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Cln3 Gene Detail
Summary
  • Symbol
    Cln3
  • Name
    CLN3 lysosomal/endosomal transmembrane protein, battenin
  • Synonyms
    battenin
  • Feature Type
    protein coding gene
  • IDs
    MGI:107537
    NCBI Gene: 12752
  • Alliance
    gene page
  • Transcription Start Sites
    17 TSS
Location &
Maps
more
  • Sequence Map
    Chr7:126170571-126184991 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 7, 69.16 cM
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    745 from dbSNP Build 142
  • Strain Annotations
    18
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_107537
 protein coding gene Chr7:126170379-126184991 (-)
129S1/SvImJ MGP_129S1SvImJ_G0032986
 protein coding gene Chr7:130854396-130869089 (-)
A/J MGP_AJ_G0032969
 protein coding gene Chr7:127392227-127406424 (-)
AKR/J MGP_AKRJ_G0032901
 protein coding gene Chr7:130613197-130629278 (-)
BALB/cJ MGP_BALBcJ_G0032974
 protein coding gene Chr7:127049565-127063967 (-)
C3H/HeJ MGP_C3HHeJ_G0032684
 protein coding gene Chr7:130544149-130558995 (-)
C57BL/6NJ MGP_C57BL6NJ_G0033480
 protein coding gene Chr7:135942859-135959185 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0030452
 protein coding gene Chr7:128582598-128595072 (-)
CAST/EiJ MGP_CASTEiJ_G0032012
 protein coding gene Chr7:122332786-122352567 (-)
CBA/J MGP_CBAJ_G0032657
 protein coding gene Chr7:140515082-140530860 (-)
DBA/2J MGP_DBA2J_G0032809
 protein coding gene Chr7:125368002-125382450 (-)
FVB/NJ MGP_FVBNJ_G0032762
 protein coding gene Chr7:125217650-125232154 (-)
LP/J MGP_LPJ_G0032903
 protein coding gene Chr7:132319435-132333892 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0032794
 protein coding gene Chr7:141703134-141718959 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0033499
 protein coding gene Chr7:129630394-129645831 (-)
PWK/PhJ MGP_PWKPhJ_G0031720
 protein coding gene Chr7:118354959-118370523 (-)
SPRET/EiJ MGP_SPRETEiJ_G0031566
 protein coding gene Chr7:116456938-116474440 (-)
WSB/EiJ MGP_WSBEiJ_G0032125
 protein coding gene Chr7:130597061-130613328 (-)



Homology
more
  • Human Ortholog
    CLN3, CLN3 lysosomal/endosomal transmembrane protein, battenin
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    CLN3, CLN3 lysosomal/endosomal transmembrane protein, battenin
  • Synonyms
    BTN1, BTS, JNCL, SLC29B1
  • Links
    NCBI Gene ID: 1201
    UniProt: Q13286

  • Chr Location
    16p12.1; chr16:28466653-28495575 (-)  GRCh38
Human Diseases
more
  • Diseases
    1 with Cln3 mouse models; 1 with human CLN3 associations

Human Disease Mouse Models
      
IDs
 View 7 models
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    5 with disease annotations
  • References
    7 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    49 phenotypes from 5 alleles in 7 genetic backgrounds
    88 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
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
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
    206
  • GO References
    34
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 differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
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
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
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
    837
  • Tissues
    80
  • cDNA Data
    73
  • Literature Summary
    7
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 12752 NCBI Gene Model | MGI Sequence Detail 14421 C57BL/6J ±  kb
    transcript NM_001146311 RefSeq | MGI Sequence Detail 3013 ZRU/MplStud  
    polypeptide Q61124 UniProt | EBI | MGI Sequence Detail 438 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 74
      cDNA 73
      Primer pair 1

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGD-MRK-36107, MGI:2141907
    References
    more
    • Summaries
      All 133
      Developmental Gene Expression 7
      Diseases 7
      Gene Ontology 34
      Phenotypes 88
    • 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:346716 Nyame K, et al., Glycerophosphodiesters inhibit lysosomal phospholipid catabolism in Batten disease. Mol Cell. 2024 Feb 28;
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    03/25/2025
    MGI 6.24     		The Jackson Laboratory