CAPN11 p.Cys151=
c.453C>T · rs187597064 · VCV778004
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.704%, nfe)
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 0.17 | GERP -3.9, phastCons 0.65 |
| Overall | ||
| CADD | 7.733 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.704%
European (non-Finnish) · 8,114/1,152,880 alleles
Filtering AF
0.691%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.686%
Overall
0.57%
8,899/1,561,120 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.704% | 142 |
| Admixed American | 0.541% | 185 |
| Remaining individualsnot grpmax-eligible | 0.524% | 191 |
| Middle Eastern | 0.334% | 299 |
| Ashkenazi Jewishnot grpmax-eligible | 0.139% | 718 |
| African / African-American | 0.114% | 874 |
| South Asian | 0.0284% | 3,520 |
| Finnishnot grpmax-eligible | 0.0248% | 4,026 |
| East Asian | 0.00482% | 20,755 |
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
- CAPN11
- Protein
- p.Cys151=
- Coding
- c.453C>T
- MANE Select
- NM_007058
- dbSNP
- rs187597064
- Type
- single nucleotide variant
- Location
- chr6:44172345 (GRCh38)
- Gene constraint
- LOEUF 1.194 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.10
- Residue 151
- the calpain catalytic domain
Similar variants
- CAPN11 p.Gln133Ter Likely benign ★★ same type
- CAPN11 p.Ala29Pro Uncertain significance ★ ⚠ same type
- CAPN11 p.Ala405Pro Uncertain significance ★ ⚠ same type
- CAPN11 p.Ala405Thr Uncertain significance ★ ⚠ same type
- CAPN11 p.Ala461Ser Uncertain significance ★ ⚠ same type
- CAPN11 p.Ala472Thr Uncertain significance ★ ⚠ same type
- CAPN11 p.Ala599Thr Uncertain significance ★ ⚠ same type
- CAPN11 p.Ala689Glu 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/capn11-p-cys151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown