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

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

Summary

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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
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Genomic context

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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

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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. 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

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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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

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

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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)

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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_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.

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