Test Catalog

Test Id : AGXTZ

AGXT Gene, Full Gene Analysis, Varies

Useful For
Suggests clinical disorders or settings where the test may be helpful

Confirming a diagnosis of primary hyperoxaluria type 1

 

Carrier testing for individuals with a family history of primary hyperoxaluria type 1 in the absence of known mutations in the family

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

See Hyperoxaluria Diagnostic Algorithm in Special Instructions.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

Polymerase Chain Reaction (PCR) Followed by DNA Sequence Analysis and Gene Dosage Analysis by Multiplex Ligation-Dependent Probe Amplification (MLPA)

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

AGXT Gene, Full Gene Analysis

Aliases
Lists additional common names for a test, as an aid in searching

AGXT (Alanine-Glyoxylate Aminotransferase)

Alanine-Glyoxylate Aminotransferase (AGXT)

Hyperoxaluria

PH1 (Primary Hyperoxaluria Type 1)

Primary Hyperoxaluria

Primary Hyperoxaluria Type 1 (PH1)

AGXMS

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

See Hyperoxaluria Diagnostic Algorithm in Special Instructions.

Specimen Type
Describes the specimen type validated for testing

Varies

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

Patient Preparation: A previous bone marrow transplant from an allogenic donor will interfere with testing. Call 800-533-1710 for instructions for testing patients who have received a bone marrow transplant.

Specimen Type: Whole blood

Container/Tube: Lavender top (EDTA) or yellow top (ACD)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube.

Additional Information: Specimen preferred to arrive within 96 hours of draw.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Forms

1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available in Special Instructions:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing-Spanish (T826)

2. Molecular Genetics: Congenital Inherited Diseases Patient Information (T521) in Special Instructions

3. If not ordering electronically, complete, print, and send a Renal Diagnostics Test Request (T830) with the specimen.

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

1 mL

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

All specimens will be evaluated by Mayo Clinic Laboratories for test suitability.

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

Specimen Type Temperature Time Special Container
Varies Varies (preferred)

Useful For
Suggests clinical disorders or settings where the test may be helpful

Confirming a diagnosis of primary hyperoxaluria type 1

 

Carrier testing for individuals with a family history of primary hyperoxaluria type 1 in the absence of known mutations in the family

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

See Hyperoxaluria Diagnostic Algorithm in Special Instructions.

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Primary hyperoxaluria type 1 (PH1) is a hereditary disorder of glyoxylate metabolism caused by deficiency of alanine:glyoxylate-aminotransferase (AGT), a hepatic enzyme that converts glyoxylate to glycine. Absence of AGT activity results in conversion of glyoxylate to oxalate, which is not capable of being degraded. Therefore, excess oxalate is excreted in the urine, causing kidney stones (urolithiasis), nephrocalcinosis, and kidney failure. As kidney function declines, blood levels of oxalate increase markedly, and oxalate combines with calcium to form calcium oxalate deposits in the kidney, eyes, heart, bones, and other organs, resulting in systemic disease. Pyridoxine (vitamin B6), a cofactor of AGT, is effective in reducing urine oxalate excretion in some PH1 patients.

 

Presenting symptoms of PH1 include nephrolithiasis, nephrocalcinosis, or end-stage kidney disease with or without a history of urolithiasis. Age of symptom onset is variable; however, most individuals present in childhood or adolescence with symptoms related to kidney stones. In some infants with a more severe phenotype, kidney failure may be the initial presenting feature. Less frequently, affected individuals present in adulthood with recurrent kidney stones or kidney failure. End-stage kidney disease is most often seen in the third decade of life, but can occur at any age.

 

The exact prevalence and incidence of PH1 are not known, but prevalence rates of 1 to 3 per million population and incidences of 0.1 per million/year have been estimated from population surveys.

 

Biochemical testing is indicated in patients with possible primary hyperoxaluria. Measurement of urinary oxalate is strongly preferred, with correction to adult body surface area in pediatric patients (HYOX / Hyperoxaluria Panel, Urine; OXU / Oxalate, 24 Hour, Urine). Abnormal urinary excretion of oxalate is strongly suggestive of, but not diagnostic for, this disorder, as there are other forms of inherited (type 2 and non-PH1/PH2) hyperoxaluria and secondary hyperoxaluria that may result in similarly elevated urine oxalate excretion rates. An elevated urine glycolate in the presence of hyperoxaluria is suggestive of PH1. Historically, the diagnosis of PH1 was confirmed by AGT enzyme analysis performed on liver biopsy; however, this has been replaced by molecular testing, which forms the basis of confirmatory or carrier testing in most cases.

 

PH1 is inherited as an autosomal recessive disorder caused by mutations in the AGXT gene, which encodes the enzyme AGT. Several common AGXT mutations have been identified including c.33dupC, p.Gly170Arg (c.508G->A), and p.Ile244Thr (c.731T->C). These mutations account for at least 1 of the 2 affected alleles in approximately 70% of individuals with PH1. Direct sequencing of the AGXT gene is predicted to identify 99% of alleles in individuals who are known by enzyme analysis to be affected with PH1.

 

While age of onset and severity of disease is variable and not necessarily predictable by genotype, a correlation between pyridoxine responsiveness and homozygosity for the p.Gly170Arg mutation has been observed. (Note: testing for the p.Gly170Arg mutation only is available by ordering AGXTG / Alanine:Glyoxylate Aminotransferase [AGXT] Mutation Analysis [G170R], Blood). Pyridoxine (vitamin B6) is a known cofactor of AGT and is effective in reducing urine oxalate excretion in some PH1 patients treated with pharmacologic doses. Individuals with 2 copies of the p.Gly170Arg mutation have been shown to normalize their urine oxalate when treated with pharmacologic doses of pyridoxine and those with a single copy of the mutation show reduction in urine oxalate. This is valuable because not all patients have been shown to be responsive to pyridoxine, and strategies that help to identify the individuals most likely to benefit from such targeted therapies are desirable.

Reference Values
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided.

Interpretation
Provides information to assist in interpretation of the test results

All detected alterations are evaluated according to American College of Medical Genetics recommendations.(1) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

A small percentage of individuals who are carriers or have a diagnosis of primary hyperoxaluria type 1 (PH1) may have a mutation that is not identified by this method (eg, promoter mutations). The absence of a mutation, therefore, does not eliminate the possibility of positive carrier status or the diagnosis of PH1 disease. For carrier testing, it is important to first document the presence of a PH1-gene mutation in an affected family member.

 

In some cases, DNA alterations of undetermined significance may be identified.

 

In addition to disease-related probes, this test utilizes probes localized to other chromosomal regions as internal controls. In certain circumstances, these control probes may detect other diseases or conditions for which this test was not specifically intended. Results of the control probes are not normally reported. However, in cases where clinically relevant information is identified, the ordering physician will be informed of the result and provided with recommendations for any appropriate follow-up testing.

 

Rare polymorphisms exist that could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, additional testing should be considered.

  

Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Errors in our interpretation of results may occur if information given is inaccurate or incomplete.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

1. Richards S, Aziz N, Bale S, et al: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015 May;17(5):405-424

2. Milliner DS: The primary hyperoxalurias: an algorithm for diagnosis. Am J Nephrol 2005;25(2):154-160

3. Monico CG, Rossetti S, Olson JB, Milliner DS: Pyridoxine effect in type I primary hyperoxaluria is associated with the most common mutant allele. Kidney Int 2005;67(5):1704-1709

4. Monico CG, Rossetti S, Schwanz HA, et al: Comprehensive mutation screening in 55 probands with type 1 primary hyperoxaluria shows feasibility of a gene-based diagnosis. J Am Soc Nephrol 2007;18:1905-1914

5. Rumsby G, Williams E, Coulter-Mackie M: Evaluation of mutation screening as a first line test for the diagnosis of the primary hyperoxalurias. Kidney Int 2004;66(3):959-963

6. Williams EL, Acquaviva C, Amoroso, A, et al: Primary hyperoxaluria type I: update and additional mutation analysis of the AGXT gene. Hum Mutat 2009;30:910-917

7. Williams E, Rumsby G: Selected exonic sequencing of the AGXT gene provides a genetic diagnosis in 50% of patients with primary hyperoxaluria type 1. Clin Chem 2007;53(7):1216-1221

8. Communique April 2007: Laboratory and Molecular Diagnosis of Primary Hyperoxaluria and Oxalosis

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Description
Describes how the test is performed and provides a method-specific reference

Bidirectional sequence analysis is performed to test for the presence of a mutation in all coding regions and intron/exon boundaries of the AGXT gene. Additionally, gene dosage analysis (multiplex ligation-dependent probe amplification) is used to test for the presence of large deletions and duplications in this gene.(Unpublished Mayo method)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Varies

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

14 to 20 days

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

81479-Unlisted molecular pathology procedure

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
AGXTZ AGXT Gene, Full Gene Analysis 94227-6
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
53442 Result Summary 50397-9
53443 Result 82939-0
53444 Interpretation 69047-9
53445 Additional Information 48767-8
53446 Specimen 31208-2
53447 Source 31208-2
53448 Released By 18771-6

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Create a PDF

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports