Invitae Elevated Leucine Panel


Test description

The Invitae Elevated Leucine Panel analyzes the three genes that are associated with elevated leucine on newborn screening (NBS) or plasma amino acid analysis. This panel is indicated for any individual in whom a diagnosis of MSUD is suspected due to a positive newborn screen for maple syrup urine disease (MSUD), elevated branched-chain amino acids (especially elevated leucine) on plasma amino acid analysis, the presence of alloisoleucine on plasma amino acid analysis, or clinical presentation. Newborn screening may miss intermittent MSUD, so any individual with a clinical or biochemical phenotype suggestive of MSUD should be tested, regardless of a prior negative newborn screen. Age of diagnosis and subsequent metabolic control are the greatest determinants of long-term outcome.

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Primary panel (3 genes)


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

Elevated leucine on newborn screening (NBS) may be the result of maple syrup urine disease (MSUD). MSUD is an inborn error of metabolism caused by an inability to completely break down the branched-chain amino acids (BCAAs) leucine, isoleucine, and valine. Inability to breakdown the BCAAs leads to their accumulation in blood and tissue, causing the characteristic maple-syrup urine odor that is often detectable in the urine or cerumen of affected individuals.

MSUD has a broad phenotypic spectrum that includes classic, intermediate, intermittent, and thiamin-responsive forms. Classic cases generally have a residual enzyme activity of less than 3% whereas intermediate, intermittent, and thiamin-responsive MSUD cases 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 developmental delay. Most individuals with intermediate MSUD are diagnosed between five to seven years of age. Individuals with 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 necessary cofactor. 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.

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

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

Gene Proportion of MSUD cases
DBT 20%

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.

This test is indicated for any individual with elevated branched-chain amino acids on plasma amino acid analysis. The presence of allo-isoleucine is pathognomonic for MSUD.

Newborn screening has been documented to miss intermittant forms of MSUD as biochemical abnormalities, biochemical abnormalities are generally only unmasked during times of physiologic stress.

For considerations for testing please refer to:

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, +/- 10 base pairs of adjacent intronic sequence, and select noncoding variants. Our assay provides a Q30 quality-adjusted mean coverage depth of 350x (50x minimum, or supplemented with additional analysis). Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods, except individual variants that have high quality scores and previously validated in at least ten unrelated samples.

Our analysis detects most intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. If you are requesting the detection of a specific single-exon copy number variation, please contact Client Services before placing your order.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
BCKDHA NM_000709.3
BCKDHB NM_183050.2
DBT NM_001918.3