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... See more...

Aliases for CLN3 Gene

Aliases for CLN3 Gene

  • CLN3 Lysosomal/Endosomal Transmembrane Protein, Battenin 2 3 5
  • Ceroid-Lipofuscinosis, Neuronal 3 2 3
  • Batten Disease Protein 3 4
  • CLN3, Battenin 2 3
  • Battenin 3 4
  • BTN1 2 3
  • JNCL 2 3
  • BTS 3 4
  • Juvenile Neuronal Ceroid Lipofuscinosis 2
  • Batten, Spielmeyer-Vogt Disease 2
  • Protein CLN3 4
  • CLN3 5

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 Lysosomal/Endosomal Transmembrane Protein, Battenin) is a Protein Coding gene. Diseases associated with CLN3 include Ceroid Lipofuscinosis, Neuronal, 3 and Neuronal Ceroid Lipofuscinosis. Among its related pathways are Lysosome. Gene Ontology (GO) annotations related to this gene include unfolded protein binding. An important paralog of this gene is ENSG00000261832.

UniProtKB/Swiss-Prot Summary for CLN3 Gene

  • Mediates microtubule-dependent, anterograde transport connecting the Golgi network, endosomes, autophagosomes, lysosomes and plasma membrane, and participates in several cellular processes such as regulation of lysosomal pH, lysosome protein degradation, receptor-mediated endocytosis, autophagy, transport of proteins and lipids from the TGN, apoptosis and synaptic transmission (PubMed:10924275, PubMed:18817525, PubMed:18317235, PubMed:22261744, PubMed:15471887, PubMed:20850431). Facilitates the proteins transport from trans-Golgi network (TGN)-to other membrane compartments such as transport of microdomain-associated proteins to the plasma membrane, IGF2R transport to the lysosome where it regulates the CTSD release leading to regulation of CTSD maturation and thereby APP intracellular processing (PubMed:10924275, PubMed:18817525). Moreover regulates CTSD activity in response to osmotic stress (PubMed:23840424, PubMed:28390177). Also binds galactosylceramide and transports it from the trans Golgi to the rafts, which may have immediate and downstream effects on cell survival by modulating ceramide synthesis (PubMed:18317235). At the plasma memebrane, regulates actin-dependent events including filopodia formation, cell migration, and pinocytosis through ARF1-CDC42 pathway and also the cytoskeleton organization through interaction with MYH10 and fodrin leading to the regulation of the plasma membrane association of Na+, K+ ATPase complex (PubMed:20850431). Regulates synaptic transmission in the amygdala, hippocampus, and cerebellum through regulation of synaptic vesicles density and their proximity to active zones leading to modulation of short-term plasticity and age-dependent anxious behavior, learning and memory (By similarity). Regulates autophagic vacuoles (AVs) maturation by modulating the trafficking between endocytic and autophagolysosomal/lysosomal compartments, which involves vesicle fusion leading to regulation of degradation process (By similarity). Participates also in cellular homeostasis of compounds such as, water, ions, amino acids, proteins and lipids in several tissue namely in brain and kidney through regulation of their transport and synthesis (PubMed:17482562).

Gene Wiki entry for CLN3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLN3 Gene

Genomics for CLN3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLN3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J028490 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +1.7 1740 7.3 SP1 CREB1 GATAD2A PRDM10 ZNF629 REST TFE3 SIX5 LEF1 IKZF1 APOBR CLN3 ENSG00000261832 lnc-CLN3-1 lnc-IL27-1 SULT1A2 ATXN2L ENSG00000260853 SH2B1 SPNS1
GH16J028487 Promoter 0.4 EPDnew 600.4 +7.8 7758 0.1 ZNF664 CLN3 SULT1A2 ENSG00000261832 lnc-IL27-1 piR-43164-023 EIF3CL
GH16J028479 Promoter 0.3 EPDnew 600.4 +16.0 15969 0.1 CLN3 piR-43164-023 NPIPB7 ENSG00000261832 EIF3CL
GH16J028525 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 18.1 -32.0 -31970 4.1 GATAD2A ATF7 REST TFE3 SOX13 NFKBIZ RCOR2 ZNF7 FOXA1 RXRB IL27 SULT1A2 TUFM CLN3 APOBR NPIPB7 SGF29 ENSG00000251417 lnc-APOBR-1 lnc-SGF29-2
GH16J028821 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 11.3 -328.5 -328490 4.5 ZNF221 SP1 HNRNPL CREB1 GATAD2A ATF7 PRDM10 ZNF629 TFE3 ZNF512 ATXN2L ENSG00000275807 HSALNG0110526 MN297364 TUFM NPIPB12 ENSG00000260853 ENSG00000198106 SH2B1 NFATC2IP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLN3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLN3

Top Transcription factor binding sites by QIAGEN in the CLN3 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • IRF-1

Genomic Locations for CLN3 Gene

Genomic Locations for CLN3 Gene
chr16:28,466,653-28,495,575
(GRCh38/hg38)
Size:
28,923 bases
Orientation:
Minus strand
chr16:28,477,983-28,506,896
(GRCh37/hg19)
Size:
28,914 bases
Orientation:
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:
    Q13286-CLN3_HUMAN
    Recommended name:
    Battenin
    Protein Accession:
    Q13286
    Secondary Accessions:
    • B2R7J1
    • B4DXL3
    • O00668
    • O95089
    • Q549S9
    • Q9UP09
    • Q9UP11
    • Q9UP12
    • Q9UP13
    • Q9UP14

    Protein attributes for CLN3 Gene

    Size:
    438 amino acids
    Molecular mass:
    47623 Da
    Quaternary structure:
    • Homooligomer (By similarity). Interacts with DCTN1, KIF3A, RAB7A and RILP (PubMed:22261744). Interacts with CLN5 (PubMed:19941651, PubMed:14699076). May interact with HOOK1 (PubMed:15471887). Interacts with KCNIP3; this interaction is disrupted by intracellular increase of calcium level (PubMed:17189291). Interacts with TPP1, CLN6 AND CLN8 (PubMed:17237713). Interacts with MYH10; this interaction may play a role in regulation of cytoskeleton organization (PubMed:20850431). Interacts with SBDS (PubMed:20015955). Interacts with sodium/potassium-transporting ATPase complex (via ATP1A1) and fodrin heteromer (via SPTAN1); this interaction regulates their localization at the plasma membrane (Probable). Interacts with HSPA5 (Probable). Interacts (via dileucine motif) with AP3D1 and AP1G1; this interaction facilitates lysosomal targeting (PubMed:15598649). Interacts (via dileucine motif) with AP2A2 (PubMed:15598649).
    Miscellaneous:
    • [Isoform 4]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    • [Isoform 5]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    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
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for CLN3 Gene

InterPro:
Blocks:
  • CLN3 Batten's disease protein (battenin) signature
ProtoNet:

Suggested Antigen Peptide Sequences for CLN3 Gene

GenScript: Design optimal peptide antigens:
  • Mutant CLN3 (A8JYI8_HUMAN)
  • Mutant CLN3 (A8JYI9_HUMAN)
  • cDNA FLJ60087, highly similar to Protein CLN3 (B4DFF3_HUMAN)
  • cDNA FLJ59353, highly similar to Protein CLN3 (B4DMY6_HUMAN)
  • Protein CLN3 (CLN3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13286

UniProtKB/Swiss-Prot:

CLN3_HUMAN :
  • The C-terminal (153-438) mediates KCNIP3 interaction and the cytoprotective activity (PubMed:17189291). the dileucine motif mediates AP1G1 and AP3D1 interaction (PubMed:15598649).
  • Belongs to the battenin family.
Domain:
  • The C-terminal (153-438) mediates KCNIP3 interaction and the cytoprotective activity (PubMed:17189291). the dileucine motif mediates AP1G1 and AP3D1 interaction (PubMed:15598649).
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

UniProtKB/Swiss-Prot Function:
Mediates microtubule-dependent, anterograde transport connecting the Golgi network, endosomes, autophagosomes, lysosomes and plasma membrane, and participates in several cellular processes such as regulation of lysosomal pH, lysosome protein degradation, receptor-mediated endocytosis, autophagy, transport of proteins and lipids from the TGN, apoptosis and synaptic transmission (PubMed:10924275, PubMed:18817525, PubMed:18317235, PubMed:22261744, PubMed:15471887, PubMed:20850431). Facilitates the proteins transport from trans-Golgi network (TGN)-to other membrane compartments such as transport of microdomain-associated proteins to the plasma membrane, IGF2R transport to the lysosome where it regulates the CTSD release leading to regulation of CTSD maturation and thereby APP intracellular processing (PubMed:10924275, PubMed:18817525). Moreover regulates CTSD activity in response to osmotic stress (PubMed:23840424, PubMed:28390177). Also binds galactosylceramide and transports it from the trans Golgi to the rafts, which may have immediate and downstream effects on cell survival by modulating ceramide synthesis (PubMed:18317235). At the plasma memebrane, regulates actin-dependent events including filopodia formation, cell migration, and pinocytosis through ARF1-CDC42 pathway and also the cytoskeleton organization through interaction with MYH10 and fodrin leading to the regulation of the plasma membrane association of Na+, K+ ATPase complex (PubMed:20850431). Regulates synaptic transmission in the amygdala, hippocampus, and cerebellum through regulation of synaptic vesicles density and their proximity to active zones leading to modulation of short-term plasticity and age-dependent anxious behavior, learning and memory (By similarity). Regulates autophagic vacuoles (AVs) maturation by modulating the trafficking between endocytic and autophagolysosomal/lysosomal compartments, which involves vesicle fusion leading to regulation of degradation process (By similarity). Participates also in cellular homeostasis of compounds such as, water, ions, amino acids, proteins and lipids in several tissue namely in brain and kidney through regulation of their transport and synthesis (PubMed:17482562).
UniProtKB/Swiss-Prot Induction:
Increased by osmotic stress.
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

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:0051861 glycolipid binding IDA 18317235
GO:0120146 sulfatide binding IDA 18317235
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

CRISPR Products

miRNA for CLN3 Gene

miRTarBase miRNAs that target CLN3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for 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. Golgi apparatus. Golgi apparatus membrane. Golgi apparatus, Golgi stack. Golgi apparatus, trans-Golgi network. Cell membrane. Recycling endosome. Membrane raft. Membrane, caveola. Early endosome membrane. Cell junction, synapse, synaptosome. Late endosome membrane. Cytoplasmic vesicle, autophagosome. Note=CLN3 is not present in late endosomes/lysosomes in fibroblasts and neurons (PubMed:15240864). Trafficks from cell membrane to Golgi via endosomes (PubMed:15240864). Osmotic stress changes the subcellular localization of CLN3 (PubMed:23840424). Trafficks to intracellular compartments via the plasma membranet through AP3M1-dependent mechanisms (PubMed:14644441). Excluded from the synaptic vesicles (By similarity). {ECO:0000250 UniProtKB:Q61124, ECO:0000269 PubMed:14644441, ECO:0000269 PubMed:15240864, ECO:0000269 PubMed:23840424}.

Subcellular locations from

COMPARTMENTS
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
nucleus 5
endoplasmic reticulum 5
endosome 5
lysosome 5
golgi apparatus 5
cytosol 3
extracellular 2
cytoskeleton 2
mitochondrion 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for CLN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IDA 9949212
GO:0005623 cell IEA --
GO:0005634 nucleus IDA 10191116
GO:0005737 cytoplasm IDA 10191116
GO:0005764 lysosome IBA,IMP 14644441
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

PathCards logo

SuperPathways 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:0006898 receptor-mediated endocytosis IMP 15471887
GO:0007034 vacuolar transport IBA --
GO:0007040 lysosome organization IBA,ISS --
GO:0007042 lysosomal lumen acidification IBA,IMP 11722572
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

mRNA/cDNA for CLN3 Gene

6 REFSEQ mRNAs :
52 NCBI additional mRNA sequence :
63 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLN3

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: - - - - - - - -
SP17:
SP18: - - - - - -
SP19: - - - - - -
SP20: -
SP21: - - - -
SP22: - - - - - -
SP23:
SP24:
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: -
SP11:
SP12: -
SP13:
SP14: -
SP15:
SP16: -
SP17: -
SP18:
SP19:
SP20:
SP21:
SP22:
SP23:
SP24:
SP25:

Relevant External Links for CLN3 Gene

GeneLoc Exon Structure for
CLN3

Expression for CLN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for CLN3 Gene



Protein tissue co-expression partners for CLN3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLN3

SOURCE GeneReport for Unigene cluster for CLN3 Gene:

Hs.534667

mRNA Expression by UniProt/SwissProt for CLN3 Gene:

Q13286-CLN3_HUMAN
Tissue specificity: Expressed in the cortical brain, pancreas, spleen, and testis with weaker expression in the peripheral nerve (at protein level). Highly expressed in gray matter (at protein level).

Evidence on tissue expression from TISSUES for CLN3 Gene

  • Nervous system(4.9)
  • Lung(4.5)
  • Intestine(3.4)
  • Kidney(3.2)
  • Muscle(3)
  • Skin(3)
  • Liver(2.7)
  • Blood(2.6)
  • Heart(2.4)
  • Stomach(2.2)
  • Bone(2.1)
  • Thyroid gland(2)
  • Eye(2)
  • Bone marrow(2)

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

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • immune
  • nervous
  • skeletal muscle
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • head
General:
  • 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 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
Chimpanzee
(Pan troglodytes)
Mammalia -- 31
  • 98 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia -- 31
  • 88 (a)
OneToMany
CLN3 30
  • 86.76 (n)
Dog
(Canis familiaris)
Mammalia CLN3 30 31
  • 87.75 (n)
OneToMany
Mouse
(Mus musculus)
Mammalia Cln3 30 17 31
  • 82.91 (n)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Cln3 30
  • 82.84 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 75 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 69 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 56 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia cln3 30
  • 63.29 (n)
Str.15897 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.15291 30
Zebrafish
(Danio rerio)
Actinopterygii cln3 30 31
  • 55.58 (n)
OneToMany
Dr.3167 30
Fruit Fly
(Drosophila melanogaster)
Insecta cln3 30 31
  • 52.67 (n)
OneToMany
CG5582 32
  • 40 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003934 30
  • 52.49 (n)
Worm
(Caenorhabditis elegans)
Secernentea cln-3.2 30 31 32
  • 48.94 (n)
ManyToMany
cln-3.1 31 32
  • 39 (a)
ManyToMany
cln-3.3 31 32
  • 38 (a)
ManyToMany
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AEL171C 30
  • 47.58 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YHC3 30 31 33
  • 46.35 (n)
OneToMany
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F01551g 30
  • 44.26 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU10272 30
  • 49.09 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes btn1 30
  • 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 Vase (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

ENSEMBL:
Gene Tree for CLN3 (if available)
TreeFam:
Gene Tree for CLN3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLN3: view image

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLN3 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
632772 Pathogenic: Juvenile neuronal ceroid lipofuscinosis 28,480,659(-) GGCCTCCCAAAGTGCT SPLICE_ACCEPTOR_VARIANT,SPLICE_DONOR_VARIANT
640841 Uncertain Significance: Neuronal ceroid lipofuscinosis 28,488,649(-) G/A MISSENSE_VARIANT,NONSENSE,INTRON_VARIANT
641439 Uncertain Significance: Neuronal ceroid lipofuscinosis 28,477,885(-) CA/C INTRON_VARIANT
646454 Uncertain Significance: Neuronal ceroid lipofuscinosis 28,477,748(-) T/C MISSENSE_VARIANT
646719 Uncertain Significance: Neuronal ceroid lipofuscinosis 28,482,622(-) G/A INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for CLN3 Gene

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

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

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)

Additional Variant Information for CLN3 Gene

Human Gene Mutation Database (HGMD)
CLN3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLN3

SNP Genotyping and Copy Number Assay Products

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

Disorders for CLN3 Gene

MalaCards: The human disease database

(36) MalaCards diseases for CLN3 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
ceroid lipofuscinosis, neuronal, 3
  • cln3
neuronal ceroid lipofuscinosis
  • batten disease
ceroid storage disease
  • lipofuscin storage disease
inherited retinal disorder
  • retinal dystrophy
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search CLN3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CLN3_HUMAN
  • 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:10332042, ECO:0000269 PubMed:10924275, ECO:0000269 PubMed:14699076, ECO:0000269 PubMed:17482562, 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-Sjögren) 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)

Additional Disease Information for CLN3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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 4 23
  2. Interaction between Sdo1p and Btn1p in the Saccharomyces cerevisiae model for Batten disease. (PMID: 20015955) Vitiello SP … Pearce DA (Human molecular genetics 2010) 3 4 23
  3. Novel interactions of CLN5 support molecular networking between Neuronal Ceroid Lipofuscinosis proteins. (PMID: 19941651) Lyly A … Kyttälä A (BMC cell biology 2009) 3 4 23
  4. Loss of the Batten disease gene CLN3 prevents exit from the TGN of the mannose 6-phosphate receptor. (PMID: 18817525) Metcalf DJ … Cutler DF (Traffic (Copenhagen, Denmark) 2008) 3 4 23
  5. Neuronal ceroid lipofuscinosis: a common pathway? (PMID: 17237713) Persaud-Sawin DA … Boustany RM (Pediatric research 2007) 3 4 23

Products for CLN3 Gene

Sources for CLN3 Gene