Invitae Glycine Encephalopathy Panel

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  • Test code: 06143
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top tube
  • Alternate specimens:
    DNA or saliva/assisted saliva
  • Sample requirements
  • Request a sample kit
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Test description

The Invitae Glycine Encephalopathy Panel analyzes 6 genes associated with glycine encephalopathy, also referred to as nonketotic hyperglycinemia (NKH). This test is useful for the diagnosis of individuals in whom glycine encephalopathy is suspected due to clinical symptoms or biochemical findings. This test may help distinguish neonatal glycine encephalopathy from transient glycine encephalopathy. Identification of disease-causing variants provides accurate risk assessment and carrier status for at-risk relatives.

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Primary panel (6 genes)

AMT GCSH GLDC LIAS NFU1 SLC6A9

Alternative tests to consider

For a broader analysis of the genetics of metabolic conditions:

Glycine encephalopathy – also known as nonketotic hyperglycinemia (NKH)

  • non-ketotic hyperglycinemia (NKH)
  • neonatal glycine encephalopathy
  • late-onset glycine encephalopathy
  • transient glycine encephalopathy
  • variant glycine encephalopathy

Gene Disorder Inheritance pattern
AMT Glycine encephalopathy (GCE) Autosomal recessive
GCSH
GLDC
LIAS Hyperglycinemia, lactic acidosis, and seizures (HGCLAS), also known as pyruvate dehydrogenase lipoic acid synthetase deficiency (PDHLD)
NFU1 multiple mitochondrial dysfunctions syndrome 1 (MMDS1)
SLC6A9 Glycine encephalopathy with normal serum glycine

Glycine encephalopathy is an inborn error of glycine metabolism that most commonly presents in the neonatal period. Patients with this disorder are not able to metabolize glycine properly due to a defect in the glycine cleavage system. This defect leads to toxic accumulation of glycine, especially in the brain. The age of onset in patients with glycine encephalopathy can range from neonatal to adulthood, with the most severely affected individuals presenting in the neonatal period.

Patients with glycine encephalopathy have hyperglycinemia that is detectable in both plasma and CSF. These patients will also have an elevated CSF-to-plasma glycine ratio (>0.08 in severe patients; note that this value can be lower in late-onset patients). The absence of acidosis and ketosis is important in distinguishing this disorder from other causes of hyperglycinemia (e.g., propionic acidemia, methylmalonic acidemia).

Neonatal glycine encephalopathy
This is the most common clinical subtype of glycine encephalopathy. Most patients are normal at birth but can present as early as a few hours of life. Symptoms include progressive encephalopathy leading to lethargy, muscular hypotonia, apneic attacks, hiccups, seizures, burst suppression pattern on EEG, coma, and early death. The vast majority of patients that do survive the first 15 months of life show severe intellectual impairment (IQ<20) and motor disability (inability to sit or grasp objects).

Late-onset glycine encephalopathy
This phenotype presents anytime from infancy to adulthood and has a heterogeneous clinical picture. The late-onset form may include features such as intellectual disability, hypotonia, choreic movement disorder, aggressiveness, attention deficit hyperactivity disorder (ADHD), confusion triggered by fever, and, although rarely, seizures.

Transient glycine encephalopathy
This phenotype has been reported in a few patients. These patients may present with symptoms similar to neonatal glycine encephalopathy, though the biochemical elevations typically normalize by the third month of life. Differentiating neonatal glycine encephalopathy from transient glycine encephalopathy based on biochemical findings alone is difficult. Transient glycine encephalopathy may be due to delayed maturation of the glycine cleavage system, high residual activity of the glycine cleavage system in the presence of two pathogenic variants, or a heterozygous individual.

Hyperglycinemia, lactic acidosis, and seizures (HGCLAS)
Caused by pathogenic variants in the LIAS gene, is a severe disorder characterized by a clinical picture similar to that of neonatal glycine encephalopathy. It represents a distinct, ‘variant’ form of nonketotic hyperglycinemia. Individuals typically present with hypotonia, seizures, and increased serum glycine and lactate within the first days of life, followed by development of encephalopathy and/or severe psychomotor delays, which may result in childhood death. Unlike classic glycine encephalopathy, HGCLAS appears to be caused by mitochondrial lipoate biosynthesis defects.

Multiple mitochondrial dysfunctions syndrome 1 (MMDS1)
Caused by pathogenic variants in the NFU1 gene, is another ‘variant’ form of glycine encephalopathy, characterized by infantile-onset neuronal deterioration, vacuolating leukoencephalopathy, lactic acidosis, and pulmonary hypertension. Biochemical studies show increased levels of plasma, urinary, and CSF glycine. The disorder is typically fatal by early childhood.

Glycine encephalopathy with normal serum glycine
Caused by pathogenic variants in the SLC6A9 gene, is characterized by features of severe neonatal glycine encephalopathy along with arthrogryposis multiplex congenita, joint hyperlaxity, and respiratory issues. Biochemical studies show increased CSF glycine and normal to mildly increased serum glycine, which differs from classic forms of glycine encephalopathy. The disorder is typically fatal in infancy.

In individuals with a biochemical diagnosis of glycine encephalopathy (elevated plasma and CSF glycine with an increased CSF-to-plasma glycine ratio), approximately 90%–95% will have two pathogenic variants in the AMT, GCSH, or GLDC gene. Pathogenic variants in GLDC are the most commonly identified in individuals with glycine encephalopathy (70%–75%), followed by AMT (20%) and GCSH (<1%). Approximately 5% of individuals with an enzymatically confirmed diagnosis of glycine encephalopathy do not have a pathogenic variant in any of the aforementioned genes, and may have a variant form of glycine encephalopathy.

Glycine encephalopathy is inherited in an autosomal recessive manner.

Glycine encephalopathy is a fully penetrant disorder. Patients with little or no residual enzyme activity typically have the severe neonatal presentation, and patients with higher residual enzyme activity have the attenuated, late-onset form. Phenotypic expression in the late-onset form is heterogeneous, ranging from mild language delay, intellectual disability, and chorea to pulmonary hypertension with rapid neurological deterioration.

The general prevalence of glycine encephalopathy is unknown. The birth incidence in several subpopulations have been estimated as follows:

  • British Columbia: 1 in 63,495
  • Finland: 1 in 55,000
  • Northern Finland: 1 in 12,000
  • Tunisia: 1 in 21,088

Some small, consanguineous Arab villages in Israel have a higher incidence of glycine encephalopathy.

  1. Applegarth, DA, et al. Incidence of inborn errors of metabolism in British Columbia, 1969-1996. Pediatrics. 2000; 105(1):e10. PMID: 10617747
  2. Baker, PR, et al. Variant non ketotic hyperglycinemia is caused by mutations in LIAS, BOLA3 and the novel gene GLRX5. Brain. 2014; 137(Pt 2):366-79. PMID: 24334290
  3. Dulac O, Rolland M-O. Inborn metabolic diseases: diagnosis and treatment. 5th ed. Heidelberg: Springer; 2012. Chapter 24, Nonketotic Hyperglycinemia (Glycine Encephalopathy); p. 349–356.
  4. Hadj-Taieb, S, et al. Aminoacidopathies and organic acidurias in Tunisia: a retrospective survey over 23 years. Tunis Med. 2012; 90(3):258-61. PMID: 22481200
  5. Hennermann, JB, et al. Prediction of long-term outcome in glycine encephalopathy: a clinical survey. J. Inherit. Metab. Dis. 2012; 35(2):253-61. PMID: 22002442
  6. Koyata, H, Hiraga, K. The glycine cleavage system: structure of a cDNA encoding human H-protein, and partial characterization of its gene in patients with hyperglycinemias. Am. J. Hum. Genet. 1991; 48(2):351-61. PMID: 1671321
  7. Kure, S, et al. Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia. Hum. Mutat. 2006; 27(4):343-52. PMID: 16450403
  8. Kure, S, et al. Heterozygous GLDC and GCSH gene mutations in transient neonatal hyperglycinemia. Ann. Neurol. 2002; 52(5):643-6. PMID: 12402263
  9. Kurolap, A, et al. Loss of Glycine Transporter 1 Causes a Subtype of Glycine Encephalopathy with Arthrogryposis and Mildly Elevated Cerebrospinal Fluid Glycine. Am. J. Hum. Genet. 2016; 99(5):1172-1180. PMID: 27773429
  10. Navarro-Sastre, A, et al. A fatal mitochondrial disease is associated with defective NFU1 function in the maturation of a subset of mitochondrial Fe-S proteins. Am. J. Hum. Genet. 2011; 89(5):656-67. PMID: 22077971
  11. Toone, JR, et al. Biochemical and molecular investigations of patients with nonketotic hyperglycinemia. Mol. Genet. Metab. 2000; 70(2):116-21. PMID: 10873393
  12. Van, Hove, J, et al. Glycine Encephalopathy. 2002 Nov 14. In: Pagon, RA, et al, editors. GeneReviews(®) (Internet). University of Washington, Seattle. PMID: 20301531
  13. von, Wendt, L, et al. Nonketotic hyperglycinemia. A genetic study of 13 Finnish families. Clin. Genet. 1979; 15(5):411-7. PMID: 445864

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
AMT NM_000481.3
GCSH NM_004483.4
GLDC NM_000170.2
LIAS NM_006859.3
NFU1 NM_001002755.2
SLC6A9 NM_201649.3