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 Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 5497 | AMT | 81479 | 81479,81479 | $990 | Order Options and Pricing |
Pricing Comments
Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.
Turnaround Time
3 weeks on average for standard orders or 2 weeks 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.
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.
Genetics
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.
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.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| AMT | 238310 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Glycine Encephalopathy | AR | 605899 |
Related Tests
| Name |
|---|
| GLDC-Related Glycine Encephalopathy via the GLDC Gene |
| Glycine Encephalopathy via the GCSH Gene |
Citations
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
If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.
Specimen Types
Specimen Requirements and Shipping Details
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ORDER OPTIONS
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2) Select Additional Test Options
No Additional Test Options are available for this test.