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Exome sequencing identifies ACSF3 as a cause of combined malonic and methylmalonic aciduria

Nature Genetics volume 43, pages 883–886 (2011)Cite this article

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Abstract

We used exome sequencing to identify the genetic basis of combined malonic and methylmalonic aciduria (CMAMMA). We sequenced the exome of an individual with CMAMMA and followed up with sequencing of eight additional affected individuals (cases). This included one individual who was identified and diagnosed by searching an exome database. We identify mutations in ACSF3, encoding a putative methylmalonyl-CoA and malonyl-CoA synthetase as a cause of CMAMMA. We also examined a canine model of CMAMMA, which showed pathogenic mutations in a predicted ACSF3 ortholog. ACSF3 mutant alleles occur with a minor allele frequency of 0.0058 in ∼1,000 control individuals, predicting a CMAMMA population incidence of ∼1:30,000. ACSF3 deficiency is the first human disorder identified as caused by mutations in a gene encoding a member of the acyl-CoA synthetase family, a diverse group of evolutionarily conserved proteins, and may emerge as one of the more common human metabolic disorders.

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Figure 1: Alignment of the motif regions in ACSF3 orthologs and the malonyl-CoA synthetase enzymes in bacteria.
Figure 2: MMA production by CMAMMA fibroblasts and lentiviral complementation with ACSF3.
Figure 3: ACSF3 mitochondrial localization.

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Accessions

GenBank/EMBL/DDBJ

NCBI Reference Sequence

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Acknowledgements

We thank the subjects and families for participating, E. Ostrander for the gift of unrelated Labrador DNA samples, K.M. Gibson and R. Wander for performing the malonyl-CoA decarboxylase assay on fibroblasts from subjects 2 and 9, J. Teer for bioinformatics assistance, S. Suchy for subject referral, M. Podell and W. Gahl for helpful discussions, R. Fisher, I. Bernardini, A. Gropman, L. Hecht, F. Facio, C. Gitiaux, C. Ottolenghi, D. Rabier and G. Touati for laboratory assistance and clinical care, and M. Oglesbee and A. Genders for searching for dogs related to the affected Labrador retriever. J.L.S., J.J.J., I.M., R.J.C., N.C.-C., S.D.C., J.R.S., H.M.D., M.H., K.O., N.S.H., J.C.S., C.K., L.G.B. and C.P.V. were supported by the Intramural Research Program of the NHGRI, NIH. M.D.G. was supported by NIA K23 AG021989 and R01-AG031189.

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Author notes

  1. Jennifer L Sloan, Jennifer J Johnston and Dimitar K Gavrilov: These authors contributed equally to this work.

Authors and Affiliations

  1. Genetics and Molecular Biology Branch, National Human Genome Research Institute (NHGRI), US National Institutes of Health (NIH), Bethesda, Maryland, USA

    Jennifer L Sloan, Irini Manoli, Randy J Chandler, Nuria Carrillo-Carrasco, Suma D Chandrasekaran, Justin R Sysol, Natalie S Hauser & Charles P Venditti

  2. Genetic Disease Research Branch, NHGRI, NIH, Bethesda, Maryland, USA

    Jennifer J Johnston, Caitlin Krause, Julie C Sapp & Leslie G Biesecker

  3. Department of Pharmacology, Institute for Biomedical Sciences, George Washington University, Washington, DC, USA

    Randy J Chandler

  4. Medical Genetics Branch, NHGRI, NIH, Bethesda, Maryland, USA

    Kevin O'Brien, Heidi M Dorward & Marjan Huizing

  5. Department of Pediatrics, Biochemical Genetics Laboratory, University of California, San Diego, La Jolla, California, USA

    Bruce A Barshop & William L Nyhan

  6. Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA

    Susan A Berry

  7. Department of Pediatrics, Harvard Medical School, Children's Hospital Boston, Boston, Massachusetts, USA

    Philip M James

  8. Greenwood Genetics Center, Greenwood, South Carolina, USA

    Neena L Champaigne

  9. Reference Center for Inherited Metabolic Disorders, Necker-Enfants Malades Hospital, Paris, France

    Pascale de Lonlay & Vassilli Valayannopoulos

  10. Department of Neurology, University of California, San Francisco, San Francisco, California, USA.,

    Michael D Geschwind

  11. Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA

    Dimitar K Gavrilov

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  1. Jennifer L Sloan
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Consortia

NIH Intramural Sequencing Center Group

Contributions

J.C.S. and L.G.B. developed the exome sequencing protocol. J.L.S., I.M., J.C.S., L.G.B. and C.P.V. designed the clinical research studies. The NIH Intramural Sequencing Center Group (N.I.S.C.G.) performed exome sequencing. J.J.J., J.L.S., I.M., R.J.C., L.G.B. and C.P.V. performed bioinformatic analyses. J.J.J. and C.K. performed mutational analysis and genotyping. R.J.C., N.C.-C., S.D.C. and J.R.S. performed cell culture studies and protein blot analyses. R.J.C. created viral vectors and performed cellular complementation studies. J.L.S., M.H. and H.M.D. performed immunofluorescence experiments. J.L.S., J.R.S. and I.M. performed enzymatic assays. J.L.S., I.M., N.S.H., K.O., J.C.S., B.A.B., S.A.B., P.M.J., N.L.C., P.d.L., V.V., M.D.G., W.L.N., L.G.B. and C.P.V. contributed to clinical evaluations and the delineation of the subject phenotypes. D.K.G. performed organic acid measurements. J.L.S., J.J.J., L.G.B. and C.P.V. prepared the manuscript. L.G.B. and C.P.V. conceived of and supervised the study.

Corresponding author

Correspondence to Leslie G Biesecker.

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The authors declare no competing financial interests.

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NIH Intramural Sequencing Center Group

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Supplementary Figures 1–4 and Supplementary Tables 1–3. (PDF 2074 kb)

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Sloan, J., Johnston, J., Manoli, I. et al. Exome sequencing identifies ACSF3 as a cause of combined malonic and methylmalonic aciduria. Nat Genet 43, 883–886 (2011). https://doi.org/10.1038/ng.908

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