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Aliases for CLIC5 Gene

Aliases for CLIC5 Gene

  • Chloride Intracellular Channel 5 2 3 5
  • Chloride Intracellular Channel Protein 5 3
  • DFNB102 3
  • DFNB103 3
  • MSTP130 3
  • MST130 3

External Ids for CLIC5 Gene

Previous GeneCards Identifiers for CLIC5 Gene

  • GC06M045871
  • GC06M045916
  • GC06M045977
  • GC06M045589

Summaries for CLIC5 Gene

Entrez Gene Summary for CLIC5 Gene

  • 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]

GeneCards Summary for CLIC5 Gene

CLIC5 (Chloride Intracellular Channel 5) is a Protein Coding gene. Diseases associated with CLIC5 include Deafness, Autosomal Recessive 103 and Autosomal Recessive Non-Syndromic Sensorineural Deafness Type Dfnb. Among its related pathways are Hepatic ABC Transporters and Activation of cAMP-Dependent PKA. 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 CLIC6.

UniProtKB/Swiss-Prot for CLIC5 Gene

  • Required for normal hearing (PubMed:24781754). It is necessary for the formation of stereocilia in the inner ear and normal development of the organ of Corti (By similarity). Can insert into membranes and form poorly selective ion channels that may also transport chloride ions. May play a role in the regulation of transepithelial ion absorption and secretion. Is required for the development and/or maintenance of the proper glomerular endothelial cell and podocyte architecture (PubMed:15184393, PubMed:18028448, PubMed:20335315).

Gene Wiki entry for CLIC5 Gene

Additional gene information for CLIC5 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLIC5 Gene

Genomics for CLIC5 Gene

GeneHancer (GH) Regulatory Elements for CLIC5 Gene

Promoters and enhancers for CLIC5 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
GH06J046010 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 670.5 +67.2 67209 5.7 FOXA2 KLF17 BMI1 BATF ZNF2 IRF4 ZNF48 ZNF121 GLIS2 SCRT2 CLIC5 ENPP4 ENSG00000231769 RNU6-754P GC06M045521
GH06J046128 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE 650.2 -49.4 -49368 2.7 PKNOX1 MZF1 KLF14 ZNF2 YY1 ZNF335 GLIS2 ZNF213 ZNF366 SCRT2 ENSG00000231769 ENPP4 CLIC5 TDRD6
GH06J046077 Promoter/Enhancer 1.1 EPDnew ENCODE dbSUPER 650.7 +1.1 1118 3.9 ZFHX2 FOXA2 EGR2 CLIC5 ENPP4 ENSG00000231769 RNU6-754P
GH06J046050 Enhancer 1.5 VISTA FANTOM5 Ensembl ENCODE dbSUPER 10.7 +25.7 25713 8 MAX RAD21 YY1 ZFHX2 EGR1 SCRT2 HNF4G STAT1 RXRA NR2F2 RNU6-754P CLIC5
GH06J046044 Enhancer 1.1 Ensembl ENCODE dbSUPER 10 +35.2 35203 1.3 ZBTB21 JUN HIC1 ZNF335 ZNF366 PRDM10 FOSL2 FOS RFX1 ZNF362 RNU6-754P CLIC5 LOC101926898 RCAN2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLIC5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLIC5 gene promoter:
  • C/EBPbeta
  • SREBP-1c
  • SREBP-1b
  • SREBP-1a
  • FOXO1
  • FOXO1a
  • AML1a
  • POU2F1
  • POU2F1c
  • POU2F1b

Genomic Locations for CLIC5 Gene

Genomic Locations for CLIC5 Gene
chr6:45,880,827-46,080,348
(GRCh38/hg38)
Size:
199,522 bases
Orientation:
Minus strand
chr6:45,866,188-46,048,132
(GRCh37/hg19)
Size:
181,945 bases
Orientation:
Minus strand

Genomic View for CLIC5 Gene

Genes around CLIC5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLIC5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLIC5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLIC5 Gene

Proteins for CLIC5 Gene

  • Protein details for CLIC5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NZA1-CLIC5_HUMAN
    Recommended name:
    Chloride intracellular channel protein 5
    Protein Accession:
    Q9NZA1
    Secondary Accessions:
    • B3KUF1
    • Q5T4Z0
    • Q8NBY3
    • Q96JT5
    • Q9BWZ0

    Protein attributes for CLIC5 Gene

    Size:
    410 amino acids
    Molecular mass:
    46503 Da
    Quaternary structure:
    • Component of a multimeric complex consisting of several cytoskeletal proteins, including actin, ezrin, alpha-actinin, gelsolin, and IQGAP1. Interacts with AKAP9.

    Alternative splice isoforms for CLIC5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLIC5 Gene

Post-translational modifications for CLIC5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CLIC5 Gene

Domains & Families for CLIC5 Gene

Gene Families for CLIC5 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted intracellular proteins
  • Transporters

Graphical View of Domain Structure for InterPro Entry

Q9NZA1

UniProtKB/Swiss-Prot:

CLIC5_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 CLIC5: view

Function for CLIC5 Gene

Molecular function for CLIC5 Gene

UniProtKB/Swiss-Prot Function:
Required for normal hearing (PubMed:24781754). It is necessary for the formation of stereocilia in the inner ear and normal development of the organ of Corti (By similarity). Can insert into membranes and form poorly selective ion channels that may also transport chloride ions. May play a role in the regulation of transepithelial ion absorption and secretion. Is required for the development and/or maintenance of the proper glomerular endothelial cell and podocyte architecture (PubMed:15184393, PubMed:18028448, PubMed:20335315).

Phenotypes From GWAS Catalog for CLIC5 Gene

Gene Ontology (GO) - Molecular Function for CLIC5 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 IBA --
GO:0005515 protein binding IPI 10793131
genes like me logo Genes that share ontologies with CLIC5: view
genes like me logo Genes that share phenotypes with CLIC5: view

Human Phenotype Ontology for CLIC5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for CLIC5

miRNA for CLIC5 Gene

miRTarBase miRNAs that target CLIC5

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for CLIC5 Gene

Localization for CLIC5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLIC5 Gene

Isoform 1: Cytoplasm, cell cortex. Cytoplasm, cytoskeleton. Membrane; Single-pass membrane protein. Note=Associates with the cortical actin cytoskeleton. Exists both as soluble cytoplasmic protein and as membrane protein with probably a single transmembrane domain (By similarity). {ECO:0000250}.
Isoform 2: Golgi apparatus. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Membrane; Single-pass membrane protein. Note=Colocalized with AKAP9 at the Golgi apparatus as well as, to a lesser extent, the centrosome. Exists both as soluble cytoplasmic protein and as membrane protein with probably a single transmembrane domain (By similarity). Colocalized with podocalyxin in renal glomeruli. {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 CLIC5 gene
Compartment Confidence
extracellular 5
cytoskeleton 5
golgi apparatus 5
cytosol 3
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLIC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 NOT nucleus IBA --
GO:0005737 cytoplasm IBA --
GO:0005794 Golgi apparatus IEA --
GO:0005815 microtubule organizing center IEA --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with CLIC5: view

Pathways & Interactions for CLIC5 Gene

genes like me logo Genes that share pathways with CLIC5: view

Pathways by source for CLIC5 Gene

Gene Ontology (GO) - Biological Process for CLIC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006749 NOT glutathione metabolic process IBA --
GO:0006811 ion transport IEA --
GO:0006821 chloride transport IDA 10793131
GO:0007565 female pregnancy TAS 10793131
GO:0007605 sensory perception of sound IMP 24781754
genes like me logo Genes that share ontologies with CLIC5: view

No data available for SIGNOR curated interactions for CLIC5 Gene

Drugs & Compounds for CLIC5 Gene

(1) Additional Compounds for CLIC5 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Chloride ion
  • Chloride(1-)
  • Chlorine anion
  • CL(-)
  • Bertholite
  • Chloor
16887-00-6
genes like me logo Genes that share compounds with CLIC5: view

Transcripts for CLIC5 Gene

mRNA/cDNA for CLIC5 Gene

Unigene Clusters for CLIC5 Gene

Chloride intracellular channel 5:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLIC5 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b · 10c · 10d ^ 11 ^ 12a · 12b · 12c
SP1: - - - - - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - -
SP4: -
SP5: - - - -
SP6: - - - - -
SP7: - -
SP8: - - - - -

Relevant External Links for CLIC5 Gene

GeneLoc Exon Structure for
CLIC5
ECgene alternative splicing isoforms for
CLIC5

Expression for CLIC5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLIC5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLIC5 Gene

This gene is overexpressed in Muscle - Skeletal (x15.3), Heart - Left Ventricle (x11.7), and Heart - Atrial Appendage (x4.9).

Protein differential expression in normal tissues from HIPED for CLIC5 Gene

This gene is overexpressed in Liver (24.1) and Retina (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLIC5 Gene



NURSA nuclear receptor signaling pathways regulating expression of CLIC5 Gene:

CLIC5

SOURCE GeneReport for Unigene cluster for CLIC5 Gene:

Hs.485489

mRNA Expression by UniProt/SwissProt for CLIC5 Gene:

Q9NZA1-CLIC5_HUMAN
Tissue specificity: Widely expressed in both fetal and adult human tissues (PubMed:24781754). Isoform 1 is expressed in renal glomeruli endothelial cells and podocytes (at protein level).

Evidence on tissue expression from TISSUES for CLIC5 Gene

  • Kidney(4.4)
  • Intestine(4.2)
  • Heart(2.6)
  • Muscle(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CLIC5 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • inner ear
  • middle ear
  • outer ear
  • skull
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with CLIC5: view

No data available for Protein tissue co-expression partners for CLIC5 Gene

Orthologs for CLIC5 Gene

This gene was present in the common ancestor of animals.

Orthologs for CLIC5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLIC5 34 33
  • 99.43 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Clic5 33
  • 89.16 (n)
oppossum
(Monodelphis domestica)
Mammalia CLIC5 34
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Clic5 16 34 33
  • 88.89 (n)
dog
(Canis familiaris)
Mammalia CLIC5 34 33
  • 82.3 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CLIC5 34 33
  • 81.91 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CLIC5 34
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLIC5 34 33
  • 68.35 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLIC5 34
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clic4 33
  • 77.55 (n)
African clawed frog
(Xenopus laevis)
Amphibia clic5-prov 33
zebrafish
(Danio rerio)
Actinopterygii clic5a 34 33
  • 73.53 (n)
OneToMany
clic5b 34 34
  • 54 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2945 33
fruit fly
(Drosophila melanogaster)
Insecta Clic 34 33
  • 50.58 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000943 33
  • 50.41 (n)
worm
(Caenorhabditis elegans)
Secernentea exl-1 34
  • 26 (a)
ManyToMany
exc-4 34
  • 20 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6991 34
  • 42 (a)
OneToMany
Species where no ortholog for CLIC5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 CLIC5 Gene

ENSEMBL:
Gene Tree for CLIC5 (if available)
TreeFam:
Gene Tree for CLIC5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLIC5: view image

Paralogs for CLIC5 Gene

Paralogs for CLIC5 Gene

(6) SIMAP similar genes for CLIC5 Gene using alignment to 4 proteins:

  • CLIC5_HUMAN
  • Q49AE1_HUMAN
  • Q53G01_HUMAN
  • Q8N675_HUMAN
genes like me logo Genes that share paralogs with CLIC5: view

Variants for CLIC5 Gene

Sequence variations from dbSNP and Humsavar for CLIC5 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs606231308 pathogenic, Deafness, autosomal recessive 103 45,955,212(-) A/T coding_sequence_variant, genic_upstream_transcript_variant, non_coding_transcript_variant, stop_gained
rs1000011800 -- 46,062,135(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000036528 -- 46,104,749(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000040608 -- 45,953,686(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000049165 -- 46,103,530(-) A/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CLIC5 Gene

Variant ID Type Subtype PubMed ID
dgv3309n106 CNV deletion 24896259
dgv388e215 CNV deletion 23714750
esv1008384 CNV deletion 20482838
esv1256091 CNV deletion 17803354
esv2367588 CNV deletion 18987734
esv2585595 CNV deletion 19546169
esv2732026 CNV deletion 23290073
esv2759424 CNV loss 17122850
esv3309527 CNV mobile element insertion 20981092
esv3426714 CNV insertion 20981092
esv3426956 CNV insertion 20981092
esv3608874 CNV loss 21293372
esv4021 CNV loss 18987735
nsv1021917 CNV gain 25217958
nsv1025846 CNV gain 25217958
nsv1074929 CNV deletion 25765185
nsv349891 CNV deletion 16902084
nsv474863 CNV novel sequence insertion 20440878
nsv517891 CNV gain 19592680
nsv950175 CNV duplication 24416366
nsv950176 CNV duplication 24416366
nsv957551 CNV deletion 24416366

Variation tolerance for CLIC5 Gene

Residual Variation Intolerance Score: 90.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.15; 51.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLIC5 Gene

Human Gene Mutation Database (HGMD)
CLIC5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLIC5

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLIC5 Gene

Disorders for CLIC5 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CLIC5 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal recessive 103
  • dfnb103
autosomal recessive non-syndromic sensorineural deafness type dfnb
  • autosomal recessive isolated neurosensory deafness type dfnb
- elite association - COSMIC cancer census association via MalaCards
Search CLIC5 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CLIC5_HUMAN
  • Deafness, autosomal recessive, 103 (DFNB103) [MIM:616042]: A form of sensorineural deafness with onset in early childhood. Hearing impairment progresses from mild to severe or even profound before the second decade, and is accompanied by vestibular areflexia. {ECO:0000269 PubMed:24781754}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CLIC5

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 CLIC5: view

No data available for Genatlas for CLIC5 Gene

Publications for CLIC5 Gene

  1. 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) 2 3 4 22 58
  2. Progressive hearing loss and vestibular dysfunction caused by a homozygous nonsense mutation in CLIC5. (PMID: 24781754) Seco CZ … Schraders M (European journal of human genetics : EJHG 2015) 2 3 4 58
  3. CLIC5A, a component of the ezrin-podocalyxin complex in glomeruli, is a determinant of podocyte integrity. (PMID: 20335315) Wegner B … Ballermann BJ (American journal of physiology. Renal physiology 2010) 3 4 22 58
  4. 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
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for CLIC5 Gene

Sources for CLIC5 Gene

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