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Aliases for CLDN3 Gene

Aliases for CLDN3 Gene

  • Claudin 3 2 3 5
  • Clostridium Perfringens Enterotoxin Receptor 2 2 3 4
  • CPE-Receptor 2 2 3 4
  • Ventral Prostate.1-Like Protein 2 3
  • Claudin-3 2 3
  • CPE-R 2 3 4
  • C7orf1 3 4
  • CPETR2 3 4
  • HRVP1 3 4
  • Rat Ventral Prostate.1 Protein Homolog 4
  • Ventral Prostate.1 Protein Homolog 3
  • CPE-R2 3
  • RVP1 3

External Ids for CLDN3 Gene

Previous HGNC Symbols for CLDN3 Gene

  • C7orf1
  • CPETR2

Previous GeneCards Identifiers for CLDN3 Gene

  • GC07M071823
  • GC07M072581
  • GC07M072595
  • GC07M072627
  • GC07M072821
  • GC07M073183
  • GC07M069065

Summaries for CLDN3 Gene

Entrez Gene Summary for CLDN3 Gene

  • Tight junctions represent one mode of cell-to-cell adhesion in epithelial or endothelial cell sheets, forming continuous seals around cells and serving as a physical barrier to prevent solutes and water from passing freely through the paracellular space. These junctions are comprised of sets of continuous networking strands in the outwardly facing cytoplasmic leaflet, with complementary grooves in the inwardly facing extracytoplasmic leaflet. The protein encoded by this intronless gene, a member of the claudin family, is an integral membrane protein and a component of tight junction strands. It is also a low-affinity receptor for Clostridium perfringens enterotoxin, and shares aa sequence similarity with a putative apoptosis-related protein found in rat. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLDN3 Gene

CLDN3 (Claudin 3) is a Protein Coding gene. Diseases associated with CLDN3 include Ovarian Cancer and Williams-Beuren Syndrome. Among its related pathways are Adhesion and Blood-Brain Barrier and Immune Cell Transmigration: VCAM-1/CD106 Signaling Pathways. GO annotations related to this gene include identical protein binding and structural molecule activity. An important paralog of this gene is CLDN4.

UniProtKB/Swiss-Prot for CLDN3 Gene

  • Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity.

Gene Wiki entry for CLDN3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLDN3 Gene

Genomics for CLDN3 Gene

Regulatory Elements for CLDN3 Gene

Enhancers for CLDN3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07F073736 1.8 FANTOM5 Ensembl ENCODE 2.1 +29.5 29546 7.8 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 WBSCR27 ABHD11-AS1 SPDYE7P WBSCR22 FKBP6 LOC100101148 POM121B MIR590 ABHD11 CLDN4
GH07F073821 1.6 FANTOM5 Ensembl ENCODE 1.5 -52.7 -52714 3.1 HDGF ATF1 PKNOX1 SIN3A GLIS2 ELK1 GATA2 FOS KLF13 SP5 WBSCR27 VPS37D ABHD11-AS1 CLDN4 CLDN3 GC07P073835
GH07F073773 0.8 Ensembl ENCODE 0.8 -3.6 -3626 1.7 JUN CEBPA HNF4G RAD21 YY1 WBSCR27 ABHD11-AS1 CLDN3 CLDN4
GH07F073775 0.8 ENCODE 0.8 -4.8 -4844 0.0 JUN BACH1 CDC5L ZNF316 NCOR1 NFE2 TRIM24 FOS MAFK NFE2L2 CLDN3 CLDN4
GH07F073791 1.2 Ensembl ENCODE 0.3 -22.9 -22895 3.0 HDGF PKNOX1 ATF1 ARNT CBX5 ELK1 GATA2 FOS NFYC ZHX2 WBSCR27 ABHD11 CLDN4 CLDN3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLDN3 on UCSC Golden Path with GeneCards custom track

Promoters for CLDN3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000628153 70 1201 PKNOX1 SIN3A GLIS2 SCRT2 KLF7 FOS EGR2 ZNF263 SP3 ZEB2

Genomic Location for CLDN3 Gene

73,768,997 bp from pter
73,770,270 bp from pter
1,274 bases
Minus strand

Genomic View for CLDN3 Gene

Genes around CLDN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLDN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLDN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLDN3 Gene

Proteins for CLDN3 Gene

  • Protein details for CLDN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:

    Protein attributes for CLDN3 Gene

    220 amino acids
    Molecular mass:
    23319 Da
    Quaternary structure:
    • Can form homo- and heteropolymers with other CLDN. Homopolymers interact with CLDN1 and CLDN2 homopolymers. Directly interacts with TJP1/ZO-1, TJP2/ZO-2 and TJP3/ZO-3 (By similarity).

neXtProt entry for CLDN3 Gene

Post-translational modifications for CLDN3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLDN3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLDN3 Gene

Domains & Families for CLDN3 Gene

Gene Families for CLDN3 Gene

Suggested Antigen Peptide Sequences for CLDN3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the claudin family.
  • Belongs to the claudin family.
genes like me logo Genes that share domains with CLDN3: view

Function for CLDN3 Gene

Molecular function for CLDN3 Gene

GENATLAS Biochemistry:
claudin 3,clostridium perfringens enterotoxin receptor 2,low affinity,integral membrane protein,claudin family of major structural components of tight junction (TJ) strands,mainly expressed in lung and liver,also in kidney and testis
UniProtKB/Swiss-Prot Function:
Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity.

Gene Ontology (GO) - Molecular Function for CLDN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004888 transmembrane signaling receptor activity TAS 9334247
GO:0005198 structural molecule activity IEA --
GO:0042802 identical protein binding IEA --
genes like me logo Genes that share ontologies with CLDN3: view
genes like me logo Genes that share phenotypes with CLDN3: view

Animal Models for CLDN3 Gene

MGI Knock Outs for CLDN3:

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for CLDN3 Gene

Localization for CLDN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLDN3 Gene

Cell junction, tight junction. Cell membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLDN3 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 2
nucleus 1

Gene Ontology (GO) - Cellular Components for CLDN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane TAS 9334247
GO:0005923 bicellular tight junction ISS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with CLDN3: view

Pathways & Interactions for CLDN3 Gene

genes like me logo Genes that share pathways with CLDN3: view

SIGNOR curated interactions for CLDN3 Gene

Other effect:

Gene Ontology (GO) - Biological Process for CLDN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEP 15174142
GO:0003382 epithelial cell morphogenesis ISS --
GO:0007165 signal transduction IEA --
GO:0016338 calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules IEA --
GO:0045471 response to ethanol IEA --
genes like me logo Genes that share ontologies with CLDN3: view

Drugs & Compounds for CLDN3 Gene

(3) Drugs for CLDN3 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0

(2) Additional Compounds for CLDN3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CLDN3: view

Transcripts for CLDN3 Gene

mRNA/cDNA for CLDN3 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(412) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLDN3 Gene

Claudin 3:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLDN3 Gene

No ASD Table

Relevant External Links for CLDN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLDN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLDN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLDN3 Gene

This gene is overexpressed in Colon - Transverse (x19.7), Small Intestine - Terminal Ileum (x6.9), and Pancreas (x4.7).

Protein differential expression in normal tissues from HIPED for CLDN3 Gene

This gene is overexpressed in Nasal epithelium (43.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CLDN3 Gene

Protein tissue co-expression partners for CLDN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of CLDN3 Gene:


SOURCE GeneReport for Unigene cluster for CLDN3 Gene:

genes like me logo Genes that share expression patterns with CLDN3: view

No data available for mRNA Expression by UniProt/SwissProt for CLDN3 Gene

Orthologs for CLDN3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLDN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLDN3 34 35
  • 99.39 (n)
(Canis familiaris)
Mammalia CLDN3 34 35
  • 92.81 (n)
(Bos Taurus)
Mammalia CLDN3 34 35
  • 91.02 (n)
(Mus musculus)
Mammalia Cldn3 34 16 35
  • 87.37 (n)
(Rattus norvegicus)
Mammalia Cldn3 34
  • 86 (n)
(Ornithorhynchus anatinus)
Mammalia CLDN3 35
  • 76 (a)
(Gallus gallus)
Aves CLDN3 34 35
  • 80.37 (n)
(Anolis carolinensis)
Reptilia CLDN3 35
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cldn3 34
  • 67.61 (n)
(Danio rerio)
Actinopterygii LOC792492 34
  • 68.22 (n)
cldnh 35
  • 64 (a)
cldnc 35
  • 60 (a)
cldne 34
Species where no ortholog for CLDN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLDN3 Gene

Gene Tree for CLDN3 (if available)
Gene Tree for CLDN3 (if available)

Paralogs for CLDN3 Gene

(19) SIMAP similar genes for CLDN3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CLDN3: view

Variants for CLDN3 Gene

Sequence variations from dbSNP and Humsavar for CLDN3 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs10709722 -- 73,768,942(+) GCCCC(-/G)AGGGG downstream-variant-500B
rs111495077 -- 73,771,076(+) GGTTC(C/G)ATCTC upstream-variant-2KB
rs111698034 -- 73,768,679(+) AATGT(G/T)TCGGG downstream-variant-500B
rs112155256 -- 73,771,999(+) CAAAG(C/G)GAGAC upstream-variant-2KB
rs112833390 -- 73,771,735(+) TGGCT(A/G)GGTAC upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for CLDN3 Gene

Variant ID Type Subtype PubMed ID
esv2761337 CNV loss 21179565
nsv469841 CNV loss 16826518
nsv5791 CNV insertion 18451855
nsv831028 CNV loss 17160897
nsv831029 CNV loss 17160897

Variation tolerance for CLDN3 Gene

Residual Variation Intolerance Score: 70.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.18; 23.79% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLDN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLDN3 Gene

Disorders for CLDN3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for CLDN3 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
ovarian cancer
  • malignant ovarian tumor
williams-beuren syndrome
  • fanconi schlesinger syndrome
prostate transitional cell carcinoma
  • transitional cell carcinoma of prostate
endometrial cancer
  • endometrial cancer, familial
- elite association - COSMIC cancer census association via MalaCards
Search CLDN3 in MalaCards View complete list of genes associated with diseases


  • Note=CLDN3 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region.

Relevant External Links for CLDN3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CLDN3: view

No data available for Genatlas for CLDN3 Gene

Publications for CLDN3 Gene

  1. Analysis of a human gene homologous to rat ventral prostate.1 protein. (PMID: 9441748) Peacock R.E. … Inglehearn C.F. (Genomics 1997) 2 3 4 22 64
  2. Clostridium perfringens enterotoxin utilizes two structurally related membrane proteins as functional receptors in vivo. (PMID: 9334247) Katahira J. … Sugimoto N. (J. Biol. Chem. 1997) 3 4 22 64
  3. Derepression of CLDN3 and CLDN4 during ovarian tumorigenesis is associated with loss of repressive histone modifications. (PMID: 20053926) Kwon M.J. … Shin Y.K. (Carcinogenesis 2010) 3 22 64
  4. Claudin expression profiles in Epstein-Barr virus-associated nasopharyngeal carcinoma. (PMID: 20204275) Kojima F. … Okabe H. (Oncol. Rep. 2010) 3 22 64
  5. Urine-based detection of intestinal tight junction loss. (PMID: 19525861) Thuijls G. … Buurman W.A. (J. Clin. Gastroenterol. 2010) 3 22 64

Products for CLDN3 Gene

Sources for CLDN3 Gene

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