CASP2 p.Val29=
c.87G>A · rs192384558 · VCV715721
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.5%, amr)
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 -1.3 | GERP -3.2 |
| Overall | ||
| CADD | 0.491 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.5%
Admixed American · 900/60,024 alleles
Filtering AF
1.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.39%
Overall
0.0594%
959/1,614,128 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 1.5% | 67 |
| Remaining individualsnot grpmax-eligible | 0.064% | 1,563 |
| African / African-American | 0.0173% | 5,771 |
| European (non-Finnish) | 0.000508% | 196,668 |
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
- CASP2
- Protein
- p.Val29=
- Coding
- c.87G>A
- MANE Select
- NM_032982
- dbSNP
- rs192384558
- Type
- single nucleotide variant
- Location
- chr7:143291552 (GRCh38)
- Gene constraint
- LOEUF 0.936 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.95 · 17 PDB
Similar variants
- CASP2 p.Val29Met Uncertain significance ★ ⚠ same residue
- CASP2 p.Gln331Glu Uncertain significance ★★ ⚠ same type
- CASP2 p.Ala412= Likely benign ★★ same type
- CASP2 p.Gly7= Likely benign ★★ same type
- CASP2 p.Ile387= Benign/Likely benign ★★ same type
- CASP2 p.Lys254= Benign/Likely benign ★★ same type
- CASP2 p.Thr267= Benign/Likely benign ★★ same type
- CASP2 p.Tyr151= 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/casp2-p-val29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown