#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
FAM86EP	348926	broad.mit.edu	37	4	3952899	3952899	+	RNA	SNP	A	A	T	rs17410906		TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr4:3952899A>T	ENST00000313946.8	-	0	155				AC226119.5_ENST00000281228.8_RNA					family with sequence similarity 86, member E, pseudogene																		AGCACCGGGCATACTTGACTG	0.557																																						ENST00000281228.8																			0																																																			0							g.chr4:3952899A>T			4p16.3	2011-07-01			ENSG00000251669	ENSG00000251669			28017	pseudogene	pseudogene						12477932	Standard	NR_024253		Approved		uc011bvu.2		OTTHUMG00000159867		4.37:g.3952899A>T						FAM86EP_ENST00000313946.8_RNA								0	208	-									RNA	SNP	ENST00000313946.8	37																																																																																						0.557	FAM86EP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000357822.1			4	66	0	0	0	1	0	4	66				
GTF2E1	2960	broad.mit.edu	37	3	120489597	120489597	+	Silent	SNP	C	C	T			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr3:120489597C>T	ENST00000283875.5	+	3	564	c.471C>T	c.(469-471)tgC>tgT	p.C157C		NM_005513.2	NP_005504.2	P29083	T2EA_HUMAN	general transcription factor IIE, polypeptide 1, alpha 56kDa	157					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)	22				GBM - Glioblastoma multiforme(114;0.159)		GTACTTTTTGCCATACAGAGG	0.418																																						ENST00000283875.5																			0				NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)	22						c.(469-471)tgC>tgT		general transcription factor IIE, polypeptide 1, alpha 56kDa							119.0	120.0	120.0					3																	120489597		2203	4300	6503	SO:0001819	synonymous_variant	2960				interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding|zinc ion binding	g.chr3:120489597C>T	S67859	CCDS3002.1	3q21-q24	2010-03-23	2002-08-29		ENSG00000153767	ENSG00000153767		"""General transcription factors"""	4650	protein-coding gene	gene with protein product		189962	"""general transcription factor IIE, polypeptide 1 (alpha subunit, 56kD)"""			1454543, 8162052	Standard	NM_005513		Approved	TFIIE-A, FE	uc003edz.4	P29083	OTTHUMG00000159667	ENST00000283875.5:c.471C>T	3.37:g.120489597C>T							p.C157C	NM_005513.2	NP_005504.2	P29083	T2EA_HUMAN		GBM - Glioblastoma multiforme(114;0.159)	3	564	+			157					Q16103	Silent	SNP	ENST00000283875.5	37	c.471C>T	CCDS3002.1																																																																																				0.418	GTF2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356770.1	NM_005513		4	128	0	0	0	1	0	4	128				
LINC00969	440993	broad.mit.edu	37	3	195400799	195400799	+	lincRNA	SNP	G	G	A	rs7635172		TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr3:195400799G>A	ENST00000445430.1	+	0	1395									long intergenic non-protein coding RNA 969																		CAAACTCGCTGTTGGACCTGG	0.597																																						ENST00000445430.1																			0																																																			0							g.chr3:195400799G>A	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195400799G>A														0	1395	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.597	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			3	24	0	0	0	1	0	3	24				
NUPL2	11097	broad.mit.edu	37	7	23224892	23224892	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr7:23224892G>A	ENST00000258742.5	+	2	584	c.325G>A	c.(325-327)Gag>Aag	p.E109K	NUPL2_ENST00000410002.3_Missense_Mutation_p.E109K|AC005082.1_ENST00000366347.4_Intron|NUPL2_ENST00000487595.1_3'UTR	NM_007342.2	NP_031368.1	O15504	NUPL2_HUMAN	nucleoporin like 2	109	Interaction with HIV-1 Vpr.				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 export from nucleus (GO:0006611)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nuclear export signal receptor activity (GO:0005049)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TAGTCCTGATGAGCAGAAAGA	0.353																																						ENST00000258742.5																			0				breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						c.(325-327)Gag>Aag		nucleoporin like 2							82.0	86.0	85.0					7																	23224892		2203	4300	6503	SO:0001583	missense	11097				carbohydrate metabolic process|glucose transport|mRNA transport|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nuclear pore	nuclear export signal receptor activity|nucleic acid binding|zinc ion binding	g.chr7:23224892G>A	U97198	CCDS5379.1	7p15	2003-08-07			ENSG00000136243	ENSG00000136243			17010	protein-coding gene	gene with protein product	"""nucleoporin-like protein 1"""					10358091, 9450185	Standard	NM_007342		Approved	NLP_1, CG1, hCG1, H_RG271G13.9	uc003svu.3	O15504	OTTHUMG00000096955	ENST00000258742.5:c.325G>A	7.37:g.23224892G>A	ENSP00000258742:p.Glu109Lys					NUPL2_ENST00000410002.3_Missense_Mutation_p.E109K|AC005082.1_ENST00000366347.4_Intron|NUPL2_ENST00000487595.1_3'UTR	p.E109K	NM_007342.2	NP_031368.1	O15504	NUPL2_HUMAN			2	584	+			109			Interaction with HIV-1 Vpr.		A4D143|B4DP42|Q49AE7|Q9BS49	Missense_Mutation	SNP	ENST00000258742.5	37	c.325G>A	CCDS5379.1	.	.	.	.	.	.	.	.	.	.	G	9.683	1.149729	0.21288	.	.	ENSG00000136243	ENST00000258742;ENST00000410002;ENST00000413919	T;T;T	0.41758	0.99;0.99;0.99	5.97	5.08	0.68730	.	0.951386	0.08868	N	0.881940	T	0.36220	0.0959	L	0.40543	1.245	0.25302	N	0.989275	B	0.22003	0.063	B	0.18561	0.022	T	0.18461	-1.0336	10	0.10636	T	0.68	-0.2654	15.2645	0.73651	0.069:0.0:0.931:0.0	.	109	O15504	NUPL2_HUMAN	K	109	ENSP00000258742:E109K;ENSP00000387330:E109K;ENSP00000401475:E109K	ENSP00000258742:E109K	E	+	1	0	NUPL2	23191417	0.821000	0.29204	0.332000	0.25469	0.372000	0.29890	3.168000	0.50801	2.832000	0.97577	0.585000	0.79938	GAG		0.353	NUPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214017.2	NM_007342		4	83	0	0	0	1	0	4	83				
CUL1	8454	broad.mit.edu	37	7	148427233	148427233	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr7:148427233C>T	ENST00000325222.4	+	2	298	c.19C>T	c.(19-21)Cag>Tag	p.Q7*	CUL1_ENST00000602748.1_Nonsense_Mutation_p.Q7*|AC005229.1_ENST00000578165.1_RNA|CUL1_ENST00000409469.1_Nonsense_Mutation_p.Q7*	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	7					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			AACCCGGAGCCAGAACCCCCA	0.527																																						ENST00000325222.4																			0				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40						c.(19-21)Cag>Tag		cullin 1							107.0	104.0	105.0					7																	148427233		2203	4300	6503	SO:0001587	stop_gained	8454				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding	g.chr7:148427233C>T	U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.19C>T	7.37:g.148427233C>T	ENSP00000326804:p.Gln7*					CUL1_ENST00000602748.1_Nonsense_Mutation_p.Q7*|CUL1_ENST00000409469.1_Nonsense_Mutation_p.Q7*	p.Q7*	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00291)		2	298	+	Melanoma(164;0.15)		7					D3DWG3|O60719|Q08AL6|Q8IYW1	Nonsense_Mutation	SNP	ENST00000325222.4	37	c.19C>T	CCDS34772.1	.	.	.	.	.	.	.	.	.	.	C	41	8.537347	0.98854	.	.	ENSG00000055130	ENST00000409469;ENST00000325222;ENST00000433865	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	-3.7713	20.0155	0.97477	0.0:1.0:0.0:0.0	.	.	.	.	X	7	.	ENSP00000326804:Q7X	Q	+	1	0	CUL1	148058166	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.349000	0.79376	2.742000	0.94016	0.591000	0.81541	CAG		0.527	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		32	74	0	0	0	1	0	32	74				
CUL1	8454	broad.mit.edu	37	7	148427298	148427298	+	Missense_Mutation	SNP	C	C	G			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr7:148427298C>G	ENST00000325222.4	+	2	363	c.84C>G	c.(82-84)atC>atG	p.I28M	CUL1_ENST00000602748.1_Missense_Mutation_p.I28M|AC005229.1_ENST00000578165.1_RNA|CUL1_ENST00000409469.1_Missense_Mutation_p.I28M	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	28					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			GAGCCGGCATCCAGCAGGTGT	0.547																																						ENST00000325222.4																			0				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40						c.(82-84)atC>atG		cullin 1							103.0	90.0	94.0					7																	148427298		2203	4300	6503	SO:0001583	missense	8454				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding	g.chr7:148427298C>G	U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.84C>G	7.37:g.148427298C>G	ENSP00000326804:p.Ile28Met					CUL1_ENST00000602748.1_Missense_Mutation_p.I28M|CUL1_ENST00000409469.1_Missense_Mutation_p.I28M	p.I28M	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00291)		2	363	+	Melanoma(164;0.15)		28					D3DWG3|O60719|Q08AL6|Q8IYW1	Missense_Mutation	SNP	ENST00000325222.4	37	c.84C>G	CCDS34772.1	.	.	.	.	.	.	.	.	.	.	C	18.71	3.681871	0.68042	.	.	ENSG00000055130	ENST00000409469;ENST00000325222;ENST00000433865	T;T	0.80033	-1.33;-1.33	5.79	1.87	0.25490	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.82084	0.4960	M	0.68593	2.085	0.80722	D	1	D	0.53745	0.962	P	0.55615	0.78	T	0.79065	-0.1956	10	0.62326	D	0.03	-25.454	5.4826	0.16731	0.1315:0.5367:0.0:0.3318	.	28	Q13616	CUL1_HUMAN	M	28	ENSP00000387160:I28M;ENSP00000326804:I28M	ENSP00000326804:I28M	I	+	3	3	CUL1	148058231	0.995000	0.38212	1.000000	0.80357	0.964000	0.63967	0.376000	0.20535	0.347000	0.23924	-1.083000	0.02208	ATC		0.547	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		29	67	0	0	0	1	0	29	67				
