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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SLC6A1
solute carrier family 6 member 1
Chromosome 3 Β· 3p25.3
NCBI Gene: 6529Ensembl: ENSG00000157103.13HGNC: HGNC:11042UniProt: A0A2R8Y4I3
100PubMed Papers
21Diseases
2Drugs
184Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTransporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
FDA Approved TargetOMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
sodium ion import across plasma membraneplasma membranechloride transmembrane transportgamma-aminobutyric acid:sodium:chloride symporter activityepilepsy with myoclonic atonic seizuresSeizuregenetic disorderIntellectual disability
✦AI Summary

SLC6A1 encodes GAT1 (GABA transporter 1), which mediates the sodium- and chloride-dependent reuptake of gamma-aminobutyric acid (GABA) from synapses into neurons and astrocytes 1. This transporter plays a pivotal role in GABAergic neurotransmission by clearing GABA from the synaptic cleft and facilitating its storage in presynaptic vesicles 2. The protein functions through a complex intracellular trafficking process involving molecular chaperones, quality control mechanisms, and delivery to the cell surface 2. Pathogenic variants in SLC6A1 cause a broad spectrum of neurological disorders, including myoclonic-atonic epilepsy and developmental epileptic encephalopathies 3. Many disease-causing mutations impair protein folding and membrane targeting, leading to loss of transporter function and disrupted GABAergic signaling 23. Complete loss of GABA uptake function is associated with more severe clinical phenotypes 3. Haploinsufficient deletions of SLC6A1, as seen in 3p- syndrome, also significantly reduce GABA uptake capacity 4. Gene therapy approaches using AAV9 vectors have shown promise in preclinical models, normalizing EEG patterns and improving behavioral deficits 1. Additionally, pharmacological chaperones like 4-phenylbutyrate can rescue some misfolded variants and provide therapeutic benefits 24.

Sources cited
1
SLC6A1 encodes GAT1 which mediates sodium- and chloride-dependent GABA reuptake, and gene therapy shows efficacy in mouse models
PMID: 39589822
2
GAT1 plays pivotal role in GABA uptake and undergoes complex intracellular trafficking with quality control mechanisms
PMID: 39268250
3
SLC6A1 variants cause broad phenotypic spectrum with complete loss-of-function associated with severe disease
PMID: 37647852
4
Haploinsufficient deletions reduce GABA uptake and 4-phenylbutyrate treatment shows therapeutic benefits
PMID: 39923323
⚠Limited data available β€” This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜21
epilepsy with myoclonic atonic seizuresOpen Targets
0.77Strong
SeizureOpen Targets
0.59Moderate
genetic disorderOpen Targets
0.54Moderate
Intellectual disabilityOpen Targets
0.50Moderate
Neurodevelopmental delayOpen Targets
0.48Moderate
epilepsyOpen Targets
0.48Moderate
Neurodevelopmental disorderOpen Targets
0.43Moderate
AnxietyOpen Targets
0.37Weak
autosomal dominant non-syndromic intellectual disabilityOpen Targets
0.37Weak
Abnormality of refractionOpen Targets
0.35Weak
childhood-onset epilepsy syndromeOpen Targets
0.34Weak
developmental and epileptic encephalopathy 94Open Targets
0.34Weak
Global developmental delayOpen Targets
0.33Weak
Rolandic epilepsyOpen Targets
0.33Weak
self-limited epilepsy with centrotemporal spikesOpen Targets
0.33Weak
smoking initiationOpen Targets
0.33Weak
placental retentionOpen Targets
0.33Weak
overnutritionOpen Targets
0.32Weak
generalized anxiety disorderOpen Targets
0.32Weak
obesityOpen Targets
0.32Weak
Myoclonic-atonic epilepsyUniProt
Pathogenic Variants184
NM_003042.4(SLC6A1):c.1000G>A (p.Ala334Thr)Likely pathogenic
Seizure;Intellectual disability|SLC6A1-related disorder|Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2025β†’ Residue 334
NM_003042.4(SLC6A1):c.223G>A (p.Gly75Arg)Pathogenic
not provided|Epilepsy with myoclonic atonic seizures|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 75
NM_003042.4(SLC6A1):c.1084G>A (p.Gly362Arg)Pathogenic
not provided|Neurodevelopmental delay|Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2025β†’ Residue 362
NM_003042.4(SLC6A1):c.1435C>T (p.Arg479Ter)Pathogenic
not provided|Epilepsy with myoclonic atonic seizures|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 479
