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Aliases for CLCNKA Gene

Aliases for CLCNKA Gene

  • Chloride Voltage-Gated Channel Ka 2 3 5
  • Chloride Channel Ka 2 3 4
  • Chloride Channel, Voltage-Sensitive Ka 2 3
  • 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 Voltage-Gated Channel Ka) is a Protein Coding gene. Diseases associated with CLCNKA include Bartter Syndrome, Type 4B, Digenic and Bartter Syndrome, Type 4A. Among its related pathways are Hepatic ABC Transporters and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. GO annotations related to this gene include ion channel activity and voltage-gated chloride channel activity. An important paralog of this gene is CLCNKB.

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

Additional gene information for CLCNKA Gene

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

Genomics for CLCNKA Gene

Regulatory Elements for CLCNKA Gene

Enhancers for CLCNKA Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H016012 1.9 FANTOM5 Ensembl ENCODE dbSUPER 28 -1.8 -1840 9.7 HDGF PKNOX1 ARNT ZFP64 ARID4B ZNF766 ZNF207 ZNF143 FOS SP5 HSPB7 CLCNKA ENSG00000237938 CROCCP3 ARHGEF19 RPS16P1 CROCC SPEN CASP9 ENSG00000224621
GH01H015791 2 FANTOM5 Ensembl ENCODE dbSUPER 25.6 -221.4 -221373 11.3 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 MEF2D GLIS1 RCOR2 CLCNKA FAM231A HSPB7 FBLIM1 ENSG00000237938 RPS16P1 CD24P1 RNU1-1 SPEN ZBTB17
GH01H015961 1.8 FANTOM5 Ensembl ENCODE dbSUPER 18.6 -54.3 -54279 5.8 HDGF PKNOX1 TBL1XR1 RB1 BMI1 YBX1 BATF ZNF121 ZNF143 FOS CLCNKA PLEKHM2 ZBTB17 CROCC CLCNKB CASP9 SZRD1 SPEN ENSG00000234607 GC01P015946
GH01H015829 2 FANTOM5 Ensembl ENCODE dbSUPER 15.1 -184.9 -184875 9.6 MLX FEZF1 DMAP1 YY1 ZNF143 SP3 NFYC ZC3H11A PPARGC1A MEF2D ZBTB17 FAM231A SPEN ENSG00000237938 CROCC CLCNKA NECAP2 CD24P1 RNU1-1 FLJ37453
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLCNKA on UCSC Golden Path with GeneCards custom track

Genomic Locations for CLCNKA Gene

Genomic Locations for CLCNKA Gene
15,176 bases
Plus strand

Genomic View for CLCNKA Gene

Genes around CLCNKA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLCNKA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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 (PubMed:17562318). 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

Post-translational modifications for CLCNKA Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLCNKA Gene

No data available for DME Specific Peptides for CLCNKA Gene

Domains & Families for CLCNKA Gene

Gene Families for CLCNKA Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for CLCNKA Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the chloride channel (TC 2.A.49) family. CLCNKA subfamily.
  • 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 EnzymeRegulation:
Activated by extracellular calcium and inhibited by extracellular protons.
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.

Phenotypes From GWAS Catalog for CLCNKA Gene

Gene Ontology (GO) - Molecular Function for CLCNKA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005244 voltage-gated ion channel activity IEA --
GO:0005247 voltage-gated chloride channel activity TAS,IBA --
GO:0005254 chloride channel activity IEA --
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

Human Phenotype Ontology for CLCNKA Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets 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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLCNKA gene
Compartment Confidence
plasma membrane 5
extracellular 1

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 IEA --
GO:0016021 integral component of membrane IEA --
GO:0034707 chloride channel complex IEA --
genes like me logo Genes that share ontologies with CLCNKA: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLCNKA Gene

Pathways & Interactions for CLCNKA Gene

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

Pathways by source 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:0006811 ion transport IEA --
GO:0006821 chloride transport IEA --
GO:0007588 excretion TAS 8041726
GO:0034220 ion transmembrane transport TAS --
genes like me logo Genes that share ontologies with CLCNKA: view

No data available for SIGNOR curated interactions for CLCNKA Gene

Drugs & Compounds for CLCNKA Gene

(6) Drugs for CLCNKA Gene - From: DrugBank, DGIdb, IUPHAR, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Niflumic Acid Approved Pharma Channel blocker, inhibitor, Target, inducer Ca2+-activated Cl- channel blocker 0
3-phenyl-CPP Pharma Channel blocker 0
DIDS Pharma Channel blocker 0

(4) Additional Compounds for CLCNKA Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Chloride ion
  • Bertholite
  • Chloor
  • Chlor
  • Chlore
  • Chloride
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

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 (x25.9), Thyroid (x6.9), and Pituitary (x5.1).

NURSA nuclear receptor signaling pathways regulating expression of CLCNKA Gene:


SOURCE GeneReport for Unigene cluster for CLCNKA Gene:


mRNA Expression by UniProt/SwissProt for CLCNKA Gene:

Tissue specificity: Expressed predominantly in the kidney. All nephron segments expressing BSND also express CLCNK proteins.

Evidence on tissue expression from TISSUES for CLCNKA Gene

  • Kidney(4.6)
  • Intestine(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CLCNKA Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • ear
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • pituitary gland
  • skull
  • chest wall
  • clavicle
  • diaphragm
  • esophagus
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • stomach
  • pelvis
  • placenta
  • rectum
  • ureter
  • urinary bladder
  • uterus
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with CLCNKA: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners 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 33 34
  • 97.72 (n)
(Canis familiaris)
Mammalia -- 34
  • 87 (a)
(Bos Taurus)
Mammalia -- 34
  • 84 (a)
(Mus musculus)
Mammalia Clcnka 34
  • 83 (a)
Clcnkb 33 16 34
  • 82.12 (n)
(Rattus norvegicus)
Mammalia Clcnkb 33
  • 81.44 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 60 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 37 (a)
(Gallus gallus)
Aves -- 34
  • 61 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 62 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.2959 33
African clawed frog
(Xenopus laevis)
Amphibia clcnka-A 33
(Danio rerio)
Actinopterygii clcnk 34
  • 42 (a)
fruit fly
(Drosophila melanogaster)
Insecta ClC-a 34
  • 23 (a)
(Caenorhabditis elegans)
Secernentea clh-2 34
  • 25 (a)
clh-3 34
  • 25 (a)
clh-1 34
  • 23 (a)
clh-4 34
  • 22 (a)
Species where no ortholog for CLCNKA was found in the sources mined by GeneCards:
  • 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

(3) 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
rs121909137 Pathogenic, Bartter syndrome 4B, neonatal, with sensorineural deafness (BARTS4B) [MIM:613090] 16,024,773(+) CAGTG(C/G)CTGTA intron-variant, reference, missense
rs121909138 Pathogenic 16,027,432(+) GCGAG(C/T)AGGGT reference, stop-gained
rs373577135 Uncertain significance 16,022,693(+) CCCCT(A/G)TCCCC reference, missense
rs387907405 Uncertain significance 16,029,219(+) AGCTC(G/T)ACCCC reference, missense
rs387907406 Uncertain significance 16,027,407(+) TTCCG(C/G)CTCCT reference, synonymous-codon

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

Variant ID Type Subtype PubMed ID
nsv997887 CNV gain 25217958
nsv954844 CNV deletion 24416366
nsv833758 CNV gain+loss 17160897
nsv829570 CNV gain 20364138
nsv545635 CNV loss 21841781
nsv545634 CNV gain 21841781
nsv545628 CNV gain+loss 21841781
nsv545627 CNV loss 21841781
nsv524045 CNV loss 19592680
nsv520148 CNV loss 19592680
nsv517651 CNV gain+loss 19592680
nsv508936 CNV insertion 20534489
nsv473735 CNV novel sequence insertion 20440878
nsv470698 CNV loss 18288195
nsv460629 CNV gain 19166990
nsv1161228 CNV duplication 26073780
esv8597 CNV loss 19470904
esv3585328 CNV loss 21293372
esv2760188 CNV gain+loss 21179565
esv2744364 CNV deletion 23290073
esv2674711 CNV deletion 23128226
esv2665318 CNV deletion 23128226
esv25815 CNV gain 19812545
dgv2n64 CNV gain 17921354
dgv156n54 CNV gain 21841781
dgv155n54 CNV gain 21841781
dgv13n27 CNV gain 19166990
dgv12n27 CNV loss 19166990
dgv10e214 CNV gain 21293372

Variation tolerance for CLCNKA Gene

Residual Variation Intolerance Score: 88.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.69; 78.55% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLCNKA Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for CLCNKA Gene

MalaCards: The human disease database

(9) MalaCards diseases for CLCNKA Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
bartter syndrome, type 4b, digenic
  • bartter disease type 4b
bartter syndrome, type 4a
  • sensorineural deafness with mild renal dysfunction
diabetes insipidus
deafness, autosomal recessive 96
  • autosomal recessive nonsyndromic deafness 96
deafness, autosomal recessive 36
  • autosomal recessive nonsyndromic deafness 36
- elite association - COSMIC cancer census association via MalaCards


  • Bartter syndrome 4B, neonatal, with sensorineural deafness (BARTS4B) [MIM:613090]: A digenic form of Bartter syndrome, an autosomal 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. BARTS4B 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}.

Relevant External Links for CLCNKA

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CLCNKA: view

No data available for Genatlas for CLCNKA Gene

Publications for CLCNKA Gene

  1. Haplotype diversity in four genes (CLCNKA, CLCNKB, BSND, NEDD4L) involved in renal salt reabsorption. (PMID: 17652939) Sile S … Williams SM (Human heredity 2008) 3 22 45 60
  2. Common genetic variants and haplotypes in renal CLCNKA gene are associated to salt-sensitive hypertension. (PMID: 17510212) Barlassina C … Cusi D (Human molecular genetics 2007) 3 22 45 60
  3. Cloning, tissue distribution, and intrarenal localization of ClC chloride channels in human kidney. (PMID: 8544406) Takeuchi Y … Sasaki S (Kidney international 1995) 2 3 22 60
  4. Two highly homologous members of the ClC chloride channel family in both rat and human kidney. (PMID: 8041726) Kieferle S … Jentsch TJ (Proceedings of the National Academy of Sciences of the United States of America 1994) 3 4 22 60
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 45 60

Products for CLCNKA Gene

Sources for CLCNKA Gene

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