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  • Test code: 06192
  • 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
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Invitae 3-Methylcrotonyl-CoA Carboxylase Panel

Test description

The Invitae 3-Methylcrotonyl-CoA Carboxyalse Deficiency Panel analyzes the two genes that are associated with 3-Methylcrotonyl-CoA Carboxyalse (3MCC) deficiency. This test is useful for the diagnosis of patients who are suspected to have 3MCC deficiency according to clinical symptoms, biochemical findings, or abnormal newborn-screening results.

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Primary panel (2 genes)

Alternative tests to consider

The Invitae Organic Acidemias Panel and the Invitae Elevated C5-OH Panel have been designed to provide a broad genetic analysis of these classes of disorders. Depending on the individual’s clinical and family history, one of these broader panels may be appropriate. They can be ordered at no additional cost.

  • 3-methylcrotonyl-CoA carboxylase (3MCC) deficiency

Patients with 3MCC deficiency show a wide range of phenotypic severity, from asymptomatic to more severe. Traditionally, diagnosis relied on ascertainment of symptomatic patients. A wide range of symptoms have been reported, including developmental delay, intellectual disability, seizures, hypotonia, hypoglycemia, metabolic acidosis, ketosis, Reye syndrome, hyperammonemia, secondary carnitine depletion, and even coma or death; however, with the advent of expanded newborn screening, it is now recognized that the vast majority (>90%) of diagnosed individuals are asymptomatic, despite the presence of the characteristic biochemical abnormalities. No phenotype-genotype correlations exist, and recent studies have suggested that symptoms in at least some clinically affected individuals may have an alternative underlying cause.

Patients with 3MCC deficiency typically have biochemical laboratory findings, including elevations of 3-hydroxyisovaleric acid and 3-methylcrotonylglycine on urine organic acid analysis; and elevation of 3-hydroxyisovalerylcarnitine (C5-OH) on newborn screening or plasma acylcarnitine analysis. Asymptomatic mothers may also be diagnosed due to elevated C5-OH in their healthy babies’ newborn-screening result.

Approximately 99% of patients with isolated 3MCC deficiency will have two pathogenic variants in either the MCCC1 or MCCC2 gene.

3MCC deficiency is inherited in an autosomal recessive pattern.

The general prevalence for 3MCC deficiency is estimated at 1 in 41,700–84,700 individuals.

  1. Thomsen, JA, et al. Is L-Carnitine Supplementation Beneficial in 3-Methylcrotonyl-CoA Carboxylase Deficiency?. JIMD Rep. 2015; 21:79-88. PMID: 25732994
  2. Kör, D, et al. An asymptomatic mother diagnosed with 3-methylcrotonyl-CoA carboxylase deficiency after newborn screening. J. Pediatr. Endocrinol. Metab. 2015; 28(5-6):669-71. PMID: 25381946
  3. Shepard, PJ, et al. Consanguinity and rare mutations outside of MCCC genes underlie nonspecific phenotypes of MCCD. Genet. Med. 2015; 17(8):660-7. PMID: 25356967
  4. Feuchtbaum, L, et al. Birth prevalence of disorders detectable through newborn screening by race/ethnicity. Genet. Med. 2012; 14(11):937-45. PMID: 22766612
  5. Lam, C, et al. Analysis of cases of 3-methylcrotonyl CoA carboxylase deficiency (3-MCCD) in the California newborn screening program reported in the state database. Mol. Genet. Metab. 2013; 110(4):477-83. PMID: 24103308
  6. Stadler, SC, et al. Newborn screening for 3-methylcrotonyl-CoA carboxylase deficiency: population heterogeneity of MCCA and MCCB mutations and impact on risk assessment. Hum. Mutat. 2006; 27(8):748-59. PMID: 16835865
  7. Grünert, SC, et al. 3-methylcrotonyl-CoA carboxylase deficiency: clinical, biochemical, enzymatic and molecular studies in 88 individuals. Orphanet J Rare Dis. 2012; 7:31. PMID: 22642865
  8. 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.
  9. American College of Medical Genetics. NBS ACT Sheet. Organic Acidemias. https://www.acmg.net/StaticContent/ACT/C5-OH.pdf Accessed February 2016.

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 in the transcript listed below. In addition, analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any specific limitations in the analysis of these genes are also listed in the table below.

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
MCCC1 NM_020166.4
MCCC2 NM_022132.4