CAPRIN2 p.Val688Ile
c.2062G>A · VCV3995305
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.104 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.9 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 24.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
African / African-American · 20/74,952 alleles
Filtering AF
0.0177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0147%
Overall
0.00254%
41/1,613,444 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0267% | 3,748 |
| Admixed American | 0.005% | 19,982 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,237 |
| European (non-Finnish) | 0.00136% | 73,732 |
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
- CAPRIN2
- Protein
- p.Val688Ile
- Coding
- c.2062G>A
- MANE Select
- NM_001385503
- Type
- single nucleotide variant
- Location
- chr12:30716667 (GRCh38)
- Gene constraint
- LOEUF 0.58 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.42 · 5 PDB
- Residue 688
- the 'disordered' region
Similar variants
- CAPRIN2 c.1800+5C>T Benign ★★ same type
- CAPRIN2 p.Met253Thr Benign ★★ same type
- CAPRIN2 p.Ser668= Benign ★★ same type
- CAPRIN2 p.Thr763= Benign ★★ same type
- CAPRIN2 p.Tyr806= Benign ★★ same type
- CAPRIN2 c.-12A>G Uncertain significance ★ same type
- CAPRIN2 c.-2A>C Uncertain significance ★ same type
- CAPRIN2 c.-30G>A Uncertain significance ★ 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/caprin2-p-val688ile (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown