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SLC6A15 solute carrier family 6 member 15 [ Homo sapiens (human) ]

Gene ID: 55117, updated on 3-Nov-2024

Summary

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Official Symbol
SLC6A15provided by HGNC
Official Full Name
solute carrier family 6 member 15provided by HGNC
Primary source
HGNC:HGNC:13621
See related
Ensembl:ENSG00000072041 MIM:607971; AllianceGenome:HGNC:13621
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
V7-3; NTT73; SBAT1; hv7-3
Summary
This gene encodes a member of the solute carrier family 6 protein family which transports neutral amino acids. The encoded protein is thought to play a role in neuronal amino acid transport (PMID: 16185194) and may be associated with major depression (PMID: 21521612). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]
Expression
Biased expression in brain (RPKM 5.0), placenta (RPKM 1.2) and 3 other tissues See more
Orthologs
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Genomic context

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See SLC6A15 in Genome Data Viewer
Location:
12q21.31
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (84859491..84912799, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (84838955..84892203, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (85253270..85306578, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene WD repeat domain 12 pseudogene Neighboring gene uncharacterized LOC105369875 Neighboring gene NANOG hESC enhancer GRCh37_chr12:85083456-85083957 Neighboring gene NANOG hESC enhancer GRCh37_chr12:85117712-85118213 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:85198877-85199735 Neighboring gene uncharacterized LOC124903121 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:85305148-85305696 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:85306245-85306792 Neighboring gene uncharacterized LOC102724680 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:85306793-85307339 Neighboring gene NANOG hESC enhancer GRCh37_chr12:85397904-85398436 Neighboring gene Sharpr-MPRA regulatory region 14945 Neighboring gene tetraspanin 19

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. The neuronal transporter gene SLC6A15 confers risk to major depression. Kohli MA, et al. Neuron, 2011 Apr 28. PMID 21521612, Free PMC Article
  2. A Combined Study of SLC6A15 Gene Polymorphism and the Resting-State Functional Magnetic Resonance Imaging in First-Episode Drug-Naive Major Depressive Disorder. Wang L, et al. Genet Test Mol Biomarkers, 2017 Sep. PMID 28915082
  3. Effects of a Polymorphism of the Neuronal Amino Acid Transporter SLC6A15 Gene on Structural Integrity of White Matter Tracts in Major Depressive Disorder. Choi S, et al. PLoS One, 2016. PMID 27723767, Free PMC Article
  4. SLC6A15 acts as a tumor suppressor to inhibit migration and invasion in human papillary thyroid cancer. Chen Y, et al. J Cell Biochem, 2021 Aug. PMID 33690923
  5. SLC6A15 rs1545843 and depression: implications from brain imaging data. Li M, et al. Am J Psychiatry, 2013 Jul. PMID 23820837

See all (67) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SLC6A15 acts as a tumor suppressor to inhibit migration and invasion in human papillary thyroid cancer.
    Title: SLC6A15 acts as a tumor suppressor to inhibit migration and invasion in human papillary thyroid cancer.
  2. Fine-scale haplotype mapping of MUT, AACS, SLC6A15 and PRKCA genes indicates association with insulin resistance of metabolic syndrome and relationship with branched chain amino acid metabolism or regulation.
    Title: Fine-scale haplotype mapping of MUT, AACS, SLC6A15 and PRKCA genes indicates association with insulin resistance of metabolic syndrome and relationship with branched chain amino acid metabolism or regulation.
  3. We observed an association between the SLC6A15 rs1545843 and resting-state brain function of the corpus callosum, cingulum and the frontal, parietal, and temporal lobes in MDD patients, which may be involved in the pathogenesis of Major Depressive Disorder. There was no interaction between rs1545843 genotypes and disease status.
    Title: A Combined Study of SLC6A15 Gene Polymorphism and the Resting-State Functional Magnetic Resonance Imaging in First-Episode Drug-Naive Major Depressive Disorder.
  4. This study provides the first evidence that, at least among Han Chinese patients with PD, AA genotype at rs1545843 in the SLC6A15 gene.
    Title: Association between gene polymorphism and depression in Parkinson's disease: A case-control study.
  5. an association between the risk allele of the SLC6A15 gene rs1545843 and the White Matter Tracts integrity of the PHC in Major Depressive Disorder patients, which is known to play an important role in the neural circuit involved in emotion processing.
    Title: Effects of a Polymorphism of the Neuronal Amino Acid Transporter SLC6A15 Gene on Structural Integrity of White Matter Tracts in Major Depressive Disorder.
  6. The SLC6A15 gene plays a role in adrenocorticotropic hormone (ACTH) and cortisol secretion during cognitive impairments in unipolar depression.
    Title: A variant of the neuronal amino acid transporter SLC6A15 is associated with ACTH and cortisol responses and cognitive performance in unipolar depression.
  7. SNP rs1545843 associated with with local gray matter volume in median cingulate gyrus
    Title: SLC6A15 rs1545843 and depression: implications from brain imaging data.
  8. The data from human genetics(SLC6A15), expression studies, brain imaging, and animal models suggest a pathophysiological mechanism for MD that may be accessible to drug targeting.
    Title: The neuronal transporter gene SLC6A15 confers risk to major depression.
  9. The substrate profile of the NTT4/XT1-dependent activity is similar to that of the closely related B(0)AT2/SBAT1 (SLC6A15), including a submillimolar apparent affinity for proline and leucine and a low millimolar apparent affinity for glutamine.
    Title: Synaptic Vesicle Protein NTT4/XT1 (SLC6A17) Catalyzes Na+-coupled Neutral Amino Acid Transport.
  10. SBAT1-mediated transport of BCAA, particularly leucine, may be an important source of amino nitrogen for neurotransmitter synthesis in glutamatergic and GABAergic neurons.
    Title: Characterization of a branched-chain amino-acid transporter SBAT1 (SLC6A15) that is expressed in human brain.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study of behavioral disinhibition.
EBI GWAS Catalog
The neuronal transporter gene SLC6A15 confers risk to major depression.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10316, MGC87066, DKFZp761I0921

