CAPN3 p.Glu582Ter
c.1743dup · VCV3731383
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Rare
Conditions
1
autosomal recessive limb-girdle muscular dystrophy type 2A
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 13 of 24 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 0.87, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CAPN3
- Protein
- p.Glu582Ter
- Coding
- c.1743dup
- MANE Select
- NM_000070
- Type
- Duplication
- Location
- chr15:42402999 (GRCh38)
- Gene constraint
- LOEUF 0.896 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 79.18 · 5 PDB
- Residue 582
- the 'domain iii' region
Disease context
autosomal recessive limb-girdle muscular dystrophy type 2A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Calpain-3-related limb-girdle muscular dystrophy R1 (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- CAPN3 p.Glu582fs Pathogenic ★★★ same residue
- CAPN3 p.Arg110fs Pathogenic ★★★ same condition
- CAPN3 p.Asn760fs Pathogenic ★★★ same condition
- CAPN3 p.Leu87fs Pathogenic ★★★ same condition
- CAPN3 p.Tyr75fs Pathogenic ★★★ same condition
- CAPN3 c.2115+1_2115+2dup Likely pathogenic ★★ same condition
- CAPN3 p.Arg289fs Pathogenic ★★ same condition
- CAPN3 p.Asn296delinsArgTer Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/capn3-p-glu582ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown