NLRP3
Chr 1ADNLR family pyrin domain containing 3
Also known as: AGTAVPRL, AII, AVP, C1orf7, CIAS1, CLR1.1, DFNA34, FCAS
This gene encodes a pyrin-like protein containing a pyrin domain, a nucleotide-binding site (NBS) domain, and a leucine-rich repeat (LRR) motif. This protein interacts with the apoptosis-associated speck-like protein PYCARD/ASC, which contains a caspase recruitment domain, and is a member of the NLRP3 inflammasome complex. This complex functions as an upstream activator of NF-kappaB signaling, and it plays a role in the regulation of inflammation, the immune response, and apoptosis. The SARS-CoV 3a protein, a transmembrane pore-forming viroporin, has been shown to activate the NLRP3 inflammasome via the formation of ion channels in macrophages. Mutations in this gene are associated with familial cold autoinflammatory syndrome (FCAS), Muckle-Wells syndrome (MWS), chronic infantile neurological cutaneous and articular (CINCA) syndrome, neonatal-onset multisystem inflammatory disease (NOMID), keratoendotheliitis fugax hereditarian, and deafness, autosomal dominant 34, with or without inflammation. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. Alternative 5' UTR structures are suggested by available data; however, insufficient evidence is available to determine if all of the represented 5' UTR splice patterns are biologically valid. [provided by RefSeq, Aug 2020]
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Moderately missense-constrained (top ~2.5%)
This gene — mechanism propensity
This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Literature Evidence
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
References
ClinVar Variant Classifications
794 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 1 | 20 | 0 | 0 | 21 |
Likely Pathogenic | 0 | 31 | 0 | 0 | 31 |
VUS | 20 | 370 | 17 | 4 | 411 |
Likely Benign | 0 | 5 | 57 | 147 | 209 |
Benign | 1 | 0 | 26 | 3 | 30 |
Conflicting | — | 24 | |||
| Total | 22 | 426 | 100 | 154 | 726 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →39 pathogenic / likely-pathogenic (of 51) ClinVar copy-number / structural variants overlap NLRP3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →
Protein Context — Lollipop Plot
NLRP3 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
Circadian Rhythm Deregulation in Patients With CAPS
RECRUITINGEffects of Different Fish Oil Types on Type 2 Diabetes Risk Factors in High-Risk Adults
NOT YET RECRUITINGTargeting Risk Factors for Diabetes in Subjects With Normal Blood Cholesterol Using Omega-3 Fatty Acids
RECRUITINGEffects of Gender-Affirming Hormone Therapy on Cardiovascular, Metabolic, and Mental Health Outcomes in Transgender Adults.
NOT YET RECRUITINGImmuno-inflammatory Response of Erdosteine in COPD
NOT YET RECRUITINGEGR2 and NLRP3 Pathways in Obstructive Sleep Apnea-Related Cognitive and Mood Disorders
RECRUITINGStudies of the Natural History, Pathogenesis, and Outcome of Autoinflammatory Diseases Including Juvenile Dermatomyositis
RECRUITINGEffects of Specific Amino Acid Supplementation and Lifestyle Factors on Brain Ageing
RECRUITINGSystemic Activation of Inflammasomes and Frailty in Older Candidates to Kidney Transplantation
NOT YET RECRUITINGNon-Ablative Laser to Treat Scarring Alopecia With Hair Follicle Gene Expression Analysis
RECRUITINGAdipose Tissue and Inflammation in Coronary Heart Disease
ACTIVE NOT RECRUITINGProbiotics in Mild Alzheimer's Disease
RECRUITINGExternal Resources
Links to major genomics databases and tools