Is CPEB2 p.Thr474Ile (c.1421C>T) pathogenic?

CPEB2 p.Thr474Ile (c.1421C>T) is classified Uncertain significance in CPEB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-07). Very rare (popmax 0.00242%, nfe).

How common is CPEB2 p.Thr474Ile (c.1421C>T) in the general population?

CPEB2 p.Thr474Ile (c.1421C>T) is very rare (popmax 0.00242%, nfe) (gnomAD).

CPEB2 p.Thr474Ile

c.1421C>T · VCV3835862

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00242%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.052	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.7	GERP 0.44, phastCons 1
Regional constraint	o/e 1.34	unconstrained · MANE · 50 kb · p 8.8e-28 · regional, not allelic
Overall
CADD	21.9	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00242% European (non-Finnish) · 28/1,157,064 alleles

Filtering AF 0.00168% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00145%

Overall 0.00213% 30/1,409,778 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00242%	41,324
Remaining individualsnot grpmax-eligible	0.00167%	60,014
African / African-American	0.00143%	70,144

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.Thr474Ile
Coding: c.1421C>T
MANE Select: NM_001177382
Type: single nucleotide variant
Location: chr4:15004094 (GRCh38)
Gene constraint: LOEUF 1.328 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.86
Residue 474: the rrm 2 domain

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

Similar variants

CPEB2 p.Thr474Ala Uncertain significance ★ same residue
CPEB2 p.Thr474Ser 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

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-thr474ile (accessed [today's date]).

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