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Familial Episodic Pain Type 2 Syndrome via the SCN10A 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
4651 SCN10A$990.00 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 104 patients presenting with idiopathic peripheral neuropathic pain, 9 cases were determined to harbor a causative sequence variant in the SCN10A gene (Faber et al. 2012). In another report, one patient who tested negative for causative variants in the SCN9A gene was determined to carry a causative variant in the SCN10A gene (Huang et al. 2013).

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Clinical Features

Familial episodic pain syndrome type 2 (FEPS2) is an adult small fiber neuropathy that is characterized by paroxysmal pain involving the distal lower extremities (Faber et al. 2012; Huang et al. 2013). This disorder initially presents as a sudden and intense burning or stabbing pain in the feet that is generally caused by heat, cold, chemicals, or certain surfaces. The pain may also be continuous or evoked by a particular stimulus (Themistocleous et al. 2014). This clinical presentation is caused by a decrease in the number of intraepidermal nerve fibers in the distal region of the leg (Bakkers et al. 2010; Laedermann et al. 2013; Ramachandra et al. 2013). Other features of FEPS2 include allodynia (hypersensitivity to touch) and hyperalgesia (elevated response to a pain stimulus). Certain individuals with FEPS2 may also develop pruritic responses (Themistocleous et al. 2014). FEPS2 episodes can be relieved by warmth, although the affected areas may develop red discoloration. Assessment of nerve conduction of the affected extremities generally shows normal properties, although quantitative testing of sensory capacities of both feet, and in rare cases hands, usually indicates abnormal thresholds for warm and cold temperatures (Hovaguimian & Gibbons 2011). Mutations in two other genes, TRPA1 on chromosome 8q13.3 (Faber et al. 2012) and SCN11A on chromosome 3p22.2 (Zhang et al. 2013) may also cause FEPS.   

Genetics

FEPS2 is an autosomal dominant neurologic disorder caused by heterozygous missense mutations involving the voltage-gated sodium channel type X, alpha subunit (SCN10A) gene (Faber et al. 2012). Voltage-gated sodium channels serve as integral membrane components that play a major role in the generation of the initial action potential of nerve cells. These channels consist of a large alpha subunit that directly interacts with several smaller beta protein subunits (Zhao et al. 2011). Although a wide range of voltage-gated sodium channels exist, each type can be differentiated according to their primary structure, protein kinetics, as well as sensitivity to the tetrodotoxin (TTX) neurotoxin (Rajamani et al. 2008). Sodium channels that are relatively resistant to TTX generally accumulate within the area where nerve injury has occurred, thus resulting in chronic pain (Gold et al. 2003). 

The SCN10A gene maps to chromosome 3p22.2, consists of 27 exons, and encodes a TTX-resistant sodium channel, Nav1.8, which is required in maintaining the excitability of epidermal neurons when skin is exposed to cool temperatures and in other functions of the peripheral sensory nervous system (Abrahamsen et al. 2008). SCN10A has also been implicated in the development of cardiac pain and dysrhythmia, possibly serving gap junction proteins and functioning in cardiac innervation and conduction (Facer et al. 2011; Ritchie et al. 2013; Verkerk et al. 2012; van den Boogaard et al. 2014), as well as in lingual nerve neuromas (Bird et al. 2013). About 30 causative variants have been reported in the SCN10A gene, the great majority of which are missense variants (Faber et al. 2012; Savio-Galimberti et al. 2014).

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 SCN10A test candidates have a family history of FEPS along with a positive skin biopsy result for small fiber neuropathy, which includes a decreased density of intradermal nerve fibers and complete epidermal denervation (Devigili et al. 2008; Latronico et al. 2013; Shipton 2013).

Gene

Official Gene Symbol OMIM ID
SCN10A 604427
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Episodic Pain Syndrome, Familial, 2 615551

Related Tests

Name
Chronic Joint Pain and Dysfunction via the MMP13 Gene
Episodic Pain Syndrome Sequencing Panel
Familial Episodic Pain Type 3 (FEPS3) Syndrome, Hereditary Sensory and Autonomic Neuropathy Type VII (HSAN7), and other Pain-Related Disorders via the SCN11A Gene
Hereditary Motor and Sensory Neuropathy IIB (HMSN2B) via the RAB7A Gene
Hereditary Sensory and Autonomic Neuropathy Type V (HSAN5) via the NGF Gene
Increased Pain Sensitivity via the COMT Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Abrahamsen B, Zhao J, Asante CO, Cendan CM, Marsh S, Martinez-Barbera JP, Nassar MA, Dickenson AH, Wood JN. 2008. The cell and molecular basis of mechanical, cold, and inflammatory pain. Science 321: 702-705.  PubMed ID: 18669863
  • Bakkers M, Faber CG, Drent M, Hermans MC, van Nes SI, Lauria G, De Baets M, Merkies IS. 2010. Pain and autonomic dysfunction in patients with sarcoidosis and small fibre neuropathy. Journal of Neurology 257: 2086-2090. PubMed ID: 20644950
  • Bird EV, Christmas CR, Loescher AR, Smith KG, Robinson PP, Black JA, Waxman SG, Boissonade FM. 2013. Correlation of Nav1.8 and Nav1.9 sodium channel expression with neuropathic pain in human subjects with lingual nerve neuromas. Molecular Pain 9:52. PubMed ID: 24144460
  • Devigili G, Tugnoli V, Penza P, Camozzi F, Lombardi R, Melli G, Broglio L, Granieri E, Lauria G. 2008. The diagnostic criteria for small fibre neuropathy: From symptoms to neuropathology. Brain 131(Pt 7): 1912-1925.  PubMed ID: 18524793
  • Faber CG, Lauria G, Merkies IS, Cheng X, Han C, Ahn HS, Persson AK, Hoeijmakers JG, Gerrits MM, Pierro T, Lombardi R, Kapetis D, Dib-Hajj SD, Waxman SG. 2012. Gain-of-function Nav1.8 mutations in painful neuropathy. Proceedings of the National Academy of Sciences USA 109: 19444-19449. PubMed ID: 23115331
  • Facer P, Punjabi PP, Abrari A, Kaba RA, Severs NJ, Chambers J, Kooner JS, Anand P. 2011. Localisation of SCN10A gene product Na(v)1.8 and novel pain-related ion channels in human heart. International Heart Journal 52: 146-152.  PubMed ID: 21646736
  • Gold MS, Weinreich D, Kim CS, Wang R, Treanor J, Porreca F, Lai J. 2003. Redistribution of Na(V)1.8 in uninjured axons enables neuropathic pain. Journal of Neuroscience 23: 158-166. PubMed ID: 12514212
  • Hovaguimian A, Gibbons CH. 2011. Diagnosis and treatment of pain in small-fiber neuropathy. Current Pain and Headache Reports 15: 193-200. PubMed ID: 21286866
  • Huang J, Yang Y, Zhao P, Gerrits MM, Hoeijmakers JG, Bekelaar K, Merkies IS, Faber CG, Dib-Hajj SD, Waxman SG. 2013. Small-fiber neuropathy Nav1.8 mutation shifts activation to hyperpolarized potentials and increases excitability of dorsal root ganglion neurons. Journal of Neuroscience 33: 14087-14097. PubMed ID: 23986244
  • Laedermann CJ, Cachemaille M, Kirschmann G, Pertin M, Gosselin RD, Chang I, Albesa M, Towne C, Schneider BL, Kellenberger S, Abriel H, Decosterd I. 2013. Dysregulation of voltage-gated sodium channels by ubiquitin ligase NEDD4-2 in neuropathic pain. Journal of Clinical Investigation 123:3002-3013. PubMed ID: 23778145
  • Latronico N, Filosto M, Fagoni N, Gheza L, Guarneri B, Todeschini A, Lombardi R, Padovani A, Lauria G. 2013. Small nerve fiber pathology in critical illness. PLoS One 8: e75696.  PubMed ID: 24098716
  • Rajamani S, Shryock JC, Belardinelli L. 2008. Block of tetrodotoxin-sensitive, Na(V)1.7 and tetrodotoxin-resistant, Na(V)1.8, Na+ channels by ranolazine. Channels (Austin) 2: 449-460. PubMed ID: 19077543
  • Ramachandra R, McGrew SY, Baxter JC, Howard JR, Elmslie KS. 2013. NaV1.8 channels are expressed in large, as well as small, diameter sensory afferent neurons. Channels (Austin) 7: 34-37. PubMed ID: 23064159
  • Ritchie MD, Denny JC, Zuvich RL, Crawford DC, Schildcrout JS, Bastarache L, Ramirez AH, Mosley JD, Pulley JM, Basford MA, Bradford Y, Rasmussen LV, Pathak J, Chute CG, Kullo IJ, McCarty CA, Chisholm RL, Kho AN, Carlson CS, Larson EB, Jarvik GP, Sotoodehnia N; Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) QRS Group, Manolio TA, Li R, Masys DR, Haines JL, Roden DM. 2013. Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk. Circulation 127: 1377-1385. PubMed ID: 23463857
  • Savio-Galimberti E, Weeke P, Muhammad R, Blair M, Ansari S, Short L, Atack TC, Kor K, Vanoye CG, Olesen MS, LuCamp, Yang T, George AL Jr, Roden DM, Darbar D. 2014. SCN10A/Nav1.8 modulation of peak and late sodium currents in patients with early onset atrial fibrillation. Cardiovascular Research 104: 355-363. PubMed ID: 25053638
  • Shipton EA. 2013. Skin matters: Identifying pain mechanisms and predicting treatment outcomes. Neurology Research International 2013: 329364. PubMed ID: 23766902
  • Themistocleous AC, Ramirez JD, Serra J, Bennett DL. 2014. The clinical approach to small fibre neuropathy and painful channelopathy. Practical Neurology 0: 1-12. PubMed ID: 24778270
  • van den Boogaard M, Smemo S, Burnicka-Turek O, Arnolds DE, van de Werken HJ, Klous P, McKean D, Muehlschlegel JD, Moosmann J, Toka O, Yang XH, Koopmann TT, Adriaens ME, Bezzina CR, de Laat W, Seidman C, Seidman JG, Christoffels VM, Nobrega MA, Barnett P, Moskowitz IP. 2014. A common genetic variant within SCN10A modulates cardiac SCN5A expression. Journal of Clinical Investigation 124: 1844-1852. PubMed ID: 24642470
  • Verkerk AO, Remme CA, Schumacher CA, Scicluna BP, Wolswinkel R, de Jonge B, Bezzina CR, Veldkamp MW. 2012. Functional Nav1.8 channels in intracardiac neurons: the link between SCN10A and cardiac electrophysiology. Circulation Research 111: 333-343. PubMed ID: 22723301
  • Zhang XY, Wen J, Yang W, Wang C, Gao L, Zheng LH, Wang T, Ran K, Li Y, Li X, Xu M, Luo J, Feng S, Ma X, Ma H, Chai Z, Zhou Z, Yao J, Zhang X, Liu JY. 2013. Gain-of-function mutations in SCN11A cause familial episodic Pain. American Journal of Human Genetics 93: 957–966. PubMed ID: 24207120
  • Zhao J, O'Leary ME, Chahine M.Regulation of Nav1.6 and Nav1.8 peripheral nerve Na+ channels by auxiliary β-subunits. 2011. Journal of Neurophysiolpgy 106: 608-619. PubMed ID: 21562192
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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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