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Symbol CLN3 contributors: mct/npt/pgu - updated : 25-10-2017
HGNC name ceroid-lipofuscinosis, neuronal 3
HGNC id 2074
Corresponding disease
CLN3 ceroid lipofuscinosis, neuronal, 3
Location 16p11.2      Physical location : 28.488.600 - 28.503.623
Synonym name
  • battenin
  • Batten disease protein
  • protein CLN3
  • Synonym symbol(s) BTS, CLN3P, WHI1, FUN10, DAF1, JNCL, MGC102840
    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
    Physical map
    MGC18079 16p12.1 hypothetical protein MGC18079 XPO6 16p12 exportin 6 LOC390687 16 similar to Glyceraldehyde 3-phosphate dehydrogenase, liver (GAPDH) LOC388228 16 similar to SH3-binding kinase LOC388229 16 similar to Group X secretory phospholipase A2 precursor (Phosphatidylcholine 2-acylhydrolase GX) (GX sPLA2) (sPLA2-X) EIF3S8 16p11.2 eukaryotic translation initiation factor 3, subunit 8, 110kDa LOC283890 16p12.1 similar to nuclear pore complex interacting protein LOC388230 16 similar to MGC9515 protein LOC388231 16 LOC388231 SULT1A1 16p12.1 sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1 SULT1A2 16p12-p11.2 sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2 LOC112869 16p12.1 hypothetical protein BC011981 P8 16p11.2 p8 protein (candidate of metastasis 1) IL27  interleukin 27 LOC388232 16 similar to apolipoprotein B48 receptor CLN3 16p12.1-p11.2 ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) LOC388233 16 similar to MGC9515 protein APOB48R 16p11 apolipoprotein B48 receptor LOC388234 16 similar to nuclear pore complex interacting protein LOC390688 16 similar to CDC37-like gene LOC388235 16 LOC388235 LOC388236 16 similar to MGC9515 protein A2LP 16p11 ataxin 2 related protein TUFM 16p11.2 Tu translation elongation factor, mitochondrial SH2B 16p12.1 Tu translation elongation factor, mitochondrial ATP2A1 16p12.1 ATPase, Ca++ transporting, cardiac muscle, fast twitch 1 FRA 16p12.1 Fos-related antigen CD19 16p11.2 CD19 antigen FLJ14639 16p12.1 hypothetical protein FLJ14639 SPINL 16p12.1 spinster-like LAT 16p11.2 linker for activation of T cells LOC388237 16 similar to nuclear pore complex interacting protein LOC388238 16 similar to RRN3 LOC283892 16p12.1 hypothetical gene supported by NM_017869; AK023827 LOC283895 16p12.1 hypothetical LOC283895 LOC388239 16 similar to nuclear pore complex interacting protein LOC388240 16 similar to MGC9515 protein LOC388241 16 similar to PI-3-kinase-related kinase SMG-1 isoform 2; lambda/iota protein kinase C-interacting protein; phosphatidylinositol 3-kinase-related protein kinase
    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
    Type widely
       expressed in (based on citations)
    SystemCellPubmedSpeciesStageRna symbol
    Endocrineislet cell (alpha,beta...)
    cell lineage
    cell lines
    at STAGE
    physiological period fetal
  • expressed in the developing eye but is not required for its development
  • 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
    interspecies ortholog to yeast BTN1
  • battenin family
  • CATEGORY regulatory , transport
    SUBCELLULAR LOCALIZATION     plasma membrane
  • 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
    PHYSIOLOGICAL PROCESS cellular trafficking transport
    text endocytic and exocytic neuronal transport processes
    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
    small molecule
  • 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
    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
    Variant & Polymorphism
    Candidate gene
    Therapy target
  • Cln3 deficient mouse model
  • canine model of juvenile Batten disease