Normal function · from ai-gene-review (P51798, commit 79fe13b38970) · AI-generated, not KB evidence

CLCN7 encodes ClC-7, a member of the CLC family that functions as an electrogenic 2Cl(-)/1H(+) antiporter (exchanger) rather than a passive chloride channel. It resides in the membranes of late endosomes and lysosomes, and in osteoclasts it localizes to the ruffled border bounding the resorption lacuna. ClC-7 forms an obligate heteromeric complex with the accessory beta-subunit OSTM1, which is required for ClC-7 protein stability and transport activity. By coupling chloride flux to the outwardly directed proton gradient, ClC-7 provides the counter-ion movement that allows the V-ATPase to acidify the lysosomal lumen and the osteoclast resorption space, and it raises luminal chloride concentration. Loss-of-function variants cause osteopetrosis (recessive OPTB4 and dominant Albers-Schonberg OPTA2) together with lysosomal storage and neurodegeneration, whereas certain gain-of-function variants cause a distinct hypopigmentation, organomegaly and delayed-myelination syndrome.

ClC-7 functions as an electrogenic 2Cl(-)/1H(+) antiporter in the lysosomal membrane, exchanging two chloride ions for one proton and thereby providing the counter-ion conductance that supports V-ATPase-driven luminal acidification and raises luminal chloride concentration.
molecular function: chloride:proton antiporter activity · directly involved in: chloride transmembrane transport · locations: lysosomal membrane
ClC-7 acts as the alpha-subunit of an obligate heteromeric complex with the beta-subunit OSTM1, which is required for ClC-7 protein stability and transport activity; the assembled CLCN7-OSTM1 complex is the functional transport unit in lysosomes and the osteoclast ruffled border.
molecular function: chloride:proton antiporter activity · locations: lysosomal membrane · in complex: chloride channel complex
ClC-7 transport is tonically inhibited by the lysosome-specific signaling lipid PI(3,5)P2, which binds a site at the transmembrane-cytosolic interface; relief of this inhibition (e.g. on PI(3,5)P2 depletion) activates the antiporter and modulates lysosomal acidification. Gain-of-function HOD variants (Y715C, K285T) line this lipid-binding pocket and reduce PI(3,5)P2 inhibition, causing excess transport. This regulatory lipid-binding function is well established but not currently captured in GOA.
In the knowledge base · computed from kb/ at build time

Disorders

Relationship is the entry's genetic[].relationship_type. untyped means the entry has a genetic record for the gene but does not type it; its free-text association is shown instead.

DisorderRelationshipWhere the gene appears
Hypopigmentation, Organomegaly, and Delayed Myelination and Development causative de novo gain of function
mechanism: De Novo Heterozygous CLCN7 Missense Variant
Osteopetrosis causative
mechanism: Defective osteoclast acidification
subtype: ADO2; ARO; ARO4
scoped to subtype: ADO2, ARO4
Autosomal Dominant Osteopetrosis Type II untyped
Pathogenic Variants
ClinGen gene–disease validity · snapshot 2026-10-03 · matched to entries by MONDO

An entry matches when ClinGen's MONDO disease is the entry's own disease term, a subtype term, or an exact-match mapping. An amber status marks an entry ClinGen supports the gene for (Definitive, Strong or Moderate) whose own record does not type it. A Limited, Disputed or Refuted tier on such an entry is not a gap.

ClinGen diseaseMOIClassificationdismech entry
autosomal dominant osteopetrosis 2 MONDO:0008156 AD Definitive
2023-12-04
Osteopetrosis causative
autosomal recessive osteopetrosis 4 MONDO:0012676 AR Definitive
2023-10-04
Osteopetrosis causative
hypopigmentation, organomegaly, and delayed myelination and development MONDO:0032805 AD Definitive
2026-01-09

Identity from HGNC (snapshot 2026-10-01). Page layers are described in the gene pages documentation.