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    CLN5 CLN5 intracellular trafficking protein [ Homo sapiens (human) ]

    Gene ID: 1203, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CLN5provided by HGNC
    Official Full Name
    CLN5 intracellular trafficking proteinprovided by HGNC
    Primary source
    HGNC:HGNC:2076
    See related
    Ensembl:ENSG00000102805 MIM:608102; AllianceGenome:HGNC:2076
    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
    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 thyroid (RPKM 44.6), kidney (RPKM 19.6) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLN5 in Genome Data Viewer
    Location:
    13q22.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (76992081..77005117)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (76215721..76228757)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (77566216..77579252)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5412 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5413 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5414 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:77566521-77567720 Neighboring gene ribosomal protein L7 pseudogene 44 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7838 Neighboring gene DEAH-box helicase 9 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5417 Neighboring gene F-box and leucine rich repeat protein 3 Neighboring gene MYC binding protein 2 Neighboring gene MYCBP2 antisense RNA 1 Neighboring gene MYCBP2 antisense RNA 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Lysosomal dysfunction, autophagic defects, and CLN5 accumulation underlie the pathogenesis of KCTD7-mutated neuronal ceroid lipofuscinoses. Wang Y, et al. Autophagy, 2023 Jun. PMID 36368077, Free PMC Article
    2. The ultrastructural characteristics of the abnormal cytosomes in Batten-Kufs' disease. Carpenter S, et al. Brain, 1977 Mar. PMID 193610
    3. Defined chromosomal assignment of CLN5 demonstrates that at least four genetic loci are involved in the pathogenesis of human ceroid lipofuscinoses. Savukoski M, et al. Am J Hum Genet, 1994 Oct. PMID 7942847, Free PMC Article
    4. Efficient construction of a physical map by fiber-FISH of the CLN5 region: refined assignment and long-range contig covering the critical region on 13q22. Klockars T, et al. Genomics, 1996 Jul 1. PMID 8661106
    5. CLN5, a novel gene encoding a putative transmembrane protein mutated in Finnish variant late infantile neuronal ceroid lipofuscinosis. Savukoski M, et al. Nat Genet, 1998 Jul. PMID 9662406

    See all (59) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Batten disease gene product CLN5 is the lysosomal bis(monoacylglycero)phosphate synthase.
      Title: The Batten disease gene product CLN5 is the lysosomal bis(monoacylglycero)phosphate synthase.
    2. Lysosomal dysfunction, autophagic defects, and CLN5 accumulation underlie the pathogenesis of KCTD7-mutated neuronal ceroid lipofuscinoses.
      Title: Lysosomal dysfunction, autophagic defects, and CLN5 accumulation underlie the pathogenesis of KCTD7-mutated neuronal ceroid lipofuscinoses.
    3. Cln5 represents a new type of cysteine-based S-depalmitoylase linked to neurodegeneration.
      Title: Cln5 represents a new type of cysteine-based S-depalmitoylase linked to neurodegeneration.
    4. Deficiency of the Lysosomal Protein CLN5 Alters Lysosomal Function and Movement.
      Title: Deficiency of the Lysosomal Protein CLN5 Alters Lysosomal Function and Movement.
    5. CLN5 in heterozygosis may protect against the development of tumors in a VHL patient.
      Title: CLN5 in heterozygosis may protect against the development of tumors in a VHL patient.
    6. Association of the Recurrent Rare Variant c.415T>C p.Phe139Leu in CLN5 With a Recessively Inherited Macular Dystrophy.
      Title: Association of the Recurrent Rare Variant c.415T>C p.Phe139Leu in CLN5 With a Recessively Inherited Macular Dystrophy.
    7. Novel likely disease-causing CLN5 variants identified in Pakistani patients with neuronal ceroid lipofuscinosis.
      Title: Novel likely disease-causing CLN5 variants identified in Pakistani patients with neuronal ceroid lipofuscinosis.
    8. The Neuronal Ceroid Lipofuscinoses-Linked Loss of Function CLN5 and CLN8 Variants Disrupt Normal Lysosomal Function.
      Title: The Neuronal Ceroid Lipofuscinoses-Linked Loss of Function CLN5 and CLN8 Variants Disrupt Normal Lysosomal Function.
    9. This is the first report of whole gene deletion in combination with a novel pathogenic sequence variant in a CLN5 patient. The two mutations detected with whole exome sequencing simultaneously proved the advantage of the sequencing technology for genetic diagnostics
      Title: A novel pathogenic frameshift variant unmasked by a large de novo deletion at 13q21.33-q31.1 in a Chinese patient with neuronal ceroid lipofuscinosis type 5.
    10. This study demonstrated that Novel Mutations in CLN5 of Chinese Patients With Neuronal Ceroid Lipofuscinosis.
      Title: Novel Mutations in CLN5 of Chinese Patients With Neuronal Ceroid Lipofuscinosis.
    Submit: New GeneRIF Correction See all GeneRIFs (31)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Neuronal ceroid lipofuscinosis 5
    MedGen: C1850442 OMIM: 256731 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ90628

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables D-mannose binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables bis(monoacylglycero)phosphate synthase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables hydrolase activity, acting on glycosyl bonds IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables long-chain fatty acyl-CoA hydrolase activity 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 brain development IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in glycosylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 neurogenesis IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in neuron maturation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of GTP binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein catabolic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in retrograde transport, endosome to Golgi IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in signal peptide processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in vacuolar lumen IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    bis(monoacylglycero)phosphate synthase CLN5
    Names
    BMP synthase CLN5
    S-depalmitoylase CLN5
    ceroid-lipofuscinosis neuronal protein 5
    ceroid-lipofuscinosis, neuronal 5
    palmitoyl protein thioesterase CLN5
    NP_001353553.1
    NP_006484.2

    NCBI Reference Sequences (RefSeq)

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    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_009064.1 RefSeqGene

      Range
      5001..15594
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_692

    mRNA and Protein(s)

    1. NM_001366624.2 → NP_001353553.1  bis(monoacylglycero)phosphate synthase CLN5 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC001226
      Consensus CDS
      CCDS91815.1
      UniProtKB/TrEMBL
      A0A087WZY0, A0A1B0GTI0, A0A1B0GTR6
      Related
      ENSP00000489809.2, ENST00000636780.2
      Conserved Domains (1) summary
      pfam15014
      Location:53 → 188
      CLN5; Ceroid-lipofuscinosis neuronal protein 5

    2. NM_006493.4 → NP_006484.2  bis(monoacylglycero)phosphate synthase CLN5 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC001226
      Consensus CDS
      CCDS9456.2
      UniProtKB/Swiss-Prot
      B3KQK7, O75503
      UniProtKB/TrEMBL
      A0A1B0GWI2
      Related
      ENSP00000366673.5, ENST00000377453.9
      Conserved Domains (1) summary
      pfam15014
      Location:53 → 349
      CLN5; Ceroid-lipofuscinosis neuronal protein 5

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      76992081..77005117
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      76215721..76228757
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75503.2 GenPept UniProtKB/Swiss-Prot:O75503

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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