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    SLC12A2 solute carrier family 12 member 2 [ Homo sapiens (human) ]

    Gene ID: 6558, updated on 18-Jun-2019

    Summary

    Official Symbol
    SLC12A2provided by HGNC
    Official Full Name
    solute carrier family 12 member 2provided by HGNC
    Primary source
    HGNC:HGNC:10911
    See related
    Ensembl:ENSG00000064651 MIM:600840
    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
    BSC; BSC2; NKCC1; PPP1R141
    Summary
    The protein encoded by this gene mediates sodium and chloride transport and reabsorption. The encoded protein is a membrane protein and is important in maintaining proper ionic balance and cell volume. This protein is phosphorylated in response to DNA damage. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
    Expression
    Broad expression in colon (RPKM 25.6), stomach (RPKM 18.8) and 22 other tissues See more
    Orthologs

    Genomic context

    See SLC12A2 in Genome Data Viewer
    Location:
    5q23.3
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (128083766..128189688)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (127419483..127525380)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 192 Neighboring gene cullin 1 pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 1184 Neighboring gene uncharacterized LOC101929964 Neighboring gene KDEL motif containing 1 pseudogene 1 Neighboring gene fibrillin 2 Neighboring gene uncharacterized LOC105379167

    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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    A genome-wide association study of schizophrenia using brain activation as a quantitative phenotype.
    NHGRI GWA Catalog
    A pilot genome-wide association study shows genomic variants enriched in the non-tumor cells of patients with well-differentiated neuroendocrine tumors of the ileum.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Cation-coupled Chloride cotransporters, organism-specific biosystem (from REACTOME)
      Cation-coupled Chloride cotransporters, organism-specific biosystemThe cation-chloride cotransporter family (SLC12 gene family) are membrane proteins that cotranslocate chloride (Cl-) with either Na+, K+, or both cations electroneutrally. The general topology of the...
    • Pancreatic secretion, organism-specific biosystem (from KEGG)
      Pancreatic secretion, organism-specific biosystemThe pancreas performs both exocrine and endocrine functions. The exocrine pancreas consists of two parts, the acinar and duct cells. The primary functions of pancreatic acinar cells are to synthesiz...
    • Pancreatic secretion, conserved biosystem (from KEGG)
      Pancreatic secretion, conserved biosystemThe pancreas performs both exocrine and endocrine functions. The exocrine pancreas consists of two parts, the acinar and duct cells. The primary functions of pancreatic acinar cells are to synthesiz...
    • SLC-mediated transmembrane transport, organism-specific biosystem (from REACTOME)
      SLC-mediated transmembrane transport, organism-specific biosystemProteins with transporting functions can be roughly classified into 3 categories: ATP-powered pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the m...
    • Salivary secretion, organism-specific biosystem (from KEGG)
      Salivary secretion, organism-specific biosystemSaliva has manifold functions in maintaining the integrity of the oral tissues, in protecting teeth from caries, in the tasting and ingestion of food, in speech and in the tolerance of tenures, for e...
    • Salivary secretion, conserved biosystem (from KEGG)
      Salivary secretion, conserved biosystemSaliva has manifold functions in maintaining the integrity of the oral tissues, in protecting teeth from caries, in the tasting and ingestion of food, in speech and in the tolerance of tenures, for e...
    • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
      Transmembrane transport of small molecules, organism-specific biosystem
      Transmembrane transport of small molecules
    • Transport of inorganic cations/anions and amino acids/oligopeptides, organism-specific biosystem (from REACTOME)
      Transport of inorganic cations/anions and amino acids/oligopeptides, organism-specific biosystemTeleologically, one might argue that inorganic cation and anion transport would be evolutionarily among the oldest transport functions. Eight families comprise the group that transports exclusively i...
    • Vibrio cholerae infection, organism-specific biosystem (from KEGG)
      Vibrio cholerae infection, organism-specific biosystemCholera toxin (CTX) is one of the main virulence factors of Vibrio cholerae. Once secreted, CTX B-chain (CTXB) binds to ganglioside GM1 on the surface of the host's cells. After binding takes place, ...
    • Vibrio cholerae infection, conserved biosystem (from KEGG)
      Vibrio cholerae infection, conserved biosystemCholera toxin (CTX) is one of the main virulence factors of Vibrio cholerae. Once secreted, CTX B-chain (CTXB) binds to ganglioside GM1 on the surface of the host's cells. After binding takes place, ...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC104233

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ammonium transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    ammonium transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    potassium:chloride symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase 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:potassium:chloride symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    T cell chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    aging IEA
    Inferred from Electronic Annotation
    more info
     
    ammonium transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    ammonium transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    ammonium transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell volume homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cellular response to chemokine IMP
    Inferred from Mutant Phenotype
    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 
    gamma-aminobutyric acid signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    hyperosmotic response IEA
    Inferred from Electronic Annotation
    more info
     
    ion transport TAS
    Traceable Author Statement
    more info
     
    positive regulation of cell volume IEA
    Inferred from Electronic Annotation
    more info
     
    potassium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    potassium ion import across plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sodium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sodium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    transepithelial ammonium transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transepithelial chloride transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    apical plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular exosome HDA PubMed 
    extracellular vesicle HDA 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 2
    Names
    basolateral Na-K-Cl symporter
    bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1
    protein phosphatase 1, regulatory subunit 141
    solute carrier family 12 (sodium/potassium/chloride transporter), member 2
    solute carrier family 12 (sodium/potassium/chloride transporters), member 2

    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_042286.1 RefSeqGene

      Range
      5001..110898
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001046.3NP_001037.1  solute carrier family 12 member 2 isoform 1

      See identical proteins and their annotated locations for NP_001037.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AA425438, AA425619, AA843086, AC011332, AK025062, AV708692, AY280459, BC033003, BM978607, U30246
      Consensus CDS
      CCDS4144.1
      UniProtKB/Swiss-Prot
      P55011
      UniProtKB/TrEMBL
      Q53ZR1
      Related
      ENSP00000262461.2, ENST00000262461.7
      Conserved Domains (3) summary
      TIGR00930
      Location:2161212
      2a30; K-Cl cotransporter
      pfam03522
      Location:8011212
      SLC12; Solute carrier family 12
      pfam08403
      Location:202263
      AA_permease_N; Amino acid permease N-terminal
    2. NM_001256461.2NP_001243390.1  solute carrier family 12 member 2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC008577, AC011332, AI493213, AY280459, BC144221
      Consensus CDS
      CCDS58965.1
      UniProtKB/TrEMBL
      B7ZM24, Q53ZR1
      Related
      ENSP00000340878.4, ENST00000343225.4
      Conserved Domains (3) summary
      TIGR00930
      Location:2161196
      2a30; K-Cl cotransporter
      pfam03522
      Location:8011196
      SLC12; Solute carrier family 12
      pfam08403
      Location:202263
      AA_permease_N; Amino acid permease N-terminal

    RNA

    1. NR_046207.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice junction in the 3' end that truncates the coding sequence compared to variant 1. The resulting transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is therefore thought not to be proten-coding.
      Source sequence(s)
      AC008577, AC011332, AI493213, AY280459, BC033003

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

      Range
      128083766..128189688
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011543588.2XP_011541890.1  solute carrier family 12 member 2 isoform X1

      Conserved Domains (1) summary
      pfam08403
      Location:202263
      AA_permease_N; Amino acid permease N-terminal
    2. XM_017009771.1XP_016865260.1  solute carrier family 12 member 2 isoform X2

    RNA

    1. XR_001742214.1 RNA Sequence

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