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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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CLCNKA
chloride voltage-gated channel Ka
Chromosome 1 Β· 1p36.13
NCBI Gene: 1187Ensembl: ENSG00000186510.13HGNC: HGNC:2026UniProt: P51800
33PubMed Papers
21Diseases
0Drugs
5Pathogenic Variants
FUNCTIONAL ROLE
Ion ChannelTransporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
chloride channel activityidentical protein bindingprotein bindingvoltage-gated chloride channel activityBartter syndromeheart failuresystolic heart failureneurodegenerative disease
✦AI Summary

CLCNKA encodes a voltage-gated chloride channel that functions as a homodimeric anion-selective transporter with selectivity for chloride over bromide, nitrate, and iodide 12. The channel contains two independent fast gates controlling each subunit and a slow common gate regulating both simultaneously, displaying linear current-voltage relationships when complexed with the regulatory subunit Barttin (BSND) 123. CLCNKA mediates transepithelial chloride transport in the thin ascending limb of Henle's loop, essential for generating the hypertonic medullary interstitium required for urine concentration 4. The channel also conducts chloride currents in the inner ear's stria vascularis to establish the endocochlear potential necessary for normal hearing 435. Clinically, CLCNKA variants associate with salt-sensitive hypertension; polymorphisms rs848307 and rs1739843 upstream of CLCNKA significantly correlate with blood pressure changes after sodium loading 67. Loss-of-function mutations cause Bartter syndrome 4B with neonatal sensorineural hearing loss, though some patients present with hearing loss as the dominant phenotype without renal involvement 8. Mutations in CLCNKA combined with CLCNKB deletions or individual CLCNKA mutations result in complex polyuro-polydipsic syndromes with electrolyte wasting 9. Additionally, CLCNKA variants associate with dilated cardiomyopathy risk 10.

Sources cited
1
CLCNKA is chloride-selective, forms homodimeric channels with independent and common gates
PMID: 11734858
2
Ion selectivity (Cl > Br > NO3 > I) and double-barreled gating mechanism
PMID: 12111250
3
CLCNKA:BSND assembly and linear current-voltage relationship with fast gating
PMID: 18310267
4
Role in transepithelial chloride transport in Henle's loop and endocochlear potential in inner ear
PMID: 15044642
5
CLCNKA function in cochlear chloride currents for hearing
PMID: 19646679
6
CLCNKA SNPs (rs848307, rs1739843, rs1010069, rs1805152) associated with salt-sensitive hypertension
PMID: 17510212
7
CLCNKA loss-of-function causes Bartter syndrome 4B with sensorineural hearing loss
PMID: 38069401
8
CLCNKA mutations cause complex polyuro-polydipsic syndrome with electrolyte wasting
PMID: 16093448
9
CLCNKA variants associated with dilated cardiomyopathy risk
PMID: 32916098
10
CLCNKA tag SNPs interact with dietary factors to influence essential hypertension risk
PMID: 25919862
Disease Associationsβ“˜21
Bartter syndromeOpen Targets
0.50Moderate
heart failureOpen Targets
0.42Moderate
systolic heart failureOpen Targets
0.41Moderate
neurodegenerative diseaseOpen Targets
0.41Moderate
Bartter syndrome type 4Open Targets
0.41Moderate
cardiomyopathyOpen Targets
0.41Moderate
deafnessOpen Targets
0.40Weak
congestive heart failureOpen Targets
0.37Weak
cardioverter defibrillatorOpen Targets
0.36Weak
hypertrophic cardiomyopathyOpen Targets
0.35Weak
sensorineural hearing lossOpen Targets
0.34Weak
Sensorineural hearing impairmentOpen Targets
0.34Weak
diabetes mellitusOpen Targets
0.34Weak
type 2 diabetes mellitusOpen Targets
0.33Weak
essential hypertensionOpen Targets
0.33Weak
hypertensionOpen Targets
0.31Weak
dilated cardiomyopathyOpen Targets
0.30Weak
aortic stenosisOpen Targets
0.28Weak
Increased blood pressureOpen Targets
0.26Weak
hearing loss, autosomal recessiveOpen Targets
0.26Weak
Bartter syndrome 4B, neonatal, with sensorineural deafnessUniProt
Pathogenic Variants5
NM_004070.4(CLCNKA):c.1801C>T (p.Gln601Ter)Likely pathogenic
Bartter disease type 4B
β˜…β˜†β˜†β˜†2025β†’ Residue 601
NM_004070.4(CLCNKA):c.1885G>T (p.Glu629Ter)Likely pathogenic
Bartter disease type 4B
β˜…β˜†β˜†β˜†2023β†’ Residue 629
NM_004070.4(CLCNKA):c.1985G>T (p.Gly662Val)Pathogenic
Deafness|Hearing loss, autosomal recessive
β˜†β˜†β˜†β˜†2018β†’ Residue 662
NM_004070.4(CLCNKA):c.778C>T (p.Gln260Ter)Pathogenic
Bartter disease type 4B
β˜†β˜†β˜†β˜†2008β†’ Residue 260
NM_004070.4(CLCNKA):c.240G>C (p.Trp80Cys)Pathogenic
Bartter disease type 4B
β˜†β˜†β˜†β˜†2004β†’ Residue 80
View on ClinVar β†—
Related Genes
SLC12A1Protein interaction91%AQP2Protein interaction81%CLCNKBShared pathway80%KLF15Protein interaction80%BSNDProtein interaction77%SLC12A3Protein interaction76%
Tissue Expression6 tissues
Ovary
100%
Bone Marrow
29%
Heart
26%
Lung
22%
Liver
16%
Brain
5%
Gene Interaction Network
Click a node to explore
CLCNKASLC12A1AQP2CLCNKBKLF15BSNDSLC12A3
PROTEIN STRUCTURE
Preparing viewer…
PDB2PFI Β· 1.60 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.96LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.78 [0.64–0.96]
RankingsWhere CLCNKA stands among ~20K protein-coding genes
  • #11,305of 20,598
    Most Researched33
  • #3,613of 5,498
    Most Pathogenic Variants5
  • #9,037of 17,882
    Most Constrained (LOEUF)0.96
Genes detectedCLCNKA
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Common genetic variants and haplotypes in renal CLCNKA gene are associated to salt-sensitive hypertension.
PMID: 17510212
Hum Mol Genet Β· 2007
1.00
2
Expanding Genotype-Phenotype Correlation of
PMID: 38069401
Int J Mol Sci Β· 2023
0.90
3
The Genetic Makeup of the Electrocardiogram.
PMID: 32916098
Cell Syst Β· 2020
0.80
4
Molecular biology of hereditary diabetes insipidus.
PMID: 16093448
J Am Soc Nephrol Β· 2005
0.70
5
Associations between CLCNKA_B tag SNPs with essential hypertension and interactions between genetic and environmental factors in an island population in China.
PMID: 25919862
Clin Exp Hypertens Β· 2015
0.60