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CLN3 Gene

protein-coding   GIFtS: 63
GCID: GC16M028488

Ceroid-Lipofuscinosis, Neuronal 3

(Previous names: Batten, Spielmeyer-Vogt disease)
(Previous symbol: BTS)
  See CLN3-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Ceroid-Lipofuscinosis, Neuronal 31 2     Juvenile Neuronal Ceroid Lipofuscinosis1
BTS1 2 3 5     JNCL2
Batten Disease Protein2 3     battenin2
Batten, Spielmeyer-Vogt Disease1     Protein CLN33

External Ids:    HGNC: 20741   Entrez Gene: 12012   Ensembl: ENSG000001886037   OMIM: 6070425   UniProtKB: Q132863   

Export aliases for CLN3 gene to outside databases

Previous GC identifers: GC16P028406 GC16P028790 GC16P028559 GC16P028601 GC16M028396 GC16M026514


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CLN3 Gene:
This gene encodes a protein that is involved in lysosomal function. Mutations in this, as well as other neuronal
ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease or
collectively known as neuronal ceroid lipofuscinoses (NCLs). Many alternatively spliced transcript variants have
been found for this gene. (provided by RefSeq, Jul 2008)

GeneCards Summary for CLN3 Gene:
CLN3 (ceroid-lipofuscinosis, neuronal 3) is a protein-coding gene. Diseases associated with CLN3 include juvenile batten disease, and batten disease. GO annotations related to this gene include unfolded protein binding. An important paralog of this gene is ENSG00000261832.

UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286
Function: Involved in microtubule-dependent, anterograde transport of late endosomes and lysosomes

Gene Wiki entry for CLN3 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000016.9  NC_018927.2  NT_187260.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the CLN3 gene promoter:
         AP-1   ATF-2   c-Jun   IRF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLN3 promoter sequence
   Search Chromatin IP Primers for CLN3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLN3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16p12.1   Ensembl cytogenetic band:  16p11.2   HGNC cytogenetic band: 16p12

CLN3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLN3 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M028488:  view genomic region     (about GC identifiers)

Start:
28,477,983 bp from pter      End:
28,506,896 bp from pter
Size:
28,914 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286 (See protein sequence)
Recommended Name: Battenin precursor  
Size: 438 amino acids; 47623 Da
Subunit: Interacts with DCTN1 and KIF3A. Interacts with RAB7A and RILP
Secondary accessions: B2R7J1 O00668 O95089 Q549S9 Q9UP09 Q9UP11 Q9UP12 Q9UP13 Q9UP14
Alternative splicing: 6 isoforms:  Q13286-1   Q13286-2   Q13286-3   Q13286-4   Q13286-5   Q13286-6   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for CLN3: NX_Q13286

Explore proteomics data for CLN3 at MOPED

Post-translational modifications: 

  • Highly glycosylated1
  • Farnesylation is important for trafficking to lysosomes1
  • Ubiquitination2 at Lys262
  • Glycosylation2 at Asn71, Thr80, Asn85, Asn310
  • Modification sites at PhosphoSitePlus

  • See CLN3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (6 alternative transcripts): 
    NP_000077.1  NP_001035897.1  NP_001273033.1  NP_001273034.1  NP_001273038.1  NP_001273039.1  

    ENSEMBL proteins: 
     ENSP00000454466   ENSP00000454229   ENSP00000329171   ENSP00000350457   ENSP00000350523  
     ENSP00000455387   ENSP00000379014   ENSP00000455549   ENSP00000456693   ENSP00000454680  
     ENSP00000456117   ENSP00000455342   ENSP00000455603   ENSP00000456414   ENSP00000456013  
     ENSP00000458015   ENSP00000456122   ENSP00000457615   ENSP00000454899   ENSP00000455365  
     ENSP00000353116   ENSP00000353073   ENSP00000346650   ENSP00000347660   ENSP00000443221  
     ENSP00000349586  

    CLN3 Human Recombinant Protein Products:

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    Novus Biologicals CLN3 Protein
    Novus Biologicals CLN3 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for CLN3 

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    LSBio Antibodies in human, mouse, rat for CLN3

    CLN3 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for CLN3 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR018460 Battenin_disease_Cln3_subgr
     IPR003492 Battenin_disease_Cln3
     IPR016196 MFS_dom_general_subst_transpt

    Graphical View of Domain Structure for InterPro Entry Q13286

    ProtoNet protein and cluster: Q13286

    1 Blocks protein domain: IPB003492 CLN3 Batten's disease protein (battenin) signature

    UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286
    Similarity: Belongs to the battenin family


    Find genes that share domains with CLN3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CLN3_HUMAN, Q13286
    Function: Involved in microtubule-dependent, anterograde transport of late endosomes and lysosomes

         Genatlas biochemistry entry for CLN3:
    integral lysosomal membrane protein battenin,highly conserved,with alternatively spliced forms,expressed in
    astrocytes,capillary endothelium and neurons of gray matter of the brain in peripheral nerve,pancreatic islet
    cells and within the seminiferous tubules of the testis,involved in synaptic trafficking through the endoplasmic
    reticulum and Golgi,potentially protecting neurons from apoptosis mediated by ceramide,yeast BTN1 ortholog

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI12134079
    GO:0051082unfolded protein binding TAS8980123
         
    Find genes that share ontologies with CLN3           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for CLN3:
     Decreased Tat-dependent transc  Decreased p24 protein expressi 

         10 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Cln3):
     behavior/neurological  cellular  homeostasis/metabolism  liver/biliary system  mortality/aging 
     nervous system  no phenotypic analysis  renal/urinary system  reproductive system  vision/eye 

    Find genes that share phenotypes with CLN3           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for CLN3: Cln3tm1Mkat Cln3tm1Mem Cln3tm1Nbm Cln3tm1.1Mem

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CLN3
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CLN3
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CLN3

    miRNA
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    miRTarBase miRNAs that target CLN3:
    hsa-mir-7-5p (MIRT025765), hsa-mir-877-3p (MIRT037057)

    Block miRNA regulation of human, mouse, rat CLN3 using miScript Target Protectors
    Search for qRT-PCR Assays for microRNAs that regulate CLN3
    SwitchGear 3'UTR luciferase reporter plasmidCLN3 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CLN3

    Gene Editing
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    GenScript: all cDNA clones in your preferred vector (see all 2): CLN3 (NM_001042432)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CLN3
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLN3

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLN3


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CLN3_HUMAN, Q13286: Lysosome membrane; Multi-pass membrane protein. Late endosome
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum5
    endosome5
    golgi apparatus5
    lysosome5
    nucleus5
    plasma membrane5
    vacuole5
    mitochondrion4

    Gene Ontology (GO): Selected cellular component terms (see all 21):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000139Golgi membrane IDA10191111
    GO:0005634nucleus IDA10191116
    GO:0005737cytoplasm IDA10191116
    GO:0005739mitochondrion TAS8980123
    GO:0005764lysosome IDA10924275

    Find genes that share ontologies with CLN3           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for CLN3 About    
    See pathways by source

    SuperPathContained pathways About
    1Lysosome
    Lysosome


    Find genes that share SuperPaths with CLN3           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    1 Kegg Pathway  (Kegg details for CLN3):
        Lysosome

        Pathway & Disease-focused RT2 Profiler PCR Arrays including CLN3: 
              GABA & Glutamate in human mouse rat
              Autophagy in human mouse rat
              Prostate Cancer in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for CLN3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for CLN3 (Q132863 ENSP000003530734) via UniProtKB, MINT, STRING, and/or I2D (see all 715)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 32):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000046autophagic vacuole fusion ISS--
    GO:0001508action potential ISS--
    GO:0001575globoside metabolic process IMP15240864
    GO:0006457protein folding TAS8980123
    GO:0006520cellular amino acid metabolic process ISS--

    Find genes that share ontologies with CLN3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CLN3

    8 Novoseek inferred chemical compound relationships for CLN3 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    mannose 6-phosphate 42.5 2 17286803 (1), 9878558 (1)
    ceramide 33.6 7 10191118 (3), 16151633 (2)
    atp 10.8 2 11589015 (1), 10356317 (1)
    arginine 4.06 3 14660799 (2), 17896996 (1)
    glutamate 1.58 2 9490299 (1), 9450775 (1)
    lysine 0 1 9450775 (1)
    lipid 0 4 17896996 (1), 18317235 (1), 17237713 (1), 15094366 (1)
    serine 0 1 9878558 (1)



    Find genes that share compounds with CLN3           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for CLN3 gene (6 alternative transcripts): 
    NM_000086.2  NM_001042432.1  NM_001286104.1  NM_001286105.1  NM_001286109.1  NM_001286110.1  

    Unigene Cluster for CLN3:

    Ceroid-lipofuscinosis, neuronal 3
    Hs.534667  [show with all ESTs]
    Unigene Representative Sequence: AK090709
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 41):
    ENST00000564091 ENST00000569430 ENST00000333496 ENST00000563874(uc002dqa.2 uc010vcx.1)
    ENST00000357806(uc021tfs.1) ENST00000357857 ENST00000567963(uc002dpx.1)
    ENST00000395653 ENST00000565354 ENST00000568422 ENST00000566057 ENST00000569030
    ENST00000565316 ENST00000568452 ENST00000568076 ENST00000561689 ENST00000565140
    ENST00000568558(uc002dpy.1)
    miRNA
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    GenScript: all cDNA clones in your preferred vector (see all 2): CLN3 (NM_001042432)
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      QuantiTect SYBR Green Assays in human, mouse, rat CLN3
      QuantiFast Probe-based Assays in human, mouse, rat CLN3

    Additional mRNA sequence: 

    AF015593.1 AF015594.1 AF015595.1 AF015596.1 AF015597.1 AF015598.1 AF015599.1 AF015600.1 
    AF015601.1 AF015602.1 AF077956.1 AF077957.1 AF077958.1 AF077959.1 AF077960.1 AF077961.1 
    AF077962.1 AF077966.1 AF077970.1 AF077971.1 AF077972.1 AF078168.1 AF078169.1 AK090709.1 
    AK294070.1 AK294250.1 AK295500.1 AK297690.1 AK302027.1 AK302138.1 AK313002.1 BC002394.2 
    BC004433.1 BC111068.1 U32680.1 

    37 DOTS entries (see top 24):

    DT.87018129  DT.100867986  DT.95239976  DT.100831826  DT.95368403  DT.100868011  DT.92457282  DT.95368415 
    DT.92457287  DT.92457300  DT.97860083  DT.100868007  DT.100868000  DT.120696604  DT.120696706  DT.92457289 
    DT.92457297  DT.100868006  DT.120696247  DT.100844156  DT.120695125  DT.91867272  DT.100868014  DT.102843670 
    DT.92457283  DT.120695944  DT.120696919  DT.120697066  DT.87018137  DT.92457277  DT.95368405  DT.97860081 
    DT.100682236  DT.113032  DT.120696832  DT.120698214  DT.95093459 

    Selected AceView cDNA sequences (see all 260):

    BI761771 BQ067057 AL536863 CA444377 BM726882 CR613621 AL555221 AU121777 
    CR605499 BM923971 BI490061 AK090709 T08995 BM795168 BG696720 BU150620 
    CR597053 AF077971 CR601899 AU099671 BX393642 AI355261 BU619787 CB117283 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for CLN3 (see all 25)    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b · 4c · 4d · 4e · 4f · 4g · 4h ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b · 13c ^
    SP1:                                -     -     -     -     -                             -                                                     -               
    SP2:                                                                                      -                                                     -               
    SP3:                                                                                      -                       -                             -               
    SP4:                                                                                      -                                                     -               
    SP5:                                                                                      -                                                     -               

    ExUns: 14a · 14b ^ 15a · 15b ^ 16 ^ 17a · 17b · 17c ^ 18 ^ 19a · 19b · 19c · 19d · 19e
    SP1:        -                                                                           
    SP2:        -                                                                           
    SP3:        -                                                                           
    SP4:        -                                                                           
    SP5:              -     -                                                               


    ECgene alternative splicing isoforms for CLN3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CLN3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCTTCTGAAT
    CLN3 Expression
    About this image

    CLN3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLN3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.534667
        Pathway & Disease-focused RT2 Profiler PCR Arrays including CLN3: 
              GABA & Glutamate in human mouse rat
              Autophagy in human mouse rat
              Prostate Cancer in human mouse rat

    Primer
    Products:
    OriGene qPCR primer pairs and template standards for CLN3
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CLN3
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for CLN3 gene from Selected species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cln31 , 5 ceroid lipofuscinosis, neuronal 3, juvenile (Batten, more1, 5 82.91(n)1
    86.04(a)1
      7 (69.16 cM)5
    127521  NM_009907.31  NP_034037.31 
     1265712075 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    56(a)
    1 → many
    GL343287.1(735505-750833)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.152912 Xenopus laevis transcribed sequence with weak similarity more 76.05(n)    48012878 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.31672 Transcribed sequence with weak similarity to protein more 72.42(n)    57057328 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG55823
    cln31
    cln31 40(a)3
    52.67(n)1
    46.26(a)1
      75A43
    399811  NM_140754.21  NP_649011.11 
    worm
    (Caenorhabditis elegans)
    Secernentea cln-3.13
    cln-3.21
    Human CLN3 protein like3
    cln-3.21
    40(a)
    (best of 3)3
    48.94(n)1
    45.8(a)1
      V(11266193-11268210)3
    1721711  NM_059155.61  NP_491556.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes YHC3(YJL059W)4
    YHC31
    Vacuolar membrane protein involved in the ATP-dependent more4
    YHC31
    46.35(n)1
    44.32(a)1
      10(324964-326190)4
    8533871, 4  NP_012476.11, 4 


    ENSEMBL Gene Tree for CLN3 (if available)
    TreeFam Gene Tree for CLN3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CLN3 gene
    ENSG000002618322  

    Find genes that share paralogs with CLN3           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CLN3 (see all 538)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0051344
    Ceroid lipofuscinosis, neuronal, 3 (CLN3)4--see VAR_0051342 V F mis40--------
    VAR_0051324
    Ceroid lipofuscinosis, neuronal, 3 (CLN3)4--see VAR_0051322 L P mis40--------
    VAR_0051314
    Ceroid lipofuscinosis, neuronal, 3 (CLN3)4--see VAR_0051312 L P mis40--------
    VAR_0051354
    Ceroid lipofuscinosis, neuronal, 3 (CLN3)4--see VAR_0051352 R C mis40--------
    VAR_0668944
    Ceroid lipofuscinosis, neuronal, 3 (CLN3)4--see VAR_0668942 G R mis40--------
    VAR_0668934
    Ceroid lipofuscinosis, neuronal, 3 (CLN3)4--see VAR_0668932 G A mis40--------
    VAR_0051364
    Ceroid lipofuscinosis, neuronal, 3 (CLN3)4--see VAR_0051362 R H mis40--------
    VAR_0051334
    Ceroid lipofuscinosis, neuronal, 3 (CLN3)4--see VAR_0051332 E K mis40--------
    VAR_0668924
    Ceroid lipofuscinosis, neuronal, 3 (CLN3)4--see VAR_0668922 C R mis40--------
    rs1386653621,2
    C--26531542(+) TGGCT-/GGGTGGC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CLN3 (28477983 - 28506896 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for CLN3:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2673092CNV Deletion23128226
    nsv509608CNV Insertion20534489
    nsv103376CNV Loss16902084
    nsv833180CNV Loss17160897
    nsv9415CNV Gain18304495
    nsv905688CNV Gain21882294
    dgv842e1CNV Complex17122850
    dgv843e1CNV Complex17122850

    Human Gene Mutation Database (HGMD): CLN3
    Locus Specific Mutation Databases (LSDB): CLN3

    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for CLN3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607042   
    OMIM disorders: 204200  
    UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286
  • Ceroid lipofuscinosis, neuronal, 3 (CLN3) [MIM:204200]: A form of neuronal ceroid lipofuscinosis.
    Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by
    intracellular accumulation of autofluorescent liposomal material, and clinically by seizures, dementia, visual
    loss, and/or cerebral atrophy. The hallmark of CLN3 is the ultrastructural pattern of lipopigment with a
    fingerprint profile, which can have 3 different appearances: pure within a lysosomal residual body; in
    conjunction with curvilinear or rectilinear profiles; and as a small component within large membrane-bound
    lysosomal vacuoles. The combination of fingerprint profiles within lysosomal vacuoles is a regular feature of
    blood lymphocytes from patients with neuronal ceroid lipofuscinosis type 3. Note=The disease is caused by
    mutations affecting the gene represented in this entry

  • 8 diseases for CLN3:    
    About MalaCards
    juvenile batten disease    batten disease    neuronal ceroid lipofuscinosis    neuronal ceroid-lipofuscinoses
    northern epilepsy    peripheral retinal degeneration    lafora disease    late-infantile neuronal ceroid lipofuscinosis

    3 diseases from the University of Copenhagen DISEASES database for CLN3:
    Neuronal ceroid lipofuscinosis     Neurodegenerative disease     Blindness

    Find genes that share disorders with CLN3           About GenesLikeMe

    Selected Novoseek inferred disease relationships for CLN3 gene (see all 12)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    batten disease 98.3 95 10527801 (4), 11590129 (4), 10916181 (3), 14699076 (3) (see all 55)
    neuronal ceroid lipofuscinoses 96 9 15032383 (2), 11001812 (1), 17896996 (1), 18552385 (1) (see all 6)
    lincl 92.4 8 11339651 (2), 9097964 (1), 9458173 (1), 10446748 (1) (see all 6)
    neurodegenerative diseases 79.3 17 14644441 (2), 11589015 (1), 20015955 (1), 17896996 (1) (see all 16)
    lysosomal storage diseases 73.2 1 18314010 (1)
    lafora disease 58.5 1 11579433 (1)
    neurodegeneration 55.7 2 10191118 (1), 11921051 (1)
    retinal degeneration 53.9 2 10964839 (1), 18265413 (1)
    chromosome deletion 53.2 2 9490299 (1), 9450775 (1)
    visual loss 46.4 1 16720047 (1)

    Genatlas disease: CLN3
    ceroid-lipofuscinosis,neuronal 3,juvenile,Batten (Spielmeyer-Vogt-Sjogren) disease,progressive neurodegenerative
    disease with an onset between 5 and 10 years,characterized by retinitis pigmentosa and a rapid loss of vision
    with macular and peripheral retinal degeneration,cognitive and motor dysfunction,seizures in childhood,a fatal
    outcome within a decade,and a characteristic fingerprint profile inclusions in different cells,including the
    variant form with granular osmiophilic deposits (GROD)

    GeneTests: CLN3
    GeneReviews: CLN3
    Genetic Association Database (GAD): CLN3
    Human Genome Epidemiology (HuGE) Navigator: CLN3 (2 documents)

    Export disorders for CLN3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for CLN3 gene, integrated from 10 sources (see all 178):
    (articles sorted by number of sources associating them with CLN3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Expression studies of CLN3 protein (battenin) in fusion with the green fluorescent protein in mammalian cells in vitro. (PubMed id 10191115)1, 2, 9 Golabek A.A....Wisniewski K.E. (Mol. Genet. Metab. 1999)
    2. Genomic structure and complete nucleotide sequence of the Batten disease gene, CLN3. (PubMed id 9119403)1, 2, 9 Mitchison H.M.... Mole S.E. (Genomics 1997)
    3. C-terminal prenylation of the CLN3 membrane glycoprotein is required for efficient endosomal sorting to lysosomes. (PubMed id 17286803)1, 2, 9 Storch S.... Braulke T. (Traffic 2007)
    4. Spectrum of mutations in the Batten disease gene, CLN3. (PubMed id 9311735)1, 2, 9 Munroe P.B.... Mole S.E. (Am. J. Hum. Genet. 1997)
    5. Molecular screening of Batten disease: identification of a missense mutation (E295K) in the CLN3 gene. (PubMed id 9490299)1, 2, 9 Zhong N.... Brown W.T. (Hum. Genet. 1998)
    6. Isolation of a novel gene underlying Batten disease, CLN3. (PubMed id 7553855)1, 2, 9 Lerner T.J.... Mole S.E. (Cell 1995)
    7. CLN3p impacts galactosylceramide transport, raft morphology, and lipid content. (PubMed id 18317235)1, 3, 9 Rusyn E....Boustany R.M. (Pediatr. Res. 2008)
    8. Neuronal ceroid lipofuscinosis protein CLN3 interacts with motor proteins and modifies location of late endosomal compartments. (PubMed id 22261744)1, 2 Uusi-Rauva K.... Jalanko A. (Cell. Mol. Life Sci. 2012)
    9. Genotype does not predict severity of behavioural phenotype in juvenile neuronal ceroid lipofuscinosis (Batten disease). (PubMed id 20187884)1, 4 Adams H.R....Mink J.W. (Dev Med Child Neurol 2010)
    10. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. (PubMed id 21102463)1, 4 Franke A....Parkes M. (Nat. Genet. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1201 HGNC: 2074 AceView: CLN3 Ensembl:ENSG00000188603 euGenes: HUgn1201
    ECgene: CLN3 Kegg: 1201 H-InvDB: CLN3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for CLN3 Pharmacogenomics, SNPs, Pathways
    NCL CLN3http://www.ucl.ac.uk/ncl/cln3.shtml
    Mutations of the CLN3 genehttp://www.retina-international.org/files/sci-news/cln3mut.htm
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=CLN3[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CLN3 gene:
    Search GeneIP for patents involving CLN3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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