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Aliases for CLN5 Gene

Aliases for CLN5 Gene

  • CLN5, Intracellular Trafficking Protein 2 3 5
  • 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 (CLN5, Intracellular Trafficking Protein) is a Protein Coding gene. Diseases associated with CLN5 include Ceroid Lipofuscinosis, Neuronal, 5 and Neuronal Ceroid Lipofuscinosis. Among its related pathways are Lysosome. Gene Ontology (GO) annotations related to this gene include mannose binding. An important paralog of this gene is ENSG00000283208.

UniProtKB/Swiss-Prot for CLN5 Gene

  • Plays a role in influencing the retrograde trafficking of lysosomal sorting receptors SORT1 and IGF2R from the endosomes to the trans-Golgi network by controlling the recruitment of retromer complex to the endosomal membrane. Regulates the localization and activation of RAB7A which is required to recruit the retromer complex to the endosomal membrane (PubMed:22431521).

Gene Wiki entry for CLN5 Gene

Additional gene information for CLN5 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLN5 Gene

Genomics for CLN5 Gene

GeneHancer (GH) Regulatory Elements for CLN5 Gene

Promoters and enhancers for CLN5 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH13J076990 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 663.6 +2.1 2082 3.8 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 IRF4 YY1 SLC30A9 POLR2B CLN5 ENSG00000283208 FBXL3 MYCBP2-AS1
GH13J076995 Promoter 0.5 EPDnew 650.7 +4.5 4473 0.1 CLN5 ENSG00000283208 FBXL3 MYCBP2-AS1
GH13J077025 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 9.7 +36.2 36181 3.5 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 YY1 POLR2B ZNF766 FBXL3 MYCBP2-AS1 ENSG00000274898 MYCBP2-AS2 CLN5 ENSG00000283208
GH13J077338 Enhancer 1.2 Ensembl ENCODE dbSUPER 15.4 +348.6 348579 1.8 PKNOX1 SMAD1 BMI1 YBX1 IRF4 ATF7 ETV6 IKZF2 RUNX3 CREM CLN5 MYCBP2 LOC105370271
GH13J077324 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4.4 +335.6 335644 3.1 HDGF FOXA2 PKNOX1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 MYCBP2 CLN5 FBXL3 KCTD12 GC13P077273
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLN5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLN5 gene promoter:
  • Nkx2-2
  • Gfi-1
  • FOXD3
  • Sox5
  • HNF-3beta
  • Sox9
  • AML1a
  • MEF-2A
  • aMEF-2

Genomic Locations for CLN5 Gene

Genomic Locations for CLN5 Gene
28,484 bases
Plus strand
11,858 bases
Plus strand

Genomic View for CLN5 Gene

Genes around CLN5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLN5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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:
    • Interacts with SORT1, RAB5A and RAB7A (PubMed:22431521). Interacts with PPT1, TPP1, CLN3, CLN6, CLN8, ATP5F1A and ATP5F1B (By similarity).
    • Sequence=AAC27614.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for CLN5 Gene

Post-translational modifications for CLN5 Gene

  • N-glycosylated with both high mannose and complex type sugars. Glycosylation is important for proper folding and trafficking to the lysosomes.
  • Ceroid-lipofuscinosis neuronal protein 5: The type II membrane signal anchor is proteolytically cleaved to produce a mature form that is transported to the lysosomes (Ceroid-lipofuscinosis neuronal protein 5, secreted form) (PubMed:24038957, PubMed:20052765).
  • Can undergo proteolytic cleavage at the C-terminus, probably by a cysteine protease and may involve the removal of approximately 10-15 residues from the C-terminal end (PubMed:26342652).
  • Glycosylation at posLast=352352, Asn281, Asn271, posLast=255255, Asn203, posLast=178178, Asn143, and Asn130
  • Ubiquitination at posLast=105105 and posLast=6565
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CLN5 Gene

Domains & Families for CLN5 Gene

Gene Families for CLN5 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

Protein Domains for CLN5 Gene


Suggested Antigen Peptide Sequences for CLN5 Gene

Graphical View of Domain Structure for InterPro Entry



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

Function for CLN5 Gene

Molecular function for CLN5 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in influencing the retrograde trafficking of lysosomal sorting receptors SORT1 and IGF2R from the endosomes to the trans-Golgi network by controlling the recruitment of retromer complex to the endosomal membrane. Regulates the localization and activation of RAB7A which is required to recruit the retromer complex to the endosomal membrane (PubMed:22431521).
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

Human Phenotype Ontology for CLN5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CLN5 Gene

MGI Knock Outs for CLN5:
  • Cln5 Cln5<tm1Pltn>

Animal Model Products

miRNA for CLN5 Gene

miRTarBase miRNAs that target CLN5

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for CLN5 Gene

Localization for CLN5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLN5 Gene

Ceroid-lipofuscinosis neuronal protein 5, secreted form: Lysosome.
Ceroid-lipofuscinosis neuronal protein 5: Membrane; Single-pass type II membrane protein. Note=An amphipathic anchor region facilitates its association with the membrane. {ECO:0000269 PubMed:24038957}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLN5 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
lysosome 5
golgi apparatus 5
mitochondrion 3
cytosol 3
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for CLN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA,IDA 11971870
GO:0005765 lysosomal membrane IDA 12134079
GO:0005783 endoplasmic reticulum IDA 12134079
GO:0005794 Golgi apparatus IDA 12134079
GO:0005829 cytosol IEA --
genes like me logo Genes that share ontologies with CLN5: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLN5 Gene

Pathways & Interactions for CLN5 Gene

SuperPathway Contained pathways
1 Lysosome
genes like me logo Genes that share pathways with CLN5: view

Pathways by source for CLN5 Gene

1 KEGG 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:0007042 lysosomal lumen acidification IMP 11722572
GO:0007420 brain development IEP 10992246
GO:0022008 neurogenesis IEP 10992246
GO:0030163 protein catabolic process NAS 10740217
genes like me logo Genes that share ontologies with CLN5: view

No data available for SIGNOR curated interactions for CLN5 Gene

Drugs & Compounds for CLN5 Gene

No Compound Related Data Available

Transcripts for CLN5 Gene

mRNA/cDNA for CLN5 Gene

(2) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(156) Selected AceView cDNA sequences:
(19) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLN5 Gene

Ceroid-lipofuscinosis, neuronal 5:
Representative Sequences:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for CLN5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CLN5 Gene

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

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLN5 Gene

NURSA nuclear receptor signaling pathways regulating expression of CLN5 Gene:


SOURCE GeneReport for Unigene cluster for CLN5 Gene:


mRNA Expression by UniProt/SwissProt for CLN5 Gene:

Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for CLN5 Gene

  • Nervous system(4.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CLN5 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • head
  • peripheral nervous system
genes like me logo Genes that share expression patterns with CLN5: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-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
(Pan troglodytes)
Mammalia CLN5 34 33
  • 98.94 (n)
(Bos Taurus)
Mammalia CLN5 34 33
  • 91.69 (n)
(Canis familiaris)
Mammalia CLN5 34 33
  • 90.84 (n)
(Mus musculus)
Mammalia Cln5 16 34 33
  • 81.9 (n)
(Rattus norvegicus)
Mammalia RGD1564125 33
  • 81.44 (n)
(Ornithorhynchus anatinus)
Mammalia CLN5 34
  • 81 (a)
(Monodelphis domestica)
Mammalia CLN5 34
  • 75 (a)
(Gallus gallus)
Aves CLN5 34 33
  • 73.98 (n)
(Anolis carolinensis)
Reptilia CLN5 34
  • 67 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cln5 33
  • 70.57 (n)
(Danio rerio)
Actinopterygii cln5 34 33
  • 61.11 (n)
CLN5 (2 of 2) 34
  • 60 (a)
Species where no ortholog for CLN5 was found in the sources mined by GeneCards:
  • 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)
Evolutionary constrained regions (ECRs) for CLN5: view image

Paralogs for CLN5 Gene

Paralogs for CLN5 Gene

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

Variants for CLN5 Gene

Sequence variations from dbSNP and Humsavar for CLN5 Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
rs104894385 pathogenic, Ceroid lipofuscinosis neuronal 5 76,992,176(+) G/A/T coding_sequence_variant, missense_variant, stop_gained
rs104894386 pathogenic, likely-pathogenic, Ceroid lipofuscinosis neuronal 5, Ceroid lipofuscinosis, neuronal, 5 (CLN5) [MIM:256731], Ceroid lipofuscinosis, neuronal, 5 (CLN5) [MIM:256731] 76,995,077(+) G/A/C coding_sequence_variant, missense_variant
rs1057516390 likely-pathogenic, Ceroid lipofuscinosis neuronal 5 76,995,901(+) G/ splice_acceptor_variant
rs1057516814 likely-pathogenic, Ceroid lipofuscinosis neuronal 5 76,992,171(+) TC/G coding_sequence_variant, frameshift
rs1057517134 likely-pathogenic, Ceroid lipofuscinosis neuronal 5 76,992,250(+) GCCACTGGCCGGTGCC/GCC coding_sequence_variant, frameshift

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

Variant ID Type Subtype PubMed ID
nsv528367 CNV loss 19592680
nsv832652 CNV gain 17160897
nsv832653 CNV loss 17160897

Variation tolerance for CLN5 Gene

Residual Variation Intolerance Score: 79.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.34; 88.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLN5 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for CLN5 Gene

MalaCards: The human disease database

(15) MalaCards diseases for CLN5 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
ceroid lipofuscinosis, neuronal, 5
  • cln5
neuronal ceroid lipofuscinosis
  • batten disease
ceroid storage disease
  • lipofuscin storage disease
neuronal ceroid-lipofuscinoses
  • neuronal ceroid-lipofuscinosis, infantile
ceroid lipofuscinosis, neuronal, 2
  • cln2
- elite association - COSMIC cancer census association via MalaCards
Search CLN5 in MalaCards View complete list of genes associated with diseases


  • 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:20052765, ECO:0000269 PubMed:21990111, ECO:0000269 PubMed:24038957, ECO:0000269 PubMed:24058541, ECO:0000269 PubMed:26342652, ECO:0000269 PubMed:9662406}. Note=The disease is caused by mutations affecting the gene represented in this entry.

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

Additional Disease Information for CLN5

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CLN5: view

Publications for CLN5 Gene

  1. The neuronal ceroid lipofuscinosis protein CLN5: new insights into cellular maturation, transport, and consequences of mutations. (PMID: 20052765) Schmiedt ML … Kyttälä A (Human mutation 2010) 3 4 22 58
  2. Mutations in CLN7/MFSD8 are a common cause of variant late-infantile neuronal ceroid lipofuscinosis. (PMID: 19201763) Kousi M … Lehesjoki AE (Brain : a journal of neurology 2009) 3 22 44 58
  3. Retention of lysosomal protein CLN5 in the endoplasmic reticulum causes neuronal ceroid lipofuscinosis in Asian sibship. (PMID: 19309691) Lebrun AH … Schulz A (Human mutation 2009) 3 4 22 58
  4. Revelation of a novel CLN5 mutation in early juvenile neuronal ceroid lipofuscinosis. (PMID: 17607606) Cannelli N … Santorelli FM (Neuropediatrics 2007) 3 4 22 58
  5. Two novel CLN5 mutations in a Portuguese patient with vLINCL: insights into molecular mechanisms of CLN5 deficiency. (PMID: 16814585) Bessa C … Ribeiro MG (Molecular genetics and metabolism 2006) 3 4 22 58

Products for CLN5 Gene

Sources for CLN5 Gene

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