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    CLN3 CLN3 lysosomal/endosomal transmembrane protein, battenin [ Homo sapiens (human) ]

    Gene ID: 1201, updated on 7-Sep-2023

    Summary

    Official Symbol
    CLN3provided by HGNC
    Official Full Name
    CLN3 lysosomal/endosomal transmembrane protein, batteninprovided by HGNC
    Primary source
    HGNC:HGNC:2074
    See related
    Ensembl:ENSG00000188603 MIM:607042; AllianceGenome:HGNC:2074
    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; BTN1; 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]
    Expression
    Ubiquitous expression in placenta (RPKM 23.0), colon (RPKM 17.0) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CLN3 in Genome Data Viewer
    Location:
    16p12.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (28466653..28492082, complement)
    RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (28903667..28920379) , (28747320..28747572, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (28477974..28503403, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 3 subunit C like Neighboring gene cell division cycle 37 pseudogene 2 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:28459200-28460080 Neighboring gene nuclear pore complex interacting protein family member B7 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:28503277-28504066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:28510584-28511084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:28511085-28511585 Neighboring gene apolipoprotein B receptor Neighboring gene interleukin 27

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Neuronal ceroid lipofuscinosis 3
    MedGen: C0751383 OMIM: 204200 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

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

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC102840

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium-dependent protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables glycolipid binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sulfatide binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Golgi to lysosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in L-arginine transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in actin cytoskeleton organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in action potential ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in amyloid precursor protein catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in associative learning ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in autophagosome maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in autophagosome-lysosome fusion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in blood vessel endothelial cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in glycerophospholipid biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in glycolipid transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular water homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ionotropic glutamate receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in learning or memory ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in lysosomal lumen acidification IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in lysosomal lumen acidification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lysosomal lumen pH elevation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lysosomal protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in lysosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in lysosome organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in membrane organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of catalytic activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of neuron apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of proteolysis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuromuscular process controlling balance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neurotransmitter metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in phagosome-lysosome docking ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in phagosome-lysosome fusion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in plasma membrane raft organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of Golgi to plasma membrane protein transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of caveolin-mediated endocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of pinocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of protein phosphorylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein localization to plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein processing ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in receptor-mediated endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of arginine biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of autophagosome maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of autophagosome size IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of cellular response to osmotic stress IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of cytosolic calcium ion concentration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of fibroblast migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of filopodium assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of modification of synaptic structure ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of phagosome maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of protein localization to plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of protein processing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of short-term neuronal synaptic plasticity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of synaptic transmission, GABAergic ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of synaptic transmission, glutamatergic ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in renal potassium excretion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in vesicle transport along microtubule IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in Golgi apparatus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in Golgi stack IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in autolysosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in autophagosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in caveola IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in caveola IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in early endosome membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in late endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosomal membrane HDA PubMed 
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane raft IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in neuron projection IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in recycling endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in synaptic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    battenin
    Names
    CLN3, battenin
    batten disease protein
    ceroid-lipofuscinosis, neuronal 3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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/Swiss-Prot
      B2R7J1, B4DXL3, O00668, O95089, Q13286, Q549S9, Q9UP09, Q9UP11, Q9UP12, Q9UP13, Q9UP14
      UniProtKB/TrEMBL
      A0A024QZB8, A0A1B0GWD3
      Related
      ENSP00000353073.9, ENST00000359984.12
      Conserved Domains (1) summary
      pfam02487
      Location:40437
      CLN3; CLN3 protein
    2. NM_001042432.2NP_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/Swiss-Prot
      B2R7J1, B4DXL3, O00668, O95089, Q13286, Q549S9, Q9UP09, Q9UP11, Q9UP12, Q9UP13, Q9UP14
      UniProtKB/TrEMBL
      A0A024QZB8, A0A1B0GWD3
      Related
      ENSP00000490105.1, ENST00000636147.2
      Conserved Domains (1) summary
      pfam02487
      Location:40437
      CLN3; CLN3 protein
    3. NM_001286104.2NP_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)
      AC138894, AK302027, DA703317
      Consensus CDS
      CCDS73855.1
      UniProtKB/Swiss-Prot
      Q13286
      UniProtKB/TrEMBL
      A0A1B0GWD3
      Related
      ENSP00000353116.3, ENST00000360019.8
      Conserved Domains (1) summary
      pfam02487
      Location:40413
      CLN3; CLN3 protein
    4. NM_001286105.2NP_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)
      AC138894, AK297690, AK302027, BP252176
      UniProtKB/Swiss-Prot
      Q13286
      UniProtKB/TrEMBL
      B4DMY6, O95086
      Conserved Domains (1) summary
      pfam02487
      Location:27337
      CLN3; CLN3 protein
    5. NM_001286109.2NP_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
      O95086, Q2TA70
      Conserved Domains (1) summary
      pfam02487
      Location:1359
      CLN3; CLN3 protein
    6. NM_001286110.2NP_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)
      AC138894, AK294070, BP252176, DA869025
      Consensus CDS
      CCDS73854.1
      UniProtKB/TrEMBL
      B4DFF3, H3BPM8, O95086
      Related
      ENSP00000350523.9, ENST00000357857.14
      Conserved Domains (1) summary
      pfam02487
      Location:1383
      CLN3; CLN3 protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      28466653..28492082 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      28747320..28747572 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    2. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      28903667..28920379
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)