About   Help   FAQ
Cln3 Gene Detail
Summary
  • Symbol
    Cln3
  • Name
    ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)
  • Synonyms
    battenin
  • Feature Type
    protein coding gene
  • IDs
    MGI:107537
    NCBI Gene: 12752
  • Gene Overview
    MyGene.info: CLN3
  • Alliance
    gene page
Location & Maps
more
  • Sequence Map
    Chr7:126571207-126585817 bp, - strand
  • From VEGA annotation of GRCm38

    Mouse Genome Browser
  • Download
    Sequence
      14611 bp   ±  kb flank

  • Genome Browsers
    VEGA | Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 7, 69.16 cM
  • Mapping Data
    2 experiments
Homology
more
  • Human Ortholog
    CLN3, CLN3, battenin
  • Vertebrate Orthologs
    7
  • Human Ortholog
    CLN3, CLN3, battenin
    Orthology source: HomoloGene, HGNC
  • Synonyms
    BTN1, BTS, JNCL
  • Links
    NCBI Gene ID: 1201
    neXtProt AC: NX_Q13286
    UniProt: Q13286

  • Chr Location
    16p12.1; chr16:28466653-28492302 (-)  GRCh38.p7
Human Diseases
more
  • Diseases
    1 with Cln3 mouse models; 1 with human CLN3 associations

Human Disease Mouse Models
      
IDs
 View 6 models
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    4 with disease annotations
  • References
    6 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    44 phenotypes from 4 alleles in 6 genetic backgrounds
    62 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
immune system
integument
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
neoplasm
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
vision/eye

Click cells to view annotations.
Nullizygous mutations can result in neuronal ceroid lipofuscinosis, degeneration of the retina, cerebral cortex and cerebellum, hypertrophy of hippocampal interneuron populations, gliosis, neurological deficits, and premature death. Homozygotes for a null allele show impaired water and K+ balance.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    73
  • GO References
    19
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell death
cell differentiation
cell proliferation
cellular component organization
establishment of localization
homeostatic process
immune system process
lipid metabolic process
nucleic acid-templated transcription
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
non-membrane-bounded organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    81
  • Tissues
    59
  • cDNA Data
    72
  • Literature Summary
    4
  • Comparison Matrix
    Gene Expression + Phenotype
    • Interactions
    less
    Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic OTTMUSG00000019900 VEGA Gene Model | MGI Sequence Detail 14611 C57BL/6J ±  kb
    transcript OTTMUST00000047437 VEGA | MGI Sequence Detail 3203 Not Applicable  
    polypeptide OTTMUSP00000021443 VEGA | MGI Sequence Detail 438 Not Applicable  
    For the selected sequence
    Polymorphisms
    less
    • SNPs within 2kb
      113 from dbSNP Build 142
    • RFLP
      1
    Protein
    Information
    less
    • UniProt
      10 Sequences
    • InterPro Domains
      IPR003492 Batten's disease protein Cln3
      IPR018460 Batten's disease protein Cln3, subgroup
      IPR036259 MFS transporter superfamily
    Molecular
    Reagents
    less
    • All nucleic 72
      cDNA 72

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGD-MRK-36107, MGI:2141907
    References
    more
    • Summaries
      All 97
      Developmental Gene Expression 4
      Diseases 6
      Gene Ontology 19
      Phenotypes 62
    • Earliest
      J:34626 Lee RL, et al., Isolation and chromosomal mapping of a mouse homolog of the Batten disease gene CLN3. Genomics. 1996 Aug 1;35(3):617-9
    • Latest
      J:259406 Burkovetskaya M, et al., Age-dependent alterations in neuronal activity in the hippocampus and visual cortex in a mouse model of Juvenile Neuronal Ceroid Lipofuscinosis (CLN3). Neurobiol Dis. 2017 Apr;100:19-29
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
    Citing These Resources
    Funding Information
    Warranty Disclaimer & Copyright Notice
    Send questions and comments to User Support.     		last database update
    07/31/2018
    MGI 6.12     		The Jackson Laboratory