NLRP11

NLR family pyrin domain containing 11, the group of NLR family|Pyrin domain containing

Basic information

Region (hg38): 19:55785396-55836800

Previous symbols: [ "NALP11" ]

Links

ENSG00000179873 ∙ NCBI:204801 ∙ OMIM:609664 ∙ HGNC:22945 ∙ Uniprot:P59045 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NLRP11 gene.

• Inborn genetic diseases (45 variants)
• not provided (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLRP11 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		1
missense			41	4	3	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	5	3

Variants in NLRP11

This is a list of pathogenic ClinVar variants found in the NLRP11 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55785540-T-C			not provided (-)
19-55785653-G-A			Benign (Jul 18, 2018)
19-55785656-G-A		not specified	Likely benign (Mar 01, 2024)
19-55785661-C-G		not specified	Uncertain significance (May 05, 2023)
19-55785717-G-A		not specified	Uncertain significance (Nov 09, 2023)
19-55785723-T-C		not specified	Likely benign (Mar 27, 2023)
19-55785798-T-G			Benign (Aug 28, 2018)
19-55785821-A-G		not specified	Uncertain significance (Dec 03, 2021)
19-55788829-C-T		not specified	Uncertain significance (Feb 27, 2024)
19-55788832-G-A		not specified	Uncertain significance (Dec 28, 2022)
19-55788864-C-G		not specified	Uncertain significance (Oct 05, 2022)
19-55788879-T-C		not specified	Uncertain significance (Feb 27, 2023)
19-55788918-G-A			not provided (-)
19-55788939-G-T		not specified	Uncertain significance (Feb 28, 2024)
19-55788942-C-A		not specified	Uncertain significance (Mar 12, 2024)
19-55788964-T-G		not specified	Uncertain significance (May 18, 2022)
19-55789307-C-T		not specified	Uncertain significance (Oct 26, 2022)
19-55792360-G-A			not provided (-)
19-55792364-T-A		not specified	Uncertain significance (Jun 09, 2022)
19-55792410-T-A		not specified	Uncertain significance (Nov 17, 2023)
19-55792423-T-A		not specified	Uncertain significance (Apr 25, 2023)
19-55792440-A-C			Benign (Jul 18, 2018)
19-55792503-T-C			not provided (-)
19-55796089-A-G		not specified	Likely benign (Dec 12, 2022)
19-55796093-G-T		not specified	Uncertain significance (Nov 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLRP11	protein_coding	protein_coding	ENST00000443188	9	51397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.15e-9	0.993	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.646	524	567	0.924	0.0000298	6842
Missense in Polyphen		92	132.69	0.69332		1794
Synonymous	-1.74	253	220	1.15	0.0000125	1963
Loss of Function	2.52	20	36.4	0.549	0.00000193	460

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00102
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000164	0.000163
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000256	0.000255
Middle Eastern	0.000164	0.000163
South Asian	0.000262	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in inflammation. {ECO:0000305}.

Recessive Scores

• pRec: 0.0656

Intolerance Scores

• loftool: 0.740
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.27

Haploinsufficiency Scores

• pHI: 0.0449
• hipred: N
• hipred_score: 0.251

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0704

Gene Damage Prediction

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

Gene ontology

• Biological process: oxidation-reduction process
• Molecular function: RNA binding;ATP binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen