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Functional assays combined with pre-mRNA splicing analysis improve variant classification and diagnostics for individuals with Neurofibromatosis type 1 and Legius syndrome.
  • +15
  • Mark Nellist,
  • Hannie C.W. Douben,
  • Marianne Hoogeveen-Westerveld,
  • Jesse Louwen,
  • Marian Kroos-de Haan,
  • Mattijs Punt,
  • Babeth van Ommeren,
  • Leontine van Unen,
  • P. Elfferich,
  • Esmee Kasteleijn,
  • Yolande Van Bever,
  • Margreethe van Vliet,
  • Rianne Oostenbrink,
  • Jasper Saris,
  • Anja Wagner,
  • Yvette van Ierland,
  • Tjakko J. van Ham,
  • Rick Van Minkelen
Mark Nellist
Erasmus MC Afdeling Klinische Genetica

Corresponding Author:[email protected]

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Hannie C.W. Douben
Erasmus MC
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Marianne Hoogeveen-Westerveld
Erasmus MC
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Jesse Louwen
Erasmus MC Afdeling Klinische Genetica
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Marian Kroos-de Haan
Erasmus MC Afdeling Klinische Genetica
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Mattijs Punt
Erasmus MC
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Babeth van Ommeren
Erasmus MC Afdeling Klinische Genetica
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Leontine van Unen
Erasmus MC Afdeling Klinische Genetica
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P. Elfferich
Erasmus MC Afdeling Klinische Genetica
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Esmee Kasteleijn
Erasmus MC Afdeling Klinische Genetica
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Yolande Van Bever
Erasmus MC Afdeling Klinische Genetica
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Margreethe van Vliet
Erasmus MC Afdeling Klinische Genetica
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Rianne Oostenbrink
Erasmus MC
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Jasper Saris
Erasmus MC Afdeling Klinische Genetica
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Anja Wagner
Erasmus MC Afdeling Klinische Genetica
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Yvette van Ierland
Erasmus MC
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Tjakko J. van Ham
Erasmus MC Afdeling Klinische Genetica
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Rick Van Minkelen
Erasmus MC
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Abstract

Neurofibromatosis type 1 (NF1) and Legius syndrome (LS) are caused by inactivating variants in NF1 and SPRED1. NF1 encodes neurofibromin (NF), a GTPase activating protein (GAP) for RAS, that interacts with the SPRED1 product, Sprouty-related protein with an EVH (Ena/Vasp homology) domain 1 (SPRED1). Establishing a clinical and molecular diagnosis of NF1 or LS can be challenging due to the phenotypic diversity, the size and complexity of the NF1 and SPRED1 loci and uncertainty over the effects of variants on pre-mRNA splicing and NF/SPRED1 function. The purpose of this work was to improve NF1 and SPRED1 variant classification. To help establish the pathogenicity of NF1 and SPRED1 variants identified in individuals with NF1 or LS, we employed 4 assays: (i) analysis of patient RNA by RT-PCR; (ii) in vitro exon trap analysis of NF1 pre-mRNA splicing; (iii) in vitro analysis of NF RAS GAP activity; and (iv) in vitro analysis of the NF-SPRED1 interaction. In 69/105 (66%) cases we obtained evidence to support variant pathogenicity according to American College of Medical Genetics guidelines, demonstrating the utility of functional approaches for NF1 and SPRED1 variant classification and NF and LS diagnostics.
09 May 2022Submitted to Human Mutation
10 May 2022Assigned to Editor
10 May 2022Submission Checks Completed
23 May 2022Reviewer(s) Assigned
14 Jun 2022Review(s) Completed, Editorial Evaluation Pending
16 Jun 2022Editorial Decision: Revise Major