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Aliases for CLN5 Gene

Aliases for CLN5 Gene

  • Ceroid-Lipofuscinosis, Neuronal 5 2 3
  • Ceroid-Lipofuscinosis Neuronal Protein 5 3
  • Protein CLN5 4
  • NCL 3

External Ids for CLN5 Gene

Previous GeneCards Identifiers for CLN5 Gene

  • GC13P075532
  • GC13P071559
  • GC13P076501
  • GC13P075362
  • GC13P076462
  • GC13P077564
  • GC13P058263

Summaries for CLN5 Gene

Entrez Gene Summary for CLN5 Gene

  • 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]

GeneCards Summary for CLN5 Gene

CLN5 (Ceroid-Lipofuscinosis, Neuronal 5) is a Protein Coding gene. Diseases associated with CLN5 include ceroid lipofuscinosis, neuronal, 5 and ceroid lipofuscinosis, neuronal, 1. Among its related pathways are Lysosome and Translational Control. GO annotations related to this gene include mannose binding.

Gene Wiki entry for CLN5 Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLN5 Gene

Genomics for CLN5 Gene

Regulatory Elements for CLN5 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for CLN5 Gene

76,990,660 bp from pter
77,002,517 bp from pter
11,858 bases
Plus strand

Genomic View for CLN5 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLN5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLN5 Gene

Proteins for CLN5 Gene

  • Protein details for CLN5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Ceroid-lipofuscinosis neuronal protein 5
    Protein Accession:
    Secondary Accessions:
    • B3KQK7

    Protein attributes for CLN5 Gene

    358 amino acids
    Molecular mass:
    41497 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAC27614.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for CLN5 Gene

Proteomics data for CLN5 Gene at MOPED

Post-translational modifications for CLN5 Gene

  • Glycosylated.
  • Ubiquitination at Lys65 and Lys105
  • Glycosylation at Asn130, Asn143, Asn178, Asn203, Asn255, Asn271, Asn281, and Asn352
  • Modification sites at PhosphoSitePlus

Other Protein References for CLN5 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for CLN5 Gene

Domains for CLN5 Gene

Protein Domains for CLN5 Gene


Suggested Antigen Peptide Sequences for CLN5 Gene

Graphical View of Domain Structure for InterPro Entry



  • O75503
  • Belongs to the CLN5 family.
genes like me logo Genes that share domains with CLN5: view

No data available for Gene Families for CLN5 Gene

Function for CLN5 Gene

Molecular function for CLN5 Gene

GENATLAS Biochemistry:
putative lysosomal membrane protein,ubiquitously expressed,in adult and fetal tissues

Gene Ontology (GO) - Molecular Function for CLN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12134079
GO:0005537 mannose binding IDA 16399764
genes like me logo Genes that share ontologies with CLN5: view
genes like me logo Genes that share phenotypes with CLN5: view

Animal Models for CLN5 Gene

MGI Knock Outs for CLN5:

Animal Model Products

miRNA for CLN5 Gene

miRTarBase miRNAs that target CLN5

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLN5

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for CLN5 Gene

Localization for CLN5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLN5 Gene


Subcellular locations from

Jensen Localization Image for CLN5 Gene COMPARTMENTS Subcellular localization image for CLN5 gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 5
lysosome 5
vacuole 5
mitochondrion 3
cytosol 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for CLN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IDA 11971870
GO:0005765 lysosomal membrane IDA 12134079
GO:0005775 vacuolar lumen --
GO:0005783 endoplasmic reticulum IDA 12134079
GO:0005794 Golgi apparatus IDA 12134079
genes like me logo Genes that share ontologies with CLN5: view

Pathways for CLN5 Gene

genes like me logo Genes that share pathways with CLN5: view

Pathways by source for CLN5 Gene

2 KEGG pathways for CLN5 Gene
1 GeneGo (Thomson Reuters) pathway for CLN5 Gene

Gene Ontology (GO) - Biological Process for CLN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006465 signal peptide processing IDA 20052765
GO:0007040 lysosome organization --
GO:0007042 lysosomal lumen acidification IMP 11722572
GO:0007420 brain development IEP 10992246
GO:0007601 visual perception --
genes like me logo Genes that share ontologies with CLN5: view

Transcripts for CLN5 Gene

mRNA/cDNA for CLN5 Gene

Unigene Clusters for CLN5 Gene

Ceroid-lipofuscinosis, neuronal 5:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLN5

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLN5 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6
SP1: - - -
SP3: - -
SP4: -

Relevant External Links for CLN5 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLN5 Gene

mRNA expression in normal human tissues for CLN5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues for CLN5 Gene

This gene is overexpressed in Vitreous humor (22.3) and Spleen (12.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for CLN5 Gene

SOURCE GeneReport for Unigene cluster for CLN5 Gene Hs.30213

mRNA Expression by UniProt/SwissProt for CLN5 Gene

Tissue specificity: Ubiquitous
genes like me logo Genes that share expressions with CLN5: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and Expression partners for CLN5 Gene

Orthologs for CLN5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLN5 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CLN5 35
  • 91.69 (n)
  • 89.46 (a)
CLN5 36
  • 84 (a)
(Canis familiaris)
Mammalia CLN5 35
  • 90.84 (n)
  • 90.1 (a)
CLN5 36
  • 85 (a)
(Mus musculus)
Mammalia Cln5 35
  • 81.9 (n)
  • 78.53 (a)
Cln5 16
Cln5 36
  • 74 (a)
(Pan troglodytes)
Mammalia CLN5 35
  • 98.94 (n)
  • 98.28 (a)
CLN5 36
  • 98 (a)
(Rattus norvegicus)
Mammalia RGD1564125 35
  • 81.44 (n)
  • 80 (a)
(Monodelphis domestica)
Mammalia CLN5 36
  • 75 (a)
(Ornithorhynchus anatinus)
Mammalia CLN5 36
  • 81 (a)
(Gallus gallus)
Aves CLN5 35
  • 73.98 (n)
  • 74.39 (a)
CLN5 36
  • 71 (a)
(Anolis carolinensis)
Reptilia CLN5 36
  • 67 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cln5 35
  • 70.57 (n)
  • 71.57 (a)
(Danio rerio)
Actinopterygii cln5 35
  • 61.11 (n)
  • 59.29 (a)
cln5 36
  • 59 (a)
CLN5 (2 of 2) 36
  • 60 (a)
Species with no ortholog for CLN5:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLN5 Gene

Gene Tree for CLN5 (if available)
Gene Tree for CLN5 (if available)

Paralogs for CLN5 Gene

No data available for Paralogs for CLN5 Gene

Variants for CLN5 Gene

Sequence variations from dbSNP and Humsavar for CLN5 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type MAF
rs1579 -- 76,999,413(-) TCTCT(C/T)CTACC intron-variant
rs605153 -- 76,995,766(+) TGACA(A/G)TAGCA intron-variant
rs642394 -- 76,991,520(+) TATCA(C/T)TGGCC upstream-variant-2KB
rs654196 -- 76,991,837(+) GGTCA(A/G)TTCAT upstream-variant-2KB
rs700357 -- 76,993,410(-) CTTCA(A/G)CCACA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLN5 Gene

Variant ID Type Subtype PubMed ID
nsv832652 CNV Gain 17160897
nsv832653 CNV Loss 17160897
nsv528367 CNV Loss 19592680

Relevant External Links for CLN5 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLN5 Gene

Disorders for CLN5 Gene

(1) OMIM Diseases for CLN5 Gene (608102)


  • Ceroid lipofuscinosis, neuronal, 5 (CLN5) [MIM:256731]: A form of neuronal ceroid lipofuscinosis. Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by intracellular accumulation of autofluorescent liposomal material, and clinically by seizures, dementia, visual loss, and/or cerebral atrophy. The lipopigment patterns observed most often in neuronal ceroid lipofuscinosis type 5 comprise mixed combinations of granular, curvilinear, and fingerprint profiles. {ECO:0000269 PubMed:15728307, ECO:0000269 PubMed:16814585, ECO:0000269 PubMed:17607606, ECO:0000269 PubMed:19309691, ECO:0000269 PubMed:21990111, ECO:0000269 PubMed:9662406}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for CLN5 Gene

(12) Novoseek inferred disease relationships for CLN5 Gene

Disease -log(P) Hits PubMed IDs
ceroid lipofuscinosis, neuronal, late infantile, variant 98 5
neuronal ceroid lipofuscinoses 97.1 7
lincl 95.8 13
neurodegenerative diseases 75.9 3
batten disease 64.3 1

Genatlas disease for CLN5 Gene

ceroid-lipofuscinosis,neuronal 5,late infantile,Jansky-Bielschowsky disease variant,characterized by an onset five years motor clumsiness,followed by progressive visual failure with macular and peripheral retinal degeneration,mental and motor deterioration and later by myoclonia and siezures,including the Finnish variant with an onset between 13 or 30 years

Relevant External Links for CLN5

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with CLN5: view

Publications for CLN5 Gene

  1. CLN5, a novel gene encoding a putative transmembrane protein mutated in Finnish variant late infantile neuronal ceroid lipofuscinosis. (PMID: 9662406) Savukoski M. … Peltonen L. (Nat. Genet. 1998) 3 4 23
  2. Lysosomal localization of the neuronal ceroid lipofuscinosis CLN5 protein. (PMID: 11971870) Isosomppi J. … Peltonen L. (Hum. Mol. Genet. 2002) 3 4 23
  3. Two novel CLN5 mutations in a Portuguese patient with vLINCL: insights into molecular mechanisms of CLN5 deficiency. (PMID: 16814585) Bessa C. … Ribeiro M.G. (Mol. Genet. Metab. 2006) 3 4 23
  4. Revelation of a novel CLN5 mutation in early juvenile neuronal ceroid lipofuscinosis. (PMID: 17607606) Cannelli N. … Santorelli F.M. (Neuropediatrics 2007) 3 4 23
  5. Retention of lysosomal protein CLN5 in the endoplasmic reticulum causes neuronal ceroid lipofuscinosis in Asian sibship. (PMID: 19309691) Lebrun A.-H. … Schulz A. (Hum. Mutat. 2009) 3 4 23

Products for CLN5 Gene

Sources for CLN5 Gene

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