NAA40
protein-codingN-alpha-acetyltransferase 40, NatD catalytic subunit, the group of GCN5 related N-acetyltransferases|N-alpha-acetyltransferase subunits
Gene summary
Enables histone H2A acetyltransferase activity; histone H4 acetyltransferase activity; and protein N-terminal-serine acetyltransferase activity. Predicted to be involved in chromatin remodeling. Predicted to act upstream of or within lipid metabolic process. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
- NAT11
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.4 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 NAA40 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024771.4. 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 | 1 | 1 | ||||
| missense | 30 | 30 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 31 | 0 | 0 | 31 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079047.2 | 8 | MANE Select | |
| Ensembl | ENSP00000367024.4 | 8 | MANE Select | |
| RefSeq | NP_001287729.1 | 7 | Standard | |
| Ensembl | ENSP00000440304.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metapathway biotransformation Phase I and II
Biological Process
- N-terminal protein amino acid acetylation
- lipid metabolic process
- histone H4 acetylation
- histone H2A acetylation
- regulation of chromatin silencing at rDNA
Molecular Function
- H4 histone acetyltransferase activity
- H2A histone acetyltransferase activity
- peptide-serine-N-acetyltransferase activity
Cellular Component
- nucleus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000377793
- Coding exons
- 8
- Length
- 18370
- Individuals with no LoFs
- 125728
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 20
- Defined
- 125748
- p
- 0.0000795
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.24 | 102 | 144 | 0.709 | 0.00000853 | 1579 |
| Missense (PolyPhen) | 19 | 32.135 | 0.59126 | 393 | ||
| Synonymous | -0.230 | 54 | 51.9 | 1.04 | 0.00000308 | 409 |
| Loss of Function | 0.690 | 14 | 17.1 | 0.820 | 0.00000104 | 180 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00026 | 0.00025 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000088 | 0.000088 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: N-alpha-acetyltransferase that specifically mediates the acetylation of the N-terminal residues of histones H4 and H2A (PubMed:21935442, PubMed:25619998). In contrast to other N-alpha- acetyltransferase, has a very specific selectivity for histones H4 and H2A N-terminus and specifically recognizes the 'Ser-Gly-Arg- Gly sequence' (PubMed:21935442, PubMed:25619998). Acts as a negative regulator of apoptosis (PubMed:26666750). May play a role in hepatic lipid metabolism (By similarity). {ECO:0000250|UniProtKB:Q8VE10, ECO:0000269|PubMed:21935442, ECO:0000269|PubMed:25619998, ECO:0000269|PubMed:26666750}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- LoFtool
- 0.355
- RVIS EVS
- -0.47
- RVIS percentile EVS
- 23.25
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |