Is CPEB2 p.Ala79Thr (c.235G>A) pathogenic?

CPEB2 p.Ala79Thr (c.235G>A) is classified Uncertain significance in CPEB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-26). Very rare (popmax 0.00782%, nfe).

How common is CPEB2 p.Ala79Thr (c.235G>A) in the general population?

CPEB2 p.Ala79Thr (c.235G>A) is very rare (popmax 0.00782%, nfe) (gnomAD).

CPEB2 p.Ala79Thr

c.235G>A · VCV3496339

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00782%, nfe)

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 5.4	GERP -0.2, phastCons 1
Regional constraint	o/e 1.34	unconstrained · MANE · 50 kb · p 8.8e-28 · regional, not allelic
Overall
CADD	18.38	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00782% European (non-Finnish) · 89/1,137,978 alleles

Filtering AF 0.00646% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.006%

Overall 0.00677% 102/1,506,272 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0154%	6,501
European (non-Finnish)grpmax	0.00782%	12,786
African / African-American	0.00576%	17,360

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Ala79Thr
Coding: c.235G>A
MANE Select: NM_001177382
Type: single nucleotide variant
Location: chr4:15002908 (GRCh38)
Gene constraint: LOEUF 1.328 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.86
Residue 79: the 'disordered' region

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

Similar variants

CPEB2 p.Ala79Pro 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-ala79thr (accessed [today's date]).

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