Is SLC2A2 p.Ser112fs (c.333del) pathogenic?

SLC2A2 p.Ser112fs (c.333del) is classified Pathogenic in SLC2A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-18). Associated with glycogen storage disease due to GLUT2 deficiency.

What condition is associated with SLC2A2 p.Ser112fs (c.333del)?

SLC2A2 p.Ser112fs (c.333del) is associated with glycogen storage disease due to GLUT2 deficiency (ClinVar).

How is Fanconi-Bickel syndrome inherited?

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

SLC2A2 p.Ser112fs

c.333del · VCV4731480

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

glycogen storage disease due to GLUT2 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 3 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.7, phastCons 1

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

Variant & gene context

Gene: SLC2A2
Protein: p.Ser112fs
Coding: c.333del
MANE Select: NM_000340
Type: Deletion
Location: chr3:171014507 (GRCh38)
Gene constraint: LOEUF 0.858 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.56

Full SLC2A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

glycogen storage disease due to GLUT2 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Fanconi-Bickel syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

SLC2A2 p.Leu153_Ile154del Pathogenic/Likely pathogenic ★★ same condition
SLC2A2 p.Tyr164del Uncertain significance ★★ same condition
SLC2A2 c.775+1del Pathogenic ★ same condition
SLC2A2 p.Gly223fs Pathogenic ★ same condition
SLC2A2 p.Leu140fs Likely pathogenic ★ same condition
SLC2A2 p.Leu224fs Likely pathogenic ★ same condition
SLC2A2 p.Phe237fs Pathogenic ★ same condition
SLC2A2 p.Phe427fs 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/slc2a2-p-ser112fs (accessed [today's date]).

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