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Aliases for SLC24A2 Gene

Aliases for SLC24A2 Gene

  • Solute Carrier Family 24 Member 2 2 3 4 5
  • Solute Carrier Family 24 (Sodium/Potassium/Calcium Exchanger), Member 2 2 3
  • Na(+)/K(+)/Ca(2+)-Exchange Protein 2 3 4
  • Retinal Cone Na-Ca+K Exchanger 3 4
  • NCKX2 3 4
  • Sodium/Potassium/Calcium Exchanger 2 3

External Ids for SLC24A2 Gene

Previous GeneCards Identifiers for SLC24A2 Gene

  • GC09M019846
  • GC09M019704
  • GC09M019505
  • GC09M019468

Summaries for SLC24A2 Gene

Entrez Gene Summary for SLC24A2 Gene

  • 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]

GeneCards Summary for SLC24A2 Gene

SLC24A2 (Solute Carrier Family 24 Member 2) is a Protein Coding gene. Diseases associated with SLC24A2 include Brain Injury and Achromatopsia. 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 calcium ion binding and calcium channel activity. An important paralog of this gene is SLC24A1.

UniProtKB/Swiss-Prot for SLC24A2 Gene

  • Critical component of the visual transduction cascade, controlling the calcium concentration of outer segments during light and darkness. Light causes a rapid lowering of cytosolic free calcium in the outer segment of both retinal rod and cone photoreceptors and the light-induced lowering of calcium is caused by extrusion via this protein which plays a key role in the process of light adaptation. Transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+).

Additional gene information for SLC24A2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC24A2 Gene

Genomics for SLC24A2 Gene

GeneHancer (GH) Regulatory Elements for SLC24A2 Gene

Promoters and enhancers for SLC24A2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09I019792 Enhancer 0.8 ENCODE dbSUPER 550.8 +1.3 1303 0.1 ZNF335 GLIS1 SIN3A FEZF1 ZIC2 ZBTB26 EZH2 ZBTB17 SLC24A2 C11orf98P1
GH09I019788 Enhancer 0.7 ENCODE dbSUPER 550.8 +0.6 627 0.2 ZNF335 MAZ POLR2A VEZF1 ZBTB26 EZH2 SLC24A2 C11orf98P1
GH09I019786 Promoter/Enhancer 0.7 EPDnew dbSUPER 550.8 +2.8 2779 0.1 SLC24A2 C11orf98P1
GH09I019789 Enhancer 0.7 ENCODE dbSUPER 550.8 +1.1 1137 0.2 ZNF335 ZNF777 GLIS1 SIN3A ZBTB26 EZH2 ZBTB17 SLC24A2 C11orf98P1
GH09I019791 Enhancer 0.7 ENCODE dbSUPER 550.8 +1.5 1467 0.2 GLIS1 SIN3A FEZF1 ZIC2 EZH2 ZBTB17 SLC24A2 C11orf98P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLC24A2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC24A2 gene promoter:

Genomic Locations for SLC24A2 Gene

Genomic Locations for SLC24A2 Gene
chr9:19,507,452-19,789,695
(GRCh38/hg38)
Size:
282,244 bases
Orientation:
Minus strand
chr9:19,507,450-19,788,591
(GRCh37/hg19)

Genomic View for SLC24A2 Gene

Genes around SLC24A2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC24A2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC24A2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC24A2 Gene

Proteins for SLC24A2 Gene

  • Protein details for SLC24A2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UI40-NCKX2_HUMAN
    Recommended name:
    Sodium/potassium/calcium exchanger 2
    Protein Accession:
    Q9UI40
    Secondary Accessions:
    • B7ZLL8
    • Q9NTN5
    • Q9NZQ4

    Protein attributes for SLC24A2 Gene

    Size:
    661 amino acids
    Molecular mass:
    73664 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SLC24A2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC24A2 Gene

Post-translational modifications for SLC24A2 Gene

Other Protein References for SLC24A2 Gene

No data available for DME Specific Peptides for SLC24A2 Gene

Domains & Families for SLC24A2 Gene

Gene Families for SLC24A2 Gene

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

Protein Domains for SLC24A2 Gene

Suggested Antigen Peptide Sequences for SLC24A2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UI40

UniProtKB/Swiss-Prot:

NCKX2_HUMAN :
  • Belongs to the Ca(2+):cation antiporter (CaCA) (TC 2.A.19) family. SLC24A subfamily.
Family:
  • Belongs to the Ca(2+):cation antiporter (CaCA) (TC 2.A.19) family. SLC24A subfamily.
genes like me logo Genes that share domains with SLC24A2: view

Function for SLC24A2 Gene

Molecular function for SLC24A2 Gene

UniProtKB/Swiss-Prot Function:
Critical component of the visual transduction cascade, controlling the calcium concentration of outer segments during light and darkness. Light causes a rapid lowering of cytosolic free calcium in the outer segment of both retinal rod and cone photoreceptors and the light-induced lowering of calcium is caused by extrusion via this protein which plays a key role in the process of light adaptation. Transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+).

Phenotypes From GWAS Catalog for SLC24A2 Gene

Gene Ontology (GO) - Molecular Function for SLC24A2 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 IDA,TAS --
GO:0015293 symporter activity IEA --
GO:0015297 antiporter activity IEA --
genes like me logo Genes that share ontologies with SLC24A2: view
genes like me logo Genes that share phenotypes with SLC24A2: view

Animal Models for SLC24A2 Gene

MGI Knock Outs for SLC24A2:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLC24A2 Gene

Localization for SLC24A2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC24A2 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
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 SLC24A2 gene
Compartment Confidence
plasma membrane 5
cytosol 1

Gene Ontology (GO) - Cellular Components for SLC24A2 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 --
GO:0031226 intrinsic component of plasma membrane IEA --
genes like me logo Genes that share ontologies with SLC24A2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC24A2 Gene

Pathways & Interactions for SLC24A2 Gene

genes like me logo Genes that share pathways with SLC24A2: view

Interacting Proteins for SLC24A2 Gene

Selected Interacting proteins: Q9UI40-NCKX2_HUMAN for SLC24A2 Gene via IID

Gene Ontology (GO) - Biological Process for SLC24A2 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 SLC24A2: view

No data available for SIGNOR curated interactions for SLC24A2 Gene

Drugs & Compounds for SLC24A2 Gene

(2) Drugs for SLC24A2 Gene - From: HMDB and Novoseek

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

(1) Additional Compounds for SLC24A2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Sodium
  • Sodium ion
7440-23-5
genes like me logo Genes that share compounds with SLC24A2: view

Transcripts for SLC24A2 Gene

mRNA/cDNA for SLC24A2 Gene

(7) REFSEQ mRNAs :
(8) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC24A2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b
SP1:
SP2: -

Relevant External Links for SLC24A2 Gene

GeneLoc Exon Structure for
SLC24A2
ECgene alternative splicing isoforms for
SLC24A2

Expression for SLC24A2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC24A2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC24A2 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x6.4), Brain - Putamen (basal ganglia) (x6.0), Brain - Caudate (basal ganglia) (x5.7), Brain - Spinal cord (cervical c-1) (x5.0), Brain - Cortex (x4.8), Brain - Anterior cingulate cortex (BA24) (x4.5), Brain - Hippocampus (x4.4), and Brain - Substantia nigra (x4.4).

Protein differential expression in normal tissues from HIPED for SLC24A2 Gene

This gene is overexpressed in Frontal cortex (57.8) and Spinal cord (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLC24A2 Gene



Protein tissue co-expression partners for SLC24A2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SLC24A2 Gene:

SLC24A2

SOURCE GeneReport for Unigene cluster for SLC24A2 Gene:

Hs.283014

Evidence on tissue expression from TISSUES for SLC24A2 Gene

  • Eye(4.4)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with SLC24A2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC24A2 Gene

Orthologs for SLC24A2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC24A2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLC24A2 33 34
  • 99.6 (n)
dog
(Canis familiaris)
Mammalia SLC24A2 33 34
  • 92.69 (n)
cow
(Bos Taurus)
Mammalia SLC24A2 33 34
  • 90.57 (n)
mouse
(Mus musculus)
Mammalia Slc24a2 33 16 34
  • 87.85 (n)
rat
(Rattus norvegicus)
Mammalia Slc24a2 33
  • 87.59 (n)
oppossum
(Monodelphis domestica)
Mammalia SLC24A2 34
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SLC24A2 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLC24A2 33 34
  • 75.54 (n)
lizard
(Anolis carolinensis)
Reptilia SLC24A2 34
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia slc24a2 33
  • 69.8 (n)
zebrafish
(Danio rerio)
Actinopterygii SLC24A2 (2 of 2) 34
  • 69 (a)
OneToMany
SLC24A2 (1 of 2) 34
  • 66 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Nckx30C 35 33 34
  • 58.75 (n)
CG1090 35
  • 44 (a)
worm
(Caenorhabditis elegans)
Secernentea ncx-4 35 34
  • 54 (a)
ncx-5 34
  • 41 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 49 (a)
OneToMany
Species where no ortholog for SLC24A2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • wheat (Triticum aestivum)

Evolution for SLC24A2 Gene

ENSEMBL:
Gene Tree for SLC24A2 (if available)
TreeFam:
Gene Tree for SLC24A2 (if available)

Paralogs for SLC24A2 Gene

Paralogs for SLC24A2 Gene

(4) SIMAP similar genes for SLC24A2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SLC24A2: view

Variants for SLC24A2 Gene

Sequence variations from dbSNP and Humsavar for SLC24A2 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs61745273 likely-benign, not provided 19,516,337(-) T/C coding_sequence_variant, missense_variant
rs1000002585 -- 19,946,936(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000005744 -- 19,697,299(-) G/C intron_variant
rs1000005781 -- 19,544,758(-) C/G intron_variant
rs1000006635 -- 19,661,858(-) A/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC24A2 Gene

Variant ID Type Subtype PubMed ID
esv2000234 CNV deletion 18987734
esv22657 CNV loss 19812545
esv2333274 CNV deletion 18987734
esv25330 CNV loss 19812545
esv2559680 CNV deletion 19546169
esv2667371 CNV deletion 23128226
esv2671085 CNV deletion 23128226
esv2676649 CNV deletion 23128226
esv2738265 CNV deletion 23290073
esv34141 CNV loss 18971310
esv3544642 CNV deletion 23714750
esv3619911 CNV gain 21293372
esv3619913 CNV gain 21293372
esv3619916 CNV loss 21293372
esv3619917 CNV loss 21293372
esv3619919 CNV loss 21293372
nsv1015645 CNV gain 25217958
nsv1023799 CNV loss 25217958
nsv1075609 CNV deletion 25765185
nsv1124405 CNV deletion 24896259
nsv415862 CNV deletion 16902084
nsv466286 CNV gain 19166990
nsv476928 CNV novel sequence insertion 20440878
nsv507508 OTHER sequence alteration 20534489
nsv511417 CNV loss 21212237
nsv512091 CNV loss 21212237
nsv524474 CNV gain 19592680
nsv613730 CNV gain 21841781
nsv613732 CNV gain 21841781
nsv613734 CNV gain 21841781
nsv831524 CNV gain+loss 17160897
nsv957104 CNV deletion 24416366

Variation tolerance for SLC24A2 Gene

Residual Variation Intolerance Score: 14.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.60; 45.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC24A2 Gene

Human Gene Mutation Database (HGMD)
SLC24A2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC24A2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC24A2 Gene

Disorders for SLC24A2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SLC24A2 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
brain injury
achromatopsia
  • achm
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SLC24A2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SLC24A2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLC24A2 Gene

Publications for SLC24A2 Gene

  1. Molecular cloning and functional expression of the potassium-dependent sodium-calcium exchanger from human and chicken retinal cone photoreceptors. (PMID: 10662833) Prinsen CF … Schnetkamp PP (The Journal of neuroscience : the official journal of the Society for Neuroscience 2000) 2 3 4 58
  2. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 44 58
  3. A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. (PMID: 19734545) Need AC … Goldstein DB (Human molecular genetics 2009) 3 44 58
  4. SLC24A5 encodes a trans-Golgi network protein with potassium-dependent sodium-calcium exchange activity that regulates human epidermal melanogenesis. (PMID: 18166528) Ginger RS … Green MR (The Journal of biological chemistry 2008) 3 22 58
  5. Exchangers NCKX2, NCKX3, and NCKX4: identification of Thr-551 as a key residue in defining the apparent K(+) affinity of NCKX2. (PMID: 17172467) Visser F … Lytton J (The Journal of biological chemistry 2007) 3 22 58

Products for SLC24A2 Gene

Sources for SLC24A2 Gene

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