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CLN3 CLN3 lysosomal/endosomal transmembrane protein, battenin [ Homo sapiens (human) ]

Gene ID: 1201, updated on 1-Aug-2020

Summary

Official Symbol
CLN3provided by HGNC
Official Full Name
CLN3 lysosomal/endosomal transmembrane protein, batteninprovided by HGNC
Primary source
HGNC:HGNC:2074
See related
Ensembl:ENSG00000188603 Ensembl:ENSG00000261832 MIM:607042
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
BTS; BTN1; JNCL
Summary
This gene encodes a protein that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease or collectively known as neuronal ceroid lipofuscinoses (NCLs). Many alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in placenta (RPKM 23.0), colon (RPKM 17.0) and 25 other tissues See more
Orthologs

Genomic context

See CLN3 in Genome Data Viewer
Location:
16p12.1
Exon count:
16
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (28466653..28492082, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (28488600..28505897, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 3 subunit C like Neighboring gene microRNA 6862-1 Neighboring gene uncharacterized LOC112268171 Neighboring gene cell division cycle 37 pseudogene 2 Neighboring gene nuclear pore complex interacting protein family member B7 Neighboring gene apolipoprotein B receptor Neighboring gene interleukin 27

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Juvenile neuronal ceroid lipofuscinosis
MedGen: C0751383 OMIM: 204200 GeneReviews: Neuronal Ceroid-Lipofuscinoses
Compare labs

NHGRI GWAS Catalog

Description
Common variants at five new loci associated with early-onset inflammatory bowel disease.
NHGRI GWA Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of ceroid-lipofuscinosis, neuronal 3 (CLN3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Nef nef Genome-wide shRNA screening identifies CLN3, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC102840

Gene Ontology Provided by GOA

Function Evidence Code Pubs
glycolipid binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sulfatide binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
Golgi to lysosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
action potential ISS
Inferred from Sequence or Structural Similarity
more info
 
amyloid precursor protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
arginine transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
arginine transport IDA
Inferred from Direct Assay
more info
PubMed 
associative learning ISS
Inferred from Sequence or Structural Similarity
more info
 
autophagosome maturation ISS
Inferred from Sequence or Structural Similarity
more info
 
autophagosome-lysosome fusion ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular water homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
glycerophospholipid biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
glycolipid transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
ionotropic glutamate receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
learning or memory ISS
Inferred from Sequence or Structural Similarity
more info
 
lysosomal lumen acidification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lysosomal lumen acidification IMP
Inferred from Mutant Phenotype
more info
PubMed 
lysosomal lumen pH elevation IDA
Inferred from Direct Assay
more info
PubMed 
lysosomal protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
lysosome organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lysosome organization ISS
Inferred from Sequence or Structural Similarity
more info
 
membrane organization ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of catalytic activity ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of neuron apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of proteolysis ISS
Inferred from Sequence or Structural Similarity
more info
 
neuromuscular process controlling balance ISS
Inferred from Sequence or Structural Similarity
more info
 
neurotransmitter metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
phagosome-lysosome docking ISS
Inferred from Sequence or Structural Similarity
more info
 
phagosome-lysosome fusion ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane raft organization ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of Golgi to plasma membrane protein transport ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of caveolin-mediated endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of pinocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
protein processing ISS
Inferred from Sequence or Structural Similarity
more info
 
receptor-mediated endocytosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of arginine biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of autophagosome maturation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cellular response to osmotic stress IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cytosolic calcium ion concentration ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of fibroblast migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of intracellular pH IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of modification of synaptic structure ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of phagosome maturation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of protein localization to plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of protein processing IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of short-term neuronal synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of synaptic transmission, GABAergic ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of synaptic transmission, glutamatergic ISS
Inferred from Sequence or Structural Similarity
more info
 
renal potassium excretion ISS
Inferred from Sequence or Structural Similarity
more info
 
vesicle transport along microtubule IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
Golgi apparatus IMP
Inferred from Mutant Phenotype
more info
PubMed 
Golgi membrane IDA
Inferred from Direct Assay
more info
PubMed 
Golgi stack IDA
Inferred from Direct Assay
more info
PubMed 
autolysosome ISS
Inferred from Sequence or Structural Similarity
more info
 
autophagosome ISS
Inferred from Sequence or Structural Similarity
more info
 
caveola IDA
Inferred from Direct Assay
more info
PubMed 
caveola IMP
Inferred from Mutant Phenotype
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
early endosome membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
integral component of endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
late endosome IDA
Inferred from Direct Assay
more info
PubMed 
late endosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
late endosome ISS
Inferred from Sequence or Structural Similarity
more info
 
late endosome membrane IEA
Inferred from Electronic Annotation
more info
 
lysosomal membrane HDA PubMed 
lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
lysosomal membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
lysosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lysosome IDA
Inferred from Direct Assay
more info
PubMed 
lysosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
membrane raft IDA
Inferred from Direct Assay
more info
PubMed 
membrane raft IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuron projection IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
recycling endosome IDA
Inferred from Direct Assay
more info
PubMed 
synaptic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
vacuole IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
battenin
Names
CLN3, battenin
batten disease protein
ceroid-lipofuscinosis, neuronal 3

NCBI Reference Sequences (RefSeq)

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_008654.2 RefSeqGene

    Range
    5001..30650
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_689

mRNA and Protein(s)

  1. NM_000086.2NP_000077.1  battenin isoform a

    See identical proteins and their annotated locations for NP_000077.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AF077962, AI138575, AU105965, DA869025, U32680
    Consensus CDS
    CCDS10632.1
    UniProtKB/Swiss-Prot
    Q13286
    UniProtKB/TrEMBL
    A0A024QZB8
    Related
    ENSP00000353073.9, ENST00000359984.12
    Conserved Domains (1) summary
    pfam02487
    Location:40437
    CLN3; CLN3 protein
  2. NM_001042432.2NP_001035897.1  battenin isoform a

    See identical proteins and their annotated locations for NP_001035897.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AF077957, AI138575, DA552461, DB101039
    Consensus CDS
    CCDS10632.1
    UniProtKB/Swiss-Prot
    Q13286
    UniProtKB/TrEMBL
    A0A024QZB8
    Related
    ENSP00000490105.1, ENST00000636147.1
    Conserved Domains (1) summary
    pfam02487
    Location:40437
    CLN3; CLN3 protein
  3. NM_001286104.2NP_001273033.1  battenin isoform b

    See identical proteins and their annotated locations for NP_001273033.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC138894, AK302027, DA703317
    Consensus CDS
    CCDS73855.1
    UniProtKB/Swiss-Prot
    Q13286
    Related
    ENSP00000353116.3, ENST00000360019.8
    Conserved Domains (1) summary
    pfam02487
    Location:40413
    CLN3; CLN3 protein
  4. NM_001286105.2NP_001273034.1  battenin isoform c

    See identical proteins and their annotated locations for NP_001273034.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and lacks two exons compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (c) with a shorter and distinct N-terminus compared to isoform a.
    Source sequence(s)
    AC138894, AK297690, AK302027, BP252176
    UniProtKB/Swiss-Prot
    Q13286
    UniProtKB/TrEMBL
    B4DMY6
    Conserved Domains (1) summary
    pfam02487
    Location:27337
    CLN3; CLN3 protein
  5. NM_001286109.2NP_001273038.1  battenin isoform d

    See identical proteins and their annotated locations for NP_001273038.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence, the 3' UTR, and lacks an alternate in-frame exon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (d) with a shorter N-terminus and missing an alternate internal segment compared to isoform a.
    Source sequence(s)
    BC111068, BP252176, DA869025
    Consensus CDS
    CCDS73853.1
    UniProtKB/TrEMBL
    Q2TA70
    Related
    ENSP00000454253.1, ENST00000568224.4
    Conserved Domains (1) summary
    pfam02487
    Location:1359
    CLN3; CLN3 protein
  6. NM_001286110.2NP_001273039.1  battenin isoform e

    See identical proteins and their annotated locations for NP_001273039.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (e) with a shorter N-terminus and missing an alternate internal segment compared to isoform a.
    Source sequence(s)
    AC138894, AK294070, BP252176, DA869025
    Consensus CDS
    CCDS73854.1
    UniProtKB/TrEMBL
    B4DFF3
    Related
    ENSP00000350523.9, ENST00000357857.14
    Conserved Domains (1) summary
    pfam02487
    Location:1383
    CLN3; CLN3 protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    28466653..28492082 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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