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

Summary

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: mouse all
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Genomic context

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_000012.12 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?

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.
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.
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.
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.
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.
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.
SNP rs1545843 associated with with local gray matter volume in median cingulate gyrus
Title: SLC6A15 rs1545843 and depression: implications from brain imaging data.
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.
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.
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.

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

SHGC-53313 (e-PCR)
- UniSTS:33860

SHGC-68514 (e-PCR)
- UniSTS:170081

A004A20 (e-PCR)
- UniSTS:2148

RH45707 (e-PCR)
- UniSTS:22903

SHGC-30472 (e-PCR)
- UniSTS:34175

G64530 (e-PCR)
- UniSTS:163768

D12S1214E (e-PCR)
- UniSTS:78273

G64783 (e-PCR)
- UniSTS:164805

SLC6A15_9875 (e-PCR)
- UniSTS:468701

RH92709 (e-PCR)
- UniSTS:88301

G64529 (e-PCR)
- UniSTS:163834

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)

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
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
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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

84859491..84912799 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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