CAPRIN2 p.Pro373Leu
c.1118C>T · VCV3484894
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0154%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.053 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -0.66, phastCons 1 |
| Overall | ||
| CADD | 19.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0154%
South Asian · 14/91,074 alleles
Filtering AF
0.0092%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00735%
Overall
0.00266%
43/1,613,926 alleles · ultra-rare
exomes 39/1,461,862 · genomes 4/152,064 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0154% | 6,505 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,810 |
| Admixed American | 0.00167% | 59,992 |
| European (non-Finnish) | 0.00161% | 62,106 |
| African / African-American | 0.00134% | 74,880 |
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.Pro373Leu
- Coding
- c.1118C>T
- MANE Select
- NM_001385503
- Type
- single nucleotide variant
- Location
- chr12:30729069 (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-pro373leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown