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

    Gene ID: 23446, updated on 10-Dec-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, Dec 2024]
    Expression
    Ubiquitous expression in colon (RPKM 21.5), thyroid (RPKM 20.3) and 25 other tissues See more
    Orthologs
    mouse all
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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, Free PMC Article
    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
    		not available

    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 variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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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    NEW Try the new Transcript table

    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

      UniProtKB/TrEMBL
      A0A8V8TN05

    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

      UniProtKB/TrEMBL
      A0A8V8TN05

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

      UniProtKB/TrEMBL
      A0A8V8TN05

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

      UniProtKB/TrEMBL
      A0A8V8TN05

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

      UniProtKB/TrEMBL
      A0A8V8TN05

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

      UniProtKB/TrEMBL
      A0A8V8TN05

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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