Is CEBPA p.Lys276= (c.828G>A) pathogenic?

CEBPA p.Lys276= (c.828G>A) is classified Likely benign in CEBPA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-31). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CEBPA p.Lys276= (c.828G>A)?

CEBPA p.Lys276= (c.828G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CEBPA p.Lys276= (c.828G>A) in the general population?

CEBPA p.Lys276= (c.828G>A) is absent from gnomAD v4.1 (gnomAD).

CEBPA p.Lys276=

c.828G>A · VCV4000021

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.9	GERP -1.8, phastCons 1
Overall
CADD	19.42	PHRED · no single calibrated threshold — expert panels disagree

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.Lys276=
Coding: c.828G>A
MANE Select: NM_004364
Type: single nucleotide variant
Location: chr19:33301587 (GRCh38)
Gene constraint: LOEUF 1.372 · pLI 0.26 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.67 · 2 PDB
Residue 276: the 'interaction with foxo1' region; the 'disordered' 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.Lys276Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
CEBPA p.Lys276Met Uncertain significance ★ ⚠ same residue
CEBPA p.Lys276Thr Uncertain significance ★ ⚠ same residue
CEBPA c.-1C>A Uncertain significance ★★ same condition
CEBPA c.-4C>G Uncertain significance ★★ same condition
CEBPA p.Ala118Thr Uncertain significance ★★ ⚠ same condition
CEBPA p.Ala154Val Uncertain significance ★★ ⚠ same condition
CEBPA p.Ala199Val 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-lys276 (accessed [today's date]).

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