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Relevance to Autism

Autistic features and/or stereotypy has been observed in a subset of individuals with both PPP3CA-associated disorders (Myers et al., 2017; Mizuguchi et al., 2018; Panneerselvam et al., 2021). Genotype-phenotype correlation of 5 novel patients and 16 previously unpublished patients with PPP3CA variants in Panneerselvam et al., 2021 found that while autistic features were overall a commonly observed phenotype in individuals with PPP3CA variants (11/20, 55%), they were more frequently observed in individuals with missense variants in the catalytic domain (7/9, 78%) or the auto-inhibitory domain (2/3, 67%) of PPP3CA compared to individuals with truncating variants in the regulatory domain of the protein (1/7, 14%). Mizuguchi et al., 2018 had previously shown that missense variants in the catalytic domain of PPP3CA exhibit loss-of-function properties, whereas missense variants in the auto-inhibitory domain display gain-of-function properties. A rare de novo missense variant in PPP3CA has also been identified in an ASD proband from the Autism Sequencing Consortium in Satterstrom et al., 2020.

Molecular Function

The protein encoded by the PPP3CA gene is a calcium-dependent, calmodulin-stimulated protein phosphatase which plays an essential role in the transduction of intracellular Ca2+-mediated signals. Heterozygous variants in this gene are responsible for two distinct disorders: arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development (ACCIID; OMIM 618265), and developmental and epileptic encephalopathy-91 (DEE91; OMIM 617711).

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures
DD, ID, epilepsy/seizures
Autistic features, stereotypy
Support
Early-onset infant epileptic encephalopathy associated with a de novo PPP3CA gene mutation
DD, epilepsy/seizures
Support
ID, epilepsy/seizures
Support
Novel calcineurin A (PPP3CA) variant associated with epilepsy, constitutive enzyme activation and downregulation of protein expression
DD, epilepsy/seizures
Support
Integrating de novo and inherited variants in 42
ASD
Support
Loss-of-function and gain-of-function mutations in PPP3CA cause two distinct disorders
DD, ID, epilepsy/seizures
Autistic features, stereotypy
Support
Prevalence and phenotypic impact of rare potentially damaging variants in autism spectrum disorder
ASD
Support
Clinical and Genetic Study on a Chinese Patient with Infantile Onset Epileptic Encephalopathy carrying a PPP3CA Null Variant: a case report
DD, epilepsy/seizures
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD
Support
Developmental and epileptic encephalopathy 91, DD,
Support
Reanalysis of whole exome sequencing data in patients with epilepsy and intellectual disability/mental retardation
DD, epilepsy/seizures
Support
DD, ID, epilepsy/seizures
Recent Recommendation
PPP3CA truncating variants clustered in the regulatory domain cause early-onset refractory epilepsy
DD
ASD or autistic features, epilepsy/seizures

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1251R001 
 stop_gained 
 c.1333C>T 
 p.Gln445Ter 
 De novo 
  
  
 GEN1251R002 
 missense_variant 
 c.275A>G 
 p.His92Arg 
 De novo 
  
  
 GEN1251R003 
 missense_variant 
 c.1339G>A 
 p.Ala447Thr 
 De novo 
  
  
 GEN1251R004 
 missense_variant 
 c.843C>G 
 p.His281Gln 
 De novo 
  
  
 GEN1251R005 
 missense_variant 
 c.844G>A 
 p.Glu282Lys 
 De novo 
  
  
 GEN1251R006 
 missense_variant 
 c.844G>A 
 p.Glu282Lys 
 De novo 
  
  
 GEN1251R007 
 missense_variant 
 c.702C>G 
 p.Asp234Glu 
 De novo 
  
 Simplex 
 GEN1251R008 
 missense_variant 
 c.449A>T 
 p.Asn150Ile 
 Unknown 
 Not maternal 
 Simplex 
 GEN1251R009 
 missense_variant 
 c.275A>G 
 p.His92Arg 
 De novo 
  
 Simplex 
 GEN1251R010 
 frameshift_variant 
 c.1290dup 
 p.Met431HisfsTer20 
 De novo 
  
 Simplex 
 GEN1251R011 
 missense_variant 
 c.1408T>G 
 p.Phe470Val 
 De novo 
  
 Simplex 
 GEN1251R012 
 missense_variant 
 c.1417G>A 
 p.Ala473Thr 
 De novo 
  
 Simplex 
 GEN1251R013 
 stop_gained 
 c.1324C>T 
 p.Gln442Ter 
 De novo 
  
 Simplex 
 GEN1251R014 
 frameshift_variant 
 c.1255_1256del 
 p.Ser419CysfsTer31 
 De novo 
  
 Simplex 
 GEN1251R015 
 frameshift_variant 
 c.1283dup 
 p.Thr429AsnfsTer22 
 De novo 
  
 Simplex 
 GEN1251R016 
 missense_variant 
 c.1533C>G 
 p.Asp511Glu 
 De novo 
  
  
 GEN1251R017 
 frameshift_variant 
 c.1283insC 
 p.Thr429AsnfsTer22 
 De novo 
  
 Simplex 
 GEN1251R018 
 frameshift_variant 
 c.1299dup 
 p.Ser434GlnfsTer17 
 De novo 
  
  
 GEN1251R019 
 frameshift_variant 
 c.1308_1309insACTT 
 p.Leu437ThrfsTer15 
 De novo 
  
  
 GEN1251R020 
 missense_variant 
 c.1417G>T 
 p.Ala473Ser 
 De novo 
  
  
 GEN1251R021 
 missense_variant 
 c.760A>G 
 p.Arg254Gly 
 De novo 
  
  
 GEN1251R022 
 missense_variant 
 c.844G>A 
 p.Glu282Lys 
 De novo 
  
  
 GEN1251R023 
 missense_variant 
 c.1456C>T 
 p.Arg486Cys 
 Unknown 
  
  
 GEN1251R024 
 missense_variant 
 c.762G>C 
 p.Arg254Ser 
 De novo 
  
  
 GEN1251R025 
 missense_variant 
 c.278G>A 
 p.Gly93Glu 
 De novo 
  
  
 GEN1251R026 
 frameshift_variant 
 c.1268_1271dup 
 p.Lys424AsnfsTer28 
 De novo 
  
 Simplex 
 GEN1251R027 
 missense_variant 
 c.844G>A 
 p.Glu282Lys 
 Unknown 
  
  
 GEN1251R028 
 frameshift_variant 
 c.1255_1256del 
 p.Ser419CysfsTer31 
 De novo 
  
  
  et al.  
 GEN1251R029 
 splice_site_variant 
 c.1340-1G>C 
  
 De novo 
  
 Simplex 
  et al.  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
4
Duplication
 1
 
4
Duplication
 1
 
4
Deletion-Duplication
 2
 

No Animal Model Data Available

 

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