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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CLCN1
chloride voltage-gated channel 1
Chromosome 7 Β· 7q34
NCBI Gene: 1180Ensembl: ENSG00000188037.15HGNC: HGNC:2019UniProt: P35523
139PubMed Papers
22Diseases
0Drugs
342Pathogenic Variants
FUNCTIONAL ROLE
Ion ChannelTransporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingchloride transmembrane transportplasma membranevoltage-gated chloride channel activitymyotonia congenita, autosomal recessiveThomsen and Becker diseaseMyotoniaTip-toe gait
✦AI Summary

CLCN1 encodes ClC-1, a voltage-gated chloride channel that generates most plasma membrane chloride conductance in skeletal muscle, stabilizing resting membrane potential and enabling action potential repolarization 1. The channel functions as a homodimer with double-barreled architecture: each subunit contains an independent ion conduction pathway controlled by fast glutamate gates, while a common slow gate regulates both subunits simultaneously, with significant open probability at resting potential further increasing upon depolarization [UniProt references]. ClC-1 exhibits chloride selectivity over other anions and maintains skeletal muscle excitability through regulated ion transport [UniProt references]. Loss-of-function CLCN1 mutations cause myotonia congenita, a nondystrophic myotonia characterized by delayed muscle relaxation, stiffness, pain, and weakness 2. Both autosomal dominant (Thomsen's disease) and recessive (Becker's disease) inheritance patterns occur, with ~130 known mutations 1. In a large German cohort (48 CLCN1 patients), myotonia occurred in 83.3%, myalgia in 57.4%, and cold-sensitivity was prominent; electromyography revealed myotonic runs in 89.1% 3. Cardiac involvement occurs in approximately 8-9% of patients, sometimes requiring pacemakers 3. Variant location predicts inheritance pattern: voltage-dependence alterations cluster in transmembrane domains one-two, loss-of-function variants in domains two-three, while intracellular domain variants show no dominant features 4. Mexiletine and lamotrigine provide symptomatic relief in approximately 50% of treated patients 3.

Sources cited
1
CLCN1 mutations cause myotonia congenita via reduced sarcolemmal chloride conductance; ~130 known mutations; discusses pathophysiology of chloride channel dysfunction
PMID: 19185184
2
CLCN1 loss-of-function mutations cause nondystrophic myotonias with myotonia, stiffness, pain, and fatigue; diagnosis based on EMG and genetic confirmation
PMID: 32270509
3
In 48 NDM-CLCN1 patients: myotonia in 83.3%, myalgia in 57.4%, cold-sensitivity prominent; myotonic EMG runs in 89.1%; cardiac involvement in 8.5%; mexiletine and lamotrigine most effective
PMID: 33263785
4
Variant location predicts inheritance pattern and pathogenic mechanism; voltage-dependence variants cluster in first half of transmembrane domains; loss-of-function variants in second half; intracellular domain variants show no dominant features
PMID: 34529042
⚠Limited data available β€” This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜22
myotonia congenita, autosomal recessiveOpen Targets
0.76Strong
Thomsen and Becker diseaseOpen Targets
0.75Strong
MyotoniaOpen Targets
0.59Moderate
Tip-toe gaitOpen Targets
0.51Moderate
hyperkalemic periodic paralysisOpen Targets
0.46Moderate
Abnormality of the musculatureOpen Targets
0.45Moderate
Smith-Lemli-Opitz syndromeOpen Targets
0.43Moderate
genetic disorderOpen Targets
0.42Moderate
EMG: myotonic dischargesOpen Targets
0.41Moderate
congenital myotoniaOpen Targets
0.37Weak
myocardial infarctionOpen Targets
0.34Weak
VertigoOpen Targets
0.34Weak
cerebral palsyOpen Targets
0.34Weak
HeadacheOpen Targets
0.34Weak
Myotonia of the upper limbOpen Targets
0.34Weak
rasopathyOpen Targets
0.34Weak
RigidityOpen Targets
0.34Weak
hypokalemic periodic paralysis, type 1Open Targets
0.33Weak
myopathyOpen Targets
0.27Weak
Skeletal muscle hypertrophyOpen Targets
0.27Weak
Myotonia congenita, autosomal dominantUniProt
Myotonia congenita, autosomal recessiveUniProt
Pathogenic Variants342
NM_000083.3(CLCN1):c.1453A>G (p.Met485Val)Pathogenic
not provided|Congenital myotonia, autosomal dominant form;Congenital myotonia, autosomal recessive form|Batten-Turner congenital myopathy|Congenital myotonia, autosomal recessive form|CLCN1-related disorder|CLCN1-related myotonia congenita
β˜…β˜…β˜†β˜†2026β†’ Residue 485
NM_000083.3(CLCN1):c.2680C>T (p.Arg894Ter)Pathogenic
Congenital myotonia, autosomal recessive form|Congenital myotonia, autosomal dominant form|Batten-Turner congenital myopathy|not provided|EMG: myopathic abnormalities;Myopathy|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|Tip-toe gait|Cerebral palsy|Abnormality of the musculature|CLCN1-related disorder|Myotonia levior;Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|Skeletal muscle channelopathy
β˜…β˜…β˜†β˜†2026β†’ Residue 894
NM_000083.3(CLCN1):c.1261C>T (p.Arg421Cys)Pathogenic
not provided|Congenital myotonia, autosomal dominant form;Congenital myotonia, autosomal recessive form|Congenital myotonia, autosomal recessive form
β˜…β˜…β˜†β˜†2026β†’ Residue 421
