Human Gene SLC12A3 (ENST00000563236.6_7) from GENCODE V47lift37
  Description: solute carrier family 12 member 3, transcript variant 3 (from RefSeq NM_001126108.2)
Gencode Transcript: ENST00000563236.6_7
Gencode Gene: ENSG00000070915.10_16
Transcript (Including UTRs)
   Position: hg19 chr16:56,899,119-56,949,762 Size: 50,644 Total Exon Count: 26 Strand: +
Coding Region
   Position: hg19 chr16:56,899,148-56,947,317 Size: 48,170 Coding Exon Count: 26 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:56,899,119-56,949,762)mRNA (may differ from genome)Protein (1021 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: S12A3_HUMAN
DESCRIPTION: RecName: Full=Solute carrier family 12 member 3; AltName: Full=Na-Cl cotransporter; Short=NCC; AltName: Full=Na-Cl symporter; AltName: Full=Thiazide-sensitive sodium-chloride cotransporter;
FUNCTION: Key mediator of sodium and chloride reabsorption in this nephron segment, accounting for a significant fraction of renal sodium reabsorption.
ENZYME REGULATION: Activated by WNK3.
SUBUNIT: Interacts with KLHL3.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Predominant in kidney.
PTM: Ubiquitinated; ubiquitination is essential for regulation of endocytosis (By similarity). May be ubiquitinated by the BCR(KLHL3) complex.
DISEASE: Defects in SLC12A3 are the cause of Gitelman syndrome (GS) [MIM:263800]. GS is an autosomal recessive disorder characterized by hypokalemic alkalosis in combination with hypomagnesemia, low urinary calcium, and increased renin activity associated with normal blood pressure. Patients are often asymptomatic or present transient periods of muscular weakness and tetany, usually accompanied by abdominal pain, vomiting and fever. The phenotype is highly heterogeneous in terms of age at onset and severity. Cardinal features such as hypocalciuria and hypomagnesemia might also change during the life cycle of a given patient. GS has overlapping features with Bartter syndrome.
MISCELLANEOUS: Target of thiazide diuretics used in the treatment of high blood pressure (PubMed:8528245).
SIMILARITY: Belongs to the SLC12A transporter family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SLC12A3";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SLC12A3
Diseases sorted by gene-association score: gitelman syndrome* (1726), hypokalemia (38), chondrocalcinosis (24), bartter syndrome, type 3 (20), renal tubular transport disease (14), bartter disease (12), pseudohypoaldosteronism (12), arthrogryposis, distal, type 3 (10), ureterolithiasis (10), basilar artery occlusion (8), intracranial hypertension (8), dent disease (6), sesame syndrome (6), mineral metabolism disease (6), renal hypertension (5), pendred syndrome (5), hypertension, essential (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 32.22 RPKM in Kidney - Cortex
Total median expression: 33.58 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -8.8029-0.303 Picture PostScript Text
3' UTR -827.502445-0.338 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004841 - AA-permease_dom
IPR013612 - AA_permease_N
IPR004842 - Na/K/Cl_cotransptS
IPR002948 - NaCl_cotranspt

Pfam Domains:
PF00324 - Amino acid permease
PF03522 - Solute carrier family 12
PF08403 - Amino acid permease N-terminal

ModBase Predicted Comparative 3D Structure on P55017
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005215 transporter activity
GO:0005515 protein binding
GO:0015293 symporter activity
GO:0015377 cation:chloride symporter activity
GO:0015378 sodium:chloride symporter activity

Biological Process:
GO:0006811 ion transport
GO:0006814 sodium ion transport
GO:0035725 sodium ion transmembrane transport
GO:0055085 transmembrane transport
GO:1902476 chloride transmembrane transport

Cellular Component:
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016324 apical plasma membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK315298 - Homo sapiens cDNA, FLJ96318.
AK223133 - Homo sapiens mRNA, solute carrier family 12 (sodium/chloride transporters), member 3 variant, clone: KDN02262.
X91220 - H.sapiens mRNA for Na-Cl electroneutral thiazide-sensitive cotransporter.
U44128 - Human thiazide-sensitive Na-Cl cotransporter (hTSC) mRNA, complete cds.
AB463268 - Synthetic construct DNA, clone: pF1KB7293, Homo sapiens SLC12A3 gene for solute carrier family 12 (sodium/chloride transporters), member 3, without stop codon, in Flexi system.
BC111850 - Synthetic construct Homo sapiens clone IMAGE:40080836, MGC:133390 SLC12A3 protein (SLC12A3) mRNA, encodes complete protein.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P55017 (Reactome details) participates in the following event(s):

R-HSA-426130 SLC12A3 cotransports Cl-, Na+ from extracellular region to cytosol
R-HSA-426117 Cation-coupled Chloride cotransporters
R-HSA-425393 Metabolism of nitrogenous molecules
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: A8MSJ2, C9JNN9, ENST00000563236.1, ENST00000563236.2, ENST00000563236.3, ENST00000563236.4, ENST00000563236.5, NCC , NM_001126108, P55017, S12A3_HUMAN, SLC12A3 , TSC, uc325rsm.1, uc325rsm.2
UCSC ID: ENST00000563236.6_7
RefSeq Accession: NM_001126108.2
Protein: P55017 (aka S12A3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.