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Gene

CLCN4

Cl-/H+ antiporter 4

Summary

Cytogenetic location
Xp22.2
Coordinates
Chromosome X: 10,156,975–10,237,660 (GRCh38)
Exons
13 exons across 80.7 kb
Protein
760 amino acids
Also known as
CLC4, ClC-4
MANE Select transcript
ENST00000380833.9NM_001830.4
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 reports relevant to this gene

  • Epilepsy (Full Panel)

    • X-Linked Complex Neurodevelopmental Disorder

      A complex neurodevelopmental disorder that is transmitted via X-linked inheritance, and is characterized by intellectual disability, autism and epilepsy.

      • ClinGen rates the link definitive
      • 1 GenCC submitter rates it definitive or strong

Broader groupings

How CLCN4 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 CLCN4 sits. CLCN4 and 8 genes near it on chromosome X, from 9,697,318 to 10,697,317.Chromosome XXp22.2p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q289.8 Mb10 Mb10.2 Mb10.4 Mb10.6 MbTBL1X: 9,463,258–9,741,723, forward strandTBL1XGPR143: 9,724,039–9,786,297, reverse strandGPR143SHROOM2: 9,786,378–9,949,443, forward strandSHROOM2: 9,786,429–9,968,352, forward strandCLDN34: 9,961,424–9,968,352, forward strandCLDN34WWC3: 10,015,254–10,144,592, forward strandWWC3CLCN4: 10,156,975–10,237,660, forward strandCLCN4MID1: 10,445,310–10,833,730, reverse strandMID1: 10,566,888–10,576,955, reverse strandDiagram of CLCN4: 13 exons on the forward strand of chromosome XExon 3: 1 known disease-causing siteExon 5: 2 known disease-causing sitesExon 7: 3 known disease-causing sitesExon 8: 4 known disease-causing sitesExon 9: 5 known disease-causing sitesExon 10: 4 known disease-causing sitesExon 11: 5 known disease-causing sitesExon 12: 3 known disease-causing sitesExon 1: 10,156,975–10,157,100, 126 basesExon 2: 10,158,289–10,158,551, 263 basesExon 3: 10,185,022–10,185,176, 155 basesExon 4: 10,187,515–10,187,614, 100 basesExon 5: 10,194,911–10,195,098, 188 basesExon 6: 10,197,939–10,198,061, 123 basesExon 7: 10,206,358–10,206,564, 207 basesExon 8: 10,206,696–10,206,776, 81 basesExon 9: 10,208,045–10,208,590, 546 basesExon 10: 10,212,467–10,212,653, 187 basesExon 11: 10,213,681–10,214,079, 399 basesExon 12: 10,220,661–10,220,877, 217 basesExon 13: 10,233,494–10,237,660, 4,167 bases124681012135′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 6.8 kb of the gene's 80.7 kb; 2,283 of those bases code for the protein.

How a genome test reads CLCN4

27

positions in CLCN4 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 80.7 kb of CLCN4, introns included, not only the 6.8 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.). CLCN4 gene: Cl-/H+ antiporter 4. Retrieved 16 October 2026, from https://dantelabs.com/genes/clcn4

Vancouver

Dante Labs. CLCN4 gene: Cl-/H+ antiporter 4 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/clcn4

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