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Intellectual disability

Gene: ATP11A

Amber List (moderate evidence)
ATP11A (ATPase phospholipid transporting 11A)
EnsemblGeneIds (GRCh38): ENSG00000068650
EnsemblGeneIds (GRCh37): ENSG00000068650
OMIM: 605868, Gene2Phenotype
ATP11A is in 6 panels

3 reviews

Sarah Leigh (Genomics England Curator)

I don't know

Comment on publications: PMID: 39432785 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: 25 Feb 2025, 4:49 p.m. | Last Modified: 25 Feb 2025, 4:49 p.m.
Panel Version: 8.99
Three heterozygous ATP11A variants have been associated with Leukodystrophy, hypomyelinating, 24 (OMIM:619851), in four unrelated cases with varying severity of neurological disorders (PMID: 34403372;39432785). It would appear that these variants interfere with the normal translocation of phosphatidylserine and phosphatidylethanolamine from the outer leaflet to the inner leaflet, resulting in an increased sphingomyelin (SM) levels on the cell surface, resulting in a greater susceptibility to SM phosphodiesterase-mediated cell lysis. Experiments in mice also support the role of ATP11A variants in neurological disorders (PMID: 34403372;39432785).
Intellectual disability was a feature of 2/4 cases reported (PMID: 34403372;39432785).
Created: 25 Feb 2025, 4:48 p.m. | Last Modified: 25 Feb 2025, 4:48 p.m.
Panel Version: 8.98
Created: 25 Feb 2025, 4:48 p.m.
Last Modified: 25 Feb 2025, 4:48 p.m.
Panel version: 8.98

Ivone Leong (Genomics England Curator)

Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. There is currently only 1 case and a mouse model which showed neurological deficit phenotypes (including tremors, abnormal gait, hind limb clasping and reduction in brain size. The patient was a 26 yo male born to healthy non-consanguineous Japanese parents. At birth his length was -3.3. SD and OFC was -1.3 SD. Developed epilepsy at 2 weeks followed by global developmental delay and mild hypothyroidism and cataracts.He suffered gradual lost of developmental milestones. At 18 yo, height was -4.6 SD and OFC was -4.0 SD.

As there is currently not enough evidence to support a gene-disease association, this gene has been given an Amber rating.
Created: 13 Oct 2021, 12:10 p.m. | Last Modified: 13 Oct 2021, 12:10 p.m.
Panel Version: 3.1353
Created: 13 Oct 2021, 12:10 p.m.
Last Modified: 13 Oct 2021, 12:10 p.m.
Panel version: 3.1353

Zornitza Stark (Australian Genomics)

I don't know

PMID: 34403372:
- Single de novo missense variant reported in a patient with developmental delay and neurological deterioration.
- Patient MRI showed severe cerebral atrophy, ventriculomegaly, hypomyelination leukodystrophy, thinned corpus callosum. Axonal neuropathy suggested.
- K/I heterozygous mice died perinatally.
- Functional studies on missense variant show plasma membrane lipid content impairment, reduced ATPase activity etc.

gnomAD: some NMD PTCs present, good quality variants found with 4-5 hets.
Sources: Literature
Created: 11 Oct 2021, 9:24 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Neurodevelopmental disorder

Publications

Created: 11 Oct 2021, 9:24 a.m.

Panel version: 3.1335

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
Phenotypes
  • Neurodevelopmental disorder
Tags
watchlist
OMIM
605868
Clinvar variants
Variants in ATP11A
Penetrance
None
Publications
Panels with this gene

History Filter Activity

25 Feb 2025, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: ATP11A were set to 34403372; 39432785

25 Feb 2025, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: ATP11A were set to 34403372; 39432785

25 Feb 2025, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: ATP11A were set to 34403372

13 Oct 2021, Gel status: 2

Added Tag

Ivone Leong (Genomics England Curator)

Tag watchlist tag was added to gene: ATP11A.

13 Oct 2021, Gel status: 2

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: atp11a has been classified as Amber List (Moderate Evidence).

11 Oct 2021, Gel status: 0

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

Zornitza Stark (Australian Genomics)

gene: ATP11A was added gene: ATP11A was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: ATP11A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ATP11A were set to 34403372 Phenotypes for gene: ATP11A were set to Neurodevelopmental disorder Review for gene: ATP11A was set to AMBER