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GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PPP3CA
protein phosphatase 3 catalytic subunit alpha
Chromosome 4 Β· 4q24
NCBI Gene: 5530Ensembl: ENSG00000138814.18HGNC: HGNC:9314UniProt: A0A0S2Z4B5
233PubMed Papers
22Diseases
1Drugs
49Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub Gene
RESEARCH IMPACT
Trending
CLINICAL
FDA Approved TargetOMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
negative regulation of angiotensin-activated signaling pathwaycalmodulin bindingdendritic spinepositive regulation of cell adhesiondevelopmental and epileptic encephalopathy 91arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual developmentlupus nephritisinfantile epileptic encephalopathy
✦AI Summary

PPP3CA encodes the catalytic alpha subunit of calcineurin, a calcium-dependent, calmodulin-stimulated protein phosphatase essential for transducing intracellular Ca2+-mediated signals 1. The enzyme dephosphorylates numerous substrates containing PxIxIT and LxVP motifs, including transcription factors (NFATC1, ELK1, TFEB), cytoskeletal proteins (cofilin via SSH1), and signaling molecules (DARPP32, KLHL3) 1. PPP3CA functions in the calcineurin-NFAT signaling cascade, promoting nuclear translocation of NFAT transcription factors to regulate gene expression 1. Physiologically, it is required for kidney development and function, salivary gland secretion, keratinocyte differentiation, and bone cell differentiation; it also regulates sleep-wake cycles as a sleep-promoting phosphatase competing with PKA at excitatory post-synapses 2. Pathogenic PPP3CA variants cause rare developmental and epileptic encephalopathy (DEE), with phenotype severity dependent on mutation type and location 3. Truncating mutations and variants in the regulatory domain produce drug-resistant early-onset epilepsy with developmental impairment, while calmodulin-binding domain variants cause milder childhood-onset seizures 3. Alternative splicing isoforms show CNS tissue-specificity and may influence disease manifestations 4. PPP3CA alterations also associate with multi-organ fibrosis pathogenesis 5 and cerebrospinal fluid proteomic changes in Alzheimer's disease 6. Overall, PPP3CA dysfunction impairs calcium-dependent signaling across multiple physiological systems.

Sources cited
1
PPP3CA encodes calcineurin, a serine/threonine phosphatase activated by calcium-calmodulin binding; dephosphorylates diverse substrates including transcription factors, receptors, channels, and mitochondrial proteins
PMID: 32859215
2
PPP3CA functions as sleep-promoting phosphatase at excitatory post-synapses, competing with PKA to regulate sleep-wake cycles; knockout studies show dramatic sleep duration changes
PMID: 39506111
3
Pathogenic PPP3CA variants cause developmental and epileptic encephalopathy with phenotype severity dependent on mutation type and location; regulatory domain variants produce more severe drug-resistant epilepsy
PMID: 39305655
4
PPP3CA alternative splicing isoforms show tissue-specificity in central nervous system; isoform imbalance may explain varied disease manifestations
PMID: 39707491
5
PPP3CA variants associate with multi-organ fibrosis pathways involving immune function
PMID: 38806679
6
PPP3CA is among proteomic markers in cerebrospinal fluid associated with Alzheimer's disease, relating to protein phosphorylation and neuronal mechanisms
PMID: 39373095
Disease Associationsβ“˜22
developmental and epileptic encephalopathy 91Open Targets
0.78Strong
arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual developmentOpen Targets
0.72Strong
lupus nephritisOpen Targets
0.56Moderate
infantile epileptic encephalopathyOpen Targets
0.50Moderate
type 2 diabetes mellitusOpen Targets
0.45Moderate
genetic disorderOpen Targets
0.45Moderate
obesityOpen Targets
0.39Weak
developmental and epileptic encephalopathyOpen Targets
0.37Weak
Neurodevelopmental disorderOpen Targets
0.37Weak
autosomal dominant non-syndromic intellectual disabilityOpen Targets
0.37Weak
immune system diseaseOpen Targets
0.37Weak
SeizureOpen Targets
0.37Weak
undetermined early-onset epileptic encephalopathyOpen Targets
0.37Weak
psoriasisOpen Targets
0.35Weak
Epileptic encephalopathyOpen Targets
0.34Weak
Intellectual disabilityOpen Targets
0.34Weak
intermediate uveitisOpen Targets
0.32Weak
panuveitisOpen Targets
0.32Weak
posterior uveitisOpen Targets
0.32Weak
VertigoOpen Targets
0.31Weak
Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual developmentUniProt
Epileptic encephalopathy, infantile or early childhood, 1UniProt
Pathogenic Variants49
NM_000944.5(PPP3CA):c.1283dup (p.Thr429fs)Pathogenic
Developmental and epileptic encephalopathy 91|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 429
NM_000944.5(PPP3CA):c.702C>A (p.Asp234Glu)Pathogenic
not provided|Developmental and epileptic encephalopathy 91
β˜…β˜…β˜†β˜†2025β†’ Residue 234
NM_000944.5(PPP3CA):c.1251_1252del (p.Ser417fs)Pathogenic
Developmental and epileptic encephalopathy 91
β˜…β˜…β˜†β˜†2025β†’ Residue 417
NM_000944.5(PPP3CA):c.275A>G (p.His92Arg)Pathogenic
Developmental and epileptic encephalopathy 91|Seizure;Intellectual disability|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 92
NM_000944.5(PPP3CA):c.1255_1256del (p.Ser419fs)Pathogenic
Developmental and epileptic encephalopathy 91|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 419
NM_000944.5(PPP3CA):c.1308_1311dup (p.Ser438fs)Pathogenic
Developmental and epileptic encephalopathy 91
β˜…β˜…β˜†β˜†2025β†’ Residue 438
NM_000944.5(PPP3CA):c.1339G>A (p.Ala447Thr)Pathogenic
Developmental and epileptic encephalopathy 91|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 447
NM_000944.5(PPP3CA):c.762G>T (p.Arg254Ser)Pathogenic
Developmental and epileptic encephalopathy 91|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 254
NM_000944.5(PPP3CA):c.844G>A (p.Glu282Lys)Pathogenic
Developmental and epileptic encephalopathy 91|Inborn genetic diseases|not provided|Epileptic encephalopathy|Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development;Developmental and epileptic encephalopathy 91
β˜…β˜…β˜†β˜†2024β†’ Residue 282
NM_000944.5(PPP3CA):c.1366G>T (p.Glu456Ter)Pathogenic
See cases|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 456
NM_000944.5(PPP3CA):c.1340-2A>GPathogenic
not provided
β˜…β˜…β˜†β˜†2021
NM_000944.5(PPP3CA):c.1340-2A>CLikely pathogenic
Developmental and epileptic encephalopathy 91
β˜…β˜†β˜†β˜†2025
NM_000944.5(PPP3CA):c.353A>G (p.Asp118Gly)Likely pathogenic
Developmental and epileptic encephalopathy 91
β˜…β˜†β˜†β˜†2025β†’ Residue 118
NM_000944.5(PPP3CA):c.1255_1258dup (p.Val420fs)Pathogenic
Developmental and epileptic encephalopathy 91
β˜…β˜†β˜†β˜†2025β†’ Residue 420
NM_000944.5(PPP3CA):c.1333_1336dup (p.Ser446fs)Pathogenic
Developmental and epileptic encephalopathy 91
β˜…β˜†β˜†β˜†2025β†’ Residue 446
NM_000944.5(PPP3CA):c.1284_1287dup (p.Gly430fs)Pathogenic
Developmental and epileptic encephalopathy 91
β˜…β˜†β˜†β˜†2025β†’ Residue 430
NM_000944.5(PPP3CA):c.1354_1356delinsCAATA (p.Ile452fs)Pathogenic
Developmental and epileptic encephalopathy 91
β˜…β˜†β˜†β˜†2025β†’ Residue 452
NM_000944.5(PPP3CA):c.1375A>T (p.Lys459Ter)Likely pathogenic
Developmental and epileptic encephalopathy 91
β˜…β˜†β˜†β˜†2025β†’ Residue 459
NM_000944.5(PPP3CA):c.1338dup (p.Ala447fs)Pathogenic
Developmental and epileptic encephalopathy 91
β˜…β˜†β˜†β˜†2025β†’ Residue 447
NM_000944.5(PPP3CA):c.1411G>T (p.Glu471Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 471
View on ClinVar β†—
Drug Targets1
VOCLOSPORINApproved
Serine/threonine protein phosphatase 2B catalytic subunit, alpha isoform inhibitor
Related Genes
BADProtein interaction100%RCAN1Protein interaction100%FKBP1AProtein interaction100%NFATC1Protein interaction100%NFATC2Protein interaction100%NFATC3Protein interaction100%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
12%
Ovary
9%
Lung
9%
Heart
8%
Liver
6%
Gene Interaction Network
Click a node to explore
PPP3CABADRCAN1FKBP1ANFATC1NFATC2NFATC3
PROTEIN STRUCTURE
Preparing viewer…
PDB2W73 Β· 1.45 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.24Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.13 [0.07–0.24]
RankingsWhere PPP3CA stands among ~20K protein-coding genes
  • #1,714of 20,598
    Most Researched233 Β· top 10%
  • #846of 1,025
    FDA-Approved Drug Targets1
  • #1,346of 5,498
    Most Pathogenic Variants49 Β· top quartile
  • #720of 17,882
    Most Constrained (LOEUF)0.24 Β· top 5%
Genes detectedPPP3CA
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
PPP3CA gene-related developmental and epileptic encephalopathy: Expanding the electro-clinical phenotype.
PMID: 39305655
Seizure Β· 2024
1.00
2
A 20-year Clinical and Genetic Neuromuscular Cohort Analysis in Lebanon: An International Effort.
PMID: 34602496
J Neuromuscul Dis Β· 2022
0.90
3
Calcineurin.
PMID: 32859215
Cell Commun Signal Β· 2020
0.80
4
Postsynaptic competition between calcineurin and PKA regulates mammalian sleep-wake cycles.
PMID: 39506111
Nature Β· 2024
0.70
5
OR2T6 modulates autophagy through the PPP3CA-mediated pathways to suppress gastric cancer.
PMID: 41214150
Cell Death Differ Β· 2026
0.64