Invitae Elevated Phenylalanine Panel


Test description

The Invitae Elevated Phenylalanine Panel analyzes five genes that are known to cause increased phenylalanine on newborn screening (NBS) or plasma amino acid analysis. Hyperphenylalaninemia is most commonly due to impaired function of phenylalanine hydroxylase (PAH), the enzyme that catabolizes the amino acid phenylalanine to tyrosine, but it can also be due to defects in the regeneration or biosynthesis of the enzyme co-factor tetrahydrobiopterin (BH4).

Any individual with a positive newborn screen for phenylketonuria (PKU), elevated plasma phenylalanine, abnormal urine pterins (tetrahydrobiopterin compounds), or a suspected diagnosis of hyperphenylalaninemia based on clinical presentation or laboratory results should be tested for hyperphenylalaninemias. Age of diagnosis and subsequent metabolic management are some of the greatest determinants of long-term outcome.

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Primary panel (5 genes)


  • 6-pyruvoyltetrahydropterin synthase
  • GTP cyclohydrolase deficiency (dopa-responsive dystonia)
  • phenylketonuria, tetrahydrobiopterin deficient hyperphenylalaninemia
  • pterin-4-α -carbinolamine dehydratase deficiency
  • quinoid dihydropteridine reductase deficiency

The hyperphenylalaninemias are a diverse group of conditions that result from the disruption of phenylalanine homeostasis. This disruption can occur due to impaired catabolism of the amino acid phenylalanine by the enzyme phenylalanine hydroxylase (PAH), causing phenylketonuria (PKU); it can also occur due to defects of the enzymatic cofactor tetrahydrobiopterin (BH4):

An affected individual is homozygous or compound heterozygous for pathogenic variants in the same gene (except for GCH1, which has autosomal recessive and dominant forms). Biallelic variants in any of the five genes can cause hyperphenylalaninemia.

Gene Function Clinical condition
GCH1 Tetrahydrobiopterin biosynthesis GTP cyclohydrlase deficiency (a.k.a. dopa-responsive dystonia)
PAH Phenylalanine catabolism Phenylketonuria
PCBD1 Tetrahydrobiopterin recycling Pterin-4-α -carbinolamine dehydratase deficiency
PTS Tetrahydrobiopterin biosynthesis 6-pyruvoyltetrahydropterin synthase (PTS)
QDPR Tetrahydrobiopterin recycling Quinoid dihydropteridine reductase deficiency

Phenylketonuria (PKU) is the most common cause of hyperphenylalaninemia and is due to a deficiency of the enzyme phenylalanine hydroxylase (PAH). This enzyme catalyzes the hydroxylation of the amino acid phenylalanine to tyrosine. Reduction in PAH activity leads to a metabolic block with the accumulation of excess phenylalanine and metabolic byproducts such as phenylketones. Additionally, there is a reduction of tyrosine (a precursor for neurotransmitter synthesis), so neurotransmitter production and other downstream pathways are also impacted.

Phenylketonuria has wide clinical heterogeneity ranging from benign hyperphenylalaninemia to severe, classic PKU. All forms present with a normal birth and neonatal period, but excess phenylalanine is neurotoxic and, if left untreated, a progressive, insidious neurocognitive impairment occurs proportionate to the phenylalanine elevation. Symptoms can include microcephaly, epilepsy, mental retardation, behavior problems, eczema, pigmentation lighter than the family constellation, decreased myelin formation, and reduced dopamine, norepinephrine, and serotonin production. Additionally, excessive phenylalanine and its metabolic byproduct, phenylketones, have been attributed to the musty/mousy odor detectable in some untreated individuals.

All forms of PAH-hyperphenylalaninemia are treatable with dietary phenylalanine restriction commensurate to the amount of residual PAH activity. Classic, severe cases tolerate <500 mg dietary phenylalanine/day; mild to moderate phenylketonurics tolerate approximately <700 mg of phenylalanine, and benign hyperphenylketonurics maintain a plasma phenylalanine level of 10 mg/dL (<600 umol/L) on an unrestricted diet (normal <2 mg/dL). Affected individuals that are detected in the newborn period and placed on a phenylalanine-restricted diet can achieve normal intelligence, though there is an increased risk for learning difficulties and emotional problems despite the most stringent metabolic control. Any dietary interventions must be managed by a metabolic nutritionist to avoid any nutritional deficiencies.

Less common hyperphenylalaninemias are due to defects in tetrahydrobiopterin (BH4) biosynthesis or recycling. BH4 serves as a cofactor for PAH, the amino acid hydroxylases tyrosine hydroxylase (TH) and tryptophan hydroxylase (TPH), nitric oxide synthase, and glyceryl-ether monooxygenase. TH and TPH are involved in biosynthesis of the neurotransmitters dopamine and serotonin, so BH4 defects alter neurotransmitter levels, which results in significant neurologic symptoms.

Pathogenic variants in GCH1 and PTS result in the BH4 biosynthesis disorders GTP cyclohydrolase deficiency (aka dopa-responsive dystonia) and 6-pyruvoyltetrahydropterin synthase deficiency.

GTP cyclohydrolase deficiency presents with an autosomal dominant and an autosomal recessive form. Approximately 90% of individuals present with the autosomal dominant form, which is typically characterized by a postural dystonia that appears around age six years (often the foot), then subsides around ten years of age, when a postural tremor appears; later, parkinsonism develops. Diurnal fluctuation of the symptoms (increase of symptoms in the evening and lessening in the morning) is characteristic of the condition. Intellectual function generally remains normal, as does autonomic function. This form is remarkably responsive to low doses of oral L-dopa supplementation. The recessive form presents with hyperphenylalaninemia within the first six months of life, significant developmental delay, truncal hypotonia, hypertonia of the extremities, tremors, seizures, and, at times, autonomic dysfunction. Treatment involves oral L-dopa replacement and BH4 supplementation.

PTS deficiency presents with severe and attenuated forms. The severe form results in a clinical presentation similar to that of autosomal dominant GCH1 deficiency and includes hyperphenylalaninemia and neurotransmitter deficiencies. The initial presentation includes abnormal movements and developmental delay in the first few months of life. The attenuated form is considered peripheral and has an excellent prognosis with treatment that includes supplemental BH4 and dietary phenylalanine restriction.

Pathogenic variants in PCBD1 and QDPR lead to complications of biopterin recycling. Variants in PCBD1 cause elevated levels of phenylalanine and urine pterins (though neurotransmitter levels are normal) and result in a clinically benign condition. Affected individuals are usually picked up through newborn screening and reported cases have remained asymptomatic without treatment. Pathogenic variants in QDPR often leads to severe developmental delay, brain abnormalities, and sudden death for incompletely understood reasons. Treatment involves any combination of dietary phenylalanine restriction and BH4 and neurotransmitter supplementation; the degree of responsiveness varies.

For patients with a biochemical diagnosis of hyperphenylalaninemia, at least 97% will have two pathogenic variants in PAH. The remaining <3% will have a BH4 defect.
Of the <3% with a BH4 defect:

  • approximately 60% are due to 6-pyruvoyltetrahydropterin synthase (PTS) deficiency
  • approximately 30% are due to quinoid dihydropteridine reductase deficiency (QDPR)
  • approximately 5% are due to GTP cyclohydrolase deficiency
  • approximately 5% are due to pterin-4-α-carbinolamine dehydratase deficiency (PCBD1)

Variants in PAH, PTS, PCBD1, and QDPR are inherited in an autosomal recessive manner. GCH1 variants have autosomal recessive and dominant inheritance; 90% of cases are dominantly inherited. Females are affected more frequently by variants in GCH1 (2:1) than males (6:1). Additionally, greater penetrance of GCH1 variants has been reported in females (87%–100% penetrance) than in males (35%–55% penetrance).

The general population incidence of PAH hyperphenylalaninemia is 1 in 10,000–20,000. Incidence varies on country of origin and has been reported at 1 in 2600 in Turkey and 1 in 143,000 in Japan. An estimated <3% of hyperphenylalaninemia cases are due to a BH4 defect.

This panel may be appropriate for any individual with:

  • an elevated plasma phenylalanine level on plasma amino acid analysis
  • an elevated plasma phenylalanine level on newborn screening
  • abnormal urine pterin screening

For considerations for testing please refer to:

  1. American College of Medical Genetics. NBS ACT Sheet. Phenylketonuria (PKU). Accessed February 2016.
  2. Blau N, Thöny B, Cotton RH, Hyland K. The online metabolic and molecular bases of inherited disease. New York: McGraw-Hill; retrieved January 2016. Chapter 78, Disorders of tetrahydrobiopterin and related biogenic amines.
  3. Duch, DS and Smith, GK. Biosynthesis and function of tetrahydrobiopterin. J. Nutrit Biochem. 1991; 2(8):411-23.
  4. Furukawa, Y. GTP Cyclohydrolase 1-Deficient Dopa-Responsive Dystonia. 2002 Feb 21. In: Pagon, RA, et al, editors. GeneReviews(®) (Internet). University of Washington, Seattle. PMID: 20301681
  5. Longo, N. Disorders of biopterin metabolism. J. Inherit. Metab. Dis. 2009; 32(3):333-42. PMID: 19234759
  6. Mitchell, JJ. Phenylalanine Hydroxylase Deficiency. 2000 Jan 10. In: Pagon, RA, et al, editors. GeneReviews(®) (Internet). University of Washington, Seattle. PMID: 20301677
  7. Segawa, M, et al. Autosomal dominant guanosine triphosphate cyclohydrolase I deficiency (Segawa disease). Ann. Neurol. 2003; 54 Suppl 6:S32-45. PMID: 12891652
  8. Thöny, B, Blau, N. Mutations in the BH4-metabolizing genes GTP cyclohydrolase I, 6-pyruvoyl-tetrahydropterin synthase, sepiapterin reductase, carbinolamine-4a-dehydratase, and dihydropteridine reductase. Hum. Mutat. 2006; 27(9):870-8. PMID: 16917893
  9. Thöny, B, et al. Mutations in the pterin-4alpha-carbinolamine dehydratase (PCBD) gene cause a benign form of hyperphenylalaninemia. Hum. Genet. 1998; 103(2):162-7. PMID: 9760199
  10. Waisbren, S, White, DA. Screening for cognitive and social-emotional problems in individuals with PKU: tools for use in the metabolic clinic. Mol. Genet. Metab. 2010; 99 Suppl 1:S96-9. PMID: 20123479

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence, and select noncoding variants. Our assay provides a Q30 quality-adjusted mean coverage depth of 350x (50x minimum, or supplemented with additional analysis). Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods, except individual variants that have high quality scores and previously validated in at least ten unrelated samples.

Our analysis detects most intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. If you are requesting the detection of a specific single-exon copy number variation, please contact Client Services before placing your order.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
GCH1 NM_000161.2
PAH NM_000277.1
PCBD1 NM_000281.3
PTS NM_000317.2
QDPR NM_000320.2