SLC6A12 solute carrier family 6 member 12 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC6A12provided by HGNC
Official Full Name: solute carrier family 6 member 12provided by HGNC
Primary source: HGNC:HGNC:11045
See related: Ensembl:ENSG00000111181 MIM:603080; AllianceGenome:HGNC:11045
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: BGT1; GAT2; BGT-1
Summary: Enables gamma-aminobutyric acid:sodium:chloride symporter activity. Involved in gamma-aminobutyric acid transport and monocarboxylic acid transport. Predicted to be located in basolateral plasma membrane. Predicted to be active in cell projection and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in liver (RPKM 12.1), kidney (RPKM 10.0) and 5 other tissues See more
Orthologs: all
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Genomic context

Location:: 12p13.33

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (183848..214157, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (179876..211078, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (299247..323323, 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?

Overexpression of solute carrier family 6 member 12 promotes cell injury in Parkinson's disease via MAPK signaling pathway.
Title: Overexpression of solute carrier family 6 member 12 promotes cell injury in Parkinson's disease via MAPK signaling pathway.
Protein kinases as regulators of osmolyte accumulation under stress conditions: An overview.
Title: Protein kinases as regulators of osmolyte accumulation under stress conditions: An overview.
This review gathers the current structural and functional knowledge on BGT1 with emphasis on brain relevance, discusses all available compounds, and tries to shed light on the molecular determinants driving BGT1 selectivity--{REVIEW}
Title: Structural and molecular aspects of betaine-GABA transporter 1 (BGT1) and its relation to brain function.
The SLC6A12 expression levels in peripheral blood mononuclear cells were significantly higher in TLE patients.
Title: Combined effect between two functional polymorphisms of SLC6A12 gene is associated with temporal lobe epilepsy.
T40 may be important for the trafficking and insertion of BGT1 in the plasma membrane
Title: Mutation of a single threonine in the cytoplasmic NH2 terminus disrupts trafficking of renal betaine-GABA transporter 1 during hypertonic stress.
JAK2 is a novel regulator of the GABA transporter BGT1.
Title: Up-regulation of the betaine/GABA transporter BGT1 by JAK2.
This study found that rs216250 of SLC6A12 was correlated with the Scale for the Assessment of Negative Symptoms (SANS) scores.
Title: Association between the SLC6A12 gene and negative symptoms of schizophrenia in a Korean population.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Association of SLC6A12 variants with aspirin-intolerant asthma in a Korean population.
Results showed that two polymorphisms and a haplotype in SLC6A12, were significantly associated with AIA after multiple testing corrections.
Title: Association of SLC6A12 variants with aspirin-intolerant asthma in a Korean population.
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 See all GeneRIFs (12)

Phenotypes

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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 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

PMC139224P1 (e-PCR)
- UniSTS:270885

WI-18098 (e-PCR)
- UniSTS:25249

RH79135 (e-PCR)
- UniSTS:71859

SLC6A12_1341 (e-PCR)
- UniSTS:281019

G41013 (e-PCR)
- UniSTS:73162

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables amino acid transmembrane transporter activity	TAS Traceable Author Statement 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 monocarboxylic acid transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

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 amino acid transport	TAS Traceable Author Statement more info
involved_in gamma-aminobutyric acid reuptake	TAS Traceable Author Statement more info
involved_in gamma-aminobutyric acid transport	IDA Inferred from Direct Assay more info	PubMed
involved_in glycine betaine transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in monocarboxylic acid transport	IDA Inferred from Direct Assay more info	PubMed
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info

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 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	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 betaine transporter

Names: Na(+)/Cl(-) betaine/GABA transporter; betaine/GABA transporter-1; gamma-aminobutyric acid transporter; solute carrier family 6 (neurotransmitter transporter), member 12; solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12

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_001122847.3 → NP_001116319.1 sodium- and chloride-dependent betaine transporter

See identical proteins and their annotated locations for NP_001116319.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.

Source sequence(s)

AC007406, BC036838, DA093632

Consensus CDS

CCDS8501.1

UniProtKB/Swiss-Prot

A0AV52, B2R992, D3DUN8, P48065

UniProtKB/TrEMBL

B3KWG3

Related

ENSP00000352702.4, ENST00000359674.8

Conserved Domains (1) summary

cd11511
Location:35 → 575

SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain
NM_001122848.3 → NP_001116320.1 sodium- and chloride-dependent betaine transporter

See identical proteins and their annotated locations for NP_001116320.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.

