CAPN12 p.Ala410=
c.1230A>T · rs866494898 · VCV3040929
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0191%, eas)
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 -3.7 | GERP -3.1 |
| Overall | ||
| CADD | 2.065 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0191%
East Asian · 2/10,458 alleles
Filtering AF
0.0138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0126%
Overall
0.0148%
70/474,018 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0191% | 5,229 |
| European (non-Finnish) | 0.0174% | 5,758 |
| African / African-American | 0.0141% | 7,107 |
| Remaining individualsnot grpmax-eligible | 0.0109% | 9,167 |
| Admixed American | 0.00518% | 19,294 |
| South Asian | 0.00385% | 25,974 |
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
- CAPN12
- Protein
- p.Ala410=
- Coding
- c.1230A>T
- MANE Select
- NM_144691
- dbSNP
- rs866494898
- Type
- single nucleotide variant
- Location
- chr19:38737288 (GRCh38)
- Gene constraint
- LOEUF 1.398 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.63
- Residue 410
- the 'domain iii' region; the 'disordered' region
Similar variants
- CAPN12 c.1362+80A>G Benign ★★ same type
- CAPN12 c.1374+85A>C Benign ★★ same type
- CAPN12 c.1583+12G>A Benign ★★ same type
- CAPN12 c.1584-39C>T Benign ★★ same type
- CAPN12 c.1686+152A>G Benign ★★ same type
- CAPN12 c.1745-17C>T Benign ★★ same type
- CAPN12 c.1815+25G>A Benign ★★ same type
- CAPN12 c.1815+57C>T 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/capn12-p-ala410 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown