Is CPEB1 p.Cys54Phe (c.161G>T) pathogenic?

CPEB1 p.Cys54Phe (c.161G>T) is classified Uncertain significance in CPEB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-26). Absent from gnomAD v4.1.

How common is CPEB1 p.Cys54Phe (c.161G>T) in the general population?

CPEB1 p.Cys54Phe (c.161G>T) is absent from gnomAD v4.1 (gnomAD).

CPEB1 p.Cys54Phe

c.161G>T · VCV4656045

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.389	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 1.8, phastCons 1
Overall
CADD	25.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CPEB1
Protein: p.Cys54Phe
Coding: c.161G>T
MANE Select: NM_001365242
Type: single nucleotide variant
Location: chr15:82627303 (GRCh38)
Gene constraint: LOEUF 0.177 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 66.05 · 5 PDB

Full CPEB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-cys54phe (accessed [today's date]).

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