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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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CLCN7
Cl-/H+ antiporter 7
Chromosome 16 Β· 16p13.3
NCBI Gene: 1186Ensembl: ENSG00000103249.20HGNC: HGNC:2025UniProt: P51798
117PubMed Papers
23Diseases
0Drugs
93Pathogenic Variants
FUNCTIONAL ROLE
Transporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
membranetransepithelial chloride transportlysosomal membraneprotein bindingAutosomal recessive malignant osteopetrosisAlbers-SchΓΆnberg osteopetrosisautosomal recessive osteopetrosis 4autosomal dominant osteopetrosis 2
✦AI Summary

CLCN7 encodes a slowly voltage-gated chloride/proton (Cl-/H+) antiporter that mediates 2Cl-/H+ exchange across lysosomal and late endosomal membranes 1. Operating as a counter-ion transporter paired with v-ATPase complexes, ClC-7 maintains intravesicular ion homeostasis and contributes to lysosomal acidification 1. The protein functions as a dimer, with conserved gating glutamate residues characteristic of antiporters 1. Loss-of-function CLCN7 mutations cause osteopetrosis through defective osteoclast bone resorption. Biallelic mutations result in autosomal recessive osteopetrosis (ARO) with variable neurodegeneration and lysosomal storage 1, while heterozygous mutations cause autosomal dominant osteopetrosis type 2 (ADO2), characterized by generalized osteosclerosis and "bone-in-bone" radiographic features, though disease penetrance is ~66% 23. Missense mutations typically reduce chloride currents through dominant-negative mechanisms 1. Paradoxically, gain-of-function CLCN7 variants cause hypopigmentation, organomegaly, and delayed myelination (HOD syndrome) without osteopetrosis 4. These mutations shift voltage-dependent gating to less positive potentials, increasing Cl- uptake and inducing pathologically enlarged lysosomes across multiple tissues 4. Currently, no disease-specific treatments exist; management focuses on monitoring complications 3.

Sources cited
1
ClC-7 is a Cl-/H+ exchanger functioning in osteoclasts and lysosomal/late endosomal compartments; biallelic mutations cause ARO with variable neurodegeneration; heterozygous mutations cause ADO2; explains electrophysiological properties and variants
PMID: 36513280
2
ADO2 characterized by generalized osteosclerosis, bone-in-bone appearance, and cranial nerve complications; results from CLCN7 mutations; wide disease phenotype; no disease-specific treatment available
PMID: 36863500
3
Five different missense CLCN7 mutations identified in ADO2 families; disease penetrance 66%; dominant-negative mechanism proposed; missense mutations predominate
PMID: 12929941
4
Gain-of-function CLCN7 mutations (p.Y715C, p.K285T) cause HOD syndrome without osteopetrosis; mutations shift voltage-dependent gating to less positive potentials; induce pathologically enlarged vacuoles; mechanism distinct from loss-of-function
PMID: 38838776
5
ARO patient osteoclasts with CLCN7 mutations (p.G292E, p.R403Q) showed loss-of-function with inability to resorb bone; demonstrates disease modeling applications
PMID: 33905594
Disease Associationsβ“˜23
Autosomal recessive malignant osteopetrosisOpen Targets
0.81Strong
Albers-SchΓΆnberg osteopetrosisOpen Targets
0.79Strong
autosomal recessive osteopetrosis 4Open Targets
0.76Strong
autosomal dominant osteopetrosis 2Open Targets
0.73Strong
hypopigmentation, organomegaly, and delayed myelination and developmentOpen Targets
0.70Moderate
genetic disorderOpen Targets
0.45Moderate
osteopetrosisOpen Targets
0.43Moderate
Intermediate osteopetrosisOpen Targets
0.39Weak
Abnormality of the skeletal systemOpen Targets
0.27Weak
alcohol drinkingOpen Targets
0.09Suggestive
12q14 microdeletion syndromeOpen Targets
0.08Suggestive
age-related macular degenerationOpen Targets
0.08Suggestive
pyknoachondrogenesisOpen Targets
0.08Suggestive
melorheostosisOpen Targets
0.08Suggestive
osteomesopyknosisOpen Targets
0.08Suggestive
amelogenesis imperfectaOpen Targets
0.07Suggestive
osteoporosisOpen Targets
0.07Suggestive
melorheostosis with osteopoikilosisOpen Targets
0.07Suggestive
bladder calculusOpen Targets
0.07Suggestive
Dentin dysplasia - sclerotic bonesOpen Targets
0.07Suggestive
Hypopigmentation, organomegaly, and delayed myelination and developmentUniProt
Osteopetrosis, autosomal dominant 2UniProt
Osteopetrosis, autosomal recessive 4UniProt
Pathogenic Variants93
