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Gene

CLCN5

Cl-/H+ antiporter 5

Summary

Cytogenetic location
Xp11.23
Coordinates
Chromosome X: 49,922,596–50,099,230 (GRCh38)
Exons
15 exons across 176.6 kb
Protein
816 amino acids
Inheritance
X-linked recessive
Also known as
DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5
Previous symbols
NPHL2, NPHL1
MANE Select transcript
ENST00000376091.8NM_001127898.4
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

  • Dent Disease and Lowe Syndrome

    • Dent DiseaseX-linked recessive

      An X-linked kidney tubule disorder caused by variants in CLCN5 or OCRL, with low-molecular-weight proteinuria, high urine calcium, kidney stones and progressive chronic kidney disease in males.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing allows monitoring and measures to reduce urine calcium and slow kidney damage, and testing of female relatives who may be carriers.

Inheritance

X-linked recessive
The change is on the X chromosome, so one copy affects males, who have one X, while females with one are usually carriers. A carrier mother passes it on to each child with a one-in-two chance.

How CLCN5 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome X, with a bracket where CLCN5 sits. CLCN5 and 15 genes near it on chromosome X, from 49,510,913 to 50,510,912.Chromosome XXp11.23p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2849.6 Mb49.8 Mb50 Mb50.2 Mb50.4 MbGAGE12B: 49,529,869–49,529,985, forward strandGAGE12C: 49,532,177–49,539,541, forward strandGAGE12D: 49,541,733–49,549,097, forward strandGAGE12E: 49,551,289–49,558,645, forward strandGAGE12F: 49,560,842–49,568,209, forward strandGAGE12G: 49,570,400–49,577,757, forward strandGAGE12GGAGE12H: 49,579,945–49,587,304, forward strandGAGE12HGAGE2A: 49,589,476–49,596,834, forward strandGAGE2AGAGE1: 49,599,020–49,608,538, forward strandGAGE1PAGE1: 49,687,445–49,696,024, reverse strandPAGE1PAGE4: 49,752,516–49,835,255, forward strandPAGE4USP27X: 49,879,484–49,882,558, forward strandUSP27XCLCN5: 49,922,596–50,099,230, forward strandCLCN5AKAP4: 50,190,777–50,201,007, reverse strandAKAP4CCNB3: 50,202,713–50,351,914, forward strandCCNB3DGKK: 50,365,405–50,470,850, reverse strandDGKKDiagram of CLCN5: 15 exons on the forward strand of chromosome XExon 5: 4 known disease-causing sitesExon 6: 7 known disease-causing sitesExon 7: 3 known disease-causing sitesExon 8: 1 known disease-causing siteExon 9: 7 known disease-causing sitesExon 10: 4 known disease-causing sitesExon 11: 14 known disease-causing sitesExon 12: 11 known disease-causing sitesExon 13: 14 known disease-causing sitesExon 14: 4 known disease-causing sitesExon 15: 1 known disease-causing siteExon 1: 49,922,596–49,922,792, 197 basesExon 2: 49,923,407–49,923,482, 76 basesExon 3: 49,925,171–49,925,314, 144 basesExon 4: 50,042,316–50,042,462, 147 basesExon 5: 50,069,879–50,070,030, 152 basesExon 6: 50,072,489–50,072,588, 100 basesExon 7: 50,075,795–50,075,982, 188 basesExon 8: 50,080,594–50,080,716, 123 basesExon 9: 50,081,641–50,081,847, 207 basesExon 10: 50,085,980–50,086,060, 81 basesExon 11: 50,086,328–50,086,870, 543 basesExon 12: 50,088,698–50,088,884, 187 basesExon 13: 50,090,116–50,090,514, 399 basesExon 14: 50,090,670–50,090,886, 217 basesExon 15: 50,092,129–50,099,230, 7,102 bases1510155′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 9.9 kb of the gene's 176.6 kb; 2,451 of those bases code for the protein.

How a genome test reads CLCN5

82

positions in CLCN5 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 176.6 kb of CLCN5, introns included, not only the 9.9 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.). CLCN5 gene: Cl-/H+ antiporter 5. Retrieved 16 October 2026, from https://dantelabs.com/genes/clcn5

Vancouver

Dante Labs. CLCN5 gene: Cl-/H+ antiporter 5 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/clcn5

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