Source sequence(s)

AC007406, AI241640, BC036838, DA390883, DA406088, L42300

Consensus CDS

CCDS8501.1

UniProtKB/Swiss-Prot

A0AV52, B2R992, D3DUN8, P48065

UniProtKB/TrEMBL

B3KWG3

Related

ENSP00000508194.1, ENST00000684302.1

Conserved Domains (1) summary

cd11511
Location:35 → 575

SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain
NM_001206931.2 → NP_001193860.1 sodium- and chloride-dependent betaine transporter

See identical proteins and their annotated locations for NP_001193860.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.

Source sequence(s)

AC007406, AK313690

Consensus CDS

CCDS8501.1

UniProtKB/Swiss-Prot

A0AV52, B2R992, D3DUN8, P48065

UniProtKB/TrEMBL

B3KWG3

Related

ENSP00000444268.1, ENST00000536824.5

Conserved Domains (1) summary

cd11511
Location:35 → 575

SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain
NM_003044.5 → NP_003035.3 sodium- and chloride-dependent betaine transporter

See identical proteins and their annotated locations for NP_003035.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) and variants 2, 3 and 4 encode the same protein.

Source sequence(s)

AC007406, U27699

Consensus CDS

CCDS8501.1

UniProtKB/Swiss-Prot

A0AV52, B2R992, D3DUN8, P48065

UniProtKB/TrEMBL

B3KWG3

Related

ENSP00000399136.2, ENST00000424061.6

Conserved Domains (1) summary

cd11511
Location:35 → 575

SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; 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

183848..214157 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047429417.1 → XP_047285373.1 sodium- and chloride-dependent betaine transporter isoform X5
XM_005253748.4 → XP_005253805.1 sodium- and chloride-dependent betaine transporter isoform X3

UniProtKB/TrEMBL

B3KWG3

Conserved Domains (1) summary

cl00456
Location:35 → 570

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_047429416.1 → XP_047285372.1 sodium- and chloride-dependent betaine transporter isoform X3
XM_011521010.2 → XP_011519312.1 sodium- and chloride-dependent betaine transporter isoform X1

See identical proteins and their annotated locations for XP_011519312.1

UniProtKB/Swiss-Prot

A0AV52, B2R992, D3DUN8, P48065

UniProtKB/TrEMBL

B3KWG3

Conserved Domains (1) summary

cd11511
Location:35 → 575

SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain
XM_047429419.1 → XP_047285375.1 sodium- and chloride-dependent betaine transporter isoform X6
XM_047429418.1 → XP_047285374.1 sodium- and chloride-dependent betaine transporter isoform X6
XM_005253747.5 → XP_005253804.1 sodium- and chloride-dependent betaine transporter isoform X2

UniProtKB/TrEMBL

B3KWG3

Conserved Domains (1) summary

cl00456
Location:35 → 567

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_006719005.4 → XP_006719068.1 sodium- and chloride-dependent betaine transporter isoform X4

UniProtKB/TrEMBL

B3KWG3

Conserved Domains (1) summary

cl00456
Location:35 → 567

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

179876..211078 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054373001.1 → XP_054228976.1 sodium- and chloride-dependent betaine transporter isoform X5
XM_054372996.1 → XP_054228971.1 sodium- and chloride-dependent betaine transporter isoform X1
XM_054373003.1 → XP_054228978.1 sodium- and chloride-dependent betaine transporter isoform X6
XM_054373002.1 → XP_054228977.1 sodium- and chloride-dependent betaine transporter isoform X6
XM_054372998.1 → XP_054228973.1 sodium- and chloride-dependent betaine transporter isoform X3
XM_054372999.1 → XP_054228974.1 sodium- and chloride-dependent betaine transporter isoform X3
XM_054372997.1 → XP_054228972.1 sodium- and chloride-dependent betaine transporter isoform X2
XM_054373000.1 → XP_054228975.1 sodium- and chloride-dependent betaine transporter isoform X4