NAA20

Chr 20AR

N-alpha-acetyltransferase 20, NatB catalytic subunit

Also known as: MRT73, NAT3, NAT3P, NAT5, NAT5P, dJ1002M8.1

NCBI Gene: 51126 ENSG00000173418 UniProt: P61599 OMIM: 610833

The NAA20 protein is the catalytic subunit of the NatB complex, which acetylates N-terminal methionine residues of specific peptides and is required for maintaining actomyosin fiber structure and cellular migration. Mutations cause autosomal recessive intellectual developmental disorder. The gene shows relatively low constraint to loss-of-function variants (pLI 0.006, LOEUF 1.03), consistent with its recessive inheritance pattern.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

NAT5 is a component of N-acetyltransferase complex B (NatB). Human NatB performs cotranslational N(alpha)-terminal acetylation of methionine residues when they are followed by asparagine (Starheim et al., 2008 [PubMed 18570629]).[supplied by OMIM, Apr 2009]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Intellectual developmental disorder, autosomal recessive 73MIM #619717

Clinical highlights

Gene–disease validity (ClinGen)

Moderate · syndromic intellectual disability · AR · ClinGen 2026

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.03

LOEUF

GOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.03LOEUF

pLI 0.006

Z-score 1.52

OE 0.49 (0.25–1.03)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.31Z-score

OE missense 0.63 (0.52–0.78)

65 obs / 102.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.49 (0.25–1.03)

0≤0.351.4

Missense OE?0.63 (0.52–0.78)

0≤0.61.4

Synonymous OE?1.11

0≤1.21.6

LoF obs/exp: 5 / 10.2Missense obs/exp: 65 / 102.4Syn Z: -0.55

Background carrier burden — how many people carry a rare variant somewhere in NAA20?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 960

184 rare PASS variants

Rare truncating (LoF)

1 in 2,300

74 rare PASS variants

Rare synonymous (reference)

1 in 730

86 rare PASS variants

Rare missense and truncating variants are carried at similar rates in NAA20; this gene does not show strong loss-of-function constraint by this measure. 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 1,100	1 in 2,600
South Asian	~43k	1 in 870	1 in 1,500
Remaining (unassigned)	~30k	1 in 790	none seen
European (Finnish)	~27k	1 in 310	1 in 620
Admixed American	~22k	1 in 680	≈ 1 in 17,000
African / African American	~21k	1 in 510	1 in 860
East Asian	~20k	1 in 750	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 620	none seen
Middle Eastern	~2,884	≈ 1 in 1,400	≈ 1 in 960

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): 5 of 6 coding exons well covered in gnomAD exomes; exon 2 marginal. Genomes: all 6.? see exons ↓