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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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CLCN5
Cl-/H+ antiporter 5
Chromosome X · Xp11.23
NCBI Gene: 1184Ensembl: ENSG00000171365.17HGNC: HGNC:2023UniProt: A8K4H5
115PubMed Papers
24Diseases
0Drugs
141Pathogenic Variants
FUNCTIONAL ROLE
Transporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
voltage-gated chloride channel activityprotein bindingidentical protein bindingrenal system processDent disease type 1hypophosphatemic rickets, X-linked recessiveDent diseaseproteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis
✦AI Summary

CLCN5 encodes ClC-5, an electrogenic Cl⁻/H⁺ antiporter that functions as a proton-coupled chloride transporter, exchanging chloride ions against protons 1. ClC-5 localizes to endosomal and lysosomal membranes and is strongly expressed in renal proximal tubules, where it plays a critical role in endocytic protein uptake and prevention of proteinuria 2. The protein functions as part of an endosomal macromolecular complex responsible for albumin and low-molecular-weight protein reabsorption 3. Recent structural studies confirm ClC-5 interacts with TMEM9 and TMEM9B as subunits of chloride-proton antiporter complexes in early endosomes 4. CLCN5 mutations cause Dent disease 1 (also termed low molecular weight proteinuria with hypercalciuria and nephrocalcinosis), an X-linked renal tubular disorder characterized by proximal tubule dysfunction 5. The disease manifests primarily in males with low-molecular-weight proteinuria, hypercalciuria, nephrolithiasis, nephrocalcinosis, and progressive renal failure 6. Approximately 60% of Dent disease patients carry CLCN5 mutations 7. Progression to end-stage renal failure occurs in 30-80% of affected males between the 3rd and 5th decades 5. Management focuses on supportive care, treatment of hypercalciuria, and prevention of nephrolithiasis, with prognosis generally favorable in most patients.

Sources cited
1
CLCN5 functions as a proton-coupled chloride transporter exchanging chloride ions against protons
PMID: 20466723
2
ClC-5 is involved in preventing protein loss in the kidney and is defective in Dent disease
PMID: 32289351
3
ClC-5 is part of the endocytic complex for albumin and low-molecular-weight protein uptake in renal proximal tubules
PMID: 32019767
4
ClC-5 interacts with TMEM9 and TMEM9B in early endosomal chloride-proton antiporter complexes
PMID: 40437099
5
CLCN5 mutations cause Dent disease 1, characterized by proximal tubule dysfunction and progressive renal failure in 30-80% of males
PMID: 20946626
6
Dent disease presents with hypercalciuria, low molecular weight proteinuria, nephrocalcinosis, and proximal tubular dysfunction
PMID: 30454742
7
Approximately 60% of Dent disease patients have causative CLCN5 mutations
PMID: 36646056
Disease Associationsⓘ24
Dent disease type 1Open Targets
0.85Strong
hypophosphatemic rickets, X-linked recessiveOpen Targets
0.76Strong
Dent diseaseOpen Targets
0.73Strong
proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosisOpen Targets
0.71Strong
hypophosphatemic ricketsOpen Targets
0.56Moderate
genetic disorderOpen Targets
0.47Moderate
nephrotic syndromeOpen Targets
0.42Moderate
Low-molecular-weight proteinuriaOpen Targets
0.27Weak
HyperkalemiaOpen Targets
0.27Weak
Multiple small medullary renal cystsOpen Targets
0.27Weak
X-linked dominant hypophosphatemic ricketsOpen Targets
0.27Weak
X-linked hypophosphatemiaOpen Targets
0.27Weak
focal segmental glomerulosclerosisOpen Targets
0.09Suggestive
familial idiopathic steroid-resistant nephrotic syndromeOpen Targets
0.08Suggestive
uridine-cytidineuriaOpen Targets
0.08Suggestive
hyperprolinemia type 1Open Targets
0.08Suggestive
isolated sedoheptulokinase deficiencyOpen Targets
0.08Suggestive
pentosuriaOpen Targets
0.08Suggestive
IGA glomerulonephritisOpen Targets
0.08Suggestive
lipoprotein glomerulopathyOpen Targets
0.07Suggestive
Dent disease 1UniProt
Hypophosphatemic rickets, X-linked recessiveUniProt
Low molecular weight proteinuria with hypercalciuria and nephrocalcinosisUniProt
Nephrolithiasis, X-linked recessive, with renal failureUniProt
Pathogenic Variants141
NM_001127898.4(CLCN5):c.292C>T (p.Arg98Ter)Pathogenic
not provided|Dent disease type 1|Hypophosphatemic rickets, X-linked recessive;Dent disease type 1;Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;X-linked recessive nephrolithiasis with renal failure
★★☆☆2025→ Residue 98
NM_001127898.4(CLCN5):c.310C>T (p.Arg104Ter)Pathogenic
Dent disease type 1|CLCN5-related disorder|Familial X-linked hypophosphatemic vitamin D refractory rickets|Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;Dent disease type 1;Hypophosphatemic rickets, X-linked recessive;X-linked recessive nephrolithiasis with renal failure|not provided
★★☆☆2025→ Residue 104
NM_001127898.4(CLCN5):c.2362C>T (p.Arg788Ter)Pathogenic
