CLDN4
claudin 4, the group of Claudins
Basic information
Region (hg38): 7:73799542-73832690
Previous symbols: [ "CPETR", "CPETR1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLDN4 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 13 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 2 | 0 |
Variants in CLDN4
This is a list of pathogenic ClinVar variants found in the CLDN4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-73831234-C-T | Likely benign (Jan 01, 2022) | |||
| 7-73831262-G-A | not specified | Uncertain significance (Aug 08, 2024) | ||
| 7-73831329-C-T | not specified | Uncertain significance (Jan 20, 2025) | ||
| 7-73831391-T-C | not specified | Uncertain significance (Jul 14, 2022) | ||
| 7-73831419-T-A | not specified | Uncertain significance (May 25, 2022) | ||
| 7-73831422-C-T | not specified | Uncertain significance (Jan 01, 2025) | ||
| 7-73831443-G-A | not specified | Uncertain significance (Dec 04, 2024) | ||
| 7-73831445-G-A | not specified | Uncertain significance (May 05, 2023) | ||
| 7-73831469-G-A | not specified | Uncertain significance (Mar 21, 2024) | ||
| 7-73831485-T-C | not specified | Uncertain significance (Jul 27, 2024) | ||
| 7-73831538-G-A | not specified | Uncertain significance (May 05, 2023) | ||
| 7-73831598-A-T | not specified | Uncertain significance (Dec 28, 2022) | ||
| 7-73831600-A-G | not specified | Likely benign (Dec 10, 2024) | ||
| 7-73831664-G-A | not specified | Uncertain significance (Dec 12, 2024) | ||
| 7-73831701-G-T | not specified | Uncertain significance (Sep 26, 2023) | ||
| 7-73831719-T-C | not specified | Uncertain significance (Aug 16, 2022) | ||
| 7-73831761-C-A | not specified | Uncertain significance (May 30, 2023) | ||
| 7-73831769-G-A | not specified | Uncertain significance (Sep 08, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CLDN4 | protein_coding | protein_coding | ENST00000435050 | 1 | 33143 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000698 | 0.308 | 125714 | 0 | 25 | 125739 | 0.0000994 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.760 | 124 | 150 | 0.825 | 0.0000103 | 1337 |
| Missense in Polyphen | 41 | 54.757 | 0.74876 | 497 | ||
| Synonymous | -0.930 | 86 | 75.7 | 1.14 | 0.00000597 | 471 |
| Loss of Function | -0.171 | 6 | 5.57 | 1.08 | 2.42e-7 | 47 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000177 | 0.000177 |
| Ashkenazi Jewish | 0.000487 | 0.000397 |
| East Asian | 0.000272 | 0.000272 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000903 | 0.0000879 |
| Middle Eastern | 0.000272 | 0.000272 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Channel-forming tight junction protein that mediates paracellular chloride transport in the kidney. Plays a critical role in the paracellular reabsorption of filtered chloride in the kidney collecting ducts. Claudins play a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity. {ECO:0000250|UniProtKB:O35054}.;
- Disease
- DISEASE: Note=CLDN4 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
- 0.257
Intolerance Scores
- loftool
- 0.258
- rvis_EVS
- -0.58
- rvis_percentile_EVS
- 18.44
Haploinsufficiency Scores
- pHI
- 0.246
- hipred
- Y
- hipred_score
- 0.638
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cldn4
- Phenotype
- normal phenotype; 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); hematopoietic system 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); renal/urinary system phenotype; cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- female pregnancy;circadian rhythm;calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules;response to progesterone;establishment of skin barrier;renal absorption;chloride transmembrane transport
- Cellular component
- plasma membrane;integral component of plasma membrane;bicellular tight junction;basal plasma membrane;apical plasma membrane;apicolateral plasma membrane;lateral plasma membrane;chloride channel complex
- Molecular function
- transmembrane signaling receptor activity;structural molecule activity;chloride channel activity;protein binding;identical protein binding