Is CEBPE p.Ala171fs (c.509dup) pathogenic?

CEBPE p.Ala171fs (c.509dup) is classified Pathogenic in CEBPE (ClinVar, No assertion criteria, 1 submitter; last evaluated 2001-05-01). Absent from gnomAD; Associated with specific granule deficiency 1.

What condition is associated with CEBPE p.Ala171fs (c.509dup)?

CEBPE p.Ala171fs (c.509dup) is associated with specific granule deficiency 1 (ClinVar).

How common is CEBPE p.Ala171fs (c.509dup) in the general population?

CEBPE p.Ala171fs (c.509dup) is absent from gnomAD (gnomAD).

CEBPE p.Ala171fs

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.509dup · rs2140291802 · VCV8855

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

specific granule deficiency 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon within the last 50 nt of the penultimate exon (1 of 2, 0 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 2.2, 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.Ala171fs
Coding: c.509dup
MANE Select: NM_001805
dbSNP: rs2140291802
Type: Duplication
Location: chr14:23118582 (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 171: a UniProt-annotated variant site (in sgd1)

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

Disease context

specific granule deficiency 1 — 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.Ala171Asp Uncertain significance ★★ ⚠ same residue
CEBPE p.Ala171Gly Uncertain significance ★ ⚠ same residue
CEBPE p.Ala171Thr Uncertain significance ★ ⚠ same residue
CEBPE p.Leu69Phe Uncertain significance ★★ ⚠ same condition
CEBPE p.Arg135Ter Pathogenic ★ same condition
CEBPE p.Val218Ala Likely pathogenic ★ ⚠ same condition
CEBPE p.Ser281Asn Conflicting classifications of pathogenicity ★ ⚠ same condition
CEBPE p.Asp84fs Pathogenic 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-ala171fs (accessed [today's date]).

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