CASP2 p.Pro354=
c.1062G>A · rs561597102 · VCV709219
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00501%, 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 2.1 | GERP 0.55, phastCons 1 |
| Overall | ||
| CADD | 12.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00501%
Admixed American · 3/59,856 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000669%
Overall
0.00103%
15/1,460,820 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00501% | 19,952 |
| East Asian | 0.00223% | 44,864 |
| South Asian | 0.0022% | 45,429 |
| European (non-Finnish) | 0.000763% | 131,055 |
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.Pro354=
- Coding
- c.1062G>A
- MANE Select
- NM_032982
- dbSNP
- rs561597102
- Type
- single nucleotide variant
- Location
- chr7:143303878 (GRCh38)
- Gene constraint
- LOEUF 0.936 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.95 · 17 PDB
- Residue 354
- a UniProt-annotated variant site (in mrt80; likely pathogenic); the 'disordered' region
Similar variants
- CASP2 p.Pro354Ala 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-pro354 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown