CPEB1 p.Pro405Leu
c.1214C>T · rs185845489 · VCV2602806
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0179%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.06 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 8.6 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 22.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0179%
East Asian · 8/44,738 alleles
Filtering AF
0.00886%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00643%
Overall
0.00391%
63/1,611,896 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0179% | 5,592 |
| Admixed American | 0.00504% | 19,855 |
| European (non-Finnish) | 0.00399% | 25,089 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,204 |
| Finnishnot grpmax-eligible | 0.00156% | 63,986 |
| African / African-American | 0.00134% | 74,802 |
| South Asian | 0.0011% | 90,744 |
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
- CPEB1
- Protein
- p.Pro405Leu
- Coding
- c.1214C>T
- MANE Select
- NM_001365242
- dbSNP
- rs185845489
- Type
- single nucleotide variant
- Location
- chr15:82552547 (GRCh38)
- Gene constraint
- LOEUF 0.177 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.05 · 5 PDB
- Residue 405
- the rrm 1 domain; the 'necessary for stress granule assembly and correct localization in dcp1 bodies' region
Similar variants
- CPEB1 p.Ala109Val Uncertain significance ★ same type
- CPEB1 p.Ala147Asp Uncertain significance ★ same type
- CPEB1 p.Arg136Gly Uncertain significance ★ same type
- CPEB1 p.Arg196Cys Uncertain significance ★ same type
- CPEB1 p.Arg200Gln Uncertain significance ★ same type
- CPEB1 p.Arg200Trp Uncertain significance ★ same type
- CPEB1 p.Arg233His Uncertain significance ★ same type
- CPEB1 p.Arg452Lys 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/cpeb1-p-pro405leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown