CLN6

Protein identityUniProt · HPA

UniProt accession

Q9NWW5

Gene

CLN6

Ensembl

ENSG00000128973

Chromosome

15

Canonical length

311 aa

Protein class

Disease related genes, Human disease related genes, Potential drug targets, Predicted intracellular proteins, Predicted membrane proteins, Transporters

Subcellular location

Nucleoli,Endoplasmic reticulum,Vesicles

OverviewNCBI Gene

This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely encode proteins involved in the degradation of post-translationally modified proteins in lysosomes. The primary defect in NCL disorders is thought to be associated with lysosomal storage function. [provided by RefSeq, Oct 2008]

Canonical amino-acid sequenceUniProt

311 residues, UniProt reviewed canonical sequence.

>Q9NWW5|CLN6
     1  MEATRRRQHL GATGGPGAQL GASFLQARHG SVSADEAART APFHLDLWFY FTLQNWVLDF
    61  GRPIAMLVFP LEWFPLNKPS VGDYFHMAYN VITPFLLLKL IERSPRTLPR SITYVSIIIF
   121  IMGASIHLVG DSVNHRLLFS GYQHHLSVRE NPIIKNLKPE TLIDSFELLY YYDEYLGHCM
   181  WYIPFFLILF MYFSGCFTAS KAESLIPGPA LLLVAPSGLY YWYLVTEGQI FILFIFTFFA
   241  MLALVLHQKR KRLFLDSNGL FLFSSFALTL LLVALWVAWL WNDPVLRKKY PGVIYVPEPW
   301  AFYTLHVSSR H

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CLN6 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability

Other membrane

Secreted

No

Transmembrane segments

6

Mean surface accessibility (rSASA)

0.32

Highest tissue expression

28 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CLN6.

Disease | AllUniProt

Conditions CLN6 is implicated in, by any mechanism.

• Ceroid lipofuscinosis, neuronal, 6 (CLN6) MIM:601780
• Ceroid lipofuscinosis, neuronal, 4A (Kufs type), autosomal recessive (CLN4A) MIM:204300

Disease | GeneticClinVar

121 pathogenic / likely-pathogenic of 822 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• Neuronal ceroid lipofuscinosis
• Ceroid lipofuscinosis, neuronal, 6A
• Ceroid lipofuscinosis, neuronal, 6B (Kufs type)
• Abnormality of the nervous system
• Inborn genetic diseases

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)

1.13

gnomAD pLI

0

gnomAD missense Z

-0.01

DepMap mean gene effect

-0.2

DepMap dependency class

selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• cholesterol metabolic process
• ganglioside metabolic process
• glycosaminoglycan metabolic process
• locomotion involved in locomotory behavior
• lysosomal lumen acidification
• lysosome organization
• positive regulation of proteolysis
• protein catabolic process
• visual perception

Molecular functions

• lysophosphatidic acid binding
• protein homodimerization activity
• sulfatide binding

Cellular components

• early endosome
• endoplasmic reticulum
• endoplasmic reticulum lumen
• endoplasmic reticulum membrane
• membrane
• membrane raft
• nucleolus

Protein domainsUniProt · Pfam · InterPro

• Ceroid-lipofuscinosis neuronal protein 6
• Ceroid-lipofuscinosis neuronal protein 6

KeywordsUniProt

• Endoplasmic reticulum
• Membrane
• Neurodegeneration
• Neuronal ceroid lipofuscinosis
• Transmembrane
• Transmembrane helix

InteractionsUniProt · HPA

Protein binding partners of CLN6 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• CLN3
• CLN5
• CRMP2
• DPYSL2