| Alias_names | solute carrier family 24, member 5 |
| solute carrier family 24 (sodium/potassium/calcium exchanger), member 5 |
| Alias_symbol (synonym) | JSX |
| OCA6 |
| Other alias | Oculocutaneous Albinism 6 |
| Na(+)/K(+)/Ca(2+)-Exchange Protein 5 |
| Solute Carrier Family 24, Member 5 |
| NCKX5 |
| P |
| Solute Carrier Family 24 Member 5 |
| Ion Transporter JSX |
| SHEP4 |
| HGNC (Hugo) |
SLC24A5 |
| LocusID (NCBI) |
283652 |
| Atlas_Id |
73332 |
| Location |
15q21.1 [Link to chromosome band 15q21] |
| Location_base_pair |
Starts at 48120972 and ends at 48142392 bp from pter ( according to hg19-Feb_2009) [Mapping SLC24A5.png] |
| |  |
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| | Cytogenetic band showing SLC24A5 locus (Ref: http://www.genecards.org/cgi-bin/carddisp.pl?gene=SLC24A5&keywords=SLC24A5) |
| |
| Description | The gene encodes a cation exchanger which is 500 amino acids protein of molecular mass 54888 Da; this multi-pass membrane protein is an intracellular potassium-dependent sodium/calcium exchanger with 2 large hydrophilic loops and 2 sets of multiple trans-membrane-spanning segments. The first large hydrophilic loop is located extracellularly at the N-terminus while the other is cytoplasmic and separates the two sets of transmembrane domains. It belongs to sodium/potassium/calcium exchanger family, SLC24A subfamily. |
| Expression | Due to its localization in the melanosomal membrane, SLC24A5 is thought to be expressed in the melanocytes (Wilson S et al., 2013). Interestingly, the expression of the gene in the following tissue types are evident by its existence in the corresponding cDNA libraries: B-cell, brain, cerebellum, cerebrum, colon, embryonic tissue, fetus, gastrointestinal tract, kidney, liver, lung, lymph node, lymphoreticular, mammary gland, nervous, pancreas, pancreatic islet, placenta, prostate, skin, stem cell, stomach, testis, thymus, uterus and vascular tissue (http://cgap.nci.nih.gov/Genes/GeneInfo?ORG=Hs&CID=710240). |
| Localisation | SLC24A5 is expressed in the trans-Golgi network of melanocytes (Wilson S et al., 2013). |
| Function | The precise function of SLC24A5 is not yet known. However, the potential functions include: (a) transporting 1 Ca2+ and 1 K+ to the melanosome in exchange for 4 cytoplasmic Na (Lamason RL et al., 2005); (b) Influencing natural variation in skin pigmentation via an unknown mechanism affecting cellular sterol levels (Wilson S et al., 2013). |
| Homology | It belongs to Solute Carrier Family 24 (http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=202). |
| Germinal | SLC24A5 mutations are responsible for Oculocutaneous Albinism type 6 (OCA6). Only 9 SLC24A5 mutations have been reported till date - one patient from India, one from China, two from France, three from Portugal, one from Belgium and one from Syria (Mondal et al. 2012; Wei et al., 2013; Fanny et al., 2014). Patients are generally characterized by light hair at birth that darkens with age, white skin, transparent irises, photophobia, nystagmus, foveal hypoplasia and reduced visual acuity. In a man from eastern India who had extreme hypopigmentation resulting in pinkish-white skin, but with dark brown hair and brown irises, was found to have a 4-bp insertion in the SLC24A5 gene as homozygous genotype (Mondal et al, 2012). |
| Somatic | Somatic variations in SLC24A5 have been identified in cancers (https://dcc.icgc.org/mutations/MU45848787; http://cancer.sanger.ac.uk/cosmic/search?q=SLC24A5), but no causality have been reported. |
| SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans |
| Lamason RL, Mohideen MA, Mest JR, Wong AC, Norton HL, Aros MC, Jurynec MJ, Mao X, Humphreville VR, Humbert JE, Sinha S, Moore JL, Jagadeeswaran P, Zhao W, Ning G, Makalowska I, McKeigue PM, O'donnell D, Kittles R, Parra EJ, Mangini NJ, Grunwald DJ, Shriver MD, Canfield VA, Cheng KC |
| Science 2005 Dec 16;310(5755):1782-6 |
| PMID 16357253 |
| |
| Molecular basis of albinism in India: evaluation of seven potential candidate genes and some new findings |
| Mondal M, Sengupta M, Samanta S, Sil A, Ray K |
| Gene 2012 Dec 15;511(2):470-4 |
| PMID 23010199 |
| |
| SLC24A5 mutations are associated with non-syndromic oculocutaneous albinism |
| Morice-Picard F, Lasseaux E, François S, Simon D, Rooryck C, Bieth E, Colin E, Bonneau D, Journel H, Walraedt S, Leroy BP, Meire F, Lacombe D, Arveiler B |
| J Invest Dermatol 2014 Feb;134(2):568-71 |
| PMID 23985994 |
| |
| Exome sequencing identifies SLC24A5 as a candidate gene for nonsyndromic oculocutaneous albinism |
| Wei AH, Zang DJ, Zhang Z, Liu XZ, He X, Yang L, Wang Y, Zhou ZY, Zhang MR, Dai LL, Yang XM, Li W |
| J Invest Dermatol 2013 Jul;133(7):1834-40 |
| PMID 23364476 |
| |
| NCKX5, a natural regulator of human skin colour variation, regulates the expression of key pigment genes MC1R and alpha-MSH and alters cholesterol homeostasis in normal human melanocytes |
| Wilson S, Ginger RS, Dadd T, Gunn D, Lim FL, Sawicka M, Sandel M, Schnetkamp PP, Green MR |
| Adv Exp Med Biol 2013;961:95-107 |
| PMID 23224873 |
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| Nomenclature |
|---|
| HGNC (Hugo) | SLC24A5 20611 |
| Cards |
|---|
| Atlas | SLC24A5ID73332ch15q21 |
| Entrez_Gene (NCBI) | SLC24A5 283652 solute carrier family 24 member 5 |
| Aliases | JSX; NCKX5; OCA6; SHEP4 |
| GeneCards (Weizmann) | SLC24A5 |
| Ensembl hg19 (Hinxton) | ENSG00000188467 [Gene_View] |
| Ensembl hg38 (Hinxton) | ENSG00000188467 [Gene_View] ENSG00000188467 [Sequence] chr15:48120972-48142392 [Contig_View] SLC24A5 [Vega] |
| ICGC DataPortal | ENSG00000188467 |
| TCGA cBioPortal | SLC24A5 |
| AceView (NCBI) | SLC24A5 |
| Genatlas (Paris) | SLC24A5 |
| WikiGenes | 283652 |
| SOURCE (Princeton) | SLC24A5 |
| Genetics Home Reference (NIH) | SLC24A5 |
| Genomic and cartography |
|---|
| GoldenPath hg38 (UCSC) | SLC24A5 - chr15:48120972-48142392 + 15q21.1 [Description] (hg38-Dec_2013) |
| GoldenPath hg19 (UCSC) | SLC24A5 - 15q21.1 [Description] (hg19-Feb_2009) |
| GoldenPath | SLC24A5 - 15q21.1 [CytoView hg19] SLC24A5 - 15q21.1 [CytoView hg38] |
| ImmunoBase | ENSG00000188467 |
| Mapping of homologs : NCBI | SLC24A5 [Mapview hg19] SLC24A5 [Mapview hg38] |
| OMIM | 113750 609802 |
| Gene and transcription |
|---|
| Genbank (Entrez) | AF348468 BC073944 BC110836 BC113628 BC113630 |
| RefSeq transcript (Entrez) | NM_205850 |
| RefSeq genomic (Entrez) | |
| Consensus coding sequences : CCDS (NCBI) | SLC24A5 |
| Cluster EST : Unigene | Hs.710240 [ NCBI ] |
| CGAP (NCI) | Hs.710240 |
| Alternative Splicing Gallery | ENSG00000188467 |
| Gene Expression | SLC24A5 [ NCBI-GEO ] SLC24A5 [ EBI - ARRAY_EXPRESS ]
SLC24A5 [ SEEK ] SLC24A5 [ MEM ] |
| Gene Expression Viewer (FireBrowse) | SLC24A5 [ Firebrowse - Broad ] |
| SOURCE (Princeton) | Expression in : [Datasets] [Normal Tissue Atlas] [carcinoma Classsification] [NCI60] |
| Genevestigator | Expression in : [tissues] [cell-lines] [cancer] [perturbations] |
| BioGPS (Tissue expression) | 283652 |
| GTEX Portal (Tissue expression) | SLC24A5 |
| Human Protein Atlas | ENSG00000188467-SLC24A5 [pathology] [cell] [tissue] |
| Protein : pattern, domain, 3D structure |
|---|
| UniProt/SwissProt | Q71RS6 [function] [subcellular_location] [family_and_domains] [pathology_and_biotech] [ptm_processing] [expression] [interaction] |
| NextProt | Q71RS6 [Sequence] [Exons] [Medical] [Publications] |
| With graphics : InterPro | Q71RS6 |
| Splice isoforms : SwissVar | Q71RS6 |
| PhosPhoSitePlus | Q71RS6 |
| Domains : Interpro (EBI) | K/Na/Ca-exchanger NaCa_Exmemb SLC24A5 |
| Domain families : Pfam (Sanger) | Na_Ca_ex (PF01699) |
| Domain families : Pfam (NCBI) | pfam01699 |
| Conserved Domain (NCBI) | SLC24A5 |
| DMDM Disease mutations | 283652 |
| Blocks (Seattle) | SLC24A5 |
| Superfamily | Q71RS6 |
| Human Protein Atlas [tissue] | ENSG00000188467-SLC24A5 [tissue] |
| Peptide Atlas | Q71RS6 |
| HPRD | 18055 |
| IPI | IPI00409687 IPI00853386 |
| Protein Interaction databases |
|---|
| DIP (DOE-UCLA) | Q71RS6 |
| IntAct (EBI) | Q71RS6 |
| FunCoup | ENSG00000188467 |
| BioGRID | SLC24A5 |
| STRING (EMBL) | SLC24A5 |
| ZODIAC | SLC24A5 |
| Ontologies - Pathways |
|---|
| QuickGO | Q71RS6 |
| Ontology : AmiGO | calcium channel activity trans-Golgi network trans-Golgi network ion transport cellular calcium ion homeostasis calcium, potassium:sodium antiporter activity calcium, potassium:sodium antiporter activity calcium, potassium:sodium antiporter activity symporter activity integral component of membrane melanocyte differentiation trans-Golgi network membrane ion transmembrane transport sodium ion transmembrane transport melanosome negative regulation of melanin biosynthetic process response to stimulus calcium ion transmembrane transport potassium ion transmembrane transport anion transmembrane transport |
| Ontology : EGO-EBI | calcium channel activity trans-Golgi network trans-Golgi network ion transport cellular calcium ion homeostasis calcium, potassium:sodium antiporter activity calcium, potassium:sodium antiporter activity calcium, potassium:sodium antiporter activity symporter activity integral component of membrane melanocyte differentiation trans-Golgi network membrane ion transmembrane transport sodium ion transmembrane transport melanosome negative regulation of melanin biosynthetic process response to stimulus calcium ion transmembrane transport potassium ion transmembrane transport anion transmembrane transport |
| REACTOME | Q71RS6 [protein] |
| REACTOME Pathways | R-HSA-425561 [pathway] |
| NDEx Network | SLC24A5 |
| Atlas of Cancer Signalling Network | SLC24A5 |
| Wikipedia pathways | SLC24A5 |
| Orthology - Evolution |
|---|
| OrthoDB | 283652 |
| GeneTree (enSembl) | ENSG00000188467 |
| Phylogenetic Trees/Animal Genes : TreeFam | SLC24A5 |
| HOGENOM | Q71RS6 |
| Homologs : HomoloGene | SLC24A5 |
| Homology/Alignments : Family Browser (UCSC) | SLC24A5 |
| Gene fusions - Rearrangements |
|---|
| Fusion : Fusion_Hub | CCDC80--SLC24A5 LYSMD2--SLC24A5 SLC24A5--SLC24A5 |
| Fusion : Quiver | SLC24A5 |
| Polymorphisms : SNP and Copy number variants |
|---|
| NCBI Variation Viewer | SLC24A5 [hg38] |
| dbSNP Single Nucleotide Polymorphism (NCBI) | SLC24A5 |
| dbVar | SLC24A5 |
| ClinVar | SLC24A5 |
| 1000_Genomes | SLC24A5 |
| Exome Variant Server | SLC24A5 |
| ExAC (Exome Aggregation Consortium) | ENSG00000188467 |
| GNOMAD Browser | ENSG00000188467 |
| Varsome Browser | SLC24A5 |
| Genetic variants : HAPMAP | 283652 |
| Genomic Variants (DGV) | SLC24A5 [DGVbeta] |
| DECIPHER | SLC24A5 [patients] [syndromes] [variants] [genes] |
| CONAN: Copy Number Analysis | SLC24A5 |
| Mutations |
|---|
| ICGC Data Portal | SLC24A5 |
| TCGA Data Portal | SLC24A5 |
| Broad Tumor Portal | SLC24A5 |
| OASIS Portal | SLC24A5 [ Somatic mutations - Copy number] |
| Somatic Mutations in Cancer : COSMIC | SLC24A5 [overview] [genome browser] [tissue] [distribution] |
| Somatic Mutations in Cancer : COSMIC3D | SLC24A5 |
| Mutations and Diseases : HGMD | SLC24A5 |
| LOVD (Leiden Open Variation Database) | Whole genome datasets |
| LOVD (Leiden Open Variation Database) | LOVD 3.0 shared installation |
| BioMuta | search SLC24A5 |
| DgiDB (Drug Gene Interaction Database) | SLC24A5 |
| DoCM (Curated mutations) | SLC24A5 (select the gene name) |
| CIViC (Clinical Interpretations of Variants in Cancer) | SLC24A5 (select a term) |
| intoGen | SLC24A5 |
| Cancer3D | SLC24A5(select the gene name) |
| Impact of mutations | [PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser] |
| Diseases |
|---|
| OMIM | 113750 609802 |
| Orphanet | 22481 |
| DisGeNET | SLC24A5 |
| Medgen | SLC24A5 |
| Genetic Testing Registry | SLC24A5
|
| NextProt | Q71RS6 [Medical] |
| TSGene | 283652 |
| GENETests | SLC24A5 |
| Target Validation | SLC24A5 |
| Huge Navigator |
SLC24A5 [HugePedia] |
| snp3D : Map Gene to Disease | 283652 |
| BioCentury BCIQ | SLC24A5 |
| ClinGen | SLC24A5 |
| Clinical trials, drugs, therapy |
|---|
| Chemical/Protein Interactions : CTD | 283652 |
| Chemical/Pharm GKB Gene | PA134868972 |
| Clinical trial | SLC24A5 |
| Miscellaneous |
|---|
| canSAR (ICR) | SLC24A5 (select the gene name) |
| DataMed Index | SLC24A5 |
| Probes |
|---|
| Litterature |
|---|
| PubMed | 32 Pubmed reference(s) in Entrez |
| GeneRIFs | Gene References Into Functions (Entrez) |
| CoreMine | SLC24A5 |
| EVEX | SLC24A5 |
| GoPubMed | SLC24A5 |
| iHOP | SLC24A5 |
