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Aliases for CLCN1 Gene

Aliases for CLCN1 Gene

  • Chloride Channel, Voltage-Sensitive 1 2 3
  • Chloride Channel Protein, Skeletal Muscle 3 4
  • Chloride Channel 1, Skeletal Muscle 2 3
  • ClC-1 3 4
  • CLC1 3 4
  • Chloride Channel Protein 1 3
  • 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 Channel, Voltage-Sensitive 1) is a Protein Coding gene. Diseases associated with CLCN1 include myotonia congenita, recessive and myotonia congenita, dominant. Among its related pathways are Activation of cAMP-Dependent PKA and Activation of cAMP-Dependent PKA. GO annotations related to this gene include chloride 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

Start:
143,316,126 bp from pter
End:
143,352,083 bp from pter
Size:
35,958 bases
Orientation:
Plus strand

Genomic View for CLCN1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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:
    • Homotetramer.
    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:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for CLCN1 Gene

Domains for CLCN1 Gene

Gene Families for CLCN1 Gene

HGNC:
  • CLCN :Ion channels / Chloride channels : Voltage-sensitive
IUPHAR :

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 :
  • P35523
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

Gene Ontology (GO) - Molecular Function for CLCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity --
GO:0005247 voltage-gated chloride channel activity IEA --
GO:0005254 chloride channel activity TAS 1379744
GO:0005515 protein binding IPI 25416956
GO:0030554 adenyl nucleotide binding --
genes like me logo Genes that share ontologies with CLCN1: view
genes like me logo Genes that share phenotypes with CLCN1: view

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLCN1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for CLCN1 Gene

Localization for CLCN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCN1 Gene

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 4

Gene Ontology (GO) - Cellular Components for CLCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 9122265
GO:0016020 membrane --
GO:0034707 chloride channel complex IEA --
GO:0042383 sarcolemma IEA --
genes like me logo Genes that share ontologies with CLCN1: view

Pathways 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 9122265
GO:0006821 chloride transport --
GO:0006936 muscle contraction TAS 1379744
GO:0019227 neuronal action potential propagation IEA --
GO:0034220 ion transmembrane transport TAS --
genes like me logo Genes that share ontologies with CLCN1: view

Compounds for CLCN1 Gene

(1) HMDB Compounds for CLCN1 Gene

Compound Synonyms Cas Number PubMed IDs
Chlorine
  • Cl2
16887-00-6

(7) IUPHAR Ligand for CLCN1 Gene

Ligand Type Action Affinity Pubmed IDs
Zn2+ Channel blocker None 6
S-(-)CPP Channel blocker None
fenofibric acid Channel blocker None
niflumic acid Channel blocker None
S-(-)CPB Channel blocker None
Cd2+ Channel blocker None
9-A-C Channel blocker None

(2) Novoseek inferred chemical compound relationships for CLCN1 Gene

Compound -log(P) Hits PubMed IDs
chloride 85.3 62
sodium 40.9 5
genes like me logo Genes that share compounds with CLCN1: view

Transcripts for CLCN1 Gene

mRNA/cDNA for CLCN1 Gene

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

Unigene Clusters for CLCN1 Gene

Chloride channel, voltage-sensitive 1:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLCN1

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for CLCN1

Flow Cytometry Products

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 (38.0).

Integrated Proteomics: protein expression 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 expressions with CLCN1: view

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 35
  • 99.43 (n)
  • 99.6 (a)
CLCN1 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CLCN1 35
  • 87.74 (n)
  • 89.26 (a)
CLCN1 36
  • 89 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CLCN1 35
  • 87.26 (n)
  • 89.55 (a)
CLCN1 36
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Clcn1 35
  • 85.89 (n)
  • 88.32 (a)
Clcn1 16
Clcn1 36
  • 87 (a)
OneToOne
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 35
  • 64.95 (n)
  • 67.88 (a)
clcn1a 36
  • 55 (a)
OneToMany
clcn1b 36
  • 65 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta ClC-a 36
  • 33 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea clh-1 36
  • 31 (a)
ManyToMany
clh-2 36
  • 33 (a)
ManyToMany
clh-3 36
  • 33 (a)
ManyToMany
clh-4 36
  • 28 (a)
ManyToMany
clh-3 37
  • 39 (a)
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

Selected 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 MAF
rs940864 -- 143,342,218(-) TTAAC(C/T)CTAAG intron-variant
rs940865 -- 143,335,547(-) TTTTA(A/G)TTTAG intron-variant
rs940867 -- 143,326,901(-) TATAG(A/C)ACCAT intron-variant
rs1525788 -- 143,335,256(-) GTCCT(C/G)TATAT intron-variant
rs1880650 -- 143,341,026(-) aaggc(C/G)cttgt intron-variant

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

Relevant External Links for CLCN1 Gene

HapMap Linkage Disequilibrium report
CLCN1
Human Gene Mutation Database (HGMD)
CLCN1
Locus Specific Mutation Databases (LSDB)
CLCN1

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

Disorders for CLCN1 Gene

(2) OMIM Diseases for CLCN1 Gene (118425)

UniProtKB/Swiss-Prot

CLCN1_HUMAN
  • Myotonia congenita, autosomal dominant (MCD) [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:7581380, ECO:0000269 PubMed:7981750, ECO:0000269 PubMed:8112288, ECO:0000269 PubMed:8533761, 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 (MCR) [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:1379744, ECO:0000269 PubMed:7874130, ECO:0000269 PubMed:7951242, ECO:0000269 PubMed:7981681, ECO:0000269 PubMed:8571958}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(8) Novoseek inferred disease relationships for CLCN1 Gene

Disease -log(P) Hits PubMed IDs
myotonia congenita 98.6 53
myotonia generalized becker 95.4 2
myotonic disorders 91.7 3
promm 82.6 2
myotonic dystrophy 79 4

Relevant External Links for CLCN1

GeneTests
CLCN1
GeneReviews
CLCN1
Genetic Association Database (GAD)
CLCN1
Human Genome Epidemiology (HuGE) Navigator
CLCN1
genes like me logo Genes that share disorders with CLCN1: view

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
  2. Myotonia levior is a chloride channel disorder. (PMID: 7581380) Lehmann-Horn F. … George A.L. Jr. (Hum. Mol. Genet. 1995) 3 4 23
  3. Genomic organization of the human muscle chloride channel ClC-1 and analysis of novel mutations leading to Becker-type myotonia. (PMID: 7951242) Lorenz C. … Jentsch T.J. (Hum. Mol. Genet. 1994) 3 4 23
  4. Multimeric structure of ClC-1 chloride channel revealed by mutations in dominant myotonia congenita (Thomsen). (PMID: 8112288) Steinmeyer K. … Jentsch T.J. (EMBO J. 1994) 3 4 23
  5. Spectrum of mutations in the major human skeletal muscle chloride channel gene (CLCN1) leading to myotonia. (PMID: 8533761) Meyer-Kleine C. … Koch M.C. (Am. J. Hum. Genet. 1995) 3 4 23

Products for CLCN1 Gene

Sources for CLCN1 Gene

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