Cited by 98BRCA gene mutations in cancerRNA Research and SplicingGenomics and Rare Diseases

Intronic variants in BRCA1 and BRCA2 that affect RNA splicing can be reliably selected by splice-site prediction programs

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Vreeswijk, Maaike P.G., Kraan, Jaennelle N., van der Klift, Heleen M., Vink, Geraldine R., Cornelisse, Cees J., Wijnen, Juul T., Bakker, Egbert, van Asperen, Christi J. +1 more·2009·Human Mutation

Abstract

A large number of sequence variants identified in BRCA1 and BRCA2 cannot be distinguished as either disease-causing mutations or neutral variants. These so-called unclassified variants (UVs) include variants that are located in the intronic sequences of BRCA1 and BRCA2. The purpose of this study was to assess the use of splice-site prediction programs (SSPPs) to select intronic variants in BRCA1 and BRCA2 that are likely to affect RNA splicing. We performed in vitro molecular characterization of RNA of six intronic variants in BRCA1 and BRCA2. In four cases (BRCA1, c.81-6T>A and c.4986+5G>T; BRCA2, c.7617+2T>G and c.8754+5G>A) a deleterious effect on RNA splicing was seen, whereas the c.135-15_-12del variant in BRCA1 showed no effect on RNA splicing. In the case of the BRCA2 c.68-7T>A variant, RNA analysis was not sufficient to establish the clinical significance. Six SSPPs were used to predict whether an effect on RNA splicing was expected for these six variants as well as for 23 intronic variants in BRCA1 for which the effect on RNA splicing has been published. Out of a total of 174 predictions, 161 (93%) were informative (i.e., the wild-type splice-site was recognized). No false-negative predictions were observed; an effect on RNA splicing was always predicted by these programs. In four cases (2.5%) a false-positive prediction was observed. For DNA diagnostic laboratories, these programs are therefore very useful to select intronic variants that are likely to affect RNA splicing for further analysis.

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Authors
Vreeswijk, M. P. G., Kraan, J. N., van der Klift, H. M., Vink, G. R., Cornelisse, C. J., Wijnen, J. T., Bakker, E., van Asperen, C. J., & Devilee, P.
Affiliations
Leiden University Medical Center (NL)
Corresponding author
Vreeswijk, Maaike P.G.
Venue
Human Mutation
Published
2009-01
Volume
30
Issue
1
Pages
107-114
ISSN
  • 1059-7794 (ISSN-L)
  • 1098-1004
OpenAlex
W2013639985
Cited by
98
References
47
Citations by year
2025: 1 · 2023: 2 · 2022: 4 · 2021: 5 · 2020: 3 · 2019: 9 · 2018: 9 · 2017: 7 · 2016: 10 · 2015: 5 · 2014: 5 · 2013: 7 · 2012: 6
FWCI
4.75
Type
journal article
Language
en
Open access
Locations
  • Human Mutation (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Keywords
BRCA1, BRCA2, intronic variants, splice site prediction, RNA splicing, unclassified variants, variant interpretation, false positive prediction
MeSH terms
Adult, Base Sequence, Breast Neoplasms, Female, Humans, Introns, Molecular Sequence Data, RNA Splicing, Software, Genetic Variation, Sequence Analysis, RNA, BRCA1 Protein, RNA Splice Sites, BRCA2 Protein

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