Is CEPT1 p.Pro80Ala (c.238C>G) pathogenic?

CEPT1 p.Pro80Ala (c.238C>G) is classified Uncertain significance in CEPT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-11). AlphaMissense: likely pathogenic (0.9077); Absent from gnomAD v4.1.

How common is CEPT1 p.Pro80Ala (c.238C>G) in the general population?

CEPT1 p.Pro80Ala (c.238C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CEPT1 p.Pro80Ala (c.238C>G)?

AlphaMissense predicts likely pathogenic (score 0.9077) — an in-silico prediction, not a clinical call.

CEPT1 p.Pro80Ala

c.238C>G · VCV4001234

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9077 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9077	likely pathogenic
REVEL	0.817	moderately pathogenic-leaning
SaProt	LLR -15.30	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 6.5, phastCons 1
Regional constraint	o/e 0.57	unconstrained · MANE · 36 kb · p 4e-20 · regional, not allelic
Overall
CADD	26.8	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: CEPT1
Protein: p.Pro80Ala
Coding: c.238C>G
MANE Select: NM_006090
Type: single nucleotide variant
Location: chr1:111147952 (GRCh38)
Gene constraint: LOEUF 0.359 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 89.27 · 2 PDB

Full CEPT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEPT1 p.Ile120Val Benign ★★ same type
CEPT1 p.Ala121Thr Uncertain significance ★ ⚠ same type
CEPT1 p.Arg207Gln Uncertain significance ★ ⚠ same type
CEPT1 p.Arg267Cys Uncertain significance ★ ⚠ same type
CEPT1 p.Arg267His Uncertain significance ★ ⚠ same type
CEPT1 p.Arg386Cys Uncertain significance ★ ⚠ same type
CEPT1 p.Arg45Lys Uncertain significance ★ ⚠ same type
CEPT1 p.Arg5Gln 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/cept1-p-pro80ala (accessed [today's date]).

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