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Cldn6 Gene Detail
Summary
  • Symbol
    Cldn6
  • Name
    claudin 6
  • Feature Type
    protein coding gene
  • IDs
    MGI:1859284
    NCBI Gene: 54419
  • Alliance
    genome feature page
  • Transcription Start Sites
    6 TSS
Location &
Maps
more
  • Sequence Map
    Chr17:23898345-23901417 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 17, 11.99 cM
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    123 from dbSNP Build 142
  • Strain Annotations
    19
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1859284
 protein coding gene Chr17:23898223-23901420 (+)
129S1/SvImJ ENSMUSG00200037537
 protein coding gene Chr17:19322832-19326034 (+)
A/J ENSMUSG00195035620
 protein coding gene Chr17:20341031-20344233 (+)
AKR/J ENSMUSG00220022010
 protein coding gene Chr17:19396239-19399436 (+)
BALB/cJ ENSMUSG00180014487
 protein coding gene Chr17:19623643-19626845 (+)
C3H/HeJ ENSMUSG00175033759
 protein coding gene Chr17:19409345-19412542 (+)
C57BL/6NJ ENSMUSG00215039801
 protein coding gene Chr17:19405955-19409152 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0021153
 protein coding gene Chr17:19514032-19517120 (+)
CAST/EiJ ENSTCUG00005022099
 protein coding gene Chr17:19988309-19991519 (+)
CBA/J ENSMUSG00210033573
 protein coding gene Chr17:19248204-19251401 (+)
DBA/2J ENSMUSG00185050950
 protein coding gene Chr17:21429844-21433046 (+)
FVB/NJ ENSMUSG00205017396
 protein coding gene Chr17:19699326-19702523 (+)
JF1/MsJ ENSUMUG00000053315
 protein coding gene Chr17:20904368-20907577 (+)
LP/J ENSMUSG00230054762
 protein coding gene Chr17:22827749-22830951 (+)
NOD/ShiLtJ ENSMUSG00190023507
 protein coding gene Chr17:19328118-19331320 (+)
NZO/HlLtJ ENSMUSG00225049750
 protein coding gene Chr17:24750814-24754016 (+)
PWK/PhJ ENSLUMG00010019383
 protein coding gene Chr17:18799820-18803030 (+)
SPRET/EiJ ENSMSPG00010032510
 protein coding gene Chr17:20153272-20156615 (+)
WSB/EiJ ENSIUOG00005034265
 protein coding gene Chr17:20076727-20079924 (+)



Homology
more
  • Human Ortholog
    CLDN6, claudin 6
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    CLDN6, claudin 6
  • Links
    NCBI Gene ID: 9074
    UniProt: P56747

  • Chr Location
    16p13.3; chr16:3014705-3020071 (-)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    1 phenotype from 1 allele in 1 genetic background
    10 phenotypes from multigenic genotypes
    3 images
    12 phenotype references
Mice homozygous for a null allele do not exhibit overt abnormalities.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    27
  • GO References
    12
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
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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
    825
  • Tissues
    171
  • cDNA Data
    49
  • Literature Summary
    30
Sequences &
Gene Models
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Representative SequencesLengthStrain/SpeciesFlank
genomic 54419 NCBI Gene Model | MGI Sequence Detail 3073 C57BL/6J ±  kb
transcript NM_001439480 RefSeq | MGI Sequence Detail 1524 C57BL/6  
polypeptide Q9Z262 UniProt | EBI | MGI Sequence Detail 219 Not Applicable  
For the selected sequence
Protein
Information
less
Molecular
Reagents
less
  • All nucleic 58
    cDNA 49
    Primer pair 6
    Other 3
    Antibodies 4

    Microarray probesets 5
Other
Accession IDs
less
MGI:2146955
References
more
  • Summaries
    All 81
    Developmental Gene Expression 30
    Gene Ontology 12
    Phenotypes 12
  • Earliest
    J:58914 Itoh M, et al., Direct binding of three tight junction-associated MAGUKs, ZO-1, ZO-2, and ZO-3, with the COOH termini of claudins. J Cell Biol. 1999 Dec 13;147(6):1351-63
  • Latest
    J:367359 Menezes NA, et al., Cell-context response to germ layer differentiation signals is predetermined by the epigenome in regionalized epiblast populations. Nat Commun. 2025 May 29;16(1):5000
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)
Citing These Resources
Funding Information
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Send questions and comments to User Support. 		last database update
09/08/2026
MGI 6.24 		The Jackson Laboratory