NM_000083.3(CLCN1):c.47G>A (p.Trp16Ter)Pathogenic
Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|Congenital myotonia, autosomal recessive form|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 16
NM_000083.3(CLCN1):c.1013G>A (p.Arg338Gln)Pathogenic
not provided|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|Congenital myotonia, autosomal dominant form|Congenital myotonia, autosomal recessive form|CLCN1-related disorder
β˜…β˜…β˜†β˜†2026β†’ Residue 338
NM_000083.3(CLCN1):c.2831dup (p.Gly945fs)Pathogenic
not provided|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|Skeletal muscle channelopathy
β˜…β˜…β˜†β˜†2026β†’ Residue 945
NM_000083.3(CLCN1):c.689G>A (p.Gly230Glu)Pathogenic
Congenital myotonia, autosomal dominant form|Batten-Turner congenital myopathy|not provided|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|Congenital myotonia, autosomal recessive form|CLCN1-related disorder
β˜…β˜…β˜†β˜†2026β†’ Residue 230
NM_000083.3(CLCN1):c.2172+1G>TPathogenic
Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|not provided
β˜…β˜…β˜†β˜†2026
NM_000083.3(CLCN1):c.1444G>C (p.Gly482Arg)Pathogenic
Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|not provided|Congenital myotonia, autosomal recessive form
β˜…β˜…β˜†β˜†2026β†’ Residue 482
NM_000083.3(CLCN1):c.1238T>G (p.Phe413Cys)Pathogenic
Congenital myotonia, autosomal recessive form|Congenital myotonia, autosomal dominant form|not provided|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|Tip-toe gait|CLCN1-related disorder|Skeletal muscle channelopathy
β˜…β˜…β˜†β˜†2026β†’ Residue 413
NM_000083.3(CLCN1):c.1478C>A (p.Ala493Glu)Pathogenic
Congenital myotonia, autosomal recessive form|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 493
NM_000083.3(CLCN1):c.854G>A (p.Gly285Glu)Pathogenic
not provided|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|Smith-Lemli-Opitz syndrome|Tip-toe gait|CLCN1-related disorder|Skeletal muscle channelopathy
β˜…β˜…β˜†β˜†2026β†’ Residue 285
NM_000083.3(CLCN1):c.2364+2T>APathogenic
not provided|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|Congenital myotonia, autosomal recessive form
β˜…β˜…β˜†β˜†2026
NM_000083.3(CLCN1):c.920T>C (p.Phe307Ser)Pathogenic
Batten-Turner congenital myopathy|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|not provided|Congenital myotonia, autosomal dominant form|CLCN1-related disorder|Congenital myotonia, autosomal recessive form
β˜…β˜…β˜†β˜†2026β†’ Residue 307
NM_000083.3(CLCN1):c.1785G>A (p.Trp595Ter)Pathogenic
Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form
β˜…β˜…β˜†β˜†2026β†’ Residue 595
NM_000083.3(CLCN1):c.180+3A>TPathogenic
not provided|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|Congenital myotonia, autosomal recessive form|Congenital myotonia, autosomal dominant form|Skeletal muscle channelopathy
β˜…β˜…β˜†β˜†2026
NM_000083.3(CLCN1):c.490T>C (p.Trp164Arg)Likely pathogenic
Congenital myotonia, autosomal dominant form;Congenital myotonia, autosomal recessive form|Skeletal muscle channelopathy
β˜…β˜…β˜†β˜†2026β†’ Residue 164
NM_000083.3(CLCN1):c.1444G>A (p.Gly482Arg)Pathogenic
Congenital myotonia, autosomal recessive form|not provided|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form|Congenital myotonia, autosomal dominant form
β˜…β˜…β˜†β˜†2026β†’ Residue 482
NM_000083.3(CLCN1):c.762C>G (p.Cys254Trp)Pathogenic
Congenital myotonia, autosomal dominant form;Congenital myotonia, autosomal recessive form|Batten-Turner congenital myopathy|Congenital myotonia, autosomal recessive form
β˜…β˜…β˜†β˜†2026β†’ Residue 254
NM_000083.3(CLCN1):c.2058C>G (p.Tyr686Ter)Pathogenic
not provided|Congenital myotonia, autosomal recessive form;Congenital myotonia, autosomal dominant form
β˜…β˜…β˜†β˜†2026β†’ Residue 686
View on ClinVar β†—
Related Genes
CELF1Protein interaction99%CNBPProtein interaction96%DMPKProtein interaction94%ATP2A1Protein interaction93%MBNL1Protein interaction93%MBNL2Protein interaction81%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
60%
Lung
30%
Liver
25%
Ovary
10%
Heart
0%
Gene Interaction Network
Click a node to explore
CLCN1CELF1CNBPDMPKATP2A1MBNL1MBNL2
PROTEIN STRUCTURE
Preparing viewer…
PDB8WXI Β· 2.57 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.03LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.86 [0.73–1.03]
RankingsWhere CLCN1 stands among ~20K protein-coding genes
  • #3,304of 20,598
    Most Researched139 Β· top quartile
  • #171of 5,498
    Most Pathogenic Variants342 Β· top 5%
  • #10,112of 17,882
    Most Constrained (LOEUF)1.03
Genes detectedCLCN1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Guidelines on clinical presentation and management of nondystrophic myotonias.
PMID: 32270509
Muscle Nerve Β· 2020
1.00
2
Non-dystrophic myotonias: clinical and mutation spectrum of 70 German patients.
PMID: 33263785
J Neurol Β· 2021
0.90
3
Translating genetic and functional data into clinical practice: a series of 223 families with myotonia.
PMID: 34529042
Brain Β· 2022
0.80
4
A 20-year Clinical and Genetic Neuromuscular Cohort Analysis in Lebanon: An International Effort.
PMID: 34602496
J Neuromuscul Dis Β· 2022
0.70
5
Myotonia congenita.
PMID: 19185184
Adv Genet Β· 2008
0.60