CAPN15 p.Pro265=
c.795G>A · VCV4926926
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0136%, 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 -0.08 | GERP -2.5, phastCons 0.005 |
| Overall | ||
| CADD | 1.688 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0136%
East Asian · 6/44,038 alleles
Filtering AF
0.00588%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.004%
Overall
0.0021%
33/1,568,104 alleles · ultra-rare
exomes 28/1,415,890 · genomes 5/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0136% | 7,340 |
| Remaining individualsnot grpmax-eligible | 0.00496% | 20,175 |
| South Asian | 0.00343% | 29,189 |
| Admixed American | 0.00173% | 57,700 |
| European (non-Finnish) | 0.00164% | 60,961 |
| African / African-American | 0.00135% | 74,158 |
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
- CAPN15
- Protein
- p.Pro265=
- Coding
- c.795G>A
- MANE Select
- NM_005632
- Type
- single nucleotide variant
- Location
- chr16:547633 (GRCh38)
- Gene constraint
- LOEUF 0.974 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.65
- Residue 265
- the 'disordered' region
Similar variants
- CAPN15 p.Pro265Leu Uncertain significance ★ ⚠ same residue
- CAPN15 p.Pro265Ser Uncertain significance ★ ⚠ same residue
- CAPN15 c.2192+8C>T Uncertain significance ★★ same type
- CAPN15 p.Arg428Trp Uncertain significance ★★ ⚠ same type
- CAPN15 p.Arg867Cys Uncertain significance ★★ ⚠ same type
- CAPN15 p.Arg867His Uncertain significance ★★ ⚠ same type
- CAPN15 p.Cys363Arg Uncertain significance ★★ ⚠ same type
- CAPN15 p.Glu776Ala 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/capn15-p-pro265 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown