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    SLC24A1 solute carrier family 24 member 1 [ Homo sapiens (human) ]

    Gene ID: 9187, updated on 3-Nov-2024

    Summary

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    Official Symbol
    SLC24A1provided by HGNC
    Official Full Name
    solute carrier family 24 member 1provided by HGNC
    Primary source
    HGNC:HGNC:10975
    See related
    Ensembl:ENSG00000074621 MIM:603617; AllianceGenome:HGNC:10975
    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
    NCKX; RODX; NCKX1; CSNB1D; HsT17412
    Summary
    This gene encodes a member of the potassium-dependent sodium/calcium exchanger protein family. The encoded protein plays an important role in sodium/calcium exchange in retinal rod and cone photoreceptors by mediating the extrusion of one calcium ion and one potassium ion in exchange for four sodium ions. Mutations in this gene may play a role in congenital stationary night blindness. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
    Expression
    Ubiquitous expression in thyroid (RPKM 3.0), testis (RPKM 2.7) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See SLC24A1 in Genome Data Viewer
    Location:
    15q22.31
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (65611350..65661002)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (63420643..63470640)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (65903688..65953340)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene 3-hydroxyacyl-CoA dehydratase 3 Neighboring gene small nucleolar RNA U13 Neighboring gene NANOG hESC enhancer GRCh37_chr15:65871212-65871790 Neighboring gene integrator complex subunit 14 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9602 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:65910767-65911352 Neighboring gene uncharacterized LOC102723464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6557 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:65943238-65943423 Neighboring gene DENN domain containing 4A Neighboring gene small nucleolar RNA, C/D box 13E Neighboring gene microRNA 4511

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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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    Related articles in PubMed

    1. The SLC24 Na+/Ca2+-K+ exchanger family: vision and beyond. Schnetkamp PP. Pflugers Arch, 2004 Feb. PMID 14770312
    2. How does the retinal rod Na-Ca+K exchanger regulate cytosolic free Ca2+? Schnetkamp PP. J Biol Chem, 1995 Jun 2. PMID 7539424
    3. Chromosomal localization and genomic organization of the human retinal rod Na-Ca+K exchanger. Tucker JE, et al. Hum Genet, 1998 Oct. PMID 9856482
    4. Mutated alleles of the rod and cone Na-Ca+K-exchanger genes in patients with retinal diseases. Sharon D, et al. Invest Ophthalmol Vis Sci, 2002 Jun. PMID 12037007
    5. Topology of the retinal cone NCKX2 Na/Ca-K exchanger. Kinjo TG, et al. Biochemistry, 2003 Mar 4. PMID 12600216

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. We report the association of many previously unreported variants with retinal disease, as well as new disease phenotypes associated with known genes, including the first association of the SLC24A1 gene with retinitis pigmentosa
      Title: Panel-Based Population Next-Generation Sequencing for Inherited Retinal Degenerations.
    2. The index patient and his affected brother carry a homozygous single-nucleotide variants (SNVs) in sodium-calcium, potassium exchanger (SLC24A1) (c.2401G > T).
      Title: Next-generation sequencing confirms the implication of SLC24A1 in autosomal-recessive congenital stationary night blindness.
    3. A mutation in SLC24A1 is implicated in autosomal-recessive congenital stationary night blindness.
      Title: A mutation in SLC24A1 implicated in autosomal-recessive congenital stationary night blindness.
    Submit: New GeneRIF Correction

    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
    Congenital stationary night blindness 1D
    MedGen: C3151193 OMIM: 613830 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of hematological and biochemical traits in a Japanese population.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of solute carrier family 24 (sodium/potassium/calcium exchanger), member 1 (SLC24A1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    capsid gag The interaction of HIV-1 CA with human cellular solute carrier family 24, member 1 protein (SLC24A1) is identified by yeast two-hybrid screen PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0702

    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables calcium, potassium:sodium antiporter activity NAS
    Non-traceable Author Statement
    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 across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    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 calcium ion transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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 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 monoatomic ion transport TAS
    Traceable Author Statement
    more info
    		  
    involved_in potassium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to light intensity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in sodium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in visual perception NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in outer membrane NAS
    Non-traceable Author Statement
    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 1
    Names
    Na(+)/K(+)/Ca(2+)-exchange protein 1
    Na/Ca-K exchanger 1
    retinal rod Na+/Ca+/K+ exchanger
    solute carrier family 24 (sodium/potassium/calcium exchanger), member 1

    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

    1. NG_031968.2 RefSeqGene

      Range
      15534..49856
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001254740.2 → NP_001241669.1  sodium/potassium/calcium exchanger 1 isoform 2

      See identical proteins and their annotated locations for NP_001241669.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AC011939, AC027220, AK300633
      UniProtKB/TrEMBL
      B4DUG1
      Conserved Domains (1) summary
      pfam01699
      Location:263 → 414
      Na_Ca_ex; Sodium/calcium exchanger protein

    2. NM_001301031.1 → NP_001287960.1  sodium/potassium/calcium exchanger 1 isoform 3

      See identical proteins and their annotated locations for NP_001287960.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
      Source sequence(s)
      AI026072, AK304006, BC117263, BM129630, BM681488, EL947516, EL948740
      Consensus CDS
      CCDS73742.1
      UniProtKB/TrEMBL
      B4E1W0
      Related
      ENSP00000381991.4, ENST00000399033.8
      Conserved Domains (2) summary
      TIGR00927
      Location:1 → 1069
      2A1904; K+-dependent Na+/Ca+ exchanger
      pfam01699
      Location:458 → 602
      Na_Ca_ex; Sodium/calcium exchanger protein

    3. NM_001301032.1 → NP_001287961.1  sodium/potassium/calcium exchanger 1 isoform 4

      See identical proteins and their annotated locations for NP_001287961.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, and lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
      Source sequence(s)
      AB014602, AF026132, AI026072, BM129630, BM681488, EL947516, EL948740
      Consensus CDS
      CCDS73743.1
      UniProtKB/TrEMBL
      B4E1W0
      Related
      ENSP00000439190.1, ENST00000546330.1
      Conserved Domains (2) summary
      TIGR00927
      Location:1 → 1081
      2A1904; K+-dependent Na+/Ca+ exchanger
      pfam01699
      Location:458 → 602
      Na_Ca_ex; Sodium/calcium exchanger protein

    4. NM_001301033.2 → NP_001287962.1  sodium/potassium/calcium exchanger 1 isoform 5

      See identical proteins and their annotated locations for NP_001287962.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks an alternate in-frame exon in the central coding region, and contains alternate 3' exon structure and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (5) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AB014602, AC011939, AC027220, AK304006
      Consensus CDS
      CCDS73744.1
      UniProtKB/TrEMBL
      B4E1W0, F5H127
      Related
      ENSP00000439693.1, ENST00000537259.5
      Conserved Domains (1) summary
      cl27511
      Location:1 → 1000
      Na_Ca_ex; Sodium/calcium exchanger protein

    5. NM_001411142.1 → NP_001398071.1  sodium/potassium/calcium exchanger 1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC011939, AC027220
      Consensus CDS
      CCDS92023.1
      UniProtKB/TrEMBL
      F5H483
      Related
      ENSP00000445163.1, ENST00000544319.6

    6. NM_004727.3 → NP_004718.1  sodium/potassium/calcium exchanger 1 isoform 1

      See identical proteins and their annotated locations for NP_004718.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC011939, AC027220, AF062922
      Consensus CDS
      CCDS45284.1
      UniProtKB/Swiss-Prot
      O43485, O60721, O75184, Q17RM9
      UniProtKB/TrEMBL
      B4E1W0
      Related
      ENSP00000261892.6, ENST00000261892.11
      Conserved Domains (1) summary
      TIGR00927
      Location:1 → 1099
      2A1904; K+-dependent Na+/Ca+ exchanger

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      65611350..65661002
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024450103.2 → XP_024305871.1  sodium/potassium/calcium exchanger 1 isoform X1

      UniProtKB/Swiss-Prot
      O43485, O60721, O75184, Q17RM9
      UniProtKB/TrEMBL
      B4E1W0
      Conserved Domains (1) summary
      TIGR00927
      Location:1 → 1099
      2A1904; K+-dependent Na+/Ca+ exchanger

    2. XM_011522219.2 → XP_011520521.1  sodium/potassium/calcium exchanger 1 isoform X1

      See identical proteins and their annotated locations for XP_011520521.1

      UniProtKB/Swiss-Prot
      O43485, O60721, O75184, Q17RM9
      UniProtKB/TrEMBL
      B4E1W0
      Conserved Domains (1) summary
      TIGR00927
      Location:1 → 1099
      2A1904; K+-dependent Na+/Ca+ exchanger

    3. XM_024450105.2 → XP_024305873.1  sodium/potassium/calcium exchanger 1 isoform X1

      UniProtKB/Swiss-Prot
      O43485, O60721, O75184, Q17RM9
      UniProtKB/TrEMBL
      B4E1W0
      Conserved Domains (1) summary
      TIGR00927
      Location:1 → 1099
      2A1904; K+-dependent Na+/Ca+ exchanger

    4. XM_047433325.1 → XP_047289281.1  sodium/potassium/calcium exchanger 1 isoform X2

    5. XM_024450104.2 → XP_024305872.1  sodium/potassium/calcium exchanger 1 isoform X1

      UniProtKB/Swiss-Prot
      O43485, O60721, O75184, Q17RM9
      UniProtKB/TrEMBL
      B4E1W0
      Conserved Domains (1) summary
      TIGR00927
      Location:1 → 1099
      2A1904; K+-dependent Na+/Ca+ exchanger

    6. XM_047433326.1 → XP_047289282.1  sodium/potassium/calcium exchanger 1 isoform X2

    7. XM_047433330.1 → XP_047289286.1  sodium/potassium/calcium exchanger 1 isoform X7

    8. XM_011522222.4 → XP_011520524.1  sodium/potassium/calcium exchanger 1 isoform X7

      See identical proteins and their annotated locations for XP_011520524.1

      UniProtKB/TrEMBL
      B4E1W0
      Conserved Domains (2) summary
      TIGR00927
      Location:1 → 1018
      2A1904; K+-dependent Na+/Ca+ exchanger
      pfam01699
      Location:458 → 602
      Na_Ca_ex; Sodium/calcium exchanger protein

    9. XM_047433333.1 → XP_047289289.1  sodium/potassium/calcium exchanger 1 isoform X10

    10. XM_047433334.1 → XP_047289290.1  sodium/potassium/calcium exchanger 1 isoform X11

    11. XM_047433338.1 → XP_047289294.1  sodium/potassium/calcium exchanger 1 isoform X15

    12. XM_011522221.4 → XP_011520523.1  sodium/potassium/calcium exchanger 1 isoform X3

      See identical proteins and their annotated locations for XP_011520523.1

      UniProtKB/TrEMBL
      B4E1W0
      Conserved Domains (2) summary
      TIGR00927
      Location:1 → 1069
      2A1904; K+-dependent Na+/Ca+ exchanger
      pfam01699
      Location:458 → 602
      Na_Ca_ex; Sodium/calcium exchanger protein

    13. XM_047433327.1 → XP_047289283.1  sodium/potassium/calcium exchanger 1 isoform X4

    14. XM_047433335.1 → XP_047289291.1  sodium/potassium/calcium exchanger 1 isoform X13

    15. XM_017022724.3 → XP_016878213.1  sodium/potassium/calcium exchanger 1 isoform X5

      UniProtKB/TrEMBL
      B4E1W0

    16. XM_047433331.1 → XP_047289287.1  sodium/potassium/calcium exchanger 1 isoform X8

    17. XM_017022725.3 → XP_016878214.1  sodium/potassium/calcium exchanger 1 isoform X12

      UniProtKB/TrEMBL
      B4E1W0

    18. XM_047433328.1 → XP_047289284.1  sodium/potassium/calcium exchanger 1 isoform X6

    19. XM_047433332.1 → XP_047289288.1  sodium/potassium/calcium exchanger 1 isoform X9

    20. XM_047433336.1 → XP_047289292.1  sodium/potassium/calcium exchanger 1 isoform X14

    21. XM_005254781.5 → XP_005254838.1  sodium/potassium/calcium exchanger 1 isoform X16

      Conserved Domains (2) summary
      TIGR00927
      Location:1 → 637
      2A1904; K+-dependent Na+/Ca+ exchanger
      pfam01699
      Location:458 → 602
      Na_Ca_ex; Sodium/calcium exchanger protein

    22. XM_011522226.4 → XP_011520528.1  sodium/potassium/calcium exchanger 1 isoform X17

      Conserved Domains (2) summary
      TIGR00927
      Location:1 → 637
      2A1904; K+-dependent Na+/Ca+ exchanger
      pfam01699
      Location:458 → 602
      Na_Ca_ex; Sodium/calcium exchanger protein

    23. XM_047433339.1 → XP_047289295.1  sodium/potassium/calcium exchanger 1 isoform X18

    RNA

    1. XR_007064494.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      63420643..63470640
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379191.1 → XP_054235166.1  sodium/potassium/calcium exchanger 1 isoform X1

      UniProtKB/Swiss-Prot
      O43485, O60721, O75184, Q17RM9

    2. XM_054379190.1 → XP_054235165.1  sodium/potassium/calcium exchanger 1 isoform X1

      UniProtKB/Swiss-Prot
      O43485, O60721, O75184, Q17RM9

    3. XM_054379193.1 → XP_054235168.1  sodium/potassium/calcium exchanger 1 isoform X1

      UniProtKB/Swiss-Prot
      O43485, O60721, O75184, Q17RM9

    4. XM_054379192.1 → XP_054235167.1  sodium/potassium/calcium exchanger 1 isoform X1

      UniProtKB/Swiss-Prot
      O43485, O60721, O75184, Q17RM9

    5. XM_054379194.1 → XP_054235169.1  sodium/potassium/calcium exchanger 1 isoform X2

    6. XM_054379195.1 → XP_054235170.1  sodium/potassium/calcium exchanger 1 isoform X2

    7. XM_054379200.1 → XP_054235175.1  sodium/potassium/calcium exchanger 1 isoform X7

    8. XM_054379201.1 → XP_054235176.1  sodium/potassium/calcium exchanger 1 isoform X7

    9. XM_054379204.1 → XP_054235179.1  sodium/potassium/calcium exchanger 1 isoform X10

    10. XM_054379205.1 → XP_054235180.1  sodium/potassium/calcium exchanger 1 isoform X11

    11. XM_054379209.1 → XP_054235184.1  sodium/potassium/calcium exchanger 1 isoform X15

    12. XM_054379198.1 → XP_054235173.1  sodium/potassium/calcium exchanger 1 isoform X5

    13. XM_054379196.1 → XP_054235171.1  sodium/potassium/calcium exchanger 1 isoform X3

    14. XM_054379202.1 → XP_054235177.1  sodium/potassium/calcium exchanger 1 isoform X8

    15. XM_054379206.1 → XP_054235181.1  sodium/potassium/calcium exchanger 1 isoform X12

    16. XM_054379199.1 → XP_054235174.1  sodium/potassium/calcium exchanger 1 isoform X6

    17. XM_054379197.1 → XP_054235172.1  sodium/potassium/calcium exchanger 1 isoform X4

    18. XM_054379203.1 → XP_054235178.1  sodium/potassium/calcium exchanger 1 isoform X9

    19. XM_054379208.1 → XP_054235183.1  sodium/potassium/calcium exchanger 1 isoform X14

    20. XM_054379207.1 → XP_054235182.1  sodium/potassium/calcium exchanger 1 isoform X13

    21. XM_054379210.1 → XP_054235185.1  sodium/potassium/calcium exchanger 1 isoform X16

    22. XM_054379211.1 → XP_054235186.1  sodium/potassium/calcium exchanger 1 isoform X17

    23. XM_054379212.1 → XP_054235187.1  sodium/potassium/calcium exchanger 1 isoform X18

    RNA

    1. XR_008489031.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O60721.1 GenPept UniProtKB/Swiss-Prot:O60721

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