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Creatine Deficiency Syndrome via the GATM 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
GATM 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11881GATM81479 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

Cerebral creatine deficiency syndromes (CCDSs) are inborn errors of creatine metabolism (Mercimek-Mahmutoglu and Stockler-Ipsiroglu, “Creatine Deficiency Syndromes”, GeneReviews, www.genereviews.org). L-Arginine:glycine amidinotranferase (AGAT) deficiency (OMIM #612718) is an autosomal recessive inborn error of creatine biosynthesis. The AGAT enzyme normally catalyzes the first step in creatine synthesis; it transfers the amidino group from arginine to glycine, thus forming ornithine and guanidinoacetate (an immediate precursor of creatine) (Item et al. Am J Hum Genet 69: 1127-1133, 2001). Characteristic biochemical findings in affected individuals include low levels of guanidinoacetate in plasma and urine (Verma. Neurology 75:186-188, 2010). In vivo proton magnetic resonance spectroscopy will reveal low brain creatine levels (Verma 2010). Clinical manifestations of AGAT deficiency include developmental delay, mental retardation, severe language impairment, autistic-like behavior, and failure to thrive. Myopathy in adults and hypotonia in infancy have also been reported. Oral creatine supplementation has been associated with improvement in development as well as muscle weakness (Bianchi et al. Ann Neurol 47:511-513, 2000; Johnston et al. 2005 Am Soc Hum Genet Meeting Abstract, P. 58, Abstract #205; Edvardson et al. Mol Genet Metab 101:228-232, 2010; Verma 2010).


L-Arginine:glycine amidinotransferase is encoded by exons 1-9 of the GATM gene (OMIM #602360) located on chromosome 15. AGAT deficiency is a rare autosomal recessive disorder, with only four different variants having been published. All four variants are severe and lead to premature protein termination. These four pathogenic variants include two nonsense variants and two frameshifts (including one resulting from a splice donor variant that caused exon 3 skipping) (Johnston et al. 2005).

Clinical Sensitivity - Sequencing with CNV PGxome

At least one GATM variant has been identified in all individuals with enzymatically-confirmed GATM deficiency (Item et al. 2001; Johnston et al. 2005). Furthermore, all gene variants reported to date are detectable using standard polymerase chain reaction and automated sequencing methodologies.

Testing Strategy

This test provides full coverage of all coding exons of the GATM 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 arginine:glycine amidinotranferase (AGAT) deficiency. Testing is also indicated for family members of patients who have known GATM variants. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in GATM.


Official Gene Symbol OMIM ID
GATM 602360
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
AGAT Deficiency AR 612718


  • Bianchi, M. C., et.al. (2000). "Reversible brain creatine deficiency in two sisters with normal blood creatine level." Ann Neurol 47(4): 511-3. PubMed ID: 10762163
  • Edvardson, S., et.al. (2010). "l-arginine:glycine amidinotransferase (AGAT) deficiency: clinical presentation and response to treatment in two patients with a novel mutation." Mol Genet Metab 101(2-3): 228-32. PubMed ID: 20682460
  • Item, C. B., et.al. (2001). "Arginine:glycine amidinotransferase deficiency: the third inborn error of creatine metabolism in humans." Am J Hum Genet 69(5): 1127-33. PubMed ID: 11555793
  • Johnston, K (2005). "The second family with AGAT deficiency (creatine biosynthesis defect): diagnosis, treatment and the first prenatal diagnosis."." The American Society of Human Genetics."
  • 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
  • Verma, A. (2010). "Arginine:glycine amidinotransferase deficiency: a treatable metabolic encephalomyopathy." Neurology 75(2): 186-8. PubMed ID: 20625172


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

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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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