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Cldn1 Gene Detail
Summary
  • Symbol
    Cldn1
  • Name
    claudin 1
  • Feature Type
    protein coding gene
  • IDs
    MGI:1276109
    NCBI Gene: 12737
  • Alliance
    genome feature page
  • Transcription Start Sites
    7 TSS
Location &
Maps
more
  • Sequence Map
    Chr16:26175395-26190589 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 16, 18.00 cM
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    520 from dbSNP Build 142
  • Strain Annotations
    19
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1276109
 protein coding gene Chr16:26175392-26190591 (-)
129S1/SvImJ ENSMUSG00200035162
 protein coding gene Chr16:23193204-23208387 (-)
A/J ENSMUSG00195028696
 protein coding gene Chr16:22733314-22748505 (-)
AKR/J ENSMUSG00220029970
 protein coding gene Chr16:23051357-23066546 (-)
BALB/cJ ENSMUSG00180027755
 protein coding gene Chr16:22969834-22985029 (-)
C3H/HeJ ENSMUSG00175034449
 protein coding gene Chr16:23123267-23138450 (-)
C57BL/6NJ ENSMUSG00215018365
 protein coding gene Chr16:22847391-22862592 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0020627
 protein coding gene Chr16:23514197-23529636 (-)
CAST/EiJ ENSTCUG00005034420
 protein coding gene Chr16:23445338-23460467 (-)
CBA/J ENSMUSG00210032284
 protein coding gene Chr16:23144801-23159984 (-)
DBA/2J ENSMUSG00185018017
 protein coding gene Chr16:23083704-23098889 (-)
FVB/NJ ENSMUSG00205016998
 protein coding gene Chr16:23069800-23084996 (-)
JF1/MsJ ENSUMUG00000028322
 protein coding gene Chr16:23297661-23312782 (-)
LP/J ENSMUSG00230030460
 protein coding gene Chr16:25653767-25668950 (-)
NOD/ShiLtJ ENSMUSG00190028532
 protein coding gene Chr16:23229748-23244938 (-)
NZO/HlLtJ ENSMUSG00225037444
 protein coding gene Chr16:28905055-28920262 (-)
PWK/PhJ ENSLUMG00010031076
 protein coding gene Chr16:23131164-23146320 (-)
SPRET/EiJ ENSMSPG00010017690
 protein coding gene Chr16:23068164-23081307 (-)
WSB/EiJ ENSIUOG00005031744
 protein coding gene Chr16:23354589-23369777 (-)



Homology
more
  • Human Ortholog
    CLDN1, claudin 1
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    CLDN1, claudin 1
  • Synonyms
    CLD1, ILVASC, SEMP1
  • Links
    NCBI Gene ID: 9076
    UniProt: O95832

  • Chr Location
    3q28; chr3:190305707-190322446 (-)  GRCh38
Human Diseases
more
  • Diseases
    1 with Cldn1 mouse models; 2 with human CLDN1 associations

Human Disease Mouse Models
      
IDs
 View 2 models
      
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    2 with disease annotations
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    26 phenotypes from 4 alleles in 5 genetic backgrounds
    4 images
    18 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.
Animals homozygous for a mutation in this gene have wrinkled skin and die within 1 day after birth.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    84
  • GO References
    24
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
    851
  • Tissues
    118
  • cDNA Data
    75
  • Literature Summary
    63
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 12737 NCBI Gene Model | MGI Sequence Detail 15195 C57BL/6J ±  kb
    transcript NM_016674 RefSeq | MGI Sequence Detail 3263 C57BL/6  
    polypeptide O88551 UniProt | EBI | MGI Sequence Detail 211 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 82
      cDNA 75
      Primer pair 7
      Antibodies 11

      Microarray probesets 5
    Other
    Accession IDs
    less
    MGI:2146462
    References
    more
    • Summaries
      All 175
      Developmental Gene Expression 63
      Diseases 1
      Gene Ontology 24
      Phenotypes 18
    • Earliest
      J:48635 Furuse M, et al., Claudin-1 and -2: novel integral membrane proteins localizing at tight junctions with no sequence similarity to occludin. J Cell Biol. 1998 Jun 29;141(7):1539-50
    • Latest
      J:390258 Dalal V, et al., Transcription factor 21 deletion from podocyte precursors as a model for congenital nephrotic syndrome. Am J Physiol Renal Physiol. 2026 Jun 1;330(6):F746-F760
    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
    09/01/2026
    MGI 6.24     		The Jackson Laboratory