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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

SLC24A5 Gene

protein-coding GIFtS: 54
GCID: GC15P048413

solute carrier family 24, member 5

Explore 7 diseases affiliated with
SLC24A5 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Solute Carrier Family 24, Member 5¹ ²		Ion Transporter JSX²
JSX¹ ² ³		Sodium/Potassium/Calcium Exchanger 5²
NCKX5² ³ ⁵		Solute Carrier Family 24 (Sodium/Potassium/Calcium Exchanger), Member 5²
Na(+)/K(+)/Ca(2+)-Exchange Protein 5² ³		Solute Carrier Family 24 Member 5³
SHEP4² ⁵

External Ids:	HGNC: 20611¹	Entrez Gene: 283652²	Ensembl: ENSG00000188467⁷	OMIM: 609802⁵	UniProtKB: Q71RS6³

Export aliases for SLC24A5 gene to outside databases

Previous GC identifers: GC00U900962 GC15P046118 GC15P046200 GC15P025246

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for SLC24A5:

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)

UniProtKB/Swiss-Prot: NCKX5_HUMAN, Q71RS6

Function: Cation exchanger involved in pigmentation, possibly by participating in ion transport in melanosomes.

Probably transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+)

Gene Wiki entry for SLC24A5

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000015.9 NC_018926.1 NT_010194.17

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the SLC24A5 gene promoter:
STAT1 NCX/Ncx MyoD STAT1beta POU6F1 (c2) GATA-1 STAT1alpha S8 Cart-1 MRF-2
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SLC24A5 promoter sequence

Search SABiosciences Chromatin IP Primers for SLC24A5

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SLC24A5

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 15q21.1 Ensembl cytogenetic band: 15q21.1 HGNC cytogenetic band: 15q21.1

SLC24A5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLC24A5 gene location

GeneLoc information about chromosome 15 GeneLoc Exon Structure

GeneLoc location for GC15P048413: view genomic region (about GC identifiers)

Start:	48,413,169 bp from pter	End:	48,434,869 bp from pter
Size:	21,701 bases	Orientation:	plus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: NCKX5_HUMAN, Q71RS6 (See protein sequence)

Recommended Name: Sodium/potassium/calcium exchanger 5 precursor

Size: 500 amino acids; 54888 Da

Subcellular location: Membrane; Multi-pass membrane protein (By similarity). Melanosome. Note=Enriched in late-stage

melanosomes

Secondary accessions: A5X8Z8 Q14CT4 Q6DKH3

Explore the universe of human proteins at neXtProt for SLC24A5: NX_Q71RS6

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q71RS6

SLC24A5 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_995322.1

ENSEMBL proteins:

ENSP00000341550 ENSP00000453395 ENSP00000389966

Reactome Protein details: Q71RS6
Human Recombinant Protein Products for SLC24A5:

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	Uscn Proteins for SLC24A5

Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005886	plasma membrane	TAS	--
GO:0016021	integral to membrane	IEA	--
GO:0042470	melanosome	IEA	--

SLC24A5 for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

SLC24A5 for domains About GeneDecksing

2 InterPro domains/families:

IPR004481 K/Na/Ca-exchanger

IPR004837 NaCa_Exmemb

Graphical View of Domain Structure for InterPro Entry Q71RS6

ProtoNet protein and cluster: Q71RS6

1 Blocks protein family: IPB004837 Sodium/calcium exchanger membrane region

UniProtKB/Swiss-Prot: NCKX5_HUMAN, Q71RS6

Similarity: Belongs to the sodium/potassium/calcium exchanger family. SLC24A subfamily

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: NCKX5_HUMAN, Q71RS6

Function: Cation exchanger involved in pigmentation, possibly by participating in ion transport in melanosomes.

Probably transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+)

Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0015293	symporter activity	IEA	--
GO:0015297	antiporter activity	IEA	--

SLC24A5 for ontologies About GeneDecksing

Phenotypes:
1 GenomeRNAi human phenotype for SLC24A5:

Small cells

5 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Slc24a5):

craniofacial

hearing/vestibular/ear

integument

pigmentation

vision/eye

SLC24A5 for phenotypes About GeneDecksing

Animal Models:

inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for SLC24A5

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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLC24A5

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways About this table

See pathways by source

Super-pathway

contained gene-specific pathways

SLC-mediated transmembrane transport

SLC-mediated transmembrane transport

1.00

Transmembrane transport of small molecules

0.50

Amino acid and oligopeptide SLC transporters

Transport of inorganic cations/anions and amino acids/oligopeptides

0.52

Sodium-coupled transporters and pumps

Sodium/Calcium exchangers

0.30

Pathway sources
See GeneCards unified pathways
Show all pathways

4 Reactome Pathways for SLC24A5

	Sodium/Calcium exchangers
	SLC-mediated transmembrane transport
	Transmembrane transport of small molecules
	Transport of inorganic cations/anions and amino acids/oligopeptides

SLC24A5 for pathways About GeneDecksing

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for SLC24A5

Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6): About this table

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:0050896	response to stimulus	IEA	--

SLC24A5 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

EMD Millipore small molecules for SLC24A5:
Small Molecule - inhibitor

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for SLC24A5

2 HMDB Compounds for SLC24A5 About this table

Compound	Synonyms	CAS #	PubMed Ids
Calcium	Ca (see all 2)	7440-70-2	--
Sodium	Sodium (see all 2)	7440-23-5	--

Search CenterWatch for drugs/clinical trials and news about SLC24A5 / NCKX5

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for SLC24A5 gene:

NM_205850.2

Unigene Cluster for SLC24A5:

Solute carrier family 24, member 5

Hs.710240 [show with all ESTs]

Unigene Representative Sequence: BC110836

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000341459(uc001zwe.3 uc010bel.3) ENST00000482911(uc001zwd.3)

ENST00000449382(uc001zwk.3) ENST00000463289

miRNA Products:		Browse 3'-UTR reporter clones for miRNA target validation Browse OriGene MicroRNA Expression Plasmids
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Additional cDNA sequence:

AF348468.1 BC073944.1 BC110836.1 BC113628.1 BC113630.1 BC143950.1 DQ665306.1 DQ665307.1

6 DOTS entries:

DT.102845416 DT.409979 DT.91741899 DT.121018825 DT.100788905 DT.112605

24/42 AceView cDNA sequences (see all 42):

BE221473 BM263399 AA885702 BF445399 AF348468 BI858597 AA625302 AI302242

BU188045 BC073944 AI240404 NM_205850 AI969605 BU183014 BG762279 T05299

H96671 AA625334 BF979157 BF938949 BF732396 BQ423791 BU608093 AI082695

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

SLC24A5 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

About this image

SLC24A5 expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

1 LifeMap In Vivo Development Anatomical Compartment/Cell

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Brain

Choroid Plexus

Mature Choroid Plexus Cells

Selective marker (cell-identifying gene)

Choroid Plexus

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See SLC24A5 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SLC24A5

SOURCE GeneReport for Unigene cluster: Hs.710240

SABiosciences Custom PCR Arrays for SLC24A5

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for SLC24A5 gene from 5/19 species (see all 19) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	SLC24A5¹	solute carrier family 24, member 5	71.95(n) 72.89(a)		415431 NM_001038497.2 NP_001033586.2
lizard (Anolis carolinensis)	Reptilia	SLC24A5⁶	--	67(a)	1 ↔ 1	GL343561.1(312127-321076)
tropical clawed frog (Xenopus tropicalis)	Amphibia	BX739745.1²	--	72.7(n)		BX739745.1
zebrafish (Danio rerio)	Actinopterygii	slc24a5¹	solute carrier family 24, member 5	63.5(n) 68.6(a)		570312 NM_001030280.1 NP_001025451.1
fruit fly (Drosophila melanogaster)	Insecta	CG12061⁶ CG2893⁶ (see all 4)	--	31(a) 29(a) (see all 4)	possible ortholog possible ortholog (see all 4)	XHet(14884-26496) XHet(2141-13174)

ENSEMBL Gene Tree for SLC24A5 (if available)
TreeFam Gene Tree for SLC24A5 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for SLC24A5 gene

SLC24A4² SLC8A2² SLC24A2² SLC8A3² SLC24A3² SLC8A1² SLC24A6² SLC24A1²

4 SIMAP similar genes for SLC24A5 using alignment to 3 protein entries: NCKX5_HUMAN (see all proteins):

SLC24A1 SLC24A4 SLC24A2 SLC24A3

SLC24A5 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

UniProtKB/Swiss-Prot: NCKX5_HUMAN, Q71RS6

Polymorphism: 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

Polymorphism: 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

SNP ID	Valid	Clinical significance	Chr 15 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs1426654^1,2	C,F,A,H	other	77122342(+)	`CAGGCA/GCAACT`	2	T A	mis¹ ese³		36		WA NA EA CA CSAM NS EU	9077
rs7359271^1,2	C	--	25244782(+)	`ATGTAA/GGCCAC`	1	--	us2k¹		0	--	--	--	--
rs79875456^1,2		--	25244787(+)	`GGCCAC/GTCCCC`	1	--	us2k¹		2		CSA WA	120
rs7359278^1,2	C,F,H	--	25245087(+)	`TACTAG/AGCATA`	1	--	us2k¹		8		NS EA NA	836
rs78065868^1,2		--	25245459(+)	`AGGTCG/ATTCTG`	1	--	us2k¹		1		NA	120
rs58102225^1,2	C	--	25247008(+)	`TTTCAT/CGATTT`	1	--	int¹		2		WA	120
rs77575793^1,2		--	25248336(+)	`AACCTC/TCACCC`	1	--	int¹		1		NA	120
rs79856063^1,2	F	--	25248399(+)	`ATGAAT/CGTAAA`	1	--	int¹		1		WA	118
rs76084158^1,2	F	--	25248968(+)	`GTTTTT/CACACA`	1	--	int¹		1		EA	120
rs77294837^1,2		--	25250457(+)	`GAAACG/AGGCTT`	1	--	int¹		1		WA	118

HapMap Linkage Disequilibrium report for SLC24A5 (48413169 - 48434869 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for SLC24A5: --
Human Gene Mutation Database (HGMD): SLC24A5

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SLC24A5

DNA2.0 Custom Variant and Variant Library Synthesis for SLC24A5

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

SLC24A5 for disorders           About GeneDecksing

OMIM gene information: 609802
OMIM disorders: 113750
7 diseases for SLC24A5:    About MalaCards

skin/hair/eye pigmentation 4, fair/dark skin loeys-dietz syndrome patent ductus arteriosus oculocutaneous albinism

ocular albinism albinism skin cancer

2 diseases from the University of Copenhagen DISEASES database for SLC24A5:

Oculocutaneous albinism Ocular albinism

Human Genome Epidemiology (HuGE) Navigator: SLC24A5 (10 documents)

Export disorders for SLC24A5 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for SLC24A5 gene, integrated from 9 sources (see all 17):
(articles sorted by number of sources associating them with SLC24A5)

Utopia: connect your pdf to the dynamic
world of online information

SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. (PubMed id 16357253)^{1, 2, 9} Lamason R.L.... Cheng K.C. (2005)
Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes. (PubMed id 17081065)^{1, 2, 9} Chi A....Hunt D.F. (2006)
A genomewide association study of skin pigmentation in a South Asian population. (PubMed id 17999355)^{1, 2} Stokowski R.P....Cox D.R. (2007)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
SLC24A5 encodes a trans-Golgi network protein with potassium-dependent sodium-calcium exchange activity that regulates human epidermal melanogenesis. (PubMed id 18166528)^{1, 9} Ginger R.S....Green M.R. (2008)
Analysis of cultured human melanocytes based on polymorphisms within the SLC45A2/MATP, SLC24A5/NCKX5, and OCA2/P loci. (PubMed id 18650849)^{1, 9} Cook A.L....Sturm R.A. (2009)
Genetic associations of brain structural networks in schizophrenia: a preliminary study. (PubMed id 20691427)¹ Jagannathan K....Pearlson G.D. (2010)
Birth prevalence and mutation spectrum in danish patients with autosomal recessive albinism. (PubMed id 19060277)¹ GrA...Rosenberg T. (2009)
Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. (PubMed id 19384953)¹ Nan H....Han J. (2009)
A pilot multivariate parallel ICA study to investigat e differential linkage between neural networks and genetic profiles in schizoph renia. (PubMed id 19944766)¹ Meda S.A....Pearlson G.D. (2009)

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		AND	OR
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 283652	HGNC: 20611	AceView: SLC24A5	Ensembl:ENSG00000188467	euGenes: HUgn283652
ECgene: SLC24A5	H-InvDB: SLC24A5

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for SLC24A5	Pharmacogenomics, SNPs, Pathways
Protein Spotlight	http://web.expasy.org/spotlight/back_issues/sptlt074.shtml

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solute carrier family 24, member 5

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SLC24A5 Gene

solute carrier family 24, member 5

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