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 1 is a member of the p64 family; the protein localizes principally to the cell nucleus and exhibits both nucle... See more...

Aliases for CLIC1 Gene

Aliases for CLIC1 Gene

  • Chloride Intracellular Channel 1 2 3 5
  • NCC27 2 3 4
  • G6 2 3 4
  • Regulatory Nuclear Chloride Ion Channel Protein 3 4
  • Chloride Intracellular Channel Protein 1 3 4
  • Nuclear Chloride Ion Channel 27 3 4
  • Chloride Channel ABP 3 4
  • P64CLCP 2 3
  • CLCNL1 2 3
  • HRNCC 3 4
  • Nuclear Chloride Ion Channel Protein 3
  • RNCC Protein 3
  • CL1C1 3
  • CLIC1 5

External Ids for CLIC1 Gene

Previous GeneCards Identifiers for CLIC1 Gene

  • GC06U990013
  • GC06M031752
  • GC06M031469
  • GC06M031802
  • GC06M031806
  • GC06M031698
  • GC06M031484
  • GC06M031731
  • GC06M032075
  • GC06M032146
  • GC06M032216
  • GC06M032375
  • GC06M031742
  • GC06M031751
  • GC06M031818
  • GC06M031865
  • GC06M031897
  • GC06M031948
  • GC06M031991
  • GC06M032030
  • GC06M032621
  • GC06M033042

Summaries for CLIC1 Gene

Entrez Gene Summary for CLIC1 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 1 is a member of the p64 family; the protein localizes principally to the cell nucleus and exhibits both nuclear and plasma membrane chloride ion channel activity. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLIC1 Gene

CLIC1 (Chloride Intracellular Channel 1) is a Protein Coding gene. Diseases associated with CLIC1 include Gallbladder Cancer and Colorectal Cancer. 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 CLIC4.

UniProtKB/Swiss-Prot Summary for CLIC1 Gene

  • Can insert into membranes and form chloride ion channels. Channel activity depends on the pH. Membrane insertion seems to be redox-regulated and may occur only under oxydizing conditions. Involved in regulation of the cell cycle.

Gene Wiki entry for CLIC1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLIC1 Gene

Genomics for CLIC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLIC1 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 CLIC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLIC1

Top Transcription factor binding sites by QIAGEN in the CLIC1 gene promoter:
  • Evi-1
  • GATA-2
  • Nkx2-5
  • p53
  • Sp1

Genomic Locations for CLIC1 Gene

Latest Assembly
chr6:31,730,581-31,739,763
(GRCh38/hg38)
Size:
9,183 bases
Orientation:
Minus strand

Previous Assembly
chr6:31,698,358-31,705,095
(GRCh37/hg19 by Entrez Gene)
Size:
6,738 bases
Orientation:
Minus strand

chr6:31,698,358-31,707,540
(GRCh37/hg19 by Ensembl)
Size:
9,183 bases
Orientation:
Minus strand

Alternative Locations (GRCh38/hg38)

  • chr6(ALT_REF_LOCI_2):3,207,869-3,214,610 (-)
  • chr6(ALT_REF_LOCI_3):2,978,342-2,985,081 (-)
  • chr6(ALT_REF_LOCI_4):3,035,628-3,042,369 (-)
  • chr6(ALT_REF_LOCI_5):3,072,456-3,079,197 (-)
  • chr6(ALT_REF_LOCI_6):2,986,392-2,993,137 (-)
  • chr6(ALT_REF_LOCI_7):3,029,877-3,036,620 (-)

Genomic View for CLIC1 Gene

Genes around CLIC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLIC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLIC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for CLIC1 Gene

  • Protein details for CLIC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O00299-CLIC1_HUMAN
    Recommended name:
    Chloride intracellular channel protein 1
    Protein Accession:
    O00299
    Secondary Accessions:
    • Q15089
    • Q502X1

    Protein attributes for CLIC1 Gene

    Size:
    241 amino acids
    Molecular mass:
    26923 Da
    Quaternary structure:
    • Monomer. Homodimer (in vitro). Interacts with TRAPPC2. Dimerization requires a conformation change that leads to the exposure of a large hydrophobic surface. In vivo, this may lead to membrane insertion. Interacts with AKAP9.
    Miscellaneous:
    • The protein seems to have very low affinity for glutathione, even though glutathione binding was observed in protein crystals.

    Three dimensional structures from OCA and Proteopedia for CLIC1 Gene

neXtProt entry for CLIC1 Gene

Post-translational modifications for CLIC1 Gene

  • Hydrogen peroxide treatment causes a conformation change, leading to dimerization and formation of an intramolecular disulfide bond between Cys-24 and Cys-59.
  • Ubiquitination at Lys49, Lys57, Lys119, Lys131, Lys135, Lys138, Lys166, and Lys183
  • Modification sites at PhosphoSitePlus

Other Protein References for CLIC1 Gene

No data available for DME Specific Peptides for CLIC1 Gene

Domains & Families for CLIC1 Gene

Gene Families for CLIC1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transporters

Protein Domains for CLIC1 Gene

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

Suggested Antigen Peptide Sequences for CLIC1 Gene

GenScript: Design optimal peptide antigens:
  • Regulatory nuclear chloride ion channel protein (CLIC1_HUMAN)
  • cDNA, FLJ94671, Homo sapiens chloride intracellular channel 1 (CLIC1), mRNA (Q5SRT3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O00299

UniProtKB/Swiss-Prot:

CLIC1_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.
  • 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.
Family:
  • Belongs to the chloride channel CLIC family.
genes like me logo Genes that share domains with CLIC1: view

Function for CLIC1 Gene

Molecular function for CLIC1 Gene

UniProtKB/Swiss-Prot Function:
Can insert into membranes and form chloride ion channels. Channel activity depends on the pH. Membrane insertion seems to be redox-regulated and may occur only under oxydizing conditions. Involved in regulation of the cell cycle.

Phenotypes From GWAS Catalog for CLIC1 Gene

Gene Ontology (GO) - Molecular Function for CLIC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005244 voltage-gated ion channel activity IEA --
GO:0005254 chloride channel activity IDA 9139710
GO:0005515 protein binding IPI 12163479
GO:0045296 cadherin binding HDA 25468996
genes like me logo Genes that share ontologies with CLIC1: view
genes like me logo Genes that share phenotypes with CLIC1: view

Animal Models for CLIC1 Gene

MGI Knock Outs for CLIC1:
  • Clic1 Clic1<tm1.1Breit>

Animal Models for research

  • Taconic Biosciences Mouse Models for CLIC1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLIC1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CLIC1 Gene

Localization for CLIC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLIC1 Gene

Nucleus. Nucleus membrane. Single-pass membrane protein. Cytoplasm. Cell membrane. Single-pass membrane protein. Note=Mostly in the nucleus including in the nuclear membrane (PubMed:9139710, PubMed:12681486). Small amount in the cytoplasm and the plasma membrane (PubMed:9139710). Exists both as soluble cytoplasmic protein and as membrane protein with probably a single transmembrane domain (PubMed:11940526, PubMed:11551966, PubMed:14613939). {ECO:0000269 PubMed:11551966, ECO:0000269 PubMed:11940526, ECO:0000269 PubMed:12681486, ECO:0000269 PubMed:14613939, ECO:0000269 PubMed:9139710}.

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 CLIC1 gene
Compartment Confidence
extracellular 5
nucleus 5
plasma membrane 4
mitochondrion 3
cytosol 3
cytoskeleton 2
endoplasmic reticulum 2
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CLIC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space HDA 22664934
GO:0005634 nucleus IBA,TAS 16130169
GO:0005635 nuclear envelope IDA 9139710
GO:0005737 cytoplasm IEA,IDA 10793131
GO:0005739 mitochondrion IEA --
genes like me logo Genes that share ontologies with CLIC1: view

Pathways & Interactions for CLIC1 Gene

PathCards logo

SuperPathways for CLIC1 Gene

SuperPathway Contained pathways
1 Activation of cAMP-Dependent PKA
.77
.77
.56
2 Neuroscience
3 Neuropathic Pain-Signaling in Dorsal Horn Neurons
.40
4 Hepatic ABC Transporters
.41
genes like me logo Genes that share pathways with CLIC1: view

Pathways by source for CLIC1 Gene

5 Qiagen pathways for CLIC1 Gene
  • Activation of cAMP-Dependent PKA
  • cAMP Pathway
  • Cholera Infection
  • Hepatic ABC Transporters
  • PKA Signaling
1 Cell Signaling Technology pathway for CLIC1 Gene

Gene Ontology (GO) - Biological Process for CLIC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006749 glutathione metabolic process IEA --
GO:0006811 ion transport IEA --
GO:0006821 chloride transport IDA 9139710
GO:0007165 signal transduction TAS 16130169
GO:0034220 ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with CLIC1: view

No data available for SIGNOR curated interactions for CLIC1 Gene

Drugs & Compounds for CLIC1 Gene

(4) Drugs for CLIC1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Copper Approved, Investigational Pharma Target 276
Dihydroartemisinin Approved, Experimental, Investigational Pharma Target, ligand 123
Chloride ion Experimental Pharma 0

(2) Additional Compounds for CLIC1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CLIC1: view

Transcripts for CLIC1 Gene

mRNA/cDNA for CLIC1 Gene

3 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
5 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 CLIC1

Alternative Splicing Database (ASD) splice patterns (SP) for CLIC1 Gene

No ASD Table

Relevant External Links for CLIC1 Gene

GeneLoc Exon Structure for
CLIC1

Expression for CLIC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLIC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLIC1 Gene

This gene is overexpressed in Whole Blood (x10.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLIC1 Gene



Protein tissue co-expression partners for CLIC1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLIC1

SOURCE GeneReport for Unigene cluster for CLIC1 Gene:

Hs.414565

mRNA Expression by UniProt/SwissProt for CLIC1 Gene:

O00299-CLIC1_HUMAN
Tissue specificity: Expression is prominent in heart, placenta, liver, kidney and pancreas.

Evidence on tissue expression from TISSUES for CLIC1 Gene

  • Liver(4.8)
  • Skin(4.7)
  • Pancreas(4.6)
  • Lung(4.6)
  • Intestine(4.4)
  • Nervous system(4.2)
  • Stomach(4.1)
  • Blood(4)
  • Kidney(3.5)
  • Heart(3.1)
  • Spleen(3.1)
  • Bone(3)
  • Muscle(2.6)
  • Eye(2.4)
  • Lymph node(2.3)
  • Bone marrow(2.2)
genes like me logo Genes that share expression patterns with CLIC1: view

Primer products for research

No data available for Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLIC1 Gene

Orthologs for CLIC1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CLIC1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CLIC1 29 30
  • 99.17 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CLIC1 30
  • 93 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia CLIC1 29 30
  • 92.39 (n)
OneToMany
-- 30
  • 92 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia CLIC1 29 30
  • 91.7 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Clic1 29 16 30
  • 90.04 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Clic1 29
  • 89.9 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia CLIC1 30
  • 80 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CLIC1 30
  • 87 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia clic1 29
  • 69.47 (n)
MGC75951 29
African clawed frog
(Xenopus laevis)
Amphibia CLIC1 29
Zebrafish
(Danio rerio)
Actinopterygii clic1 29 30
  • 67.22 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Clic 30
  • 21 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea exl-1 30
  • 25 (a)
ManyToMany
exc-4 30
  • 20 (a)
ManyToMany
Thale Cress
(Arabidopsis thaliana)
eudicotyledons DHAR1 29
  • 45.2 (n)
Rice
(Oryza sativa)
Liliopsida Os05g0116100 29
  • 50.61 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.6991 30
  • 42 (a)
OneToMany
Species where no ortholog for CLIC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Chicken (Gallus gallus)
  • 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 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)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for CLIC1 Gene

ENSEMBL:
Gene Tree for CLIC1 (if available)
TreeFam:
Gene Tree for CLIC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLIC1: view image
Alliance of Genome Resources:
Additional Orthologs for CLIC1

Paralogs for CLIC1 Gene

(6) SIMAP similar genes for CLIC1 Gene using alignment to 2 proteins:

  • CLIC1_HUMAN
  • Q5SRT3_HUMAN

Pseudogenes.org Pseudogenes for CLIC1 Gene

genes like me logo Genes that share paralogs with CLIC1: view

Variants for CLIC1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CLIC1 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 CLIC1 Gene

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259

Variation tolerance for CLIC1 Gene

Residual Variation Intolerance Score: 64.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.27; 52.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLIC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLIC1
Leiden Open Variation Database (LOVD)
CLIC1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLIC1 Gene

Disorders for CLIC1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CLIC1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
gallbladder cancer
  • gallbladder ca
colorectal cancer
  • crc
- elite association - COSMIC cancer census association via MalaCards
Search CLIC1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLIC1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CLIC1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLIC1 Gene

Publications for CLIC1 Gene

  1. Molecular cloning and expression of a chloride ion channel of cell nuclei. (PMID: 9139710) Valenzuela SM … Breit SN (The Journal of biological chemistry 1997) 2 3 4 22
  2. The intracellular chloride ion channel protein CLIC1 undergoes a redox-controlled structural transition. (PMID: 14613939) Littler DR … Curmi PM (The Journal of biological chemistry 2004) 3 4 22
  3. AKAP350 at the Golgi apparatus. II. Association of AKAP350 with a novel chloride intracellular channel (CLIC) family member. (PMID: 12163479) Shanks RA … Goldenring JR (The Journal of biological chemistry 2002) 3 4 22
  4. Crystal structure of a soluble form of the intracellular chloride ion channel CLIC1 (NCC27) at 1.4-A resolution. (PMID: 11551966) Harrop SJ … Curmi PM (The Journal of biological chemistry 2001) 3 4 22
  5. The nuclear chloride ion channel NCC27 is involved in regulation of the cell cycle. (PMID: 11195932) Valenzuela SM … Breit SN (The Journal of physiology 2000) 3 4 22

Products for CLIC1 Gene