CAPN10 p.Ala396=
c.1188C>T · rs377409925 · VCV746446
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0174%, afr)
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 -0.7 | GERP -1.2 |
| Overall | ||
| CADD | 2.798 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0174%
African / African-American · 13/74,910 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00813%
Overall
0.000806%
13/1,613,532 alleles · ultra-rare
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.Ala396=
- Coding
- c.1188C>T
- MANE Select
- NM_023083
- dbSNP
- rs377409925
- Type
- single nucleotide variant
- Location
- chr2:240595214 (GRCh38)
- Gene constraint
- LOEUF 1.121 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.91
- Residue 396
- the 'domain iii 1' region
Similar variants
- CAPN10 p.Ala396Thr 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-ala396 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown