CAPN12 p.Ser535=
c.1605C>T · rs141009431 · VCV732597
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.541%, 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 3 | GERP -0.31, phastCons 1 |
| Overall | ||
| CADD | 11.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.541%
African / African-American · 403/74,488 alleles
Filtering AF
0.497%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.48%
Overall
0.0291%
469/1,610,902 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.541% | 185 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,081 |
| Admixed American | 0.0317% | 3,152 |
| Middle Eastern | 0.0166% | 6,040 |
| South Asian | 0.0022% | 45,446 |
| European (non-Finnish) | 0.00119% | 84,247 |
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.Ser535=
- Coding
- c.1605C>T
- MANE Select
- NM_144691
- dbSNP
- rs141009431
- Type
- single nucleotide variant
- Location
- chr19:38735523 (GRCh38)
- Gene constraint
- LOEUF 1.398 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.63
- Residue 535
- the 'domain iii' 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-ser535 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown