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Aliases for CLIC1 Gene

Aliases for CLIC1 Gene

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

External Ids for CLIC1 Gene

Previous GeneCards Identifiers for CLIC1 Gene

  • GC06U990013
  • GC06M031752
  • GC06M031469
  • GC06M031802
  • GC06M031806
  • GC06M031698
  • GC06M031484
  • GC06M031731
  • GC06M031742
  • GC06M031751
  • GC06M031818
  • GC06M031865
  • GC06M031897

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 Blackwater Fever and Hyperornithinemia-Hyperammonemia-Homocitrullinuria Syndrome. 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 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

Additional gene information for CLIC1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLIC1 Gene

Genomics for CLIC1 Gene

GeneHancer (GH) Regulatory Elements for CLIC1 Gene

Promoters and enhancers for CLIC1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I031733 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 559.2 +2.3 2308 8.5 CLOCK MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 MSH5 CLIC1 DDX39B LY6G5B ATF6B LSM2 CSNK2B SKIV2L GPANK1 BAG6
GH06I031619 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 18 +118.5 118536 4 CLOCK ZFP64 FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC GC06P031990 GC06P032044 GC06P032046 GC06P032049 GC06P032051 GC06P032055 GC06P032056 GC06P032063 GC06P032065 GC06P032066
GH06I032175 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 17.9 -438.0 -437997 5.1 DMAP1 YBX1 YY1 E2F8 ZNF143 ZNF548 SP3 NFYC GLIS1 NR2C1 RNF5 AGPAT1 BRD2 LSM2 LY6G5B DDX39B ATF6B GPANK1 VARS BAG6
GH06I031545 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 18 +192.2 192231 3.2 CLOCK MLX YBX1 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 NFKBIL1 ATP6V1G2 ATP6V1G2-DDX39B DDX39B DHX16 ATF6B LY6G5B LSM2 MDC1 TCF19
GH06I031813 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.8 -86.1 -86113 25.6 CLOCK ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 C6orf48 HSPA1B HSPA1A HSPA1L GC06P032039 ATF6B DDX39B LY6G5B LSM2 BAG6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CLIC1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLIC1 gene promoter:

Genomic Locations for CLIC1 Gene

Genomic Locations for CLIC1 Gene
chr6:31,730,581-31,739,763
(GRCh38/hg38)
Size:
9,183 bases
Orientation:
Minus strand
chr6:31,698,358-31,707,540
(GRCh37/hg19)

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 posLast=4949, Lys57, posLast=135135, posLast=138138, and posLast=183183
  • 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

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:0004364 NOT glutathione transferase activity IBA --
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 IDA 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:

Animal Model Products

  • Taconic Biosciences Mouse Models for CLIC1

Clone Products

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. Small amount in the cytoplasm and the plasma membrane. Exists both as soluble cytoplasmic protein and as membrane protein with probably a single transmembrane domain.

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
cytosol 4
mitochondrion 3
endoplasmic reticulum 2
cytoskeleton 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 IDA,HDA 22664934
GO:0005634 nucleus TAS 16130169
GO:0005635 nuclear envelope IDA 9139710
GO:0005737 cytoplasm IDA 10793131
GO:0005739 mitochondrion IEA --
genes like me logo Genes that share ontologies with CLIC1: view

Pathways & Interactions for CLIC1 Gene

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

Pathways by source for CLIC1 Gene

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 NOT glutathione metabolic process IBA --
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006821 chloride transport IDA 9139710
GO:0007165 signal transduction TAS 16130169
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

(2) Drugs for CLIC1 Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Copper Approved, Investigational Pharma Target 202

(3) Additional Compounds for CLIC1 Gene - From: Novoseek and HMDB

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 CLIC1: view

Transcripts for CLIC1 Gene

Unigene Clusters for CLIC1 Gene

Chloride intracellular channel 1:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for CLIC1 Gene

GeneLoc Exon Structure for
CLIC1
ECgene alternative splicing isoforms for
CLIC1

Expression for CLIC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for CLIC1 Gene



Protein tissue co-expression partners for CLIC1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLIC1 Gene:

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(4.9)
  • Pancreas(4.6)
  • Lung(4.5)
  • Skin(4.5)
  • Intestine(4.4)
  • Nervous system(4.2)
  • Blood(4.1)
  • Stomach(3.8)
  • Kidney(3.5)
  • Heart(3.2)
  • Muscle(3.1)
  • Spleen(2.6)
  • Bone(2.4)
  • Eye(2.2)
genes like me logo Genes that share expression patterns with CLIC1: view

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 33 34
  • 99.17 (n)
oppossum
(Monodelphis domestica)
Mammalia CLIC1 34
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CLIC1 33 34
  • 92.39 (n)
-- 34
  • 92 (a)
OneToMany
cow
(Bos Taurus)
Mammalia CLIC1 33 34
  • 91.7 (n)
mouse
(Mus musculus)
Mammalia Clic1 33 16 34
  • 90.04 (n)
rat
(Rattus norvegicus)
Mammalia Clic1 33
  • 89.9 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLIC1 34
  • 80 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLIC1 34
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clic1 33
  • 69.47 (n)
MGC75951 33
African clawed frog
(Xenopus laevis)
Amphibia CLIC1 33
zebrafish
(Danio rerio)
Actinopterygii clic1 33 34
  • 67.22 (n)
fruit fly
(Drosophila melanogaster)
Insecta Clic 34
  • 21 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea exl-1 34
  • 25 (a)
ManyToMany
exc-4 34
  • 20 (a)
ManyToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons DHAR1 33
  • 45.2 (n)
rice
(Oryza sativa)
Liliopsida Os05g0116100 33
  • 50.61 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6991 34
  • 42 (a)
OneToMany
Species where no ortholog for CLIC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for CLIC1 Gene

Paralogs for CLIC1 Gene

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

Pseudogenes.org Pseudogenes for CLIC1 Gene

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

Variants for CLIC1 Gene

Sequence variations from dbSNP and Humsavar for CLIC1 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000211682 -- 31,732,963(-) A/T intron_variant
rs1000238815 -- 31,730,980(-) T/C coding_sequence_variant, synonymous_variant
rs1000242585 -- 31,732,712(-) A/G intron_variant
rs1000265313 -- 31,731,565(-) G/C intron_variant
rs1000398315 -- 31,738,731(-) TT/T upstream_transcript_variant

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLIC1 Gene

Disorders for CLIC1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for CLIC1 Gene - From: DISEASES

- 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

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 58
  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 58
  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 58
  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 58
  5. Identification of a novel member of the chloride intracellular channel gene family (CLIC5) that associates with the actin cytoskeleton of placental microvilli. (PMID: 10793131) Berryman M … Bretscher A (Molecular biology of the cell 2000) 3 4 22 58

Products for CLIC1 Gene