CLDND1

Chr 3

claudin domain containing 1

Also known as: C3orf4, CLDN-25, GENX-3745, Z38

NCBI Gene: 56650ENSG00000080822UniProt: Q9NY35OMIM: 619677

The protein negatively regulates cellular permeability to small molecules at the cell surface. Mutations cause autosomal recessive deafness-90, which presents as hearing loss. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.617), suggesting some intolerance to complete protein loss.

OMIMResearchSummary from RefSeq, UniProt
LOEUF 0.62
Clinical Summary— CLDND1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.27) despite low pLI — interpret in context.
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.62LOEUF
pLI 0.164
Z-score 2.61
OE 0.27 (0.13–0.62)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.09Z-score
OE missense 0.98 (0.86–1.12)
155 obs / 158.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.27 (0.13–0.62)
0≤0.351.4
Missense OE0.98 (0.86–1.12)
0≤0.61.4
Synonymous OE1.08
0≤1.21.6
LoF obs/exp: 4 / 14.8Missense obs/exp: 155 / 158.2Syn Z: -0.47

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

CLDND1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival
Lukashina N et al.·Int J Mol Sci
2021Functional
Blood DNA methylation signatures are associated with social determinants of health among survivors of childhood cancer
Song N et al.·Epigenetics
2022
Association of DNA methylation with hypertension and blood pressure: a 7-year longitudinal study from KORA F4/FF4.
Lai L et al.·BMC Med
2026Natural history
Long-Read Transcriptome Sequencing and Functional Validation Reveals Novel and Oncogenic Gene Fusions in Fusion Panel-Negative Gliomas.
Rybacki K et al.·bioRxiv
2026Functional
Identifying a CD8T cell signature in the tumor microenvironment to forecast gastric cancer outcomes from sequencing data
Zeng X et al.·J Gastrointest Oncol
2024
Top 5 full-text resultsSearch PubTator3 ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
MicroRNA‑199a‑3p suppresses non‑small cell lung cancer progression by targeting FTO to enhance m6A‑mediated downregulation of MZF1 and its transcriptional activation of CLDND1.
Cui Y et al.·Mol Med Rep
2026Open Access
CLDND1 as a prognostic ferroptosis-associated biomarker in oral squamous cell carcinoma.
Zang X et al.·Biochem Biophys Res Commun
2025
MiR-595 and Cldnd1: Potential related factors for bone loss in postmenopausal women with hip osteoporotic fracture.
Jingyue S et al.·PLoS One
2024Open Access
EGF-Dependent Activation of ELK1 Contributes to the Induction of CLDND1 Expression Involved in Tight Junction Formation.
Matsuoka H et al.·Biomedicines
2022Open Access
Transcription of CLDND1 in human brain endothelial cells is regulated by the myeloid zinc finger 1.
Shima A et al.·Clin Exp Pharmacol Physiol
2021
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients