#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
RP11-146E13.4	0	broad.mit.edu	37	14	19857036	19857036	+	lincRNA	SNP	A	A	G	rs374719458		TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr14:19857036A>G	ENST00000548109.1	+	0	72																											CTGGATAATAAAGTTCATCTC	0.373																																						ENST00000548109.1																			0																																																			0							g.chr14:19857036A>G																													14.37:g.19857036A>G														0	72	+									RNA	SNP	ENST00000548109.1	37																																																																																						0.373	RP11-146E13.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000409408.1			3	23	0	0	0	1	0	3	23				
SDHAP1	255812	broad.mit.edu	37	3	195690271	195690271	+	RNA	SNP	T	T	C	rs201745109	byFrequency	TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr3:195690271T>C	ENST00000427841.1	-	0	2224					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		TTGTCGATTATGGGTCTATAT	0.403																																					Ovarian(67;1158 1227 12109 20189 43170)	ENST00000427841.1																			0																																																			0							g.chr3:195690271T>C	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.195690271T>C								NR_003264.2						0	2224	-									RNA	SNP	ENST00000427841.1	37																																																																																						0.403	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			3	21	0	0	0	1	0	3	21				
RANBP2	5903	broad.mit.edu	37	2	109371498	109371498	+	Silent	SNP	G	G	A	rs373469365	byFrequency	TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr2:109371498G>A	ENST00000283195.6	+	16	2466	c.2340G>A	c.(2338-2340)ccG>ccA	p.P780P		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	780					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)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						ATTCTACACCGTCTCCTACCA	0.353													G|||	3	0.000599042	0.0008	0.0	5008	,	,		15081	0.001		0.0	False		,,,				2504	0.001					ENST00000283195.6																		RANBP2/ALK(34)	0				NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						c.(2338-2340)ccG>ccA		RAN binding protein 2							98.0	103.0	101.0					2																	109371498		2198	4282	6480	SO:0001819	synonymous_variant	5903				carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding	g.chr2:109371498G>A	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2340G>A	2.37:g.109371498G>A							p.P780P	NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN			16	2466	+			780					Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	c.2340G>A	CCDS2079.1																																																																																				0.353	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		5	342	0	0	0	1	0	5	342				
CATSPERG	57828	broad.mit.edu	37	19	38858384	38858384	+	Silent	SNP	C	C	T	rs2302184		TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr19:38858384C>T	ENST00000409235.3	+	25	3013	c.2898C>T	c.(2896-2898)gaC>gaT	p.D966D	CATSPERG_ENST00000215069.4_3'UTR|CATSPERG_ENST00000410018.1_Silent_p.D926D	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	966					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						ACAGTGAGGACGAAATCTACC	0.597													C|||	1	0.000199681	0.0	0.0	5008	,	,		17275	0.0		0.0	False		,,,				2504	0.001					ENST00000409235.3																			0				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						c.(2896-2898)gaC>gaT		catsper channel auxiliary subunit gamma		C		0,4406		0,0,2203	227.0	238.0	234.0		2898	-3.5	0.3	19	dbSNP_100	234	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CATSPERG	NM_021185.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		966/1160	38858384	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57828				cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane		g.chr19:38858384C>T	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"""chromosome 19 open reading frame 15"", ""cation channel, sperm-associated, gamma"""	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.2898C>T	19.37:g.38858384C>T						CATSPERG_ENST00000410018.1_Silent_p.D926D|CATSPERG_ENST00000215069.4_3'UTR	p.D966D	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN			25	3013	+			966					A6NEG6|Q659E1	Silent	SNP	ENST00000409235.3	37	c.2898C>T	CCDS12514.2																																																																																				0.597	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185		93	158	0	0	0	1	0	93	158				
TRIOBP	11078	broad.mit.edu	37	22	38122318	38122318	+	Missense_Mutation	SNP	C	C	T	rs560619122		TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr22:38122318C>T	ENST00000406386.3	+	7	4010	c.3755C>T	c.(3754-3756)tCc>tTc	p.S1252F		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1252					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					TCTGGGGGCTCCCGGGGCTCA	0.716													C|||	1	0.000199681	0.0	0.0	5008	,	,		12887	0.0		0.001	False		,,,				2504	0.0					ENST00000406386.3																			0				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						c.(3754-3756)tCc>tTc		TRIO and F-actin binding protein							19.0	25.0	23.0					22																	38122318		1884	4061	5945	SO:0001583	missense	11078				actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding	g.chr22:38122318C>T	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.3755C>T	22.37:g.38122318C>T	ENSP00000384312:p.Ser1252Phe					RP1-37E16.12_ENST00000455236.1_RNA	p.S1252F	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN			7	4010	+	Melanoma(58;0.0574)		1252					B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	c.3755C>T	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.980577	0.53827	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.26810	1.71	5.38	1.86	0.25419	.	.	.	.	.	T	0.14442	0.0349	L	0.27053	0.805	0.80722	D	1	P	0.38167	0.621	B	0.30572	0.117	T	0.09751	-1.0660	9	0.72032	D	0.01	.	8.2176	0.31521	0.2766:0.6467:0.0:0.0767	.	1252	Q9H2D6	TARA_HUMAN	F	1252	ENSP00000384312:S1252F	ENSP00000384312:S1252F	S	+	2	0	TRIOBP	36452264	1.000000	0.71417	0.999000	0.59377	0.422000	0.31414	2.547000	0.45786	1.223000	0.43536	0.456000	0.33151	TCC		0.716	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			6	47	0	0	0	1	0	6	47				
AUTS2	26053	broad.mit.edu	37	7	69364311	69364311	+	Missense_Mutation	SNP	C	C	T	rs142957106	byFrequency	TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr7:69364311C>T	ENST00000342771.4	+	2	670	c.349C>T	c.(349-351)Cgc>Tgc	p.R117C	AUTS2_ENST00000403018.2_Missense_Mutation_p.R117C|AUTS2_ENST00000406775.2_Missense_Mutation_p.R117C	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	117								p.R117C(1)		breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		TGTGGAGAAACGCCAGACGCC	0.488																																						ENST00000342771.4																			1	Substitution - Missense(1)	p.R117C(1)	breast(1)	breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50						c.(349-351)Cgc>Tgc		autism susceptibility candidate 2		C	CYS/ARG,CYS/ARG,CYS/ARG	9,4397	15.5+/-35.6	0,9,2194	94.0	86.0	88.0		349,349,349	4.8	1.0	7	dbSNP_134	88	0,8600		0,0,4300	yes	missense,missense,missense	AUTS2	NM_001127231.1,NM_001127232.1,NM_015570.2	180,180,180	0,9,6494	TT,TC,CC		0.0,0.2043,0.0692	possibly-damaging,possibly-damaging,possibly-damaging	117/1236,117/267,117/1260	69364311	9,12997	2203	4300	6503	SO:0001583	missense	26053							g.chr7:69364311C>T	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.349C>T	7.37:g.69364311C>T	ENSP00000344087:p.Arg117Cys					AUTS2_ENST00000406775.2_Missense_Mutation_p.R117C|AUTS2_ENST00000403018.2_Missense_Mutation_p.R117C	p.R117C	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)	2	670	+		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)	117					A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	37	c.349C>T	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.230260	0.58777	0.002043	0.0	ENSG00000158321	ENST00000406775;ENST00000342771;ENST00000403018	T;T	0.36520	1.25;1.29	5.65	4.75	0.60458	.	0.216528	0.32608	N	0.005861	T	0.37999	0.1024	N	0.22421	0.69	0.40142	D	0.976844	P;P;D	0.71674	0.956;0.956;0.998	B;B;P	0.53861	0.401;0.401;0.736	T	0.18999	-1.0319	9	.	.	.	-15.6291	16.5834	0.84720	0.0:0.8697:0.1303:0.0	.	117;117;117	Q8WXX7-2;Q8WXX7;Q6PJU5	.;AUTS2_HUMAN;.	C	117	ENSP00000385263:R117C;ENSP00000344087:R117C	.	R	+	1	0	AUTS2	69002247	0.966000	0.33281	1.000000	0.80357	0.997000	0.91878	1.521000	0.35910	1.587000	0.49959	0.655000	0.94253	CGC		0.488	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			27	44	0	0	0	1	0	27	44				
