Atlas of Genetics and Cytogenetics in Oncology and Haematology


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CLN3 (CLN3, battenin)

Identity

Alias_namesBTS
Batten, Spielmeyer-Vogt disease
ceroid-lipofuscinosis, neuronal 3
Alias_symbol (synonym)JNCL
BTN1
Other alias
HGNC (Hugo) CLN3
LocusID (NCBI) 1201
Atlas_Id 56249
Location 16p12.1  [Link to chromosome band 16p12]
Location_base_pair Starts at 28477279 and ends at 28492082 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
CLN3 (16p11.2) / C15orf32 (15q26.1)CLN3 (16p11.2) / CLN3 (16p11.2)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)CLN3   2074
LRG (Locus Reference Genomic)LRG_689
Cards
Entrez_Gene (NCBI)CLN3  1201  CLN3, battenin
AliasesBTN1; BTS; JNCL
GeneCards (Weizmann)CLN3
Ensembl hg19 (Hinxton)ENSG00000188603 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000188603 [Gene_View]  chr16:28477279-28492082 [Contig_View]  CLN3 [Vega]
ICGC DataPortalENSG00000188603
TCGA cBioPortalCLN3
AceView (NCBI)CLN3
Genatlas (Paris)CLN3
WikiGenes1201
SOURCE (Princeton)CLN3
Genetics Home Reference (NIH)CLN3
Genomic and cartography
GoldenPath hg38 (UCSC)CLN3  -     chr16:28477279-28492082 -  16p12.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CLN3  -     16p12.1   [Description]    (hg19-Feb_2009)
EnsemblCLN3 - 16p12.1 [CytoView hg19]  CLN3 - 16p12.1 [CytoView hg38]
Mapping of homologs : NCBICLN3 [Mapview hg19]  CLN3 [Mapview hg38]
OMIM204200   607042   
Gene and transcription
Genbank (Entrez)###############################################################################################################################################################################################################################################################
RefSeq transcript (Entrez)NM_000086 NM_001042432 NM_001286104 NM_001286105 NM_001286109 NM_001286110
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CLN3
Cluster EST : UnigeneHs.534667 [ NCBI ]
CGAP (NCI)Hs.534667
Alternative Splicing GalleryENSG00000188603
Gene ExpressionCLN3 [ NCBI-GEO ]   CLN3 [ EBI - ARRAY_EXPRESS ]   CLN3 [ SEEK ]   CLN3 [ MEM ]
Gene Expression Viewer (FireBrowse)CLN3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1201
GTEX Portal (Tissue expression)CLN3
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13286   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ13286  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ13286
Splice isoforms : SwissVarQ13286
PhosPhoSitePlusQ13286
Domains : Interpro (EBI)Battenin_disease_Cln3    Battenin_disease_Cln3_subgr    MFS_dom   
Domain families : Pfam (Sanger)CLN3 (PF02487)   
Domain families : Pfam (NCBI)pfam02487   
Conserved Domain (NCBI)CLN3
DMDM Disease mutations1201
Blocks (Seattle)CLN3
SuperfamilyQ13286
Human Protein AtlasENSG00000188603
Peptide AtlasQ13286
HPRD08450
IPIIPI00012448   IPI00217835   IPI00217836   IPI00217837   IPI00217838   IPI00639963   IPI00384849   IPI00640605   IPI00186092   IPI00028312   IPI00642284   IPI00383566   IPI00383568   IPI00010906   IPI00383669   IPI00384850   
Protein Interaction databases
DIP (DOE-UCLA)Q13286
IntAct (EBI)Q13286
FunCoupENSG00000188603
BioGRIDCLN3
STRING (EMBL)CLN3
ZODIACCLN3
Ontologies - Pathways
QuickGOQ13286
Ontology : AmiGOGolgi membrane  action potential  globoside metabolic process  protein binding  nucleus  cytoplasm  mitochondrion  lysosome  lysosomal membrane  early endosome  late endosome  late endosome  autophagosome  endoplasmic reticulum  Golgi apparatus  Golgi stack  trans-Golgi network  plasma membrane  caveola  cellular amino acid metabolic process  ceramide metabolic process  glucosylceramide metabolic process  galactosylceramide metabolic process  sphingomyelin metabolic process  receptor-mediated endocytosis  lysosome organization  lysosomal lumen acidification  synaptic vesicle  associative learning  arginine transport  integral component of membrane  macroautophagy  protein processing  protein catabolic process  integral component of endoplasmic reticulum membrane  ionotropic glutamate receptor signaling pathway  lysosomal lumen pH elevation  neurotransmitter metabolic process  amyloid precursor protein catabolic process  neuron projection  negative regulation of apoptotic process  negative regulation of catalytic activity  negative regulation of neuron apoptotic process  membrane raft  negative regulation of proteolysis  vesicle transport along microtubule  neuromuscular process controlling balance  unfolded protein binding  regulation of cytosolic calcium ion concentration  membrane organization  autophagosome maturation  
Ontology : EGO-EBIGolgi membrane  action potential  globoside metabolic process  protein binding  nucleus  cytoplasm  mitochondrion  lysosome  lysosomal membrane  early endosome  late endosome  late endosome  autophagosome  endoplasmic reticulum  Golgi apparatus  Golgi stack  trans-Golgi network  plasma membrane  caveola  cellular amino acid metabolic process  ceramide metabolic process  glucosylceramide metabolic process  galactosylceramide metabolic process  sphingomyelin metabolic process  receptor-mediated endocytosis  lysosome organization  lysosomal lumen acidification  synaptic vesicle  associative learning  arginine transport  integral component of membrane  macroautophagy  protein processing  protein catabolic process  integral component of endoplasmic reticulum membrane  ionotropic glutamate receptor signaling pathway  lysosomal lumen pH elevation  neurotransmitter metabolic process  amyloid precursor protein catabolic process  neuron projection  negative regulation of apoptotic process  negative regulation of catalytic activity  negative regulation of neuron apoptotic process  membrane raft  negative regulation of proteolysis  vesicle transport along microtubule  neuromuscular process controlling balance  unfolded protein binding  regulation of cytosolic calcium ion concentration  membrane organization  autophagosome maturation  
Pathways : KEGGLysosome   
NDEx NetworkCLN3
Atlas of Cancer Signalling NetworkCLN3
Wikipedia pathwaysCLN3
Orthology - Evolution
OrthoDB1201
GeneTree (enSembl)ENSG00000188603
Phylogenetic Trees/Animal Genes : TreeFamCLN3
HOVERGENQ13286
HOGENOMQ13286
Homologs : HomoloGeneCLN3
Homology/Alignments : Family Browser (UCSC)CLN3
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCLN3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CLN3
dbVarCLN3
ClinVarCLN3
1000_GenomesCLN3 
Exome Variant ServerCLN3
ExAC (Exome Aggregation Consortium)CLN3 (select the gene name)
Genetic variants : HAPMAP1201
Genomic Variants (DGV)CLN3 [DGVbeta]
DECIPHERCLN3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCLN3 
Mutations
ICGC Data PortalCLN3 
TCGA Data PortalCLN3 
Broad Tumor PortalCLN3
OASIS PortalCLN3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCLN3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCLN3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch CLN3
DgiDB (Drug Gene Interaction Database)CLN3
DoCM (Curated mutations)CLN3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CLN3 (select a term)
intoGenCLN3
Cancer3DCLN3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM204200    607042   
Orphanet19109   
MedgenCLN3
Genetic Testing Registry CLN3
NextProtQ13286 [Medical]
TSGene1201
GENETestsCLN3
Target ValidationCLN3
Huge Navigator CLN3 [HugePedia]
snp3D : Map Gene to Disease1201
BioCentury BCIQCLN3
ClinGenCLN3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1201
Chemical/Pharm GKB GenePA26601
Clinical trialCLN3
Miscellaneous
canSAR (ICR)CLN3 (select the gene name)
Probes
Litterature
PubMed94 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCLN3
EVEXCLN3
GoPubMedCLN3
iHOPCLN3
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 25 19:02:51 CEST 2017

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