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    CLN6 ceroid-lipofuscinosis, neuronal 6, late infantile, variant [ Homo sapiens (human) ]

    Gene ID: 54982, updated on 20-Apr-2017
    Official Symbol
    CLN6provided by HGNC
    Official Full Name
    ceroid-lipofuscinosis, neuronal 6, late infantile, variantprovided by HGNC
    Primary source
    HGNC:HGNC:2077
    See related
    Ensembl:ENSG00000128973 MIM:606725; Vega:OTTHUMG00000133286
    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
    nclf; CLN4A; HsT18960
    Summary
    This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely encode proteins involved in the degradation of post-translationally modified proteins in lysosomes. The primary defect in NCL disorders is thought to be associated with lysosomal storage function. [provided by RefSeq, Oct 2008]
    Orthologs
    Location:
    15q23
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 15 NC_000015.10 (68206992..68229742, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (68499330..68522081, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene protein inhibitor of activated STAT 1 Neighboring gene uncharacterized LOC105370871 Neighboring gene calmodulin like 4 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 40 Neighboring gene fem-1 homolog B

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with ceroid-lipofuscinosis, neuronal 6, late infantile, variant (CLN6) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ20561

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    cellular macromolecule catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    cholesterol metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    ganglioside metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    glycosaminoglycan metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    locomotion involved in locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    lysosomal lumen acidification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of proteolysis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein catabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum lumen IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    ceroid-lipofuscinosis neuronal protein 6
    Names
    ceroid-lipofuscinosis neuronal 6 late infantile

    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_008764.2 RefSeqGene

      Range
      32470..55220
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_017882.2NP_060352.1  ceroid-lipofuscinosis neuronal protein 6

      See identical proteins and their annotated locations for NP_060352.1

      Status: REVIEWED

      Source sequence(s)
      AK027604, BC010849, BC013130, BM149330, CA446197, CN427564
      Consensus CDS
      CCDS10227.1
      UniProtKB/Swiss-Prot
      Q9NWW5
      UniProtKB/TrEMBL
      A0A024R601
      Related
      ENSP00000249806.5, OTTHUMP00000164387, ENST00000249806.10, OTTHUMT00000257066
      Conserved Domains (1) summary
      pfam15156
      Location:30309
      CLN6; Ceroid-lipofuscinosis neuronal protein 6

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p7 Primary Assembly

      Range
      68206992..68229742 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018926.2 Alternate CHM1_1.1

      Range
      68617284..68640038 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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