HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CLDN9
claudin 9
Chromosome 16 · 16p13.3
NCBI Gene: 9080Ensembl: ENSG00000213937.4HGNC: HGNC:2051UniProt: O95484
33PubMed Papers
21Diseases
0Drugs
3Pathogenic Variants
FUNCTIONAL ROLE
Receptor
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
cell junctionvirus receptor activityprotein bindingplasma membranehearing loss, autosomal recessive 116hearing lossautosomal dominant nonsyndromic hearing lossHearing impairment
✦AI Summary

CLDN9 (claudin 9) is a tight junction protein that mediates cell-cell adhesion and forms paracellular barriers in epithelial tissues 1. While primarily functioning in maintaining tight junction integrity, CLDN9 has emerged as a significant oncogenic factor across multiple cancer types. In hepatocellular carcinoma (HCC), CLDN9 upregulation enhances metastatic potential through Tyk2/Stat3 signaling activation, promoting hepatocyte invasion and migration 2. Similarly, in glioblastoma multiforme, CLDN9 downregulation correlates with reduced tumor cell migration and invasion, and its expression inversely associates with activated CD8 T cells and dendritic cells, suggesting immunotherapeutic implications 3. In endometrial cancer, high CLDN9 expression independently predicts poor prognosis with a 5-year disease-specific survival rate of 62.8% versus 87.8% for low expression cases 4. CLDN9 dysregulation also appears prognostically significant in gastric cancer and non-functioning pituitary adenomas 567. Clinically, biallelic CLDN9 variants cause autosomal recessive deafness through impaired tight junction formation in inner ear epithelia, establishing CLDN9 as a bona fide deafness gene 1. CLDN9 shows promise as a multi-cancer biomarker and immunotherapeutic target for precision oncology approaches 8.

Sources cited
1
CLDN9 is an integral membrane protein forming epithelial tight junctions in inner ear; biallelic variants cause autosomal recessive deafness with mild to profound hearing loss
PMID: 34265170
2
CLDN9 upregulation in HCC enhances metastatic potential via Tyk2/Stat3 signaling pathway activation
PMID: 31418417
3
CLDN9 downregulation in glioblastoma correlates with reduced cell migration/invasion; expression inversely correlates with activated CD8 T cells and dendritic cells
PMID: 40533749
4
High CLDN9 expression independently predicts poor prognosis in endometrial cancer with 5-year disease-specific survival of 62.8% versus 87.8% for low expression
PMID: 36129146
5
CLDN9 identified as hub gene in tumor microenvironment-related prognostic model for gastric cancer
PMID: 37238607
6
CLDN9 upregulation increases invasiveness in non-functioning pituitary adenomas through STAT3 activation
PMID: 38131177
7
CLDN9 is significantly associated with patient survival in gastric cancer progression
PMID: 39447404
8
CLDN9 is aberrantly expressed in hepatocellular carcinoma with potential as prognostic indicator and therapeutic target
PMID: 38185042
Disease Associationsⓘ21
hearing loss, autosomal recessive 116Open Targets
0.64Moderate
hearing lossOpen Targets
0.27Weak
autosomal dominant nonsyndromic hearing lossOpen Targets
0.13Weak
Hearing impairmentOpen Targets
0.12Weak
nonsyndromic genetic hearing lossOpen Targets
0.12Weak
Pendred syndromeOpen Targets
0.12Weak
gastric cancerOpen Targets
0.08Suggestive
cancerOpen Targets
0.08Suggestive
endometrial cancerOpen Targets
0.08Suggestive
breast cancerOpen Targets
0.08Suggestive
glioblastoma multiformeOpen Targets
0.07Suggestive
deafnessOpen Targets
0.07Suggestive
neoplasmOpen Targets
0.06Suggestive
hearing loss, autosomal recessiveOpen Targets
0.05Suggestive
Non-syndromic genetic deafnessOpen Targets
0.05Suggestive
hearing loss, autosomal dominant 87Open Targets
0.04Suggestive
hearing loss, autosomal dominant 86Open Targets
0.04Suggestive
hearing loss, autosomal dominant 85Open Targets
0.04Suggestive
autosomal recessive nonsyndromic hearing loss 9Open Targets
0.04Suggestive
X-linked nonsyndromic hearing lossOpen Targets
0.04Suggestive
Deafness, autosomal recessive, 116UniProt
Pathogenic Variants3
NM_020982.4(CLDN9):c.346C>T (p.Arg116Cys)Likely pathogenic
Hearing loss, autosomal recessive 116
★☆☆☆2024→ Residue 116
NM_020982.4(CLDN9):c.370_372dup (p.Ile124dup)Pathogenic
Hearing loss|Hearing loss, autosomal recessive 116
★☆☆☆2021→ Residue 124
NM_020982.4(CLDN9):c.86del (p.Leu29fs)Pathogenic
Hearing loss, autosomal recessive 116
☆☆☆☆2024→ Residue 29
View on ClinVar ↗
Related Genes
TJP1Protein interaction98%OCLNProtein interaction96%TJP3Protein interaction87%TJP2Protein interaction85%CLDN6Protein interaction83%CLDN7Protein interaction79%
Tissue Expression6 tissues
Brain
100%
Liver
95%
Bone Marrow
91%
Lung
22%
Heart
11%
Ovary
1%
Gene Interaction Network
Click a node to explore
CLDN9TJP1OCLNTJP3TJP2CLDN6CLDN7
PROTEIN STRUCTURE
Preparing viewer…
PDB6OV2 · 3.20 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
1.71LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF1.15 [0.78–1.71]
RankingsWhere CLDN9 stands among ~20K protein-coding genes
  • #11,306of 20,598
    Most Researched33
  • #4,105of 5,498
    Most Pathogenic Variants3
  • #16,152of 17,882
    Most Constrained (LOEUF)1.71
Genes detectedCLDN9
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Comprehensive analysis reveals CLDN9 is a new biomarker in human cancers and immunotherapeutic target for glioblastoma multiforme.
PMID: 40533749
Cancer Cell Int · 2025
1.00
2
Claudins and hepatocellular carcinoma.
PMID: 38185042
Biomed Pharmacother · 2024
0.90
3
Claudin‑9 is a novel prognostic biomarker for endometrial cancer.
PMID: 36129146
Int J Oncol · 2022
0.80
4
Epigenetic and Tumor Microenvironment for Prognosis of Patients with Gastric Cancer.
PMID: 37238607
Biomolecules · 2023
0.70
5
Variants of human CLDN9 cause mild to profound hearing loss.
PMID: 34265170
Hum Mutat · 2021
0.60