NAA50

Chr 3

N-alpha-acetyltransferase 50, NatE catalytic subunit

Also known as: MAK3, NAT13, NAT13P, NAT5, NAT5P, SAN, hNaa50p

NCBI Gene: 80218 ENSG00000121579 UniProt: Q9GZZ1 OMIM: 610834

NAA50 encodes an N-terminal acetyltransferase that acetylates the amino terminus of proteins retaining their initiating methionine and functions as part of the NatA complex, playing a critical role in sister chromatid cohesion during mitosis. The gene is highly constrained against loss-of-function variants (LOEUF 0.545), but specific disease associations and inheritance patterns have not been established from the provided data. Further clinical and genetic studies are needed to define the phenotypic spectrum associated with NAA50 variants.

OMIM ResearchSummary from RefSeq, UniProt

Enables histone H4 acetyltransferase activity and protein-N-terminal amino-acid acetyltransferase activity. Involved in N-terminal protein amino acid acetylation; establishment of mitotic sister chromatid cohesion; and mitotic sister chromatid cohesion, centromeric. Located in cytosol and nucleolus. Part of NatA complex. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOEUF 0.55

Clinical Summary— NAA50

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.73) — some intolerance to loss-of-function variants.

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ClinVar Variants

9 VUS of 22 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.55LOEUF

pLI 0.735

Z-score 2.42

OE 0.11 (0.04–0.55)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.78Z-score

OE missense 0.46 (0.36–0.60)

40 obs / 86.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.11 (0.04–0.55)

0≤0.351.4

Missense OE?0.46 (0.36–0.60)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 1 / 8.7Missense obs/exp: 40 / 86.6Syn Z: -0.05

ClinVar Variant Classifications

22 submitted variants in ClinVar

ClinVar

Classification Summary

VUS9

Benign3

VUS

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	9	0	0	9
Likely Benign	0	0	0	0
Benign	0	1	2	3
Total	9	1	2	12

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

30 pathogenic / likely-pathogenic (of 31) ClinVar copy-number / structural variants overlap NAA50 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →