Is CEBPA p.Pro39fs (c.115_121del) pathogenic?

CEBPA p.Pro39fs (c.115121del) is classified Pathogenic in CEBPA (ClinVar, No assertion criteria, 1 submitter; last evaluated 2001-03-01). Absent from gnomAD; Associated with acute myeloid leukemia.

What condition is associated with CEBPA p.Pro39fs (c.115_121del)?

CEBPA p.Pro39fs (c.115_121del) is associated with acute myeloid leukemia (ClinVar).

How common is CEBPA p.Pro39fs (c.115_121del) in the general population?

CEBPA p.Pro39fs (c.115_121del) is absent from gnomAD (gnomAD).

CEBPA p.Pro39fs

c.115_121del · rs587776848 · VCV17566

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

acute myeloid leukemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (1 of 1) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.3	GERP 0.073, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CEBPA
Protein: p.Pro39fs
Coding: c.115_121del
MANE Select: NM_004364
dbSNP: rs587776848
Type: Deletion
Location: chr19:33302294 (GRCh38)
Gene constraint: LOEUF 1.372 · pLI 0.26 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.67 · 2 PDB
Residue 39: 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.Pro39Arg Uncertain significance ★★ ⚠ same residue
CEBPA p.Pro39= Uncertain significance ★ same residue
CEBPA p.Pro39Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
CEBPA p.Pro39Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
CEBPA p.Ala111fs Pathogenic ★★ same condition
CEBPA p.Gln83fs Pathogenic/Likely pathogenic ★★ same condition
CEBPA p.Glu89del Uncertain significance ★★ same condition
CEBPA p.Pro45_Ile55delinsLeu 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-pro39fs (accessed [today's date]).

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