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Protein

Ceroid-lipofuscinosis neuronal protein 5

Gene

CLN5

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Plays a role in influencing the retrograde trafficking of lysosomal sorting receptors SORT1 and IGF2R from the endosomes to the trans-Golgi network by controlling the recruitment of retromer complex to the endosomal membrane. Regulates the localization and activation of RAB7A which is required to recruit the retromer complex to the endosomal membrane (PubMed:22431521).1 Publication

GO - Molecular functioni

  • mannose binding Source: UniProtKB

GO - Biological processi

  • brain development Source: UniProtKB
  • glycosylation Source: UniProtKB
  • lysosomal lumen acidification Source: UniProtKB
  • neurogenesis Source: UniProtKB
  • neuron maturation Source: UniProtKB
  • positive regulation of GTP binding Source: UniProtKB
  • protein catabolic process Source: UniProtKB
  • retrograde transport, endosome to Golgi Source: UniProtKB
  • signal peptide processing Source: UniProtKB

Names & Taxonomyi

Protein namesi
Recommended name:
Ceroid-lipofuscinosis neuronal protein 5
Short name:
Protein CLN5
Cleaved into the following chain:
Gene namesi
Name:CLN5
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 13

Organism-specific databases

EuPathDBiHostDB:ENSG00000102805.13
HGNCiHGNC:2076 CLN5
MIMi608102 gene
neXtProtiNX_O75503

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 23Cytoplasmic1 PublicationAdd BLAST23
Transmembranei24 – 41Helical; Signal-anchor for type II membrane proteinSequence analysisAdd BLAST18
Topological domaini42 – 358Lumenal1 PublicationAdd BLAST317

Keywords - Cellular componenti

Lysosome, Membrane

Pathology & Biotechi

Involvement in diseasei

Ceroid lipofuscinosis, neuronal, 5 (CLN5)10 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:256731
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04270063R → H in CLN5; retained in the endoplasmic reticulum rather than reaching the lysosome. 3 PublicationsCorresponds to variant dbSNP:rs104894386Ensembl.1
Natural variantiVAR_04270263R → P in CLN5; Retained in the endoplasmic reticulum rather than reaching the lysosome. 2 PublicationsCorresponds to variant dbSNP:rs104894386Ensembl.1
Natural variantiVAR_06689677C → Y in CLN5. 1 PublicationCorresponds to variant dbSNP:rs267606738Ensembl.1
Natural variantiVAR_066897143N → S in CLN5; loss of glycosylation; effectively transported to the lysosome. 2 PublicationsCorresponds to variant dbSNP:rs386833975Ensembl.1
Natural variantiVAR_066898149L → P in CLN5. 1 PublicationCorresponds to variant dbSNP:rs386833976Ensembl.1
Natural variantiVAR_066899156P → S in CLN5. 1 PublicationCorresponds to variant dbSNP:rs386833977Ensembl.1
Natural variantiVAR_066900158W → R in CLN5. 1 PublicationCorresponds to variant dbSNP:rs147065248Ensembl.1
Natural variantiVAR_066901158W → S in CLN5. 1 PublicationCorresponds to variant dbSNP:rs386833978Ensembl.1
Natural variantiVAR_042701209Y → D in CLN5. 2 PublicationsCorresponds to variant dbSNP:rs386833981Ensembl.1
Natural variantiVAR_005137230D → N in CLN5; creates a new N-glycosylation site; retained in the endoplasmic reticulum rather than reaching the lysosome. 6 PublicationsCorresponds to variant dbSNP:rs28940280Ensembl.1
Natural variantiVAR_066903325Y → C in CLN5. 1 PublicationCorresponds to variant dbSNP:rs148862100Ensembl.1
Natural variantiVAR_059032330W → C in CLN5; retained in the endoplasmic reticulum rather than reaching the lysosome. 1 PublicationCorresponds to variant dbSNP:rs386833968Ensembl.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi130N → Q: Loss of glycosylation. Retained in the endoplasmic reticulum rather than reaching the lysosome. 1 Publication1
Mutagenesisi143N → Q: Loss of glycosylation. Effectively transported to the lysosome. 1 Publication1
Mutagenesisi178N → Q: Loss of glycosylation. Effectively transported to the lysosome. 1 Publication1
Mutagenesisi203N → Q: Loss of glycosylation. Retained in the endoplasmic reticulum rather than reaching the lysosome. 1 Publication1
Mutagenesisi255N → Q: Loss of glycosylation. Retained in the endoplasmic reticulum rather than reaching the lysosome. 1 Publication1
Mutagenesisi271N → Q: Loss of glycosylation. Retained in the endoplasmic reticulum rather than reaching the lysosome. 1 Publication1
Mutagenesisi281N → Q: Loss of glycosylation. Partially retained in the endoplasmic reticulum. 1 Publication1
Mutagenesisi352N → Q: Loss of glycosylation. Retained in the Golgi apparatus rather than reaching the lysosome. 1 Publication1

Keywords - Diseasei

Disease mutation, Epilepsy, Neurodegeneration, Neuronal ceroid lipofuscinosis

Organism-specific databases

DisGeNETi1203
GeneReviewsiCLN5
MalaCardsiCLN5
MIMi256731 phenotype
OpenTargetsiENSG00000102805
Orphaneti228360 CLN5 disease
PharmGKBiPA26603

Polymorphism and mutation databases

BioMutaiCLN5

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_0000438009? – 358Ceroid-lipofuscinosis neuronal protein 5, secreted form
ChainiPRO_00000898601 – 358Ceroid-lipofuscinosis neuronal protein 5Add BLAST358

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi130N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi143N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi178N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi203N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi255N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi271N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi281N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi352N-linked (GlcNAc...) asparagine1 Publication1

Post-translational modificationi

N-glycosylated with both high mannose and complex type sugars. Glycosylation is important for proper folding and trafficking to the lysosomes.4 Publications
Ceroid-lipofuscinosis neuronal protein 5: The type II membrane signal anchor is proteolytically cleaved to produce a mature form that is transported to the lysosomes (Ceroid-lipofuscinosis neuronal protein 5, secreted form) (PubMed:24038957, PubMed:20052765).2 Publications
Can undergo proteolytic cleavage at the C-terminus, probably by a cysteine protease and may involve the removal of approximately 10-15 residues from the C-terminal end (PubMed:26342652).1 Publication

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiO75503
MaxQBiO75503
PaxDbiO75503
PeptideAtlasiO75503
PRIDEiO75503
ProteomicsDBi50054

PTM databases

GlyConnecti1108
iPTMnetiO75503
PhosphoSitePlusiO75503

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiENSG00000102805 Expressed in 228 organ(s), highest expression level in left lobe of thyroid gland
CleanExiHS_CLN5
ExpressionAtlasiO75503 baseline and differential
GenevisibleiO75503 HS

Organism-specific databases

HPAiHPA041788

Interactioni

Subunit structurei

Interacts with SORT1, RAB5A and RAB7A (PubMed:22431521). Interacts with PPT1, TPP1, CLN3, CLN6, CLN8, ATP5F1A and ATP5F1B (By similarity).By similarity1 Publication

Protein-protein interaction databases

BioGridi107614, 44 interactors
IntActiO75503, 3 interactors
MINTiO75503
STRINGi9606.ENSP00000366673

Structurei

3D structure databases

SMRiO75503
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni304 – 343Membrane-anchoring1 PublicationAdd BLAST40

Sequence similaritiesi

Belongs to the CLN5 family.Curated

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IJEH Eukaryota
ENOG4110RH0 LUCA
GeneTreeiENSGT00390000010065
HOGENOMiHOG000060233
HOVERGENiHBG005345
InParanoidiO75503
KOiK12390
PhylomeDBiO75503
TreeFamiTF330864

Family and domain databases

InterProiView protein in InterPro
IPR026138 CLN5
PANTHERiPTHR15380 PTHR15380, 1 hit
PfamiView protein in Pfam
PF15014 CLN5, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry has 1 described isoform and 12 potential isoforms that are computationally mapped.Show allAlign All

O75503-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAQEVDTAQG AEMRRGAGAA RGRASWCWAL ALLWLAVVPG WSRVSGIPSR
60 70 80 90 100
RHWPVPYKRF DFRPKPDPYC QAKYTFCPTG SPIPVMEGDD DIEVFRLQAP
110 120 130 140 150
VWEFKYGDLL GHLKIMHDAI GFRSTLTGKN YTMEWYELFQ LGNCTFPHLR
160 170 180 190 200
PEMDAPFWCN QGAACFFEGI DDVHWKENGT LVQVATISGN MFNQMAKWVK
210 220 230 240 250
QDNETGIYYE TWNVKASPEK GAETWFDSYD CSKFVLRTFN KLAEFGAEFK
260 270 280 290 300
NIETNYTRIF LYSGEPTYLG NETSVFGPTG NKTLGLAIKR FYYPFKPHLP
310 320 330 340 350
TKEFLLSLLQ IFDAVIVHKQ FYLFYNFEYW FLPMKFPFIK ITYEEIPLPI

RNKTLSGL
Length:358
Mass (Da):41,497
Last modified:April 29, 2008 - v2
Checksum:i07E49D4913685190
GO

Computationally mapped potential isoform sequencesi

There are 12 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A1B0GVL0A0A1B0GVL0_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN5
125Annotation score:
A0A0A0MRU5A0A0A0MRU5_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN5
358Annotation score:
A0A1B0GTV7A0A1B0GTV7_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN5
249Annotation score:
A0A024R644A0A024R644_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN5 hCG_28176
407Annotation score:
A0A087WZY0A0A087WZY0_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN5
205Annotation score:
A0A1C7CYZ2A0A1C7CYZ2_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN5
210Annotation score:
A0A1B0GUE8A0A1B0GUE8_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN5
271Annotation score:
A0A1B0GWI2A0A1B0GWI2_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN5
304Annotation score:
A0A1B0GV94A0A1B0GV94_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN5
277Annotation score:
A0A1B0GTR6A0A1B0GTR6_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN5
216Annotation score:
There are more potential isoformsShow all

Sequence cautioni

The sequence AAC27614 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti57Y → C in BAG52069 (PubMed:14702039).Curated1
Sequence conflicti92I → T in BAG52069 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06689526W → R1 PublicationCorresponds to variant dbSNP:rs199727787Ensembl.1
Natural variantiVAR_04270063R → H in CLN5; retained in the endoplasmic reticulum rather than reaching the lysosome. 3 PublicationsCorresponds to variant dbSNP:rs104894386Ensembl.1
Natural variantiVAR_04270263R → P in CLN5; Retained in the endoplasmic reticulum rather than reaching the lysosome. 2 PublicationsCorresponds to variant dbSNP:rs104894386Ensembl.1
Natural variantiVAR_06689677C → Y in CLN5. 1 PublicationCorresponds to variant dbSNP:rs267606738Ensembl.1
Natural variantiVAR_066897143N → S in CLN5; loss of glycosylation; effectively transported to the lysosome. 2 PublicationsCorresponds to variant dbSNP:rs386833975Ensembl.1
Natural variantiVAR_066898149L → P in CLN5. 1 PublicationCorresponds to variant dbSNP:rs386833976Ensembl.1
Natural variantiVAR_066899156P → S in CLN5. 1 PublicationCorresponds to variant dbSNP:rs386833977Ensembl.1
Natural variantiVAR_066900158W → R in CLN5. 1 PublicationCorresponds to variant dbSNP:rs147065248Ensembl.1
Natural variantiVAR_066901158W → S in CLN5. 1 PublicationCorresponds to variant dbSNP:rs386833978Ensembl.1
Natural variantiVAR_066902193N → K1 PublicationCorresponds to variant dbSNP:rs138611001Ensembl.1
Natural variantiVAR_042701209Y → D in CLN5. 2 PublicationsCorresponds to variant dbSNP:rs386833981Ensembl.1
Natural variantiVAR_059031219E → A. Corresponds to variant dbSNP:rs11842935Ensembl.1
Natural variantiVAR_005137230D → N in CLN5; creates a new N-glycosylation site; retained in the endoplasmic reticulum rather than reaching the lysosome. 6 PublicationsCorresponds to variant dbSNP:rs28940280Ensembl.1
Natural variantiVAR_005138319K → R1 PublicationCorresponds to variant dbSNP:rs1800209Ensembl.1
Natural variantiVAR_066903325Y → C in CLN5. 1 PublicationCorresponds to variant dbSNP:rs148862100Ensembl.1
Natural variantiVAR_059032330W → C in CLN5; retained in the endoplasmic reticulum rather than reaching the lysosome. 1 PublicationCorresponds to variant dbSNP:rs386833968Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF068227 mRNA Translation: AAC27614.1 Different initiation.
AK075109 mRNA Translation: BAG52069.1
AC001226 Genomic DNA No translation available.
RefSeqiNP_006484.1, NM_006493.2
UniGeneiHs.30213

Genome annotation databases

EnsembliENST00000377453; ENSP00000366673; ENSG00000102805
GeneIDi1203
KEGGihsa:1203
UCSCiuc058xoc.1 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Web resourcesi

NCL CLN5

Neural Ceroid Lipofuscinoses mutation db

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF068227 mRNA Translation: AAC27614.1 Different initiation.
AK075109 mRNA Translation: BAG52069.1
AC001226 Genomic DNA No translation available.
RefSeqiNP_006484.1, NM_006493.2
UniGeneiHs.30213

3D structure databases

SMRiO75503
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi107614, 44 interactors
IntActiO75503, 3 interactors
MINTiO75503
STRINGi9606.ENSP00000366673

PTM databases

GlyConnecti1108
iPTMnetiO75503
PhosphoSitePlusiO75503

Polymorphism and mutation databases

BioMutaiCLN5

Proteomic databases

EPDiO75503
MaxQBiO75503
PaxDbiO75503
PeptideAtlasiO75503
PRIDEiO75503
ProteomicsDBi50054

Protocols and materials databases

DNASUi1203
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000377453; ENSP00000366673; ENSG00000102805
GeneIDi1203
KEGGihsa:1203
UCSCiuc058xoc.1 human

Organism-specific databases

CTDi1203
DisGeNETi1203
EuPathDBiHostDB:ENSG00000102805.13
GeneCardsiCLN5
GeneReviewsiCLN5
HGNCiHGNC:2076 CLN5
HPAiHPA041788
MalaCardsiCLN5
MIMi256731 phenotype
608102 gene
neXtProtiNX_O75503
OpenTargetsiENSG00000102805
Orphaneti228360 CLN5 disease
PharmGKBiPA26603
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IJEH Eukaryota
ENOG4110RH0 LUCA
GeneTreeiENSGT00390000010065
HOGENOMiHOG000060233
HOVERGENiHBG005345
InParanoidiO75503
KOiK12390
PhylomeDBiO75503
TreeFamiTF330864

Miscellaneous databases

ChiTaRSiCLN5 human
GeneWikiiCLN5
GenomeRNAii1203
PROiPR:O75503
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000102805 Expressed in 228 organ(s), highest expression level in left lobe of thyroid gland
CleanExiHS_CLN5
ExpressionAtlasiO75503 baseline and differential
GenevisibleiO75503 HS

Family and domain databases

InterProiView protein in InterPro
IPR026138 CLN5
PANTHERiPTHR15380 PTHR15380, 1 hit
PfamiView protein in Pfam
PF15014 CLN5, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiCLN5_HUMAN
AccessioniPrimary (citable) accession number: O75503
Secondary accession number(s): B3KQK7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: April 29, 2008
Last modified: October 10, 2018
This is version 154 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  2. SIMILARITY comments
    Index of protein domains and families
  3. Human chromosome 13
    Human chromosome 13: entries, gene names and cross-references to MIM
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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