AMT-Related Glycine Encephalopathy via the AMT Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
5497 AMT 81479 81479,81479 $640 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
5497AMT81479 81479 $640 Order Options and Pricing

Pricing Comments

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

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

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.


Genetic Counselors


Clinical Features and Genetics

Clinical Features

Glycine encephalopathy, also known as nonketotic hyperglycinemia (NKH), is an inborn error of glycine metabolism caused by defects in the glycine cleavage multi-enzyme system (GCS) (Hamosh et al. 2002. PubMed ID: 20301531). Affected children have a large accumulation of glycine in the body resulting in various neurological symptoms. The majority of patients with glycine encephalopathy present in the neonatal period, while some patients can develop the disease in infancy. Regardless of age at onset, 20% of all affected children present with atypical, less severe phenotypes.

Affected neonates develop severe symptoms including progressive lethargy, hypotonia, and myoclonic jerks leading to apnea and often death. Surviving infants have hypotonia, profound intellectual disability, developmental delay and intractable seizures. The atypical form has disease onset from late infancy to adulthood and the clinical outcomes range from milder features to rapidly progressive severe disease.


Glycine encephalopathy is an autosomal recessive disorder. GLDC, AMT and GCSH are the three known genes associated with the disease (Kure et al. 2006. PubMed ID: 16450403). These three genes encode the P, T and H proteins of the glycine cleavage multi-enzyme system (GCS), respectively.

Genetic defects of AMT (9 coding exons) account for approximately 20% of glycine encephalopathy cases. Documented pathogenic AMT variants include missense and various types of truncating variants. Large deletions and duplications involving AMT have not been reported (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PG-Select

Genetic defects of AMT account for approximately 20% of glycine encephalopathy (Hamosh et al. 2002. PubMed ID: 20301531). Large deletions/duplications involving AMT have not been reported (Human Gene Mutation Database). As an estimation, therefore, pathogenic AMT sequence variants can be found in approximately 20% of patients with glycine encephalopathy.

Testing Strategy

This panel provides full coverage of all coding exons of the AMT gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for this test are patients with glycine encephalopathy. Testing is also indicated for family members of patients who have known AMT pathogenic variants. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in AMT.


Official Gene Symbol OMIM ID
AMT 238310
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Glycine Encephalopathy AR 605899

Related Tests

GLDC-Related Glycine Encephalopathy via the GLDC Gene
Glycine Encephalopathy via the GCSH Gene


  • Human Gene Mutation Database (Bio-base).
  • Kure et al. 2006. PubMed ID: 16450403
  • Van Hove et al. 2019. PubMed ID: 20301531


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.

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

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View Ordering Instructions

1) Select Test Type

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.

Total Price: $
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