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SLC44A1 solute carrier family 44 member 1 [ Homo sapiens (human) ]

Gene ID: 23446, updated on 2-Nov-2024

Summary

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Official Symbol
SLC44A1provided by HGNC
Official Full Name
solute carrier family 44 member 1provided by HGNC
Primary source
HGNC:HGNC:18798
See related
Ensembl:ENSG00000070214 MIM:606105; AllianceGenome:HGNC:18798
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
CD92; CTL1; CDW92; CHTL1; CONATOC
Summary
Enables choline transmembrane transporter activity and ethanolamine transmembrane transporter activity. Involved in choline transport; ethanolamine transport; and transmembrane transport. Located in several cellular components, including cytosol; mitochondrial outer membrane; and nucleoplasm. Implicated in high grade glioma. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in colon (RPKM 21.5), thyroid (RPKM 20.3) and 25 other tissues See more
Orthologs
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Genomic context

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See SLC44A1 in Genome Data Viewer
Location:
9q31.1-q31.2
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (105244651..105438504)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (117419258..117613150)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (108006932..108200785)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:107753226-107754425 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:107755941-107756769 Neighboring gene cancer/testis associated transcript 70 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:107814850-107816049 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:107832754-107833953 Neighboring gene uncharacterized LOC105376197 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:107875055-107875555 Neighboring gene RN7SK pseudogene 191 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:107899749-107900728 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:107901709-107902688 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:107900729-107901708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:107902689-107903668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20149 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28737 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:107935529-107936117 Neighboring gene uncharacterized LOC112268038 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:108006574-108007478 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:108007479-108008382 Neighboring gene MPRA-validated peak7312 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:108061257-108062456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28738 Neighboring gene MPRA-validated peak7314 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28740 Neighboring gene fibronectin type III and SPRY domain containing 1 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28742 Neighboring gene RALGAPA1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28744 Neighboring gene FKTN antisense RNA 1 Neighboring gene fukutin

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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 Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Polymorphisms in the choline transporter SLC44A1 are associated with reduced cognitive performance in normotypic but not prenatal alcohol-exposed children. Smith SM, et al. Am J Clin Nutr, 2024 Jan. PMID 38176775,
  2. Mechanism of choline deficiency and membrane alteration in postural orthostatic tachycardia syndrome primary skin fibroblasts. Schenkel LC, et al. FASEB J, 2015 May. PMID 25466896, Free PMC Article
  3. Functional expression of choline transporter-like protein 1 (CTL1) in small cell lung carcinoma cells: a target molecule for lung cancer therapy. Inazu M, et al. Pharmacol Res, 2013 Oct. PMID 23948665
  4. The ubiquitous choline transporter SLC44A1. Michel V, et al. Cent Nerv Syst Agents Med Chem, 2012 Jun. PMID 22483272
  5. Choline transporter-like 1 deficiency causes a new type of childhood-onset neurodegeneration. Fagerberg CR, et al. Brain, 2020 Jan 1. PMID 31855247

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Polymorphisms in the choline transporter SLC44A1 are associated with reduced cognitive performance in normotypic but not prenatal alcohol-exposed children.
    Title: Polymorphisms in the choline transporter SLC44A1 are associated with reduced cognitive performance in normotypic but not prenatal alcohol-exposed children.
  2. Functional Expression of Choline Transporters in Human Neural Stem Cells and Its Link to Cell Proliferation, Cell Viability, and Neurite Outgrowth.
    Title: Functional Expression of Choline Transporters in Human Neural Stem Cells and Its Link to Cell Proliferation, Cell Viability, and Neurite Outgrowth.
  3. Choline transporter-like proteins 1 and 2 are newly identified plasma membrane and mitochondrial ethanolamine transporters.
    Title: Choline transporter-like proteins 1 and 2 are newly identified plasma membrane and mitochondrial ethanolamine transporters.
  4. Protein kinase C promotes choline transporterlike protein 1 function via improved cell surface expression in immortalized human hepatic cells.
    Title: Protein kinase C promotes choline transporter‑like protein 1 function via improved cell surface expression in immortalized human hepatic cells.
  5. Choline transporter-like 1 deficiency causes a new type of childhood-onset neurodegeneration.
    Title: Choline transporter-like 1 deficiency causes a new type of childhood-onset neurodegeneration.
  6. SLC44A1 acts as a choline transporter both in the plasma membrane and in the mitochondria. Novel aspects of choline transport regulation in the muscle, nervous system, and cancer are reviewed. Review.
    Title: Choline transport for phospholipid synthesis: An emerging role of choline transporter-like protein 1.
  7. Study of genome-wide epigenetic changes in bronchial epithelial cells of asthmatic patients, following cells treatment with vitamin D3 and Poly (I:C)(a viral analogue) allows the identification of biologically plausible candidate genes for viral infections and asthma, such as DUSP10 and SLC44A1.
    Title: Epigenome-wide effects of vitamin D on asthma bronchial epithelial cells.
  8. SLC44A1 and KLF13 may be involved in tumorigenesis and the metastasis of colon cancer by miRNA regulation
    Title: Integrated analysis of gene expression signatures associated with colon cancer from three datasets.
  9. The differential expression pattern of CTL1 and CTL2 suggests that CTL1 is the key transporter involved in choline transport from maternal circulation and both transporters are likely involved in stromal and endothelial cell choline transport.
    Title: Characterization of choline transporters in the human placenta over gestation.
  10. This study showed that SLC44A1-PRKCA fusion seems to be a specific characteristic of Papillary glioneuronal tumors with a high diagnostic value.
    Title: Papillary glioneuronal tumors: histological and molecular characteristics and diagnostic value of SLC44A1-PRKCA fusion.
Submit: New GeneRIF Correction See all GeneRIFs (20)

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
Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline
MedGen: C5394335 OMIM: 618868 GeneReviews: Not available
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EBI GWAS Catalog

Description
Meta-analysis of genome-wide association data identifies two loci influencing age at menarche.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables antiporter activity IEA
Inferred from Electronic Annotation
more info
  
enables choline transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables choline transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables choline transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables choline transmembrane transporter activity TAS
Traceable Author Statement
more info
 PubMed 
enables ethanolamine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in choline catabolic process 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 choline transport TAS
Traceable Author Statement
more info
 PubMed 
involved_in ethanolamine transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in phosphatidylcholine biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transmembrane transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in transmembrane transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in transmembrane transport TAS
Traceable Author Statement
more info
  
involved_in transport across blood-brain barrier NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in membrane HDA PubMed 
located_in membrane TAS
Traceable Author Statement
more info
 PubMed 
located_in mitochondrial outer membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial outer membrane TAS
Traceable Author Statement
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
choline transporter-like protein 1
Names
CDW92 antigen
solute carrier family 44 (choline transporter), member 1

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)

  1. NM_001286730.2 → NP_001273659.1  choline transporter-like protein 1 isoform b

    Status: VALIDATED

    Source sequence(s)
    AJ272365, AL161627, BC049203, DA073110
    Consensus CDS
    CCDS75868.1
    UniProtKB/TrEMBL
    A0A8V8TN05
    Related
    ENSP00000363855.1, ENST00000374723.5
    Conserved Domains (1) summary
    pfam04515
    Location:293 → 604
    Choline_transpo; Plasma-membrane choline transporter

  2. NM_001330731.2 → NP_001317660.1  choline transporter-like protein 1 isoform c

    Status: VALIDATED

    Source sequence(s)
    AL590368, AU125248, BE502051, BM799970, DA616095, DB297628
    Consensus CDS
    CCDS83390.1
    UniProtKB/TrEMBL
    A0A8V8TN05
    Related
    ENSP00000363856.1, ENST00000374724.1

  3. NM_080546.5 → NP_536856.2  choline transporter-like protein 1 isoform a

    See identical proteins and their annotated locations for NP_536856.2

    Status: VALIDATED

    Source sequence(s)
    AL161627, BC049203, CF994263
    Consensus CDS
    CCDS6763.1
    UniProtKB/Swiss-Prot
    A6NLZ9, Q5VUB3, Q8WVB0, Q8WWI5, Q96KU3, Q9NY69
    UniProtKB/TrEMBL
    A0A8V8TN05
    Related
    ENSP00000363852.3, ENST00000374720.8
    Conserved Domains (1) summary
    pfam04515
    Location:293 → 604
    Choline_transpo; Plasma-membrane choline transporter

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

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    105244651..105438504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005251855.5 → XP_005251912.1  choline transporter-like protein 1 isoform X2

    UniProtKB/TrEMBL
    A0A8V8TN05
    Related
    ENSP00000514271.1, ENST00000699290.1
    Conserved Domains (1) summary
    pfam04515
    Location:293 → 604
    Choline_transpo; Plasma-membrane choline transporter

  2. XM_006717028.4 → XP_006717091.1  choline transporter-like protein 1 isoform X3

    UniProtKB/TrEMBL
    A0A8V8TN05
    Conserved Domains (1) summary
    pfam04515
    Location:311 → 622
    Choline_transpo; Plasma-membrane choline transporter

  3. XM_006717029.4 → XP_006717092.1  choline transporter-like protein 1 isoform X4

    UniProtKB/TrEMBL
    A0A8V8TN05
    Conserved Domains (1) summary
    pfam04515
    Location:311 → 622
    Choline_transpo; Plasma-membrane choline transporter

  4. XM_006717027.4 → XP_006717090.1  choline transporter-like protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A8V8TN05
    Conserved Domains (1) summary
    pfam04515
    Location:311 → 622
    Choline_transpo; Plasma-membrane choline transporter

  5. XM_047423117.1 → XP_047279073.1  choline transporter-like protein 1 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    117419258..117613150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362555.1 → XP_054218530.1  choline transporter-like protein 1 isoform X2

  2. XM_054362556.1 → XP_054218531.1  choline transporter-like protein 1 isoform X3

  3. XM_054362557.1 → XP_054218532.1  choline transporter-like protein 1 isoform X4

  4. XM_054362554.1 → XP_054218529.1  choline transporter-like protein 1 isoform X1

  5. XM_054362558.1 → XP_054218533.1  choline transporter-like protein 1 isoform X5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_022109.2: Suppressed sequence

    Description
    NM_022109.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WWI5.1 GenPept UniProtKB/Swiss-Prot:Q8WWI5

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