Dystonia Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
3017 ANO3 81479,81479 Order Options and Pricing
ATP1A3 81479,81479
CYP27A1 81479,81479
DDC 81479,81479
GCH1 81405,81479
GNAL 81479,81479
PNKD 81406,81479
PRKRA 81479,81479
PRRT2 81479,81479
SGCE 81406,81405
SLC2A1 81405,81479
SPR 81479,81479
TAF1 81479,81479
TH 81406,81479
THAP1 81404,81479
TOR1A 81404,81479
TUBB4A 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
3017Genes x (17)81479 81404, 81405, 81406, 81479 $890 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our PGxome Custom Panel tool.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

For Reflex to PGxome pricing click here.

Turnaround Time

18 days on average for standard orders or 14 days on average for STAT orders.

Once a specimen has started the testing process in our lab, the most accurate prediction of TAT will be displayed in the myPrevent portal as an Estimated Report Date (ERD) range. We calculate the ERD for each specimen as testing progresses; therefore the ERD range may differ from our published average TAT. View more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

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Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Dystonia has been recently redefined by an international panel as: “a movement disorder characterized by sustained and intermittent muscle contractions, causing abnormal, often repetitive, movements, postures or both. Dystonic movements are typically patterned, twisting and may be tremulous. Dystonia is often initiated or worsened by voluntary action and associated with overflow muscle activation” (Albanese et al. 2013. PubMed ID: 23649720). Dystonia can affect muscles in many parts of the body. Examples of dystonic movements include: oromandibular dystonia (face, jaw, and tongue), cervical dystonia (i.e. torticollis and laterocollis of the neck), limb dystonia (legs, feet, hands, arms), laryngeal dystonia or spasmodic dysphonia (vocal cords), and belpharospasm (excessive blinking and forceful closure of eyelids) (Pablo-Fernandez and Warner. 2017. PubMed ID: 28910989). Dystonic movements are uncontrollable, painful, and for some patients can be disabling (Dystonias Fact Sheet). Dystonia is a clinically heterogeneous disorder and is classified according to 4 major criteria: 1) age of onset, 2) body distribution, 3) temporal pattern, and 4) occurrence in the absence or presence of other features (e.g. movement, neurological, or metabolic disorders) (Klein et al. 2017. PubMed ID: 20301334).  

The onset of dystonia can occur at any age from infancy to late adulthood. Determination of age of on-set is beneficial for diagnostic testing and prognosis evaluation as patients with earlier onset tend to have a more severe and progressive disease course than patients with later onset. Some patients experience dystonia in only one part of their body, known as focal dystonia. Other patients experience dystonia in two or more parts of their body. These patients are further classified based on the affected body regions:  segmental (contiguous body regions), multifocal (non-contiguous body regions), hemidystonia (ipsilateral body regions), and generalized (three or more parts of the body are affected, including the trunk and one leg). For patients that have severe forms of dystonia, symptoms can often begin focally and then progress to a generalized form. (Klein et al. 2017. PubMed ID: 20301334)

Temporal patterns for dystonia can be persistent throughout the day, action-specific (e.g. writer’s cramp), diurnal, or paroxysmal (triggered by events such as a sudden movement, fatigue, and consumption of coffee or alcohol). Dystonia can occur in the absence or presence of other features. The term “isolated dystonia” is used to classify patients that present with dystonia and have no evidence of brain degeneration or other disease features (Klein et al. 2017. PubMed ID: 20301334). Combined dystonia occurs patients present with dystonia plus additional movement phenotypes such as Parkinsonism, myoclonus, and dyskinesia (Weissbach et al. 2020. PubMed ID: 33099685). Complex dystonia is the co-occurrence of dystonia with other neurological or systemic disorders. There are many types of disorders that can include dystonia (e.g. Huntington disease, Wilson disease, and Krabbe disease); however, dystonia may not be a prominent or consistent feature of these diseases (For a list of disorders see Klein et al. 2017. PubMed ID: 20301334).

Behind essential tremor and Parkinson disease, dystonia is the 3rd most common movement disorder (American Association of Neurological Surgeons). Dystonia, in its various forms, affects people worldwide with a higher incidence in women than in men. Adult on-set isolated dystonia is the most common form of dystonia and is estimated to affect about 16 in 100,000 individuals (Steeves et al. 2012. PubMed ID: 23114997), with cervical dystonia being the most prevalent (~5 out of 100,000 cases) (Pablo-Fernandez and Warner. 2017. PubMed ID: 28910989). Steeves et al. speculated that the number of isolated dystonia cases may be an underestimate as many cases of dystonia go undiagnosed or misdiagnosed. Combined dystonia represents a much smaller subgroup when compared to isolated dystonia, and although prevalence data is limited, it has been estimated to occur at a rate of <20-25% of isolated dystonia (The International Parkinson and Movement Disorder Society). 

