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Protein

Ceroid-lipofuscinosis neuronal protein 6

Gene

CLN6

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

Functioni

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

GO - Biological processi

  • cellular macromolecule catabolic process Source: Ensembl
  • cholesterol metabolic process Source: UniProtKB
  • ganglioside metabolic process Source: UniProtKB
  • glycosaminoglycan metabolic process Source: UniProtKB
  • locomotion involved in locomotory behavior Source: Ensembl
  • lysosomal lumen acidification Source: UniProtKB
  • lysosome organization Source: GO_Central
  • positive regulation of proteolysis Source: UniProtKB
  • protein catabolic process Source: UniProtKB
  • visual perception Source: Ensembl

Names & Taxonomyi

Protein namesi
Recommended name:
Ceroid-lipofuscinosis neuronal protein 6
Short name:
Protein CLN6
Gene namesi
Name:CLN6
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 15

Organism-specific databases

EuPathDBiHostDB:ENSG00000128973.11
HGNCiHGNC:2077 CLN6
MIMi606725 gene
neXtProtiNX_Q9NWW5

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
Transmembranei56 – 76HelicalSequence analysisAdd BLAST21
Transmembranei81 – 101HelicalSequence analysisAdd BLAST21
Transmembranei111 – 131HelicalSequence analysisAdd BLAST21
Transmembranei179 – 199HelicalSequence analysisAdd BLAST21
Transmembranei204 – 224HelicalSequence analysisAdd BLAST21
Transmembranei225 – 245HelicalSequence analysisAdd BLAST21
Transmembranei260 – 280HelicalSequence analysisAdd BLAST21

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Involvement in diseasei

Ceroid lipofuscinosis, neuronal, 6 (CLN6)7 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 6 comprise mixed combinations of granular, curvilinear, and fingerprint profiles.
See also OMIM:601780
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06690517G → S in CLN6; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs763944821EnsemblClinVar.1
Natural variantiVAR_02154962R → H in CLN6. 1 PublicationCorresponds to variant dbSNP:rs751486476EnsemblClinVar.1
Natural variantiVAR_06690690N → K in CLN6. 1 Publication1
Natural variantiVAR_066907104S → F in CLN6. 1 Publication1
Natural variantiVAR_015683123G → D in CLN6. 1 PublicationCorresponds to variant dbSNP:rs104894484EnsemblClinVar.1
Natural variantiVAR_066908149R → C in CLN6. 1 PublicationCorresponds to variant dbSNP:rs747229909EnsemblClinVar.1
Natural variantiVAR_015684154Missing in CLN6. 1 Publication1
Natural variantiVAR_058436159P → L in CLN6. 1 PublicationCorresponds to variant dbSNP:rs919850756EnsemblClinVar.1
Natural variantiVAR_066909169L → P in CLN6. 1 Publication1
Natural variantiVAR_015685171Missing in CLN6. 1 Publication1
Natural variantiVAR_066910186F → S in CLN6. 1 Publication1
Natural variantiVAR_058437221Y → C in CLN6. 1 PublicationCorresponds to variant dbSNP:rs764571295EnsemblClinVar.1
Natural variantiVAR_021551221Y → S in CLN6. 1 PublicationCorresponds to variant dbSNP:rs764571295EnsemblClinVar.1
Natural variantiVAR_066911234F → L in CLN6. 2 PublicationsCorresponds to variant dbSNP:rs959199004Ensembl.1
Natural variantiVAR_021552241M → T in CLN6. 1 Publication1
Natural variantiVAR_066912252R → H in CLN6. 1 PublicationCorresponds to variant dbSNP:rs374681194EnsemblClinVar.1
Natural variantiVAR_066913259G → S in CLN6. 1 PublicationCorresponds to variant dbSNP:rs150363441Ensembl.1
Natural variantiVAR_021553265Missing in CLN6. 2 Publications1
Natural variantiVAR_066914297P → T in CLN6. 1 PublicationCorresponds to variant dbSNP:rs1194940137Ensembl.1
Natural variantiVAR_021554299P → L in CLN6. 1 PublicationCorresponds to variant dbSNP:rs758921701EnsemblClinVar.1
Natural variantiVAR_015686300W → R in CLN6. 1 PublicationCorresponds to variant dbSNP:rs750937323EnsemblClinVar.1
Ceroid lipofuscinosis, neuronal, 4A (CLN4A)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn 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.
See also OMIM:204300
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0658346R → T in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774636EnsemblClinVar.1
Natural variantiVAR_06583647L → F in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774635EnsemblClinVar.1
Natural variantiVAR_06583767L → P in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774633EnsemblClinVar.1
Natural variantiVAR_06583877N → K in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774641EnsemblClinVar.1
Natural variantiVAR_065839103R → Q in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774634EnsemblClinVar.1
Natural variantiVAR_065840149R → H in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774638EnsemblClinVar.1
Natural variantiVAR_065841238F → T in CLN4A; requires 2 nucleotide substitutions. 1 Publication1

Keywords - Diseasei

Disease mutation, Neurodegeneration, Neuronal ceroid lipofuscinosis

Organism-specific databases

DisGeNETi54982
GeneReviewsiCLN6
MalaCardsiCLN6
MIMi204300 phenotype
601780 phenotype
OpenTargetsiENSG00000128973
Orphaneti228340 CLN4A disease
228363 CLN6 disease
PharmGKBiPA26604

Polymorphism and mutation databases

BioMutaiCLN6
DMDMi32129457

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000898621 – 311Ceroid-lipofuscinosis neuronal protein 6Add BLAST311

Proteomic databases

EPDiQ9NWW5
MaxQBiQ9NWW5
PaxDbiQ9NWW5
PeptideAtlasiQ9NWW5
PRIDEiQ9NWW5
ProteomicsDBi82991

PTM databases

iPTMnetiQ9NWW5
PhosphoSitePlusiQ9NWW5

Expressioni

Gene expression databases

BgeeiENSG00000128973 Expressed in 135 organ(s), highest expression level in spleen
CleanExiHS_CLN6
ExpressionAtlasiQ9NWW5 baseline and differential
GenevisibleiQ9NWW5 HS

Organism-specific databases

HPAiHPA066046
HPA074162

Interactioni

Subunit structurei

Interacts with CRMP2 (PubMed:19235893). Interacts with CLN5 (PubMed:19941651).2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
A0A142I5B94EBI-6165897,EBI-20625235From Zika virus (isolate ZIKV/Human/Cambodia/FSS13025/2010).

GO - Molecular functioni

Protein-protein interaction databases

BioGridi120318, 10 interactors
IntActiQ9NWW5, 59 interactors
STRINGi9606.ENSP00000249806

Structurei

3D structure databases

ProteinModelPortaliQ9NWW5
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IJBC Eukaryota
ENOG410ZY0K LUCA
GeneTreeiENSGT00400000022240
HOGENOMiHOG000013091
HOVERGENiHBG039396
InParanoidiQ9NWW5
KOiK12359
OrthoDBiEOG091G0CFY
PhylomeDBiQ9NWW5
TreeFamiTF333294

Family and domain databases

InterProiView protein in InterPro
IPR029255 CLN6
PANTHERiPTHR16244 PTHR16244, 1 hit
PfamiView protein in Pfam
PF15156 CLN6, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 14 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q9NWW5-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MEATRRRQHL GATGGPGAQL GASFLQARHG SVSADEAART APFHLDLWFY
60 70 80 90 100
FTLQNWVLDF GRPIAMLVFP LEWFPLNKPS VGDYFHMAYN VITPFLLLKL
110 120 130 140 150
IERSPRTLPR SITYVSIIIF IMGASIHLVG DSVNHRLLFS GYQHHLSVRE
160 170 180 190 200
NPIIKNLKPE TLIDSFELLY YYDEYLGHCM WYIPFFLILF MYFSGCFTAS
210 220 230 240 250
KAESLIPGPA LLLVAPSGLY YWYLVTEGQI FILFIFTFFA MLALVLHQKR
260 270 280 290 300
KRLFLDSNGL FLFSSFALTL LLVALWVAWL WNDPVLRKKY PGVIYVPEPW
310
AFYTLHVSSR H
Length:311
Mass (Da):35,919
Last modified:October 1, 2000 - v1
Checksum:iC718E6F2DC20CE0F
GO
Isoform 2 (identifier: Q9NWW5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-28: MEATRRRQHLGATGGPGAQLGASFLQAR → MAAVAGKERR...LRKLKFKGKK

Note: No experimental confirmation available.
Show »
Length:343
Mass (Da):39,484
Checksum:i861D47B5F541CDB0
GO

Computationally mapped potential isoform sequencesi

There are 14 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H3BUT1H3BUT1_HUMAN
Ceroid-lipofuscinosis neuronal 6 la...
CLN6 hCG_23813
248Annotation score:
H3BUV4H3BUV4_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN6
213Annotation score:
H3BTY4H3BTY4_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN6
158Annotation score:
A0A0S2Z5D0A0A0S2Z5D0_HUMAN
Ceroid-lipofuscinosis neuronal 6 la...
CLN6
171Annotation score:
A0A1B0GTU6A0A1B0GTU6_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN6
251Annotation score:
A0A1B0GUD2A0A1B0GUD2_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN6
215Annotation score:
H3BNF1H3BNF1_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN6
105Annotation score:
A0A1B0GTV3A0A1B0GTV3_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN6 hCG_23813
108Annotation score:
A0A1B0GU90A0A1B0GU90_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN6
76Annotation score:
A0A1B0GTD3A0A1B0GTD3_HUMAN
Ceroid-lipofuscinosis neuronal prot...
CLN6
86Annotation score:
There are more potential isoformsShow all

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti281W → R in BAB55226 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0658346R → T in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774636EnsemblClinVar.1
Natural variantiVAR_06690412A → T1 PublicationCorresponds to variant dbSNP:rs112239768EnsemblClinVar.1
Natural variantiVAR_06690517G → S in CLN6; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs763944821EnsemblClinVar.1
Natural variantiVAR_06583534A → T1 PublicationCorresponds to variant dbSNP:rs146198681EnsemblClinVar.1
Natural variantiVAR_06583647L → F in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774635EnsemblClinVar.1
Natural variantiVAR_02154962R → H in CLN6. 1 PublicationCorresponds to variant dbSNP:rs751486476EnsemblClinVar.1
Natural variantiVAR_06583767L → P in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774633EnsemblClinVar.1
Natural variantiVAR_02155072E → Q2 PublicationsCorresponds to variant dbSNP:rs104894483EnsemblClinVar.1
Natural variantiVAR_06583877N → K in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774641EnsemblClinVar.1
Natural variantiVAR_06690690N → K in CLN6. 1 Publication1
Natural variantiVAR_065839103R → Q in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774634EnsemblClinVar.1
Natural variantiVAR_066907104S → F in CLN6. 1 Publication1
Natural variantiVAR_015683123G → D in CLN6. 1 PublicationCorresponds to variant dbSNP:rs104894484EnsemblClinVar.1
Natural variantiVAR_066908149R → C in CLN6. 1 PublicationCorresponds to variant dbSNP:rs747229909EnsemblClinVar.1
Natural variantiVAR_065840149R → H in CLN4A. 1 PublicationCorresponds to variant dbSNP:rs154774638EnsemblClinVar.1
Natural variantiVAR_015684154Missing in CLN6. 1 Publication1
Natural variantiVAR_058436159P → L in CLN6. 1 PublicationCorresponds to variant dbSNP:rs919850756EnsemblClinVar.1
Natural variantiVAR_066909169L → P in CLN6. 1 Publication1
Natural variantiVAR_015685171Missing in CLN6. 1 Publication1
Natural variantiVAR_066910186F → S in CLN6. 1 Publication1
Natural variantiVAR_058437221Y → C in CLN6. 1 PublicationCorresponds to variant dbSNP:rs764571295EnsemblClinVar.1
Natural variantiVAR_021551221Y → S in CLN6. 1 PublicationCorresponds to variant dbSNP:rs764571295EnsemblClinVar.1
Natural variantiVAR_066911234F → L in CLN6. 2 PublicationsCorresponds to variant dbSNP:rs959199004Ensembl.1
Natural variantiVAR_065841238F → T in CLN4A; requires 2 nucleotide substitutions. 1 Publication1
Natural variantiVAR_021552241M → T in CLN6. 1 Publication1
Natural variantiVAR_066912252R → H in CLN6. 1 PublicationCorresponds to variant dbSNP:rs374681194EnsemblClinVar.1
Natural variantiVAR_066913259G → S in CLN6. 1 PublicationCorresponds to variant dbSNP:rs150363441Ensembl.1
Natural variantiVAR_021553265Missing in CLN6. 2 Publications1
Natural variantiVAR_066914297P → T in CLN6. 1 PublicationCorresponds to variant dbSNP:rs1194940137Ensembl.1
Natural variantiVAR_021554299P → L in CLN6. 1 PublicationCorresponds to variant dbSNP:rs758921701EnsemblClinVar.1
Natural variantiVAR_015686300W → R in CLN6. 1 PublicationCorresponds to variant dbSNP:rs750937323EnsemblClinVar.1
Natural variantiVAR_065842308S → T1 PublicationCorresponds to variant dbSNP:rs143578698EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0561971 – 28MEATR…FLQAR → MAAVAGKERRARGRPRPETL GAIPRREGGEAGLSRAFKPL AQAPLSCETSLRKLKFKGKK in isoform 2. 1 PublicationAdd BLAST28

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK000568 mRNA Translation: BAA91260.1
AK027604 mRNA Translation: BAB55226.1
AK291175 mRNA Translation: BAF83864.1
AK293197 mRNA Translation: BAG56737.1
CR457244 mRNA Translation: CAG33525.1
AC107871 Genomic DNA No translation available.
CH471082 Genomic DNA Translation: EAW77811.1
BC010849 mRNA Translation: AAH10849.1
BC013130 mRNA Translation: AAH13130.1
CCDSiCCDS10227.1 [Q9NWW5-1]
RefSeqiNP_060352.1, NM_017882.2 [Q9NWW5-1]
UniGeneiHs.584921

Genome annotation databases

EnsembliENST00000249806; ENSP00000249806; ENSG00000128973 [Q9NWW5-1]
ENST00000538696; ENSP00000445770; ENSG00000128973 [Q9NWW5-2]
GeneIDi54982
KEGGihsa:54982
UCSCiuc002arf.3 human [Q9NWW5-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Web resourcesi

NCL CLN6

Neural Ceroid Lipofuscinoses mutation db

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK000568 mRNA Translation: BAA91260.1
AK027604 mRNA Translation: BAB55226.1
AK291175 mRNA Translation: BAF83864.1
AK293197 mRNA Translation: BAG56737.1
CR457244 mRNA Translation: CAG33525.1
AC107871 Genomic DNA No translation available.
CH471082 Genomic DNA Translation: EAW77811.1
BC010849 mRNA Translation: AAH10849.1
BC013130 mRNA Translation: AAH13130.1
CCDSiCCDS10227.1 [Q9NWW5-1]
RefSeqiNP_060352.1, NM_017882.2 [Q9NWW5-1]
UniGeneiHs.584921

3D structure databases

ProteinModelPortaliQ9NWW5
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120318, 10 interactors
IntActiQ9NWW5, 59 interactors
STRINGi9606.ENSP00000249806

PTM databases

iPTMnetiQ9NWW5
PhosphoSitePlusiQ9NWW5

Polymorphism and mutation databases

BioMutaiCLN6
DMDMi32129457

Proteomic databases

EPDiQ9NWW5
MaxQBiQ9NWW5
PaxDbiQ9NWW5
PeptideAtlasiQ9NWW5
PRIDEiQ9NWW5
ProteomicsDBi82991

Protocols and materials databases

DNASUi54982
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000249806; ENSP00000249806; ENSG00000128973 [Q9NWW5-1]
ENST00000538696; ENSP00000445770; ENSG00000128973 [Q9NWW5-2]
GeneIDi54982
KEGGihsa:54982
UCSCiuc002arf.3 human [Q9NWW5-1]

Organism-specific databases

CTDi54982
DisGeNETi54982
EuPathDBiHostDB:ENSG00000128973.11
GeneCardsiCLN6
GeneReviewsiCLN6
HGNCiHGNC:2077 CLN6
HPAiHPA066046
HPA074162
MalaCardsiCLN6
MIMi204300 phenotype
601780 phenotype
606725 gene
neXtProtiNX_Q9NWW5
OpenTargetsiENSG00000128973
Orphaneti228340 CLN4A disease
228363 CLN6 disease
PharmGKBiPA26604
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IJBC Eukaryota
ENOG410ZY0K LUCA
GeneTreeiENSGT00400000022240
HOGENOMiHOG000013091
HOVERGENiHBG039396
InParanoidiQ9NWW5
KOiK12359
OrthoDBiEOG091G0CFY
PhylomeDBiQ9NWW5
TreeFamiTF333294

Miscellaneous databases

ChiTaRSiCLN6 human
GeneWikiiCLN6
GenomeRNAii54982
PROiPR:Q9NWW5
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000128973 Expressed in 135 organ(s), highest expression level in spleen
CleanExiHS_CLN6
ExpressionAtlasiQ9NWW5 baseline and differential
GenevisibleiQ9NWW5 HS

Family and domain databases

InterProiView protein in InterPro
IPR029255 CLN6
PANTHERiPTHR16244 PTHR16244, 1 hit
PfamiView protein in Pfam
PF15156 CLN6, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiCLN6_HUMAN
AccessioniPrimary (citable) accession number: Q9NWW5
Secondary accession number(s): A8K560
, B4DDH6, Q6IAB1, Q96SR0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 16, 2003
Last sequence update: October 1, 2000
Last modified: November 7, 2018
This is version 155 of the entry and version 1 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. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
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