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Mitochondrial Trifunctional Protein Deficiency and Long-Chain 3-Hydroxyacyl CoA Dehydrogenase Deficiency via the HADHA Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
5257 HADHA 81406 81406,81479 $640 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
5257HADHA81406 81406,81479 $640 Order Options and Pricing

Pricing Comments

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

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

  • Kym Bliven, PhD

Clinical Features and Genetics

Clinical Features

Mitochondrial trifunctional protein (MTP) deficiency is a rare disorder of long-chain fatty acid oxidation. MTP deficiency can be classified into two biochemical phenotypes: general (complete) MTP deficiency, which results in reduced activity from all three enzymes of the MTP complex, and isolated long-chain 3-hydroxyacyl CoA dehydrogenase (LCHAD) deficiency. Of the two disorders, LCHAD deficiency is more common, with an estimated incidence of 1 in 75,000 and 1 in 100,000 in the American and European populations, respectively (Shahrokhi et al. 2017. PubMed ID: 28112527). Except for differences in enzymatic activities, however, the LCHAD and general MTP deficiencies are clinically indistinguishable (Boutron et al. 2011. PubMed ID: 21549624).

MTP deficiency may be categorized into three types depending on onset and severity of disease: lethal type (neonatal-onset), intermediate/hepatic type (infantile-onset), and neuromyopathic type (adult-onset) (Spiekerkoetter et al. 2004. PubMed ID: 14630990; Boutron et al. 2011. PubMed ID: 21549624). Neonatal-onset is generally characterized by severe cardiomyopathy, hypoketotic hypoglycemia, and neonatal death. During infantile-onset, patients initially present during a period of prolonged fasting or illness, and symptoms may include feeding difficulties, breathing difficulties, lethargy, hypoketotic hypoglycemia, hypotonia, lactic academia, hepatopathy, cardiomyopathy, retinopathy, and coma (Karall et al. 2015. PubMed ID: 25888220; Shahrokhi et al. 2017. PubMed ID: 28112527). In adolescents and adults, hypotonia, rhabdomyolysis, and peripheral neuropathy are more common clinical symptoms of this disease. Regardless of age, all affected individuals show increased levels of long-chain 3-OH-acylcarnitines upon blood acylcarnitine (AC) analysis.

Without treatment, the early-onset form of this disorder is associated with high morbidity and mortality. However, early diagnosis of this disorder in affected patients can result in relatively favorable outcomes, prompting the inclusion of trifunctional protein deficiency into newborn screening programs in several places across the world, including a number of states within the U.S. (https://www.babysfirsttest.org/). Molecular diagnostics may help to confirm a positive result. Treatment largely consists of restricting intake of long-chain fatty acids, avoidance of fasting, and careful monitoring during stress (including prolonged exercise) or illness to avoid a metabolic crisis (Karall et al. 2015. PubMed ID: 25888220). L-carnitine supplementation may also be recommended.

Additionally, if a mother is carrying an affected fetus, she may be at increased risk of developing maternal HELLP (hypertension, elevated liver enzymes, and low platelet) or AFLP (acute fatty liver of pregnancy) syndromes during the pregnancy. In rare instances, AFLP syndrome may be life-threatening to the mother (Ibdah. 2006. PubMed ID: 17167825). Therefore, understanding recurrence risk for this disorder may be important for future pregnancies.  

Genetics

The mitochondrial trifunctional protein (MTP) is an inner mitochondrial membrane protein that consists of four α-subunits with LCEH (long-chain 2,3-enoyl-CoA hydratase) and LCHAD (long-chain 3-hydroxyacyl CoA dehydrogenase) activities, and four β-subunits that have LCKT (long-chain 3-ketoacyl-CoA thiolase) activity (Uchida et al. 1992. PubMed ID: 1730633). These enzymes catalyze the three final steps of the β-oxidation cycle of long-chain fatty acids. Two nuclear genes, HADHA and HADHB, encode the α and β subunits of the MTP complex, respectively (Boutron et al. 2011. PubMed ID: 21549624).

Defects in HADHA or HADHB can result in general MTP deficiency, a condition where all three enzyme activities of the MTP complex are significantly reduced; of the two, defects in HADHA are more prevalent (Boutron et al. 2011. PubMed ID: 21549624; Shahrokhi et al. 2017. PubMed ID: 28112527). One particular HADHA missense variant (p.Glu510Gln) may result in an isolated LCHAD deficiency, leaving the remaining two enzyme activities unaffected. Both disorders are inherited in an autosomal recessive manner. 

Approximately 60 causative variants have been reported in the HADHA gene to date (Human Gene Mutation Database). The majority of these variants are missense, but splicing and nonsense variants have also been described, as well as a number of small deletions and insertions/duplications. Two gross deletions of one or more exons have also been reported. To our knowledge, no causative variants have arisen de novo in any of the previously reported probands, and therefore all known pathogenic variants are known or suspected to have been inherited from a carrier parent.

The most common pathogenic variant in HADHA is p.Glu510Gln (also known as p.Glu474Gln), which accounted for 54/90 pathogenic alleles (60%) in one study (Boutron et al. 2011. PubMed ID: 21549624). This variant, located in the LCHAD catalytic domain, appears to affect only LCHAD function and results in isolated LCHAD deficiency when present in the homozygous state. This variant is listed at a minor allele frequency of up to ~0.39% in at least one sub-population (European (Finnish)) in the gnomAD public population database (gnomAD).

Mice lacking the mitochondrial trifunctional protein are viable, but they exhibit intrauterine fetal growth retardation, hypoglycemia, and early neonatal death (Ibdah et al. 2001. PubMed ID: 11390422). The HADHA gene is listed as nonessential in the Online Gene Essentiality (OGEE) database (Online Gene Essentiality, ogee.medgenius.info).  

Clinical Sensitivity - Sequencing with CNV PG-Select

Clinical sensitivity for this test is expected to be high for patients with a biochemical diagnosis of long-chain 3-hydroxyacyl CoA dehydrogenase (LCHAD) deficiency or mitochondrial trifunctional protein (MTP) deficiency. In a cohort of 52 patients with biochemically-diagnosed MTP deficiency, Boutron and colleagues identified causative variants in 52 (100%) patients; 45 (~86.5%) had homozygous or compound heterozygous pathogenic variants in HADHA, while the remaining 7 (13.5%) patients carried homozygous or compound heterozygous pathogenic variants in HADHB (Boutron et al. 2011. PubMed ID: 21549624).

Gross deletions/duplications are expected to be a rare cause of MTP/LCHAD deficiency. Only two gross deletions have been reported in the HADHA gene to date (Human Gene Mutation Database).

Testing Strategy

This test is performed using Next-Generation sequencing with additional Sanger sequencing as necessary.

This test provides full coverage of all coding exons of the HADHA gene plus coverage of 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.

Indications for Test

HADHA sequencing could be considered for patients who present with symptoms consistent with mitochondrial trifunctional protein deficiency. Targeted testing is indicated for family members of patients who have known pathogenic variants in HADHA. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in HADHA.

Gene

Official Gene Symbol OMIM ID
HADHA 600890
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Citations

  • Boutron et al. 2011. PubMed ID: 21549624
  • Genome Aggregation Database (gnomAD).
  • Human Gene Mutation Database (Biobase).
  • Ibdah et al. 2001. PubMed ID: 11390422
  • Ibdah. 2006. PubMed ID: 17167825
  • Karall et al. 2015. PubMed ID: 25888220
  • Online Gene Essentiality (OGEE).
  • Shahrokhi et al. 2017. PubMed ID: 28112527
  • Spiekerkoetter et al. 2004. PubMed ID: 14630990
  • Uchida et al. 1992. PubMed ID: 1730633

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

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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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