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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.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
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
ASD
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
DD
ADHD
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

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 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 
  
  
  et al.  
 GEN786R070 
 frameshift_variant 
 c.1267_1270del 
 p.Leu423IlefsTer9 
 De novo 
  
  
  et al.  
 GEN786R071 
 missense_variant 
 c.619T>C 
 p.Trp207Arg 
 De novo 
  
  
  et al.  
 GEN786R072 
 missense_variant 
 c.1258G>A 
 p.Glu420Lys 
 De novo 
  
 Simplex 
  et al.  
 GEN786R073 
 missense_variant 
 c.751G>T 
 p.Asp251Tyr 
 Unknown 
  
  
  et al.  
 GEN786R074 
 missense_variant 
 c.752A>C 
 p.Asp251Ala 
 Unknown 
  
  
  et al.  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
6
Deletion-Duplication
 12
 
6
Deletion-Duplication
 1
 
6
Deletion
 1
 
6
Deletion
 1
 

No Animal Model Data Available

 

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