This gene encodes a member of the potassium-dependent sodium/calcium exchanger protein family. The encoded protein plays an important role in sodium/calcium exchange in retinal rod and cone photoreceptors by mediating the extrusion of one calcium ion and one potassium ion in exchange for four sodium ions. Mutations in this gene may play a role in congenital stationary night bli... See more...

Aliases for SLC24A1 Gene

Aliases for SLC24A1 Gene

  • Solute Carrier Family 24 Member 1 2 3 4 5
  • NCKX1 2 3 4
  • Solute Carrier Family 24 (Sodium/Potassium/Calcium Exchanger), Member 1 2 3
  • Sodium/Potassium/Calcium Exchanger 1 3 4
  • Na(+)/K(+)/Ca(2+)-Exchange Protein 1 3 4
  • HsT17412 2 3
  • KIAA0702 2 4
  • CSNB1D 2 3
  • NCKX 2 3
  • RODX 2 3
  • Retinal Rod Na+/Ca+/K+ Exchanger 3
  • Retinal Rod Na-Ca+K Exchanger 4
  • SLC24A1 5

External Ids for SLC24A1 Gene

Previous GeneCards Identifiers for SLC24A1 Gene

  • GC15P061706
  • GC15P059013
  • GC15P063482
  • GC15P063630
  • GC15P063690
  • GC15P065914
  • GC15P042738
  • GC15P066001

Summaries for SLC24A1 Gene

Entrez Gene Summary for SLC24A1 Gene

  • This gene encodes a member of the potassium-dependent sodium/calcium exchanger protein family. The encoded protein plays an important role in sodium/calcium exchange in retinal rod and cone photoreceptors by mediating the extrusion of one calcium ion and one potassium ion in exchange for four sodium ions. Mutations in this gene may play a role in congenital stationary night blindness. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

GeneCards Summary for SLC24A1 Gene

SLC24A1 (Solute Carrier Family 24 Member 1) is a Protein Coding gene. Diseases associated with SLC24A1 include Night Blindness, Congenital Stationary, Type 1D and Congenital Stationary Night Blindness. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include symporter activity and calcium, potassium:sodium antiporter activity. An important paralog of this gene is SLC24A2.

UniProtKB/Swiss-Prot Summary for SLC24A1 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(+).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLC24A1 Gene

Genomics for SLC24A1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SLC24A1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC24A1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLC24A1

Top Transcription factor binding sites by QIAGEN in the SLC24A1 gene promoter:
  • AML1a
  • HEN1
  • Pax-2
  • Pax-2a
  • Pax-2b
  • PPAR-gamma1
  • PPAR-gamma2
  • STAT1
  • STAT1alpha
  • STAT1beta

Genomic Locations for SLC24A1 Gene

Genomic Locations for SLC24A1 Gene
chr15:65,611,313-65,661,002
(GRCh38/hg38)
Size:
49,690 bases
Orientation:
Plus strand
chr15:65,903,704-65,953,333
(GRCh37/hg19)
Size:
49,630 bases
Orientation:
Plus strand

Genomic View for SLC24A1 Gene

Genes around SLC24A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC24A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC24A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC24A1 Gene

Proteins for SLC24A1 Gene

  • Protein details for SLC24A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60721-NCKX1_HUMAN
    Recommended name:
    Sodium/potassium/calcium exchanger 1
    Protein Accession:
    O60721
    Secondary Accessions:
    • O43485
    • O75184
    • Q17RM9

    Protein attributes for SLC24A1 Gene

    Size:
    1099 amino acids
    Molecular mass:
    121374 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SLC24A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC24A1 Gene

Post-translational modifications for SLC24A1 Gene

  • The uncleaved signal sequence is required for efficient membrane targeting and proper membrane integration.
  • Glycosylation at Asn290
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SLC24A1 Gene

Domains & Families for SLC24A1 Gene

Gene Families for SLC24A1 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC24A1 Gene

InterPro:
Blocks:
  • Sodium/calcium exchanger membrane region
ProtoNet:

Suggested Antigen Peptide Sequences for SLC24A1 Gene

GenScript: Design optimal peptide antigens:
  • Retinal rod Na-Ca+K exchanger (NCKX1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O60721

UniProtKB/Swiss-Prot:

NCKX1_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 SLC24A1: view

Function for SLC24A1 Gene

Molecular function for SLC24A1 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(+).
GENATLAS Biochemistry:
solute carrier family 24 (sodium/potassium/calcium exchanger),calcium extrusion protein,exclusively expressed in retinal rod photoreceptor,outer segments

Phenotypes From GWAS Catalog for SLC24A1 Gene

Gene Ontology (GO) - Molecular Function for SLC24A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005262 calcium channel activity IBA 21873635
GO:0005515 protein binding IPI 17474147
GO:0008273 calcium, potassium:sodium antiporter activity NAS 9478004
GO:0015293 symporter activity IEA --
GO:0015297 antiporter activity IEA --
genes like me logo Genes that share ontologies with SLC24A1: view
genes like me logo Genes that share phenotypes with SLC24A1: view

Human Phenotype Ontology for SLC24A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLC24A1 Gene

MGI Knock Outs for SLC24A1:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC24A1

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC24A1

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for SLC24A1 Gene

Localization for SLC24A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC24A1 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 SLC24A1 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 3
endoplasmic reticulum 2
cytosol 2
extracellular 1
mitochondrion 1
nucleus 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SLC24A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS,IBA 21873635
GO:0016020 membrane TAS 9478004
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SLC24A1: view

Pathways & Interactions for SLC24A1 Gene

genes like me logo Genes that share pathways with SLC24A1: view

Pathways by source for SLC24A1 Gene

1 KEGG pathway for SLC24A1 Gene
1 Qiagen pathway for SLC24A1 Gene
  • Visual Cycle in Retinal Rods

Interacting Proteins for SLC24A1 Gene

Gene Ontology (GO) - Biological Process for SLC24A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport TAS --
GO:0006816 calcium ion transport NAS 7539424
GO:0006874 cellular calcium ion homeostasis IDA 26631410
GO:0007601 visual perception NAS 9856482
GO:0009642 response to light intensity NAS 9856482
genes like me logo Genes that share ontologies with SLC24A1: view

No data available for SIGNOR curated interactions for SLC24A1 Gene

Drugs & Compounds for SLC24A1 Gene

(4) Drugs for SLC24A1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6556

(1) Additional Compounds for SLC24A1 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Na(+)
  • Na+
  • SODIUM ion
7440-23-5
genes like me logo Genes that share compounds with SLC24A1: view

Transcripts for SLC24A1 Gene

mRNA/cDNA for SLC24A1 Gene

5 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC24A1

Alternative Splicing Database (ASD) splice patterns (SP) for SLC24A1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15
SP1: -
SP2:
SP3:
SP4: -
SP5:
SP6: - - - - - -

Relevant External Links for SLC24A1 Gene

GeneLoc Exon Structure for
SLC24A1

Expression for SLC24A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SLC24A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Eye (Sensory Organs)

Protein differential expression in normal tissues from HIPED for SLC24A1 Gene

This gene is overexpressed in Cervix (32.6), Retina (17.5), and Pancreatic juice (16.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLC24A1 Gene



Protein tissue co-expression partners for SLC24A1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLC24A1

SOURCE GeneReport for Unigene cluster for SLC24A1 Gene:

Hs.173092

mRNA Expression by UniProt/SwissProt for SLC24A1 Gene:

O60721-NCKX1_HUMAN
Tissue specificity: Expressed in the retina, particularly in the inner segment, outer and inner nuclear layers, and ganglion cell layer.

Evidence on tissue expression from TISSUES for SLC24A1 Gene

  • Eye(4.6)
  • Nervous system(4.4)
  • Lung(4.3)
  • Heart(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC24A1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • immune
  • integumentary
  • nervous
  • skeletal muscle
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
General:
  • blood
  • peripheral nervous system
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with SLC24A1: view

No data available for mRNA differential expression in normal tissues for SLC24A1 Gene

Orthologs for SLC24A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC24A1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SLC24A1 30 31
  • 98.51 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SLC24A1 30 31
  • 83.24 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SLC24A1 30 31
  • 82.87 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Slc24a1 30
  • 77.27 (n)
Mouse
(Mus musculus)
Mammalia Slc24a1 30 17 31
  • 75.89 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SLC24A1 31
  • 59 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SLC24A1 31
  • 53 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SLC24A1 30 31
  • 70.93 (n)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia slc24a1 30
  • 67.09 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.17601 30
Zebrafish
(Danio rerio)
Actinopterygii slc24a1 30 31
  • 65.84 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG1090 32
  • 38 (a)
Nckx30C 31
  • 36 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ncx-5 30 31
  • 57.44 (n)
ManyToMany
ncx-4 31 32
  • 46 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 49 (a)
OneToMany
Species where no ortholog for SLC24A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Lizard (Anolis carolinensis)
  • 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 Vase (Ciona intestinalis)
  • 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 SLC24A1 Gene

ENSEMBL:
Gene Tree for SLC24A1 (if available)
TreeFam:
Gene Tree for SLC24A1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SLC24A1: view image

Paralogs for SLC24A1 Gene

Paralogs for SLC24A1 Gene

(37) SIMAP similar genes for SLC24A1 Gene using alignment to 5 proteins:

  • NCKX1_HUMAN
  • F5H127_HUMAN
  • F5H483_HUMAN
  • H0YH06_HUMAN
  • Q17RM9_HUMAN
genes like me logo Genes that share paralogs with SLC24A1: view

Variants for SLC24A1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLC24A1 Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
713480 Conflicting Interpretations: Congenital stationary night blindness, type 1D; not provided 65,625,733(+) C/T SYNONYMOUS_VARIANT
838529 Uncertain Significance: not provided 65,644,441(+) GAGA/G INFRAME_DELETION
842714 Uncertain Significance: not provided 65,653,895(+) A/G MISSENSE_VARIANT,INTRON_VARIANT
843907 Uncertain Significance: not provided 65,625,525(+) G/A MISSENSE_VARIANT
843908 Uncertain Significance: not provided 65,645,629(+) C/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for SLC24A1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SLC24A1 Gene

Variant ID Type Subtype PubMed ID
nsv820238 CNV loss 19587683
nsv833042 CNV loss 17160897
nsv833043 CNV loss 17160897

Variation tolerance for SLC24A1 Gene

Residual Variation Intolerance Score: 52.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.00; 84.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC24A1 Gene

Human Gene Mutation Database (HGMD)
SLC24A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC24A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC24A1 Gene

Disorders for SLC24A1 Gene

MalaCards: The human disease database

(12) MalaCards diseases for SLC24A1 Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
night blindness, congenital stationary, type 1d
  • csnb, complete, autosomal recessive
congenital stationary night blindness
  • congenital essential nyctalopia
retinitis pigmentosa
  • retinitis pigmentosa 1
fundus dystrophy
  • retinal dystrophy
inherited retinal disorder
  • retinal dystrophy
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

NCKX1_HUMAN
  • Night blindness, congenital stationary, 1D (CSNB1D) [MIM:613830]: An autosomal recessive form of congenital stationary night blindness, a non-progressive retinal disorder characterized by impaired night vision. CSNB1D is characterized by a Riggs type of electroretinogram (proportionally reduced a- and b-waves). Patients have visual acuity within the normal range and no symptoms of myopia and/or nystagmus. {ECO:0000269 PubMed:20850105}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with SLC24A1: view

No data available for Genatlas for SLC24A1 Gene

Publications for SLC24A1 Gene

  1. Chromosomal localization and genomic organization of the human retinal rod Na-Ca+K exchanger. (PMID: 9856482) Tucker JE … Schnetkamp PP (Human genetics 1998) 2 3 4 23
  2. The retinal rod Na(+)/Ca(2+),K(+) exchanger contains a noncleaved signal sequence required for translocation of the N terminus. (PMID: 10608890) McKiernan CJ … Friedlander M (The Journal of biological chemistry 1999) 3 4 23
  3. A mutation in SLC24A1 implicated in autosomal-recessive congenital stationary night blindness. (PMID: 20850105) Riazuddin SA … Hejtmancik JF (American journal of human genetics 2010) 3 4
  4. The SLC24 Na+/Ca2+-K+ exchanger family: vision and beyond. (PMID: 14770312) Schnetkamp PP (Pflugers Archiv : European journal of physiology 2004) 3 23
  5. Topology of the retinal cone NCKX2 Na/Ca-K exchanger. (PMID: 12600216) Kinjo TG … Schnetkamp PP (Biochemistry 2003) 3 23

Products for SLC24A1 Gene

Sources for SLC24A1 Gene