CAPRIN1 p.Val225=
c.675A>C · VCV4911207
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00136%, nfe)
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 -0.73 | GERP -3.6 |
| Overall | ||
| CADD | 0.902 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00136%
European (non-Finnish) · 16/1,176,012 alleles
Filtering AF
0.000805%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000652%
Overall
0.000994%
16/1,609,566 alleles · very rare
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
- CAPRIN1
- Protein
- p.Val225=
- Coding
- c.675A>C
- MANE Select
- NM_005898
- Type
- single nucleotide variant
- Location
- chr11:34076629 (GRCh38)
- Gene constraint
- LOEUF 0.372 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.64 · 6 PDB
- Residue 225
- a β-strand
Similar variants
- CAPRIN1 p.Val225Ala Uncertain significance ★ ⚠ same residue
- CAPRIN1 p.Arg458Ter Pathogenic ★★ same type
- CAPRIN1 p.Arg132Cys Uncertain significance ★★ ⚠ same type
- CAPRIN1 p.Gln206Arg Uncertain significance ★★ ⚠ same type
- CAPRIN1 p.Pro424Leu Uncertain significance ★★ ⚠ same type
- CAPRIN1 p.Pro528Thr Uncertain significance ★★ ⚠ same type
- CAPRIN1 c.1122+19G>A Benign ★★ same type
- CAPRIN1 c.217-5C>G Likely 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/caprin1-p-val225 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown