ENY2
protein-codingENY2 transcription and export complex 2 subunit, the group of SAGA complex|Transcription and export complex 2
Gene summary
Enables transcription coactivator activity. Involved in poly(A)+ mRNA export from nucleus; positive regulation of DNA-templated transcription; and regulation of transcription by RNA polymerase II. Part of SAGA complex and nucleus. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ENY2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020189.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 5 | 5 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 7 | 0 | 0 | 7 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_064574.1 | 5 | MANE Select | |
| Ensembl | ENSP00000429986.1 | 5 | MANE Select | |
| RefSeq | NP_001180486.1 | 4 | Standard | |
| Ensembl | ENSP00000339861.7 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Chromatin modifying enzymes
- HATs acetylate histones
- Chromatin organization
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
Molecular Function
- chromatin binding
- transcription coactivator activity
- protein binding
- nuclear receptor transcription coactivator activity
Cellular Component
- SAGA complex
- nuclear pore
- nucleoplasm
- mitochondrion
- transcription export complex 2
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000521688
- Coding exons
- 5
- Length
- 11630
- Individuals with no LoFs
- 123867
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 123868
- p
- 0.00000404
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.43 | 24 | 53.5 | 0.449 | 0.00000270 | 663 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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}.;
Intolerance Scores
- RVIS EVS
- 0.15
- RVIS percentile EVS
- 63.81
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- N
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.925
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |