GLUT1 deficiency syndrome: genes and variants

Genes linked to GLUT1 deficiency syndrome

• SLC2A1: Solute carrier family 2, facilitated glucose transporter member 1

  It provides basal glucose uptake in many tissues and is the principal route for glucose entry across the blood-brain barrier. Haploinsufficiency causes GLUT1 deficiency syndrome with epilepsy, developmental impairment, and movement disorders from inadequate brain glucose delivery.

  53 disease-causing and 226 uncertain variants in SLC2A1 are linked to GLUT1 deficiency syndrome.

Where GLUT1 deficiency syndrome variants cluster

• SLC2A1 Transmembrane (positions 121–144): 9 of 53 disease-causing changes, 3.5× more than its size predicts.
• SLC2A1 Cytoplasmic (positions 329–334): 4 of 53 disease-causing changes, 6.2× more than its size predicts.
• SLC2A1 Cytoplasmic (positions 145–155): 4 of 53 disease-causing changes, 3.4× more than its size predicts.
• SLC2A1 Transmembrane (positions 402–422): 5 of 53 disease-causing changes, 2.2× more than its size predicts.
• SLC2A1 Extracellular (positions 294–306): 3 of 53 disease-causing changes, 2.1× more than its size predicts.

Known disease-causing variants in GLUT1 deficiency syndrome

Uncertain variants in GLUT1 deficiency syndrome that look disease-causing

Same protein, different disease

• Encephalopathy due to GLUT1 deficiency is also caused by SLC2A1 variants; they fall in the same places as the GLUT1 deficiency syndrome variants (32 disease-causing).
• Childhood onset GLUT1 deficiency syndrome 2 is also caused by SLC2A1 variants; they fall partly in the same places as the GLUT1 deficiency syndrome variants (18 disease-causing).
• Hereditary cryohydrocytosis with reduced stomatin is also caused by SLC2A1 variants; they fall mostly in different places as the GLUT1 deficiency syndrome variants (5 disease-causing).
• Epilepsy, idiopathic generalized, susceptibility to, 13 is also caused by SLC2A1 variants; they fall mostly in different places as the GLUT1 deficiency syndrome variants (4 disease-causing).

Diseases related to GLUT1 deficiency syndrome

• Epilepsy, idiopathic generalized, susceptibility to, 13, also linked to SLC2A1
• Encephalopathy due to GLUT1 deficiency, also linked to SLC2A1
• Idiopathic generalized epilepsy, also linked to SLC2A1
• Childhood onset GLUT1 deficiency syndrome 2, also linked to SLC2A1
• Self-limited epilepsy with centrotemporal spikes, also linked to SLC2A1
• Developmental disorder, also linked to SLC2A1
• Hereditary cryohydrocytosis with reduced stomatin, also linked to SLC2A1

Frequently asked questions

Which genes are linked to GLUT1 deficiency syndrome?

In CATVariant, GLUT1 deficiency syndrome is linked to 1 analyzed protein: SLC2A1 (Solute carrier family 2, facilitated glucose transporter member 1).

How many genetic variants are linked to GLUT1 deficiency syndrome?

307 variants: 53 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 226 are of uncertain significance or have conflicting reports.

Which uncertain variants in GLUT1 deficiency syndrome look disease-causing?

7 uncertain variants reach the likely-pathogenic range of the ACMG/AMP points scale on computable evidence, for example SLC2A1 Y293H, SLC2A1 R93Q, SLC2A1 M96T, SLC2A1 G332R and SLC2A1 G332S. These are leads for expert review, not diagnoses.

About this data

Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.

Download every variant as CSV · Browse all diseases · Methods · About the Center