SLC6A13 solute carrier family 6 member 13 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC6A13provided by HGNC
Official Full Name: solute carrier family 6 member 13provided by HGNC
Primary source: HGNC:HGNC:11046
See related: Ensembl:ENSG00000010379 MIM:615097; AllianceGenome:HGNC:11046
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GAT2; GAT3; GAT-2
Summary: Enables gamma-aminobutyric acid:sodium:chloride symporter activity. Involved in amino acid import across plasma membrane and monocarboxylic acid transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in kidney (RPKM 28.5) and liver (RPKM 1.5) See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.33

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (220622..262836, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (217551..259667, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (329788..372002, complement)

Chromosome 12 - NC_000012.12 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 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?

Transcription factor ASCL1 targets SLC6A13 to inhibit the progression of hepatocellular carcinoma via the glycine-inflammasome signaling.
Title: Transcription factor ASCL1 targets SLC6A13 to inhibit the progression of hepatocellular carcinoma via the glycine-inflammasome signaling.
Evidence for a Revised Ion/Substrate Coupling Stoichiometry of GABA Transporters.
Title: Evidence for a Revised Ion/Substrate Coupling Stoichiometry of GABA Transporters.
Neurotransmitter transporters including SLC6A6 and SLC6A13 mediate the uptake of 5-aminolevulinic acid (ALA) and can play roles in the enhancement of ALA-induced accumulation of protoporphyrin in cancerous cells.
Title: Neurotransmitter transporter family including SLC6A6 and SLC6A13 contributes to the 5-aminolevulinic acid (ALA)-induced accumulation of protoporphyrin IX and photodamage, through uptake of ALA by cancerous cells.
Results suggest that gamma-aminobutyric acid transporter 2 GAT-2 is a high selectivity/low affinity transporter.
Title: High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Meta-analysis and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: New loci associated with kidney function and chronic kidney disease.
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.
homology models of hGAT-2 and hGAT-3 were built and searched for (i) substrate conformation, (ii) prediction of substrate (inhibitor) interaction, and (iii) distinguishable allosteric Zn2+ inhibition by combining docking and MD calculations.
Title: Substrate-Na+ complex formation: coupling mechanism for gamma-aminobutyrate symporters.
Observational study of gene-disease association. (HuGE Navigator)
Title: L-type voltage-dependent calcium channel alpha subunit 1C is a novel candidate gene associated with secondary hyperparathyroidism: an application of haplotype-based analysis for multiple linked single nucleotide polymorphisms.

Submit: New GeneRIF Correction

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
An atlas of genetic influences on human blood metabolites. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic determinants influencing human serum metabolome among African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
New loci associated with kidney function and chronic kidney disease. 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

D12S2046 (e-PCR)
- UniSTS:53031

RH93085 (e-PCR)
- UniSTS:91761

D12S1256 (e-PCR)
- UniSTS:76206

PMC311068P1 (e-PCR)
- UniSTS:272879

WI-17955 (e-PCR)
- UniSTS:41716

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables amino acid transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables amino acid:sodium symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables creatine transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info
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	TAS Traceable Author Statement more info
enables monocarboxylic acid transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables taurine transmembrane transporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables taurine:sodium symporter activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in amino acid import across plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in amino acid transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in creatine transmembrane transport	ISS Inferred from Sequence or Structural Similarity more info
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 monocarboxylic acid transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of nitrogen compound transport	IDA Inferred from Direct Assay more info	PubMed
involved_in nitrogen compound transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in taurine transmembrane transport	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 basolateral plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cell projection	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular exosome	HDA more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in presynapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sodium- and chloride-dependent GABA transporter 2

Names: GABA transport protein; GABA transporter 2; solute carrier family 6 (neurotransmitter transporter), member 13; solute carrier family 6 (neurotransmitter transporter, GABA), member 13

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_001190997.3 → NP_001177926.1 sodium- and chloride-dependent GABA transporter 2 isoform 2

See identical proteins and their annotated locations for NP_001177926.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks two consecutive exons in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AK296127, DB540466

Consensus CDS

CCDS53729.1

UniProtKB/Swiss-Prot

Q9NSD5

Related

ENSP00000407104.2, ENST00000445055.6

Conserved Domains (1) summary

cl00456
Location:32 → 483

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_001243392.2 → NP_001230321.1 sodium- and chloride-dependent GABA transporter 2 isoform 3

See identical proteins and their annotated locations for NP_001230321.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks a splice site and a large portion of the coding region, compared to variant 1. The encoded isoform (3) is significantly shorter and has a disctinct C-terminus, compared to isoform 1.

Source sequence(s)

AI802118, BC020867

Consensus CDS

CCDS58198.1

UniProtKB/Swiss-Prot

Q9NSD5

Related

ENSP00000389316.1, ENST00000436453.1

Conserved Domains (1) summary

cl00456
Location:32 → 68

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
NM_016615.5 → NP_057699.2 sodium- and chloride-dependent GABA transporter 2 isoform 1

See identical proteins and their annotated locations for NP_057699.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AK313511, BM662288, DA374290, DB540466

Consensus CDS

CCDS8502.1

UniProtKB/Swiss-Prot

B4DJL1, Q8TCC2, Q8WW56, Q9NSD5

UniProtKB/TrEMBL

B4DJS3

Related

ENSP00000339260.4, ENST00000343164.9

Conserved Domains (1) summary

cd11507
Location:32 → 575

SLC6sbd_GAT2; Na(+)- and Cl(-)-dependent GABA transporter 2; 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_000012.12 Reference GRCh38.p14 Primary Assembly

Range

220622..262836 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047429420.1 → XP_047285376.1 sodium- and chloride-dependent GABA transporter 2 isoform X2
XM_017019845.2 → XP_016875334.1 sodium- and chloride-dependent GABA transporter 2 isoform X3

Conserved Domains (1) summary

cl00456
Location:1 → 332

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_006719008.4 → XP_006719071.1 sodium- and chloride-dependent GABA transporter 2 isoform X3

Conserved Domains (1) summary

cl00456
Location:1 → 332

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_017019842.2 → XP_016875331.1 sodium- and chloride-dependent GABA transporter 2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

217551..259667 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054373005.1 → XP_054228980.1 sodium- and chloride-dependent GABA transporter 2 isoform X2
XM_054373004.1 → XP_054228979.1 sodium- and chloride-dependent GABA transporter 2 isoform X1
XM_054373007.1 → XP_054228982.1 sodium- and chloride-dependent GABA transporter 2 isoform X3
XM_054373006.1 → XP_054228981.1 sodium- and chloride-dependent GABA transporter 2 isoform X3