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

Gene ID: 1203, updated on 14-Apr-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
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Genomic context

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Location:
13q22.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (76992081..77005117)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (76215721..76228757)
105.20220307 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: 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

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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. Cln5 represents a new type of cysteine-based S-depalmitoylase linked to neurodegeneration. Luebben AV, et al. Sci Adv, 2022 Apr 15. PMID 35427157, Free PMC Article
  3. Deficiency of the Lysosomal Protein CLN5 Alters Lysosomal Function and Movement. Basak I, et al. Biomolecules, 2021 Sep 27. PMID 34680045, Free PMC Article
  4. Association of the Recurrent Rare Variant c.415T>C p.Phe139Leu in CLN5 With a Recessively Inherited Macular Dystrophy. Magliyah MS, et al. JAMA Ophthalmol, 2021 Mar 1. PMID 33507209, Free PMC Article
  5. CLN5 in heterozygosis may protect against the development of tumors in a VHL patient. de Rojas-P I, et al. Orphanet J Rare Dis, 2020 Jun 2. PMID 32487141, Free PMC Article

See all (57) 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
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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)

Genotypes

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 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 mannose 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 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

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_2023_10

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

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