Phenotypic Mutation 'Park3' (pdf version)
AllelePark3
Mutation Type missense
Chromosome11
Coordinate59,456,676 bp (GRCm39)
Base Change A ⇒ G (forward strand)
Gene Nlrp3
Gene Name NLR family, pyrin domain containing 3
Synonym(s) Mmig1, Cias1, NALP3, cryopyrin, Pypaf1
Chromosomal Location 59,432,395-59,457,781 bp (+) (GRCm39)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a pyrin-like protein containing a pyrin domain, a nucleotide-binding site (NBS) domain, and a leucine-rich repeat (LRR) motif. This protein interacts with the apoptosis-associated speck-like protein PYCARD/ASC, which contains a caspase recruitment domain, and is a member of the NALP3 inflammasome complex. This complex functions as an upstream activator of NF-kappaB signaling, and it plays a role in the regulation of inflammation, the immune response, and apoptosis. Mutations in this gene are associated with familial cold autoinflammatory syndrome (FCAS), Muckle-Wells syndrome (MWS), chronic infantile neurological cutaneous and articular (CINCA) syndrome, and neonatal-onset multisystem inflammatory disease (NOMID). Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. Alternative 5' UTR structures are suggested by available data; however, insufficient evidence is available to determine if all of the represented 5' UTR splice patterns are biologically valid. [provided by RefSeq, Oct 2008]
PHENOTYPE: Mice homozygous for null mutations exhibit attenuated inflammatory responses related to decrease secretion of IL-1beta and IL-18. Mice heterozygous for activating mutations suffer from autoinflammatory attacks that lead to organ failure and death before weaning. [provided by MGI curators]
Accession Number

NCBI RefSeq: NM_145827.3; MGI: 2653833

MappedYes 
Amino Acid Change Aspartic acid changed to Glycine
Institutional SourceBeutler Lab
Gene Model predicted gene model for protein(s): [ENSMUSP00000078440] [ENSMUSP00000098707]
AlphaFold Q8R4B8
SMART Domains Protein: ENSMUSP00000078440
Gene: ENSMUSG00000032691
AA Change: D946G

DomainStartEndE-ValueType
PYRIN 4 87 6.39e-33 SMART
FISNA 135 206 1.45e-22 SMART
Pfam:NACHT 216 385 6.7e-52 PFAM
low complexity region 533 539 N/A INTRINSIC
low complexity region 688 697 N/A INTRINSIC
LRR_RI 737 764 1.07e-9 SMART
LRR 766 793 5.13e1 SMART
LRR 794 821 3.86e-7 SMART
LRR 823 850 1.62e0 SMART
LRR 851 878 3.39e-3 SMART
LRR 880 907 1.2e2 SMART
LRR 908 935 2.24e-3 SMART
LRR 937 964 2.16e2 SMART
LRR 965 992 8.73e-6 SMART
Predicted Effect probably benign

PolyPhen 2 Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)
(Using ENSMUST00000079476)
SMART Domains Protein: ENSMUSP00000098707
Gene: ENSMUSG00000032691
AA Change: D946G

DomainStartEndE-ValueType
PYRIN 4 87 6.39e-33 SMART
FISNA 135 206 1.45e-22 SMART
Pfam:NACHT 216 385 6.7e-52 PFAM
low complexity region 533 539 N/A INTRINSIC
low complexity region 688 697 N/A INTRINSIC
LRR_RI 737 764 1.07e-9 SMART
LRR 766 793 5.13e1 SMART
LRR 794 821 3.86e-7 SMART
LRR 823 850 1.62e0 SMART
LRR 851 878 3.39e-3 SMART
LRR 880 907 1.2e2 SMART
LRR 908 935 2.24e-3 SMART
LRR 937 964 2.16e2 SMART
LRR 965 992 8.73e-6 SMART
Predicted Effect probably benign

PolyPhen 2 Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)
(Using ENSMUST00000101148)
Meta Mutation Damage Score 0.3192 question?
Is this an essential gene? Probably nonessential (E-score: 0.076) question?
Phenotypic Category Autosomal Dominant
Candidate Explorer Status loading ...
Single pedigree
Linkage Analysis Data
Penetrance  
Alleles Listed at MGI

