NLRP3

Chr 1AD

NLR 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]

GeneReviewsOMIMResearchGenerating clinical summary…
GOFmechanismADLOEUF 0.525 OMIM phenotypes
Clinical SummaryNLRP3
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.33) despite low pLI — interpret in context.
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ClinVar Variants
52 unique Pathogenic / Likely Pathogenic· 411 VUS of 794 total submissions
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Clinical Trials
12 active or recruiting trials — potential therapeutic options may be available
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GeneReview available — NLRP3
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint?
0.52LOEUF
pLI 0.001
Z-score 3.94
OE 0.33 (0.210.52)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
2.14Z-score
OE missense 0.74 (0.690.81)
414 obs / 556.1 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.33 (0.210.52)
00.351.4
Missense OE?0.74 (0.690.81)
00.61.4
Synonymous OE?1.28
01.21.6
LoF obs/exp: 13 / 39.8Missense obs/exp: 414 / 556.1Syn Z: -3.41
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveNLRP3-related familial cold autoinflammatory syndromeOTHERAD
definitiveNLRP3-related chronic neurologic cutaneous and articular syndrome (CINCA)OTHERAD
strongNLRP3-related cold urticaria, familialGOFAD

This gene — mechanism propensity

DN
0.76top 25%
GOF
0.77top 25%
LOF
0.1598th %ile

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.

GOFprediction above median · 1 literature citation · 98% of P/LP are missense
DNprediction above median · 1 literature citation

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

DNThese findings strongly suggested that the mutated protein exerts a dominant-negative or a gain-of-function effect over the wildtype product and that the null mutation of 1 allele would probably have no effect or would lead to a different phenotypic expression because of haploinsufficiency.1
GOFThe discovery that dominant gain-of-function mutations in NLRP3 cause the cryopyrin-associated periodic syndromes (CAPS) and trigger spontaneous inflammasome activation and IL-1β oversecretion led to successful treatment with IL-1-blocking agents.2

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

794 submitted variants in ClinVar

Classification Summary

Pathogenic21
Likely Pathogenic31
VUS411
Likely Benign209
Benign30
Conflicting24
21
Pathogenic
31
Likely Pathogenic
411
VUS
209
Likely Benign
30
Benign
24
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
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
Total22426100154726

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.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

Cryopyrin Associated Periodic SyndromeFamilial Cold UrticariaMuckle-Wells Syndrome

Circadian Rhythm Deregulation in Patients With CAPS

RECRUITING
NCT06544018Phase NAHospices Civils de LyonStarted 2026-02-25
Genetic analysis of NLRP3Circadian rhythm measurementSaliva sampling
Type 2 DiabetesPrediabetes (Insulin Resistance, Impaired Glucose Tolerance)Prediabetes / Type 2 Diabetes

Effects of Different Fish Oil Types on Type 2 Diabetes Risk Factors in High-Risk Adults

NOT YET RECRUITING
NCT07575438Phase PHASE2May Faraj, PDt, PhDStarted 2026-07
Fish OilFish OilCorn oil control
Type 2 DiabetesInflammationInsulin Sensitivity/Resistance

Targeting Risk Factors for Diabetes in Subjects With Normal Blood Cholesterol Using Omega-3 Fatty Acids

RECRUITING
NCT04485871Phase NAInstitut de Recherches Cliniques de MontrealStarted 2019-12-19
Omega-3 fatty acids
Transgender Individuals

Effects of Gender-Affirming Hormone Therapy on Cardiovascular, Metabolic, and Mental Health Outcomes in Transgender Adults.

NOT YET RECRUITING
NCT07394400Milagros Rocha BarajasStarted 2026-02-14
COPD

Immuno-inflammatory Response of Erdosteine in COPD

NOT YET RECRUITING
NCT07329946Phase NAPierachille Santus, MD, PhDStarted 2026-09-01
ErdosteineStandard of Care (SOC)
Obstructive Sleep Apnea-Hypopnea SyndromeAnxiety DisordersDepressive Disorders

EGR2 and NLRP3 Pathways in Obstructive Sleep Apnea-Related Cognitive and Mood Disorders

RECRUITING
NCT07120711Xinhua Hospital, Shanghai Jiao Tong University School of MedicineStarted 2025-07-01
EGR2/NLRP3 pathway activityfatty tissue
Autoinflammatory DiseaseJuvenile Dermatomyositis

Studies of the Natural History, Pathogenesis, and Outcome of Autoinflammatory Diseases Including Juvenile Dermatomyositis

RECRUITING
NCT00059748National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)Started 2003-05-09
Late-Life Depression

Effects of Specific Amino Acid Supplementation and Lifestyle Factors on Brain Ageing

RECRUITING
NCT07497347Phase NAIRCCS Centro San Giovanni di Dio FatebenefratelliStarted 2026-03-01
L-serine supplementationPlacebo
Chronic Kidney FailureFrailtyAging

Systemic Activation of Inflammasomes and Frailty in Older Candidates to Kidney Transplantation

NOT YET RECRUITING
NCT06887075Phase NAUniversity Hospital, BordeauxStarted 2025-04-15
Blood sampleGeriatric assessment standardized
Scarring Alopecia

Non-Ablative Laser to Treat Scarring Alopecia With Hair Follicle Gene Expression Analysis

RECRUITING
NCT06946550Phase NAMontefiore Medical CenterStarted 2025-12-09
1470nm non-ablative fractional laser
Coronary Heart Disease

Adipose Tissue and Inflammation in Coronary Heart Disease

ACTIVE NOT RECRUITING
NCT02760914Oslo University HospitalStarted 2016-06
Neurodegenerative DiseasesCognition Disorders in Old Age

Probiotics in Mild Alzheimer's Disease

RECRUITING
NCT06181513Phase EARLY_PHASE1University of NicosiaStarted 2022-12-19
Probiotic Blend Capsule