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Aliases for CLN3 Gene

Aliases for CLN3 Gene

  • Ceroid-Lipofuscinosis, Neuronal 3 2 3
  • Batten Disease Protein 3 4
  • BTS 3 4
  • Juvenile Neuronal Ceroid Lipofuscinosis 2
  • Batten, Spielmeyer-Vogt Disease 2
  • Protein CLN3 4
  • Battenin 2
  • JNCL 3

External Ids for CLN3 Gene

Previous HGNC Symbols for CLN3 Gene

  • BTS

Previous GeneCards Identifiers for CLN3 Gene

  • GC16P028406
  • GC16P028790
  • GC16P028559
  • GC16P028601
  • GC16M028396
  • GC16M026514

Summaries for CLN3 Gene

Entrez Gene Summary for CLN3 Gene

  • This gene encodes a protein that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease or collectively known as neuronal ceroid lipofuscinoses (NCLs). Many alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLN3 Gene

CLN3 (Ceroid-Lipofuscinosis, Neuronal 3) is a Protein Coding gene. Diseases associated with CLN3 include juvenile batten disease and cln3 disease. Among its related pathways are Lysosome. GO annotations related to this gene include unfolded protein binding. An important paralog of this gene is ENSG00000261832.

UniProtKB/Swiss-Prot for CLN3 Gene

  • Involved in microtubule-dependent, anterograde transport of late endosomes and lysosomes.

Gene Wiki entry for CLN3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLN3 Gene

Genomics for CLN3 Gene

Regulatory Elements for CLN3 Gene

Epigenetics Products

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

Genomic Location for CLN3 Gene

28,466,653 bp from pter
28,495,575 bp from pter
28,923 bases
Minus strand

Genomic View for CLN3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLN3 Gene

Proteins for CLN3 Gene

  • Protein details for CLN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2R7J1
    • B4DXL3
    • O00668
    • O95089
    • Q549S9
    • Q9UP09
    • Q9UP11
    • Q9UP12
    • Q9UP13
    • Q9UP14

    Protein attributes for CLN3 Gene

    438 amino acids
    Molecular mass:
    47623 Da
    Quaternary structure:
    • Interacts with DCTN1 and KIF3A. Interacts with RAB7A and RILP.

    Alternative splice isoforms for CLN3 Gene

neXtProt entry for CLN3 Gene

Proteomics data for CLN3 Gene at MOPED

Post-translational modifications for CLN3 Gene

Antibody Products

No data available for DME Specific Peptides for CLN3 Gene

Domains & Families for CLN3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the battenin family.
  • Belongs to the battenin family.
genes like me logo Genes that share domains with CLN3: view

No data available for Gene Families for CLN3 Gene

Function for CLN3 Gene

Molecular function for CLN3 Gene

GENATLAS Biochemistry:
integral lysosomal membrane protein battenin,highly conserved,with alternatively spliced forms,expressed in astrocytes,capillary endothelium and neurons of gray matter of the brain in peripheral nerve,pancreatic islet cells and within the seminiferous tubules of the testis,involved in synaptic trafficking through the endoplasmic reticulum and Golgi,potentially protecting neurons from apoptosis mediated by ceramide,yeast BTN1 ortholog
UniProtKB/Swiss-Prot Function:
Involved in microtubule-dependent, anterograde transport of late endosomes and lysosomes.

Gene Ontology (GO) - Molecular Function for CLN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12134079
GO:0051082 unfolded protein binding TAS 8980123
genes like me logo Genes that share ontologies with CLN3: view
genes like me logo Genes that share phenotypes with CLN3: view

Animal Models for CLN3 Gene

MGI Knock Outs for CLN3:

Animal Model Products

miRNA for CLN3 Gene

miRTarBase miRNAs that target CLN3

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLN3

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CLN3 Gene

Localization for CLN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLN3 Gene

Lysosome membrane; Multi-pass membrane protein. Late endosome.

Subcellular locations from

Jensen Localization Image for CLN3 Gene COMPARTMENTS Subcellular localization image for CLN3 gene
Compartment Confidence
endoplasmic reticulum 5
endosome 5
golgi apparatus 5
lysosome 5
nucleus 5
plasma membrane 5
vacuole 5
mitochondrion 4
cytosol 3
cytoskeleton 1
extracellular 1

Gene Ontology (GO) - Cellular Components for CLN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IDA 9949212
GO:0005622 intracellular --
GO:0005634 nucleus IDA 10191116
GO:0005737 cytoplasm IDA 10191116
GO:0005739 mitochondrion TAS 8980123
genes like me logo Genes that share ontologies with CLN3: view

Pathways & Interactions for CLN3 Gene

SuperPathways for CLN3 Gene

Superpath Contained pathways
1 Lysosome
genes like me logo Genes that share pathways with CLN3: view

Pathways by source for CLN3 Gene

1 KEGG pathway for CLN3 Gene

PCR Array Products

Gene Ontology (GO) - Biological Process for CLN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001508 action potential ISS --
GO:0001575 globoside metabolic process IMP 15240864
GO:0006520 cellular amino acid metabolic process ISS --
GO:0006672 ceramide metabolic process IDA 15240864
GO:0006678 glucosylceramide metabolic process IMP 15240864
genes like me logo Genes that share ontologies with CLN3: view

No data available for SIGNOR curated interactions for CLN3 Gene

Drugs & Compounds for CLN3 Gene

(4) Drugs for CLN3 Gene - From: NovoSeek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
ATP Pharma Activator 0
arginine Nutra 346
lysine Nutra 70
serine Nutra 420

(4) Additional Compounds for CLN3 Gene - From: NovoSeek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Mannose 6-phosphate
  • alpha-D-Mannose-6-P
  • alpha-D-Mannose-6-phosphate
  • alpha-delta-Mannose-6-P
  • alpha-delta-Mannose-6-phosphate
  • D-Mannose 6-phosphate
genes like me logo Genes that share compounds with CLN3: view

Transcripts for CLN3 Gene

Unigene Clusters for CLN3 Gene

Ceroid-lipofuscinosis, neuronal 3:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLN3

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLN3 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b · 4c · 4d · 4e · 4f · 4g · 4h ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b · 13c ^
SP1: - - - - - - -
SP2: - -
SP3: - - -
SP4: - -
SP5: - -
SP6: - - - -
SP7: - - -
SP8: - - - -
SP9: - - - -
SP10: - - - - -
SP11: - -
SP12: - - - - - -
SP13: - - - - - - - - - - -
SP14: - - - - - - - - -
SP15: - - - - - -
SP16: - - - - - - - -
SP18: - - - - - -
SP19: - - - - - -
SP20: -
SP21: - - - -
SP22: - - - - - -
SP25: -

ExUns: 14a · 14b ^ 15a · 15b ^ 16 ^ 17a · 17b · 17c ^ 18 ^ 19a · 19b · 19c · 19d · 19e
SP1: -
SP2: -
SP3: -
SP4: -
SP5: - -
SP6: -
SP7: -
SP8: -
SP9: -
SP10: -
SP12: -
SP14: -
SP16: -
SP17: -

Relevant External Links for CLN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLN3 Gene

mRNA expression in normal human tissues for CLN3 Gene

mRNA differential expression in normal tissues according to GTEx for CLN3 Gene

This gene is overexpressed in Whole Blood (x7.3) and Colon - Transverse (x4.0).

Protein differential expression in normal tissues from HIPED for CLN3 Gene

This gene is overexpressed in Adrenal (49.5), Amniocyte (10.3), and Urine (7.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for CLN3 Gene

SOURCE GeneReport for Unigene cluster for CLN3 Gene Hs.534667

genes like me logo Genes that share expression patterns with CLN3: view

Protein tissue co-expression partners for CLN3 Gene

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for CLN3 Gene

Orthologs for CLN3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CLN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CLN3 35
  • 86.76 (n)
  • 87.67 (a)
-- 36
  • 88 (a)
(Canis familiaris)
Mammalia CLN3 35
  • 87.75 (n)
  • 89.27 (a)
CLN3 36
  • 89 (a)
(Mus musculus)
Mammalia Cln3 35
  • 82.91 (n)
  • 86.04 (a)
Cln3 16
Cln3 36
  • 85 (a)
(Rattus norvegicus)
Mammalia Cln3 35
  • 82.84 (n)
  • 84.67 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 69 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 75 (a)
(Pan troglodytes)
Mammalia -- 36
  • 98 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 56 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cln3 35
  • 63.29 (n)
  • 60 (a)
Str.15897 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.15291 35
(Danio rerio)
Actinopterygii cln3 35
  • 55.58 (n)
  • 54.43 (a)
Dr.3167 35
cln3 36
  • 48 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG5582 37
  • 40 (a)
cln3 35
  • 52.67 (n)
  • 46.26 (a)
cln3 36
  • 40 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003934 35
  • 52.49 (n)
  • 44.3 (a)
(Caenorhabditis elegans)
Secernentea cln-3.1 37
  • 40 (a)
cln-3.2 37
  • 40 (a)
cln-3.3 37
  • 39 (a)
cln-3.2 35
  • 48.94 (n)
  • 45.8 (a)
cln-3.1 36
  • 39 (a)
cln-3.2 36
  • 41 (a)
cln-3.3 36
  • 38 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL171C 35
  • 47.58 (n)
  • 42.47 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F01551g 35
  • 44.26 (n)
  • 38.02 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YHC3 35
  • 46.35 (n)
  • 44.32 (a)
YHC3 36
  • 36 (a)
YHC3 38
bread mold
(Neurospora crassa)
Ascomycetes NCU10272 35
  • 49.09 (n)
  • 42.9 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes btn1 35
  • 43.06 (n)
  • 35.83 (a)
Species with no ortholog for CLN3:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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)

Evolution for CLN3 Gene

Gene Tree for CLN3 (if available)
Gene Tree for CLN3 (if available)

Paralogs for CLN3 Gene

Paralogs for CLN3 Gene

genes like me logo Genes that share paralogs with CLN3: view

Variants for CLN3 Gene

Sequence variations from dbSNP and Humsavar for CLN3 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type MAF
rs34834 -- 28,490,184(-) attac(A/G)ggcgt intron-variant
rs34835 -- 28,487,970(-) CTAGG(C/T)GCTAT intron-variant
rs34836 -- 28,483,502(-) gttca(C/T)acctg intron-variant
rs34837 -- 28,483,153(-) gtata(G/T)tactt intron-variant
rs34838 -- 28,483,029(-) cctcc(C/T)gggtt intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLN3 Gene

Variant ID Type Subtype PubMed ID
dgv842e1 CNV Complex 17122850
dgv843e1 CNV Complex 17122850
nsv833180 CNV Loss 17160897
nsv905688 CNV Gain 21882294
nsv509608 CNV Insertion 20534489
nsv9415 CNV Gain 18304495
nsv103376 CNV Loss 16902084
esv2673092 CNV Deletion 23128226

Variation tolerance for CLN3 Gene

Residual Variation Intolerance Score: 18.82% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.77; 83.29% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLN3 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLN3 Gene

Disorders for CLN3 Gene

MalaCards: The human disease database

(15) MalaCards diseases for CLN3 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, NovoSeek, and GeneCards

Disorder Aliases PubMed IDs
juvenile batten disease
  • juvenile neuronal ceroid lipofuscinosis
cln3 disease
  • neuronal ceroid lipofuscinosis 3
ceroid lipofuscinosis, neuronal, 3
  • batten disease
neuronal ceroid-lipofuscinoses
  • ceroid lipofuscinosis, neuronal, 1
neuronal ceroid lipofuscinosis
  • neuronal ceroid-lipofuscinoses
- elite association
Search CLN3 in MalaCards View complete list of genes associated with diseases


  • Ceroid lipofuscinosis, neuronal, 3 (CLN3) [MIM:204200]: 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 hallmark of CLN3 is the ultrastructural pattern of lipopigment with a fingerprint profile, which can have 3 different appearances: pure within a lysosomal residual body; in conjunction with curvilinear or rectilinear profiles; and as a small component within large membrane-bound lysosomal vacuoles. The combination of fingerprint profiles within lysosomal vacuoles is a regular feature of blood lymphocytes from patients with neuronal ceroid lipofuscinosis type 3. {ECO:0000269 PubMed:21990111, ECO:0000269 PubMed:9311735, ECO:0000269 PubMed:9490299}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for CLN3 Gene

ceroid-lipofuscinosis,neuronal 3,juvenile,Batten (Spielmeyer-Vogt-Sjogren) disease,progressive neurodegenerative disease with an onset between 5 and 10 years,characterized by retinitis pigmentosa and a rapid loss of vision with macular and peripheral retinal degeneration,cognitive and motor dysfunction,seizures in childhood,a fatal outcome within a decade,and a characteristic fingerprint profile inclusions in different cells,including the variant form with granular osmiophilic deposits (GROD)

Relevant External Links for CLN3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CLN3: view

Publications for CLN3 Gene

  1. CLN3p impacts galactosylceramide transport, raft morphology, and lipid content. (PMID: 18317235) Rusyn E. … Boustany R.M. (Pediatr. Res. 2008) 2 23 67
  2. Interaction between Sdo1p and Btn1p in the Saccharomyces cerevisiae model for Batten disease. (PMID: 20015955) Vitiello S.P. … Pearce D.A. (Hum. Mol. Genet. 2010) 23 67
  3. A 30-year follow-up of a neuronal ceroid lipofuscinosis patient with mutations in CLN3 and protracted disease course. (PMID: 19135632) Aberg L. … Autti T. (Pediatr. Neurol. 2009) 23 67
  4. The fission yeast model for the lysosomal storage disorder Batten disease predicts disease severity caused by mutations in CLN3. (PMID: 19132115) Haines R.L. … Mole S.E. (Dis Model Mech 2009) 23 67
  5. Protracted course of juvenile ceroid lipofuscinosis associated with a novel CLN3 mutation (p.Y199X). (PMID: 19489875) Sarpong A. … Schuelke M. (Clin. Genet. 2009) 23 67

Products for CLN3 Gene

Sources for CLN3 Gene

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