All mutations/alleles(16) : Chemically induced (ENU)(5) Targeted(11)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00421:Nlrp3 APN 11 59456769 missense probably damaging 0.99
IGL00573:Nlrp3 APN 11 59455942 missense possibly damaging 0.93
IGL01025:Nlrp3 APN 11 59442713 missense probably benign 0.21
IGL01637:Nlrp3 APN 11 59440204 missense probably damaging 0.99
IGL02010:Nlrp3 APN 11 59440361 missense probably benign
IGL02334:Nlrp3 APN 11 59455909 missense probably benign
IGL02417:Nlrp3 APN 11 59456849 unclassified probably benign
IGL02578:Nlrp3 APN 11 59439227 missense probably damaging 1.00
IGL02710:Nlrp3 APN 11 59456802 missense probably damaging 0.99
IGL02816:Nlrp3 APN 11 59446608 missense probably benign 0.03
IGL03157:Nlrp3 APN 11 59440372 missense possibly damaging 0.80
IGL03334:Nlrp3 APN 11 59439842 missense probably damaging 1.00
Flogiston UTSW 11 59449274 missense probably benign 0.00
nd1 UTSW 11 59456800 missense probably benign 0.45
Nd14 UTSW 11 59446701 missense possibly damaging 0.89
Nd3 UTSW 11 59456800 missense probably benign 0.45
nd5 UTSW 11 59456705 missense probably benign 0.01
nd6 UTSW 11 59440180 missense probably damaging 1.00
nd7 UTSW 11 59446701 missense possibly damaging 0.89
Nd9 UTSW 11 59440180 missense probably damaging 1.00
Park2 UTSW 11 59455954 nonsense probably null
Park4 UTSW 11 59440357 missense probably benign 0.19
Park5 UTSW 11 59439302 missense probably damaging 0.99
Park6 UTSW 11 59439862 missense probably damaging 1.00
Park7 UTSW 11 59438836 nonsense probably null
Park8 UTSW 11 59457025 missense probably benign 0.19
R0008:Nlrp3 UTSW 11 59449274 missense probably benign 0.00
R0008:Nlrp3 UTSW 11 59449274 missense probably benign 0.00
R0052:Nlrp3 UTSW 11 59455954 nonsense probably null
R0362:Nlrp3 UTSW 11 59439623 missense possibly damaging 0.49
R0416:Nlrp3 UTSW 11 59446750 splice site probably benign
R0649:Nlrp3 UTSW 11 59439368 missense possibly damaging 0.83
R0740:Nlrp3 UTSW 11 59439082 missense probably benign 0.01
R0863:Nlrp3 UTSW 11 59456676 missense probably benign 0.02
R1300:Nlrp3 UTSW 11 59446594 missense possibly damaging 0.86
R1414:Nlrp3 UTSW 11 59440357 missense probably benign 0.19
R1622:Nlrp3 UTSW 11 59439302 missense probably damaging 0.99
R1654:Nlrp3 UTSW 11 59433949 missense probably benign 0.03
R1715:Nlrp3 UTSW 11 59434177 missense probably damaging 1.00
R1754:Nlrp3 UTSW 11 59449228 missense possibly damaging 0.80
R1837:Nlrp3 UTSW 11 59439742 missense probably benign 0.00
R1905:Nlrp3 UTSW 11 59439862 missense probably damaging 1.00
R2281:Nlrp3 UTSW 11 59439962 missense possibly damaging 0.70
R4296:Nlrp3 UTSW 11 59440487 missense possibly damaging 0.89
R4305:Nlrp3 UTSW 11 59438836 nonsense probably null
R4540:Nlrp3 UTSW 11 59442725 missense possibly damaging 0.83
R4591:Nlrp3 UTSW 11 59440048 missense probably benign 0.00
R4816:Nlrp3 UTSW 11 59439127 missense probably benign 0.32
R4913:Nlrp3 UTSW 11 59440064 missense probably benign 0.09
R4970:Nlrp3 UTSW 11 59439554 missense probably damaging 1.00
R5051:Nlrp3 UTSW 11 59457025 missense probably benign 0.19
R5112:Nlrp3 UTSW 11 59439554 missense probably damaging 1.00
R5185:Nlrp3 UTSW 11 59455910 missense probably benign 0.05
R5417:Nlrp3 UTSW 11 59439889 missense probably damaging 1.00
R5709:Nlrp3 UTSW 11 59446574 nonsense probably null
R5869:Nlrp3 UTSW 11 59438960 missense probably damaging 1.00
R5898:Nlrp3 UTSW 11 59437678 missense probably benign 0.00
R5953:Nlrp3 UTSW 11 59437617 missense probably benign
R5979:Nlrp3 UTSW 11 59439797 missense probably benign 0.06
R6359:Nlrp3 UTSW 11 59439392 missense probably damaging 0.97
R6723:Nlrp3 UTSW 11 59456018 missense probably damaging 1.00
R7261:Nlrp3 UTSW 11 59439272 missense possibly damaging 0.83
R7349:Nlrp3 UTSW 11 59438912 missense probably damaging 1.00
R7388:Nlrp3 UTSW 11 59455892 missense probably benign 0.00
R7715:Nlrp3 UTSW 11 59433829 splice site probably null
R7916:Nlrp3 UTSW 11 59442689 missense probably benign 0.00
R8222:Nlrp3 UTSW 11 59439614 missense probably damaging 0.98
R8360:Nlrp3 UTSW 11 59440229 missense probably benign 0.02
R8390:Nlrp3 UTSW 11 59442616 missense possibly damaging 0.47
R8550:Nlrp3 UTSW 11 59440097 missense probably damaging 1.00
R8738:Nlrp3 UTSW 11 59440216 missense probably benign 0.00
R8940:Nlrp3 UTSW 11 59455870 missense probably benign 0.26
R8990:Nlrp3 UTSW 11 59439584 missense probably damaging 0.99
R9324:Nlrp3 UTSW 11 59434141 missense probably damaging 1.00
R9673:Nlrp3 UTSW 11 59440148 missense probably damaging 1.00
RF031:Nlrp3 UTSW 11 59449378 frame shift probably null
RF040:Nlrp3 UTSW 11 59449378 frame shift probably null
Z1088:Nlrp3 UTSW 11 59442686 missense possibly damaging 0.67
Mode of Inheritance Autosomal Dominant
Local Stock Sperm
MMRRC Submission 038251-MU
Last Updated 2019-09-04 9:48 PM by Diantha La Vine
Record Created 2014-09-18 10:25 PM by Hexin Shi
Record Posted 2015-01-23
Phenotypic Description

Figure 1. Park3 mice secreted decreased amounts of IL-1β in response to priming with lipopolysaccharide (LPS) followed by nigericin treatment. IL-1β levels were determined by ELISA. Image is from gene-based superpedigree analysis of pedigrees R0008 (green), R0052 (light blue), R0416 (red), R0362 (yellow), R1622 (glue/gray), R0863 (purple), and R1414 (gold), each harboring different Nlrp3 alleles (Chr11: 59549531, 59565850, 59548476, 59565128, 59558448, 59555924, and 59548797). Normalized log data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

The Park3 phenotype was identified among G3 mice of the pedigree R0863 some of which showed attenuated inflammatory responses related to decrease secretion of the proinflammatory cytokine interleukin (IL)-1β in response to priming with lipopolysaccharide (LPS) followed by nigericin treatment (Figure 1).

Nature of Mutation
Figure 2. Linkage mapping of the reduced IL-1β secretion after nigericin treatment using an dominant model of inheritance and gene-based superpedigree analysis. Manhattan plot shows -log10 P values (Y-axis) plotted against the chromosome positions of 493 mutations (X-axis) identified in the G1 males of pedigrees R0008, R0052, R0362, R0416, R0863, R1414, and R1622. Normalized phenotype data are shown without consideration of G2 dam identity. Horizontal pink and red lines represent thresholds of P = 0.05, and the threshold for P = 0.05 after applying Bonferroni correction, respectively.

Whole exome HiSeq sequencing of the G1 grandsire identified 62 mutations. The Nlrp3 inflammasome phenotype was linked to a mutation in Nlrp3 by continuous variable mapping and gene-based superpedigree analysis: normalized data from pedigrees R0008, R0052, R0362, R0416, R0863, R1414, and R1622 were analyzed using a dominant model of inheritance (P = 5.797 x 10-8), wherein 28 variant homozygotes and 65 heterozygotes departed phenotypically from 48 homozygous reference mice (Figure 2). The Nlrp3 mutation in Park3 is an A to G transition at base pair 59,565,850 (v38) on chromosome 11, or base pair 24,282 in the GenBank genomic region NC_000077. The mutation corresponds to residue 3,063 in the mRNA sequence NM_145827 within exon 4 of 10 total exons.

3047 CAGATGCTGGAATTAGACAACTGCAGCCTCACC

941  -Q--M--L--E--L--D--N--C--S--L--T-

The mutated nucleotide is indicated in red.  The mutation results in an aspartic acid (D) to glycine (G) substitution at position 946 (D946G) in the NLRP3 protein, and is strongly predicted by Polyphen-2 to be benign (score = 0.017).

Illustration of Mutations in
Gene & Protein
Protein Prediction
Figure 3. Domain structure of NLRP3. Shown are the pyrin domain (PYD), NACHT domain, NACHT-associated domain (NAD), and leucine-rich repeat (LRR) domain. Together, the NACHT and NAD domains are known as the nucleotide-binding domain (NBD). The Park3 mutation results in an aspartic acid to glycine substitution at position 946. This image is interactive. Other mutations found in NLRP3 are noted in red. Click on each mutation for more specific information.

The Nlrp3 gene encodes a 1,033 amino acid protein that is a member of the nucleotide-binding and oligomerization domain (NOD)-like receptor (NLR) or CATERPILLER [for CARD, transcription enhancer, R(purine)-binding, pyrin, lots of leucine repeats] family [Figure 3; (1)]. NLRP3 has a C-terminal leucine-rich repeat (LRR) domain, a central oligomerization NACHT usually with a C-terminal extension known as the NACHT associated domain (NAD), and an N-terminal effector domain. The N-terminus of NLRP3 contains a pyrin domain (PYD). The Park3 mutation (D945G) is within the LRR domain.

For more information about Nlrp3, please see the record for ND1.

Putative Mechanism

NLRP3 is able to oligomerize through its NBD domain and assemble into large caspase-1-activating multiprotein complexes termed inflammasomes upon the detection of pathogenic or other danger signals in the cytoplasm. A large variety of agents have been shown to activate the NLRP3 inflammasome, and NLRP3 plays an important role in the innate immune response. The phenotype of the Park3 mice suggests that the mutated protein, if expressed, is inactive or has reduced activity.

Primers PCR Primer
Park3_pcr_F: CCCTGATGCAAATCTGTGTCTGAGG
Park3_pcr_R: CAAACCACACTCACTGTAGGCTCTG

Sequencing Primer
Park3_seq_F: cctggcttgcctggaac
Park3_seq_R: TTGTTGCCCAGGTTCAGCTT
Genotyping

PCR program

1) 94°C 2:00
2) 94°C 0:30
3) 55°C 0:30
4) 72°C 1:00
5) repeat steps (2-4) 40x
6) 72°C 10:00
7) 4°C hold


The following sequence of 758 nucleotides is amplified (chromosome 11, + strand):


1   ccctgatgca aatctgtgtc tgaggagtga ggcgttcttg gtgtccatta gtgagaaatg
61  ggaagtttct agatggtata cagcttaaag gctaagcccc tgccaccaca gtcctgccaa
121 ctgcaaacat tcatttggtc cattgatact ttgtggaaat ctgaggggaa cataatgttt
181 agaaaaagtc aattgacaaa tttctgttac tattttggtc tgttcaaccc agtaccttgg
241 gaaaagaaac ttccatctaa agaggggaga aaagaaacca tatcatatga agcagcttca
301 cgctggtcag tctgtggttt gttgttgttg ttgttttcaa gacagggttt atctgtgtag
361 ccctggcttg cctggaactc actctgtaga ccaggttggc ttcgaactca gaaatccgcc
421 tgcttctgcc tcccaagtgc tgggattaaa ggtgtgcacc accactgccc agcccaatct
481 gcgcttttta tgcaaatgaa actgcaggtt tggagacccg gaagtatgga tggtcaaggc
541 tattttcttt atatcaccct tctcttctca aagattagac aactgcagcc tcacctcaca
601 cagctgctgg aatctctcca caattctgac ccacaaccac agccttcgga agctgaacct
661 gggcaacaat gatcttggcg atctgtgcgt ggtgaccctc tgtgaggtgc tgaaacagca
721 gggctgcctc ctgcagagcc tacagtgagt gtggtttg


Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red.

References

1. Ting, J. P., Lovering, R. C., Alnemri, E. S., Bertin, J., Boss, J. M., Davis, B. K., Flavell, R. A., Girardin, S. E., Godzik, A., Harton, J. A., Hoffman, H. M., Hugot, J. P., Inohara, N., Mackenzie, A., Maltais, L. J., Nunez, G., Ogura, Y., Otten, L. A., Philpott, D., Reed, J. C., Reith, W., Schreiber, S., Steimle, V., and Ward, P. A. (2008) The NLR Gene Family: A Standard Nomenclature. Immunity. 28, 285-287.

Science Writers Anne Murray
Illustrators Katherine Timer
AuthorsBruce Beutler, Hexin Shi, Ying Wang, Zhao Zhang, Doan Dao