Detection of splicing aberrations caused by BRCA1 and BRCA2 sequence variants encoding missense substitutions: Implications for prediction of pathogenicity

Logan C. Walker, Phillip J. Whiley, Fergus J. Couch, Daniel J. Farrugia, Sue Healey, Diana M. Eccles, Feng Lin, Samantha A. Butler, Sheila A. Goff, Bryony A. Thompson, Sunil R. Lakhani, Leonard M. Da Silva, Sean V. Tavtigian, David E. Goldgar, Melissa A. Brown, Amanda B. Spurdle

Research output: Contribution to journalArticle

49 Scopus citations

Abstract

Missense substitutions in high-risk cancer susceptibility genes create clinical uncertainty in the genetic counseling process. Multifactorial likelihood classification approaches and in vitro assays are useful for the classification of exonic sequence variants in BRCA1 and BRCA2, but these currently rely on the assumption that changes in protein function are the major biological mechanism of pathogenicity. This study investigates the potentially pathogenic role of aberrant splicing for exonic variants predicted to encode missense substitutions using patientderived RNA. No splicing aberrations were identified for BRCA1c.5054C>T and BRCA2c.7336A>G, c.8839G>A, and c.9154C>T. However, RT-PCR analysis identified a major splicing aberration for BRCA1c.4868C>G(p.Ala1623Gly), a variant encoding a missense substitution considered likely to be neutral. Splicing aberrations were also observed for BRCA2c.7988A>T(p.Glu2663Val) and c.8168A>G(p.Asp2723Gly), but both variant and wildtype alleles were shown to be present in full-length mRNA transcripts, suggesting that variant protein may be translated. BRCA2 protein function assays indicated that BRCA2p.Glu2663Val, p.Asp2723Gly and p.Arg3052Trp missense proteins have abrogated function consistent with pathogenicity. Multifactorial likelihood analysis provided evidence for pathogenicity for BRCA1 c.5054C>T(p.Thr1685Ile) and BRCA2c.7988A>T(p.Glu2663Val), c.8168A>G(p.Asp2723Gly) and c.9154C>T(p.Arg3052Trp), supporting experimentally derived evidence. These findings highlight the need for improved bioinformatic prediction of splicing aberrations and to refine multifactorial likelihood models used to assess clinical significance.

Original languageEnglish (US)
Pages (from-to)E1484-E1505
JournalHuman mutation
Volume31
Issue number6
DOIs
StatePublished - Jun 2010

Keywords

  • BRCA1
  • BRCA2
  • Clinical significance
  • Splicing
  • Variants

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Fingerprint Dive into the research topics of 'Detection of splicing aberrations caused by BRCA1 and BRCA2 sequence variants encoding missense substitutions: Implications for prediction of pathogenicity'. Together they form a unique fingerprint.

  • Cite this

    Walker, L. C., Whiley, P. J., Couch, F. J., Farrugia, D. J., Healey, S., Eccles, D. M., Lin, F., Butler, S. A., Goff, S. A., Thompson, B. A., Lakhani, S. R., Da Silva, L. M., Tavtigian, S. V., Goldgar, D. E., Brown, M. A., & Spurdle, A. B. (2010). Detection of splicing aberrations caused by BRCA1 and BRCA2 sequence variants encoding missense substitutions: Implications for prediction of pathogenicity. Human mutation, 31(6), E1484-E1505. https://doi.org/10.1002/humu.21267