ANKRD27	84079	broad.mit.edu	37	19	33149850	33149850	+	Silent	SNP	C	C	T			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr19:33149850C>T	ENST00000306065.4	-	2	230	c.72G>A	c.(70-72)ttG>ttA	p.L24L	ANKRD27_ENST00000587352.1_Silent_p.L24L	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	24					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					CTTTGCTGCACAAGTCAGGGC	0.498																																						ENST00000306065.4																			0				breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42						c.(70-72)ttG>ttA		ankyrin repeat domain 27 (VPS9 domain)							92.0	86.0	88.0					19																	33149850		2203	4300	6503	SO:0001819	synonymous_variant	84079				early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity	g.chr19:33149850C>T	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.72G>A	19.37:g.33149850C>T						ANKRD27_ENST00000587352.1_Silent_p.L24L|ANKRD27_ENST00000586693.2_5'UTR	p.L24L	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN			2	230	-	Esophageal squamous(110;0.137)		24					Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Silent	SNP	ENST00000306065.4	37	c.72G>A	CCDS32986.1																																																																																				0.498	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139		17	19	0	0	0	1	0	17	19				
TMEM132E	124842	broad.mit.edu	37	17	32959839	32959839	+	Nonsense_Mutation	SNP	G	G	A			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr17:32959839G>A	ENST00000321639.5	+	7	1657	c.1329G>A	c.(1327-1329)tgG>tgA	p.W443*		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	443						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		TGACAGTCTGGGTCCCCAAGC	0.587																																						ENST00000321639.5																			0				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57						c.(1327-1329)tgG>tgA		transmembrane protein 132E							185.0	164.0	171.0					17																	32959839		2203	4300	6503	SO:0001587	stop_gained	124842					integral to membrane		g.chr17:32959839G>A	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1329G>A	17.37:g.32959839G>A	ENSP00000316532:p.Trp443*						p.W443*	NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.231)	7	1657	+			443					Q8WUF4|Q8WVA5	Nonsense_Mutation	SNP	ENST00000321639.5	37	c.1329G>A	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	G	41	8.558026	0.98861	.	.	ENSG00000181291	ENST00000321639	.	.	.	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.8622	16.6219	0.84932	0.0:0.0:1.0:0.0	.	.	.	.	X	443	.	ENSP00000316532:W443X	W	+	3	0	TMEM132E	29983952	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	9.657000	0.98554	2.388000	0.81334	0.551000	0.68910	TGG		0.587	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		40	104	0	0	0	1	0	40	104				
GSK3A	2931	broad.mit.edu	37	19	42738596	42738596	+	Silent	SNP	G	G	A			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr19:42738596G>A	ENST00000222330.3	-	6	940	c.813C>T	c.(811-813)gtC>gtT	p.V271V	GSK3A_ENST00000398249.4_Silent_p.V189V	NM_019884.2	NP_063937.2	P49840	GSK3A_HUMAN	glycogen synthase kinase 3 alpha	271	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cardiac left ventricle morphogenesis (GO:0003214)|cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|cellular response to interleukin-3 (GO:0036016)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transferase activity (GO:0051348)|negative regulation of type B pancreatic cell development (GO:2000077)|negative regulation of UDP-glucose catabolic process (GO:0010905)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of heart contraction (GO:0045823)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein phosphorylation (GO:0006468)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of systemic arterial blood pressure (GO:0003073)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cytosol (GO:0005829)	ATP binding (GO:0005524)|protein kinase A catalytic subunit binding (GO:0034236)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(3)|large_intestine(3)|lung(6)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	19		Prostate(69;0.00682)				GCTCCCCTCGGACCAACTGCT	0.592																																						ENST00000398249.4																			0				endometrium(3)|large_intestine(3)|lung(6)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	19						c.(565-567)gtC>gtT		glycogen synthase kinase 3 alpha							99.0	89.0	92.0					19																	42738596		2203	4300	6503	SO:0001819	synonymous_variant	2931				insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of insulin receptor signaling pathway|negative regulation of transferase activity|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process	beta-catenin destruction complex|cytosol	ATP binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|tau-protein kinase activity	g.chr19:42738596G>A		CCDS12599.1	19q13	2008-02-15			ENSG00000105723	ENSG00000105723			4616	protein-coding gene	gene with protein product		606784				9809441	Standard	NM_019884		Approved		uc002otb.1	P49840	OTTHUMG00000150722	ENST00000222330.3:c.813C>T	19.37:g.42738596G>A						GSK3A_ENST00000222330.3_Silent_p.V271V	p.V189V			P49840	GSK3A_HUMAN			5	2280	-		Prostate(69;0.00682)	271			Protein kinase.		O14959	Silent	SNP	ENST00000222330.3	37	c.567C>T	CCDS12599.1																																																																																				0.592	GSK3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319782.1			13	35	0	0	0	1	0	13	35				
CMYA5	202333	broad.mit.edu	37	5	79028017	79028017	+	Missense_Mutation	SNP	T	T	A			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr5:79028017T>A	ENST00000446378.2	+	2	3460	c.3429T>A	c.(3427-3429)agT>agA	p.S1143R		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1143					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GGGAGGCAAGTTCATCAGTAG	0.423																																						ENST00000446378.2																			0				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128						c.(3427-3429)agT>agA		cardiomyopathy associated 5							75.0	72.0	73.0					5																	79028017		1949	4144	6093	SO:0001583	missense	202333					perinuclear region of cytoplasm		g.chr5:79028017T>A	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.3429T>A	5.37:g.79028017T>A	ENSP00000394770:p.Ser1143Arg						p.S1143R	NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)	2	3460	+		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)	1143					A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	c.3429T>A	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	T	9.041	0.989710	0.18966	.	.	ENSG00000164309	ENST00000446378	T	0.39406	1.08	5.96	3.55	0.40652	.	1.248360	0.05270	N	0.517447	T	0.42177	0.1191	M	0.67953	2.075	0.09310	N	1	B	0.30281	0.275	B	0.25140	0.058	T	0.36866	-0.9730	10	0.72032	D	0.01	.	5.6313	0.17512	0.0:0.164:0.154:0.6819	.	1143	Q8N3K9	CMYA5_HUMAN	R	1143	ENSP00000394770:S1143R	ENSP00000394770:S1143R	S	+	3	2	CMYA5	79063773	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.961000	0.29267	0.495000	0.27882	0.533000	0.62120	AGT		0.423	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		5	48	0	0	0	1	0	5	48				
NELL1	4745	broad.mit.edu	37	11	21555934	21555934	+	Missense_Mutation	SNP	T	T	C			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr11:21555934T>C	ENST00000357134.5	+	16	1812	c.1660T>C	c.(1660-1662)Tca>Cca	p.S554P	NELL1_ENST00000532434.1_Intron|NELL1_ENST00000298925.5_Missense_Mutation_p.S582P|NELL1_ENST00000529218.1_3'UTR|NELL1_ENST00000325319.5_Missense_Mutation_p.S497P	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	554	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						TGATGAATGTTCAGAGGGAAT	0.458																																						ENST00000298925.5																			0				NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						c.(1744-1746)Tca>Cca		NEL-like 1 (chicken)							157.0	141.0	146.0					11																	21555934		2203	4300	6503	SO:0001583	missense	4745				cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity	g.chr11:21555934T>C	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.1660T>C	11.37:g.21555934T>C	ENSP00000349654:p.Ser554Pro					NELL1_ENST00000529218.1_3'UTR|NELL1_ENST00000532434.1_Intron|NELL1_ENST00000357134.5_Missense_Mutation_p.S554P|NELL1_ENST00000325319.5_Missense_Mutation_p.S497P	p.S582P			Q92832	NELL1_HUMAN			17	1897	+			554			EGF-like 5; calcium-binding (Potential).		B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	37	c.1744T>C	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	T	13.79	2.342732	0.41498	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319	D;D;D	0.92249	-3.0;-3.0;-3.0	5.37	-1.15	0.09709	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.255253	0.30676	N	0.009110	D	0.86377	0.5918	L	0.56769	1.78	0.23776	N	0.99688	B;B;B	0.21147	0.018;0.052;0.01	B;B;B	0.17433	0.018;0.012;0.008	T	0.76487	-0.2941	10	0.66056	D	0.02	-3.9838	4.0764	0.09906	0.2511:0.0:0.4211:0.3278	.	497;582;554	F5H6I3;B3KXR2;Q92832	.;.;NELL1_HUMAN	P	582;554;497	ENSP00000298925:S582P;ENSP00000349654:S554P;ENSP00000317837:S497P	ENSP00000298925:S582P	S	+	1	0	NELL1	21512510	1.000000	0.71417	0.984000	0.44739	0.987000	0.75469	0.773000	0.26661	-0.199000	0.10317	-0.917000	0.02746	TCA		0.458	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		43	52	0	0	0	1	0	43	52				
RPA1	6117	broad.mit.edu	37	17	1795214	1795214	+	Missense_Mutation	SNP	C	C	A			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr17:1795214C>A	ENST00000254719.5	+	15	1749	c.1639C>A	c.(1639-1641)Ctt>Att	p.L547I		NM_002945.3	NP_002936.1	P27694	RFA1_HUMAN	replication protein A1, 70kDa	547					base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of cell proliferation (GO:0008284)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|DNA replication factor A complex (GO:0005662)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|single-stranded DNA binding (GO:0003697)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)	10						TGCTGCTTATCTTGGGGAATT	0.343								Nucleotide excision repair (NER)																														ENST00000254719.5																			0				breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)	10						c.(1639-1641)Ctt>Att	Nucleotide excision repair (NER)	replication protein A1, 70kDa							74.0	77.0	76.0					17																	1795214		2203	4300	6503	SO:0001583	missense	6117				cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	actin cytoskeleton|cytoplasm|DNA replication factor A complex|PML body	metal ion binding|protein binding|single-stranded DNA binding	g.chr17:1795214C>A	M63488	CCDS11014.1	17p13.3	2008-02-05	2002-08-29		ENSG00000132383	ENSG00000132383			10289	protein-coding gene	gene with protein product		179835	"""replication protein A1 (70kD)"""			8454588	Standard	NM_002945		Approved	REPA1, RPA70, HSSB, RF-A, RP-A	uc002fto.2	P27694	OTTHUMG00000090579	ENST00000254719.5:c.1639C>A	17.37:g.1795214C>A	ENSP00000254719:p.Leu547Ile						p.L547I	NM_002945.3	NP_002936.1	P27694	RFA1_HUMAN			15	1749	+			547					A8K0Y9|Q59ES9	Missense_Mutation	SNP	ENST00000254719.5	37	c.1639C>A	CCDS11014.1	.	.	.	.	.	.	.	.	.	.	C	11.04	1.521118	0.27211	.	.	ENSG00000132383	ENST00000254719	T	0.57595	0.39	5.72	2.58	0.30949	Nucleic acid-binding, OB-fold-like (1);Replication factor A, C-terminal (1);Nucleic acid-binding, OB-fold (1);	0.057244	0.64402	N	0.000001	T	0.61726	0.2370	L	0.60957	1.885	0.58432	D	0.999996	P	0.51653	0.947	D	0.69479	0.964	T	0.56643	-0.7945	10	0.41790	T	0.15	-5.8117	6.266	0.20928	0.2463:0.5711:0.1187:0.064	.	547	P27694	RFA1_HUMAN	I	547	ENSP00000254719:L547I	ENSP00000254719:L547I	L	+	1	0	RPA1	1741964	0.998000	0.40836	0.154000	0.22540	0.048000	0.14542	1.979000	0.40608	0.326000	0.23384	-0.187000	0.12897	CTT		0.343	RPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207118.2	NM_002945		24	39	1	0	6.12954e-19	1	7.3159e-19	24	39				
TBC1D10A	83874	broad.mit.edu	37	22	30691024	30691024	+	Missense_Mutation	SNP	A	A	G			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr22:30691024A>G	ENST00000215790.7	-	5	709	c.545T>C	c.(544-546)gTg>gCg	p.V182A	RP1-130H16.18_ENST00000447976.1_Missense_Mutation_p.V56A|TBC1D10A_ENST00000403477.3_Missense_Mutation_p.V189A|TBC1D10A_ENST00000403362.1_Missense_Mutation_p.V94A	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	182	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)			cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						GGCCTTCAGCACACGGAATAG	0.637																																						ENST00000215790.7																			0				cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						c.(544-546)gTg>gCg		TBC1 domain family, member 10A							55.0	53.0	54.0					22																	30691024		2203	4300	6503	SO:0001583	missense	83874					intracellular|microvillus	guanyl-nucleotide exchange factor activity|PDZ domain binding|Rab GTPase activator activity	g.chr22:30691024A>G	AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"""EBP50-PDZ interactor of 64 kD"""	610020	"""TBC1 domain family, member 10"""	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.545T>C	22.37:g.30691024A>G	ENSP00000215790:p.Val182Ala					RP1-130H16.18_ENST00000447976.1_Missense_Mutation_p.V56A|TBC1D10A_ENST00000403362.1_Missense_Mutation_p.V94A|TBC1D10A_ENST00000403477.3_Missense_Mutation_p.V189A	p.V182A	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN			5	709	-			182			Rab-GAP TBC.		B3KXT8|O76053|Q20WK7|Q543A2	Missense_Mutation	SNP	ENST00000215790.7	37	c.545T>C	CCDS13874.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.313120	0.81358	.	.	ENSG00000248751;ENSG00000099992;ENSG00000099992;ENSG00000099992;ENSG00000099992	ENST00000434291;ENST00000215790;ENST00000403477;ENST00000403362;ENST00000393906	T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23	4.24	3.17	0.36434	Rab-GAP/TBC domain (4);	0.060021	0.64402	D	0.000003	T	0.50854	0.1640	H	0.96142	3.775	0.58432	D	0.999994	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.79108	0.983;0.992;0.983;0.992	T	0.59484	-0.7446	10	0.87932	D	0	.	9.1913	0.37200	0.8371:0.0:0.0:0.1629	.	182;189;182;182	Q20WK7;B3KXT8;Q9BXI6;A7E244	.;.;TB10A_HUMAN;.	A	56;182;189;94;94	ENSP00000401535:V56A;ENSP00000215790:V182A;ENSP00000384996:V189A;ENSP00000385050:V94A;ENSP00000377484:V94A	ENSP00000331267:V43A	V	-	2	0	TBC1D10A;RP1-130H16.18	29021024	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	9.040000	0.93783	0.747000	0.32809	0.459000	0.35465	GTG		0.637	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937		18	26	0	0	0	1	0	18	26				
MBLAC1	255374	broad.mit.edu	37	7	99725140	99725140	+	Missense_Mutation	SNP	A	A	C			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr7:99725140A>C	ENST00000398075.2	+	2	521	c.122A>C	c.(121-123)gAc>gCc	p.D41A	RP11-506M12.1_ENST00000494221.1_RNA	NM_203397.1	NP_981942.1	A4D2B0	MBLC1_HUMAN	metallo-beta-lactamase domain containing 1	41							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|skin(1)	7						GTGCGCGCCGACGGCTCCGTG	0.746																																						ENST00000398075.2																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|skin(1)	7						c.(121-123)gAc>gCc		metallo-beta-lactamase domain containing 1							9.0	11.0	11.0					7																	99725140		1951	4125	6076	SO:0001583	missense	255374						hydrolase activity|metal ion binding	g.chr7:99725140A>C	BC031288	CCDS43620.1	7q22	2014-02-12	2009-04-08		ENSG00000214309	ENSG00000214309			22180	protein-coding gene	gene with protein product							Standard	XM_005250250		Approved	MGC49416	uc003utp.3	A4D2B0	OTTHUMG00000154846	ENST00000398075.2:c.122A>C	7.37:g.99725140A>C	ENSP00000381150:p.Asp41Ala						p.D41A	NM_203397.1	NP_981942.1	A4D2B0	MBLC1_HUMAN			2	521	+			41					Q8N5X8	Missense_Mutation	SNP	ENST00000398075.2	37	c.122A>C	CCDS43620.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.088055	0.55968	.	.	ENSG00000214309	ENST00000398075;ENST00000421390	T;T	0.57907	1.06;0.37	4.23	4.23	0.50019	.	0.000000	0.64402	U	0.000020	T	0.42359	0.1199	L	0.29908	0.895	0.34261	D	0.679939	D	0.54047	0.964	P	0.44811	0.461	T	0.60393	-0.7272	10	0.72032	D	0.01	.	9.8943	0.41309	1.0:0.0:0.0:0.0	.	41	A4D2B0	MBLC1_HUMAN	A	41	ENSP00000381150:D41A;ENSP00000406055:D41A	ENSP00000381150:D41A	D	+	2	0	MBLAC1	99563076	0.999000	0.42202	0.849000	0.33467	0.070000	0.16714	3.647000	0.54403	1.913000	0.55393	0.459000	0.35465	GAC		0.746	MBLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337353.1	NM_203397		4	5	0	0	0	1	0	4	5				
