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0  structures 97  species 0  interactions 125  sequences 3  architectures

Family: CLN5 (PF15014)

Summary: Ceroid-lipofuscinosis neuronal protein 5

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This is the Wikipedia entry entitled "CLN5". More...

CLN5 Edit Wikipedia article

CLN5
Identifiers
Aliases CLN5, NCL, ceroid-lipofuscinosis, neuronal 5
External IDs MGI: 2442253 HomoloGene: 4738 GeneCards: CLN5
RNA expression pattern
PBB GE CLN5 204084 s at fs.png

PBB GE CLN5 204085 s at fs.png

PBB GE CLN5 214252 s at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_006493

NM_001033242

RefSeq (protein)

NP_006484

NP_001028414.1
NP_001028414

Location (UCSC) Chr 13: 76.99 – 77.02 Mb Chr 14: 103.07 – 103.08 Mb
PubMed search [1] [2]
Wikidata
View/Edit Human View/Edit Mouse

Ceroid-lipofuscinosis neuronal protein 5 is a protein that in humans is encoded by the CLN5 gene.[3][4][5]

The neuronal ceroid lipofuscinoses (CLN or NCL) are a group of autosomal recessive, progressive encephalopathies in children. They are characterized by psychomotor deterioration, visual failure, and the accumulation of autofluorescent lipopigment in neurons and other cell types. The main childhood forms are the infantile type (Santavuori-Haltia disease; MIM 256730), the late infantile type (Jansky-Bielschowsky disease; MIM 204500), and the juvenile type (Batten disease; MIM 204200) based on the age of onset, clinical course, neurologic and ophthalmologic findings, and ultrastructural analysis (Carpenter et al., 1977 [PubMed 193610]).[supplied by OMIM][5]

References

  1. ^ "Human PubMed Reference:". 
  2. ^ "Mouse PubMed Reference:". 
  3. ^ Savukoski M, Kestila M, Williams R, Jarvela I, Sharp J, Harris J, Santavuori P, Gardiner M, Peltonen L (Oct 1994). "Defined chromosomal assignment of CLN5 demonstrates that at least four genetic loci are involved in the pathogenesis of human ceroid lipofuscinoses". Am J Hum Genet. 55 (4): 695–701. PMC 1918303Freely accessible. PMID 7942847. 
  4. ^ Klockars T, Savukoski M, Isosomppi J, Laan M, Jarvela I, Petrukhin K, Palotie A, Peltonen L (Sep 1996). "Efficient construction of a physical map by fiber-FISH of the CLN5 region: refined assignment and long-range contig covering the critical region on 13q22". Genomics. 35 (1): 71–8. doi:10.1006/geno.1996.0324. PMID 8661106. 
  5. ^ a b "Entrez Gene: CLN5 ceroid-lipofuscinosis, neuronal 5". 

External links

Further reading



This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Ceroid-lipofuscinosis neuronal protein 5 Provide feedback

No Pfam abstract.

Literature references

  1. Savukoski M, Klockars T, Holmberg V, Santavuori P, Lander ES, Peltonen L;, Nat Genet. 1998;19:286-288.: CLN5, a novel gene encoding a putative transmembrane protein mutated in Finnish variant late infantile neuronal ceroid lipofuscinosis. PUBMED:9662406 EPMC:9662406

  2. Houweling PJ, Cavanagh JA, Palmer DN, Frugier T, Mitchell NL, Windsor PA, Raadsma HW, Tammen I;, Biochim Biophys Acta. 2006;1762:890-897.: Neuronal ceroid lipofuscinosis in Devon cattle is caused by a single base duplication (c.662dupG) in the bovine CLN5 gene. PUBMED:16935476 EPMC:16935476

  3. Frugier T, Mitchell NL, Tammen I, Houweling PJ, Arthur DG, Kay GW, van Diggelen OP, Jolly RD, Palmer DN;, Neurobiol Dis. 2008;29:306-315.: A new large animal model of CLN5 neuronal ceroid lipofuscinosis in Borderdale sheep is caused by a nucleotide substitution at a consensus splice site (c.571+1G>A) leading to excision of exon 3. PUBMED:17988881 EPMC:17988881

  4. Melville SA, Wilson CL, Chiang CS, Studdert VP, Lingaas F, Wilton AN;, Genomics. 2005;86:287-294.: A mutation in canine CLN5 causes neuronal ceroid lipofuscinosis in Border collie dogs. PUBMED:16033706 EPMC:16033706


This tab holds annotation information from the InterPro database.

InterPro entry IPR026138

This protein family consist of CLN5 and CLN5-like proteins. Defects in CLN5 are the cause of neuronal ceroid lipofuscinosis type 5 (CLN5), also known as Finnish variant late-infantile neuronal ceroid lipofuscinosis (vLINCL). Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterised by intracellular accumulation of autofluorescent liposomal material [PUBMED:9662406, PUBMED:15728307, PUBMED:16814585, PUBMED:17607606, PUBMED:19309691, PUBMED:21990111, PUBMED:16935476, PUBMED:16033706].

Gene Ontology

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Domain organisation

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Alignments

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  Seed
(10)
Full
(125)
Representative proteomes UniProt
(163)
NCBI
(317)
Meta
(1)
RP15
(28)
RP35
(47)
RP55
(83)
RP75
(110)
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Key: ✓ available, x not generated, not available.

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  Seed
(10)
Full
(125)
Representative proteomes UniProt
(163)
NCBI
(317)
Meta
(1)
RP15
(28)
RP35
(47)
RP55
(83)
RP75
(110)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(10)
Full
(125)
Representative proteomes UniProt
(163)
NCBI
(317)
Meta
(1)
RP15
(28)
RP35
(47)
RP55
(83)
RP75
(110)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Seed source: Jackhmmer:O75503
Previous IDs: none
Type: Family
Author: Eberhardt R
Number in seed: 10
Number in full: 125
Average length of the domain: 267.20 aa
Average identity of full alignment: 66 %
Average coverage of the sequence by the domain: 85.95 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 34.7 29.4
Noise cut-off 24.9 24.6
Model length: 303
Family (HMM) version: 5
Download: download the raw HMM for this family

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