SLC5A7 solute carrier family 5 member 7 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC5A7provided by HGNC
Official Full Name: solute carrier family 5 member 7provided by HGNC
Primary source: HGNC:HGNC:14025
See related: Ensembl:ENSG00000115665 MIM:608761; AllianceGenome:HGNC:14025
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: CHT; CHT1; CMS20; HMN7A; HMND7; hCHT1; DHMNVP
Summary: 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]
Expression: Low expression observed in reference dataset See more
Orthologs: all
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Genomic context

Location:: 2q12.3

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (107986524..108013994)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (108448101..108475570)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (108602980..108630450)

Chromosome 2 - NC_000002.12 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Congenital myasthenic syndrome secondary to pathogenic variants in the SLC5A7 gene: report of two cases.
Title: Congenital myasthenic syndrome secondary to pathogenic variants in the SLC5A7 gene: report of two cases.
CircFBXW4 Suppresses Colorectal Cancer Progression by Regulating the MiR-338-5p/SLC5A7 Axis.
Title: CircFBXW4 Suppresses Colorectal Cancer Progression by Regulating the MiR-338-5p/SLC5A7 Axis.
Genetic analysis of a family affected by congenital myasthenic syndrome due to a Novel mutation in the SLC5A7 gene.
Title: Genetic analysis of a family affected by congenital myasthenic syndrome due to a Novel mutation in the SLC5A7 gene.
Targeted demethylation of the SLC5A7 promotor inhibits colorectal cancer progression.
Title: Targeted demethylation of the SLC5A7 promotor inhibits colorectal cancer progression.
Choline-induced SLC5A7 impairs colorectal cancer growth by stabilizing p53 protein.
Title: Choline-induced SLC5A7 impairs colorectal cancer growth by stabilizing p53 protein.
Our observation regarding defective myelination in the recessive form of the SLC5A7-related disorder could suggest that pathogenicity of CHT1 variants is not limited strictly to the transport of choline but may also influence myelination with a combined functional effect.
Title: The novel p.Ser263Phe mutation in the human high-affinity choline transporter 1 (CHT1/SLC5A7) causes a lethal form of fetal akinesia syndrome.
Biallelic loss-of-function SLC5A7 variants cause congenital myasthenic syndrome, while a monoallelic truncatingvariant in the last exon of SLC5A7 was reported in 2 unrelated hereditary motor neuropathy 7 families from Wales
Title: Confirmation of SLC5A7-related distal hereditary motor neuropathy 7 in a family outside Wales.
SLC5A7 genotype significantly predicted respiratory sinus arrhythmia (RSA) stress responsivity (beta=-0.023; p=0.028) and heart rate (HR) stress responsivity (beta=0.004; p=0.002). T-allele carriers exhibited RSA suppression and HR acceleration in response to stress while G/G homozygotes did not suppress RSA and exhibited less HR acceleration.
Title: Polymorphic variation in the SLC5A7 gene influences infant autonomic reactivity and self-regulation: A neurobiological model for ANS stress responsivity and infant temperament.
Lack of association between SLC5A7 polymorphisms and Tourette syndrome in a Chinese Han population
Title: Lack of association between SLC5A7 polymorphisms and Tourette syndrome in a Chinese Han population.
Here we describe an autosomal recessive presynaptic congenital myasthenic syndrome presenting with a broad clinical phenotype due to homozygous SLC5a7 missense mutations. Phenotype ranges from classical presentation of a congenital myasthenic syndrome in one patient (p.Pro210Leu), to severe neurodevelopmental delay with brain atrophy (p.Ser94Arg) and extend the clinical outcomes to infantile lethality (p.Val112Glu).
Title: Choline transporter mutations in severe congenital myasthenic syndrome disrupt transporter localization.

Submit: New GeneRIF Correction See all GeneRIFs (29)

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

Associated conditions

Description	Tests
Congenital myasthenic syndrome MedGen: C0751882 GeneReviews: Congenital Myasthenic Syndromes Overview	Compare labs
Congenital myasthenic syndrome 20 MedGen: C4310694 OMIM: 617143 GeneReviews: Not available	Compare labs
Neuronopathy, distal hereditary motor, type 7A MedGen: C1834703 OMIM: 158580 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables choline binding	IEA Inferred from Electronic Annotation more info
enables choline transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables choline transmembrane transporter activity	IEA Inferred from Electronic Annotation more info
enables choline transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables choline transmembrane transporter activity	TAS Traceable Author Statement more info
enables choline:sodium symporter activity	EXP Inferred from Experiment more info	PubMed
enables choline:sodium symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables choline:sodium symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables choline:sodium symporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transmembrane transporter activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in acetylcholine biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in acetylcholine biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in acetylcholine biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in acetylcholine biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in bile acid and bile salt transport	TAS Traceable Author Statement more info
involved_in choline transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in choline transport	IDA Inferred from Direct Assay more info	PubMed
involved_in choline transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuromuscular synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in neurotransmitter transport	TAS Traceable Author Statement more info
involved_in synaptic transmission, cholinergic	IBA Inferred from Biological aspect of Ancestor more info
involved_in transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IEA Inferred from Electronic Annotation more info
is_active_in dendrite	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
located_in early endosome membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in neuromuscular junction	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	IEA Inferred from Electronic Annotation more info
is_active_in perikaryon	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in presynapse	IEA Inferred from Electronic Annotation more info
located_in presynaptic membrane	EXP Inferred from Experiment more info	PubMed
located_in presynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in presynaptic membrane	IEA Inferred from Electronic Annotation more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: high affinity choline transporter 1

Names: Motor neuronopathy, distal hereditary, type VIIA; Motor neuronopathy, distal hereditary, with vocal cord paresis; high affinity choline transporter; hemicholinium-3-sensitive choline transporter; solute carrier family 5 (sodium/choline cotransporter), member 7

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.

Genomic

NG_042267.1 RefSeqGene

Range

5011..32481

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001305005.3 → NP_001291934.1 high affinity choline transporter 1 isoform a

See identical proteins and their annotated locations for NP_001291934.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AC009963, AK315280, DA714970

Consensus CDS

CCDS2074.1

UniProtKB/Swiss-Prot

Q53TF2, Q9GZV3

UniProtKB/TrEMBL

B2RCU2

Related

ENSP00000387346.1, ENST00000409059.5

Conserved Domains (1) summary

cd11474
Location:8 → 495

SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain
NM_001305006.3 → NP_001291935.1 high affinity choline transporter 1 isoform b

See identical proteins and their annotated locations for NP_001291935.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate exon in the 5' end compared to variant 1. This difference causes translation initiation at a downstream AUG and results in an isoform (b) with a shorter N-terminus compared to isoform a.

Source sequence(s)

AC009963, AK300801

UniProtKB/TrEMBL

B4DUU7

Conserved Domains (1) summary

cd11474
Location:1 → 390

SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain
NM_001305007.3 → NP_001291936.1 high affinity choline transporter 1 isoform c

See identical proteins and their annotated locations for NP_001291936.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate internal splice junction compared to variant 1. This difference causes translation initiation at a downstream AUG and results in an isoform (c) with a shorter N-terminus compared to isoform 1.

Source sequence(s)

AC009963, BC111524, DA714970

UniProtKB/TrEMBL

Q2T9H3

Conserved Domains (1) summary

cd11474
Location:1 → 248

SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain
NM_021815.5 → NP_068587.1 high affinity choline transporter 1 isoform a

See identical proteins and their annotated locations for NP_068587.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AC009963, BC111525, DA714970

Consensus CDS

CCDS2074.1

UniProtKB/Swiss-Prot

Q53TF2, Q9GZV3

UniProtKB/TrEMBL

B2RCU2

Related

ENSP00000264047.2, ENST00000264047.3

Conserved Domains (1) summary

cd11474
Location:8 → 495

SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

107986524..108013994

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047445369.1 → XP_047301325.1 high affinity choline transporter 1 isoform X1

UniProtKB/Swiss-Prot

Q53TF2, Q9GZV3

UniProtKB/TrEMBL

B2RCU2
XM_047445370.1 → XP_047301326.1 high affinity choline transporter 1 isoform X2

UniProtKB/TrEMBL

B2RCU2

Related

ENSP00000620114.1, ENST00000950055.1
XM_017004629.3 → XP_016860118.1 high affinity choline transporter 1 isoform X4

UniProtKB/TrEMBL

B4DUU7

Conserved Domains (1) summary

cd11474
Location:1 → 390

SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain
XM_011511580.3 → XP_011509882.1 high affinity choline transporter 1 isoform X3

UniProtKB/TrEMBL

B4DUU7

Conserved Domains (1) summary

cd11474
Location:14 → 411

SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

108448101..108475570

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054343269.1 → XP_054199244.1 high affinity choline transporter 1 isoform X1

UniProtKB/Swiss-Prot

Q53TF2, Q9GZV3

UniProtKB/TrEMBL

B2RCU2
XM_054343270.1 → XP_054199245.1 high affinity choline transporter 1 isoform X2

UniProtKB/TrEMBL

B2RCU2
XM_054343272.1 → XP_054199247.1 high affinity choline transporter 1 isoform X4

UniProtKB/TrEMBL

B4DUU7
XM_054343271.1 → XP_054199246.1 high affinity choline transporter 1 isoform X3

UniProtKB/TrEMBL

B4DUU7