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Malonyl-CoA Decarboxylase Deficiency via the MLYCD 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
MLYCD 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8567MLYCD81479 81479,81479 $990 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.

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 platform).

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

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

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks 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.


Genetic Counselors


  • Maxime Cadieux-Dion, PhD

Clinical Features and Genetics

Clinical Features

Malonyl-CoA decarboxylase deficiency is a rare inborn error of metabolism caused by defects in the MLYCD gene. Although the clinical presentation is variable, patients with this disorder may present with developmental delay, seizures, hypoglycemia, cardiomyopathy and structural brain abnormalities (FitzPatrick et al. 1999; Celato et al. 2013; Liu et al. 2016). Biochemically, this disorder is characterized by elevated malonylcarnitine on an acylcarnitine profile and the presence of malonic and methylmalonic acid in the urine (FitzPatrick et al. 1999; Celato et al. 2013; Baertling et al. 2014). Metabolic acidosis is also frequently observed (Celato et al. 2013; Liu et al. 2016). More severely affected patients may die in infancy (Polinati et al. 2015).

Treatment of MLYCD deficient patients is generally via dietary modification as well as medications to treat cardiomyopathy, if needed. While this treatment may not prevent or eliminate all symptoms, there does seem to be benefit to diagnosing affected patients early in life so that treatment can begin as soon as possible (Baertling et al. 2014).


Malonyl-CoA decarboxylase deficiency is an autosomal recessive disorder caused by defects in the MLYCD gene, which is located on chromosome 16 at 16q23.3. Over 35 pathogenic variants have been reported in the MLYCD gene, approximately one-third of which have been missense variants. Nearly half of the reported variants are splice site or protein truncating variants, and approximately one-fifth of reported variants are larger copy number variants (Human Gene Mutation Database). Most reported MLYCD variants seem to be private, familial variants.

The malonyl-CoA decarboxylase enzyme catalyzes the conversion of malonyl-CoA to acetyl-CoA and carbon dioxide (Sacksteder et al. 1999). The malonyl-CoA metabolite has at least two functions in mammalian cells. First, it is used in the de novo synthesis and elongation of fatty acids in lipogenic tissues. Secondly, malonyl-CoA acts as an inhibitor of the carnitine palmitoyltransferase I (CPTI) enzyme, thereby regulating mitochondrial fatty acid β-oxidation in non-lipogenic tissues (Sacksteder et al. 1999; Polinati et al. 2015). For these reasons, MLYCD deficient patients often have some phenotypic overlap with patients who have a defect in fatty acid oxidation (Salomons et al. 2007).

Clinical Sensitivity - Sequencing with CNV PGxome

Based on collective totals of many of the patients reported in the literature, the clinical sensitivity of MLYCD gene sequencing for patients with confirmed malonyl-CoA decarboxylase deficiency is estimated to be ~73% (22 pathogenic MLYCD alleles out of 30 alleles, with only one patient counted if multiple family members were affected) (FitzPatrick et al. 1999; Salomons et al. 2007; Celato et al. 2013; Baertling et al. 2014; Polinati et al. 2015; Liu et al. 2016). The remaining ~27% of alleles contained exonic or larger deletions that may not be detected by this test.

Testing Strategy

This test provides full coverage of all coding exons of the MLYCD 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

Patients with malonic and methylmalonic aciduria and/or elevated malonylcarnitine are good candidates for this test, as are those with phenotypic features consistent with MLYCD deficiency. Testing is also indicated for family members of patients with known MLYCD pathogenic variants. We will also sequence the MLYCD gene to determine carrier status.


Official Gene Symbol OMIM ID
MLYCD 606761
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Malonyl-CoA Decarboxylase Deficiency AR 248360


  • Baertling F. et al. 2014. European Journal of Pediatrics. 173: 1719-22. PubMed ID: 25233985
  • Celato A. et al. 2013. Brain & Development. 35: 675-80. PubMed ID: 23177061
  • FitzPatrick D.R. et al. 1999. American Journal of Human Genetics. 65: 318-26. PubMed ID: 10417274
  • Human Gene Mutation Database (Bio-base).
  • Liu H. et al. 2016. American Journal of Medical Genetics. Part A. 170: 1347-51. PubMed ID: 26858006
  • Polinati P.P. et al. 2015. Brain & Development. 37: 107-13. PubMed ID: 24613099
  • Sacksteder K.A. et al. 1999. The Journal of Biological Chemistry. 274: 24461-8. PubMed ID: 10455107
  • Salomons G.S. et al. 2007. Journal of Inherited Metabolic Disease. 30: 23-8. PubMed ID: 17186413


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

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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