Dystonia can be inherited or acquired (traumatic brain injury, drug/pharmaceutical use, and infections). Evaluation of physical symptoms, family history, and laboratory testing which can include blood and urine tests, brain imaging, and EMG measurements can all aid in the diagnosis of dystonia. Although clinical classification guidelines have been developed, extensive phenotypic overlap exists between some forms of dystonia and can make diagnosis based on phenotype alone challenging (Klein et al. 2017. PubMed ID: 20301334; Pablo-Fernandez and Warner. 2017. PubMed ID: 28910989). Molecular genetic testing can help determine whether a patient has an inherited from of dystonia and can assist in proper diagnosis, prognosis prediction, therapeutic planning, and reproductive planning. A study analyzing both whole genome and exome sequencing of patients with different forms of dystonia was able to identify a genetic diagnosis for ~12% of those patients. The diagnostic yield was highest among patients that were young at the time of testing, had an earlier age of dystonia onset, and had a combined dystonia phenotype (Kumar et al. 2019. PubMed ID:  31731261).

There is no cure for dystonia; however, several therapies such as Botulinum toxin (Botox) injections, deep brain stimulation, and medications can be administered to help manage symptoms. Of note, patients with combined forms of dystonia related to genetic variants in the GCH1, TH, or SPR genes have shown benefit from treatment with Levodopa (Cloud and Jinnah. 2012. PubMed ID: 20001425). 

Genetics

About 20% of dystonia cases are familial (Lohmann and Klein. 2017. PubMed ID: 28283962). Dystonia is genetically heterogeneous, and to date, fifteen genes with >600 pathogenic variants have been confirmed to be involved in the etiology of isolated and combined dystonia: TOR1A, THAP1, GNAL, ANO3, TAF1, GCH1, TH, SPR, ATP1A3, PRKRA, SGCE, PNKD, PRRT2, SLC2A1, and TUBB4A (Klein et al. 2017. PubMed ID: 20301334; Lohmann and Klein. 2017. PubMed ID: 28283962). These genes along with two genes associated with complex dystonia, DDC and CYP27A1, are included in this test. In most cases of familial dystonia, the disease is inherited in an autosomal dominant manner with variable penetrance and expressivity. However, autosomal recessive inheritance is documented in several families with combined dystonia, and X-linked inheritance is associated with variants in the TAF1 gene. The genes included in this panel are summarized in the following table.

Gene Associated Features or Disease Traditional Nomenclature Inheritance Additional Phenotypic Information Average Age of Onset (Age Range)
Isolated Dystonia
TOR1A N/A DYT1 AD Early-onset, generalized dystonia 13 years (1-28 years)
THAP1 N/A DYT6 AD Adolescent-onset mixed type dystonia 19 years (5-38 years)
GNAL N/A DYT25 AD Adult onset craniocervical dystonia ~40 years (7-54 years)
ANO3 N/A DYT24 AD Adult onset craniocervical dystonia (19-39 years)
Combined Dystonia
TUBB4A With  leukoencephalopathy DYT4 AD Adolescent-adult onset mixed dystonia (whispering dysphonia) 31 years (7-87 years)
TAF1 With neurodevelopmental disorder DYT3 X-linked Severe Neonatal
GCH1 With Parkinsonism DYT5a AD Dopa-responsive dystonia ~6 years
TH With Parkinsonism DYT5b AR Dopa-responsive dystonia (12 months – 12 years)
SPR With Parkinsonism Not assigned AR Dopa-responsive dystonia and cognitive impairment  
ATP1A3 With Parkinsonism DYT12 AD Rapid-onset dystonia 23 years (3 – 59 years)
PRKRA With Parkinsonism DYT16 AR Young-onset dystonia (2-18 years)
SGCE With Myoclonus DYT11 AD Early onset and psychiatric features 10th – 20th decade (6 months – 80 years)
PNKD Paroxysmal and dyskinesia DYT8 AD Paroxysmal nonkinesigenic dyskinesia (1-20 years)
PRRT2 Paroxysmal and dyskinesia DYT10 AD Paroxysmal kinesigenic choreoathetosis and infantile convulsions 10 years (1-20 years)
SLC2A1 Paroxysmal and dyskinesia DYT18 AD Paroxysmal exertion-induced dyskinesia  
Complex Dystonia
DDC Aromatic L-amino acid decarboxylase deficiency (AADCD) N/A AR Dystonia reported in ~54% of AADC cases ~2.5 years
CYP27A1 Cerebrotendinous Xanthomatosis (CTX) N/A AR Dystonia may be underdiagnosed in CTX ~19  years

Dystonia was initially classified based on genetic locus symbols that were assigned to the successive loci identified from genetic linkage analyses of informative families with a history of the various forms of the disease. Twenty five subtypes, designated DYT1 to DYT25, were defined (see column in table). The causative genes for several of these loci have not yet been identified; while several different DYT types corresponded to the same genes. In addition, a few reported loci have not been replicated since the initial publications (Klein et al. 2017. PubMed ID: 20301334; Camargo et al. 2015. PubMed ID: 25992527).

