Human Gene CLN5 (ENST00000377453.9_9) from GENCODE V47lift37
  Description: CLN5 intracellular trafficking protein, transcript variant 1 (from RefSeq NM_006493.4)
Gencode Transcript: ENST00000377453.9_9
Gencode Gene: ENSG00000102805.16_14
Transcript (Including UTRs)
   Position: hg19 chr13:77,566,216-77,579,252 Size: 13,037 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr13:77,566,234-77,575,104 Size: 8,871 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:77,566,216-77,579,252)mRNA (may differ from genome)Protein (358 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CLN5_HUMAN
DESCRIPTION: RecName: Full=Ceroid-lipofuscinosis neuronal protein 5; Short=Protein CLN5; Flags: Precursor;
INTERACTION: P05787:KRT8; NbExp=1; IntAct=EBI-1043514, EBI-297852;
SUBCELLULAR LOCATION: Lysosome.
TISSUE SPECIFICITY: Ubiquitous.
PTM: Glycosylated.
DISEASE: Defects in CLN5 are the cause of neuronal ceroid lipofuscinosis type 5 (CLN5) [MIM:256731]; also known as Finnish variant late-infantile neuronal ceroid lipofuscinosis (vLINCL). 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 5 comprise mixed combinations of granular, curvilinear, and fingerprint profiles.
SIMILARITY: Belongs to the CLN5 family.
SEQUENCE CAUTION: Sequence=AAC27614.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
WEB RESOURCE: Name=NCL CLN5; Note=Neural Ceroid Lipofuscinoses mutation db; URL="http://www.ucl.ac.uk/ncl/cln5.shtml";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CLN5";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CLN5
Diseases sorted by gene-association score: ceroid lipofuscinosis, neuronal, 5* (1704), neuronal ceroid-lipofuscinoses* (153), ceroid lipofuscinosis, neuronal, 2 (30), neuronal ceroid lipofuscinosis (15), peripheral retinal degeneration (13), ceroid lipofuscinosis, neuronal, 3 (13), ceroid lipofuscinosis, neuronal, 1 (11), ceroid lipofuscinosis, neuronal, 10 (10), ceroid lipofuscinosis, neuronal, 8, northern epilepsy variant (10), ceroid lipofuscinosis, neuronal, 9 (10), ceroid lipofuscinosis, neuronal, 7 (9), ceroid lipofuscinosis, neuronal, 11 (7), visual epilepsy (3), lipid storage disease (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.88 RPKM in Thyroid
Total median expression: 177.00 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -2.3018-0.128 Picture PostScript Text
3' UTR -1110.904148-0.268 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR026138 - CLN5

Pfam Domains:
PF15014 - Ceroid-lipofuscinosis neuronal protein 5

ModBase Predicted Comparative 3D Structure on O75503
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0005537 mannose binding

Biological Process:
GO:0006465 signal peptide processing
GO:0007042 lysosomal lumen acidification
GO:0007420 brain development
GO:0022008 neurogenesis
GO:0030163 protein catabolic process
GO:0042147 retrograde transport, endosome to Golgi
GO:0042551 neuron maturation
GO:0070085 glycosylation
GO:1904426 positive regulation of GTP binding

Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AF068227 - Homo sapiens putative transmembrane protein (CLN5) mRNA, complete cds.
LF210193 - JP 2014500723-A/17696: Polycomb-Associated Non-Coding RNAs.
AB528107 - Synthetic construct DNA, clone: pF1KE0566, Homo sapiens CLN5 gene for ceroid-lipofuscinosis, neuronal 5, without stop codon, in Flexi system.
BC146274 - Synthetic construct Homo sapiens clone IMAGE:100015168, MGC:180232 ceroid-lipofuscinosis, neuronal 5 (CLN5) mRNA, encodes complete protein.
BC153154 - Synthetic construct Homo sapiens clone IMAGE:100016512, MGC:184226 ceroid-lipofuscinosis, neuronal 5 (CLN5) mRNA, encodes complete protein.
AK304001 - Homo sapiens cDNA FLJ54235 complete cds, highly similar to Ceroid-lipofuscinosis neuronal protein 5.
AK075109 - Homo sapiens cDNA FLJ90628 fis, clone PLACE1003407, highly similar to Ceroid-lipofuscinosis neuronal protein 5.
LF335513 - JP 2014500723-A/143016: Polycomb-Associated Non-Coding RNAs.
LF335514 - JP 2014500723-A/143017: Polycomb-Associated Non-Coding RNAs.
LF335516 - JP 2014500723-A/143019: Polycomb-Associated Non-Coding RNAs.
LF335517 - JP 2014500723-A/143020: Polycomb-Associated Non-Coding RNAs.
LF335518 - JP 2014500723-A/143021: Polycomb-Associated Non-Coding RNAs.
LF335519 - JP 2014500723-A/143022: Polycomb-Associated Non-Coding RNAs.
LF335520 - JP 2014500723-A/143023: Polycomb-Associated Non-Coding RNAs.
JD091224 - Sequence 72248 from Patent EP1572962.
JD261529 - Sequence 242553 from Patent EP1572962.
JD329964 - Sequence 310988 from Patent EP1572962.
LF335521 - JP 2014500723-A/143024: Polycomb-Associated Non-Coding RNAs.
JD312844 - Sequence 293868 from Patent EP1572962.
JD094333 - Sequence 75357 from Patent EP1572962.
LF335522 - JP 2014500723-A/143025: Polycomb-Associated Non-Coding RNAs.
JD237666 - Sequence 218690 from Patent EP1572962.
JD111806 - Sequence 92830 from Patent EP1572962.
JD235624 - Sequence 216648 from Patent EP1572962.
JD289791 - Sequence 270815 from Patent EP1572962.
JD233271 - Sequence 214295 from Patent EP1572962.
JD439252 - Sequence 420276 from Patent EP1572962.
JD269276 - Sequence 250300 from Patent EP1572962.
JD303345 - Sequence 284369 from Patent EP1572962.
JD451219 - Sequence 432243 from Patent EP1572962.
JD376139 - Sequence 357163 from Patent EP1572962.
JD454132 - Sequence 435156 from Patent EP1572962.
JD498027 - Sequence 479051 from Patent EP1572962.
JD286708 - Sequence 267732 from Patent EP1572962.
JD511542 - Sequence 492566 from Patent EP1572962.
JD251013 - Sequence 232037 from Patent EP1572962.
JD380507 - Sequence 361531 from Patent EP1572962.
JD319519 - Sequence 300543 from Patent EP1572962.
JD431527 - Sequence 412551 from Patent EP1572962.
JD532687 - Sequence 513711 from Patent EP1572962.
JD531720 - Sequence 512744 from Patent EP1572962.
JD138362 - Sequence 119386 from Patent EP1572962.
JD176192 - Sequence 157216 from Patent EP1572962.
JD138361 - Sequence 119385 from Patent EP1572962.
JD176191 - Sequence 157215 from Patent EP1572962.
JD176190 - Sequence 157214 from Patent EP1572962.
MA445770 - JP 2018138019-A/17696: Polycomb-Associated Non-Coding RNAs.
MA571090 - JP 2018138019-A/143016: Polycomb-Associated Non-Coding RNAs.
MA571091 - JP 2018138019-A/143017: Polycomb-Associated Non-Coding RNAs.
MA571093 - JP 2018138019-A/143019: Polycomb-Associated Non-Coding RNAs.
MA571094 - JP 2018138019-A/143020: Polycomb-Associated Non-Coding RNAs.
MA571095 - JP 2018138019-A/143021: Polycomb-Associated Non-Coding RNAs.
MA571096 - JP 2018138019-A/143022: Polycomb-Associated Non-Coding RNAs.
MA571097 - JP 2018138019-A/143023: Polycomb-Associated Non-Coding RNAs.
MA571098 - JP 2018138019-A/143024: Polycomb-Associated Non-Coding RNAs.
MA571099 - JP 2018138019-A/143025: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KQK7, CLN5_HUMAN, ENST00000377453.1, ENST00000377453.2, ENST00000377453.3, ENST00000377453.4, ENST00000377453.5, ENST00000377453.6, ENST00000377453.7, ENST00000377453.8, NM_006493, O75503, uc318npx.1, uc318npx.2
UCSC ID: ENST00000377453.9_9
RefSeq Accession: NM_006493.4
Protein: O75503 (aka CLN5_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CLN5:
ataxias (Hereditary Ataxia Overview)
dystonia-ov (Hereditary Dystonia Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.