NM_001287.6(CLCN7):c.296A>G (p.Tyr99Cys)Pathogenic
Autosomal dominant osteopetrosis 2|Autosomal recessive osteopetrosis 4|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 99
NM_001287.6(CLCN7):c.2299C>T (p.Arg767Trp)Pathogenic
Autosomal dominant osteopetrosis 2|Autosomal recessive osteopetrosis 4|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 767
NM_001287.6(CLCN7):c.746C>T (p.Pro249Leu)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 249
NM_001287.6(CLCN7):c.856C>T (p.Arg286Trp)Pathogenic
not provided|Autosomal dominant osteopetrosis 2|Disorder of bone
β˜…β˜…β˜†β˜†2025β†’ Residue 286
NM_001287.6(CLCN7):c.2284C>T (p.Arg762Trp)Pathogenic
not provided|Autosomal recessive osteopetrosis 4
β˜…β˜…β˜†β˜†2025β†’ Residue 762
NM_001287.6(CLCN7):c.857G>A (p.Arg286Gln)Pathogenic
Autosomal dominant osteopetrosis 2|Inborn genetic diseases|Abnormality of the skeletal system|not provided|CLCN7-related disorder|Autosomal recessive osteopetrosis 4|Disorder of bone
β˜…β˜…β˜†β˜†2025β†’ Residue 286
NM_001287.6(CLCN7):c.643G>A (p.Gly215Arg)Pathogenic
Autosomal dominant osteopetrosis 2|not provided|CLCN7-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 215
NM_001287.6(CLCN7):c.1576C>T (p.Arg526Trp)Pathogenic
not provided|Autosomal dominant osteopetrosis 2
β˜…β˜…β˜†β˜†2025β†’ Residue 526
NM_001287.6(CLCN7):c.739-18G>APathogenic
Autosomal dominant osteopetrosis 2|not provided|Autosomal recessive osteopetrosis 4
β˜…β˜…β˜†β˜†2025
NM_001287.6(CLCN7):c.139C>T (p.Gln47Ter)Pathogenic
not provided|Autosomal recessive osteopetrosis 4
β˜…β˜…β˜†β˜†2025β†’ Residue 47
NM_001287.6(CLCN7):c.163C>T (p.Arg55Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 55
NM_001287.6(CLCN7):c.2116_2147dup (p.Pro716_Arg717insTer)Likely pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 716
NM_001287.6(CLCN7):c.1617+119G>APathogenic
Autosomal recessive osteopetrosis 4|not provided
β˜…β˜…β˜†β˜†2024
NM_001287.6(CLCN7):c.1194G>A (p.Trp398Ter)Pathogenic
not provided|Autosomal recessive osteopetrosis 4;Autosomal dominant osteopetrosis 2;Hypopigmentation, organomegaly, and delayed myelination and development
β˜…β˜…β˜†β˜†2024β†’ Residue 398
NM_001287.6(CLCN7):c.641A>G (p.Asn214Ser)Pathogenic
Autosomal recessive osteopetrosis 4|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 214
NM_001287.6(CLCN7):c.295T>C (p.Tyr99His)Likely pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 99
NM_001287.6(CLCN7):c.746C>G (p.Pro249Arg)Pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 249
NM_001287.6(CLCN7):c.2144A>G (p.Tyr715Cys)Pathogenic
not provided|Hypopigmentation, organomegaly, and delayed myelination and development|Autosomal recessive osteopetrosis 4;Autosomal dominant osteopetrosis 2;Hypopigmentation, organomegaly, and delayed myelination and development
β˜…β˜…β˜†β˜†2022β†’ Residue 715
NM_001287.6(CLCN7):c.1828_1829del (p.Ser610fs)Pathogenic
Autosomal recessive osteopetrosis 4
β˜…β˜†β˜†β˜†2025β†’ Residue 610
NM_001287.6(CLCN7):c.2231C>T (p.Ser744Phe)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 744
View on ClinVar β†—
Related Genes
CA2Protein interaction100%TCIRG1Protein interaction96%PLEKHM1Protein interaction92%ATP12AProtein interaction83%ATP4AProtein interaction83%SNX10Protein interaction78%
Tissue Expression6 tissues
Bone Marrow
100%
Lung
86%
Liver
74%
Ovary
66%
Heart
43%
Brain
37%
Gene Interaction Network
Click a node to explore
CLCN7CA2TCIRG1PLEKHM1ATP12AATP4ASNX10
PROTEIN STRUCTURE
Preparing viewer…
PDB9G6C Β· 1.80 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.82LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.66 [0.53–0.82]
RankingsWhere CLCN7 stands among ~20K protein-coding genes
  • #4,028of 20,598
    Most Researched117 Β· top quartile
  • #824of 5,498
    Most Pathogenic Variants93 Β· top quartile
  • #6,962of 17,882
    Most Constrained (LOEUF)0.82
Genes detectedCLCN7
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Autosomal dominant osteopetrosis.
PMID: 36863500
Bone Β· 2023
1.00
2
CLCN7, a gene shared by autosomal recessive and autosomal dominant osteopetrosis.
PMID: 36513280
Bone Β· 2023
0.90
3
Gain-of-function variants in CLCN7 cause hypopigmentation and lysosomal storage disease.
PMID: 38838776
J Biol Chem Β· 2024
0.80
4
Chloride channel 7 (ClCN7) gene mutations and autosomal dominant osteopetrosis, type II.
PMID: 12929941
J Bone Miner Res Β· 2003
0.70
5
Metabolomics study of osteopetrosis caused by
PMID: 40018371
Front Endocrinol (Lausanne) Β· 2024
0.60