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FLASH GENE
Symbol CLN3 contributors: mct/npt/pgu - updated : 25-10-2017
HGNC name ceroid-lipofuscinosis, neuronal 3
HGNC id 2074
DNA
TYPE functioning gene
STRUCTURE 15.02 kb     15 Exon(s)
10 Kb 5' upstream gene genomic sequence study
regulatory sequence Promoter
text structure
  • transcriptional regulation of CLN3 in response to the accumulation of free histones is not mediated by any of the known transcription factors operating on the CLN3 promoter
  • MAPPING cloned Y linked N status confirmed
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    15 - 1915 47.6 438 - 2008 18688960
    - - 1879 - 438 in normal brain, overexpressed in brains of patients with Batten disease 2006 16515873
    also called CLN3L or variant 2
    EXPRESSION
    Type widely
       expressed in (based on citations)
    organ(s)
    cells
    SystemCellPubmedSpeciesStageRna symbol
    Endocrineislet cell (alpha,beta...)
    Nervousastrocyte
    Nervousneuron
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    physiological period fetal
    Text
  • expressed in the developing eye but is not required for its development
  • PROTEIN
    PHYSICAL PROPERTIES Hydrophobic
    STRUCTURE
    motifs/domains
  • five transmembrane domains
  • several Alu repeats, phosphorylated on both serine and threonine residues
  • four predicted N glycosylation sites
  • a dileucine motif and a cluster of acidic amino acids in the second cytoplasmic domain are required for efficient lysosomal targeting
  • a galactosylceramide binding domain that may be involved in its trafficking from Golgi to rafts via recycling endosomes
  • HOMOLOGY
    interspecies ortholog to yeast BTN1
    Homologene
    FAMILY
  • battenin family
  • CATEGORY regulatory , transport
    SUBCELLULAR LOCALIZATION     plasma membrane
        intracellular
    intracellular,cytoplasm,organelle,membrane
    intracellular,cytoplasm,organelle,Golgi
    intracellular,cytoplasm,organelle,endosome
    intracellular,cytoplasm,organelle,lysosome
    intracellular,nucleus
    text
  • integral transmembrane protein, localizing to membrane lipid rafts
  • lysosomal protein trafficked in synapses through the ER-Golgi intermediary compartment ERGIC
  • in lysosomes in non-neuronal cells and in endosomes in neuronal cells.
  • localized in synaptosomes but not targetted to synaptic vesicles
  • predominantly a lysosomal protein
  • basic FUNCTION
  • palmitoyl-protein Delta-9 desaturase, which converts membrane-associated palmitoylated proteins to their respective palmitoylated derivatives
  • potentially protecting neurons from apoptosis mediated by ceramide
  • chaperone involved in the folding/unfolding or assembly/disassembly of other proteins, regulating cell growth and apoptosis
  • multimembrane-spanning protein involved in recycling of synaptic vesicles through the endosomal lysosome
  • inhibitor of amyloid beta protein precursor and cathepsin
  • a N terminus probably involved in protein-protein interactions and a C terminal required for movement from ER to Golgi and prenylation
  • may have a role in regulating intracellular levels of arginine possibly through control of the transport of this amino acid into lysosomes
  • playing a role in neuronal proteolipid trafficking and synaptic transmission
  • negatively regulating cellular level of calsenilin, suppressing neuronal cell death mediated by calsenilin and dysregulation of intracellular Ca2+
  • involved in the regulation of plasma membrane fodrin cytoskeleton and consequently, the plasma membrane association of Na(+), K(+) ATPase (ATP1B1)
  • may traffic across the cells from the Golgi apparatus to plasma membranes via endosomes/lysosomes or synaptosomes in neuronal cells
  • mediates several regulatory pathways by coupling the cell-cycle progression in G1 to physiological conditions, including nitrogen deprivation, daughter cell G1-delay and changes in glucose levels
  • may be involved in the cellular response to stress
  • specific role for CLN3 in the oxidative stress response, suggesting that a compromise of this response may be a fundamental defect leading to neurodegeneration in Batten disease
  • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS cellular trafficking transport
    text endocytic and exocytic neuronal transport processes
    PATHWAY
    metabolism
    signaling
    a component
  • constituent of integral lysosomal membrane protein battenin
  • interacts with the plasma membrane-associated cytoskeletal and endocytic fodrin and the associated Na(+), K(+) ATPase (ATP1B1)
  • may be a component of, or trafficked by, the vesicles from the perinuclear recycling compartment to the plasma membrane
  • INTERACTION
    DNA
    RNA
    small molecule
    protein
  • interacting with RAB proteins
  • CLN5, CLN6, and CLN8 complement each otherwith respect to growth and apoptosis
  • calsenilin-binding partner (KCNIP3)
  • interacting with FLNA (CAV1-dependent target in IGF1-stimulated cancer cell migration)
  • interaction with the mammalian HOOK1 protein suggests an interaction with cytoskeleton and a role in membrane trafficking, possibly by regulating vesicular transport and/or fusion
  • interacting with Notch and Jun N-terminal kinase signalling pathways (potential role for the RNA splicing and localization machinery in regulating CLN3 function)
  • interacts with cytoskeleton-associated nonmuscle myosin-IIB (MYH10)
  • functional and physical interaction between CLN3 and myosin-IIB (MYH10)
  • direct involvement of CLN3 in the regulation of CTSD activity
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) CLN3
    related resource Neuronal Ceroid Lipofuscinoses
    Neuronal Ceroid Lipofuscinoses
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    constitutional     --over  
    seems to cause neurodegeneration via a process that does not require apoptosis
    constitutional     --over  
    is sufficient to confer increased resistance to oxidative stress
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS
  • Cln3 deficient mouse model
  • canine model of juvenile Batten disease