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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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CLSTN1
calsyntenin 1
Chromosome 1 · 1p36.22
NCBI Gene: 22883Ensembl: ENSG00000171603.19HGNC: HGNC:17447UniProt: B4E3Q1
51PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
X11-like protein bindingamyloid-beta bindingprotein bindingkinesin bindingatrial fibrillationconnective tissue diseaseage-related macular degenerationatrial flutter
✦AI Summary

CLSTN1 (calsyntenin 1) is a neuronal cell adhesion protein that plays multiple roles in neural development, synaptic function, and disease pathogenesis. In neural development, CLSTN1 functions as part of the CTNNBIP1-CLSTN1 fusion transcript that regulates neural progenitor cell maintenance and differentiation through fine-tuning of Wnt/β-catenin signaling 1. This fusion transcript is essential for proper human neocortical and retinal development, preventing precocious neuronal differentiation 12. At the cellular level, CLSTN1 localizes to plasma membranes, intracellular vesicular structures, and cell-cell contact regions where it mediates cell adhesion and potentially synaptic signaling 3. The protein's expression and localization are regulated by MAP4 kinases, which suppress CLSTN1 recruitment to cell-cell contacts 3. In disease contexts, CLSTN1 exhibits tumor-suppressive properties, as reduced expression increases invasiveness in medulloblastoma 3. Alternative splicing of CLSTN1 is crucial for epithelial-mesenchymal transition regulation in breast cancer metastasis 4. Additionally, CLSTN1 shows potential as a therapeutic target, being associated with type 2 diabetes mellitus risk and involved in neuroprotection through S-nitrosation mechanisms in ischemic stroke 56. CLSTN1 expression is also altered in trigeminal neuralgia and regulated by DNA methylation in obesity-associated immune cells 78.

Sources cited
1
CTNNBIP1-CLSTN1 fusion transcript regulates neural progenitor maintenance and Wnt/β-catenin signaling in human neocortical development
PMID: 34192541
2
CLSTN1 fusion transcript prevents precocious neuronal differentiation in retinal development
PMID: 38165397
3
CLSTN1 localizes to plasma membrane and cell-cell contacts, suppresses invasiveness in medulloblastoma, and is regulated by MAP4 kinases
PMID: 39762313
4
Alternative splicing of CLSTN1 is crucial for epithelial-mesenchymal transition in breast cancer metastasis
PMID: 31980632
5
CLSTN1 is associated with type 2 diabetes mellitus risk as a potential therapeutic target
PMID: 40204939
6
CLSTN1 S-nitrosation is involved in neuroprotection mechanisms in ischemic stroke
PMID: 40494828
7
CLSTN1 protein levels are altered in trigeminal neuralgia patients
PMID: 38158702
8
CLSTN1 expression is regulated by DNA methylation in CD4+ T cells associated with obesity
PMID: 29956501
Disease Associationsⓘ20
atrial fibrillationOpen Targets
0.32Weak
connective tissue diseaseOpen Targets
0.27Weak
age-related macular degenerationOpen Targets
0.15Weak
atrial flutterOpen Targets
0.11Weak
Miyoshi myopathyOpen Targets
0.10Weak
neoplasmOpen Targets
0.10Suggestive
multiple myelomaOpen Targets
0.09Suggestive
gastric cancerOpen Targets
0.08Suggestive
oral squamous cell carcinomaOpen Targets
0.07Suggestive
Mobius syndromeOpen Targets
0.07Suggestive
acute lymphoblastic leukemiaOpen Targets
0.06Suggestive
dilated cardiomyopathyOpen Targets
0.05Suggestive
osteoarthritisOpen Targets
0.05Suggestive
primary familial polycythemia due to EPO receptor mutationOpen Targets
0.05Suggestive
hemoglobin D diseaseOpen Targets
0.04Suggestive
X-linked sideroblastic anemia 1Open Targets
0.04Suggestive
Alzheimer diseaseOpen Targets
0.04Suggestive
hemolytic anemia due to diphosphoglycerate mutase deficiencyOpen Targets
0.04Suggestive
hemoglobin E diseaseOpen Targets
0.04Suggestive
Adult-onset autosomal recessive sideroblastic anemiaOpen Targets
0.04Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
KLC2Protein interaction99%KLC3Protein interaction98%KLC1Protein interaction92%KLC4Protein interaction92%APBA2Protein interaction85%APPProtein interaction81%
Tissue Expression6 tissues
Brain
100%
Ovary
44%
Heart
28%
Bone Marrow
18%
Lung
17%
Liver
6%
Gene Interaction Network
Click a node to explore
CLSTN1KLC2KLC3KLC1KLC4APBA2APP
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt O94985
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.34Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.25 [0.18–0.34]
RankingsWhere CLSTN1 stands among ~20K protein-coding genes
  • #8,657of 20,598
    Most Researched51
  • #1,477of 17,882
    Most Constrained (LOEUF)0.34 · top 10%
Genes detectedCLSTN1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
The CTNNBIP1-CLSTN1 fusion transcript regulates human neocortical development.
PMID: 34192541
Cell Rep · 2021
1.00
2
RNA fusion in human retinal development.
PMID: 38165397
Elife · 2024
0.90
3
MAP4 kinase-regulated reduced CLSTN1 expression in medulloblastoma is associated with increased invasiveness.
PMID: 39762313
Sci Rep · 2025
0.80
4
Identification and validation of five novel protein targets for type 2 diabetes mellitus.
PMID: 40204939
Sci Rep · 2025
0.70
5
Design, Synthesis, and Anti-ischemic Stroke Activity Evaluation of Novel GSNOR Inhibitors.
PMID: 40494828
J Med Chem · 2025
0.60