CLDN3
Basic information
Region (hg38): 7:73768997-73770270
Previous symbols: [ "C7orf1", "CPETR2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001306.4. 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 | 0 | |||||
| missense | 22 | 22 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 22 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CLDN3 | protein_coding | protein_coding | ENST00000395145 | 1 | 1273 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.522 | 0.463 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.33 | 106 | 152 | 0.697 | 0.00000997 | 1375 |
| Missense in Polyphen | 25 | 55.875 | 0.44743 | 584 | ||
| Synonymous | 1.15 | 69 | 82.2 | 0.839 | 0.00000621 | 506 |
| Loss of Function | 1.95 | 1 | 6.28 | 0.159 | 2.74e-7 | 52 |
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, through calcium- independent cell-adhesion activity. {ECO:0000250|UniProtKB:Q9Z0G9}.;
- Disease
- DISEASE: 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.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Tight junction - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);EMT transition in Colorectal Cancer;Tight junction interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication
(Consensus)
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- loftool
- rvis_EVS
- 0.42
- rvis_percentile_EVS
- 76.81
Haploinsufficiency Scores
- pHI
- 0.196
- hipred
- N
- hipred_score
- 0.481
- ghis
- 0.553
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- 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
- Cldn3
- Phenotype
Gene ontology
- Biological process
- response to hypoxia;epithelial cell morphogenesis;calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules;response to ethanol;protein homooligomerization;protein heterooligomerization;bicellular tight junction assembly
- Cellular component
- cytoplasm;integral component of plasma membrane;bicellular tight junction;integral component of membrane;apicolateral plasma membrane;lateral plasma membrane
- Molecular function
- transmembrane signaling receptor activity;structural molecule activity;identical protein binding