NAA60

Chr 16AR

N-alpha-acetyltransferase 60, NatF catalytic subunit

Also known as: HAT4, IBGC9, NAT15, NatF, hNaa60

NCBI Gene: 79903ENSG00000122390UniProt: Q9H7X0OMIM: 614246

The protein is an N-alpha-acetyltransferase that acetylates N-terminal residues of transmembrane proteins and is required for normal chromosomal segregation during cell division. Biallelic mutations cause basal ganglia calcification, idiopathic, 9, an autosomal recessive disorder affecting the brain's basal ganglia structures. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.596), suggesting some tolerance to inactivating mutations.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
DNmechanismARLOEUF 0.601 OMIM phenotype
Clinical Summary— NAA60
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.52) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
41 unique Pathogenic / Likely Pathogenic· 41 VUS of 102 total submissions
Explore recent and relevant literature in Research Assistant →
📖
GeneReview available — NAA60
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.60LOEUF
pLI 0.517
Z-score 2.44
OE 0.19 (0.08–0.60)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.93Z-score
OE missense 0.78 (0.67–0.91)
111 obs / 142.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.19 (0.08–0.60)
0≤0.351.4
Missense OE0.78 (0.67–0.91)
0≤0.61.4
Synonymous OE0.99
0≤1.21.6
LoF obs/exp: 2 / 10.6Missense obs/exp: 111 / 142.2Syn Z: 0.06
DN
0.6356th %ile
GOF
0.5268th %ile
LOF
0.4037th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

102 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic40
Likely Pathogenic1
VUS41
Likely Benign5
Benign2
40
Pathogenic
1
Likely Pathogenic
41
VUS
5
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
2
4
34
0
40
Likely Pathogenic
0
0
1
0
1
VUS
0
25
16
0
41
Likely Benign
0
2
0
3
5
Benign
0
2
0
0
2
Total23351389

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

View in ClinVar →

Protein Context — Lollipop Plot

NAA60 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients