CASP2 p.Asn302=
c.906C>T · rs750534880 · VCV3049220
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00891%, eas)
Conditions
1
CASP2-related disorder
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 -4.1 | GERP -5.8 |
| Overall | ||
| CADD | 4.877 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00891%
East Asian · 4/44,888 alleles
Filtering AF
0.00358%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00321%
Overall
0.00378%
61/1,614,030 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00891% | 11,222 |
| European (non-Finnish) | 0.00458% | 21,853 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| Admixed American | 0.00167% | 60,006 |
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.Asn302=
- Coding
- c.906C>T
- MANE Select
- NM_032982
- dbSNP
- rs750534880
- Type
- single nucleotide variant
- Location
- chr7:143300233 (GRCh38)
- Gene constraint
- LOEUF 0.936 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.95 · 17 PDB
- Residue 302
- a UniProt-annotated variant site (in mrt80; likely pathogenic); a turn
Disease context
CASP2-related disorder
Similar variants
- CASP2 c.876+9A>G Likely benign same condition
- CASP2 p.Ala19Thr Likely benign same condition
- CASP2 p.His337= Likely benign same condition
- CASP2 p.Pro178Ala Likely benign same condition
- 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
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-asn302 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown