Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CLCN4 Gene

Aliases for CLCN4 Gene

  • Chloride Channel, Voltage-Sensitive 4 2 3
  • Chloride Channel Protein 4 3 4
  • Chloride Transporter ClC-4 3 4
  • Chloride Channel 4 2 3
  • ClC-4 3 4
  • H(+)/Cl(-) Exchange Transporter 4 3
  • ClC-4A 3
  • CLC4 3

External Ids for CLCN4 Gene

Previous GeneCards Identifiers for CLCN4 Gene

  • GC0XP009154
  • GC0XP008940
  • GC0XP009471
  • GC0XP009536
  • GC0XP009934
  • GC0XP007954

Summaries for CLCN4 Gene

Entrez Gene Summary for CLCN4 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. Chloride channel 4 has an evolutionary conserved CpG island and is conserved in both mouse and hamster. This gene is mapped in close proximity to APXL (Apical protein Xenopus laevis-like) and OA1 (Ocular albinism type I), which are both located on the human X chromosome at band p22.3. The physiological role of chloride channel 4 remains unknown but may contribute to the pathogenesis of neuronal disorders. Alternate splicing results in two transcript variants that encode different proteins. [provided by RefSeq, Mar 2012]

GeneCards Summary for CLCN4 Gene

CLCN4 (Chloride Channel, Voltage-Sensitive 4) is a Protein Coding gene. Diseases associated with CLCN4 include ocular albinism and dent disease. 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 antiporter activity. An important paralog of this gene is CLCN7.

UniProtKB/Swiss-Prot for CLCN4 Gene

  • Proton-coupled chloride transporter. Functions as antiport system and exchanges chloride ions against protons.

Gene Wiki entry for CLCN4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLCN4 Gene

Genomics for CLCN4 Gene

Regulatory Elements for CLCN4 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for CLCN4 Gene

10,156,945 bp from pter
10,237,660 bp from pter
80,716 bases
Plus strand

Genomic View for CLCN4 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLCN4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLCN4 Gene

Proteins for CLCN4 Gene

  • Protein details for CLCN4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    H(+)/Cl(-) exchange transporter 4
    Protein Accession:
    Secondary Accessions:
    • A1L3U1
    • B7Z5Z4
    • Q9UBU1

    Protein attributes for CLCN4 Gene

    760 amino acids
    Molecular mass:
    84917 Da
    Quaternary structure:
    No Data Available
    • The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons. The presence of conserved gating glutamate residues is typical for family members that function as antiporters

    Alternative splice isoforms for CLCN4 Gene


neXtProt entry for CLCN4 Gene

Proteomics data for CLCN4 Gene at MOPED

Post-translational modifications for CLCN4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLCN4 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for CLCN4 Gene

Domains for CLCN4 Gene

Gene Families for CLCN4 Gene

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

Graphical View of Domain Structure for InterPro Entry



  • P51793
  • Contains 2 CBS domains.
  • Belongs to the chloride channel (TC 2.A.49) family. ClC-4/CLCN4 subfamily.
genes like me logo Genes that share domains with CLCN4: view

Function for CLCN4 Gene

Molecular function for CLCN4 Gene

GENATLAS Biochemistry:
chloride voltage-gated channel 4,brain and heart
UniProtKB/Swiss-Prot Function:
Proton-coupled chloride transporter. Functions as antiport system and exchanges chloride ions against protons.

Gene Ontology (GO) - Molecular Function for CLCN4 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 IDA 10564087
GO:0005524 ATP binding IEA --
GO:0015297 antiporter activity IEA --
genes like me logo Genes that share ontologies with CLCN4: view

Phenotypes for CLCN4 Gene

genes like me logo Genes that share phenotypes with CLCN4: view

Animal Models for CLCN4 Gene

MGI Knock Outs for CLCN4:

Animal Model Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLCN4

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for CLCN4 Gene

Localization for CLCN4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCN4 Gene

Early endosome membrane; Multi-pass membrane protein. Late endosome membrane; Multi-pass membrane protein.

Subcellular locations from

Jensen Localization Image for CLCN4 Gene COMPARTMENTS Subcellular localization image for CLCN4 gene
Compartment Confidence
endosome 5
plasma membrane 3
cytosol 1
golgi apparatus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for CLCN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010008 endosome membrane TAS --
GO:0016020 membrane --
GO:0016021 integral component of membrane IEA --
GO:0031901 early endosome membrane IEA --
GO:0031902 late endosome membrane IEA --
genes like me logo Genes that share ontologies with CLCN4: view

Pathways for CLCN4 Gene

genes like me logo Genes that share pathways with CLCN4: view

Gene Ontology (GO) - Biological Process for CLCN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport TAS 8069296
GO:0006821 chloride transport IDA 10564087
GO:0034220 ion transmembrane transport TAS --
GO:0044070 regulation of anion transport --
GO:0055085 transmembrane transport TAS --
genes like me logo Genes that share ontologies with CLCN4: view

Compounds for CLCN4 Gene

(1) HMDB Compounds for CLCN4 Gene

Compound Synonyms Cas Number PubMed IDs
  • Cl2

(2) IUPHAR Ligand for CLCN4 Gene

Ligand Type Action Affinity Pubmed IDs
Zn2+ Channel blocker None 6
Cd2+ Channel blocker None

(3) Novoseek inferred chemical compound relationships for CLCN4 Gene

Compound -log(P) Hits PubMed IDs
chloride 78.2 12
hydrogen 28.5 1
glutamate 16.4 1
genes like me logo Genes that share compounds with CLCN4: view

Transcripts for CLCN4 Gene

Unigene Clusters for CLCN4 Gene

Chloride channel, voltage-sensitive 4:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLCN4

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLCN4 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: - -
SP2: - -
SP3: - - - -
SP4: - - -

Relevant External Links for CLCN4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLCN4 Gene

mRNA expression in normal human tissues for CLCN4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLCN4 Gene

This gene is overexpressed in Muscle - Skeletal (6.6) and Brain - Frontal Cortex (BA9) (4.1).

Protein differential expression in normal tissues for CLCN4 Gene

This gene is overexpressed in Frontal cortex (36.5) and Retina (32.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for CLCN4 Gene

SOURCE GeneReport for Unigene cluster for CLCN4 Gene Hs.495674

mRNA Expression by UniProt/SwissProt for CLCN4 Gene

Tissue specificity: Abundant in skeletal muscle and also detectable in brain and heart
genes like me logo Genes that share expressions with CLCN4: view

Expression partners for CLCN4 Gene

In Situ Assay Products

Orthologs for CLCN4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CLCN4 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CLCN4 35
  • 90.22 (n)
  • 97.76 (a)
CLCN4 36
  • 98 (a)
(Canis familiaris)
Mammalia CLCN4 35
  • 91.45 (n)
  • 99.21 (a)
CLCN4 36
  • 99 (a)
(Mus musculus)
Mammalia Clcn4-2 35
  • 88.26 (n)
  • 98.53 (a)
Clcn4-2 16
Clcn4-2 36
  • 99 (a)
(Rattus norvegicus)
Mammalia Clcn4 35
  • 87.93 (n)
  • 99.07 (a)
(Monodelphis domestica)
Mammalia CLCN4 36
  • 98 (a)
(Ornithorhynchus anatinus)
Mammalia CLCN4 36
  • 97 (a)
(Pan troglodytes)
Mammalia CLCN4 36
  • 100 (a)
(Gallus gallus)
Aves CLCN4 35
  • 81.27 (n)
  • 97.24 (a)
CLCN4 36
  • 97 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 23 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clcn4 35
  • 78.64 (n)
  • 94.74 (a)
Str.12434 35
(Danio rerio)
Actinopterygii clcn4 35
  • 78.18 (n)
  • 90.31 (a)
Dr.7965 35
clcn4 36
  • 89 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.174 35
fruit fly
(Drosophila melanogaster)
Insecta CG5284 37
  • 57 (a)
ClC-c 36
  • 51 (a)
(Caenorhabditis elegans)
Secernentea clh-5 36
  • 52 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GEF1 36
  • 30 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU06444 35
  • 52.05 (n)
  • 44.71 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 58 (a)
Species with no ortholog for CLCN4:
  • 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for CLCN4 Gene

Gene Tree for CLCN4 (if available)
Gene Tree for CLCN4 (if available)

Paralogs for CLCN4 Gene

Paralogs for CLCN4 Gene

Selected SIMAP similar genes for CLCN4 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with CLCN4: view

Variants for CLCN4 Gene

Sequence variations from dbSNP and Humsavar for CLCN4 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs3833 -- 10,237,541(-) AACAC(G/T)TTGCT utr-variant-3-prime
rs10610 -- 10,233,636(+) AAAAA(A/G)AAATA utr-variant-3-prime
rs756826 -- 10,173,460(+) GGTTC(C/G)GCTGC intron-variant
rs1000670 -- 10,213,295(-) CAGGG(G/T)ACAGA intron-variant
rs1003368 -- 10,211,943(+) TCAGC(C/T)ACCAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLCN4 Gene

Variant ID Type Subtype PubMed ID
dgv2438e1 CNV Complex 17122850
nsv519068 CNV Gain 19592680
nsv6795 CNV Insertion 18451855

Relevant External Links for CLCN4 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLCN4 Gene

Disorders for CLCN4 Gene

MalaCards: The human disease database

MalaCards: The human disease database.

Search for CLCN4 Gene in MalaCards »

(2) Diseases for CLCN4 Gene including...

(1) University of Copenhagen DISEASES for CLCN4 Gene

(1) Novoseek inferred disease relationships for CLCN4 Gene

Disease -log(P) Hits PubMed IDs
cystic fibrosis 19.7 1

Relevant External Links for CLCN4

Genetic Association Database (GAD)
genes like me logo Genes that share disorders with CLCN4: view

No data available for OMIM , UniProtKB/Swiss-Prot and Genatlas for CLCN4 Gene

Publications for CLCN4 Gene

  1. A gene from the Xp22.3 region shares homology with voltage-gated chloride channels. (PMID: 8069296) van Slegtenhorst M.A. … Ballabio A. (Hum. Mol. Genet. 1994) 2 3 4 23
  2. Identification of an acid-activated Cl- channel from human skeletal muscles. (PMID: 10564087) Kawasaki M. … Sasaki S. (Am. J. Physiol. 1999) 3 4 23
  3. A new region of conservation is defined between human and mouse X chromosomes. (PMID: 8661129) Dinulos M.B. … Disteche C.M. (Genomics 1996) 3 23
  4. Intragenic TaqI restriction fragment length polymorphism (RFLP) in CICN4, between the loci for X-linked ocular albinism (OA1) and microphthalmia with linear skin defects syndrome (MLS). (PMID: 7759088) Schnur R.E. … Wick P.A. (Hum. Genet. 1995) 3 23
  5. Expression of CLCN voltage-gated chloride channel genes in human blood vessels. (PMID: 10198195) Lamb F.S. … Schutte B.C. (J. Mol. Cell. Cardiol. 1999) 3 23

Products for CLCN4 Gene

Sources for CLCN4 Gene

Back to Top