UCSF Pharmacogenetics of Membrane Transporters
Gene View
Common Name:NCKX
HGNC Symbol:SLC24A1
HGNC Description:solute carrier family 24 (sodium/potassium/calcium exchanger), member 1
HGNC ID:10975
Chromosome:Chr.15(+): 65903618-65953334 GRCh37
OMIM Phenotype:None
Nucleotide RefSeq:NM_004727
Protein RefSeq:NP_004718
Evidence:Substrate In Vitro Evidence: NCKX1 was expressed stably in BTI-TN-5B1-4 insect cells (High Five cells), and found to be a potassium-dependent sodium-calcium exchanger (Prinsen CFM, Szerencsei RT, Schnetkamp PPM. Molecular cloning and functional expression the potassium-dependent sodium-calcium exchanger from human and chicken retinal cone photoreceptors. J Neurosci 20:1424-1434, 2000). Substrate In Vivo Evidence: In 815 patients with retinal disease, 27 novel sequence variants were found in the NCKX1 gene. Six of these were thought to be likely pathogenic mutations (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: Tissue distribution of NCKX1 has not been well studied. NCKX1 was originally cloned from bovine retina, and is thought to be the retinal potassium-dependent sodium/calcium exchanger (Reiländer H, Achilles A, Friedel U, Maul G, Lottspeich F, Cook NJ. Primary structure and functional expression of the Na/Ca,K-exchanger from bovine rod photoreceptors. EMBO J 11:1689-1695, 1992). More recently, NCKX1 mRNA was found to be expressed in human platelets by RT-PCR (Kimura J, Jeanclos EM, Donnelly RJ, Lytton J, Reeves JP, Aviv A. Physiological and molecular characterization of the Na+/Ca2+ exchanger in human platelets. Am J Physiol 277:H911-H917, 1999).
Tissues:Retina, platelets
PharmGKB ID:PA35851
HPRD ID:04685
Substrates:Na+, Ca2+
Trivial Names:NCKX, RODX, NCKX1, CSNB1D, HsT17412
Transcripts:NM_004727.2 [Chr.15(+): 65914270-65948598 GRCh37]
XM_005254780.1 [Chr.15(+): 65903618-65953334 GRCh37]
XM_005254778.1 [Chr.15(+): 65903618-65947090 GRCh37]
XM_005254779.1 [Chr.15(+): 65903618-65947090 GRCh37]
XM_005254781.1 [Chr.15(+): 65903618-65942824 GRCh37]
NM_001254740.1 [Chr.15(+): 65935243-65948598 GRCh37]
ENST00000261892 [Chr.15(+): 65914270-65948598 GRCh37]
ENST00000339868 [Chr.15(+): 65914270-65948598 GRCh37]
ENST00000399033 [Chr.15(+): 65916337-65946448 GRCh37]
ENST00000425561 [Chr.15(+): 65903716-65918195 GRCh37]
ENST00000434116 [Chr.15(+): 65903704-65945267 GRCh37]
ENST00000449142 [Chr.15(+): 65935243-65946529 GRCh37]
ENST00000505666 [Chr.15(+): 65945077-65947851 GRCh37]
ENST00000535950 [Chr.15(+): 65904150-65916356 GRCh37]
ENST00000537259 [Chr.15(+): 65903743-65953333 GRCh37]
ENST00000539516 [Chr.15(+): 65936266-65942946 GRCh37]
ENST00000544319 [Chr.15(+): 65914347-65946418 GRCh37]
ENST00000546330 [Chr.15(+): 65916419-65946417 GRCh37]
Annotation History:View Events (43)

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.

Expression values:
No expression data exists for SLC24A1.

Variant Data

View all PMT variants for SLC24A1 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.