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Malformations of cortical development

Gene: PPP2R1A

Amber List (moderate evidence)
PPP2R1A (protein phosphatase 2 scaffold subunit Aalpha)
EnsemblGeneIds (GRCh38): ENSG00000105568
EnsemblGeneIds (GRCh37): ENSG00000105568
OMIM: 605983, Gene2Phenotype
PPP2R1A is in 5 panels

1 review

Ida Ertmanska (Genomics England Curator)

Green List (high evidence)

Comment on list classification: Comment on list classification: There are numerous individuals reported in literature with heterozygous PPP2R1A variants and a neurodevelopmental syndrome, which includes brain malformations (corpus callosum agenesis/hypoplasia, ventriculomegaly, and/or periventricular leukomalacia) in 40-67% of patients. Hence, this gene should be promoted to Green for Malformations of cortical development at the next update.
Created: 13 Mar 2026, 12:12 p.m. | Last Modified: 13 Mar 2026, 12:12 p.m.
Panel Version: 7.38
PMID: 33106617 Lenaerts et al., 2021
Report of 30 individuals with 16 different de novo variants in PPP2R1A. Shared phenotype: developmental delay (97%), hypotonia (93%), hypermobile joints (58%), CC hypoplasia/agenesis (56%), epilepsy (38%), macrocephaly (38%). Macrocephaly and epilepsy were mutually exclusive. Intellectual disability ranged from mild to severe, based on functional effects of each variant.

Functional evidence: HEK293T cells transfected with PPP2R1A mutants - variants from patients with less severe ID, no seizures, and sometimes macrocephaly typically showed normal B55α and STRN3 binding, while more severe ID, seizures, and sometimes microcephaly correlated with lost B55α binding and increased STRN3 binding.

22/33 (67%) of patients with PPP2R1A-Related Neurodevelopmental Disorder presented with corpus callosum hypo-/aplasia according to GeneReviews (https://www.ncbi.nlm.nih.gov/books/NBK580243/)

PPP2R1A is now associated with AD Houge-Janssens syndrome 2, OMIM:616362 (OMIM accessed 13th Mar 2026). PPP2R1A is Definitve in ClinGen for an AD complex neurodevelopmental disorder (Nov 2022).
Sources: Literature
Created: 13 Mar 2026, 11:48 a.m. | Last Modified: 13 Mar 2026, 12:13 p.m.
Panel Version: 7.38

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Houge-Janssens syndrome 2, OMIM:616362; Houge-Janssens syndrome 2, MONDO:0014605

Publications

Created: 13 Mar 2026, 11:48 a.m.
Last Modified: 13 Mar 2026, 12:13 p.m.
Panel version: 7.37

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • Houge-Janssens syndrome 2, OMIM:616362
  • Houge-Janssens syndrome 2, MONDO:0014605
Tags
Q1_26_promote_green
OMIM
605983
Clinvar variants
Variants in PPP2R1A
Penetrance
None
Publications
Panels with this gene

History Filter Activity

13 Mar 2026, Gel status: 2

Entity classified by Genomics England curator

Ida Ertmanska (Genomics England Curator)

Gene: ppp2r1a has been classified as Amber List (Moderate Evidence).

13 Mar 2026, Gel status: 1

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

Ida Ertmanska (Genomics England Curator)

gene: PPP2R1A was added gene: PPP2R1A was added to Malformations of cortical development. Sources: Literature Q1_26_promote_green tags were added to gene: PPP2R1A. Mode of inheritance for gene: PPP2R1A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PPP2R1A were set to 33106617 Phenotypes for gene: PPP2R1A were set to Houge-Janssens syndrome 2, OMIM:616362; Houge-Janssens syndrome 2, MONDO:0014605 Review for gene: PPP2R1A was set to GREEN