NAA15

Chr 4AD

N-alpha-acetyltransferase 15, NatA auxiliary subunit

Also known as: Ga19, MRD50, NARG1, NAT1P, NATH, TBDN, TBDN100

NCBI Gene: 80155 ENSG00000164134 UniProt: Q9BXJ9 OMIM: 608000

The protein serves as the auxiliary subunit of the N-terminal acetyltransferase A (NatA) complex, which transfers acetyl groups from acetyl-coenzyme A to the alpha-amino group of nascent polypeptides, a modification essential for normal cell function. Mutations cause autosomal dominant intellectual developmental disorder with behavioral abnormalities through loss-of-function mechanisms. The gene is highly intolerant to loss-of-function variants, consistent with haploinsufficiency as the likely pathogenic mechanism.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

N-alpha-acetylation is among the most common post-translational protein modifications in eukaryotic cells. This process involves the transfer of an acetyl group from acetyl-coenzyme A to the alpha-amino group on a nascent polypeptide and is essential for normal cell function. This gene encodes the auxillary subunit of the N-terminal acetyltransferase A (NatA) complex. [provided by RefSeq, Jan 2017]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Intellectual developmental disorder, autosomal dominant 50, with behavioral abnormalitiesMIM #617787

Clinical highlights

Gene–disease validity (ClinGen)

Definitive · syndromic intellectual disability · AD · ClinGen 2022

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

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P/LP submissions

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P/LP missense

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LOEUF

LOF

Mechanism· G2P

Some data sources returned errors (1)

gnomad: Error: gnomAD API error: 400

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in NAA15?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

783 rare PASS variants

Rare truncating (LoF)

1 in 3,000

88 rare PASS variants

Rare synonymous (reference)

1 in 98

394 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NAA15. 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 130	1 in 4,700
South Asian	~43k	1 in 150	1 in 1,700
Remaining (unassigned)	~30k	1 in 86	≈ 1 in 30,000
European (Finnish)	~27k	1 in 220	1 in 5,300
Admixed American	~22k	1 in 76	1 in 1,500
African / African American	~21k	1 in 100	1 in 2,000
East Asian	~20k	1 in 150	1 in 2,200
Ashkenazi Jewish	~13k	1 in 400	≈ 1 in 4,100
Middle Eastern	~2,884	1 in 110	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): 12 of 20 coding exons well covered in gnomAD exomes; exons 3, 8, 9, 15, 16 and 3 more marginal. Genomes: all 20.? see exons ↓