CAPN3 p.Ile317fs
c.949dup · VCV3577105
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
2
muscular dystrophy, limb-girdle, autosomal dominant 4
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 7 of 24 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 3.9 | GERP 1.8, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CAPN3
- Protein
- p.Ile317fs
- Coding
- c.949dup
- MANE Select
- NM_000070
- Type
- Duplication
- Location
- chr15:42392640 (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 317
- the calpain catalytic domain
Disease context
muscular dystrophy, limb-girdle, autosomal dominant 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: autosomal recessive limb-girdle muscular dystrophy type 2A
For Calpain-3-related limb-girdle muscular dystrophy D4 (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adult
- Prevalence
- <1 / 1 000 000 (Worldwide)
Similar variants
- CAPN3 p.Ile317Thr Uncertain significance ★★ ⚠ same residue
- CAPN3 p.Ile317Val Uncertain significance ★★ ⚠ same residue
- CAPN3 p.Ile317= Likely benign ★ 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
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-ile317fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown