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FLASH GENE
Symbol CLRN1 contributors: mct/npt - updated : 11-04-2023
HGNC name clarin 1
HGNC id 12605
Corresponding disease
RP61 retinitis pigmentosa 61
USH3A Usher syndrome, type III
Location 3q25.1      Physical location : 150.643.950 - 150.690.786
Synonym name
  • Usher syndrome 3A
  • Usher syndrome type-3 protein
  • Synonym symbol(s) CLAR1, USH3A, USH3
    DNA
    TYPE functioning gene
    STRUCTURE 46.84 kb     4 Exon(s)
    regulatory sequence Promoter (CAAT box)
    alternative promoter
    cytosine-phosphate-guanine/HTF
    MAPPING cloned Y linked N status provisional
    Map cen - D3S1299 - D3S3413 - CLRN1 - D3S1315 - UCRP - MED12L - GPR171 - P2RY14 - D3S3625 - D3S1594 - qter
    Authors Joensuu (01)
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    3 - 2359 25.7 232 ubiquitous 2020 31968401
  • also called USH3A Ia
  • 4 polyA site 1444 13.4 120 ubiquitous 2020 31968401
    also called USH3A Ic
    - polyA site 704 - 30 ubiquitous 2020 31968401
    also called USH3A Ib
    4 - 2398 - 245 - 2020 31968401
    4 - 2259 - 185 - 2020 31968401
    EXPRESSION
    Type ubiquitous
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Hearing/Equilibriumearinner   
    Visualeyeretina    Homo sapiens
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Muscularstriatumskeletal  
    Nervouscentral   
    Nervousperipherous   
    cells
    SystemCellPubmedSpeciesStageRna symbol
    Hearing / Equilibriumcochlea cell
    Hearing / Equilibriumstereocilia
    Visualganglion cell Homo sapiens
    VisualMuller cell Homo sapiens
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • cytosolic N terminus
  • two helical transmembrane domain
  • endoplasmic reticulum membrane retention signal TKGH at the C terminus
  • four transmembrane alpha helices (Tian 2009)
  • without any signal peptide
  • a prokar lipoprotein domain
  • secondary structure only alpha-helix but no beta sheets
    conjugated GlycoP
    HOMOLOGY
    interspecies ortholog to murine Ush3a
    intraspecies paralog to clarin 2
    paralog to clarin 3
    Homologene
    FAMILY
  • small integral membrane glycoprotein family
  • clarin family
  • claudin 2 super family
  • CATEGORY regulatory
    SUBCELLULAR LOCALIZATION     plasma membrane
        intracellular
    intracellular,cytoplasm,organelle,membrane
    intracellular,cytoplasm,organelle,endoplasmic reticulum
    text localization dependent on its interaction with F-actin, because disruption of F-actin led to diffuse localization of CLRN1 on the plasma membrane (Tian 2009)
    basic FUNCTION
  • playing a role in the hair cells and photoreceptor synaptic functions
  • possible role in the regulation and homeostasis of actin filaments (Tian 2009)
  • forms membranous cholesterol-rich compartments on plasma membranes and interacts with and regulates the machinery involved in actin filament organization (Tian 2009)
  • may play a vital role in creating and assembling membrane microdomains involved in adhesion strengthening and signaling (Geng 2009)
  • plays a novel role in hair cell development and function (may be having necessary role for normal sensory transduction, hair cell to afferent communication and/or primary afferent neural activation) (Geng 2009)
  • CDH23, PCDH15 and ADGRV1 have been implicated in the development of cochlear hair cell stereocilia, while CLRN1 has been suggested to also play a role in synaptogenesis
  • is likely functionally important for mechanotransduction channel activity and for proper localization of synaptic components, establishing a critical role for CLRN1 at the apical and basal poles of hair cells
  • hair cell expression of CLRN1 is likely essential for postnatal preservation of hair cell structure and hearing
  • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism
    signaling neurotransmission , sensory transduction/hearing , sensory transduction/vision
    a component
    INTERACTION
    DNA
    RNA
    small molecule
    protein
  • MYO7A
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) USH3A , RP61
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS
  • Clrn1 knockout (KO) mice develop hair cell defects by postnatal day 2 (P2) and are deaf by P21-P25