CPEB2 p.Pro350Ser
c.1048C>T · VCV3835867
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00458%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.023 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.88 | GERP -0.33, phastCons 1 |
| Regional constraint | o/e 1.34 | unconstrained · MANE · 50 kb · p 8.8e-28 · regional, not allelic |
| Overall | ||
| CADD | 19.73 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00458%
African / African-American · 3/65,542 alleles
Filtering AF
0.00122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000637%
Overall
0.000304%
4/1,315,400 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00458% | 21,847 |
| European (non-Finnish) | 9.65e-05% | 1,036,550 |
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.Pro350Ser
- Coding
- c.1048C>T
- MANE Select
- NM_001177382
- Type
- single nucleotide variant
- Location
- chr4:15003721 (GRCh38)
- Gene constraint
- LOEUF 1.328 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.86
- Residue 350
- the rrm 1 domain
Similar variants
- CPEB2 p.Pro350Ala Uncertain significance ★ same residue
- 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
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-pro350ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown