#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-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	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	78	0	0	0	1	0	3	78				
HLA-DQB2	3120	broad.mit.edu	37	6	32726684	32726684	+	Missense_Mutation	SNP	T	T	C			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr6:32726684T>C	ENST00000437316.2	-	3	652	c.589A>G	c.(589-591)Atc>Gtc	p.I197V	HLA-DQB2_ENST00000411527.1_Missense_Mutation_p.I197V|HLA-DQB2_ENST00000435145.2_Missense_Mutation_p.I197V			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	201	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)|toxic substance binding (GO:0015643)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						CAGGTGTAGATGTCTCCACGC	0.567																																						ENST00000435145.2																			0				endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						c.(589-591)Atc>Gtc		major histocompatibility complex, class II, DQ beta 2																																				SO:0001583	missense	3120				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	integral to membrane|MHC class II protein complex		g.chr6:32726684T>C	M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4945	protein-coding gene	gene with protein product		615161		HLA-DXB		2564844	Standard	NM_001198858		Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.589A>G	6.37:g.32726684T>C	ENSP00000396330:p.Ile197Val					HLA-DQB2_ENST00000411527.1_Missense_Mutation_p.I197V|HLA-DQB2_ENST00000437316.2_Missense_Mutation_p.I197V	p.I197V			Q5SR06	Q5SR06_HUMAN			3	650	-			197					A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	Missense_Mutation	SNP	ENST00000437316.2	37	c.589A>G		.	.	.	.	.	.	.	.	.	.	T	0	-2.697852	0.00097	.	.	ENSG00000232629	ENST00000437316;ENST00000435145;ENST00000411527	T;T;T	0.02682	4.2;4.2;4.2	3.29	-0.72	0.11195	.	0.616617	0.15137	N	0.278509	T	0.00178	0.0005	N	0.00140	-2.01	0.19775	N	0.99995	B;B	0.06786	0.001;0.001	B;B	0.13407	0.009;0.004	T	0.31447	-0.9943	10	0.02654	T	1	.	6.956	0.24572	0.0:0.4031:0.0:0.5969	.	197;197	A2ADX3;Q5SR06	.;.	V	197	ENSP00000396330:I197V;ENSP00000410512:I197V;ENSP00000390431:I197V	ENSP00000390431:I197V	I	-	1	0	HLA-DQB2	32834662	0.027000	0.19231	0.775000	0.31657	0.092000	0.18411	0.590000	0.23954	-0.065000	0.13021	-1.585000	0.00851	ATC		0.567	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076216.2			4	66	0	0	0	1	0	4	66				
SYNE1	23345	broad.mit.edu	37	6	152501297	152501297	+	Missense_Mutation	SNP	C	C	G			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr6:152501297C>G	ENST00000367255.5	-	129	24035	c.23434G>C	c.(23434-23436)Gaa>Caa	p.E7812Q	SYNE1_ENST00000448038.1_Missense_Mutation_p.E7741Q|SYNE1_ENST00000356820.4_Missense_Mutation_p.E2336Q|SYNE1_ENST00000341594.5_Missense_Mutation_p.E7424Q|SYNE1_ENST00000265368.4_Missense_Mutation_p.E7812Q|SYNE1_ENST00000423061.1_Missense_Mutation_p.E7741Q|SYNE1_ENST00000347037.5_5'Flank	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7812					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ATCATTTCTTCAATGAGAATG	0.388										HNSCC(10;0.0054)																												ENST00000367255.5																			0				NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524						c.(23434-23436)Gaa>Caa		spectrin repeat containing, nuclear envelope 1							192.0	182.0	186.0					6																	152501297		2203	4300	6503	SO:0001583	missense	23345				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding	g.chr6:152501297C>G	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.23434G>C	6.37:g.152501297C>G	ENSP00000356224:p.Glu7812Gln	HNSCC(10;0.0054)				SYNE1_ENST00000448038.1_Missense_Mutation_p.E7741Q|SYNE1_ENST00000341594.5_Missense_Mutation_p.E7424Q|SYNE1_ENST00000265368.4_Missense_Mutation_p.E7812Q|SYNE1_ENST00000423061.1_Missense_Mutation_p.E7741Q|SYNE1_ENST00000356820.4_Missense_Mutation_p.E2336Q	p.E7812Q	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)	129	24035	-		Ovarian(120;0.0955)	7812					E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	c.23434G>C	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	20.6	4.021432	0.75275	.	.	ENSG00000131018	ENST00000367255;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000367251	T;T;T;T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92;-0.92;-0.92;-0.92	5.21	4.33	0.51752	.	0.000000	0.64402	D	0.000007	T	0.80999	0.4732	M	0.69823	2.125	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.85130	0.997;0.997;0.995;0.997;0.984	T	0.82311	-0.0520	10	0.46703	T	0.11	.	15.2995	0.73936	0.1408:0.8592:0.0:0.0	.	7812;7812;7741;7741;14	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	Q	7812;458;7741;7812;7741;7424;2336;734	ENSP00000356224:E7812Q;ENSP00000356226:E458Q;ENSP00000396024:E7741Q;ENSP00000265368:E7812Q;ENSP00000390975:E7741Q;ENSP00000341887:E7424Q;ENSP00000349276:E2336Q;ENSP00000356220:E734Q	ENSP00000265368:E7812Q	E	-	1	0	SYNE1	152542990	1.000000	0.71417	0.999000	0.59377	0.735000	0.41995	7.681000	0.84073	1.174000	0.42811	0.655000	0.94253	GAA		0.388	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		29	48	0	0	0	1	0	29	48				
SLC22A10	387775	broad.mit.edu	37	11	63070001	63070001	+	Missense_Mutation	SNP	C	C	T	rs375615317		TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr11:63070001C>T	ENST00000332793.6	+	7	1273	c.1271C>T	c.(1270-1272)aCg>aTg	p.T424M	SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000544661.1_Intron|SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000526800.1_Intron	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	424						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	TTGGCCAACACGTTTGTGCCC	0.433													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20554	0.0		0.0	False		,,,				2504	0.0					ENST00000332793.6																			0				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						c.(1270-1272)aCg>aTg		solute carrier family 22, member 10		C	MET/THR	0,3774		0,0,1887	117.0	104.0	108.0		1271	-1.5	0.0	11		108	3,8217		0,3,4107	no	missense	SLC22A10	NM_001039752.3	81	0,3,5994	TT,TC,CC		0.0365,0.0,0.025	possibly-damaging	424/542	63070001	3,11991	1887	4110	5997	SO:0001583	missense	387775					integral to membrane	transmembrane transporter activity	g.chr11:63070001C>T	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"""Solute carriers"""	18057	protein-coding gene	gene with protein product		607580	"""solute carrier family 22 (organic anion/cation transporter), member 10"""			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.1271C>T	11.37:g.63070001C>T	ENSP00000327569:p.Thr424Met					SLC22A10_ENST00000544661.1_Intron|SLC22A10_ENST00000526800.1_Intron|SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000525620.1_Intron	p.T424M	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN			7	1273	+			424					Q68CJ0	Missense_Mutation	SNP	ENST00000332793.6	37	c.1271C>T	CCDS41661.1	.	.	.	.	.	.	.	.	.	.	C	6.882	0.532082	0.13127	0.0	3.65E-4	ENSG00000184999	ENST00000332793	T	0.59083	0.29	3.62	-1.45	0.08828	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.601467	0.15348	N	0.267112	T	0.30634	0.0771	N	0.19112	0.55	0.09310	N	1	P	0.43231	0.801	B	0.36378	0.223	T	0.21348	-1.0248	9	.	.	.	.	4.5441	0.12073	0.0:0.4311:0.3459:0.223	.	424	Q63ZE4	S22AA_HUMAN	M	424	ENSP00000327569:T424M	.	T	+	2	0	SLC22A10	62826577	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	-0.600000	0.05693	-0.090000	0.12462	0.579000	0.79373	ACG		0.433	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		33	54	0	0	0	1	0	33	54				
POTEC	388468	broad.mit.edu	37	18	14513764	14513764	+	Missense_Mutation	SNP	C	C	T	rs201788045		TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr18:14513764C>T	ENST00000358970.5	-	10	1429	c.1430G>A	c.(1429-1431)cGg>cAg	p.R477Q		NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	477								p.R477Q(12)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						AAGTTGTTTCCGGGTATCATT	0.358																																						ENST00000358970.5																			12	Substitution - Missense(12)	p.R477Q(12)	endometrium(4)|kidney(3)|urinary_tract(2)|prostate(2)|soft_tissue(1)	NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						c.(1429-1431)cGg>cAg		POTE ankyrin domain family, member C							13.0	9.0	10.0					18																	14513764		683	1543	2226	SO:0001583	missense	388468							g.chr18:14513764C>T	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.1430G>A	18.37:g.14513764C>T	ENSP00000351856:p.Arg477Gln						p.R477Q	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN			10	1429	-			477						Missense_Mutation	SNP	ENST00000358970.5	37	c.1430G>A	CCDS45835.1	492	0.22527472527472528	61	0.12398373983739837	82	0.2265193370165746	187	0.3269230769230769	162	0.21372031662269128	c	0.001	-3.539655	0.00009	.	.	ENSG00000183206	ENST00000358970	T	0.20881	2.04	1.34	0.0657	0.14358	.	.	.	.	.	T	0.00012	0.0000	N	0.00116	-2.08	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42430	-0.9452	9	0.06757	T	0.87	.	3.4153	0.07373	0.0:0.2473:0.0:0.7527	.	477	B2RU33	POTEC_HUMAN	Q	477	ENSP00000351856:R477Q	ENSP00000351856:R477Q	R	-	2	0	POTEC	14503764	0.885000	0.30320	0.063000	0.19743	0.005000	0.04900	1.581000	0.36558	0.005000	0.14708	-1.615000	0.00797	CGG		0.358	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		5	143	0	0	0	1	0	5	143				
OR11L1	391189	broad.mit.edu	37	1	248004826	248004826	+	Missense_Mutation	SNP	C	C	T			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr1:248004826C>T	ENST00000355784.2	-	1	428	c.373G>A	c.(373-375)Gcc>Acc	p.A125T		NM_001001959.1	NP_001001959.1	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L, member 1	125						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			CTGCAGATGGCCAGGTAACGG	0.592																																						ENST00000355784.2																			0				NS(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57						c.(373-375)Gcc>Acc		olfactory receptor, family 11, subfamily L, member 1							46.0	42.0	43.0					1																	248004826		2203	4300	6503	SO:0001583	missense	391189				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248004826C>T	AB065646	CCDS31098.1	1q44	2013-09-24			ENSG00000197591	ENSG00000197591		"""GPCR / Class A : Olfactory receptors"""	14998	protein-coding gene	gene with protein product							Standard	NM_001001959		Approved		uc001idn.1	Q8NGX0	OTTHUMG00000040193	ENST00000355784.2:c.373G>A	1.37:g.248004826C>T	ENSP00000348033:p.Ala125Thr						p.A125T	NM_001001959.1	NP_001001959.1	Q8NGX0	O11L1_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0319)		1	428	-	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		125						Missense_Mutation	SNP	ENST00000355784.2	37	c.373G>A	CCDS31098.1	.	.	.	.	.	.	.	.	.	.	C	18.55	3.648372	0.67358	.	.	ENSG00000197591	ENST00000355784	T	0.00912	5.55	4.42	4.42	0.53409	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36268	U	0.002690	T	0.08935	0.0221	M	0.93550	3.43	0.47094	D	0.999314	D	0.76494	0.999	D	0.79784	0.993	T	0.01940	-1.1243	10	0.87932	D	0	.	17.1903	0.86877	0.0:1.0:0.0:0.0	.	125	Q8NGX0	O11L1_HUMAN	T	125	ENSP00000348033:A125T	ENSP00000348033:A125T	A	-	1	0	OR11L1	246071449	0.998000	0.40836	1.000000	0.80357	0.067000	0.16453	3.877000	0.56123	2.450000	0.82876	0.543000	0.68304	GCC		0.592	OR11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096850.1	NM_001001959		3	29	0	0	0	1	0	3	29				
SIRT3	23410	broad.mit.edu	37	11	219035	219035	+	Missense_Mutation	SNP	G	G	C			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr11:219035G>C	ENST00000382743.4	-	6	1078	c.976C>G	c.(976-978)Cct>Gct	p.P326A	SIRT3_ENST00000525319.1_Missense_Mutation_p.P245A|SIRT3_ENST00000524564.1_Missense_Mutation_p.P262A|SIRT3_ENST00000529382.1_Missense_Mutation_p.P184A|SIRT3_ENST00000532956.1_Missense_Mutation_p.P272A	NM_001017524.2|NM_012239.5	NP_001017524.1|NP_036371.1	Q9NTG7	SIR3_HUMAN	sirtuin 3	326	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				aerobic respiration (GO:0009060)|peptidyl-lysine deacetylation (GO:0034983)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)	membrane (GO:0016020)|mitochondrion (GO:0005739)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|zinc ion binding (GO:0008270)			endometrium(1)|lung(5)|urinary_tract(1)	7		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		CTGGCAAAAGGCTCCACCTGA	0.602																																						ENST00000382743.4																			0				endometrium(1)|lung(5)|urinary_tract(1)	7						c.(976-978)Cct>Gct		sirtuin 3							36.0	34.0	35.0					11																	219035		2203	4300	6503	SO:0001583	missense	23410				chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding	g.chr11:219035G>C	AF083108	CCDS7691.1, CCDS53590.1	11p15.5	2010-06-25	2010-06-25		ENSG00000142082	ENSG00000142082			14931	protein-coding gene	gene with protein product		604481	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 3"", ""sirtuin (silent mating type information regulation 2 homolog) 3 (S. cerevisiae)"""			10381378, 18215119	Standard	NM_012239		Approved	SIR2L3	uc001lok.4	Q9NTG7	OTTHUMG00000119074	ENST00000382743.4:c.976C>G	11.37:g.219035G>C	ENSP00000372191:p.Pro326Ala					SIRT3_ENST00000529382.1_Missense_Mutation_p.P184A|SIRT3_ENST00000525319.1_Missense_Mutation_p.P245A|SIRT3_ENST00000524564.1_Missense_Mutation_p.P262A|SIRT3_ENST00000532956.1_Missense_Mutation_p.P272A	p.P326A	NM_001017524.2|NM_012239.5	NP_001017524.1|NP_036371.1	Q9NTG7	SIRT3_HUMAN		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)	6	1078	-		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)	326			Deacetylase sirtuin-type.		B7Z5U6|Q9Y6E8	Missense_Mutation	SNP	ENST00000382743.4	37	c.976C>G	CCDS7691.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.205757	0.79127	.	.	ENSG00000142082	ENST00000382743;ENST00000525319;ENST00000524564;ENST00000532956;ENST00000529382	T;T;T;T;T	0.56776	0.44;0.44;0.44;1.91;0.44	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.85173	0.5636	H	0.99507	4.6	0.58432	D	0.999999	D;B;D;D;B	0.89917	1.0;0.243;1.0;0.999;0.37	D;B;D;D;B	0.97110	1.0;0.113;0.996;0.999;0.068	D	0.91900	0.5531	10	0.87932	D	0	-16.968	17.833	0.88688	0.0:0.0:1.0:0.0	.	272;326;245;262;326	E9PM75;B7Z7G4;E9PK80;E9PN58;Q9NTG7	.;.;.;.;SIRT3_HUMAN	A	326;245;262;272;184	ENSP00000372191:P326A;ENSP00000435464:P245A;ENSP00000432937:P262A;ENSP00000433077:P272A;ENSP00000437216:P184A	ENSP00000372191:P326A	P	-	1	0	SIRT3	209035	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	9.805000	0.99149	2.543000	0.85770	0.555000	0.69702	CCT		0.602	SIRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239288.3			4	14	0	0	0	1	0	4	14				
KIF21B	23046	broad.mit.edu	37	1	200960121	200960121	+	Missense_Mutation	SNP	G	G	C	rs540134751		TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr1:200960121G>C	ENST00000422435.2	-	18	2927	c.2611C>G	c.(2611-2613)Cgc>Ggc	p.R871G	KIF21B_ENST00000461742.2_Missense_Mutation_p.R871G|KIF21B_ENST00000332129.2_Missense_Mutation_p.R871G|KIF21B_ENST00000360529.5_Missense_Mutation_p.R871G	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	871					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TTCCACTGGCGCACGATGCTG	0.617																																						ENST00000332129.2																			0				autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						c.(2611-2613)Cgc>Ggc		kinesin family member 21B							96.0	98.0	97.0					1																	200960121		2203	4300	6503	SO:0001583	missense	23046				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity	g.chr1:200960121G>C	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.2611C>G	1.37:g.200960121G>C	ENSP00000411831:p.Arg871Gly					KIF21B_ENST00000422435.2_Missense_Mutation_p.R871G|KIF21B_ENST00000360529.5_Missense_Mutation_p.R871G|KIF21B_ENST00000461742.2_Missense_Mutation_p.R871G	p.R871G	NM_001252102.1|NM_001252103.1|NM_017596.3	NP_001239031.1|NP_001239032.1|NP_060066.2	O75037	KI21B_HUMAN			18	2927	-			871					B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	c.2611C>G	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.164057	0.38217	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.71934	-0.26;-0.58;-0.61;-0.33	4.65	4.65	0.58169	.	0.058169	0.64402	D	0.000002	D	0.82797	0.5115	M	0.71581	2.175	0.51012	D	0.999904	D;D;D;D	0.71674	0.993;0.997;0.997;0.998	D;D;D;D	0.80764	0.982;0.987;0.987;0.994	D	0.83479	0.0063	9	.	.	.	.	16.8837	0.86070	0.0:0.0:1.0:0.0	.	871;871;871;871	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	G	871	ENSP00000328494:R871G;ENSP00000353724:R871G;ENSP00000433808:R871G;ENSP00000411831:R871G	.	R	-	1	0	KIF21B	199226744	1.000000	0.71417	1.000000	0.80357	0.004000	0.04260	4.968000	0.63728	2.283000	0.76528	0.561000	0.74099	CGC		0.617	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		29	43	0	0	0	1	0	29	43				
