Is CEBPA p.Pro188Arg (c.561_563delinsCCG) pathogenic?

CEBPA p.Pro188Arg (c.561563delinsCCG) is classified Likely benign in CEBPA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-29). Associated with Inborn genetic diseases.

What condition is associated with CEBPA p.Pro188Arg (c.561_563delinsCCG)?

CEBPA p.Pro188Arg (c.561_563delinsCCG) is associated with Inborn genetic diseases (ClinVar).

CEBPA p.Pro188Arg

c.561_563delinsCCG · VCV4611174

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 8.8	GERP -1.5, phastCons 1
Regional constraint	o/e 1.14	unconstrained · MANE · 260 bp · p 0.13 · regional, not allelic
Region caveats
Repeat context	tandem	G-rich low complexity, simple repeat · ambiguous alignment · confidence, not pathogenicity

Variant & gene context

Gene: CEBPA
Protein: p.Pro188Arg
Coding: c.561_563delinsCCG
MANE Select: NM_004364
Type: Indel
Location: chr19:33301852 (GRCh38)
Gene constraint: LOEUF 1.372 · pLI 0.26 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.67 · 2 PDB
Residue 188: the 'required to induce adipocyte differentiation' region; the 'disordered' region; the 'required to functionally cooperate with srebf1 in promoter activation' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CEBPA p.Pro188_Pro189dup Uncertain significance ★★ same residue
CEBPA p.Pro188_Pro189del Conflicting classifications of pathogenicity ★ same residue
CEBPA p.Pro188Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
CEBPA p.Pro188= Likely benign ★ same residue
CEBPA p.Ala199Leu Uncertain significance ★★ same condition
CEBPA p.Ala265Met Uncertain significance ★★ same condition
CEBPA p.Ala93Lys Uncertain significance ★★ same condition
CEBPA p.Asp322Ile 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-pro188arg (accessed [today's date]).

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