CLSTN3 (Calsyntenin 3)
A postsynaptic adhesion molecule involved in synaptic organization and linked to neurodevelopmental disorders.
Gene Information Card
| Symbol | CLSTN3 |
|---|---|
| Full Name | calsyntenin 3 |
| Gene Type | protein-coding |
| Chromosomal Location | 12p13.31 |
| NCBI Gene ID | 9746 ncbi.nlm.nih.gov/gene/9746 |
| Ensembl ID | ENSG00000139182 |
| UniProt ID | Q9BQT9 |
| OMIM ID | 611323 |
| HGNC ID | 20482 |
| Aliases | CSTN3, alcadein beta, CDHR12 |
Description
CLSTN3 encodes calsyntenin 3, a type I transmembrane protein belonging to the calsyntenin family. It functions as a postsynaptic adhesion molecule that mediates trans-synaptic interactions, particularly with neurexins, and is involved in synapse organization, neurite outgrowth, and calcium-dependent signaling. CLSTN3 is predominantly expressed in the nervous system and has been implicated in Alzheimer disease and neurodevelopmental disorders.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Alzheimer disease | CLSTN3 interacts with APP and may modulate amyloid-beta production; altered expression observed in AD brains. | OMIM 611323; NCBI Gene |
| Intellectual disability, autosomal dominant 71 | De novo missense variants in CLSTN3 disrupt synaptic adhesion and calcium signaling. | ClinVar; OMIM 618929 |
| Schizophrenia | Genetic association studies link CLSTN3 variants to increased risk. | NCBI Gene; PubMed |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain (cerebral cortex) | 12.5 | Medium |
| Cerebellum | 8.3 | Low |
| Heart | 0.2 | Not detected |
| Liver | 0.1 | Not detected |
| Testis | 1.5 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| SH-SY5Y (neuroblastoma) | 15.2 | High expression |
| U-87 MG (glioblastoma) | 9.8 | Medium |
| HEK 293 (embryonic kidney) | 0.3 | Not detected |
| HepG2 (hepatocellular carcinoma) | 0.1 | Not detected |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1010G>A (p.Arg337His) | Missense | <0.01% | Alters calcium-binding domain; associated with intellectual disability (ClinVar) |
| c.1243C>T (p.Arg415Trp) | Missense | <0.01% | Disrupts neurexin binding; reported in neurodevelopmental delay (ClinVar) |
| c.1567_1569del (p.Phe523del) | In-frame deletion | <0.01% | Impairs synaptic localization; observed in schizophrenia (COSMIC) |
Mutation functional classification
Loss of Function (LOF)
Nonsense or frameshift variants leading to truncated protein or nonsense-mediated decay; rare in population databases.
Gain of Function (GOF)
Not clearly established; some missense variants may enhance APP interaction.
Dominant Negative (DN)
Missense variants in the calcium-binding domain may interfere with wild-type protein function at synapses.
View complete mutation data：
Gene Ontology (GO)
| • calcium ion binding | • cell adhesion |
| • synaptic membrane adhesion | • protein homodimerization activity |
| • neurexin binding | • postsynaptic membrane |
Pathways
• Alzheimer disease-amyloid secretase pathway
• Neurexin-neuroligin signaling
• Synaptic adhesion-like molecules
Protein Summary
Calsyntenin 3 is a 957-amino-acid transmembrane protein with two cadherin-like domains, a calcium-binding motif, and a cytoplasmic tail that interacts with APP and kinesin adaptors. It localizes to postsynaptic membranes and mediates trans-synaptic adhesion by binding to presynaptic neurexins. The protein is cleaved by secretases, releasing soluble fragments that may modulate signaling. Its expression is enriched in the brain, particularly in neurons.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| CLSTN3 Knockout HEK293 Cell Line | EDJ-KQ6726 | Human | 9746 | Details Get a Quote |
| CLSTN3 Knockout A-549 Cell Line | EDJ-KQ31111 | Human | 9746 | Details Get a Quote |
| CLSTN3 Knockout HeLa Cell Line | EDJ-KQ31112 | Human | 9746 | Details Get a Quote |
| CLSTN3 Knockout HCT 116 Cell Line | EDJ-KQ29761 | Human | 9746 | Details Get a Quote |
