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
E1484-E1505
Walker, Logan C.
d6db41bd-937e-44aa-bff6-33686387939a
Whiley, Phillip J.
72aef9ff-59e4-4f42-a1dc-a60a0cd7ab48
Couch, Fergus J.
778e32f1-0b19-4cf4-b38f-69dd027cad3a
Farrugia, Daniel J.
751487ee-9795-4104-9111-b235ad164cb4
Healey, Sue
5d595192-5381-464d-85cc-71ad09a05065
Eccles, Diana
5b59bc73-11c9-4cf0-a9d5-7a8e523eee23
Lin, Feng
07c7383d-53a3-41bb-82f4-98c24495fd01
Butler, Samantha A.
8b42b817-aec9-4a67-ba6e-60d27c189d37
Goff, Sheila A.
087b5b5e-4508-43f5-891e-21c5317d9c4c
Thompson, Bryony A.
51634e1f-4096-4595-abbe-cd79b92def23
Lakhani, Sunil R.
cc43b574-e4be-476f-b1f5-bb97f9658ada
Da Silva, Leonard M.
a4625ca7-f0af-4d4d-8232-18086e4ff1d6
Tavtigian, Sean V.
6ce776c6-2813-48a1-bb6a-64ec81e13a03
Goldgar, David E.
102af7b6-41ab-46c0-9d76-43359c897e2e
Brown, Melissa A.
898b5f8f-6b40-47db-b76e-2a702f759c26
Spurdle, Amanda B.
8158d468-cc96-4e39-9bac-fcaaa7061a72
June 2010
Walker, Logan C.
d6db41bd-937e-44aa-bff6-33686387939a
Whiley, Phillip J.
72aef9ff-59e4-4f42-a1dc-a60a0cd7ab48
Couch, Fergus J.
778e32f1-0b19-4cf4-b38f-69dd027cad3a
Farrugia, Daniel J.
751487ee-9795-4104-9111-b235ad164cb4
Healey, Sue
5d595192-5381-464d-85cc-71ad09a05065
Eccles, Diana
5b59bc73-11c9-4cf0-a9d5-7a8e523eee23
Lin, Feng
07c7383d-53a3-41bb-82f4-98c24495fd01
Butler, Samantha A.
8b42b817-aec9-4a67-ba6e-60d27c189d37
Goff, Sheila A.
087b5b5e-4508-43f5-891e-21c5317d9c4c
Thompson, Bryony A.
51634e1f-4096-4595-abbe-cd79b92def23
Lakhani, Sunil R.
cc43b574-e4be-476f-b1f5-bb97f9658ada
Da Silva, Leonard M.
a4625ca7-f0af-4d4d-8232-18086e4ff1d6
Tavtigian, Sean V.
6ce776c6-2813-48a1-bb6a-64ec81e13a03
Goldgar, David E.
102af7b6-41ab-46c0-9d76-43359c897e2e
Brown, Melissa A.
898b5f8f-6b40-47db-b76e-2a702f759c26
Spurdle, Amanda B.
8158d468-cc96-4e39-9bac-fcaaa7061a72
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), .
(doi:10.1002/humu.21267).
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
This record has no associated files available for download.
More information
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
Catalogue record
Date deposited: 05 Apr 2011 13:28
Last modified: 15 Mar 2024 02:40
Export record
Altmetrics
Contributors
Author:
Logan C. Walker
Author:
Phillip J. Whiley
Author:
Fergus J. Couch
Author:
Daniel J. Farrugia
Author:
Sue Healey
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
Download statistics
Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.
View more statistics