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... See more...

Aliases for CLN6 Gene

Aliases for CLN6 Gene

  • CLN6 Transmembrane ER Protein 2 3 5
  • Ceroid-Lipofuscinosis Neuronal Protein 6 3 4
  • HsT18960 2 3
  • Nclf 2 3
  • Ceroid-Lipofuscinosis, Neuronal 6, Late Infantile, Variant 2
  • Ceroid-Lipofuscinosis, Neuronal 6, Late Infantile 3
  • Ceroid-Lipofuscinosis Neuronal 6 Late Infantile 3
  • CLN6, Transmembrane ER Protein 2
  • Protein CLN6 4
  • FLJ20561 2
  • CLN4A 3
  • CLN6 5

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 (CLN6 Transmembrane ER Protein) is a Protein Coding gene. Diseases associated with CLN6 include Ceroid Lipofuscinosis, Neuronal, 6 and Ceroid Lipofuscinosis, Neuronal, 4A, Autosomal Recessive. Gene Ontology (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 Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLN6 Gene

Genomics for CLN6 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLN6 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
GH15J068227 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 613.9 +28.0 27968 3.6 CREB1 PRDM10 ZNF629 TFE3 ZNF692 BACH1 FOS TARDBP LARP7 MTA2 CLN6 ENSG00000260007 FEM1B RNU6-1 LOC101929076 SKOR1 piR-55985-056 CALML4 lnc-CLN6-3
GH15J068256 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas dbSUPER 606.9 +0.1 89 1.8 CEBPG GATAD2A IRF2 SP1 POLR2A EZH2 GTF2F1 CEBPA SOX13 CEBPB CLN6 lnc-CLN6-3 piR-55985-057 FEM1B IQCH-AS1 ENSG00000260007
GH15J068260 Promoter/Enhancer 0.5 Ensembl dbSUPER 606.2 -1.2 -1190 0.4 CLN6 lnc-CLN6-3 ENSG00000260657 piR-42491-070 FEM1B
GH15J068209 Promoter 0.3 EPDnew 600.3 +49.1 49097 0.1 CLN6 CALML4 piR-41126-005 ENSG00000260007
GH15J068203 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 13.4 +51.5 51510 4.2 TEAD4 LEF1 IKZF1 POLR2A JUND ETV6 SP1 HDAC1 SOX6 EP300 CALML4 CLN6 HSALNG0106791 ENSG00000260007 PIAS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLN6 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLN6

Top Transcription factor binding sites by QIAGEN in the CLN6 gene promoter:
  • AREB6
  • c-Myc
  • E47
  • Egr-1
  • Egr-3
  • GATA-3
  • Lmo2
  • Max1
  • RORalpha2
  • RP58

Genomic Locations for CLN6 Gene

Genomic Locations for CLN6 Gene
chr15:68,206,992-68,257,211
(GRCh38/hg38)
Size:
50,220 bases
Orientation:
Minus strand
chr15:68,499,330-68,549,549
(GRCh37/hg19)
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). Interacts with CLN3 (PubMed:17237713).

    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

Gene Families for CLN6 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CLN6 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CLN6 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57025, highly similar to Ceroid-lipofuscinosis neuronal protein 6 (B4DDH6_HUMAN)
  • Ceroid-lipofuscinosis neuronal protein 6 (CLN6_HUMAN)
genes like me logo Genes that share domains with CLN6: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CLN6 Gene

Function for CLN6 Gene

Phenotypes From GWAS Catalog for CLN6 Gene

Gene Ontology (GO) - Molecular Function for CLN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17237713
GO:0035727 lysophosphatidic acid binding IDA 18317235
GO:0042803 protein homodimerization activity IDA 15010453
GO:0120146 sulfatide binding IDA 18317235
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 Cln6<tm1b(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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
endosome 5
nucleus 4
plasma membrane 3
mitochondrion 2
lysosome 2
extracellular 1
cytoskeleton 1
cytosol 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (3)
  • Nucleoli (1)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005730 nucleolus IDA --
GO:0005769 early endosome IDA 17237713
GO:0005783 endoplasmic reticulum IDA 15265688
GO:0005788 endoplasmic reticulum lumen IDA 15010453
genes like me logo Genes that share ontologies with CLN6: view

Pathways & Interactions for CLN6 Gene

PathCards logo

SuperPathways for CLN6 Gene

No Data Available

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 IBA 21873635
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

mRNA/cDNA for CLN6 Gene

1 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
25 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 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

Expression for CLN6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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)
  • Nervous system(2.8)
  • Eye(2.2)
  • Skin(2)

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

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
Regions:
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

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 30 31
  • 91 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CLN6 30 31
  • 89.5 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Cln6 30 17 31
  • 87.76 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Cln6 30
  • 86.89 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia CLN6 31
  • 83 (a)
OneToOne
Chimpanzee
(Pan troglodytes)
Mammalia CLN6 31
  • 82 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CLN6 31
  • 82 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CLN6 30 31
  • 76.31 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CLN6 31
  • 82 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia cln6 30
  • 70.43 (n)
Str.6976 30
Zebrafish
(Danio rerio)
Actinopterygii cln6a 30 31
  • 67.59 (n)
OneToMany
cln6b 31
  • 62 (a)
OneToMany
Dr.14969 30
Species where no ortholog for CLN6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 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)
  • Worm (Caenorhabditis elegans)

Evolution for CLN6 Gene

ENSEMBL:
Gene Tree for CLN6 (if available)
TreeFam:
Gene Tree for CLN6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLN6: view image

Paralogs for CLN6 Gene

No data available for Paralogs for CLN6 Gene

Variants for CLN6 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLN6 Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
640764 Uncertain Significance: Neuronal ceroid lipofuscinosis 68,211,830(-) A/G MISSENSE_VARIANT
656898 Uncertain Significance: Neuronal ceroid lipofuscinosis 68,211,755(-) G/A MISSENSE_VARIANT
658242 Uncertain Significance: Neuronal ceroid lipofuscinosis 68,214,363(-) G/A MISSENSE_VARIANT
658763 Uncertain Significance: Neuronal ceroid lipofuscinosis 68,209,743(-) G/A MISSENSE_VARIANT
661634 Uncertain Significance: Neuronal ceroid lipofuscinosis 68,211,311(-) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for CLN6 Gene

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)

Additional Variant Information for CLN6 Gene

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

SNP Genotyping and Copy Number Assay Products

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

(38) MalaCards diseases for CLN6 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- 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, 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.

Additional Disease Information for CLN6

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 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 AE (Brain : a journal of neurology 2009) 3 4 23 41
  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 RB … Mole SE (American journal of human genetics 2002) 2 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. Neuronal ceroid lipofuscinosis: a common pathway? (PMID: 17237713) Persaud-Sawin DA … Boustany RM (Pediatric research 2007) 3 4 23
  5. CLN6, which is associated with a lysosomal storage disease, is an endoplasmic reticulum protein. (PMID: 15265688) Mole SE … Cutler DF (Experimental cell research 2004) 3 4 23

Products for CLN6 Gene

Sources for CLN6 Gene