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Aliases for CLN6 Gene

Aliases for CLN6 Gene

  • Ceroid-Lipofuscinosis, Neuronal 6, Late Infantile, Variant 2 3
  • CLN4A 3 6
  • Ceroid-Lipofuscinosis Neuronal Protein 6 3
  • Protein CLN6 4
  • HsT18960 3
  • Nclf 3

External Ids for CLN6 Gene

Previous GeneCards Identifiers for CLN6 Gene

  • GC15M064339
  • GC15M061598
  • GC15M066063
  • GC15M066215
  • GC15M066286
  • GC15M068499
  • GC15M045330

Summaries for CLN6 Gene

Entrez Gene Summary for CLN6 Gene

  • This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely encode proteins involved in the degradation of post-translationally modified proteins in lysosomes. The primary defect in NCL disorders is thought to be associated with lysosomal storage function. [provided by RefSeq, Oct 2008]

GeneCards Summary for CLN6 Gene

CLN6 (Ceroid-Lipofuscinosis, Neuronal 6, Late Infantile, Variant) is a Protein Coding gene. Diseases associated with CLN6 include ceroid lipofuscinosis, neuronal, 6 and ceroid lipofuscinosis, neuronal, kufs type, adult onset. GO annotations related to this gene include protein homodimerization activity.

Gene Wiki entry for CLN6 Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLN6 Gene

Genomics for CLN6 Gene

Regulatory Elements for CLN6 Gene

Genomic Location for CLN6 Gene

Start:
68,206,992 bp from pter
End:
68,257,211 bp from pter
Size:
50,220 bases
Orientation:
Minus strand

Genomic View for CLN6 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLN6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLN6 Gene

Proteins for CLN6 Gene

  • Protein details for CLN6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NWW5-CLN6_HUMAN
    Recommended name:
    Ceroid-lipofuscinosis neuronal protein 6
    Protein Accession:
    Q9NWW5
    Secondary Accessions:
    • A8K560
    • B4DDH6
    • Q6IAB1
    • Q96SR0

    Protein attributes for CLN6 Gene

    Size:
    311 amino acids
    Molecular mass:
    35919 Da
    Quaternary structure:
    • Interacts with CRMP2.

    Alternative splice isoforms for CLN6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLN6 Gene

Proteomics data for CLN6 Gene at MOPED

Post-translational modifications for CLN6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLN6 Gene

No data available for DME Specific Peptides for CLN6 Gene

Domains for CLN6 Gene

Protein Domains for CLN6 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CLN6 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CLN6: view

No data available for Gene Families and UniProtKB/Swiss-Prot for CLN6 Gene

Function for CLN6 Gene

Gene Ontology (GO) - Molecular Function for CLN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19235893
GO:0042803 protein homodimerization activity IDA 15010453
genes like me logo Genes that share ontologies with CLN6: view

Phenotypes for CLN6 Gene

genes like me logo Genes that share phenotypes with CLN6: view

No data available for Molecular function , Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for CLN6 Gene

Localization for CLN6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLN6 Gene

Endoplasmic reticulum membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CLN6 Gene COMPARTMENTS Subcellular localization image for CLN6 gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 3
lysosome 2
vacuole 2
endosome 1

Gene Ontology (GO) - Cellular Components for CLN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus --
GO:0005654 nucleoplasm IDA --
GO:0005783 endoplasmic reticulum IDA --
GO:0005788 endoplasmic reticulum lumen IDA 15010453
GO:0005789 endoplasmic reticulum membrane IEA --
genes like me logo Genes that share ontologies with CLN6: view

Pathways for CLN6 Gene

SuperPathways for CLN6 Gene

No Data Available

Interacting Proteins for CLN6 Gene

Gene Ontology (GO) - Biological Process for CLN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001573 ganglioside metabolic process IMP 16857350
GO:0007040 lysosome organization --
GO:0007042 lysosomal lumen acidification IMP 11722572
GO:0007601 visual perception IEA --
GO:0008203 cholesterol metabolic process IMP 16857350
genes like me logo Genes that share ontologies with CLN6: view

No data available for Pathways by source for CLN6 Gene

Compounds for CLN6 Gene

(1) Novoseek inferred chemical compound relationships for CLN6 Gene

Compound -log(P) Hits PubMed IDs
lipid 0 1
genes like me logo Genes that share compounds with CLN6: view

Transcripts for CLN6 Gene

Unigene Clusters for CLN6 Gene

Ceroid-lipofuscinosis, neuronal 6, late infantile, variant:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CLN6 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b · 3c ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d
SP1: - - - -
SP2: - - -
SP3: - - - - -
SP4: - - - - -
SP5: -
SP6: -
SP7: - - - - - - - - -
SP8:

Relevant External Links for CLN6 Gene

GeneLoc Exon Structure for
CLN6
ECgene alternative splicing isoforms for
CLN6

Expression for CLN6 Gene

mRNA expression in normal human tissues for CLN6 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for CLN6 Gene

SOURCE GeneReport for Unigene cluster for CLN6 Gene Hs.584921

genes like me logo Genes that share expressions with CLN6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for CLN6 Gene

Orthologs for CLN6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLN6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLN6 36
  • 82 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CLN6 35
  • 91 (n)
  • 91 (a)
CLN6 36
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CLN6 35
  • 89.5 (n)
  • 91.56 (a)
CLN6 36
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Cln6 35
  • 87.76 (n)
  • 91.15 (a)
Cln6 16
Cln6 36
  • 90 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CLN6 36
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CLN6 36
  • 83 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cln6 35
  • 86.89 (n)
  • 90.16 (a)
chicken
(Gallus gallus)
Aves CLN6 35
  • 76.31 (n)
  • 75.88 (a)
CLN6 36
  • 75 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLN6 36
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cln6 35
  • 70.43 (n)
  • 73.09 (a)
Str.6976 35
zebrafish
(Danio rerio)
Actinopterygii cln6a 35
  • 67.59 (n)
  • 70 (a)
cln6a 36
  • 68 (a)
OneToMany
cln6b 36
  • 62 (a)
OneToMany
Dr.14969 35
Species with no ortholog for CLN6:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for CLN6 Gene

ENSEMBL:
Gene Tree for CLN6 (if available)
TreeFam:
Gene Tree for CLN6 (if available)

Paralogs for CLN6 Gene

No data available for Paralogs for CLN6 Gene

Variants for CLN6 Gene

Sequence variations from dbSNP and Humsavar for CLN6 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type MAF
rs1012521 -- 68,216,305(-) GCTGG(A/T)CTGGC intron-variant
rs1012522 -- 68,216,187(-) CTCCC(C/T)TCACT intron-variant
rs1400432 -- 68,210,266(-) GGAGC(C/T)GGTGT intron-variant
rs2292746 -- 68,214,137(-) GCCTG(C/G)GGCCC intron-variant
rs3743088 -- 68,229,580(-) CATGG(A/G)GGCGA reference, missense

Relevant External Links for CLN6 Gene

HapMap Linkage Disequilibrium report
CLN6
Human Gene Mutation Database (HGMD)
CLN6
Locus Specific Mutation Databases (LSDB)
CLN6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for CLN6 Gene

Disorders for CLN6 Gene

(2) OMIM Diseases for CLN6 Gene (606725)

UniProtKB/Swiss-Prot

CLN6_HUMAN
  • Ceroid lipofuscinosis, neuronal, 6 (CLN6) [MIM:601780]: 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 lipopigment patterns observed most often in neuronal ceroid lipofuscinosis type 6 comprise mixed combinations of granular, curvilinear, and fingerprint profiles. {ECO:0000269 PubMed:11727201, ECO:0000269 PubMed:11791207, ECO:0000269 PubMed:12673792, ECO:0000269 PubMed:12815591, ECO:0000269 PubMed:19201763, ECO:0000269 PubMed:21990111, ECO:0000269 Ref.2}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Ceroid lipofuscinosis, neuronal, 4A (CLN4A) [MIM:204300]: An adult-onset 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. CLN4A has no visual involvement and is characterized by progressive myoclonic epilepsy. {ECO:0000269 PubMed:21549341}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for CLN6 Gene

(5) Novoseek inferred disease relationships for CLN6 Gene

Disease -log(P) Hits PubMed IDs
neuronal ceroid lipofuscinoses 95.9 1
ceroid lipofuscinosis, neuronal, late infantile, variant 95.7 4
lincl 93.9 4
neurodegenerative diseases 72.8 1
blindness 28.1 2

Relevant External Links for CLN6

GeneTests
CLN6
GeneReviews
CLN6
Genetic Association Database (GAD)
CLN6
Human Genome Epidemiology (HuGE) Navigator
CLN6
genes like me logo Genes that share disorders with CLN6: view

Publications for CLN6 Gene

  1. The gene mutated in variant late-infantile neuronal ceroid lipofuscinosis (CLN6) and in nclf mutant mice encodes a novel predicted transmembrane protein. (PMID: 11727201) Wheeler R.B. … Mole S.E. (Am. J. Hum. Genet. 2002) 2 3 4 23
  2. Mutations in CLN7/MFSD8 are a common cause of variant late-infantile neuronal ceroid lipofuscinosis. (PMID: 19201763) Kousi M. … Lehesjoki A.-E. (Brain 2009) 3 4 23 48
  3. Novel mutations in the CLN6 gene causing a variant late infantile neuronal ceroid lipofuscinosis. (PMID: 12673792) Teixeira C.A. … Boustany R.-M.N. (Hum. Mutat. 2003) 3 4 23
  4. Mutations in a novel CLN6-encoded transmembrane protein cause variant neuronal ceroid lipofuscinosis in man and mouse. (PMID: 11791207) Gao H. … MacDonald M.E. (Am. J. Hum. Genet. 2002) 3 4 23
  5. CLN6, which is associated with a lysosomal storage disease, is an endoplasmic reticulum protein. (PMID: 15265688) Mole S.E. … Cutler D.F. (Exp. Cell Res. 2004) 3 4 23

Products for CLN6 Gene

Sources for CLN6 Gene

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