Exome sequencing identifies a DNAJB6 mutation in a family with dominantly-inherited limb-girdle muscular dystrophy

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Abstract

Limb-girdle muscular dystrophy primarily affects the muscles of the hips and shoulders (the “limb-girdle” muscles), although it is a heterogeneous disorder that can present with varying symptoms. There is currently no cure. We sought to identify the genetic basis of limb-girdle muscular dystrophy type 1 in an American family of Northern European descent using exome sequencing. Exome sequencing was performed on DNA samples from two affected siblings and one unaffected sibling and resulted in the identification of eleven candidate mutations that co-segregated with the disease. Notably, this list included a previously reported mutation in DNAJB6, p.Phe89Ile, which was recently identified as a cause of limb-girdle muscular dystrophy type 1D. Additional family members were Sanger sequenced and the mutation in DNAJB6 was only found in affected individuals. Subsequent haplotype analysis indicated that this DNAJB6 p.Phe89Ile mutation likely arose independently of the previously reported mutation. Since other published mutations are located close by in the G/F domain of DNAJB6, this suggests that the area may represent a mutational hotspot. Exome sequencing provided an unbiased and effective method for identifying the genetic etiology of limb-girdle muscular dystrophy type 1 in a previously genetically uncharacterized family. This work further confirms the causative role of DNAJB6 mutations in limb-girdle muscular dystrophy type 1D.

Introduction

Autosomal dominant limb-girdle muscular dystrophies (LGMD1) are a genetically and clinically heterogeneous group of disorders. LGMD1 often presents with progressive proximal muscle weakness of the upper and lower extremities; however several forms may present with primarily distal weakness, and clinical heterogeneity may exist even within the same family [1]. To date, mutations in five causative genes have been associated with LGMD1, including the MYOT gene encoding myotilin in LGMD1A [2], the LMNA gene encoding lamin A/C in LGMD1B [3], the CAV3 gene which encodes caveolin in LGMD1C [4]. More recently, mutations in the DNAJB6 gene have been described in LGMD1D patients [5], [6], [7] and mutations in Transportin 3 (TNPO3) gene have been linked to LGMD1F [8], [9]. Additional loci linked to LGMD1 have been mapped, but causative genes have not been identified [1].

Using exome sequencing, we sought to determine the genetic basis for LGMD1 in an American family of Northern European descent that presented with an autosomal dominant pattern of inheritance. Exome sequencing has been used to great effect to identify the underlying mutations in a number of diseases, including recently in LGMD1 [5], [8].

Section snippets

Patients and methods

All aspects of this study were approved by the Stanford University Institutional Review Board and written informed consent was received.

Proband (III-3, Fig. 1A arrowhead) presented at 55 years of age to clinic, with a history of slow running and difficulty climbing stairs, beginning shortly after high school. He began using a cane in his late 30s, two canes in his 40s, and at 56 years of age, developed acute worsening of upper and lower extremity strength owing to severe cervical spinal cord

Exome sequencing

Exome sequencing was performed for two affected brothers (Fig. 1A red asterisks; III-1 and III-3) and one unaffected sister (III-2); average coverage depth was 60X. Eleven novel variants shared between the two affected brothers (III-1 and III-3) but not present in the unaffected sister (III-2) were identified (Supplemental Table 1). Included in the list of disease-segregating variants was a variation in the DNAJB6 gene, c.265T > A, producing a p.Phe89Ile substitution, which is located in the G/F

Discussion

Using the unbiased technique of exome sequencing, we identified a mutation in DNAJB6 in a family with LGMD1. LGMD1D was originally described in several Finnish families with linkage to chromosome 7q36 and recently three studies in Finnish, Italian, American, and Japanese families revealed the causative gene to be DNAJB6 [5], [6], [7], [15], [18]. The nomenclature of LGMD associated with DNAJB6 mutations is confusing, with some groups utilizing the HUGO Gene Nomenclature Committee’s locus

Acknowledgements

We thank the patients and their family for participating in this study. Supported by NIH Director’s New Innovator Award DP2OD004417 (A.D.G.), NIH Grants NS065317 (A.D.G.) and NS073660 (A.D.G.). A.D.G. is a Pew Scholar in the Biomedical Sciences, supported by The Pew Charitable Trusts, and a Rita Allen Foundation Scholar. A.R.R. is supported by an Alzheimer’s Disease Research Grant from the BrightFocus Foundation. J.D.B. is supported by the NIH-NHGRI Stanford Genome Science training grant. We

References (24)

  • J. Sarparanta et al.

    Mutations affecting the cytoplasmic functions of the co-chaperone DNAJB6 cause limb-girdle muscular dystrophy

    Nat Genet

    (2012)
  • A. Torella et al.

    Next-generation sequencing identifies transportin 3 as the causative gene for LGMD1F

    PLoS One

    (2013)
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    1

    These authors contributed equally to the manuscript.

    2

    Current address: University of California Irvine School of Medicine, Irvine, CA, USA.

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