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Aliases for CLN6 Gene

Aliases for CLN6 Gene

  • Ceroid-Lipofuscinosis, Neuronal 6, Late Infantile, Variant 2 3 5
  • Ceroid-Lipofuscinosis Neuronal 6 Late Infantile 3
  • Ceroid-Lipofuscinosis Neuronal Protein 6 3
  • Protein CLN6 4
  • HsT18960 3
  • CLN4A 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 CIViC summary , 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

Enhancers for CLN6 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
GH15G068203 1.4 Ensembl ENCODE dbSUPER 13.4 +51.5 51510 4.2 HDAC1 TBP ATF1 TBL1XR1 ARNT ARID4B ZBTB40 RAD21 YY1 SCRT2 CLN6 CALML4 LOC105370871
GH15G068227 1.1 ENCODE 13.9 +28.0 27969 3.6 HDGF PKNOX1 MLX CREB3L1 ARNT WRNIP1 ARID4B SIN3A ZBTB7B ZNF766 IQCH-AS1 CLN6 FEM1B PIAS1 RNU6-1 LOC101929076 SKOR1 ENSG00000260007 CALML4
GH15G068232 1 Ensembl ENCODE 14 +24.1 24069 1.6 ELF3 PKNOX1 SAP130 ZNF644 RARA ZNF335 PRDM10 CREM MTA2 GFI1B CLN6 CALML4 ENSG00000260007 HMGN2P40
GH15G068186 1.2 Ensembl ENCODE dbSUPER 11.3 +69.6 69604 2.0 ZNF263 TAF1 HLF MAX REST RAD21 YY1 ZFHX2 POLR2A ZNF341 CLN6 LOC105370871 CALML4
GH15G068208 1 Ensembl ENCODE 13.3 +47.1 47081 2.9 CTCF MAX KLF17 EBF1 ZIC2 RAD21 ZNF664 ZFHX2 GLIS2 EGR1 CLN6 CALML4 ENSG00000260007
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLN6 on UCSC Golden Path with GeneCards custom track

Promoters for CLN6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000078451 11 801 ELF3 ARID4B SIN3A ZNF48 RAD21 YY1 THAP11 ZNF202 CEBPB REST

Genomic Location for CLN6 Gene

Chromosome:
15
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

Genes around CLN6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLN6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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 (PubMed:19235893). Interacts with CLN5 (PubMed:19941651).

    Alternative splice isoforms for CLN6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLN6 Gene

Post-translational modifications for CLN6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CLN6 Gene

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

Human Phenotype Ontology for CLN6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CLN6 Gene

MGI Knock Outs for CLN6:
  • Cln6 tm1b(EUCOMM)Hmgu

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CLN6

No data available for Molecular function , Enzyme Numbers (IUBMB) , Transcription Factor Targets 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. Endoplasmic reticulum.

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 CLN6 gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 3
nucleus 2
lysosome 2
mitochondrion 1
endosome 1

Gene Ontology (GO) - Cellular Components for CLN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA,IEA 15265688
GO:0005788 endoplasmic reticulum lumen IDA 15010453
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA,IDA 19946888
GO:0016021 integral component of membrane IEA,NAS 11727201
genes like me logo Genes that share ontologies with CLN6: view

Pathways & Interactions 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 IEA --
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 and SIGNOR curated interactions for CLN6 Gene

Drugs & Compounds for CLN6 Gene

(1) Additional Compounds for CLN6 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CLN6

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for CLN6 Gene

Protein differential expression in normal tissues from HIPED for CLN6 Gene

This gene is overexpressed in Ovary (8.7) and Retina (7.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLN6 Gene



Protein tissue co-expression partners for CLN6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLN6 Gene:

CLN6

SOURCE GeneReport for Unigene cluster for CLN6 Gene:

Hs.584921

Evidence on tissue expression from TISSUES for CLN6 Gene

  • Lung(4.3)
  • Adrenal gland(4.2)
  • Liver(4.2)
  • Nervous system(2.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CLN6 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
General:
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with CLN6: view

Primer Products

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
cow
(Bos Taurus)
Mammalia CLN6 34 35
  • 91 (n)
dog
(Canis familiaris)
Mammalia CLN6 34 35
  • 89.5 (n)
mouse
(Mus musculus)
Mammalia Cln6 34 16 35
  • 87.76 (n)
rat
(Rattus norvegicus)
Mammalia Cln6 34
  • 86.89 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLN6 35
  • 83 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CLN6 35
  • 82 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia CLN6 35
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLN6 34 35
  • 76.31 (n)
lizard
(Anolis carolinensis)
Reptilia CLN6 35
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cln6 34
  • 70.43 (n)
Str.6976 34
zebrafish
(Danio rerio)
Actinopterygii cln6a 34 35
  • 67.59 (n)
cln6b 35
  • 62 (a)
OneToMany
Dr.14969 34
Species where no ortholog for CLN6 was found in the sources mined by GeneCards:
  • 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
rs112239768 other, Ceroid lipofuscinosis, neuronal, 6 (CLN6) [MIM:601780] 68,229,551(+) CGTCG(C/T)TCCCA reference, missense
rs150363441 Uncertain significance, Ceroid lipofuscinosis, neuronal, 6 (CLN6) [MIM:601780] 68,208,301(+) GAGGC(C/G/T)GTTGC reference, missense
rs154774633 Pathogenic, Ceroid lipofuscinosis, neuronal, 4A (CLN4A) [MIM:204300] 68,214,387(-) GCAGC(C/T)GGTAT reference, missense
rs154774634 Pathogenic, Ceroid lipofuscinosis, neuronal, 4A (CLN4A) [MIM:204300] 68,211,853(-) CGAGC(A/G)GTCCC reference, missense
rs154774635 Pathogenic, Ceroid lipofuscinosis, neuronal, 4A (CLN4A) [MIM:204300] 68,218,595(-) TCGAC(C/T)TCTGG reference, missense

Variation tolerance for CLN6 Gene

Residual Variation Intolerance Score: 66.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.73; 32.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLN6 Gene

Human Gene Mutation Database (HGMD)
CLN6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
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

MalaCards: The human disease database

(21) MalaCards diseases for CLN6 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
ceroid lipofuscinosis, neuronal, 6
  • neuronal ceroid lipofuscinosis 6
ceroid lipofuscinosis, neuronal, kufs type, adult onset
  • ceroid lipofuscinosis, neuronal, 4a, autosomal recessive
neuronal ceroid lipofuscinosis
  • hereditary ceroid lipofuscinosis
neuronal ceroid-lipofuscinoses
  • neuronal ceroid-lipofuscinosis, infantile
ceroid lipofuscinosis, neuronal, 2
  • neuronal ceroid lipofuscinosis 2
- elite association - COSMIC cancer census association via MalaCards
Search CLN6 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CLN6_HUMAN
  • 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.
  • 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.

Relevant External Links for CLN6

Genetic Association Database (GAD)
CLN6
Human Genome Epidemiology (HuGE) Navigator
CLN6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLN6
genes like me logo Genes that share disorders with CLN6: view

No data available for Genatlas for CLN6 Gene

Publications for CLN6 Gene

  1. 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 22 46 64
  2. 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 22 64
  3. Novel interactions of CLN5 support molecular networking between Neuronal Ceroid Lipofuscinosis proteins. (PMID: 19941651) Lyly A. … KyttAolAo A. (BMC Cell Biol. 2009) 3 4 22 64
  4. 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 22 64
  5. 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 22 64

Products for CLN6 Gene

Sources for CLN6 Gene

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