Cln6 ceroid-lipofuscinosis, neuronal 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cln6provided by MGI
Official Full Name: ceroid-lipofuscinosis, neuronal 6provided by MGI
Primary source: MGI:MGI:2159324
See related: Ensembl:ENSMUSG00000032245 AllianceGenome:MGI:2159324
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: nclf; D9Bwg1455e; 1810065L06Rik
Summary: Predicted to enable lysophosphatidic acid binding activity; protein homodimerization activity; and sulfatide binding activity. Acts upstream of or within several processes, including locomotion involved in locomotory behavior; lysosome organization; and visual perception. Predicted to be located in several cellular components, including early endosome; endoplasmic reticulum lumen; and membrane raft. Predicted to be active in endoplasmic reticulum and membrane. Is expressed in several structures, including central nervous system and retina. Used to study neuronal ceroid lipofuscinosis 6. Human ortholog(s) of this gene implicated in neuronal ceroid lipofuscinosis; neuronal ceroid lipofuscinosis 4A; and neuronal ceroid lipofuscinosis 6. Orthologous to human CLN6 (CLN6 transmembrane ER protein). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in testis adult (RPKM 42.3), placenta adult (RPKM 37.5) and 26 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 B; 9 33.89 cM

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (62746067..62759288)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (62838785..62852006)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CLN6 deficiency causes selective changes in the lysosomal protein composition.
Title: CLN6 deficiency causes selective changes in the lysosomal protein composition.
An altered secretome is an early marker of the pathogenesis of CLN6 Batten disease.
Title: An altered secretome is an early marker of the pathogenesis of CLN6 Batten disease.
A CLN6-CLN8 complex recruits lysosomal enzymes at the ER for Golgi transfer.
Title: A CLN6-CLN8 complex recruits lysosomal enzymes at the ER for Golgi transfer.
Bipolar cell-specific expression of CLN6 slowed significantly the loss of photoreceptor function and photoreceptor cells. This study shows that the deficiency of a gene normally expressed in bipolar cells can cause the loss of photoreceptors and that this can be prevented by bipolar cell-directed treatment.
Title: Prevention of Photoreceptor Cell Loss in a Cln6(nclf) Mouse Model of Batten Disease Requires CLN6 Gene Transfer to Bipolar Cells.
Data indicate that ceroid-lipofuscinosis, neuronal 6 protein Cln6(nclf) mutation leads to deficits in motor coordination, vision, memory, and learning.
Title: A murine model of variant late infantile ceroid lipofuscinosis recapitulates behavioral and pathological phenotypes of human disease.
These findings implicate Cln6 in the survival and maturation of specific neuronal populations during development and make it possible to compare regional Cln6 expression with the distribution of subsequent pathology.
Title: High expression of disease-related Cln6 in the cerebral cortex, purkinje cells, dentate gyrus, and hippocampal ca1 neurons.
Data show a progressive breakdown of axons and synapses in the brains of two different models of NCL: Ppt1(-/-) model of infantile NCL and Cln6(nclf) model of variant late-infantile NCL.
Title: Molecular correlates of axonal and synaptic pathology in mouse models of Batten disease.
We concluded that alterations in neurite maturation resulting from a loss of CLN6-CRMP-2 interaction may contribute to neuronal dysfunction and pathology in vLINCL.
Title: Protein product of CLN6 gene responsible for variant late-onset infantile neuronal ceroid lipofuscinosis interacts with CRMP-2.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)
Spontaneous (1) 1 citation
Targeted (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW743417 (e-PCR)
- UniSTS:208391

AW822070 (e-PCR)
- UniSTS:208392

NoName (e-PCR)
- UniSTS:492552

RH125063 (e-PCR)
- UniSTS:161885

D9Bwg1455e (e-PCR), detects polymorphism
- UniSTS:142743

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables lysophosphatidic acid binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables sulfatide binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cholesterol metabolic process	ISO Inferred from Sequence Orthology more info
involved_in cholesterol metabolic process	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in ganglioside metabolic process	ISO Inferred from Sequence Orthology more info
involved_in ganglioside metabolic process	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in glycosaminoglycan metabolic process	ISO Inferred from Sequence Orthology more info
involved_in glycosaminoglycan metabolic process	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within locomotion involved in locomotory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lysosomal lumen acidification	ISO Inferred from Sequence Orthology more info
involved_in lysosomal lumen acidification	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in lysosome organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within lysosome organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within macromolecule catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of proteolysis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of proteolysis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within visual perception	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in early endosome	ISO Inferred from Sequence Orthology more info
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in endoplasmic reticulum lumen	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum lumen	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane raft	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: ceroid-lipofuscinosis neuronal protein 6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.