Arginine:Glycine Amidinotransferase (GATM) Deficiency Sequencing
Ordering Recommendation

Preferred molecular test following biochemical testing suggestive of arginine:glycine amidinotransferase (AGAT) deficiency.

Polymerase Chain Reaction/Sequencing
14-21 days
New York DOH Approval Status
Specimens from New York clients will be sent out to a New York DOH approved laboratory, if possible.
Specimen Required
Patient Preparation
Lavender (EDTA), pink (K2EDTA), or yellow (ACD Solution A or B). 
Specimen Preparation
Transport 3 mL whole blood. (Min: 1 mL) 
Storage/Transport Temperature
Unacceptable Conditions
Ambient: 72 hours; Refrigerated: 1 week; Frozen: Unacceptable 
Reference Interval
By report
Interpretive Data
Background Information for Arginine:Glycine Amidinotransferase (GATM) Deficiency Sequencing:
Intellectual disability and seizure disorder of variable severity. May also include speech / language delays, movement disorder, and behavioral disorders such as autism, hyperactivity, and self-injury.
Incidence: Unknown. Less than 15 cases have been described.
Inheritance: Autosomal recessive.
Cause: Pathogenic GATM gene mutations.
Clinical Sensitivity: Based on limited data, may be as high as 99 percent.
Methodology: Bidirectional sequencing of the entire coding region and intron/exon boundaries of the GATM gene.
Analytical Sensitivity and Specificity: 99 percent.
Limitations: Diagnostic errors can occur due to rare sequence variations. Regulatory region mutations, deep intronic mutations, and large deletions/duplications will not be detected. Mutations in genes other than GATM are not evaluated.

Counseling and informed consent are recommended for genetic testing. Consent forms are available online at

Compliance Statement C: For human genetic inheritable conditions and mutations. This test was developed and its performance characteristics determined by ARUP Laboratories. The U. S. Food and Drug Administration has not approved or cleared this test; however, FDA clearance or approval is not currently required for clinical use. The results are not intended to be used as the sole means for clinical diagnosis or patient management decisions.

Counseling and informed consent are recommended for genetic testing. Consent forms are available online.

Hotline History
Component Test Code*Component Chart NameLOINC
2011145AGAT (GATM) Sequencing Specimen31208-2
2011146AGAT (GATM) Sequencing Interpretation35474-6
* Component test codes cannot be used to order tests. The information provided here is not sufficient for interface builds; for a complete test mix, please click the sidebar link to access the Interface Map.
  • AGAT Deficiency, GAMT, Guanidinoacetate Methyltransferase, GAA, SLC6A8, creatine deficiency, creatin