Is CEBPA p.Pro153= (c.459G>C) pathogenic?

CEBPA p.Pro153= (c.459G>C) is classified Likely benign in CEBPA (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-02). Very rare (popmax 0.000105%, nfe); Associated with acute myeloid leukemia.

What condition is associated with CEBPA p.Pro153= (c.459G>C)?

CEBPA p.Pro153= (c.459G>C) is associated with acute myeloid leukemia (ClinVar).

How common is CEBPA p.Pro153= (c.459G>C) in the general population?

CEBPA p.Pro153= (c.459G>C) is very rare (popmax 0.000105%, nfe) (gnomAD).

CEBPA p.Pro153=

c.459G>C · rs779373951 · VCV1114260

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000105%, nfe)

Conditions

acute myeloid leukemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.2	GERP -2.4
Overall
CADD	9.543	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000105% European (non-Finnish) · 1/949,050 alleles

Overall 0.000676% 1/147,976 alleles · very rare

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: CEBPA
Protein: p.Pro153=
Coding: c.459G>C
MANE Select: NM_004364
dbSNP: rs779373951
Type: single nucleotide variant
Location: chr19:33301956 (GRCh38)
Gene constraint: LOEUF 1.372 · pLI 0.26 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.67 · 2 PDB
Residue 153: the 'required to induce adipocyte differentiation' 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.Pro153Arg Uncertain significance ★★ ⚠ same residue
CEBPA p.Pro153Gln Uncertain significance ★ ⚠ same residue
CEBPA p.Pro153Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
CEBPA p.Pro153_Ala174del Uncertain significance ★ same residue
CEBPA p.Pro153Ala Uncertain significance ★ ⚠ same residue
CEBPA p.Pro153Thr Uncertain significance ★ ⚠ same residue
CEBPA p.Glu59Ter Pathogenic ★★ same condition
CEBPA p.Ala113Ser 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-pro153 (accessed [today's date]).

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