CLSTN3
protein-codingcalsyntenin 3, the group of Cadherin related
Gene summary
Enables cell-cell adhesion mediator activity and neurexin family protein binding activity. Involved in L-ascorbic acid metabolic process and regulation of synapse assembly. Predicted to be located in several cellular components, including Golgi membrane; postsynaptic density; and postsynaptic membrane. Predicted to be part of protein-containing complex. Predicted to be active in several cellular components, including endoplasmic reticulum membrane; lipid droplet; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~29.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CLSTN3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014718.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 4 | 1 | 7 | ||
| missense | 143 | 1 | 1 | 145 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 149 | 5 | 2 | 156 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055533.2 | 18 | MANE Select | |
| Ensembl | ENSP00000266546.6 | 18 | MANE Select | |
| Ensembl | ENSP00000497486.1 | 3 | Standard | |
| Ensembl | ENSP00000443490.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of cell growth
- homophilic cell adhesion via plasma membrane adhesion molecules
- synapse assembly
- synaptic transmission, glutamatergic
- positive regulation of synaptic transmission
Molecular Function
- calcium ion binding
Cellular Component
- Golgi membrane
- endoplasmic reticulum membrane
- cell surface
- protein-containing complex
- postsynaptic membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000266546
- Coding exons
- 18
- Length
- 29248
- Individuals with no LoFs
- 125730
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 16
- Defined
- 125746
- p
- 0.0000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.50 | 487 | 589 | 0.826 | 0.0000366 | 6244 |
| Missense (PolyPhen) | 75 | 130.35 | 0.57539 | 1478 | ||
| Synonymous | -0.166 | 246 | 243 | 1.01 | 0.0000155 | 1910 |
| Loss of Function | 4.98 | 7 | 41.7 | 0.168 | 0.00000195 | 481 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000080 | 0.000079 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May modulate calcium-mediated postsynaptic signals. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of beta-APP40 secretion, due to the retardation of intracellular APP maturation. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- LoFtool
- 0.364
- RVIS EVS
- -1.65
- RVIS percentile EVS
- 2.76
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.293
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |