• Test code: 06147
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top tube
  • Alternate specimens:
    DNA or saliva/assisted saliva
  • Sample requirements
  • Request a sample kit

Invitae Maple Syrup Urine Disease Panel

Test description

The Invitae Maple Syrup Urine Disease panel analyzes up to 5 genes that are associated with maple syrup urine disease (MSUD). This test is indicated for any individual with a positive newborn screen for MSUD, elevated branched-chain amino acids on plasma amino acid analysis (especially elevated leucine), the presence of alloisoleucine on plasma amino acid analysis, or a suspected diagnosis of MSUD based on clinical presentation. Newborn screening may miss intermittent MSUD, so any individual with a clinical or biochemical phenotype suggestive of MSUD should be tested, even if a prior newborn screen was negative. Age of diagnosis and subsequent metabolic control are the greatest determinants of long-term outcome.

Order test

Primary panel (4 genes)
Add-on DLD Gene (1 gene)

Dihydrolipoamide dehydrogenase (DLD) forms the E3 subunit of the BCKDH enzyme complex. This same E3 subunit is also a part of two other enzyme complexes, pyruvate dehydrogenase (PDC) complex and alpha-ketoglutarate dehydrogenase (αKGDH) complex. Individuals with biallelic pathogenic variants in the DLD gene present with biochemical findings similar to those observed in MSUD cases, although the clinical phenotype differs and varies from severe neonatal onset disease to a milder isolated liver presentation in adulthood.


Alternative tests to consider

The Invitae Organic Acidemias Panel has been designed to provide a broad genetic analysis of this class of disorders. Depending on the individual’s clinical and family history, this broader panel may be appropriate. It can be ordered at no additional cost.

  • maple syrup urine disease (MSUD)
    • classic MSUD
    • intermediate MSUD
    • intermittent MSUD
    • thiamin-responsive MSUD

MSUD is an inborn error of metabolism that results from an inability to completely catabolize the branched-chain amino acids (BCAAs) leucine, isoleucine, and valine. The second step of BCAA catabolism involves oxidative decarboxylation by the branched-chain alpha keto-acid dehydrogenase (BCKDH) complex. Impairment in any of the BCKDH subunits results in a metabolic block that leads to elevated plasma and tissue concentrations of BCAAs. The accumulation of BCAAs and their metabolic by-products causes the characteristic odor that is often detectable in the urine and cerumen of affected individuals.

MSUD is caused by decreased activity of the branched-chain alpha keto-acid dehydrogenase complex. It is a mitochondrial multienzyme complex that is composed of several subunits (E1α, E1β, E2, E3) and its activity is controlled by specific regulatory molecules. PP2Cm is a phosphatase that reactivates the BCKDH complex in the presence of excess branched- chain amino acids. Defects in PP2Cm leads to an inactive BCKDH complex and also causes accumulation of branched- chain amino acids.

A deficiency in the E2, E1α, or E1β subunits causes isolated MSUD. Impairment of the E3 subunit produces a phenotypically and biochemically distinct condition called dihydrolipoamide dehydrogenase deficiency (congenital lactic acidosis, branched-chain ketoaciduria, 2-ketoglutaric aciduria) that is not tested for in this MSUD panel (available on Invitae Elevated Leucine Panel). PP2Cm defects result in a milder, variant form of MSUD, but minimal data exists regarding this condition.

MSUD is genetically heterogeneous (see the table below). An affected individual is homozygous or compound heterozygous for pathogenic variants in the same gene. No cases have been identified with pathogenic variants in different genes. Biallelic variants in any of the three genes can cause any of the four clinical phenotypes. Pathogenic variants are most common in BCKDHA and BCKDHB. Thiamin responsive patients have been found to have a greater incidence of missense DBT variants that result in a full-length mutant protein.

Gene Subunit Name
BCKDHA E1α Branched-chain keto acid dehydrogenase E1, alpha subunit
BCKDHB E1β Branched-chain keto acid dehydrogenase E1, beta subunit
DBT E2 Dihydrolipoamide branched-chain transacylase E2
PPM1K Regulatory E2 phosphatase Protein phosphatase 2Cm (PP2Cm)

MSUD has a broad phenotypic spectrum: classic, intermediate, intermittent, and thiamin-responsive. Classic cases generally have a residual enzyme activity of less than 3% while intermediate, intermittent, and thiamin-responsive MSUD have variable residual enzyme activity ranging from 3%–40%.

Classic MSUD represents most known cases and presents in the neonatal period following protein catabolism. Affected neonates present within the first 48 hours of life with irritability, poor feeding, and rapid onset of ketoacidosis. If untreated, the patients rapidly deteriorate and may become lethargic with intermittent apnea, neurologic abnormalities, and even coma and respiratory failure. Intermediate MSUD has greater enzymatic activity and may present in infancy with feeding problems, growth delays, and developmental delay, or in later childhood with an insidious developmental delay. Most individuals with intermediate MSUD are diagnosed between five and seven years of age. Cases of intermittent MSUD are clinically well during infancy and childhood but present with clinical and biochemical abnormalities during times of illness or physiologic stress. Patients with thiamin-responsive MSUD also present later in life; their enzymatic activity can be increased with thiamin supplementation because thiamin is a cofactor for the BCKDH complex. All forms of MSUD are susceptible to periods of acute metabolic decompensation due to BCAA build-up. Such episodes are frequently precipitated by infection, injury, or physiologic stress.

MSUD is treatable by lifetime dietary restriction of branched-chain amino acids and aggressive intervention during metabolic crisis. Dietary therapy must be managed by a nutritionist to prevent malnutrition. Some cases are responsive to pharmacologic doses of thiamin. Thiamin treatment does not eliminate the need for dietary intervention, but it reduces the degree of restriction. Some affected individuals have been successfully treated by liver transplant.

For patients with a clinical and biochemical diagnosis of MSUD, approximately 100% will have two pathogenic variants in one of these four genes.

Gene Proportion of MSUD cases
DBT 20%
PPM1K Rare

MSUD is inherited in an autosomal recessive manner.

MSUD is fully penetrant, with a broad phenotypic spectrum.

The general population incidence of MSUD has been reported as 1 in 120,000–500,000. This may be underestimated due to intermittent biochemical presentations and a mild disease that results in a subclinical phenotype.

MSUD has a much higher incidence in the Old Order Mennonite population of southeastern Pennsylvania due to a BCKDHA founder mutation (p.Y393N). Incidence has been reported as high as 1 in 176 live births.

There is an increased carrier frequency of 1 in 113 among the Ashkenazi Jewish population for the p.R133P mutation in BCKDHB.

Any individual with a positive newborn screen for MSUD, elevated branched-chain amino acids upon plasma amino-acid analysis (especially elevated leucine), the presence of alloisoleucine upon plasma amino-acid analysis, or a suspected diagnosis of MSUD based on clinical presentation, should be tested for MSUD. Newborn screening may miss intermittent MSUD, so any individual with a clinical or biochemical phenotype suggestive of MSUD should be tested, even if a prior newborn screen had a negative result. Age of diagnosis and subsequent metabolic control are the greatest determinants of long-term outcome.

  1. Frazier, DM, et al. Nutrition management guideline for maple syrup urine disease: an evidence- and consensus-based approach. Mol. Genet. Metab. 2014; 112(3):210-7. PMID: 24881969
  2. Fisher, CW, et al. Molecular phenotypes in cultured maple syrup urine disease cells. Complete E1 alpha cDNA sequence and mRNA and subunit contents of the human branched chain alpha-keto acid dehydrogenase complex. J. Biol. Chem. 1989; 264(6):3448-53. PMID: 2914958
  3. Bhattacharya, K, et al. Newborn screening may fail to identify intermediate forms of maple syrup urine disease. J. Inherit. Metab. Dis. 2006; 29(4):586. PMID: 16830261
  4. Chuang, DT, et al. Lessons from genetic disorders of branched-chain amino acid metabolism. J. Nutr. 2006; 136(1 Suppl):243S-9S. PMID: 16365091
  5. Chuang, JL, et al. Structural and biochemical basis for novel mutations in homozygous Israeli maple syrup urine disease patients: a proposed mechanism for the thiamin-responsive phenotype. J. Biol. Chem. 2004; 279(17):17792-800. PMID: 14742428
  6. Oyarzabal, A, et al. A novel regulatory defect in the branched-chain α-keto acid dehydrogenase complex due to a mutation in the PPM1K gene causes a mild variant phenotype of maple syrup urine disease. Hum. Mutat. 2013; 34(2):355-62. PMID: 23086801
  7. Strauss, KA, et al. Maple Syrup Urine Disease. 2006 Jan 30. In: Pagon, RA, et al, editors. GeneReviews(®) (Internet). University of Washington, Seattle. PMID: 20301495
  8. Lu, G, et al. Protein phosphatase 2Cm is a critical regulator of branched-chain amino acid catabolism in mice and cultured cells. J. Clin. Invest. 2009; 119(6):1678-87. PMID: 19411760
  9. Schiff M, Ogier de Baulny H, Dionisi-Vici C. Inborn metabolic diseases: diagnosis and treatment. 6th ed. Heidelberg: Springer; 2016. Chapter 18, Branched-chain organic acidurias/acidaemias; p. 289–293.
  10. Chuang DT, Shih VE. The metabolic and molecular bases of inherited disease. New York: McGraw-Hill; 2001. Chapter 87, Maple syrup urine disease (branched-chain ketoaciduria); p. 1971–2006.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below. In addition, the analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
BCKDHA NM_000709.3
BCKDHB NM_183050.2
DBT NM_001918.3
DLD NM_000108.4
PPM1K NM_152542.4