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Intellectual disability

Gene: SLC2A1

Green List (high evidence)
SLC2A1 (solute carrier family 2 member 1)
EnsemblGeneIds (GRCh38): ENSG00000117394
EnsemblGeneIds (GRCh37): ENSG00000117394
OMIM: 138140, Gene2Phenotype
SLC2A1 is in 24 panels

8 reviews

Ida Ertmanska (Genomics England Curator)

Green List (high evidence)

Comment on mode of inheritance: There are numerous patients reported in literature with monoallelic SLC2A1 variants and GLUT1 deficiency syndrome (characterised by early-onset epileptic encephalopathy associated with hypoglycorrhachia, delayed development, acquired microcephaly, motor incoordination, and spasticity). There are only two probands reported to date with biallelic SLC2A1 variants and GLUT1 deficiency syndrome. While their heterozygous family members were reported as asymptomatic, GLUT1DS presents with variable and often mild symptoms. Hence, the mode of inheritance should be changed to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted on this panel, until more biallelic cases are reported.
Created: 8 Oct 2026, 1:21 p.m. | Last Modified: 8 Oct 2026, 1:21 p.m.
Panel Version: 11.36
PMID: 41561681 Previtali et al., 2026 - MONOALLELIC COHORT
Retrospective evaluation of 32 adults with genetically confirmed GLUT1DS from Italian medical centres. 17/32 variants in SLC2A1 were confirmed to be de novo, 10 inherited from a parent, and 5 of unknown inheritance. 24/32 patients had epilepsy, 26 had paroxysmal movement disorders. Fatigue was present in 12 individuals and migraine in 6. Psychomotor delay was observed in 15/32 subjects. Subsequently, 11/32 individuals received a diagnosis of intellectual disability. Mean age at symptom onset was 4 yrs. Brain MRI was unremarkable in most cases (15/20). Mostly missense variants detected.
Study highlights that "GLUT1DS presents with variable symptoms, often unrecognised or too mild to prompt clinical attention." Several adults in the study were diagnosed in adulthood - some asymptomatic and only following their child’s diagnosis.

BIALLELIC CASES:
PMID: 20687207 Rotstein et al., 2011
F1 - male proband seen at 3 yrs, with seizures, dev delay, progressive postnatal microcephaly, hypoglycorrhachia on CSF analysis. He had spasticity with distant lower limb dystonia. Parents and sister unaffected. He was found to carry comp het SLC2A1 (old name GLUT1) variants: c.945A>G, p.K256V (maternally inherited) and c.556G>T, p.R126L (de novo). The same patient as P13 in PMID: 10980529.
F2 - two affectes sisters, aged 6 and 2.5 yrs. Seems to be the same family as in PMID: 20221955.
Only SLC2A1 was analysed, method not described.

PMID: 20221955 Klepper et al., 2009
Report of a 6yo female patient from a consanguineous Arab family from Qatar, with moderate global developmental delay, epilepsy, ataxia, hypotonia, and hypoglycorrhachia (CSF glucose 36 mg/dL; CSF lactate 1.09 mmol/L; CSF/blood glucose ratio 0.44). Symptom onset was around 18 months of age, with frequent falls and an ataxic gait. She harboured a homozygous SLC2A1: c.1402C>T (p.Arg468Trp) variant - also homozygous in her younger sister who was asymptomatic. Unaffected parents were het for the variant. 3 hets reported in gnomAD v4.1.2, no hmz. Method: targeted sequencing of SLC2A1.

PMID: 10980529 Wang et al., 2000
Report of 15 children with infantile seizures, acquired microcephaly, low CSF/blood glucose ratio, and dev delay, harbouring SLC2A1 variants. Method: PCR sequencing of SLC2A1 only. 7 patients had het nonsense variants in SLC2A1, 3 had splicing variants, and 1 harboured a large deletion. 4 patients had missense variants, including Patient 13 with comp het SLC2A1 variants R126L and K256V
(K256V inherited from an asymptomatic mother).
Variants R126L (SLC2A1 c.377G>T (p.Arg126Leu)) & K256V (SLC2A1: c.766_767delinsGT (p.Lys256Val)) are not reported in gnomAD v4.1.2.

SLC2A1 association with AD GLUT1 deficiency syndrome is classified as Definitive in ClinGen (Intellectual Disability and Autism GCEP, Apr 2019). The gene is associated with several disease entities in OMIM: AD {Epilepsy, idiopathic generalized, susceptibility to, 12}, MIM:614847; AD Dystonia 9, MIM:601042; AD GLUT1 deficiency syndrome 2, childhood onset, MIM:612126; AD, AR GLUT1 deficiency syndrome 1, infantile onset, severe, MIM:606777; AD Stomatin-deficient cryohydrocytosis with neurologic defects, OMIM:608885 (accessed 7th Oct 2026).
Created: 8 Oct 2026, 1:21 p.m. | Last Modified: 8 Oct 2026, 1:21 p.m.
Panel Version: 11.36

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
GLUT1 deficiency syndrome 2, childhood onset, OMIM:612126; childhood onset GLUT1 deficiency syndrome 2, MONDO:0012805; GLUT1 deficiency syndrome 1, infantile onset, severe, OMIM:606777; encephalopathy due to GLUT1 deficiency, MONDO:0011724; Stomatin-deficient cryohydrocytosis with neurologic defects, OMIM:608885

Publications

Created: 8 Oct 2026, 1:21 p.m.
Last Modified: 8 Oct 2026, 1:21 p.m.
Panel version: 11.36

Louise Daugherty (Genomics England Curator)

Comment on phenotypes: reformatted to remove format issue
Created: 12 Jan 2018, 11:20 a.m.
Comment on phenotypes: reformatted to remove format issue
Created: 12 Jan 2018, 11:20 a.m.
Created: 12 Jan 2018, 11:20 a.m.

Panel version: 1.634

Louise Daugherty (Genomics England Curator)

Comment on phenotypes: reformatted to remove format issue
Created: 12 Jan 2018, 11:20 a.m.
Created: 12 Jan 2018, 11:20 a.m.

Panel version: 1.634

Louise Daugherty (Genomics England Curator)

Comment on phenotypes: reformatted to remove format issue
Created: 12 Jan 2018, 11:20 a.m.
Created: 12 Jan 2018, 11:20 a.m.

Panel version: 1.634

Caroline Wright (Sanger)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
GLUT1 DEFICIENCY SYNDROME TYPE 1 (GLUT1DS1)

Publications

Created: 5 Nov 2017, 2:42 a.m.

Panel version: 0

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf;in_gilissen_2014_known;in_omim_20150205_epilepsies;in_movement_disorder_list;in_UKGTN_v12 . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 8:26 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; find_uk10k; gilissen_2014_known; omim_20150205_epilepsies; manju_list; UKGTN_v12; Nijmegen_ID_diagnostic; Nijmegen_ID_candidates; gonzalez_mantilla_2016; GEL_ID_green_20160217; neuro_20160418_strict; Loss of function. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 1:22 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Publications

  • 25529582
  • 24896178
  • omim.org
  • Personal communication with NIHRBRRD BRIDGE SPEED
  • Version 12 ukgtn.nhs.uk

Created: 2 Aug 2017, 10:36 p.m.

Panel version: 1.354

Sarah Leigh (Genomics England Curator)

Comment on mode of inheritance: Intellectual disability reported as a phenotypic feature in GLUT1 deficiency syndrome 1, infantile onset, severe 606777 which can be either mono or biallelic
Created: 12 Jan 2017, 4:30 p.m.
Created: 12 Jan 2017, 4:30 p.m.

Panel version: 1.26

Lu Raymond (university of cambridge )

Green List (high evidence)

Created: 23 Feb 2016, 10:46 a.m.

Panel version: 0.306

Details

Mode of Inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Victorian Clinical Genetics Services
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • GLUT1 deficiency syndrome 2, childhood onset, OMIM:612126
  • childhood onset GLUT1 deficiency syndrome 2, MONDO:0012805
  • GLUT1 deficiency syndrome 1, infantile onset, severe, OMIM:606777
  • encephalopathy due to GLUT1 deficiency, MONDO:0011724
  • Stomatin-deficient cryohydrocytosis with neurologic defects, OMIM:608885
Tags
Q4_26_MOI
OMIM
138140
Clinvar variants
Variants in SLC2A1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

8 Oct 2026, Gel status: 3

Set Phenotypes

Ida Ertmanska (Genomics England Curator)

Phenotypes for gene: SLC2A1 were changed from GLUT1 deficiency syndrome 1, 606777; GLUT1 deficiency syndrome 2, 612126; {Epilepsy, idiopathic generalized, suscpetibility to, 12}, 614847; Dystonia 9, 601042; GLUT1 DEFICIENCY SYNDROME TYPE 1 (GLUT1DS1) to GLUT1 deficiency syndrome 2, childhood onset, OMIM:612126; childhood onset GLUT1 deficiency syndrome 2, MONDO:0012805; GLUT1 deficiency syndrome 1, infantile onset, severe, OMIM:606777; encephalopathy due to GLUT1 deficiency, MONDO:0011724; Stomatin-deficient cryohydrocytosis with neurologic defects, OMIM:608885

8 Oct 2026, Gel status: 3

Set publications

Ida Ertmanska (Genomics England Curator)

Publications for gene: SLC2A1 were set to

8 Oct 2026, Gel status: 3

Added Tag

Ida Ertmanska (Genomics England Curator)

Tag Q4_26_MOI tag was added to gene: SLC2A1.

29 Sep 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to SLC2A1.

12 Mar 2018, Gel status: 3

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

12 Jan 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for SLC2A1 were set to GLUT1 deficiency syndrome 1, 606777; GLUT1 deficiency syndrome 2, 612126; {Epilepsy, idiopathic generalized, suscpetibility to, 12}, 614847; Dystonia 9, 601042; GLUT1 DEFICIENCY SYNDROME TYPE 1 (GLUT1DS1)

12 Jan 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for SLC2A1 were set to GLUT1 deficiency syndrome 1, 606777; GLUT1 deficiency syndrome 2, 612126; {Epilepsy, idiopathic generalized, suscpetibility to, 12}, 614847; Dystonia 9, 601042; GLUT1 DEFICIENCY SYNDROME TYPE 1 (GLUT1DS1)

12 Jan 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for SLC2A1 were set to GLUT1 deficiency syndrome 1, 606777; GLUT1 deficiency syndrome 2, 612126; {Epilepsy, idiopathic generalized, suscpetibility to, 12}, 614847; Dystonia 9, 601042; GLUT1 DEFICIENCY SYNDROME TYPE 1 (GLUT1DS1)

12 Jan 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for SLC2A1 were set to GLUT1 deficiency syndrome 1, 606777; GLUT1 deficiency syndrome 2, 612126; {Epilepsy, idiopathic generalized, suscpetibility to, 12}, 614847; Dystonia 9, 601042; GLUT1 DEFICIENCY SYNDROME TYPE 1 (GLUT1DS1)

12 Jan 2017, Gel status: 4

Set Mode of Inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for SLC2A1 was changed to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

12 Jan 2017, Gel status: 4

Set Mode of Inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for SLC2A1 was changed to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

13 Nov 2015, Gel status: 4

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 4

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 1

Set Mode of Inheritance, Added New Source

Ellen McDonagh (Genomics England Curator)

SLC2A1 was added to Intellectual disabilitypanel. Source: Expert Review Green Model of inheritance for gene SLC2A1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

SLC2A1 was added to Intellectual disabilitypanel. Sources: Radboud University Medical Center, Nijmegen