PTPRN	5798	broad.mit.edu	37	2	220166408	220166408	+	Missense_Mutation	SNP	G	G	A	rs139651840	byFrequency	TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr2:220166408G>A	ENST00000295718.2	-	7	1268	c.1028C>T	c.(1027-1029)gCg>gTg	p.A343V	PTPRN_ENST00000409251.3_Missense_Mutation_p.A343V|AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000423636.2_Missense_Mutation_p.A253V	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	343					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CCCATAGCCCGCCAGCACAGC	0.612													G|||	6	0.00119808	0.0045	0.0	5008	,	,		17983	0.0		0.0	False		,,,				2504	0.0					ENST00000295718.2																			0				breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						c.(1027-1029)gCg>gTg		protein tyrosine phosphatase, receptor type, N		G	VAL/ALA,VAL/ALA,VAL/ALA	15,4391	22.3+/-47.3	0,15,2188	24.0	27.0	26.0		1028,758,1028	4.4	0.4	2	dbSNP_134	26	0,8600		0,0,4300	yes	missense,missense,missense	PTPRN	NM_001199763.1,NM_001199764.1,NM_002846.3	64,64,64	0,15,6488	AA,AG,GG		0.0,0.3404,0.1153	probably-damaging,probably-damaging,probably-damaging	343/951,253/890,343/980	220166408	15,12991	2203	4300	6503	SO:0001583	missense	5798				response to reactive oxygen species	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity	g.chr2:220166408G>A		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.1028C>T	2.37:g.220166408G>A	ENSP00000295718:p.Ala343Val					PTPRN_ENST00000409251.3_Missense_Mutation_p.A343V|PTPRN_ENST00000423636.2_Missense_Mutation_p.A253V|AC114803.3_ENST00000417355.1_RNA	p.A343V	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)	7	1268	-		Renal(207;0.0474)	343					B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	c.1028C>T	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.855986	0.51376	0.003404	0.0	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.26223	1.75;1.75;1.75	5.32	4.45	0.53987	.	0.336628	0.25055	N	0.033492	T	0.28034	0.0691	L	0.27053	0.805	0.27332	N	0.956743	P;D	0.76494	0.84;0.999	B;P	0.53450	0.06;0.726	T	0.05784	-1.0864	10	0.48119	T	0.1	.	11.8144	0.52202	0.0821:0.0:0.9179:0.0	.	343;343	Q6NSL1;Q16849	.;PTPRN_HUMAN	V	343;343;343;253	ENSP00000386638:A343V;ENSP00000295718:A343V;ENSP00000444244:A253V	ENSP00000295718:A343V	A	-	2	0	PTPRN	219874652	1.000000	0.71417	0.416000	0.26546	0.072000	0.16883	3.827000	0.55745	1.240000	0.43803	0.561000	0.74099	GCG		0.612	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			17	36	0	0	0	1	0	17	36				
SLFN12	55106	broad.mit.edu	37	17	33738370	33738370	+	Missense_Mutation	SNP	C	C	T			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr17:33738370C>T	ENST00000394562.1	-	6	2247	c.1724G>A	c.(1723-1725)cGa>cAa	p.R575Q	SLFN12_ENST00000452764.3_Missense_Mutation_p.R575Q|SLFN12_ENST00000304905.5_Missense_Mutation_p.R575Q|RP11-686D22.8_ENST00000587012.1_RNA|SLFN12_ENST00000460530.1_5'UTR			Q8IYM2	SLN12_HUMAN	schlafen family member 12	575							ATP binding (GO:0005524)			breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GGTGAGCCTTCGACAAGATTT	0.318																																						ENST00000394562.1																			0				breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						c.(1723-1725)cGa>cAa		schlafen family member 12							55.0	61.0	59.0					17																	33738370		2201	4300	6501	SO:0001583	missense	55106						ATP binding	g.chr17:33738370C>T	AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.1724G>A	17.37:g.33738370C>T	ENSP00000378063:p.Arg575Gln					SLFN12_ENST00000452764.3_Missense_Mutation_p.R575Q|SLFN12_ENST00000304905.5_Missense_Mutation_p.R575Q|SLFN12_ENST00000460530.1_5'UTR	p.R575Q			Q8IYM2	SLN12_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)	6	2247	-		Ovarian(249;0.17)	575					A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	c.1724G>A	CCDS11295.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.695395	0.30052	.	.	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764	T;T;T	0.03920	3.76;3.76;3.76	3.05	-0.674	0.11369	.	.	.	.	.	T	0.02304	0.0071	N	0.08118	0	0.09310	N	1	B	0.30634	0.288	B	0.24269	0.052	T	0.44159	-0.9346	9	0.87932	D	0	.	4.9962	0.14240	0.1358:0.4333:0.4309:0.0	.	575	Q8IYM2	SLN12_HUMAN	Q	575	ENSP00000378063:R575Q;ENSP00000302077:R575Q;ENSP00000394903:R575Q	ENSP00000302077:R575Q	R	-	2	0	SLFN12	30762483	0.001000	0.12720	0.000000	0.03702	0.022000	0.10575	0.005000	0.13129	0.126000	0.18424	-0.437000	0.05841	CGA		0.318	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042		4	87	0	0	0	1	0	4	87				
SLCO2A1	6578	broad.mit.edu	37	3	133664084	133664084	+	Missense_Mutation	SNP	G	G	T	rs147644142	byFrequency	TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr3:133664084G>T	ENST00000310926.4	-	10	1589	c.1316C>A	c.(1315-1317)cCg>cAg	p.P439Q	SLCO2A1_ENST00000493729.1_Missense_Mutation_p.P363Q	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	439	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	AGGAGACTGCGGATGTATAGA	0.532																																						ENST00000310926.4																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30						c.(1315-1317)cCg>cAg		solute carrier organic anion transporter family, member 2A1							117.0	127.0	124.0					3																	133664084		2203	4300	6503	SO:0001583	missense	6578				sodium-independent organic anion transport	integral to plasma membrane|membrane fraction	prostaglandin transmembrane transporter activity|protein binding	g.chr3:133664084G>T		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"""Solute carriers"""	10955	protein-coding gene	gene with protein product		601460	"""solute carrier family 21 (prostaglandin transporter), member 2"", ""matrin F/G 1"""	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.1316C>A	3.37:g.133664084G>T	ENSP00000311291:p.Pro439Gln					SLCO2A1_ENST00000493729.1_Missense_Mutation_p.P363Q	p.P439Q	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN			10	1589	-			439			Kazal-like.		Q86V98|Q8IUN2	Missense_Mutation	SNP	ENST00000310926.4	37	c.1316C>A	CCDS3084.1	.	.	.	.	.	.	.	.	.	.	G	7.619	0.676464	0.14841	.	.	ENSG00000174640	ENST00000310926;ENST00000493729	T;T	0.37411	1.2;1.2	5.63	1.71	0.24356	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.811849	0.11321	N	0.576002	T	0.27349	0.0671	N	0.11818	0.18	0.09310	N	0.999997	B;B;P	0.52170	0.083;0.058;0.951	B;B;P	0.57548	0.046;0.042;0.823	T	0.13335	-1.0513	10	0.17369	T	0.5	.	2.6018	0.04868	0.1653:0.1292:0.5013:0.2042	.	258;363;439	B7Z8J8;E7EU40;Q92959	.;.;SO2A1_HUMAN	Q	439;363	ENSP00000311291:P439Q;ENSP00000418893:P363Q	ENSP00000311291:P439Q	P	-	2	0	SLCO2A1	135146774	0.205000	0.23458	0.039000	0.18376	0.918000	0.54935	0.298000	0.19120	0.751000	0.32900	0.491000	0.48974	CCG		0.532	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630		16	124	1	0	6.94344e-10	1	7.5561e-10	16	124				
GPR125	166647	broad.mit.edu	37	4	22390725	22390725	+	Silent	SNP	C	C	T			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr4:22390725C>T	ENST00000334304.5	-	18	2978	c.2709G>A	c.(2707-2709)cgG>cgA	p.R903R	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	903					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)	p.R903R(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				GTGCGTTTGGCCGACTGCCGT	0.418																																						ENST00000334304.5																			1	Substitution - coding silent(1)	p.R903R(1)	lung(1)	breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56						c.(2707-2709)cgG>cgA		G protein-coupled receptor 125							206.0	217.0	213.0					4																	22390725		2203	4300	6503	SO:0001819	synonymous_variant	166647				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity	g.chr4:22390725C>T	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"""	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.2709G>A	4.37:g.22390725C>T						GPR125_ENST00000282943.5_5'UTR	p.R903R	NM_145290.2	NP_660333.2	Q8IWK6	GP125_HUMAN			18	2978	-		Breast(46;0.198)	903					Q6UXK9|Q86SQ5|Q8TC55	Silent	SNP	ENST00000334304.5	37	c.2709G>A	CCDS33964.1																																																																																				0.418	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			5	185	0	0	0	1	0	5	185				
AKAP9	10142	broad.mit.edu	37	7	91699396	91699396	+	Missense_Mutation	SNP	T	T	G			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr7:91699396T>G	ENST00000359028.2	+	28	6644	c.6419T>G	c.(6418-6420)cTt>cGt	p.L2140R	AKAP9_ENST00000356239.3_Missense_Mutation_p.L2128R|AKAP9_ENST00000358100.2_Missense_Mutation_p.L2140R			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2140	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TGCAGTGAGCTTTTGCTCTCT	0.348			T	BRAF	papillary thyroid																																	ENST00000359028.2				Dom	yes		7	7q21-q22	10142	T	A kinase (PRKA) anchor protein (yotiao) 9			E	BRAF		papillary thyroid		0				NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155						c.(6418-6420)cTt>cGt		A kinase (PRKA) anchor protein 9							103.0	116.0	112.0					7																	91699396		2203	4300	6503	SO:0001583	missense	10142				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding	g.chr7:91699396T>G	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.6419T>G	7.37:g.91699396T>G	ENSP00000351922:p.Leu2140Arg					AKAP9_ENST00000356239.3_Missense_Mutation_p.L2128R|AKAP9_ENST00000358100.2_Missense_Mutation_p.L2140R	p.L2140R			Q99996	AKAP9_HUMAN	STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		28	6644	+	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		2140			Glu-rich.		A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37	c.6419T>G		.	.	.	.	.	.	.	.	.	.	T	15.72	2.916279	0.52546	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120	T;T;T	0.05025	3.53;3.52;3.51	5.3	4.06	0.47325	.	0.000000	0.35291	N	0.003309	T	0.24812	0.0602	M	0.81802	2.56	0.49915	D	0.999838	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.91635	0.982;0.999;0.995	T	0.01287	-1.1395	10	0.87932	D	0	.	12.1534	0.54062	0.0:0.0:0.1428:0.8572	.	2140;2128;2128	Q99996;Q99996-2;Q99996-3	AKAP9_HUMAN;.;.	R	2128;2140;2140;2140	ENSP00000348573:L2128R;ENSP00000351922:L2140R;ENSP00000350813:L2140R	ENSP00000348573:L2128R	L	+	2	0	AKAP9	91537332	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	5.372000	0.66156	2.141000	0.66446	0.455000	0.32223	CTT		0.348	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		42	45	0	0	0	1	0	42	45				
