PPP3CAprotein phosphatase 3 catalytic subunit alpha
Autism Reports / Total Reports
3 / 13Rare Variants / Common Variants
28 / 0Aliases
PPP3CA, ACCIID, CALN, CALNA, CALNA1, CCN1, CNA1, DEE91, IECEE, IECEE1, PPP2BAssociated Syndromes
-Chromosome Band
4q24Associated Disorders
ASD, EPSRelevance 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 Genotype-phenotype correlation of 5 novel patients and 16 previously unpublished patients with PPP3CA variants in Panneerselvam et al., 2021 found that while autistic features were overall a commonly observed phenotype in individuals with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
SFARI Genomic Platforms
Reports related to PPP3CA (13 Reports)
# | Type | Title | Author, Year | Autism Report | Associated Disorders |
---|---|---|---|---|---|
1 | Primary | - | Myers CT et al. (2017) | No | Autistic features, stereotypy |
2 | Support | - | Mizuguchi T et al. (2018) | No | Autistic features, stereotypy |
3 | Support | - | Rydzanicz M et al. (2019) | No | - |
4 | Support | - | Qian Y et al. (2018) | No | - |
5 | Support | - | Li J et al. (2019) | No | - |
6 | Support | Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism | Satterstrom FK et al. (2020) | Yes | - |
7 | Support | - | Yang S et al. (2020) | No | - |
8 | Recent Recommendation | - | Panneerselvam S et al. (2021) | No | ASD or autistic features, epilepsy/seizures |
9 | Support | - | Mahjani B et al. (2021) | Yes | - |
10 | Support | - | Zhou X et al. (2022) | Yes | - |
11 | Support | - | Ko YJ et al. (2023) | No | - |
12 | Support | - | Lucie Sedlackova et al. (2024) | No | - |
13 | Support | - | Erica Rosina et al. (2024) | No | - |
Rare Variants (28)
Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Parental Transmission | Family Type | PubMed ID | Author, Year |
---|---|---|---|---|---|---|---|---|
c.1333C>T | p.Gln445Ter | stop_gained | De novo | - | - | 28942967 | Myers CT et al. (2017) | |
c.844G>A | p.Glu282Lys | missense_variant | Unknown | - | - | 37645600 | Ko YJ et al. (2023) | |
c.278G>A | p.Gly93Glu | missense_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
c.762G>C | p.Arg254Ser | missense_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
c.275A>G | p.His92Arg | missense_variant | De novo | - | - | 28942967 | Myers CT et al. (2017) | |
c.843C>G | p.His281Gln | missense_variant | De novo | - | - | 28942967 | Myers CT et al. (2017) | |
c.844G>A | p.Glu282Lys | missense_variant | De novo | - | - | 28942967 | Myers CT et al. (2017) | |
c.1339G>A | p.Ala447Thr | missense_variant | De novo | - | - | 28942967 | Myers CT et al. (2017) | |
c.1456C>T | p.Arg486Cys | missense_variant | Unknown | - | - | 34615535 | Mahjani B et al. (2021) | |
c.1324C>T | p.Gln442Ter | stop_gained | De novo | - | Simplex | 30254215 | Rydzanicz M et al. (2019) | |
c.1340-1G>C | - | splice_site_variant | De novo | - | Simplex | 38041506 | Erica Rosina et al. (2024) | |
c.1533C>G | p.Asp511Glu | missense_variant | De novo | - | - | 31981491 | Satterstrom FK et al. (2020) | |
c.760A>G | p.Arg254Gly | missense_variant | De novo | - | - | 33963760 | Panneerselvam S et al. (2021) | |
c.844G>A | p.Glu282Lys | missense_variant | De novo | - | - | 33963760 | Panneerselvam S et al. (2021) | |
c.1417G>T | p.Ala473Ser | missense_variant | De novo | - | - | 33963760 | Panneerselvam S et al. (2021) | |
c.275A>G | p.His92Arg | missense_variant | De novo | - | Simplex | 29432562 | Mizuguchi T et al. (2018) | |
c.702C>G | p.Asp234Glu | missense_variant | De novo | - | Simplex | 29432562 | Mizuguchi T et al. (2018) | |
c.1408T>G | p.Phe470Val | missense_variant | De novo | - | Simplex | 29432562 | Mizuguchi T et al. (2018) | |
c.1417G>A | p.Ala473Thr | missense_variant | De novo | - | Simplex | 29432562 | Mizuguchi T et al. (2018) | |
c.1283dup | p.Thr429AsnfsTer22 | frameshift_variant | De novo | - | Simplex | 30904718 | Li J et al. (2019) | |
c.1283insC | p.Thr429AsnfsTer22 | frameshift_variant | De novo | - | Simplex | 32593294 | Yang S et al. (2020) | |
c.1299dup | p.Ser434GlnfsTer17 | frameshift_variant | De novo | - | - | 33963760 | Panneerselvam S et al. (2021) | |
c.1268_1271dup | p.Lys424AsnfsTer28 | frameshift_variant | De novo | - | Simplex | 37645600 | Ko YJ et al. (2023) | |
c.1255_1256del | p.Ser419CysfsTer31 | frameshift_variant | De novo | - | Simplex | 30455226 | Qian Y et al. (2018) | |
c.1290dup | p.Met431HisfsTer20 | frameshift_variant | De novo | - | Simplex | 29432562 | Mizuguchi T et al. (2018) | |
c.449A>T | p.Asn150Ile | missense_variant | Unknown | Not maternal | Simplex | 29432562 | Mizuguchi T et al. (2018) | |
c.1255_1256del | p.Ser419CysfsTer31 | frameshift_variant | De novo | - | - | 38008000 | Lucie Sedlackova et al. (2024) | |
c.1308_1309insACTT | p.Leu437ThrfsTer15 | frameshift_variant | De novo | - | - | 33963760 | Panneerselvam S et al. (2021) |
Common Variants
No common variants reported.
SFARI Gene score
Suggestive Evidence, Syndromic
Score Delta: Score remained at 3S
criteria met
See SFARI Gene'scoring criteriaThe literature is replete with relatively small studies of candidate genes, using either common or rare variant approaches, which do not reach the criteria set out for categories 1 and 2. Genes that had two such lines of supporting evidence were placed in category 3, and those with one line of evidence were placed in category 4. Some additional lines of "accessory evidence" (indicated as "acc" in the score cards) could also boost a gene from category 4 to 3.
The syndromic category includes mutations that are associated with a substantial degree of increased risk and consistently linked to additional characteristics not required for an ASD diagnosis. If there is independent evidence implicating a gene in idiopathic ASD, it will be listed as "#S" (e.g., 2S, 3S, etc.). If there is no such independent evidence, the gene will be listed simply as "S."
4/1/2022
Increased from to 3S
Krishnan Probability Score
Score 0.60870123685605
Ranking 278/25841 scored genes
[Show Scoring Methodology]
ExAC Score
Score 0.99814878870211
Ranking 1234/18225 scored genes
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Sanders TADA Score
Score 0.93650262999599
Ranking 13217/18665 scored genes
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Zhang D Score
Score 0.4766182216649
Ranking 688/20870 scored genes
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