Sodium/potassium/calcium exchanger 5

Last updated
SLC24A5
Identifiers
Aliases SLC24A5 , JSX, NCKX5, OCA6, SHEP4, solute carrier family 24 member 5
External IDs OMIM: 609802 MGI: 2677271 HomoloGene: 18400 GeneCards: SLC24A5
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_205850

NM_175034

RefSeq (protein)

NP_995322

NP_778199

Location (UCSC) Chr 15: 48.12 – 48.14 Mb Chr 2: 124.91 – 124.93 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Sodium/potassium/calcium exchanger 5 (NCKX5), also known as solute carrier family 24 member 5 (SLC24A5), is a protein that in humans is encoded by the SLC24A5 gene that has a major influence on natural skin colour variation. [5] The NCKX5 protein is a member of the potassium-dependent sodium/calcium exchanger family. Sequence variation in the SLC24A5 gene, particularly a non-synonymous SNP changing the amino acid at position 111 in NCKX5 from alanine to threonine, has been associated with differences in skin pigmentation. [6]

Contents

The SLC24A5 gene's derived threonine or Ala111Thr allele (rs1426654 [7] ) has been shown to be a major factor in the light skin tone of Europeans compared to Sub-Saharan Africans, and is believed to represent as much as 25–40% of the average skin tone difference between Europeans and West Africans. [5] [8] Possibly originating as long as 19,000 years ago, it has been the subject of selection in the ancestors of Europeans as recently as within the last 5,000 years, [9] and is fixed in modern European populations. [10] [11] [12] It was introduced into Khoisan people via "back-to-Africa" migration around 2,000 years ago is partly responsible for their differing skin tone to most other African populations. [13]

Gene

In human, the SLC24A5 gene is located on the long (q) arm of chromosome 15 at position 21.1. SLC24A5 location.png
In human, the SLC24A5 gene is located on the long (q) arm of chromosome 15 at position 21.1.

The SLC24A5 gene, in humans, is located on the long (q) arm of chromosome 15 on position 21.1, from base pair 46,200,461 to base pair 46,221,881. [5]

Protein

NCKX5 is 43 kDa protein that is partially localized to the trans-Golgi network in melanocytes. Removal of the NCKX5 protein disrupts melanogenesis in human and mouse melanocytes, causing a significant reduction in melanin pigment production. Site-directed mutagenesis corresponding to a non-synonymous single nucleotide polymorphism in SLC24A5 alters a residue in NCKX5 (A111T) that is important for NCKX5 sodium-calcium exchanger activity. [6]

Effect on skin color

Global frequency distribution of the SLC24A5 gene's ancestral Ala111 allele (yellow) and its derived Ala111Thr allele (blue). Ala111Thr allele frequency distribution0.png
Global frequency distribution of the SLC24A5 gene's ancestral Ala111 allele (yellow) and its derived Ala111Thr allele (blue).

SLC24A5 appears to have played a key role in the evolution of light skin in humans of European ancestry. The gene's function in pigmentation was discovered in zebrafish as a result of the positional cloning of the gene responsible for the "golden" variety of this common pet store fish. Evidence in the International HapMap Project database of genetic variation in human populations showed that Europeans, represented by the "CEU" population, had two primary alleles differing by only one nucleotide, changing the 111th amino acid from alanine to threonine, abbreviated "A111T". [5] [14] [15]

The derived threonine allele (Ala111Thr; also known as A111T or Thr111) represented 98.7 to 100% of the alleles in European samples, while the ancestral or alanine form was found in 93 to 100% of samples of Sub-Saharan Africans, East Asians and Indigenous Americans. The variation is a SNP polymorphism rs1426654, which had been previously shown to be second among 3011 tabulated SNPs ranked as ancestry-informative markers. This single change in SLC24A5 explains between 25 and 38% of the difference in skin melanin index between peoples of sub-Saharan African and European ancestry. [5]

The SNP rs2470102 independently affects skin pigmentation variation among the South Asian population. [16]

Furthermore, the European mutation is associated with the largest region of diminished genetic variation in the CEU HapMap population, suggesting the possibility that the A111T mutation may be the subject of the single largest degree of selection in human populations of European ancestry. [5] It is hypothesized that selection for the derived allele is based on the need for sunlight to produce the essential nutrient vitamin D. In northerly latitudes, where there is less sun, greater requirement for body coverage due to colder climate, and frequently, diets poor in vitamin D, making lighter skin more suitable for survival. [17]

The earliest known sample of the threonine allele is 13,000 years old from Satsurblia Cave in Georgia. [18] The allele was widespread from Anatolia to Ukraine and Iran at the beginning of the Neolithic. [19] [20] [21]

This allele forms part of the HIrisplex DNA test system used to estimate pigmentation in forensic investigations. [22] [23]

See also

Related Research Articles

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<span class="mw-page-title-main">Melanin</span> Group of natural pigments found in most organisms

Melanin consist of oligomers or polymers arranged in a disordered manner which among other functions provide the pigments of many organisms. Melanin pigments are produced in a specialized group of cells known as melanocytes. They have been described as "among the last remaining biological frontiers with the unknown".

<span class="mw-page-title-main">Melanocyte</span> Melanin-producing cells of the skin

Melanocytes are melanin-producing neural crest-derived cells located in the bottom layer of the skin's epidermis, the middle layer of the eye, the inner ear, vaginal epithelium, meninges, bones, and heart. Melanin is a dark pigment primarily responsible for skin color. Once synthesized, melanin is contained in special organelles called melanosomes which can be transported to nearby keratinocytes to induce pigmentation. Thus darker skin tones have more melanosomes present than lighter skin tones. Functionally, melanin serves as protection against UV radiation. Melanocytes also have a role in the immune system.

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<span class="mw-page-title-main">Single-nucleotide polymorphism</span> Single nucleotide in genomic DNA at which different sequence alternatives exist

In genetics and bioinformatics, a single-nucleotide polymorphism is a germline substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of considered population.

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<span class="mw-page-title-main">Membrane-associated transporter protein</span> Protein

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<span class="mw-page-title-main">Western Hunter-Gatherer</span> Archaeogenetic name for an ancestral genetic component

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<span class="mw-page-title-main">Eastern Hunter-Gatherer</span> Archaeogenetic name for an ancestral genetic component

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<span class="mw-page-title-main">Scandinavian Hunter-Gatherer</span> Archaeogenetic name for an ancestral genetic component

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References

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Further reading