Is CEBPE p.Phe264Val (c.790T>G) pathogenic?

CEBPE p.Phe264Val (c.790T>G) is classified Uncertain significance in CEBPE (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-08). AlphaMissense: likely pathogenic (0.9862); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CEBPE p.Phe264Val (c.790T>G)?

CEBPE p.Phe264Val (c.790T>G) is associated with Inborn genetic diseases (ClinVar).

How common is CEBPE p.Phe264Val (c.790T>G) in the general population?

CEBPE p.Phe264Val (c.790T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CEBPE p.Phe264Val (c.790T>G)?

AlphaMissense predicts likely pathogenic (score 0.9862) — an in-silico prediction, not a clinical call.

CEBPE p.Phe264Val

c.790T>G · rs757448387 · VCV3141870

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9862 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,818)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9862	likely pathogenic · top 10% in CEBPE
REVEL	0.443	indeterminate
SaProt	LLR -10.25	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.4, phastCons 1
Regional constraint	o/e 1.11	unconstrained · MANE · 170 bp · p 0.34 · regional, not allelic
Overall
CADD	25.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,818). 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: CEBPE
Protein: p.Phe264Val
Coding: c.790T>G
MANE Select: NM_001805
dbSNP: rs757448387
Type: single nucleotide variant
Location: chr14:23117543 (GRCh38)
Gene constraint: LOEUF 0.848 · pLI 0.05 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.89 · 1 PDB
Residue 264: the bzip domain; a UniProt-annotated variant site (in sgd1)

Full CEBPE 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

CEBPE p.Ala119Val Uncertain significance ★★ ⚠ same condition
CEBPE p.Arg135Gln Uncertain significance ★★ ⚠ same condition
CEBPE p.Arg265Cys Uncertain significance ★★ ⚠ same condition
CEBPE p.Glu19Gln Uncertain significance ★★ ⚠ same condition
CEBPE p.Gly28Arg Uncertain significance ★★ ⚠ same condition
CEBPE p.Gly49Arg Uncertain significance ★★ ⚠ same condition
CEBPE p.His194Asn Uncertain significance ★★ ⚠ same condition
CEBPE p.Leu173Val 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/cebpe-p-phe264val (accessed [today's date]).

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