JAG1	182	broad.mit.edu	37	20	10622217	10622217	+	Missense_Mutation	SNP	C	C	T			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr20:10622217C>T	ENST00000254958.5	-	23	3322	c.2807G>A	c.(2806-2808)tGt>tAt	p.C936Y	JAG1_ENST00000423891.2_Missense_Mutation_p.C777Y	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	936					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						GGAAGACCGACACTCGCCCAC	0.567									Alagille Syndrome																													ENST00000254958.5																			0				biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						c.(2806-2808)tGt>tAt		jagged 1							87.0	86.0	86.0					20																	10622217		2203	4300	6503	SO:0001583	missense	182	Alagille Syndrome	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity	g.chr20:10622217C>T	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.2807G>A	20.37:g.10622217C>T	ENSP00000254958:p.Cys936Tyr					JAG1_ENST00000423891.2_Missense_Mutation_p.C777Y	p.C936Y	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN			23	3322	-			936					A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	37	c.2807G>A	CCDS13112.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872171	0.91587	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.95853	-3.83;-3.74	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.98607	0.9534	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.99293	1.0899	10	0.87932	D	0	.	19.8471	0.96713	0.0:1.0:0.0:0.0	.	936	P78504	JAG1_HUMAN	Y	936;777	ENSP00000254958:C936Y;ENSP00000389519:C777Y	ENSP00000254958:C936Y	C	-	2	0	JAG1	10570217	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.487000	0.81328	2.688000	0.91661	0.655000	0.94253	TGT		0.567	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		83	108	0	0	0	1	0	83	108				
PPM1D	8493	broad.mit.edu	37	17	58734108	58734108	+	Missense_Mutation	SNP	A	A	G			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr17:58734108A>G	ENST00000305921.3	+	5	1398	c.1166A>G	c.(1165-1167)gAt>gGt	p.D389G		NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1D	389					G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of cell proliferation (GO:0008285)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			ACCAATGAAGATGAGTTATAC	0.468																																						ENST00000305921.3																			0				haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15						c.(1165-1167)gAt>gGt		protein phosphatase, Mg2+/Mn2+ dependent, 1D							134.0	123.0	127.0					17																	58734108		2203	4300	6503	SO:0001583	missense	8493				negative regulation of cell proliferation|protein dephosphorylation|response to radiation	nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein binding|protein serine/threonine phosphatase activity	g.chr17:58734108A>G	U78305	CCDS11625.1	17q23.3	2014-09-17	2010-03-05		ENSG00000170836	ENSG00000170836		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9277	protein-coding gene	gene with protein product	"""wild-type p53-induced phosphatase 1"", ""protein phosphatase 2C, delta isoform"""	605100	"""protein phosphatase 1D magnesium-dependent, delta isoform"""			9177166	Standard	NM_003620		Approved	Wip1, PP2C-DELTA	uc002iyt.2	O15297		ENST00000305921.3:c.1166A>G	17.37:g.58734108A>G	ENSP00000306682:p.Asp389Gly						p.D389G	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)		5	1398	+	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		389					Q53XP4|Q6P991|Q8IVR6	Missense_Mutation	SNP	ENST00000305921.3	37	c.1166A>G	CCDS11625.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.151767	0.78001	.	.	ENSG00000170836	ENST00000305921;ENST00000544712;ENST00000392995	T;T	0.52526	0.66;0.72	5.88	5.88	0.94601	.	0.218479	0.47852	D	0.000207	T	0.37433	0.1003	N	0.24115	0.695	0.58432	D	0.999991	D	0.53151	0.958	B	0.42692	0.395	T	0.22730	-1.0208	10	0.42905	T	0.14	-21.2357	14.9154	0.70792	1.0:0.0:0.0:0.0	.	389	O15297	PPM1D_HUMAN	G	389;237;389	ENSP00000306682:D389G;ENSP00000376720:D389G	ENSP00000306682:D389G	D	+	2	0	PPM1D	56088890	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.302000	0.78861	2.256000	0.74724	0.524000	0.50904	GAT		0.468	PPM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449474.1	NM_003620		30	60	0	0	0	1	0	30	60				
SPEN	23013	broad.mit.edu	37	1	16259547	16259547	+	Missense_Mutation	SNP	G	G	A			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr1:16259547G>A	ENST00000375759.3	+	11	7016	c.6812G>A	c.(6811-6813)gGc>gAc	p.G2271D		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2271	Interaction with MSX2. {ECO:0000250}.|RID.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GCTGTATCTGGCATCCTGGAA	0.557																																						ENST00000375759.3																			0				NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149						c.(6811-6813)gGc>gAc		spen family transcriptional repressor							90.0	95.0	93.0					1																	16259547		2203	4300	6503	SO:0001583	missense	23013				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding	g.chr1:16259547G>A		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.6812G>A	1.37:g.16259547G>A	ENSP00000364912:p.Gly2271Asp						p.G2271D	NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)	11	7016	+		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)	2271			Interaction with MSX2 (By similarity).|RID.		Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	c.6812G>A	CCDS164.1	.	.	.	.	.	.	.	.	.	.	G	10.78	1.447025	0.25987	.	.	ENSG00000065526	ENST00000375759	T	0.08720	3.06	5.05	5.05	0.67936	.	.	.	.	.	T	0.15912	0.0383	L	0.47716	1.5	0.32056	N	0.59631	D	0.89917	1.0	D	0.83275	0.996	T	0.09862	-1.0655	9	0.12766	T	0.61	-17.9182	5.0846	0.14675	0.1279:0.0:0.6701:0.202	.	2271	Q96T58	MINT_HUMAN	D	2271	ENSP00000364912:G2271D	ENSP00000364912:G2271D	G	+	2	0	SPEN	16132134	0.979000	0.34478	1.000000	0.80357	0.354000	0.29330	1.268000	0.33062	2.339000	0.79563	0.462000	0.41574	GGC		0.557	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		4	126	0	0	0	1	0	4	126				
EMR2	30817	broad.mit.edu	37	19	14854471	14854471	+	Missense_Mutation	SNP	T	T	C			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr19:14854471T>C	ENST00000315576.3	-	19	2760	c.2309A>G	c.(2308-2310)cAg>cGg	p.Q770R	EMR2_ENST00000353876.1_Missense_Mutation_p.Q677R|EMR2_ENST00000392965.3_Missense_Mutation_p.Q712R|EMR2_ENST00000346057.1_Missense_Mutation_p.Q721R|EMR2_ENST00000594076.1_Missense_Mutation_p.Q677R|EMR2_ENST00000353005.1_Missense_Mutation_p.Q628R|EMR2_ENST00000595839.1_Missense_Mutation_p.Q628R|EMR2_ENST00000596991.2_Missense_Mutation_p.Q759R|EMR2_ENST00000594294.1_Missense_Mutation_p.Q721R|EMR2_ENST00000601345.1_Missense_Mutation_p.Q759R|EMR2_ENST00000392967.2_Missense_Mutation_p.Q759R	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	770					cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						GAAGACACCCTGCAGGCTGTT	0.607																																						ENST00000315576.3																			0				breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						c.(2308-2310)cAg>cGg		egf-like module containing, mucin-like, hormone receptor-like 2							171.0	151.0	158.0					19																	14854471		2203	4300	6503	SO:0001583	missense	30817				cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity	g.chr19:14854471T>C	AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	3337	protein-coding gene	gene with protein product		606100	"""egf-like module containing, mucin-like, hormone receptor-like sequence 2"""				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.2309A>G	19.37:g.14854471T>C	ENSP00000319883:p.Gln770Arg					EMR2_ENST00000353005.1_Missense_Mutation_p.Q628R|EMR2_ENST00000595839.1_Missense_Mutation_p.Q628R|EMR2_ENST00000392965.3_Missense_Mutation_p.Q712R|EMR2_ENST00000601345.1_Missense_Mutation_p.Q759R|EMR2_ENST00000596991.2_Missense_Mutation_p.Q759R|EMR2_ENST00000594294.1_Missense_Mutation_p.Q721R|EMR2_ENST00000353876.1_Missense_Mutation_p.Q677R|EMR2_ENST00000594076.1_Missense_Mutation_p.Q677R|EMR2_ENST00000346057.1_Missense_Mutation_p.Q721R|EMR2_ENST00000392967.2_Missense_Mutation_p.Q759R	p.Q770R	NM_013447.2	NP_038475.2	Q9UHX3	EMR2_HUMAN			19	2760	-			770					B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	c.2309A>G	CCDS32935.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.816829	0.70912	.	.	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000392965	T;T;T;T;T;T	0.59906	0.23;0.23;0.23;0.23;0.23;0.23	5.21	4.19	0.49359	GPCR, family 2-like (1);GPCR, family 2, secretin-like, conserved site (1);	.	.	.	.	D	0.83963	0.5368	H	0.98833	4.345	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;0.998;0.997;0.996;0.998;0.999;0.999;0.997	D	0.86430	0.1760	9	0.87932	D	0	.	9.749	0.40464	0.1546:0.0:0.0:0.8454	.	712;677;770;628;721;770;770;759	E7ESD7;Q9UHX3-4;A0JNV7;Q9UHX3-5;Q9UHX3-3;A8K6W1;Q9UHX3;Q9UHX3-2	.;.;.;.;.;.;EMR2_HUMAN;.	R	770;759;721;677;628;712	ENSP00000319883:Q770R;ENSP00000376694:Q759R;ENSP00000263380:Q721R;ENSP00000319454:Q677R;ENSP00000319838:Q628R;ENSP00000376692:Q712R	ENSP00000319883:Q770R	Q	-	2	0	EMR2	14715471	1.000000	0.71417	1.000000	0.80357	0.602000	0.36980	4.347000	0.59373	0.815000	0.34398	0.491000	0.48974	CAG		0.607	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2			8	134	0	0	0	1	0	8	134				