SRCAP	10847	broad.mit.edu	37	16	30735845	30735845	+	Silent	SNP	C	C	G			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr16:30735845C>G	ENST00000262518.4	+	25	5485	c.5100C>G	c.(5098-5100)ctC>ctG	p.L1700L	SRCAP_ENST00000395059.2_Silent_p.L1638L|SRCAP_ENST00000344771.4_Silent_p.L1542L	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1700	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CTCAGACACTCTCTTTGGGAA	0.572																																						ENST00000262518.4																			0				NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136						c.(5098-5100)ctC>ctG		Snf2-related CREBBP activator protein							109.0	117.0	114.0					16																	30735845		2197	4300	6497	SO:0001819	synonymous_variant	10847				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity	g.chr16:30735845C>G	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.5100C>G	16.37:g.30735845C>G						SRCAP_ENST00000395059.2_Silent_p.L1638L|SRCAP_ENST00000344771.4_Silent_p.L1542L	p.L1700L	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Colorectal(24;0.198)		25	5485	+			1700			Pro-rich.		B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	37	c.5100C>G	CCDS10689.2																																																																																				0.572	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		4	164	0	0	0	1	0	4	164				
FAM86EP	348926	broad.mit.edu	37	4	3952901	3952901	+	RNA	SNP	A	A	T			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr4:3952901A>T	ENST00000313946.8	-	0	155				AC226119.5_ENST00000281228.8_RNA					family with sequence similarity 86, member E, pseudogene																		CACCGGGCATACTTGACTGAC	0.552																																						ENST00000281228.8																			0																																																			0							g.chr4:3952901A>T			4p16.3	2011-07-01			ENSG00000251669	ENSG00000251669			28017	pseudogene	pseudogene						12477932	Standard	NR_024253		Approved		uc011bvu.2		OTTHUMG00000159867		4.37:g.3952901A>T						FAM86EP_ENST00000313946.8_RNA								0	206	-									RNA	SNP	ENST00000313946.8	37																																																																																						0.552	FAM86EP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000357822.1			4	66	0	0	0	1	0	4	66				
CLCN2	1181	broad.mit.edu	37	3	184076767	184076767	+	Silent	SNP	G	G	A			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr3:184076767G>A	ENST00000265593.4	-	2	387	c.216C>T	c.(214-216)tgC>tgT	p.C72C	CLCN2_ENST00000457512.1_Silent_p.C72C|POLR2H_ENST00000456318.1_5'Flank|EIF2B5_ENST00000444495.1_Intron|POLR2H_ENST00000438240.1_5'Flank|CLCN2_ENST00000434054.2_Silent_p.C72C|CLCN2_ENST00000344937.7_Silent_p.C72C|CLCN2_ENST00000475279.1_5'Flank|CLCN2_ENST00000423355.2_5'UTR	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	72					cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	TCTCACCGCGGCATCGGGCGC	0.652																																						ENST00000265593.4																			0				breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27						c.(214-216)tgC>tgT		chloride channel, voltage-sensitive 2	Lubiprostone(DB01046)						41.0	47.0	45.0					3																	184076767		2203	4299	6502	SO:0001819	synonymous_variant	1181					chloride channel complex	voltage-gated chloride channel activity	g.chr3:184076767G>A	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"""Ion channels / Chloride channels : Voltage-sensitive"""	2020	protein-coding gene	gene with protein product		600570	"""chloride channel 2"""			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.216C>T	3.37:g.184076767G>A						CLCN2_ENST00000344937.7_Silent_p.C72C|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000434054.2_Silent_p.C72C|CLCN2_ENST00000423355.2_5'UTR|CLCN2_ENST00000457512.1_Silent_p.C72C	p.C72C	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		2	387	-	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		72					B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Silent	SNP	ENST00000265593.4	37	c.216C>T	CCDS3263.1																																																																																				0.652	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			4	95	0	0	0	1	0	4	95				
BCL11B	64919	broad.mit.edu	37	14	99641455	99641455	+	Missense_Mutation	SNP	A	A	C			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr14:99641455A>C	ENST00000357195.3	-	4	1727	c.1718T>G	c.(1717-1719)gTg>gGg	p.V573G	BCL11B_ENST00000345514.2_Missense_Mutation_p.V502G|BCL11B_ENST00000443726.2_Missense_Mutation_p.V379G	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	573	Gly-rich.				alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		gaccccgggcACCCCACCACC	0.711			T	TLX3	T-ALL																																	ENST00000345514.2				Dom	yes		14	14q32.1	64919	T	B-cell CLL/lymphoma 11B  (CTIP2)			L	TLX3		T-ALL		0				NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34						c.