SLC6A1 solute carrier family 6 member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC6A1provided by HGNC
Official Full Name: solute carrier family 6 member 1provided by HGNC
Primary source: HGNC:HGNC:11042
See related: Ensembl:ENSG00000157103 MIM:137165; AllianceGenome:HGNC:11042
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MAE; GAT1; GABATR; hGAT-1; GABATHG
Summary: The protein encoded by this gene is a gamma-aminobutyric acid (GABA) transporter that localizes to the plasma membrane. The encoded protein removes GABA from the synaptic cleft, restoring it to presynaptic terminals. [provided by RefSeq, Jan 2017]
Expression: Biased expression in brain (RPKM 26.6), liver (RPKM 15.1) and 2 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p25.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (10992748..11039247)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (10987230..11033712)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (11034434..11080933)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Abnormal Weakening of DNA Methylation around the SLC6A1 Gene Promoter in Temporal Lobe Epilepsy.
Title: Abnormal Weakening of DNA Methylation around the SLC6A1 Gene Promoter in Temporal Lobe Epilepsy.
Beyond the Diagnosis: Evaluation of Quality-of-Life Measures and Family Functioning in SLC6A1-Related Neurodevelopmental Disorder.
Title: Beyond the Diagnosis: Evaluation of Quality-of-Life Measures and Family Functioning in SLC6A1-Related Neurodevelopmental Disorder.
SLC6A1 variant pathogenicity, molecular function and phenotype: a genetic and clinical analysis.
Title: SLC6A1 variant pathogenicity, molecular function and phenotype: a genetic and clinical analysis.
Patient-derived SLC6A1 variant S295L results in an epileptic phenotype similar to haploinsufficient mice.
Title: Patient-derived SLC6A1 variant S295L results in an epileptic phenotype similar to haploinsufficient mice.
Ketone bodies promote stroke recovery via GAT-1-dependent cortical network remodeling.
Title: Ketone bodies promote stroke recovery via GAT-1-dependent cortical network remodeling.
Assessing the impact of the de novo SLC6A1 mutation in schizophrenia through a comprehensive case study.
Title: Assessing the impact of the de novo SLC6A1 mutation in schizophrenia through a comprehensive case study.
Experimental and Bioinformatic Insights into the Effects of Epileptogenic Variants on the Function and Trafficking of the GABA Transporter GAT-1.
Title: Experimental and Bioinformatic Insights into the Effects of Epileptogenic Variants on the Function and Trafficking of the GABA Transporter GAT-1.
Astrocytic GABA transporter 1 deficit in novel SLC6A1 variants mediated epilepsy: Connected from protein destabilization to seizures in mice and humans.
Title: Astrocytic GABA transporter 1 deficit in novel SLC6A1 variants mediated epilepsy: Connected from protein destabilization to seizures in mice and humans.
New Genetic Variants in CYP2B6 and SLC6A Support the Role of Oxidative Stress in Familial Meniere's Disease.
Title: New Genetic Variants in CYP2B6 and SLC6A Support the Role of Oxidative Stress in Familial Ménière's Disease.
Structural basis of GABA reuptake inhibition.
Title: Structural basis of GABA reuptake inhibition.

Submit: New GeneRIF Correction See all GeneRIFs (57)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Myoclonic-atonic epilepsy MedGen: CN231318 OMIM: 616421 GeneReviews: SLC6A1-Related Neurodevelopmental Disorder	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2019-09-25) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2019-09-25) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies three common variants associated with serologic response to vitamin E supplementation in men. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S3997 (e-PCR)
- UniSTS:24930

RH103850 (e-PCR)
- UniSTS:98175

Slc6a1 (e-PCR), detects polymorphism
- UniSTS:531382

WI-14944 (e-PCR)
- UniSTS:5314

SLC6A1_849 (e-PCR)
- UniSTS:277749

SLC6A1_V155 (e-PCR)
- UniSTS:277749

SGC30830 (e-PCR)
- UniSTS:48382

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables gamma-aminobutyric acid transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables gamma-aminobutyric acid:sodium:chloride symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables gamma-aminobutyric acid:sodium:chloride symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables gamma-aminobutyric acid:sodium:chloride symporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables gamma-aminobutyric acid:sodium:chloride symporter activity	TAS Traceable Author Statement more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sodium:chloride symporter activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in amino acid transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of associative learning	ISS Inferred from Sequence or Structural Similarity more info
involved_in chemical synaptic transmission	TAS Traceable Author Statement more info	PubMed
involved_in chloride transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in gamma-aminobutyric acid import	IDA Inferred from Direct Assay more info	PubMed
involved_in gamma-aminobutyric acid import	ISS Inferred from Sequence or Structural Similarity more info
involved_in gamma-aminobutyric acid reuptake	TAS Traceable Author Statement more info
involved_in inorganic anion import across plasma membrane	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of memory	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of synaptic transmission, GABAergic	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gamma-aminobutyric acid secretion	IEA Inferred from Electronic Annotation more info
involved_in response to calcium ion	IEA Inferred from Electronic Annotation more info
involved_in response to cocaine	IEA Inferred from Electronic Annotation more info
involved_in response to estradiol	IEA Inferred from Electronic Annotation more info
involved_in response to lead ion	IEA Inferred from Electronic Annotation more info
involved_in response to methamphetamine hydrochloride	IEA Inferred from Electronic Annotation more info
involved_in response to purine-containing compound	IEA Inferred from Electronic Annotation more info
involved_in response to sucrose	IEA Inferred from Electronic Annotation more info
involved_in response to toxic substance	IEA Inferred from Electronic Annotation more info
involved_in sodium ion import across plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of synapse organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in transport across blood-brain barrier	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in GABA-ergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
located_in presynaptic membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sodium- and chloride-dependent GABA transporter 1

