Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CLDN5 Gene

Aliases for CLDN5 Gene

  • Claudin 5 2 3 5
  • Transmembrane Protein Deleted In Velocardiofacial Syndrome 2 3
  • Transmembrane Protein Deleted In VCFS 3 4
  • TMDVCF 3 4
  • TMVCF 3 4
  • AWAL 3 4
  • Claudin-5 3
  • CPETRL1 3
  • BEC1 3

External Ids for CLDN5 Gene

Previous HGNC Symbols for CLDN5 Gene

  • AWAL

Previous GeneCards Identifiers for CLDN5 Gene

  • GC22M016450
  • GC22M017885
  • GC22M003131

Summaries for CLDN5 Gene

Entrez Gene Summary for CLDN5 Gene

  • This gene encodes a member of the claudin family. Claudins are integral membrane proteins and components of tight junction strands. Tight junction strands serve as a physical barrier to prevent solutes and water from passing freely through the paracellular space between epithelial or endothelial cell sheets. Mutations in this gene have been found in patients with velocardiofacial syndrome. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, May 2018]

GeneCards Summary for CLDN5 Gene

CLDN5 (Claudin 5) is a Protein Coding gene. Diseases associated with CLDN5 include Velocardiofacial Syndrome and Gray Platelet Syndrome. Among its related pathways are Blood-Brain Barrier and Immune Cell Transmigration: VCAM-1/CD106 Signaling Pathways and Sertoli-Sertoli Cell Junction Dynamics. Gene Ontology (GO) annotations related to this gene include identical protein binding and structural molecule activity. An important paralog of this gene is CLDN3.

UniProtKB/Swiss-Prot for CLDN5 Gene

  • Plays a major role in tight junction-specific obliteration of the intercellular space.

Gene Wiki entry for CLDN5 Gene

Additional gene information for CLDN5 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLDN5 Gene

Genomics for CLDN5 Gene

GeneHancer (GH) Regulatory Elements for CLDN5 Gene

Promoters and enhancers for CLDN5 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
GH22J019521 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 650.7 +4.4 4417 3 HNRNPUL1 MXI1 SUZ12 BACH1 ZIC2 ZFHX2 POLR2B POLR2A RBM22 EZH2 CLDN5 UFD1 MED15 RPL7AP70 DGCR11 LOC105372860 PIR41958
GH22J019527 Enhancer 0.6 ENCODE 650.7 -0.2 -230 1.4 MCM3 MAFG NR2F2 FOSL1 MCM7 ZSCAN16 POLR2A IKZF1 ZFP91 CLDN5 RPL7AP70 MED15 SCARF2 CLTCL1 DGCR11 LINC00895
GH22J019576 Enhancer 1.3 FANTOM5 Ensembl ENCODE 13.2 -49.5 -49502 1.7 HDGF HDAC1 ATF1 KLF17 ZNF335 ZNF766 GLIS2 EGR1 FOS ATF7 CLDN5 CDC45 UFD1 CLTCL1 LINC00895 GC22P019632
GH22J019579 Enhancer 1.1 FANTOM5 Ensembl ENCODE 14.7 -52.3 -52277 1.6 USF1 JUN MAX BMI1 ETV6 IKZF2 L3MBTL2 CAVIN1 BHLHE40 GTF2A2 DGCR8 TRMT2A CLDN5 MED15 DGCR11 UFD1 CDC45 RANBP1 LINC01311 LOC100420177
GH22J019607 Enhancer 1.1 Ensembl ENCODE dbSUPER 11.7 -80.2 -80151 1.1 KLF1 FOXA2 TAF1 KLF17 MAX RAD21 YY1 GATA2 EGR1 RNF2 CLDN5 CDC45 UFD1 GC22P019632 LINC00895
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLDN5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLDN5 gene promoter:
  • c-Myb
  • PPAR-alpha
  • TBP
  • Spz1
  • ATF-2
  • CRE-BP1
  • Zic3
  • MyoD
  • GATA-1
  • AP-2alpha

Genomic Locations for CLDN5 Gene

Genomic Locations for CLDN5 Gene
4,522 bases
Minus strand
4,522 bases
Minus strand

Genomic View for CLDN5 Gene

Genes around CLDN5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLDN5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLDN5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLDN5 Gene

Proteins for CLDN5 Gene

  • Protein details for CLDN5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B3KS11
    • Q53XW2
    • Q8WUW3

    Protein attributes for CLDN5 Gene

    218 amino acids
    Molecular mass:
    23147 Da
    Quaternary structure:
    • Directly interacts with TJP1/ZO-1, TJP2/ZO-2 and TJP3/ZO-3. Interacts with MPDZ (By similarity).

neXtProt entry for CLDN5 Gene

Post-translational modifications for CLDN5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CLDN5 Gene

Domains & Families for CLDN5 Gene

Gene Families for CLDN5 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for CLDN5 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 CLDN5: view

Function for CLDN5 Gene

Molecular function for CLDN5 Gene

UniProtKB/Swiss-Prot Function:
Plays a major role in tight junction-specific obliteration of the intercellular space.
GENATLAS Biochemistry:
claudin 5,clostridium perfringens enterotoxin receptor-like,transmembrane protein,integral membrane protein,claudin family of major structural components of tight junction (TJ) strands,expressed in lung,heart,skeletal muscle,homolog to rat ventral prostate protein,deleted in velocardiofacial syndrome,DiGeorge region

Phenotypes From GWAS Catalog for CLDN5 Gene

Gene Ontology (GO) - Molecular Function for CLDN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity IEA --
GO:0042802 identical protein binding ISS --
genes like me logo Genes that share ontologies with CLDN5: view
genes like me logo Genes that share phenotypes with CLDN5: view

Animal Models for CLDN5 Gene

MGI Knock Outs for CLDN5:

Animal Model Products

CRISPR Products

miRNA for CLDN5 Gene

miRTarBase miRNAs that target CLDN5

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLDN5

Clone Products

  • Addgene plasmids for CLDN5

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CLDN5 Gene

Localization for CLDN5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLDN5 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 CLDN5 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 2
nucleus 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for CLDN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IDA,IEA 25978380
GO:0005911 cell-cell junction IDA 18065521
GO:0005923 bicellular tight junction IEA,ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane TAS,IEA 9192844
genes like me logo Genes that share ontologies with CLDN5: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLDN5 Gene

Pathways & Interactions for CLDN5 Gene

genes like me logo Genes that share pathways with CLDN5: view

Gene Ontology (GO) - Biological Process for CLDN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003151 outflow tract morphogenesis TAS 9192844
GO:0007043 cell-cell junction assembly IMP 23288152
GO:0007179 transforming growth factor beta receptor signaling pathway IDA 21168935
GO:0007612 learning TAS 9192844
GO:0016338 calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules ISS --
genes like me logo Genes that share ontologies with CLDN5: view

No data available for SIGNOR curated interactions for CLDN5 Gene

Drugs & Compounds for CLDN5 Gene

(1) Drugs for CLDN5 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for CLDN5 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CLDN5: view

Transcripts for CLDN5 Gene

Unigene Clusters for CLDN5 Gene

Claudin 5:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLDN5

Clone Products

  • Addgene plasmids for CLDN5

Alternative Splicing Database (ASD) splice patterns (SP) for CLDN5 Gene

No ASD Table

Relevant External Links for CLDN5 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLDN5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLDN5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLDN5 Gene

This gene is overexpressed in Adipose - Subcutaneous (x4.1).

Protein differential expression in normal tissues from HIPED for CLDN5 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (21.6), Platelet (15.6), and Lung (15.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLDN5 Gene

NURSA nuclear receptor signaling pathways regulating expression of CLDN5 Gene:


SOURCE GeneReport for Unigene cluster for CLDN5 Gene:


Evidence on tissue expression from TISSUES for CLDN5 Gene

  • Nervous system(4.9)
  • Lung(4.6)
  • Heart(3.3)
  • Blood(2.8)
  • Eye(2.1)
  • Intestine(2.1)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with CLDN5: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLDN5 Gene

Orthologs for CLDN5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLDN5 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLDN5 34 33
  • 99.56 (n)
(Canis familiaris)
Mammalia CLDN5 33
  • 92.97 (n)
(Bos Taurus)
Mammalia CLDN5 34 33
  • 90.52 (n)
(Mus musculus)
Mammalia Cldn5 16 34 33
  • 87 (n)
(Rattus norvegicus)
Mammalia Cldn5 33
  • 86.09 (n)
(Ornithorhynchus anatinus)
Mammalia CLDN5 34
  • 71 (a)
(Gallus gallus)
Aves CLDN5 34 33
  • 76.85 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia cldn5 33
  • 68.83 (n)
(Danio rerio)
Actinopterygii cldn5a 34 33
  • 67.75 (n)
cldn5b 34
  • 55 (a)
cldnk 34
  • 49 (a)
FP102191.1 34
  • 40 (a)
Species where no ortholog for CLDN5 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)
  • lizard (Anolis carolinensis)
  • 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 CLDN5 Gene

Gene Tree for CLDN5 (if available)
Gene Tree for CLDN5 (if available)
Evolutionary constrained regions (ECRs) for CLDN5: view image

Paralogs for CLDN5 Gene

Paralogs for CLDN5 Gene

(18) SIMAP similar genes for CLDN5 Gene using alignment to 2 proteins:

  • D3DX19_HUMAN
genes like me logo Genes that share paralogs with CLDN5: view

Variants for CLDN5 Gene

Sequence variations from dbSNP and Humsavar for CLDN5 Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1001152998 -- 19,523,146(-) C/G 3_prime_UTR_variant
rs1001412506 -- 19,528,532(-) C/T upstream_transcript_variant
rs1001730761 -- 19,526,481(-) T/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1001851757 -- 19,523,168(-) G/A 3_prime_UTR_variant
rs1002010191 -- 19,527,528(-) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for CLDN5 Gene

Variant ID Type Subtype PubMed ID
dgv4478n100 CNV loss 25217958
esv2751940 CNV gain 17911159
esv3575418 CNV gain 25503493
esv3893434 CNV gain 25118596
nsv588216 CNV gain 21841781
nsv834127 CNV loss 17160897

Variation tolerance for CLDN5 Gene

Residual Variation Intolerance Score: 66.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.81; 83.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLDN5 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 CLDN5 Gene

Disorders for CLDN5 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CLDN5 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
velocardiofacial syndrome
  • cayler cardiofacial syndrome
gray platelet syndrome
  • gps
- elite association - COSMIC cancer census association via MalaCards
Search CLDN5 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLDN5

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CLDN5: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLDN5 Gene

Publications for CLDN5 Gene

  1. Identification, characterization, and precise mapping of a human gene encoding a novel membrane-spanning protein from the 22q11 region deleted in velo-cardio-facial syndrome. (PMID: 9192844) Sirotkin H … Kucherlapati R (Genomics 1997) 2 3 4 22 58
  2. Expression pattern of claudins 5 and 7 distinguishes solid-pseudopapillary from pancreatoblastoma, acinar cell and endocrine tumors of the pancreas. (PMID: 19194274) Comper F … Scarpa A (The American journal of surgical pathology 2009) 3 22 58
  3. Diagnostic utility of expression of claudins in non-small cell lung cancer: different expression profiles in squamous cell carcinomas and adenocarcinomas. (PMID: 19231096) Jung JH … Lee KY (Pathology, research and practice 2009) 3 22 58
  4. Structure and function of extracellular claudin domains. (PMID: 19538285) Krause G … Müller SL (Annals of the New York Academy of Sciences 2009) 3 22 58
  5. Claudin-5 overexpression correlates with aggressive behavior in serous ovarian adenocarcinoma. (PMID: 20044634) Turunen M … Santala M (Anticancer research 2009) 3 22 58

Products for CLDN5 Gene

  • Addgene plasmids for CLDN5

Sources for CLDN5 Gene

Loading form....