Chloride channels are a diverse group of proteins that regulate fundamental cellular processes including stabilization of cell membrane potential, transepithelial transport, maintenance of intracellular pH, and regulation of cell volume. Chloride intracellular channel 3 is a member of the p64 family and is predominantly localized in the nucleus and stimulates chloride ion chann... See more...

Aliases for CLIC3 Gene

Aliases for CLIC3 Gene

  • Chloride Intracellular Channel 3 2 3 5
  • Chloride Intracellular Channel Protein 3 3 4
  • CLIC3 5

External Ids for CLIC3 Gene

Previous GeneCards Identifiers for CLIC3 Gene

  • GC09P131140
  • GC09M131578
  • GC09M133330
  • GC09M135246
  • GC09M137164
  • GC09M139008
  • GC09M139889
  • GC09M109348

Summaries for CLIC3 Gene

Entrez Gene Summary for CLIC3 Gene

  • Chloride channels are a diverse group of proteins that regulate fundamental cellular processes including stabilization of cell membrane potential, transepithelial transport, maintenance of intracellular pH, and regulation of cell volume. Chloride intracellular channel 3 is a member of the p64 family and is predominantly localized in the nucleus and stimulates chloride ion channel activity. In addition, this protein may participate in cellular growth control, based on its association with ERK7, a member of the MAP kinase family. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLIC3 Gene

CLIC3 (Chloride Intracellular Channel 3) is a Protein Coding gene. Diseases associated with CLIC3 include Adenosquamous Gallbladder Carcinoma. Among its related pathways are Activation of cAMP-Dependent PKA and Hepatic ABC Transporters. Gene Ontology (GO) annotations related to this gene include chloride channel activity and voltage-gated chloride channel activity. An important paralog of this gene is CLIC1.

UniProtKB/Swiss-Prot Summary for CLIC3 Gene

  • Can insert into membranes and form chloride ion channels. May participate in cellular growth control.

Gene Wiki entry for CLIC3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLIC3 Gene

Genomics for CLIC3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLIC3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLIC3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLIC3

Top Transcription factor binding sites by QIAGEN in the CLIC3 gene promoter:
  • Egr-2
  • Egr-3
  • Elk-1
  • GATA-2
  • HTF
  • ITF-2
  • Olf-1
  • Sp1
  • Tal-1beta

Genomic Locations for CLIC3 Gene

Latest Assembly
chr9:136,994,608-136,997,929
(GRCh38/hg38)
Size:
3,322 bases
Orientation:
Minus strand

Previous Assembly
chr9:139,889,060-139,891,020
(GRCh37/hg19 by Entrez Gene)
Size:
1,961 bases
Orientation:
Minus strand

chr9:139,889,087-139,891,255
(GRCh37/hg19 by Ensembl)
Size:
2,169 bases
Orientation:
Minus strand

Genomic View for CLIC3 Gene

Genes around CLIC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLIC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLIC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLIC3 Gene

Proteins for CLIC3 Gene

  • Protein details for CLIC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95833-CLIC3_HUMAN
    Recommended name:
    Chloride intracellular channel protein 3
    Protein Accession:
    O95833
    Secondary Accessions:
    • Q5SPZ7

    Protein attributes for CLIC3 Gene

    Size:
    236 amino acids
    Molecular mass:
    26648 Da
    Quaternary structure:
    • Associated with the C-terminal of MAPK15.
    SequenceCaution:
    • Sequence=AAD16450.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CLIC3 Gene

neXtProt entry for CLIC3 Gene

Post-translational modifications for CLIC3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLIC3 Gene

Antibodies for research

  • Abcam antibodies for CLIC3

No data available for DME Specific Peptides for CLIC3 Gene

Domains & Families for CLIC3 Gene

Gene Families for CLIC3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transporters

Protein Domains for CLIC3 Gene

InterPro:
Blocks:
  • Glutathione S-transferase, N-terminal
  • Intracellular chloride (Cl-) channel signature

Suggested Antigen Peptide Sequences for CLIC3 Gene

GenScript: Design optimal peptide antigens:
  • Chloride intracellular channel protein 3 (CLIC3_HUMAN)
  • Chloride intracellular channel 3, isoform CRA_b (Q6FGP1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O95833

UniProtKB/Swiss-Prot:

CLIC3_HUMAN :
  • Members of this family may change from a globular, soluble state to a state where the N-terminal domain is inserted into the membrane and functions as chloride channel. A conformation change of the N-terminal domain is thought to expose hydrophobic surfaces that trigger membrane insertion (By similarity).
  • Belongs to the chloride channel CLIC family.
Domain:
  • Members of this family may change from a globular, soluble state to a state where the N-terminal domain is inserted into the membrane and functions as chloride channel. A conformation change of the N-terminal domain is thought to expose hydrophobic surfaces that trigger membrane insertion (By similarity).
Family:
  • Belongs to the chloride channel CLIC family.
genes like me logo Genes that share domains with CLIC3: view

Function for CLIC3 Gene

Molecular function for CLIC3 Gene

UniProtKB/Swiss-Prot Function:
Can insert into membranes and form chloride ion channels. May participate in cellular growth control.
GENATLAS Biochemistry:
membrane chloride intracellular channel 3

Gene Ontology (GO) - Molecular Function for CLIC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005244 voltage-gated ion channel activity IEA --
GO:0005254 chloride channel activity IBA,IMP 9880541
GO:0005515 protein binding IPI 9880541
genes like me logo Genes that share ontologies with CLIC3: view
genes like me logo Genes that share phenotypes with CLIC3: view

Animal Models for research

  • Taconic Biosciences Mouse Models for CLIC3

miRNA for CLIC3 Gene

miRTarBase miRNAs that target CLIC3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLIC3

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CLIC3 Gene

Localization for CLIC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLIC3 Gene

Nucleus. Membrane. Single-pass membrane protein. Cytoplasm. Note=Predominantly nuclear. Some protein was found in the cytoplasm. Exists both as soluble cytoplasmic protein and as membrane protein with probably a single transmembrane domain (By similarity). {ECO:0000250}.

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 CLIC3 gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 4
plasma membrane 3
mitochondrion 2
endosome 2
lysosome 2
cytoskeleton 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLIC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 9880541
GO:0005737 cytoplasm IEA,IDA 9880541
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with CLIC3: view

Pathways & Interactions for CLIC3 Gene

PathCards logo

SuperPathways for CLIC3 Gene

SuperPathway Contained pathways
1 Activation of cAMP-Dependent PKA
.77
.77
.56
2 Neuropathic Pain-Signaling in Dorsal Horn Neurons
.40
3 Hepatic ABC Transporters
.41
genes like me logo Genes that share pathways with CLIC3: view

Pathways by source for CLIC3 Gene

5 Qiagen pathways for CLIC3 Gene
  • Activation of cAMP-Dependent PKA
  • cAMP Pathway
  • Cholera Infection
  • Hepatic ABC Transporters
  • PKA Signaling

Gene Ontology (GO) - Biological Process for CLIC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006749 glutathione metabolic process IEA --
GO:0006811 ion transport IEA --
GO:0006821 chloride transport IMP 9880541
GO:0007165 signal transduction TAS 9880541
GO:0034220 ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with CLIC3: view

No data available for SIGNOR curated interactions for CLIC3 Gene

Drugs & Compounds for CLIC3 Gene

(1) Drugs for CLIC3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Chloride ion Experimental Pharma 0

(1) Additional Compounds for CLIC3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CLIC3: view

Transcripts for CLIC3 Gene

mRNA/cDNA for CLIC3 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLIC3

Alternative Splicing Database (ASD) splice patterns (SP) for CLIC3 Gene

No ASD Table

Relevant External Links for CLIC3 Gene

GeneLoc Exon Structure for
CLIC3

Expression for CLIC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLIC3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLIC3 Gene

This gene is overexpressed in Esophagus - Mucosa (x16.3), Vagina (x6.5), Skin - Not Sun Exposed (Suprapubic) (x5.5), Skin - Sun Exposed (Lower leg) (x5.1), Thyroid (x4.8), and Cervix - Ectocervix (x4.2).

