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    SLC12A3 solute carrier family 12 member 3 [ Homo sapiens (human) ]

    Gene ID: 6559, updated on 26-Aug-2018

    Summary

    Official Symbol
    SLC12A3provided by HGNC
    Official Full Name
    solute carrier family 12 member 3provided by HGNC
    Primary source
    HGNC:HGNC:10912
    See related
    Ensembl:ENSG00000070915 MIM:600968; Vega:OTTHUMG00000133284
    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
    NCC; TSC; NCCT
    Summary
    This gene encodes a renal thiazide-sensitive sodium-chloride cotransporter that is important for electrolyte homeostasis. This cotransporter mediates sodium and chloride reabsorption in the distal convoluted tubule. Mutations in this gene cause Gitelman syndrome, a disease similar to Bartter's syndrome, that is characterized by hypokalemic alkalosis combined with hypomagnesemia, low urinary calcium, and increased renin activity associated with normal blood pressure. This cotransporter is the target for thiazide diuretics that are used for treating high blood pressure. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Restricted expression toward kidney (RPKM 65.2) See more
    Orthologs

    Genomic context

    See SLC12A3 in Genome Data Viewer
    Location:
    16q13
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (56865207..56915850)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (56899119..56949762)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene nucleoporin 93 Neighboring gene microRNA 138-2 Neighboring gene ribosomal protein S24 pseudogene 17 Neighboring gene microRNA 6863 Neighboring gene homocysteine inducible ER protein with ubiquitin like domain 1 Neighboring gene cholesteryl ester transfer protein

    Genomic regions, transcripts, and products

    Expression

    • 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Familial hypokalemia-hypomagnesemia
    MedGen: C0268450 OMIM: 263800 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
    NHGRI GWA Catalog
    Polymorphism in the CETP gene region, HDL cholesterol, and risk of future myocardial infarction: Genomewide analysis among 18 245 initially healthy women from the Women's Genome Health Study.
    NHGRI GWA Catalog

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ96318

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    potassium:chloride symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    sodium ion transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sodium:chloride symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sodium:chloride symporter activity TAS
    Traceable Author Statement
    more info
     
    sodium:potassium:chloride symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    cell volume homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chloride ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chloride transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chloride transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    ion transport TAS
    Traceable Author Statement
    more info
     
    potassium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    potassium ion import IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sodium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sodium ion transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    sodium ion transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    apical plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular exosome HDA PubMed 
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    solute carrier family 12 member 3
    Names
    Na-Cl cotransporter
    Na-Cl symporter
    NaCl electroneutral thiazide-sensitive cotransporter
    solute carrier family 12 (sodium/chloride transporter), member 3
    thiazide-sensitive Na-Cl cotransporter
    thiazide-sensitive sodium-chloride cotransporter

    NCBI Reference Sequences (RefSeq)

    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_009386.1 RefSeqGene

      Range
      5001..55644
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000339.2NP_000330.2  solute carrier family 12 member 3 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC012181, AK315298, BF510426, U44128
      Consensus CDS
      CCDS10770.1
      UniProtKB/Swiss-Prot
      P55017
      Related
      ENSP00000402152.2, OTTHUMP00000164385, ENST00000438926.6, OTTHUMT00000257064
      Conserved Domains (3) summary
      TIGR00930
      Location:591029
      2a30; K-Cl cotransporter
      pfam03522
      Location:6551029
      SLC12; Solute carrier family 12
      pfam08403
      Location:45115
      AA_permease_N; Amino acid permease N-terminal
    2. NM_001126107.1NP_001119579.1  solute carrier family 12 member 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a protein (isoform 2) that is 1 aa shorter than isoform 1.
      Source sequence(s)
      AC012181, AK315298, BF510426, U44128
      Consensus CDS
      CCDS45491.1
      UniProtKB/Swiss-Prot
      P55017
      Related
      ENSP00000457552.1, OTTHUMP00000254444, ENST00000566786.5, OTTHUMT00000432335
      Conserved Domains (3) summary
      TIGR00930
      Location:591028
      2a30; K-Cl cotransporter
      pfam03522
      Location:6541028
      SLC12; Solute carrier family 12
      pfam08403
      Location:45114
      AA_permease_N; Amino acid permease N-terminal
    3. NM_001126108.1NP_001119580.1  solute carrier family 12 member 3 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a protein (isoform 3) that is 9 aa shorter than isoform 1.
      Source sequence(s)
      AC012181, AK315298, BF510426, X91220
      Consensus CDS
      CCDS58464.1
      UniProtKB/Swiss-Prot
      P55017
      Related
      ENSP00000456149.1, OTTHUMP00000254445, ENST00000563236.5, OTTHUMT00000432337
      Conserved Domains (3) summary
      TIGR00930
      Location:591020
      2a30; K-Cl cotransporter
      pfam03522
      Location:6551020
      SLC12; Solute carrier family 12
      pfam08403
      Location:45115
      AA_permease_N; Amino acid permease N-terminal

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

      Range
      56865207..56915850
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005256119.2XP_005256176.1  solute carrier family 12 member 3 isoform X1

      UniProtKB/TrEMBL
      J3QSS1
      Related
      ENSP00000262502.5, OTTHUMP00000254446, ENST00000262502.5, OTTHUMT00000432338
      Conserved Domains (3) summary
      TIGR00930
      Location:591019
      2a30; K-Cl cotransporter
      pfam03522
      Location:6541019
      SLC12; Solute carrier family 12
      pfam08403
      Location:45114
      AA_permease_N; Amino acid permease N-terminal
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