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Gene

CLCN3

Cl-/H+ antiporter 3

Summary

Cytogenetic location
4q33
Coordinates
Chromosome 4: 169,620,578–169,723,673 (GRCh38)
Exons
13 exons across 103.1 kb
Protein
818 amino acids
Also known as
CLC3, ClC-3
MANE Select transcript
ENST00000513761.6NM_001829.4
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

No Genome Test report reads CLCN3 yet. The test sequences your whole genome, so your data includes it all the same.

How CLCN3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 4, with a bracket where CLCN3 sits. CLCN3 and 5 genes near it on chromosome 4, from 169,172,126 to 170,172,125.Chromosome 44q33p16.3p16.2p16.1p15.33p15.32p15.31p15.2p15.1p14p13p12p11q11q12q13.1q13.2q13.3q21.1q21.21q21.22q21.23q21.3q22.1q22.2q22.3q23q24q25q26q27q28.1q28.2q28.3q31.1q31.21q31.22q31.23q31.3q32.1q32.2q32.3q33q34.1q34.2q34.3q35.1q35.2169.2 Mb169.4 Mb169.6 Mb169.8 Mb170 MbSH3RF1: 169,094,259–169,271,185, reverse strandSH3RF1NEK1: 169,369,704–169,612,646, reverse strandNEK1CLCN3: 169,620,578–169,723,673, forward strandCLCN3HPF1: 169,729,465–169,757,972, reverse strandHPF1MFAP3L: 169,986,597–170,033,031, reverse strandMFAP3LAADAT: 170,059,663–170,091,699, reverse strandAADATDiagram of CLCN3: 13 exons on the forward strand of chromosome 4Exon 3: 2 known disease-causing sitesExon 7: 2 known disease-causing sitesExon 8: 1 known disease-causing siteExon 9: 2 known disease-causing sitesExon 10: 1 known disease-causing siteExon 11: 2 known disease-causing sitesExon 12: 1 known disease-causing siteExon 1: 169,620,578–169,621,063, 486 basesExon 2: 169,635,913–169,636,088, 176 basesExon 3: 169,680,050–169,680,207, 158 basesExon 4: 169,687,658–169,687,757, 100 basesExon 5: 169,689,043–169,689,230, 188 basesExon 6: 169,690,530–169,690,652, 123 basesExon 7: 169,692,114–169,692,320, 207 basesExon 8: 169,695,612–169,695,692, 81 basesExon 9: 169,697,189–169,697,734, 546 basesExon 10: 169,703,998–169,704,184, 187 basesExon 11: 169,706,868–169,707,266, 399 basesExon 12: 169,713,079–169,713,295, 217 basesExon 13: 169,719,907–169,723,673, 3,767 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 6.6 kb of the gene's 103.1 kb; 2,457 of those bases code for the protein.

How a genome test reads CLCN3

11

positions in CLCN3 where ClinVar classes a change as pathogenic or likely pathogenic

7 of them (64%) fall in regions short reads find hard.

  • Segmental duplications (7 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 103.1 kb of CLCN3, introns included, not only the 6.6 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.
  • 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.). CLCN3 gene: Cl-/H+ antiporter 3. Retrieved 16 October 2026, from https://dantelabs.com/genes/clcn3

Vancouver

Dante Labs. CLCN3 gene: Cl-/H+ antiporter 3 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/clcn3

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