CAPRIN2 p.Met253Thr
c.758T>C · rs61735414 · VCV785399
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.31%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.112 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP 0.51, phastCons 1 |
| Overall | ||
| CADD | 16.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.31%
African / African-American · 2,483/74,978 alleles
Filtering AF
3.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.16%
Overall
0.184%
2,968/1,613,146 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.31% | 30 |
| Remaining individualsnot grpmax-eligible | 0.247% | 406 |
| Middle Eastern | 0.215% | 466 |
| Admixed American | 0.2% | 500 |
| European (non-Finnish) | 0.0162% | 6,175 |
| South Asian | 0.00769% | 13,003 |
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.Met253Thr
- Coding
- c.758T>C
- MANE Select
- NM_001385503
- dbSNP
- rs61735414
- Type
- single nucleotide variant
- Location
- chr12:30731402 (GRCh38)
- Gene constraint
- LOEUF 0.58 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.42 · 5 PDB
- Residue 253
- an α-helix
Similar variants
- CAPRIN2 c.1800+5C>T 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
- CAPRIN2 c.-32C>T 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-met253thr (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown