SLC24A2 solute carrier family 24 member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC24A2provided by HGNC
Official Full Name: solute carrier family 24 member 2provided by HGNC
Primary source: HGNC:HGNC:10976
See related: Ensembl:ENSG00000155886 MIM:609838; AllianceGenome:HGNC:10976
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: NCKX2
Summary: This gene encodes a member of the calcium/cation antiporter superfamily of transport proteins. The encoded protein belongs to the SLC24 branch of exchangers, which can mediate the extrusion of one Ca2+ ion and one K+ ion in exchange for four Na+ ions. This family member is a retinal cone/brain exchanger that can mediate a light-induced decrease in free Ca2+ concentration. This protein may also play a neuroprotective role during ischemic brain injury. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
Expression: Restricted expression toward brain (RPKM 17.5) See more
Orthologs: mouse all
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Genomic context

Location:: 9p22.1-p21.3

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (19507455..20307892, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (19520160..20321675, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (19507453..19789035, complement)

Chromosome 9 - NC_000009.12 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?

A Genome-Wide Scan on Individual Typology Angle Found Variants at SLC24A2 Associated with Skin Color Variation in Chinese Populations.
Title: A Genome-Wide Scan on Individual Typology Angle Found Variants at SLC24A2 Associated with Skin Color Variation in Chinese Populations.
Multiomics Integrated Analysis Identifies SLC24A2 as a Potential Link between Type 2 Diabetes and Cancer.
Title: Multiomics Integrated Analysis Identifies SLC24A2 as a Potential Link between Type 2 Diabetes and Cancer.
residues in the two regions with the highest degree of homology between the different NCKX isoforms (alpha-1 and alpha-2 repeats) were examined to determine which residues are important for Ca(2+) coordination.
Title: Residues important for Ca(2+) ion transport in the neuronal K(+)-dependent Na(+)-Ca(2+) exchanger (NCKX2).
a new mutation in SLC24A2 gene was identified to decrease the stability of SLC24A2
Title: A SLC24A2 Gene Variant Uncovered in Pancreatic Ductal Adenocarcinoma by Whole Exome Sequencing.
Functional and structural properties of the NCKX2 Na(+)-Ca (2+)/K (+) exchanger: a comparison with the NCX1 Na (+)/Ca (2+) exchanger.
Title: Functional and structural properties of the NCKX2 Na(+)-Ca (2+)/K (+) exchanger: a comparison with the NCX1 Na (+)/Ca (2+) exchanger.
identified 31 residues that, when substituted, result in shifts in Na(+) affinity, either toward higher or lower K(m) values when compared with wild type NCKX2 (K(m) for Na(+) 58 mm)
Title: Residues contributing to the Na(+)-binding pocket of the SLC24 Na(+)/Ca(2+)-K(+) Exchanger NCKX2.
Observational study of gene-disease association. (HuGE Navigator)
Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
non-synonymous single nucleotide polymorphism in SLC24A5 alters a residue that is important for NCKX5 and NCKX2 activity
Title: SLC24A5 encodes a trans-Golgi network protein with potassium-dependent sodium-calcium exchange activity that regulates human epidermal melanogenesis.
Glu(188) and Asp(548) are the central residues of a single cation binding pocket that can accommodate both K(+) and Ca(2+). Furthermore, a single set of residues lines a transport pathway for both K(+) and Ca(2+).
Title: Residues contributing to the Ca2+ and K+ binding pocket of the NCKX2 Na+/Ca2+-K+ exchanger.
Several residues in helix H2 of NCKX2 are in the proximity of residues in helices H8 and to aspartate575 in H9; the residues found here are conserved in NCKX1-5 isoforms.
Title: Site-directed disulfide mapping of residues contributing to the Ca2+ and K+ binding pocket of the NCKX2 Na+/Ca2+-K+ exchanger.

