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]

Primary Disease Associations & Inheritance

CINCA syndromeMIM #607115
AD
Deafness, autosomal dominant 34, with or without inflammationMIM #617772
AD
Familial cold inflammatory syndrome 1MIM #120100
AD
Keratoendothelitis fugax hereditariaMIM #148200
AD
Muckle-Wells syndromeMIM #191900
AD
UniProtFamilial cold autoinflammatory syndrome 1
UniProtChronic infantile neurologic cutaneous and articular syndrome
519
ClinVar variants
53
Pathogenic / LP
0.00
pLI score
12
Active trials
Clinical SummaryNLRP3
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.33) despite low pLI — interpret in context.
📋
ClinVar Variants
53 Pathogenic / Likely Pathogenic· 292 VUS of 519 total submissions
💊
Clinical Trials
12 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
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?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
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?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.33 (0.210.52)
00.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.74 (0.690.81)
00.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.28
01.21.6
LoF obs/exp: 13 / 39.8Missense obs/exp: 414 / 556.1Syn Z: -3.41

ClinVar Variant Classifications

519 submitted variants in ClinVar

Classification Summary

Pathogenic32
Likely Pathogenic21
VUS292
Likely Benign159
Benign4
Conflicting11
32
Pathogenic
21
Likely Pathogenic
292
VUS
159
Likely Benign
4
Benign
11
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
8
24
0
32
Likely Pathogenic
0
19
2
0
21
VUS
7
259
22
4
292
Likely Benign
0
5
49
105
159
Benign
0
0
3
1
4
Conflicting
11
Total7291100110519

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

NLRP3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

NLRP3-related familial cold autoinflammatory syndrome

definitive
ADUndeterminedAltered Gene Product Structure
Skin
G2P ↗
missense variantinframe deletioninframe insertion

NLRP3-related chronic neurologic cutaneous and articular syndrome (CINCA)

definitive
ADUndeterminedAltered Gene Product Structure
Skin
G2P ↗
missense variantinframe deletioninframe insertion

NLRP3-related cold urticaria, familial

strong
ADGain Of FunctionAltered Gene Product Structure
Skin
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

CINCA syndrome

MIM #607115

Molecular basis of disorder known

Autosomal dominant

Deafness, autosomal dominant 34, with or without inflammation

MIM #617772

Molecular basis of disorder known

Autosomal dominant

Familial cold inflammatory syndrome 1

MIM #120100

Molecular basis of disorder known

Autosomal dominant

Keratoendothelitis fugax hereditaria

MIM #148200

Molecular basis of disorder known

Autosomal dominant

Muckle-Wells syndrome

MIM #191900

Molecular basis of disorder known

Autosomal dominant
📖
GeneReview available — NLRP3
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

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
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
Periodontitis, Adult

Non-surgical Periodontal Treatment in Smokers on SIRT-1, NLRP3 Inflammasome and LncRNAs

NOT YET RECRUITING
NCT06351722Necmettin Erbakan UniversityStarted 2024-05-15
Before non-surgical periodontal treatmentnon-surgical periodontal treatment3rd month after non-surgical periodontal treatment
Coronary Heart Disease

Adipose Tissue and Inflammation in Coronary Heart Disease

ACTIVE NOT RECRUITING
NCT02760914Oslo University HospitalStarted 2016-06
Leishmaniasis

Mediterranean Visceral Leishmaniasis With Leishmania Infantum

ACTIVE NOT RECRUITING
NCT03784248Centre Hospitalier Universitaire de NiceStarted 2019-07-03
blood donation and isolation of leuco-platelet layers
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
Vitiligo

TRPM2 Gene Polymorphism, NLRP3 Inflammasome Expression in Vitiligo Patients

ACTIVE NOT RECRUITING
NCT07232238Aswan UniversityStarted 2025-10-20
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
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
Heart Failure, SystolicHeart Failure NYHA Class IVMetabolic Disturbance

Mechanistic Studies of Nicotinamide Riboside in Human Heart Failure

ACTIVE NOT RECRUITING
NCT04528004Phase EARLY_PHASE1University of WashingtonStarted 2020-09-26
Nicotinamide ribosidePlacebo
NOMIDDIRANLRC4-MAS

Natural History, Pathogenesis, and Outcome of Autoinflammatory Diseases (NOMID/CAPS, DIRA, CANDLE, SAVI, NLRC4-MAS, Still'S-like Diseases, and Other Undifferentiated Autoinflammatory Diseases)

RECRUITING
NCT02974595National Institute of Allergy and Infectious Diseases (NIAID)Started 2016-12-09
Nephrotic Syndrome

Transcriptome Analysis in Idiopathic Nephrotic Syndrome: Steroid Responsiveness

RECRUITING
NCT06325137IRCCS Burlo GarofoloStarted 2023-03-16
Transcriptome analyses