Seroatlas · Human Serome Atlas

CAPN3

Calpain-3

Also known as: CAN3_HUMAN, CANP3, LGMD2, LGMD2A, nCL-1, p94

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
P20807
Gene
CAPN3
Ensembl
ENSG00000092529
Chromosome
15
Canonical length
821 aa
Protein class
Disease related genes, Enzymes, Human disease related genes, Metabolic proteins, Potential drug targets, Predicted intracellular proteins
Quaternary structure
Homodimer

OverviewNCBI Gene

Calpain, a heterodimer consisting of a large and a small subunit, is a major intracellular protease, although its function has not been well established. This gene encodes a muscle-specific member of the calpain large subunit family that specifically binds to titin. Mutations in this gene are associated with limb-girdle muscular dystrophies type 2A. Alternate promoters and alternative splicing result in multiple transcript variants encoding different isoforms and some variants are ubiquitously expressed. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

821 residues, UniProt reviewed canonical sequence.

>P20807|CAPN3
     1  MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
    61  FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
   121  ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
   181  CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
   241  IRDAPSDMYK IMKKAIERGS LMGCSIDDGT NMTYGTSPSG LNMGELIARM VRNMDNSLLQ
   301  DSDLDPRGSD ERPTRTIIPV QYETRMACGL VRGHAYSVTG LDEVPFKGEK VKLVRLRNPW
   361  GQVEWNGSWS DRWKDWSFVD KDEKARLQHQ VTEDGEFWMS YEDFIYHFTK LEICNLTADA
   421  LQSDKLQTWT VSVNEGRWVR GCSAGGCRNF PDTFWTNPQY RLKLLEEDDD PDDSEVICSF
   481  LVALMQKNRR KDRKLGASLF TIGFAIYEVP KEMHGNKQHL QKDFFLYNAS KARSKTYINM
   541  REVSQRFRLP PSEYVIVPST YEPHQEGEFI LRVFSEKRNL SEEVENTISV DRPVKKKKTK
   601  PIIFVSDRAN SNKELGVDQE SEEGKGKTSP DKQKQSPQPQ PGSSDQESEE QQQFRNIFKQ
   661  IAGDDMEICA DELKKVLNTV VNKHKDLKTH GFTLESCRSM IALMDTDGSG KLNLQEFHHL
   721  WNKIKAWQKI FKHYDTDQSG TINSYEMRNA VNDAGFHLNN QLYDIITMRY ADKHMNIDFD
   781  SFICCFVRLE GMFRAFHAFD KDGDGIIKLN VLEWLQLTMY A

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CAPN3 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Intracellular
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.31
Highest tissue expression
849 nTPM

Expression across tissuesHPA

Tissue

  • skeletal muscle: 849 nTPM
  • tongue: 352 nTPM
  • spinal cord: 318 nTPM
  • midbrain: 185 nTPM
  • epididymis: 155 nTPM
  • basal ganglia: 126 nTPM

Single-cell type

  • oligodendrocytes: 301 nCPM
  • microglia: 18 nCPM
  • astrocytes: 17 nCPM
  • melanocytes: 16 nCPM
  • ependymal cells: 11 nCPM
  • myonuclei: 8.8 nCPM

Immune cell

  • classical monocyte: 1 nTPM
  • naive CD8 T-cell: 0.9 nTPM
  • neutrophil: 0.9 nTPM
  • MAIT T-cell: 0.8 nTPM
  • gdT-cell: 0.7 nTPM
  • NK-cell: 0.6 nTPM

Brain region

  • white matter: 350 nTPM
  • medulla oblongata: 224 nTPM
  • basal ganglia: 207 nTPM
  • midbrain: 186 nTPM
  • cerebellum: 186 nTPM
  • thalamus: 170 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CAPN3.

Disease | AllUniProt

Conditions CAPN3 is implicated in, by any mechanism.

  • Muscular dystrophy, limb-girdle, autosomal recessive 1 (LGMDR1) MIM:253600
  • Muscular dystrophy, limb-girdle, autosomal dominant 4 (LGMDD4) MIM:618129

Disease | GeneticClinVar

529 pathogenic / likely-pathogenic of 2,131 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
0.97
gnomAD pLI
0
gnomAD missense Z
-0.03
DepMap mean gene effect
0.02
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of CAPN3 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads CAPN3 as an antibody target. Whether an autoantibody or antibody against CAPN3 could matter depends on whether native CAPN3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CAPN3 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label CAPN3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/CAPN3. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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