Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	114548
Gene name Gene Name - the full gene name approved by the HGNC.	NLR family pyrin domain containing 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	NLRP3
Synonyms (NCBI Gene) Gene synonyms aliases	AGTAVPRL, AII, AVP, C1orf7, CIAS1, CLR1.1, DFNA34, FCAS, FCAS1, FCU, KEFH, MWS, NALP3, PYPAF1
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1q44
Summary Summary of gene provided in NCBI Entrez Gene.	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 r

Show/Hide all(33)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28937896	T>C	Pathogenic	Coding sequence variant, missense variant
rs35829419	C>A	Benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs114158404	C>A,G,T	Conflicting-interpretations-of-pathogenicity	Missense variant, intron variant, coding sequence variant
rs117287351	G>A,C,T	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, coding sequence variant
rs121908146	C>T	Pathogenic	Missense variant, coding sequence variant
rs121908147	G>A,C	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Missense variant, coding sequence variant
rs121908148	A>G	Pathogenic	Missense variant, coding sequence variant
rs121908149	C>T	Pathogenic, not-provided	Missense variant, coding sequence variant
rs121908150	C>T	Pathogenic	Stop gained, coding sequence variant
rs121908151	G>A,C	Pathogenic, not-provided	Missense variant, coding sequence variant
rs121908152	T>C	Pathogenic, not-provided	Missense variant, coding sequence variant
rs121908153	G>A,C	Pathogenic, not-provided	Missense variant, coding sequence variant
rs121908154	T>C	Pathogenic, not-provided	Missense variant, coding sequence variant
rs139814109	C>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Missense variant, coding sequence variant
rs141389711	G>A	Conflicting-interpretations-of-pathogenicity	Intron variant, coding sequence variant, missense variant
rs145268073	G>A,C	Uncertain-significance, conflicting-interpretations-of-pathogenicity, not-provided, likely-benign	Coding sequence variant, missense variant
rs147946775	A>G	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Intron variant, missense variant, coding sequence variant
rs151344629	C>T	Pathogenic, not-provided	Missense variant, coding sequence variant
rs180177431	T>C	Likely-pathogenic, not-provided	Missense variant, coding sequence variant
rs180177441	G>A	Likely-pathogenic, not-provided	Missense variant, coding sequence variant
rs180177442	G>C,T	Likely-pathogenic, not-provided	Missense variant, coding sequence variant
rs180177445	A>C	Likely-pathogenic, not-provided	Missense variant, coding sequence variant
rs180177452	A>C,G	Uncertain-significance, not-provided, pathogenic	Intron variant, missense variant, coding sequence variant
rs180177458	G>A	Likely-pathogenic, not-provided	Missense variant, coding sequence variant
rs180177465	A>C,G	Likely-pathogenic, uncertain-significance, not-provided	Missense variant, coding sequence variant
rs180177484	G>A	Pathogenic, not-provided	Missense variant, coding sequence variant
rs180177493	C>T	Not-provided, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs200154873	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs1057518827	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1057524777	G>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1131691298	A>C	Pathogenic	Missense variant, coding sequence variant
rs1553287287	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1553293095	G>A	Uncertain-significance, pathogenic	Coding sequence variant, missense variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT016468	hsa-miR-193b-3p	Microarray	20304954
MIRT048559	hsa-miR-100-5p	CLASH	23622248
MIRT735167	hsa-miR-223-3p	Luciferase reporter assay, qRT-PCR, Western blot	28302726
MIRT732474	hsa-miR-155-3p	ELISA, Flow cytometry, qRT-PCR, Western blotting	33909229
MIRT734746	hsa-miR-138-5p	Luciferase reporter assay, Western blotting, RNA-seq, ELISA	33628043
MIRT735028	hsa-miR-141-3p	Western blotting, Microarray, Immunohistochemistry (IHC), Immunofluorescence, qRT-PCR, Flow cytometry	32984347
MIRT735167	hsa-miR-223-3p	Luciferase reporter assay, Western blotting, qRT-PCR, ELISA	33650318
MIRT735168	hsa-miR-22-3p	Luciferase reporter assay, Western blotting, qRT-PCR, ELISA	33650318
MIRT735167	hsa-miR-223-3p	qRT-PCR	32090515
MIRT732474	hsa-miR-155-3p	Western blotting, qRT-PCR, Flow cytometry, ELISA	33909229
MIRT755595	hsa-miR-3653-3p	qRT-PCR, in vitro cullelar assays	37946206
MIRT735167	hsa-miR-223-3p	Luciferase reporter assay, Western blotting, qRT-PCR	37359091
MIRT1187263	hsa-miR-561	CLIP-seq
MIRT1187264	hsa-miR-223	CLIP-seq
MIRT1187265	hsa-miR-4662a-3p	CLIP-seq
MIRT1187266	hsa-miR-4781-5p	CLIP-seq
MIRT1187263	hsa-miR-561	CLIP-seq
MIRT1187267	hsa-miR-633	CLIP-seq
MIRT1187268	hsa-miR-935	CLIP-seq
MIRT1187269	hsa-miR-1283	CLIP-seq
MIRT1187270	hsa-miR-1305	CLIP-seq
MIRT1187271	hsa-miR-4680-3p	CLIP-seq
MIRT2391607	hsa-miR-2355-3p	CLIP-seq
MIRT2391608	hsa-miR-4289	CLIP-seq
MIRT2391609	hsa-miR-4711-3p	CLIP-seq
MIRT2391610	hsa-miR-616	CLIP-seq
MIRT2391611	hsa-miR-626	CLIP-seq
MIRT2391612	hsa-miR-676	CLIP-seq
MIRT2455259	hsa-miR-4679	CLIP-seq
MIRT2455260	hsa-miR-549	CLIP-seq

Show/Hide all(108)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IDA	23229815
GO:0000139	Component	Golgi membrane	IEA
GO:0000166	Function	Nucleotide binding	IEA
GO:0002221	Process	Pattern recognition receptor signaling pathway	NAS	22258606
GO:0002376	Process	Immune system process	IEA
GO:0002674	Process	Negative regulation of acute inflammatory response	IMP	11687797
GO:0002830	Process	Positive regulation of type 2 immune response	ISS
GO:0005515	Function	Protein binding	IPI	11786556, 15020601, 15030775, 19158675, 19337385, 22461501, 22801494, 23582325, 23809162, 23871209, 24531343, 24630722, 26347139, 26814970, 28229991, 31189953, 31231549, 31421660, 32814053, 34341353, 34589402, 38593810, 39225180
GO:0005524	Function	ATP binding	IDA	17483456, 36442502
GO:0005524	Function	ATP binding	IEA
GO:0005576	Component	Extracellular region	IEA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	34512673
GO:0005737	Component	Cytoplasm	IDA	17164409, 39225180
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	NAS	28263976
GO:0005737	Component	Cytoplasm	TAS	15967716
GO:0005739	Component	Mitochondrion	IDA	23582325
GO:0005739	Component	Mitochondrion	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005794	Component	Golgi apparatus	IEA
GO:0005815	Component	Microtubule organizing center	IDA	28656979, 39173637
GO:0005815	Component	Microtubule organizing center	IEA
GO:0005829	Component	Cytosol	IDA	11786556
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006915	Process	Apoptotic process	NAS	12032915
GO:0006952	Process	Defense response	TAS	15967716
GO:0006954	Process	Inflammatory response	IDA	16407889, 17483456, 18403674, 18604214
GO:0006954	Process	Inflammatory response	IEA
GO:0006954	Process	Inflammatory response	IMP	12093792, 28847925
GO:0007165	Process	Signal transduction	NAS	11786556
GO:0007231	Process	Osmosensory signaling pathway	NAS	22981536
GO:0009306	Process	Protein secretion	IDA	33883744
GO:0009595	Process	Detection of biotic stimulus	IDA	18604214
GO:0009595	Process	Detection of biotic stimulus	IEA
GO:0009595	Process	Detection of biotic stimulus	TAS	15967716
GO:0009615	Process	Response to virus	IEA
GO:0016020	Component	Membrane	IDA	30487600
GO:0016020	Component	Membrane	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IDA	17483456, 31086327, 31086329
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0030674	Function	Protein-macromolecule adaptor activity	IDA	1189953
GO:0031021	Component	Interphase microtubule organizing center	ISS
GO:0032691	Process	Negative regulation of interleukin-1 beta production	IMP	12483741
GO:0032731	Process	Positive regulation of interleukin-1 beta production	IDA	15326478
GO:0032731	Process	Positive regulation of interleukin-1 beta production	IDA	15030775, 16407889, 17483456, 18403674, 18604214, 23582325, 25686105, 30487600, 31086327, 31086329, 31189953
GO:0032731	Process	Positive regulation of interleukin-1 beta production	IEA
GO:0032731	Process	Positive regulation of interleukin-1 beta production	IMP	28847925
GO:0032731	Process	Positive regulation of interleukin-1 beta production	ISO
GO:0032741	Process	Positive regulation of interleukin-18 production	IDA	15326478
GO:0032753	Process	Positive regulation of interleukin-4 production	ISS
GO:0035591	Function	Signaling adaptor activity	IDA	27432880, 35114687, 35254907, 35559676
GO:0035591	Function	Signaling adaptor activity	IEA
GO:0035655	Process	Interleukin-18-mediated signaling pathway	IDA	14528293
GO:0042802	Function	Identical protein binding	IPI	23582325, 24630722
GO:0042834	Function	Peptidoglycan binding	TAS	15967716
GO:0043531	Function	ADP binding	IDA	35114687, 35254907
GO:0043565	Function	Sequence-specific DNA binding	IBA
GO:0043565	Function	Sequence-specific DNA binding	ISS
GO:0044546	Process	NLRP3 inflammasome complex assembly	IDA	17483456, 23582325, 25686105, 27043286, 27432880, 28465465, 28656979, 28943315, 30487600, 31189953, 33231615, 34554188, 34615873, 35114687, 35254907, 35559676, 36442502, 39173637
GO:0044546	Process	NLRP3 inflammasome complex assembly	IEA
GO:0045087	Process	Innate immune response	IEA
GO:0045630	Process	Positive regulation of T-helper 2 cell differentiation	ISS
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	ISS
GO:0050727	Process	Regulation of inflammatory response	IBA
GO:0050728	Process	Negative regulation of inflammatory response	IMP	12483741, 16531551, 17178985
GO:0050729	Process	Positive regulation of inflammatory response	IDA	15326478, 32109412, 33883744
GO:0050729	Process	Positive regulation of inflammatory response	IDA	25686105, 31086327, 31086329, 31189953, 35114687, 35254907, 35559676
GO:0050729	Process	Positive regulation of inflammatory response	IEA
GO:0050729	Process	Positive regulation of inflammatory response	NAS	29255148
GO:0051092	Process	Positive regulation of NF-kappaB transcription factor activity	IDA	19158675
GO:0051260	Process	Protein homooligomerization	IDA	35114687, 35254907, 35559676, 36442502
GO:0051260	Process	Protein homooligomerization	IEA
GO:0051604	Process	Protein maturation	IDA	15326478, 31189953, 32109412
GO:0051604	Process	Protein maturation	IDA	31189953
GO:0060090	Function	Molecular adaptor activity	IDA	1189953
GO:0061702	Component	Canonical inflammasome complex	IEA
GO:0070269	Process	Pyroptotic inflammatory response	IDA	33883744, 36227980
GO:0070269	Process	Pyroptotic inflammatory response	NAS	26611636
GO:0070273	Function	Phosphatidylinositol-4-phosphate binding	IDA	30487600
GO:0070273	Function	Phosphatidylinositol-4-phosphate binding	IEA
GO:0070498	Process	Interleukin-1-mediated signaling pathway	IDA	1919436
GO:0071222	Process	Cellular response to lipopolysaccharide	IDA	28847925
GO:0071222	Process	Cellular response to lipopolysaccharide	IEA
GO:0071222	Process	Cellular response to lipopolysaccharide	IMP	12483741
GO:0072559	Component	NLRP3 inflammasome complex	IBA
GO:0072559	Component	NLRP3 inflammasome complex	IDA	15030775, 36442502
GO:0072559	Component	NLRP3 inflammasome complex	IEA
GO:0072559	Component	NLRP3 inflammasome complex	IPI	29255148
GO:0098586	Process	Cellular response to virus	IDA	33231615
GO:0140297	Function	DNA-binding transcription factor binding	IBA
GO:0140297	Function	DNA-binding transcription factor binding	ISS
GO:0140299	Function	Molecular sensor activity	IDA	16407889, 18403674, 18604214
GO:0140299	Function	Molecular sensor activity	IEA
GO:0140608	Function	Cysteine-type endopeptidase activator activity	IDA	31189953
GO:0140693	Function	Molecular condensate scaffold activity	IDA	35114687
GO:1900227	Process	Positive regulation of NLRP3 inflammasome complex assembly	IDA	31189953
GO:1901223	Process	Negative regulation of non-canonical NF-kappaB signal transduction	IBA
GO:1901223	Process	Negative regulation of non-canonical NF-kappaB signal transduction	IDA	14662828
GO:1901224	Process	Positive regulation of non-canonical NF-kappaB signal transduction	IPI	15817483
GO:1901981	Function	Phosphatidylinositol phosphate binding	IDA	34554188
GO:2000553	Process	Positive regulation of T-helper 2 cell cytokine production	ISS

MIM	HGNC	e!Ensembl
606416	16400	ENSG00000162711

Protein

UniProt ID

Q96P20

Protein name

NACHT, LRR and PYD domains-containing protein 3 (EC 3.6.4.-) (Angiotensin/vasopressin receptor AII/AVP-like) (Caterpiller protein 1.1) (CLR1.1) (Cold-induced autoinflammatory syndrome 1 protein) (Cryopyrin) (PYRIN-containing APAF1-like protein 1)

Protein function

Sensor component of the NLRP3 inflammasome, which mediates inflammasome activation in response to defects in membrane integrity, leading to secretion of inflammatory cytokines IL1B and IL18 and pyroptosis (PubMed:16407889, PubMed:18403674, PubMe

PDB

2NAQ , 3QF2 , 6NPY , 7ALV , 7PZC , 7PZD , 7VTP , 7ZGU , 8EJ4 , 8ERT , 8ETR , 8RI2 , 8SWF , 8SWK , 8SXN , 8WSM , 8ZEM , 9DH3 , 9GU4 , 9MGY , 9MIE , 9MIG

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02758	PYRIN	9 → 85	PAAD/DAPIN/Pyrin domain	Domain
PF14484	FISNA	140 → 210	Fish-specific NACHT associated domain	Family
PF05729	NACHT	220 → 389	NACHT domain	Domain
PF17779	NOD2_WH	464 → 520	NOD2 winged helix domain	Domain
PF17776	NLRC4_HD2	522 → 645	NLRC4 helical domain HD2	Domain
PF13516	LRR_6	739 → 762	Leucine Rich repeat	Repeat
PF13516	LRR_6	796 → 819	Leucine Rich repeat	Repeat

Tissue specificity

TISSUE SPECIFICITY: Predominantly expressed in macrophages (PubMed:33231615, PubMed:34133077). Also expressed in dendritic cells, B- and T-cells (at protein level) (PubMed:11786556, PubMed:17164409). Expressed in LPS-treated granulocytes, but not in resti

Sequence

MKMASTRCKLARYLEDLEDVDLKKFKMHLEDYPPQKGCIPLPRGQTEKADHVDLATLMID
FNGEEKAWAMAVWIFAAINRRDLYEKAKRDEPKWGSDNARVSNPTVICQEDSIEEEWMGL
LEYLSRISICKMKKDYRKKYRKYVRSRFQCIEDRNARLGESVSLNKRYTRLRLIKEHRSQ
QEREQELLAIGKTKTCESPVSPIKMELLFDPDDEHSEPVHTVVFQGAAGIGKTILARKMM
LDWASGTLYQDRFDYLFYIHCREVSLVTQRSLGDLIMSCCPDPNPPIHKIVRKPSRILFL
MDGFDELQGAFDEHIGPLCTDWQKAERGDILLSSLIRKKLLPEASLLITTRPVALEKLQH
LLDHPRHVEILGFSEAKRKEYFFKYFSDEAQARAAFSLIQENEVLFTMCFIPLVCWIVCT
GLKQQMESGKSLAQTSKTTTAVYVFFLSSLLQPRGGSQEHGLCAHLWGLCSLAADGIWNQ
KILFEESDLRNHGLQKADVSAFLRMNLFQKEVDCEKFYSFIHMTFQEFFAAMYYLLEEEK
EGRTNVPGSRLKLPSRDVTVLLENYGKFEKGYLIFVVRFLFGLVNQERTSYLEKKLSCKI
SQQIRLELLKWIEVKAKAKKLQIQPSQLELFYCLYEMQEEDFVQRAMDYFPKIEINLSTR
MDHMVSSFCIENCHRVESLSLGFLHNMPKEEEEEEKEGRHLDMVQCVLPSSSHAACSHGL
VNSHLTSSFCRGLFSVLSTSQSLTELDLSDNSLGDPGMRVLCETLQHPGCNIRRLWLGRC
GLSHECCFDISLVLSSNQKLVELDLSDNALGDFGIRLLCVGLKHLLCNLKKLWLVSCCLT
SACCQDLASVLSTSHSLTRLYVGENALGDSGVAILCEKAKNPQCNLQKLGLVNSGLTSVC
CSALSSVLSTNQNLTHLYLRGNTLGDKGIKLLCEGLLHPDCKLQVLELDNCNLTSHCCWD
LSTLLTSSQSLRKLSLGNNDLGDLGVMMFCEVLKQQSCLLQNLGLSEMYFNYETKSALET
LQEEKPELTVVFEPSW

Sequence length

1036

Interactions

View interactions

	KEGG		Reactome
	Necroptosis NOD-like receptor signaling pathway Cytosolic DNA-sensing pathway C-type lectin receptor signaling pathway Pathogenic Escherichia coli infection Shigellosis Salmonella infection Pertussis Yersinia infection Influenza A Coronavirus disease - COVID-19 Lipid and atherosclerosis		Metalloprotease DUBs The NLRP3 inflammasome Purinergic signaling in leishmaniasis infection

Show/Hide Causal Diseases (3)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Autoinflammatory Disease	Autoinflammatory syndrome	rs151344629, rs121908148, rs180177431, rs121908150, rs121908146	N/A
Cold Autoinflammatory Syndrome	familial cold autoinflammatory syndrome 1	rs121908148, rs180177431, rs180177435, rs180177503, rs180177469, rs121908149, rs180177468, rs180177437, rs180177473, rs180177470, rs121908150, rs180177445, rs180177452, rs180177456, rs180177433 View all (19 more)	N/A
Keratitis Fugax Hereditaria	keratitis fugax hereditaria	rs200154873	N/A

Show/Hide Unknown Diseases (5)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
hearing impairment	Hearing impairment	N/A	N/A	ClinVar
Hearing Loss	Hearing loss, autosomal dominant 34, with or without inflammation	N/A	N/A	ClinVar
Hemolytic Uremic Syndrome	Atypical hemolytic-uremic syndrome	N/A	N/A	ClinVar
Muckle-Wells Syndrome	Muckle-Wells syndrome	N/A	N/A	GenCC
Periodic Syndrome	cryopyrin-associated periodic syndrome	N/A	N/A	GenCC

Show/Hide Text Mining Associations (18)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Alzheimer Disease	Associate	36835494
Bone Diseases	Associate	38270300
Brain Ischemia	Associate	34866334
Carcinoma Pancreatic Ductal	Associate	38018872
Cerebral Infarction	Associate	34866334
Deafness	Associate	27965898
Diabetes Mellitus	Associate	36378718
Hepatitis Alcoholic	Associate	25149528
Idiopathic Noncirrhotic Portal Hypertension	Associate	26820153
Inflammation	Associate	35363405, 35978267, 38018872, 38270300
Liver Cirrhosis	Associate	26773180
Liver Diseases Alcoholic	Associate	26773180
Nervous System Diseases	Associate	34866334
Neuroinflammatory Diseases	Associate	34866334, 36378718, 37334594
Nonsyndromic sensorineural hearing loss	Associate	27965898
Osteoarthritis Knee	Associate	30755787
Osteoglophonic dwarfism	Associate	35403328
Pneumonia	Associate	36347039

NLRP3 (NLR family pyrin domain containing 3)