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Familial Episodic Pain Type 3 (FEPS3) Syndrome, Hereditary Sensory and Autonomic Neuropathy Type VII (HSAN7), and other Pain-Related Disorders via the SCN11A Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

NGS Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
4855 SCN11A$690.00 81479 Add to Order
Pricing Comment

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 targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

In a study involving 58 unrelated individuals with early-onset severe sensory loss, one patient was determined to have a pathogenic sequence variant within the SCN11A gene (Leipold et al. 2013). In another study involving 393 patients diagnosed with painful peripheral neuropathy, 12 patients were determined to harbor causative variants within the SCN11A gene (Huang et al. 2014). It should be noted that in this particular study, screening for sequence variants in the SCN11A gene was only performed on patients who tested negative for variants involving the other more commonly involved sodium channel genes, namely SCN9A and SCN10A.

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Clinical Features

Familial episodic pain syndrome type 3 (FEPS3) pertains to sporadic hypersensitivity to inflammatory pain that mainly involves distal lower extremities, with occasional occurrence in the upper extremities such as the joints of the fingers and arms. Episodic pain generally occurs late in the day and relapses once every 2-5 days for a total of 9-19 recurrences for each cycle (Zhang et al. 2013). The condition is exacerbated by fatigue, particularly when an individual contracts a viral infection such as a cold or has undergone profuse sweating after engaging in intense physical activities (Lolignier et al. 2011). The affected region is extremely cold, and pain is often alleviated by the application of a hot compress and the administration of ant-inflammatory drugs. Most cases of FEPS3 subside with aging. Neurologic assessment of individuals with FEPS3 generally shows normal sensitivities involving joints to light touch, as well as to pin pricks. Hereditary sensory and autonomic neuropathy type VII (HSAN7) is a congenital, neurologic disorder that is characterized by an inability to perceive pain. Because this condition does not allow an individual to experience the unique sensation of pain, this often results in self-mutilations, as well as the occurrence of slow-healing injuries, lacerations, and multiple fractures. Individuals with HSAN7 generally present a mild degree of muscular weakness and slow motor development, as well as gastrointestinal disturbances. Muscle assessments such biopsies and electromyography usually show normal findings. A slight reduction in motor and sensory nerve conduction velocities is often observed in individuals diagnosed with HSAN7. Patients also present normal magnetic resonance imaging (MRI) findings and no signs of intellectual disability (Leipold et al. 2013).

Genetics

FEPS3 and HSAN7 are autosomal dominant neurologic disorders caused by heterozygous variants in the voltage-gated sodium channel type XI, alpha subunit (SCN11A) gene, which has been mapped to 3p22.2 (Dib-Hajj et al. 1998). The SCN11A gene consists of 26 exons and encodes a tetrodotoxin (TTX)-resistant protein channel, Nav1.9, initially termed NaN, which is highly expressed in the neurons of the dorsal root ganglion and is stimulated by the occurrence of a negative action potential (Dib-Hajj et al. 1999). Nav1.9 is structurally similar to another sodium channel, Nav1.8, which is encoded by an adjacent gene, SCN10A (Faber et al. 2012). The protein channel Nav1.9 mediates the activity of brain-derived neurotrophic factor (BDNF)-evoked depolarization of membrane potentials (Cummins et al. 2000; Wilson-Gerwing et al. 2008; Vanoye et al. 2013) through the action of tyrosine kinases (Benn et al. 2001; Fang et al. 2005). Reports have shown that variants involving the SCN11A gene may cause either hypersensitivity or insensitivity to pain, which may be due to elevated electrical activities that induce the opening of sodium channels or the depolarization of the sodium channels that block an individual's perception of pain, respectively (Zhang et al. 2013; Leipold et al. 2013; Huang et al. 2014). About 10 causative sequence variants have been reported in the SCN11A gene, which include mostly missense variants (Huang et al. 2014; Leipold et al. 2013; Zhang et al. 2013). To date, there is no distinction between mutations that cause FEPS3 or HSAN7, and both neurologic disorders are caused by gain-of-function sequence variants within the SCN11A gene. Other previous names of the SCN11A gene include SCN12A, peripheral nerve sodium channel 5 (PN5), and sensory neuron sodium channel 2 (SNS-2). Sequence variants in other types of voltage-gated cation channels such as TRPA1 (Kremeyer et al. 2010) and Nav1.8 (Faber et al. 2012) may also cause FEPS3, and sequence variants of enzymes such as DNMT1 (Klein et al. 2011, 2013), WNK1 (Davidson et al. 2012; Potulska-Chromik et al. 2012), and SPTLC2 (Rotthier et al. 2010; Murphy et al. 2013) may also result in HSAN. Two unrelated Chinese families spanning five generations (consisting of 43 and 26 members, respectively) were diagnosed with FEPS3 and harbored missense substitutions in the SCN11A gene (Zhang et al. 2013). Electrophysiologic examination of the affected family members showed that the mutant proteins presented higher electrical activities, which in turn induces the opening of other ion channels, resulting in a hyperexcitable state that contributes to the development of FEPS3. Two unrelated patients with HSAN7 have been reported with de novo heterozygous missense substitutions involving the SCN11A gene (Leipold et al. 2013). It has been suggested that the excessive influx of sodium ions into cells might have caused depolarization, which in turn resulted in the blockage of other ion channels that play essential roles in the generation of an action potential in neurons of the dorsal root ganglia (Persson et al. 2009; Bosmans et al. 2011).

Testing Strategy

For this NextGen test, the full coding regions plus ~20 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

The ideal SCN11A test candidates should either have a family history of FEPS involving the lower extremities and triggered by fatigue, as well as dorsal root ganglia showing elevated electrical activities (Zhang et al. 2013) or a family history of HSAN7 (congenital insensitivity to pain), coupled with muscle hypotonia and gastrointestinal dysfunction (Leipold et al. 2013).

Gene

Official Gene Symbol OMIM ID
SCN11A 604385
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Name
Chronic Joint Pain and Dysfunction via the MMP13 Gene
Episodic Pain Syndrome Sequencing Panel
Familial Episodic Pain Type 2 Syndrome via the SCN10A Gene
Hereditary Motor and Sensory Neuropathy IIB (HMSN2B) via the RAB7A Gene
Hereditary Sensory and Autonomic Neuropathy Sequencing Panel
Hereditary Sensory and Autonomic Neuropathy Type V (HSAN5) via the NGF Gene
Increased Pain Sensitivity via the COMT Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Leipold E, Liebmann L, Korenke GC, Heinrich T, Giesselmann S, Baets J, Ebbinghaus M, Goral RO, Stödberg T, Hennings JC, Bergmann M, Altmüller J, Thiele H, Wetzel A, Nürnberg P, Timmerman V, De Jonghe P, Blum R, Schaible HG, Weis J, Heinemann SH, Hübner CA, Kurth I. 2013. A de novo gain-of-function mutation in SCN11A causes loss of pain perception. Nature Genetics 45: 1399-1404. PubMed ID: 24036948
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TEST METHODS

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 ~20 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 covered by Sanger sequencing.  All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed 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, Common Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org).  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 ~20 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.

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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.
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.

SPECIMEN TYPES
WHOLE BLOOD

(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.

DNA

(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.

CELL CULTURE

(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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