CLDN4
gene geneOn this page
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
| Field | Value |
|---|---|
| HGNC ID | HGNC:2046 |
| Approved symbol | CLDN4 |
| Name | claudin 4 |
| Location | 7q11.23 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | CPE-R, WBSCR8, hCPE-R |
| Ensembl gene | ENSG00000189143 |
| Ensembl biotype | protein_coding |
| OMIM | 602909 |
| Entrez | 1364 |
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
| Exon | Start | End |
|---|---|---|
| ENSE00001371777 | 73830996 | 73832690 |
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:
| Tissue | QTL | q-value | Slope | Lead variant |
|---|---|---|---|---|
| Adipose Subcutaneous | eqtl | 2.3e-38 | -0.49 | 7:73824000:C:T |
| Brain Cerebellar Hemisphere | eqtl | 1.2e-26 | -0.77 | 7:73827962:T:TTAGTCACTTCTG |
| Brain Cerebellum | eqtl | 1.9e-19 | -0.76 | 7:73821936:G:A |
| Brain Nucleus accumbens basal ganglia | eqtl | 1.6e-16 | -0.74 | 7:73827962:T:TTAGTCACTTCTG |
| Brain Caudate basal ganglia | eqtl | 2.6e-16 | -0.66 | 7:73832131:A:G |
| Thyroid | eqtl | 5.1e-12 | -0.17 | 7:73856561:C:T |
| Nerve Tibial | eqtl | 3.4e-11 | -0.38 | 7:73824842:T:C |
| Adipose Visceral Omentum | eqtl | 8.2e-11 | -0.43 | 7:73832874:G:A |
| Brain Putamen basal ganglia | eqtl | 8.3e-11 | -0.73 | 7:73832131:A:G |
| Brain Hippocampus | eqtl | 4.6e-10 | -0.49 | 7:73846917:G:A |
| Pituitary | eqtl | 1.8e-08 | -0.32 | 7:73846340:C:T |
| Brain Frontal Cortex BA9 | eqtl | 1.8e-08 | -0.53 | 7:73827962:T:TTAGTCACTTCTG |
| Brain Cortex | eqtl | 5.4e-08 | -0.47 | 7:73829456:T:G |
| Pancreas | eqtl | 1.3e-06 | -0.26 | 7:73847487:T:C |
| Esophagus Muscularis | eqtl | 2.0e-06 | -0.25 | 7:73829456:T:G |
| Cells Cultured fibroblasts | eqtl | 2.4e-06 | -0.24 | 7:73828809:T:C |
| Brain Anterior cingulate cortex BA24 | eqtl | 3.9e-05 | -0.48 | 7:73808747:C:T |
| Adrenal Gland | eqtl | 5.2e-05 | -0.46 | 7:73832131:A:G |
| Heart Left Ventricle | eqtl | 1.7e-04 | -0.39 | 7:73812477:C:T |
| Brain Hypothalamus | eqtl | 2.0e-04 | -0.38 | 7:73858574:G:C |
FANTOM5 promoters
4 alternative TSS:
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 79028 | 49.9824 | 658 |
| 79027 | 0.1018 | 59 |
| 79026 | 0.0740 | 34 |
| 79023 | 0.0710 | 12 |
Top tissues by expression
showing 100 of 287 tissues by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| mucosa of transverse colon | UBERON:0004991 | 99.36 | gold quality |
| right uterine tube | UBERON:0001302 | 98.28 | gold quality |
| endometrium epithelium | UBERON:0004811 | 98.19 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 98.19 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 97.62 | gold quality |
| skin of abdomen | UBERON:0001416 | 97.58 | gold quality |
| skin of leg | UBERON:0001511 | 97.38 | gold quality |
| minor salivary gland | UBERON:0001830 | 97.34 | gold quality |
| rectum | UBERON:0001052 | 97.27 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 96.95 | gold quality |
| esophagus mucosa | UBERON:0002469 | 96.92 | gold quality |
| mucosa of sigmoid colon | UBERON:0004993 | 96.75 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 96.53 | gold quality |
| body of pancreas | UBERON:0001150 | 96.35 | gold quality |
| saliva-secreting gland | UBERON:0001044 | 96.17 | gold quality |
| colonic mucosa | UBERON:0000317 | 96.11 | gold quality |
| thyroid gland | UBERON:0002046 | 96.11 | gold quality |
| metanephros cortex | UBERON:0010533 | 95.87 | gold quality |
| mouth mucosa | UBERON:0003729 | 95.85 | gold quality |
| nasal cavity epithelium | UBERON:0005384 | 95.18 | gold quality |
| islet of Langerhans | UBERON:0000006 | 94.86 | gold quality |
| zone of skin | UBERON:0000014 | 94.63 | gold quality |
| gall bladder | UBERON:0002110 | 94.43 | gold quality |
| pancreas | UBERON:0001264 | 94.31 | gold quality |
| mucosa of urinary bladder | UBERON:0001259 | 94.04 | gold quality |
| cervix epithelium | UBERON:0004801 | 93.56 | gold quality |
| upper lobe of left lung | UBERON:0008952 | 93.36 | gold quality |
| cervix squamous epithelium | UBERON:0006922 | 92.92 | silver quality |
| upper lobe of lung | UBERON:0008948 | 92.81 | gold quality |
| transverse colon | UBERON:0001157 | 92.46 | gold quality |
| amniotic fluid | UBERON:0000173 | 92.38 | gold quality |
| right lung | UBERON:0002167 | 92.13 | gold quality |
| parotid gland | UBERON:0001831 | 92.02 | gold quality |
| tongue squamous epithelium | UBERON:0006919 | 91.95 | silver quality |
| duodenum | UBERON:0002114 | 91.44 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 91.40 | gold quality |
| mammary duct | UBERON:0001765 | 91.22 | gold quality |
| epithelium of mammary gland | UBERON:0003244 | 90.91 | gold quality |
| oral cavity | UBERON:0000167 | 89.88 | gold quality |
| small intestine | UBERON:0002108 | 89.78 | gold quality |
| epithelium of bronchus | UBERON:0002031 | 89.66 | gold quality |
| epithelium of nasopharynx | UBERON:0001951 | 89.53 | silver quality |
| bronchus | UBERON:0002185 | 89.25 | gold quality |
| upper arm skin | UBERON:0004263 | 89.04 | silver quality |
| mucosa of paranasal sinus | UBERON:0005030 | 88.93 | silver quality |
| prostate gland | UBERON:0002367 | 88.84 | gold quality |
| adult mammalian kidney | UBERON:0000082 | 88.52 | gold quality |
| oviduct epithelium | UBERON:0004804 | 88.20 | gold quality |
| bronchial epithelial cell | CL:0002328 | 88.16 | gold quality |
| fallopian tube | UBERON:0003889 | 87.82 | gold quality |
| palpebral conjunctiva | UBERON:0001812 | 87.75 | gold quality |
| lung | UBERON:0002048 | 87.28 | gold quality |
| squamous epithelium | UBERON:0006914 | 87.17 | silver quality |
| tonsil | UBERON:0002372 | 87.03 | gold quality |
| urinary bladder | UBERON:0001255 | 86.93 | gold quality |
| epithelium of esophagus | UBERON:0001976 | 86.90 | gold quality |
| lower lobe of lung | UBERON:0008949 | 86.83 | silver quality |
| vermiform appendix | UBERON:0001154 | 86.69 | gold quality |
| vagina | UBERON:0000996 | 86.55 | gold quality |
| nasal cavity mucosa | UBERON:0001826 | 86.55 | gold quality |
| seminal vesicle | UBERON:0000998 | 86.54 | gold quality |
| gingiva | UBERON:0001828 | 86.29 | gold quality |
| jejunal mucosa | UBERON:0000399 | 85.94 | gold quality |
| placenta | UBERON:0001987 | 85.73 | gold quality |
| intestine | UBERON:0000160 | 85.64 | gold quality |
| esophagus squamous epithelium | UBERON:0006920 | 85.45 | gold quality |
| gingival epithelium | UBERON:0001949 | 85.21 | silver quality |
| colonic epithelium | UBERON:0000397 | 85.17 | gold quality |
| ileal mucosa | UBERON:0000331 | 84.69 | gold quality |
| kidney | UBERON:0002113 | 84.57 | gold quality |
| large intestine | UBERON:0000059 | 84.33 | gold quality |
| colon | UBERON:0001155 | 84.02 | gold quality |
| periodontal ligament | UBERON:0008266 | 83.17 | silver quality |
| buccal mucosa cell | CL:0002336 | 83.00 | silver quality |
| caecum | UBERON:0001153 | 82.51 | gold quality |
| mammary gland | UBERON:0001911 | 82.49 | gold quality |
| thoracic mammary gland | UBERON:0005200 | 82.31 | gold quality |
| cortex of kidney | UBERON:0001225 | 81.48 | gold quality |
| pharyngeal mucosa | UBERON:0000355 | 81.13 | gold quality |
| uterine cervix | UBERON:0000002 | 80.56 | gold quality |
| endometrium | UBERON:0001295 | 80.29 | gold quality |
| trachea | UBERON:0003126 | 80.24 | gold quality |
| left uterine tube | UBERON:0001303 | 80.15 | gold quality |
| esophagus | UBERON:0001043 | 79.77 | gold quality |
| corpus epididymis | UBERON:0004359 | 79.29 | gold quality |
| adenohypophysis | UBERON:0002196 | 78.76 | gold quality |
| pituitary gland | UBERON:0000007 | 78.55 | gold quality |
| metanephros | UBERON:0000081 | 78.41 | gold quality |
| caput epididymis | UBERON:0004358 | 77.81 | gold quality |
| decidua | UBERON:0002450 | 77.68 | silver quality |
| mammalian vulva | UBERON:0000997 | 77.41 | silver quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 76.94 | silver quality |
| nephron tubule | UBERON:0001231 | 76.70 | silver quality |
| jejunum | UBERON:0002115 | 74.77 | gold quality |
| body of stomach | UBERON:0001161 | 74.68 | gold quality |
| endocervix | UBERON:0000458 | 74.28 | gold quality |
| oocyte | CL:0000023 | 73.05 | gold quality |
| female reproductive system | UBERON:0000474 | 73.05 | gold quality |
| upper leg skin | UBERON:0004262 | 72.99 | gold quality |
| sigmoid colon | UBERON:0001159 | 72.98 | gold quality |
Single-cell (SCXA)
Detected in 28 experiment(s), a significant marker in 26.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-81547 | yes | 10858.75 |
| E-MTAB-9841 | yes | 8529.45 |
| E-MTAB-8221 | yes | 4379.17 |
| E-GEOD-114530 | yes | 3994.78 |
| E-GEOD-124472 | yes | 3907.15 |
| E-MTAB-10287 | yes | 3711.28 |
| E-MTAB-10885 | yes | 3248.31 |
| E-CURD-114 | yes | 2150.08 |
| E-HCAD-10 | yes | 2002.85 |
| E-MTAB-6701 | yes | 1483.62 |
| E-GEOD-130473 | yes | 1430.23 |
| E-HCAD-23 | yes | 940.72 |
| E-MTAB-10662 | yes | 806.94 |
| E-MTAB-8530 | yes | 697.74 |
| E-MTAB-8142 | yes | 541.87 |
HPA expression
RNA tissue specificity: Tissue enhanced
53 HPA tissues / cells by nTPM:
| Tissue / cell | Axis | nTPM | Protein (IHC) |
|---|---|---|---|
| Urinary bladder | tissue | 282.7 | high |
| Colon | tissue | 215.5 | high |
| Small intestine | tissue | 179.5 | high |
| Salivary gland | tissue | 159.9 | medium |
| Duodenum | tissue | 119.3 | high |
| Esophagus | tissue | 116.8 | medium |
| Rectum | tissue | 115.9 | high |
| Vagina | tissue | 107.3 | low |
| Prostate | tissue | 76.2 | medium |
| Fallopian tube | tissue | 71.3 | medium |
| Thyroid gland | tissue | 69.4 | medium |
| Pancreas | tissue | 62.4 | high |
| Lung | tissue | 49.7 | low |
| Parathyroid gland | tissue | 48.7 | low |
| Gallbladder | tissue | 45.9 | medium |
| Breast | tissue | 42.5 | medium |
| Seminal vesicle | tissue | 36.9 | medium |
| Skin 1 | tissue | 35.8 | high |
| Tonsil | tissue | 35.2 | medium |
| Placenta | tissue | 34.1 | high |
| Kidney | tissue | 29.8 | high |
| Endometrium 1 | tissue | 25.1 | medium |
| Epididymis | tissue | 23.1 | medium |
| Appendix | tissue | 21.7 | high |
| Cervix | tissue | 20.6 | low |
| Pituitary gland | tissue | 13.6 | |
| Choroid plexus | tissue | 11.2 | |
| Stomach 1 | tissue | 10.7 | not detected |
| Thymus | tissue | 10.0 | |
| Smooth muscle | tissue | 6.9 | not detected |
| Liver | tissue | 4.5 | not detected |
| Adipose tissue | tissue | 2.5 | not detected |
| Postcentral gyrus | tissue | 1.1 | |
| Locus coeruleus | tissue | 1.0 | |
| Lymph node | tissue | 0.9 | not detected |
| Nucleus accumbens | tissue | 0.8 | |
| Hippocampus | tissue | 0.8 | low |
| Spleen | tissue | 0.6 | not detected |
| Skeletal muscle | tissue | 0.3 | not detected |
| Superior colliculi | tissue | 0.3 | |
| Spinal cord | tissue | 0.3 | |
| Testis | tissue | 0.2 | not detected |
| Heart muscle | tissue | 0.2 | not detected |
| Retina | tissue | 0.2 | |
| Tongue | tissue | 0.2 | |
| Bone marrow | tissue | 0.2 | not detected |
| Ovary | tissue | 0.1 | not detected |
| Hypothalamus | tissue | 0.1 | |
| Cerebellum | tissue | 0.1 | low |
| Adrenal gland | tissue | 0.1 | not detected |
| Cerebral cortex | tissue | 0.0 | low |
| Bronchus | tissue | -1.0 | medium |
| Oral mucosa | tissue | -1.0 | medium |
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:
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-4692 | 100.00 | 67.32 | 2066 |
| HSA-MIR-4481 | 100.00 | 66.42 | 1669 |
| HSA-MIR-6856-5P | 100.00 | 65.47 | 1298 |
| HSA-MIR-6758-5P | 100.00 | 66.21 | 1470 |
| HSA-MIR-4514 | 99.99 | 67.10 | 1870 |
| HSA-MIR-520D-5P | 99.98 | 73.34 | 4883 |
| HSA-MIR-524-5P | 99.98 | 73.43 | 4882 |
| HSA-MIR-4745-5P | 99.98 | 65.95 | 1028 |
| HSA-MIR-2110 | 99.96 | 66.68 | 1930 |
| HSA-MIR-6756-5P | 99.82 | 67.97 | 2466 |
| HSA-MIR-1296-3P | 99.72 | 64.04 | 636 |
| HSA-MIR-4530 | 99.69 | 66.47 | 1509 |
| HSA-MIR-6766-5P | 99.68 | 67.70 | 2325 |
| HSA-MIR-6887-3P | 99.66 | 67.83 | 1778 |
| HSA-MIR-1827 | 99.63 | 68.57 | 3265 |
| HSA-MIR-497-3P | 99.61 | 69.71 | 1990 |
| HSA-MIR-186-3P | 99.51 | 66.24 | 1685 |
| HSA-MIR-1207-5P | 99.49 | 69.11 | 2983 |
| HSA-MIR-582-5P | 99.47 | 70.79 | 2635 |
| HSA-MIR-3125 | 99.14 | 68.49 | 2269 |
| HSA-MIR-491-5P | 99.13 | 65.98 | 1468 |
| HSA-MIR-5701 | 98.97 | 69.54 | 1502 |
| HSA-MIR-939-3P | 98.97 | 65.07 | 2347 |
| HSA-MIR-4656 | 98.79 | 66.22 | 1306 |
| HSA-MIR-6511A-5P | 98.13 | 67.47 | 1770 |
| HSA-MIR-649 | 97.96 | 67.21 | 704 |
| HSA-MIR-6847-5P | 97.93 | 66.74 | 1808 |
| HSA-MIR-7113-5P | 97.88 | 67.33 | 1735 |
| HSA-MIR-1914-5P | 97.83 | 66.21 | 807 |
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
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Cldn13 | ENSMUSG00000008843 |
| rattus_norvegicus | Cldn4 | ENSRNOG00000001476 |
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 reabsorption | 2 |
| increased urine chloride ion level | 2 |
| decreased circulating calcium level | 1 |
| abnormal renal/urinary system morphology | 1 |
| hydronephrosis | 1 |
| ureter urothelium hyperplasia | 1 |
| decreased body weight | 1 |
| polyuria | 1 |
| premature death | 1 |
| increased hematocrit | 1 |
| increased circulating aldosterone level | 1 |
| increased circulating bicarbonate level | 1 |
| decreased circulating chloride level | 1 |
| alkalosis | 1 |
| abnormal ureter physiology | 1 |
| decreased mean systemic arterial blood pressure | 1 |
| increased urine calcium level | 1 |
| increased circulating potassium level | 1 |
| increased urine sodium level | 1 |
| abnormal renal sodium reabsorption | 1 |
| abnormal renal calcium reabsorption | 1 |
| abnormal kidney pelvis urothelium morphology | 1 |
| increased kidney cell proliferation | 1 |
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.
| Organism | UniProt | Identity | Method |
|---|---|---|---|
| Pongo abelii | Q5R8E5 | 99.6% | Diamond |
| Chlorocebus aethiops | O19005 | 99.0% | Diamond |
| Macaca fascicularis | Q4R3L1 | 98.1% | Diamond |
| Bos taurus | Q3MHK4 | 97.1% | Diamond |
| Canis lupus familiaris | Q95KM5 | 94.5% | Diamond |
| Sus scrofa | C3VMW3 | 85.8% | Diamond |
| Danio rerio | Q6DHP1 | 70.2% | 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).
| Symbol | Type | Entrez |
|---|---|---|
| CLDN3 | protein-coding | 1365 |
| METTL27 | protein-coding | 155368 |
| ABHD11 | protein-coding | 83451 |
| TMEM270 | protein-coding | 135886 |
| ELN-AS1 | ncRNA | 107986809 |
| ELN | protein-coding | 2006 |
| LIMK1 | protein-coding | 3984 |
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)
| ID | Name | Type |
|---|---|---|
| IPR003550 | Claudin4 | Family |
| IPR004031 | PMP22/EMP/MP20/Claudin | Family |
| IPR006187 | Claudin | Family |
| IPR017974 | Claudin_CS | Conserved_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:
| PDB | Title | Method | Resolution (Å) |
|---|---|---|---|
| 9CMI | Cryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin … | ELECTRON MICROSCOPY | 2.83 |
| 8U4V | Cryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin … | ELECTRON MICROSCOPY | 2.99 |
| 7KP4 | Crystal structure of human claudin-4 in complex with Clostridium perfringens enterotoxin … | X-RAY DIFFRACTION | 3.37 |
| 5B2G | Crystal structure of human claudin-4 in complex with C-terminal fragment of Clostridium … | X-RAY DIFFRACTION | 3.5 |
| 9CMH | Cryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin | ELECTRON MICROSCOPY | 4 |
| 7TDN | CryoEM Structure of sFab COP-3 Complex with human claudin-4 and Clostridium perfringens … | ELECTRON MICROSCOPY | 5 |
| 8U5B | Cryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin … | ELECTRON MICROSCOPY | 5.3 |
| 7TDM | CryoEM Structure of sFab COP-2 Complex with human claudin-4 and Clostridium perfringens … | ELECTRON MICROSCOPY | 6.9 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-O14493-F1 | 84.50 | 0.54 |
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)
| Type | Positions |
|---|---|
| Phosphotyrosine | 208 |
Disulfide bonds (1)
| Type | Positions |
|---|---|
| Disulfide bond | 54–64 |
Mutagenesis-validated functional residues (6)
| Position | Phenotype |
|---|---|
| 35 | decreases interaction with clostridium perfringens cpe. |
| 35 | abolishes interaction with clostridium perfringens cpe. |
| 40 | no effect on interaction with clostridium perfringens cpe. |
| 40 | strongly decreases interaction with clostridium perfringens cpe. |
| 53 | decreases interaction with clostridium perfringens cpe. |
| 208 | loss 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:
| ID | Pathway | Evidence |
|---|---|---|
| R-HSA-446728 | Cell junction organization | — |
| R-HSA-1500931 | Cell-Cell communication | — |
| R-HSA-421270 | Cell-cell junction organization | — |
| R-HSA-420029 | Tight junction interactions | electronic |
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:
| Category | Pathways |
|---|---|
| Cell-cell junction organization | 1 |
| Cell junction organization | 1 |
| Cell-Cell communication | 1 |
GO top-level categories
41 GO namespaces:
| Category | Terms |
|---|---|
| plasma membrane region | 3 |
| transport | 2 |
| cellular anatomical structure | 2 |
| multi-organism reproductive process | 1 |
| multi-multicellular organism process | 1 |
| rhythmic process | 1 |
| cell-cell adhesion | 1 |
| cell morphogenesis | 1 |
| regulation of anatomical structure morphogenesis | 1 |
| cell migration | 1 |
| regulation of cell migration | 1 |
| positive regulation of cell motility | 1 |
| response to steroid hormone | 1 |
| response to ketone | 1 |
| skin epidermis development | 1 |
| renal system process | 1 |
| wound healing | 1 |
| regulation of wound healing | 1 |
| positive regulation of response to wounding | 1 |
| monoatomic anion transport | 1 |
| inorganic anion transport | 1 |
| monoatomic ion transport | 1 |
| transmembrane transport | 1 |
| chloride transport | 1 |
| monoatomic anion transmembrane transport | 1 |
| signaling receptor activity | 1 |
| molecular_function | 1 |
| monoatomic anion channel activity | 1 |
| chloride transmembrane transporter activity | 1 |
| protein binding | 1 |
| binding | 1 |
| membrane | 1 |
| cell periphery | 1 |
| anchoring junction | 1 |
| apical junction complex | 1 |
| tight junction | 1 |
| basal part of cell | 1 |
| apical part of cell | 1 |
| plasma membrane | 1 |
| monoatomic ion channel complex | 1 |
| cell-cell junction | 1 |
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 term | NS | Evidence |
|---|---|---|
| establishment of skin barrier | BP | mutant phenotype |
| positive regulation of cell migration | BP | mutant phenotype |
| positive regulation of wound healing | BP | mutant phenotype |
| regulation of cell morphogenesis | BP | mutant phenotype |
| bicellular tight junction | CC | direct assay |
| cell-cell junction | CC | direct assay |
| plasma membrane | CC | direct assay |
| tight junction | CC | direct assay |
Protein interactions and networks
STRING
showing 15 of 1,460 interactions by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CLDN4 | TJP1 | Q07157 | 934 |
| CLDN4 | CLDN12 | P56749 | 928 |
| CLDN4 | OCLN | Q16625 | 923 |
| CLDN4 | TJP2 | Q9UDY2 | 747 |
| CLDN4 | MARVELD2 | Q8N4S9 | 653 |
| CLDN4 | CDH1 | P12830 | 650 |
| CLDN4 | TJP3 | O95049 | 648 |
| CLDN4 | F11R | Q9Y624 | 645 |
| CLDN4 | KRT8 | P05787 | 581 |
| CLDN4 | EPCAM | P16422 | 569 |
| CLDN4 | TUBB2A | Q13885 | 513 |
| CLDN4 | CGN | Q9P2M7 | 499 |
| CLDN4 | KRT5 | P13647 | 498 |
| CLDN4 | IL1B | P01584 | 498 |
| CLDN4 | MUC2 | Q02817 | 482 |
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:
| Partner | Interaction type | MIscore | Records |
|---|---|---|---|
| AQP6 | physical association | 0.560 | 3 |
| ARL13B | physical association | 0.560 | 3 |
| CLEC14A | physical association | 0.560 | 3 |
| FAM209A | physical association | 0.560 | 3 |
| FFAR2 | physical association | 0.560 | 3 |
| GJA8 | physical association | 0.560 | 3 |
| GOLM1 | physical association | 0.560 | 3 |
| HSD17B13 | physical association | 0.560 | 3 |
| ICAM3 | physical association | 0.560 | 3 |
| MFSD14B | physical association | 0.560 | 3 |
| SYT2 | physical association | 0.560 | 3 |
| TMEM237 | physical association | 0.560 | 3 |
| TMEM52B | physical association | 0.560 | 3 |
| TRIM59 | physical association | 0.560 | 3 |
| TSPO2 | physical association | 0.560 | 3 |
| PATJ | direct interaction | 0.440 | 7 |
| GRIP1 | direct interaction | 0.440 | 5 |
| GRIP2 | direct interaction | 0.440 | 5 |
| DLG1 | direct interaction | 0.440 | 3 |
| DLG3 | direct interaction | 0.440 | 3 |
| FRMPD2 | direct interaction | 0.440 | 3 |
| IL16 | direct interaction | 0.440 | 3 |
| MAGI2 | direct interaction | 0.440 | 3 |
| MPDZ | direct interaction | 0.440 | 3 |
| PDZK1 | direct interaction | 0.440 | 3 |
| SCRIB | direct interaction | 0.440 | 3 |
| WHRN | direct interaction | 0.440 | 3 |
| APBA2 | direct interaction | 0.440 | 2 |
| DLG2 | direct interaction | 0.440 | 2 |
| DLG4 | direct interaction | 0.440 | 2 |
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:
| A | Effect | B | Mechanism |
|---|---|---|---|
| SNAI1 | “down-regulates quantity by repression” | CLDN4 | “transcriptional regulation” |
| CLDN4 | down-regulates | Epithelial-mesenchymal_transition | |
| EPHA2 | “down-regulates activity” | CLDN4 | phosphorylation |
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:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Ras activation upon Ca2+ influx through NMDA receptor | 5 | 52.9× | 1e-06 |
| Unblocking of NMDA receptors, glutamate binding and activation | 5 | 50.4× | 1e-06 |
| Negative regulation of NMDA receptor-mediated neuronal transmission | 5 | 50.4× | 1e-06 |
| Assembly and cell surface presentation of NMDA receptors | 10 | 47.0× | 7e-13 |
| Dopamine Neurotransmitter Release Cycle | 5 | 46.0× | 2e-06 |
| Long-term potentiation | 5 | 44.1× | 2e-06 |
| Neurexins and neuroligins | 12 | 43.8× | 5e-15 |
| Protein-protein interactions at synapses | 8 | 39.4× | 1e-09 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| establishment or maintenance of epithelial cell apical/basal polarity | 9 | 64.6× | 4e-12 |
| protein localization to synapse | 6 | 56.7× | 1e-07 |
| receptor clustering | 7 | 53.9× | 9e-09 |
| regulation of postsynaptic membrane neurotransmitter receptor levels | 6 | 36.7× | 1e-06 |
| cell-cell adhesion | 9 | 11.3× | 6e-06 |
| protein-containing complex assembly | 8 | 11.2× | 3e-05 |
| chemical synaptic transmission | 7 | 6.7× | 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):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 27 |
| Likely benign | 2 |
| Benign | 0 |
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 ID | HGVS | Classification | Review | Submitters |
|---|---|---|---|---|
| 978415 | NC_000007.14:g.73773313_74086695del | Pathogenic | no assertion criteria provided | 1 |
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) | Effect | Δscore | Sites |
|---|---|---|---|
| 7:73832663 | acceptor_gain | 0.4800 | |
| 7:73832661 | acceptor_gain | 0.4700 | |
| 7:73831679 | donor_gain | 0.3800 | |
| 7:73831827 | donor_gain | 0.3700 | |
| 7:73831788 | donor_gain | 0.3600 | |
| 7:73832666 | acceptor_gain | 0.3500 | |
| 7:73832214 | acceptor_gain | 0.3300 | |
| 7:73831822 | donor_gain | 0.3200 | |
| 7:73831785 | donor_gain | 0.3100 | |
| 7:73831833 | donor_gain | 0.2900 |
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:
| Residue | Likely-pathogenic substitutions | Mean am_pathogenicity | Max am_pathogenicity |
|---|---|---|---|
| M52 | 8 | 0.811 | 0.961 |
| D68 | 8 | 0.775 | 0.915 |
| C54 | 7 | 0.991 | 0.994 |
| C64 | 7 | 0.988 | 0.997 |
| F147 | 7 | 0.984 | 0.998 |
| W30 | 7 | 0.980 | 0.996 |
| W51 | 7 | 0.978 | 0.996 |
| F35 | 7 | 0.961 | 0.994 |
| W168 | 7 | 0.935 | 0.997 |
| W47 | 7 | 0.890 | 0.968 |
| W138 | 7 | 0.853 | 0.959 |
| E159 | 7 | 0.843 | 0.953 |
| F125 | 7 | 0.784 | 0.881 |
| G49 | 6 | 0.986 | 0.998 |
| G161 | 6 | 0.980 | 0.996 |
| P28 | 6 | 0.969 | 0.988 |
| R81 | 6 | 0.943 | 0.994 |
| S58 | 6 | 0.932 | 0.974 |
| G60 | 6 | 0.929 | 0.986 |
| G17 | 6 | 0.917 | 0.995 |
HPA cancer prognostics
RNA cancer specificity: Low cancer specificity
Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.
3 prognostic cancer types:
| Cancer | Prognostic | p-value |
|---|---|---|
| Kidney Renal Clear Cell Carcinoma (TCGA) | favorable | 1.95e-09 |
| Kidney Renal Clear Cell Carcinoma (validation) | favorable | 5.05e-05 |
| Ovary Serous Cystadenocarcinoma (TCGA) | unfavorable | 0.00023 |
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:
| Descriptor | Name | Tree numbers |
|---|---|---|
| D018980 | Williams Syndrome | C10.597.606.360.970; 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.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | decreases methylation, increases expression, decreases expression | 7 |
| Valproic Acid | affects cotreatment, increases expression | 5 |
| deoxynivalenol | affects localization, decreases expression, increases expression | 3 |
| trichostatin A | affects cotreatment, increases expression | 3 |
| sodium arsenite | decreases expression, increases expression | 3 |
| Estradiol | affects cotreatment, decreases expression | 3 |
| Tobacco Smoke Pollution | increases expression | 3 |
| Cadmium Chloride | increases expression | 3 |
| ochratoxin A | affects reaction, decreases expression | 2 |
| mercuric bromide | increases expression, affects cotreatment | 2 |
| trans-10,cis-12-conjugated linoleic acid | increases expression | 2 |
| 2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide | affects expression, affects reaction, decreases expression, affects cotreatment | 2 |
| Panobinostat | increases expression, affects cotreatment | 2 |
| Air Pollutants | increases abundance, increases expression | 2 |
| Phenylmercuric Acetate | affects cotreatment, increases expression | 2 |
| Quercetin | affects localization, increases expression | 2 |
| Smoke | decreases expression, increases abundance, increases expression | 2 |
| Cyclosporine | increases expression | 2 |
| Okadaic Acid | increases expression | 2 |
| aristolochic acid I | increases expression | 1 |
| propionaldehyde | decreases expression, increases expression | 1 |
| sanguinarine | decreases expression | 1 |
| bisphenol A | decreases expression | 1 |
| 2,5,2’,5’-tetrachlorobiphenyl | increases expression | 1 |
| quercitrin | affects expression | 1 |
| butyraldehyde | increases expression | 1 |
| tetrathiomolybdate | decreases expression | 1 |
| benzo(e)pyrene | increases methylation | 1 |
| diallyl disulfide | decreases expression | 1 |
| 2,3-bis(3’-hydroxybenzyl)butyrolactone | affects cotreatment, decreases expression | 1 |
Cellosaurus cell lines
2 cell lines: 1 cancer cell line, 1 transformed cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_C3VA | HT-1080/hCLDN-4 | Cancer cell line | Male |
| CVCL_D3PN | CHO/CLDN4 | Transformed cell line | Female |
Clinical trials (associated diseases)
Via MONDO — disease-level, not drug-specific.
28 trials:
| NCT | Phase | Status | Title |
|---|---|---|---|
| NCT00768820 | Phase 4 | RECRUITING | The Psychiatric and Cognitive Phenotypes in Velocardiofacial Syndrome |
| NCT04807517 | Phase 4 | COMPLETED | Buspirone Treatment of Anxiety in Williams Syndrome |
| NCT00876200 | Phase 2 | COMPLETED | Efficacy of Minoxidil in Children With Williams-Beuren Syndrome |
| NCT06087757 | Phase 2 | ACTIVE_NOT_RECRUITING | Clemastine Treatment in Individuals With Williams Syndrome |
| NCT06315699 | Phase 2 | COMPLETED | Clemastine Fumarate in the Treatment of Neurodevelopmental Delays in Williams Syndrome |
| NCT00004351 | Not specified | COMPLETED | Study of Phenotype and Genotype Correlations in Patients With Contiguous Gene Deletion Syndromes |
| NCT00013962 | Not specified | COMPLETED | Vitamin D Metabolism and the Williams Syndrome |
| NCT01132885 | Not specified | RECRUITING | Defining the Brain Phenotype of Children With Williams Syndrome |
| NCT01793168 | Not specified | RECRUITING | Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford |
| NCT01864304 | Not specified | COMPLETED | Fat Distribution and Glucose Metabolism in Williams Syndrome |
| NCT02212314 | Not specified | COMPLETED | Response Inhibition Training for Children With Williams Syndrome |
| NCT02692846 | Not specified | COMPLETED | WS-SAVE Study (Williams Syndrome Skin and Vessel Elasticity Study) |
| NCT02706639 | Not specified | COMPLETED | Williams Syndrome (WS) and Supravalvar Aortic Stenosis (SVAS) DNA and Tissue Bank |
| NCT02840448 | Not specified | COMPLETED | Impact of Elastin Mediated Vascular Stiffness on End Organs |
| NCT03758651 | Not specified | COMPLETED | Williams Syndrome Strength, Hormones, Activity & Adiposity, DNA Programming, Eating Study |
| NCT03827525 | Not specified | UNKNOWN | Cognitive and Behavioral Therapy of Anxiety in Williams Syndrome |
| NCT03836300 | Not specified | ENROLLING_BY_INVITATION | Parent and Infant Inter(X)Action Intervention (PIXI) |
| NCT04051086 | Not specified | UNKNOWN | Quantification of Elastin Markers Synthesis in Williams-Beuren Syndrome and 7q11.23 Micro-duplication Syndrome |
| NCT04095585 | Not specified | COMPLETED | Molecular Characterization of Patients Affected by Williams Syndrome and Autism. |
| NCT04463316 | Not specified | RECRUITING | GROWing Up With Rare GENEtic Syndromes |
| NCT04610424 | Not specified | UNKNOWN | Cooperative Parent Mediated Therapy in Children With Fragile X Syndrome and Williams Syndrome |
| NCT05430763 | Not specified | WITHDRAWN | Motor Deficits and Signal Conduction in Individuals With Williams Syndrome |
| NCT06740162 | Not specified | RECRUITING | Physical Activity and Community EmPOWERment Project |
| NCT06930417 | Not specified | RECRUITING | Characterization and Natural History of Williams Syndrome and Other Chromosome 7q11.23 Variants |
| NCT07285720 | Not specified | RECRUITING | Phonological Constraints on Language Development in Individuals With Williams Syndrome |
| NCT07493096 | Not specified | RECRUITING | Intensive Multimodal Neurorehabilitation Targeting Neuroplasticity in Pediatric Neurodevelopmental and Chromosomal Disorders |
| NCT07509879 | Not specified | NOT_YET_RECRUITING | Research on the Molecular Mechanism of Cognitive Differences Between Williams Syndrome and Autism Spectrum Disorder |
| NCT07537374 | Not specified | NOT_YET_RECRUITING | A Case-Control Observational Study of Peripheral Blood-Derived iPSC Models to Investigate Oligodendrocyte Lineage Development in Children With Williams Syndrome and Healthy Controls |
Related Atlas pages
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