Names: GABA transporter 1; solute carrier family 6 (neurotransmitter transporter), member 1; solute carrier family 6 (neurotransmitter transporter, GABA), member 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_053003.1 RefSeqGene

Range

5020..51519

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001348250.2 → NP_001335179.1 sodium- and chloride-dependent GABA transporter 1 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform.

Source sequence(s)

AC024910

Consensus CDS

CCDS2603.1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5

Related

ENSP00000494346.1, ENST00000642767.1

Conserved Domains (1) summary

cd11506
Location:2 → 599

SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain
NM_001348251.2 → NP_001335180.1 sodium- and chloride-dependent GABA transporter 1 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses two alternate splice junctions compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform (a).

Source sequence(s)

AC024910

Consensus CDS

CCDS87043.1

UniProtKB/TrEMBL

A0A2R8Y4I3, A0A2R8Y867

Related

ENSP00000493813.1, ENST00000644314.1

Conserved Domains (1) summary

cl00456
Location:1 → 479

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001348252.2 → NP_001335181.1 sodium- and chloride-dependent GABA transporter 1 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate splice junction and lacks an alternate exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 4 and 5 both encode the same isoform (c).

Source sequence(s)

AC024910

Consensus CDS

CCDS87044.1

UniProtKB/TrEMBL

A0A2R8Y867, B7Z3C5

Related

ENSP00000494002.1, ENST00000646072.1

Conserved Domains (1) summary

cl00456
Location:1 → 421

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001348253.2 → NP_001335182.1 sodium- and chloride-dependent GABA transporter 1 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses two alternate splice junctions and lacks an alternate exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 4 and 5 both encode the same isoform (c).

Source sequence(s)

AC024910

Consensus CDS

CCDS87044.1

UniProtKB/TrEMBL

A0A2R8Y867, B7Z3C5

Related

ENSP00000495375.1, ENST00000645776.1

Conserved Domains (1) summary

cl00456
Location:1 → 421

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_003042.4 → NP_003033.3 sodium- and chloride-dependent GABA transporter 1 isoform a

See identical proteins and their annotated locations for NP_003033.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AC024910, BC033904, BC057291, DA162953

Consensus CDS

CCDS2603.1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5

Related

ENSP00000287766.4, ENST00000287766.10

Conserved Domains (1) summary

cd11506
Location:2 → 599

SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

10992748..11039247

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011534027.4 → XP_011532329.1 sodium- and chloride-dependent GABA transporter 1 isoform X1

See identical proteins and their annotated locations for XP_011532329.1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5

Conserved Domains (1) summary

cd11506
Location:2 → 599

SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain
XM_005265411.6 → XP_005265468.1 sodium- and chloride-dependent GABA transporter 1 isoform X1

See identical proteins and their annotated locations for XP_005265468.1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5

Related

ENSP00000494136.1, ENST00000643396.1

Conserved Domains (1) summary

cd11506
Location:2 → 599

SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain
XM_017007071.3 → XP_016862560.1 sodium- and chloride-dependent GABA transporter 1 isoform X1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5

Related

ENSP00000496348.1, ENST00000642515.1

Conserved Domains (1) summary

cd11506
Location:2 → 599

SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain
XM_017007072.3 → XP_016862561.1 sodium- and chloride-dependent GABA transporter 1 isoform X1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5

Conserved Domains (1) summary

cd11506
Location:2 → 599

SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

10987230..11033712

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054347613.1 → XP_054203588.1 sodium- and chloride-dependent GABA transporter 1 isoform X1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5
XM_054347617.1 → XP_054203592.1 sodium- and chloride-dependent GABA transporter 1 isoform X1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5
XM_054347612.1 → XP_054203587.1 sodium- and chloride-dependent GABA transporter 1 isoform X1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5
XM_054347616.1 → XP_054203591.1 sodium- and chloride-dependent GABA transporter 1 isoform X1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5
XM_054347615.1 → XP_054203590.1 sodium- and chloride-dependent GABA transporter 1 isoform X1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5
XM_054347614.1 → XP_054203589.1 sodium- and chloride-dependent GABA transporter 1 isoform X1

UniProtKB/Swiss-Prot

P30531, Q8N4K8

UniProtKB/TrEMBL

A0A2R8YDD5