GENE REFERENCE / HGNC:2019

CLCN1

chloride voltage-gated channel 1

protein-coding gene7q34Gene information

What does this gene do?

The CLCN1 gene provides instructions for making a type of protein called a chloride channel. 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.

The CLCN1 gene provides instructions for making a chloride channel called ClC-1. These channels are found only in muscles used for movement (skeletal muscles). For the body to move normally, skeletal muscles must tense (contract) and relax in a coordinated way. Muscle contraction and relaxation are controlled by the flow of certain ions into and out of muscle cells. ClC-1 channels, which span the cell membrane, control the flow of chloride ions into these cells. This influx stabilizes the cells' electrical charge, which prevents muscles from contracting abnormally.

ClC-1 channels are made of two identical protein subunits, each produced from the CLCN1 gene. Although each subunit forms a separate opening (pore) that allows chloride ions to pass through, the two proteins work together to regulate the flow of chloride ions into skeletal muscle cells.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2020-02.

ClinGen reviews

We found no matching ClinGen review in the data used here. This does not rule out a link between the gene and a condition.

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: 1,845
Submissions for variants in or overlapping this gene: 3,448
Submissions explicitly reporting this gene: 3,357
Alleles reported pathogenic / likely pathogenic: 375
VariationIDs with uncertain significance: 638
VariationIDs with conflicting classifications: 125

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 CLCN1?

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 375 alleles in CLCN1 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 CLCN1.

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

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