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Aliases for CLCN1 Gene

Aliases for CLCN1 Gene

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

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 Ion channel transport. GO annotations related to this gene include ion channel activity and adenyl nucleotide binding. An important paralog of this gene is CLCN2.

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 CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLCN1 Gene

Genomics for CLCN1 Gene

Regulatory Elements for CLCN1 Gene

Enhancers for CLCN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07G143345 1.2 Ensembl ENCODE 34.5 +29.5 29500 1.0 FOXA2 ATF1 GLI4 ZNF2 ZNF48 YY1 GLIS2 KLF7 KDM4B REST CLCN1 HINT1P1 ZYX LOC100507507 LOC105375545 CASP2 RN7SL535P TMEM139 EPHA1-AS1 EPHA1
GH07G143346 0.7 ENCODE 35.9 +30.1 30077 0.2 SOX5 CTCF ESRRA ETV1 JUNB HMG20A RBBP5 RAD21 ZGPAT CREM CLCN1 HINT1P1 LOC100507507 ZYX CASP2 RN7SL535P LOC105375545 TMEM139 EPHA1 EPHA1-AS1
GH07G143378 2 FANTOM5 Ensembl ENCODE dbSUPER 10.6 +70.1 70069 15.9 HDGF PKNOX1 MLX CREB3L1 WRNIP1 ARID4B SIN3A YBX1 ZNF2 ZBTB7B ZYX EPHA1-AS1 EPHA1 CLCN1 HINT1P1 OR2A1 FAM131B LOC100507507 TAS2R60 ARHGEF35
GH07G143258 1.5 FANTOM5 Ensembl ENCODE 11.1 -56.9 -56858 2.2 FOXA2 YY1 TCF12 ZNF766 GATA2 CBX5 FOS SP3 CAVIN1 JUNB TMEM139 CASP2 LOC105375545 RN7SL535P EPHA1-AS1 EPHA1 FAM131B HINT1P1 CLCN1 ZYX
GH07G143238 1 Ensembl ENCODE 11.4 -76.1 -76104 2.4 CTCF RB1 TBL1XR1 DDX20 CEBPG RAD21 YY1 GATA2 HNF4G ZNF143 HINT1P1 CLCN1 FAM131B LOC105375546 GSTK1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLCN1 on UCSC Golden Path with GeneCards custom track

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

Post-translational modifications for CLCN1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLCN1 Gene

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 :
  • Belongs to the chloride channel (TC 2.A.49) family. ClC-1/CLCN1 subfamily.
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:0005244 voltage-gated ion channel activity IEA --
GO:0005247 voltage-gated chloride channel activity IEA,TAS --
GO:0005254 chloride channel activity IEA --
GO:0005515 protein binding IPI 25416956
GO:0042803 protein homodimerization activity IDA 26502825
genes like me logo Genes that share ontologies with CLCN1: view
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

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLCN1 gene
Compartment Confidence
plasma membrane 5
extracellular 1
endosome 1

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 IDA 26502825
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0034707 chloride channel complex 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 IEA --
GO:0006811 ion transport IEA --
GO:0006821 chloride transport IEA --
GO:0006936 muscle contraction IMP 22521272
GO:0019227 neuronal action potential propagation IEA --
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

(10) Drugs for CLCN1 Gene - From: ApexBio, DGIdb, and IUPHAR

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 33

(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

(3) ApexBio Compounds for CLCN1 Gene

Compound Action Cas Number
9-AC 723-62-6
DCPIB 82749-70-0
NPPB inhibitor of chloride channel 107254-86-4
genes like me logo Genes that share compounds with CLCN1: view

Drug Products

Transcripts for CLCN1 Gene

mRNA/cDNA for CLCN1 Gene

(4) 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:

CRISPR Products

Inhibitory RNA Products

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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



Protein tissue co-expression partners for CLCN1 Gene

NURSA nuclear receptor signaling pathways regulating expression of CLCN1 Gene:

CLCN1

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.

Evidence on tissue expression from TISSUES for CLCN1 Gene

  • Muscle(2.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CLCN1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • nervous
  • skeletal muscle
Organs:
Head and neck:
  • head
  • mouth
  • pharynx
Thorax:
  • esophagus
Abdomen:
  • stomach
Limb:
  • arm
  • foot
  • forearm
  • lower limb
  • upper limb
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with CLCN1: view

Primer 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 34 35
  • 99.43 (n)
cow
(Bos Taurus)
Mammalia CLCN1 34 35
  • 87.74 (n)
dog
(Canis familiaris)
Mammalia CLCN1 34 35
  • 87.26 (n)
rat
(Rattus norvegicus)
Mammalia Clcn1 34
  • 86.06 (n)
mouse
(Mus musculus)
Mammalia Clcn1 34 16 35
  • 85.89 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLCN1 35
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLCN1 34 35
  • 66.7 (n)
lizard
(Anolis carolinensis)
Reptilia CLCN1 35
  • 66 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii clcn1b 35
  • 65 (a)
OneToMany
clcn1a 34 35
  • 64.95 (n)
fruit fly
(Drosophila melanogaster)
Insecta ClC-a 35
  • 33 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea clh-3 36 35
  • 39 (a)
clh-2 35
  • 33 (a)
ManyToMany
clh-1 35
  • 31 (a)
ManyToMany
clh-4 35
  • 28 (a)
ManyToMany
Species where no ortholog for CLCN1 was found in the sources mined by GeneCards:
  • 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
rs121912799 Pathogenic, Myotonia congenita, autosomal recessive (MCAR) [MIM:255700] 143,332,490(+) TCAAT(G/T)CATGG intron-variant, nc-transcript-variant, reference, missense
rs121912801 Pathogenic, Myotonia congenita, autosomal recessive (MCAR) [MIM:255700] 143,339,527(+) GGAAG(G/T)CTGGT nc-transcript-variant, reference, missense
rs121912805 Pathogenic, Myotonia congenita, autosomal recessive (MCAR) [MIM:255700] 143,330,789(+) GCATC(A/G)AGGTC nc-transcript-variant, upstream-variant-2KB, reference, missense
rs121912807 Pathogenic, Myotonia congenita, autosomal recessive (MCAR) [MIM:255700] 143,339,534(+) TGGTA(A/G)GAGAA nc-transcript-variant, reference, missense
rs146457619 Pathogenic, Myotonia congenita, autosomal recessive (MCAR) [MIM:255700] 143,339,304(+) GCTTC(A/G)TGCCT nc-transcript-variant, reference, missense

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

Variant ID Type Subtype PubMed ID
nsv5984 CNV deletion 18451855
nsv5985 CNV insertion 18451855
nsv831169 CNV loss 17160897
nsv949966 CNV deletion 24416366

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

Human Gene Mutation Database (HGMD)
CLCN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLCN1

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

Disorders for CLCN1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
myotonia congenita, recessive
  • becker muscular dystrophy
myotonia congenita, dominant
  • thomsen disease
myotonia congenita
  • congenital myotonia, autosomal dominant form
myotonia
nondystrophic myotonia
  • ndm
- 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:26096614, ECO:0000269 PubMed:27666773, ECO:0000269 PubMed:7581380, ECO:0000269 PubMed:7981750, ECO:0000269 PubMed:8112288, ECO:0000269 PubMed:8533761, ECO:0000269 PubMed:8845168, 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:22641783, ECO:0000269 PubMed:26007199, ECO:0000269 PubMed:26096614, ECO:0000269 PubMed:26502825, ECO:0000269 PubMed:26510092, ECO:0000269 PubMed:7874130, ECO:0000269 PubMed:7951242, ECO:0000269 PubMed:7981681, ECO:0000269 PubMed:8533761, ECO:0000269 PubMed:8571958, ECO:0000269 PubMed:8845168, 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 22 64
  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 4 22 64
  3. In tandem analysis of CLCN1 and SCN4A greatly enhances mutation detection in families with non-dystrophic myotonia. (PMID: 18337730) Trip J. … Ginjaar I.B. (Eur. J. Hum. Genet. 2008) 3 22 46 64
  4. High frequency of co-segregating CLCN1 mutations among myotonic dystrophy type 2 patients from Finland and Germany. (PMID: 18807109) Suominen T. … Udd B. (J. Neurol. 2008) 3 22 46 64
  5. Decrement of compound muscle action potential is related to mutation type in myotonia congenita. (PMID: 12661046) Colding-JA … Vissing J. (Muscle Nerve 2003) 3 4 22 64

Products for CLCN1 Gene

Sources for CLCN1 Gene

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