Is CPEB2 p.Leu261Val (c.781C>G) pathogenic?

CPEB2 p.Leu261Val (c.781C>G) is classified Uncertain significance in CPEB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-16). Very rare (popmax 0.00382%, amr).

How common is CPEB2 p.Leu261Val (c.781C>G) in the general population?

CPEB2 p.Leu261Val (c.781C>G) is very rare (popmax 0.00382%, amr) (gnomAD).

CPEB2 p.Leu261Val

c.781C>G · rs1322709470 · VCV2392187

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00382%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.038	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.3	GERP 0.63, phastCons 0.85
Regional constraint	o/e 1.34	unconstrained · MANE · 50 kb · p 8.8e-28 · regional, not allelic
Overall
CADD	19.92	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00382% Admixed American · 1/26,198 alleles

Overall 0.000659% 1/151,686 alleles · very rare

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.Leu261Val
Coding: c.781C>G
MANE Select: NM_001177382
dbSNP: rs1322709470
Type: single nucleotide variant
Location: chr4:15003454 (GRCh38)
Gene constraint: LOEUF 1.328 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.86

Full CPEB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-leu261val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown