NAA40

Chr 11

N-alpha-acetyltransferase 40, NatD catalytic subunit

Also known as: NAT11, NatD, PATT1, hNatD

NCBI Gene: 79829 ENSG00000110583 UniProt: Q86UY6

The NAA40 protein is an N-alpha-acetyltransferase that specifically acetylates the N-terminal residues of histones H4 and H2A, recognizing a distinct serine-glycine-arginine-glycine sequence and acting as a negative regulator of apoptosis. Mutations cause Ogden syndrome, a rare X-linked disorder characterized by severe intellectual disability, distinctive craniofacial features, cryptorchidism, and hypotonia with early infantile onset. The gene shows tolerance to loss-of-function variants (LOEUF 1.281), suggesting the pathogenic variants may involve other mechanisms.

ResearchSummary from RefSeq, UniProt

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]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.28

LOEUF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.28LOEUF

pLI 0.000

Z-score 0.69

OE 0.82 (0.54–1.28)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.24Z-score

OE missense 0.71 (0.60–0.84)

102 obs / 143.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.82 (0.54–1.28)

0≤0.351.4

Missense OE?0.71 (0.60–0.84)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 14 / 17.1Missense obs/exp: 102 / 143.8Syn Z: -0.23

Background carrier burden — how many people carry a rare variant somewhere in NAA40?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 220

254 rare PASS variants

Rare truncating (LoF)

1 in 4,900

47 rare PASS variants

Rare synonymous (reference)

1 in 170

140 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NAA40. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 300	1 in 4,800
South Asian	~43k	1 in 170	1 in 6,100
Remaining (unassigned)	~30k	1 in 170	1 in 6,000
European (Finnish)	~27k	1 in 490	1 in 3,300
Admixed American	~22k	1 in 220	≈ 1 in 7,400
African / African American	~21k	1 in 390	≈ 1 in 6,000
East Asian	~20k	1 in 380	none seen
Ashkenazi Jewish	~13k	1 in 410	none seen
Middle Eastern	~2,884	1 in 240	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 8 of 8 coding exons well covered in gnomAD exomes. Genomes: 7 of 8 (exon 1 below).? see exons ↓