Methionine Adenosyltransferase I/III Deficiency via the MAT1A 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
8479 MAT1A 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8479MAT1A81479 81479(x2) $890 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 backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days 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.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • McKenna Kyriss, PhD

Clinical Features and Genetics

Clinical Features

Methionine adenosyltransferase (MAT) I/III deficiency is characterized by isolated persistent hypermethioninemia and occasionally unusual breath odor. Most individuals with isolated hypermethioninemia are free of major clinical difficulties, although rare cases of individuals with neurologic abnormalities, including intellectual impairment, increased tendon reflexes, dystonia, and nystagmus, have been reported (Mudd 2011; Chien et al. 2015). The product of MAT, S-adenosylmethionine (AdoMet), is a major methyl donor for a large number of biologically important compounds, including two liver-synthesized myelin phospholipids, phosphatidylcholine and sphingomyelin. In a review of 30 affected patients, 27 individuals were found to have normal intelligence and no neurological signs, while three patients were found to have intellectual impairment (Mudd et al. 1995). It has been reported that at least two individuals with complete absence of MATI/III activity developed brain demyelination at 11 years of age (Chamberlin et al. 1996). Although it has been suggested that MATI/III plays an essential role in maintaining myelin structure in the brain, not all patients with truncating pathogenic variants have neurologic involvement (Hazelwood et al. 1998). In a recent study, 32 out of 64 patients with MATI/III deficiency were reported to have some evidence of CNS abnormalities, and the authors suggest that patients with higher levels of methionine are more likely to present with CNS abnormalities (Chien et al. 2015).

Most cases of hypermethioninemia are initially detected by newborn screening, as high levels of serum methionine may serve as an indicator of hyperhomocysteinemia associated with cystathionine β-synthase deficiency. Although methionine S-adenosyltransferase deficiency usually does not require treatment (Andria et al. 2012), dietary therapy may help to maintain myelin structure in individuals with severe MAT I/III deficiency (Chamberlin et al. 1996; Hirabayashi et al. 2013). Treatment with supplemental AdoMet may help improve neurological development and myelination (Furujo et al. 2012).

Genetics

Methionine adenosyltransferase (MAT) I/III deficiency is an autosomal genetic disorder caused by a deficiency of methionine adenosyltransferase I alpha. The disease is associated with pathogenic variants in the MAT1A gene located on chromosome 10q22. Pathogenic variants within the MAT1A gene encoding methionine adenosyltransferase I alpha are the only known cause of the disease, and nearly 60 different variants have been reported (Human Gene Mutation Database). Causative variants have been reported in all nine coding exons, with missense and nonsense variants serving as the main cause of disease.

Most MAT1A pathogenic variants show autosomal recessive inheritance, but autosomal dominant inheritance has also been reported. In all cases described to date, the autosomal dominant form of disease has been linked to heterozygosity for a single sequence variant, c.791G>A (p.Arg264His) (Chamberlin et al. 1997). In vitro studies suggest that residue 264 is involved in salt bridge formation that is essential for subunit dimerization, and the dominant effect of the R264 mutation is exerted by the formation of enzymatically inactive R264/H264 dimers (Chamberlin et al. 2000).

Most cases of hypermethioninemia are initially detected by newborn screening. Population screening suggests the incidence of MATI/III deficiency may be as high as 1 in 25,000 to 1 in 30,000 live births (Baric 2009). Methionine adenosyltransferase I/III deficiency can be found in ethnically diverse populations, including Europeans, Americans, Spaniards (Couce et al. 2013), Koreans (Kim et al. 2002), Taiwanese (Chien et al. 2005), and Japanese (Nagao et al. 2013).

The MAT1A gene is primarily expressed in the liver; it encodes an α1 subunit that can form two different isozymes, a homotetramer (MAT I) or homodimer (MAT III). MAT catalyzes the biosynthesis of S-adenosylmethionine (also known as AdoMet or SAM) from methionine and ATP (Catoni 1953). AdoMet is the source of methyl groups for most biological methylations and is important in both transmethylation and transsulfuration pathways.

Clinical Sensitivity - Sequencing with CNV PGxome

A comprehensive review of the literature suggests that the clinical sensitivity of this test should be high. Of the 61 biochemically/enzymatically diagnosed patients for whom MAT1A gene sequencing was performed, 59 patients carried two pathogenic variants. One patient was reported to be heterozygous for a single variant, and one patient was reported with one sequencing variant and one multi-exonic deletion (Chien et al. 2015). This suggests a clinical sensitivity of ~98% for direct sequencing of the MAT1A gene. In addition, of 18 Spanish patients detected by newborn screening programs (Couce et al. 2013), 15 were reported to be heterozygous for the known R264H dominantly inherited variant, while two of the remaining three patients were compound heterozygous for two variants and the last patient was found to carry only a single heterozygous variant. This suggests a clinical sensitivity of ~95% for direct sequencing of the MAT1A gene.

Testing Strategy

This test provides full coverage of all coding exons of the MAT1A 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 hypermethioninemia or known methionine adenosyltransferase deficiency. MATI/III deficiency should be differentiated from other causes of hypermethioninemia, including cystathionine β-synthase deficiency, tyrosinemia type I, prematurity, and severe hepatocellular disease (Mudd et al. 1995). Because MAT1A primarily shows hepatic expression, genetic testing may allow diagnostic confirmation of this disorder without the need for liver biopsy. It has been recommended that DNA-based diagnosis should be performed for isolated hypermethioninemic individuals with unusually high plasma methionine levels to assess if therapy aimed at the prevention of neurological manifestations is warranted (Chou 2000). This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in MAT1A.

Gene

Official Gene Symbol OMIM ID
MAT1A 610550
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Methionine Adenosyltransferase I/III Deficiency AD,AR 250850

Citations

  • Andria G. et al. 2012. Disorders of Sulfur Amino Acid Metabolism. In: Saudubray J-M, van den Berghe G, and Walter JH, editors. ┬áInborn Metabolic Diseases: Diagnosis and Treatment, 5e. Berlin, Germany: Springer-Verlag, p 317-318.
  • Baric I. 2009. Journal of Inherited Metabolic Disease. 32: 459-71. PubMed ID: 19585268
  • Catoni G.L. 1953. The Journal of Biological Chemistry. 204: 403-16. PubMed ID: 13084611
  • Chamberlin et al. 1996. PubMed ID: 8770875
  • Chamberlin M.E. et al. 1997. American Journal of Human Genetics. 60: 540-6. PubMed ID: 9042912
  • Chamberlin M.E. et al. 2000. American Journal of Human Genetics. 66: 347-55. PubMed ID: 10677294
  • Chien et al. 2015. PubMed ID: 26289392
  • Chien Y.H. et al. 2005. Early Human Development. 81: 529-33. PubMed ID: 15935930
  • Chou J.Y. 2000. Pharmacology & Therapeutics. 85: 1-9. PubMed ID: 10674710
  • Couce et al. 2013. PubMed ID: 23993429
  • Furujo M et al. 2012. Molecular Genetics and Metabolism. 107: 253-6. PubMed ID: 22951388
  • Hazelwood et al. 1998. PubMed ID: 9482646
  • Hirabayashi K. et al. 2013. Gene. 530: 104-8. PubMed ID: 23973726
  • Human Gene Mutation Database (Bio-base).
  • Kim S.Z. et al. 2002. Journal of Inherited Metabolic Disease. 25: 661-71. PubMed ID: 12705496
  • Mudd et al. 1995. PubMed ID: 7573050
  • Mudd. 2011. PubMed ID: 21308989
  • Nagao M. et al. 2013. Molecular Genetics and Metabolism. 110: 460-4. PubMed ID: 24231718

Ordering/Specimens

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


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

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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