U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    SLC44A2 solute carrier family 44 member 2 (CTL2 blood group) [ Homo sapiens (human) ]

    Gene ID: 57153, updated on 3-Apr-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    SLC44A2provided by HGNC
    Official Full Name
    solute carrier family 44 member 2 (CTL2 blood group)provided by HGNC
    Primary source
    HGNC:HGNC:17292
    See related
    Ensembl:ENSG00000129353 MIM:606106; AllianceGenome:HGNC:17292
    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
    CTL2; PP1292
    Summary
    Enables choline transmembrane transporter activity. Involved in choline transport and transmembrane transport. Located in mitochondrion and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in placenta (RPKM 82.0), spleen (RPKM 69.3) and 25 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    19p13.2
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (10602455..10644557)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (10728929..10771033)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10713131..10755233)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene adaptor related protein complex 1 subunit mu 2 Neighboring gene MPRA-validated peak3354 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10703269-10703793 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10704320-10704844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10085 Neighboring gene LSM2 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10734687-10735268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10747236-10747758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10763030-10763532 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10763533-10764034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13983 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10087 Neighboring gene ILF3 divergent transcript Neighboring gene interleukin enhancer binding factor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10801737-10802532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10802533-10803326

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Lack of the human choline transporter-like protein SLC44A2 causes hearing impairment and a rare red blood phenotype. Koehl B, et al. EMBO Mol Med, 2023 Mar 8. PMID 36695047, Free PMC Article
    2. The Effect of Common Variants in SLC44A2 on the Contribution to the Risk of Deep Cein Thrombosis after Orthopedic Surgery. Zhi L, et al. J Atheroscler Thromb, 2021 Mar 1. PMID 32581188, Free PMC Article
    3. Association between SLC44A2 rs2288904 polymorphism and risk of recurrent venous thromboembolism among Thai patients. Apipongrat D, et al. Thromb Res, 2019 Feb. PMID 30634167
    4. SLC44A2 single nucleotide polymorphisms, isoforms, and expression: Association with severity of Meniere's disease? Nair TS, et al. Genomics, 2016 Dec. PMID 27829169, Free PMC Article
    5. Genotype frequency of human neutrophil antigen-3 polymorphisms in the Yi, Han, and Tibetan populations of China. Chen Q, et al. Transfusion, 2016 Mar. PMID 26593331, Free PMC Article

    See all (58) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Lack of the human choline transporter-like protein SLC44A2 causes hearing impairment and a rare red blood phenotype.
      Title: Lack of the human choline transporter-like protein SLC44A2 causes hearing impairment and a rare red blood phenotype.
    2. The Effect of Common Variants in SLC44A2 on the Contribution to the Risk of Deep Cein Thrombosis after Orthopedic Surgery.
      Title: The Effect of Common Variants in SLC44A2 on the Contribution to the Risk of Deep Cein Thrombosis after Orthopedic Surgery.
    3. Impaired adhesion of neutrophils expressing Slc44a2/HNA-3b to VWF protects against NETosis under venous shear rates.
      Title: Impaired adhesion of neutrophils expressing Slc44a2/HNA-3b to VWF protects against NETosis under venous shear rates.
    4. 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.
    5. 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.
    6. Activated alphaIIbbeta3 on platelets mediates flow-dependent NETosis via SLC44A2.
      Title: Activated α(IIb)β(3) on platelets mediates flow-dependent NETosis via SLC44A2.
    7. SLC44A2*01 allele is associated with venous thromboembolism and constitutes a potential marker for recurrent venous thromboembolism among Thai patients.
      Title: Association between SLC44A2 rs2288904 polymorphism and risk of recurrent venous thromboembolism among Thai patients.
    8. Variants in SLC44A2 gene is associated with thrombosis.
      Title: Genome-wide association analysis of self-reported events in 6135 individuals and 252 827 controls identifies 8 loci associated with thrombosis.
    9. SLC44A2 SNPs are associated with Meniere's disease severity.
      Title: SLC44A2 single nucleotide polymorphisms, isoforms, and expression: Association with severity of Meniere's disease?
    10. Although circulating nucleosomes and elastase - alpha 1-antitrypsin complexes are at present the best characterized biomarkers for neutrophil extracellular traps formation and neutrophil activation, their lack of association with rs2288904 genotype does not exclude a role for SLC44A2 in neutrophil activation (and possibly NET formation) in Venous Thromboembolism.
      Title: Circulating nucleosomes and elastase α1-antitrypsin complexes and the novel thrombosis susceptibility locus SLC44A2.
    Submit: New GeneRIF Correction See all GeneRIFs (28)

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • FLJ44586, DKFZp666A071

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables antiporter activity 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 TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables ethanolamine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in choline transport IDA
    Inferred from Direct Assay
    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 positive regulation of canonical NF-kappaB signal transduction HMP PubMed 
    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 TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in lysosomal membrane HDA PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in specific granule membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    choline transporter-like protein 2
    Names
    solute carrier family 44 (choline transporter), member 2
    testicular tissue protein Li 47

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001145056.2 → NP_001138528.1  choline transporter-like protein 2 isoform 2

      See identical proteins and their annotated locations for NP_001138528.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region compared to variant 1. The encoded isoform (2) has a shorter, distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC011475, AK027519, BI602883, DA628435
      Consensus CDS
      CCDS54216.1
      UniProtKB/TrEMBL
      A0A024R798, A0A088QCU6
      Related
      ENSP00000385135.3, ENST00000407327.8
      Conserved Domains (1) summary
      pfam04515
      Location:335 → 673
      Choline_transpo; Plasma-membrane choline transporter

    2. NM_001363611.2 → NP_001350540.1  choline transporter-like protein 2 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC011475, AU310140, BC040556, DA673268, DA749803, HY323543
      Consensus CDS
      CCDS86700.1
      UniProtKB/TrEMBL
      A0A024R798
      Conserved Domains (1) summary
      pfam04515
      Location:337 → 675
      Choline_transpo; Plasma-membrane choline transporter

    3. NM_020428.4 → NP_065161.3  choline transporter-like protein 2 isoform 1

      See identical proteins and their annotated locations for NP_065161.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant encodes isoform 1.
      Source sequence(s)
      AC011475, BC040556, DA673268, DA749803
      Consensus CDS
      CCDS12245.1
      UniProtKB/Swiss-Prot
      B2RBB1, B3KNH3, B4DFJ0, F2Q9D7, Q658V1, Q658Z2, Q6PJV7, Q8IWA5, Q8N2F0, Q9NY68
      UniProtKB/TrEMBL
      A0A024R798
      Related
      ENSP00000336888.4, ENST00000335757.10
      Conserved Domains (1) summary
      pfam04515
      Location:337 → 675
      Choline_transpo; Plasma-membrane choline transporter

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      10602455..10644557
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439113.1 → XP_047295069.1  choline transporter-like protein 2 isoform X2

    2. XM_047439112.1 → XP_047295068.1  choline transporter-like protein 2 isoform X1

      Related
      ENSP00000466664.1, ENST00000586078.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      10728929..10771033
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321513.1 → XP_054177488.1  choline transporter-like protein 2 isoform X2

    2. XM_054321514.1 → XP_054177489.1  choline transporter-like protein 2 isoform X3

    3. XM_054321512.1 → XP_054177487.1  choline transporter-like protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IWA5.3 GenPept UniProtKB/Swiss-Prot:Q8IWA5

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous