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8 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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PCDHA3
protocadherin alpha 3
Chromosome 5 · 5q31.3
NCBI Gene: 56145Ensembl: ENSG00000255408.4HGNC: HGNC:8669UniProt: Q9Y5H8
18PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
plasma membranecell adhesioncell adhesion molecule bindingnervous system developmentThrombocytosisFamilial prostate cancerprostate cancermajor depressive disorder
✦AI Summary

PCDHA3 is a calcium-dependent cell adhesion protein predominantly expressed in the nervous system 1 that plays critical roles in neuronal connectivity and cell identity. As part of the clustered protocadherin-alpha family, PCDHA3 interacts with beta1-integrin to promote cell adhesion and forms oligomers with other protocadherin proteins at membrane sites 1. During neuronal maturation, PCDHA3 expression is dramatically downregulated by myelination 1. In cancer biology, PCDHA3 acts as a tumor suppressor; overexpression impairs lung squamous cell carcinoma proliferation, invasion, and migration by inhibiting epithelial-mesenchymal transition signatures 2. PCDHA3 has been implicated in neuropsychiatric disorders: maternal immune activation downregulates PCDHA3 in fetal mouse brains, linking genetic and environmental risk factors in schizophrenia pathogenesis 3. Ultra-rare missense mutations in PCDHA3 have been identified in schizophrenia cases, causing cytoplasmic aggregates and failure of homophilic plasma membrane interactions 4. Additionally, PCDHA3 variants segregate with familial restless legs syndrome 5 and have been associated with short root anomaly in Japanese populations 6, suggesting broader developmental roles beyond the nervous system.

Sources cited
1
PCDHA3 suppresses lung squamous cell carcinoma proliferation, invasion, and migration by inhibiting EMT signatures
PMID: 34086268
2
PCDHA3 is downregulated in fetal brains following maternal immune activation and linked to schizophrenia pathogenesis
PMID: 34859219
3
PCDHA3 variants segregate with familial restless legs syndrome
PMID: 23192925
4
PCDHA3 is involved in miRNA-mediated regulation of endometrial cancer cell proliferation and migration
PMID: 33751805
5
Recurrent PCDHA3 mutations in schizophrenia cases cause cytoplasmic aggregates and impaired homophilic interactions
PMID: 33756103
6
PCDHA3 variants are associated with short root anomaly in Japanese populations
PMID: 40988636
7
PCDHA3 is a calcium-dependent cell adhesion protein that interacts with beta1-integrin and is downregulated during myelination
PMID: 16697637
Disease Associationsⓘ20
ThrombocytosisOpen Targets
0.12Weak
Familial prostate cancerOpen Targets
0.11Weak
prostate cancerOpen Targets
0.11Weak
major depressive disorderOpen Targets
0.09Suggestive
schizophreniaOpen Targets
0.05Suggestive
intelligenceOpen Targets
0.04Suggestive
ocular hypotensionOpen Targets
0.03Suggestive
cervical carcinomaOpen Targets
0.02Suggestive
neoplasmOpen Targets
0.02Suggestive
Reunion island Larsen syndromeOpen Targets
0.01Suggestive
Reunion Island's Larsen syndromeOpen Targets
0.01Suggestive
squamous cell lung carcinomaOpen Targets
0.01Suggestive
cancerOpen Targets
0.01Suggestive
exstrophy-epispadias complexOpen Targets
0.00Suggestive
migraine disorderOpen Targets
0.00Suggestive
Facioscapulohumeral dystrophyOpen Targets
0.00Suggestive
head and neck malignant neoplasiaOpen Targets
0.00Suggestive
lung cancerOpen Targets
0.00Suggestive
Neurodevelopmental disorderOpen Targets
0.00Suggestive
Usher syndrome type 1Open Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
PCDHGA8Shared pathway100%PCDHA9Shared pathway100%PCDHGA12Shared pathway100%PCDHB1Shared pathway100%PCDHGB7Shared pathway100%PCDHGB6Shared pathway100%
Tissue Expression6 tissues
Ovary
100%
Brain
66%
Lung
35%
Heart
23%
Bone Marrow
4%
Liver
1%
Gene Interaction Network
Click a node to explore
PCDHA3PCDHGA8PCDHA9PCDHGA12PCDHB1PCDHGB7PCDHGB6
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9Y5H8
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.81LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.63 [0.49–0.81]
RankingsWhere PCDHA3 stands among ~20K protein-coding genes
  • #14,769of 20,598
    Most Researched18
  • #6,860of 17,882
    Most Constrained (LOEUF)0.81
Genes detectedPCDHA3
Sources retrieved8 papers
Response time—
📄 Sources
8▼
1
Protocadherin alpha 3 inhibits lung squamous cell carcinoma metastasis and epithelial-mesenchymal transition.
PMID: 34086268
Genes Genomics · 2022
1.00
2
Maternal immune activation downregulates schizophrenia genes in the foetal mouse brain.
PMID: 34859219
Brain Commun · 2021
0.88
3
Exome sequencing in a family with restless legs syndrome.
PMID: 23192925
Mov Disord · 2012
0.75
4
LncRNA-ZXF1 stabilizes P21 expression in endometrioid endometrial carcinoma by inhibiting ubiquitination-mediated degradation and regulating the miR-378a-3p/PCDHA3 axis.
PMID: 33751805
Mol Oncol · 2022
0.63
5
Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia.
PMID: 33756103
Neuron · 2021
0.50