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

Gene ID: 25769, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (19507455..20307892, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (19520160..20321675, complement)
105.20220307 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
  • 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. Multiomics Integrated Analysis Identifies SLC24A2 as a Potential Link between Type 2 Diabetes and Cancer. Bian Q, et al. J Diabetes Res, 2022. PMID 35601016, Free PMC Article
  2. 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
  3. Residues important for Ca(2+) ion transport in the neuronal K(+)-dependent Na(+)-Ca(2+) exchanger (NCKX2). Jalloul AH, et al. Cell Calcium, 2018 Sep. PMID 30173760
  4. A SLC24A2 Gene Variant Uncovered in Pancreatic Ductal Adenocarcinoma by Whole Exome Sequencing. Wang L, et al. Tohoku J Exp Med, 2017 Apr. PMID 28413183
  5. Residues contributing to the Na(+)-binding pocket of the SLC24 Na(+)/Ca(2+)-K(+) Exchanger NCKX2. Altimimi HF, et al. J Biol Chem, 2010 May 14. PMID 20231282, Free PMC Article

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
  

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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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_2023_10

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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