ATP10B	23120	broad.mit.edu	37	5	160063209	160063209	+	Missense_Mutation	SNP	T	T	A			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr5:160063209T>A	ENST00000327245.5	-	11	1954	c.1108A>T	c.(1108-1110)Aca>Tca	p.T370S	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	370					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATGATCATTGTGAGGAACATG	0.483																																						ENST00000327245.5																			0				NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75						c.(1108-1110)Aca>Tca		ATPase, class V, type 10B							69.0	68.0	68.0					5																	160063209		1896	4116	6012	SO:0001583	missense	23120				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity	g.chr5:160063209T>A	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.1108A>T	5.37:g.160063209T>A	ENSP00000313600:p.Thr370Ser					CTC-348L5.1_ENST00000523598.1_RNA	p.T370S	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		11	1954	-	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	370					Q9H725	Missense_Mutation	SNP	ENST00000327245.5	37	c.1108A>T	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.489288	0.84962	.	.	ENSG00000118322	ENST00000327245	T	0.44482	0.92	5.18	4.01	0.46588	ATPase, P-type, ATPase-associated domain (1);	0.054440	0.64402	N	0.000001	T	0.53094	0.1775	L	0.44542	1.39	0.58432	D	0.999997	D;P;D;D	0.89917	1.0;0.542;1.0;1.0	D;P;D;D	0.97110	1.0;0.58;1.0;0.998	T	0.47222	-0.9134	9	.	.	.	.	10.9856	0.47520	0.1397:0.0:0.0:0.8603	.	414;370;342;370	B4DHG1;O94823-2;O94823-3;O94823	.;.;.;AT10B_HUMAN	S	370	ENSP00000313600:T370S	.	T	-	1	0	ATP10B	159995787	1.000000	0.71417	0.949000	0.38748	0.985000	0.73830	7.946000	0.87746	0.902000	0.36520	-0.531000	0.04308	ACA		0.483	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		20	29	0	0	0	1	0	20	29				
VPS11	55823	broad.mit.edu	37	11	118947656	118947656	+	Missense_Mutation	SNP	G	G	T			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr11:118947656G>T	ENST00000300793.6	+	9	1327	c.1285G>T	c.(1285-1287)Gcc>Tcc	p.A429S	VPS11_ENST00000527798.1_3'UTR	NM_021729.4	NP_068375.3	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11 homolog (S. cerevisiae)	430					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	29	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)		GTTTCTGGATGCCCAGCGCAT	0.537																																						ENST00000300793.6																			0				autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	29						c.(1285-1287)Gcc>Tcc		vacuolar protein sorting 11 homolog (S. cerevisiae)							88.0	94.0	92.0					11																	118947656		2142	4237	6379	SO:0001583	missense	55823				protein transport	endocytic vesicle|HOPS complex|late endosome membrane|lysosomal membrane	nucleotide binding|protein binding|zinc ion binding	g.chr11:118947656G>T	AB027508	CCDS73404.1	11q23	2008-02-05	2006-12-19			ENSG00000160695		"""RING-type (C3HC4) zinc fingers"""	14583	protein-coding gene	gene with protein product		608549	"""vacuolar protein sorting 11 (yeast homolog)"""				Standard	NM_021729		Approved	RNF108, PEP5	uc010ryx.2	Q9H270		ENST00000300793.6:c.1285G>T	11.37:g.118947656G>T	ENSP00000475301:p.Ala429Ser					VPS11_ENST00000527798.1_3'UTR	p.A429S	NM_021729.4	NP_068375.3	Q9H270	VPS11_HUMAN		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)	9	1327	+	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)	430					Q8WY89|Q96EP8|Q9H6D9|Q9HCS6	Missense_Mutation	SNP	ENST00000300793.6	37	c.1285G>T																																																																																					0.537	VPS11-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021729		4	24	1	0	0.00909568	1	0.00934834	4	24				
DENND3	22898	broad.mit.edu	37	8	142202641	142202641	+	Missense_Mutation	SNP	C	C	T	rs143494640		TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr8:142202641C>T	ENST00000262585.2	+	22	3553	c.3275C>T	c.(3274-3276)gCg>gTg	p.A1092V	DENND3_ENST00000424248.1_Missense_Mutation_p.A1040V|DENND3_ENST00000523308.1_Missense_Mutation_p.A142V|DENND3_ENST00000519811.1_Missense_Mutation_p.A1172V	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	1092					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			CAGCTGTGGGCGGCCTGTGCA	0.667																																						ENST00000519811.1																			0				breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55						c.(3514-3516)gCg>gTg		DENN/MADD domain containing 3		C	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	47.0	52.0	50.0		3275	2.7	0.4	8	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	no	missense	DENND3	NM_014957.2	64	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	benign	1092/1199	142202641	3,13003	2203	4300	6503	SO:0001583	missense	22898							g.chr8:142202641C>T	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"""DENN/MADD domain containing"", ""WD repeat domain containing"""	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.3275C>T	8.37:g.142202641C>T	ENSP00000262585:p.Ala1092Val					DENND3_ENST00000523308.1_Missense_Mutation_p.A142V|DENND3_ENST00000262585.2_Missense_Mutation_p.A1092V|DENND3_ENST00000424248.1_Missense_Mutation_p.A1040V	p.A1172V			A2RUS2	DEND3_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.105)		22	3585	+	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		1092					B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	37	c.3515C>T	CCDS34947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.30|13.30	2.195140|2.195140	0.38806|0.38806	4.54E-4|4.54E-4	1.16E-4|1.16E-4	ENSG00000105339|ENSG00000105339	ENST00000262585;ENST00000424248;ENST00000519811;ENST00000523308|ENST00000520725	T;T;T;T|.	0.38401|.	1.75;1.75;1.75;1.14|.	5.49|5.49	2.71|2.71	0.32032|0.32032	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);|.	0.508551|.	0.23756|.	N|.	0.044877|.	T|T	0.28896|0.28896	0.0717|0.0717	N|N	0.17872|0.17872	0.535|0.535	0.28323|0.28323	N|N	0.922149|0.922149	B;P;B|.	0.44734|.	0.163;0.842;0.095|.	B;B;B|.	0.35931|.	0.015;0.214;0.015|.	T|T	0.22382|0.22382	-1.0218|-1.0218	10|5	0.20046|.	T|.	0.44|.	-27.7715|-27.7715	9.1161|9.1161	0.36758|0.36758	0.0:0.7166:0.0:0.2834|0.0:0.7166:0.0:0.2834	.|.	1172;142;1092|.	E9PF32;A2RUS2-3;A2RUS2|.	.;.;DEND3_HUMAN|.	V|W	1092;1040;1172;142|46	ENSP00000262585:A1092V;ENSP00000410594:A1040V;ENSP00000428714:A1172V;ENSP00000430912:A142V|.	ENSP00000262585:A1092V|.	A|R	+|+	2|1	0|2	DENND3|DENND3	142271823|142271823	0.095000|0.095000	0.21747|0.21747	0.408000|0.408000	0.26446|0.26446	0.890000|0.890000	0.51754|0.51754	0.632000|0.632000	0.24583|0.24583	0.270000|0.270000	0.21984|0.21984	0.561000|0.561000	0.74099|0.74099	GCG|CGG		0.667	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		18	25	0	0	0	1	0	18	25				
LRRC24	441381	broad.mit.edu	37	8	145749890	145749890	+	Missense_Mutation	SNP	G	G	A			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr8:145749890G>A	ENST00000529415.2	-	3	490	c.373C>T	c.(373-375)Cgc>Tgc	p.R125C	LRRC24_ENST00000533758.1_Missense_Mutation_p.R125C|LRRC14_ENST00000292524.1_3'UTR			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	125						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TAGAGCACGCGCAGCTGGGCC	0.711																																						ENST00000529415.2																			0				breast(2)|endometrium(1)|kidney(1)|lung(1)	5						c.(373-375)Cgc>Tgc		leucine rich repeat containing 24							8.0	11.0	10.0					8																	145749890		1813	3927	5740	SO:0001583	missense	441381					integral to membrane		g.chr8:145749890G>A	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"""Immunoglobulin superfamily / I-set domain containing"""	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.373C>T	8.37:g.145749890G>A	ENSP00000434849:p.Arg125Cys					LRRC24_ENST00000533758.1_Missense_Mutation_p.R125C|LRRC14_ENST00000292524.1_3'UTR	p.R125C			Q50LG9	LRC24_HUMAN	OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)		3	490	-	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		125						Missense_Mutation	SNP	ENST00000529415.2	37	c.373C>T	CCDS34969.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.771448	0.90108	.	.	ENSG00000254402	ENST00000529415;ENST00000533758	T;T	0.61274	0.12;0.12	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.78929	0.4361	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.993;1.0	T	0.82995	-0.0180	10	0.87932	D	0	.	15.4632	0.75377	0.0:0.0:1.0:0.0	.	125;125	G3V1D8;Q50LG9	.;LRC24_HUMAN	C	125	ENSP00000434849:R125C;ENSP00000435653:R125C	ENSP00000434849:R125C	R	-	1	0	LRRC24	145720698	0.998000	0.40836	0.991000	0.47740	0.994000	0.84299	3.134000	0.50538	2.500000	0.84329	0.655000	0.94253	CGC		0.711	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678		5	5	0	0	0	1	0	5	5				
