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    SLC24A2 solute carrier family 24 member 2 [ Homo sapiens (human) ]

    Gene ID: 25769, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SLC24A2provided by HGNC
    Official Full Name
    solute carrier family 24 member 2provided by HGNC
    Primary source
    HGNC:HGNC:10976
    See related
    Ensembl:ENSG00000155886 MIM:609838; AllianceGenome:HGNC:10976
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NCKX2
    Summary
    This gene encodes a member of the calcium/cation antiporter superfamily of transport proteins. The encoded protein belongs to the SLC24 branch of exchangers, which can mediate the extrusion of one Ca2+ ion and one K+ ion in exchange for four Na+ ions. This family member is a retinal cone/brain exchanger that can mediate a light-induced decrease in free Ca2+ concentration. This protein may also play a neuroprotective role during ischemic brain injury. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
    Expression
    Restricted expression toward brain (RPKM 17.5) See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC24A2 in Genome Data Viewer
    Location:
    9p22.1-p21.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (19507455..20307892, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (19520160..20321675, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (19507453..19789035, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr9:19407977-19408834 and GRCh37_chr9:19408835-19409690 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:19446057-19447256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28222 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:19457239-19457834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:19460877-19461378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19795 Neighboring gene uncharacterized LOC105375988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:19492981-19493504 Neighboring gene microtubule associated protein 1 light chain 3 beta pseudogene 1 Neighboring gene alkaline ceramidase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28224 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:19698798-19699484 Neighboring gene C11orf98 pseudogene 1 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:19787951-19788598 Neighboring gene uncharacterized LOC124902128 Neighboring gene MPRA-validated peak7210 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:19801277-19801836 Neighboring gene Sharpr-MPRA regulatory region 6135 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:19967668-19968507 Neighboring gene CDC like kinase 3 pseudogene 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:19999298-20000497 Neighboring gene glutaredoxin 3 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:20111206-20111956 Neighboring gene Sharpr-MPRA regulatory region 8935 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:20276506-20277705 Neighboring gene Sharpr-MPRA regulatory region 2682 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:20290423-20290924 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:20302065-20302742 Neighboring gene uncharacterized LOC124902129 Neighboring gene MLLT3 super elongation complex subunit Neighboring gene survival of motor neuron 1, telomeric pseudogene

    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 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. A Genome-Wide Scan on Individual Typology Angle Found Variants at SLC24A2 Associated with Skin Color Variation in Chinese Populations. Wang F, et al. J Invest Dermatol, 2022 Apr. PMID 34570997
    2. Studies on the oligomeric state of the sodium/calcium + potassium exchanger NCKX2. Yoo SS, et al. Ann N Y Acad Sci, 2002 Nov. PMID 12502543
    3. Scanning mutagenesis of the alpha repeats and of the transmembrane acidic residues of the human retinal cone Na/Ca-K exchanger. Winkfein RJ, et al. Biochemistry, 2003 Jan 21. PMID 12525183
    4. Role of cysteine residues in the NCKX2 Na+/Ca(2+)-K+ Exchanger: generation of a functional cysteine-free exchanger. Kinjo TG, et al. Biochemistry, 2004 Jun 22. PMID 15196038
    5. Residues contributing to the Ca2+ and K+ binding pocket of the NCKX2 Na+/Ca2+-K+ exchanger. Kang KJ, et al. J Biol Chem, 2005 Feb 25. PMID 15583008

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A Genome-Wide Scan on Individual Typology Angle Found Variants at SLC24A2 Associated with Skin Color Variation in Chinese Populations.
      Title: A Genome-Wide Scan on Individual Typology Angle Found Variants at SLC24A2 Associated with Skin Color Variation in Chinese Populations.
    2. Multiomics Integrated Analysis Identifies SLC24A2 as a Potential Link between Type 2 Diabetes and Cancer.
      Title: Multiomics Integrated Analysis Identifies SLC24A2 as a Potential Link between Type 2 Diabetes and Cancer.
    3. residues in the two regions with the highest degree of homology between the different NCKX isoforms (alpha-1 and alpha-2 repeats) were examined to determine which residues are important for Ca(2+) coordination.
      Title: Residues important for Ca(2+) ion transport in the neuronal K(+)-dependent Na(+)-Ca(2+) exchanger (NCKX2).
    4. a new mutation in SLC24A2 gene was identified to decrease the stability of SLC24A2
      Title: A SLC24A2 Gene Variant Uncovered in Pancreatic Ductal Adenocarcinoma by Whole Exome Sequencing.
    5. Functional and structural properties of the NCKX2 Na(+)-Ca (2+)/K (+) exchanger: a comparison with the NCX1 Na (+)/Ca (2+) exchanger.
      Title: Functional and structural properties of the NCKX2 Na(+)-Ca (2+)/K (+) exchanger: a comparison with the NCX1 Na (+)/Ca (2+) exchanger.
    6. identified 31 residues that, when substituted, result in shifts in Na(+) affinity, either toward higher or lower K(m) values when compared with wild type NCKX2 (K(m) for Na(+) 58 mm)
      Title: Residues contributing to the Na(+)-binding pocket of the SLC24 Na(+)/Ca(2+)-K(+) Exchanger NCKX2.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    8. non-synonymous single nucleotide polymorphism in SLC24A5 alters a residue that is important for NCKX5 and NCKX2 activity
      Title: SLC24A5 encodes a trans-Golgi network protein with potassium-dependent sodium-calcium exchange activity that regulates human epidermal melanogenesis.
    9. Glu(188) and Asp(548) are the central residues of a single cation binding pocket that can accommodate both K(+) and Ca(2+). Furthermore, a single set of residues lines a transport pathway for both K(+) and Ca(2+).
      Title: Residues contributing to the Ca2+ and K+ binding pocket of the NCKX2 Na+/Ca2+-K+ exchanger.
    10. Several residues in helix H2 of NCKX2 are in the proximity of residues in helices H8 and to aspartate575 in H9; the residues found here are conserved in NCKX1-5 isoforms.
      Title: Site-directed disulfide mapping of residues contributing to the Ca2+ and K+ binding pocket of the NCKX2 Na+/Ca2+-K+ exchanger.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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

    EBI GWAS Catalog

    Description
    A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB.
    EBI GWAS Catalog
    Genome-wide association study of body mass index in 23 000 individuals with and without asthma.
    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)

    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

    • FLJ45149

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium, potassium:sodium antiporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium, potassium:sodium antiporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables calcium, potassium:sodium antiporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables symporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in calcium ion import IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in calcium ion import across plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in calcium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in calcium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in establishment of localization in cell IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intracellular calcium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within intracellular calcium ion homeostasis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in learning IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in long-term synaptic depression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in long-term synaptic potentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in memory IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within monoatomic ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in monoatomic ion transport TAS
    Traceable Author Statement
    more info
    		  
    involved_in neuron cellular homeostasis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in potassium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in sodium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in photoreceptor inner segment ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    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 RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    sodium/potassium/calcium exchanger 2
    Names
    Na(+)/K(+)/Ca(2+)-exchange protein 2
    Na/Ca-K exchanger 2
    retinal cone Na-Ca+K exchanger
    solute carrier family 24 (sodium/potassium/calcium exchanger), member 2

    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.

    Genomic

    1. NG_029734.2 RefSeqGene

      Range
      523855..805437
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001193288.3 → NP_001180217.1  sodium/potassium/calcium exchanger 2 isoform 2

      See identical proteins and their annotated locations for NP_001180217.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1. Variants 2 and 4 encode the same isoform.
      Source sequence(s)
      AL133281, AL158077, AL158206
      Consensus CDS
      CCDS55297.1
      UniProtKB/Swiss-Prot
      Q9UI40
      Related
      ENSP00000286344.3, ENST00000286344.4
      Conserved Domains (1) summary
      TIGR00927
      Location:115 → 644
      2A1904; K+-dependent Na+/Ca+ exchanger

    2. NM_001375850.1 → NP_001362779.1  sodium/potassium/calcium exchanger 2 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL133281, AL158077, AL158206
      Consensus CDS
      CCDS6493.1
      UniProtKB/Swiss-Prot
      B7ZLL8, Q9NTN5, Q9NZQ4, Q9UI40
      Conserved Domains (1) summary
      TIGR00927
      Location:115 → 661
      2A1904; K+-dependent Na+/Ca+ exchanger

    3. NM_001375851.1 → NP_001362780.1  sodium/potassium/calcium exchanger 2 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL133281, AL158077, AL158206
      Consensus CDS
      CCDS55297.1
      Conserved Domains (1) summary
      TIGR00927
      Location:115 → 644
      2A1904; K+-dependent Na+/Ca+ exchanger

    4. NM_020344.4 → NP_065077.1  sodium/potassium/calcium exchanger 2 isoform 1

      See identical proteins and their annotated locations for NP_065077.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). Variants 1 and 3 encode the same isoform.
      Source sequence(s)
      AL133281, AL158077, AL158206
      Consensus CDS
      CCDS6493.1
      UniProtKB/Swiss-Prot
      B7ZLL8, Q9NTN5, Q9NZQ4, Q9UI40
      Related
      ENSP00000344801.1, ENST00000341998.7
      Conserved Domains (1) summary
      TIGR00927
      Location:115 → 661
      2A1904; K+-dependent Na+/Ca+ exchanger

    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
      19507455..20307892 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017014592.2 → XP_016870081.1  sodium/potassium/calcium exchanger 2 isoform X1

      UniProtKB/Swiss-Prot
      B7ZLL8, Q9NTN5, Q9NZQ4, Q9UI40
      Conserved Domains (1) summary
      TIGR00927
      Location:115 → 661
      2A1904; K+-dependent Na+/Ca+ exchanger

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      19520160..20321675 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362637.1 → XP_054218612.1  sodium/potassium/calcium exchanger 2 isoform X1

      UniProtKB/Swiss-Prot
      B7ZLL8, Q9NTN5, Q9NZQ4, Q9UI40
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UI40.1 GenPept UniProtKB/Swiss-Prot:Q9UI40

    Gene LinkOut

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

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