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Cln6 Gene Detail
Summary
  • Symbol
    Cln6
  • Name
    ceroid-lipofuscinosis, neuronal 6
  • Synonyms
    1810065L06Rik, D9Bwg1455e
  • Feature Type
    protein coding gene
  • IDs
    MGI:2159324
    NCBI Gene: 76524
  • Alliance
    gene page
  • Transcription Start Sites
    11 TSS
Location &
Maps
more
  • Sequence Map
    Chr9:62746067-62759288 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 9, 33.89 cM
  • Mapping Data
    4 experiments
Strain
Comparison
more
  • SNPs within 2kb
    537 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_2159324
 protein coding gene Chr9:62746067-62759288 (+)
129S1/SvImJ MGP_129S1SvImJ_G0034924
 protein coding gene Chr9:62404846-62424107 (+)
A/J MGP_AJ_G0034904
 protein coding gene Chr9:60341934-60355504 (+)
AKR/J MGP_AKRJ_G0034834
 protein coding gene Chr9:61752945-61766815 (+)
BALB/cJ MGP_BALBcJ_G0034897
 protein coding gene Chr9:60071387-60096728 (+)
C3H/HeJ MGP_C3HHeJ_G0034607
 protein coding gene Chr9:62256657-62269832 (+)
C57BL/6NJ MGP_C57BL6NJ_G0035416
 protein coding gene Chr9:64126939-64141374 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0032327
 protein coding gene Chr9:59998853-60012354 (+)
CAST/EiJ MGP_CASTEiJ_G0033928
 protein coding gene Chr9:62399652-62412710 (+)
CBA/J MGP_CBAJ_G0034578
 protein coding gene Chr9:66335874-66348761 (+)
DBA/2J MGP_DBA2J_G0034737
 protein coding gene Chr9:60140994-60154049 (+)
FVB/NJ MGP_FVBNJ_G0034679
 protein coding gene Chr9:59429187-59442222 (+)
LP/J MGP_LPJ_G0034820
 protein coding gene Chr9:62695778-62709915 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0034722
 protein coding gene Chr9:67681620-67696163 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0035438
 protein coding gene Chr9:61829664-61848796 (+)
PWK/PhJ MGP_PWKPhJ_G0033632
 protein coding gene Chr9:60265335-60279937 (+)
SPRET/EiJ MGP_SPRETEiJ_G0033465
 protein coding gene Chr9:62109846-62122686 (+)
WSB/EiJ MGP_WSBEiJ_G0034041
 protein coding gene Chr9:61737302-61751748 (+)



Homology
more
  • Human Ortholog
    CLN6, CLN6 transmembrane ER protein
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    CLN6, CLN6 transmembrane ER protein
  • Synonyms
    CLN4A, CLN6A, HsT18960, nclf
  • Links
    NCBI Gene ID: 54982
    neXtProt AC: NX_Q9NWW5
    UniProt: Q9NWW5

  • Chr Location
    15q23; chr15:68206992-68257211 (-)  GRCh38
Human Diseases
more
  • Diseases
    1 with Cln6 mouse models; 3 with human CLN6 associations

Human Disease Mouse Models
      
IDs
 View 1 model
      
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    1 with disease annotations
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    14 phenotypes from 2 alleles in 3 genetic backgrounds
    37 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.
Homozygous mutants have progressive retinal atrophy, limb paralysis, and seizures that lead to early death.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    21
  • GO References
    5
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
    761
  • Tissues
    38
  • cDNA Data
    55
  • Literature Summary
    2
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 76524 NCBI Gene Model | MGI Sequence Detail 13222 C57BL/6J ±  kb
    transcript NM_001033175 RefSeq | MGI Sequence Detail 2142 ZRU/MplStud  
    polypeptide NP_001028347 RefSeq | MGI Sequence Detail 308 ZRU/MplStud  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      5 Sequences
    • InterPro Domains
      IPR029255 Ceroid-lipofuscinosis neuronal protein 6
    Molecular
    Reagents
    less
    • All nucleic 57
      cDNA 56
      Primer pair 1

      Microarray probesets 3
    Other
    Accession IDs
    less
    MGD-MRK-34102, MGI:106408, MGI:1202067, MGI:1923774, MGI:2143349
    References
    more
    • Summaries
      All 65
      Developmental Gene Expression 2
      Diseases 1
      Gene Ontology 5
      Phenotypes 37
    • Earliest
      J:44483 Brady KP, et al., Genetic mapping of 262 loci derived from expressed sequences in a murine interspecific cross using single-strand conformational polymorphism analysis. Genome Res. 1997 Nov;7(11):1085-93
    • Latest
      J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136
    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
    12/10/2024
    MGI 6.24     		The Jackson Laboratory