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

Detection of splicing aberrations caused by BRCA1 and BRCA2 sequence variants encoding missense substitutions: implications for prediction of pathogenicity
Detection of splicing aberrations caused by BRCA1 and BRCA2 sequence variants encoding missense substitutions: implications for prediction of pathogenicity
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 patient-derived 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
1059-7794
E1484-E1505
Walker, Logan C.
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Whiley, Phillip J.
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Couch, Fergus J.
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Farrugia, Daniel J.
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Healey, Sue
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Eccles, Diana
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Lin, Feng
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Butler, Samantha A.
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Goff, Sheila A.
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Thompson, Bryony A.
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Lakhani, Sunil R.
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Da Silva, Leonard M.
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Tavtigian, Sean V.
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Goldgar, David E.
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Brown, Melissa A.
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Spurdle, Amanda B.
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Walker, Logan C.
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Whiley, Phillip J.
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Couch, Fergus J.
778e32f1-0b19-4cf4-b38f-69dd027cad3a
Farrugia, Daniel J.
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Healey, Sue
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Eccles, Diana
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Lin, Feng
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Butler, Samantha A.
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Goff, Sheila A.
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Thompson, Bryony A.
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Lakhani, Sunil R.
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Da Silva, Leonard M.
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Tavtigian, Sean V.
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Goldgar, David E.
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Brown, Melissa A.
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Spurdle, Amanda B.
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Walker, Logan C., Whiley, Phillip J., Couch, Fergus J., Farrugia, Daniel J., Healey, Sue, Eccles, Diana, Lin, Feng, Butler, Samantha A., Goff, Sheila A., Thompson, Bryony A., Lakhani, Sunil R., Da Silva, Leonard M., Tavtigian, Sean V., Goldgar, David E., Brown, Melissa A. and Spurdle, Amanda 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. (doi:10.1002/humu.21267).

Record type: Article

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 patient-derived 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

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Published date: June 2010

Identifiers

Local EPrints ID: 180161
URI: http://eprints.soton.ac.uk/id/eprint/180161
ISSN: 1059-7794
PURE UUID: c3c998f2-8d86-46ea-814a-0063f78cc16a
ORCID for Diana Eccles: ORCID iD orcid.org/0000-0002-9935-3169

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Date deposited: 05 Apr 2011 13:28
Last modified: 15 Mar 2024 02:40

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Contributors

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

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