{"gene":"CLDN16","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2000,"finding":"CLDN16 (PCLN-1/paracellin-1) encodes a renal tight junction protein predominantly expressed in the thick ascending limb (TAL) of the loop of Henle, where it mediates paracellular reabsorption of divalent cations (Ca2+ and Mg2+). Mutations in the first extracellular loop (e.g., Leu151) disrupt the intercellular bridging function critical for paracellular conductance.","method":"Linkage analysis, mutational analysis, and mapping of mutations to functional protein domains (extracellular loop)","journal":"European journal of human genetics : EJHG","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic mapping plus domain-level mutation analysis in multiple families; no in vitro reconstitution, but replicated across cohorts","pmids":["10878661"],"is_preprint":false},{"year":2007,"finding":"Complete loss-of-function mutations in both CLDN16 alleles result in significantly earlier disease onset and faster GFR decline compared to mutations that retain partial protein function, establishing a dose-dependent relationship between residual claudin-16 activity and renal paracellular Ca2+/Mg2+ transport capacity.","method":"Expression studies of mutant proteins combined with clinical genotype-phenotype correlation in 71 FHHNC patients across 17+ mutations","journal":"Journal of the American Society of Nephrology : JASN","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional expression studies classifying partial vs. complete loss of function, combined with large clinical cohort; single study but multiple mutations and orthogonal clinical data","pmids":["18003771"],"is_preprint":false},{"year":2010,"finding":"Targeted deletion of murine Cldn16 causes hypercalciuria and hypomagnesemia, confirming that CLDN16 is required for renal paracellular Ca2+ and Mg2+ reabsorption in the thick ascending loop of Henle. Loss of CLDN16 triggers compensatory upregulation of transcellular Ca2+ and Mg2+ transport genes including Trpv5, Trpm6, calbindin-D9k, Cnnm2, and Atp13a4.","method":"Targeted gene knockout mouse model with urinary electrolyte measurements, gene expression profiling, and hormonal assays (PTH, 1,25(OH)2D3)","journal":"American journal of physiology. Renal physiology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean knockout model with defined physiological phenotype and compensatory gene expression profiling; multiple orthogonal readouts in a dedicated mechanistic study","pmids":["20147368"],"is_preprint":false},{"year":2008,"finding":"Mutations affecting the second extracellular loop of claudin-16 (e.g., Arg216Cys missense and a splice-site mutation truncating 64 amino acids in the second extracellular loop) cause complete loss of function of the protein, establishing the second extracellular loop as essential for CLDN16 function in paracellular transport.","method":"Mutation analysis with domain mapping and clinical loss-of-function correlation in affected siblings","journal":"BMC nephrology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — domain-level mutation mapping in a single family case report; no in vitro reconstitution","pmids":["18816383"],"is_preprint":false},{"year":2019,"finding":"Several CLDN16 exonic mutations previously classified as missense variants alter pre-mRNA splicing: mutations c.453G>T and c.446G>T inactivate exonic splicing enhancers and promote use of an internal cryptic acceptor splice site; c.571G>A causes partial exon 3 skipping; c.593G>C and c.593G>A disrupt the acceptor splice site of intron 3, causing complete exon 4 skipping.","method":"Minigene splicing assay for 12 CLDN16 exonic mutations","journal":"BMC medical genetics","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — direct functional minigene assay establishing splicing mechanism; single lab but multiple mutations tested with clear molecular readouts","pmids":["30621608"],"is_preprint":false},{"year":2023,"finding":"CLDN16 expression in high-grade serous ovarian cancer cells is upregulated via PKC, PI3K, and estrogen signaling pathways, and the protein localizes predominantly to the cytoplasm rather than at tight junctions in this cancer context.","method":"Immunoblotting, immunofluorescence, and pathway inhibitor/activator experiments in OVCAR-3 cells","journal":"Experimental cell research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, limited cell-line experiments, no mechanistic epistasis; findings in a non-renal cancer context with small sample sizes","pmids":["36889572"],"is_preprint":false},{"year":2025,"finding":"CLDN16 knockdown in papillary thyroid cancer cells inhibits cell migration, invasion, and iodine uptake, demonstrating a pro-tumorigenic functional role for CLDN16 in PTC cell behavior.","method":"Knockdown experiments with migration, invasion, and iodine-uptake assays in PTC cells","journal":"European journal of endocrinology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab knockdown study with defined cellular phenotypes but no upstream pathway placement or mechanistic detail","pmids":["39996468"],"is_preprint":false},{"year":2025,"finding":"CLDN16 knockdown in pancreatic adenocarcinoma cells enhances invasiveness and reduces apoptosis, identifying CLDN16 as a pro-tumorigenic factor in PAAD.","method":"Functional knockdown validation with invasion and apoptosis assays in pancreatic cancer cells","journal":"Cellular and molecular life sciences : CMLS","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single in vitro knockdown study, no pathway mechanistic detail, single lab","pmids":["41407964"],"is_preprint":false}],"current_model":"CLDN16 (paracellin-1) is a tight junction protein expressed in the thick ascending limb of the loop of Henle, where it forms a paracellular channel essential for reabsorption of Ca2+ and Mg2+; loss-of-function mutations cause familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC), with disease severity proportional to residual protein function, and its absence triggers compensatory upregulation of transcellular Ca2+/Mg2+ transport proteins including Trpv5, Trpm6, and calbindin-D9k."},"narrative":{"mechanistic_narrative":"CLDN16 (paracellin-1) is a renal tight junction protein expressed predominantly in the thick ascending limb of the loop of Henle, where it forms the paracellular pathway for reabsorption of the divalent cations Ca2+ and Mg2+ [PMID:10878661, PMID:20147368]. Targeted deletion of murine Cldn16 produces hypercalciuria and hypomagnesemia, and the loss of paracellular transport triggers compensatory upregulation of transcellular Ca2+/Mg2+ transport genes including Trpv5, Trpm6, calbindin-D9k, Cnnm2, and Atp13a4 [PMID:20147368]. The bridging function depends on both extracellular loops: mutations in the first and second extracellular loops abolish paracellular conductance [PMID:10878661, PMID:18816383], and the degree of residual claudin-16 activity scales inversely with disease severity, establishing a dose-dependent relationship between protein function and renal divalent-cation handling [PMID:18003771]. Loss-of-function mutations in CLDN16 cause familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC) [PMID:18003771], and a substantial fraction of exonic mutations act not by amino-acid substitution but by disrupting pre-mRNA splicing through inactivation of exonic splicing enhancers, cryptic splice-site activation, and exon skipping [PMID:30621608]. Beyond its renal role, the mechanistic basis of CLDN16 function in non-renal tissues has not been characterized in the available corpus.","teleology":[{"year":2000,"claim":"Established the gene's identity and core role: linking CLDN16 to renal paracellular divalent-cation reabsorption and identifying the extracellular loop as the functional determinant of intercellular bridging.","evidence":"Linkage analysis and mutation-to-domain mapping in FHHNC families","pmids":["10878661"],"confidence":"Medium","gaps":["No in vitro reconstitution of channel activity","Selectivity mechanism for Ca2+ vs Mg2+ not defined","Partner claudins not identified"]},{"year":2007,"claim":"Resolved whether disease severity tracks with residual protein function, showing a dose-dependent relationship between claudin-16 activity and renal Ca2+/Mg2+ transport capacity.","evidence":"Mutant expression studies plus genotype-phenotype correlation across 71 FHHNC patients","pmids":["18003771"],"confidence":"Medium","gaps":["Functional classification based on expression, not direct conductance measurement","Single study cohort"]},{"year":2008,"claim":"Extended the structure-function map by establishing the second extracellular loop, not only the first, as essential for CLDN16 function.","evidence":"Domain-level mutation mapping in affected siblings","pmids":["18816383"],"confidence":"Low","gaps":["Single family case report with no in vitro reconstitution","No biophysical assay of loop function"]},{"year":2010,"claim":"Confirmed causal necessity in vivo and revealed the compensatory transcellular response when paracellular transport is lost.","evidence":"Cldn16 knockout mouse with urinary electrolyte, gene expression, and hormonal profiling","pmids":["20147368"],"confidence":"High","gaps":["Molecular mechanism of compensatory gene induction unknown","Direct measurement of paracellular conductance not performed","Ion selectivity mechanism unresolved"]},{"year":2019,"claim":"Reclassified the molecular consequence of multiple exonic mutations, showing splicing disruption rather than coding change underlies a portion of pathogenic alleles.","evidence":"Minigene splicing assays for 12 CLDN16 exonic mutations","pmids":["30621608"],"confidence":"Medium","gaps":["Splicing outcomes from minigenes not confirmed in patient tissue","Single lab"]},{"year":2025,"claim":"Probed non-renal contexts, reporting cytoplasmic localization and pro-tumorigenic effects of CLDN16 across ovarian, thyroid, and pancreatic cancer cells.","evidence":"Pathway inhibitor/activator and knockdown phenotyping in OVCAR-3, PTC, and PAAD cell lines","pmids":["36889572","39996468","41407964"],"confidence":"Low","gaps":["Single-lab in vitro studies with no mechanistic epistasis","Connection to canonical tight-junction function unclear","No in vivo validation"]},{"year":null,"claim":"How CLDN16 achieves divalent-cation selectivity and which partner claudins or tight-junction proteins it requires to form a functional paracellular channel remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No reconstituted channel assay defining ion selectivity","Interacting claudins not identified in the corpus","No structural model of the channel"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[0,2]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,2]}],"pathway":[{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[0,2]},{"term_id":"R-HSA-1500931","term_label":"Cell-Cell communication","supporting_discovery_ids":[0]}],"complexes":["tight junction"],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y5I7","full_name":"Claudin-16","aliases":["Paracellin-1","PCLN-1"],"length_aa":235,"mass_kda":26.1,"function":"Forms paracellular channels: coassembles with CLDN19 into tight junction strands with cation-selective channels through the strands, conveying epithelial permeability in a process known as paracellular tight junction permeability (PubMed:16234325, PubMed:18188451, PubMed:28028216). Involved in the maintenance of ion gradients along the nephron. In the thick ascending limb (TAL) of Henle's loop, facilitates sodium paracellular permeability from the interstitial compartment to the lumen, contributing to the lumen-positive transepithelial potential that drives paracellular magnesium and calcium reabsorption (PubMed:10390358, PubMed:11518780, PubMed:14628289, PubMed:16528408, PubMed:28028216)","subcellular_location":"Cell junction, tight junction; Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q9Y5I7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CLDN16","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CLDN16","total_profiled":1310},"omim":[{"mim_id":"611718","title":"HYPOMAGNESEMIA 4, RENAL; HOMG4","url":"https://www.omim.org/entry/611718"},{"mim_id":"610036","title":"CLAUDIN 19; CLDN19","url":"https://www.omim.org/entry/610036"},{"mim_id":"603959","title":"CLAUDIN 16; CLDN16","url":"https://www.omim.org/entry/603959"},{"mim_id":"602014","title":"HYPOMAGNESEMIA 1, INTESTINAL; HOMG1","url":"https://www.omim.org/entry/602014"},{"mim_id":"248250","title":"HYPOMAGNESEMIA 3, RENAL; HOMG3","url":"https://www.omim.org/entry/248250"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"kidney","ntpm":59.3}],"url":"https://www.proteinatlas.org/search/CLDN16"},"hgnc":{"alias_symbol":["PCLN1","HOMG3"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y5I7","domains":[{"cath_id":"1.20.140.150","chopping":"87-97_143-263","consensus_level":"medium","plddt":88.3625,"start":87,"end":263}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y5I7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y5I7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y5I7-F1-predicted_aligned_error_v6.png","plddt_mean":77.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CLDN16","jax_strain_url":"https://www.jax.org/strain/search?query=CLDN16"},"sequence":{"accession":"Q9Y5I7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y5I7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y5I7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y5I7"}},"corpus_meta":[{"pmid":"18003771","id":"PMC_18003771","title":"CLDN16 genotype predicts renal decline in familial hypomagnesemia with hypercalciuria and nephrocalcinosis.","date":"2007","source":"Journal of the American Society of Nephrology : JASN","url":"https://pubmed.ncbi.nlm.nih.gov/18003771","citation_count":88,"is_preprint":false},{"pmid":"20147368","id":"PMC_20147368","title":"Targeted deletion of murine Cldn16 identifies extra- and intrarenal compensatory mechanisms of Ca2+ and Mg2+ wasting.","date":"2010","source":"American journal of physiology. Renal physiology","url":"https://pubmed.ncbi.nlm.nih.gov/20147368","citation_count":84,"is_preprint":false},{"pmid":"10878661","id":"PMC_10878661","title":"Familial hypomagnesaemia with hypercalciuria and nephrocalcinosis maps to chromosome 3q27 and is associated with mutations in the PCLN-1 gene.","date":"2000","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/10878661","citation_count":84,"is_preprint":false},{"pmid":"22422540","id":"PMC_22422540","title":"Familial hypomagnesemia with hypercalciuria and nephrocalcinosis: phenotype-genotype correlation and outcome in 32 patients with CLDN16 or CLDN19 mutations.","date":"2012","source":"Clinical journal of the American Society of Nephrology : CJASN","url":"https://pubmed.ncbi.nlm.nih.gov/22422540","citation_count":77,"is_preprint":false},{"pmid":"14586675","id":"PMC_14586675","title":"Two heterozygous mutations of CLDN16 in a Japanese patient with FHHNC.","date":"2003","source":"Pediatric nephrology (Berlin, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/14586675","citation_count":30,"is_preprint":false},{"pmid":"21669885","id":"PMC_21669885","title":"Clinical and molecular characterization of Turkish patients with familial hypomagnesaemia: novel mutations in TRPM6 and CLDN16 genes.","date":"2011","source":"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association","url":"https://pubmed.ncbi.nlm.nih.gov/21669885","citation_count":28,"is_preprint":false},{"pmid":"16047219","id":"PMC_16047219","title":"Familial hypomagnesemia with hypercalciuria and nephrocalcinosis associated with CLDN16 mutations.","date":"2005","source":"Pediatric nephrology (Berlin, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/16047219","citation_count":25,"is_preprint":false},{"pmid":"25477417","id":"PMC_25477417","title":"Retrospective cohort study of familial hypomagnesaemia with hypercalciuria and nephrocalcinosis due to CLDN16 mutations.","date":"2014","source":"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association","url":"https://pubmed.ncbi.nlm.nih.gov/25477417","citation_count":24,"is_preprint":false},{"pmid":"18816383","id":"PMC_18816383","title":"Familial hypomagnesaemia with hypercalciuria and nephrocalcinosis (FHHNC): compound heterozygous mutation in the claudin 16 (CLDN16) gene.","date":"2008","source":"BMC nephrology","url":"https://pubmed.ncbi.nlm.nih.gov/18816383","citation_count":23,"is_preprint":false},{"pmid":"16595585","id":"PMC_16595585","title":"Hydrochlorothiazide in CLDN16 mutation.","date":"2006","source":"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association","url":"https://pubmed.ncbi.nlm.nih.gov/16595585","citation_count":16,"is_preprint":false},{"pmid":"26136118","id":"PMC_26136118","title":"Identification of the first large deletion in the CLDN16 gene in a patient with FHHNC and late-onset of chronic kidney disease: case report.","date":"2015","source":"BMC nephrology","url":"https://pubmed.ncbi.nlm.nih.gov/26136118","citation_count":13,"is_preprint":false},{"pmid":"17123117","id":"PMC_17123117","title":"A novel PCLN-1 gene mutation in familial hypomagnesemia with hypercalciuria and atypical phenotype.","date":"2006","source":"Pediatric nephrology (Berlin, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/17123117","citation_count":13,"is_preprint":false},{"pmid":"25852890","id":"PMC_25852890","title":"Two novel mutations of the CLDN16 gene cause familial hypomagnesaemia with hypercalciuria and nephrocalcinosis.","date":"2014","source":"Clinical kidney journal","url":"https://pubmed.ncbi.nlm.nih.gov/25852890","citation_count":10,"is_preprint":false},{"pmid":"12584272","id":"PMC_12584272","title":"Exclusion of mutations in FXYD2, CLDN16 and SLC12A3 in two families with primary renal Mg2+ loss.","date":"2003","source":"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association","url":"https://pubmed.ncbi.nlm.nih.gov/12584272","citation_count":9,"is_preprint":false},{"pmid":"24321194","id":"PMC_24321194","title":"A novel CLDN16 mutation in a large family with familial hypomagnesaemia with hypercalciuria and nephrocalcinosis.","date":"2013","source":"BMC research notes","url":"https://pubmed.ncbi.nlm.nih.gov/24321194","citation_count":8,"is_preprint":false},{"pmid":"32869508","id":"PMC_32869508","title":"Novel compound heterozygous mutations of CLDN16 in a patient with familial hypomagnesemia with hypercalciuria and nephrocalcinosis.","date":"2020","source":"Molecular genetics & genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32869508","citation_count":8,"is_preprint":false},{"pmid":"27067446","id":"PMC_27067446","title":"A novel mutation in CLDN16 results in rare familial hypomagnesaemia with hypercalciuria and nephrocalcinosis in a Chinese family.","date":"2016","source":"Clinica chimica acta; international journal of clinical chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/27067446","citation_count":7,"is_preprint":false},{"pmid":"17347984","id":"PMC_17347984","title":"Hypomagnesemia and nephrocalcinosis in a patient with two heterozygous mutations in the CLDN16 gene.","date":"2007","source":"Journal of nephrology","url":"https://pubmed.ncbi.nlm.nih.gov/17347984","citation_count":7,"is_preprint":false},{"pmid":"30621608","id":"PMC_30621608","title":"Exonic CLDN16 mutations associated with familial hypomagnesemia with hypercalciuria and nephrocalcinosis can induce deleterious mRNA alterations.","date":"2019","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30621608","citation_count":5,"is_preprint":false},{"pmid":"34761296","id":"PMC_34761296","title":"Familial Hypomagnesemia with Hypercalciuria and Nephrocalcinosis Due to CLDN16 Gene Mutations: Novel Findings in Two Cases with Diverse Clinical Features.","date":"2021","source":"Calcified tissue international","url":"https://pubmed.ncbi.nlm.nih.gov/34761296","citation_count":4,"is_preprint":false},{"pmid":"36889572","id":"PMC_36889572","title":"Overexpression of CLDN16 in ovarian cancer is modulated by PI3K and PKC pathways.","date":"2023","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/36889572","citation_count":3,"is_preprint":false},{"pmid":"32710267","id":"PMC_32710267","title":"Hypomagnesemia with Hypercalciuria Leading to Nephrocalcinosis, Amelogenesis Imperfecta, and Short Stature in a Child Carrying a Homozygous Deletion in the CLDN16 Gene.","date":"2020","source":"Calcified tissue international","url":"https://pubmed.ncbi.nlm.nih.gov/32710267","citation_count":3,"is_preprint":false},{"pmid":"30102483","id":"PMC_30102483","title":"A novel homozygous W99G mutation in CLDN-16 gene causing familial hypomagnesemic hypercalciuric nephrocalcinosis in Turkish siblings.","date":"2018","source":"The Turkish journal of pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/30102483","citation_count":3,"is_preprint":false},{"pmid":"35714216","id":"PMC_35714216","title":"A Novel Mutation in CLDN16 Gene Causing Familial Hypomagnesemia, Hypercalciuria, Nephrocalcinosis in An Iranian Family.","date":"2022","source":"Iranian journal of kidney diseases","url":"https://pubmed.ncbi.nlm.nih.gov/35714216","citation_count":2,"is_preprint":false},{"pmid":"39996468","id":"PMC_39996468","title":"A new broom sweeps clean: CLDN16 surpasses the BRAF-V600E mutation as an unrivaled biomarker in papillary thyroid cancer.","date":"2025","source":"European journal of endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/39996468","citation_count":2,"is_preprint":false},{"pmid":"38078932","id":"PMC_38078932","title":"Identification of a Novel Homozygous Missense Mutation in the CLDN16 Gene to Decipher the Ambiguous Clinical Presentation Associated with Autosomal Dominant Hypocalcaemia and Familial Hypomagnesemia with Hypercalciuria and Nephrocalcinosis in an Indian Family.","date":"2023","source":"Calcified tissue international","url":"https://pubmed.ncbi.nlm.nih.gov/38078932","citation_count":2,"is_preprint":false},{"pmid":"31357502","id":"PMC_31357502","title":"In-Depth Bioinformatic Study of the CLDN16 Gene and Protein: Prediction of Subcellular Localization to Mitochondria.","date":"2019","source":"Medicina (Kaunas, Lithuania)","url":"https://pubmed.ncbi.nlm.nih.gov/31357502","citation_count":1,"is_preprint":false},{"pmid":"31232269","id":"PMC_31232269","title":"A novel CLDN16 mutation in familial hypomagnesemia with hypercalciuria and nephrocalcinosis
.","date":"2019","source":"Clinical nephrology","url":"https://pubmed.ncbi.nlm.nih.gov/31232269","citation_count":1,"is_preprint":false},{"pmid":"41306405","id":"PMC_41306405","title":"Recurrent Nephrolithiasis and Beyond: The Long Diagnostic Odyssey of a Case of CLDN16 Mutation.","date":"2025","source":"Clinical case reports","url":"https://pubmed.ncbi.nlm.nih.gov/41306405","citation_count":0,"is_preprint":false},{"pmid":"41407964","id":"PMC_41407964","title":"Multi-omics analysis reveals cell adhesion molecules as key regulators of immune cell infiltration and adverse outcomes and in vitro validation of CLDN16 in pancreatic adenocarcinoma.","date":"2025","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/41407964","citation_count":0,"is_preprint":false},{"pmid":"41896308","id":"PMC_41896308","title":"Familial hypomagnesemia with hypercalciuria and nephrocalcinosis caused by CLDN16/CLDN19 mutations in four Chinese families.","date":"2026","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/41896308","citation_count":0,"is_preprint":false},{"pmid":"40826740","id":"PMC_40826740","title":"Whole exome sequencing reveals a pathogenic homozygous CLDN16 mutation in a 17-year-old patient with familial hypomagnesemia with hypercalciuria and nephrocalcinosis: A case report.","date":"2025","source":"Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40826740","citation_count":0,"is_preprint":false},{"pmid":"40807067","id":"PMC_40807067","title":"Familial MEN1 Syndrome with Atypical Renal Features and a Coexisting CLDN16 Variant: A Case Series.","date":"2025","source":"Journal of clinical medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40807067","citation_count":0,"is_preprint":false},{"pmid":"41884086","id":"PMC_41884086","title":"X-linked hypophosphatemia in the presence of a CLDN16 variant: implications for renal handling and disease severity.","date":"2026","source":"JCEM case reports","url":"https://pubmed.ncbi.nlm.nih.gov/41884086","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.08.22.24312447","title":"Unveiling Genetic Associations: Investigating<i>CLDN16, GRID2, NRG3,</i>and<i>CACNG4</i>Gene Polymorphisms with Insulin Resistance Risk Among Normal BMI Individuals in the Indian Population","date":"2024-08-23","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.22.24312447","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":21205,"output_tokens":1938,"usd":0.046343,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8875,"output_tokens":2220,"usd":0.049938,"stage2_stop_reason":"end_turn"},"total_usd":0.096281,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"CLDN16 (PCLN-1/paracellin-1) encodes a renal tight junction protein predominantly expressed in the thick ascending limb (TAL) of the loop of Henle, where it mediates paracellular reabsorption of divalent cations (Ca2+ and Mg2+). Mutations in the first extracellular loop (e.g., Leu151) disrupt the intercellular bridging function critical for paracellular conductance.\",\n      \"method\": \"Linkage analysis, mutational analysis, and mapping of mutations to functional protein domains (extracellular loop)\",\n      \"journal\": \"European journal of human genetics : EJHG\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic mapping plus domain-level mutation analysis in multiple families; no in vitro reconstitution, but replicated across cohorts\",\n      \"pmids\": [\"10878661\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Complete loss-of-function mutations in both CLDN16 alleles result in significantly earlier disease onset and faster GFR decline compared to mutations that retain partial protein function, establishing a dose-dependent relationship between residual claudin-16 activity and renal paracellular Ca2+/Mg2+ transport capacity.\",\n      \"method\": \"Expression studies of mutant proteins combined with clinical genotype-phenotype correlation in 71 FHHNC patients across 17+ mutations\",\n      \"journal\": \"Journal of the American Society of Nephrology : JASN\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional expression studies classifying partial vs. complete loss of function, combined with large clinical cohort; single study but multiple mutations and orthogonal clinical data\",\n      \"pmids\": [\"18003771\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Targeted deletion of murine Cldn16 causes hypercalciuria and hypomagnesemia, confirming that CLDN16 is required for renal paracellular Ca2+ and Mg2+ reabsorption in the thick ascending loop of Henle. Loss of CLDN16 triggers compensatory upregulation of transcellular Ca2+ and Mg2+ transport genes including Trpv5, Trpm6, calbindin-D9k, Cnnm2, and Atp13a4.