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CLN6 (ceroid-lipofuscinosis, neuronal 6, late infantile, variant)

Identity

Alias_symbol (synonym)FLJ20561
HsT18960
nclf
Other aliasCLN4A
HGNC (Hugo) CLN6
LocusID (NCBI) 54982
Atlas_Id 61895
Location 15q23  [Link to chromosome band 15q23]
Location_base_pair Starts at 68206992 and ends at 68229742 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
CHST2 (3q24) / CLN6 (15q23)CLN6 (15q23) / C15orf59 (15q24.1)CLN6 (15q23) / CHST2 (3q24)
CLN6 (15q23) / FBXL17 (5q21.3)CLN6 (15q23) / PAQR5 (15q23)PRCD (17q25.1) / CLN6 (15q23)
CLN6 PAQR5CLN6 C15orf59CLN6 FBXL17

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)CLN6   2077
LRG (Locus Reference Genomic)LRG_832
Cards
Entrez_Gene (NCBI)CLN6  54982  ceroid-lipofuscinosis, neuronal 6, late infantile, variant
AliasesCLN4A; HsT18960; nclf
GeneCards (Weizmann)CLN6
Ensembl hg19 (Hinxton)ENSG00000128973 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000128973 [Gene_View]  chr15:68206992-68229742 [Contig_View]  CLN6 [Vega]
ICGC DataPortalENSG00000128973
TCGA cBioPortalCLN6
AceView (NCBI)CLN6
Genatlas (Paris)CLN6
WikiGenes54982
SOURCE (Princeton)CLN6
Genetics Home Reference (NIH)CLN6
Genomic and cartography
GoldenPath hg38 (UCSC)CLN6  -     chr15:68206992-68229742 -  15q23   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CLN6  -     15q23   [Description]    (hg19-Feb_2009)
EnsemblCLN6 - 15q23 [CytoView hg19]  CLN6 - 15q23 [CytoView hg38]
Mapping of homologs : NCBICLN6 [Mapview hg19]  CLN6 [Mapview hg38]
OMIM204300   601780   606725   
Gene and transcription
Genbank (Entrez)AK000568 AK027604 AK074753 AK124013 AK291175
RefSeq transcript (Entrez)NM_017882
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CLN6
Cluster EST : UnigeneHs.584921 [ NCBI ]
CGAP (NCI)Hs.584921
Alternative Splicing GalleryENSG00000128973
Gene ExpressionCLN6 [ NCBI-GEO ]   CLN6 [ EBI - ARRAY_EXPRESS ]   CLN6 [ SEEK ]   CLN6 [ MEM ]
Gene Expression Viewer (FireBrowse)CLN6 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)54982
GTEX Portal (Tissue expression)CLN6
Human Protein AtlasENSG00000128973-CLN6 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NWW5   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NWW5  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NWW5
Splice isoforms : SwissVarQ9NWW5
PhosPhoSitePlusQ9NWW5
Domains : Interpro (EBI)CLN6   
Domain families : Pfam (Sanger)CLN6 (PF15156)   
Domain families : Pfam (NCBI)pfam15156   
Conserved Domain (NCBI)CLN6
DMDM Disease mutations54982
Blocks (Seattle)CLN6
SuperfamilyQ9NWW5
Human Protein Atlas [tissue]ENSG00000128973-CLN6 [tissue]
Peptide AtlasQ9NWW5
HPRD05991
IPIIPI00016597   IPI00910505   IPI00922070   
Protein Interaction databases
DIP (DOE-UCLA)Q9NWW5
IntAct (EBI)Q9NWW5
FunCoupENSG00000128973
BioGRIDCLN6
STRING (EMBL)CLN6
ZODIACCLN6
Ontologies - Pathways
QuickGOQ9NWW5
Ontology : AmiGOganglioside metabolic process  protein binding  endoplasmic reticulum  endoplasmic reticulum lumen  endoplasmic reticulum membrane  lysosomal lumen acidification  visual perception  cholesterol metabolic process  membrane  integral component of membrane  protein catabolic process  glycosaminoglycan metabolic process  locomotion involved in locomotory behavior  protein homodimerization activity  cellular macromolecule catabolic process  positive regulation of proteolysis  
Ontology : EGO-EBIganglioside metabolic process  protein binding  endoplasmic reticulum  endoplasmic reticulum lumen  endoplasmic reticulum membrane  lysosomal lumen acidification  visual perception  cholesterol metabolic process  membrane  integral component of membrane  protein catabolic process  glycosaminoglycan metabolic process  locomotion involved in locomotory behavior  protein homodimerization activity  cellular macromolecule catabolic process  positive regulation of proteolysis  
NDEx NetworkCLN6
Atlas of Cancer Signalling NetworkCLN6
Wikipedia pathwaysCLN6
Orthology - Evolution
OrthoDB54982
GeneTree (enSembl)ENSG00000128973
Phylogenetic Trees/Animal Genes : TreeFamCLN6
HOVERGENQ9NWW5
HOGENOMQ9NWW5
Homologs : HomoloGeneCLN6
Homology/Alignments : Family Browser (UCSC)CLN6
Gene fusions - Rearrangements
Fusion: TCGA_MDACCCLN6 PAQR5
Fusion: TCGA_MDACCCLN6 C15orf59
Fusion: TCGA_MDACCCLN6 FBXL17
Tumor Fusion PortalCLN6
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCLN6 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CLN6
dbVarCLN6
ClinVarCLN6
1000_GenomesCLN6 
Exome Variant ServerCLN6
ExAC (Exome Aggregation Consortium)ENSG00000128973
GNOMAD BrowserENSG00000128973
Genetic variants : HAPMAP54982
Genomic Variants (DGV)CLN6 [DGVbeta]
DECIPHERCLN6 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCLN6 
Mutations
ICGC Data PortalCLN6 
TCGA Data PortalCLN6 
Broad Tumor PortalCLN6
OASIS PortalCLN6 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCLN6  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCLN6
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Mendelian genes
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch CLN6
DgiDB (Drug Gene Interaction Database)CLN6
DoCM (Curated mutations)CLN6 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CLN6 (select a term)
intoGenCLN6
Cancer3DCLN6(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM204300    601780    606725   
Orphanet19114    19107   
DisGeNETCLN6
MedgenCLN6
Genetic Testing Registry CLN6
NextProtQ9NWW5 [Medical]
TSGene54982
GENETestsCLN6
Target ValidationCLN6
Huge Navigator CLN6 [HugePedia]
snp3D : Map Gene to Disease54982
BioCentury BCIQCLN6
ClinGenCLN6
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD54982
Chemical/Pharm GKB GenePA26604
Clinical trialCLN6
Miscellaneous
canSAR (ICR)CLN6 (select the gene name)
Probes
Litterature
PubMed39 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCLN6
EVEXCLN6
GoPubMedCLN6
iHOPCLN6
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 13:31:03 CET 2017

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