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Methlymalonyl-CoA Epimerase Deficiency via the MCEE Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
2192 MCEE$540.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity

At this time, the sensitivity of this test is difficult to estimate due to the low number of cases reported in the literature. Analytical sensitivity may be high as the only reported causative variants are detectable by sequencing.  

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Clinical Features

Methylmalonic acidemia (MMA) without homocystinuria is caused either by errors in the biochemical pathway in which propionyl-CoA is converted to succinyl-CoA, or by defects in the generation of the enzymatic cofactor adenosylcobalamin (AdoCbl) (Dobson et al 2006; Manoli et al. 2016). The vast majority of diagnosed cases of MMA are caused by variants in the MUT gene, followed by the MMAA, MMAB, MMADHC and MCEE genes. Very few patients have been reported to have variants in the MCEE gene, so a cohesive clinical picture has yet to emerge. Symptoms reported in the few MCEE patients thus far include failure to gain weight, gastroesophageal reflux, tachypnea, vomiting and diarrhea. Biochemically, these patients have been found to exhibit mild to moderately increased levels of serum methylmalonic acid and methylcitric acid, as well as severe metabolic acidosis. Plasma total homocysteine levels have been reported to be normal (Bikker et al. 2006; Dobson et al 2006; Gradinger et al. 2007; Manoli et al. 2016). One patient presented with progressive delayed motor development; however, this patient was the child of consanguineous parents and was also diagnosed with sepiapterin deficiency, to which the motor delays were largely attributed (Bikker et al. 2006). MCEE deficiency has also been reported to occur in asymptomatic individuals (Bikker et al. 2006; Dobson et al 2006; Gradinger et al. 2007).

Treatment of the reported patients has included a protein-restricted diet and vitamin B12 supplementation, although too few reports exist to be certain of the efficacy of this regimen (Bikker et al. 2006; Dobson et al 2006).

Genetics

Methlymalonyl-CoA Epimerase Deficiency is thought to be an autosomal recessive disorder, and MCEE is the only gene in which defects occur. To date, fewer than five causative variants have been reported in the MCEE gene (Human Gene Mutation Database; Gradinger et al. 2007). Two of these variants (p.Arg47* and p.Lys60Gln) have been reported in the homozygous state, while the third (p.Arg143Cys) has been reported in the heterozygous state in two patients for whom a second variant was not identified. Of these variants, the p.Arg47* variant appears to be the most common as it has been reported in at least three families (Bikker et al. 2006; Dobson et al 2006; Gradinger et al. 2007).

Methlymalonyl-CoA Epimerase Deficiency is caused by defects in the Methlymalonyl-CoA Epimerase enzyme, which is responsible for the interconversion of the D- and L-methylmalonyl-CoA. The D- and L-methylmalonyl-CoA products are intermediates in the pathway whereby propionyl-CoA is converted to succinyl-CoA (Dobson et al. 2007).

Testing Strategy

This test involves bidirectional Sanger sequencing using genomic DNA of all coding exons of the MCEE gene plus ~20 bp of flanking non-coding DNA on each side. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results.

This testing also includes coverage for the following intronic variant, as well as ~20 bp of adjacent sequence: c.379-644A>G.

Indications for Test

Individuals with elevated serum methylmalonic acid are good candidates for this test, particularly if cellular complementation and/or studies are not able to pinpoint the suspected type of methylmalonic acidemia. Family members of patients known to have MCEE variants are also good candidates, and we will also sequence the MCEE gene to determine carrier status.

Gene

Official Gene Symbol OMIM ID
MCEE 608419
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Methylmalonyl-CoA Epimerase Deficiency AR 251120

Related Tests

Name
Disorders Related to Metabolism of Cobalamin, Folate and Homocysteine Sequencing Panel
Methylmalonic Acidemia Sequencing Panel
Organic Aciduria Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Bikker H. et al. 2006. Human Mutation. 27: 640-3. PubMed ID: 16752391
  • Dobson C.M. et al. 2006. Molecular Genetics and Metabolism. 88: 327-33. PubMed ID: 16697227
  • Gradinger A.B. et al. 2007. Human Mutation. 28: 1045. PubMed ID: 17823972
  • Human Gene Mutation Database (Bio-base).
  • Manoli I. et al. 2016. Isolated Methylmalonic Acidemia. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301409
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TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

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Ordering Options


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.
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.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.

CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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