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Aliases for SLC24A3 Gene

Aliases for SLC24A3 Gene

  • Solute Carrier Family 24 Member 3 2 3 4 5
  • Solute Carrier Family 24 (Sodium/Potassium/Calcium Exchanger), Member 3 2 3
  • Na(+)/K(+)/Ca(2+)-Exchange Protein 3 3 4
  • NCKX3 3 4
  • Sodium/Potassium/Calcium Exchanger 3 3
  • Sodium Calcium Exchanger 3

External Ids for SLC24A3 Gene

Previous GeneCards Identifiers for SLC24A3 Gene

  • GC20P019181
  • GC20P019188

Summaries for SLC24A3 Gene

Entrez Gene Summary for SLC24A3 Gene

  • Plasma membrane sodium/calcium exchangers are an important component of intracellular calcium homeostasis and electrical conduction. Potassium-dependent sodium/calcium exchangers such as SLC24A3 are believed to transport 1 intracellular calcium and 1 potassium ion in exchange for 4 extracellular sodium ions (Kraev et al., 2001 [PubMed 11294880]).[supplied by OMIM, Mar 2008]

GeneCards Summary for SLC24A3 Gene

SLC24A3 (Solute Carrier Family 24 Member 3) is a Protein Coding gene. Diseases associated with SLC24A3 include Corneal Dystrophy, Posterior Polymorphous, 1. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Visual Cycle in Retinal Rods. Gene Ontology (GO) annotations related to this gene include symporter activity and calcium, potassium:sodium antiporter activity. An important paralog of this gene is SLC24A4.

UniProtKB/Swiss-Prot for SLC24A3 Gene

  • Transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+).

Additional gene information for SLC24A3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC24A3 Gene

Genomics for SLC24A3 Gene

GeneHancer (GH) Regulatory Elements for SLC24A3 Gene

Promoters and enhancers for SLC24A3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20I019211 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 550.8 +0.1 87 2.2 CTCF MXI1 MAX SIN3A ZNF76 ZNF335 ZFHX2 GLIS2 POLR2A ZNF444 ENSG00000235996 SLC24A3
GH20I019254 Enhancer 0.9 FANTOM5 Ensembl ENCODE 19.9 +41.9 41940 0.8 RFX1 FOS SLC24A3 ENSG00000235996 GC20P019232 LOC100130264
GH20I019274 Enhancer 1 Ensembl ENCODE dbSUPER 17.5 +62.9 62907 2.5 ZNF687 RXRA NFIB NR2F2 FOXA1 GATA3 FOXP2 MAFK TCF7L2 SLC24A3 ENSG00000235996 LOC100130264 GC20P019232
GH20I019427 Enhancer 0.9 Ensembl ENCODE 14.9 +215.7 215655 1.4 SMARCE1 ESRRA GATAD2B DPF2 KLF4 THRB ZNF217 CTBP1 JUND GATA3 SLC24A3 ENSG00000235996 PIR38492 PIR62332
GH20I019657 Enhancer 1.1 FANTOM5 Ensembl ENCODE 10.8 +445.7 445666 1 L3MBTL2 CBFB HLF BHLHE40 ELF1 BATF IRF4 RELA IKZF1 ZSCAN29 SLC24A3 ENSG00000235996 CFAP61 PIR51262 PIR38492
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLC24A3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC24A3 gene promoter:

Genomic Locations for SLC24A3 Gene

Genomic Locations for SLC24A3 Gene
510,292 bases
Plus strand

Genomic View for SLC24A3 Gene

Genes around SLC24A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC24A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC24A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC24A3 Gene

Proteins for SLC24A3 Gene

  • Protein details for SLC24A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sodium/potassium/calcium exchanger 3
    Protein Accession:
    Secondary Accessions:
    • B1AKV7
    • Q9BQJ9
    • Q9BQL7
    • Q9BQY3
    • Q9H519

    Protein attributes for SLC24A3 Gene

    644 amino acids
    Molecular mass:
    71992 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SLC24A3 Gene

Post-translational modifications for SLC24A3 Gene

No Post-translational modifications

Other Protein References for SLC24A3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SLC24A3 Gene

Domains & Families for SLC24A3 Gene

Gene Families for SLC24A3 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC24A3 Gene

Suggested Antigen Peptide Sequences for SLC24A3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Ca(2+):cation antiporter (CaCA) (TC 2.A.19) family. SLC24A subfamily.
  • Belongs to the Ca(2+):cation antiporter (CaCA) (TC 2.A.19) family. SLC24A subfamily.
genes like me logo Genes that share domains with SLC24A3: view

Function for SLC24A3 Gene

Molecular function for SLC24A3 Gene

UniProtKB/Swiss-Prot Function:
Transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+).

Phenotypes From GWAS Catalog for SLC24A3 Gene

Gene Ontology (GO) - Molecular Function for SLC24A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005262 calcium channel activity IBA --
GO:0005509 calcium ion binding IBA --
GO:0008273 calcium, potassium:sodium antiporter activity TAS --
GO:0015293 symporter activity IEA --
GO:0015297 antiporter activity IEA --
genes like me logo Genes that share ontologies with SLC24A3: view
genes like me logo Genes that share phenotypes with SLC24A3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SLC24A3 Gene

Localization for SLC24A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC24A3 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC24A3 gene
Compartment Confidence
plasma membrane 5

Gene Ontology (GO) - Cellular Components for SLC24A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SLC24A3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC24A3 Gene

Pathways & Interactions for SLC24A3 Gene

genes like me logo Genes that share pathways with SLC24A3: view

Interacting Proteins for SLC24A3 Gene

Selected Interacting proteins: Q9HC58-NCKX3_HUMAN for SLC24A3 Gene via IID

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for SLC24A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport TAS --
GO:0006813 potassium ion transport IEA --
GO:0006814 sodium ion transport IEA --
GO:0006816 calcium ion transport IEA --
genes like me logo Genes that share ontologies with SLC24A3: view

No data available for SIGNOR curated interactions for SLC24A3 Gene

Drugs & Compounds for SLC24A3 Gene

(9) Drugs for SLC24A3 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0

(8) Additional Compounds for SLC24A3 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Sodium
  • Sodium ion
genes like me logo Genes that share compounds with SLC24A3: view

Transcripts for SLC24A3 Gene

mRNA/cDNA for SLC24A3 Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(68) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SLC24A3 Gene

Solute carrier family 24 (sodium/potassium/calcium exchanger), member 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC24A3 Gene

No ASD Table

Relevant External Links for SLC24A3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLC24A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC24A3 Gene

mRNA differential expression in normal tissues according to GTEx for SLC24A3 Gene

This gene is overexpressed in Brain - Hippocampus (x4.4).

Protein differential expression in normal tissues from HIPED for SLC24A3 Gene

This gene is overexpressed in Heart (52.9) and Peripheral blood mononuclear cells (11.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLC24A3 Gene

Protein tissue co-expression partners for SLC24A3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC24A3 Gene:


SOURCE GeneReport for Unigene cluster for SLC24A3 Gene:


mRNA Expression by UniProt/SwissProt for SLC24A3 Gene:

Tissue specificity: Abundant in the brain. Expressed at low levels in the aorta, uterus and intestine.

Evidence on tissue expression from TISSUES for SLC24A3 Gene

  • Nervous system(4.5)
  • Muscle(4.4)
genes like me logo Genes that share expression patterns with SLC24A3: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC24A3 Gene

Orthologs for SLC24A3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC24A3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC24A3 33 34
  • 98.71 (n)
(Monodelphis domestica)
Mammalia SLC24A3 34
  • 94 (a)
(Canis familiaris)
Mammalia SLC24A3 33 34
  • 90.44 (n)
(Mus musculus)
Mammalia Slc24a3 33 16 34
  • 89.47 (n)
(Rattus norvegicus)
Mammalia Slc24a3 33
  • 89.25 (n)
(Bos Taurus)
Mammalia SLC24A3 33 34
  • 88.8 (n)
(Ornithorhynchus anatinus)
Mammalia SLC24A3 34
  • 84 (a)
(Gallus gallus)
Aves SLC24A3 33 34
  • 79.34 (n)
(Anolis carolinensis)
Reptilia SLC24A3 34
  • 79 (a)
(Danio rerio)
Actinopterygii slc24a3 33 34
  • 68.72 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010975 33
  • 53.09 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG2893 35 33 34
  • 52.8 (n)
CG12061 35 34
  • 37 (a)
CG1090 35
  • 35 (a)
CG17167 34
  • 29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1993 34
  • 32 (a)
Species where no ortholog for SLC24A3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SLC24A3 Gene

Gene Tree for SLC24A3 (if available)
Gene Tree for SLC24A3 (if available)

Paralogs for SLC24A3 Gene

Paralogs for SLC24A3 Gene

(4) SIMAP similar genes for SLC24A3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SLC24A3: view

Variants for SLC24A3 Gene

Sequence variations from dbSNP and Humsavar for SLC24A3 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000005342 -- 19,507,318(+) G/C intron_variant
rs1000007644 -- 19,513,753(+) C/G/T intron_variant
rs1000017187 -- 19,305,864(+) C/T intron_variant
rs1000023847 -- 19,696,596(+) T/C intron_variant
rs1000026385 -- 19,475,863(+) T/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC24A3 Gene

Variant ID Type Subtype PubMed ID
nsv952996 CNV deletion 24416366
nsv833938 CNV loss 17160897
nsv833937 CNV gain 17160897
nsv585671 CNV loss 21841781
nsv527125 CNV loss 19592680
nsv474514 CNV novel sequence insertion 20440878
nsv3317 CNV insertion 18451855
nsv3316 CNV insertion 18451855
nsv3315 CNV deletion 18451855
nsv1119487 CNV insertion 24896259
nsv1109356 CNV deletion 24896259
nsv1072527 CNV deletion 25765185
nsv1056243 CNV gain 25217958
esv3645457 CNV gain 21293372
esv3645455 CNV loss 21293372
esv3423159 CNV insertion 20981092
esv3309667 CNV mobile element insertion 20981092
esv3303482 CNV mobile element insertion 20981092
esv2670085 CNV deletion 23128226
esv2652551 CNV insertion 19546169

Variation tolerance for SLC24A3 Gene

Residual Variation Intolerance Score: 74.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.90; 94.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC24A3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC24A3 Gene

Disorders for SLC24A3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SLC24A3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
corneal dystrophy, posterior polymorphous, 1
  • ppcd1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SLC24A3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SLC24A3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLC24A3 Gene

Publications for SLC24A3 Gene

  1. Molecular cloning of a third member of the potassium-dependent sodium-calcium exchanger gene family, NCKX3. (PMID: 11294880) Kraev A … Lytton J (The Journal of biological chemistry 2001) 3 4 22 58
  2. Genome-wide association study of lung function decline in adults with and without asthma. (PMID: 22424883) Imboden M … Probst-Hensch NM (The Journal of allergy and clinical immunology 2012) 3 44 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Genome-wide association scan identifies variants near Matrix Metalloproteinase (MMP) genes on chromosome 11q21-22 strongly associated with serum MMP-1 levels. (PMID: 20031604) Cheng YC … Pollin TI (Circulation. Cardiovascular genetics 2009) 3 44 58
  5. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4 58

Products for SLC24A3 Gene

Sources for SLC24A3 Gene

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