PCDHA9
Protocadherin Alpha 9
Gene Information Card
| Symbol | PCDHA9 |
|---|---|
| Full Name | Protocadherin Alpha 9 |
| Gene Type | protein-coding |
| Chromosomal Location | 5q31.3 |
| NCBI Gene ID | 56145 ncbi.nlm.nih.gov/gene/56145 |
| Ensembl ID | ENSG00000204970 |
| UniProt ID | Q9Y5I2 |
| OMIM ID | 606322 |
| HGNC ID | 8673 |
| Aliases | PCDH-ALPHA9, CNR1 |
Description
PCDHA9 (Protocadherin Alpha 9) is a protein-coding gene belonging to the protocadherin alpha gene cluster on chromosome 5. This gene encodes a member of the cadherin superfamily of calcium-dependent cell adhesion proteins. The protocadherin alpha cluster is primarily expressed in the brain and is involved in neural circuit formation, synaptic specificity, and cell-cell recognition. Alternative splicing generates multiple isoforms.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Autism Spectrum Disorder | Altered protocadherin expression may disrupt synaptic adhesion and neural connectivity | PMID: 23453885 |
| Schizophrenia | Dysregulation of PCDHA cluster genes implicated in synaptic pruning deficits | PMID: 25662881 |
| Epilepsy | Rare variants in PCDHA9 may affect neuronal network stability | ClinVar: VCV000429496 |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | High |
| Cerebral Cortex | 15.2 | High |
| Cerebellum | 10.8 | High |
| Hippocampus | 14.1 | High |
| Testis | 2.3 | Low |
| Heart | 0.5 | Not detected |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| SH-SY5Y | 8.7 | Neuroblastoma cell line |
| SK-N-SH | 7.2 | Neuroblastoma cell line |
| HEK293 | 0.3 | Low expression |
| HeLa | 0.1 | Not detected |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1234G>A (p.Gly412Arg) | Missense | <0.01% | Unknown functional impact; reported in ClinVar |
| c.567C>T (p.Pro189Leu) | Missense | <0.01% | Likely benign |
| c.2101_2102insA | Frameshift | <0.01% | Predicted loss-of-function |
Mutation functional classification
Loss of Function (LOF)
Frameshift insertions or nonsense mutations predicted to truncate the protein, likely impairing cell adhesion.
Gain of Function (GOF)
No documented gain-of-function mutations for PCDHA9.
Dominant Negative (DN)
No evidence for dominant-negative effects in PCDHA9.
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 assembly |
| • nervous system development |
Pathways
• Cell adhesion molecules (CAMs)
• Neuronal system
• Cadherin signaling pathway
Protein Summary
The PCDHA9 protein is a single-pass type I membrane protein with extracellular cadherin repeats that mediate homophilic cell adhesion. It is predominantly expressed in the brain and localizes to synapses, where it contributes to the formation and maintenance of neuronal connections. The protein undergoes proteolytic processing and may interact with intracellular signaling molecules.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| PCDHA9 Knockout HEK293 Cell Line | EDJ-KQ50903 | Human | 9752 | Details Get a Quote |
| PCDHA9 Knockout HeLa Cell Line | EDJ-KQ55247 | Human | 9752 | Details Get a Quote |
| PCDHA9 Knockout A-549 Cell Line | EDJ-KQ63725 | Human | 9752 | Details Get a Quote |
| PCDHA9 Knockout HCT 116 Cell Line | EDJ-KQ72186 | Human | 9752 | Details Get a Quote |
