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Aliases for CLCNKA Gene

Aliases for CLCNKA Gene

  • Chloride Channel, Voltage-Sensitive Ka 2 3
  • Chloride Channel Ka 2 3 4
  • ClC-K1 3 4
  • Chloride Channel Protein ClC-Ka 3
  • Chloride Channel, Kidney, A 3
  • HClC-Ka 3
  • CLCK1 3

External Ids for CLCNKA Gene

Previous GeneCards Identifiers for CLCNKA Gene

  • GC01U990022
  • GC01P9E0033
  • GC01P015711
  • GC01P016094
  • GC01P016220
  • GC01P016345
  • GC01P014867

Summaries for CLCNKA Gene

Entrez Gene Summary for CLCNKA Gene

  • This gene is a member of the CLC family of voltage-gated chloride channels. The encoded protein is predicted to have 12 transmembrane domains, and requires a beta subunit called barttin to form a functional channel. It is thought to function in salt reabsorption in the kidney and potassium recycling in the inner ear. The gene is highly similar to CLCNKB, which is located 10 kb downstream from this gene. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLCNKA Gene

CLCNKA (Chloride Channel, Voltage-Sensitive Ka) is a Protein Coding gene. Diseases associated with CLCNKA include bartter syndrome, type 4b, digenic and bartter syndrome type 4. Among its related pathways are Activation of cAMP-Dependent PKA and Diuretics Pathway, Pharmacodynamics. GO annotations related to this gene include voltage-gated chloride channel activity and adenyl nucleotide binding. An important paralog of this gene is CLCN7.

UniProtKB/Swiss-Prot for CLCNKA Gene

  • Voltage-gated chloride channel. Chloride channels have several functions including the regulation of cell volume; membrane potential stabilization, signal transduction and transepithelial transport. May be important in urinary concentrating mechanisms

Gene Wiki entry for CLCNKA Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLCNKA Gene

Genomics for CLCNKA Gene

Regulatory Elements for CLCNKA Gene

Genomic Location for CLCNKA Gene

16,018,875 bp from pter
16,034,050 bp from pter
15,176 bases
Plus strand

Genomic View for CLCNKA Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLCNKA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLCNKA Gene

Proteins for CLCNKA Gene

  • Protein details for CLCNKA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Chloride channel protein ClC-Ka
    Protein Accession:
    Secondary Accessions:
    • B4DPD3
    • E7EPH6
    • Q5T5P8
    • Q5T5Q4
    • Q7Z6D1
    • Q86VT1

    Protein attributes for CLCNKA Gene

    687 amino acids
    Molecular mass:
    75285 Da
    Quaternary structure:
    • Homodimer. Interacts with BSND. Forms heteromers with BSND in the thin ascending limb of Henle (By similarity).

    Three dimensional structures from OCA and Proteopedia for CLCNKA Gene

    Alternative splice isoforms for CLCNKA Gene


neXtProt entry for CLCNKA Gene

Proteomics data for CLCNKA Gene at MOPED

Post-translational modifications for CLCNKA Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLCNKA Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for CLCNKA Gene

Domains for CLCNKA Gene

Gene Families for CLCNKA Gene

  • CLCN :Ion channels / Chloride channels : Voltage-sensitive

Suggested Antigen Peptide Sequences for CLCNKA Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • P51800
  • Contains 2 CBS domains.
  • Belongs to the chloride channel (TC 2.A.49) family. CLCNKA subfamily.
genes like me logo Genes that share domains with CLCNKA: view

Function for CLCNKA Gene

Molecular function for CLCNKA Gene

GENATLAS Biochemistry: chloride voltage-gated channel A,kidney specific,highly expressed in the thin ascending limb of Henle loop,involved in the concentration function,putative candidate gene for nephrogenic diabetes insipidus,as in mice;tightly linked to CLCNKB (11kb apart)
UniProtKB/Swiss-Prot Function: Voltage-gated chloride channel. Chloride channels have several functions including the regulation of cell volume; membrane potential stabilization, signal transduction and transepithelial transport. May be important in urinary concentrating mechanisms

Gene Ontology (GO) - Molecular Function for CLCNKA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity --
GO:0005247 voltage-gated chloride channel activity IEA --
GO:0030554 adenyl nucleotide binding --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CLCNKA: view
genes like me logo Genes that share phenotypes with CLCNKA: view

Animal Models for CLCNKA Gene

MGI Knock Outs for CLCNKA:

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for CLCNKA Gene

Localization for CLCNKA Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCNKA Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Jensen Localization Image for CLCNKA Gene COMPARTMENTS Subcellular localization image for CLCNKA gene
Compartment Confidence
plasma membrane 4

Gene Ontology (GO) - Cellular Components for CLCNKA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 8041726
GO:0016020 membrane --
GO:0034707 chloride channel complex IEA --
genes like me logo Genes that share ontologies with CLCNKA: view

Pathways for CLCNKA Gene

genes like me logo Genes that share pathways with CLCNKA: view

Pathways by source for CLCNKA Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Interacting Proteins for CLCNKA Gene

Gene Ontology (GO) - Biological Process for CLCNKA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport TAS 8041726
GO:0006821 chloride transport --
GO:0007588 excretion TAS 8041726
GO:0034220 ion transmembrane transport TAS --
GO:0034765 regulation of ion transmembrane transport --
genes like me logo Genes that share ontologies with CLCNKA: view

Compounds for CLCNKA Gene

(1) HMDB Compounds for CLCNKA Gene

Compound Synonyms Cas Number PubMed IDs
  • Cl2

(1) Drugbank Compounds for CLCNKA Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Niflumic Acid
  • 2-(3-(Trifluoromethyl)-phenyl)aminonicotinic acid
4394-00-7 target inducer

(3) IUPHAR Ligand for CLCNKA Gene

Ligand Type Action Affinity Pubmed IDs
DIDS Channel blocker None
3-phenyl-CPP Channel blocker None
niflumic acid Channel blocker None

(6) Novoseek inferred chemical compound relationships for CLCNKA Gene

Compound -log(P) Hits PubMed IDs
chloride 75.7 9
magnesium 34.3 2
potassium 25.7 2
sodium 23.1 2
nacl 18.3 1
genes like me logo Genes that share compounds with CLCNKA: view

Transcripts for CLCNKA Gene

Unigene Clusters for CLCNKA Gene

Chloride channel, voltage-sensitive Ka:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLCNKA

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLCNKA Gene

No ASD Table

Relevant External Links for CLCNKA Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLCNKA Gene

mRNA expression in normal human tissues for CLCNKA Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLCNKA Gene

This gene is overexpressed in Kidney - Cortex (25.9), Thyroid (6.9), and Pituitary (5.1).

SOURCE GeneReport for Unigene cluster for CLCNKA Gene Hs.591533

mRNA Expression by UniProt/SwissProt for CLCNKA Gene

Tissue specificity: Expressed predominantly in the kidney. All nephron segments expressing BSND also express CLCNK proteins.
genes like me logo Genes that share expressions with CLCNKA: view

In Situ Assay Products

No data available for Protein expression for CLCNKA Gene

Orthologs for CLCNKA Gene

This gene was present in the common ancestor of animals.

Orthologs for CLCNKA Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLCNKA 35
  • 97.72 (n)
  • 96.35 (a)
  • 97 (a)
(Bos Taurus)
Mammalia -- 36
  • 84 (a)
(Canis familiaris)
Mammalia -- 36
  • 87 (a)
(Mus musculus)
Mammalia Clcnka 16
Clcnka 36
  • 83 (a)
Clcnkb 35
  • 82.12 (n)
  • 81.2 (a)
Clcnkb 36
  • 81 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 37 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 60 (a)
(Rattus norvegicus)
Mammalia Clcnkb 35
  • 81.44 (n)
  • 80.47 (a)
(Gallus gallus)
Aves -- 36
  • 61 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 62 (a)
African clawed frog
(Xenopus laevis)
Amphibia clcnka-A 35
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.2959 35
(Danio rerio)
Actinopterygii clcnk 36
  • 42 (a)
fruit fly
(Drosophila melanogaster)
Insecta ClC-a 36
  • 23 (a)
(Caenorhabditis elegans)
Secernentea clh-1 36
  • 23 (a)
clh-2 36
  • 25 (a)
clh-3 36
  • 25 (a)
clh-4 36
  • 22 (a)
Species with no ortholog for CLCNKA:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CLCNKA Gene

Gene Tree for CLCNKA (if available)
Gene Tree for CLCNKA (if available)

Paralogs for CLCNKA Gene

Paralogs for CLCNKA Gene

Selected SIMAP similar genes for CLCNKA Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CLCNKA: view

Variants for CLCNKA Gene

Sequence variations from dbSNP and Humsavar for CLCNKA Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs883867 -- 16,031,590(-) AGCAG(C/G/T)GCTGG intron-variant
rs945425 -- 16,021,917(+) CTCCA(C/T)GGTAA upstream-variant-2KB
rs1010069 -- 16,026,442(-) ATCTC(C/T)CCAAC intron-variant
rs1537803 -- 16,023,767(-) TATGT(C/T)GGGGC intron-variant
rs1805152 - 16,030,006(+) CCGTC(A/G)CCTTC missense, reference

Structural Variations from Database of Genomic Variants (DGV) for CLCNKA Gene

Variant ID Type Subtype PubMed ID
nsv871162 CNV Gain 21882294
nsv508936 CNV Insertion 20534489
dgv174n71 CNV Loss 21882294
nsv833758 CNV Gain+Loss 17160897
nsv871695 CNV Loss 21882294
nsv517651 CNV Gain+Loss 19592680
dgv175n71 CNV Gain 21882294
dgv176n71 CNV Loss 21882294
nsv520148 CNV Loss 19592680
nsv871485 CNV Loss 21882294
nsv524045 CNV Loss 19592680
dgv12n27 CNV Loss 19166990
nsv460629 CNV Gain 19166990
nsv470698 CNV Loss 18288195
dgv13n27 CNV Gain 19166990
nsv870526 CNV Loss 21882294
esv25815 CNV Gain 19812545
esv2744364 CNV Deletion 23290073
dgv2n64 CNV Gain 17921354
esv8597 CNV Loss 19470904
esv2674711 CNV Deletion 23128226
esv2665318 CNV Deletion 23128226
dgv177n71 CNV Loss 21882294
nsv829570 CNV Gain 20364138

Relevant External Links for CLCNKA Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLCNKA Gene

Disorders for CLCNKA Gene

(1) OMIM Diseases for CLCNKA Gene (602024)


  • Bartter syndrome 4B (BS4B) [MIM:613090]: A digenic, recessive disorder characterized by impaired salt reabsorption in the thick ascending loop of Henle with pronounced salt wasting, hypokalemic metabolic alkalosis, and varying degrees of hypercalciuria. Bartter syndrome type 4B is associated with sensorineural deafness. {ECO:0000269 PubMed:15044642, ECO:0000269 PubMed:18310267}. Note=The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry. Loss-of-function of both CLCNKA and CLCNKB results in the disease phenotype (PubMed:18310267). {ECO:0000269 PubMed:18310267}.

(3) University of Copenhagen DISEASES for CLCNKA Gene

Relevant External Links for CLCNKA

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with CLCNKA: view

Publications for CLCNKA Gene

  1. Two highly homologous members of the ClC chloride channel family in both rat and human kidney. (PMID: 8041726) Kieferle S. … Jentsch T. (Proc. Natl. Acad. Sci. U.S.A. 1994) 3 4 23
  2. Cloning, tissue distribution, and intrarenal localization of ClC chloride channels in human kidney. (PMID: 8544406) Takeuchi Y. … Sasaki S. (Kidney Int. 1995) 2 3 23
  3. Common genetic variants and haplotypes in renal CLCNKA gene are associated to salt-sensitive hypertension. (PMID: 17510212) Barlassina C. … Cusi D. (Hum. Mol. Genet. 2007) 3 23 48
  4. Haplotype diversity in four genes (CLCNKA, CLCNKB, BSND, NEDD4L) involved in renal salt reabsorption. (PMID: 17652939) Sile S. … Williams S.M. (Hum. Hered. 2008) 3 23 48
  5. Mechanisms of Disease: the kidney-specific chloride channels ClCKA and ClCKB, the Barttin subunit, and their clinical relevance. (PMID: 18094726) KrAomer B.K. … Waldegger S. (Nat Clin Pract Nephrol 2008) 3 23

Products for CLCNKA Gene

  • antibodies-online peptides for CLCNKA
  • antibodies-online antibodies for CLCNKA
  • antibodies-online kits for CLCNKA

Sources for CLCNKA Gene

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