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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, Neonatal, With Sensorineural Deafness and Infantile Bartter Syndrome With Sensorineural Deafness. Among its related pathways are Activation of cAMP-Dependent PKA and Diuretics Pathway, Pharmacodynamics. Gene Ontology (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

GeneHancer (GH) Regulatory Elements for CLCNKA Gene

Promoters and enhancers for CLCNKA Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I016012 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 578 -1.8 -1839 9.7 HDGF PKNOX1 ARNT ZFP64 ARID4B ZNF766 ZNF207 ZNF143 FOS SP5 HSPB7 CLCNKA CROCCP3 CROCC CASP9 LINC01772 CLCNKB PLEKHM2 ZBTB17 RPS16P1
GH01I016021 Promoter/Enhancer 0.7 EPDnew dbSUPER 550.8 +3.1 3142 0.1 CLCNKA HSPB7 LOC440568
GH01I015791 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 25.6 -221.4 -221372 11.3 CLOCK MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF263 CLCNKA HSPB7 FBLIM1 ENSG00000237938 RPS16P1 SPEN ZBTB17 ENSG00000233078 FAM131C ARHGEF19-AS1
GH01I015846 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 15.9 -169.2 -169176 6.4 CLOCK FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 MEF2D SPEN FLJ37453 ENSG00000237938 ZBTB17 ARHGEF19 HSPB7 CLCNKA NECAP2 RPS16P1 RPL22P3
GH01I016048 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 22.7 +29.8 29802 1.1 HDAC1 PKNOX1 NFRKB KLF17 ZBTB40 ZNF335 EGR1 SCRT2 ATF7 SP3 CLCNKB CLCNKA HSPB7 ENSG00000233078 FAM131C CROCCP2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CLCNKA on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLCNKA gene promoter:

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:0042802 identical protein binding IPI 17562318
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, Target, inducer, inhibitor 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: Novoseek and HMDB

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

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 Variation AA Info Type
rs121909137 pathogenic, Bartter syndrome, type 4b, Bartter syndrome 4B, neonatal, with sensorineural deafness (BARTS4B) [MIM:613090] 16,024,773(+) G/C/T coding_sequence_variant, intron_variant, missense_variant
rs121909138 pathogenic, Bartter syndrome, type 4b 16,027,432(+) C/T coding_sequence_variant, stop_gained
rs143389794 likely-benign, not specified 16,030,552(+) C/G/T coding_sequence_variant, synonymous_variant
rs528421254 likely-benign, not specified 16,033,179(+) C/T coding_sequence_variant, missense_variant
rs373577135 uncertain-significance, not provided 16,022,693(+) G/A/T coding_sequence_variant, missense_variant

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

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

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)

Additional Variant Information 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, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- 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}.

Additional Disease Information for CLCNKA

Genetic Association Database
Human Genome Epidemiology 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 44 58
  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 44 58
  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 58
  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 58
  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 44 58

Products for CLCNKA Gene

Sources for CLCNKA Gene

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