ENY2

ENY2 transcription and export complex 2 subunit, the group of SAGA complex|Transcription and export complex 2

Basic information

Region (hg38): 8:109334323-109345954

Links

ENSG00000120533

∙ NCBI:56943 ∙ OMIM:619015 ∙ HGNC:24449 ∙ Uniprot:Q9NPA8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ENY2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENY2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			3 clinvar			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in ENY2

This is a list of pathogenic ClinVar variants found in the ENY2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
8-109336150-C-T	not specified	Uncertain significance (May 10, 2024)	2277697
8-109336182-A-G	not specified	Uncertain significance (Feb 15, 2023)	2484057
8-109340491-G-C	not specified	Uncertain significance (Apr 25, 2023)	2515513

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENY2	protein_coding	protein_coding	ENST00000521688	5	11630

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.875	0.124	123867	0	1	123868	0.00000404

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	24	53.5	0.449	0.00000270	663
Missense in Polyphen		3	11.898	0.25213		176
Synonymous	-1.24	25	18.2	1.37	0.00000103	172
Loss of Function	2.41	0	6.78	0.00	2.84e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000465	0.0000465
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in mRNA export coupled transcription activation by association with both the TREX-2 and the SAGA complexes. The transcription regulatory histone acetylation (HAT) complex SAGA is a multiprotein complex that activates transcription by remodeling chromatin and mediating histone acetylation and deubiquitination. Within the SAGA complex, participates in a subcomplex that specifically deubiquitinates both histones H2A and H2B. The SAGA complex is recruited to specific gene promoters by activators such as MYC, where it is required for transcription. Required for nuclear receptor-mediated transactivation. The TREX-2 complex functions in docking export-competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket). TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. {ECO:0000269|PubMed:18206972, ECO:0000269|PubMed:21746879}.;
Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Intolerance Scores

loftool
rvis_EVS: 0.15
rvis_percentile_EVS: 63.81

Haploinsufficiency Scores

pHI: 0.926
hipred: Y
hipred_score: 0.734
ghis: 0.610

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: N
essential_gene_gene_trap: H
gene_indispensability_pred: E
gene_indispensability_score: 0.925

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

Gene name: Eny2
Phenotype

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;histone deubiquitination;poly(A)+ mRNA export from nucleus;positive regulation of transcription, DNA-templated;negative regulation of insulin secretion involved in cellular response to glucose stimulus
Cellular component: SAGA complex;nuclear pore;nucleoplasm;mitochondrion;transcription export complex 2;DUBm complex
Molecular function: chromatin binding;transcription coactivator activity;protein binding;nuclear receptor transcription coactivator activity