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Arginine:Glycine Amidinotransferase (GATM) Deficiency Sequencing
2011144
Ordering Recommendation

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

Mnemonic
AGAT FGS
Methodology
Polymerase Chain Reaction/Sequencing
Performed
Varies
Reported
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.
ARUP Consult®
Disease Topics
Specimen Required
Patient Preparation
 
Collect
Lavender (EDTA), pink (K2EDTA), or yellow (ACD Solution A or B). 
Specimen Preparation
Transport 3 mL whole blood. (Min: 1 mL) 
Storage/Transport Temperature
Refrigerated. 
Unacceptable Conditions
 
Remarks
 
Stability
Ambient: 72 hours; Refrigerated: 1 week; Frozen: Unacceptable 
Reference Interval
By report
Interpretive Data
Background Information for Arginine:Glycine Amidinotransferase (GATM) Deficiency Sequencing:
Characteristics:
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 www.aruplab.com.

Compliance Statement C: The performance characteristics of this test were validated by ARUP Laboratories. The U.S. Food and Drug Administration (FDA) has not approved or cleared this test. However, FDA approval or clearance is currently not required for clinical use of this test. The results are not intended to be used as the sole means for clinical diagnosis or patient management decisions. ARUP is authorized under Clinical Laboratory Improvement Amendments (CLIA) and by all states to perform high-complexity testing. Counseling and informed consent are recommended for genetic testing. Consent forms are available online.

Components
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.
Aliases
  • AGAT Deficiency, GAMT, Guanidinoacetate Methyltransferase, GAA, SLC6A8, creatine deficiency, creatin