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Aliases for CLN6 Gene

Aliases for CLN6 Gene

  • CLN6, Transmembrane ER Protein 2 3 5
  • Ceroid-Lipofuscinosis, Neuronal 6, Late Infantile, Variant 2
  • Ceroid-Lipofuscinosis, Neuronal 6, Late Infantile 3
  • 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 (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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for CLN6 Gene

Promoters and enhancers for CLN6 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15I068227 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 563.9 +28.0 27968 3.6 HDGF PKNOX1 CLOCK SMAD1 MLX ARNT ARID4B SIN3A ZBTB7B ZNF766 CLN6 ENSG00000260007 PIAS1 FEM1B RNU6-1 LOC101929076 SKOR1 IQCH-AS1 CALML4
GH15I068256 Promoter/Enhancer 1.6 Ensembl ENCODE dbSUPER 557 +0.2 153 1.6 ELF3 FOXA2 ARID4B SIN3A ZNF48 RAD21 YY1 THAP11 ZNF202 RXRA CLN6 FEM1B IQCH-AS1 HMGN2P40
GH15I068258 Enhancer 0.5 Ensembl dbSUPER 550.8 -1.7 -1690 0.2 ZNF449 CLN6 GC15P069504
GH15I068203 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 13.4 +51.5 51510 4.2 HDAC1 ATF1 ARNT ARID4B ZBTB40 RAD21 YY1 SCRT2 ETV6 CREM CALML4 CLN6 LOC105370871 ENSG00000260007
GH15I068208 Enhancer 0.9 Ensembl ENCODE 13.3 +47.1 47081 2.9 CTCF KLF17 EBF1 ZIC2 RAD21 ZFHX2 GLIS2 POLR2A EGR1 PATZ1 CLN6 CALML4 ENSG00000260007
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CLN6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLN6 gene promoter:

Genomic Locations for CLN6 Gene

Genomic Locations for CLN6 Gene
50,220 bases
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:
    Recommended name:
    Ceroid-lipofuscinosis neuronal protein 6
    Protein Accession:
    Secondary Accessions:
    • A8K560
    • B4DDH6
    • Q6IAB1
    • Q96SR0

    Protein attributes for CLN6 Gene

    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


neXtProt entry for CLN6 Gene

Post-translational modifications for CLN6 Gene

No Post-translational modifications

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


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 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

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CLN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA,IDA 15265688
GO:0005788 endoplasmic reticulum lumen IDA 15010453
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane HDA,IEA 19946888
GO:0016021 integral component of membrane NAS,IEA 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

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: - - - - - - - - -

Relevant External Links for CLN6 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

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:


SOURCE GeneReport for Unigene cluster for CLN6 Gene:


Evidence on tissue expression from TISSUES for CLN6 Gene

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

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

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • 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
(Bos Taurus)
Mammalia CLN6 33 34
  • 91 (n)
(Canis familiaris)
Mammalia CLN6 33 34
  • 89.5 (n)
(Mus musculus)
Mammalia Cln6 33 16 34
  • 87.76 (n)
(Rattus norvegicus)
Mammalia Cln6 33
  • 86.89 (n)
(Ornithorhynchus anatinus)
Mammalia CLN6 34
  • 83 (a)
(Monodelphis domestica)
Mammalia CLN6 34
  • 82 (a)
(Pan troglodytes)
Mammalia CLN6 34
  • 82 (a)
(Gallus gallus)
Aves CLN6 33 34
  • 76.31 (n)
(Anolis carolinensis)
Reptilia CLN6 34
  • 82 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cln6 33
  • 70.43 (n)
Str.6976 33
(Danio rerio)
Actinopterygii cln6a 33 34
  • 67.59 (n)
cln6b 34
  • 62 (a)
Dr.14969 33
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

Gene Tree for CLN6 (if available)
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 Variation AA Info Type
rs1022134304 uncertain-significance, Neuronal Ceroid-Lipofuscinosis, Recessive 68,207,608(-) A/T 3_prime_UTR_variant
rs1043527424 uncertain-significance, Neuronal Ceroid-Lipofuscinosis, Recessive 68,208,008(-) G/A 3_prime_UTR_variant
rs104894483 pathogenic, likely-benign, benign, Ceroid lipofuscinosis neuronal 6, not provided, not specified, Neuronal ceroid lipofuscinosis 68,214,373(-) C/A/G/T coding_sequence_variant, missense_variant, stop_gained
rs104894484 pathogenic, Ceroid lipofuscinosis neuronal 6, Ceroid lipofuscinosis, neuronal, 6 (CLN6) [MIM:601780] 68,211,793(-) C/T coding_sequence_variant, missense_variant
rs104894486 pathogenic, Ceroid lipofuscinosis neuronal 6 68,209,639(-) G/C coding_sequence_variant, stop_gained

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

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

Disorder Aliases PubMed IDs
ceroid lipofuscinosis, neuronal, 6
  • ceroid lipofuscinosis, neuronal, 5
ceroid lipofuscinosis, neuronal, 4a, autosomal recessive
  • cln4a
adult neuronal ceroid lipofuscinosis
  • adult ncl
cln4 disease
  • cln4b
ceroid storage disease
  • lipofuscin storage disease
- elite association - COSMIC cancer census association via MalaCards
Search CLN6 in MalaCards View complete list of genes associated with diseases


  • 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.

Additional Disease Information for CLN6

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 22 44 58
  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 22 58
  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 22 58
  4. 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 22 58
  5. Novel mutations in the CLN6 gene causing a variant late infantile neuronal ceroid lipofuscinosis. (PMID: 12673792) Teixeira CA … Boustany RM (Human mutation 2003) 3 4 22 58

Products for CLN6 Gene

Sources for CLN6 Gene

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