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Familial Hemiplegic Migraine 1 (FHM1) via the CACNA1A 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
4293 CACNA1A$1290.00 81407 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

Previous studies have shown that 4% to 94% of FHM cases may be FHM1, depending on the specific population being assessed. For example, in a study conducted in the United States, 15 of 16 probands of families affected by hemiplegic migraine and cerebellar signs harbored sequence variants in the CACNA1A gene (94%; Ducros et al. 2001). On the other hand, in a study involving Spanish patients with FHM, 4 out of 18 patients presented causative sequence variants in the CACNA1A gene (22%; Carreno et al. 2013). A Danish investigation showed that only 7% of FHM cases were of the FHM1 type (Thomsen et al. 2007). An Australian-based study reported that 7 out of 168 patients with FHM tested positive for pathogenic CACNA1A sequence variants (4%; Stuart et al. 2012).

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Clinical Features

Familial hemiplegic migraine (FHM) is a rare neurologic condition that belongs to the category of migraine with aura, which is an idiopathic, episodic disorder involving the cerebral cortex or the brain stem. The aura generally develops within 5 to 20 minutes after exposure to typical migraine triggers such as food, odor, stress, exertion and head trauma. The aura could then persist for almost an hour. Headache, nausea, or hypersensitivity to light (photophobia) usually develops after the occurrence of aura symptoms, which could last from 4 to 72 hours; however, some FHM cases are headache-free (Thomsen et al. 2002). FHM also results in sensory loss such as paresthesia or numbness of the limbs or the face, and dysphasia or speech impairment (Terwindt et al. 1998). It also affects motor functions, thus resulting in hemiparesis or weakness of the limbs. Most episodes of FHM with aura occur with at least another symptom such as mental retardation, ataxia (lack of muscle coordination), dysarthia (motor speech disorder), or recurrent coma (Jurkat-Rott et al. 2004; Spadaro et al. 2004; Barros et al. 2012). Neurologic symptoms associated with an FHM episode may last for several hours or days, significantly longer than the common migraine headache (Ducros et al. 2001). The onset of FHM is usually earlier than typical cases of migraine headaches, often beginning in the first or second decade of life. The number of FHM attacks decreases with age. Familial hemiplegic migraine type 1 (FHM1) presents with cerebellar symptoms that range from involuntary eye movements (nystagmus) to late-onset, progressive disambiguation (ataxia) (Ophoff et al. 1996). FHM is diagnosed when the following criteria are observed: occurrence of migraine with aura, the developed aura is coupled with prolonged hemiparesis, and the same condition occurs in at least one first-degree relative such as a parent, sibling, or child. Other forms of FHM include FHM2 and FHM3 (Jurkat-Rott et al. 2004; Vahedi et al. 2009).

Genetics

FHM1 is a rare autosomal dominant neurologic disorder caused by variations in the CACNA1A gene, which encodes a voltage-dependent P/Q-type calcium channel subunit alpha-1A. The gene is located on chromosomal band 19p13.2, consists of 47 exons, and is approximately 417 kb in length (Ophoff et al. 1996). A total of 160 pathogenic sequence variants have been reported in the CACNA1A gene, which consist of ~100 missense/nonsense, 11 splicing, 11 small insertions, 15 gross deletions, 1 complex rearrangement, and 4 repeat variations (Stenson et al. 2014). Two other disorders have been associated with sequence variations occurring in the CACNA1A gene, namely episodic ataxia type 2 (EA2) and spinocerebellar ataxia type 6 (SCA6) (Ishikawa et al. 1997; Riant et al. 2010). Phenotype overlap has been reported between FHM1 and SCA6 and EA2; however, significantly greater overlap has been reported between EA2 and SCA6 (Jodice et al. 1997; Alonso et al. 2003).

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.

This test is currently not validated to identify pathogenic variants in the CAG repeat region that lie in the 3’ region of CACNA1A; such mild CAG expansions have been primarily associated with spinocerebellar ataxia 6 (Ishikawa et al. 1997).

Indications for Test

The ideal CACNA1A test candidates are individuals who experience hemiplegic migraine with aura involving the cerebral cortex or the brain stem, visual disturbances, paresthesia, and dysphasia. The most significant criterion in diagnosing FHM is hemiparesis or weakness of a limb (Thomsen et al. 2002). Visual disturbances may occur in the form of blind spots (scotoma), flashing lights (photopsia), zigzag patterns (fortification spectra), and double vision (diplopia). Dyphasia usually develops in right-sided hemiplegia.

Gene

Official Gene Symbol OMIM ID
CACNA1A 601011
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Familial Hemiplegic Migraine Type 1 141500

Related Tests

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

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Alonso I, Barros J, Tuna A, Coelho J, Sequeiros J, Silveira I, Coutinho P. 2003. Phenotypes of spinocerebellar ataxia type 6 and familial hemiplegic migraine caused by a unique CACNA1A missense mutation in patients from a large family. Archives of Neurology 60: 610–614. PubMed ID: 12707077
  • Barros J, Mendes A, Matos I, Pereira-Monteiro J. 2012. Psychotic aura symptoms in familial hemiplegic migraine type 2 (ATP1A2). Journal of Headache Pain 13(7): 581-585. PubMed ID: 22661290
  • Carreño O, Corominas R, Serra SA, Sintas C, Fernández-Castillo N, Vila-Pueyo M, Toma C, Gené GG, Pons R, Llaneza M, Sobrido MJ, Grinberg D, Valverde MÁ, Fernández-Fernández JM, Macaya A, Cormand B. 2013. Molecular Genetics and Genomic Medicine 1(4): 206-222. PubMed ID: 24498617
  • Ducros A, Denier C, Joutel A, Cecillon M, Lescoat C, Vahedi K, Darcel F, Vicaut E, Bousser MG, Tournier-Lasserve E. 2001. The clinical spectrum of familial hemiplegic migraine associated with mutations in a neuronal calcium channel. New England Journal of Medicine 345: 17–24. PubMed ID: 11439943
  • Ishikawa K, Tanaka H, Saito M, Ohkoshi N, Fujita T, Yoshizawa K, Ikeuchi T, Watanabe M, Hayashi A, Takiyama Y, Nishizawa M, Nakano I, Matsubayashi K, Miwa M, Shoji S, Kanazawa I, Tsuji S, Mizusawa H. 1997. Japanese families with autosomal dominant pure cerebellar ataxia map to chromosome 19p13.1-p13.2 and are strongly associated with mild CAG expansions in the spinocerebellar ataxia type 6 gene in chromosome 19p13.1. Amercan Journal of Human Genetics 61(2): 336-346. PubMed ID: 9311738
  • Jodice C, Mantuano E, Veneziano L, Trettel F, Sabbadini G, Calandriello L, Francia A, Spadaro M, Pierelli F, Salvi F, Ophoff RA, Frants RR, Frontali M. 1997. Episodic ataxia type 2 (EA2) and spinocerebellar ataxia type 6 (SCA6) due to CAG repeat expansion in the CACNA1A gene on chromosome 19p. Human Molecular Genetics 6:1973–1978. PubMed ID: 9302278
  • Jurkat-Rott K, Freilinger T, Dreier JP, Herzog J, Göbel H, Petzold GC, Montagna P, Gasser T, Lehmann-Horn F, Dichgans M. 2004. Variability of familial hemiplegic migraine with novel A1A2 Na+/K+-ATPase variants. Neurology 62(10): 1857-1861. PubMed ID: 15159495
  • Kordasiewicz HB, Thompson RM, Clark HB, Gomez CM. 2006. C-termini of P/Q-type Ca2+ channel alpha1A subunits translocate to nuclei and promote polyglutamine-mediated toxicity. Human Molecular Genetics 15(10): 1587-1599. PubMed ID: 16595610
  • Ophoff R.A. et al. 1996. Cell 87: 543-52. PubMed ID: 8898206
  • Riant F, Lescoat C, Vahedi K, Kaphan E, Toutain A, Soisson T, Wiener-Vacher SR, Tournier-Lasserve E. 2010. Identification of CACNA1A large deletions in four patients with episodic ataxia. Neurogenetics 11(1): 101-106. PubMed ID: 19633872
  • Spadaro M, Ursu S, Lehmann-Horn F, Veneziano L, Antonini G, Giunti P, Frontali M, Jurkat-Rott K. 2004. A G301R Na+/K+ -ATPase mutation causes familial hemiplegic migraine type 2 with cerebellar signs. Neurogenetics 5(3): 177-185. PubMed ID: 15459825
  • Stenson P.D. et al. 2014. Human Genetics. 133: 1-9. PubMed ID: 24077912
  • Stuart S. et al. 2012. Twin Research and Human Genetics 15: 120-5. PubMed ID: 22784462
  • Terwindt G, Kors E, Haan J, Vermeulen F, Van Den Maagdenberg A, Frants R, Ferrari M. 2003. Mutation analysis of the CACNA1A calcium channel subunit gene in 27 patients with sporadic hemiplegic migraine. Headache 43: 303. PubMed ID: 12056940
  • Thomsen LL, Eriksen MK, Roemer SF, Andersen I, Olesen J, Russell MB. 2002. A population-based study of familial hemiplegic migraine suggests revised diagnostic criteria. Brain 125(Pt 6): 1379-1391. PubMed ID: 12023326
  • Thomsen LL, Kirchmann M, Bjornsson A, Stefansson H, Jensen RM, Fasquel AC, Petursson H, Stefansson M, Frigge ML, Kong A, Gulcher J, Stefansson K, Olesen J. 2007. The genetic spectrum of a population-based sample of familial hemiplegic migraine. Brain 130(Pt 2): 346-356. PubMed ID: 17142831
  • Vahedi K, Depienne C, Le Fort D, Riant F, Chaine P, Trouillard O, Gaudric A, Morris MA, Leguern E, Tournier-Lasserve E, Bousser MG. 2009. Elicited repetitive daily blindness: a new phenotype associated with hemiplegic migraine and SCN1A mutations. Neurology 72(13): 1178-1183. PubMed ID: 19332696
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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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