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables amino acid transmembrane transporter activity TAS
Traceable Author Statement
more info
  
enables branched-chain amino acid:sodium symporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables neurotransmitter transmembrane transporter activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables neutral L-amino acid:sodium symporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables proline:sodium symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in L-leucine transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in L-leucine transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in amino acid transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in amino acid transport TAS
Traceable Author Statement
more info
  
involved_in carboxylic acid transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in neurotransmitter transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in neutral amino acid transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proline 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
  
Component Evidence Code Pubs
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane NAS
Non-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
  

General protein information

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Preferred Names
sodium-dependent neutral amino acid transporter B(0)AT2
Names
homolog of rat orphan transporter v7-3
orphan sodium- and chloride-dependent neurotransmitter transporter NTT73
orphan transporter v7-3
sodium- and chloride-dependent neurotransmitter transporter NTT73
sodium-coupled branched-chain amino-acid transporter 1
sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7
solute carrier family 6 (neurotransmitter transporter), member 15
solute carrier family 6 (neutral amino acid transporter), member 15
transporter v7-3

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)

  1. NM_001146335.3 → NP_001139807.1  sodium-dependent neutral amino acid transporter B(0)AT2 isoform 3

    See identical proteins and their annotated locations for NP_001139807.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks the 5' coding exon, resulting in a downstream AUG start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AF351619, AI368909, AK001178, AK294945
    Consensus CDS
    CCDS53816.1
    UniProtKB/TrEMBL
    Q68CX0
    Related
    ENSP00000450145.1, ENST00000552192.5
    Conserved Domains (1) summary
    cl00456
    Location:1 → 533
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  2. NM_018057.7 → NP_060527.2  sodium-dependent neutral amino acid transporter B(0)AT2 isoform 2

    See identical proteins and their annotated locations for NP_060527.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC018922, AK022853, CF529868, DA247242
    Consensus CDS
    CCDS9027.1
    UniProtKB/TrEMBL
    Q8TBM6
    Related
    ENSP00000390706.2, ENST00000450363.4
    Conserved Domains (1) summary
    cl00456
    Location:61 → 263
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  3. NM_182767.6 → NP_877499.1  sodium-dependent neutral amino acid transporter B(0)AT2 isoform 1

    See identical proteins and their annotated locations for NP_877499.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC018922, AF265577, AI368909, DA247242
    Consensus CDS
    CCDS9026.1
    UniProtKB/Swiss-Prot
    A8K592, B7Z2P7, E7ESJ5, Q9H2J7, Q9H9F5
    UniProtKB/TrEMBL
    Q68CX0
    Related
    ENSP00000266682.5, ENST00000266682.10
    Conserved Domains (1) summary
    cd11522
    Location:61 → 640
    SLC6sbd_SBAT1; Sodium-coupled branched-chain amino-acid 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

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    84859491..84912799 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538525.4 → XP_011536827.1  sodium-dependent neutral amino acid transporter B(0)AT2 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T8B7, A0A7P0T8I1
    Related
    ENSP00000505134.1, ENST00000679989.1
    Conserved Domains (1) summary
    cl00456
    Location:61 → 498
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    84838955..84892203 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372387.1 → XP_054228362.1  sodium-dependent neutral amino acid transporter B(0)AT2 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T8I1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H2J7.1 GenPept UniProtKB/Swiss-Prot:Q9H2J7

Gene LinkOut

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