Skip to content
Use your HSA or FSA funds

Gene

CLCN1

chloride voltage-gated channel 1

Summary

Cytogenetic location
7q34
Coordinates
Chromosome 7: 143,316,111–143,352,083 (GRCh38)
Exons
23 exons across 36 kb
Protein
988 amino acids
Also known as
CLC1, ClC-1
MANE Select transcript
ENST00000343257.7NM_000083.3
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

  • Dystonia, Myotonia, Paroxysmal Dyskinesia

    • Thomsen And Becker Disease

      A rare, genetic, skeletal muscle channelopathy characterized by slow muscle relaxation after contraction (myotonia).

      • 2 GenCC submitters rate it definitive or strong

How CLCN1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 7, with a bracket where CLCN1 sits. CLCN1 and 23 genes near it on chromosome 7, from 142,834,097 to 143,834,096.Chromosome 77q34p22.3p22.2p22.1p21.3p21.2p21.1p15.3p15.2p15.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.21q11.22q11.23q21.11q21.12q21.13q21.2q21.3q22.1q22.2q22.3q31.1q31.2q31.31q31.32q31.33q32.1q32.2q32.3q33q34q35q36.1q36.2q36.3143 Mb143.2 Mb143.4 Mb143.6 Mb143.8 MbEPHB6: 142,854,809–142,872,810, forward strandEPHB6TRPV6: 142,871,208–142,885,781, reverse strandTRPV6TRPV5: 142,904,277–142,933,746, reverse strandTRPV5SOFU1: 142,939,343–142,949,915, forward strandSOFU1KEL: 142,941,114–142,962,369, reverse strandKELOR9A2: 143,026,200–143,027,132, reverse strandOR9A2OR6V1: 143,052,341–143,053,282, forward strandOR6V1PIP: 143,132,077–143,139,746, forward strandPIPTAS2R39: 143,183,419–143,184,435, forward strandTAS2R39TAS2R40: 143,222,037–143,223,079, forward strandTAS2R40GSTK1: 143,244,093–143,272,483, forward strandGSTK1TMEM139: 143,279,937–143,288,240, forward strandTMEM139CASP2: 143,288,215–143,307,696, forward strandCASP2CLCN1: 143,316,111–143,352,083, forward strandCLCN1FAM131B: 143,353,395–143,362,815, reverse strandFAM131BZYX: 143,381,076–143,391,111, forward strandZYXEPHA1: 143,390,289–143,408,880, reverse strandEPHA1TAS2R60: 143,443,453–143,444,409, forward strandTAS2R60TAS2R41: 143,477,873–143,478,796, forward strandTAS2R41OR10AC1: 143,509,256–143,519,469, reverse strandOR10AC1CTAGE15: 143,571,801–143,574,387, forward strandCTAGE15TCAF2: 143,620,952–143,732,460, forward strandTCAF2TCAF2C: 143,639,230–143,647,646, reverse strandTCAF2CCTAGE6: 143,755,089–143,757,696, reverse strandCTAGE6Diagram of CLCN1: 23 exons on the forward strand of chromosome 7Exon 1: 15 known disease-causing sitesExon 2: 8 known disease-causing sitesExon 3: 12 known disease-causing sitesExon 4: 10 known disease-causing sitesExon 5: 17 known disease-causing sitesExon 6: 10 known disease-causing sitesExon 7: 13 known disease-causing sitesExon 8: 30 known disease-causing sitesExon 9: 9 known disease-causing sitesExon 10: 4 known disease-causing sitesExon 11: 9 known disease-causing sitesExon 12: 19 known disease-causing sitesExon 13: 9 known disease-causing sitesExon 14: 11 known disease-causing sitesExon 15: 25 known disease-causing sitesExon 16: 11 known disease-causing sitesExon 17: 23 known disease-causing sitesExon 18: 6 known disease-causing sitesExon 19: 4 known disease-causing sitesExon 20: 1 known disease-causing siteExon 21: 6 known disease-causing sitesExon 22: 8 known disease-causing sitesExon 23: 11 known disease-causing sitesExon 1: 143,316,111–143,316,392, 282 basesExon 2: 143,319,755–143,319,875, 121 basesExon 3: 143,320,664–143,320,795, 132 basesExon 4: 143,321,365–143,321,493, 129 basesExon 5: 143,321,715–143,321,848, 134 basesExon 6: 143,323,309–143,323,386, 78 basesExon 7: 143,324,414–143,324,492, 79 basesExon 8: 143,330,772–143,330,897, 126 basesExon 9: 143,331,232–143,331,316, 85 basesExon 10: 143,331,551–143,331,652, 102 basesExon 11: 143,332,419–143,332,503, 85 basesExon 12: 143,332,724–143,332,873, 150 basesExon 13: 143,339,253–143,339,322, 70 basesExon 14: 143,339,511–143,339,621, 111 basesExon 15: 143,341,929–143,342,142, 214 basesExon 16: 143,342,372–143,342,505, 134 basesExon 17: 143,345,521–143,345,762, 242 basesExon 18: 143,346,140–143,346,251, 112 basesExon 19: 143,346,579–143,346,658, 80 basesExon 20: 143,346,911–143,346,949, 39 basesExon 21: 143,350,372–143,350,476, 105 basesExon 22: 143,350,568–143,350,654, 87 basesExon 23: 143,351,594–143,352,083, 490 bases15101520235′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 3.2 kb of the gene's 36 kb; 2,967 of those bases code for the protein.

How a genome test reads CLCN1

318

positions in CLCN1 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 36 kb of CLCN1, introns included, not only the 3.2 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.). CLCN1 gene: chloride voltage-gated channel 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/clcn1

Vancouver

Dante Labs. CLCN1 gene: chloride voltage-gated channel 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/clcn1

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test