Protein differential expression in normal tissues from HIPED for CLIC3 Gene

This gene is overexpressed in Cervix (39.1) and Hair follicle (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLIC3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLIC3

SOURCE GeneReport for Unigene cluster for CLIC3 Gene:

Hs.64746

mRNA Expression by UniProt/SwissProt for CLIC3 Gene:

O95833-CLIC3_HUMAN
Tissue specificity: Detected in placenta (at protein level). Widely expressed. High expression is found in placenta followed by lung and heart. Low expression in skeletal muscle, kidney and pancreas.

Evidence on tissue expression from TISSUES for CLIC3 Gene

  • Nervous system(4.2)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with CLIC3: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLIC3 Gene

Orthologs for CLIC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for CLIC3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CLIC3 29 30
  • 99.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CLIC3 29 30
  • 89.55 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CLIC3 29 30
  • 86.16 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Clic3 29 16 30
  • 83.76 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Clic3 29
  • 83.76 (n)
Oppossum
(Monodelphis domestica)
Mammalia CLIC3 30
  • 72 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CLIC3 30
  • 65 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LOC417293 29
  • 74.67 (n)
CLIC3 30
  • 66 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CLIC3 30
  • 67 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia clic3 29
  • 64.78 (n)
Zebrafish
(Danio rerio)
Actinopterygii clica 29 30
  • 59.53 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Clic 30
  • 21 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea exl-1 30
  • 23 (a)
ManyToMany
exc-4 30
  • 17 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.6991 30
  • 32 (a)
OneToMany
Species where no ortholog for CLIC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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 Vase (Ciona intestinalis)
  • 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 CLIC3 Gene

ENSEMBL:
Gene Tree for CLIC3 (if available)
TreeFam:
Gene Tree for CLIC3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLIC3: view image
Alliance of Genome Resources:
Additional Orthologs for CLIC3

Paralogs for CLIC3 Gene

(6) SIMAP similar genes for CLIC3 Gene using alignment to 3 proteins:

  • CLIC3_HUMAN
  • Q5SQ17_HUMAN
  • Q6FGP1_HUMAN
genes like me logo Genes that share paralogs with CLIC3: view

Variants for CLIC3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLIC3 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs2292923 -- p.Pro38His

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CLIC3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CLIC3 Gene

Variant ID Type Subtype PubMed ID
dgv13007n54 CNV loss 21841781
esv2422220 CNV deletion 17116639
nsv469918 CNV loss 18288195
nsv524322 CNV loss 19592680
nsv615991 CNV loss 21841781
nsv818738 CNV gain 17921354
nsv951206 CNV deletion 24416366

Variation tolerance for CLIC3 Gene

Residual Variation Intolerance Score: 77.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.25; 52.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLIC3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLIC3
Leiden Open Variation Database (LOVD)
CLIC3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLIC3 Gene

Disorders for CLIC3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CLIC3 Gene - From: COP

Disorder Aliases PubMed IDs
adenosquamous gallbladder carcinoma
  • adenosquamous carcinoma of gallbladder
- elite association - COSMIC cancer census association via MalaCards
Search CLIC3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLIC3

genes like me logo Genes that share disorders with CLIC3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLIC3 Gene

Publications for CLIC3 Gene

  1. Molecular cloning and characterization of a mitogen-activated protein kinase-associated intracellular chloride channel. (PMID: 9880541) Qian Z … Rosner MR (The Journal of biological chemistry 1999) 2 3 4 22
  2. Expression and cellular localisation of chloride intracellular channel 3 in human placenta and fetal membranes. (PMID: 17027078) Money TT … Gude NM (Placenta 2007) 3 4 22
  3. Structure of human CLIC3 at 2 A resolution. (PMID: 20146363) Littler DR … Curmi PM (Proteins 2010) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for CLIC3 Gene

Sources for CLIC3 Gene