This gene is a member of the potassium-dependent sodium/calcium exchanger family and encodes an intracellular membrane protein with 2 large hydrophilic loops and 2 sets of multiple transmembrane-spanning segments. Sequence variation in this gene has been associated with differences in skin pigmentation. [provided by RefSeq, Jul 2008] See more...

Aliases for SLC24A5 Gene

Aliases for SLC24A5 Gene

  • Solute Carrier Family 24 Member 5 2 3 4 5
  • JSX 2 3 4
  • Solute Carrier Family 24 (Sodium/Potassium/Calcium Exchanger), Member 5 2 3
  • Oculocutaneous Albinism 6 (Autosomal Recessive) 2 3
  • Sodium/Potassium/Calcium Exchanger 5 3 4
  • Na(+)/K(+)/Ca(2+)-Exchange Protein 5 3 4
  • NCKX5 3 4
  • OCA6 2 3
  • Solute Carrier Family 24, Member 5 2
  • Ion Transporter JSX 3
  • SLC24A5 5
  • SHEP4 3

External Ids for SLC24A5 Gene

Previous GeneCards Identifiers for SLC24A5 Gene

  • GC00U900962
  • GC15P046118
  • GC15P046200
  • GC15P048413
  • GC15P025246

Summaries for SLC24A5 Gene

Entrez Gene Summary for SLC24A5 Gene

  • This gene is a member of the potassium-dependent sodium/calcium exchanger family and encodes an intracellular membrane protein with 2 large hydrophilic loops and 2 sets of multiple transmembrane-spanning segments. Sequence variation in this gene has been associated with differences in skin pigmentation. [provided by RefSeq, Jul 2008]

GeneCards Summary for SLC24A5 Gene

SLC24A5 (Solute Carrier Family 24 Member 5) is a Protein Coding gene. Diseases associated with SLC24A5 include Albinism, Oculocutaneous, Type Vi and Oculocutaneous Albinism. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. Gene Ontology (GO) annotations related to this gene include symporter activity and calcium, potassium:sodium antiporter activity. An important paralog of this gene is SLC24A3.

UniProtKB/Swiss-Prot Summary for SLC24A5 Gene

  • Cation exchanger involved in pigmentation, possibly by participating in ion transport in melanosomes. Predominant sodium-Calcium exchanger in melanocytes. Probably transports 1 Ca(2+) and 1 K(+) to the melanosome in exchange for 4 cytoplasmic Na(+).

Gene Wiki entry for SLC24A5 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLC24A5 Gene

Genomics for SLC24A5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SLC24A5 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
GH15J048120 Promoter 0.3 EPDnew 600.7 0.0 -19 0.1 SLC24A5 piR-48965-047 SEMA6D
GH15J048122 Enhancer 0.2 Ensembl 600.7 +1.8 1811 0.4 SLC24A5 lnc-MYEF2-6 CTXN2
GH15J048096 Enhancer 0.8 FANTOM5 Ensembl ENCODE 22.6 -24.2 -24180 0.8 CEBPB FOS BATF JUND BHLHE40 POLR2A SLC24A5 SEMA6D HSALNG0105731 piR-48965-047
GH15J048084 Enhancer 0.7 Ensembl ENCODE 11.3 -35.0 -34982 2.4 CTCF RAD21 SCRT2 ZNF316 MAFF SMC3 MAFK MAFG RCOR1 ZNF654 HSALNG0105731 SLC24A5 piR-48965-047 SEMA6D
GH15J048062 Enhancer 0.8 Ensembl 10 -58.6 -58605 1.2 PRDM10 ZNF629 ZNF692 PRDM1 PATZ1 GABPA SCRT2 ZBTB44 ZNF639 TCF7L2 HSALNG0105726 SLC24A5 piR-31199-118 SEMA6D
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC24A5 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLC24A5

Top Transcription factor binding sites by QIAGEN in the SLC24A5 gene promoter:
  • Cart-1
  • GATA-1
  • MRF-2
  • MyoD
  • NCX
  • POU6F1 (c2)
  • S8
  • STAT1
  • STAT1alpha
  • STAT1beta

Genomic Locations for SLC24A5 Gene

Genomic Locations for SLC24A5 Gene
chr15:48,120,990-48,142,672
(GRCh38/hg38)
Size:
21,683 bases
Orientation:
Plus strand
chr15:48,413,169-48,434,869
(GRCh37/hg19)
Size:
21,701 bases
Orientation:
Plus strand

Genomic View for SLC24A5 Gene

Genes around SLC24A5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC24A5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC24A5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC24A5 Gene

Proteins for SLC24A5 Gene

  • Protein details for SLC24A5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q71RS6-NCKX5_HUMAN
    Recommended name:
    Sodium/potassium/calcium exchanger 5
    Protein Accession:
    Q71RS6
    Secondary Accessions:
    • A5X8Z8
    • A5X8Z9
    • Q14CT4
    • Q6DKH3

    Protein attributes for SLC24A5 Gene

    Size:
    500 amino acids
    Molecular mass:
    54888 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SLC24A5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC24A5 Gene

Post-translational modifications for SLC24A5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SLC24A5 Gene

No data available for DME Specific Peptides for SLC24A5 Gene

Domains & Families for SLC24A5 Gene

Gene Families for SLC24A5 Gene

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

Protein Domains for SLC24A5 Gene

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

Suggested Antigen Peptide Sequences for SLC24A5 Gene

GenScript: Design optimal peptide antigens:
  • Solute carrier family 24, member 5 (A5X8Z8_HUMAN)
  • Solute carrier family 24 member 5 (NCKX5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q71RS6

UniProtKB/Swiss-Prot:

NCKX5_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 SLC24A5: view

Function for SLC24A5 Gene

Molecular function for SLC24A5 Gene

UniProtKB/Swiss-Prot Function:
Cation exchanger involved in pigmentation, possibly by participating in ion transport in melanosomes. Predominant sodium-Calcium exchanger in melanocytes. Probably transports 1 Ca(2+) and 1 K(+) to the melanosome in exchange for 4 cytoplasmic Na(+).

Phenotypes From GWAS Catalog for SLC24A5 Gene

Gene Ontology (GO) - Molecular Function for SLC24A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005262 calcium channel activity IBA 21873635
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 SLC24A5: view
genes like me logo Genes that share phenotypes with SLC24A5: view

Human Phenotype Ontology for SLC24A5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLC24A5 Gene

MGI Knock Outs for SLC24A5:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC24A5

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC24A5

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for SLC24A5 Gene

Localization for SLC24A5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC24A5 Gene

Golgi apparatus, trans-Golgi network membrane. Multi-pass membrane protein. Melanosome. Note=Enriched in late-stage melanosomes (PubMed:17081065).

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 SLC24A5 gene
Compartment Confidence
golgi apparatus 5
plasma membrane 3
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for SLC24A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005802 trans-Golgi network IDA 18166528
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SLC24A5: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC24A5 Gene

Pathways & Interactions for SLC24A5 Gene

genes like me logo Genes that share pathways with SLC24A5: view

Interacting Proteins for SLC24A5 Gene

Gene Ontology (GO) - Biological Process for SLC24A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport TAS --
GO:0006813 potassium ion transport IEA --
GO:0006814 sodium ion transport IEA --
GO:0006816 calcium ion transport IEA --
GO:0006874 cellular calcium ion homeostasis IBA 21873635
genes like me logo Genes that share ontologies with SLC24A5: view

No data available for SIGNOR curated interactions for SLC24A5 Gene

Drugs & Compounds for SLC24A5 Gene

(1) Drugs for SLC24A5 Gene - From: HMDB

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

(1) Additional Compounds for SLC24A5 Gene - From: 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 SLC24A5: view

Transcripts for SLC24A5 Gene

mRNA/cDNA for SLC24A5 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
4 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 SLC24A5

Alternative Splicing Database (ASD) splice patterns (SP) for SLC24A5 Gene

No ASD Table

Relevant External Links for SLC24A5 Gene

GeneLoc Exon Structure for
SLC24A5

Expression for SLC24A5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SLC24A5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC24A5 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x6.5) and Brain - Cerebellum (x5.8).

Protein differential expression in normal tissues from HIPED for SLC24A5 Gene

This gene is overexpressed in CD8 Tcells (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLC24A5 Gene



Protein tissue co-expression partners for SLC24A5 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLC24A5

SOURCE GeneReport for Unigene cluster for SLC24A5 Gene:

Hs.710240

Evidence on tissue expression from TISSUES for SLC24A5 Gene

  • Nervous system(4.7)
  • Eye(4.3)
  • Kidney(4.2)
  • Skin(2.9)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC24A5 Gene

Germ Layers:
  • ectoderm
Systems:
  • integumentary
  • nervous
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
General:
  • hair
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with SLC24A5: view

No data available for mRNA Expression by UniProt/SwissProt for SLC24A5 Gene

Orthologs for SLC24A5 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC24A5 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SLC24A5 30 31
  • 99.6 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SLC24A5 30 31
  • 90.87 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SLC24A5 30 31
  • 90.05 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Slc24a5 30 17 31
  • 83.83 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SLC24A5 31
  • 80 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SLC24A5 31
  • 64 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SLC24A5 30 31
  • 71.81 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SLC24A5 31
  • 72 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia slc24a5 30
  • 70.67 (n)
Zebrafish
(Danio rerio)
Actinopterygii slc24a5 30 31
  • 63.61 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG1090 31
  • 30 (a)
OneToOne
Species where no ortholog for SLC24A5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for SLC24A5 Gene

ENSEMBL:
Gene Tree for SLC24A5 (if available)
TreeFam:
Gene Tree for SLC24A5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SLC24A5: view image

Paralogs for SLC24A5 Gene

Paralogs for SLC24A5 Gene

(4) SIMAP similar genes for SLC24A5 Gene using alignment to 2 proteins:

  • NCKX5_HUMAN
  • H0YLZ0_HUMAN
genes like me logo Genes that share paralogs with SLC24A5: view

Variants for SLC24A5 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for SLC24A5 Gene

NCKX5_HUMAN-Q71RS6
Genetic variants in SLC24A5 define the skin/hair/eye pigmentation variation locus 4 (SHEP4) [MIM:113750]. Hair, eye and skin pigmentation are among the most visible examples of human phenotypic variation, with a broad normal range that is subject to substantial geographic stratification. In the case of skin, individuals tend to have lighter pigmentation with increasing distance from the equator. By contrast, the majority of variation in human eye and hair color is found among individuals of European ancestry, with most other human populations fixed for brown eyes and black hair.
NCKX5_HUMAN-Q71RS6
The Ala-111 allele predominates (93 to 100%) in African and East Asian populations. In contrast, the Thr-111 allele is nearly fixed (98.7 to 100%) in European populations, is associated with a substantial reduction in regional heterozygosity, and correlates with lighter skin pigmentation in admixed populations.

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLC24A5 Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
627611 Pathogenic: Skin/hair/eye pigmentation, variation in, 4 48,134,897(+) C/G NONSENSE,THREE_PRIME_UTR_VARIANT
667388 Likely Pathogenic: Oculocutaneous albinism 48,139,176(+) G/A SPLICE_DONOR_VARIANT,THREE_PRIME_UTR_VARIANT
722159 Likely Benign: not provided 48,142,336(+) G/A SYNONYMOUS_VARIANT,THREE_PRIME_UTR_VARIANT
727005 Likely Benign: not provided 48,139,019(+) T/G MISSENSE_VARIANT,THREE_PRIME_UTR_VARIANT
744273 Likely Benign: not provided 48,139,029(+) C/A MISSENSE_VARIANT,THREE_PRIME_UTR_VARIANT

Additional dbSNP identifiers (rs#s) for SLC24A5 Gene

Structural Variations from Database of Genomic Variants (DGV) for SLC24A5 Gene

Variant ID Type Subtype PubMed ID
nsv569337 CNV loss 21841781
nsv569338 CNV loss 21841781
nsv832999 CNV gain 17160897

Variation tolerance for SLC24A5 Gene

Residual Variation Intolerance Score: 36.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.77; 33.45% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC24A5 Gene

Human Gene Mutation Database (HGMD)
SLC24A5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC24A5

Disorders for SLC24A5 Gene

MalaCards: The human disease database

(20) MalaCards diseases for SLC24A5 Gene - From: OMIM, ClinVar, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

NCKX5_HUMAN
  • Albinism, oculocutaneous, 6 (OCA6) [MIM:113750]: A disorder characterized by a reduction or complete loss of melanin in the skin, hair and eyes. Patients show reduced or lacking pigmentation often accompanied by eye symptoms such as photophobia, strabismus, moderate to severe visual impairment, and nystagmus. {ECO:0000269 PubMed:23364476}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SLC24A5

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SLC24A5: view

No data available for Genatlas for SLC24A5 Gene

Publications for SLC24A5 Gene

  1. Exome sequencing identifies SLC24A5 as a candidate gene for nonsyndromic oculocutaneous albinism. (PMID: 23364476) Wei AH … Li W (The Journal of investigative dermatology 2013) 2 3 4
  2. 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 4 23
  3. A genomewide association study of skin pigmentation in a South Asian population. (PMID: 17999355) Stokowski RP … Cox DR (American journal of human genetics 2007) 3 4 41
  4. Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes. (PMID: 17081065) Chi A … Hunt DF (Journal of proteome research 2006) 3 4 23
  5. SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. (PMID: 16357253) Lamason RL … Cheng KC (Science (New York, N.Y.) 2005) 3 4 23

Products for SLC24A5 Gene

Sources for SLC24A5 Gene