Dent disease type 1|not provided|Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;Dent disease type 1;Hypophosphatemic rickets, X-linked recessive;X-linked recessive nephrolithiasis with renal failure
★★☆☆2025→ Residue 788
NM_001127898.4(CLCN5):c.2152C>T (p.Arg718Ter)Pathogenic
Dent disease type 1|not provided
★★☆☆2025→ Residue 718
NM_001127898.4(CLCN5):c.1844G>A (p.Ser615Asn)Likely pathogenic
CLCN5-related disorder|not provided
★★☆☆2025→ Residue 615
NM_001127898.4(CLCN5):c.2119C>T (p.Arg707Ter)Pathogenic
Dent disease type 1|not provided|Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis|Dent disease|Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;Dent disease type 1;Hypophosphatemic rickets, X-linked recessive;X-linked recessive nephrolithiasis with renal failure
★★☆☆2025→ Residue 707
NM_001127898.4(CLCN5):c.1756C>T (p.Arg586Trp)Pathogenic
Dent disease type 1|Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;Dent disease type 1;Hypophosphatemic rickets, X-linked recessive;X-linked recessive nephrolithiasis with renal failure|not provided
★★☆☆2025→ Residue 586
NM_001127898.4(CLCN5):c.941C>T (p.Ser314Leu)Pathogenic
Hypophosphatemic rickets, X-linked recessive|Dent disease type 1|not provided|X-linked recessive nephrolithiasis with renal failure;Hypophosphatemic rickets, X-linked recessive;Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;Dent disease type 1|CLCN5-related disorder
★★☆☆2025→ Residue 314
NM_001127898.4(CLCN5):c.328del (p.Ser110fs)Pathogenic
Inborn genetic diseases|not provided
★★☆☆2025→ Residue 110
NM_001127898.4(CLCN5):c.871T>C (p.Cys291Arg)Likely pathogenic
Nephrotic syndrome|Hypophosphatemic rickets, X-linked recessive;Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;Dent disease type 1;X-linked recessive nephrolithiasis with renal failure|not provided
★★☆☆2025→ Residue 291
NM_001127898.4(CLCN5):c.1275T>G (p.Tyr425Ter)Pathogenic
Hypophosphatemic rickets, X-linked recessive;Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;Dent disease type 1;X-linked recessive nephrolithiasis with renal failure|not provided
★★☆☆2025→ Residue 425
NM_001127898.4(CLCN5):c.1249C>T (p.Arg417Ter)Pathogenic
Dent disease type 1|not provided|Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;Dent disease type 1;Hypophosphatemic rickets, X-linked recessive;X-linked recessive nephrolithiasis with renal failure|Thyroid cancer, nonmedullary, 1
★★☆☆2024→ Residue 417
NM_001127898.4(CLCN5):c.1014+1G>APathogenic
X-linked recessive nephrolithiasis with renal failure;Dent disease type 1;Hypophosphatemic rickets, X-linked recessive;Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis|X-linked recessive nephrolithiasis with renal failure
★★☆☆2024
NM_001127898.4(CLCN5):c.1329dup (p.Asn444fs)Pathogenic
Dent disease type 1|not provided
★★☆☆2024→ Residue 444
NM_001127898.4(CLCN5):c.2060dup (p.Tyr687Ter)Likely pathogenic
Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis|Dent disease type 1
★★☆☆2024→ Residue 687
NM_001127898.4(CLCN5):c.1633C>T (p.Gln545Ter)Likely pathogenic
Dent disease type 1|Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;X-linked recessive nephrolithiasis with renal failure;Dent disease type 1;Hypophosphatemic rickets, X-linked recessive
★★☆☆2024→ Residue 545
NM_001127898.4(CLCN5):c.933+1G>APathogenic
not provided|Dent disease type 1;Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis;Hypophosphatemic rickets, X-linked recessive;X-linked recessive nephrolithiasis with renal failure
★★☆☆2024
NM_001127898.4(CLCN5):c.1773TGT[1] (p.Val593del)Pathogenic
not provided
★★☆☆2024→ Residue 593
NM_001127898.4(CLCN5):c.1609C>T (p.Arg537Ter)Pathogenic
Dent disease type 1|not provided
★★☆☆2022→ Residue 537
NM_001127898.4(CLCN5):c.845del (p.Gly282fs)Pathogenic
not provided
★★☆☆2022→ Residue 282
View on ClinVar ↗
Related Genes
CUBNProtein interaction85%SLC34A3Protein interaction84%SLC9A3Protein interaction82%CFL1Protein interaction81%CFL2Protein interaction81%BSNDProtein interaction81%
Tissue Expression6 tissues
Liver
100%
Ovary
61%
Lung
29%
Brain
24%
Bone Marrow
14%
Heart
9%
Gene Interaction Network
Click a node to explore
CLCN5CUBNSLC34A3SLC9A3CFL1CFL2BSND
PROTEIN STRUCTURE
Preparing viewer…
PDB2J9L · 2.30 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.47Moderately Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.31 [0.22–0.47]
RankingsWhere CLCN5 stands among ~20K protein-coding genes
  • #4,108of 20,598
    Most Researched115 · top quartile
  • #538of 5,498
    Most Pathogenic Variants141 · top 10%
  • #2,712of 17,882
    Most Constrained (LOEUF)0.47 · top quartile
Genes detectedCLCN5
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Hypercalciuria.
PMID: 11195313
Joint Bone Spine · 2000
1.00
2
X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes.
PMID: 25644381
Mol Psychiatry · 2016
0.90
3
EndoMAP.v1 charts the structural landscape of human early endosome complexes.
PMID: 40437099
Nature · 2025
0.80
4
Dent's disease.
PMID: 20946626
Orphanet J Rare Dis · 2010
0.70
5
A Study on the CLCN5 Gene in Iranian Patients: A Report of Novel and Recurrent Mutations.
PMID: 36646056
Nephron · 2023
0.60