Is SLC2A1 p.Ser55fs (c.163_164dup) pathogenic?

SLC2A1 p.Ser55fs (c.163164dup) is classified Pathogenic in SLC2A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-07). No gnomAD frequency available for this variant; Associated with GLUT1 deficiency syndrome 1, autosomal recessive.

What condition is associated with SLC2A1 p.Ser55fs (c.163_164dup)?

SLC2A1 p.Ser55fs (c.163_164dup) is associated with GLUT1 deficiency syndrome 1, autosomal recessive (ClinVar).

How common is SLC2A1 p.Ser55fs (c.163_164dup) in the general population?

SLC2A1 p.Ser55fs (c.163_164dup) is no gnomAD frequency available for this variant (gnomAD).

SLC2A1 p.Ser55fs

c.163_164dup · rs2524999574 · VCV2022504

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

GLUT1 deficiency syndrome 1, autosomal recessive

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 3 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.2	GERP 0.56, 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: SLC2A1
Protein: p.Ser55fs
Coding: c.163_164dup
MANE Select: NM_006516
dbSNP: rs2524999574
Type: Microsatellite
Location: chr1:42931156 (GRCh38)
Gene constraint: LOEUF 0.139 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 90.30 · 5 PDB
Residue 55: an α-helix

Full SLC2A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

GLUT1 deficiency syndrome 1, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SLC2A1 p.Val166del Pathogenic ★ same condition
SLC2A1 p.Val83fs Pathogenic ★ same condition
SLC2A1 c.1279-11_1279-8del Conflicting classifications of pathogenicity ★ same condition
SLC2A1 p.59TTL[1] Uncertain significance ★ same condition
SLC2A1 p.Glu221del Uncertain significance ★ same condition
SLC2A1 p.Leu204del Uncertain significance ★ same condition
SLC2A1 p.Phe379del Conflicting classifications of pathogenicity ★ same condition
SLC2A1 p.Ser55Thr Uncertain significance ★ ⚠ same residue

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/slc2a1-p-ser55fs (accessed [today's date]).

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