Submit: New GeneRIF Correction See all GeneRIFs (16)

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

EBI GWAS Catalog

Description
A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of body mass index in 23 000 individuals with and without asthma. 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

SHGC-7540 (e-PCR)
- UniSTS:4149

RH119062 (e-PCR)
- UniSTS:138306

RH121296 (e-PCR)
- UniSTS:138562

D9S162 (e-PCR), detects polymorphism
- UniSTS:46935

RH103060 (e-PCR)
- UniSTS:97394

D9S162 (e-PCR), detects polymorphism
- UniSTS:70016

G42174 (e-PCR)
- UniSTS:105092

D9S1684 (e-PCR), detects polymorphism
- UniSTS:31129

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 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 import across plasma membrane	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 calcium ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
involved_in intracellular calcium ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intracellular calcium ion homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in learning	IEA Inferred from Electronic Annotation more info
involved_in long-term synaptic depression	IBA Inferred from Biological aspect of Ancestor more info
involved_in long-term synaptic potentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in memory	IEA Inferred from Electronic Annotation 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 neuron cellular homeostasis	IEA Inferred from Electronic Annotation more info
involved_in potassium ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in sodium ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in photoreceptor inner segment	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	RCA inferred from Reviewed Computational Analysis more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: sodium/potassium/calcium exchanger 2

Names: Na(+)/K(+)/Ca(2+)-exchange protein 2; Na/Ca-K exchanger 2; retinal cone Na-Ca+K exchanger; solute carrier family 24 (sodium/potassium/calcium exchanger), member 2

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.

Genomic

NG_029734.2 RefSeqGene

Range

523855..805437

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001193288.3 → NP_001180217.1 sodium/potassium/calcium exchanger 2 isoform 2

See identical proteins and their annotated locations for NP_001180217.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1. Variants 2 and 4 encode the same isoform.

Source sequence(s)

AL133281, AL158077, AL158206

Consensus CDS

CCDS55297.1

UniProtKB/Swiss-Prot

Q9UI40

Related

ENSP00000286344.3, ENST00000286344.4

Conserved Domains (1) summary

TIGR00927
Location:115 → 644

2A1904; K+-dependent Na+/Ca+ exchanger
NM_001375850.1 → NP_001362779.1 sodium/potassium/calcium exchanger 2 isoform 1

Status: REVIEWED

Source sequence(s)

AL133281, AL158077, AL158206

Consensus CDS

CCDS6493.1

UniProtKB/Swiss-Prot

B7ZLL8, Q9NTN5, Q9NZQ4, Q9UI40

Conserved Domains (1) summary

TIGR00927
Location:115 → 661

2A1904; K+-dependent Na+/Ca+ exchanger
NM_001375851.1 → NP_001362780.1 sodium/potassium/calcium exchanger 2 isoform 2

Status: REVIEWED

Source sequence(s)

AL133281, AL158077, AL158206

Consensus CDS

CCDS55297.1

Conserved Domains (1) summary

TIGR00927
Location:115 → 644

2A1904; K+-dependent Na+/Ca+ exchanger
NM_020344.4 → NP_065077.1 sodium/potassium/calcium exchanger 2 isoform 1

See identical proteins and their annotated locations for NP_065077.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). Variants 1 and 3 encode the same isoform.

Source sequence(s)

AL133281, AL158077, AL158206

Consensus CDS

CCDS6493.1

UniProtKB/Swiss-Prot

B7ZLL8, Q9NTN5, Q9NZQ4, Q9UI40

Related

ENSP00000344801.1, ENST00000341998.7

Conserved Domains (1) summary

TIGR00927
Location:115 → 661

2A1904; K+-dependent Na+/Ca+ exchanger

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

19507455..20307892 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017014592.2 → XP_016870081.1 sodium/potassium/calcium exchanger 2 isoform X1

UniProtKB/Swiss-Prot

B7ZLL8, Q9NTN5, Q9NZQ4, Q9UI40

Conserved Domains (1) summary

TIGR00927
Location:115 → 661

2A1904; K+-dependent Na+/Ca+ exchanger