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

Gene ID: 6558, updated on 17-Sep-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; 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
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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 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
Compare labs
Hearing loss, autosomal dominant 78
MedGen: C5436768 OMIM: 619081 GeneReviews: Not available
Compare labs
Kilquist syndrome
MedGen: C5436756 OMIM: 619080 GeneReviews: Not available
Compare labs

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
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)

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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_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

    UniProtKB/TrEMBL
    G3XAL9
    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

    UniProtKB/TrEMBL
    G3XAL9
  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