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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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CLSTN3
calsyntenin 3
Chromosome 12 · 12p13.31
NCBI Gene: 9746Ensembl: ENSG00000139182.16HGNC: HGNC:18371UniProt: Q9BQT9
27PubMed Papers
0Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
neurexin family protein bindingcell-cell adhesion mediator activityprotein bindingpositive regulation of synapse assembly
✦AI Summary

CLSTN3 (calsyntenin-3) is a transmembrane protein with distinct tissue-specific functions. In brown adipose tissue, the adipocyte-selective CLSTN3β isoform enforces multilocular lipid droplet morphology by localizing to endoplasmic reticulum-lipid droplet contact sites and inhibiting CIDEA/CIDEC-mediated lipid droplet fusion, thereby promoting efficient fatty acid oxidation and thermogenesis 1. Conversely, in white adipose tissue, CLSTN3 overexpression impairs lipolysis and promotes metabolic dysfunction; the obesity-associated rs7296261 variant increases CLSTN3 expression and disrupts adipose tissue function via interaction with APP and mitochondrial dysfunction 2. Beyond metabolism, CLSTN3 functions as a potent suppressor of TLR-mediated inflammation by inhibiting OST complex assembly and reducing N-glycosylation-dependent TLR4 membrane translocation 3. Reduced CLSTN3 expression correlates with elevated inflammatory markers in sepsis and other inflammatory diseases. CLSTN3 has emerged as a biomarker across multiple disease contexts, including associations with colorectal cancer, psoriatic arthritis, and ALS risk 4 5 6, suggesting pleiotropic roles in immunity and neurodegeneration. In neuroinflammatory contexts, CLSTN3 elevation exacerbates intracerebral hemorrhage-induced neuronal injury via miR-488 regulation 7.

Sources cited
1
CLSTN3β localizes to ER-LD contact sites and inhibits CIDEA/CIDEC-mediated lipid droplet fusion to promote multilocularity and fatty acid oxidation in brown adipocytes
PMID: 36477540
2
Obesity-associated CLSTN3 variant rs7296261 increases expression in white adipose tissue and impairs lipolysis via APP-mediated mitochondrial dysfunction
PMID: 35753632
3
CLSTN3 suppresses TLR-triggered inflammation by inhibiting OST complex assembly and reducing N-glycosylation and membrane localization of TLRs; reduced in inflammatory diseases
PMID: 41849401
4
Decreased circulating CLSTN3 levels are genetically associated with increased colorectal cancer risk
PMID: 37726845
5
Higher CLSTN3 levels are genetically associated with increased psoriatic arthritis risk
PMID: 39953266
6
CLSTN3 is significantly altered in cerebrospinal fluid of ALS patients compared to healthy controls
PMID: 37238921
7
CircAFF2 promotes neuronal injury in intracerebral hemorrhage by increasing CLSTN3 via sponging miR-488
PMID: 37884088
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
CLSTN1Shared pathway75%NRXN1Protein interaction71%NRXN2Protein interaction71%CLSTN2Shared pathway60%LRRC24Shared pathway33%AMIGO2Shared pathway33%
Tissue Expression

No tissue expression data available for this gene.

Gene Interaction Network
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CLSTN3CLSTN1NRXN1NRXN2CLSTN2LRRC24AMIGO2
PROTEIN STRUCTURE
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AlphaFoldAI-predicted · UniProt Q9BQT9
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.51Moderately Constrained
pLIⓘ
0.86Intermediate
Observed/Expected LoF0.38 [0.29–0.51]
RankingsWhere CLSTN3 stands among ~20K protein-coding genes
  • #12,533of 20,598
    Most Researched27
  • #3,093of 17,882
    Most Constrained (LOEUF)0.51 · top quartile
Genes detectedCLSTN3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Identification of novel protein biomarkers and drug targets for colorectal cancer by integrating human plasma proteome with genome.
PMID: 37726845
Genome Med · 2023
1.00
2
CLSTN3β enforces adipocyte multilocularity to facilitate lipid utilization.
PMID: 36477540
Nature · 2023
0.90
3
CLSTN3 gene variant associates with obesity risk and contributes to dysfunction in white adipose tissue.
PMID: 35753632
Mol Metab · 2022
0.80
4
An integrated multi-omics analysis identifies protein biomarkers and potential drug targets for psoriatic arthritis.
PMID: 39953266
Commun Biol · 2025
0.70
5
Discovery of Biomarkers for Amyotrophic Lateral Sclerosis from Human Cerebrospinal Fluid Using Mass-Spectrometry-Based Proteomics.
PMID: 37238921
Biomedicines · 2023
0.60