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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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CLSTN2
calsyntenin 2
Chromosome 3 · 3q23
NCBI Gene: 64084Ensembl: ENSG00000158258.16HGNC: HGNC:17448UniProt: Q9H4D0
32PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
positive regulation of synaptic transmissionpositive regulation of synapse assemblyhomophilic cell-cell adhesioncell surfaceintelligenceattention deficit hyperactivity disorderautism spectrum disorderretinopathy
✦AI Summary

CLSTN2 (calsyntenin 2) is a postsynaptic cell adhesion molecule that mediates synapse formation and plasticity. It functions as a neurexin-binding protein at the postsynaptic membrane, promoting synapse development and assembly 1. CLSTN2 is expressed in the medial temporal lobe and contributes to episodic memory performance through interactive effects with other genetic variants 2. In episodic memory tasks, CLSTN2 polymorphisms (rs6439886) show interactive effects with KIBRA variants, where the C-allele can enhance memory performance in certain genetic backgrounds but reduces performance in KIBRA C-allele homozygotes 2. This gene-gene interaction effect is particularly pronounced in cognitively compromised populations, such as elderly individuals with depression 3. Beyond neurocognitive functions, CLSTN2 has been identified as a surface marker of midbrain dopaminergic progenitors, enabling enrichment of dopaminergic neurons (up to 80%) for cell-based Parkinson's disease therapies 1. Additionally, CLSTN2 shows genome-wide significant association with HDL-mediated cholesterol efflux capacity, a cardiovascular risk factor 4. CLSTN2 has been identified as a candidate disease gene in genetic screening studies 5, though some studies in elderly cohorts found no significant associations between CLSTN2 polymorphisms and memory decline or hippocampal atrophy 67.

Sources cited
1
CLSTN2 is a surface marker of midbrain dopaminergic progenitors and enables enrichment and transplantation for Parkinson's disease cell therapy
PMID: 35700056
2
CLSTN2 polymorphisms show interactive effects with KIBRA on episodic memory performance, with the C-allele showing context-dependent effects
PMID: 19804789
3
CLSTN2 genetic variants show interactive effects with KIBRA on episodic memory in elderly depressed individuals
PMID: 25080189
4
CLSTN2 locus is associated with HDL-mediated cholesterol efflux capacity in genome-wide association study
PMID: 36812656
5
CLSTN2 identified as candidate disease gene in clinical next-generation sequencing diagnostic panel study
PMID: 28600779
6
No significant influence of CLSTN2 SNP on memory tests in 75-76 year old cohort
PMID: 21643791
7
CLSTN2 polymorphisms not associated with episodic memory or hippocampal volume in older adults in cross-sectional and longitudinal analyses
PMID: 26415670
Disease Associationsⓘ20
intelligenceOpen Targets
0.40Moderate
attention deficit hyperactivity disorderOpen Targets
0.34Weak
autism spectrum disorderOpen Targets
0.32Weak
retinopathyOpen Targets
0.27Weak
diabetes mellitusOpen Targets
0.27Weak
bone remodeling diseaseOpen Targets
0.25Weak
prostate diseaseOpen Targets
0.25Weak
Phenotypic abnormalityOpen Targets
0.25Weak
blood vessel replacementOpen Targets
0.24Weak
Keratoconjunctivitis siccaOpen Targets
0.24Weak
pericarditisOpen Targets
0.19Weak
inflammation of heart layerOpen Targets
0.17Weak
smoking initiationOpen Targets
0.12Weak
ulcerative colitisOpen Targets
0.09Suggestive
hereditary attention deficit-hyperactivity disorderOpen Targets
0.08Suggestive
attention deficit-hyperactivity disorder 8Open Targets
0.08Suggestive
osteosarcomaOpen Targets
0.07Suggestive
intellectual disability, autosomal recessive 59Open Targets
0.07Suggestive
schizophrenia 15Open Targets
0.07Suggestive
Potocki-Lupski syndromeOpen Targets
0.06Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
KLC2Protein interaction99%NMNAT3Protein interaction90%KLC4Protein interaction70%CLSTN3Shared pathway60%CLSTN1Shared pathway50%AMIGO2Shared pathway25%
Tissue Expression6 tissues
Ovary
100%
Brain
41%
Heart
10%
Liver
1%
Lung
1%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
CLSTN2KLC2NMNAT3KLC4CLSTN3CLSTN1AMIGO2
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9H4D0
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.58Moderately Constrained
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.45 [0.36–0.58]
RankingsWhere CLSTN2 stands among ~20K protein-coding genes
  • #11,485of 20,598
    Most Researched32
  • #3,849of 17,882
    Most Constrained (LOEUF)0.58 · top quartile
Genes detectedCLSTN2
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
The landscape of genetic diseases in Saudi Arabia based on the first 1000 diagnostic panels and exomes.
PMID: 28600779
Hum Genet · 2017
1.00
2
Human midbrain dopaminergic neuronal differentiation markers predict cell therapy outcomes in a Parkinson's disease model.
PMID: 35700056
J Clin Invest · 2022
0.90
3
KIBRA and CLSTN2 polymorphisms exert interactive effects on human episodic memory.
PMID: 19804789
Neuropsychologia · 2010
0.80
4
KLKB1 and CLSTN2 are associated with HDL-mediated cholesterol efflux capacity in a genome-wide association study.
PMID: 36812656
Atherosclerosis · 2023
0.70
5
PMID: 35474272
Clin J Am Soc Nephrol · 2022
0.60