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    CLN6 CLN6 transmembrane ER protein [ Homo sapiens (human) ]

    Gene ID: 54982, updated on 3-Nov-2024

    Summary

    Official Symbol
    CLN6provided by HGNC
    Official Full Name
    CLN6 transmembrane ER proteinprovided by HGNC
    Primary source
    HGNC:HGNC:2077
    See related
    Ensembl:ENSG00000128973 MIM:606725; AllianceGenome:HGNC:2077
    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; CLN6A; 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]
    Expression
    Ubiquitous expression in bone marrow (RPKM 12.1), colon (RPKM 10.8) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See CLN6 in Genome Data Viewer
    Location:
    15q23
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (68206992..68257211, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (66025741..66075904, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (68499330..68549549, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene protein inhibitor of activated STAT 1 Neighboring gene uncharacterized LOC105370871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68492859-68493630 Neighboring gene Sharpr-MPRA regulatory region 569 Neighboring gene calmodulin like 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68503536-68504076 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9642 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:68521930-68522109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9643 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:68549209-68549856 Neighboring gene uncharacterized LOC124903593 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 40 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:68564472-68565671 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:68570079-68570980 Neighboring gene NANOG hESC enhancer GRCh37_chr15:68577826-68578327 Neighboring gene fem-1 homolog B

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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
    Ceroid lipofuscinosis, neuronal, 6A
    MedGen: C5551375 OMIM: 601780 GeneReviews: Not available
    Compare labs
    Ceroid lipofuscinosis, neuronal, 6B (Kufs type)
    MedGen: C5561927 OMIM: 204300 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

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

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ20561

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables lysophosphatidic acid binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sulfatide binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cholesterol metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ganglioside metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in glycosaminoglycan metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in locomotion involved in locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lysosomal lumen acidification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lysosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of proteolysis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein catabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum lumen IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in membrane HDA PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    ceroid-lipofuscinosis neuronal protein 6
    Names
    ceroid-lipofuscinosis neuronal 6 late infantile
    ceroid-lipofuscinosis, neuronal 6, late infantile

    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_008764.2 RefSeqGene

      Range
      32484..55220
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_832

    mRNA and Protein(s)

    1. NM_001411068.1NP_001397997.1  ceroid-lipofuscinosis neuronal protein 6 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC107871
      Consensus CDS
      CCDS92032.1
      Related
      ENSP00000445770.1, ENST00000538696.5
    2. NM_017882.3NP_060352.1  ceroid-lipofuscinosis neuronal protein 6 isoform 1

      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
      A8K560, B4DDH6, Q6IAB1, Q96SR0, Q9NWW5
      UniProtKB/TrEMBL
      A0A024R601, A0A0S2Z5G3
      Related
      ENSP00000249806.5, ENST00000249806.11
      Conserved Domains (1) summary
      pfam15156
      Location:30309
      CLN6; Ceroid-lipofuscinosis neuronal protein 6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      68206992..68257211 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      66025741..66075904 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)