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SLC12A1 solute carrier family 12 member 1 [ Homo sapiens (human) ]

Gene ID: 6557, updated on 13-Feb-2019

Summary

Official Symbol
SLC12A1provided by HGNC
Official Full Name
solute carrier family 12 member 1provided by HGNC
Primary source
HGNC:HGNC:10910
See related
Ensembl:ENSG00000074803 MIM:600839
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
BSC1; NKCC2
Summary
This gene encodes a kidney-specific sodium-potassium-chloride cotransporter that is expressed on the luminal membrane of renal epithelial cells of the thick ascending limb of Henle's loop and the macula densa. It plays a key role in concentrating urine and accounts for most of the NaCl resorption. It is sensitive to such diuretics as furosemide and bumetanide. Some Bartter-like syndromes result from defects in this gene. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional splice variants have been described but their biological validity in humans has not been experimentally proven.[provided by RefSeq, May 2010]
Expression
Restricted expression toward kidney (RPKM 306.7) See more
Orthologs

Genomic context

See SLC12A1 in Genome Data Viewer
Location:
15q21.1
Exon count:
29
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 15 NC_000015.10 (48206301..48304078)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (48498498..48596275)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 24 member 5 Neighboring gene myelin expression factor 2 Neighboring gene uncharacterized LOC105370807 Neighboring gene cortexin 2 Neighboring gene uncharacterized LOC112267905 Neighboring gene uncharacterized LOC107984756 Neighboring gene uncharacterized LOC107984758 Neighboring gene uncharacterized LOC107984755 Neighboring gene uncharacterized LOC107984757 Neighboring gene deoxyuridine triphosphatase

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

Associated conditions

Description Tests
Bartter syndrome, type 1, antenatal
MedGen: C1866495 OMIM: 601678 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC48843

Gene Ontology Provided by GOA

Function Evidence Code Pubs
potassium:chloride symporter activity IBA
Inferred from Biological aspect of Ancestor
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
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 
ion transmembrane transport ISS
Inferred from Sequence or Structural Similarity
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 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 
Component Evidence Code Pubs
apical plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular exosome HDA PubMed 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
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 1
Names
NKCC2A variant A
Na-K-2Cl cotransporter
bumetanide-sensitive sodium-(potassium)-chloride cotransporter 2
kidney-specific Na-K-Cl symporter
solute carrier family 12 (sodium/potassium/chloride transporter), member 1
solute carrier family 12 (sodium/potassium/chloride transporters), member 1

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_021301.1 RefSeqGene

    Range
    5001..102778
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000338.2NP_000329.2  solute carrier family 12 member 1 isoform A

    See identical proteins and their annotated locations for NP_000329.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform A. Isoforms A and F are the same length but differ in the region of amino acids 214-238.
    Source sequence(s)
    AA917702, AC023355, BC040138, DA632985, U58130
    Consensus CDS
    CCDS10129.2
    UniProtKB/Swiss-Prot
    Q13621
    UniProtKB/TrEMBL
    Q8IUN5
    Related
    ENSP00000370381.3, ENST00000380993.7
    Conserved Domains (3) summary
    TIGR00930
    Location:1041099
    2a30; K-Cl cotransporter
    pfam03522
    Location:6941099
    SLC12; Solute carrier family 12
    pfam08403
    Location:90156
    AA_permease_N; Amino acid permease N-terminal
  2. NM_001184832.1NP_001171761.1  solute carrier family 12 member 1 isoform F

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame exon in the 5' coding region, compared to variant 1, and encodes isoform F. Isoforms A and F are the same length but differ in the region of amino acids 214-238.
    Source sequence(s)
    AA917702, AC023355, AK298312, DA632985, U58130
    Consensus CDS
    CCDS53940.1
    UniProtKB/Swiss-Prot
    Q13621
    UniProtKB/TrEMBL
    B4DPF4
    Related
    ENSP00000379822.3, ENST00000396577.7
    Conserved Domains (3) summary
    TIGR00930
    Location:1041099
    2a30; K-Cl cotransporter
    pfam03522
    Location:6941099
    SLC12; Solute carrier family 12
    pfam08403
    Location:90156
    AA_permease_N; Amino acid permease N-terminal

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.p12 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p12 Primary Assembly

    Range
    48206301..48304078
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005254606.2XP_005254663.1  solute carrier family 12 member 1 isoform X1

    Conserved Domains (3) summary
    TIGR00930
    Location:1041099
    2a30; K-Cl cotransporter
    pfam03522
    Location:6941099
    SLC12; Solute carrier family 12
    pfam08403
    Location:90156
    AA_permease_N; Amino acid permease N-terminal
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