ANP32E
protein-codingacidic nuclear phosphoprotein 32 family member E, the group of ANP32 acidic nuclear phosphoproteins
Gene summary
Enables histone binding activity; histone chaperone activity; and protein folding chaperone. Predicted to be involved in regulation of apoptotic process. Located in nucleus. Part of Swr1 complex. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.7 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 ANP32E variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_030920.5. 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 | 2 | 2 | ||||
| missense | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 23 | 0 | 0 | 23 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_112182.1 | 7 | MANE Select | |
| Ensembl | ENSP00000463154.1 | 7 | MANE Select | |
| RefSeq | NP_001129950.1 | 6 | Standard | |
| RefSeq | NP_001129951.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of catalytic activity
- histone exchange
Molecular Function
- phosphatase inhibitor activity
- histone binding
Cellular Component
- Swr1 complex
- nucleus
- cytoplasmic vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000314136
- Coding exons
- 7
- Length
- 17788
- Individuals with no LoFs
- 125709
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125716
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.05 | 66 | 132 | 0.498 | 0.00000636 | 1786 |
| Missense (PolyPhen) | 11 | 33.979 | 0.32373 | 537 | ||
| Synonymous | 1.27 | 40 | 51.6 | 0.775 | 0.00000275 | 443 |
| Loss of Function | 3.09 | 2 | 14.9 | 0.134 | 7.52e-7 | 203 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000054 | 0.000035 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00066 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Histone chaperone that specifically mediates the genome- wide removal of histone H2A.Z/H2AFZ from the nucleosome: removes H2A.Z/H2AFZ from its normal sites of deposition, especially from enhancer and insulator regions. Not involved in deposition of H2A.Z/H2AFZ in the nucleosome. May stabilize the evicted H2A.Z/H2AFZ-H2B dimer, thus shifting the equilibrium towards dissociation and the off-chromatin state (PubMed:24463511). Inhibits activity of protein phosphatase 2A (PP2A). Does not inhibit protein phosphatase 1. May play a role in cerebellar development and synaptogenesis. {ECO:0000269|PubMed:24463511}.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- LoFtool
- 0.580
- RVIS EVS
- 0.17
- RVIS percentile EVS
- 65.33
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.991
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | High |