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Aliases for SLC5A7 Gene

Aliases for SLC5A7 Gene

  • Solute Carrier Family 5 Member 7 2 3 4 5
  • Solute Carrier Family 5 (Sodium/Choline Cotransporter), Member 7 2 3
  • CHT1 3 4
  • CHT 3 4
  • High Affinity Choline Transporter; Hemicholinium-3-Sensitive Choline Transporter 3
  • Solute Carrier Family 5 (Choline Transporter), Member 7 2
  • Hemicholinium-3-Sensitive Choline Transporter 4
  • High Affinity Choline Transporter 1 3
  • CMS20 3
  • HMN7A 3

External Ids for SLC5A7 Gene

Previous GeneCards Identifiers for SLC5A7 Gene

  • GC02P106508
  • GC02P107083
  • GC02P108207
  • GC02P108224
  • GC02P108061
  • GC02P108602
  • GC02P102202

Summaries for SLC5A7 Gene

Entrez Gene Summary for SLC5A7 Gene

  • This gene encodes a sodium ion- and chloride ion-dependent high-affinity transporter that mediates choline uptake for acetylcholine synthesis in cholinergic neurons. The protein transports choline from the extracellular space into presynaptic terminals for synthesis into acetylcholine. Increased choline uptake results from increased density of this protein in synaptosomal plasma membranes in response to depolarization of cholinergic terminals. Dysfunction of cholinergic signaling has been implicated in various disorders including depression, attention-deficit disorder, and schizophrenia. An allelic variant of this gene is associated with autosomal dominant distal hereditary motor neuronopathy type VIIA. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

GeneCards Summary for SLC5A7 Gene

SLC5A7 (Solute Carrier Family 5 Member 7) is a Protein Coding gene. Diseases associated with SLC5A7 include Neuronopathy, Distal Hereditary Motor, Type Viia and Distal Hereditary Motor Neuropathy Type 7. Among its related pathways are Transmission across Chemical Synapses and Sympathetic Nerve Pathway (Pre- and Post- Ganglionic Junction). GO annotations related to this gene include transporter activity and choline transmembrane transporter activity.

UniProtKB/Swiss-Prot for SLC5A7 Gene

  • Imports choline from the extracellular space to the neuron with high affinity. Choline uptake is the rate-limiting step in acetylcholine synthesis. Sodium ion- and chloride ion-dependent.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC5A7 Gene

Genomics for SLC5A7 Gene

Regulatory Elements for SLC5A7 Gene

Genomic Location for SLC5A7 Gene

107,986,487 bp from pter
108,014,207 bp from pter
27,721 bases
Plus strand

Genomic View for SLC5A7 Gene

Genes around SLC5A7 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC5A7 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC5A7 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC5A7 Gene

Proteins for SLC5A7 Gene

  • Protein details for SLC5A7 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    High affinity choline transporter 1
    Protein Accession:
    Secondary Accessions:
    • Q53TF2

    Protein attributes for SLC5A7 Gene

    580 amino acids
    Molecular mass:
    63204 Da
    Quaternary structure:
    • Homooligomerizes at cell surface (PubMed:23132865). Interacts with SEC14L1; may regulate SLC5A7 (PubMed:17092608).
    • Specifically inhibited by nanomolar concentrations of hemicholinium 3.

neXtProt entry for SLC5A7 Gene

Post-translational modifications for SLC5A7 Gene

Other Protein References for SLC5A7 Gene

Antibody Products

  • Abcam antibodies for SLC5A7
  • Santa Cruz Biotechnology (SCBT) Antibodies for SLC5A7

No data available for DME Specific Peptides for SLC5A7 Gene

Domains & Families for SLC5A7 Gene

Gene Families for SLC5A7 Gene


Protein Domains for SLC5A7 Gene


Suggested Antigen Peptide Sequences for SLC5A7 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the sodium:solute symporter (SSF) (TC 2.A.21) family.
  • Belongs to the sodium:solute symporter (SSF) (TC 2.A.21) family.
genes like me logo Genes that share domains with SLC5A7: view

Function for SLC5A7 Gene

Molecular function for SLC5A7 Gene

UniProtKB/Swiss-Prot Function:
Imports choline from the extracellular space to the neuron with high affinity. Choline uptake is the rate-limiting step in acetylcholine synthesis. Sodium ion- and chloride ion-dependent.

Gene Ontology (GO) - Molecular Function for SLC5A7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005307 choline:sodium symporter activity IMP 12237312
GO:0015220 choline transmembrane transporter activity TAS --
GO:0015293 symporter activity IEA --
GO:0033265 choline binding IEA,IBA --
genes like me logo Genes that share ontologies with SLC5A7: view
genes like me logo Genes that share phenotypes with SLC5A7: view

Human Phenotype Ontology for SLC5A7 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLC5A7 Gene

MGI Knock Outs for SLC5A7:

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SLC5A7 Gene

Localization for SLC5A7 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC5A7 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC5A7 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytosol 1
endosome 1

Gene Ontology (GO) - Cellular Components for SLC5A7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,IDA 11027560
GO:0030424 axon IBA --
genes like me logo Genes that share ontologies with SLC5A7: view

Pathways & Interactions for SLC5A7 Gene

genes like me logo Genes that share pathways with SLC5A7: view

Gene Ontology (GO) - Biological Process for SLC5A7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006814 sodium ion transport IEA --
GO:0007269 neurotransmitter secretion TAS --
GO:0007271 synaptic transmission, cholinergic IEA,IBA --
genes like me logo Genes that share ontologies with SLC5A7: view

No data available for SIGNOR curated interactions for SLC5A7 Gene

Drugs & Compounds for SLC5A7 Gene

(6) Drugs for SLC5A7 Gene - From: DrugBank, ApexBio, DGIdb, IUPHAR, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Choline Approved Nutra Transporter, substrate 148
[<sup>3</sup>H]hemicholinium-3 Pharma 0
hemicholinium-3 Pharma Inhibition, Inhibitor 0
ML352 Pharma Non-competitive inhibitor of the presynaptic choline transporter 0

(2) Additional Compounds for SLC5A7 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Chloride ion
  • Bertholite
  • Chloor
  • Chlor
  • Chlore
  • Chloride
  • Sodium
  • Sodium ion

(1) ApexBio Compounds for SLC5A7 Gene

Compound Action Cas Number
ML352 Non-competitive inhibitor of the presynaptic choline transporter 1649450-12-3
genes like me logo Genes that share compounds with SLC5A7: view

Transcripts for SLC5A7 Gene

mRNA/cDNA for SLC5A7 Gene

(7) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(11) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SLC5A7 Gene

Solute carrier family 5 (choline transporter), member 7:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC5A7 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9

Relevant External Links for SLC5A7 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLC5A7 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SLC5A7 Gene

mRNA differential expression in normal tissues according to GTEx for SLC5A7 Gene

This gene is overexpressed in Brain - Putamen (basal ganglia) (x8.4), Brain - Caudate (basal ganglia) (x7.5), Colon - Sigmoid (x5.6), and Bladder (x4.7).

Protein differential expression in normal tissues from HIPED for SLC5A7 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SLC5A7 Gene

Protein tissue co-expression partners for SLC5A7 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC5A7 Gene:


SOURCE GeneReport for Unigene cluster for SLC5A7 Gene:


mRNA Expression by UniProt/SwissProt for SLC5A7 Gene:

Tissue specificity: Expressed in putamen, spinal cord and medulla. Specific for cholinergic neurons.
genes like me logo Genes that share expression patterns with SLC5A7: view

Primer Products

Orthologs for SLC5A7 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC5A7 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC5A7 34 35
  • 99.71 (n)
(Canis familiaris)
Mammalia SLC5A7 34 35
  • 88.89 (n)
(Monodelphis domestica)
Mammalia SLC5A7 35
  • 88 (a)
(Ornithorhynchus anatinus)
Mammalia SLC5A7 35
  • 88 (a)
(Rattus norvegicus)
Mammalia Slc5a7 34
  • 87.47 (n)
(Mus musculus)
Mammalia Slc5a7 34 16 35
  • 86.78 (n)
(Bos Taurus)
Mammalia SLC5A7 34 35
  • 84.25 (n)
(Gallus gallus)
Aves SLC5A7 34 35
  • 78.26 (n)
(Anolis carolinensis)
Reptilia SLC5A7 35
  • 83 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia slc5a7 34
  • 73.01 (n)
(Danio rerio)
Actinopterygii SLC5A7 (2 of 2) 35
  • 73 (a)
SLC5A7 (1 of 2) 35
  • 72 (a)
si:dkey-24h22.4 34
  • 69.04 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG7708 36 34 35
  • 57.95 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002366 34
  • 57.64 (n)
(Caenorhabditis elegans)
Secernentea cho-1 36 34 35
  • 56.23 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 59 (a)
-- 35
  • 57 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.11892 34
Species where no ortholog for SLC5A7 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC5A7 Gene

Gene Tree for SLC5A7 (if available)
Gene Tree for SLC5A7 (if available)

Paralogs for SLC5A7 Gene

No data available for Paralogs for SLC5A7 Gene

Variants for SLC5A7 Gene

Sequence variations from dbSNP and Humsavar for SLC5A7 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs147656110 Pathogenic 108,008,651(+) TGCAC(A/G)GAACA reference, missense
rs193921021 Uncertain significance 108,010,293(+) ATCTG(C/T)AACAG reference, missense
rs1013940 Benign 107,992,192(-) TCCAA(C/T)TGGTG intron-variant, upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs3731684 Benign 108,002,058(-) CTTCA(A/G)GTAAG intron-variant
rs10187243 -- 107,994,358(+) GAGGG(A/C)GGATC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SLC5A7 Gene

Variant ID Type Subtype PubMed ID
nsv834326 CNV gain 17160897
nsv527686 CNV gain 19592680
nsv527491 CNV loss 19592680
nsv469771 CNV loss 16826518
nsv438365 CNV loss 16468122
esv3591917 CNV gain 21293372
esv3591916 CNV gain 21293372
esv3591913 CNV gain 21293372
esv2759081 CNV gain 17122850
esv2720498 CNV deletion 23290073
dgv724e199 CNV deletion 23128226
dgv4036n100 CNV gain 25217958
dgv4035n100 CNV gain 25217958
dgv4034n100 CNV gain 25217958
dgv153e55 CNV gain 17911159

Variation tolerance for SLC5A7 Gene

Residual Variation Intolerance Score: 37.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.20; 61.99% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SLC5A7 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC5A7 Gene

Disorders for SLC5A7 Gene

MalaCards: The human disease database

(8) MalaCards diseases for SLC5A7 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, and DISEASES

Disorder Aliases PubMed IDs
neuronopathy, distal hereditary motor, type viia
  • distal hereditary motor neuropathy, type viia
distal hereditary motor neuropathy type 7
  • distal spinal muscular atrophy with vocal cord paralysis
presynaptic congenital myasthenic syndromes
  • congenital myasthenic syndromes, presynaptic
anal canal adenocarcinoma
  • adenocarcinoma of anal canal
anus adenocarcinoma
  • adenocarcinoma of anus
- elite association - COSMIC cancer census association via MalaCards


  • Neuronopathy, distal hereditary motor, 7A (HMN7A) [MIM:158580]: A neuromuscular disorder. Distal hereditary motor neuronopathies constitute a heterogeneous group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The overall clinical picture consists of a classical distal muscular atrophy syndrome in the legs without clinical sensory loss. The disease starts with weakness and wasting of distal muscles of the anterior tibial and peroneal compartments of the legs. Later on, weakness and atrophy may expand to the proximal muscles of the lower limbs and/or to the distal upper limbs. HMN7A is characterized by onset in the second decade of progressive distal muscle wasting and weakness affecting the upper and lower limbs and resulting in walking difficulties and hand grip. There is significant muscle atrophy of the hands and lower limbs. The disorder is associated with vocal cord paresis due to involvement of the tenth cranial nerve. {ECO:0000269 PubMed:23141292}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SLC5A7

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SLC5A7: view

No data available for Genatlas for SLC5A7 Gene

Publications for SLC5A7 Gene

  1. Molecular cloning of a human, hemicholinium-3-sensitive choline transporter. (PMID: 11027560) Apparsundaram S. … Blakely R.D. (Biochem. Biophys. Res. Commun. 2000) 2 3 4 22 64
  2. Human choline transporter gene variation is associated with corticolimbic reactivity and autonomic-cholinergic function. (PMID: 16876130) Neumann S.A. … Hariri A.R. (Biol. Psychiatry 2006) 3 22 46 64
  3. Heart rate variability is associated with polymorphic variation in the choline transporter gene. (PMID: 15784779) Neumann S.A. … Manuck S.B. (Psychosom Med 2005) 3 22 46 64
  4. Single nucleotide polymorphism of the human high affinity choline transporter alters transport rate. (PMID: 12237312) Okuda T. … Gurwitz D. (J. Biol. Chem. 2002) 3 4 22 64
  5. Functional characterization of the human high-affinity choline transporter. (PMID: 11068039) Okuda T. … Haga T. (FEBS Lett. 2000) 3 4 22 64

Products for SLC5A7 Gene

Sources for SLC5A7 Gene

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