Developmental Brain Disorder Gene Database

Missense Gene

Gene

Return to Missense Gene Listing Page

Missense

SLC6A1

HGNC:11042 (protein-coding gene)

solute carrier family 6 member 1

Unique Cases:: 28

Disorders:: ID, ASD, EP, ADHD, SCZ

Last Updated:: January 4, 2024

Gene Summary:

Gene Function: Mediates transport of gamma-aminobutyric acid (GABA) together with sodium and chloride and is responsible for the reuptake of GABA from the synapse (PubMed:30132828). The translocation of GABA, however, may also occur in the reverse direction leading to the release of GABA (By similarity). The direction and magnitude of GABA transport is a consequence of the prevailing thermodynamic conditions, determined by membrane potential and the intracellular and extracellular concentrations of Na(+), Cl(-... (Source: Uniprot)

Previous symbols: No previous symbols

Alias symbols: GAT1, GABATR, GABATHG, GAT-1, hGAT-1

Chromosomal Location: 3p25.3

Genomic Coordinates: GRCh37:chr3:11034420-11080935; GRCh38:chr3:10992748-11039247

Associated Disorders: Intellectual Disability, Autism, Epilepsy, Attention Deficit Hyperactivity Disorder

Predictive Scores:

HI Score (Decipher): 15.39

pLI (gnomAD): 1.00

LOEUF (gnomAD): 0.15

Classifications from External Sources:

SFARI Score (SFARI): 1

DDG2P Classification (DDG2P): No Classification

ClinGen Classification (ClinGen): No Classification

GenCC Classification (GenCC): Strong2 Supportive1 Definitive1

Cases:

Publications:

Yuan H et. al., Concurrent pathogenic variants in SLC6A1/NOTCH1/PRIMPOL genes in a Chinese patient with myoclonic-atonic epilepsy, mild aortic valve stenosis and high myopia., BMC Med Genet, 2020

Tang S et. al., Phenotypic and genetic spectrum of epilepsy with myoclonic atonic seizures., Epilepsia, 2020

Snoeijen-Schouwenaars FM et. al., Diagnostic exome sequencing in 100 consecutive patients with both epilepsy and intellectual disability., Epilepsia, 2019

Coe BP et. al., Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity., Nat Genet, 2019

Peng J et. al., Next-generation sequencing improves treatment efficacy and reduces hospitalization in children with drug-resistant epilepsy., CNS Neurosci Ther, 2019

Aspromonte MC et. al., Characterization of intellectual disability and autism comorbidity through gene panel sequencing., Hum Mutat, 2019

Fernández-Marmiesse A et. al., Rare Variants in 48 Genes Account for 42% of Cases of Epilepsy With or Without Neurodevelopmental Delay in 246 Pediatric Patients., Front Neurosci, 2019

Chérot E et. al., Using medical exome sequencing to identify the causes of neurodevelopmental disorders: Experience of 2 clinical units and 216 patients., Clin Genet, 2018

Munnich A et. al., Impact of on-site clinical genetics consultations on diagnostic rate in children and young adults with autism spectrum disorder., Mol Autism, 2019

Takata A et. al., Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy., Nat Commun, 2019

Salinas V et. al., Clinical next generation sequencing in developmental and epileptic encephalopathies: Diagnostic relevance of data re-analysis and variants re-interpretation., Eur J Med Genet, 2021

Jiang T et. al., Application of Trio-Whole Exome Sequencing in Genetic Diagnosis and Therapy in Chinese Children With Epilepsy., Front Mol Neurosci, 2021

Rees E et. al., De novo mutations identified by exome sequencing implicate rare missense variants in SLC6A1 in schizophrenia., Nat Neurosci, 2020

Varesio C et. al., Diagnostic Yield and Cost-Effectiveness of "Dynamic" Exome Analysis in Epilepsy with Neurodevelopmental Disorders: A Tertiary-Center Experience in Northern Italy., Diagnostics (Basel), 2021

Brea-Fernández AJ et. al., Trio-based exome sequencing reveals a high rate of the de novo variants in intellectual disability., Eur J Hum Genet, 2022

Lindstrand A et. al., Genome sequencing is a sensitive first-line test to diagnose individuals with intellectual disability., Genet Med, 2022

Miyake N et. al., Molecular diagnosis of 405 individuals with autism spectrum disorder., Eur J Hum Genet, 2023

External References:

NCBI: Gene

Integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

NCBI: Gene

Gene Reviews

An international point-of-care resource for busy clinicians, provides clinically relevant and medically actionable information for inherited conditions in a standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families.

Gene Reviews

DECIPHER

DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants. DECIPHER enhances clinical diagnosis by retrieving information from a variety of bioinformatics resources relevant to the variant found in the patient.

DECIPHER

SFARI

SFARI Gene is an evolving online database designed to permit quick entrée into the genetics of autism, and to help researchers track the ever-expanding genetic risk factors that emerge in the literature.

SFARI

ClinGen

ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.

ClinGen

GenCC

The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases.

GenCC

gnomAD

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.