ZNF746	155061	broad.mit.edu	37	7	149191569	149191569	+	Missense_Mutation	SNP	G	G	A			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr7:149191569G>A	ENST00000340622.3	-	2	330	c.50C>T	c.(49-51)aCg>aTg	p.T17M	ZNF746_ENST00000458143.2_Missense_Mutation_p.T17M|ZNF746_ENST00000461958.2_Missense_Mutation_p.T17M			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	17					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			GGCCTGAATCGTGGCTGCCAT	0.532																																						ENST00000461958.2																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						c.(49-51)aCg>aTg		zinc finger protein 746							60.0	63.0	62.0					7																	149191569		2203	4299	6502	SO:0001583	missense	155061				negative regulation of transcription, DNA-dependent|neuron death|regulation of cell death|transcription, DNA-dependent	cytoplasm|nucleus	transcription regulatory region DNA binding|ubiquitin protein ligase binding|zinc ion binding	g.chr7:149191569G>A	AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"""Zinc fingers, C2H2-type"", ""-"""	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.50C>T	7.37:g.149191569G>A	ENSP00000345140:p.Thr17Met					ZNF746_ENST00000340622.3_Missense_Mutation_p.T17M|ZNF746_ENST00000458143.2_Missense_Mutation_p.T17M	p.T17M			Q6NUN9	ZN746_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00358)		2	246	-	Melanoma(164;0.165)		17					A8K6Z9|Q6ZRF9	Missense_Mutation	SNP	ENST00000340622.3	37	c.50C>T	CCDS5897.1	.	.	.	.	.	.	.	.	.	.	.	19.16	3.773491	0.69992	.	.	ENSG00000181220	ENST00000340622;ENST00000458143;ENST00000461958	T;T	0.10005	2.95;2.92	4.64	4.64	0.57946	.	0.149607	0.30969	N	0.008505	T	0.18676	0.0448	N	0.22421	0.69	0.21762	N	0.999558	D;D	0.89917	0.999;1.0	D;D	0.68353	0.949;0.957	T	0.03025	-1.1081	10	0.87932	D	0	-16.1073	13.0146	0.58749	0.0:0.0:1.0:0.0	.	17;17	Q6NUN9-2;Q6NUN9	.;ZN746_HUMAN	M	17;17;4	ENSP00000345140:T17M;ENSP00000395007:T17M	ENSP00000345140:T17M	T	-	2	0	ZNF746	148822502	0.184000	0.23200	0.703000	0.30354	0.970000	0.65996	2.397000	0.44477	2.119000	0.64992	0.514000	0.50259	ACG		0.532	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557		14	74	0	0	0	1	0	14	74				
CD200R1	131450	broad.mit.edu	37	3	112644012	112644012	+	Missense_Mutation	SNP	T	T	A			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr3:112644012T>A	ENST00000471858.1	-	5	961	c.729A>T	c.(727-729)ttA>ttT	p.L243F	CD200R1_ENST00000308611.3_Missense_Mutation_p.L266F|CD200R1_ENST00000295863.4_Intron	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	243					regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						ATGGAATATATAATTTTGCTG	0.299																																						ENST00000471858.1																			0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						c.(727-729)ttA>ttT		CD200 receptor 1							51.0	56.0	55.0					3																	112644012		2203	4298	6501	SO:0001583	missense	131450				interspecies interaction between organisms|regulation of immune response	extracellular region|integral to membrane|plasma membrane	receptor activity	g.chr3:112644012T>A	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.729A>T	3.37:g.112644012T>A	ENSP00000418928:p.Leu243Phe					CD200R1_ENST00000295863.4_Intron|CD200R1_ENST00000308611.3_Missense_Mutation_p.L266F	p.L243F	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN			5	961	-			243					B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	37	c.729A>T	CCDS2970.1	.	.	.	.	.	.	.	.	.	.	T	12.73	2.025755	0.35701	.	.	ENSG00000163606	ENST00000471858;ENST00000308611	T;T	0.18502	2.23;2.21	4.26	-3.07	0.05363	.	1.263890	0.05901	N	0.630039	T	0.19725	0.0474	M	0.73962	2.25	0.09310	N	1	P;P	0.45011	0.764;0.848	B;P	0.44359	0.261;0.447	T	0.21827	-1.0234	10	0.48119	T	0.1	.	0.9234	0.01320	0.1554:0.2804:0.1604:0.4038	.	243;266	Q8TD46;Q8TD46-4	MO2R1_HUMAN;.	F	243;266	ENSP00000418928:L243F;ENSP00000311035:L266F	ENSP00000311035:L266F	L	-	3	2	CD200R1	114126702	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.282000	0.02799	-0.647000	0.05444	-0.264000	0.10439	TTA		0.299	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806		15	30	0	0	0	1	0	15	30				
TRPC4AP	26133	broad.mit.edu	37	20	33665958	33665958	+	Missense_Mutation	SNP	G	G	A	rs200326780		TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr20:33665958G>A	ENST00000252015.2	-	2	277	c.188C>T	c.(187-189)aCg>aTg	p.T63M	TRPC4AP_ENST00000432634.2_Missense_Mutation_p.T63M|TRPC4AP_ENST00000451813.2_Missense_Mutation_p.T63M			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	63	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			GTCCCTCTCCGTCAAAAAAGT	0.443																																						ENST00000252015.2																			0				breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32						c.(187-189)aCg>aTg		transient receptor potential cation channel, subfamily C, member 4 associated protein		G	MET/THR,MET/THR	0,4406		0,0,2203	105.0	96.0	99.0		188,188	-0.4	0.1	20		99	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	TRPC4AP	NM_015638.2,NM_199368.1	81,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	63/798,63/790	33665958	1,13005	2203	4300	6503	SO:0001583	missense	26133				protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding	g.chr20:33665958G>A	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 158"""	608430	"""chromosome 20 open reading frame 188"""	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.188C>T	20.37:g.33665958G>A	ENSP00000252015:p.Thr63Met					TRPC4AP_ENST00000451813.1_Missense_Mutation_p.T63M|TRPC4AP_ENST00000432634.2_Missense_Mutation_p.T63M	p.T63M			Q8TEL6	TP4AP_HUMAN	BRCA - Breast invasive adenocarcinoma(18;0.00936)		2	277	-			63			Interaction with TNFRSF1A (By similarity).		E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	37	c.188C>T	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	G	9.154	1.017072	0.19355	0.0	1.16E-4	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000432634;ENST00000541994	.	.	.	5.03	-0.364	0.12553	.	0.622984	0.17610	N	0.168111	T	0.07143	0.0181	N	0.08118	0	0.24980	N	0.991602	B;B;P	0.42757	0.0;0.004;0.789	B;B;B	0.22152	0.0;0.001;0.038	T	0.31251	-0.9950	9	0.45353	T	0.12	.	4.5179	0.11945	0.2048:0.0:0.291:0.5042	.	63;63;63	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	M	63;63;63;48	.	ENSP00000252015:T63M	T	-	2	0	TRPC4AP	33129619	0.213000	0.23551	0.050000	0.19076	0.650000	0.38633	0.949000	0.29109	0.169000	0.19679	-0.222000	0.12452	ACG		0.443	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		24	21	0	0	0	1	0	24	21				
TMEM173	340061	broad.mit.edu	37	5	138857857	138857857	+	Missense_Mutation	SNP	G	G	A	rs199795457		TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr5:138857857G>A	ENST00000330794.4	-	6	1090	c.757C>T	c.(757-759)Cgg>Tgg	p.R253W	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	253	c-di-GMP-binding domain (CBD).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACACTTACCCGCTGCCCGTTC	0.577													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18364	0.0		0.0	False		,,,				2504	0.0					ENST00000330794.4																			0				endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9						c.(757-759)Cgg>Tgg		transmembrane protein 173		G	TRP/ARG	0,4406		0,0,2203	95.0	100.0	98.0		757	3.7	0.3	5		98	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TMEM173	NM_198282.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	253/380	138857857	1,13005	2203	4300	6503	SO:0001583	missense	340061				activation of innate immune response|apoptosis|cellular response to exogenous dsRNA|defense response to virus|innate immune response|interferon-beta production|positive regulation of defense response to virus by host|positive regulation of protein binding|positive regulation of protein import into nucleus, translocation|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane|perinuclear region of cytoplasm|plasma membrane	protein homodimerization activity|protein kinase binding|transcription factor binding	g.chr5:138857857G>A		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.757C>T	5.37:g.138857857G>A	ENSP00000331288:p.Arg253Trp						p.R253W	NM_198282.2	NP_938023.1	Q86WV6	TM173_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		6	1090	-			253					A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	37	c.757C>T	CCDS4215.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	20.3	3.974904	0.74360	0.0	1.16E-4	ENSG00000184584	ENST00000330794;ENST00000510817	T;T	0.34472	1.87;1.36	5.67	3.71	0.42584	.	1.133100	0.06456	N	0.728679	T	0.41373	0.1156	L	0.46157	1.445	0.09310	N	1	D	0.71674	0.998	P	0.46975	0.533	T	0.39035	-0.9633	10	0.66056	D	0.02	-4.8775	12.4879	0.55883	0.0:0.0:0.7477:0.2523	.	253	Q86WV6	TM173_HUMAN	W	253	ENSP00000331288:R253W;ENSP00000427455:R253W	ENSP00000331288:R253W	R	-	1	2	TMEM173	138838041	0.006000	0.16342	0.345000	0.25642	0.270000	0.26580	1.496000	0.35638	2.676000	0.91093	0.561000	0.74099	CGG		0.577	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282		39	50	0	0	0	1	0	39	50				
AGAP11	119385	broad.mit.edu	37	10	88759210	88759210	+	RNA	SNP	C	C	T	rs373805034		TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr10:88759210C>T	ENST00000444431.1	+	0	340				RP11-96C23.14_ENST00000444180.3_RNA|RP11-96C23.5_ENST00000433214.2_RNA			Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase activating protein 11						regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)										GTTTAGGTTGCCAAGCTGTTC	0.333																																						ENST00000444431.1																			0													ankyrin repeat and GTPase domain Arf GTPase activating protein 11																																						119385				regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding	g.chr10:88759210C>T			10q23.2	2013-01-11			ENSG00000151303	ENSG00000151303		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	29421	protein-coding gene	gene with protein product						11853319	Standard	NM_133447		Approved	KIAA1975	uc001kee.2	Q8TF27	OTTHUMG00000018667		10.37:g.88759210C>T						RP11-96C23.14_ENST00000444180.3_RNA|RP11-96C23.5_ENST00000433214.2_RNA				Q8TF27	AGA11_HUMAN			0	340	+								B9EIP7|D3DWE4	RNA	SNP	ENST00000444431.1	37																																																																																						0.333	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447		5	24	0	0	0	1	0	5	24				
DUOX1	53905	broad.mit.edu	37	15	45453998	45453998	+	Silent	SNP	C	C	A	rs368964201		TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr15:45453998C>A	ENST00000321429.4	+	31	4326	c.3919C>A	c.(3919-3921)Cgg>Agg	p.R1307R	CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000389037.3_Silent_p.R1307R|DUOX1_ENST00000561166.1_Silent_p.R953R	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1307	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GCAGTGGGTGCGGATCGCTTG	0.647																																						ENST00000321429.4																			0				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57						c.(3919-3921)Cgg>Agg		dual oxidase 1							89.0	78.0	81.0					15																	45453998		2198	4298	6496	SO:0001819	synonymous_variant	53905				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity	g.chr15:45453998C>A	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.3919C>A	15.37:g.45453998C>A						CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000389037.3_Silent_p.R1307R|DUOX1_ENST00000561166.1_Silent_p.R953R	p.R1307R	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)	31	4326	+		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)	1307			FAD-binding FR-type.		A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	c.3919C>A	CCDS32221.1																																																																																				0.647	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		19	37	1	0	6.44725e-10	1	7.45464e-10	19	37				
SETD2	29072	broad.mit.edu	37	3	47125274	47125274	+	Missense_Mutation	SNP	G	G	C			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr3:47125274G>C	ENST00000409792.3	-	12	6038	c.5996C>G	c.(5995-5997)cCa>cGa	p.P1999R	SETD2_ENST00000492397.1_5'UTR	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1999					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGTTTTATCTGGCTGTTCTTG	0.413			"""N, F, S, Mis"""		clear cell renal carcinoma																																	ENST00000409792.3				Rec	yes		3	3p21.31	29072	"""N, F, S, Mis"""	SET domain containing 2			E			clear cell renal carcinoma		0				breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141						c.(5995-5997)cCa>cGa		SET domain containing 2							235.0	212.0	220.0					3																	47125274		2203	4300	6503	SO:0001583	missense	29072				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding	g.chr3:47125274G>C	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5996C>G	3.37:g.47125274G>C	ENSP00000386759:p.Pro1999Arg					SETD2_ENST00000492397.1_5'UTR	p.P1999R	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)	12	6038	-		Acute lymphoblastic leukemia(5;0.0169)	1999					O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	c.5996C>G	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	G	14.40	2.524853	0.44969	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	T	0.21734	1.99	5.59	5.59	0.84812	.	0.233852	0.30356	N	0.009820	T	0.28962	0.0719	L	0.29908	0.895	0.29012	N	0.886781	D;P	0.53312	0.959;0.915	P;B	0.52598	0.703;0.374	T	0.02789	-1.1110	10	0.45353	T	0.12	.	19.5917	0.95518	0.0:0.0:1.0:0.0	.	1999;1999	F2Z317;Q9BYW2	.;SETD2_HUMAN	R	1999	ENSP00000386759:P1999R	ENSP00000386759:P1999R	P	-	2	0	SETD2	47100278	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.315000	0.59172	2.614000	0.88457	0.650000	0.86243	CCA		0.413	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		68	108	0	0	0	1	0	68	108				
CTBS	1486	broad.mit.edu	37	1	85039999	85040007	+	In_Frame_Del	DEL	GCAGCGCCA	GCAGCGCCA	-	rs142534762|rs3217269|rs199701060|rs201060055	byFrequency	TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr1:85039999_85040007delGCAGCGCCA	ENST00000370630.5	-	1	140_148	c.92_100delTGGCGCTGC	c.(91-102)ctggcgctgcgg>cgg	p.LAL31del	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	31					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		GCCGCGAGCCgcagcgccagcagcgccag	0.718														1537	0.306909	0.5038	0.2954	5008	,	,		11352	0.0556		0.2624	False		,,,				2504	0.3538					ENST00000370630.4																			0				breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9						c.(91-102)cgg>c		chitobiase, di-N-acetyl-				865,21,1798		349,2,165,3,13,810						-3.6	0.0		dbSNP_134	4	1279,4,4361		415,1,448,1,1,1956	no	codingComplex	CTBS	NM_004388.2		764,3,613,4,14,2766	A1A1,A1A2,A1R,A2A2,A2R,RR		22.7321,33.0104,26.0447				2144,25,6159				SO:0001651	inframe_deletion	1486					lysosome	cation binding	g.chr1:85039999_85040007delGCAGCGCCA	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.92_100delTGGCGCTGC	1.37:g.85040008_85040016delGCAGCGCCA	ENSP00000359664:p.Leu31_Leu33del					CTBS_ENST00000477677.1_5'UTR	p.LALR31del	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN		all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)	1	140_148	-			31					Q5VX50	In_Frame_Del	DEL	ENST00000370630.5	37	c.92_100delTGGCGCTGC	CCDS698.1																																																																																				0.718	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388		2	4						2	4	---	---	---	---
OTOP1	133060	broad.mit.edu	37	4	4228274	4228282	+	In_Frame_Del	DEL	CCACAGCAG	CCACAGCAG	-	rs75328065|rs199840382|rs111245977|rs377667898|rs200554408|rs201436152	byFrequency	TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr4:4228274_4228282delCCACAGCAG	ENST00000296358.4	-	1	334_342	c.310_318delCTGCTGTGG	c.(310-318)ctgctgtggdel	p.LLW104del		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	104					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.L104_W106delLLW(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ACCACAGCATCCACAGCAGCTGCAGCAGC	0.727																																						ENST00000296358.4																			1	Deletion - In frame(1)	p.L104_W106delLLW(1)	upper_aerodigestive_tract(1)	NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						c.(310-318)del		otopetrin 1																																				SO:0001651	inframe_deletion	133060				biomineral tissue development	extracellular space|integral to membrane		g.chr4:4228274_4228282delCCACAGCAG	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.310_318delCTGCTGTGG	4.37:g.4228274_4228282delCCACAGCAG	ENSP00000296358:p.Leu104_Trp106del						p.LLW104del	NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (64;0.168)	1	334_342	-			104					A1L476	In_Frame_Del	DEL	ENST00000296358.4	37	c.310_318delCTGCTGTGG	CCDS3372.1																																																																																				0.727	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		7	21						7	21	---	---	---	---
