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SLC6A4 solute carrier family 6 member 4 [ Homo sapiens (human) ]

Gene ID: 6532, updated on 16-Sep-2018

Summary

Official Symbol
SLC6A4provided by HGNC
Official Full Name
solute carrier family 6 member 4provided by HGNC
Primary source
HGNC:HGNC:11050
See related
Ensembl:ENSG00000108576 MIM:182138; Vega:OTTHUMG00000132751
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
HTT; 5HTT; OCD1; SERT; 5-HTT; SERT1; hSERT; 5-HTTLPR
Summary
This gene encodes an integral membrane protein that transports the neurotransmitter serotonin from synaptic spaces into presynaptic neurons. The encoded protein terminates the action of serotonin and recycles it in a sodium-dependent manner. This protein is a target of psychomotor stimulants, such as amphetamines and cocaine, and is a member of the sodium:neurotransmitter symporter family. A repeat length polymorphism in the promoter of this gene has been shown to affect the rate of serotonin uptake and may play a role in sudden infant death syndrome, aggressive behavior in Alzheimer disease patients, and depression-susceptibility in people experiencing emotional trauma. [provided by RefSeq, Jul 2008]
Expression
Biased expression in lung (RPKM 18.0), small intestine (RPKM 13.9) and 3 other tissues See more
Orthologs

Genomic context

See SLC6A4 in Genome Data Viewer
Location:
17q11.2
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (30194319..30235968, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (28521337..28562986, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene EF-hand calcium binding domain 5 Neighboring gene syntaxin 18 pseudogene 1 Neighboring gene microRNA 3184 Neighboring gene microRNA 423 Neighboring gene nuclear speckle splicing regulatory protein 1 Neighboring gene uncharacterized LOC107984991 Neighboring gene serotonin transporter intronic VNTR enhancer Neighboring gene solute carrier family 6 member 4 gene promoter Neighboring gene uncharacterized LOC105371720 Neighboring gene bleomycin hydrolase Neighboring gene RNA, U6 small nuclear 1267, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Anxiety
MedGen: C1842981 OMIM: 607834 GeneReviews: Not available
Compare labs
Obsessive-compulsive disorder
MedGen: C0028768 OMIM: 164230 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2012-05-10)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2012-05-10)

ClinGen Genome Curation Page

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 clade B Tat up-regulates IDO and down-regulates 5-HTT gene and protein expressions in immature dendritic cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • Monoamine Transport, organism-specific biosystem (from WikiPathways)
    Monoamine Transport, organism-specific biosystem
    Monoamine Transport
  • NRF2 pathway, organism-specific biosystem (from WikiPathways)
    NRF2 pathway, organism-specific biosystemNRF2 is part of a group of transcription factors called nuclear receptors. It is activated under oxidative stress conditions and subsequently activates several antioxidative genes and proteins.
  • Neuronal System, organism-specific biosystem (from REACTOME)
    Neuronal System, organism-specific biosystemThe human brain contains at least 100 billion neurons, each with the ability to influence many other cells. Clearly, highly sophisticated and efficient mechanisms are needed to enable communication a...
  • Neurotransmitter Clearance In The Synaptic Cleft, organism-specific biosystem (from REACTOME)
    Neurotransmitter Clearance In The Synaptic Cleft, organism-specific biosystemNeurotransmitter released in the synaptic cleft binds to specific receptors on the post-synaptic cell and the excess of the neurotransmitter is cleared to prevent over activation of the post-synapti...
  • Serotonergic synapse, organism-specific biosystem (from KEGG)
    Serotonergic synapse, organism-specific biosystemSerotonin (5-Hydroxytryptamine, 5-HT) is a monoamine neurotransmitter that plays important roles in physiological functions such as learning and memory, emotion, sleep, pain, motor function and endoc...
  • Serotonin Transporter Activity, organism-specific biosystem (from WikiPathways)
    Serotonin Transporter Activity, organism-specific biosystem
    Serotonin Transporter Activity
  • Serotonin clearance from the synaptic cleft, organism-specific biosystem (from REACTOME)
    Serotonin clearance from the synaptic cleft, organism-specific biosystemSerotonergic neurotransmission affects a wide range of behaviors, from food intake and reproductive activity, to sensory processing and motor activity, to cognition and emotion. One such key regulato...
  • Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
    Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...
  • Synaptic Vesicle Pathway, organism-specific biosystem (from WikiPathways)
    Synaptic Vesicle Pathway, organism-specific biosystemPathway depicting synaptic transmission of neurotransmitters from the presynaptic nerve terminal to the synaptic cleft upon depolarization. Synaptotagmin mediated transport along the nerve cell cytos...
  • Transmission across Chemical Synapses, organism-specific biosystem (from REACTOME)
    Transmission across Chemical Synapses, organism-specific biosystemChemical synapses are specialized junctions that are used for communication between neurons, neurons and muscle or gland cells. The synapse involves a pre-synaptic neuron and a post-synaptic neuron,...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab GTPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
actin filament binding ISS
Inferred from Sequence or Structural Similarity
more info
 
