GENE REFERENCE / HGNC:1480

CAPN3

calpain 3

protein-coding gene15q15.1Gene information

What does this gene do?

The CAPN3 gene provides instructions for making an enzyme called calpain-3, which is found within muscle fiber structures called sarcomeres. Sarcomeres are needed for the tensing of muscle fibers (contraction). When linked together, sarcomeres form myofibrils, which are the basic units of muscle fibers.

Calpain-3 cuts (cleaves) damaged proteins into shorter segments so that they can be easily removed from the sarcomere. The process of making new proteins and breaking down older proteins within the sarcomere is known as sarcomere remodeling. This process enables the muscle cells to adapt to the body's needs.

In addition to maintaining the sarcomeres, calpain-3 also interacts with other proteins to help regulate calcium transport within muscle fibers.

Source: MedlinePlus, National Library of Medicine. Source publication: 2025-11-19. Source review: 2025-11.

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
muscular dystrophy, limb-girdle, autosomal dominantMONDO:0015151 · Evaluated 2025-05-13	Autosomal dominant	DefinitiveMuscular Dystrophies and Myopathies Gene Curation Expert Panel
autosomal recessive limb-girdle muscular dystrophyMONDO:0015152 · Evaluated 2024-08-29	Autosomal recessive	DefinitiveMuscular Dystrophies and Myopathies 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: 2,203
Submissions for variants in or overlapping this gene: 5,025
Submissions explicitly reporting this gene: 4,983
Alleles reported pathogenic / likely pathogenic: 567
VariationIDs with uncertain significance: 706
VariationIDs with conflicting classifications: 154

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 CAPN3?

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 567 alleles in CAPN3 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 CAPN3.

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

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