NLRP4

NLR family pyrin domain containing 4, the group of NLR family|Pyrin domain containing

Basic information

Region (hg38): 19:55836540-55881855

Previous symbols: [ "NALP4" ]

Links

ENSG00000160505 ∙ NCBI:147945 ∙ OMIM:609645 ∙ HGNC:22943 ∙ Uniprot:Q96MN2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NLRP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLRP4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			62	7	1	70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	62	9	2

Variants in NLRP4

This is a list of pathogenic ClinVar variants found in the NLRP4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-55836542-G-A			not provided (-)
19-55836725-T-G			not provided (-)
19-55836825-G-A			not provided (-)
19-55836940-G-T			not provided (-)
19-55836941-G-T			not provided (-)
19-55852091-C-G		not specified	Uncertain significance (Feb 21, 2024)
19-55852096-T-A		not specified	Uncertain significance (Nov 13, 2024)
19-55852104-T-G		not specified	Uncertain significance (Apr 08, 2024)
19-55852149-C-G		not specified	Uncertain significance (Nov 30, 2022)
19-55852150-A-G		not specified	Uncertain significance (Aug 30, 2021)
19-55852166-A-T		not specified	Likely benign (Sep 20, 2023)
19-55852184-T-G		not specified	Uncertain significance (Sep 18, 2024)
19-55852210-T-C		not specified	Uncertain significance (Oct 03, 2023)
19-55852211-G-T		not specified	Uncertain significance (Sep 22, 2022)
19-55852217-A-T		not specified	Uncertain significance (Mar 13, 2023)
19-55852237-G-A		not specified	Uncertain significance (Nov 23, 2024)
19-55852259-T-A		not specified	Uncertain significance (Jan 20, 2023)
19-55852291-A-G		not specified	Likely benign (Apr 27, 2022)
19-55857719-G-A			Likely benign (Mar 01, 2023)
19-55857760-T-G		not specified	Uncertain significance (Sep 08, 2024)
19-55857777-G-T		not specified	Uncertain significance (Apr 09, 2024)
19-55857815-C-T		not specified	Uncertain significance (Aug 21, 2023)
19-55857838-C-T		not specified	Uncertain significance (Jul 12, 2023)
19-55857839-G-GA			not provided (-)
19-55857848-TCATTCAAGGA-T			not provided (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLRP4	protein_coding	protein_coding	ENST00000301295	9	45277

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.18e-9	0.996	125443	1	304	125748	0.00121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.737	600	551	1.09	0.0000319	6575
Missense in Polyphen		108	118.65	0.91022		1595
Synonymous	-3.64	301	231	1.30	0.0000150	1872
Loss of Function	2.64	20	37.4	0.534	0.00000177	474

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00231	0.00194
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.00103	0.000925
Finnish	0.000833	0.000832
European (Non-Finnish)	0.00156	0.00153
Middle Eastern	0.00103	0.000925
South Asian	0.00174	0.00170
Other	0.000658	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in inflammation and recognition of cytosolic pathogen-associated molecular patterns (PAMPs) not intercepted by membrane-bound receptors. Acts as a negative regulator of the type I interferon signaling pathway by serving as an adapter to promote DTX4-mediated ubiquitination of activated TBK1, and its subsequent degradation. Suppresses NF-kappaB induction by the cytokines TNFA and IL1B, suggesting that it operates at a point of convergence in these two cytokine signaling pathways. {ECO:0000269|PubMed:12093792, ECO:0000269|PubMed:22388039}.
• Pathway: Nucleotide-binding Oligomerization Domain (NOD) pathway;IRF3 mediated activation of type 1 IFN;ZBP1(DAI) mediated induction of type I IFNs;STING mediated induction of host immune responses;Regulation of innate immune responses to cytosolic DNA;Innate Immune System;Immune System;IRF3-mediated induction of type I IFN;TNFalpha;Cytosolic sensors of pathogen-associated DNA (Consensus)

Recessive Scores

• pRec: 0.0970

Intolerance Scores

• loftool: 0.141
• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.0750
• hipred: N
• hipred_score: 0.251

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.408

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nlrp4e

Gene ontology

• Biological process: inflammatory response;regulation of type I interferon production
• Cellular component: cytosol
• Molecular function: ATP binding