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    CLN3 ceroid-lipofuscinosis, neuronal 3 [ Homo sapiens (human) ]

    Gene ID: 1201, updated on 26-Jan-2016
    Official Symbol
    CLN3provided by HGNC
    Official Full Name
    ceroid-lipofuscinosis, neuronal 3provided by HGNC
    Primary source
    HGNC:HGNC:2074
    See related
    Ensembl:ENSG00000188603; Ensembl:ENSG00000261832; HPRD:08450; MIM:607042; Vega:OTTHUMG00000097024; Vega:OTTHUMG00000175737
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BTS; JNCL
    Summary
    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]
    Orthologs
    See CLN3 in Epigenomics, MapViewer
    Location:
    16p12.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) 16 NC_000016.10 (28466653..28492302, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (28488600..28505897, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 3 subunit C-like Neighboring gene microRNA 6862-1 Neighboring gene cell division cycle 37 pseudogene 2 Neighboring gene nuclear pore complex interacting protein family member B7 Neighboring gene uncharacterized LOC105371165 Neighboring gene apolipoprotein B receptor

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Juvenile neuronal ceroid lipofuscinosis
    MedGen: C0751383 OMIM: 204200 GeneReviews: Neuronal Ceroid-Lipofuscinoses
    Compare labs

    NHGRI GWAS Catalog

    Description
    Common variants at five new loci associated with early-onset inflammatory bowel disease.
    NHGRI GWA Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    NHGRI GWA Catalog

    Replication interactions

    Interaction Pubs
    Knockdown of ceroid-lipofuscinosis, neuronal 3 (CLN3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Genome-wide shRNA screening identifies CLN3, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

    Go to the HIV-1, Human Interaction Database

    • Lysosome, organism-specific biosystem (from KEGG)
      Lysosome, organism-specific biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
    • Lysosome, conserved biosystem (from KEGG)
      Lysosome, conserved biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC102840

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    unfolded protein binding TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    action potential ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    amyloid precursor protein catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    arginine transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    associative learning ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    autophagosome maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cellular amino acid metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    ceramide metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    galactosylceramide metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    globoside metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    glucosylceramide metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    ionotropic glutamate receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    lysosomal lumen acidification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    lysosomal lumen pH elevation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lysosome organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    macroautophagy NAS
    Non-traceable Author Statement
    more info
    PubMed 
    membrane organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of catalytic activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of macroautophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of neuron apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of proteolysis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    neuromuscular process controlling balance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    neurotransmitter metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein catabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    protein processing ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    receptor-mediated endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cytosolic calcium ion concentration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    sphingomyelin metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    vacuolar transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    vesicle transport along microtubule IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Golgi membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Golgi stack IDA
    Inferred from Direct Assay
    more info
    PubMed 
    autophagosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    caveola IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    late endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mitochondrion TAS
    Traceable Author Statement
    more info
    PubMed 
    neuron projection IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    synaptic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    battenin
    Names
    batten disease protein

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008654.2 RefSeqGene

      Range
      5001..30650
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_689

    mRNA and Protein(s)

    1. NM_000086.2NP_000077.1  battenin isoform a

      See identical proteins and their annotated locations for NP_000077.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (a).
      Source sequence(s)
      AF077962, AI138575, AU105965, DA869025, U32680
      Consensus CDS
      CCDS10632.1
      UniProtKB/TrEMBL
      A0A024QZB8
      UniProtKB/Swiss-Prot
      Q13286
      Conserved Domains (1) summary
      cl15430
      Location:37438
      Nucleoside_tran; Nucleoside transporter
    2. NM_001042432.1NP_001035897.1  battenin isoform a

      See identical proteins and their annotated locations for NP_001035897.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 2 encode the same isoform (a).
      Source sequence(s)
      AF077957, AI138575, DA552461, DB101039
      Consensus CDS
      CCDS10632.1
      UniProtKB/TrEMBL
      A0A024QZB8
      UniProtKB/Swiss-Prot
      Q13286
      Related
      ENSP00000353116, ENST00000360019
      Conserved Domains (1) summary
      cl15430
      Location:37438
      Nucleoside_tran; Nucleoside transporter
    3. NM_001286104.1NP_001273033.1  battenin isoform b

      See identical proteins and their annotated locations for NP_001273033.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AK302027, DA703317
      Consensus CDS
      CCDS73855.1
      UniProtKB/Swiss-Prot
      Q13286
      Related
      ENSP00000329171, OTTHUMP00000254078, ENST00000333496, OTTHUMT00000430940
      Conserved Domains (1) summary
      cl15430
      Location:37414
      Nucleoside_tran; Nucleoside transporter
    4. NM_001286105.1NP_001273034.1  battenin isoform c

      See identical proteins and their annotated locations for NP_001273034.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and lacks two exons compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (c) with a shorter and distinct N-terminus compared to isoform a.
      Source sequence(s)
      AK297690, AK302027, BP252176
      UniProtKB/TrEMBL
      B4DMY6
      UniProtKB/Swiss-Prot
      Q13286
      Related
      ENSP00000379014, OTTHUMP00000254082, ENST00000395653, OTTHUMT00000430945
      Conserved Domains (1) summary
      cl15430
      Location:26338
      Nucleoside_tran; Nucleoside transporter
    5. NM_001286109.1NP_001273038.1  battenin isoform d

      See identical proteins and their annotated locations for NP_001273038.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence, the 3' UTR, and lacks an alternate in-frame exon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (d) with a shorter N-terminus and missing an alternate internal segment compared to isoform a.
      Source sequence(s)
      BC111068, BP252176, DA869025
      Consensus CDS
      CCDS73853.1
      UniProtKB/TrEMBL
      Q2TA70
      Related
      ENSP00000454253, OTTHUMP00000254076, ENST00000568224, OTTHUMT00000430938
      Conserved Domains (1) summary
      cl15430
      Location:1360
      Nucleoside_tran; Nucleoside transporter
    6. NM_001286110.1NP_001273039.1  battenin isoform e

      See identical proteins and their annotated locations for NP_001273039.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (e) with a shorter N-terminus and missing an alternate internal segment compared to isoform a.
      Source sequence(s)
      AK294070, BP252176, DA869025
      Consensus CDS
      CCDS73854.1
      UniProtKB/TrEMBL
      B4DFF3
      Related
      ENSP00000350523, OTTHUMP00000254080, ENST00000357857, OTTHUMT00000430943
      Conserved Domains (1) summary
      cl15430
      Location:1384
      Nucleoside_tran; Nucleoside transporter

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p2 Primary Assembly

      Range
      28466653..28492302 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018927.2 Alternate CHM1_1.1

      Range
      29489652..29515233 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)