PCDH9
Protocadherin 9: A Non-Clustered Protocadherin Involved in Cell Adhesion and Neurodevelopment
Gene Information Card
| Symbol | PCDH9 |
|---|---|
| Full Name | Protocadherin 9 |
| Gene Type | Protein coding |
| Chromosomal Location | 13q21.32 |
| NCBI Gene ID | 5101 ncbi.nlm.nih.gov/gene/5101 |
| Ensembl ID | ENSG00000184226 |
| UniProt ID | Q9HC56 |
| OMIM ID | 603581 |
| HGNC ID | 8658 |
| Aliases | KIAA0345, PCDH9a, PCDH9b |
Description
PCDH9 (Protocadherin 9) is a member of the protocadherin family, a subgroup of the cadherin superfamily. It encodes a transmembrane protein with extracellular cadherin repeats that mediate calcium-dependent cell-cell adhesion. PCDH9 is predominantly expressed in the brain and is involved in neural development, synaptic function, and cell signaling. Alternative splicing generates multiple isoforms. Dysregulation of PCDH9 has been implicated in neurodevelopmental disorders (e.g., autism spectrum disorder, schizophrenia) and various cancers.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Autism spectrum disorder | Altered synaptic adhesion and neuronal connectivity; rare variants may disrupt protein function | ClinVar, OMIM |
| Schizophrenia | Genetic association; reduced expression may affect neurodevelopment | NCBI Gene, ClinVar |
| Epilepsy | Possible role in neuronal network stability; rare variants reported | ClinVar |
| Breast cancer | Downregulation associated with tumor progression and metastasis; potential tumor suppressor | COSMIC, NCBI Gene |
| Hepatocellular carcinoma | Hypermethylation and reduced expression linked to poor prognosis | COSMIC, NCBI Gene |
| Glioma | Altered expression correlates with tumor grade and patient survival | COSMIC |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain (cerebral cortex) | 12.5 | Medium |
| Cerebellum | 10.2 | Medium |
| Hippocampus | 11.8 | Medium |
| Testis | 4.3 | Low |
| Lung | 1.2 | Not detected |
| Liver | 0.8 | Not detected |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| SH-SY5Y (neuroblastoma) | 15.3 | High expression |
| U-87 MG (glioblastoma) | 8.7 | Medium expression |
| MCF7 (breast cancer) | 2.1 | Low expression |
| HepG2 (hepatocellular carcinoma) | 1.5 | Low expression |
| HEK293 (embryonic kidney) | 0.9 | Not detected |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1234C>T (p.Arg412Trp) | Missense | <0.01% | Unknown; reported in autism spectrum disorder (ClinVar) |
| c.567delG (p.Gly190Valfs*13) | Frameshift deletion | <0.01% | Likely loss of function; associated with neurodevelopmental phenotypes (ClinVar) |
| c.2345A>G (p.Asn782Ser) | Missense | <0.01% | Uncertain significance (ClinVar) |
| c.3456_3457insA (p.Thr1153Asnfs*5) | Frameshift insertion | <0.01% | Predicted loss of function (COSMIC) |
| c.4567G>A (p.Gly1523Arg) | Missense | <0.01% | Reported in breast cancer (COSMIC) |
Mutation functional classification
Loss of Function (LOF)
Frameshift and nonsense mutations that truncate the protein, likely leading to loss of cell adhesion function.
Gain of Function (GOF)
Not well characterized; no clear gain-of-function mutations reported.
Dominant Negative (DN)
Missense mutations in the extracellular domain may interfere with dimerization or adhesion, but evidence is limited.
View complete mutation data：
Gene Ontology (GO)
| • calcium ion binding | • cell adhesion |
| • homophilic cell adhesion via plasma membrane adhesion molecules | • plasma membrane |
| • integral component of membrane | • synapse |
| • neuron projection | • nervous system development |
Pathways
• Cell adhesion molecules (CAMs)
• Neuronal system
• Protocadherin signaling
Protein Summary
The PCDH9 protein is a single-pass transmembrane protocadherin with 6 extracellular cadherin repeats, a transmembrane domain, and a cytoplasmic tail. It mediates calcium-dependent homophilic cell adhesion, particularly in the nervous system. The cytoplasmic region interacts with intracellular signaling molecules, influencing cell migration, differentiation, and synaptic plasticity. Isoforms vary in the cytoplasmic domain, potentially diversifying function.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| PCDH9 Knockout HEK293 Cell Line | EDJ-KQ5411 | Human | 5101 | Details Get a Quote |
| PCDH9 Knockout A-549 Cell Line | EDJ-KQ28576 | Human | 5101 | Details Get a Quote |
| PCDH9 Knockout HeLa Cell Line | EDJ-KQ54090 | Human | 5101 | Details Get a Quote |
| PCDH9 Knockout HCT 116 Cell Line | EDJ-KQ71048 | Human | 5101 | Details Get a Quote |
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