CPEB2 p.Pro515Leu
c.1544C>T · VCV3835865
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00283%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.046 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.5 | GERP -0.44, phastCons 1 |
| Regional constraint | o/e 1.34 | unconstrained · MANE · 50 kb · p 8.8e-28 · regional, not allelic |
| Overall | ||
| CADD | 22.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00283%
East Asian · 1/35,302 alleles
Overall
0.000224%
3/1,341,440 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00283% | 35,302 |
| South Asian | 0.00125% | 79,872 |
| European (non-Finnish) | 8.86e-05% | 1,128,168 |
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
- CPEB2
- Protein
- p.Pro515Leu
- Coding
- c.1544C>T
- MANE Select
- NM_001177382
- Type
- single nucleotide variant
- Location
- chr4:15004217 (GRCh38)
- Gene constraint
- LOEUF 1.328 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.86
- Residue 515
- the rrm 2 domain
Similar variants
- CPEB2 p.Ala113Val Uncertain significance ★ same type
- CPEB2 p.Ala27Val Uncertain significance ★ same type
- CPEB2 p.Ala287Ser Uncertain significance ★ same type
- CPEB2 p.Ala288Val Uncertain significance ★ same type
- CPEB2 p.Ala494Ser Uncertain significance ★ same type
- CPEB2 p.Ala517Thr Uncertain significance ★ same type
- CPEB2 p.Ala540Val Uncertain significance ★ same type
- CPEB2 p.Ala541Thr 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/cpeb2-p-pro515leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown