NLRP11

protein-coding

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

Gene summary

This gene is a member of the the NOD-like receptor protein (NLRP) gene family and encodes a protein with an N-terminal pyrin death (PYD) domain and nucleoside triphosphate hydrolase (NACHT) domain and a C-terminal leucine-rich repeats (LRR) region. This gene has been shown to regulate caspases in the proinflammatory signal transduction pathway and, based on studies of other members of the NLRP gene family with similar domain structure, is predicted to form part of the multiprotein inflammasome complex. Alternative splicing produces multiple transcript variants encoding distince isoforms. [provided by RefSeq, May 2017]

Previous symbols:

NALP11

MANE transcript

NM_001394894.2

Inheritance

—

ClinVar variants

U:157B:19

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr19:55,785,397-55,836,800

External References & Databases

Ensembl (ENSG00000179873)

Transcript & Mutation Effects

hg38 • Region Span ~51.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NLRP11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 162

not providedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394894.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	2 clinvar		7
missense			151 clinvar	14 clinvar	3 clinvar	168
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	157	16	3	176

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394894.2	RefSeq	NP_001381823.1	9	MANE Select
ENST00000589093.6	Ensembl	ENSP00000466285.1	9	MANE Select
NM_001297743.3	RefSeq	NP_001284672.1	8	Standard
NM_001385451.2	RefSeq	NP_001372380.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000443188
Coding exons: 9
Length: 51397
Individuals with no LoFs: 125676
Homozygous LoFs: 0
Heterozygous LoFs: 72
Defined: 125748
p: 0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.646	524	567	0.924	0.0000298	6842
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00016	0.00016	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00026	0.00025	rare
South Asian	0.00026	0.00026	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0704

Gene Damage Prediction

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