(1504-1506)gTg>gGg		B-cell CLL/lymphoma 11B (zinc finger protein)							5.0	8.0	7.0					14																	99641455		2053	3959	6012	SO:0001583	missense	64919					nucleus	zinc ion binding	g.chr14:99641455A>C	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"""Zinc fingers, C2H2-type"""	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.1718T>G	14.37:g.99641455A>C	ENSP00000349723:p.Val573Gly					BCL11B_ENST00000357195.3_Missense_Mutation_p.V573G|BCL11B_ENST00000443726.2_Missense_Mutation_p.V379G	p.V502G	NM_022898.1	NP_075049.1	Q9C0K0	BC11B_HUMAN		COAD - Colon adenocarcinoma(157;0.103)	3	1771	-		Melanoma(154;0.0866)|all_epithelial(191;0.241)	573					Q9H162	Missense_Mutation	SNP	ENST00000357195.3	37	c.1505T>G	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	A	0.347	-0.946942	0.02304	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.11063	2.82;2.83;2.81	3.69	-1.74	0.08056	.	6.479460	0.00166	N	0.000002	T	0.04952	0.0133	N	0.08118	0	0.09310	N	1	B;B	0.31705	0.031;0.336	B;B	0.28232	0.007;0.087	T	0.18304	-1.0341	10	0.27082	T	0.32	.	2.2852	0.04124	0.5572:0.2104:0.0908:0.1416	.	502;573	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	G	573;502;379	ENSP00000349723:V573G;ENSP00000280435:V502G;ENSP00000387419:V379G	ENSP00000280435:V502G	V	-	2	0	BCL11B	98711208	0.238000	0.23825	0.021000	0.16686	0.430000	0.31655	0.922000	0.28734	-0.383000	0.07858	0.459000	0.35465	GTG		0.711	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		4	5	0	0	0	1	0	4	5				
SNRNP200	23020	broad.mit.edu	37	2	96950283	96950283	+	Missense_Mutation	SNP	T	T	C	rs560485569	byFrequency	TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr2:96950283T>C	ENST00000323853.5	-	31	4282	c.4205A>G	c.(4204-4206)aAc>aGc	p.N1402S	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1402	Helicase ATP-binding 2. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						CACCTTCTTGTTGAGCCTGTC	0.527													T|||	8	0.00159744	0.0	0.0	5008	,	,		20196	0.0		0.0	False		,,,				2504	0.0082					ENST00000323853.5																			0				breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						c.(4204-4206)aAc>aGc		small nuclear ribonucleoprotein 200kDa (U5)							164.0	135.0	145.0					2																	96950283		2203	4300	6503	SO:0001583	missense	23020					catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding	g.chr2:96950283T>C	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.4205A>G	2.37:g.96950283T>C	ENSP00000317123:p.Asn1402Ser					SNRNP200_ENST00000349783.5_Intron	p.N1402S	NM_014014.4	NP_054733.2	O75643	U520_HUMAN			31	4282	-			1402			Helicase ATP-binding 2.		O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	37	c.4205A>G	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.480158	0.44044	.	.	ENSG00000144028	ENST00000323853;ENST00000543553	T	0.36340	1.26	5.62	-1.2	0.09554	DEAD-like helicase (2);ATPase, AAA+ type, core (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.269700	0.41097	N	0.000946	T	0.24160	0.0585	L	0.40543	1.245	0.80722	D	1	B	0.09022	0.002	B	0.12156	0.007	T	0.02975	-1.1087	10	0.62326	D	0.03	-18.0298	6.2261	0.20708	0.1183:0.3779:0.0:0.5039	.	1402	O75643	U520_HUMAN	S	1402;36	ENSP00000317123:N1402S	ENSP00000317123:N1402S	N	-	2	0	SNRNP200	96314010	1.000000	0.71417	0.986000	0.45419	0.949000	0.60115	0.639000	0.24690	-0.434000	0.07275	-0.263000	0.10527	AAC		0.527	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		35	57	0	0	0	1	0	35	57				
LINC00969	440993	broad.mit.edu	37	3	195400795	195400795	+	lincRNA	SNP	C	C	T	rs7615357	byFrequency	TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr3:195400795C>T	ENST00000445430.1	+	0	1391									long intergenic non-protein coding RNA 969																		GGGGCAAACTCGCTGTTGGAC	0.592																																						ENST00000445430.1																			0																																																			0							g.chr3:195400795C>T	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195400795C>T														0	1391	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.592	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			3	24	0	0	0	1	0	3	24				
MAPKBP1	23005	broad.mit.edu	37	15	42115806	42115806	+	Missense_Mutation	SNP	C	C	T	rs149990798		TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr15:42115806C>T	ENST00000456763.2	+	30	3974	c.3778C>T	c.(3778-3780)Cgc>Tgc	p.R1260C	MAPKBP1_ENST00000514566.1_Intron|MAPKBP1_ENST00000457542.2_Missense_Mutation_p.R1254C|RP11-23P13.4_ENST00000512295.1_RNA|RP11-23P13.4_ENST00000510176.1_RNA|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.R1137C|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.R1093C	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	1260										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		CAAGATATCCCGCAGTATCTC	0.627																																						ENST00000457542.2																			0				breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56						c.(3760-3762)Cgc>Tgc		mitogen-activated protein kinase binding protein 1		C	CYS/ARG,CYS/ARG	1,4405		0,1,2202	68.0	64.0	65.0		3778,3760	6.0	1.0	15	dbSNP_134	65	0,8600		0,0,4300	no	missense,missense	MAPKBP1	NM_001128608.1,NM_014994.2	180,180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	1260/1515,1254/1509	42115806	1,13005	2203	4300	6503	SO:0001583	missense	23005							g.chr15:42115806C>T	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"""WD repeat domain containing"""	29536	protein-coding gene	gene with protein product			"""mitogen activated protein kinase binding protein 1"""			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.3778C>T	15.37:g.42115806C>T	ENSP00000393099:p.Arg1260Cys					MAPKBP1_ENST00000456763.2_Missense_Mutation_p.R1260C|MAPKBP1_ENST00000514566.1_Intron|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.R1093C|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.R1137C	p.R1254C	NM_014994.2	NP_055809.2	O60336	MABP1_HUMAN		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)	29	4046	+		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)	1260					A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	37	c.3760C>T	CCDS45239.1	.	.	.	.	.	.	.	.	.	.	.	22.6	4.305773	0.81247	2.27E-4	0.0	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000260357;ENST00000456763	T;T;T;T	0.65549	0.16;0.16;-0.16;0.2	5.98	5.98	0.97165	.	0.054914	0.64402	D	0.000001	T	0.70657	0.3249	L	0.34521	1.04	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.998;0.993	T	0.72327	-0.4327	10	0.87932	D	0	-17.467	14.7177	0.69284	0.1454:0.8546:0.0:0.0	.	1093;1137;1093;1260;1254	F8WC21;O60336-3;B4DYK7;O60336;O60336-6	.;.;.;MABP1_HUMAN;.	C	1254;1137;1093;1260	ENSP00000397570:R1254C;ENSP00000221214:R1137C;ENSP00000260357:R1093C;ENSP00000393099:R1260C	ENSP00000221214:R1137C	R	+	1	0	MAPKBP1	39903098	1.000000	0.71417	0.974000	0.42286	0.860000	0.49131	5.375000	0.66173	2.837000	0.97791	0.591000	0.81541	CGC		0.627	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		29	30	0	0	0	1	0	29	30				
PRSS3P2	154754	broad.mit.edu	37	7	142482229	142482229	+	RNA	SNP	T	T	A			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr7:142482229T>A	ENST00000603901.1	+	0	609					NR_001296.3		Q8NHM4	TRY6_HUMAN	protease, serine, 3 pseudogene 2						endothelial cell migration (GO:0043542)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.P203P(1)									CTGGTGGCCCTGTGGTCTGCA	0.493																																						ENST00000603901.1																			1	Substitution - coding silent(1)	p.P203P(1)	prostate(1)																																																0							g.chr7:142482229T>A			7q34	2012-03-06			ENSG00000250606	ENSG00000275896			43788	pseudogene	pseudogene	"""trypsinogen C"""						Standard	NR_001296		Approved	TRY6	uc011ksq.2	Q8NHM4	OTTHUMG00000158904		7.37:g.142482229T>A								NR_001296.3						0	609	+									RNA	SNP	ENST00000603901.1	37																																																																																						0.493	PRSS3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470000.1	NR_001296		4	61	0	0	0	1	0	4	61				
PRSS3P2	154754	broad.mit.edu	37	7	142482242	142482242	+	RNA	SNP	G	G	A			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr7:142482242G>A	ENST00000603901.1	+	0	622					NR_001296.3		Q8NHM4	TRY6_HUMAN	protease, serine, 3 pseudogene 2						endothelial cell migration (GO:0043542)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)										GGTCTGCAATGGACAGCTTCA	0.493																																						ENST00000603901.1																			0																																																			0							g.chr7:142482242G>A			7q34	2012-03-06			ENSG00000250606	ENSG00000275896			43788	pseudogene	pseudogene	"""trypsinogen C"""						Standard	NR_001296		Approved	TRY6	uc011ksq.2	Q8NHM4	OTTHUMG00000158904		7.37:g.142482242G>A								NR_001296.3						0	622	+									RNA	SNP	ENST00000603901.1	37																																																																																						0.493	PRSS3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470000.1	NR_001296		4	65	0	0	0	1	0	4	65				
MACF1	23499	broad.mit.edu	37	1	39799059	39799060	+	Frame_Shift_Ins	INS	-	-	G			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr1:39799059_39799060insG	ENST00000372915.3	+	36	6901_6902	c.6814_6815insG	c.(6814-6816)aggfs	p.R2272fs	MACF1_ENST00000476350.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000564288.1_Frame_Shift_Ins_p.R2267fs|MACF1_ENST00000567887.1_Frame_Shift_Ins_p.R2304fs|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000289893.4_Frame_Shift_Ins_p.R707fs|MACF1_ENST00000361689.2_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	2272					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AGATAGTGGCAGGGAAATTTTT	0.391																																						ENST00000564288.1																			0				breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203						c.(6799-6801)ggafs		microtubule-actin crosslinking factor 1																																				SO:0001589	frameshift_variant	23499				cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding	g.chr1:39799059_39799060insG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.6817dupG	1.37:g.39799062_39799062dupG	ENSP00000362006:p.Arg2272fs					MACF1_ENST00000567887.1_Frame_Shift_Ins_p.G2304fs|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000372915.3_Frame_Shift_Ins_p.G2272fs|MACF1_ENST00000476350.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000289893.4_Frame_Shift_Ins_p.G707fs|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000317713.7_Intron	p.G2267fs			Q9UPN3	MACF1_HUMAN	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		37	7576_7577	+	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	2272					B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Frame_Shift_Ins	INS	ENST00000372915.3	37	c.6799_6800insG																																																																																					0.391	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		15	71						15	71	---	---	---	---
HSPD1P6	645548	broad.mit.edu	37	3	36810381	36810381	+	RNA	DEL	T	T	-			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr3:36810381delT	ENST00000424886.1	-	0	405									heat shock 60kDa protein 1 (chaperonin) pseudogene 6																		GAGTGAGGCCttttttttttt	0.542																																						ENST00000424886.1																			0																																																			0							g.chr3:36810381delT			3p22.3	2010-06-25	2002-08-29	2008-09-22	ENSG00000230067	ENSG00000230067			5267	pseudogene	pseudogene			"""heat shock 60kD protein 1 (chaperonin) pseudogene 6"""	HSPDP6			Standard	NG_008828		Approved	HSPD1-6P			OTTHUMG00000155803		3.37:g.36810381delT														0	405	-									RNA	DEL	ENST00000424886.1	37																																																																																						0.542	HSPD1P6-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341724.1	XR_017400		2	4						2	4	---	---	---	---
LOC101243545	101243545	broad.mit.edu	37	3	161146872	161146873	+	lincRNA	DEL	AT	AT	-	rs139058677		TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr3:161146872_161146873delAT	ENST00000473595.1	+	0	1231				RP11-3P17.5_ENST00000602890.1_lincRNA	NR_102265.1																						TGGTGAAAAGATATATATATAT	0.342																																						ENST00000473595.1																			0																																																			0							g.chr3:161146872_161146873delAT																													3.37:g.161146882_161146883delAT								NR_102265.1						0	1231	+									RNA	DEL	ENST00000473595.1	37																																																																																						0.342	RP11-3P17.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000353185.1			6	12						6	12	---	---	---	---
POU4F2	5458	broad.mit.edu	37	4	147560457	147560458	+	In_Frame_Ins	INS	-	-	GGC	rs530695040|rs72269802|rs5862765		TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr4:147560457_147560458insGGC	ENST00000281321.3	+	1	413_414	c.165_166insGGC	c.(166-168)ggc>GGCggc	p.56_56G>GG	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	56	Poly-Gly.				axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					ACGCTggtggtggcggcggcgg	0.762																																						ENST00000281321.3																			0				NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33						c.(163-168)gggcgg>ggGGCgcgg		POU class 4 homeobox 2																																				SO:0001652	inframe_insertion	5458				estrogen receptor signaling pathway|MAPKKK cascade|negative regulation of transcription from RNA polymerase II promoter	nuclear speck	RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription	g.chr4:147560457_147560458insGGC	U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9219	protein-coding gene	gene with protein product		113725	"""POU domain, class 4, transcription factor 2"", ""POU domain class 4, transcription factor 2"""	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.196_198dupGGC	4.37:g.147560464_147560466dupGGC	ENSP00000281321:p.Gly68dup					AC093887.1_ENST00000584185.1_RNA	p.55_56GR>GAR	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN			1	413_414	+	all_hematologic(180;0.151)		55			Poly-Gly.		B1PJR6|B2RC84|Q13883|Q14987	In_Frame_Ins	INS	ENST00000281321.3	37	c.165_166insGGC	CCDS34074.1																																																																																				0.762	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		5	11						5	11	---	---	---	---
