SLC6A11 solute carrier family 6 member 11 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC6A11provided by HGNC
Official Full Name: solute carrier family 6 member 11provided by HGNC
Primary source: HGNC:HGNC:11044
See related: Ensembl:ENSG00000132164 MIM:607952; AllianceGenome:HGNC:11044
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: GAT3; GAT4; GAT-3
Summary: The protein encoded by this gene is a sodium-dependent transporter that uptakes gamma-aminobutyric acid (GABA), an inhibitory neurotransmitter, which ends the GABA neurotransmission. Defects in this gene may result in epilepsy, behavioral problems, or intellectual problems. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]
Expression: Biased expression in brain (RPKM 2.2), esophagus (RPKM 0.8) and 3 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p25.3

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (10816228..10940714)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (10810506..10935188)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (10857913..10982400)

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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Downregulation of GABA Transporter 3 (GAT3) is Associated with Deficient Oxidative GABA Metabolism in Human Induced Pluripotent Stem Cell-Derived Astrocytes in Alzheimer's Disease.
Title: Downregulation of GABA Transporter 3 (GAT3) is Associated with Deficient Oxidative GABA Metabolism in Human Induced Pluripotent Stem Cell-Derived Astrocytes in Alzheimer's Disease.
GAT-1 (rs2697153) and GAT-3 (rs2272400) polymorphisms are associated with febrile seizures and temporal lobe epilepsy.
Title: GAT-1 (rs2697153) and GAT-3 (rs2272400) polymorphisms are associated with febrile seizures and temporal lobe epilepsy.
we performed GATA4 mutation screening for 119 patients with 46, XY DSD without heart anomalies
Title: GATA4 mutations are uncommon in patients with 46,XY disorders of sex development without heart anomaly.
GAT-3 expression was selectively decreased in the central amygdala of alcohol-dependent people compared to those who died of unrelated causes.
Title: A molecular mechanism for choosing alcohol over an alternative reward.
GABA-transporter 3 was reduced by about 62% in severe hippocampal sclerosis samples
Title: Hippocampal GABA transporter distribution in patients with temporal lobe epilepsy and hippocampal sclerosis.
3p25.3 microdeletion of GABA transporters SLC6A1 and SLC6A11 results in intellectual disability, epilepsy and stereotypic behavior.
Title: 3p25.3 microdeletion of GABA transporters SLC6A1 and SLC6A11 results in intellectual disability, epilepsy and stereotypic behavior.
results suggest that GABA receptor signaling pathway was associated with the increased susceptibility to TD in Korean schizophrenic patients
Title: Gaba transporter SLC6A11 gene polymorphism associated with tardive dyskinesia.
Binding assays employing membrane preparations obtained from a stably GAT3 expressing HEK293 cell line and DDPM-1007 as nonlabeled GAT3 marker were performed. In these experiments specific binding of DDPM-1007 at GAT3 could be unambiguously detected.
Title: Development and validation of an LC-ESI-MS/MS quantification method for a potential γ-aminobutyric acid transporter 3 (GAT3) marker and its application in preliminary MS binding assays.
The results suggest that GAT3 c.1572T may be one of the contributing factors with a modest effect on antiepileptic drug (AEDs) pharmacoresistance in the epileptic brain.
Title: Association of a synonymous GAT3 polymorphism with antiepileptic drug pharmacoresistance.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

Submit: New GeneRIF Correction See all GeneRIFs (12)

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

EBI GWAS Catalog

Description
Genome-wide association analysis implicates the involvement of eight loci with response to tocilizumab for the treatment of rheumatoid arthritis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide Interrogation of Longitudinal FEV1 in Children with Asthma. 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)

General gene information

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Markers

SHGC-145517 (e-PCR)
- UniSTS:174623

SHGC-141816 (e-PCR)
- UniSTS:171094

RH18458 (e-PCR)
- UniSTS:55920

SHGC-144538 (e-PCR)
- UniSTS:174274

SHGC-36836 (e-PCR)
- UniSTS:83436

G19637 (e-PCR)
- UniSTS:41966

A001T39 (e-PCR)
- UniSTS:41967

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables amino acid binding	IEA Inferred from Electronic Annotation 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	TAS Traceable Author Statement more info
enables monocarboxylic acid transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables taurine:sodium symporter activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in amino acid transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in amino acid transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in gamma-aminobutyric acid reuptake	TAS Traceable Author Statement more info
involved_in monocarboxylic acid transport	IDA Inferred from Direct Assay more info	PubMed
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in taurine transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in GABA-ergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in cell projection	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
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 3

Names: GABA transporter 3; solute carrier family 6 (neurotransmitter transporter), member 11; solute carrier family 6 (neurotransmitter transporter, GABA), member 11

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.

mRNA and Protein(s)

NM_001317406.3 → NP_001304335.1 sodium- and chloride-dependent GABA transporter 3 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the C-terminus compared to isoform 1.

Source sequence(s)

AC018495, BC036083

Consensus CDS

CCDS82734.1

UniProtKB/Swiss-Prot

P48066

Related

ENSP00000404120.1, ENST00000454147.1

Conserved Domains (1) summary

cl00456
Location:49 → 208

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_014229.3 → NP_055044.1 sodium- and chloride-dependent GABA transporter 3 isoform 1

See identical proteins and their annotated locations for NP_055044.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AC027128, AK312719, S75989

Consensus CDS

CCDS2602.1

UniProtKB/Swiss-Prot

B2R6U6, P48066, Q8IYC9

Related

ENSP00000254488.2, ENST00000254488.7

Conserved Domains (1) summary

cd11508
Location:49 → 590

SLC6sbd_GAT3; Na(+)- and Cl(-)-dependent GABA transporter 3; solute-binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

10816228..10940714

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011534033.3 → XP_011532335.1 sodium- and chloride-dependent GABA transporter 3 isoform X2

Conserved Domains (1) summary

cl00456
Location:49 → 374

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_047448764.1 → XP_047304720.1 sodium- and chloride-dependent GABA transporter 3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

10810506..10935188

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054347622.1 → XP_054203597.1 sodium- and chloride-dependent GABA transporter 3 isoform X2
XM_054347621.1 → XP_054203596.1 sodium- and chloride-dependent GABA transporter 3 isoform X1