CLDN5
claudin 5, the group of Claudins
Basic information
Region (hg38): 22:19523024-19527545
Previous symbols: [ "AWAL", "TMVCF" ]
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (15 variants)
- not_provided (10 variants)
- CLDN5-related_neurodevelopmental_disorder (3 variants)
- Neurodevelopmental_disorder (1 variants)
- CLDN5-associated_neurodevelopmental_disorder (1 variants)
- Neurodevelopmental_abnormality (1 variants)
- CLDN5_deficiency (1 variants)
- Syndromic_disease (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001363066.2. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 16 | 24 | ||||
| nonsense | 3 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 3 | 1 | 19 | 4 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CLDN5 | protein_coding | protein_coding | ENST00000406028 | 1 | 4522 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.895 | 0.104 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.44 | 108 | 159 | 0.679 | 0.00000720 | 1835 |
| Missense in Polyphen | 19 | 55.492 | 0.34239 | 595 | ||
| Synonymous | 0.384 | 74 | 78.3 | 0.945 | 0.00000376 | 696 |
| Loss of Function | 2.50 | 0 | 7.31 | 0.00 | 3.18e-7 | 68 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a major role in tight junction-specific obliteration of the intercellular space. {ECO:0000250}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Tight junction - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Exercise-induced Circadian Regulation;Transcriptional regulation by RUNX1;EMT transition in Colorectal Cancer;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Tight junction interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication;RUNX1 regulates expression of components of tight junctions;Transcriptional regulation by RUNX1
(Consensus)
Recessive Scores
- pRec
- 0.286
Haploinsufficiency Scores
- pHI
- 0.205
- hipred
- N
- hipred_score
- 0.493
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.694
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cldn5
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- cldn5a
- Affected structure
- neuroepithelial cell
- Phenotype tag
- abnormal
- Phenotype quality
- increased permeability
Gene ontology
- Biological process
- outflow tract morphogenesis;cell-cell junction assembly;transforming growth factor beta receptor signaling pathway;learning;calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules;roof of mouth development;face morphogenesis;positive regulation of establishment of endothelial barrier;regulation of bicellular tight junction assembly
- Cellular component
- plasma membrane;cell-cell junction;bicellular tight junction;integral component of membrane;apicolateral plasma membrane;cell junction;cortical actin cytoskeleton
- Molecular function
- structural molecule activity;identical protein binding