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Gene

CAPN3

calpain 3

Summary

Cytogenetic location
15q15.1
Coordinates
Chromosome 15: 42,359,501–42,412,317 (GRCh38)
Exons
24 exons across 52.8 kb
Protein
821 amino acids
Also known as
CANP3, p94, nCL-1
Previous symbols
LGMD2, LGMD2A
MANE Select transcript
ENST00000397163.8NM_000070.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Limb-Girdle Muscular Dystrophy

    • Limb-girdle Muscular Dystrophy is defined as a collection of numerous subtypes with differing inheritance patterns (with diagnostic sufficiency being varied too). Carriers of variants related to the condition should seek guidance from a muscular-skeletal specialist for a definitive diagnosis.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong

How CAPN3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome 15, with a bracket where CAPN3 sits. CAPN3 and 17 genes near it on chromosome 15, from 41,885,909 to 42,885,908.Chromosome 1515q15.1p13p12p11.2p11.1q11.1q11.2q12q13.1q13.2q13.3q14q15.1q15.2q15.3q21.1q21.2q21.3q22.1q22.2q22.31q22.32q22.33q23q24.1q24.2q24.3q25.1q25.2q25.3q26.1q26.2q26.342 Mb42.2 Mb42.4 Mb42.6 Mb42.8 MbSPTBN5: 41,848,146–41,894,053, reverse strandSPTBN5EHD4: 41,895,928–41,972,614, reverse strandEHD4PLA2G4E: 41,981,394–42,051,190, reverse strandPLA2G4EPLA2G4D: 42,067,009–42,094,565, reverse strandPLA2G4DPLA2G4F: 42,139,034–42,156,659, reverse strandPLA2G4FVPS39: 42,158,701–42,208,326, reverse strandVPS39TMEM87A: 42,209,667–42,274,128, reverse strandTMEM87AGANC: 42,273,196–42,353,666, forward strandGANC: 42,348,103–42,412,317, forward strandCAPN3: 42,359,501–42,412,317, forward strandCAPN3ZNF106: 42,412,823–42,491,150, reverse strandZNF106SNAP23: 42,491,233–42,545,358, forward strandSNAP23: 42,497,395–42,548,786, reverse strandLRRC57: 42,534,627–42,548,802, reverse strandLRRC57HAUS2: 42,548,828–42,572,263, forward strandHAUS2STARD9: 42,575,574–42,720,998, forward strandSTARD9CDAN1: 42,723,544–42,737,156, reverse strandCDAN1TTBK2: 42,738,730–42,920,850, reverse strandTTBK2Diagram of CAPN3: 24 exons on the forward strand of chromosome 15Exon 1: 38 known disease-causing sitesExon 2: 16 known disease-causing sitesExon 3: 16 known disease-causing sitesExon 4: 28 known disease-causing sitesExon 5: 33 known disease-causing sitesExon 6: 12 known disease-causing sitesExon 7: 13 known disease-causing sitesExon 8: 13 known disease-causing sitesExon 9: 10 known disease-causing sitesExon 10: 25 known disease-causing sitesExon 11: 26 known disease-causing sitesExon 12: 2 known disease-causing sitesExon 13: 27 known disease-causing sitesExon 14: 2 known disease-causing sitesExon 15: 2 known disease-causing sitesExon 16: 15 known disease-causing sitesExon 17: 13 known disease-causing sitesExon 18: 12 known disease-causing sitesExon 19: 7 known disease-causing sitesExon 20: 13 known disease-causing sitesExon 21: 22 known disease-causing sitesExon 22: 22 known disease-causing sitesExon 23: 1 known disease-causing siteExon 24: 6 known disease-causing sitesExon 1: 42,359,501–42,360,114, 614 bases. 5 variants with a page in exon 1. List themExon 2: 42,384,483–42,384,552, 70 bases. 3 variants with a page in exon 2. List themExon 3: 42,386,167–42,386,285, 119 basesExon 4: 42,387,753–42,387,886, 134 bases. 3 variants with a page in exon 4. List themExon 5: 42,388,928–42,389,096, 169 bases. 7 variants with a page in exon 5. List themExon 6: 42,389,953–42,390,096, 144 bases. 2 variants with a page in exon 6. List themExon 7: 42,392,639–42,392,722, 84 bases. 2 variants with a page in exon 7. List themExon 8: 42,394,256–42,394,341, 86 bases. 2 variants with a page in exon 8. List themExon 9: 42,396,800–42,396,877, 78 bases. 1 variant with a page in exon 9. List themExon 10: 42,399,492–42,399,652, 161 bases. 13 variants with a page in exon 10. List themExon 11: 42,401,641–42,401,810, 170 bases. 8 variants with a page in exon 11. List themExon 12: 42,402,124–42,402,135, 12 basesExon 13: 42,402,794–42,403,002, 209 bases. 7 variants with a page in exon 13. List themExon 14: 42,403,741–42,403,777, 37 bases. 1 variant with a page in exon 14. List themExon 15: 42,405,926–42,405,943, 18 basesExon 16: 42,408,211–42,408,324, 114 bases. 3 variants with a page in exon 16. List themExon 17: 42,409,303–42,409,380, 78 bases. 1 variant with a page in exon 17. List themExon 18: 42,409,787–42,409,844, 58 basesExon 19: 42,409,931–42,409,995, 65 bases. 1 variant with a page in exon 19. List themExon 20: 42,410,428–42,410,496, 69 bases. 4 variants with a page in exon 20. List themExon 21: 42,410,588–42,410,666, 79 bases. 2 variants with a page in exon 21. List themExon 22: 42,410,884–42,411,000, 117 bases. 7 variants with a page in exon 22. List themExon 23: 42,411,287–42,411,345, 59 bases. 1 variant with a page in exon 23. List themExon 24: 42,411,747–42,412,317, 571 bases15101520245′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 3.3 kb of the gene's 52.8 kb; 2,466 of those bases code for the protein.

How a genome test reads CAPN3

452

positions in CAPN3 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 52.8 kb of CAPN3, introns included, not only the 3.3 kb of exons.

Variants with a page (80)

The CAPN3 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
A702Vc.2105C>TExon 1942,409,985Pathogenic3 stars out of 4 reviewed by expert panel
A798Ec.2393C>AExon 2342,411,299Pathogenic3 stars out of 4 reviewed by expert panel
c.499-1G>AIntron 342,387,752Pathogenic3 stars out of 4 reviewed by expert panel
c.1115+5G>CIntron 842,394,346Pathogenic3 stars out of 4 reviewed by expert panel
c.1194-2A>GIntron 942,399,490Pathogenic3 stars out of 4 reviewed by expert panel
c.1194-2delIntron 942,399,489Pathogenic3 stars out of 4 reviewed by expert panel
c.1194-9A>GIntron 942,399,483Pathogenic3 stars out of 4 reviewed by expert panel
c.1524G>AExon 1142,401,810Pathogenic3 stars out of 4 reviewed by expert panel
c.1746-20C>GIntron 1342,403,721Pathogenic3 stars out of 4 reviewed by expert panel
c.1782G>AExon 1442,403,777Likely pathogenic3 stars out of 4 reviewed by expert panel

See all 80 CAPN3 variants →

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). CAPN3 gene: calpain 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/capn3

Vancouver

Dante Labs. CAPN3 gene: calpain 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/capn3

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