NLRP9

NLR family pyrin domain containing 9, the group of NLR family|Pyrin domain containing

Basic information

Region (hg38): 19:55708438-55738402

Previous symbols: [ "NALP9" ]

Links

ENSG00000185792 ∙ NCBI:338321 ∙ OMIM:609663 ∙ HGNC:22941 ∙ Uniprot:Q7RTR0 ∙ 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 NLRP9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLRP9 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				1	4	5
missense			72	8	3	83
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	72	10	7

Variants in NLRP9

This is a list of pathogenic ClinVar variants found in the NLRP9 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55708926-C-A		not specified	Uncertain significance (Oct 01, 2024)
19-55708944-C-T		not specified	Uncertain significance (Dec 02, 2022)
19-55708945-G-A			Likely benign (Oct 01, 2022)
19-55709044-C-G		not specified	Likely benign (May 15, 2024)
19-55711772-C-T			not provided (-)
19-55711818-C-T		not specified	Uncertain significance (Aug 27, 2024)
19-55711821-T-G		not specified	Uncertain significance (Oct 22, 2024)
19-55711824-G-A		not specified	Uncertain significance (Feb 12, 2025)
19-55711875-A-G		not specified	Uncertain significance (Jan 27, 2025)
19-55711891-G-A			not provided (-)
19-55711891-G-T		not specified	Uncertain significance (Mar 27, 2023)
19-55711912-C-T		not specified	Uncertain significance (Mar 21, 2024)
19-55711914-A-T		not specified	Uncertain significance (Oct 19, 2024)
19-55711918-G-C		not specified	Uncertain significance (Dec 20, 2024)
19-55711924-C-A		not specified	Likely benign (Feb 10, 2025)
19-55711927-C-T		not specified	Uncertain significance (Mar 08, 2025)
19-55711933-C-T		not specified	Uncertain significance (Feb 19, 2025)
19-55711948-G-A			Benign (Jul 17, 2018)
19-55711948-G-C		not specified	Uncertain significance (Mar 30, 2022)
19-55711956-G-A		not specified	Uncertain significance (Aug 04, 2021)
19-55712306-G-A			not provided (-)
19-55712422-G-A			Benign (Dec 31, 2019)
19-55712429-T-A		not specified	Uncertain significance (Feb 21, 2024)
19-55712430-C-G		not specified	Uncertain significance (Jul 08, 2022)
19-55712463-A-G		not specified	Uncertain significance (Jan 27, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLRP9	protein_coding	protein_coding	ENST00000332836	9	29971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.86e-25	0.000455	125314	2	432	125748	0.00173

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.643	564	523	1.08	0.0000269	6555
Missense in Polyphen		114	120.71	0.94437		1771
Synonymous	-1.66	244	213	1.14	0.0000125	1845
Loss of Function	0.0291	37	37.2	0.995	0.00000191	492

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00390	0.00382
Ashkenazi Jewish	0.00233	0.00228
East Asian	0.00439	0.00430
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.00124	0.00123
Middle Eastern	0.00439	0.00430
South Asian	0.00316	0.00304
Other	0.00116	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As the sensor component of the NLRP9 inflammasome, plays a crucial role in innate immunity and inflammation. In response to pathogens, including rotavirus, initiates the formation of the inflammasome polymeric complex, made of NLRP9, PYCARD and CASP1. Recruitment of proCASP1 to the inflammasome promotes its activation and CASP1-catalyzed IL1B and IL18 maturation and release in the extracellular milieu. The active cytokines stimulate inflammatory responses. Inflammasomes can also induce pyroptosis, an inflammatory form of programmed cell death. NLRP9 inflammasome activation may be initiated by DHX9 interaction with viral double-stranded RNA (dsRNA), preferentially to short dsRNA segments. {ECO:0000269|PubMed:28636595}.

Recessive Scores

• pRec: 0.0823

Intolerance Scores

• loftool: 0.693
• rvis_EVS: -0.1
• rvis_percentile_EVS: 45.68

Haploinsufficiency Scores

• pHI: 0.0815
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nlrp9b
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype; digestive/alimentary phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Gene ontology

• Biological process: inflammatory response;positive regulation of interleukin-18 production;innate immune response;defense response to virus;pyroptosis
• Cellular component: inflammasome complex
• Molecular function: protein binding;ATP binding