Clinical, neuroimaging and molecular characteristics ofPPP2R5D-related neurodevelopmental disorders: an expanded series with functional characterisation and genotype–phenotype analysis

Abstract

BackgroundVariants in PPP2R5D, affecting the regulatory B56δ subunit of protein phosphatase 2A (PP2A), have been identified in individuals with neurodevelopmental abnormalities. However, the molecular and clinical spectra remain incompletely understood.MethodsIndividuals with PPP2R5D variants were enrolled through Simons Variation in Individuals Project/Simons Searchlight. Data were collected from medical history interviews, medical record review, online validated instruments and neuroimaging review. Genetic variants were biochemically characterised.ResultsWe studied 76 individuals with PPP2R5D variants, including 68 with pathogenic de novo variants, four with a variant of uncertain significance (VUS) and four siblings with a novel dominantly inherited pathogenic variant. Among 13 pathogenic variants, eight were novel and two (p.Glu198Lys and p.Glu200Lys) were highly recurrent. Functional analysis revealed impaired PP2A A/C-subunit binding, decreased short linear interaction motif-dependent substrate binding or both—with the most severe phenotypes associated with variants that completely retained one of these binding characteristics and lost the other—further supporting a dominant-negative disease mechanism. p.Glu198Lys showed the highest C-binding defect and a more severe clinical phenotype. The inherited p.Glu197Gly variant had a mild substrate binding defect, and three of four VUS had no biochemical impact. Common clinical phenotypes were language, intellectual or learning disabilities (80.6%), hypotonia (75.0%), macrocephaly (66.7%), seizures (45.8%) and autism spectrum disorder (26.4%). The mean composite Vineland score was 59.8, and most participants were in the ‘moderate to low’ and ‘low’ adaptive levels in all domains.ConclusionOur study delineates the most common features of PPP2R5D-related neurodevelopmental disorders, expands the clinical and molecular spectrum and identifies genotype–phenotype correlations.

Clinical and molecular characteristics of a novel rare de novo variant in PPP2CA in a patient with a developmental disorder, autism, and epilepsy

“…Through these B subunits, trimeric PP2A complexes achieve their substrate specificity, regulation, subcellular localization, and tissue-specific expression ( Slupe et al, 2011 ; Lambrecht et al, 2013 ). Despite this major structural complexity, PP2A-related NDDs are characterized by alterations in just a subset of PP2A holoenzymes, and the molecular characterization of PPP2CA (encoding the catalytic Cα subunit), PPP2R1A (encoding the scaffolding Aα subunit), and PPP2R5D (encoding the regulatory B56δ subunit) variants have been consistent so far with a loss-of-function mechanism for most, if not, all of them ( Houge et al, 2015 ; Reynhout et al, 2019 ; Lenaerts et al, 2020 ; Oyama et al, 2022 ). Although PP2A affected individuals exhibit common clinical features, including hypotonia, developmental delay (DD) (motoric skills, speech), intellectual disability (ID), differences in brain size, autism (ASD), and seizures, they also show a broad heterogeneity in the severity of their presentation—within individuals affected in different PP2A genes, as well as within individuals affected in the same PP2A gene.…”

“…PP2A-related neurodevelopmental disorders (NDDs) are a group of rare genetic diseases characterized by heterozygous de novo mutations in PPP2CA ( Reynhout et al, 2019 ) (OMIM: #618354), PPP2R1A ( Houge et al, 2015 ; Lenaerts et al, 2020 ; Douzgou et al, 2022 ) (OMIM: #616362), or PPP2R5D ( Houge et al, 2015 ; Loveday et al, 2015 ; Shang et al, 2016 ; Mirzaa et al, 2019 ; Oyama et al, 2022 ) (OMIM: #616355). These three PP2A genes belong to nineteen human genes encoding the protein phosphatase 2A (PP2A) family of Ser/Thr phosphatases ( Janssens and Goris, 2001 ; Lambrecht et al, 2013 ), a group of dephosphorylating enzymes with pleiotropic functions in cell signaling and organismal physiology ( Janssens and Goris, 2001 ; Reynhout and Janssens, 2019 ).…”

The role of serine/threonine phosphatases in human development: Evidence from congenital disorders

“…This nicely correlated with the clinical findings, where severity of the phenotype was less when both binding partners were affected. In contrast, in the two subgroups where only one of the two binding partners were affected, the phenotypes were found to be more severe, consistent with a stronger dominant-negative effect (Oyama et al, 2022). However, downstream molecular effects of PPP2R5D mutations remain poorly understood, with one variant of B56δ (p.Glu420Lys) leading to a constitutive activation of the Akt-mTOR pathway when reconstituted in HEK293 cells (Papke et al, 2021).…”

“…Patients with de novo variants of PPP2R5D most commonly present with intellectual and developmental delay, hypotonia, macrocephaly, distinct facial features ( e.g. frontal bossing) and less common symptoms, such as epilepsy, autism spectrum disorder, ADHD and early-onset Parkinsonism ( Houge et al, 2015 ; Loveday et al, 2015 ; Shang et al, 2016 ; Yeung et al, 2017 ; Mirzaa et al, 2019 ; Kim et al, 2020 ; Hetzelt et al, 2021 ; Walker et al, 2021 ; Yan et al, 2021 ; Oyama et al, 2022 ) (OMIM# 616355 ). Thus far, seventeen variants have been reported for PPP2R5D which are spread throughout the whole protein, but some seem to cluster around a conserved acidic loop, or a canonical short linear interaction motif-binding site ( Figure 3C ) ( Verbinnen et al, 2021 ).…”

“…Current literature states that these de novo variants act in a dominant-negative fashion, showing decrease in both A- and C-subunit binding, thus potentially trapping the substrate ( Houge et al, 2015 ). Recently, however, it was found that different variants affect formation of the holoenzyme differently, and three distinct biochemical groups were identified: one where only C-binding was affected, one where only a common SLIM-containing interactor was affected, and one where both were affected ( Oyama et al, 2022 ). This nicely correlated with the clinical findings, where severity of the phenotype was less when both binding partners were affected.…”