CAPN5 p.Phe272del
c.811TTC[1] · rs781942330 · VCV1953996
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP -0.56, phastCons 1 |
| Overall | ||
| CADD | 18.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,012 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000682%
11/1,613,250 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,004 |
| European (non-Finnish) | 0.000678% | 147,498 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CAPN5
- Protein
- p.Phe272del
- Coding
- c.811TTC[1]
- MANE Select
- NM_004055
- dbSNP
- rs781942330
- Type
- Microsatellite
- Location
- chr11:77115505 (GRCh38)
- Gene constraint
- LOEUF 0.928 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 91.71 · 1 PDB
- Residue 272
- the calpain catalytic domain; an α-helix
Similar variants
- CAPN5 p.Phe272Leu Uncertain significance ★★ ⚠ same residue
- CAPN5 p.Phe272Val Uncertain significance ★★ ⚠ same residue
- CAPN5 p.Ala183del Uncertain significance ★ same type
- CAPN5 p.Ile542del Uncertain significance ★ same type
- CAPN5 p.Phe385del Uncertain significance ★ same type
- CAPN5 c.1603+6CT[3] Likely benign ★ 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/capn5-p-phe272del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown