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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 3 of 3.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_176820.4	NP_789790.2	9	yes	-
ENST00000332836.7	ENSP00000331857.2	9	yes	-
ENST00000590200.1	ENSP00000465253.1	9	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NLRP9 gene.

• not_specified (155 variants)
• not_provided (20 variants)
• Congenital_stationary_night_blindness (1 variants)

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. These statistics are base on transcript: NM_176820.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	4	5	11
missense			144	15	3	162
nonsense						0
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	146	20	8

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
		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

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

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