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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 Papillary Carcinoma and Williams-Beuren Syndrome. Among its related pathways are Cytoskeletal Signaling and Blood-Brain Barrier and Immune Cell Transmigration: VCAM-1/CD106 Signaling Pathways. Gene Ontology (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

Additional gene information for CLDN3 Gene

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

Genomics for CLDN3 Gene

GeneHancer (GH) Regulatory Elements for CLDN3 Gene

Promoters and enhancers for CLDN3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07J073766 Promoter/Enhancer 1.6 Ensembl ENCODE dbSUPER 650.7 +0.9 940 4.9 PKNOX1 CLOCK SIN3A ZBTB7B ZNF121 GLIS2 KLF7 FOS SP3 RXRA CLDN3 GC07M073770 GC07M073769 METTL27 ABHD11-AS1 GC07P073744
GH07J073736 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 2.1 +29.5 29545 7.8 CLOCK ZFP64 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 ZNF610 GLIS1 ABHD11 GC07P073742 GC07P073741 METTL27 STAG3L3 POM121B ABHD11-AS1 POM121 NSUN5P2 MIR590
GH07J073821 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 1.5 -52.7 -52714 3.1 HDGF PKNOX1 CLOCK ATF1 ARNT NEUROD1 SIN3A GLIS2 CBX5 GATA2 METTL27 VPS37D ABHD11-AS1 CLDN4 CLDN3 GC07P073835
GH07J073773 Enhancer 0.9 ENCODE dbSUPER 0.7 -3.6 -3626 1.7 HDAC1 FOXA2 RXRA NFIB JUN MAX REST RAD21 YY1 SP1 METTL27 ABHD11-AS1 CLDN3 CLDN4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLDN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLDN3 gene promoter:
  • ATF
  • Sp1
  • NRSF form 2
  • NRSF form 1
  • GR
  • GR-beta

Genomic Locations for CLDN3 Gene

Genomic Locations for CLDN3 Gene
1,274 bases
Minus strand
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

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Potential drug targets
  • Predicted membrane proteins
  • Transporters

Protein Domains 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

UniProtKB/Swiss-Prot Function:
Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity.
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

Phenotypes From GWAS Catalog for CLDN3 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLDN3

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 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (3)
See all subcellular structures

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,IEA --
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 Approved 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:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLDN3

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 CGAP 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, 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:


Evidence on tissue expression from TISSUES for CLDN3 Gene

  • Intestine(5)
  • Liver(4.3)
  • Pancreas(3.9)
  • Kidney(2.7)
  • Blood(2)
genes like me logo Genes that share expression patterns with CLDN3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33
  • 99.39 (n)
(Canis familiaris)
Mammalia CLDN3 34 33
  • 92.81 (n)
(Bos Taurus)
Mammalia CLDN3 34 33
  • 91.02 (n)
(Mus musculus)
Mammalia Cldn3 16 34 33
  • 87.37 (n)
(Rattus norvegicus)
Mammalia Cldn3 33
  • 86 (n)
(Ornithorhynchus anatinus)
Mammalia CLDN3 34
  • 76 (a)
(Gallus gallus)
Aves CLDN3 34 33
  • 80.37 (n)
(Anolis carolinensis)
Reptilia CLDN3 34
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cldn3 33
  • 67.61 (n)
(Danio rerio)
Actinopterygii LOC792492 33
  • 68.22 (n)
cldnh 34
  • 64 (a)
cldnc 34
  • 60 (a)
cldne 33
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)
Evolutionary constrained regions (ECRs) for CLDN3: view image

Paralogs for CLDN3 Gene

Paralogs for CLDN3 Gene

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

  • Q75L79_HUMAN
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 Variation AA Info Type
rs1000919133 -- 73,771,592(-) G/A upstream_transcript_variant
rs1001433654 -- 73,771,989(-) G/A upstream_transcript_variant
rs1003490578 -- 73,769,593(-) C/T coding_sequence_variant, missense_variant
rs1003831227 -- 73,770,020(-) G/A coding_sequence_variant, synonymous_variant
rs1005430918 -- 73,769,294(-) G/A 3_prime_UTR_variant

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)

Additional Variant Information for CLDN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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
papillary carcinoma
  • carcinoma papillary
williams-beuren syndrome
  • wbs
prostate transitional cell carcinoma
  • transitional cell carcinoma of prostate
ovarian cancer
  • ovarian cancer, somatic
- 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.

Additional Disease Information for CLDN3

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 RE … Inglehearn CF (Genomics 1997) 2 3 4 22 58
  2. Clostridium perfringens enterotoxin utilizes two structurally related membrane proteins as functional receptors in vivo. (PMID: 9334247) Katahira J … Sugimoto N (The Journal of biological chemistry 1997) 3 4 22 58
  3. Urine-based detection of intestinal tight junction loss. (PMID: 19525861) Thuijls G … Buurman WA (Journal of clinical gastroenterology 2010) 3 22 58
  4. Derepression of CLDN3 and CLDN4 during ovarian tumorigenesis is associated with loss of repressive histone modifications. (PMID: 20053926) Kwon MJ … Shin YK (Carcinogenesis 2010) 3 22 58
  5. Claudin expression profiles in Epstein-Barr virus-associated nasopharyngeal carcinoma. (PMID: 20204275) Kojima F … Okabe H (Oncology reports 2010) 3 22 58

Products for CLDN3 Gene

Sources for CLDN3 Gene

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