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Creatine Deficiency Syndrome via the GAMT 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
GAMT 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9615GAMT81479 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. If the Sanger option is selected, CNV detection may be ordered through Test #600.

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

Guanidinoacetate N-methyltransferase (GAMT) deficiency (OMIM #612736) is an inborn error of creatine biosynthesis causing cerebral creatine deficiency syndrome (CCDS). GAMT enzyme normally catalyzes the transfer of a methyl group from S-adenosylmethionine to guanidinoacetate, thus forming creatine (Stockler et al. Am J Hum Genet 58:914-922, 1996; Schulze. Molecular and Cellular Biochemistry 244:143-150, 2003.). Characteristic biochemical findings include low urinary creatinine (reflecting a low body creatine pool) and accumulation of guanidinoacetate in urine, plasma, and CSF (Mercimek-Mahmutoglu et al. Neurology 67:480-484, 2006). Direct measurement of total creatine levels in the brain is possible by in vivo proton magnetic resonance spectroscopy (Stromberger et al. J Inherit Metab Dis 26: 299-308, 2003). Clinical manifestations of GAMT deficiency include intellectual disability (usually severe), epileptic seizures, and extrapyramidal movement disorder. Dietary treatment, including oral creatine and ornithine supplementation together with arginine restriction, has been shown to result in clinical and biochemical improvement (Gordon. Brain Dev 32:79-81, 2010).


Guanidinoacetate N-methyltransferase is encoded by exons 1-6 of the GAMT gene (OMIM #601240) located on chromosome 19p13.3. GAMT deficiency is an autosomal recessive disorder, with over 25 different variants having been reported. While the majority of variants are missense, several insertions, deletions, and splice site variants are also recognized causes of disease. The two most common variants include c.59G>C in exon 1 (commonly found in patients of Portuguese or Spanish origin) and c.327G>A in exon 2 (Mercimek-Mahmutoglu et al., “Creatine Deficiency Syndromes”, GeneReviews, 2011, http://www.ncbi.nlm.nih.gov/books/NBK3794/).

Clinical Sensitivity - Sequencing with CNV PGxome

At least one GAMT variant has been identified in all individuals with enzymatically-confirmed GAMT deficiency (Mercimek-Mahmutoglu et al. Neurology 67:480-484, 2006).

The sensitivity of duplication/deletion testing for this rare disorder is currently unknown.

Testing Strategy

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

Candidates for this test are patients with biochemical findings or clinical symptoms consistent with guanidinoaceteate N-methyltransferase (GAMT) deficiency. Such individuals include those with unexplained, severe intellectual disability in association with epileptic seizures and progressive extrapyramidal symptoms (Mercimek-Mahmutoglu et al. Neurology 67:480-484, 2006). Testing is also indicated for family members of patients who have known GAMT variants. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in GAMT.


Official Gene Symbol OMIM ID
GAMT 601240
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Deficiency Of Guanidinoacetate Methyltransferase AR 612736


  • Gordon, N. (2010). "Guanidinoacetate methyltransferase deficiency (GAMT)." Brain Dev 32(2): 79-81. PubMed ID: 19289269
  • Mercimek-Mahmotoglu, S. et al.  "Creatine Deficiency Syndromes".  In: GeneReviews (edited by R.A. Pagon et al.), Seattle, 1993.   Last Updated: August 2011.  PubMed ID: 20301745
  • Mercimek-Mahmutoglu, S., et.al. (2006). "GAMT deficiency: features, treatment, and outcome in an inborn error of creatine synthesis." Neurology 67(3): 480-4. PubMed ID: 16855203
  • Schulze, A. (2003). "Creatine deficiency syndromes." Mol Cell Biochem 244(1-2): 143-50. PubMed ID: 12701824
  • Stockler, S., et.al. (1996). "Guanidinoacetate methyltransferase deficiency: the first inborn error of creatine metabolism in man." Am J Hum Genet 58(5): 914-22. PubMed ID: 8651275
  • Stromberger, C., et.al. (2003). "Clinical characteristics and diagnostic clues in inborn errors of creatine metabolism." J Inherit Metab Dis 26(2-3): 299-308. PubMed ID: 12889668


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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View Ordering Instructions

1) Select Test Method (Platform)

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2) Select Additional Test Options

No Additional Test Options are available for this test.

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