Is CEBPA p.Ala25Pro (c.73G>C) pathogenic?

CEBPA p.Ala25Pro (c.73G>C) is classified Uncertain significance in CEBPA (ClinVar, Single submitter, 1 submitter; last evaluated 2018-09-19). AlphaMissense: likely benign (0.0879); Absent from gnomAD v4.1; Associated with acute myeloid leukemia.

What condition is associated with CEBPA p.Ala25Pro (c.73G>C)?

CEBPA p.Ala25Pro (c.73G>C) is associated with acute myeloid leukemia (ClinVar).

How common is CEBPA p.Ala25Pro (c.73G>C) in the general population?

CEBPA p.Ala25Pro (c.73G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CEBPA p.Ala25Pro (c.73G>C)?

AlphaMissense predicts likely benign (score 0.0879) — an in-silico prediction, not a clinical call.

CEBPA p.Ala25Pro

c.73G>C · rs1600024440 · VCV664158

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0879 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

acute myeloid leukemia

Computational evidence

Protein change
AlphaMissense	0.0879	likely benign
REVEL	0.099	moderately benign-leaning
SaProt	LLR -6.02	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.7	GERP 1.2, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 293 bp · p 0.38 · regional, not allelic
Overall
CADD	21.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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: CEBPA
Protein: p.Ala25Pro
Coding: c.73G>C
MANE Select: NM_004364
dbSNP: rs1600024440
Type: single nucleotide variant
Location: chr19:33302342 (GRCh38)
Gene constraint: LOEUF 1.372 · pLI 0.26 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.67 · 2 PDB
Residue 25: the 'required to repress e2f1:tfdp1-mediated transcription, to inhibit cell cycle and to induce adipocyte differentiation' region; the 'disordered' region

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

Disease context

acute myeloid leukemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CEBPA p.Ala25Val Uncertain significance ★★ ⚠ same residue
CEBPA p.Ala25= Likely benign ★ same residue
CEBPA p.Ala25Ser Uncertain significance ★ ⚠ same residue
CEBPA p.Glu59Ter Pathogenic ★★ same condition
CEBPA p.Ala113Ser Uncertain significance ★★ ⚠ same condition
CEBPA p.Ala118Thr Uncertain significance ★★ ⚠ same condition
CEBPA p.Ala118Val Uncertain significance ★★ ⚠ same condition
CEBPA p.Ala124Val Uncertain significance ★★ ⚠ same condition

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/cebpa-p-ala25pro (accessed [today's date]).

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