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Aliases for CLCN1 Gene

Aliases for CLCN1 Gene

  • Chloride Voltage-Gated Channel 1 2 3
  • Chloride Channel, Voltage-Sensitive 1 2 3 5
  • Chloride Channel Protein, Skeletal Muscle 3 4
  • Chloride Channel 1, Skeletal Muscle 2 3
  • ClC-1 3 4
  • CLC1 3 4
  • Autosomal Dominant 2
  • Thomsen Disease 2

External Ids for CLCN1 Gene

Previous GeneCards Identifiers for CLCN1 Gene

  • GC07P141339
  • GC07P142407
  • GC07P142484
  • GC07P142530
  • GC07P142723
  • GC07P143013
  • GC07P137350

Summaries for CLCN1 Gene

Entrez Gene Summary for CLCN1 Gene

  • The CLCN family of voltage-dependent chloride channel genes comprises nine members (CLCN1-7, Ka and Kb) which demonstrate quite diverse functional characteristics while sharing significant sequence homology. The protein encoded by this gene regulates the electric excitability of the skeletal muscle membrane. Mutations in this gene cause two forms of inherited human muscle disorders: recessive generalized myotonia congenita (Becker) and dominant myotonia (Thomsen). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]

GeneCards Summary for CLCN1 Gene

CLCN1 (Chloride Voltage-Gated Channel 1) is a Protein Coding gene. Diseases associated with CLCN1 include myotonia congenita, recessive and myotonia congenita, dominant. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Hepatic ABC Transporters. GO annotations related to this gene include ion channel activity and adenyl nucleotide binding. An important paralog of this gene is CLCN7.

UniProtKB/Swiss-Prot for CLCN1 Gene

  • Voltage-gated chloride channel. Chloride channels have several functions including the regulation of cell volume; membrane potential stabilization, signal transduction and transepithelial transport.

Gene Wiki entry for CLCN1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLCN1 Gene

Genomics for CLCN1 Gene

Regulatory Elements for CLCN1 Gene

Genomic Location for CLCN1 Gene

Chromosome:
7
Start:
143,316,126 bp from pter
End:
143,353,862 bp from pter
Size:
37,737 bases
Orientation:
Plus strand

Genomic View for CLCN1 Gene

Genes around CLCN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLCN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLCN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLCN1 Gene

Proteins for CLCN1 Gene

  • Protein details for CLCN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P35523-CLCN1_HUMAN
    Recommended name:
    Chloride channel protein 1
    Protein Accession:
    P35523
    Secondary Accessions:
    • A4D2H5
    • Q2M202

    Protein attributes for CLCN1 Gene

    Size:
    988 amino acids
    Molecular mass:
    108626 Da
    Quaternary structure:
    • Homodimer.
    Miscellaneous:
    • The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons. The absence of conserved gating glutamate residues is typical for family members that function as channels.

neXtProt entry for CLCN1 Gene

Proteomics data for CLCN1 Gene at MOPED

Post-translational modifications for CLCN1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLCN1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for CLCN1 Gene

Domains & Families for CLCN1 Gene

Gene Families for CLCN1 Gene

Suggested Antigen Peptide Sequences for CLCN1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P35523

UniProtKB/Swiss-Prot:

CLCN1_HUMAN :
  • Contains 2 CBS domains.
  • Belongs to the chloride channel (TC 2.A.49) family. ClC-1/CLCN1 subfamily.
Domain:
  • Contains 2 CBS domains.
Family:
  • Belongs to the chloride channel (TC 2.A.49) family. ClC-1/CLCN1 subfamily.
genes like me logo Genes that share domains with CLCN1: view

Function for CLCN1 Gene

Molecular function for CLCN1 Gene

GENATLAS Biochemistry:
chloride voltage-gated channel 1,skeletal muscle
UniProtKB/Swiss-Prot Function:
Voltage-gated chloride channel. Chloride channels have several functions including the regulation of cell volume; membrane potential stabilization, signal transduction and transepithelial transport.
genes like me logo Genes that share phenotypes with CLCN1: view

Human Phenotype Ontology for CLCN1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CLCN1 Gene

Localization for CLCN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCN1 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CLCN1 Gene COMPARTMENTS Subcellular localization image for CLCN1 gene
Compartment Confidence
plasma membrane 5
endosome 1
extracellular 1
lysosome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for CLCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with CLCN1: view

Pathways & Interactions for CLCN1 Gene

genes like me logo Genes that share pathways with CLCN1: view

Gene Ontology (GO) - Biological Process for CLCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport TAS --
GO:0006821 chloride transport IEA --
GO:0034220 ion transmembrane transport IEA,TAS --
GO:1902476 chloride transmembrane transport IMP,TAS 22521272
genes like me logo Genes that share ontologies with CLCN1: view

No data available for SIGNOR curated interactions for CLCN1 Gene

Drugs & Compounds for CLCN1 Gene

(7) Drugs for CLCN1 Gene - From: IUPHAR and DGIdb

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Niflumic Acid Approved Pharma Channel blocker, inhibitor Ca2+-activated Cl- channel blocker 0
<i>S</i>-(-)CPB Pharma Channel blocker 0
<i>S</i>-(-)CPP Pharma Channel blocker 0
Cd<sup>2+</sup> Pharma Channel blocker 0
Fenofibric acid Pharma Channel blocker 32

(4) Additional Compounds for CLCN1 Gene - From: IUPHAR, Novoseek, and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
9-A-C
Channel blocker
Chloride ion
  • Bertholite
  • Chloor
  • Chlor
  • Chlore
  • Chloride
16887-00-6
genes like me logo Genes that share compounds with CLCN1: view

Transcripts for CLCN1 Gene

mRNA/cDNA for CLCN1 Gene

(3) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(7) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLCN1 Gene

Chloride channel, voltage-sensitive 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CLCN1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25
SP1: - -
SP2:
SP3: -
SP4: - - - -

Relevant External Links for CLCN1 Gene

GeneLoc Exon Structure for
CLCN1
ECgene alternative splicing isoforms for
CLCN1

Expression for CLCN1 Gene

mRNA expression in normal human tissues for CLCN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLCN1 Gene

This gene is overexpressed in Muscle - Skeletal (x38.0).

Protein differential expression in normal tissues from HIPED for CLCN1 Gene

This gene is overexpressed in Lung (33.8), Liver (26.6), and Monocytes (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CLCN1 Gene



SOURCE GeneReport for Unigene cluster for CLCN1 Gene Hs.121483

mRNA Expression by UniProt/SwissProt for CLCN1 Gene

P35523-CLCN1_HUMAN
Tissue specificity: Predominantly expressed in skeletal muscles.
genes like me logo Genes that share expression patterns with CLCN1: view

Protein tissue co-expression partners for CLCN1 Gene

Primer Products

In Situ Assay Products

Orthologs for CLCN1 Gene

This gene was present in the common ancestor of animals.

Orthologs for CLCN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLCN1 36
  • 99 (a)
OneToOne
CLCN1 35
  • 99.43 (n)
  • 99.6 (a)
cow
(Bos Taurus)
Mammalia CLCN1 36
  • 89 (a)
OneToOne
CLCN1 35
  • 87.74 (n)
  • 89.26 (a)
dog
(Canis familiaris)
Mammalia CLCN1 35
  • 87.26 (n)
  • 89.55 (a)
CLCN1 36
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Clcn1 36
  • 87 (a)
OneToOne
Clcn1 16
Clcn1 35
  • 85.89 (n)
  • 88.32 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia CLCN1 36
  • 73 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Clcn1 35
  • 86.06 (n)
  • 88.83 (a)
chicken
(Gallus gallus)
Aves CLCN1 35
  • 66.7 (n)
  • 67.88 (a)
CLCN1 36
  • 67 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLCN1 36
  • 66 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii clcn1a 36
  • 55 (a)
OneToMany
clcn1b 36
  • 65 (a)
OneToMany
clcn1a 35
  • 64.95 (n)
  • 67.88 (a)
fruit fly
(Drosophila melanogaster)
Insecta ClC-a 36
  • 33 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea clh-3 37
  • 39 (a)
clh-1 36
  • 31 (a)
ManyToMany
clh-2 36
  • 33 (a)
ManyToMany
clh-3 36
  • 33 (a)
ManyToMany
clh-4 36
  • 28 (a)
ManyToMany
Species with no ortholog for CLCN1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for CLCN1 Gene

ENSEMBL:
Gene Tree for CLCN1 (if available)
TreeFam:
Gene Tree for CLCN1 (if available)

Paralogs for CLCN1 Gene

Paralogs for CLCN1 Gene

(5) SIMAP similar genes for CLCN1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with CLCN1: view

Variants for CLCN1 Gene

Sequence variations from dbSNP and Humsavar for CLCN1 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs201509501 Myotonia congenita, autosomal recessive (MCAR) 143,320,675(+) TCCAC(C/T)GCCTG nc-transcript-variant, reference, missense
rs10282312 - 143,320,714(+) AAGAC(G/T)GGATC nc-transcript-variant, reference, missense
VAR_001584 Myotonia congenita, autosomal recessive (MCAR)
VAR_001585 Myotonia congenita, autosomal recessive (MCAR)
VAR_001586 Myotonia congenita, autosomal dominant (MCAD)

Structural Variations from Database of Genomic Variants (DGV) for CLCN1 Gene

Variant ID Type Subtype PubMed ID
nsv831169 CNV Loss 17160897
nsv5984 CNV Loss 18451855
nsv5985 CNV Insertion 18451855

Variation tolerance for CLCN1 Gene

Residual Variation Intolerance Score: 40.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.83; 86.89% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLCN1 Gene

HapMap Linkage Disequilibrium report
CLCN1
Human Gene Mutation Database (HGMD)
CLCN1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLCN1 Gene

Disorders for CLCN1 Gene

MalaCards: The human disease database

(19) MalaCards diseases for CLCN1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
myotonia congenita, recessive
  • myotonia congenita autosomal recessive
myotonia congenita, dominant
  • myotonia congenita autosomal dominant
myotonia congenita
  • congenital myotonia, autosomal dominant form
myotonia
thomsen and becker disease
  • myotonia congenita
- elite association - COSMIC cancer census association via MalaCards
Search CLCN1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CLCN1_HUMAN
  • Myotonia congenita, autosomal dominant (MCAD) [MIM:160800]: A non-dystrophic skeletal muscle disorder characterized by muscle stiffness and an inability of the muscle to relax after voluntary contraction. Most patients have symptom onset in the legs, which later progresses to the arms, neck, and facial muscles. Many patients show marked hypertrophy of the lower limb muscles. The autosomal dominant form (Thomsen disease) is less common and less severe than the autosomal recessive one (Becker disease). A milder form of autosomal dominant myotonia is characterized by isolated myotonia without muscle weakness, hypotrophy, or hypertrophy (myotonia levior). {ECO:0000269 PubMed:12661046, ECO:0000269 PubMed:7581380, ECO:0000269 PubMed:7981750, ECO:0000269 PubMed:8112288, ECO:0000269 PubMed:8533761, ECO:0000269 PubMed:9122265, ECO:0000269 PubMed:9566422, ECO:0000269 PubMed:9736777}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Myotonia congenita, autosomal recessive (MCAR) [MIM:255700]: A non-dystrophic skeletal muscle disorder characterized by muscle stiffness and an inability of the muscle to relax after voluntary contraction. Most patients have symptom onset in the legs, which later progresses to the arms, neck, and facial muscles. Many patients show marked hypertrophy of the lower limb muscles. The autosomal recessive form (Becker disease) is more severe than the autosomal dominant one (Thomsen disease). {ECO:0000269 PubMed:10215406, ECO:0000269 PubMed:10644771, ECO:0000269 PubMed:11113225, ECO:0000269 PubMed:12661046, ECO:0000269 PubMed:1379744, ECO:0000269 PubMed:19697366, ECO:0000269 PubMed:22521272, ECO:0000269 PubMed:26007199, ECO:0000269 PubMed:26502825, ECO:0000269 PubMed:26510092, ECO:0000269 PubMed:7874130, ECO:0000269 PubMed:7951242, ECO:0000269 PubMed:7981681, ECO:0000269 PubMed:8571958, ECO:0000269 PubMed:9566422, ECO:0000269 PubMed:9736777}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CLCN1

Genetic Association Database (GAD)
CLCN1
Human Genome Epidemiology (HuGE) Navigator
CLCN1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLCN1
genes like me logo Genes that share disorders with CLCN1: view

No data available for Genatlas for CLCN1 Gene

Publications for CLCN1 Gene

  1. The skeletal muscle chloride channel in dominant and recessive human myotonia. (PMID: 1379744) Koch M.C. … Jentsch T.J. (Science 1992) 2 3 4 23 67
  2. Myotonia congenita in a large consanguineous Arab family: insight into the clinical spectrum of carriers and double heterozygotes of a novel mutation in the chloride channel CLCN1 gene. (PMID: 19697366) Shalata A. … Borochowitz Z.U. (Muscle Nerve 2010) 3 23
  3. Whole-body high-field MRI shows no skeletal muscle degeneration in young patients with recessive myotonia congenita. (PMID: 20047568) Kornblum C. … Wattjes M.P. (Acta Neurol. Scand. 2010) 3 23
  4. A novel CLCN1 mutation (G1652A) causing a mild phenotype of thomsen disease. (PMID: 20120005) Kumar K.R. … Sue C.M. (Muscle Nerve 2010) 3 23
  5. Novel CLCN1 mutation in carbamazepine-responsive myotonia congenita. (PMID: 20399394) Lyons M.J. … Holden K.R. (Pediatr. Neurol. 2010) 3 23

Products for CLCN1 Gene

Sources for CLCN1 Gene

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