SLC24A5 solute carrier family 24 member 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC24A5provided by HGNC
Official Full Name: solute carrier family 24 member 5provided by HGNC
Primary source: HGNC:HGNC:20611
See related: Ensembl:ENSG00000188467 MIM:609802; AllianceGenome:HGNC:20611
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: JSX; OCA6; NCKX5; SHEP4
Summary: 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]
Expression: Broad expression in brain (RPKM 6.4), adrenal (RPKM 4.4) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q21.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (48120990..48142672)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (45929094..45950765)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (48413187..48434869)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population.
Title: Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population.
Molecular characterization of SLC24A5 variants and evaluation of Nitisinone treatment efficacy in a zebrafish model of OCA6.
Title: Molecular characterization of SLC24A5 variants and evaluation of Nitisinone treatment efficacy in a zebrafish model of OCA6.
This study identifies two novel SLC24A5 frame-shift variants in two unrelated Chinese oculocutaneous albinism type 6 patients.
Title: Identification of two Chinese oculocutaneous albinism type 6 patients and mutation updates of the SLC24A5 gene.
NCKX5 is not a plasma membrane resident and is exclusively located in the trans Golgi network.
Title: Cellular localization of the K(+) -dependent Na(+) -Ca(2+) exchanger NCKX5 and the role of the cytoplasmic loop in its distribution in pigmented cells.
The derived causal allele in SLC24A5, p.Ala111Thr, significantly lightens basal skin pigmentation in the KhoeSan and explains 8 to 15% of phenotypic variance in these populations. The frequency of this allele (33 to 53%) is far greater than expected from gene flow. We show that the allele was introduced into the KhoeSan only 2,000 y ago via a back-to-Africa migration and then experienced a selective sweep.
Title: Rapid evolution of a skin-lightening allele in southern African KhoeSan.
both polymorphisms (rs1426654 and rs2470102) play an important role in the skin pigmentation diversity of South Asians
Title: Genotype-Phenotype Study of the Middle Gangetic Plain in India Shows Association of rs2470102 with Skin Pigmentation.
Letter/Case Report: OCA6 mutation in 6 year old boy with oculocutaneous albinism.
Title: Detection of the first OCA6 Italian patient in a large cohort of albino subjects.
mutations in SLC24A4 and SLC24A5 are responsible for the phenotypic defects observed in human amylogenesis imperfecta and non-syndromic oculocutaneous albinism patients.
Title: A Functional Study of Mutations in K+-dependent Na+-Ca2+ Exchangers Associated with Amelogenesis Imperfecta and Non-syndromic Oculocutaneous Albinism.
a novel homozygous mutation in SLC24A5 in two patients from French Guiana strengthens the importance of screening this gene in oculocutaneous albinism patients.
Title: Identification of a homozygous mutation of SLC24A5 (OCA6) in two patients with oculocutaneous albinism from French Guiana.
the SLC24A5 gene locus known to be associated with skin pigmentation was in the top selection signals in the Wolaita, and the alleles of single-nucleotide polymorphisms rs1426654 and rs1834640 (SLC24A5) associated with light skin pigmentation
Title: Novel genomic signals of recent selection in an Ethiopian population.

Submit: New GeneRIF Correction See all GeneRIFs (23)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Oculocutaneous albinism type 6 MedGen: C3805375 OMIM: 113750 GeneReviews: Oculocutaneous Albinism and Ocular Albinism Overview	Compare labs

EBI GWAS Catalog

Description
A genomewide association study of skin pigmentation in a South Asian population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH78227 (e-PCR)
- UniSTS:18438

MYEF2_1816 (e-PCR)
- UniSTS:277518

NoName (e-PCR)
- UniSTS:490365

RH45837 (e-PCR)
- UniSTS:30863

SHGC-132846 (e-PCR)
- UniSTS:170924

STS-N31726 (e-PCR)
- UniSTS:47311

SHGC-53423 (e-PCR)
- UniSTS:77523

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium, potassium:sodium antiporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium, potassium:sodium antiporter activity	IDA Inferred from Direct Assay more info	PubMed
enables calcium, potassium:sodium antiporter activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables symporter activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in calcium ion import	IDA Inferred from Direct Assay more info	PubMed
involved_in calcium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular calcium ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in melanin biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in melanocyte differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within monoatomic ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in monoatomic ion transport	TAS Traceable Author Statement more info
involved_in negative regulation of melanin biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in potassium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in response to stimulus	IEA Inferred from Electronic Annotation more info
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in melanosome	IEA Inferred from Electronic Annotation more info
is_active_in trans-Golgi network	IBA Inferred from Biological aspect of Ancestor more info
located_in trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed
located_in trans-Golgi network membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: sodium/potassium/calcium exchanger 5

Names: Na(+)/K(+)/Ca(2+)-exchange protein 5; Na/Ca-K exchanger 5; ion transporter JSX; oculocutaneous albinism 6 (autosomal recessive); solute carrier family 24 (sodium/potassium/calcium exchanger), member 5

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.