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	C	T			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr1:16918653C>T	ENST00000430580.2	-	6	853		c.e6+1			NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418																																						ENST00000430580.2																			0											c.e6+1		neuroblastoma breakpoint family, member 1																																				SO:0001630	splice_region_variant	55672					cytoplasm		g.chr1:16918653C>T	AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"""neuroblastoma breakpoint family"""	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.34+1G>A	1.37:g.16918653C>T								NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)	6	853	-								Q8N4E8|Q9C0H0	Splice_Site	SNP	ENST00000430580.2	37																																																																																						0.418	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940	Intron	7	67	0	0	0	1	0	7	67				
LOC101927648	101927648	broad.mit.edu	37	1	143403563	143403563	+	lincRNA	SNP	C	C	A	rs376564211		TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr1:143403563C>A	ENST00000423249.1	-	0	59																											TTTCTTTGGCCACTTTGGCTG	0.453																																						ENST00000423249.1																			0																																																			0							g.chr1:143403563C>A																													1.37:g.143403563C>A														0	59	-									RNA	SNP	ENST00000423249.1	37																																																																																						0.453	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	lincRNA	OTTHUMT00000037552.1			3	27	1	0	1	1	1	3	27				
WDFY3	23001	broad.mit.edu	37	4	85658466	85658466	+	Missense_Mutation	SNP	T	T	C			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr4:85658466T>C	ENST00000295888.4	-	41	7035	c.6628A>G	c.(6628-6630)Agt>Ggt	p.S2210G	WDFY3_ENST00000322366.6_Missense_Mutation_p.S2210G	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2210					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TGTTTCTTACTATGTATCAGT	0.393																																						ENST00000322366.6																			0				breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						c.(6628-6630)Agt>Ggt		WD repeat and FYVE domain containing 3							105.0	101.0	102.0					4																	85658466		2203	4300	6503	SO:0001583	missense	23001					cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding	g.chr4:85658466T>C	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.6628A>G	4.37:g.85658466T>C	ENSP00000295888:p.Ser2210Gly					WDFY3_ENST00000295888.4_Missense_Mutation_p.S2210G	p.S2210G			Q8IZQ1	WDFY3_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.000808)	41	7035	-		Hepatocellular(203;0.114)	2210					Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	c.6628A>G	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	T	17.30	3.355579	0.61293	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.64803	-0.12;-0.11	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.55625	0.1932	L	0.54323	1.7	0.80722	D	1	P	0.44478	0.836	B	0.38616	0.277	T	0.55477	-0.8135	10	0.22109	T	0.4	.	14.9515	0.71077	0.0:0.0:0.0:1.0	.	2210	Q8IZQ1	WDFY3_HUMAN	G	2210	ENSP00000318466:S2210G;ENSP00000295888:S2210G	ENSP00000295888:S2210G	S	-	1	0	WDFY3	85877490	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.673000	0.83973	1.938000	0.56188	0.460000	0.39030	AGT		0.393	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		31	45	0	0	0	1	0	31	45				
UBB	7314	broad.mit.edu	37	17	16285788	16285788	+	Silent	SNP	C	C	T			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr17:16285788C>T	ENST00000395837.1	+	2	748	c.567C>T	c.(565-567)ccC>ccT	p.P189P	UBB_ENST00000302182.3_Silent_p.P189P|UBB_ENST00000578649.1_3'UTR|UBB_ENST00000395839.1_Silent_p.P189P|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000535788.1_Silent_p.P113P	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	189	Ubiquitin-like 3. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)		p.P189P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AAGGCATCCCCCCCGACCAGC	0.552																																					Melanoma(163;1126 3406 34901)	ENST00000302182.3																			1	Substitution - coding silent(1)	p.P189P(1)	urinary_tract(1)	breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						c.(565-567)ccC>ccT		ubiquitin B							55.0	59.0	58.0					17																	16285788		2203	4297	6500	SO:0001819	synonymous_variant	7314				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding	g.chr17:16285788C>T		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.567C>T	17.37:g.16285788C>T						UBB_ENST00000395839.1_Silent_p.P189P|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000395837.1_Silent_p.P189P|UBB_ENST00000578649.1_3'UTR|UBB_ENST00000535788.1_Silent_p.P113P	p.P189P	NM_018955.2	NP_061828.1	P0CG47	UBB_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)	2	959	+			189			Ubiquitin-like 3.		P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	c.567C>T	CCDS11177.1																																																																																				0.552	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955		4	86	0	0	0	1	0	4	86				
CYP2D7	1564	broad.mit.edu	37	22	42538870	42538870	+	RNA	SNP	A	A	C	rs2982057	byFrequency	TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr22:42538870A>C	ENST00000428786.1	-	0	0				CYP2D7P1_ENST00000358097.4_RNA|CYP2D7P1_ENST00000424775.1_RNA|CYP2D7P1_ENST00000433992.1_RNA																							CCATAGCGCGACAGGAACACC	0.687													N|||	80	0.0159744	0.0023	0.0317	5008	,	,		11900	0.0109		0.0348	False		,,,				2504	0.0092					ENST00000433992.1																			0				endometrium(1)	1																																														0							g.chr22:42538870A>C																													22.37:g.42538870A>C						CYP2D7P1_ENST00000424775.1_RNA|CYP2D7P1_ENST00000358097.4_RNA								0	475	-									RNA	SNP	ENST00000428786.1	37			30	0.013736263736263736	1	0.0020325203252032522	5	0.013812154696132596	5	0.008741258741258742	19	0.025065963060686015	C	8.846	0.943329	0.18281	.	.	ENSG00000205702	ENST00000428297;ENST00000381321;ENST00000436260	.	.	.	3.26	3.26	0.37387	.	.	.	.	.	T	0.04724	0.0128	.	.	.	0.28613	N	0.908552	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.23154	-1.0196	7	0.02654	T	1	.	8.0614	0.30635	0.2422:0.7578:0.0:0.0	rs2982057	122;32	Q6XP50;F5H167	.;.	A	121;71;32	.	ENSP00000446103:S71A	S	-	1	0	CYP2D7P1	40868814	0.299000	0.24426	0.017000	0.16124	0.002000	0.02628	0.565000	0.23578	0.961000	0.38030	-0.290000	0.09829	TCG		0.687	RP4-669P10.16-001	KNOWN	basic|exp_conf	sense_intronic	sense_intronic	OTTHUMT00000320534.1			3	24	0	0	0	1	0	3	24				
POM121	9883	broad.mit.edu	37	7	72398976	72398976	+	Missense_Mutation	SNP	A	A	G	rs147859349		TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr7:72398976A>G	ENST00000434423.2	+	4	1076	c.1076A>G	c.(1075-1077)aAt>aGt	p.N359S	POM121_ENST00000358357.3_Missense_Mutation_p.N94S|POM121_ENST00000257622.4_Missense_Mutation_p.N94S|POM121_ENST00000446813.1_Missense_Mutation_p.N94S|POM121_ENST00000395270.1_Missense_Mutation_p.N94S			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	359	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				CTGGTGGCCAATGGAGTCCCC	0.468													.|||	1	0.000199681	0.0008	0.0	5008	,	,		16715	0.0		0.0	False		,,,				2504	0.0					ENST00000395270.1																			0				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						c.(280-282)aAt>aGt		POM121 transmembrane nucleoporin							189.0	188.0	188.0					7																	72398976		2203	4300	6503	SO:0001583	missense	9883				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore		g.chr7:72398976A>G	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.1076A>G	7.37:g.72398976A>G	ENSP00000405562:p.Asn359Ser					POM121_ENST00000358357.3_Missense_Mutation_p.N94S|POM121_ENST00000434423.2_Missense_Mutation_p.N359S|POM121_ENST00000257622.4_Missense_Mutation_p.N94S|POM121_ENST00000446813.1_Missense_Mutation_p.N94S	p.N94S	NM_001257190.1	NP_001244119.1	Q96HA1	P121A_HUMAN			7	1322	+		Lung NSC(55;0.163)	359			Pore side (Potential).|Required for targeting to the nucleus and nuclear pore complex.		A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37	c.281A>G		.	.	.	.	.	.	.	.	.	.	G	12.65	2.002131	0.35320	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.14266	2.52;2.52;2.52;2.52;2.52	3.99	3.99	0.46301	.	0.154071	0.30020	N	0.010614	T	0.13457	0.0326	L	0.57536	1.79	0.32153	N	0.584002	B;B	0.31193	0.312;0.006	B;B	0.26202	0.067;0.053	T	0.08066	-1.0740	10	0.30078	T	0.28	.	10.8045	0.46509	1.0:0.0:0.0:0.0	.	94;359	A8MXF9;Q96HA1	.;P121A_HUMAN	S	94;94;94;94;359	ENSP00000393020:N94S;ENSP00000257622:N94S;ENSP00000378687:N94S;ENSP00000351124:N94S;ENSP00000405562:N359S	ENSP00000257622:N94S	N	+	2	0	POM121	72036912	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	5.143000	0.64826	1.663000	0.50791	0.373000	0.22412	AAT		0.468	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1			5	259	0	0	0	1	0	5	259				
INTS7	25896	broad.mit.edu	37	1	212120037	212120037	+	Missense_Mutation	SNP	C	C	T			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr1:212120037C>T	ENST00000366994.3	-	18	2431	c.2327G>A	c.(2326-2328)tGc>tAc	p.C776Y	INTS7_ENST00000366993.3_Missense_Mutation_p.C762Y|INTS7_ENST00000440600.2_Missense_Mutation_p.C727Y|INTS7_ENST00000366992.3_Intron|INTS7_ENST00000469606.1_5'UTR	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	776					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		ATTGCAGAGGCATGCTGTGTG	0.358																																						ENST00000366994.3																			0				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						c.(2326-2328)tGc>tAc		integrator complex subunit 7							60.0	62.0	62.0					1																	212120037		2203	4300	6503	SO:0001583	missense	25896				snRNA processing	integrator complex	protein binding	g.chr1:212120037C>T	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"""chromosome 1 open reading frame 73"""	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.2327G>A	1.37:g.212120037C>T	ENSP00000355961:p.Cys776Tyr					INTS7_ENST00000366993.3_Missense_Mutation_p.C762Y|INTS7_ENST00000440600.2_Missense_Mutation_p.C727Y|INTS7_ENST00000366992.3_Intron|INTS7_ENST00000469606.1_5'UTR	p.C776Y	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)	18	2431	-			776					B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	37	c.2327G>A	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.658087	0.88154	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000440600	T;T;T	0.48836	0.84;0.8;0.84	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.63745	0.2537	M	0.62723	1.935	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.80764	0.994;0.994;0.994	T	0.56353	-0.7993	10	0.02654	T	1	-23.5851	20.3081	0.98638	0.0:1.0:0.0:0.0	.	727;762;776	B4DLZ6;Q9NVH2-2;Q9NVH2	.;.;INT7_HUMAN	Y	776;762;727	ENSP00000355961:C776Y;ENSP00000355960:C762Y;ENSP00000388908:C727Y	ENSP00000355960:C762Y	C	-	2	0	INTS7	210186660	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.201000	0.77847	2.795000	0.96236	0.655000	0.94253	TGC		0.358	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434		33	48	0	0	0	1	0	33	48				
TYRO3	7301	broad.mit.edu	37	15	41865222	41865222	+	Missense_Mutation	SNP	T	T	G			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr15:41865222T>G	ENST00000263798.3	+	16	2122	c.1898T>G	c.(1897-1899)aTc>aGc	p.I633S	TYRO3_ENST00000559066.1_Missense_Mutation_p.I588S	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	633	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CAGACCCTGATCCGGTTCATG	0.592																																						ENST00000263798.3																			0				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43						c.(1897-1899)aTc>aGc		TYRO3 protein tyrosine kinase							74.0	64.0	67.0					15																	41865222		2203	4300	6503	SO:0001583	missense	7301					integral to plasma membrane	ATP binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity	g.chr15:41865222T>G	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.1898T>G	15.37:g.41865222T>G	ENSP00000263798:p.Ile633Ser					TYRO3_ENST00000559066.1_Missense_Mutation_p.I588S	p.I633S	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)	16	2122	+		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)	633			Protein kinase.		O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	c.1898T>G	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	T	18.22	3.575862	0.65878	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	D	0.83335	-1.71	5.8	5.8	0.92144	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	1.293550	0.05656	N	0.585957	D	0.86343	0.5910	L	0.60067	1.865	0.36497	D	0.868808	B	0.28971	0.229	B	0.37198	0.243	T	0.74728	-0.3567	10	0.87932	D	0	-2.1716	16.1383	0.81506	0.0:0.0:0.0:1.0	.	633	Q06418	TYRO3_HUMAN	S	565;633	ENSP00000263798:I633S	ENSP00000263798:I633S	I	+	2	0	TYRO3	39652514	0.999000	0.42202	0.984000	0.44739	0.996000	0.88848	6.305000	0.72805	2.219000	0.72066	0.533000	0.62120	ATC		0.592	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2			24	61	0	0	0	1	0	24	61				
NF1	4763	broad.mit.edu	37	17	29665157	29665157	+	Splice_Site	SNP	G	G	A			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr17:29665157G>A	ENST00000358273.4	+	45	7202	c.6819G>A	c.(6817-6819)aaG>aaA	p.K2273K	NF1_ENST00000444181.2_Splice_Site_p.K66K|NF1_ENST00000417592.2_Intron|NF1_ENST00000356175.3_Splice_Site_p.K2252K	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2273					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTCTTAGCAAGGTACCTGTTC	0.388			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												ENST00000358273.4			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	"""D, Mis, N, F, S, O"""	neurofibromatosis type 1 gene			O		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""	NF1/ACCN1(2)	11	Whole gene deletion(8)|Unknown(3)	p.0?(8)|p.?(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599						c.e45+1		neurofibromin 1							125.0	117.0	119.0					17																	29665157		2203	4300	6503	SO:0001630	splice_region_variant	4763	Neurofibromatosis, type 1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	g.chr17:29665157G>A		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.6819+1G>A	17.37:g.29665157G>A		TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_ENST00000444181.2_Splice_Site_p.K66_splice|NF1_ENST00000417592.2_Intron|NF1_ENST00000356175.3_Splice_Site_p.K2252_splice	p.K2273_splice	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	45	7202	+		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)	2273					O00662|Q14284|Q14930|Q14931|Q9UMK3	Splice_Site	SNP	ENST00000358273.4	37	c.6819_splice	CCDS42292.1																																																																																				0.388	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	Silent	51	70	0	0	0	1	0	51	70				
ZNF606	80095	broad.mit.edu	37	19	58491114	58491114	+	Missense_Mutation	SNP	T	T	A			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr19:58491114T>A	ENST00000341164.4	-	7	1554	c.934A>T	c.(934-936)Aca>Tca	p.T312S	ZNF606_ENST00000536132.1_Missense_Mutation_p.T222S	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	312					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		TTTTCTCCTGTGTGAATTCCT	0.343																																						ENST00000341164.4																			0				NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						c.(934-936)Aca>Tca		zinc finger protein 606							90.0	93.0	92.0					19																	58491114		2203	4299	6502	SO:0001583	missense	80095				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:58491114T>A	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"""Zinc fingers, C2H2-type"", ""-"""	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.934A>T	19.37:g.58491114T>A	ENSP00000343617:p.Thr312Ser					ZNF606_ENST00000536132.1_Missense_Mutation_p.T222S	p.T312S	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)	7	1554	-		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)	312					A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	37	c.934A>T	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	T	12.57	1.977765	0.34848	.	.	ENSG00000166704	ENST00000341164;ENST00000536132;ENST00000551380	T;T;T	0.18016	2.24;2.24;2.24	4.29	4.29	0.51040	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.167481	0.28641	N	0.014640	T	0.29945	0.0749	L	0.61387	1.9	0.26616	N	0.972745	D	0.58268	0.982	P	0.53760	0.734	T	0.07462	-1.0771	10	0.59425	D	0.04	.	13.3681	0.60696	0.0:0.0:0.0:1.0	.	312	Q8WXB4	ZN606_HUMAN	S	312;222;312	ENSP00000343617:T312S;ENSP00000445624:T222S;ENSP00000446972:T312S	ENSP00000343617:T312S	T	-	1	0	ZNF606	63182926	0.749000	0.28305	0.974000	0.42286	0.990000	0.78478	0.919000	0.28692	2.161000	0.67846	0.533000	0.62120	ACA		0.343	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		33	48	0	0	0	1	0	33	48				
