Is CEBPE p.Pro78= (c.234C>T) pathogenic?

CEBPE p.Pro78= (c.234C>T) is classified Benign/Likely benign in CEBPE (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-25). Low-frequency (popmax 2.77%, afr); Associated with specific granule deficiency.

What condition is associated with CEBPE p.Pro78= (c.234C>T)?

CEBPE p.Pro78= (c.234C>T) is associated with specific granule deficiency (ClinVar).

How common is CEBPE p.Pro78= (c.234C>T) in the general population?

CEBPE p.Pro78= (c.234C>T) is low-frequency (popmax 2.77%, afr) (gnomAD).

CEBPE p.Pro78=

Q: How is Recurrent infections due to specific granule deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.234C>T · rs114913626 · VCV530669

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.77%, afr)

Conditions

specific granule deficiency

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 1.2	GERP -2.3, phastCons 1
Overall
CADD	8.79	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.77% African / African-American · 2,076/75,016 alleles

Filtering AF 2.67% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.63%

Overall 0.149% 2,398/1,614,018 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.77%	36
Remaining individualsnot grpmax-eligible	0.202%	496
Admixed American	0.198%	504
Middle Eastern	0.165%	605
Ashkenazi Jewishnot grpmax-eligible	0.0101%	9,865
South Asian	0.00878%	11,386
European (non-Finnish)	0.00475%	21,071

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: CEBPE
Protein: p.Pro78=
Coding: c.234C>T
MANE Select: NM_001805
dbSNP: rs114913626
Type: single nucleotide variant
Location: chr14:23118858 (GRCh38)
Gene constraint: LOEUF 0.848 · pLI 0.05 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.89 · 1 PDB

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

Disease context

specific granule deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Recurrent infections due to specific granule deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

CEBPE p.Pro78Leu Uncertain significance ★ ⚠ same residue
CEBPE p.Arg24Ter Pathogenic/Likely pathogenic ★★ same condition
CEBPE p.Ala101Val Uncertain significance ★★ ⚠ same condition
CEBPE p.Ala119Val Uncertain significance ★★ ⚠ same condition
CEBPE p.Ala171Asp Uncertain significance ★★ ⚠ same condition
CEBPE p.Ala44Thr Uncertain significance ★★ ⚠ same condition
CEBPE p.Arg125Gln Uncertain significance ★★ ⚠ same condition
CEBPE p.Arg135Gln 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-pro78 (accessed [today's date]).

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