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

Gene ID: 6559, updated on 4-Jun-2020

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
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
109.20200522 current GRCh38.p13 (GCF_000001405.39) 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 Sharpr-MPRA regulatory region 2679 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What'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 PubChem

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 ion transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
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 
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 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 
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_009386.2 RefSeqGene

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

mRNA and Protein(s)

  1. NM_000339.3NP_000330.3  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
    Consensus CDS
    CCDS10770.1
    Related
    ENSP00000402152.2, ENST00000438926.6
  2. NM_001126107.2NP_001119579.2  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
    Consensus CDS
    CCDS45491.1
    Related
    ENSP00000457552.1, ENST00000566786.5
  3. NM_001126108.2NP_001119580.2  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
    Consensus CDS
    CCDS58464.1
    Related
    ENSP00000456149.1, ENST00000563236.5

RefSeqs of Annotated Genomes: Homo sapiens Updated 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_000016.10 Reference GRCh38.p13 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, ENST00000262502.5
    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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