CAPN5 p.Thr609=
c.1827C>T · rs138592828 · VCV1169068
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.301%, 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 -0.66 | GERP -2.1, phastCons 0.008 |
| Overall | ||
| CADD | 3.452 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.301%
African / African-American · 226/75,018 alleles
Filtering AF
0.269%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.257%
Overall
0.0154%
249/1,613,962 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.301% | 332 |
| Middle Eastern | 0.0495% | 2,020 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,906 |
| Admixed American | 0.00667% | 15,002 |
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
- CAPN5
- Protein
- p.Thr609=
- Coding
- c.1827C>T
- MANE Select
- NM_004055
- dbSNP
- rs138592828
- Type
- single nucleotide variant
- Location
- chr11:77123774 (GRCh38)
- Gene constraint
- LOEUF 0.928 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 91.71 · 1 PDB
- Residue 609
- the c2 domain
Similar variants
- CAPN5 p.Thr609Ser Uncertain significance ★★ ⚠ same residue
- CAPN5 p.Arg243Leu Pathogenic ★★ ⚠ same type
- CAPN5 p.Arg289Trp Pathogenic ★★ ⚠ same type
- CAPN5 p.Ala118Val Uncertain significance ★★ ⚠ same type
- CAPN5 p.Ala183Ser Uncertain significance ★★ ⚠ same type
- CAPN5 p.Ala185Val Uncertain significance ★★ ⚠ same type
- CAPN5 p.Ala237Val Uncertain significance ★★ ⚠ same type
- CAPN5 p.Ala245Val 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/capn5-p-thr609 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown