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COVID-19 research

Gene: NLRP3

Green List (high evidence)

NLRP3 (NLR family pyrin domain containing 3)
EnsemblGeneIds (GRCh38): ENSG00000162711
EnsemblGeneIds (GRCh37): ENSG00000162711
OMIM: 606416, Gene2Phenotype
NLRP3 is in 10 panels

5 reviews

Kimberly Gilmour (Great Ormond Street Hopsital)

Green List (high evidence)

agree with green gene
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Tracy Briggs (Manchester Genomic Medicine Centre)

Green List (high evidence)

YES- this is covered on our targeted exome
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with phenotypes in OMIM and not in Gen2Phen. At least 4 variants identified in unrelated cases of Familial cold-induced inflammatory syndrome 1 120100. At least 4 variants identified in unrelated cases of Muckle-Wells syndrome 191900, 3 variants in unrelated cases of CINCA and one each in cases of Deafness, autosomal dominant 34, with or without inflammation 617772 and Keratoendothelitis fugax hereditaria 148200. Three cases represent overlapping phenotypes and so there a total of 12 variants have been reported (8th March 2018).
Created: 8 May 2018, 4:32 p.m.
Comment on phenotypes: Variants also associated with Keratoendothelitis fugax hereditaria 148200
Created: 8 May 2018, 4:19 p.m.

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

Gene rating submitted by Kimberly Gilmour and Austen Worth on behalf of London North GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email 6th September the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Gene rating submitted by Tracy Briggs, David Gokhale and Abigal Rousseau on behalf of North West GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email on 20th June the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): NLRP3 .PanelApp HGNC gene symbol check: NLRP3 . IUIS Disease: Neonatal onset multisystem inflammatory disease (NOMID) or chronic infantile neurologic cutaneous and articular syndrome (CINCA) . IUIS Inheritance: AD GOF .T cells: Decreased T cell proliferation, .B cells: N/A, .IUIS Other affected cells: PMNs, chondrocytes. IUIS Associated features: Neonatal onset rash, chronic meningitis, and arthropathy with fever and inflammation. . IUIS Major category: Autoinflammatory Disorders. IUIS Subcategory: Defects Affecting the Inflammasome. // OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): NLRP3 (also called NALP3 CIAS1 or PYPAF1) .PanelApp HGNC gene symbol check: NLRP3 . IUIS Disease: Muckle-Wells syndrome . IUIS Inheritance: AD GOF .T cells: Lymphopenia, lack of TRECS, absent proliferation in response to antigens, .B cells: N/A, .IUIS Other affected cells: PMNs Monocytes. IUIS Associated features: Urticaria, SNHL, amyloidosis. . IUIS Major category: Autoinflammatory Disorders. IUIS Subcategory: Defects Affecting the Inflammasome.
Created: 2 Jul 2018, 10:57 a.m.
This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s) GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.
Created: 20 Apr 2018, 12:25 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: CIAS1 (NLRP3), PanelApp HGNC gene symbol check: NLRP3, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Autoinflammatory disorders / CINCA syndrome / CINCA syndrome; Autoinflammatory disorders / Familial cold autoinflammatory syndrome / Familial cold autoinflammatory syndrome; Autoinflammatory disorders / Muckle-Wells syndrome / Muckle-Wells syndrome
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: NLRP3, GRID_Gene_Symbol: NLRP3, GRID_Transcript_ENS_Community submitted: ENST00000336119, GRID_Transcript_RefSeq: NM_004895.4, GRID_Transcript_ENS_used_on_Production: ENST00000336119
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
Phenotypes
  • CINCA syndrome 607115
  • Non-pruritic urticaria, arthritis, chills, fever and leukocytosis after cold exposure
  • Neonatal onset rash, chronic meningitis, and arthropathy with fever and inflammation
  • Urticaria, SNHL, amyloidosis
  • Muckle-Wells syndrome 191900
  • Autoinflammatory Disorders
  • Familial cold autoinflammatory syndrome 1 120100
  • Deafness, autosomal dominant 34, with or without inflammation 617772
OMIM
606416
Clinvar variants
Variants in NLRP3
Penetrance
None
Publications
Panels with this gene

History Filter Activity

1 Apr 2020, Gel status: 3

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Ellen McDonagh (Genomics England Curator)

gene: NLRP3 was added gene: NLRP3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018 Mode of inheritance for gene: NLRP3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: NLRP3 were set to 28847925; 11687797; 11992256; 29366613; 12522564; 12032915 Phenotypes for gene: NLRP3 were set to CINCA syndrome 607115; Non-pruritic urticaria, arthritis, chills, fever and leukocytosis after cold exposure; Neonatal onset rash, chronic meningitis, and arthropathy with fever and inflammation; Urticaria, SNHL, amyloidosis; Muckle-Wells syndrome 191900; Autoinflammatory Disorders; Familial cold autoinflammatory syndrome 1 120100; Deafness, autosomal dominant 34, with or without inflammation 617772