ATXN1	6310	broad.mit.edu	37	6	16327894	16327894	+	Missense_Mutation	SNP	C	C	A	rs201040133	byFrequency	TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr6:16327894C>A	ENST00000244769.4	-	8	1584	c.648G>T	c.(646-648)caG>caT	p.Q216H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q216H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	216	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgctgctgctgctgctgct	0.662													-|||	41	0.0081869	0.0091	0.0014	5008	,	,		12664	0.0109		0.005	False		,,,				2504	0.0123					ENST00000244769.4																			0				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44						c.(646-648)caG>caT		ataxin 1							4.0	8.0	7.0					6																	16327894		1839	3762	5601	SO:0001583	missense	6310				cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association	g.chr6:16327894C>A	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.648G>T	6.37:g.16327894C>A	ENSP00000244769:p.Gln216His					ATXN1_ENST00000436367.1_Missense_Mutation_p.Q216H	p.Q216H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN			8	1584	-	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)	216			Poly-Gln.		Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	c.648G>T	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	-	5.041	0.193181	0.09599	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.59906	0.23;0.23	.	.	.	.	.	.	.	.	T	0.13415	0.0325	N	0.08118	0	0.09310	N	1	B	0.28713	0.22	B	0.17979	0.02	T	0.14364	-1.0475	7	0.66056	D	0.02	.	.	.	.	.	216	P54253	ATX1_HUMAN	H	216	ENSP00000244769:Q216H;ENSP00000416360:Q216H	ENSP00000244769:Q216H	Q	-	3	2	ATXN1	16435873	0.005000	0.15991	0.008000	0.14137	0.119000	0.20118	-0.699000	0.05087	0.119000	0.18210	0.121000	0.15741	CAG		0.662	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		3	12	1	0	0.00909568	1	0.00934834	3	12				
PSAT1	29968	broad.mit.edu	37	9	80921289	80921289	+	Missense_Mutation	SNP	G	G	A	rs199619145		TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr9:80921289G>A	ENST00000376588.3	+	5	525	c.457G>A	c.(457-459)Gca>Aca	p.A153T	PSAT1_ENST00000347159.2_Missense_Mutation_p.A153T	NM_058179.2	NP_478059.1	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1	153					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-serine biosynthetic process (GO:0006564)|pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	O-phospho-L-serine:2-oxoglutarate aminotransferase activity (GO:0004648)|pyridoxal phosphate binding (GO:0030170)	p.A153T(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						GTATTATTGCGCAAATGAGAC	0.463																																					Colon(34;187 791 10662 18313 37609)	ENST00000376588.3																			1	Substitution - Missense(1)	p.A153T(1)	urinary_tract(1)	breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						c.(457-459)Gca>Aca		phosphoserine aminotransferase 1	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)						334.0	308.0	317.0					9																	80921289		2203	4300	6503	SO:0001583	missense	29968				L-serine biosynthetic process|pyridoxine biosynthetic process		O-phospho-L-serine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding	g.chr9:80921289G>A	BC004863	CCDS6659.1, CCDS6660.1	9q21.2	2008-08-11			ENSG00000135069	ENSG00000135069			19129	protein-coding gene	gene with protein product		610936				12633500, 3651428	Standard	NM_058179		Approved	PSA	uc004ala.3	Q9Y617	OTTHUMG00000020066	ENST00000376588.3:c.457G>A	9.37:g.80921289G>A	ENSP00000365773:p.Ala153Thr					PSAT1_ENST00000347159.2_Missense_Mutation_p.A153T	p.A153T	NM_058179.2	NP_478059.1	Q9Y617	SERC_HUMAN			5	525	+			153					Q5T7G5|Q5T7G6|Q96AW2|Q9BQ12	Missense_Mutation	SNP	ENST00000376588.3	37	c.457G>A	CCDS6660.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.551918	0.27739	.	.	ENSG00000135069	ENST00000347159;ENST00000376588	T;T	0.62941	-0.01;-0.01	5.85	4.01	0.46588	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.261328	0.43747	D	0.000534	T	0.37598	0.1009	N	0.12746	0.255	0.48236	D	0.999615	P;B	0.37864	0.61;0.076	B;B	0.28139	0.086;0.034	T	0.16305	-1.0407	10	0.27785	T	0.31	-6.2508	11.7802	0.52010	0.0661:0.1237:0.8102:0.0	.	153;153	Q9Y617-2;Q9Y617	.;SERC_HUMAN	T	153	ENSP00000317606:A153T;ENSP00000365773:A153T	ENSP00000317606:A153T	A	+	1	0	PSAT1	80111109	1.000000	0.71417	0.699000	0.30290	0.814000	0.46013	5.862000	0.69560	0.820000	0.34516	0.655000	0.94253	GCA		0.463	PSAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052777.1	NM_021154		5	448	0	0	0	1	0	5	448				
PTPRJ	5795	broad.mit.edu	37	11	48134355	48134355	+	Missense_Mutation	SNP	A	A	G			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr11:48134355A>G	ENST00000418331.2	+	3	524	c.172A>G	c.(172-174)Ata>Gta	p.I58V	PTPRJ_ENST00000440289.2_Missense_Mutation_p.I58V|PTPRJ_ENST00000526550.1_3'UTR	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	58					contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GGAAAATGGCATAACGCAGAT	0.428																																						ENST00000418331.2																			0				breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						c.(172-174)Ata>Gta		protein tyrosine phosphatase, receptor type, J							98.0	93.0	95.0					11																	48134355		2201	4298	6499	SO:0001583	missense	5795				contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity	g.chr11:48134355A>G	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.172A>G	11.37:g.48134355A>G	ENSP00000400010:p.Ile58Val					PTPRJ_ENST00000440289.2_Missense_Mutation_p.I58V|PTPRJ_ENST00000526550.1_3'UTR	p.I58V	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN			3	524	+			58					Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	c.172A>G	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	A	0.003	-2.410017	0.00193	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289;ENST00000527952	T;T	0.36878	2.57;1.23	1.28	-2.55	0.06288	.	.	.	.	.	T	0.11110	0.0271	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26395	-1.0104	9	0.05436	T	0.98	.	0.1058	0.00052	0.2369:0.1931:0.2561:0.3139	.	58;58	Q12913;Q6P4H4	PTPRJ_HUMAN;.	V	58	ENSP00000400010:I58V;ENSP00000409733:I58V	ENSP00000278456:I58V	I	+	1	0	PTPRJ	48090931	0.089000	0.21612	0.001000	0.08648	0.007000	0.05969	0.082000	0.14847	-1.322000	0.02278	-1.216000	0.01612	ATA		0.428	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			38	48	0	0	0	1	0	38	48				
MTBP	27085	broad.mit.edu	37	8	121468835	121468835	+	Silent	SNP	A	A	G			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr8:121468835A>G	ENST00000305949.1	+	7	717	c.672A>G	c.(670-672)gtA>gtG	p.V224V		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	224					cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			CTAATGTTGTATCTTTAGAAG	0.308																																						ENST00000305949.1																			0				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30						c.(670-672)gtA>gtG		Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa							88.0	102.0	97.0					8																	121468835		2203	4291	6494	SO:0001819	synonymous_variant	27085				cell cycle arrest			g.chr8:121468835A>G		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"""MDM2 (mouse double minute 2)-binding protein, 104kD"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"""			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.672A>G	8.37:g.121468835A>G							p.V224V	NM_022045.3	NP_071328.2	Q96DY7	MTBP_HUMAN	STAD - Stomach adenocarcinoma(47;0.00503)		7	717	+	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		224					B4DUR5|Q9HA89	Silent	SNP	ENST00000305949.1	37	c.672A>G	CCDS6333.1																																																																																				0.308	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045		83	91	0	0	0	1	0	83	91				
