Is CEBPE p.Val60Met (c.178G>A) pathogenic?

CEBPE p.Val60Met (c.178G>A) is classified Uncertain significance in CEBPE (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-04). AlphaMissense: likely benign (0.1223); Very rare (popmax 0.00988%, sas); Associated with specific granule deficiency.

What condition is associated with CEBPE p.Val60Met (c.178G>A)?

CEBPE p.Val60Met (c.178G>A) is associated with specific granule deficiency (ClinVar).

How common is CEBPE p.Val60Met (c.178G>A) in the general population?

CEBPE p.Val60Met (c.178G>A) is very rare (popmax 0.00988%, sas) (gnomAD).

What do computational predictors say about CEBPE p.Val60Met (c.178G>A)?

AlphaMissense predicts likely benign (score 0.1223) — an in-silico prediction, not a clinical call.

CEBPE p.Val60Met

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.178G>A · rs1376968968 · VCV1940847

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1223 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00988%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

specific granule deficiency

Computational evidence

Protein change
AlphaMissense	0.1223	likely benign
REVEL	0.05	moderately benign-leaning
SaProt	LLR -8.16	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 2.2	GERP -1.2, phastCons 0.99
Regional constraint	o/e 1.05	unconstrained · MANE · 1,383 bp · p 0.39 · regional, not allelic
Overall
CADD	19.81	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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

Grpmax group 0.00988% South Asian · 9/91,092 alleles

Filtering AF 0.00514% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00375%

Overall 0.00235% 38/1,613,926 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00988%	10,121
East Asian	0.00445%	22,447
Remaining individualsnot grpmax-eligible	0.0032%	31,240
African / African-American	0.00267%	37,450
European (non-Finnish)	0.00186%	53,635
Admixed American	0.00167%	60,016

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.Val60Met
Coding: c.178G>A
MANE Select: NM_001805
dbSNP: rs1376968968
Type: single nucleotide variant
Location: chr14:23118914 (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.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
CEBPE p.Arg167Cys 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-val60met (accessed [today's date]).

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