CASP2 p.Ile387=
c.1161C>T · rs142190608 · VCV710252
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.613%, 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 -5.4 | GERP -6.4 |
| Overall | ||
| CADD | 1.165 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.613%
African / African-American · 460/75,034 alleles
Filtering AF
0.567%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.549%
Overall
0.0334%
539/1,614,150 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.613% | 163 |
| Middle Eastern | 0.066% | 1,515 |
| Remaining individualsnot grpmax-eligible | 0.0592% | 1,689 |
| Admixed American | 0.035% | 2,858 |
| South Asian | 0.0022% | 45,540 |
| European (non-Finnish) | 0.00127% | 78,669 |
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.Ile387=
- Coding
- c.1161C>T
- MANE Select
- NM_032982
- dbSNP
- rs142190608
- Type
- single nucleotide variant
- Location
- chr7:143304717 (GRCh38)
- Gene constraint
- LOEUF 0.936 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.95 · 17 PDB
- Residue 387
- a UniProt-annotated variant site (in mrt80; likely pathogenic); an α-helix
Similar variants
- CASP2 p.Gln331Glu Uncertain significance ★★ ⚠ same type
- CASP2 p.Ala412= Likely benign ★★ same type
- CASP2 p.Gly7= 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
- CASP2 p.Val29= Benign ★★ same type
- CASP2 c.876+1G>T Pathogenic ★ 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-ile387 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown