CAPN3 p.Ser6fs
c.16dup · VCV4081228
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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 1 of 24 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.33 | GERP -5, phastCons 0.012 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CAPN3
- Protein
- p.Ser6fs
- Coding
- c.16dup
- MANE Select
- NM_000070
- Type
- Duplication
- Location
- chr15:42359820 (GRCh38)
- Gene constraint
- LOEUF 0.896 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 79.18 · 5 PDB
Similar variants
- CAPN3 p.Ser6= Likely benign ★ same residue
- CAPN3 p.Arg110fs Pathogenic ★★★ same type
- CAPN3 p.Asn760fs Pathogenic ★★★ same type
- CAPN3 p.Leu87fs Pathogenic ★★★ same type
- CAPN3 p.Pro245_Ser246insTer Pathogenic ★★★ same type
- CAPN3 p.Tyr75fs Pathogenic ★★★ same type
- CAPN3 c.2115+1_2115+2dup Likely pathogenic ★★ same type
- CAPN3 p.Arg289fs Pathogenic ★★ same type
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-ser6fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown