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

    Gene ID: 6558, updated on 27-Nov-2024

    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; AllianceGenome:HGNC:10911
    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; CCC1; BSC-2; KILQS; NKCC1; hNKCC1; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC12A2 in Genome Data Viewer
    Location:
    5q23.3
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (128083766..128189677)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (128602602..128708515)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (127419458..127525369)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 192 Neighboring gene uncharacterized LOC124901059 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:127270427-127271080 Neighboring gene SLC12A2 divergent transcript Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:127344859-127345557 Neighboring gene MPRA-validated peak5458 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23037 Neighboring gene POGLUT2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16296 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:127680731-127681930 Neighboring gene fibrillin 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:127772173-127773372 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:127871608-127872538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:127874264-127874764 Neighboring gene Sharpr-MPRA regulatory region 657 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 Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Delpire-McNeill syndrome
    MedGen: C5436771 OMIM: 619083 GeneReviews: Not available
    not available
    Hearing loss, autosomal dominant 78
    MedGen: C5436768 OMIM: 619081 GeneReviews: Not available
    not available
    Kilquist syndrome
    MedGen: C5436756 OMIM: 619080 GeneReviews: Not available
    not available

    EBI GWAS Catalog

    Description
    A genome-wide association study of schizophrenia using brain activation as a quantitative phenotype.
    EBI GWAS 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.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC104233

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables Hsp90 protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ammonium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ammonium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chloride:monoatomic cation symporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metal ion transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables potassium ion transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-folding chaperone binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sodium:potassium:chloride symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables sodium:potassium:chloride symporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sodium:potassium:chloride symporter activity TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    involved_in T cell chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ammonium transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ammonium transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell volume homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within cell volume homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell volume homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of cell volume homeostasis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cellular response to chemokine IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to potassium ion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in chloride ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in chloride transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in chloride transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in chloride transmembrane transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within gamma-aminobutyric acid signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in hyperosmotic response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inorganic anion import across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inorganic cation import across plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within intracellular chloride ion homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within intracellular chloride ion homeostasis TAS
    Traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within intracellular potassium ion homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within intracellular sodium ion homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within maintenance of blood-brain barrier ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of maintenance of blood-brain barrier TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in monoatomic ion transport TAS
    Traceable Author Statement
    more info
     
    acts_upstream_of_or_within negative regulation of vascular wound healing ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within positive regulation of aspartate secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell volume IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in potassium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in potassium ion import across plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in potassium ion import across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within regulation of matrix metallopeptidase secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within regulation of spontaneous synaptic transmission ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in sodium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sodium ion import across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sodium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in transepithelial ammonium transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in transepithelial chloride transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in apical plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in basal plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in basolateral plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell body membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in cell periphery IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell periphery ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in cell projection ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell projection membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in cytoplasmic vesicle membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in extracellular vesicle HDA PubMed 
    located_in lateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    located_in neuron projection IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuronal cell body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    solute carrier family 12 member 2
    Names
    Na-K-2Cl cotransporter 1
    basolateral Na-K-Cl symporter
    bumetanide-sensitive cotransporter type 2
    bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1
    bumetanide-sensitive sodium-(potassium)-chloride cotransporter 2
    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)

    NEW Try the new Transcript table

    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
      4976..110887
      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, Q8N713, Q8WWH7
      UniProtKB/TrEMBL
      B7ZM24, Q53ZR1
      Related
      ENSP00000262461.2, ENST00000262461.7
      Conserved Domains (1) summary
      TIGR00930
      Location:2161212
      2a30; K-Cl cotransporter
    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
      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_046207.2 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: 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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      128083766..128189677
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417591.1XP_047273547.1  solute carrier family 12 member 2 isoform X1

      Related
      ENSP00000486323.1, ENST00000628403.2
    2. XM_011543588.3XP_011541890.1  solute carrier family 12 member 2 isoform X2

      Conserved Domains (1) summary
      pfam08403
      Location:202263
      AA_permease_N; Amino acid permease N-terminal
    3. XM_047417592.1XP_047273548.1  solute carrier family 12 member 2 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      128602602..128708515
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353244.1XP_054209219.1  solute carrier family 12 member 2 isoform X1

    2. XM_054353245.1XP_054209220.1  solute carrier family 12 member 2 isoform X2

    3. XM_054353246.1XP_054209221.1  solute carrier family 12 member 2 isoform X3