Summary Statistics:
ASD Reports: 33
Recent Reports: 2
Annotated variants: 74
Associated CNVs: 4
Evidence score: 4
Gene Score: 4S
Relevance to Autism
Four de novo missense variants in the PPP2R5D gene were identified in seven unrelated patients with developmental delay/intellectual disability; five of these patients also presented with ASD (Shang et al., 2015). Two of the de novo PPP2R5D missense variants that were found in ASD cases in this report (p.Glu198Lys and p.Glu200Lys) have been previously identified in patients with intellectual disability (Deciphering Developmental Disorders Study, 2015; Loveday et al., 2015) and have been experimentally shown to result in reduced binding to the A and C subunits of protein phosphatase 2A (Houge et al., 2015). In addition to developmental delay/intellectual disability and, in some cases, ASD, individuals with PPP2R5D mutations frequently exhibit syndromic features including overgrowth, facial dysmorphism, and additional congenital anomalies. Oyama et al., 2022 studied 76 individuals withPPP2R5Dvariants, including 68 with pathogenic de novo variants and four siblings with a novel dominantly inherited pathogenic variant; functional analysis revealed impaired PP2A A/C-subunit binding, decreased short linear interaction motif-dependent substrate binding, or both, while the recurrent p.Glu198Lys missense variant showed the highest C-binding defect and a more severe clinical phenotype and the inherited p.Glu197Gly variant had a mild substrate binding defect. Furthermore, common clinical phenotypes of affected individuals in Oyama et al., 2022 were language, intellectual or learning disabilities (80.6%), hypotonia (75.0%), macrocephaly (66.7%), seizures (45.8%) and autism spectrum disorder (26.4%).
Molecular Function
This gene encodes a delta isoform of the regulatory subunit B56 subfamily and belongs to the phosphatase 2A regulatory subunit B family, which might modulate substrate selectivity and catalytic activity of protein phosphatase 2A, which is one of the four major Ser/Thr phosphatases and has been implicated in the negative control of cell growth and division.
References
Primary
De novo missense variants in PPP2R5D are associated with intellectual disability, macrocephaly, hypotonia, and autism.
DD, ID
ASD
Support
Variation in a range of mTOR-related genes associates with intracranial volume and intellectual disability.
ID
Macrocephaly
Support
DD, ID, epilepsy/seizures
ASD
Support
De novo variants in neurodevelopmental disorders-experiences from a tertiary care center
DD
Support
Large-scale discovery of novel genetic causes of developmental disorders.
DD, ID
Support
Impaired Neurodevelopmental Genes in Slovenian Autistic Children Elucidate the Comorbidity of Autism With Other Developmental Disorders
ASD
ID
Support
Expanding the genetic heterogeneity of intellectual disability.
DD, epilepsy/seizures
Macrocephaly
Support
Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders
ASD, DD
Support
The contribution of de novo coding mutations to autism spectrum disorder
ASD
Support
Clinical Targeted Panel Sequencing Analysis in Clinical Evaluation of Children with Autism Spectrum Disorder in China
ASD
Support
Hotspots of missense mutation identify neurodevelopmental disorder genes and functional domains.
ASD, DD
Support
Hogue-Janssens syndrome 1
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD
Support
Diagnostic yield of next-generation sequencing in 87 families with neurodevelopmental disorders
Learning disability
Support
Genomic diagnosis for children with intellectual disability and/or developmental delay.
ASD, ID
Hypotonia, macrocephaly
Support
Variantrecurrence in neurodevelopmental disorders: the use of publicly available genomic data identifies clinically relevant pathogenic missense v...
DD
Support
Prevalence and phenotypic impact of rare potentially damaging variants in autism spectrum disorder
ASD
Support
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder.
ASD
Support
A single center experience with publicly funded clinical exome sequencing for neurodevelopmental disorders or multiple congenital anomalies
DD, ID
ASD, epilepsy/seizures
Support
Clinical exome sequencing: results from 2819 samples reflecting 1000 families.
