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Glycine N-Methyltransferase Deficiency via the GNMT 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
GNMT 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11831GNMT81479 81479,81479 $990 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 platform).

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

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

For Sanger Sequencing click here.

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.


Genetic Counselors


  • McKenna Kyriss, PhD

Clinical Features and Genetics

Clinical Features

Defects in the Glycine N-Methyltransferase (GNMT) enzyme have been shown to lead to persistent, isolated hypermethioninemia, which is the elevation of methionine in plasma without accompanying homocystinemia. This hypermethioninemia persists beyond the first months of life (Mudd et al. 2001). Very few patients have been described with defects in the GNMT enzyme. Clinically, the identified patients have presented with hepatomegaly (in one family) and chronic elevation of serum transaminases indicative of liver disease, but not attributable to typical causes of liver disease. Biochemically, all patients were found to have persistently elevated serum methionine levels with normal levels of plasma homocysteine, tyrosine and sarcosine. In addition, serum adenosylmethionine (AdoMet) was elevated while serum adenosylhomocysteine (AdoHcy) levels were normal (Mudd et al. 2001; Luka et al. 2002; Augoustides-Savvopoulou et al. 2003).

Onset appears to be during early childhood, although it is not currently known how early hypermethioninemia would be detected in GNMT deficient individuals. Due to the small number of cases reported, the long-term prognosis of the GNMT patients is currently unknown (Mudd et al. 2001; Luka et al. 2002; Augoustides-Savvopoulou et al. 2003).


The Glycine N-Methyltransferase enzyme is encoded by the GNMT gene, located on chromosome 6 at 6p12. To date, only three GNMT deficient patients have been reported in the literature and thus far, inheritance appears to be autosomal recessive. Two of the patients were Italian siblings, who were each found to be compound heterozygous for the missense variants Leu49Pro and His177Asn (Luka et al. 2002). The third patient was of Greek origin, and was found to be homozygous for the missense variant Arg140Ser (Augoustides-Savvopoulou et al. 2003).

The GNMT enzyme is present in large amounts in liver, pancreas and prostate, and appears to be primarily a cytosolic enzyme. GNMT is involved in methionine metabolism. The enzyme methionine adenosyltransferase I/III converts methionine to adenosylmethionine (AdoMet), which is then converted to adenosylhomocysteine (AdoHcy) via the action of the GNMT enzyme. Mutations in the GNMT gene that affect activity of the GNMT enzyme lead to accumulation of methionine and AdoMet in the plasma (Mudd et al. 2001; Luka et al. 2009).

Clinical Sensitivity - Sequencing with CNV PGxome

At this time, the sensitivity of this test is difficult to estimate due to the low number of cases reported in the literature. Analytical sensitivity may be high as the only reported causative variants are detectable by sequencing (Luka et al. 2002; Augoustides-Savvopoulou et al. 2003).

Testing Strategy

This test provides full coverage of all coding exons of the GNMT 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

Patients with hypermethioninemia are good candidates for this test, particularly if they have elevated plasma AdoMet levels and normal plasma homocysteine, tyrosine and sarcosine levels. Family members of patients known to have GNMT variants are also good candidates, and we will also sequence the GNMT gene to determine carrier status.


Official Gene Symbol OMIM ID
GNMT 606628
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Glycine N-Methyltransferase Deficiency AR 606664


  • Augoustides-Savvopoulou et al. 2003. PubMed ID: 14739680
  • Luka et al. 2002. PubMed ID: 11810299
  • Luka et al. 2009. PubMed ID: 19483083
  • Mudd et al. 2001. PubMed ID: 11596649


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

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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2) Select Additional Test Options

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