GENE REFERENCE / HGNC:2025

CLCN7

Cl-/H+ antiporter 7

protein-coding gene16p13.3Gene information

What does this gene do?

The CLCN7 gene belongs to the CLC family of genes, which provide instructions for making chloride channels. These channels, which transport negatively charged chlorine atoms (chloride ions), play a key role in a cell's ability to generate and transmit electrical signals. Some CLC channels regulate the flow of chloride ions across cell membranes, while others transport chloride ions within cells.

The CLCN7 gene provides instructions for making a chloride channel called ClC-7. These channels are abundant in cells throughout the body. They are particularly important for the normal function of osteoclasts, which are specialized cells that break down bone tissue. Osteoclasts are involved in bone remodeling, a normal process in which old bone is removed and new bone is created to replace it. Bones are constantly being remodeled, and the process is carefully controlled to ensure that bones stay strong and healthy.

ClC-7 channels help regulate the relative acidity (pH) of osteoclasts. These channels transport two negatively charged chloride ions out of these cells for every positively charged hydrogen atom (hydrogen ion) that flows in. In this way, ClC-7 channels help balance the acidic environment that osteoclasts use to dissolve bone tissue. The pH inside and outside osteoclasts must be carefully controlled for these cells to break down bone effectively.

Source: MedlinePlus, National Library of Medicine. Source publication: 2026-03-02. Source review: 2010-09.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
hypopigmentation, organomegaly, and delayed myelination and developmentMONDO:0032805 · Evaluated 2026-01-09	Autosomal dominant	DefinitiveGeneral Inborn Errors of Metabolism Gene Curation Expert Panel
autosomal dominant osteopetrosis 2MONDO:0008156 · Evaluated 2023-12-04	Autosomal dominant	DefinitiveSkeletal Disorders Gene Curation Expert Panel
autosomal recessive osteopetrosis 4MONDO:0012676 · Evaluated 2023-10-04	Autosomal recessive	DefinitiveSkeletal Disorders Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 1,570
Submissions for variants in or overlapping this gene: 2,265
Submissions explicitly reporting this gene: 2,162
Alleles reported pathogenic / likely pathogenic: 104
VariationIDs with uncertain significance: 559
VariationIDs with conflicting classifications: 89

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about CLCN7?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 104 alleles in CLCN7 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in CLCN7.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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