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    CLN8 CLN8 transmembrane ER and ERGIC protein [ Homo sapiens (human) ]

    Gene ID: 2055, updated on 1-Mar-2024

    Summary

    Official Symbol
    CLN8provided by HGNC
    Official Full Name
    CLN8 transmembrane ER and ERGIC proteinprovided by HGNC
    Primary source
    HGNC:HGNC:2079
    See related
    Ensembl:ENSG00000182372 MIM:607837; AllianceGenome:HGNC:2079
    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
    EPMR; TLCD6; C8orf61
    Summary
    This gene encodes a transmembrane protein belonging to a family of proteins containing TLC domains, which are postulated to function in lipid synthesis, transport, or sensing. The protein localizes to the endoplasmic reticulum (ER), and may recycle between the ER and ER-Golgi intermediate compartment. Mutations in this gene are associated with a disorder characterized by progressive epilepsy with cognitive disabilities (EPMR), which is a subtype of neuronal ceroid lipofuscinoses (NCL). Patients with mutations in this gene have altered levels of sphingolipid and phospholipids in the brain. [provided by RefSeq, Jul 2017]
    Expression
    Ubiquitous expression in brain (RPKM 5.7), spleen (RPKM 4.0) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See CLN8 in Genome Data Viewer
    Location:
    8p23.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (1753059..1786570)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (1542478..1565133)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (1711955..1734736)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene DLG associated protein 2 Neighboring gene uncharacterized LOC124901870 Neighboring gene conserved acetylation island sequence 7 enhancer Neighboring gene DNA fragmentation factor subunit alpha pseudogene Neighboring gene uncharacterized LOC105377778 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:1703542-1704741 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:1719100-1719280 Neighboring gene Sharpr-MPRA regulatory region 8503 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:1726288-1727208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:1731879-1732378 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:1733452-1733574 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:1748222-1749421 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:1750577-1751237 Neighboring gene uncharacterized LOC105377779 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:1762347-1762848 Neighboring gene CLN8 antisense RNA 1 Neighboring gene microRNA 3674

    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 8
    MedGen: C1838570 OMIM: 600143 GeneReviews: Not available
    Compare labs
    Neuronal ceroid lipofuscinosis 8 northern epilepsy variant
    MedGen: C1864923 OMIM: 610003 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of N370S homozygous Gaucher disease reveals the candidacy of CLN8 gene as a genetic modifier contributing to extreme phenotypic variation.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ39417

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ceramide binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ceramide binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in adult walking behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in associative learning IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ceramide biosynthetic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in ceramide metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cholesterol metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in glutamate reuptake IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lipid biosynthetic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in lipid homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in lipid transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in lysosome organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mitochondrial membrane organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in musculoskeletal movement IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of neuron apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of proteolysis NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neurofilament cytoskeleton organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuromuscular process controlling balance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuromuscular process controlling posture IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in phospholipid metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in phospholipid metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in photoreceptor cell maintenance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein catabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of cell size IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retina development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retinal rod cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in social behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in somatic motor neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    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 membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endoplasmic reticulum-Golgi intermediate compartment IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum-Golgi intermediate compartment membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
     
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    protein CLN8
    Names
    ceroid-lipofuscinosis, neuronal 8

    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_008656.2 RefSeqGene

      Range
      12927..35793
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_691

    mRNA and Protein(s)

    1. NM_018941.4NP_061764.2  protein CLN8

      See identical proteins and their annotated locations for NP_061764.2

      Status: REVIEWED

      Source sequence(s)
      AC100810, AF123761, AW296697, BC007725, DA193710
      Consensus CDS
      CCDS5956.1
      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
      Related
      ENSP00000328182.4, ENST00000331222.6
      Conserved Domains (1) summary
      smart00724
      Location:64262
      TLC; TRAM, LAG1 and CLN8 homology domains

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      1753059..1786570
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047421512.1XP_047277468.1  protein CLN8 isoform X1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
    2. XM_005266022.2XP_005266079.1  protein CLN8 isoform X1

      See identical proteins and their annotated locations for XP_005266079.1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
      Conserved Domains (1) summary
      smart00724
      Location:64262
      TLC; TRAM, LAG1 and CLN8 homology domains
    3. XM_005266023.2XP_005266080.1  protein CLN8 isoform X1

      See identical proteins and their annotated locations for XP_005266080.1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
      Related
      ENSP00000490016.1, ENST00000519254.2
      Conserved Domains (1) summary
      smart00724
      Location:64262
      TLC; TRAM, LAG1 and CLN8 homology domains
    4. XM_011534746.3XP_011533048.1  protein CLN8 isoform X1

      See identical proteins and their annotated locations for XP_011533048.1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
      Conserved Domains (1) summary
      smart00724
      Location:64262
      TLC; TRAM, LAG1 and CLN8 homology domains
    5. XM_011534745.2XP_011533047.1  protein CLN8 isoform X1

      See identical proteins and their annotated locations for XP_011533047.1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
      Related
      ENSP00000489694.1, ENST00000635751.1
      Conserved Domains (1) summary
      smart00724
      Location:64262
      TLC; TRAM, LAG1 and CLN8 homology domains
    6. XM_005266021.5XP_005266078.1  protein CLN8 isoform X1

      See identical proteins and their annotated locations for XP_005266078.1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
      Related
      ENSP00000490458.1, ENST00000637156.1
      Conserved Domains (1) summary
      smart00724
      Location:64262
      TLC; TRAM, LAG1 and CLN8 homology domains
    7. XM_047421513.1XP_047277469.1  protein CLN8 isoform X2

    8. XM_011534747.3XP_011533049.1  protein CLN8 isoform X2

      See identical proteins and their annotated locations for XP_011533049.1

      Conserved Domains (1) summary
      cl02759
      Location:64181
      TRAM_LAG1_CLN8; TLC domain

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_187680.1 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      165717..199228
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330445.1XP_054186420.1  protein CLN8 isoform X1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
    2. XM_054330441.1XP_054186416.1  protein CLN8 isoform X1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
    3. XM_054330444.1XP_054186419.1  protein CLN8 isoform X1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
    4. XM_054330440.1XP_054186415.1  protein CLN8 isoform X1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
    5. XM_054330443.1XP_054186418.1  protein CLN8 isoform X1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
    6. XM_054330442.1XP_054186417.1  protein CLN8 isoform X1

      UniProtKB/Swiss-Prot
      Q86U71, Q96I95, Q9UBY8
    7. XM_054330446.1XP_054186421.1  protein CLN8 isoform X2

    8. XM_054330447.1XP_054186422.1  protein CLN8 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      1542478..1565133
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001034061.1: Suppressed sequence

      Description
      NM_001034061.1: This RefSeq was permanently suppressed because it is entirely UTR sequence.