\",\n      \"method\": \"Targeted gene knockout mouse model with urinary electrolyte measurements, gene expression profiling, and hormonal assays (PTH, 1,25(OH)2D3)\",\n      \"journal\": \"American journal of physiology. Renal physiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean knockout model with defined physiological phenotype and compensatory gene expression profiling; multiple orthogonal readouts in a dedicated mechanistic study\",\n      \"pmids\": [\"20147368\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Mutations affecting the second extracellular loop of claudin-16 (e.g., Arg216Cys missense and a splice-site mutation truncating 64 amino acids in the second extracellular loop) cause complete loss of function of the protein, establishing the second extracellular loop as essential for CLDN16 function in paracellular transport.\",\n      \"method\": \"Mutation analysis with domain mapping and clinical loss-of-function correlation in affected siblings\",\n      \"journal\": \"BMC nephrology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — domain-level mutation mapping in a single family case report; no in vitro reconstitution\",\n      \"pmids\": [\"18816383\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Several CLDN16 exonic mutations previously classified as missense variants alter pre-mRNA splicing: mutations c.453G>T and c.446G>T inactivate exonic splicing enhancers and promote use of an internal cryptic acceptor splice site; c.571G>A causes partial exon 3 skipping; c.593G>C and c.593G>A disrupt the acceptor splice site of intron 3, causing complete exon 4 skipping.\",\n      \"method\": \"Minigene splicing assay for 12 CLDN16 exonic mutations\",\n      \"journal\": \"BMC medical genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct functional minigene assay establishing splicing mechanism; single lab but multiple mutations tested with clear molecular readouts\",\n      \"pmids\": [\"30621608\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CLDN16 expression in high-grade serous ovarian cancer cells is upregulated via PKC, PI3K, and estrogen signaling pathways, and the protein localizes predominantly to the cytoplasm rather than at tight junctions in this cancer context.\",\n      \"method\": \"Immunoblotting, immunofluorescence, and pathway inhibitor/activator experiments in OVCAR-3 cells\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, limited cell-line experiments, no mechanistic epistasis; findings in a non-renal cancer context with small sample sizes\",\n      \"pmids\": [\"36889572\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CLDN16 knockdown in papillary thyroid cancer cells inhibits cell migration, invasion, and iodine uptake, demonstrating a pro-tumorigenic functional role for CLDN16 in PTC cell behavior.\",\n      \"method\": \"Knockdown experiments with migration, invasion, and iodine-uptake assays in PTC cells\",\n      \"journal\": \"European journal of endocrinology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab knockdown study with defined cellular phenotypes but no upstream pathway placement or mechanistic detail\",\n      \"pmids\": [\"39996468\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CLDN16 knockdown in pancreatic adenocarcinoma cells enhances invasiveness and reduces apoptosis, identifying CLDN16 as a pro-tumorigenic factor in PAAD.\",\n      \"method\": \"Functional knockdown validation with invasion and apoptosis assays in pancreatic cancer cells\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single in vitro knockdown study, no pathway mechanistic detail, single lab\",\n      \"pmids\": [\"41407964\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CLDN16 (paracellin-1) is a tight junction protein expressed in the thick ascending limb of the loop of Henle, where it forms a paracellular channel essential for reabsorption of Ca2+ and Mg2+; loss-of-function mutations cause familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC), with disease severity proportional to residual protein function, and its absence triggers compensatory upregulation of transcellular Ca2+/Mg2+ transport proteins including Trpv5, Trpm6, and calbindin-D9k.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CLDN16 (paracellin-1) is a renal tight junction protein expressed predominantly in the thick ascending limb of the loop of Henle, where it forms the paracellular pathway for reabsorption of the divalent cations Ca2+ and Mg2+ [#0, #2]. Targeted deletion of murine Cldn16 produces hypercalciuria and hypomagnesemia, and the loss of paracellular transport triggers compensatory upregulation of transcellular Ca2+/Mg2+ transport genes including Trpv5, Trpm6, calbindin-D9k, Cnnm2, and Atp13a4 [#2]. The bridging function depends on both extracellular loops: mutations in the first and second extracellular loops abolish paracellular conductance [#0, #3], and the degree of residual claudin-16 activity scales inversely with disease severity, establishing a dose-dependent relationship between protein function and renal divalent-cation handling [#1]. Loss-of-function mutations in CLDN16 cause familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC) [#1], and a substantial fraction of exonic mutations act not by amino-acid substitution but by disrupting pre-mRNA splicing through inactivation of exonic splicing enhancers, cryptic splice-site activation, and exon skipping [#4]. Beyond its renal role, the mechanistic basis of CLDN16 function in non-renal tissues has not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established the gene's identity and core role: linking CLDN16 to renal paracellular divalent-cation reabsorption and identifying the extracellular loop as the functional determinant of intercellular bridging.\",\n      \"evidence\": \"Linkage analysis and mutation-to-domain mapping in FHHNC families\",\n      \"pmids\": [\"10878661\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No in vitro reconstitution of channel activity\", \"Selectivity mechanism for Ca2+ vs Mg2+ not defined\", \"Partner claudins not identified\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Resolved whether disease severity tracks with residual protein function, showing a dose-dependent relationship between claudin-16 activity and renal Ca2+/Mg2+ transport capacity.\",\n      \"evidence\": \"Mutant expression studies plus genotype-phenotype correlation across 71 FHHNC patients\",\n      \"pmids\": [\"18003771\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Functional classification based on expression, not direct conductance measurement\", \"Single study cohort\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Extended the structure-function map by establishing the second extracellular loop, not only the first, as essential for CLDN16 function.\",\n      \"evidence\": \"Domain-level mutation mapping in affected siblings\",\n      \"pmids\": [\"18816383\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single family case report with no in vitro reconstitution\", \"No biophysical assay of loop function\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Confirmed causal necessity in vivo and revealed the compensatory transcellular response when paracellular transport is lost.\",\n      \"evidence\": \"Cldn16 knockout mouse with urinary electrolyte, gene expression, and hormonal profiling\",\n      \"pmids\": [\"20147368\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Molecular mechanism of compensatory gene induction unknown\", \"Direct measurement of paracellular conductance not performed\", \"Ion selectivity mechanism unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Reclassified the molecular consequence of multiple exonic mutations, showing splicing disruption rather than coding change underlies a portion of pathogenic alleles.\",\n      \"evidence\": \"Minigene splicing assays for 12 CLDN16 exonic mutations\",\n      \"pmids\": [\"30621608\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Splicing outcomes from minigenes not confirmed in patient tissue\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Probed non-renal contexts, reporting cytoplasmic localization and pro-tumorigenic effects of CLDN16 across ovarian, thyroid, and pancreatic cancer cells.\",\n      \"evidence\": \"Pathway inhibitor/activator and knockdown phenotyping in OVCAR-3, PTC, and PAAD cell lines\",\n      \"pmids\": [\"36889572\", \"39996468\", \"41407964\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single-lab in vitro studies with no mechanistic epistasis\", \"Connection to canonical tight-junction function unclear\", \"No in vivo validation\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CLDN16 achieves divalent-cation selectivity and which partner claudins or tight-junction proteins it requires to form a functional paracellular channel remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No reconstituted channel assay defining ion selectivity\", \"Interacting claudins not identified in the corpus\", \"No structural model of the channel\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"R-HSA-1500931\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"tight junction\"],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":4,"faith_total":4,"faith_pct":100.0}}