SKIDA1	387640	broad.mit.edu	37	10	21805466	21805467	+	In_Frame_Ins	INS	-	-	CCTCCT	rs112207161	byFrequency	TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr10:21805466_21805467insCCTCCT	ENST00000449193.2	-	4	3537_3538	c.1285_1286insAGGAGG	c.(1285-1287)ggg>gAGGAGGgg	p.428_429insEE	SKIDA1_ENST00000487107.1_5'Flank|SKIDA1_ENST00000444772.3_In_Frame_Ins_p.349_350insEE	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	347						nucleus (GO:0005634)		p.E428_G429insEE(2)									CCCGCTGCccccctcctcctcc	0.619														2708	0.540735	0.916	0.4063	5008	,	,		10303	0.3244		0.5408	False		,,,				2504	0.3517					ENST00000449193.2																			2	Insertion - In frame(2)	p.E428_G429insEE(2)	soft_tissue(2)								c.(1285-1287)ggg>AGGAGGggg		SKI/DACH domain containing 1				3173,56,18,597		1435,46,11,246,5,0,0,3,1,175						3.0	1.0		dbSNP_132	7	4189,51,27,3619		1322,36,14,1495,1,0,13,2,9,1051	no	codingComplex	C10orf140	NM_207371.3		2757,82,25,1741,6,0,13,5,10,1226	A1A1,A1A2,A1A3,A1R,A2A2,A2A3,A2R,A3A3,A3R,RR		46.8805,17.4558,37.2379				7362,107,45,4216				SO:0001652	inframe_insertion	387640							g.chr10:21805466_21805467insCCTCCT	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 140"""	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.1280_1285dupAGGAGG	10.37:g.21805467_21805472dupCCTCCT	ENSP00000410041:p.Glu427_Glu428dup					SKIDA1_ENST00000444772.3_In_Frame_Ins_p.349_350insRR	p.428_429insRR	NM_207371.3	NP_997254.3					4	3537_3538	-								B1ANA5|Q6ZMX4|Q8N3C3	In_Frame_Ins	INS	ENST00000449193.2	37	c.1285_1286insAGGAGG	CCDS44363.1																																																																																				0.619	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371		5	6						5	6	---	---	---	---
TECPR2	9895	broad.mit.edu	37	14	102918941	102918941	+	Frame_Shift_Del	DEL	C	C	-			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr14:102918941delC	ENST00000359520.7	+	16	3843	c.3617delC	c.(3616-3618)accfs	p.T1206fs	TECPR2_ENST00000558678.1_Frame_Shift_Del_p.T1206fs	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	1206					autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						ATGCACTGGACCAGGCTGGAC	0.637																																						ENST00000359520.7																			0				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						c.(3616-3618)acfs		tectonin beta-propeller repeat containing 2							16.0	13.0	14.0					14																	102918941		2195	4285	6480	SO:0001589	frameshift_variant	9895						protein binding	g.chr14:102918941delC	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"""KIAA0329"""	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.3617delC	14.37:g.102918941delC	ENSP00000352510:p.Thr1206fs					TECPR2_ENST00000558678.1_Frame_Shift_Del_p.T1206fs	p.T1206fs	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN			16	3843	+			1206					A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Frame_Shift_Del	DEL	ENST00000359520.7	37	c.3617delC	CCDS32162.1																																																																																				0.637	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		2	4						2	4	---	---	---	---
NPIPB5	100132247	broad.mit.edu	37	16	22545540	22545558	+	Frame_Shift_Del	DEL	CGAGCGTCTGCGGGGGCCG	CGAGCGTCTGCGGGGGCCG	-	rs369022450		TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr16:22545540_22545558delCGAGCGTCTGCGGGGGCCG	ENST00000517539.1	+	8	1311_1329	c.1236_1254delCGAGCGTCTGCGGGGGCCG	c.(1234-1254)gccgagcgtctgcgggggccgfs	p.AERLRGP412fs	NPIPB5_ENST00000415654.1_3'UTR|NPIPB5_ENST00000424340.1_Frame_Shift_Del_p.AERLRGP412fs			A8MRT5	NPIB5_HUMAN	nuclear pore complex interacting protein family, member B5	412	Pro-rich.					integral component of membrane (GO:0016021)											AGACACCTGCCGAGCGTCTGCGGGGGCCGCTTCCACCCT	0.562																																						ENST00000424340.1																			0											c.(1234-1254)gcfs		nuclear pore complex interacting protein family, member B5																																				SO:0001589	frameshift_variant	100132247							g.chr16:22545540_22545558delCGAGCGTCTGCGGGGGCCG		CCDS45443.1	16p12.2	2013-06-11			ENSG00000243716	ENSG00000243716			37233	protein-coding gene	gene with protein product							Standard	NM_001135865		Approved			A8MRT5	OTTHUMG00000163573	ENST00000517539.1:c.1236_1254delCGAGCGTCTGCGGGGGCCG	16.37:g.22545540_22545558delCGAGCGTCTGCGGGGGCCG	ENSP00000430633:p.Ala412fs					NPIPB5_ENST00000415654.1_3'UTR|NPIPB5_ENST00000517539.1_Frame_Shift_Del_p.AERLRGP412fs	p.AERLRGP412fs	NM_001135865.1	NP_001129337.1					7	1515_1533	+								B4DK13	Frame_Shift_Del	DEL	ENST00000517539.1	37	c.1236_1254delCGAGCGTCTGCGGGGGCCG	CCDS45443.1																																																																																				0.562	NPIPB5-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374343.2	NM_001135865		3	6						3	6	---	---	---	---
CDC27	996	broad.mit.edu	37	17	45219612	45219612	+	Frame_Shift_Del	DEL	A	A	-			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr17:45219612delA	ENST00000066544.3	-	11	1454	c.1361delT	c.(1360-1362)ctafs	p.L454fs	CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs|CDC27_ENST00000527547.1_Frame_Shift_Del_p.L454fs|CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs	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_ENST00000527547.1_Frame_Shift_Del_p.L454fs|CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs|CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs	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			8	26						8	26	---	---	---	---
ESF1	51575	broad.mit.edu	37	20	13756820	13756829	+	Frame_Shift_Del	DEL	CTTTCTGAAT	CTTTCTGAAT	-			TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr20:13756820_13756829delCTTTCTGAAT	ENST00000202816.1	-	3	832_841	c.725_734delATTCAGAAAG	c.(724-735)gattcagaaagcfs	p.DSES242fs		NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	242					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S243S(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						TTCACTAACGCTTTCTGAATCTTCCTCCAG	0.39																																						ENST00000202816.1																			1	Substitution - coding silent(1)	p.S243S(1)	endometrium(1)	endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						c.(724-735)gcfs		ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)																																				SO:0001589	frameshift_variant	51575				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm		g.chr20:13756820_13756829delCTTTCTGAAT		CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 6"""	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.725_734delATTCAGAAAG	20.37:g.13756820_13756829delCTTTCTGAAT	ENSP00000202816:p.Asp242fs						p.DSES242fs	NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN			3	832_841	-			242					Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Frame_Shift_Del	DEL	ENST00000202816.1	37	c.725_734delATTCAGAAAG	CCDS13117.1																																																																																				0.390	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649		19	65						19	65	---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11038813	11038814	+	RNA	INS	-	-	T	rs144107885|rs71292114		TCGA-MG-AAMC-01A-11D-A41K-08	TCGA-MG-AAMC-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	def5beb7-82b8-4e1d-b7ba-6af748d690cb	c0828412-45cb-4358-b5e6-d0e1543d9cf0	g.chr21:11038813_11038814insT	ENST00000470054.1	-	0	1389_1390							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								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)		TGACTGAGATGTAAGTTGTTGG	0.446																																						ENST00000470054.1																			0													B melanoma antigen family, member 2																																						85319							g.chr21:11038813_11038814insT	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11038814_11038814dupT												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)	0	1389_1390	-								A8K925|Q08ER0	RNA	INS	ENST00000470054.1	37																																																																																						0.446	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		7	253						7	253	---	---	---	---
