CAPN5 p.Arg21=
c.63G>A · VCV4773747
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP 0.47, phastCons 1 |
| Overall | ||
| CADD | 7.369 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,008 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000248%
4/1,613,668 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,008 |
| European (non-Finnish) | 0.000254% | 393,332 |
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.Arg21=
- Coding
- c.63G>A
- MANE Select
- NM_004055
- Type
- single nucleotide variant
- Location
- chr11:77084949 (GRCh38)
- Gene constraint
- LOEUF 0.928 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 91.71 · 1 PDB
- Residue 21
- an α-helix
Similar variants
- CAPN5 p.Arg21Trp Uncertain significance ★★ ⚠ same residue
- CAPN5 p.Arg21Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- CAPN5 p.Arg243Leu Pathogenic ★★ ⚠ same type
- CAPN5 p.Arg289Trp Pathogenic ★★ ⚠ same type
- CAPN5 p.Ala118Val Uncertain significance ★★ ⚠ same type
- CAPN5 p.Ala183Ser Uncertain significance ★★ ⚠ same type
- CAPN5 p.Ala185Val Uncertain significance ★★ ⚠ same type
- CAPN5 p.Ala237Val Uncertain significance ★★ ⚠ 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-arg21 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown