CAPN10 p.Ala252=
c.756G>A · rs1009002311 · VCV752835
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -20 | GERP -2.2 |
| Overall | ||
| CADD | 0.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,068 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.000869%
14/1,611,490 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,068 |
| African / African-American | 0.00802% | 12,475 |
| East Asian | 0.00446% | 22,401 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,374 |
| South Asian | 0.0011% | 90,926 |
| European (non-Finnish) | 0.000255% | 392,844 |
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
- CAPN10
- Protein
- p.Ala252=
- Coding
- c.756G>A
- MANE Select
- NM_023083
- dbSNP
- rs1009002311
- Type
- single nucleotide variant
- Location
- chr2:240593973 (GRCh38)
- Gene constraint
- LOEUF 1.121 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.91
- Residue 252
- the calpain catalytic domain
Similar variants
- CAPN10 p.Ala252Val Uncertain significance ★ ⚠ same residue
- CAPN10 p.Arg127Cys Uncertain significance ★★ ⚠ same type
- CAPN10 p.Gly526Ser Uncertain significance ★★ ⚠ same type
- CAPN10 p.Pro46Ser Uncertain significance ★★ ⚠ same type
- CAPN10 p.Thr339Met Uncertain significance ★★ ⚠ same type
- CAPN10 p.Ala477= Benign ★★ same type
- CAPN10 p.Ala477Thr Benign ★★ same type
- CAPN10 p.Arg555Cys 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/capn10-p-ala252 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown