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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
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CLDN16
claudin 16
Chromosome 3 Β· 3q28
NCBI Gene: 10686Ensembl: ENSG00000113946.5HGNC: HGNC:2037UniProt: Q9Y5I7
53PubMed Papers
21Diseases
0Drugs
48Pathogenic Variants
FUNCTIONAL ROLE
Transporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
PDZ domain bindingprotein bindingparacellular transportidentical protein bindingrenal hypomagnesemia 3Autosomal dominant primary hypomagnesemia with hypocalciuriathrombocytopenia 5nephrocalcinosis
✦AI Summary

CLDN16 (claudin 16) is a tight junction protein that forms paracellular cation-selective channels by coassembling with CLDN19, enabling epithelial ion permeability 1. In the thick ascending limb of Henle's loop, CLDN16 facilitates sodium paracellular permeability and the lumen-positive transepithelial potential necessary for magnesium and calcium reabsorption 2. Biallelic loss-of-function mutations in CLDN16 cause familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC), characterized by severe renal magnesium wasting, hypercalciuria, nephrocalcinosis, and progressive renal failure 3. CLDN16 mutations account for approximately 1% of genetic kidney stone disease in adult populations 4. Beyond renal physiology, CLDN16 is significantly upregulated in several cancers including breast, papillary thyroid, and ovarian cancers, where it correlates with aggressive features and metastatic potential 5 6 7. In papillary thyroid cancer, CLDN16 demonstrates superior diagnostic accuracy (ROC=0.922) compared to the standard BRAF-V600E mutation (ROC=0.742) 6. CLDN16 expression in ovarian cancer is modulated by PI3K and PKC signaling pathways 7, suggesting potential therapeutic targeting opportunities.

Sources cited
1
CLDN16 coassembles with CLDN19 to form tight junction channels with cation-selective permeability
PMID: 16234325
2
CLDN16 facilitates sodium paracellular permeability in the thick ascending limb of Henle's loop
PMID: 10390358
3
Biallelic CLDN16 mutations cause familial hypomagnesemia with hypercalciuria and nephrocalcinosis
PMID: 34761296
4
CLDN16 variants account for 8 cases (1% enrichment) among kidney stone formers with predisposing variants
PMID: 38544324
5
CLDN16 is significantly upregulated in breast cancer tissues compared to normal tissue
PMID: 20664984
6
CLDN16 is a superior biomarker for papillary thyroid cancer with higher diagnostic accuracy than BRAF-V600E
PMID: 39996468
7
CLDN16 expression in ovarian cancer is modulated by PI3K and PKC signaling pathways
PMID: 36889572
Disease Associationsβ“˜21
renal hypomagnesemia 3Open Targets
0.84Strong
Autosomal dominant primary hypomagnesemia with hypocalciuriaOpen Targets
0.64Moderate
thrombocytopenia 5Open Targets
0.34Weak
nephrocalcinosisOpen Targets
0.27Weak
renal hypomagnesemia 5 with ocular involvementOpen Targets
0.27Weak
nephrolithiasisOpen Targets
0.26Weak
genetic disorderOpen Targets
0.19Weak
focal segmental glomerulosclerosisOpen Targets
0.05Suggestive
Dent diseaseOpen Targets
0.05Suggestive
Idiopathic hypercalciuriaOpen Targets
0.05Suggestive
Autosomal recessive infantile hypercalcemiaOpen Targets
0.05Suggestive
familial idiopathic steroid-resistant nephrotic syndromeOpen Targets
0.05Suggestive
nephrotic syndromeOpen Targets
0.05Suggestive
primary hyperoxaluria type 2Open Targets
0.05Suggestive
proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosisOpen Targets
0.05Suggestive
Dent disease type 1Open Targets
0.04Suggestive
renal hypomagnesemia 2Open Targets
0.04Suggestive
Chronic Obstructive AsthmaOpen Targets
0.04Suggestive
autosomal dominant hypocalcemia 1Open Targets
0.04Suggestive
Familial isolated hypoparathyroidismOpen Targets
0.04Suggestive
Hypomagnesemia 3UniProt
Pathogenic Variants48
NM_006580.4(CLDN16):c.243G>T (p.Leu81Phe)Pathogenic
Primary hypomagnesemia|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 81
NM_006580.4(CLDN16):c.130C>T (p.Arg44Ter)Pathogenic
Primary hypomagnesemia|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 44
NM_006580.4(CLDN16):c.217+5G>APathogenic
Primary hypomagnesemia|not provided
β˜…β˜…β˜†β˜†2025
NM_006580.4(CLDN16):c.383G>A (p.Gly128Asp)Pathogenic
Primary hypomagnesemia|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 128
NM_006580.4(CLDN16):c.235C>T (p.Arg79Ter)Pathogenic
Primary hypomagnesemia|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 79
NM_006580.4(CLDN16):c.436C>T (p.Arg146Cys)Pathogenic
Primary hypomagnesemia
β˜…β˜…β˜†β˜†2025β†’ Residue 146
NM_006580.4(CLDN16):c.217+1G>ALikely pathogenic
not provided|Primary hypomagnesemia
β˜…β˜…β˜†β˜†2024
NM_006580.4(CLDN16):c.437G>A (p.Arg146His)Pathogenic
not provided|Primary hypomagnesemia
β˜…β˜…β˜†β˜†2024β†’ Residue 146
NM_006580.4(CLDN16):c.505G>A (p.Gly169Arg)Pathogenic
Primary hypomagnesemia|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 169
NM_006580.4(CLDN16):c.487G>T (p.Gly163Cys)Likely pathogenic
not provided|Primary hypomagnesemia
β˜…β˜…β˜†β˜†2022β†’ Residue 163
NM_006580.4(CLDN16):c.415G>A (p.Ala139Thr)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 139
NM_006580.4(CLDN16):c.211C>G (p.His71Asp)Likely pathogenic
Primary hypomagnesemia
β˜…β˜†β˜†β˜†2025β†’ Residue 71
NM_006580.4(CLDN16):c.152T>G (p.Val51Gly)Pathogenic
Thrombocytopenia 5|Primary hypomagnesemia
β˜…β˜†β˜†β˜†2025β†’ Residue 51
NM_006580.4(CLDN16):c.361G>A (p.Gly121Arg)Pathogenic
Primary hypomagnesemia
β˜…β˜†β˜†β˜†2025β†’ Residue 121
NM_006580.4(CLDN16):c.128G>T (p.Cys43Phe)Likely pathogenic
Primary hypomagnesemia
β˜…β˜†β˜†β˜†2025β†’ Residue 43
NM_006580.4(CLDN16):c.83G>A (p.Cys28Tyr)Likely pathogenic
Primary hypomagnesemia
β˜…β˜†β˜†β˜†2025β†’ Residue 28
NM_006580.4(CLDN16):c.37G>C (p.Ala13Pro)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 13
NM_006580.4(CLDN16):c.498T>A (p.Cys166Ter)Likely pathogenic
Primary hypomagnesemia
β˜…β˜†β˜†β˜†2024β†’ Residue 166
NM_006580.4(CLDN16):c.608_663dup (p.Arg222Ter)Likely pathogenic
Primary hypomagnesemia
β˜…β˜†β˜†β˜†2024β†’ Residue 222
NM_006580.4(CLDN16):c.236G>T (p.Arg79Leu)Likely pathogenic
Primary hypomagnesemia
β˜…β˜†β˜†β˜†2024β†’ Residue 79
View on ClinVar β†—
Related Genes
OCLNProtein interaction96%FXYD2Protein interaction92%SLC12A3Protein interaction90%TJP3Protein interaction87%CLDN23Protein interaction84%TRPM6Protein interaction83%
Tissue Expression6 tissues
Liver
100%
Ovary
18%
Lung
15%
Brain
15%
Bone Marrow
0%
Heart
0%
Gene Interaction Network
Click a node to explore
CLDN16OCLNFXYD2SLC12A3TJP3CLDN23TRPM6
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9Y5I7
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.84LoF Tolerant
pLIβ“˜
0.01Tolerant
Observed/Expected LoF0.54 [0.35–0.84]
RankingsWhere CLDN16 stands among ~20K protein-coding genes
  • #8,408of 20,598
    Most Researched53
  • #1,374of 5,498
    Most Pathogenic Variants48 Β· top quartile
  • #7,188of 17,882
    Most Constrained (LOEUF)0.84
Genes detectedCLDN16
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Prevalence and characteristics of genetic disease in adult kidney stone formers.
PMID: 38544324
Nephrol Dial Transplant Β· 2024
1.00
2
Significant elevation of CLDN16 and HAPLN3 gene expression in human breast cancer.
PMID: 20664984
Oncol Rep Β· 2010
0.90
3
In-Depth Bioinformatic Study of the CLDN16 Gene and Protein: Prediction of Subcellular Localization to Mitochondria.
PMID: 31357502
Medicina (Kaunas) Β· 2019
0.80
4
A new broom sweeps clean: CLDN16 surpasses the BRAF-V600E mutation as an unrivaled biomarker in papillary thyroid cancer.
PMID: 39996468
Eur J Endocrinol Β· 2025
0.70
5
Overexpression of CLDN16 in ovarian cancer is modulated by PI3K and PKC pathways.
PMID: 36889572
Exp Cell Res Β· 2023
0.60