CAPRIN2 p.Ile638Val
c.1912A>G · VCV3827325
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0948%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.105 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.57 | GERP -0.2 |
| Overall | ||
| CADD | 8.677 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0948%
African / African-American · 71/74,908 alleles
Filtering AF
0.0771%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0705%
Overall
0.00508%
82/1,613,764 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0948% | 1,055 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,925 |
| Admixed American | 0.00167% | 59,978 |
| South Asian | 0.0011% | 91,054 |
| European (non-Finnish) | 0.00017% | 589,929 |
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.Ile638Val
- Coding
- c.1912A>G
- MANE Select
- NM_001385503
- Type
- single nucleotide variant
- Location
- chr12:30719219 (GRCh38)
- Gene constraint
- LOEUF 0.58 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.42 · 5 PDB
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-ile638val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown