Human Gene CLCN5 (ENST00000482218.2) from GENCODE V44
  Description: Homo sapiens chloride voltage-gated channel 5 (CLCN5), transcript variant 5, mRNA. (from RefSeq NM_001272102)
RefSeq Summary (NM_001272102): This gene encodes a member of the ClC family of chloride ion channels and ion transporters. The encoded protein is primarily localized to endosomal membranes and may function to facilitate albumin uptake by the renal proximal tubule. Mutations in this gene have been found in Dent disease and renal tubular disorders complicated by nephrolithiasis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013].
Gencode Transcript: ENST00000482218.2
Gencode Gene: ENSG00000171365.17
Transcript (Including UTRs)
   Position: hg38 chrX:49,923,404-50,042,541 Size: 119,138 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg38 chrX:49,925,299-50,042,494 Size: 117,196 Coding Exon Count: 2 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsOther NamesGeneReviews
Data last updated at UCSC: 2023-08-18 09:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chrX:49,923,404-50,042,541)mRNA (may differ from genome)Protein (64 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  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: CLCN5
Diseases sorted by gene-association score: dent disease* (1724), hypophosphatemic rickets* (1348), proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis* (1300), nephrolithiasis, type i* (900), nephrolithiasis (58), nephrocalcinosis (42), rickets (23), renal tubular transport disease (19), aminoaciduria (16), fanconi syndrome (12), nephrolithiasis, calcium oxalate (11), lowe syndrome (10), hypercalciuria, absorptive (10), bartter disease (9), hypophosphatemia (8), mineral metabolism disease (5), idiopathic hypercalciuria (4)
* = Manually curated disease association

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.80 RPKM in Kidney - Cortex
Total median expression: 88.56 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 -64.70207-0.313 Picture PostScript Text
3' UTR -1.6047-0.034 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.

-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Descriptions from all associated GenBank mRNAs
  AK092049 - Homo sapiens cDNA FLJ34730 fis, clone MESAN2006580, highly similar to Chloride channel protein 5.
AK056560 - Homo sapiens cDNA FLJ31998 fis, clone NT2RP7009322, highly similar to CHLORIDE CHANNEL PROTEIN 5.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000482218.1, NM_001272102, uc064zgc.1, V9GYG7
UCSC ID: ENST00000482218.2
RefSeq Accession: NM_001272102
CCDS: CCDS69763.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CLCN5:
dent (Dent Disease)

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