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CLDN4

gene
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Also known as CPE-RWBSCR8hCPE-R

Summary

CLDN4 (claudin 4, HGNC:2046) is a protein-coding gene on chromosome 7q11.23, encoding Claudin-4 (O14493). Can associate with other claudins to regulate tight junction structural and functional strand dynamics.

The protein encoded by this intronless gene belongs to the claudin family. Claudins are integral membrane proteins that are components of the epithelial cell tight junctions, which regulate movement of solutes and ions through the paracellular space. This protein is a high-affinity receptor for Clostridium perfringens enterotoxin (CPE) and may play a role in internal organ development and function during pre- and postnatal life. This gene is deleted in Williams-Beuren syndrome, a neurodevelopmental disorder affecting multiple systems.

Source: NCBI Gene 1364 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 30 total — 1 pathogenic
  • GTEx eGene: eQTL in 32 tissues, sQTL in 0 (q < 0.05)
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.44 (unconstrained)
  • MANE Select transcript: NM_001305

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2046
Approved symbolCLDN4
Nameclaudin 4
Location7q11.23
Locus typegene with protein product
StatusApproved
AliasesCPE-R, WBSCR8, hCPE-R
Ensembl geneENSG00000189143
Ensembl biotypeprotein_coding
OMIM602909
Entrez1364

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 protein_coding_CDS_not_defined

MANE Select: ENST00000340958

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 2: 2, TSL 4: 2

ENST00000340958, ENST00000431918, ENST00000435050, ENST00000466411, ENST00000476494

RefSeq mRNA: 1 — MANE Select: NM_001305 NM_001305

CCDS: CCDS5560

Canonical transcript exons

ENST00000340958 — 1 exons

ExonStartEnd
ENSE000013717777383099673832690

Expression profiles

Bgee: expression breadth ubiquitous, 209 present calls, max score 99.36.

FANTOM5 (CAGE): breadth broad, TPM avg 50.2292 / max 1043.2680, expressed in 663 samples.

Highest expression (Bgee): mucosa of transverse colon, uterine tube, endometrium epithelium, olfactory segment of nasal mucosa, lower esophagus mucosa.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CLDN4 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 32 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 32 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Adipose Subcutaneouseqtl2.3e-38-0.497:73824000:C:T
Brain Cerebellar Hemisphereeqtl1.2e-26-0.777:73827962:T:TTAGTCACTTCTG
Brain Cerebellumeqtl1.9e-19-0.767:73821936:G:A
Brain Nucleus accumbens basal gangliaeqtl1.6e-16-0.747:73827962:T:TTAGTCACTTCTG
Brain Caudate basal gangliaeqtl2.6e-16-0.667:73832131:A:G
Thyroideqtl5.1e-12-0.177:73856561:C:T
Nerve Tibialeqtl3.4e-11-0.387:73824842:T:C
Adipose Visceral Omentumeqtl8.2e-11-0.437:73832874:G:A
Brain Putamen basal gangliaeqtl8.3e-11-0.737:73832131:A:G
Brain Hippocampuseqtl4.6e-10-0.497:73846917:G:A
Pituitaryeqtl1.8e-08-0.327:73846340:C:T
Brain Frontal Cortex BA9eqtl1.8e-08-0.537:73827962:T:TTAGTCACTTCTG
Brain Cortexeqtl5.4e-08-0.477:73829456:T:G
Pancreaseqtl1.3e-06-0.267:73847487:T:C
Esophagus Musculariseqtl2.0e-06-0.257:73829456:T:G
Cells Cultured fibroblastseqtl2.4e-06-0.247:73828809:T:C
Brain Anterior cingulate cortex BA24eqtl3.9e-05-0.487:73808747:C:T
Adrenal Glandeqtl5.2e-05-0.467:73832131:A:G
Heart Left Ventricleeqtl1.7e-04-0.397:73812477:C:T
Brain Hypothalamuseqtl2.0e-04-0.387:73858574:G:C

FANTOM5 promoters

4 alternative TSS:

Promoter IDTPM avgSamples expressed
7902849.9824658
790270.101859
790260.074034
790230.071012

Top tissues by expression

showing 100 of 287 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
mucosa of transverse colonUBERON:000499199.36gold quality
right uterine tubeUBERON:000130298.28gold quality
endometrium epitheliumUBERON:000481198.19gold quality
olfactory segment of nasal mucosaUBERON:000538698.19gold quality
lower esophagus mucosaUBERON:003583497.62gold quality
skin of abdomenUBERON:000141697.58gold quality
skin of legUBERON:000151197.38gold quality
minor salivary glandUBERON:000183097.34gold quality
rectumUBERON:000105297.27gold quality
left lobe of thyroid glandUBERON:000112096.95gold quality
esophagus mucosaUBERON:000246996.92gold quality
mucosa of sigmoid colonUBERON:000499396.75gold quality
right lobe of thyroid glandUBERON:000111996.53gold quality
body of pancreasUBERON:000115096.35gold quality
saliva-secreting glandUBERON:000104496.17gold quality
colonic mucosaUBERON:000031796.11gold quality
thyroid glandUBERON:000204696.11gold quality
metanephros cortexUBERON:001053395.87gold quality
mouth mucosaUBERON:000372995.85gold quality
nasal cavity epitheliumUBERON:000538495.18gold quality
islet of LangerhansUBERON:000000694.86gold quality
zone of skinUBERON:000001494.63gold quality
gall bladderUBERON:000211094.43gold quality
pancreasUBERON:000126494.31gold quality
mucosa of urinary bladderUBERON:000125994.04gold quality
cervix epitheliumUBERON:000480193.56gold quality
upper lobe of left lungUBERON:000895293.36gold quality
cervix squamous epitheliumUBERON:000692292.92silver quality
upper lobe of lungUBERON:000894892.81gold quality
transverse colonUBERON:000115792.46gold quality
amniotic fluidUBERON:000017392.38gold quality
right lungUBERON:000216792.13gold quality
parotid glandUBERON:000183192.02gold quality
tongue squamous epitheliumUBERON:000691991.95silver quality
duodenumUBERON:000211491.44gold quality
small intestine Peyer’s patchUBERON:000345491.40gold quality
mammary ductUBERON:000176591.22gold quality
epithelium of mammary glandUBERON:000324490.91gold quality
oral cavityUBERON:000016789.88gold quality
small intestineUBERON:000210889.78gold quality
epithelium of bronchusUBERON:000203189.66gold quality
epithelium of nasopharynxUBERON:000195189.53silver quality
bronchusUBERON:000218589.25gold quality
upper arm skinUBERON:000426389.04silver quality
mucosa of paranasal sinusUBERON:000503088.93silver quality
prostate glandUBERON:000236788.84gold quality
adult mammalian kidneyUBERON:000008288.52gold quality
oviduct epitheliumUBERON:000480488.20gold quality
bronchial epithelial cellCL:000232888.16gold quality
fallopian tubeUBERON:000388987.82gold quality
palpebral conjunctivaUBERON:000181287.75gold quality
lungUBERON:000204887.28gold quality
squamous epitheliumUBERON:000691487.17silver quality
tonsilUBERON:000237287.03gold quality
urinary bladderUBERON:000125586.93gold quality
epithelium of esophagusUBERON:000197686.90gold quality
lower lobe of lungUBERON:000894986.83silver quality
vermiform appendixUBERON:000115486.69gold quality
vaginaUBERON:000099686.55gold quality
nasal cavity mucosaUBERON:000182686.55gold quality
seminal vesicleUBERON:000099886.54gold quality
gingivaUBERON:000182886.29gold quality
jejunal mucosaUBERON:000039985.94gold quality
placentaUBERON:000198785.73gold quality
intestineUBERON:000016085.64gold quality
esophagus squamous epitheliumUBERON:000692085.45gold quality
gingival epitheliumUBERON:000194985.21silver quality
colonic epitheliumUBERON:000039785.17gold quality
ileal mucosaUBERON:000033184.69gold quality
kidneyUBERON:000211384.57gold quality
large intestineUBERON:000005984.33gold quality
colonUBERON:000115584.02gold quality
periodontal ligamentUBERON:000826683.17silver quality
buccal mucosa cellCL:000233683.00silver quality
caecumUBERON:000115382.51gold quality
mammary glandUBERON:000191182.49gold quality
thoracic mammary glandUBERON:000520082.31gold quality
cortex of kidneyUBERON:000122581.48gold quality
pharyngeal mucosaUBERON:000035581.13gold quality
uterine cervixUBERON:000000280.56gold quality
endometriumUBERON:000129580.29gold quality
tracheaUBERON:000312680.24gold quality
left uterine tubeUBERON:000130380.15gold quality
esophagusUBERON:000104379.77gold quality
corpus epididymisUBERON:000435979.29gold quality
adenohypophysisUBERON:000219678.76gold quality
pituitary glandUBERON:000000778.55gold quality
metanephrosUBERON:000008178.41gold quality
caput epididymisUBERON:000435877.81gold quality
deciduaUBERON:000245077.68silver quality
mammalian vulvaUBERON:000099777.41silver quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047376.94silver quality
nephron tubuleUBERON:000123176.70silver quality
jejunumUBERON:000211574.77gold quality
body of stomachUBERON:000116174.68gold quality
endocervixUBERON:000045874.28gold quality
oocyteCL:000002373.05gold quality
female reproductive systemUBERON:000047473.05gold quality
upper leg skinUBERON:000426272.99gold quality
sigmoid colonUBERON:000115972.98gold quality

Single-cell (SCXA)

Detected in 28 experiment(s), a significant marker in 26.

ExperimentMarker?Max mean expression
E-GEOD-81547yes10858.75
E-MTAB-9841yes8529.45
E-MTAB-8221yes4379.17
E-GEOD-114530yes3994.78
E-GEOD-124472yes3907.15
E-MTAB-10287yes3711.28
E-MTAB-10885yes3248.31
E-CURD-114yes2150.08
E-HCAD-10yes2002.85
E-MTAB-6701yes1483.62
E-GEOD-130473yes1430.23
E-HCAD-23yes940.72
E-MTAB-10662yes806.94
E-MTAB-8530yes697.74
E-MTAB-8142yes541.87

HPA expression

RNA tissue specificity: Tissue enhanced

53 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Urinary bladdertissue282.7high
Colontissue215.5high
Small intestinetissue179.5high
Salivary glandtissue159.9medium
Duodenumtissue119.3high
Esophagustissue116.8medium
Rectumtissue115.9high
Vaginatissue107.3low
Prostatetissue76.2medium
Fallopian tubetissue71.3medium
Thyroid glandtissue69.4medium
Pancreastissue62.4high
Lungtissue49.7low
Parathyroid glandtissue48.7low
Gallbladdertissue45.9medium
Breasttissue42.5medium
Seminal vesicletissue36.9medium
Skin 1tissue35.8high
Tonsiltissue35.2medium
Placentatissue34.1high
Kidneytissue29.8high
Endometrium 1tissue25.1medium
Epididymistissue23.1medium
Appendixtissue21.7high
Cervixtissue20.6low
Pituitary glandtissue13.6
Choroid plexustissue11.2
Stomach 1tissue10.7not detected
Thymustissue10.0
Smooth muscletissue6.9not detected
Livertissue4.5not detected
Adipose tissuetissue2.5not detected
Postcentral gyrustissue1.1
Locus coeruleustissue1.0
Lymph nodetissue0.9not detected
Nucleus accumbenstissue0.8
Hippocampustissue0.8low
Spleentissue0.6not detected
Skeletal muscletissue0.3not detected
Superior colliculitissue0.3
Spinal cordtissue0.3
Testistissue0.2not detected
Heart muscletissue0.2not detected
Retinatissue0.2
Tonguetissue0.2
Bone marrowtissue0.2not detected
Ovarytissue0.1not detected
Hypothalamustissue0.1
Cerebellumtissue0.1low
Adrenal glandtissue0.1not detected
Cerebral cortextissue0.0low
Bronchustissue-1.0medium
Oral mucosatissue-1.0medium

Brain sub-regions (HPA Brain Atlas): detected in 187; highest nTPM — Periaquaductal grey, lateral (4.4), Periaquaductal grey, anterior (3.0), Flocculonodular lobe (2.7), Vermis (2.5), Cerebellar cortex (2.4).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1, FOXC1, GRHL2, HNF4A, NFE2L2, SP1, STAT2, TFAP4, TWIST1, ZEB2

miRNA regulators (miRDB)

Targeting CLDN4 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 41 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5692A100.0074.406850
HSA-MIR-4692100.0067.322066
HSA-MIR-4481100.0066.421669
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-451499.9967.101870
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-4745-5P99.9865.951028
HSA-MIR-211099.9666.681930
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-1296-3P99.7264.04636
HSA-MIR-453099.6966.471509
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-6887-3P99.6667.831778
HSA-MIR-182799.6368.573265
HSA-MIR-497-3P99.6169.711990
HSA-MIR-186-3P99.5166.241685
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-582-5P99.4770.792635
HSA-MIR-312599.1468.492269
HSA-MIR-491-5P99.1365.981468
HSA-MIR-570198.9769.541502
HSA-MIR-939-3P98.9765.072347
HSA-MIR-465698.7966.221306
HSA-MIR-6511A-5P98.1367.471770
HSA-MIR-64997.9667.21704
HSA-MIR-6847-5P97.9366.741808
HSA-MIR-7113-5P97.8867.331735
HSA-MIR-1914-5P97.8366.21807

Functional genomics

gnomAD constraint: pLI 0.000128, LOEUF 1.44, missense Z 1.14 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000340958 — one region, missense o/e 0.85.

Literature-anchored findings (GeneRIF, showing 40)

  • Results support a model in which claudins 2 and 4 create paracellular channels and the first extracellular domain is sufficient to determine both paracellular charge selectivity and transepithelial electrical resistance. (PMID:12700140)
  • CLDN4, clustered with CLDN3 at human chromosome 7q11, is a four-transmembrane protein with WWCC motif, defined by W-X(17-22)-W-X(2)-C-X(8-10)-C. (PMID:12736707)
  • Claudin-4 is a potent inhibitor of the invasiveness and metastatic phenotype of pancreatic cancer cells, and a target of the transforming growth factor beta and Ras/Raf/extracellular signal-regulated kinase pathways. (PMID:14559813)
  • The tail of claudin-2 could stabilize claudin-4, with a concomitant increase in both protein level and physiologic influence. (PMID:15366421)
  • claudin 4 may play a role in the disruption of cell-to-cell adhesion in diffuse type gastric cancer and in a loss of differentiation. (PMID:15643498)
  • loss of CLDN4 expression in areas of apocrine metaplasia and in the majority of grade 1 invasive carcinomas suggests a particular role for this protein in mammary glandular cell differentiation and carcinogenesis (PMID:15743508)
  • tyrosine phosphorylation of claudin-4 attenuates association of claudin-4 with ZO-1, decreasing integration of claudin-4 into sites of cell-cell contact and enhancing paracellular permeability (PMID:16236711)
  • The expression of claudin-1, -3 and -4 was upregulated 5.7-, 1.5- and 2.4-fold, respectively, in colorectal tumor tissues in comparison to the normal ones. (PMID:16253248)
  • claudin 3 and claudin 4 may play a role in transformation of ovarian surface epithelium towards the malignant phenotype (PMID:16287068)
  • Claudin-4 expression seems to be a useful marker in differentiating biliary tract cancers from hepatocellular carcinomas and could well become a potential diagnostic tool. (PMID:16439986)
  • Sp1 epigenetic modifications have a critical role in regulation of the CLDN4 promoter in ovarian cancer cells (PMID:16714763)
  • WNK1 increases paracellular chloride permeability and phosphorylation of claudin-4 (PMID:16949040)
  • expression of claudin-4 is lower in diffuse-type gastric cancer than in intestinal-type gastric cancer (PMID:16969486)
  • Overexpression of claudin-4 is associated with uterine serous papillary carcinoma (PMID:17326053)
  • Tight junction proteins contribute to the permeability barrier in epidermal keratinocytes (PMID:17359339)
  • When compared, small-cell-lung cancers and carcinoid tumors, adenocarcinomas, and squamous cell carcinomas in CLDN4 expression. (PMID:17418912)
  • Loss of claudin expression may enhance the grade of malignancy of gastric cancer in vivo. (PMID:17459057)
  • Claudin-3 and claudin-4 receptors are highly overexpressed in carcinosarcoma (PMID:17545541)
  • Our data suggest that JUND and CLDN4 are critical mediators of the antiproliferative and antiviral effects of type I IFNs and further confirm the functional importance of the DNA-binding domain of Stat2. (PMID:17651017)
  • The modulation of claudin-4 activity by PKCepsilon may not only provide a mechanism for disrupting TJ function in ovarian cancer, but may also be important in the regulation of TJ function in normal epithelial cells. (PMID:17678893)
  • vinculin plays a role in growth regulation of neuroendocrine tumors and in expression of CLD4 (PMID:17709988)
  • Reduced claudin-4 expression correlates with loss of differentiation in thyroid neoplasms. (PMID:17962811)
  • Cdx2 plays an important role in the regulation of intestinal claudin expression not only in gastric mucosa with intestinal metaplasia but also gastric carcinoma. (PMID:18251778)
  • MMP-2, MMP-9 and claudin-4 expression may be phenotypic features, distinguishing intestinal-type and diffuse-type gastric cancer. (PMID:18283635)
  • Increased expression of claudin-3 and claudin-4 may contribute to aggressive phenotype of endometrial cancer of serous papillary or clear-cell histology. Possible targets for therapeutic intervention. (PMID:18313739)
  • Down-regulated expression of claudin-3 and claudin-4 in ectopic endometrium suggests that claudin-3 and claudin-4 might play a pathogenic role in the formation of endometriosis. (PMID:18384777)
  • Early gastric carcinomas demonstrating I-CLDN(+) phenotype have a high risk of synchronous and metachronous secondary gastric epithelial neoplasias. (PMID:18477216)
  • Claudins 1 and 4 expression was significantly associated with stage in patients with urothelial carcinoma of the upper urinary tract. (PMID:18550469)
  • Claudin-4, coding for an integral membrane cell-junction protein, was the most significantly (P<0.00001) upregulated marker in both primary and metastatic tumour specimens compared with benign prostatic hyperplasia at both RNA and protein levels (PMID:18648369)
  • High CLDN4 is associated with basal-like breast carcinomas. (PMID:18752049)
  • We found that claudin-4 contains a sequence which is phosphorylated by atypical PKC (aPKC). These findings suggest that aPKC regulates tight junction formation through the phosphorylation of claudin-4. (PMID:18786529)
  • Claudin 4 is downregulated in lobular carcinoma in situ compated with normal breast epithelium and stroma. (PMID:18954444)
  • Down-regulated expression of claudin-4 might play a pathogenic role in the formation of endometriosis. (PMID:19035134)
  • The expression of claudins-2, -3 and -4 in 16 rectal well-differentiated endocrine neoplasms was studied (PMID:19082451)
  • Down-regulation of claudin-4 might lead to altered tight junction structure and be related to the impaired epithelial function in active ulcerative colitis. (PMID:19120888)
  • Increased claudin-4 expression is associated with breast cancer. (PMID:19142967)
  • The expressions of PSCA and Claudin-4 are upregulated in the pancreatic carcinomas. (PMID:19180924)
  • Tight junction proteins claudin-1, claudin-3, claudin-4, and the adherens junction protein beta-catenin are overexpressed in colorectal carcinoma. (PMID:19184060)
  • claudin-4, in addition to 1 and 5, might be a useful differential diagnostic marker of lung cancer in Korean people. (PMID:19231096)
  • CLDN4 has a role in the optimization of the endometrium for embryo implantation. (PMID:19374770)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCldn13ENSMUSG00000008843
rattus_norvegicusCldn4ENSRNOG00000001476

Paralogs (22): CLDN11 (ENSG00000013297), CLDN18 (ENSG00000066405), CLDN15 (ENSG00000106404), CLDN16 (ENSG00000113946), CLDN10 (ENSG00000134873), CLDN17 (ENSG00000156282), CLDN8 (ENSG00000156284), CLDN14 (ENSG00000159261), CLDN1 (ENSG00000163347), CLDN19 (ENSG00000164007), CLDN3 (ENSG00000165215), CLDN2 (ENSG00000165376), CLDN20 (ENSG00000171217), CLDN22 (ENSG00000177300), CLDN7 (ENSG00000181885), CLDN5 (ENSG00000184113), CLDN6 (ENSG00000184697), CLDN24 (ENSG00000185758), CLDN9 (ENSG00000213937), CLDN25 (ENSG00000228607), CLDN34 (ENSG00000234469), CLDN23 (ENSG00000253958)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1313314) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 23 distinct phenotype terms.

Mouse phenotype (MP)Records
abnormal renal reabsorption2
increased urine chloride ion level2
decreased circulating calcium level1
abnormal renal/urinary system morphology1
hydronephrosis1
ureter urothelium hyperplasia1
decreased body weight1
polyuria1
premature death1
increased hematocrit1
increased circulating aldosterone level1
increased circulating bicarbonate level1
decreased circulating chloride level1
alkalosis1
abnormal ureter physiology1
decreased mean systemic arterial blood pressure1
increased urine calcium level1
increased circulating potassium level1
increased urine sodium level1
abnormal renal sodium reabsorption1
abnormal renal calcium reabsorption1
abnormal kidney pelvis urothelium morphology1
increased kidney cell proliferation1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Pongo abeliiQ5R8E599.6%Diamond
Chlorocebus aethiopsO1900599.0%Diamond
Macaca fascicularisQ4R3L198.1%Diamond
Bos taurusQ3MHK497.1%Diamond
Canis lupus familiarisQ95KM594.5%Diamond
Sus scrofaC3VMW385.8%Diamond
Danio rerioQ6DHP170.2%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
CLDN3protein-coding1365
METTL27protein-coding155368
ABHD11protein-coding83451
TMEM270protein-coding135886
ELN-AS1ncRNA107986809
ELNprotein-coding2006
LIMK1protein-coding3984

Protein

Protein identifiers

Claudin-4 — O14493 (reviewed: O14493)

Alternative names: Clostridium perfringens enterotoxin receptor, Williams-Beuren syndrome chromosomal region 8 protein

All UniProt accessions (2): O14493, Q75L80

UniProt curated annotations — full annotation on UniProt →

Function. Can associate with other claudins to regulate tight junction structural and functional strand dynamics. May coassemble with CLDN8 into tight junction strands containing anion-selective channels that convey paracellular chloride permeability in renal collecting ducts. May integrate into CLDN3 strands to modulate localized tight junction barrier properties. May disrupt strand assembly of channel-forming CLDN2 and CLDN15 and inhibit cation conductance. Cannot form tight junction strands on its own.

Subunit / interactions. Can form heteropolymeric strands with other claudins. Interacts with CLDN8. Interacts with CLDN1. Directly interacts with TJP1/ZO-1. Interacts with TJP2/ZO-2 and TJP3/ZO-3. Interacts with EPHA2; phosphorylates CLDN4 and may regulate tight junctions. (Microbial infection) Interacts (via both extracellular domains) with Clostridium perfringens enterotoxin CPE; the interaction may disrupt claudin assembly in tight junctions.

Subcellular location. Cell junction. Tight junction. Cell membrane.

Post-translational modifications. Phosphorylated. Phosphorylation by EPHA2 is stimulated by EFNA1 and alters interaction with TJP1.

Disease relevance. 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.

Similarity. Belongs to the claudin family.

RefSeq proteins (1): NP_001296* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003550Claudin4Family
IPR004031PMP22/EMP/MP20/ClaudinFamily
IPR006187ClaudinFamily
IPR017974Claudin_CSConserved_site

Pfam: PF00822

Catalyzed reactions (Rhea)

  • chloride(in) = chloride(out) (RHEA:29823)
  • iodide(out) = iodide(in) (RHEA:66324)
  • bromide(in) = bromide(out) (RHEA:75383)
  • fluoride(in) = fluoride(out) (RHEA:76159)

UniProt features (33 total): strand 9, mutagenesis site 6, topological domain 5, transmembrane region 4, helix 4, region of interest 2, chain 1, modified residue 1, disulfide bond 1

Structure

Experimental structures (PDB)

8 structures by resolution:

PDBTitleMethodResolution (Å)
9CMICryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin …ELECTRON MICROSCOPY2.83
8U4VCryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin …ELECTRON MICROSCOPY2.99
7KP4Crystal structure of human claudin-4 in complex with Clostridium perfringens enterotoxin …X-RAY DIFFRACTION3.37
5B2GCrystal structure of human claudin-4 in complex with C-terminal fragment of Clostridium …X-RAY DIFFRACTION3.5
9CMHCryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxinELECTRON MICROSCOPY4
7TDNCryoEM Structure of sFab COP-3 Complex with human claudin-4 and Clostridium perfringens …ELECTRON MICROSCOPY5
8U5BCryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin …ELECTRON MICROSCOPY5.3
7TDMCryoEM Structure of sFab COP-2 Complex with human claudin-4 and Clostridium perfringens …ELECTRON MICROSCOPY6.9

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O14493-F184.500.54

Antibody-complex structures (SAbDab)

5 antibodies co-crystallized with this protein: 7TDM, 7TDN, 8U4V, 8U5B, 9CMI

Human Protein Atlas

Protein class: Transporters, Transporter channels and pores, Predicted membrane proteins, Cancer-related genes, Candidate cancer biomarkers, Disease related genes, Potential drug targets, Human disease related genes, Other congenital disorders, Chromosomal abnormalities

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): plasma membrane

Antibody reliability (HPA): IH enhanced · IF supported

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1)

TypePositions
Phosphotyrosine208

Disulfide bonds (1)

TypePositions
Disulfide bond54–64

Mutagenesis-validated functional residues (6)

PositionPhenotype
35decreases interaction with clostridium perfringens cpe.
35abolishes interaction with clostridium perfringens cpe.
40no effect on interaction with clostridium perfringens cpe.
40strongly decreases interaction with clostridium perfringens cpe.
53decreases interaction with clostridium perfringens cpe.
208loss of phosphorylation by epha2.

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 4; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

4 pathways:

IDPathwayEvidence
R-HSA-446728Cell junction organization—
R-HSA-1500931Cell-Cell communication—
R-HSA-421270Cell-cell junction organization—
R-HSA-420029Tight junction interactionselectronic

MSigDB gene sets: 240 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GOBP_CIRCADIAN_RHYTHM, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_REGULATION_OF_WOUND_HEALING, ENK_UV_RESPONSE_KERATINOCYTE_UP, SHEPARD_CRASH_AND_BURN_MUTANT_UP, MODULE_64, IVANOVA_HEMATOPOIESIS_MATURE_CELL, MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN, GOBP_INORGANIC_ANION_TRANSPORT, KEGG_TIGHT_JUNCTION, TGACCTY_ERR1_Q2, NAGASHIMA_NRG1_SIGNALING_UP, RODRIGUES_NTN1_TARGETS_DN

GO Biological Process (14): female pregnancy (GO:0007565), circadian rhythm (GO:0007623), calcium-independent cell-cell adhesion (GO:0016338), regulation of cell morphogenesis (GO:0022604), positive regulation of cell migration (GO:0030335), response to progesterone (GO:0032570), establishment of skin barrier (GO:0061436), renal absorption (GO:0070293), positive regulation of wound healing (GO:0090303), paracellular transport (GO:0160184), monoatomic ion transport (GO:0006811), chloride transport (GO:0006821), monoatomic ion transmembrane transport (GO:0034220), chloride transmembrane transport (GO:1902476)

GO Molecular Function (5): transmembrane signaling receptor activity (GO:0004888), structural molecule activity (GO:0005198), chloride channel activity (GO:0005254), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (10): plasma membrane (GO:0005886), cell-cell junction (GO:0005911), bicellular tight junction (GO:0005923), basal plasma membrane (GO:0009925), apical plasma membrane (GO:0016324), apicolateral plasma membrane (GO:0016327), lateral plasma membrane (GO:0016328), chloride channel complex (GO:0034707), tight junction (GO:0070160), membrane (GO:0016020)

Reactome top-level categories

3 top-level categories:

CategoryPathways
Cell-cell junction organization1
Cell junction organization1
Cell-Cell communication1

GO top-level categories

41 GO namespaces:

CategoryTerms
plasma membrane region3
transport2
cellular anatomical structure2
multi-organism reproductive process1
multi-multicellular organism process1
rhythmic process1
cell-cell adhesion1
cell morphogenesis1
regulation of anatomical structure morphogenesis1
cell migration1
regulation of cell migration1
positive regulation of cell motility1
response to steroid hormone1
response to ketone1
skin epidermis development1
renal system process1
wound healing1
regulation of wound healing1
positive regulation of response to wounding1
monoatomic anion transport1
inorganic anion transport1
monoatomic ion transport1
transmembrane transport1
chloride transport1
monoatomic anion transmembrane transport1
signaling receptor activity1
molecular_function1
monoatomic anion channel activity1
chloride transmembrane transporter activity1
protein binding1
binding1
membrane1
cell periphery1
anchoring junction1
apical junction complex1
tight junction1
basal part of cell1
apical part of cell1
plasma membrane1
monoatomic ion channel complex1
cell-cell junction1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 8 of 29 annotations. The rest are phylogenetic / computational / electronic (IEA).

8 experimentally-supported GO terms:

GO termNSEvidence
establishment of skin barrierBPmutant phenotype
positive regulation of cell migrationBPmutant phenotype
positive regulation of wound healingBPmutant phenotype
regulation of cell morphogenesisBPmutant phenotype
bicellular tight junctionCCdirect assay
cell-cell junctionCCdirect assay
plasma membraneCCdirect assay
tight junctionCCdirect assay

Protein interactions and networks

STRING

showing 15 of 1,460 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
CLDN4TJP1Q07157934
CLDN4CLDN12P56749928
CLDN4OCLNQ16625923
CLDN4TJP2Q9UDY2747
CLDN4MARVELD2Q8N4S9653
CLDN4CDH1P12830650
CLDN4TJP3O95049648
CLDN4F11RQ9Y624645
CLDN4KRT8P05787581
CLDN4EPCAMP16422569
CLDN4TUBB2AQ13885513
CLDN4CGNQ9P2M7499
CLDN4KRT5P13647498
CLDN4IL1BP01584498
CLDN4MUC2Q02817482

IntAct

Human interaction partners of CLDN4 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

showing 30 of 85 partners by confidence:

PartnerInteraction typeMIscoreRecords
AQP6physical association0.5603
ARL13Bphysical association0.5603
CLEC14Aphysical association0.5603
FAM209Aphysical association0.5603
FFAR2physical association0.5603
GJA8physical association0.5603
GOLM1physical association0.5603
HSD17B13physical association0.5603
ICAM3physical association0.5603
MFSD14Bphysical association0.5603
SYT2physical association0.5603
TMEM237physical association0.5603
TMEM52Bphysical association0.5603
TRIM59physical association0.5603
TSPO2physical association0.5603
PATJdirect interaction0.4407
GRIP1direct interaction0.4405
GRIP2direct interaction0.4405
DLG1direct interaction0.4403
DLG3direct interaction0.4403
FRMPD2direct interaction0.4403
IL16direct interaction0.4403
MAGI2direct interaction0.4403
MPDZdirect interaction0.4403
PDZK1direct interaction0.4403
SCRIBdirect interaction0.4403
WHRNdirect interaction0.4403
APBA2direct interaction0.4402
DLG2direct interaction0.4402
DLG4direct interaction0.4402

BioGRID (72 interactions; top human partners by supporting records): ADD3 (Affinity Capture-MS), AHNAK (Affinity Capture-MS), AKAP12 (Affinity Capture-MS), AP1B1 (Affinity Capture-MS), AQP6 (Two-hybrid), ARL13B (Two-hybrid), ATP1A1 (Affinity Capture-MS), ATP2B1 (Affinity Capture-MS), BAIAP2 (Affinity Capture-MS), CLEC14A (Two-hybrid), CPD (Affinity Capture-MS), CTNND1 (Affinity Capture-MS), CXADR (Affinity Capture-MS), DCBLD2 (Affinity Capture-MS), DLG1 (Affinity Capture-MS)

SIGNOR signaling

3 signaling interactions:

AEffectBMechanism
SNAI1“down-regulates quantity by repression”CLDN4“transcriptional regulation”
CLDN4down-regulatesEpithelial-mesenchymal_transition
EPHA2“down-regulates activity”CLDN4phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 85 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Ras activation upon Ca2+ influx through NMDA receptor552.9×1e-06
Unblocking of NMDA receptors, glutamate binding and activation550.4×1e-06
Negative regulation of NMDA receptor-mediated neuronal transmission550.4×1e-06
Assembly and cell surface presentation of NMDA receptors1047.0×7e-13
Dopamine Neurotransmitter Release Cycle546.0×2e-06
Long-term potentiation544.1×2e-06
Neurexins and neuroligins1243.8×5e-15
Protein-protein interactions at synapses839.4×1e-09

GO biological processes:

GO termPartnersFoldFDR
establishment or maintenance of epithelial cell apical/basal polarity964.6×4e-12
protein localization to synapse656.7×1e-07
receptor clustering753.9×9e-09
regulation of postsynaptic membrane neurotransmitter receptor levels636.7×1e-06
cell-cell adhesion911.3×6e-06
protein-containing complex assembly811.2×3e-05
chemical synaptic transmission76.7×3e-03

Disease & clinical

Genetic variants

Variant evidence for CLDN4: 30 ClinVar records (1 pathogenic / likely pathogenic). Per-variant detail is on Sugi Variant.

ClinVar

30 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance27
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (1)

Showing all 1 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
978415NC_000007.14:g.73773313_74086695delPathogenicno assertion criteria provided1

Per-variant reference — Sugi Variant

Explore CLDN4’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 10 predictions of 36):

Position(s)EffectΔscoreSites
7:73832663acceptor_gain0.4800
7:73832661acceptor_gain0.4700
7:73831679donor_gain0.3800
7:73831827donor_gain0.3700
7:73831788donor_gain0.3600
7:73832666acceptor_gain0.3500
7:73832214acceptor_gain0.3300
7:73831822donor_gain0.3200
7:73831785donor_gain0.3100
7:73831833donor_gain0.2900

AlphaMissense

611 missense substitutions predicted likely pathogenic (of 1,340 scored), across 174 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
M5280.8110.961
D6880.7750.915
C5470.9910.994
C6470.9880.997
F14770.9840.998
W3070.9800.996
W5170.9780.996
F3570.9610.994
W16870.9350.997
W4770.8900.968
W13870.8530.959
E15970.8430.953
F12570.7840.881
G4960.9860.998
G16160.9800.996
P2860.9690.988
R8160.9430.994
S5860.9320.974
G6060.9290.986
G1760.9170.995

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

3 prognostic cancer types:

CancerPrognosticp-value
Kidney Renal Clear Cell Carcinoma (TCGA)favorable1.95e-09
Kidney Renal Clear Cell Carcinoma (validation)favorable5.05e-05
Ovary Serous Cystadenocarcinoma (TCGA)unfavorable0.00023

Disease associations

OMIM: gene MIM:602909 | disease phenotypes: MIM:194050

GenCC curated gene-disease

Mondo (1): Williams syndrome (MONDO:0008678)

Orphanet (1): Williams syndrome (Orphanet:904)

MeSH disease descriptors

1 disease descriptors:

DescriptorNameTree numbers
D018980Williams SyndromeC10.597.606.360.970; C14.280.484.048.750.535.960; C16.131.260.970; C16.320.180.970

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

90 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases methylation, increases expression, decreases expression7
Valproic Acidaffects cotreatment, increases expression5
deoxynivalenolaffects localization, decreases expression, increases expression3
trichostatin Aaffects cotreatment, increases expression3
sodium arsenitedecreases expression, increases expression3
Estradiolaffects cotreatment, decreases expression3
Tobacco Smoke Pollutionincreases expression3
Cadmium Chlorideincreases expression3
ochratoxin Aaffects reaction, decreases expression2
mercuric bromideincreases expression, affects cotreatment2
trans-10,cis-12-conjugated linoleic acidincreases expression2
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amideaffects expression, affects reaction, decreases expression, affects cotreatment2
Panobinostatincreases expression, affects cotreatment2
Air Pollutantsincreases abundance, increases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Quercetinaffects localization, increases expression2
Smokedecreases expression, increases abundance, increases expression2
Cyclosporineincreases expression2
Okadaic Acidincreases expression2
aristolochic acid Iincreases expression1
propionaldehydedecreases expression, increases expression1
sanguinarinedecreases expression1
bisphenol Adecreases expression1
2,5,2’,5’-tetrachlorobiphenylincreases expression1
quercitrinaffects expression1
butyraldehydeincreases expression1
tetrathiomolybdatedecreases expression1
benzo(e)pyreneincreases methylation1
diallyl disulfidedecreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1

Cellosaurus cell lines

2 cell lines: 1 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_C3VAHT-1080/hCLDN-4Cancer cell lineMale
CVCL_D3PNCHO/CLDN4Transformed cell lineFemale

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

28 trials:

NCTPhaseStatusTitle
NCT00768820Phase 4RECRUITINGThe Psychiatric and Cognitive Phenotypes in Velocardiofacial Syndrome
NCT04807517Phase 4COMPLETEDBuspirone Treatment of Anxiety in Williams Syndrome
NCT00876200Phase 2COMPLETEDEfficacy of Minoxidil in Children With Williams-Beuren Syndrome
NCT06087757Phase 2ACTIVE_NOT_RECRUITINGClemastine Treatment in Individuals With Williams Syndrome
NCT06315699Phase 2COMPLETEDClemastine Fumarate in the Treatment of Neurodevelopmental Delays in Williams Syndrome
NCT00004351Not specifiedCOMPLETEDStudy of Phenotype and Genotype Correlations in Patients With Contiguous Gene Deletion Syndromes
NCT00013962Not specifiedCOMPLETEDVitamin D Metabolism and the Williams Syndrome
NCT01132885Not specifiedRECRUITINGDefining the Brain Phenotype of Children With Williams Syndrome
NCT01793168Not specifiedRECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT01864304Not specifiedCOMPLETEDFat Distribution and Glucose Metabolism in Williams Syndrome
NCT02212314Not specifiedCOMPLETEDResponse Inhibition Training for Children With Williams Syndrome
NCT02692846Not specifiedCOMPLETEDWS-SAVE Study (Williams Syndrome Skin and Vessel Elasticity Study)
NCT02706639Not specifiedCOMPLETEDWilliams Syndrome (WS) and Supravalvar Aortic Stenosis (SVAS) DNA and Tissue Bank
NCT02840448Not specifiedCOMPLETEDImpact of Elastin Mediated Vascular Stiffness on End Organs
NCT03758651Not specifiedCOMPLETEDWilliams Syndrome Strength, Hormones, Activity & Adiposity, DNA Programming, Eating Study
NCT03827525Not specifiedUNKNOWNCognitive and Behavioral Therapy of Anxiety in Williams Syndrome
NCT03836300Not specifiedENROLLING_BY_INVITATIONParent and Infant Inter(X)Action Intervention (PIXI)
NCT04051086Not specifiedUNKNOWNQuantification of Elastin Markers Synthesis in Williams-Beuren Syndrome and 7q11.23 Micro-duplication Syndrome
NCT04095585Not specifiedCOMPLETEDMolecular Characterization of Patients Affected by Williams Syndrome and Autism.
NCT04463316Not specifiedRECRUITINGGROWing Up With Rare GENEtic Syndromes
NCT04610424Not specifiedUNKNOWNCooperative Parent Mediated Therapy in Children With Fragile X Syndrome and Williams Syndrome
NCT05430763Not specifiedWITHDRAWNMotor Deficits and Signal Conduction in Individuals With Williams Syndrome
NCT06740162Not specifiedRECRUITINGPhysical Activity and Community EmPOWERment Project
NCT06930417Not specifiedRECRUITINGCharacterization and Natural History of Williams Syndrome and Other Chromosome 7q11.23 Variants
NCT07285720Not specifiedRECRUITINGPhonological Constraints on Language Development in Individuals With Williams Syndrome
NCT07493096Not specifiedRECRUITINGIntensive Multimodal Neurorehabilitation Targeting Neuroplasticity in Pediatric Neurodevelopmental and Chromosomal Disorders
NCT07509879Not specifiedNOT_YET_RECRUITINGResearch on the Molecular Mechanism of Cognitive Differences Between Williams Syndrome and Autism Spectrum Disorder
NCT07537374Not specifiedNOT_YET_RECRUITINGA Case-Control Observational Study of Peripheral Blood-Derived iPSC Models to Investigate Oligodendrocyte Lineage Development in Children With Williams Syndrome and Healthy Controls

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.