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Gene

CLCNKB

chloride voltage-gated channel Kb

Summary

Cytogenetic location
1p36.13
Coordinates
Chromosome 1: 16,043,782–16,057,308 (GRCh38)
Exons
20 exons across 13.5 kb
Protein
687 amino acids
Inheritance
Autosomal recessive
Also known as
hClC-Kb, CLCKB, ClC-K2, ClC-Kb
MANE Select transcript
ENST00000375679.9NM_000085.5
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Bartter Disease

    • Bartter Disease Type 3Autosomal recessive

      Classic Bartter syndrome is a type of Bartter syndrome, characterized by a milder clinical picture than the antenatal/infantile subtype, and presenting with failure to thrive, hypokalemic alkalosis, increased levels of plasma renin and aldosterone, low blood pressure and vascular resistance to angiotensin II.

      • 2 GenCC submitters rate it definitive or strong
    • Bartter Syndrome Type 4Autosomal recessive

      A form of Bartter syndrome characterized by maternal polyhydramnios, premature delivery, salt loss, polyuria and sensorineural deafness, associated with hypokalemic and hypochloremic metabolic alkalosis, increased levels of plasma renin and aldosterone, and low to normal blood pressure. Urinary calcium excretion rates are variable, and nephrocalcinosis is typically absent.

      • 2 GenCC submitters rate it definitive or strong
    • Bartter Syndrome

      A group of inherited salt-wasting kidney tubule disorders, caused by genes such as SLC12A1, KCNJ1, CLCNKB, BSND and CASR, with low potassium, metabolic alkalosis and high urine calcium.

      • 3 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing guides salt and potassium replacement and monitoring of growth and kidney calcification.

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How CLCNKB is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where CLCNKB sits. CLCNKB and 22 genes near it on chromosome 1, from 15,550,545 to 16,550,544.Chromosome 11p36.13p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q4415.6 Mb15.8 Mb16 Mb16.2 Mb16.4 MbDNAJC16: 15,526,813–15,592,379, forward strandDNAJC16AGMAT: 15,571,699–15,585,084, reverse strandAGMATDDI2: 15,617,416–15,669,044, forward strandDDI2RSC1A1: 15,659,713–15,662,033, forward strandRSC1A1PLEKHM2: 15,681,461–15,734,771, forward strandPLEKHM2SLC25A34: 15,736,176–15,741,392, forward strandSLC25A34TMEM82: 15,742,488–15,747,982, forward strandTMEM82FBLIM1: 15,756,604–15,786,594, forward strandFBLIM1UQCRHL: 15,807,169–15,809,348, reverse strandUQCRHLSPEN: 15,836,095–15,940,456, forward strandSPENZBTB17: 15,940,148–15,976,132, reverse strandZBTB17SRARP: 16,004,229–16,009,382, forward strandHSPB7: 16,014,018–16,020,597, reverse strandHSPB7CLCNKA: 16,018,146–16,034,109, forward strandCLCNKACLCNKB: 16,043,782–16,057,308, forward strandCLCNKBFAM131C: 16,057,769–16,073,664, reverse strandFAM131CEPHA2: 16,124,337–16,156,141, reverse strandEPHA2ARHGEF19: 16,197,854–16,212,893, reverse strandARHGEF19CPLANE2: 16,231,692–16,237,214, reverse strandCPLANE2FBXO42: 16,246,840–16,352,494, reverse strandFBXO42SZRD1: 16,352,575–16,398,147, forward strandSZRD1SPATA21: 16,387,117–16,437,424, reverse strandSPATA21NECAP2: 16,440,664–16,460,092, forward strandNECAP2Diagram of CLCNKB: 20 exons on the forward strand of chromosome 1Exon 2: 3 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 5: 4 known disease-causing sitesExon 6: 2 known disease-causing sitesExon 7: 2 known disease-causing sitesExon 8: 3 known disease-causing sitesExon 9: 3 known disease-causing sitesExon 10: 2 known disease-causing sitesExon 11: 2 known disease-causing sitesExon 12: 3 known disease-causing sitesExon 13: 1 known disease-causing siteExon 14: 10 known disease-causing sitesExon 15: 5 known disease-causing sitesExon 16: 3 known disease-causing sitesExon 17: 2 known disease-causing sitesExon 18: 1 known disease-causing siteExon 19: 1 known disease-causing siteExon 1: 16,043,782–16,043,880, 99 basesExon 2: 16,044,486–16,044,592, 107 basesExon 3: 16,045,558–16,045,686, 129 basesExon 4: 16,046,535–16,046,663, 129 basesExon 5: 16,047,905–16,048,044, 140 basesExon 6: 16,048,343–16,048,420, 78 basesExon 7: 16,048,504–16,048,582, 79 basesExon 8: 16,049,120–16,049,245, 126 basesExon 9: 16,049,618–16,049,702, 85 basesExon 10: 16,049,815–16,049,916, 102 basesExon 11: 16,050,516–16,050,600, 85 basesExon 12: 16,050,875–16,051,048, 174 basesExon 13: 16,051,478–16,051,547, 70 basesExon 14: 16,051,710–16,051,820, 111 basesExon 15: 16,052,198–16,052,411, 214 basesExon 16: 16,053,639–16,053,772, 134 basesExon 17: 16,055,435–16,055,523, 89 basesExon 18: 16,055,675–16,055,758, 84 basesExon 19: 16,056,422–16,056,508, 87 basesExon 20: 16,056,869–16,057,308, 440 bases124681012141618205′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 2.6 kb of the gene's 13.5 kb; 2,064 of those bases code for the protein.

How a genome test reads CLCNKB

60

positions in CLCNKB where ClinVar classes a change as pathogenic or likely pathogenic

60 of them (100%) fall in regions short reads find hard.

  • Low mappability (13 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
  • Segmental duplications (60 sites)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 13.5 kb of CLCNKB, introns included, not only the 2.6 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). CLCNKB gene: chloride voltage-gated channel Kb. Retrieved 17 October 2026, from https://dantelabs.com/genes/clcnkb

Vancouver

Dante Labs. CLCNKB gene: chloride voltage-gated channel Kb [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/clcnkb

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