CLDN5 Gene (Protein Coding)

Claudin 5

GC22M019523
GIFtS:
43
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 velocardiofaci... See more...

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
  • Claudin-5 3 4
  • CPETRL1 2 3
  • TMDVCF 3 4
  • TMVCF 3 4
  • AWAL 3 4
  • BEC1 2 3
  • CLDN5 5

External Ids for CLDN5 Gene

Previous HGNC Symbols for CLDN5 Gene

  • AWAL
  • TMVCF

Previous GeneCards Identifiers for CLDN5 Gene

  • GC22M016450
  • GC22M017885
  • GC22M019510
  • 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 Brain Edema. 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 CLDN6.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for CLDN5 Gene

Genomics for CLDN5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CLDN5 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 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 CraniofacialAtlas 250.7 +4.3 4344 4.4 ZIC2 SAFB MYNN CBX1 POLR2A SUPT5H STAT5A ZBTB33 HNRNPL SP1 CLDN5 ENSG00000287652 UFD1 MED15 RPL7AP70 DGCR11 ENSG00000185065 CDC45 LINC00895
GH22J019527 Enhancer 0.5 ENCODE 250.7 -0.2 -230 1.4 ZSCAN16 IKZF1 MCM7 MCM3 ZFP91 FOSL1 MAFG NR2F2 CLDN5 RPL7AP70 MED15 SCARF2 CLTCL1 DGCR11 LINC00895 SEPTIN5
GH22J019576 Enhancer 1.3 FANTOM5 Ensembl ENCODE 14.7 -51.2 -51156 5.4 IKZF1 MBD2 BHLHE40 ARNT ZNF623 ZNF395 VEZF1 RUNX1 ZEB2 GABPA DGCR8 TRMT2A CLDN5 MED15 DGCR11 CDC45 UFD1 RANBP1 LINC01311 ENSG00000215493
GH22J019604 Enhancer 1.2 Ensembl ENCODE dbSUPER 11.7 -80.5 -80456 7.2 FEZF1 CEBPA MNT IKZF1 HES1 BHLHE40 MCM7 MCM3 VEZF1 RUNX1 RPL7AP70 MED15 ENSG00000273300 TRMT2A CLDN5 UFD1 CDC45 SCARF2 RPL8P5 DGCR8
GH22J019629 Enhancer 1.1 Ensembl ENCODE 12.1 -102.4 -102417 1.1 TBP MNT IRF2 CTCF BHLHE40 NONO HOMEZ THAP11 ARNT REST TRMT2A DGCR8 MED15 ENSG00000273300 CLDN5 SEPTIN5 GP1BB CDC45 UFD1 RPL7AP70
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLDN5

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

Genomic Locations for CLDN5 Gene

Latest Assembly
chr22:19,523,024-19,527,545
(GRCh38/hg38)
Size:
4,522 bases
Orientation:
Minus strand

Previous Assembly
chr22:19,510,547-19,512,860
(GRCh37/hg19 by Entrez Gene)
Size:
2,314 bases
Orientation:
Minus strand

chr22:19,510,547-19,515,068
(GRCh37/hg19 by Ensembl)
Size:
4,522 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for CLDN5 Gene

Proteins for CLDN5 Gene

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

    Protein Symbol:
    O00501-CLD5_HUMAN
    Recommended name:
    Claudin-5
    Protein Accession:
    O00501
    Secondary Accessions:
    • B3KS11
    • Q53XW2
    • Q8WUW3

    Protein attributes for CLDN5 Gene

    Size:
    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

Protein Expression for CLDN5 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CLDN5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLDN5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLDN5 Gene

Domains & Families for CLDN5 Gene

Gene Families for CLDN5 Gene

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

Protein Domains for CLDN5 Gene

InterPro:
Blocks:
  • Claudin family signature
  • Claudin-5 signature
ProtoNet:

Suggested Antigen Peptide Sequences for CLDN5 Gene

GenScript: Design optimal peptide antigens:
  • Transmembrane protein deleted in VCFS (CLD5_HUMAN)
  • Claudin 5 (Transmembrane protein deleted in velocardiofacial syndrome), isoform CRA_a (D3DX19_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O00501

UniProtKB/Swiss-Prot:

CLD5_HUMAN :
  • Belongs to the claudin family.
Family:
  • Belongs to the claudin family.
genes like me logo Genes that share domains with CLDN5: view

Function for CLDN5 Gene

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  6. Cell Lines for research

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:0005515 protein binding IPI 25323998
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 Models for research

miRNA for CLDN5 Gene

miRTarBase miRNAs that target CLDN5

Inhibitory RNAs for research

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

Clone products for research

  • 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

COMPARTMENTS
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 3
cytoskeleton 3
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
endosome 2
cytosol 2
lysosome 2
peroxisome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CLDN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA,IDA 23137377
GO:0005911 cell-cell junction IMP 25753039
GO:0005923 bicellular tight junction IEA,ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,TAS 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

Pathways by source for CLDN5 Gene

1 BioSystems pathway for CLDN5 Gene
2 GeneGo (Thomson Reuters) pathways for CLDN5 Gene
  • Cell adhesion Tight junctions
  • Cell adhesion_Endothelial cell contacts by junctional mechanisms
3 Qiagen pathways for CLDN5 Gene
  • Epithelial Tight Junctions
  • Sertoli-Sertoli Cell Junction Dynamics
  • Transendothelial Migration of Leukocytes

SIGNOR curated interactions for CLDN5 Gene

Is activated by:

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:0007155 cell adhesion IBA 21873635
GO:0007179 transforming growth factor beta receptor signaling pathway IDA 21168935
GO:0007612 learning TAS 9192844
genes like me logo Genes that share ontologies with CLDN5: view

Drugs & Compounds for CLDN5 Gene

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(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

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mRNA/cDNA for CLDN5 Gene

4 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

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

Clone products for research

  • 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
CLDN5

Expression for CLDN5 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLDN5 Gene

mRNA expression in normal human tissues for CLDN5 Gene
mRNA expression by GTEx for CLDN5 GenemRNA expression by BioGPS 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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLDN5

SOURCE GeneReport for Unigene cluster for CLDN5 Gene:

Hs.505337

Evidence on tissue expression from TISSUES for CLDN5 Gene

  • Nervous system(4.9)
  • Lung(4.7)
  • Heart(3.3)
  • Blood(2.8)
  • Muscle(2.8)
  • Intestine(2.6)
  • Eye(2.5)
  • Kidney(2.5)
  • Skin(2.4)
  • Stomach(2.1)
  • Spleen(2)
  • Liver(2)
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
Chimpanzee
(Pan troglodytes)
 Mammalia CLDN5 30 31
  • 99.56 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CLDN5 30
  • 92.97 (n)
Cow
(Bos Taurus)
 Mammalia CLDN5 30 31
  • 90.52 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Cldn5 30 17 31
  • 87 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Cldn5 30
  • 86.09 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia CLDN5 31
  • 71 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves CLDN5 30 31
  • 76.85 (n)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia cldn5 30
  • 68.83 (n)
Zebrafish
(Danio rerio)
 Actinopterygii cldn5a 30 31
  • 67.75 (n)
 OneToMany
cldn5b 31
  • 55 (a)
 OneToMany
cldnk 31
  • 49 (a)
 OneToMany
FP102191.1 31
  • 40 (a)
 OneToMany
Species where no ortholog for CLDN5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for CLDN5 (if available)
TreeFam:
Gene Tree for CLDN5 (if available)
Aminode:
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:

  • CLD5_HUMAN
  • D3DX19_HUMAN
genes like me logo Genes that share paralogs with CLDN5: view

Variants for CLDN5 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLDN5 Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
984617 Uncertain Significance: Neurodevelopmental abnormality 19,524,092(-) A/G
NM_003277.4(CLDN5):c.419T>C (p.Val140Ala) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CLDN5 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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
CLDN5

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLDN5 Gene

Disorders for CLDN5 Gene

MalaCards: The human disease database

(9) MalaCards diseases for CLDN5 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
velocardiofacial syndrome
  • vcfs
brain edema
  • intracranial swelling
lymphocytic colitis
  • colitis, lymphocytic
meningoencephalitis
demyelinating polyneuropathy
  • peripheral demyelinating neuropathy
- 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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 23
  2. Claudin-5 overexpression correlates with aggressive behavior in serous ovarian adenocarcinoma. (PMID: 20044634) Turunen M … Santala M (Anticancer research 2009) 3 23
  3. 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 23
  4. 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 23
  5. Structure and function of extracellular claudin domains. (PMID: 19538285) Krause G … Müller SL (Annals of the New York Academy of Sciences 2009) 3 23

ExternalLinks

View latest publications for CLDN5 gene in Mastermind

Products for CLDN5 Gene

  • Addgene plasmids for CLDN5

Sources for CLDN5 Gene