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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CLN3 Gene

protein-coding   GIFtS: 62
GCID: GC16M028488

ceroid-lipofuscinosis, neuronal 3

(Previous names: Batten, Spielmeyer-Vogt disease )
(Previous symbol: BTS)
 Explore 32 diseases affiliated with
CLN3 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for CLN3    

Aliases
for CLN3 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Ceroid-Lipofuscinosis, Neuronal 31 2     Batten, Spielmeyer-Vogt Disease1
BTS1 2 3 5     Battenin1
JNCL1 2     Protein CLN33
Batten Disease Protein2 3     

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


Summaries
for CLN3 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for CLN3:
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)

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

Gene Wiki entry for CLN3


Genomic Views
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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000016.9  NC_018927.1  NT_010393.16  
Regulatory elements:
   SABiosciences 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 plasmid: CLN3 promoter sequence
   Search SABiosciences Chromatin IP Primers for CLN3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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

Proteins
for CLN3 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286 (See protein sequence)
Recommended Name: Battenin  
Size: 438 amino acids; 47623 Da
Subunit: Interacts with DCTN1 and KIF3A. Interacts with RAB7A and RILP
Subcellular location: Lysosome membrane; Multi-pass membrane protein. Late endosome
Secondary accessions: B2R7J1 O00668 Q549S9 Q9UP09 Q9UP11 Q9UP12 Q9UP13 Q9UP14
Alternative splicing: 5 isoforms:  Q13286-1   Q13286-2   Q13286-3   Q13286-4   Q13286-5   (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

Post-translational modifications:

  • Highly glycosylated1
  • Farnesylation is important for trafficking to lysosomes1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q13286

    • CLN3 Protein expression data from MOPED and PaxDb:    About this image 
    CLN3 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_000077.1  NP_001035897.1  

    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  

    Human Recombinant Protein Products for CLN3: 
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    Uscn Proteins for CLN3

    Gene Ontology (GO): 5/21 cellular component terms (GO ID links to tree view) (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

    CLN3 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for CLN3 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    CLN3 for domains           About GeneDecksing

    3 InterPro domains/families:
     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 family: IPB003492 CLN3 Batten's disease protein (battenin) signature

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


    Function
    for CLN3 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    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 (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
    GO:0051082unfolded protein binding TAS8980123
         
    CLN3 for ontologies           About GeneDecksing


    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 

    CLN3 for phenotypes           About GeneDecksing

    Animal Models:
         Mouse knock-outs for CLN3: Cln3tm1Mkat Cln3tm1Mem Cln3tm1Nbm Cln3tm1.1Mem
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for CLN3 

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    Inhib. RNA
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    In Situ Assay
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    Pathways & Interactions
    for CLN3 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Lysosome
    		Lysosome1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways



    1         Kegg Pathway  (Kegg details for CLN3):
        Lysosome


    CLN3 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for CLN3

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

    5/674 Interacting proteins for CLN3 (Q132863 ENSP000003530734) via UniProtKB, MINT, STRING, and/or I2D (see all 674)
    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): 5/32 biological process terms (GO ID links to tree view) (see all 32):    About this table

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

    CLN3 for ontologies           About GeneDecksing



    Drugs & Compounds
    for CLN3 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    CLN3 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for CLN3
    8 Novoseek 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)

    Search CenterWatch for drugs/clinical trials and news about CLN3 

    Transcripts
    for CLN3 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for CLN3 gene (2 alternative transcripts): 
    NM_000086.2  NM_001042432.1  

    Unigene Cluster for CLN3:

    Ceroid-lipofuscinosis, neuronal 3
    Hs.534667  [show with all ESTs]
    Unigene Representative Sequence: AK090709
    18/41 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)

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    Inhib. RNA
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    Additional cDNA 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 

    24/37 DOTS entries (see all 37):

    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 

    24/260 AceView cDNA sequences (see all 260):

    BU619787 CR620473 CR605499 AI355261 BM781749 BM739110 CR591558 CA453983 
    BQ963046 BI870454 CR613621 BM741475 BX402900 BM772581 BX384288 BQ929206 
    AX746584 AF078168 CR601899 BM917287 AI393924 BM753441 AL555221 T08995 

    GeneLoc Exon Structure

    5/25 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

    Expression
    for CLN3 gene

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CLN3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CCTTCTGAAT
    CLN3 Expression
    About this image
    See CLN3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CLN3

    SOURCE GeneReport for Unigene cluster: Hs.534667
        SABiosciences Expression via Pathway-Focused PCR Arrays including CLN3: 

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    Orthologs
    for CLN3 gene

    (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)
    About This Section
    This gene was present in the common ancestor of animals and fungi.

    Orthologs for CLN3 gene from 7/27 species (see all 27)    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, Spielmeyer-Vogt disease) less1, 5 82.91(n)1
    86.04(a)1    		   7 (69.16 cM)5
    127521  NM_001146311.11  NP_001139783.11 
     1265712075 
    lizard
    (Anolis carolinensis)    		 Reptilia CLN36
    		 --
    		 57(a)
    		 1 → many
    		 GL343287.1(735505-750833)
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.152912 Xenopus laevis transcribed sequence with weak similarity to protein pirA57219 (H.sapiens) A57219 Batten disease-related protein CLN3 - human less 76.05(n)    48012878 
    zebrafish
    (Danio rerio)    		 Actinopterygii Dr.31672 Transcribed sequence with weak similarity to protein pirA57219 (H.sapiens) A57219 Batten disease-related protein CLN3 - human less 72.42(n)    57057328 
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG55823
    cln31    		 CG5582-PA1 40(a)3
    52.33(n)1
    45.38(a)1    		   75A43
    399811  NM_140754.11  NP_649011.11 
    worm
    (Caenorhabditis elegans)    		 Secernentea cln-3.13
    cln-3.21    		 Human CLN3 protein like3
    Protein CLN-3.21    		 40(a)
    (best of 3)3
    48.94(n)1
    45.55(a)1    		   V(11266193-11268210)3
    1721711  NM_059155.51  NP_491556.11 
    baker's yeast
    (Saccharomyces cerevisiae)    		 Saccharomycetes YHC3(YJL059W)4
    YHC31    		 Vacuolar membrane protein involved in the ATP-dependent transport of arginine into the vacuole and possibly in balancing ion homeostasis; homolog of human CLN3 involved in Batten disease (juvenile onset neuronal ceroid lipofuscinosis) less4
    Yhc3p1    		 45.75(n)1
    41.37(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
    for CLN3 gene

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

    CLN3 for paralogs           About GeneDecksing



    Genomic Variants
    for CLN3 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/352 NCBI SNPs in CLN3 are shown (see all 352)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 16 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs798429251,2
    		C,F--26513800(+) GCATGA/GATGAA 2 -- ds50011Minor allele frequency- G:0.14WA 118
    rs746889221,2
    		C--26514092(+) GCCTAC/GGTGAC 2 -- ds50011Minor allele frequency- G:0.00WA 2
    rs10649121,2
    		C--26514286(-) GCCTTC/TTGAAT 2 -- ut312Minor allele frequency- T:0.00NA 4
    rs1131127661,2
    		C--26514341(+) CCCCCG/TGCAAG 2 -- ut311Minor allele frequency- T:0.50CSA 2
    rs1138452991,2
    		--26514397(+) GGCTGG/AGAGCA 2 -- ut311Minor allele frequency- A:0.50CSA 2
    rs10648861,2
    		C--26514571(-) TGCATC/TTCTGA 4 I syn1 ese32Minor allele frequency- T:0.00NA 4
    rs740168151,2
    		C--26514912(+) GGAGAG/AGTGGC 2 -- int12Minor allele frequency- A:0.10WA 120
    rs25204251,2
    		C--26515641(-) CTTCCT/CTTAAG 2 -- int11Minor allele frequency- C:0.00NA 2
    rs1126855171,2
    		--26516098(+) CCAGCC/ACTGAC 2 -- int11Minor allele frequency- A:0.50CSA 2
    rs26503681,2
    		C,H--26516936(-) TATGGC/AAAAAG 2 -- int12Minor allele frequency- A:0.01NS NA 174

    HapMap Linkage Disequilibrium report for CLN3 (28477983 - 28506896 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 4 variations for CLN3
         3 CNVs: 30770 4937 3999
         1 Indel: 11833
    Human Gene Mutation Database (HGMD): CLN3

    Locus Specific Mutation Databases (LSDB): CLN3

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CLN3
    DNA2.0 Custom Variant and Variant Library Synthesis for CLN3

    Disorders / Diseases
    for CLN3 gene

    (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.)
    About This Section
    CLN3 for disorders           About GeneDecksing

    OMIM gene information: 607042   
    OMIM disorders: 204200  
    UniProtKB/Swiss-Prot: CLN3_HUMAN, Q13286
  • Defects in CLN3 are the cause of neuronal ceroid lipofuscinosis type 3 (CLN3) [MIM:204200]; also known as
    • Batten disease. 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 CLN3

    20/32 diseases for CLN3 (see all 32):    About MalaCards
    ceroid lipofuscinosis    neuronal ceroid-lipofuscinoses    batten disease    neuronal ceroid-lipofuscinosis
    ceroid-lipofuscinosis, neuronal-3, juvenile    neurodegenerative disease    neuronitis    blue cone monochromacy
    blue toe syndrome    lysosomal storage disease    myoclonus epilepsy    progressive myoclonus epilepsy
    juvenile batten disease    lafora disease    retinal degeneration    myoclonus
    neuroretinitis    peripheral retinal degeneration    inflammatory bowel disease    pneumothorax

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

    10/12 Novoseek 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
    Neuronal Ceroid-Lipofuscinoses

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

    Export disorders for CLN3 gene to outside databases

    Publications
    for CLN3 gene

    (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)
    About This Section

    PubMed articles for CLN3 gene, integrated from 9 sources (see all 172):
    (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. (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. (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. (2007)
    4. Spectrum of mutations in the Batten disease gene, CLN3. (PubMed id 9311735)1, 2, 9 Munroe P.B.... Mole S.E. (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. (1998)
    6. Isolation of a novel gene underlying Batten disease, CLN3. (PubMed id 7553855)1, 2, 9 Lerner T.J.... Mole S.E. (1995)
    7. CLN3p impacts galactosylceramide transport, raft morphology, and lipid content. (PubMed id 18317235)1, 3, 9 Rusyn E....Boustany R.M. (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. (2012)
    9. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)

    External Searches for CLN3 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
    OMIM
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      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing CLN3 gene

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

    Other Databases showing CLN3 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing CLN3 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    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/sites/GeneTests/lab/gene/CLN3

    Intellectual Property
    for CLN3 gene

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

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