CLSTN2
protein-codingcalsyntenin 2, the group of Cadherin related
Gene summary
Predicted to enable cell-cell adhesion mediator activity. Predicted to be involved in homophilic cell-cell adhesion; positive regulation of synapse assembly; and positive regulation of synaptic transmission. Predicted to be located in several cellular components, including Golgi membrane; postsynaptic density; and postsynaptic membrane. Predicted to be active in cell surface 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 ~642.2 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 CLSTN2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022131.3. 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 | 5 | 3 | 10 | ||
| missense | 151 | 5 | 156 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 155 | 10 | 3 | 168 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071414.2 | 17 | MANE Select | |
| Ensembl | ENSP00000402460.2 | 17 | MANE Select | |
| RefSeq | XP_016862511.1 | 17 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- homophilic cell adhesion via plasma membrane adhesion molecules
- positive regulation of synaptic transmission
- positive regulation of synapse assembly
Molecular Function
- calcium ion binding
Cellular Component
- Golgi membrane
- endoplasmic reticulum membrane
- cell surface
- postsynaptic membrane
- glutamatergic synapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000458420
- Coding exons
- 17
- Length
- 642213
- Individuals with no LoFs
- 125724
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 23
- Defined
- 125747
- p
- 0.0000915
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.680 | 511 | 556 | 0.919 | 0.0000324 | 6329 |
| Missense (PolyPhen) | 117 | 144.26 | 0.81104 | 1611 | ||
| Synonymous | -1.04 | 232 | 213 | 1.09 | 0.0000134 | 1802 |
| Loss of Function | 3.67 | 17 | 42.9 | 0.396 | 0.00000193 | 526 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000088 | 0.000088 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May modulate calcium-mediated postsynaptic signals. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.265
Intolerance Scores
- LoFtool
- 0.513
- RVIS EVS
- -0.43
- RVIS percentile EVS
- 24.72
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.256
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |