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CLN6 CLN6, transmembrane ER protein [ Homo sapiens (human) ]

Gene ID: 54982, updated on 5-Nov-2017
Official Symbol
CLN6provided by HGNC
Official Full Name
CLN6, transmembrane ER proteinprovided by HGNC
Primary source
HGNC:HGNC:2077
See related
Ensembl:ENSG00000128973 MIM:606725; Vega:OTTHUMG00000133286
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
nclf; CLN4A; HsT18960
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 12.1), colon (RPKM 10.8) and 25 other tissues See more
Orthologs
Location:
15q23
Exon count:
7
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 15 NC_000015.10 (68206992..68229742, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (68499330..68522081, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene protein inhibitor of activated STAT 1 Neighboring gene uncharacterized LOC105370871 Neighboring gene calmodulin like 4 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 40 Neighboring gene fem-1 homolog B

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

Description
Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies.
NHGRI GWA Catalog

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with ceroid-lipofuscinosis, neuronal 6, late infantile, variant (CLN6) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ20561

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cellular macromolecule catabolic process IEA
Inferred from Electronic Annotation
more info
 
cholesterol metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
ganglioside metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
glycosaminoglycan metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
locomotion involved in locomotory behavior IEA
Inferred from Electronic Annotation
more info
 
lysosomal lumen acidification IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of proteolysis IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein catabolic process NAS
Non-traceable Author Statement
more info
PubMed 
visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum lumen IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
ceroid-lipofuscinosis neuronal protein 6
Names
ceroid-lipofuscinosis neuronal 6 late infantile
ceroid-lipofuscinosis, neuronal 6, late infantile

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008764.2 RefSeqGene

    Range
    32470..55220
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_017882.2NP_060352.1  ceroid-lipofuscinosis neuronal protein 6

    See identical proteins and their annotated locations for NP_060352.1

    Status: REVIEWED

    Source sequence(s)
    AK027604, BC010849, BC013130, BM149330, CA446197, CN427564
    Consensus CDS
    CCDS10227.1
    UniProtKB/Swiss-Prot
    Q9NWW5
    UniProtKB/TrEMBL
    A0A024R601
    Related
    ENSP00000249806.5, OTTHUMP00000164387, ENST00000249806.10, OTTHUMT00000257066
    Conserved Domains (1) summary
    pfam15156
    Location:30309
    CLN6; Ceroid-lipofuscinosis neuronal protein 6

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p7 Primary Assembly

    Range
    68206992..68229742 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018926.2 Alternate CHM1_1.1

    Range
    68617284..68640038 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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