG00000102181	ENSG00000102181			18237	protein-coding gene	gene with protein product		300846	"""MIC2 like 1"", ""CD99 antigen-like 2"""	MIC2L1			Standard	NM_001184808		Approved	CD99B	uc004fek.3	Q8TCZ2	OTTHUMG00000024247	ENST00000370377.3:c.156_158delCAC	X.37:g.149984533_149984535delGTG	ENSP00000359403:p.Thr54del					CD99L2_ENST00000355149.3_Intron|CD99L2_ENST00000466436.1_Intron|CD99L2_ENST00000346693.4_5'UTR|CD99L2_ENST00000437787.2_In_Frame_Del_p.TT52del	p.TT52del	NM_001242614.1|NM_031462.3	NP_001229543.1|NP_113650.2	Q8TCZ2	C99L2_HUMAN			3	273_275	-	Acute lymphoblastic leukemia(192;6.56e-05)		52			Poly-Thr.		A8K2D5|A8K5R0|B3KWG2|B4DDL7|E7EMK5|E9PD27|Q8TAW2|Q8TCZ0|Q8TCZ1|Q9BQG9	In_Frame_Del	DEL	ENST00000370377.3	37	c.156_158delCAC	CCDS35427.1																																																																																				0.552	CD99L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000061199.1	NM_031462		13	1165						13	1165	---	---	---	---
