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Intellectual disability

Gene: NAA20

Amber List (moderate evidence)
NAA20 (N(alpha)-acetyltransferase 20, NatB catalytic subunit)
EnsemblGeneIds (GRCh38): ENSG00000173418
EnsemblGeneIds (GRCh37): ENSG00000173418
OMIM: 610833, Gene2Phenotype
NAA20 is in 3 panels

2 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There is sufficient evidence available (three unrelated families) for the promotion of this gene to green rating on the next GMS update.
Created: 3 Feb 2025, 6:49 p.m. | Last Modified: 3 Feb 2025, 6:49 p.m.
Panel Version: 8.60
Comment on publications: PMID:39814713 paper was identified by the Genomics England Applied Machine Learning (ML) team in a Biocuration-ML project for identifying new gene-disease associations using Natural Language Processing (NLP) and Generative AI techniques.
Created: 3 Feb 2025, 6:47 p.m. | Last Modified: 3 Feb 2025, 6:47 p.m.
Panel Version: 8.58
PMID:37191084 reported two sisters from a single family with compound heterozygous variants in NAA20 gene (p.Gln34Ter & p.Leu4Pro) and with a neurodevelopmental disorder involving global developmental delay, intellectual disability, microcephaly and epilepsy. There is also functional data available for p.Leu4Pro variant. In total, there are three unrelated families reported so far with GDD and ID.

This gene has now been associated with relevant phenotypes in both OMIM (MIM #619717) and Gene2Phenotype (with 'limited' rating on the DD panel).
Created: 3 Feb 2025, 6:46 p.m. | Last Modified: 3 Feb 2025, 6:46 p.m.
Panel Version: 8.57

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Intellectual developmental disorder, autosomal recessive 73, OMIM:619717

Publications

Created: 3 Feb 2025, 6:46 p.m.
Last Modified: 3 Feb 2025, 6:46 p.m.
Panel version: 8.57

Sarah Leigh (Genomics England Curator)

I don't know

Comment on list classification: There is enough evidence for this gene to be amber on this panel, based on two missense variants, which have supporting in silico and experimental evidence in cases with mild to severe intellectually disability (PMID 34230638).
Created: 13 Jul 2021, 11:14 a.m. | Last Modified: 13 Jul 2021, 11:14 a.m.
Panel Version: 3.1179
Comment on phenotypes: Currently there is no phenotype associated with this gene in OMIM, Gen2Phen or MONDO (13/07/2021).
Created: 13 Jul 2021, 11:09 a.m. | Last Modified: 13 Jul 2021, 11:09 a.m.
Panel Version: 3.1178
Not associated with a phenotype in OMIM nor Gen2Phen. Two missense variants reported as homozygotes in one family each. In silico predictions and in vitro functional studies provide evidence that these variants will adversely affect their capacity to form a NatB complex with NAA25, and in vitro acetylation assays revealed reduced catalytic activities toward different NatB substrates (PMID 34230638). Children from these two families had developmental delay, intellectual disability (mild to moderate family 1, severe family 2).
The two children in family 1 in this study had a head circumcernces of -2.3 & -1.9 SD (which is not regarded as severe microcephaly).
The three children from family 2 in this study had a head circumcernces of -3.5, -3.0 & -3.5 SD (which is regarded as severe microcephaly). Subtle dysmorphic features were also reported.
Sources: Literature
Created: 13 Jul 2021, 11:06 a.m. | Last Modified: 13 Jul 2021, 11:20 a.m.
Panel Version: 3.1179

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
autosomal recessive developmental delay, intellectual disability, and microcephaly

Publications

Created: 13 Jul 2021, 11:06 a.m.
Last Modified: 13 Jul 2021, 11:20 a.m.
Panel version: 3.1177

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • Intellectual developmental disorder, autosomal recessive 73, OMIM:619717
Tags
Q1_25_ promote_green
OMIM
610833
Clinvar variants
Variants in NAA20
Penetrance
None
Publications
Panels with this gene

History Filter Activity

3 Feb 2025, Gel status: 2

Entity classified by Genomics England curator

Achchuthan Shanmugasundram (Genomics England Curator)

Gene: naa20 has been classified as Amber List (Moderate Evidence).

3 Feb 2025, Gel status: 2

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: NAA20 were changed from autosomal recessive developmental delay, intellectual disability, and microcephaly to Intellectual developmental disorder, autosomal recessive 73, OMIM:619717

3 Feb 2025, Gel status: 2

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q1_25_ promote_green tag was added to gene: NAA20.

3 Feb 2025, Gel status: 2

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: NAA20 were set to 34230638

13 Jul 2021, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: naa20 has been classified as Amber List (Moderate Evidence).

13 Jul 2021, Gel status: 1

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: NAA20 were changed from autosomal recessive developmental delay, intellectual disability, and microcephaly to autosomal recessive developmental delay, intellectual disability, and microcephaly

13 Jul 2021, Gel status: 1

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

Sarah Leigh (Genomics England Curator)

gene: NAA20 was added gene: NAA20 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: NAA20 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: NAA20 were set to 34230638 Phenotypes for gene: NAA20 were set to autosomal recessive developmental delay, intellectual disability, and microcephaly Review for gene: NAA20 was set to AMBER