UCSF Pharmacogenetics of Membrane Transporters
Gene View
Common Name:NCKX2
HGNC Symbol:SLC24A2
HGNC Description:solute carrier family 24 (sodium/potassium/calcium exchanger), member 2
HGNC ID:10976
Superfamily:SLC
Chromosome:Chr.9(-): 19507450-19789059 GRCh37
Location:9p22.1
OMIM:609838
OMIM Phenotype:None
Accessions:AF097366
Nucleotide RefSeq:NM_020344
Protein RefSeq:NP_065077
Entrez:25769
Ensembl:ENSG00000155886
Isoforms:5
Evidence:Substrate In Vitro Evidence: The rat ortholog of NCKX2 has been functionally characterized using X. laevis oocytes, and was found to be a potassium-dependent sodium/calcium exchanger (Dong H, Light PE, French RJ, Lytton J. Electrophysiological characterization and ionic stoichiometry of the rat brain K+-dependent Na+/Ca2+ exchanger, NCKX2. J Biol Chem 276:25919-25928, 2001). Substrate In Vivo Evidence: In 166 patients with retinal disease, 14 novel sequence variants were identified in the NCKX2 gene. Three of these led to missense changes (amino acid substitutions) that are unlikely to be pathogenic (Sharon D, Yamamoto H, McGee TL, Rabe V, Szerencsei RT, Winkfein RJ, Prinsen CFM, Barnes CS, Andreasson S, Fishman GA, Schnetkamp PPM, Berson EL, Dryja TP. Mutated alleles of the rod and cone Na/Ca+K exchanger genes in patients with retinal diseases. Invest Ophthalmol Vis Sci 43:1971-1979, 2002). Tissue Distribution Evidence: In rats, NCKX mRNA was highly expressed in all brain regions examined (cerebral cortex, cerebellum, midbrain, and brainstem), moderately in eye, and weakly in heart, aorta, small intestine, large intestine, and lung (Tsoi M, Rhee K-H, Bungard D, Li XB, Lee S-L, Auer RN, Lytton J. Molecular cloning of a novel potassium-dependent sodium-calcium exchanger from rat brain. J Biol Chem 273:4155-4162, 1998).
Tissues:Brain (cerebral cortex, cerebellum, midbrain, and brainstem) (high); eye (moderate); heart, aorta, small intestine, large intestine, lung (low)
Type:protein-coding
Sets:0
PharmGKB ID:PA35852
HPRD ID:15351
Substrates:Na+, Ca2+
Trivial Names:NCKX2
Transcripts:NM_020344.3 [Chr.9(-): 19507450-19787017 GRCh37]
NM_001193288.2 [Chr.9(-): 19507450-19787017 GRCh37]
XM_005251426.1 [Chr.9(-): 19507452-19789059 GRCh37]
XM_005251427.1 [Chr.9(-): 19507452-19788808 GRCh37]
XM_005251425.1 [Chr.9(-): 19507452-19788808 GRCh37]
ENST00000286344 [Chr.9(-): 19515978-19786926 GRCh37]
ENST00000341998 [Chr.9(-): 19507450-19786926 GRCh37]
Annotation History:View Events (34)

GTEx Expression by Gene and Transcript

The heat map summarizes relative expression by tissue type at two levels of tissue detail, e.g., 'Brain' and 'Brain - Amygdala'. Choose among four calculated expression values, including mean and median RPKM values, and quantile normalized (QN) distributions of these values. (Note that differences between some distributions are subtle.) The coloring is relative to the mean of all displayed values. All values are log base 2. (See also PMT GTEx Expression Plotting.) Click on a transcript or tissue to resort the data.

Tissues:
Expression values:
No expression data exists for SLC24A2.

Variant Data

View all PMT variants for SLC24A2 on UCSC Genome Browser
Showing SNP features for transcript:   
1000 Genomes  

20141104 phase 3 variant call set of the 20130502 sequence freeze and alignments for SNPs and short indels (indels > 255 and structural variants are not included here). This variant set contains 2504 individuals from 26 populations (mouse over population column heading for population sizes).
Showing gene variants in regions defined by NCBI RefSeq exons, putative promoter, and PMT resequencing assays.
Note: Frequencies are calculated directly from reported genotypes and may vary from consensus frequencies reported by the 1000 Genomes project, which relied on additional data and the GATK tool Variant Quality Score Recalibrator.
dbSNP build 142.
Array availability: I - found on Illumina Human1M-Duo BeadChip (2011-04-21)  A - found on Affymetrix Genome-Wide SNP Array 6.0 (2011-06-21)  
Download the SNP table data as a tab-delimited file.

Transmembrane prediction:

Non-synonymous amino acid changes shown in red, indels (insertions and deletions) in blue, and synonymous changes in green. Exon(s) indicated by black outlines.