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CLIC5 chloride intracellular channel 5 [ Homo sapiens (human) ]

Gene ID: 53405, updated on 13-Apr-2024

Summary

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Official Symbol
CLIC5provided by HGNC
Official Full Name
chloride intracellular channel 5provided by HGNC
Primary source
HGNC:HGNC:13517
See related
Ensembl:ENSG00000112782 MIM:607293; AllianceGenome:HGNC:13517
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MST130; DFNB102; DFNB103; MSTP130
Summary
This gene encodes a member of the chloride intracellular channel (CLIC) family of chloride ion channels. The encoded protein associates with actin-based cytoskeletal structures and may play a role in multiple processes including hair cell stereocilia formation, myoblast proliferation and glomerular podocyte and endothelial cell maintenance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
Expression
Biased expression in lung (RPKM 21.7), heart (RPKM 20.0) and 10 other tissues See more
Orthologs
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Genomic context

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Location:
6p21.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (45880827..46129819, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (45716118..45964907, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (45866188..46097556, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RUNX2 antisense RNA 1 Neighboring gene U6 spliceosomal RNA Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:45623433-45624632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24646 Neighboring gene NANOG hESC enhancer GRCh37_chr6:45669242-45669749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17267 Neighboring gene Sharpr-MPRA regulatory region 1586 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45722353-45722853 Neighboring gene VISTA enhancer hs1461 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:45866604-45867157 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:45868755-45869954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24647 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45894464-45895128 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:45895129-45895792 Neighboring gene uncharacterized LOC124901326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45928377-45928876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45982710-45983554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45983555-45984399 Neighboring gene RNA, U6 small nuclear 754, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24650 Neighboring gene ectonucleotide pyrophosphatase/phosphodiesterase 4 Neighboring gene ectonucleotide pyrophosphatase/phosphodiesterase family member 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Bi-Allelic Novel Variants in CLIC5 Identified in a Cameroonian Multiplex Family with Non-Syndromic Hearing Impairment. Wonkam-Tingang E, et al. Genes (Basel), 2020 Oct 23. PMID 33114113, Free PMC Article
  2. Data supporting characterization of CLIC1, CLIC4, CLIC5 and DmCLIC antibodies and localization of CLICs in endoplasmic reticulum of cardiomyocytes. Ponnalagu D, et al. Data Brief, 2016 Jun. PMID 27104215, Free PMC Article
  3. Gene transcript amplification from cell lysates in continuous-flow microfluidic devices. Gonzalez A, et al. Biomed Microdevices, 2007 Oct. PMID 17492382
  4. CLIC-5A functions as a chloride channel in vitro and associates with the cortical actin cytoskeleton in vitro and in vivo. Berryman M, et al. J Biol Chem, 2004 Aug 13. PMID 15184393
  5. CLIC5: a novel ETV6 target gene in childhood acute lymphoblastic leukemia. Neveu B, et al. Haematologica, 2016 Dec. PMID 27540136, Free PMC Article

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A comprehensively prognostic and immunological analysis of chloride intracellular channel protein 5 (CLIC5) in pan-cancer and identification in ovarian cancer.
    Title: A comprehensively prognostic and immunological analysis of chloride intracellular channel protein 5 (CLIC5) in pan-cancer and identification in ovarian cancer.
  2. Bi-Allelic Novel Variants in CLIC5 Identified in a Cameroonian Multiplex Family with Non-Syndromic Hearing Impairment.
    Title: Bi-Allelic Novel Variants in CLIC5 Identified in a Cameroonian Multiplex Family with Non-Syndromic Hearing Impairment.
  3. loss of ETV6 leads to significant overexpression of CLIC5, which in turn leads to decreased lysosome-mediated apoptosis. Our data suggest that heightened CLIC5 activity could promote a permissive environment for oxidative stress-induced DNA damage accumulation, and thereby contribute to leukemogenesis.
    Title: CLIC5: a novel ETV6 target gene in childhood acute lymphoblastic leukemia.
  4. EZR, CLIC5 and PODXL are overexpressed in hepatocellular carcinoma and may have a role in cell migration and invasiveness
    Title: Co-Expression of Ezrin-CLIC5-Podocalyxin Is Associated with Migration and Invasiveness in Hepatocellular Carcinoma.
  5. The mechanism of CLIC5A action involves clustered plasma membrane phosphatidylinositol 4,5-bisphosphate accumulation, in turn facilitating ezrin activation and actin-dependent cell surface remodeling.
    Title: Clustered PI(4,5)P₂ accumulation and ezrin phosphorylation in response to CLIC5A.
  6. CLIC5 is a novel gene involved in progressive hearing impairment, vestibular and possibly mild renal dysfunction.
    Title: Progressive hearing loss and vestibular dysfunction caused by a homozygous nonsense mutation in CLIC5.
  7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  8. CLIC5A colocalizes with ezrin and podocalyxin in podocytes and is required for the development/maintenance of the proper glomerular endothelial cell and podocyte architecture.
    Title: CLIC5A, a component of the ezrin-podocalyxin complex in glomeruli, is a determinant of podocyte integrity.
  9. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: A high-density association screen of 155 ion transport genes for involvement with common migraine.
  10. Data showed that CLIC1 and CLIC5, but not CLIC4, were strongly and reversibly inhibited (or inactivated) by F-actin.
    Title: Functional reconstitution of mammalian 'chloride intracellular channels' CLIC1, CLIC4 and CLIC5 reveals differential regulation by cytoskeletal actin.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Autosomal recessive nonsyndromic hearing loss 103
MedGen: C4015050 OMIM: 616042 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide association study of periodontal pathogen colonization.
EBI GWAS Catalog
Insights into the genetic architecture of early stage age-related macular degeneration: a genome-wide association study meta-analysis.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ90663

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chloride channel activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in chloride transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in female pregnancy TAS
Traceable Author Statement
more info
 PubMed 
involved_in response to stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in visual perception IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
located_in actin cytoskeleton IDA
Inferred from Direct Assay
more info
 PubMed 
located_in apical plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cell cortex IEA
Inferred from Electronic Annotation
more info
  
located_in centrosome IEA
Inferred from Electronic Annotation
more info
  
part_of chloride channel complex IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular exosome HDA PubMed 
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
located_in stereocilium base IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
chloride intracellular channel protein 5

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_031965.2 RefSeqGene

    Range
    118959..236363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001114086.2 → NP_001107558.1  chloride intracellular channel protein 5 isoform a

    See identical proteins and their annotated locations for NP_001107558.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a, also known as also known as CLIC5B).
    Source sequence(s)
    AK097048, DQ679794
    Consensus CDS
    CCDS47438.1
    UniProtKB/Swiss-Prot
    B3KUF1, Q5T4Z0, Q8NBY3, Q96JT5, Q9BWZ0, Q9NZA1
    Related
    ENSP00000185206.6, ENST00000185206.12
    Conserved Domains (1) summary
    TIGR00862
    Location:173 → 408
    O-ClC; intracellular chloride channel protein

  2. NM_001256023.2 → NP_001242952.1  chloride intracellular channel protein 5 isoform c

    See identical proteins and their annotated locations for NP_001242952.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' and 3' UTRs and initiates translation at an alternate start codon, compared to variant 1. the encoded isoform (c) is shorter and has distinct N- and C-termini, compared to isoform a.
    Source sequence(s)
    AK075144, AL357057, BC039380, DA843541
    Consensus CDS
    CCDS59022.1
    UniProtKB/TrEMBL
    A0A5F9ZHK1
    Related
    ENSP00000439195.1, ENST00000544153.3
    Conserved Domains (1) summary
    TIGR00862
    Location:14 → 196
    O-ClC; intracellular chloride channel protein

  3. NM_001370649.1 → NP_001357578.1  chloride intracellular channel protein 5 isoform d

    Status: REVIEWED

    Source sequence(s)
    AL035701, AL357057, AL591211
    UniProtKB/TrEMBL
    B2RAZ0
    Conserved Domains (1) summary
    TIGR00862
    Location:1 → 210
    O-ClC; intracellular chloride channel protein

  4. NM_001370650.1 → NP_001357579.1  chloride intracellular channel protein 5 isoform a

    Status: REVIEWED

    Source sequence(s)
    AL035701, AL050336, AL357057, AL591211
    Consensus CDS
    CCDS47438.1
    UniProtKB/Swiss-Prot
    B3KUF1, Q5T4Z0, Q8NBY3, Q96JT5, Q9BWZ0, Q9NZA1
    Conserved Domains (1) summary
    TIGR00862
    Location:173 → 408
    O-ClC; intracellular chloride channel protein

  5. NM_016929.5 → NP_058625.2  chloride intracellular channel protein 5 isoform b

    See identical proteins and their annotated locations for NP_058625.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b, also known as CLIC5A) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AK223130, AL357057, AL591211, BC035968
    Consensus CDS
    CCDS4914.1
    UniProtKB/TrEMBL
    B2RAZ0, Q53G01
    Related
    ENSP00000344165.6, ENST00000339561.12
    Conserved Domains (1) summary
    TIGR00862
    Location:14 → 249
    O-ClC; intracellular chloride channel protein

RNA

  1. NR_045672.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    BC039380, BP369816, BQ184144, DQ679794

  2. NR_045673.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL357057, BC039380, BI559571, BQ184144, DQ679794

  3. NR_045674.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL357057, BC039380
    Related
    ENST00000486570.2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    45880827..46129819 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047418896.1 → XP_047274852.1  chloride intracellular channel protein 5 isoform X3

    UniProtKB/TrEMBL
    A0A2R8YGW2
    Related
    ENSP00000496359.1, ENST00000642250.1

  2. XM_047418898.1 → XP_047274854.1  chloride intracellular channel protein 5 isoform X5

  3. XM_011514692.4 → XP_011512994.1  chloride intracellular channel protein 5 isoform X1

    Conserved Domains (2) summary
    cd03061
    Location:173 → 260
    GST_N_CLIC; GST_N family, Chloride Intracellular Channel (CLIC) subfamily; composed of CLIC1-5, p64, parchorin and similar proteins. They are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated ...
    cl02776
    Location:267 → 355
    GST_C_family; C-terminal, alpha helical domain of the Glutathione S-transferase family

  4. XM_047418897.1 → XP_047274853.1  chloride intracellular channel protein 5 isoform X4

  5. XM_011514694.4 → XP_011512996.1  chloride intracellular channel protein 5 isoform X2

    Conserved Domains (2) summary
    cd03061
    Location:173 → 260
    GST_N_CLIC; GST_N family, Chloride Intracellular Channel (CLIC) subfamily; composed of CLIC1-5, p64, parchorin and similar proteins. They are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated ...
    cl02776
    Location:267 → 296
    GST_C_family; C-terminal, alpha helical domain of the Glutathione S-transferase family

RNA

  1. XR_926258.4 RNA Sequence

  2. XR_007059275.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    45716118..45964907 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355665.1 → XP_054211640.1  chloride intracellular channel protein 5 isoform X3

    UniProtKB/TrEMBL
    A0A2R8YGW2

  2. XM_054355667.1 → XP_054211642.1  chloride intracellular channel protein 5 isoform X5

  3. XM_054355663.1 → XP_054211638.1  chloride intracellular channel protein 5 isoform X1

  4. XM_054355666.1 → XP_054211641.1  chloride intracellular channel protein 5 isoform X4

  5. XM_054355664.1 → XP_054211639.1  chloride intracellular channel protein 5 isoform X2

RNA

  1. XR_008487348.1 RNA Sequence

  2. XR_008487349.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NZA1.3 GenPept UniProtKB/Swiss-Prot:Q9NZA1

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