Is GBE1 p.Ala92fs (c.274del) pathogenic?

GBE1 p.Ala92fs (c.274del) is classified Pathogenic in GBE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-19). Absent from gnomAD; Associated with glycogen storage disease due to glycogen branching enzyme deficiency.

What condition is associated with GBE1 p.Ala92fs (c.274del)?

GBE1 p.Ala92fs (c.274del) is associated with glycogen storage disease due to glycogen branching enzyme deficiency (ClinVar).

How common is GBE1 p.Ala92fs (c.274del) in the general population?

GBE1 p.Ala92fs (c.274del) is absent from gnomAD (gnomAD).

GBE1 p.Ala92fs

Q: How is Glycogen storage disease due to glycogen branching enzyme deficiency inherited?

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

c.274del · rs2471917414 · VCV2942178

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

glycogen storage disease due to glycogen branching enzyme 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 2 of 16
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.8	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: GBE1
Protein: p.Ala92fs
Coding: c.274del
MANE Select: NM_000158
dbSNP: rs2471917414
Type: Deletion
Location: chr3:81705483 (GRCh38)
Gene constraint: LOEUF 1.211 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.30 · 3 PDB
Residue 92: a binding site

Full GBE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

glycogen storage disease due to glycogen branching enzyme deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Glycogen storage disease due to glycogen branching enzyme deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

GBE1 p.Ala92= Likely benign ★ same residue
GBE1 c.1799_1803+8del Likely pathogenic ★★ same condition
GBE1 p.Ala16fs Pathogenic/Likely pathogenic ★★ same condition
GBE1 p.Ala9fs Pathogenic/Likely pathogenic ★★ same condition
GBE1 p.Arg156fs Pathogenic/Likely pathogenic ★★ same condition
GBE1 p.Arg468fs Pathogenic ★★ same condition
GBE1 p.Asp169fs Pathogenic/Likely pathogenic ★★ same condition
GBE1 p.Asp24fs Pathogenic/Likely 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/gbe1-p-ala92fs (accessed [today's date]).

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