CAPN11 p.Leu2=
c.6G>A · rs118045574 · VCV728666
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.685%, 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 0.76 | GERP -1.6 |
| Overall | ||
| CADD | 2.578 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.685%
East Asian · 280/40,890 alleles
Filtering AF
0.619%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.593%
Overall
0.0195%
303/1,551,368 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.685% | 146 |
| South Asian | 0.0155% | 6,466 |
| Remaining individualsnot grpmax-eligible | 0.0133% | 7,513 |
| Admixed American | 0.00196% | 50,974 |
| European (non-Finnish) | 8.72e-05% | 1,146,807 |
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.Leu2=
- Coding
- c.6G>A
- MANE Select
- NM_007058
- dbSNP
- rs118045574
- Type
- single nucleotide variant
- Location
- chr6:44158854 (GRCh38)
- Gene constraint
- LOEUF 1.194 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.10
- Residue 2
- the 'disordered' region
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-leu2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown