3-Methylcrotonyl-CoA Carboxylase (3-MCC) Deficiency: MCCC1/MCCC2 Gene Sequencing

Condition Description

3-Methylcrotonyl-CoA Carboxylase (3-MCC) deficiency is an autosomal recessive inborn error of leucine metabolism [1]. 3-MCC is a biotin-dependent enzyme in the L-leucine degradation pathway. Newborn screening which includes testing for 3-MCC by tandem mass spectrometry, may reveal increased levels of 3-hydroxyisovalerylcarnitine (C5-OH).

The clinical course has been shown to vary considerably, ranging from entirely asymptomatic to death in infancy [3]. Severe and mild phenotypes are not clearly defined, but the vast majority of individuals have mild phenotypes which may be asymptomatic, while a subgroup shows mild unspecific symptoms like fatigue and weakness during catabolic episodes or mild developmental delay.

Isolated 3-MCC deficiency, which is not responsive to treatment with biotin, can be distinguished from the biotin-responsive multiple-carboxylase deficiencies, which are due to disorders of biotin metabolism (biotinidase deficiency and holocarboxylase synthetase deficiency) and affect all four of the biotin-dependent carboxylases. Infants with elevated C5-OH may also be due to maternal 3-MCC deficiency[2].

The 3-MCC enzyme consists of two subunits encoded by the MCCC1 (MCCA) gene on 3q26 and the MCCC2 (MCCB) gene on 5q13. Sequencing analysis is available to test for mutations in the MCCC1 and MCCC2 genes, associated with 3-MCC deficiency. For patients with mutations not identified by full gene sequencing, a separate deletion/duplication assay is available using a targeted CGH array.

1. Sweetman and Williams. Branched Chain Organic Acidurias, in: C.R. Scriver, A.L. Beaudet, W. Sly, D. Valle (Eds.), The Metabolic and Molecular Bases of Inherited Disease, McGraw-Hill, New York, 2001, pp. 2135-2137.
2. Gibson et al. 3-Methylcrotonyl-coenzyme A carboxylase deficiency in Amish/Mennonite adults identified by detection of increased acylcarnitines in blood spots of their children. J Pediatr 1998, 132:519.
3. Stadler 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):748-759.
4. Baumgartner et al. The molecular basis of human 3-methylcrotonyl-CoA carboxylase deficiency. J Clin Invest 2001, 107:495-504.
5. Dantas et al. 3-Methylcrotonyl-CoA carboxylase deficiency: mutation analysis in 28 probands, 9 symptomatic and 19 detected by newborn screening. Hum Mutat 2005, 26:164-175.
6. Holzinger et al. Cloning of the human MCCA and MCCB genes and mutations therein reveal the molecular cause of 3-methylcrotonyl-CoA: carboxylase deficiency. Hum Mol Genet 2001, 10(12):1299-1306.
7. Baumgartner MR. Molecular mechanism of dominant expression in 3-methylcrotonyl-CoA carboxylase deficiency. J Inherit Metab Dis 2005, 28(3):301-9.

Genes (2)


This test is indicated for:

  • Individuals with clinical and biochemical findings consistent with 3-MCC deficiency.
  • Carrier testing in individuals with a family history of 3-MCC deficiency.


Next Generation Sequencing: In-solution hybridization of all coding exons is performed on the patient's genomic DNA. Although some deep intronic regions may also be analyzed, this assay is not meant to interrogate most promoter regions, deep intronic regions, or other regulatory elements, and does not detect single or multi-exon deletions or duplications. Direct sequencing of the captured regions is performed using next generation sequencing. The patient's gene sequences are then compared to a standard reference sequence. Potentially causative variants and areas of low coverage are Sanger-sequenced. Sequence variations are classified as pathogenic, likely pathogenic, benign, likely benign, or variants of unknown significance. Variants of unknown significance may require further studies of the patient and/or family members.


Clinical Sensitivity:

  • 52/56 mutations identified in 28 patients [5].
  • 7/8 mutations identified in 4 patients [6].
  • 4/4 mutations identified in 2 patients [7].

Analytical Sensitivity: ~99%. The majority of patients with clinical and biochemical diagnosis of 3-MCC deficiency will have gene mutations detected by sequence analysis.

Specimen Requirements

Listed below are EGL's preferred sample criteria. For any questions, please call 470.378.2200 and ask to speak with a laboratory genetic counselor (eglgc@egl-eurofins.com).
Submit only 1 of the following specimen types
DNA, Isolated

Isolation using the Perkin Elmer™Chemagen™ Chemagen™ Automated Extraction method or Qiagen™ Puregene kit for DNA extraction is recommended.
Collection and Shipping
Refrigerate until time of shipment in 100 ng/µL in TE buffer. Ship sample at room temperature with overnight delivery.

Oragene™ Saliva Collection Kit
Orangene™ Saliva Collection Kit used according to manufacturer instructions. Please contact EGL for a Saliva Collection Kit for patients that cannot provide a blood sample.
Collection and Shipping
Please do not refrigerate or freeze saliva sample. Please store and ship at room temperature.
Whole Blood (EDTA)

EDTA (Purple Top)
Infants and Young Children (<2 years of age): 2-3 ml
Children > 2 years of age to 10 years old: 3-5 ml
Older Children & Adults: 5-10 ml
Autopsy: 2-3 ml unclotted cord or cardiac blood
Collection and Shipping
Ship sample at room temperature for receipt at EGL within 72 hours of collection. Do not freeze.

Special Instructions

Please submit copies of diagnostic biochemical test results along with the sample. Contact the laboratory if further information is needed. Sequence analysis is required before deletion/duplication analysis by targeted CGH array. If sequencing is performed outside of EGL Genetics, please submit a copy of the sequencing report with the test requisition.
  • Organic Acid Analysis (OA) - Urine and Acylcarnitine Profile (AR) - Plasma are used in the diagnosis of a patient with 3-MCC deficiency.
  • Known Mutation Analysis (KM) is available to family members if mutations are identified by sequencing.
  • For comprehensive testing, 3-Methylcrotonyl-CoA Carboxylase Deficiency (3-MCC): MCCC1/MCCC2 Gene Deletion/Duplication (JZ) is available separately. This test is indicated for individuals where mutations are not identified by sequence analysis. Refer to the test requisition or contact the laboratory for more information.

Prenatal Custom Diagnostics is available to couples who are confirmed carriers of mutations. Please contact the laboratory genetic counselor to discuss appropriate testing prior to collecting a prenatal specimen.

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