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Aliases for CLIC3 Gene

Aliases for CLIC3 Gene

  • Chloride Intracellular Channel 3 2 3 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 Deafness, Autosomal Recessive 33. Among its related pathways are Hepatic ABC Transporters and Activation of cAMP-Dependent PKA. 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 for CLIC3 Gene

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

Gene Wiki entry for CLIC3 Gene

Additional gene information for CLIC3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLIC3 Gene

Genomics for CLIC3 Gene

Regulatory Elements for CLIC3 Gene

Enhancers for CLIC3 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
GH09H137166 1.8 FANTOM5 Ensembl ENCODE dbSUPER 1.9 -174.3 -174342 10 HDGF SIN3A ZNF2 ZBTB7B GLIS2 ZNF143 KLF7 SP3 REST GLIS1 MAN1B1 TPRN DPH7 INPP5E IL9RP1 ARRDC1-AS1 EXD3 TMEM203 NDOR1 GRIN1
GH09H136711 1.2 FANTOM5 ENCODE 1.3 +285.1 285080 0 HDAC1 ZEB1 ZNF121 GLIS2 RCOR1 FOS ZNF362 ZNF280D ZBTB2 ZEB2 AGPAT2 NPDC1 C9orf172 ABCA2 LCNL1 FUT7 PAXX CCDC183 CLIC3 FAM69B
GH09H136990 1.7 FANTOM5 Ensembl ENCODE 0.7 +0.8 788 10 HDGF PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 LCN12 EHMT1 SEC16A ABCA2 SDCCAG3 ANAPC2 PRR31 C9orf139 MAN1B1 SNHG7
GH09H137004 0.8 Ensembl 0.4 -7.7 -7698 0 GTF2F1 CTCF KLF1 ATF1 RB1 ETV1 KLF17 NFXL1 ZNF2 RFX5 PIR32105 CLIC3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLIC3 on UCSC Golden Path with GeneCards custom track

Genomic Location for CLIC3 Gene

Chromosome:
9
Start:
136,994,608 bp from pter
End:
136,996,803 bp from pter
Size:
2,196 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 ERK7.
    SequenceCaution:
    • Sequence=AAD16450.1; Type=Frameshift; Positions=28; 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

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • 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

Suggested Antigen Peptide Sequences for CLIC3 Gene

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

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

Gene Ontology (GO) - Molecular Function for CLIC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004364 NOT glutathione transferase activity IBA --
GO:0005244 voltage-gated ion channel activity IEA --
GO:0005254 chloride channel activity 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 Model Products

  • Taconic Biosciences Mouse Models for CLIC3

CRISPR Products

miRNA for CLIC3 Gene

miRTarBase miRNAs that target CLIC3

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CLIC3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
extracellular 5
nucleus 5
cytosol 4
plasma membrane 2
mitochondrion 1
lysosome 1
endosome 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 IEA,IDA 9880541
GO:0005737 cytoplasm IDA,IEA 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

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

Pathways by source for CLIC3 Gene

Gene Ontology (GO) - Biological Process for CLIC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006749 NOT glutathione metabolic process IBA --
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006821 chloride transport IMP 9880541
GO:0007165 signal transduction TAS 9880541
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

(2) Additional Compounds for CLIC3 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Chloride ion
  • Bertholite
  • Chloor
  • Chlor
  • Chlore
  • Chloride
16887-00-6
genes like me logo Genes that share compounds with CLIC3: view

Transcripts for CLIC3 Gene

mRNA/cDNA for CLIC3 Gene

Unigene Clusters for CLIC3 Gene

Chloride intracellular channel 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CLIC3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

No ASD Table

Relevant External Links for CLIC3 Gene

GeneLoc Exon Structure for
CLIC3
ECgene alternative splicing isoforms for
CLIC3

Expression for CLIC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for CLIC3 Gene



NURSA nuclear receptor signaling pathways regulating expression of CLIC3 Gene:

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)
genes like me logo Genes that share expression patterns with CLIC3: view

Primer Products

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 33 34
  • 99.44 (n)
cow
(Bos Taurus)
Mammalia CLIC3 33 34
  • 89.55 (n)
dog
(Canis familiaris)
Mammalia CLIC3 33 34
  • 86.16 (n)
mouse
(Mus musculus)
Mammalia Clic3 33 16 34
  • 83.76 (n)
rat
(Rattus norvegicus)
Mammalia Clic3 33
  • 83.76 (n)
oppossum
(Monodelphis domestica)
Mammalia CLIC3 34
  • 72 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CLIC3 34
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC417293 33
  • 74.67 (n)
CLIC3 34
  • 66 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLIC3 34
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clic3 33
  • 64.78 (n)
zebrafish
(Danio rerio)
Actinopterygii clica 33 34
  • 59.53 (n)
fruit fly
(Drosophila melanogaster)
Insecta Clic 34
  • 21 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea exl-1 34
  • 23 (a)
ManyToMany
exc-4 34
  • 17 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6991 34
  • 32 (a)
OneToMany
Species where no ortholog for CLIC3 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)
  • 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 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)

Paralogs for CLIC3 Gene

Paralogs for CLIC3 Gene

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

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

Variants for CLIC3 Gene

Sequence variations from dbSNP and Humsavar for CLIC3 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs1000031872 -- 136,994,144(+) AGACC(A/G)TCCAG downstream-variant-500B
rs1000515051 -- 136,999,133(+) TTCTA(C/T)TTTCT upstream-variant-2KB
rs1001006176 -- 136,995,137(+) CCAGG(C/T)CCAGG intron-variant
rs1001786088 -- 136,997,998(+) GCCCC(A/G)GCATC upstream-variant-2KB
rs1002465632 -- 136,999,032(+) TAACA(-/T)TTTTT upstream-variant-2KB

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)

Relevant External Links for CLIC3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLIC3

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: DISEASES

Disorder Aliases PubMed IDs
deafness, autosomal recessive 33
  • autosomal recessive nonsyndromic deafness 33
- elite association - COSMIC cancer census association via MalaCards
Search CLIC3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for CLIC3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 60
  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 60
  3. Structure of human CLIC3 at 2 A resolution. (PMID: 20146363) Littler DR … Curmi PM (Proteins 2010) 3 4 60
  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 60
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60

Products for CLIC3 Gene

Sources for CLIC3 Gene

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