Variants in TAF1 have been associated with an X-linked recessive form of dystonia combined with parkinsonism and severe neurodevelopmental features (XPD) documented mainly in patients from Pany Island in the Philippines (Domingo et al. 2015. PubMed ID: 25604858). The genetic defect in this form of dystonia has not been yet identified. However, linkage and haplotype analyses of affected Pany families mapped the disease locus to a 300-kb region that includes TAF1. Penetrance is complete in male patients with the disease haplotype. Most heterozygote female carriers of the disease haplotype are unaffected. However, clinical features with variable severity have been documented in several female carriers (Westenberger et al. 2013. PubMed ID: 23389859). This test does not include the isoform that contains the c.94C>T (p.Arg32Cys) variant, which is part of the disease haplotype that has been linked to familial dystonia in Pany island. This variant has not been conclusively shown to be causative (Evidente et al. 2018. PubMed ID: 20301662).

Of note, several missense variants in the TAF1 gene have been reported as disease-causing in children with several neurodevelopmental features, including facial dysmorphology, intellectual disability, and dystonia. Evidence for pathogenicity included de novo occurrence of variants in the isolated cases, and co-segregation with the disease phenotype in the familial cases (O’Rawe et al. 2015. PubMed ID: 26637982; Cheng et al. 2020. PubMed ID: 31646703).

The vast majority of variants reported in the dystonia genes included in this test are missense variants. However, protein-truncating, splicing, regulatory, and copy number variants (CNVs) have been reported in many of these genes as well.

Even though multiple genes have been identified as causative for dystonia, our knowledge of how these genes are contributing to the molecular etiology of this disease is still emerging. Unlike Parkinson’s disease where causative factors converge on a single biological pathway, dystonia can result from a wide variety of defects and changes in many different biological pathways throughout the nervous system (Jinnah and Sun. 2019. PubMed ID: 31112762). Despite the functional heterogeneity of dystonia-causing genes, it has been suggested that many of these genes can be linked to a number shared biological pathways such as dopamine signaling, calcium transport, and abnormalities of the cell cycle. Elucidation of these shared pathways has important implications such as understanding how the brain controls movement and the design of new therapeutics (Jinnah and Sun. 2019. PubMed ID: 31112762). Additional postulates of dystonia etiology have been reviewed by Quartarone and Ruge (2018. PubMed ID: 29527184).

See individual gene summaries for more information on molecular biology of gene products and spectra of pathogenic variants.

Clinical Sensitivity - Sequencing with CNV PGxome

TOR1A pathogenic variants have been identified in up to 2.5% of all isolated dystonia and is commonly associated with early onset (Grundmann et al. 2003. PubMed ID: 12975293; Ozelius and Lubarr. 2016. PubMed ID: 20301665). The pathogenic variant c.904_906del (p.Glu303del) in the TOR1A gene has been identified in up to 53% of patients with early-onset isolated dystonia in the non-Jewish populations; and in up to 90% of patients of Ashkenazi Jewish ancestry (Ozelius and Bressman 2011. PubMed ID: 21168499).

THAP1 pathogenic variants have been identified in about 2.5% of patients with cervical dystonia (LeDoux et al. 2016. PubMed ID: 27123488). Founder variants in THAP1 have been identified in Mennonite families, and over 90 pathogenic variants in THAP1 have been reported (Klein et al. 2017. PubMed ID: 20301334)

GNAL pathogenic variants have been identified in about 0.5% of patients with cervical dystonia beginning later in life (LeDoux et al. 2016. PubMed ID: 27123488; Fuchs et al. 2013. PubMed ID: 23222958).

ANO3 pathogenic variants, including de novo variants, have been identified in about 1% of patients with predominantly craniocervical dystonia (Zech et al. 2014. PubMed ID: 25142429; Zech et al. 2017. PubMed ID: 27666935).

Pathogenic variants in TUBB4A appear to be a rare cause of dystonia. To date, only two pathogenic missense variants have been identified in two Australian families with a history of dystonia and spasmodic dysphonia combined with characteristic facies and body habitus and an ataxic gait, which responded well to alcohol (Lohmann et al. 2013. PubMed ID: 23595291; Hersheson et al. 2013. PubMed ID: 23424103). Evidence for pathogenicity included co-segregation with the disease phenotype in the described family.

Pathogenic variants in TAF1 have been reported as disease-causing in unrelated patients with several neurodevelopmental features, including facial dysmorphology, intellectual disability, and dystonia. Evidence for pathogenicity included co-segregation of the variants with the disease phenotype in the familial cases, and de novo occurrence in the sporadic cases (O’Rawe et al. 2015. PubMed ID: 26637982; Cheng et al. 2020. PubMed ID: 31646703). Of note, this test does not include the isoform that contains the c.94C>T (p.Arg32Cys) variant, which is part of the disease haplotype that has been linked to familial dystonia in Pany Island.

GCH1 pathogenic variants (>250) have been identified in up to 87% of patients with clinical diagnosis of dystonia who showed marked and sustained response to levodopa treatment (Hagenah et al. 2005. PubMed ID: 15753436; Clot et al. 2009. PubMed ID: 19491146).

TH pathogenic variants have been identified in about 5% of patients with a clinical diagnosis of dystonia, who showed marked and sustained response to levodopa treatment (Clot et al. 2009. PubMed ID: 19491146).

SPR pathogenic variants have been identified in about 1.5% of patients with clinical diagnosis of dystonia, who showed marked and sustained response to levodopa treatment (Clot et al. 2009. PubMed ID: 19491146).

ATP1A3 pathogenic variants have been identified in about 50% of families with a history of abrupt onset of dystonia with Parkinsonism (Brashear et al. 2007. PubMed ID: 17282997). Over half of the variants reported in patients with this type of dystonia have been de novo (Haq et al. 2019. PubMed ID: 31361359).

PRKRA pathogenic variants have been identified in about 21.5% of patients with clinical diagnosis of progressive generalized dystonia and mild Parkinsonism. These patients do not respond to levodopa therapy (Camargos et al. 2008. PubMed ID: 18243799; Zech et al. 2014. PubMed ID: 25142429). The c.665C>T (p.Pro222Leu) variant has been reported in several patients with this form of dystonia (Quadri et al. 2016. PubMed ID: 26990861).

SGCE pathogenic variants have been identified in up to 50% of familial myoclonus-dystonia cases and in 10-15% of non-familial cases (Raymond et al. 2020. PubMed ID: 20301587). Over 65% of patients with this form of dystonia also had a psychiatric diagnosis. Maternal imprinting has been reported for the SGCE gene, and penetrance is dependent on the parental origin of the allele. The paternally-inherited allele is expressed, while the maternally-inherited alleles are silenced (Klein et al. 2017. PubMed ID: 20301334).

PNKD pathogenic variants have been identified in patients with paroxysmal nonkinesigenic dyskinesia (Chen et al. 2005. PubMed ID: 15824259) which accounts for ~2% of paroxysmal dyskinesia cases (Gardner et al. 2015. PubMed ID: 26598494). The c.20C>T (p.Ala7Val) and c.26C>T (p.Ala9Val) are commonly found in patients with this form of dystonia (Rainier et al. 2004. PubMed ID: 15262732; Lee et al. 2004. PubMed ID: 15496428).  

PRRT2 pathogenic variants have been identified in patients with paroxysmal kinesigenic dyskinesia (Ebrahimi-Fakhari et al. 2018. PubMed ID: 29334453), which represent ~40% of paroxysmal dyskinesia cases. Seventy different variants in PRRT2 have been reported with 95% of these variants leading to protein truncation. The c.649dup (p.Arg217Profs*8) variant accounts for 82% of all these cases. Additionally, deletions of 16p11.2 have also been linked to this type of dystonia, and patients may also have features of intellectual disability (Ebrahimi-Fakhari et al. 2018. PubMed ID: 29334453).

SLC2A1 pathogenic variants have been identified in patients with paroxysmal exercise-induced dyskinesia, which represent ~10% of paroxysmal dyskinesia cases (Gardner et al. 2015. PubMed ID: 26598494). SLC2A1 encodes the GLUT1 transporter.

As part of the complex dystonia group, DDC pathogenic variants cause aromatic L-amino acid decarboxylase deficiency (AADCD). Approximately 85% of patients with AADCD deficiency have a movement disorder and of that ~54% have dystonia (Wassenberg et al. 2017. PubMed ID: 28100251).

As part of the complex dystonia group, CYP27A1 pathogenic variants cause cerebrotendinous xanthomatosis (CTX). In a small study of six CTX patients, dystonia was reported in all six patients. For one patient, dystonia was the major clinical feature and lead to the diagnosis of CTX (Lagrade et al. 2012. PubMed ID: 23115103). Lagrade et al. suggest that dystonia is an underdiagnosed feature of CTX.

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 99.7% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing.

The PRKRA gene, located at 2q31.2, has a haplotype-specific pseudogene (PRKRAψ) located within the HLA DR group of 6p21.3 (Chida et al. 2001. PubMed ID: 11220620). This pseudogene is processed only when the HLA DR53 group is present. It is intron-less and ~99% similar to the eight exon PRKRA gene. Pseudogene specific primers have been developed to verify whether variants are present in the PRKRA gene or its pseudogene.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Indications for Test

Candidates for this test are patients with isolated dystonia; patients with dystonia combined with another movement disorder; and patients with dystonia and additional neurological features, regardless of the age of onset of symptoms and mode of inheritance of the disease. In addition to this panel, PreventionGenetics also offers individual gene tests for all the genes that have been conclusively implicated in dystonia (Klein et al. 2017. PubMed ID: 20301334; Lohmann and Klein. 2017. PubMed ID: 28283962).

Genes

Official Gene Symbol OMIM ID
ANO3 610110
ATP1A3 182350
CYP27A1 606530
DDC 107930
GCH1 600225
GNAL 139312
PNKD 609023
PRKRA 603424
PRRT2 614386
SGCE 604149
SLC2A1 138140
SPR 182125
TAF1 313650
TH 191290
THAP1 609520
TOR1A 605204
TUBB4A 602662
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Name
PGxome®
Autosomal Dominant DOPA-Responsive Dystonia via the GCH1 Gene
Autosomal Recessive DOPA-Responsive Dystonia via the TH Gene
DYT1 Early-Onset Isolated Dystonia via the TOR1A Gene
Infantile Parkinsonism-Dystonia Panel
Parkinson Disease and Parkinsonism Panel

Citations

  • Albanese et al. 2013. PubMed ID: 23649720
  • Brashear et al. 2007. PubMed ID: 17282997
  • Camargo et al. 2015. PubMed ID: 25992527
  • Camargos et al. 2008. PubMed ID: 18243799
  • Chen et al. 2005. PubMed ID: 15824259
  • Cheng et al. 2019. PubMed ID: 31646703
  • Chida et al. 2001. PubMed ID: 11220620
  • Clot et al. 2009. PubMed ID: 19491146
  • Cloud and Jinnah. 2010. PubMed ID: 20001425
  • Domingo et al. 2015. PubMed ID: 25604858
  • Ebrahimi-Fakhari et al. 2018. PubMed ID: 29334453
  • Evidente. 2018. PubMed ID: 20301662
  • Fuchs et al. 2013. PubMed ID: 23222958
  • Gardner et al. 2015. PubMed ID: 26598494
  • Grundmann et al. 2003. PubMed ID: 12975293
  • Hagenah et al. 2005. PubMed ID: 15753436
  • Haq et al. 2019. PubMed ID: 31361359
  • Hersheson et al. 2013. PubMed ID: 23424103
  • Jinnah and Sun. 2019. PubMed ID: 31112762
  • Klein et al. 2017. PubMed ID: 20301334
  • Kumar et al. 2019. PubMed ID: 31731261
  • Lagrade et al. 2012. PubMed ID: 23115103
  • LeDoux et al. 2016. PubMed ID: 27123488
  • Lee et al. 2004. PubMed ID: 15496428
  • Lohmann and Klein. 2017. PubMed ID: 28283962
  • Lohmann et al. 2013. PubMed ID: 23595291
  • Ozelius and Bressman 2011. PubMed ID: 21168499
  • Ozelius and Lubarr. 2016. PubMed ID: 20301665
  • O’Rawe et al. 2015. PubMed ID: 26637982
  • Pablo-Fernandez and Warner. 2017. PubMed ID: 28910989
  • Quadri et al. 2016. PubMed ID: 26990861
  • Quartarone and Ruge. 2018. PubMed ID: 29527184
  • Rainier et al. 2004. PubMed ID: 15262732
  • Raymond et al. 2020. PubMed ID: 20301587
  • Steeves et al. 2012. PubMed ID: 23114997
  • Wassenberg et al. 2017. PubMed ID: 28100251
  • Weissbach et al. 2020. PubMed ID: 33099685
  • Westenberger et al. 2013. PubMed ID: 23389859
  • Zech et al. 2014. PubMed ID: 25142429
  • Zech et al. 2017. PubMed ID: 27666935

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