HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PCDH12
protocadherin 12
Chromosome 5 Β· 5q31.3
NCBI Gene: 51294Ensembl: ENSG00000113555.6HGNC: HGNC:8657UniProt: Q7Z738
28PubMed Papers
21Diseases
0Drugs
30Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
extracellular exosomecell adhesion molecule bindingcalcium-dependent cell-cell adhesionplasma membraneMicrocephaly - brain defect - spasticity - hypernatremiadiencephalic-mesencephalic junction dysplasiamicrocephalyepilepsy
✦AI Summary

PCDH12 (protocadherin 12) is a non-clustered protocadherin family member that functions as a calcium-dependent cell adhesion molecule with critical roles in neural development and endothelial function 1. The protein belongs to the Ξ΄2 subgroup of non-clustered protocadherins and is predominantly expressed in the nervous system with spatiotemporally diverse expression patterns 1. PCDH12 mediates homophilic cell-cell adhesion and promotes cellular aggregation at intercellular junctions, playing essential roles in neural circuit formation and maintenance 1. Unlike classical cadherins, PCDH12 cannot bind to catenins and shows weak cytoskeletal association, suggesting distinct signaling mechanisms 1. Loss-of-function mutations in PCDH12 cause diencephalic-mesencephalic junction dysplasia syndrome 1 (DMJD), characterized by progressive microcephaly, brainstem malformations, developmental delay, epilepsy, and brain calcifications 23. Patient-derived cells lacking PCDH12 expression show impaired neurite outgrowth, reflecting the protein's crucial role in neural development 2. The clinical phenotype includes punctate brain calcifications in subcortical and perithalamic regions, distinguishing it from other brain calcification disorders 4. PCDH12 has also been implicated in various neuropsychiatric conditions and appears to have broader roles in endothelial function and immune-related processes 56.

Sources cited
1
PCDH12 classification as Ξ΄2 subgroup protocadherin with nervous system expression and roles in neural circuit formation
PMID: 21173574
2
Biallelic PCDH12 mutations cause DMJD syndrome with microcephaly, brainstem malformations, and impaired neurite outgrowth
PMID: 30178464
3
Clinical features of PCDH12 deficiency including developmental delay, epilepsy, and brain calcifications
PMID: 34773825
4
Brain calcifications in subcortical and perithalamic regions associated with PCDH12 variants
PMID: 28804758
5
Association of PCDH12 with neuropsychiatric disorders including bipolar disease and schizophrenia
PMID: 22765916
6
PCDH12 identified as diagnostic marker in atherosclerosis with immune-related functions
PMID: 40070840
Disease Associationsβ“˜21
Microcephaly - brain defect - spasticity - hypernatremiaOpen Targets
0.78Strong
diencephalic-mesencephalic junction dysplasiaOpen Targets
0.62Moderate
microcephalyOpen Targets
0.42Moderate
epilepsyOpen Targets
0.42Moderate
Intellectual disabilityOpen Targets
0.42Moderate
cerebellar ataxiaOpen Targets
0.27Weak
DystoniaOpen Targets
0.27Weak
Abnormal facial shapeOpen Targets
0.27Weak
Coats diseaseOpen Targets
0.27Weak
dystonic disorderOpen Targets
0.27Weak
genetic disorderOpen Targets
0.19Weak
Neurodevelopmental disorderOpen Targets
0.12Weak
Marshall syndromeOpen Targets
0.12Weak
early-onset non-syndromic cataractOpen Targets
0.11Weak
Total congenital cataractOpen Targets
0.09Suggestive
Partial congenital cataractOpen Targets
0.09Suggestive
Cataract-microcornea syndromeOpen Targets
0.09Suggestive
early-onset nuclear cataractOpen Targets
0.08Suggestive
isolated ectopia lentisOpen Targets
0.08Suggestive
early-onset zonular cataractOpen Targets
0.08Suggestive
Diencephalic-mesencephalic junction dysplasia syndrome 1UniProt
Pathogenic Variants30
NM_016580.4(PCDH12):c.922C>T (p.Arg308Ter)Pathogenic
not provided|Diencephalic-mesencephalic junction dysplasia syndrome 1
β˜…β˜…β˜†β˜†2026β†’ Residue 308
NM_016580.4(PCDH12):c.954C>A (p.Tyr318Ter)Pathogenic
Diencephalic-mesencephalic junction dysplasia|Disorder of development or morphogenesis|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 318
NM_016580.4(PCDH12):c.669dup (p.Lys224fs)Pathogenic
not provided|Diencephalic-mesencephalic junction dysplasia syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 224
NM_016580.4(PCDH12):c.2515C>T (p.Arg839Ter)Pathogenic
Diencephalic-mesencephalic junction dysplasia syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 839
NM_016580.4(PCDH12):c.451C>T (p.Arg151Ter)Pathogenic
Diencephalic-mesencephalic junction dysplasia|Diencephalic-mesencephalic junction dysplasia syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 151
NM_016580.4(PCDH12):c.1148C>G (p.Ser383Ter)Pathogenic
not provided|Diencephalic-mesencephalic junction dysplasia syndrome 1
β˜…β˜…β˜†β˜†2023β†’ Residue 383
NM_016580.4(PCDH12):c.309del (p.Cys104fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2021β†’ Residue 104
NM_016580.4(PCDH12):c.39dup (p.Pro14fs)Likely pathogenic
Diencephalic-mesencephalic junction dysplasia syndrome 1
β˜…β˜†β˜†β˜†2025β†’ Residue 14
NM_016580.4(PCDH12):c.669del (p.Lys224fs)Likely pathogenic
Diencephalic-mesencephalic junction dysplasia syndrome 1
β˜…β˜†β˜†β˜†2025β†’ Residue 224
NM_016580.4(PCDH12):c.2062C>T (p.Arg688Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 688
NM_016580.4(PCDH12):c.2675del (p.Gly892fs)Likely pathogenic
Diencephalic-mesencephalic junction dysplasia syndrome 1
β˜…β˜†β˜†β˜†2024β†’ Residue 892
NM_016580.4(PCDH12):c.1235T>C (p.Leu412Ser)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 412
NM_016580.4(PCDH12):c.1082C>G (p.Ser361Ter)Likely pathogenic
Diencephalic-mesencephalic junction dysplasia syndrome 1
β˜…β˜†β˜†β˜†2023β†’ Residue 361
NM_016580.4(PCDH12):c.2072del (p.Leu690_Leu691insTer)Likely pathogenic
Diencephalic-mesencephalic junction dysplasia syndrome 1
β˜…β˜†β˜†β˜†2023β†’ Residue 690
NM_016580.4(PCDH12):c.30del (p.Leu11fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 11
NM_016580.4(PCDH12):c.2424G>A (p.Trp808Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 808
NM_016580.4(PCDH12):c.311G>A (p.Cys104Tyr)Likely pathogenic
Diencephalic-mesencephalic junction dysplasia syndrome 1
β˜…β˜†β˜†β˜†2022β†’ Residue 104
NM_016580.4(PCDH12):c.191_192dup (p.Ala65fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 65
NM_016580.4(PCDH12):c.3009_3019del (p.Ser1003fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 1003
NM_016580.4(PCDH12):c.418C>T (p.Gln140Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 140
View on ClinVar β†—
Related Genes
PCDH17Protein interaction73%CDH5Protein interaction70%PCDHGB4Shared pathway60%PCDHGC3Shared pathway60%CDHR4Shared pathway50%PCDH11YShared pathway50%
Tissue Expression6 tissues
Heart
100%
Lung
76%
Liver
18%
Ovary
15%
Bone Marrow
12%
Brain
8%
Gene Interaction Network
Click a node to explore
PCDH12PCDH17CDH5PCDHGB4PCDHGC3CDHR4PCDH11Y
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q7Z738
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.75LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.59 [0.46–0.75]
RankingsWhere PCDH12 stands among ~20K protein-coding genes
  • #12,412of 20,598
    Most Researched28
  • #1,819of 5,498
    Most Pathogenic Variants30
  • #5,973of 17,882
    Most Constrained (LOEUF)0.75
Genes detectedPCDH12
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Non-clustered protocadherin.
PMID: 21173574
Cell Adh Migr Β· 2011
1.00
2
Identification of lipid metabolism related immune markers in atherosclerosis through machine learning and experimental analysis.
PMID: 40070840
Front Immunol Β· 2025
0.90
3
Integrative Analysis of Endothelial Cell Senescence-Related Genes in Idiopathic Pulmonary Fibrosis.
PMID: 41351492
FASEB J Β· 2025
0.80
4
Brain calcifications and
PMID: 28804758
Neurol Genet Β· 2017
0.70
5
Cadherins and neuropsychiatric disorders.
PMID: 22765916
Brain Res Β· 2012
0.60