NM_003042.4(SLC6A1):c.889G>A (p.Gly297Arg)Pathogenic
not provided|Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2025β†’ Residue 297
NM_003042.4(SLC6A1):c.1648G>A (p.Gly550Arg)Pathogenic
not provided|Global developmental delay|Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2025β†’ Residue 550
NM_003042.4(SLC6A1):c.863C>T (p.Ala288Val)Pathogenic
not provided|Inborn genetic diseases|Autism spectrum disorder;Epilepsy with myoclonic atonic seizures|Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2025β†’ Residue 288
NM_003042.4(SLC6A1):c.919G>A (p.Gly307Arg)Pathogenic
not provided|Neurodevelopmental disorder|Epilepsy with myoclonic atonic seizures|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 307
NM_003042.4(SLC6A1):c.331G>A (p.Gly111Arg)Pathogenic
not provided|Epilepsy with myoclonic atonic seizures|SLC6A1-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 111
NM_003042.4(SLC6A1):c.1531G>A (p.Val511Met)Pathogenic
not provided|Neurodevelopmental delay|Seizure|Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2025β†’ Residue 511
NM_003042.4(SLC6A1):c.1070C>T (p.Ala357Val)Pathogenic
not provided|Epilepsy with myoclonic atonic seizures|SLC6A1-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 357
NM_003042.4(SLC6A1):c.383C>T (p.Ala128Val)Pathogenic
Seizure|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 128
NM_003042.4(SLC6A1):c.1328G>A (p.Gly443Asp)Likely pathogenic
Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2024β†’ Residue 443
NM_003042.4(SLC6A1):c.373G>A (p.Val125Met)Pathogenic
Epilepsy with myoclonic atonic seizures|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 125
NM_003042.4(SLC6A1):c.875TCT[2] (p.Phe294del)Pathogenic
Intellectual disability|not provided|Epilepsy with myoclonic atonic seizures|See cases
β˜…β˜…β˜†β˜†2024β†’ Residue 294
NM_003042.4(SLC6A1):c.640_658del (p.Leu214fs)Pathogenic
not provided|Inborn genetic diseases|SLC6A1-related neurodevelopmental disorder|Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2024β†’ Residue 214
NM_003042.4(SLC6A1):c.197del (p.Asn66fs)Pathogenic
Inborn genetic diseases|Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2024β†’ Residue 66
NM_003042.4(SLC6A1):c.130C>T (p.Arg44Trp)Pathogenic
not provided|Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2024β†’ Residue 44
NM_003042.4(SLC6A1):c.131G>A (p.Arg44Gln)Pathogenic
not provided|Autosomal dominant epilepsy|Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2024β†’ Residue 44
NM_003042.4(SLC6A1):c.809T>C (p.Phe270Ser)Pathogenic
Inborn genetic diseases|Epilepsy with myoclonic atonic seizures
β˜…β˜…β˜†β˜†2024β†’ Residue 270
View on ClinVar β†—
Drug Targets2
TIAGABINEApproved
GABA transporter 1 inhibitor
epilepsy
TIAGABINE HYDROCHLORIDEApproved
GABA transporter 1 inhibitor
Seizure
Related Genes
GABRA5Protein interaction93%GABRG2Protein interaction93%PPOXProtein interaction83%GAD1Protein interaction81%GAD2Protein interaction81%PVALBProtein interaction81%
Tissue Expression6 tissues
Liver
100%
Brain
57%
Heart
7%
Ovary
3%
Lung
1%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
SLC6A1GABRA5GABRG2PPOXGAD1GAD2PVALB
PROTEIN STRUCTURE
Preparing viewer…
PDB7Y7V Β· 2.20 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.15Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.06 [0.03–0.15]
RankingsWhere SLC6A1 stands among ~20K protein-coding genes
  • #4,811of 20,598
    Most Researched100 Β· top quartile
  • #601of 1,025
    FDA-Approved Drug Targets2
  • #386of 5,498
    Most Pathogenic Variants184 Β· top 10%
  • #223of 17,882
    Most Constrained (LOEUF)0.15 Β· top 5%
Genes detectedSLC6A1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
CDKL5 deficiency disorder: clinical features, diagnosis, and management.
PMID: 35483386
Lancet Neurol Β· 2022
1.00
2
SLC6A1 variant pathogenicity, molecular function and phenotype: a genetic and clinical analysis.
PMID: 37647852
Brain Β· 2023
0.90
3
Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer's disease.
PMID: 37264161
Nat Neurosci Β· 2023
0.80
4
AAV9/SLC6A1 gene therapy rescues abnormal EEG patterns and cognitive behavioral deficiencies in Slc6a1-/- mice.
PMID: 39589822
J Clin Invest Β· 2024
0.70
5
Precision medicine for genetic epilepsy on the horizon: Recent advances, present challenges, and suggestions for continued progress.
PMID: 35716052
Epilepsia Β· 2022
0.60