Intellectual disability
Gene: NAA60

NAA60 (N(alpha)-acetyltransferase 60, NatF catalytic subunit)
EnsemblGeneIds (GRCh38): ENSG00000122390
EnsemblGeneIds (GRCh37): ENSG00000122390
OMIM: 614246, Gene2Phenotype
NAA60 is in 4 panels

1 review

Ida Ertmanska (Genomics England Curator)

Red List (low evidence)

PMID: 38480682 Chelban et al., 2024
Report of 7 unrelated families with homozygous variants in NAA60 with primary familial brain calcifications. Families originated from UK, France/Algeria, France/Morocco, UK/India, Turkey, and Saudi Arabia. 5/7 families had reported consanguinity. Sequencing method: WGS, WES.
Variants reported: c.321_327del, (p.Arg108Thrfs*3); c.338-1G>C, p.(Gly113Valfs*32); c.391C>T, (p.His131Tyr); c.130C>T, (p.Arg44Cys); c.50T>G, (p.Leu17Arg); c.428A>C, (p.Asn143Thr). No homozygotes reported in gnomAD v4.
9/10 patients had some motor features: extrapyramidal, pyramidal, cerebellar syndrome, dystonia - onset mostly in 20s-30s, one individual had symptoms from age 10 years. 3/10 individuals had mild intellectual disability, 3/10 had developmental delay from birth. 5/10 patients had some dysmorphic features. All 10 patients had some cognitive features (mostly mild): cognitive impairment (adult-onset), mild frontal syndrome, learning difficulties.
CT and brain MRI confirmed the presence of brain calcifications in all reported adult cases (9).
Phenotype and age of onset was variable, even in individuals who harboured the same variant - e.g. siblings in Family 2, homozygous for the same variant: sib II-2 had no motor features, only presented with mild frontal syndrome in her early 30s; sib II-1 presented with global developmental delay from birth, with onset of motor symptoms at age 20 - extrapyramidal and cerebellar syndrome, dystonia.

NAA60 is associated with AR Basal ganglia calcification, idiopathic, 9, autosomal recessive, 620786 in OMIM (accessed 10th Oct 2025).
In summary, while some individuals presented with intellectual disability and cognitive impairment, their symptoms were mild. Thus, these cases do not meet the eligibility criteria of moderate/severe/profound global developmental delay/intellectual disability. Based on the available evidence, this gene should be rated Red for Intellectual disability.
Sources: Literature
Created: 10 Oct 2025, 11:10 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Basal ganglia calcification, idiopathic, 9, autosomal recessive, 620786; basal ganglia calcification, idiopathic, 9, autosomal recessive, MONDO:0968977

Publications

38480682

Created: 10 Oct 2025, 11:10 a.m.

Panel version: 9.122

Details

Mode of Inheritance

BIALLELIC, autosomal or pseudoautosomal

Sources

Expert Review Red
Literature

Phenotypes

Basal ganglia calcification, idiopathic, 9, autosomal recessive, OMIM:620786
basal ganglia calcification, idiopathic, 9, autosomal recessive, MONDO:0968977

OMIM

614246

Clinvar variants

Variants in NAA60

Penetrance

None

Publications

38480682

Panels with this gene

History Filter Activity

17 Oct 2025, Gel status: 1

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: NAA60 were changed from Basal ganglia calcification, idiopathic, 9, autosomal recessive, 620786; basal ganglia calcification, idiopathic, 9, autosomal recessive, MONDO:0968977 to Basal ganglia calcification, idiopathic, 9, autosomal recessive, OMIM:620786; basal ganglia calcification, idiopathic, 9, autosomal recessive, MONDO:0968977

17 Oct 2025, Gel status: 1

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: naa60 has been classified as Red List (Low Evidence).

10 Oct 2025, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Ida Ertmanska (Genomics England Curator)

gene: NAA60 was added gene: NAA60 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: NAA60 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: NAA60 were set to 38480682 Phenotypes for gene: NAA60 were set to Basal ganglia calcification, idiopathic, 9, autosomal recessive, 620786; basal ganglia calcification, idiopathic, 9, autosomal recessive, MONDO:0968977 Review for gene: NAA60 was set to RED

Intellectual disability Gene: NAA60