Cryopyrin-Associated Periodic Syndromes via the NLRP3 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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NextGen Sequencing

Test Code Test Copy GenesPriceCPT Code Copy CPT Codes
4685 NLRP3$640.00 81479 Add to Order
Pricing Comments

Our most cost-effective testing approach is NextGen sequencing with Sanger sequencing supplemented as needed to ensure sufficient coverage and to confirm NextGen calls that are pathogenic, likely pathogenic or of uncertain significance. If, however, full gene Sanger sequencing only is desired (for purposes of insurance billing or STAT turnaround time for example), please see link below for Test Code, pricing, and turnaround time information.

For Sanger Sequencing click here.
Targeted Testing

For ordering sequencing of targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 20 days.

Clinical Sensitivity

Mutations in NLRP3 have been identified in >85% of patients with FACS and ~60% of patients with NOMID (Aksentijevich et al. 2007). Clinical sensitivity for MWS cannot be estimated because only a small number of patients have been reported. Analytical sensitivity should be high because all mutations reported are detectable by sequencing.

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Del/Dup via aCGH

Test Code Test Copy GenesPriceCPT Code Copy CPT Codes
600 NLRP3$990.00 81479 Add to Order
Pricing Comments

# of Genes Ordered

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Over 100

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Targeted Testing

For ordering sequencing of targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 20 days.

Clinical Features

Cryopyrin-Associated Periodic Syndromes (CAPS) include a group of autoinflammatory diseases due to mutations in the NLRP3 gene. CAPS are rare disorders affecting about 1 in 1,000,000 people primarily in North America and Europe (Kastner 2005). Familial Cold Autoinflammatory Syndrome (FCAS) is characterized by episodes of fever, urticarial-like rash, and joint pain after exposure to cold temperatures. Most patients initially present with rashes at birth or within the first few months of life. This rash is typically seen first on the face or extremities, and may spread to the rest of the body. Joint pain is typically found within hands, knees and ankles. Other symptoms may include conjunctivitis, sweating, drowsiness, headache and nausea. FCAS episodes are variable and may be triggered by exposure to cold temperatures for only a few minutes or an hour or more. Episodes typically last 12 hours, but may persist up to 3 days. Rarely, patients develop amyloidosis later in life. Neonatal Onset Multisystem Inflammatory Disease (NOMID), also known as Chronic Infantile Neurologic Cutaneous and Arthropathy (CINCA) syndrome, is the most severe form of recurrent fevers due to mutations in the NLRP3 gene. Initial symptoms include rash typically present at birth which persists throughout life. NOMID is characterized by persistent inflammation damaging the nervous system, skin, and joints. Other symptoms include headaches, seizures, chronic meningitis, intellectual disability, loss of hearing, and loss of vision. Persistent joint inflammation often leads to swelling, cartilage overgrowth leading to short stature, prominent forehead, and protruding eyes. Amyloidosis is seen in <2% of patients. Treatment with IL-1 receptor antagonists has been successful in controlling disease (Farasat et al. 2008). Muckle-Wells syndrome (MWS) is a rare disease characterized by recurrent and self-limited episodes of fever, urticaria, arthralgia, myalgia (Dodé et al. 2002) and conjunctivitis since childhood, which are related to exposure to cold temperatures. Late-onset sensorineural deafness is also observed. Amyloidosis is the main complication and is found in 25% of cases. Two distinct clinical phenotypes are observed: an 'inflammatory phenotype', most commonly seen in patients diagnosed in childhood characterized by relapsing fever and abdominal pain, and an 'organ -disease' phenotype in patients diagnosed during adulthood characterized by fatigue and hearing loss (Kuemmerle-Deschner et al. 2013).


FCAS, NOMID, and MWS are all autosomal dominant diseases characterized by mutations in the NLRP3 gene. Nearly all the causative mutations identified to date are missense variants within exon 3, affecting protein-protein interactions and protein secondary structure (Aksentijevich et al. 2007; Jesus et al. 2008). Specific mutations within the NLRP3 gene may not allow distinguishing between FCAS, NOMID or MWS as common missense mutations have been found within these disorders despite clinically different phenotypes. This suggests that additional modifier genes are involved in determining the disease spectrum. Patients with FCAS typically have a family history, while NOMID is often due to de novo mutations within the NLRP3 gene (Aksentijevich et al. 2002; Jesus et al. 2008). The NLRP3 gene encodes a protein called cryopyrin, a NOD-like receptor, which is a component of the inflammasome complex. When triggered by a danger signal, assembly of the inflammasome increases Interleukin 1β production to drive inflammation to fight off infections (Fujisawa et al. 2007).

Testing Strategy

For this NextGen test, the full coding regions plus ~10 bp of non-coding DNA flanking each exon are sequenced for the gene listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

Indications for Test

Candidates for this test are patients showing features consistent with CAPS (high erythrocyte sedimentation rate, c-reactive protein, and serum amyloid A protein levels) and family members of patients who have known NLRP3 mutations. The diagnosis of Muckle-Wells Syndrome (MWS) remains challenging due to the clinical heterogeneity and lack of diagnostic criteria. Individuals with episodes of fever, urticaria, arthralgia, myalgia and conjunctivitis since childhood, abdominal pain and late-onset sensorineural deafness should consider testing for mutations in NLRP3.


Official Gene Symbol OMIM ID
NLRP3 606416
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection


Genetic Counselors
  • Aksentijevich I, D Putnam C, Remmers EF, Mueller JL, Le J, Kolodner RD, Moak Z, Chuang M, Austin F, Goldbach-Mansky R, Hoffman HM, Kastner DL. 2007. The clinical continuum of cryopyrinopathies: novel CIAS1 mutations in North American patients and a new cryopyrin model. Arthritis Rheum. 56: 1273–1285. PubMed ID: 17393462
  • Aksentijevich I, Nowak M, Mallah M, Chae JJ, Watford WT, Hofmann SR, Stein L, Russo R, Goldsmith D, Dent P, Rosenberg HF, Austin F, et al. 2002. De novo CIAS1 mutations, cytokine activation, and evidence for genetic heterogeneity in patients with neonatal-onset multisystem inflammatory disease (NOMID): a new member of the expanding family of pyrin-associated autoinflammatory diseases. Arthritis Rheum. 46: 3340–3348. PubMed ID: 12483741
  • Dodé C, Dû N Le, Cuisset L, Letourneur F, Berthelot J-M, Vaudour G, Meyrier A, Watts RA, David Scott GI, Nicholls A. 2002. New Mutations of CIAS1 That Are Responsible for Muckle-Wells Syndrome and Familial Cold Urticaria: A Novel Mutation Underlies Both Syndromes. The American Journal of Human Genetics 70: 1498–1506. PubMed ID: 11992256
  • Farasat S, Aksentijevich I, Toro JR. 2008. Autoinflammatory diseases: clinical and genetic advances. Arch. Dermatol. 144: 392–402. PubMed ID: 18347298
  • Fujisawa A, Kambe N, Saito M, Nishikomori R, Tanizaki H, Kanazawa N, Adachi S, Heike T, Sagara J, Suda T, Nakahata T, Miyachi Y. 2007. Disease-associated mutations in CIAS1 induce cathepsin B-dependent rapid cell death of human THP-1 monocytic cells. Blood 109: 2903–2911. PubMed ID: 17164343
  • Jesus AA, Silva CA, Segundo GR, Aksentijevich I, Fujihira E, Watanabe M, Carneiro-Sampaio M, Duarte AJS, Oliveira JB. 2008. Phenotype-genotype analysis of cryopyrin-associated periodic syndromes (CAPS): description of a rare non-exon 3 and a novel CIAS1 missense mutation. J. Clin. Immunol. 28: 134–138. PubMed ID: 18080732
  • Kastner DL. 2005. Hereditary periodic fever syndromes. Hematol. Educ. Program Am. Soc. Hematol. Am. Soc. Hematol. Educ. Program 74–81. PubMed ID: 16304362
  • Kuemmerle-Deschner JB, Samba SD, Tyrell PN, Koné-Paut I, Marie I, Deschner N, Benseler SM. 2013. Challenges in diagnosing Muckle-Wells syndrome: Identifying two distinct phenotypes. Arthritis Care Res (Hoboken). PubMed ID: 24127202
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NextGen Sequencing using PG-Select Capture Probes

Test Procedure

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~10 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are often covered by Sanger sequencing.

For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions.  After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Analytical Validity

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.

In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.   

Analytical Limitations

Interpretation of the test results is limited by the information that is currently available.  Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~10 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

In most cases, we are unable to determine the phase of sequence variants.  In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants due to somatic mosaicism is limited.  Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood).   Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics.  However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

Deletion/Duplication Testing via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

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Ordering Options

myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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