cocaine binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
monoamine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
myosin binding IEA
Inferred from Electronic Annotation
more info
 
nitric-oxide synthase binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
serotonin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
serotonin:sodium symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
serotonin:sodium symporter activity IDA
Inferred from Direct Assay
more info
PubMed 
serotonin:sodium symporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
serotonin:sodium symporter activity TAS
Traceable Author Statement
more info
 
syntaxin-1 binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
brain morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to cGMP IEA
Inferred from Electronic Annotation
more info
 
cellular response to retinoic acid IEA
Inferred from Electronic Annotation
more info
 
circadian rhythm IEA
Inferred from Electronic Annotation
more info
 
memory IEA
Inferred from Electronic Annotation
more info
 
monoamine transport IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cerebellar granule cell precursor proliferation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of organ growth ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of synaptic transmission, dopaminergic IEA
Inferred from Electronic Annotation
more info
 
neurotransmitter biosynthetic process TAS
Traceable Author Statement
more info
 
positive regulation of cell cycle IEA
Inferred from Electronic Annotation
more info
 
positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
positive regulation of serotonin secretion IEA
Inferred from Electronic Annotation
more info
 
protein complex oligomerization ISS
Inferred from Sequence or Structural Similarity
more info
 
protein homooligomerization IEA
Inferred from Electronic Annotation
more info
 
regulation of thalamus size IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
response to nutrient IEA
Inferred from Electronic Annotation
more info
 
response to toxic substance IDA
Inferred from Direct Assay
more info
PubMed 
serotonin transport IDA
Inferred from Direct Assay
more info
PubMed 
serotonin uptake IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
serotonin uptake IDA
Inferred from Direct Assay
more info
PubMed 
serotonin uptake IMP
Inferred from Mutant Phenotype
more info
PubMed 
social behavior ISS
Inferred from Sequence or Structural Similarity
more info
 
sperm ejaculation IEA
Inferred from Electronic Annotation
more info
 
transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
vasoconstriction IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
endomembrane system IDA
Inferred from Direct Assay
more info
PubMed 
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane IC
Inferred by Curator
more info
PubMed 
integral component of postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of presynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
membrane raft IDA
Inferred from Direct Assay
more info
PubMed 
neuron projection IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
serotonergic synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
sodium-dependent serotonin transporter
Names
5-hydroxytryptamine (serotonin) transporter
5HT transporter
Na+/Cl- dependent serotonin transporter
serotonin transporter 1
solute carrier family 6 (neurotransmitter transporter), member 4
solute carrier family 6 (neurotransmitter transporter, serotonin), member 4

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_011747.2 RefSeqGene

    Range
    4969..46618
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001045.5NP_001036.1  sodium-dependent serotonin transporter

    See identical proteins and their annotated locations for NP_001036.1

    Status: REVIEWED

    Source sequence(s)
    AC104984, AK313166, AY902473, BE645279, DC345903
    Consensus CDS
    CCDS11256.1
    UniProtKB/Swiss-Prot
    P31645
    UniProtKB/TrEMBL
    B2R7Y7
    Related
    ENSP00000261707.3, ENST00000261707.7
    Conserved Domains (2) summary
    cd11513
    Location:79615
    SLC6sbd_SERT; Na(+)- and Cl(-)-dependent serotonin transporter SERT; solute-binding domain
    pfam03491
    Location:2464
    5HT_transport_N; Serotonin (5-HT) neurotransmitter transporter, N-terminus

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    30194319..30235968 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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