BTN2A2	10385	broad.mit.edu	37	6	26384091	26384093	+	In_Frame_Del	DEL	CCT	CCT	-	rs546542545		TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr6:26384091_26384093delCCT	ENST00000356709.4	+	2	153_155	c.42_44delCCT	c.(40-45)tccctc>tcc	p.L24del	BTN2A2_ENST00000352867.2_In_Frame_Del_p.L24del|BTN2A2_ENST00000469230.1_In_Frame_Del_p.L24del|BTN2A2_ENST00000416795.2_In_Frame_Del_p.L24del|BTN2A2_ENST00000432533.2_In_Frame_Del_p.L24del|BTN2A2_ENST00000482536.1_In_Frame_Del_p.L24del	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2	24					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cellular metabolic process (GO:0031324)|negative regulation of cytokine secretion (GO:0050710)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|large_intestine(5)|lung(13)	23						TGCCAGCCTCcctcctcctcctc	0.581																																						ENST00000356709.4																			0				breast(2)|endometrium(3)|large_intestine(5)|lung(13)	23						c.(40-45)tcc>tc		butyrophilin, subfamily 2, member A2																																				SO:0001651	inframe_deletion	10385				negative regulation of activated T cell proliferation|negative regulation of cellular metabolic process|negative regulation of cytokine secretion	integral to membrane		g.chr6:26384091_26384093delCCT	U90550	CCDS4606.1, CCDS4607.1, CCDS56401.1, CCDS56402.1, CCDS56403.1	6p22.1	2014-01-14			ENSG00000124508	ENSG00000124508		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1137	protein-coding gene	gene with protein product		613591				10354554, 9149941	Standard	NM_006995		Approved	BTF2, BT2.2, BTN2.2	uc003nhq.3	Q8WVV5	OTTHUMG00000014452	ENST00000356709.4:c.42_44delCCT	6.37:g.26384100_26384102delCCT	ENSP00000349143:p.Leu24del					BTN2A2_ENST00000352867.2_In_Frame_Del_p.SL14del|BTN2A2_ENST00000469230.1_In_Frame_Del_p.SL14del|BTN2A2_ENST00000416795.2_In_Frame_Del_p.SL14del|BTN2A2_ENST00000482536.1_In_Frame_Del_p.SL14del|BTN2A2_ENST00000432533.2_In_Frame_Del_p.SL14del	p.SL14del	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN			2	153_155	+			14					A6NM84|B4DE97|B4DQ01|E9PH07|O00480	In_Frame_Del	DEL	ENST00000356709.4	37	c.42_44delCCT	CCDS4606.1																																																																																				0.581	BTN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040117.1			8	127						8	127	---	---	---	---
STEAP2-AS1	100874100	broad.mit.edu	37	7	89748927	89748928	+	RNA	INS	-	-	C	rs58370593	byFrequency	TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr7:89748927_89748928insC	ENST00000478318.2	-	0	424				DPY19L2P4_ENST00000497063.1_RNA|RP5-1121E10.2_ENST00000471553.1_lincRNA					STEAP2 antisense RNA 1																		GGTGCGGGCCTCCCCCTTCCCC	0.639													?|CCCCC|CCCCCC|unsure	3349	0.66873	0.7171	0.621	5008	,	,		14308	0.8095		0.5199	False		,,,				2504	0.6452					ENST00000478318.2																			0																																																			0							g.chr7:89748927_89748928insC			7q21.13	2012-10-12	2012-08-15		ENSG00000227646	ENSG00000227646		"""Long non-coding RNAs"""	40820	non-coding RNA	RNA, long non-coding			"""STEAP2 antisense RNA 1 (non-protein coding)"""				Standard	NR_110029		Approved				OTTHUMG00000065036		7.37:g.89748932_89748932dupC						DPY19L2P4_ENST00000497063.1_RNA|RP5-1121E10.2_ENST00000471553.1_lincRNA								0	424	-									RNA	INS	ENST00000478318.2	37																																																																																						0.639	STEAP2-AS1-002	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000350909.2			4	6						4	6	---	---	---	---
TIMM23	100287932	broad.mit.edu	37	10	51623197	51623198	+	Frame_Shift_Ins	INS	-	-	C			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr10:51623197_51623198insC	ENST00000260867.4	-	1	140_141	c.17_18insG	c.(16-18)ggafs	p.G6fs	TIMM23_ENST00000374064.3_Frame_Shift_Ins_p.G6fs|TIMM23_ENST00000374065.3_Frame_Shift_Ins_p.G6fs	NM_006327.3	NP_006318.1	O14925	TIM23_HUMAN	translocase of inner mitochondrial membrane 23 homolog (yeast)	6					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			endometrium(1)|large_intestine(1)|pancreas(1)	3						TGTTGCCGCTTCCCCCGCCTCC	0.634																																						ENST00000260867.4																			0				endometrium(1)|large_intestine(1)|pancreas(1)	3						c.(16-18)gagfs		translocase of inner mitochondrial membrane 23 homolog (yeast)																																				SO:0001589	frameshift_variant	100287932				protein targeting to mitochondrion	integral to membrane|mitochondrial inner membrane presequence translocase complex|mitochondrial intermembrane space	P-P-bond-hydrolysis-driven protein transmembrane transporter activity|protein binding	g.chr10:51623197_51623198insC	AF030162	CCDS73091.1	10q11.21-q11.23	2010-03-17			ENSG00000138297				17312	protein-coding gene	gene with protein product		605034				10339406	Standard	NM_006327		Approved	TIM23	uc010qha.2	O14925	OTTHUMG00000018213	ENST00000260867.4:c.18dupG	10.37:g.51623202_51623202dupC	ENSP00000260867:p.Gly6fs					TIMM23_ENST00000374064.3_Frame_Shift_Ins_p.E6fs|TIMM23_ENST00000374065.3_Frame_Shift_Ins_p.E6fs	p.E6fs	NM_006327.3	NP_006318.1	O14925	TIM23_HUMAN			1	140_141	-			6					Q53FF8|Q5T1E6|Q6P5S5	Frame_Shift_Ins	INS	ENST00000260867.4	37	c.17_18insG	CCDS7238.1																																																																																				0.634	TIMM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048040.1	NM_006327.2		2	4						2	4	---	---	---	---