ANKFY1	51479	broad.mit.edu	37	17	4088218	4088218	+	Missense_Mutation	SNP	C	C	T			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr17:4088218C>T	ENST00000341657.4	-	12	1629	c.1594G>A	c.(1594-1596)Gca>Aca	p.A532T	ANKFY1_ENST00000574367.1_Missense_Mutation_p.A532T|ANKFY1_ENST00000570535.1_Missense_Mutation_p.A574T|CYB5D2_ENST00000573984.1_Intron|Y_RNA_ENST00000516003.1_RNA|ANKFY1_ENST00000573722.1_5'UTR	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	532					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)	p.A532T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GTCAGGGATGCGGCCTCCTTT	0.622																																						ENST00000341657.4																			1	Substitution - Missense(1)	p.A532T(1)	large_intestine(1)	breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						c.(1594-1596)Gca>Aca		ankyrin repeat and FYVE domain containing 1							78.0	87.0	84.0					17																	4088218		2176	4268	6444	SO:0001583	missense	51479					endosome membrane	metal ion binding|protein binding	g.chr17:4088218C>T	AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"""Zinc fingers, FYVE domain containing"", ""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.1594G>A	17.37:g.4088218C>T	ENSP00000343362:p.Ala532Thr					ANKFY1_ENST00000570535.1_Missense_Mutation_p.A574T|ANKFY1_ENST00000574367.1_Missense_Mutation_p.A532T|ANKFY1_ENST00000573722.1_5'UTR|CYB5D2_ENST00000573984.1_Intron	p.A532T	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN			12	1629	-			532					A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	37	c.1594G>A		.	.	.	.	.	.	.	.	.	.	C	1.594	-0.528246	0.04112	.	.	ENSG00000185722	ENST00000341657;ENST00000535427	T	0.49139	0.79	5.12	-1.28	0.09318	Ankyrin repeat-containing domain (2);	0.723299	0.14266	N	0.330497	T	0.31670	0.0804	L	0.54908	1.71	0.19945	N	0.999944	B;B;B;B	0.15141	0.001;0.012;0.001;0.0	B;B;B;B	0.14023	0.01;0.004;0.001;0.0	T	0.24621	-1.0155	10	0.14252	T	0.57	3.0E-4	2.0699	0.03611	0.1066:0.2435:0.3195:0.3305	.	473;532;532;574	F5H754;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;ANFY1_HUMAN;.;.	T	532;473	ENSP00000343362:A532T	ENSP00000343362:A532T	A	-	1	0	ANKFY1	4034967	0.000000	0.05858	0.000000	0.03702	0.151000	0.21798	-0.156000	0.10100	-0.360000	0.08138	0.655000	0.94253	GCA		0.622	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		3	61	0	0	0	1	0	3	61				
PTPN4	5775	broad.mit.edu	37	2	120690023	120690023	+	Missense_Mutation	SNP	G	G	A	rs532212706	byFrequency	TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr2:120690023G>A	ENST00000263708.2	+	14	1865	c.1094G>A	c.(1093-1095)cGg>cAg	p.R365Q	PTPN4_ENST00000544261.1_5'UTR	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	365					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	CCCTTGGCACGGAAATTAATG	0.353													G|||	5	0.000998403	0.0	0.0	5008	,	,		16955	0.0		0.0	False		,,,				2504	0.0051					ENST00000263708.2																			0				endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30						c.(1093-1095)cGg>cAg		protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	Alendronate(DB00630)						59.0	55.0	56.0					2																	120690023		2203	4300	6503	SO:0001583	missense	5775					cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity	g.chr2:120690023G>A		CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.1094G>A	2.37:g.120690023G>A	ENSP00000263708:p.Arg365Gln					PTPN4_ENST00000544261.1_5'UTR	p.R365Q	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN			14	1865	+			365					B2RBV8|Q9UDA7	Missense_Mutation	SNP	ENST00000263708.2	37	c.1094G>A	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.429199	0.83776	.	.	ENSG00000088179	ENST00000263708	T	0.72942	-0.7	5.1	4.22	0.49857	.	0.000000	0.85682	D	0.000000	D	0.84192	0.5418	M	0.79693	2.465	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	D	0.86202	0.1619	10	0.54805	T	0.06	.	16.0218	0.80503	0.0:0.1345:0.8655:0.0	.	365	P29074	PTN4_HUMAN	Q	365	ENSP00000263708:R365Q	ENSP00000263708:R365Q	R	+	2	0	PTPN4	120406493	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.675000	0.61619	1.267000	0.44247	0.563000	0.77884	CGG		0.353	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			17	20	0	0	0	1	0	17	20				
H3F3A	3020	broad.mit.edu	37	1	226252135	226252135	+	Missense_Mutation	SNP	A	A	T			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr1:226252135A>T	ENST00000366813.1	+	1	458	c.83A>T	c.(82-84)aAg>aTg	p.K28M	H3F3A_ENST00000366814.3_Missense_Mutation_p.K28M|RP11-396C23.4_ENST00000609423.1_RNA|H3F3A_ENST00000366816.1_Missense_Mutation_p.K28M|H3F3A_ENST00000366815.3_Missense_Mutation_p.K28M			P84243	H33_HUMAN	H3 histone, family 3A	28					blood coagulation (GO:0007596)|brain development (GO:0007420)|DNA replication-independent nucleosome assembly (GO:0006336)|positive regulation of cell growth (GO:0030307)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nuclear nucleosome (GO:0000788)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	nucleosomal DNA binding (GO:0031492)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)	p.K28M(79)		central_nervous_system(116)|endometrium(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	123	Breast(184;0.179)			GBM - Glioblastoma multiforme(131;0.203)		GCCGCTCGCAAGAGTGCGCCC	0.483			Mis		glioma						OREG0014293	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000366814.3				Dom	yes		1	1q42.12	3020	Mis	"""H3 histone, family 3A"""			O			glioma		79	Substitution - Missense(79)	p.K28M(79)	central_nervous_system(79)	central_nervous_system(116)|endometrium(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	123						c.(82-84)aAg>aTg		H3 histone, family 3A							27.0	29.0	28.0					1																	226252135		2200	4298	6498	SO:0001583	missense	3020							g.chr1:226252135A>T	BC029405	CCDS1550.1	1q42.12	2011-01-27			ENSG00000163041	ENSG00000163041		"""Histones / Replication-independent"""	4764	protein-coding gene	gene with protein product		601128		H3F3		3031613	Standard	NM_002107		Approved	H3.3A	uc001hpw.3	P84243	OTTHUMG00000037507	ENST00000366813.1:c.83A>T	1.37:g.226252135A>T	ENSP00000355778:p.Lys28Met		OREG0014293	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2311	H3F3A_ENST00000366813.1_Missense_Mutation_p.K28M|H3F3A_ENST00000366816.1_Missense_Mutation_p.K28M|H3F3A_ENST00000366815.3_Missense_Mutation_p.K28M	p.K28M						GBM - Glioblastoma multiforme(131;0.203)	2	204	+	Breast(184;0.179)							P06351|P33155|Q5VV55|Q5VV56|Q66I33|Q9V3W4	Missense_Mutation	SNP	ENST00000366813.1	37	c.83A>T	CCDS1550.1	.	.	.	.	.	.	.	.	.	.	A	15.18	2.756773	0.49362	.	.	ENSG00000163041	ENST00000366816;ENST00000366815;ENST00000366814;ENST00000366813	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	4.32	4.32	0.51571	Histone-fold (2);	0.000000	0.85682	D	0.000000	T	0.68201	0.2975	.	.	.	0.58432	D	0.999999	D;P	0.89917	1.0;0.899	D;P	0.83275	0.996;0.449	T	0.73490	-0.3966	9	0.87932	D	0	.	13.4389	0.61101	1.0:0.0:0.0:0.0	.	28;28	B4DEB1;P84243	.;H33_HUMAN	M	28	ENSP00000355781:K28M;ENSP00000355780:K28M;ENSP00000355779:K28M;ENSP00000355778:K28M	ENSP00000355778:K28M	K	+	2	0	H3F3A	224318758	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.093000	0.94163	1.712000	0.51347	0.533000	0.62120	AAG		0.483	H3F3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091324.1	NM_002107		19	22	0	0	0	1	0	19	22				
PFKFB4	5210	broad.mit.edu	37	3	48594202	48594202	+	Silent	SNP	G	G	A			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr3:48594202G>A	ENST00000232375.3	-	1	121	c.9C>T	c.(7-9)tcC>tcT	p.S3S	PFKFB4_ENST00000541519.1_5'UTR|PFKFB4_ENST00000545984.1_Silent_p.S3S|PFKFB4_ENST00000383734.2_Silent_p.S3S|PFKFB4_ENST00000490115.1_5'UTR|PFKFB4_ENST00000536104.1_Intron|PFKFB4_ENST00000416568.1_Silent_p.S3S	NM_004567.2	NP_004558.1	Q16877	F264_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	3	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		ATTCCCGTGGGGACGCCATCC	0.706																																						ENST00000232375.3																			0				breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|urinary_tract(1)	14						c.(7-9)tcC>tcT		6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4							43.0	42.0	42.0					3																	48594202		2203	4300	6503	SO:0001819	synonymous_variant	5210				fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity	g.chr3:48594202G>A	BC010269	CCDS2771.1	3p22-p21	2004-03-02			ENSG00000114268	ENSG00000114268			8875	protein-coding gene	gene with protein product		605320				8830046, 10095107	Standard	NM_004567		Approved		uc003ctv.3	Q16877	OTTHUMG00000133528	ENST00000232375.3:c.9C>T	3.37:g.48594202G>A						PFKFB4_ENST00000545984.1_Silent_p.S3S|PFKFB4_ENST00000541519.1_5'UTR|PFKFB4_ENST00000490115.1_5'UTR|PFKFB4_ENST00000536104.1_Intron|PFKFB4_ENST00000416568.1_Silent_p.S3S|PFKFB4_ENST00000383734.2_Silent_p.S3S	p.S3S	NM_004567.2	NP_004558.1	Q16877	F264_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)	1	121	-			3			6-phosphofructo-2-kinase.		Q5S3G5|Q5XLC2|Q64EX5	Silent	SNP	ENST00000232375.3	37	c.9C>T	CCDS2771.1																																																																																				0.706	PFKFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257503.2	NM_004567		12	39	0	0	0	1	0	12	39				
ADAMTS2	9509	broad.mit.edu	37	5	178581188	178581188	+	Frame_Shift_Del	DEL	C	C	-			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr5:178581188delC	ENST00000251582.7	-	8	1345	c.1244delG	c.(1243-1245)ggcfs	p.G415fs	ADAMTS2_ENST00000274609.5_Frame_Shift_Del_p.G415fs	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	415	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GTGCTCCATGCCCAGCCTGCG	0.697																																						ENST00000251582.7																			0				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72						c.(1243-1245)gcfs		ADAM metallopeptidase with thrombospondin type 1 motif, 2							11.0	11.0	11.0					5																	178581188		2186	4255	6441	SO:0001589	frameshift_variant	9509				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding	g.chr5:178581188delC	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.1244delG	5.37:g.178581188delC	ENSP00000251582:p.Gly415fs					ADAMTS2_ENST00000274609.5_Frame_Shift_Del_p.G415fs	p.G415fs	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)	8	1345	-	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	415			Peptidase M12B.			Frame_Shift_Del	DEL	ENST00000251582.7	37	c.1244delG	CCDS4444.1																																																																																				0.697	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		2	4						2	4	---	---	---	---
PTCHD3P1	387647	broad.mit.edu	37	10	29699336	29699337	+	RNA	INS	-	-	T			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr10:29699336_29699337insT	ENST00000427063.2	+	0	87				PTCHD3P1_ENST00000455774.1_RNA|PTCHD3P1_ENST00000445521.1_RNA|PTCHD3P1_ENST00000430295.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000609413.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000438202.1_RNA|PTCHD3P1_ENST00000608994.1_RNA|PTCHD3P1_ENST00000537908.1_RNA|PTCHD3P1_ENST00000446807.1_RNA	NR_003930.1				patched domain containing 3 pseudogene 1																		GTGTCTTTTCATTTTTTATTTT	0.366																																						ENST00000427063.2																			0																																																			0							g.chr10:29699336_29699337insT			10p11.23	2014-08-07			ENSG00000274985	ENSG00000224597			44945	pseudogene	pseudogene							Standard	NG_034006		Approved		uc001iuq.2		OTTHUMG00000187781		10.37:g.29699342_29699342dupT						PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000430295.1_RNA|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000537908.1_RNA|PTCHD3P1_ENST00000438202.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|PTCHD3P1_ENST00000445521.1_RNA		NR_003930.1						0	87	+									RNA	INS	ENST00000427063.2	37																																																																																						0.366	PTCHD3P1-003	KNOWN	basic	antisense	antisense	OTTHUMT00000047385.1	NG_034006		2	4						2	4	---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95696016	95696016	+	Frame_Shift_Del	DEL	T	T	-			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr13:95696016delT	ENST00000376887.4	-	29	3769	c.3655delA	c.(3655-3657)atcfs	p.I1219fs	ABCC4_ENST00000412704.1_Frame_Shift_Del_p.I1172fs	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	1219	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	TTCTCCCGGATTTTTTTTTGT	0.378																																						ENST00000376887.4																			0				breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						c.(3655-3657)tcfs		ATP-binding cassette, sub-family C (CFTR/MRP), member 4	Cefazolin(DB01327)						105.0	104.0	104.0					13																	95696016		2203	4300	6503	SO:0001589	frameshift_variant	10257				platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity	g.chr13:95696016delT	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"""ATP binding cassette transporters / subfamily C"""	55	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter (ABC superfamily)"", ""bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)"", ""multidrug resistance-associated protein 4"", ""multispecific organic anion transporter B"""	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.3655delA	13.37:g.95696016delT	ENSP00000366084:p.Ile1219fs					ABCC4_ENST00000412704.1_Frame_Shift_Del_p.I1172fs	p.I1219fs	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN			29	3769	-	all_neural(89;0.0878)|Medulloblastoma(90;0.163)		1219			ABC transporter 2.		A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Frame_Shift_Del	DEL	ENST00000376887.4	37	c.3655delA	CCDS9474.1																																																																																				0.378	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845		7	105						7	105	---	---	---	---
NF1	4763	broad.mit.edu	37	17	29508796	29508797	+	Frame_Shift_Ins	INS	-	-	A			TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr17:29508796_29508797insA	ENST00000358273.4	+	7	1106_1107	c.723_724insA	c.(724-726)atgfs	p.M242fs	NF1_ENST00000431387.4_Frame_Shift_Ins_p.M242fs|NF1_ENST00000356175.3_Frame_Shift_Ins_p.M242fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	242					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CACAGACTGATATGGCTGGTAA	0.317			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												ENST00000358273.4			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	"""D, Mis, N, F, S, O"""	neurofibromatosis type 1 gene			O		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""	NF1/ACCN1(2)	12	Whole gene deletion(8)|Unknown(4)	p.0?(8)|p.?(4)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599	GRCh37	CI000104	NF1	I		c.(721-726)gatggcfs		neurofibromin 1																																				SO:0001589	frameshift_variant	4763	Neurofibromatosis, type 1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	g.chr17:29508796_29508797insA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.724dupA	17.37:g.29508797_29508797dupA	ENSP00000351015:p.Met242fs	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_ENST00000356175.3_Frame_Shift_Ins_p.DG241fs|NF1_ENST00000431387.4_Frame_Shift_Ins_p.DG241fs	p.DG241fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	7	1106_1107	+		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)	241					O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Ins	INS	ENST00000358273.4	37	c.723_724insA	CCDS42292.1																																																																																				0.317	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		20	70						20	70	---	---	---	---
ROCK1P1	727758	broad.mit.edu	37	18	112402	112405	+	RNA	DEL	AACC	AACC	-	rs113232824|rs111811281|rs11080396		TCGA-TM-A84C-01A-11D-A36O-08	TCGA-TM-A84C-12A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57d62c96-bc63-4121-b4ca-6162e23ed326	9a280df1-89bd-4b0b-8cc3-185457f517bc	g.chr18:112402_112405delAACC	ENST00000608049.1	+	0	389					NR_033770.1				Rho-associated, coiled-coil containing protein kinase 1 pseudogene 1																		CCCTGCCCCGAACCACCCGACCCC	0.711																																						ENST00000576266.1																			0																																																			0							g.chr18:112402_112405delAACC			18p11.32	2012-10-04			ENSG00000263006	ENSG00000263006			37832	pseudogene	pseudogene							Standard	NR_033770		Approved		uc002kke.3		OTTHUMG00000177913		18.37:g.112402_112405delAACC														0	36_39	+									RNA	DEL	ENST00000608049.1	37																																																																																						0.711	ROCK1P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472417.1			6	8						6	8	---	---	---	---
