CAPS2 p.Ser52=
c.156C>T · rs11180461 · VCV778643
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.66%, 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 2.6 | GERP 0.53, phastCons 1 |
| Overall | ||
| CADD | 8.447 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.66%
African / African-American · 1,208/72,942 alleles
Filtering AF
1.58%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.55%
Overall
0.0957%
1,477/1,543,944 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.66% | 60 |
| Admixed American | 0.165% | 605 |
| Remaining individualsnot grpmax-eligible | 0.142% | 702 |
| East Asian | 0.135% | 740 |
| Middle Eastern | 0.0906% | 1,103 |
| South Asian | 0.00483% | 20,725 |
| European (non-Finnish) | 0.00324% | 30,903 |
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
- CAPS2
- Protein
- p.Ser52=
- Coding
- c.156C>T
- MANE Select
- NM_017954 · reported on NM_001355024
- dbSNP
- rs11180461
- Type
- single nucleotide variant
- Location
- chr12:75323198 (GRCh38)
- Structure
- AlphaFold pLDDT 79.91
- Residue 52
- the 'disordered' region
Similar variants
- GLIPR1L1 p.Ala52Thr Uncertain significance ★ ⚠ same residue
- CADPS2 c.3718-15A>C Benign ★★ same type
- CADPS2 p.Ala298Thr Benign ★★ same type
- CADPS2 p.Asp1088Asn Likely benign ★★ same type
- CADPS2 p.Glu1010Lys Benign ★★ same type
- CADPS2 p.Leu154= Likely benign ★★ same type
- CADPS2 p.Lys338= Benign ★★ same type
- CADPS2 p.Met828Val 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/caps2-p-ser52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown