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SLC24A5 (solute carrier family 24 (sodium/potassium/calcium exchanger), member 5)

Written2016-04Kunal Ray, Mainak Sengupta, Sampurna Ghosh
Academy of Scientific and Innovative Research (AcSIR), Campus at CSIR - Central Road Research Institute, Mathura Road, New Delhi - 110 025, kunalray@gmail.com (KR); University of Calcutta, Department of Genetics, 35, Ballygunge Circular Road, Kolkata - 700 019, sengupta.mainak@gmail.com); sampurna_ghosh@yahoo.in (MS, SG) India.

Abstract SLC24A5 is a member of the potassium-dependent sodium/calcium exchanger family and encodes an intracellular membrane protein. Sequence variations in this gene have been associated with differences in skin pigmentation, and the defective protein leads to Oculocutaneous albinism type VI, OCA6.

Keywords OCA6, albinism, SLC24A5

(Note : for Links provided by Atlas : click)

Identity

Alias_namessolute carrier family 24, member 5
solute carrier family 24 (sodium/potassium/calcium exchanger), member 5
Alias_symbol (synonym)JSX
OCA6
Other aliasOculocutaneous 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]
 
  Cytogenetic band showing SLC24A5 locus (Ref: http://www.genecards.org/cgi-bin/carddisp.pl?gene=SLC24A5&keywords=SLC24A5)

DNA/RNA

Description In Chromosome 15, the 21,701 bases long gene starts from 48,120,972 bp from pter and ends at 48,142,672 bp from pter; Orientation: Plus strand. It contains 9 exons.
Transcription This gene has 5 transcripts: 4 splice variants and 1 unspliced form (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&c=Gene&l=SLC24A5). The full protein coding transcript is 1617 bp long.

Protein

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).

Mutations

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.

Bibliography

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
 

Citation

This paper should be referenced as such :
Ray K, Sengupta M, Ghosh S
SLC24A5 (solute carrier family 24 (sodium/potassium/calcium exchanger), member 5);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/SLC24A5ID73332ch15q21.html


Other Cancer prone implicated (Data extracted from papers in the Atlas) [ 1 ]
  Oculocutaneous Albinism


External links

Nomenclature
HGNC (Hugo)SLC24A5   20611
Cards
AtlasSLC24A5ID73332ch15q21
Entrez_Gene (NCBI)SLC24A5  283652  solute carrier family 24 member 5
AliasesJSX; NCKX5; OCA6; SHEP4
GeneCards (Weizmann)SLC24A5
Ensembl hg19 (Hinxton)ENSG00000188467 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000188467 [Gene_View]  chr15:48120972-48142392 [Contig_View]  SLC24A5 [Vega]
ICGC DataPortalENSG00000188467
TCGA cBioPortalSLC24A5
AceView (NCBI)SLC24A5
Genatlas (Paris)SLC24A5
WikiGenes283652
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)
EnsemblSLC24A5 - 15q21.1 [CytoView hg19]  SLC24A5 - 15q21.1 [CytoView hg38]
Mapping of homologs : NCBISLC24A5 [Mapview hg19]  SLC24A5 [Mapview hg38]
OMIM113750   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 : UnigeneHs.710240 [ NCBI ]
CGAP (NCI)Hs.710240
Alternative Splicing GalleryENSG00000188467
Gene ExpressionSLC24A5 [ 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]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)283652
GTEX Portal (Tissue expression)SLC24A5
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ71RS6   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ71RS6  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ71RS6
Splice isoforms : SwissVarQ71RS6
PhosPhoSitePlusQ71RS6
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 mutations283652
Blocks (Seattle)SLC24A5
SuperfamilyQ71RS6
Human Protein AtlasENSG00000188467
Peptide AtlasQ71RS6
HPRD18055
IPIIPI00409687   IPI00853386   
Protein Interaction databases
DIP (DOE-UCLA)Q71RS6
IntAct (EBI)Q71RS6
FunCoupENSG00000188467
BioGRIDSLC24A5
STRING (EMBL)SLC24A5
ZODIACSLC24A5
Ontologies - Pathways
QuickGOQ71RS6
Ontology : AmiGOcalcium channel activity  calcium ion binding  trans-Golgi network  integral component of plasma membrane  ion transport  potassium ion transport  cellular calcium ion homeostasis  calcium, potassium:sodium antiporter activity  calcium, potassium:sodium antiporter activity  symporter activity  potassium ion binding  sodium ion binding  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  
Ontology : EGO-EBIcalcium channel activity  calcium ion binding  trans-Golgi network  integral component of plasma membrane  ion transport  potassium ion transport  cellular calcium ion homeostasis  calcium, potassium:sodium antiporter activity  calcium, potassium:sodium antiporter activity  symporter activity  potassium ion binding  sodium ion binding  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  
REACTOMEQ71RS6 [protein]
REACTOME PathwaysR-HSA-425561 [pathway]   
NDEx NetworkSLC24A5
Atlas of Cancer Signalling NetworkSLC24A5
Wikipedia pathwaysSLC24A5
Orthology - Evolution
OrthoDB283652
GeneTree (enSembl)ENSG00000188467
Phylogenetic Trees/Animal Genes : TreeFamSLC24A5
HOVERGENQ71RS6
HOGENOMQ71RS6
Homologs : HomoloGeneSLC24A5
Homology/Alignments : Family Browser (UCSC)SLC24A5
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSLC24A5 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SLC24A5
dbVarSLC24A5
ClinVarSLC24A5
1000_GenomesSLC24A5 
Exome Variant ServerSLC24A5
ExAC (Exome Aggregation Consortium)SLC24A5 (select the gene name)
Genetic variants : HAPMAP283652
Genomic Variants (DGV)SLC24A5 [DGVbeta]
DECIPHERSLC24A5 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSLC24A5 
Mutations
ICGC Data PortalSLC24A5 
TCGA Data PortalSLC24A5 
Broad Tumor PortalSLC24A5
OASIS PortalSLC24A5 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSLC24A5  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSLC24A5
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch 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)
intoGenSLC24A5
Cancer3DSLC24A5(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM113750    609802   
Orphanet22481   
MedgenSLC24A5
Genetic Testing Registry SLC24A5
NextProtQ71RS6 [Medical]
TSGene283652
GENETestsSLC24A5
Target ValidationSLC24A5
Huge Navigator SLC24A5 [HugePedia]
snp3D : Map Gene to Disease283652
BioCentury BCIQSLC24A5
ClinGenSLC24A5
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD283652
Chemical/Pharm GKB GenePA134868972
Clinical trialSLC24A5
Miscellaneous
canSAR (ICR)SLC24A5 (select the gene name)
Probes
Litterature
PubMed27 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSLC24A5
EVEXSLC24A5
GoPubMedSLC24A5
iHOPSLC24A5
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Aug 1 17:37:10 CEST 2017

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