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Aliases for CLN3 Gene

Aliases for CLN3 Gene

  • CLN3, Battenin 2 3 5
  • 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 3
  • BTN1 3
  • 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
  • GC16M028488
  • 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 (CLN3, Battenin) is a Protein Coding gene. Diseases associated with CLN3 include Ceroid Lipofuscinosis, Neuronal, 3 and Neuronal Ceroid-Lipofuscinoses. 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

Additional gene information for CLN3 Gene

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

Genomics for CLN3 Gene

Regulatory Elements for CLN3 Gene

Enhancers for CLN3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16H029258 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10.8 -769.1 -769053 11.3 HDGF PKNOX1 ATF1 FOXA2 MLX ARID4B SIN3A YBX1 TCF12 FOS SPNS1 ATXN2L NPIPB9 ENSG00000260853 ENSG00000260367 ENSG00000260953 NPIPB10P SMG1P2 NFATC2IP NPIPB8
GH16H028945 1.7 Ensembl ENCODE dbSUPER 10.8 -450.2 -450171 1.1 HDGF PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B SPNS1 SMG1P2 ENSG00000198106 ENSG00000260853 ENSG00000260367 NFATC2IP CA5AP1 ENSG00000261766 NPIPB12 SH2B1
GH16H028525 1 ENCODE 18.1 -31.8 -31845 3.8 FOXA2 MLX ARID4B DMAP1 YY1 ATF7 CAVIN1 SP5 ZHX2 NFYC SULT1A2 TUFM CLN3 APOBR NPIPB7 SGF29 ENSG00000251417 IL27 PIR42560
GH16H028531 1.5 FANTOM5 Ensembl ENCODE 11.8 -38.1 -38081 3.7 ARID4B RAD21 RARA YY1 ZNF366 MIXL1 SMARCA5 SP5 USF2 MXD4 SULT1A2 TUFM APOBR NPIPB7 SGF29 CLN3 IL27 ENSG00000251417 SULT1A1 SPNS1
GH16H028277 1.3 Ensembl ENCODE 12.8 +217.6 217621 1.5 HDGF ARID4B SIN3A DMAP1 GLI4 ZNF2 ETS1 GLIS2 ZNF143 ATF7 ENSG00000260853 SPNS1 ENSG00000260367 NFATC2IP CLN3 RRN3P2 ATXN2L ENSG00000246465 SBK1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLN3 on UCSC Golden Path with GeneCards custom track

Promoters for CLN3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000084895 1275 201 HDGF PKNOX1 ATF1 TBL1XR1 NFRKB BATF ZNF766 ZNF143 ATF7 ETV6

Genomic Locations for CLN3 Gene

Genomic Locations for CLN3 Gene
28,923 bases
Minus strand

Genomic View for CLN3 Gene

Genes around CLN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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, KIF3A, RAB7A and RILP (PubMed:22261744). Interacts with CLN5 (PubMed:19941651).

    Alternative splice isoforms for CLN3 Gene

neXtProt entry for CLN3 Gene

Post-translational modifications for CLN3 Gene

No data available for DME Specific Peptides for CLN3 Gene

Domains & Families for CLN3 Gene

Gene Families for CLN3 Gene

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

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

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.

Phenotypes From GWAS Catalog for CLN3 Gene

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

Human Phenotype Ontology for CLN3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CLN3 Gene

MGI Knock Outs for CLN3:

Animal Model Products

miRNA for CLN3 Gene

miRTarBase miRNAs that target CLN3

Clone Products

  • Addgene plasmids for CLN3

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. Lysosome.

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 CLN3 gene
Compartment Confidence
plasma membrane 5
mitochondrion 5
nucleus 5
endoplasmic reticulum 5
lysosome 5
golgi apparatus 5
endosome 5
extracellular 1
cytoskeleton 1
cytosol 1

Gene Ontology (GO) - Cellular Components for CLN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IDA 9949212
GO:0005634 nucleus IDA 10191116
GO:0005737 cytoplasm IDA 10191116
GO:0005739 mitochondrion TAS 8980123
GO:0005764 lysosome IDA,IEA 10924275
genes like me logo Genes that share ontologies with CLN3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLN3 Gene

Pathways & Interactions for CLN3 Gene

SuperPathway 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

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

(6) Drugs for CLN3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for CLN3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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:

Clone Products

  • Addgene plasmids for CLN3

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for CLN3 Gene

Protein tissue co-expression partners for CLN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of CLN3 Gene:


SOURCE GeneReport for Unigene cluster for CLN3 Gene:


Evidence on tissue expression from TISSUES for CLN3 Gene

  • Nervous system(4.9)
  • Lung(4.5)
  • Intestine(3)
  • Kidney(2.8)
  • Blood(2.2)
  • Liver(2.2)
  • Muscle(2.2)
  • Skin(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CLN3 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • immune
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • head
  • blood
  • peripheral nerve
  • peripheral nervous system
  • white blood cell
genes like me logo Genes that share expression patterns with CLN3: view

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
(Pan troglodytes)
Mammalia -- 34
  • 98 (a)
(Bos Taurus)
Mammalia -- 34
  • 88 (a)
CLN3 33
  • 86.76 (n)
(Canis familiaris)
Mammalia CLN3 33 34
  • 87.75 (n)
(Mus musculus)
Mammalia Cln3 33 16 34
  • 82.91 (n)
(Rattus norvegicus)
Mammalia Cln3 33
  • 82.84 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 75 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 69 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 56 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cln3 33
  • 63.29 (n)
Str.15897 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.15291 33
(Danio rerio)
Actinopterygii cln3 33 34
  • 55.58 (n)
Dr.3167 33
fruit fly
(Drosophila melanogaster)
Insecta cln3 33 34
  • 52.67 (n)
CG5582 35
  • 40 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003934 33
  • 52.49 (n)
(Caenorhabditis elegans)
Secernentea cln-3.2 35 33 34
  • 48.94 (n)
cln-3.1 35 34
  • 40 (a)
cln-3.3 35 34
  • 39 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL171C 33
  • 47.58 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YHC3 33 34 36
  • 46.35 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F01551g 33
  • 44.26 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU10272 33
  • 49.09 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes btn1 33
  • 43.06 (n)
Species where no ortholog for CLN3 was found in the sources mined by GeneCards:
  • 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
rs121434286 Pathogenic, Ceroid lipofuscinosis, neuronal, 3 (CLN3) [MIM:204200] 28,482,500(-) TTGCC(A/G/T)AGTAT reference, missense
rs386833694 Likely pathogenic, Ceroid lipofuscinosis, neuronal, 3 (CLN3) [MIM:204200] 28,482,161(-) CCTCC(C/T)GCTCT reference, missense
rs386833695 Likely pathogenic, Ceroid lipofuscinosis, neuronal, 3 (CLN3) [MIM:204200] 28,482,160(-) CTCCC(A/G)CTCTT reference, missense
rs386833714 Likely pathogenic, Ceroid lipofuscinosis, neuronal, 3 (CLN3) [MIM:204200] 28,487,734(-) TGTGC(C/T)CCTGG intron-variant, reference, missense
rs386833719 Likely pathogenic, Ceroid lipofuscinosis, neuronal, 3 (CLN3) [MIM:204200] 28,487,516(-) GGATT(C/T)GTGCT reference, missense

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

Variant ID Type Subtype PubMed ID
nsv974791 CNV duplication 23825009
nsv9415 CNV gain 18304495
nsv833180 CNV loss 17160897
nsv511572 CNV loss 21212237
nsv509608 CNV insertion 20534489
nsv1151158 CNV duplication 26484159
nsv1127482 CNV deletion 24896259
nsv1059555 CNV gain 25217958
nsv103376 CNV deletion 16902084
esv3638335 CNV loss 21293372
esv3553297 CNV deletion 23714750
esv2758640 CNV gain+loss 17122850
esv2673092 CNV deletion 23128226

Variation tolerance for CLN3 Gene

Residual Variation Intolerance Score: 18.8% 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

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

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

Disorders for CLN3 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
ceroid lipofuscinosis, neuronal, 3
  • batten disease
neuronal ceroid-lipofuscinoses
  • neuronal ceroid-lipofuscinosis, infantile
neuronal ceroid lipofuscinosis
  • neuronal ceroid-lipofuscinoses
peripheral retinal degeneration
  • peripheral degeneration of retina
ceroid lipofuscinosis, neuronal, 2
  • neuronal ceroid lipofuscinosis 2
- elite association - COSMIC cancer census association via MalaCards
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:22261744, 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 RM (Pediatric research 2008) 2 3 22 60
  2. C-terminal prenylation of the CLN3 membrane glycoprotein is required for efficient endosomal sorting to lysosomes. (PMID: 17286803) Storch S … Braulke T (Traffic (Copenhagen, Denmark) 2007) 3 4 22 60
  3. Expression studies of CLN3 protein (battenin) in fusion with the green fluorescent protein in mammalian cells in vitro. (PMID: 10191115) Golabek AA … Wisniewski KE (Molecular genetics and metabolism 1999) 3 4 22 60
  4. Molecular screening of Batten disease: identification of a missense mutation (E295K) in the CLN3 gene. (PMID: 9490299) Zhong N … Brown WT (Human genetics 1998) 3 4 22 60
  5. Genomic structure and complete nucleotide sequence of the Batten disease gene, CLN3. (PMID: 9119403) Mitchison HM … Mole SE (Genomics 1997) 3 4 22 60

Products for CLN3 Gene

  • Addgene plasmids for CLN3

Sources for CLN3 Gene

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