GeneBe

NLRP6

NLR family pyrin domain containing 6, the group of Pyrin domain containing|NLR family

Basic information

Region (hg38): 11:278407-285388

Previous symbols: [ "NALP6" ]

Links

ENSG00000174885 ∙ NCBI:171389 ∙ OMIM:609650 ∙ HGNC:22944 ∙ Uniprot:P59044 ∙ 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 NLRP6 gene.

  • not_specified (129 variants)
  • not_provided (39 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLRP6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001276700.2. 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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
1
clinvar
1
clinvar
 9
missense
127
clinvar
12
clinvar
1
clinvar
 140
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 134 13 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NLRP6protein_codingprotein_codingENST00000312165 86995
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.0002740.9991256670791257460.000314
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.763935040.7790.00003285566
Missense in Polyphen88134.520.654171815
Synonymous1.242182430.8990.00001681938
Loss of Function2.991128.10.3910.00000153314

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006170.000608
Ashkenazi Jewish0.00009960.0000992
East Asian0.00005510.0000544
Finnish0.0001400.000139
European (Non-Finnish)0.0004830.000475
Middle Eastern0.00005510.0000544
South Asian0.0001750.000163
Other0.0004930.000489

dbNSFP

Source: dbNSFP

Function
FUNCTION: As the sensor component of the NLRP6 inflammasome, plays a crucial role in innate immunity and inflammation. In response to pathogens and other damage-associated signals, initiates the formation of the inflammasome polymeric complex, made of NLRP6, PYCARD and CASP1 (and possibly CASP4 and CASP5). Recruitment of proCASP1 to the inflammasome promotes its activation and CASP1- catalyzed IL1B and IL18 maturation and secretion in the extracellular milieu. The precise NLRP6 activation stimulus has not been identified yet (By similarity) (PubMed:12387869). Essential for gut mucosal self-renewal and proliferation. Maintains intestinal homeostasis and a healthy intestinal microbiota. This function is, at least partially, mediated by IL18, and not IL1B, produced by nonhematopoietic cells. Influences intestinal barrier function and microbial homeostasis through the regulation of goblet cell mucus secretion. Acts by promoting autophagy in goblet cells, an essential step for mucus granule exocytosis. Its role in goblet cell physiology is inflammasome- dependent, but IL1B- and IL18-independent. During systemic bacterial infections, may negatively regulate inflammatory signaling and inhibit the influx of monocytes and neutrophils to the circulation and to the peritoneum. May promote peripheral nerve recovery following injury via an inflammasome-independent mechanism (By similarity). {ECO:0000250|UniProtKB:Q91WS2, ECO:0000250|UniProtKB:Q96P20, ECO:0000269|PubMed:12387869}.;
Pathway
NOD-like receptor signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

pRec
0.110

Intolerance Scores

loftool
0.530
rvis_EVS
1.27
rvis_percentile_EVS
93.65

Haploinsufficiency Scores

pHI
0.133
hipred
Y
hipred_score
0.728
ghis
0.409

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.377

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Nlrp6
Phenotype
endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; 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; 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); digestive/alimentary phenotype; renal/urinary system phenotype;

Gene ontology

Biological process
negative regulation of inflammatory response to antigenic stimulus;inflammatory response;G protein-coupled receptor signaling pathway;response to bacterium;regulation of autophagy;negative regulation of toll-like receptor signaling pathway;wound healing;negative regulation of I-kappaB kinase/NF-kappaB signaling;innate immune response;regulation of inflammatory response;regulation of mucus secretion;negative regulation of ERK1 and ERK2 cascade
Cellular component
plasma membrane;nuclear membrane;inflammasome complex
Molecular function
vasopressin receptor activity;ATP binding