CLDN4

claudin 4, the group of Claudins

Basic information

Region (hg38): 7:73799542-73832690

Previous symbols: [ "CPETR", "CPETR1" ]

Links

ENSG00000189143

∙ NCBI:1364 ∙ OMIM:602909 ∙ HGNC:2046 ∙ Uniprot:O14493 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLDN4 gene.

not_specified (23 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000001305.5. 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 clinvar		1
missense			22 clinvar	1 clinvar		23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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