6-Pyruvoyltetrahydropterin Synthase (PTPS) Deficiency via the PTS Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
11889 PTS 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11889PTS81479 81479(x2) $890 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

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

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

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

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Hyperphenylalaninemias due to tetrahydrobiopterin (BH4) deficiency are a result of a disruption in phenylalanine homeostasis and dopamine and serotonin biosynthesis. These disorders are caused by pathogenic variants in genes encoding enzymes involved in the biosynthesis or regeneration of BH4. The phenylalanine, tyrosine, and tryptophan hydroxylases all require BH4 as a cofactor, and lack of this cofactor results in secondary hyperphenylalaninemia and depletion of the neurotransmitters dopamine and serotonin. Early detection and treatment can reduce or prevent neurologic symptoms (Blau et al. 2014).

The most common of the tetrahydrobiopterin deficiencies is 6-pyruvoyltetrahydropterin synthase (PTPS) deficiency, which accounts for approximately 60% of all BH4 deficiencies (Blau et al. 2014). The phenotype of PTPS deficient patients is classified as severe or mild. The severe form is observed in approximately 80% of patients, and such patients develop neurologic symptoms including psychomotor retardation, delayed development, tonal abnormalities, seizures, and dystonia. Patients may also present with abnormal thermogenesis, microcephaly, swallowing difficulties and hypersalivation (Blau et al. 2014). Biochemically, patients classified with severe PTPS deficiency are found to have abnormal levels of CSF neurotransmitters (Leuzzi et al. 2010; Blau et al. 2014).

PTPS deficient patients diagnosed with the mild form are generally found to be neurologically normal and have normal neurotransmitter levels, although transient tonal abnormalities, sleeping difficulties and other neurological problems are occasionally observed (Leuzzi et al. 2010; Blau et al. 2014). PTPS deficient patients are usually detected via newborn screening due to hyperphenylalaninemia. To distinguish PTPS deficiency from PAH deficiency and other causes of hyperphenylalaninemia, additional studies must be performed, such as a urinary pterin profile, measurement of DHPR enzyme activity, a BH4 loading test, analysis of pterins, folates and neurotransmitters in CSF, and direct PTPS enzyme activity measurement (Ye et al. 2013; Blau et al. 2014). Early diagnosis and treatment is imperative. The neurological outcome, particularly in patients with severe PTPS deficiency, has been shown to be greatly improved if treatment is started before the second month of life (Leuzzi et al. 2010). A phenylalanine-restricted diet is not sufficient to control symptoms in these patients, and many must also be treated with BH4 and neurotransmitter precursor supplementation, although this does not help all patients (Oppliger et al. 1997; Blau et al. 2014).

Genetics

6-Pyruvoyltetrahydropterin synthase deficiency is inherited in an autosomal recessive manner. The PTS gene (chromosome 11q22.3, 6 exons) encodes the PTPS enzyme which is involved in the de novo biosynthesis of tetrahydrobiopterin. More specifically, PTPS converts dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin (Blau et al. 2014). To date, over 80 pathogenic variants have been reported in the PTS gene. The majority of causative variants are missense, although nonsense, splicing, small deletions and insertions, and one gross deletion have all been reported (Human Gene Mutation Database). Pathogenic variants are spread evenly along the coding sequence. Other inborn errors of BH4 metabolism can present with a similar clinical course and involve dihydropteridine reductase (QDPR gene), GTP cyclohydrolase I (GCH1 gene), and pterin-4α-carbinalamine dehydratase (PCBD1 gene) (Blau et al. 2014, Trujillano et al. 2014).

Clinical Sensitivity - Sequencing with CNV PGxome

In a total of 19 patients from different families with a clinical diagnosis of 6-pyruvoyltetrahydropterin synthase (PTPS) deficiency, pathogenic variants were detected by sequencing on 35 out of 38 alleles, suggesting an overall detection rate of ~92% (Leuzzi et al. 2010). Analytical sensitivity should also be high because nearly all reported pathogenic variants thus far are detectable by sequencing.

Testing Strategy

This test provides full coverage of all coding exons of the PTS gene 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 full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

Newborn screening indicative of hyperpheylalaninemia. Patients with decreased homovanillic acid (HVA) and 5-hydroxyindoleacetic acid (5HIAA) in CSF, increased urinary neopterin and decreased biopterin, and a high neopterin/biopterin ratio are good candidates for this test, as are individuals that exhibit clinical symptoms of tetrahydrobiopterin deficiency and family members of patients known to have PTS variants. We will also sequence the PTS gene to determine carrier status.

Gene

Official Gene Symbol OMIM ID
PTS 612719
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
6-Pyruvoyl-Tetrahydropterin Synthase Deficiency AR 261640

Related Tests

Name
Dihydropteridine Reductase (DHPR) Deficiency via the QDPR Gene
Hyperphenylalaninemia Panel
Sepiapterin Reductase (SR) Deficiency via the SPR Gene

Citations

  • Blau N.et al. 2014. Disorders of Tetrahydrobiopterin and Related Biogenic Amines. Online Metabolic & Molecular Bases of Inherited Disease, New York, NY: McGraw-Hill.
  • Human Gene Mutation Database (Bio-base).
  • Leuzzi V. et al. 2010. Clinical Genetics. 77: 249-57.  PubMed ID: 20059486
  • Oppliger T. et al. 1997. Human Mutation. 10: 25-35.  PubMed ID: 9222757
  • Trujillano D. et al. 2014. European Journal of Human Genetics : Ejhg. 22: 528-34. PubMed ID: 23942198
  • Ye J. et al. 2013. Journal of Inherited Metabolic Disease. 36: 893-901.  PubMed ID: 23138986

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

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.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

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.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


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2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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