EP400	57634	broad.mit.edu	37	12	132547093	132547094	+	In_Frame_Ins	INS	-	-	CAG	rs10902490|rs113304321|rs528214697	byFrequency	TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr12:132547093_132547094insCAG	ENST00000333577.4	+	48	8398_8399	c.8289_8290insCAG	c.(8290-8292)cag>CAGcag	p.2764_2764Q>QQ	EP400_ENST00000330386.6_In_Frame_Ins_p.2647_2647Q>QQ|EP400_ENST00000389561.2_In_Frame_Ins_p.2728_2728Q>QQ|EP400_ENST00000389562.2_In_Frame_Ins_p.2727_2727Q>QQ|EP400_ENST00000332482.4_In_Frame_Ins_p.2691_2691Q>QQ			Q96L91	EP400_HUMAN	E1A binding protein p400	2764	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.Q2726Q(9)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcaacaacagcagcagca	0.564														1869	0.373203	0.3427	0.513	5008	,	,		15674	0.2391		0.4722	False		,,,				2504	0.3517					ENST00000333577.4																			9	Substitution - coding silent(9)	p.Q2726Q(9)	lung(3)|kidney(2)|endometrium(2)|central_nervous_system(2)	NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161						c.(8287-8292)caagca>caCAGagca		E1A binding protein p400																																				SO:0001652	inframe_insertion	57634				histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity	g.chr12:132547093_132547094insCAG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8329_8331dupCAG	12.37:g.132547100_132547102dupCAG	ENSP00000333602:p.Gln2784dup					EP400_ENST00000330386.6_In_Frame_Ins_p.2646_2646Q>HR|EP400_ENST00000332482.4_In_Frame_Ins_p.2690_2690Q>HR|EP400_ENST00000389562.2_In_Frame_Ins_p.2726_2726Q>HR|EP400_ENST00000389561.2_In_Frame_Ins_p.2727_2727Q>HR	p.2763_2763Q>HR			Q96L91	EP400_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)	48	8398_8399	+	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)	2763			Interaction with ZNF42 (By similarity).|Poly-Gln.		O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	In_Frame_Ins	INS	ENST00000333577.4	37	c.8289_8290insCAG																																																																																					0.564	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		21	46						21	46	---	---	---	---
GJA3	2700	broad.mit.edu	37	13	20716593	20716593	+	Frame_Shift_Del	DEL	G	G	-			TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr13:20716593delG	ENST00000241125.3	-	2	1011	c.835delC	c.(835-837)ctgfs	p.L279fs		NM_021954.3	NP_068773.2	Q9Y6H8	CXA3_HUMAN	gap junction protein, alpha 3, 46kDa	279					cell-cell signaling (GO:0007267)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)		GCCTGTCCCAGGGGCGCAGCG	0.761																																						ENST00000241125.3																			0				NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7						c.(835-837)tgfs		gap junction protein, alpha 3, 46kDa							5.0	6.0	6.0					13																	20716593		1987	3857	5844	SO:0001589	frameshift_variant	2700				cell-cell signaling|visual perception	connexon complex|integral to membrane		g.chr13:20716593delG	AF075290	CCDS9289.1	13q12.11	2008-02-05	2007-01-16		ENSG00000121743	ENSG00000121743		"""Ion channels / Gap junction proteins (connexins)"""	4277	protein-coding gene	gene with protein product	"""connexin 46"""	121015	"""gap junction protein, alpha 3, 46kD (connexin 46)"", ""gap junction protein, alpha 3, 46kDa (connexin 46)"""	CZP3		10205266, 7342922	Standard	NM_021954		Approved	CX46	uc001umx.1	Q9Y6H8	OTTHUMG00000016510	ENST00000241125.3:c.835delC	13.37:g.20716593delG	ENSP00000241125:p.Leu279fs						p.L279fs	NM_021954.3	NP_068773.2	Q9Y6H8	CXA3_HUMAN		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)	2	1011	-		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)	279					Q0VAB7|Q9H537	Frame_Shift_Del	DEL	ENST00000241125.3	37	c.835delC	CCDS9289.1																																																																																				0.761	GJA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044059.3	NM_021954		2	4						2	4	---	---	---	---
RP13-329D4.3	0	broad.mit.edu	37	20	26113543	26113543	+	lincRNA	DEL	A	A	-	rs375245697		TCGA-FY-A40N-01A-11D-A23M-08	TCGA-FY-A40N-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f8beba9-a6ff-4e83-8ed6-e1ffc76cc9fc	b8313c2c-a5c7-404f-a9d1-0cf2355f0cfa	g.chr20:26113543delA	ENST00000416563.1	-	0	250																											TCTTTGCCTTAACAACATTAT	0.363																																						ENST00000416563.1																			0																																																			0							g.chr20:26113543delA																													20.37:g.26113543delA														0	250	-									RNA	DEL	ENST00000416563.1	37																																																																																						0.363	RP13-329D4.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000078482.1			2	4						2	4	---	---	---	---
