Is CEBPE p.Tyr7fs (c.12_18dup) pathogenic?

CEBPE p.Tyr7fs (c.1218dup) is classified Pathogenic in CEBPE (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-11). Absent from gnomAD; Associated with specific granule deficiency.

What condition is associated with CEBPE p.Tyr7fs (c.12_18dup)?

CEBPE p.Tyr7fs (c.12_18dup) is associated with specific granule deficiency (ClinVar).

How common is CEBPE p.Tyr7fs (c.12_18dup) in the general population?

CEBPE p.Tyr7fs (c.12_18dup) is absent from gnomAD (gnomAD).

CEBPE p.Tyr7fs

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.12_18dup · rs2140292375 · VCV1457601

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

specific granule deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 2
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Tyr7fs
Coding: c.12_18dup
MANE Select: NM_001805
dbSNP: rs2140292375
Type: Duplication
Location: chr14:23119073 (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 7: the 'disordered' region

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.Tyr7Cys Uncertain significance ★ ⚠ same residue
CEBPE p.Tyr7= Likely benign ★ same residue
CEBPE p.Gly68fs Pathogenic ★ same condition
CEBPE p.Ala190fs Uncertain significance ★ same condition
CEBPE c.511-24_511-19dup Likely benign ★ same condition
CEBPE p.Arg24Ter Pathogenic/Likely pathogenic ★★ same condition
CEBPE p.Ala101Val Uncertain significance ★★ ⚠ same condition
CEBPE p.Ala119Val 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-tyr7fs (accessed [today's date]).

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