NAA38

Chr 17

N-alpha-acetyltransferase 38, NatC auxiliary subunit

Also known as: LSMD1, MAK31, PFAAP2

NCBI Gene: 84316 ENSG00000183011 UniProt: Q9BRA0 OMIM: 617990

The NAA38 protein is an auxiliary component of the N-terminal acetyltransferase C complex that catalyzes acetylation of N-terminal methionine residues, protecting proteins from degradation by the N-end rule pathway. Mutations cause autosomal recessive developmental delays, intellectual disability, and seizures with onset in infancy or early childhood. The gene shows relatively low constraint to loss-of-function variation.

OMIM ResearchSummary from UniProt

Predicted to enable RNA binding activity. Involved in negative regulation of apoptotic process. Located in cytoplasm and nucleoplasm. Part of NatC complex. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOEUF 1.91

Clinical Summary— NAA38

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

109 VUS of 132 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.91LOEUF

pLI 0.000

Z-score -0.80

OE 1.36 (0.77–1.91)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.40Z-score

OE missense 1.11 (0.95–1.30)

116 obs / 104.4 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.36 (0.77–1.91)

0≤0.351.4

Missense OE?1.11 (0.95–1.30)

0≤0.61.4

Synonymous OE?1.31

0≤1.21.6

LoF obs/exp: 8 / 5.9Missense obs/exp: 116 / 104.4Syn Z: -1.65

ClinVar Variant Classifications

132 submitted variants in ClinVar

ClinVar

Classification Summary

VUS109

Likely Benign15

Benign4

109

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	1	108	0	0	109
Likely Benign	1	11	0	3	15
Benign	0	3	1	0	4
Total	2	122	1	3	128

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

View in ClinVar →

22 pathogenic / likely-pathogenic (of 31) ClinVar copy-number / structural variants overlap NAA38 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →