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

Gene ID: 53405, updated on 7-Jun-2020

Summary

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
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

Genomic context

See CLIC5 in Genome Data Viewer
Location:
6p21.1
Exon count:
14
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (45898451..46129819, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (45866188..46048085, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986519 Neighboring gene VISTA enhancer hs1461 Neighboring gene uncharacterized LOC105375078 Neighboring gene RNA, U6 small nuclear 754, pseudogene Neighboring gene ectonucleotide pyrophosphatase/phosphodiesterase 4 Neighboring gene ectonucleotide pyrophosphatase/phosphodiesterase family member 5

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Deafness, autosomal recessive 103
MedGen: C4015050 OMIM: 616042 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ90663

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chloride channel activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
voltage-gated ion channel activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
chloride transport IDA
Inferred from Direct Assay
more info
PubMed 
female pregnancy TAS
Traceable Author Statement
more info
PubMed 
regulation of ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
response to stimulus IEA
Inferred from Electronic Annotation
more info
 
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
actin cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
apical plasma membrane IEA
Inferred from Electronic Annotation
more info
 
cell cortex IEA
Inferred from Electronic Annotation
more info
 
chloride channel complex IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
microtubule organizing center IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
chloride intracellular channel protein 5

NCBI Reference Sequences (RefSeq)

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_031965.1 RefSeqGene

    Range
    5001..186893
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001114086.2NP_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
    Q9NZA1
    UniProtKB/TrEMBL
    Q53G01
    Related
    ENSP00000185206.6, ENST00000185206.12
    Conserved Domains (1) summary
    TIGR00862
    Location:173408
    O-ClC; intracellular chloride channel protein
  2. NM_001256023.1NP_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/Swiss-Prot
    Q9NZA1
    UniProtKB/TrEMBL
    Q49AE1
    Related
    ENSP00000439195.1, ENST00000544153.3
    Conserved Domains (1) summary
    cl25455
    Location:14196
    PLN02817; glutathione dehydrogenase (ascorbate)
  3. NM_001370649.1NP_001357578.1  chloride intracellular channel protein 5 isoform d

    Status: REVIEWED

    Source sequence(s)
    AL035701, AL357057, AL591211
    Conserved Domains (1) summary
    TIGR00862
    Location:1210
    O-ClC; intracellular chloride channel protein
  4. NM_001370650.1NP_001357579.1  chloride intracellular channel protein 5 isoform a

    Status: REVIEWED

    Source sequence(s)
    AL035701, AL050336, AL357057, AL591211
    Conserved Domains (1) summary
    TIGR00862
    Location:173408
    O-ClC; intracellular chloride channel protein
  5. NM_016929.5NP_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/Swiss-Prot
    Q9NZA1
    UniProtKB/TrEMBL
    Q53G01
    Related
    ENSP00000344165.6, ENST00000339561.12
    Conserved Domains (1) summary
    TIGR00862
    Location:14249
    O-ClC; intracellular chloride channel protein

RNA

  1. NR_045672.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate 5'-most exon compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    BC039380, BP369816, BQ184144, DQ679794
  2. NR_045673.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) includes two alternate internal exons and uses an alternate 5'-most exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AL357057, BC039380, BI559571, BQ184144, DQ679794
  3. NR_045674.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) includes two alternate internal exons and uses alternate 5'- and 3'-most exons, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AL357057, BC039380
    Related
    ENST00000486570.2

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    45898451..46129819 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514692.3XP_011512994.1  chloride intracellular channel protein 5 isoform X2

    Conserved Domains (2) summary
    cd03061
    Location:173260
    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:267355
    GST_C_family; C-terminal, alpha helical domain of the Glutathione S-transferase family
  2. XM_011514694.3XP_011512996.1  chloride intracellular channel protein 5 isoform X3

    Conserved Domains (2) summary
    cd03061
    Location:173260
    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:267296
    GST_C_family; C-terminal, alpha helical domain of the Glutathione S-transferase family

RNA

  1. XR_926258.3 RNA Sequence

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