Is CEBPA p.Pro22Ser (c.64C>T) pathogenic?

CEBPA p.Pro22Ser (c.64C>T) is classified Conflicting classifications of pathogenicity in CEBPA (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-05-05). AlphaMissense: likely benign (0.0859); Ultra-rare (popmax 0.0188%, sas); Associated with acute myeloid leukemia.

What condition is associated with CEBPA p.Pro22Ser (c.64C>T)?

CEBPA p.Pro22Ser (c.64C>T) is associated with acute myeloid leukemia (ClinVar).

How common is CEBPA p.Pro22Ser (c.64C>T) in the general population?

CEBPA p.Pro22Ser (c.64C>T) is ultra-rare (popmax 0.0188%, sas) (gnomAD).

What do computational predictors say about CEBPA p.Pro22Ser (c.64C>T)?

AlphaMissense predicts likely benign (score 0.0859) — an in-silico prediction, not a clinical call.

CEBPA p.Pro22Ser

c.64C>T · rs770636941 · VCV851134

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0859 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0188%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

acute myeloid leukemia

Computational evidence

Protein change
AlphaMissense	0.0859	likely benign
REVEL	0.041	moderately benign-leaning
SaProt	LLR -7.67	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 4.1	GERP -1.5, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 293 bp · p 0.38 · regional, not allelic
Overall
CADD	19.58	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0188% South Asian · 9/47,946 alleles

Filtering AF 0.0097% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00726%

Overall 0.000925% 11/1,189,500 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0188%	5,327
European (non-Finnish)	0.000191%	523,404

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.Pro22Ser
Coding: c.64C>T
MANE Select: NM_004364
dbSNP: rs770636941
Type: single nucleotide variant
Location: chr19:33302351 (GRCh38)
Gene constraint: LOEUF 1.372 · pLI 0.26 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.67 · 2 PDB
Residue 22: 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.Pro22Thr Uncertain significance ★★ ⚠ same residue
CEBPA p.Pro22= Likely benign ★★ 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
CEBPA p.Ala154Val 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-pro22ser (accessed [today's date]).

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