Autosomal dominant mental retardation-35
ID, macrocephaly, hypotonia
Support
Complex Diagnostics of Non-Specific Intellectual Developmental Disorder
DD, ID
Support
Identification of mutations in the PI3K-AKT-mTOR signalling pathway in patients with macrocephaly and developmental delay and/or autism.
DD, ID, macrocephaly
ASD
Support
Houge-Janssens syndrome 1, DD
Support
Genetic and phenotypic analysis of 101 patients with developmental delay or intellectual disability using whole-exome sequencing
DD
Support
Mutations in the PP2A regulatory subunit B family genes PPP2R5B, PPP2R5C and PPP2R5D cause human overgrowth.
DD, ID
Support
Comprehensive genome sequencing analyses identify novel gene mutations and copy number variations associated with infant developmental delay or intellectual disability (DD/ID)
DD, ID
Recent Recommendation
Clinical, neuroimaging and molecular characteristics of PPP2R5D-related neurodevelopmental disorders: an expanded series with functional characterisation and genotype-phenotype analysis
Autosomal dominant intellectual developmental diso
ASD, DD, ID, epilepsy/seizures
Recent Recommendation
B56-related protein phosphatase 2A dysfunction identified in patients with intellectual disability.
DD, ID
GEN786R001
missense_variant
c.592G>A
p.Glu198Lys
De novo
GEN786R002
missense_variant
c.592G>A
p.Glu198Lys
De novo
GEN786R003
missense_variant
c.598G>A
p.Glu200Lys
De novo
GEN786R004
missense_variant
c.805G>A
p.Glu269Lys
De novo
GEN786R005
missense_variant
c.805G>A
p.Glu269Lys
De novo
GEN786R006
missense_variant
c.1258G>A
p.Glu420Lys
De novo
GEN786R007
missense_variant
c.589G>A
p.Glu197Lys
De novo
GEN786R008
missense_variant
c.592G>A
p.Glu198Lys
De novo
Simplex
GEN786R009
missense_variant
c.592G>A
p.Glu198Lys
De novo
Simplex
GEN786R010
missense_variant
c.592G>A
p.Glu198Lys
De novo
Simplex
GEN786R011
missense_variant
c.602C>G
p.Pro201Arg
De novo
Simplex
GEN786R012
missense_variant
c.139G>A
p.Glu47Lys
De novo
Simplex
GEN786R013
missense_variant
c.598G>A
p.Glu200Lys
De novo
Simplex
GEN786R014
missense_variant
c.145G>A
p.Glu49Lys
Unknown
Simplex
GEN786R015
missense_variant
c.157C>T
p.Pro53Ser
De novo
GEN786R016
missense_variant
c.139G>A
p.Glu47Lys
De novo
GEN786R017
missense_variant
c.592G>A
p.Glu198Lys
De novo
GEN786R018
missense_variant
c.592G>A
p.Glu198Lys
De novo
GEN786R019
missense_variant
c.145G>A
p.Glu49Lys
De novo
GEN786R020
missense_variant
c.598G>A
p.Glu200Lys
De novo
GEN786R021
missense_variant
c.619T>A
p.Trp207Arg
De novo
GEN786R022
frameshift_variant
c.210del
p.Glu71SerfsTer9
De novo
Simplex
GEN786R023
missense_variant
c.1672A>G
p.Met558Val
De novo
Simplex
GEN786R024
missense_variant
c.139G>A
p.Glu47Lys
De novo
Simplex
GEN786R025
frameshift_variant
c.1645_1646del
p.Arg549AspfsTer5
De novo
Simplex
GEN786R026
missense_variant
c.139G>A
p.Glu47Lys
De novo
GEN786R027
missense_variant
c.545C>T
p.Thr182Met
Familial
Paternal
GEN786R028
missense_variant
c.656G>A
p.Arg219His
Unknown
GEN786R029
missense_variant
c.592G>A
p.Glu198Lys
Unknown
GEN786R030
missense_variant
c.274G>A
p.Glu92Lys
De novo
Simplex
GEN786R031
missense_variant
c.1258G>A
p.Glu420Lys
De novo
GEN786R032
missense_variant
c.598G>A
p.Glu200Lys
De novo
GEN786R033
missense_variant
c.592G>A
p.Glu198Lys
De novo
GEN786R034
missense_variant
c.139G>A
p.Glu47Lys
De novo
GEN786R035
missense_variant
c.139G>A
p.Glu47Lys
De novo
GEN786R036
missense_variant
c.592G>A
p.Glu198Lys
De novo
Simplex
GEN786R037
missense_variant
c.592G>A
p.Glu198Lys
De novo
GEN786R038
missense_variant
c.592G>A
p.Glu198Lys
De novo
Simplex
GEN786R039
missense_variant
c.592G>A
p.Glu198Lys
De novo
Simplex
GEN786R040
missense_variant
c.-200G>A
De novo
GEN786R041
missense_variant
c.1727C>T
p.Pro576Leu
Unknown
GEN786R042
missense_variant
c.202C>T
p.Arg68Cys
Unknown
GEN786R043
missense_variant
c.253G>A
p.Asp85Asn
Unknown
GEN786R044
missense_variant
c.263T>C
p.Phe88Ser
Unknown
GEN786R045
missense_variant
c.1150C>T
p.Leu384%3D
Unknown
GEN786R046
missense_variant
c.-183C>T
Unknown
GEN786R047
missense_variant
c.92C>T
p.Thr31Met
Unknown
GEN786R048
missense_variant
c.655C>T
p.Arg219Cys
Unknown
GEN786R049
missense_variant
c.*76C>T
Unknown
GEN786R050
missense_variant
c.139G>A
p.Glu47Lys
Unknown
GEN786R051
missense_variant
c.145G>A
p.Glu49Lys
Unknown
GEN786R052
missense_variant
c.145G>A
p.Glu49Lys
Unknown
GEN786R053
missense_variant
c.592G>A
p.Glu198Lys
De novo
Unknown
GEN786R054
missense_variant
c.592G>A
p.Glu198Lys
De novo
Simplex
GEN786R055
missense_variant
c.496G>A
p.Ala166Thr
De novo
Simplex
GEN786R056
missense_variant
c.619T>A
p.Trp207Arg
De novo
Simplex
GEN786R057
missense_variant
c.598G>A
p.Glu200Lys
Unknown
GEN786R058
missense_variant
c.592G>A
p.Glu198Lys
De novo
Simplex
GEN786R059
missense_variant
c.560C>T
p.Ser187Leu
Unknown
GEN786R060
missense_variant
c.592G>A
p.Glu198Lys
De novo
GEN786R061
missense_variant
c.758G>A
p.Arg253Gln
Unknown
GEN786R062
missense_variant
c.619T>C
p.Trp207Arg
De novo
Simplex
GEN786R063
missense_variant
c.598G>A
p.Glu200Lys
Unknown
Unknown
GEN786R064
frameshift_variant
c.225_226del
p.Gly77AlafsTer21
De novo
GEN786R065
splice_region_variant
c.70-5C>T
De novo
GEN786R066
missense_variant
c.496G>A
p.Ala166Thr
De novo
GEN786R067
missense_variant
c.523T>C
p.Phe175Leu
De novo
GEN786R068
missense_variant
c.139_140delinsAG
p.Glu47Arg
De novo
GEN786R069
missense_variant
c.751G>C
p.Asp251His
Unknown
GEN786R070
frameshift_variant
c.1267_1270del
p.Leu423IlefsTer9
De novo
GEN786R071
missense_variant
c.619T>C
p.Trp207Arg
De novo
GEN786R072
missense_variant
c.1258G>A
p.Glu420Lys
De novo
Simplex
GEN786R073
missense_variant
c.751G>T
p.Asp251Tyr
Unknown
GEN786R074
missense_variant
c.752A>C
p.Asp251Ala
Unknown
No Common Variants Available
6
Deletion-Duplication
12
No Animal Model Data Available
No Interactions Available