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CLN3 ceroid-lipofuscinosis, neuronal 3 [ Homo sapiens (human) ]

Gene ID: 1201, updated on 19-Jul-2014
Official Symbol
CLN3provided by HGNC
Official Full Name
ceroid-lipofuscinosis, neuronal 3provided by HGNC
Primary source
HGNC:2074
See related
Ensembl:ENSG00000188603; HPRD:08450; MIM:607042; Vega:OTTHUMG00000097024
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; 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]
See CLN3 in Epigenomics, MapViewer
Location:
16p12.1
Exon count:
17
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 16 NC_000016.10 (28466653..28492302, 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 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

Replication interactions

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

Go to the HIV-1, Human Protein Interaction Database

  • Lysosome, organism-specific biosystem (from KEGG)
    Lysosome, organism-specific biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
  • Lysosome, conserved biosystem (from KEGG)
    Lysosome, conserved biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC102840

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
unfolded protein binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
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 IDA
Inferred from Direct Assay
more info
PubMed 
associative learning ISS
Inferred from Sequence or Structural Similarity
more info
 
autophagic vacuole fusion ISS
Inferred from Sequence or Structural Similarity
more info
 
cell death IEA
Inferred from Electronic Annotation
more info
 
cellular amino acid metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
ceramide metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
cytosolic calcium ion homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
galactosylceramide metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
globoside metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
glucosylceramide metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
ionotropic glutamate receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
lysosomal lumen acidification IMP
Inferred from Mutant Phenotype
more info
PubMed 
lysosomal lumen pH elevation IDA
Inferred from Direct Assay
more info
PubMed 
lysosome organization ISS
Inferred from Sequence or Structural Similarity
more info
 
macroautophagy NAS
Non-traceable Author Statement
more info
PubMed 
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 catalytic activity ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of macroautophagy 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
 
protein catabolic process NAS
Non-traceable Author Statement
more info
PubMed 
protein processing ISS
Inferred from Sequence or Structural Similarity
more info
 
receptor-mediated endocytosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
sphingomyelin metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
vacuolar transport IBA
Inferred from Biological aspect of Ancestor
more info
 
vesicle transport along microtubule IMP
Inferred from Mutant Phenotype
more info
 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
Golgi membrane IDA
Inferred from Direct Assay
more info
PubMed 
Golgi stack IDA
Inferred from Direct Assay
more info
PubMed 
autophagic vacuole ISS
Inferred from Sequence or Structural Similarity
more info
 
caveola IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
early endosome IDA
Inferred from Direct Assay
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
 
late endosome ISS
Inferred from Sequence or Structural Similarity
more info
 
lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
lysosome IDA
Inferred from Direct Assay
more info
PubMed 
membrane raft IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrion TAS
Traceable Author Statement
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 
synaptic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
battenin
Names
battenin
batten disease protein

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 

    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 proteins identical to 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
    Related
    ENSP00000353073, ENST00000359984
    Conserved Domains (1) summary
    pfam02487
    Location:37438
    Blast Score: 1419
    CLN3; CLN3 protein
  2. NM_001042432.1NP_001035897.1  battenin isoform a

    See proteins identical to 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
    Related
    ENSP00000353116, ENST00000360019
    Conserved Domains (1) summary
    pfam02487
    Location:37438
    Blast Score: 1419
    CLN3; CLN3 protein
  3. NM_001286104.1NP_001273033.1  battenin isoform b

    See proteins identical to 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)
    AK302027, DA703317
    UniProtKB/TrEMBL
    B4DXL3
    Conserved Domains (1) summary
    pfam02487
    Location:37414
    Blast Score: 1294
    CLN3; CLN3 protein
  4. NM_001286105.1NP_001273034.1  battenin isoform c

    See proteins identical to 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)
    AK297690, AK302027, BP252176
    UniProtKB/TrEMBL
    B4DMY6
    UniProtKB/TrEMBL
    B4DXL3
    Conserved Domains (1) summary
    pfam02487
    Location:26338
    Blast Score: 1078
    CLN3; CLN3 protein
  5. NM_001286109.1NP_001273038.1  battenin isoform d

    See proteins identical to 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
    UniProtKB/TrEMBL
    Q2TA70
    Conserved Domains (1) summary
    pfam02487
    Location:1360
    Blast Score: 1187
    CLN3; CLN3 protein
  6. NM_001286110.1NP_001273039.1  battenin isoform e

    See proteins identical to 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)
    AK294070, BP252176, DA869025
    UniProtKB/TrEMBL
    B4DFF3
    Conserved Domains (1) summary
    pfam02487
    Location:1384
    Blast Score: 1316
    CLN3; CLN3 protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000016.10 

    Range
    28466653..28492302
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000148.1 

    Range
    26513043..26529549
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018927.2 

    Range
    29489652..29515233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)