Gene Gene information from NCBI Gene database.
Entrez ID 60482
Gene name Solute carrier family 5 member 7
Gene symbol SLC5A7
Synonyms (NCBI Gene)
CHTCHT1CMS20DHMNVPHMN7AHMND7hCHT1
Chromosome 2
Chromosome location 2q12.3
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 fo
SNPs SNP information provided by dbSNP.
6
SNP ID Visualize variation Clinical significance Consequence
rs147656110 G>A Pathogenic Missense variant, coding sequence variant
rs886039765 G>A Pathogenic, uncertain-significance Coding sequence variant, intron variant, genic upstream transcript variant, missense variant, upstream transcript variant, 5 prime UTR variant
rs886039766 C>T Pathogenic, uncertain-significance 5 prime UTR variant, coding sequence variant, missense variant
rs886039767 CATC>- Likely-pathogenic Frameshift variant, coding sequence variant, genic upstream transcript variant, intron variant, upstream transcript variant, 5 prime UTR variant
rs886039768 A>G Pathogenic Coding sequence variant, genic upstream transcript variant, intron variant, missense variant, upstream transcript variant, 5 prime UTR variant
miRNA miRNA information provided by mirtarbase database.
342
miRTarBase ID miRNA Experiments Reference
MIRT611928 hsa-miR-8485 HITS-CLIP 23824327
MIRT611927 hsa-miR-329-3p HITS-CLIP 23824327
MIRT611926 hsa-miR-362-3p HITS-CLIP 23824327
MIRT611925 hsa-miR-603 HITS-CLIP 23824327
MIRT611924 hsa-miR-4789-3p HITS-CLIP 23824327
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
53
GO ID Ontology Definition Evidence Reference
GO:0001701 Process In utero embryonic development IEA
GO:0005307 Function Choline:sodium symporter activity IBA
GO:0005307 Function Choline:sodium symporter activity IDA 11068039, 17005849
GO:0005307 Function Choline:sodium symporter activity IMP 12237312
GO:0005768 Component Endosome IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
608761 14025 ENSG00000115665
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9GZV3
Protein name High affinity choline transporter 1 (hCHT1) (Hemicholinium-3-sensitive choline transporter) (CHT) (Solute carrier family 5 member 7)
Protein function High-affinity Na(+)-coupled choline transmembrane symporter (PubMed:11027560, PubMed:11068039, PubMed:12237312, PubMed:12969261, PubMed:17005849, PubMed:23132865, PubMed:23141292, PubMed:27569547). Functions as an electrogenic, voltage-dependent
PDB 8J74 , 8J75 , 8J76 , 8J77 , 8ZQO , 8ZQP , 8ZQQ , 8ZQR , 9BFI , 9BFJ , 9BFK , 9BIM
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00474 SSF 42 442 Sodium:solute symporter family Family
Tissue specificity TISSUE SPECIFICITY: Expressed in putamen, spinal cord and medulla (PubMed:11027560, PubMed:11068039). Expressed in cholinergic neurons (PubMed:27569547). {ECO:0000269|PubMed:11027560, ECO:0000269|PubMed:11068039, ECO:0000269|PubMed:27569547}.
Sequence
Sequence length 580
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Cholinergic synapse
Choline metabolism in cancer
  Acetylcholine Neurotransmitter Release Cycle
Transport of bile salts and organic acids, metal ions and amine compounds
Defective SLC5A7 causes distal hereditary motor neuronopathy 7A (HMN7A)
Defective SLC5A7 causes distal hereditary motor neuronopathy 7A (HMN7A)
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
24
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Charcot-Marie-Tooth disease type 2 Likely pathogenic rs2104379614 RCV002221639
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital myasthenic syndrome 20 Pathogenic; Likely pathogenic rs147656110, rs886039767, rs886039768, rs2467051596, rs2467132050, rs2467132951 RCV000256186
RCV000256182
RCV000256183
RCV003484238
RCV003485004
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neuronopathy, distal hereditary motor, type 7A Likely pathogenic rs2467117257, rs2467133875 RCV003226145
RCV003494083
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Charcot-Marie-Tooth disease Conflicting classifications of pathogenicity ClinVar
Disgenet
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
CONGEN MYASTHENIC SYNDROMES PRESYNAPTIC Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
DISTAL HEREDITARY MOTOR NEUROPATHY TYPE 7 Disgenet, Orphanet
Disgenet, Orphanet
Disgenet, Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Distal spinal muscular atrophy Conflicting classifications of pathogenicity ClinVar
Disgenet
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acquired Kyphoscoliosis Acquired Kyphoscoliosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 30317601
★☆☆☆☆
Found in Text Mining only
Angelman Syndrome Angelman Syndrome BEFREE 20571502
★☆☆☆☆
Found in Text Mining only
Arthrogryposis Arthrogryposis multiplex congenita BEFREE 27569547
★☆☆☆☆
Found in Text Mining only
Arthrogryposis Arthrogryposis Pubtator 27569547 Associate
★☆☆☆☆
Found in Text Mining only
Arthrogryposis Arthrogryposis multiplex congenita HPO_DG
★☆☆☆☆
Found in Text Mining only
Atherosclerosis Atherosclerosis Pubtator 21337021 Associate
★☆☆☆☆
Found in Text Mining only
Autonomic Nervous System Diseases Autonomic nervous system disease Pubtator 27569547 Associate
★☆☆☆☆
Found in Text Mining only
Blepharoptosis Ptosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Bulbar palsy Bulbar palsy HPO_DG
★☆☆☆☆
Found in Text Mining only