Cryptic NLRP3 Mosaicism Uncovered by Deep Sequencing in Muckle-Wells Syndrome: A Case Report

Abstract

Background Muckle-Wells syndrome is part of the cryopyrin-associated periodic syndrome (CAPS) family, a group of rare autoinflammatory conditions caused by gain-of-function variants in the NLRP3 gene, leading to uncontrolled activation of the inflammasome and excessive IL-1β release. Although most patients have a detectable genetic change, a small number present with a typical CAPS phenotype but do not carry a known pathogenic variant in NLRP3 on conventional sequencing. In-depth genetic analyses have recently shown that some of these cases are explained by hidden, low-level NLRP3 mosaicism. Case Report A 21-year-old male first presented in 2012 at the age of 6 with recurrent episodes of transient, non-pruritic urticarial rash, low-grade fever, fatigue, episodic arthritis of the knees and ankles, and enthesitis predominantly involving the Achilles tendon and dorsal foot insertions. During flares, inflammatory markers were elevated (CRP 12-18 mg/L, ESR 31-38 mm/h, serum amyloid A >160,000 ng/mL), with mild normocytic anemia. Autoimmune serologies and complement levels were normal. In 2013, mild unilateral sensorineural hearing loss was identified and remained stable; MRI of the brain and internal auditory canals was normal. Initial genetic testing with a recurrent fever syndrome panel in 2014 and whole-exome sequencing in 2018 were both reported as negative. Anakinra, initiated in 2014, provided partial improvement but was discontinued due to injection-site reactions. In 2018, with worsening symptoms and elevated inflammation (CRP 47 mg/L, ESR 31 mm/h, SAA 55,264 ng/mL), canakinumab was started, leading to rapid and sustained normalization of inflammatory markers and resolution of clinical symptoms. The patient remained in long-term disease quiescence for approximately 4 years (2018-2022), after which the patient discontinued treatment and was lost to follow-up. In 2025, stored DNA was re-analyzed with high-depth sequencing for a panel of 101 known autoinflammatory genes and identified a NLRP3 variant (p. Arg260Pro, Clinvar classification pathogenic) in approximately 5% of reads. Retrospective analysis of existing whole-exome data did not identify this low-level variant. Conclusion Consistent with previous reports of NLRP3 mosaicism as a cause of CAPS, this case demonstrates that negative genetic testing does not exclude cryopyrin-associated periodic syndromes and that somatic mosaicism should be considered when the clinical phenotype is compelling. As sequencing technologies evolve, periodic re-analysis offers a critical second opportunity for diagnosis and targeted treatment.