The intronic BRCA1 c.5407-25T>A variant causing partly skipping of exon 23-a likely pathogenic variant with reduced penetrance?
Journal
European journal of human genetics : EJHG
ISSN: 1476-5438
Titre abrégé: Eur J Hum Genet
Pays: England
ID NLM: 9302235
Informations de publication
Date de publication:
08 2020
08 2020
Historique:
received:
16
10
2019
accepted:
10
03
2020
revised:
03
03
2020
pubmed:
24
3
2020
medline:
2
6
2021
entrez:
24
3
2020
Statut:
ppublish
Résumé
Rare sequence variants in the non-coding part of the BRCA genes are often reported as variants of uncertain significance (VUS), which leave patients and doctors in a challenging position. The aim of this study was to determine the pathogenicity of the BRCA1 c.5407-25T>A variant found in 20 families from Norway, France and United States with suspected hereditary breast and ovarian cancer. This was done by combining clinical and family information with allele frequency data, and assessment of the variant's effect on mRNA splicing. Mean age at breast (n = 12) and ovarian (n = 11) cancer diagnosis in female carriers was 49.9 and 60.4 years, respectively. The mean Manchester score in the 20 families was 16.4. The allele frequency of BRCA1 c.5407-25T>A was 1/64,566 in non-Finnish Europeans (gnomAD database v2.1.1). We found the variant in 1/400 anonymous Norwegian blood donors and 0/784 in-house exomes. Sequencing of patient-derived cDNA from blood, normal breast and ovarian tissue showed that BRCA1 c.5407-25T>A leads to skipping of exon 23, resulting in frameshift and protein truncation: p.(Gly1803GlnfsTer11). Western blot analysis of transiently expressed BRCA1 proteins in HeLa cells showed a reduced amount of the truncated protein compared with wild type. Noteworthily, we found that a small amount of full-length transcript was also generated from the c.5407-25T>A allele, potentially explaining the intermediate cancer burden in families carrying this variant. In summary, our results show that BRCA1 c.5407-25T>A leads to partial skipping of exon 23, and could represent a likely pathogenic variant with reduced penetrance.
Identifiants
pubmed: 32203205
doi: 10.1038/s41431-020-0612-1
pii: 10.1038/s41431-020-0612-1
pmc: PMC7382492
doi:
Substances chimiques
BRCA1 Protein
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1078-1086Références
Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, Tavtigian S, et al. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science. 1994;266:66–71.
doi: 10.1126/science.7545954
Wooster R, Bignell G, Lancaster J, Swift S, Seal S, Mangion J, et al. Identification of the breast cancer susceptibility gene BRCA2. Nature. 1995;378:789–92.
doi: 10.1038/378789a0
Foulkes WD. BRCA1 and BRCA2 - update and implications on the genetics of breast cancer: a clinical perspective. Clin Genet. 2014;85:1–4.
doi: 10.1111/cge.12291
Norwegian Breast Cancer Group. [Nasjonalt handlingsprogram med retningslinjer for diagnostikk, behandling og oppfølging av pasienter med brystkreft] Guideline. Version 13, 2019. https://helsedirektoratet.no/retningslinjer/nasjonalt-handlingsprogram-med-retningslinjer-for-diagnostikk-behandling-og-oppfolging-av-pasienter-med-brystkreft .
National Comprehensive Cancer Network. NCCN Guidelines - Genetic/familial High-Risk Assessment: Breast and Ovarian. Version 3. 2019. https://www.nccn.org/professionals/physician_gls/pdf/genetics_screening.pdf .
Plon SE, Eccles DM, Easton D, Foulkes WD, Genuardi M, Greenblatt MS, et al. Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results. Hum Mutat. 2008;29:1282–91.
doi: 10.1002/humu.20880
Dos Santos ES, Caputo SM, Castera L, Gendrot M, Briaux A, Breault M, et al. Assessment of the functional impact of germline BRCA1/2 variants located in non-coding regions in families with breast and/or ovarian cancer predisposition. Breast Cancer Res Treat. 2018;168:311–25.
doi: 10.1007/s10549-017-4602-0
Hamann U, Liu X, Bungardt N, Ulmer HU, Bastert G, Sinn HP. Similar contributions of BRCA1 and BRCA2 germline mutations to early-onset breast cancer in Germany. Eur J Hum Genet. 2003;11:464–7.
doi: 10.1038/sj.ejhg.5200988
Konstantopoulou I, Tsitlaidou M, Fostira F, Pertesi M, Stavropoulou AV, Triantafyllidou O, et al. High prevalence of BRCA1 founder mutations in Greek breast/ovarian families. Clin Genet. 2014;85:36–42.
doi: 10.1111/cge.12274
Høberg-Vetti H, Bjorvatn C, Fiane BE, Aas T, Woie K, Espelid H, et al. BRCA1/2 testing in newly diagnosed breast and ovarian cancer patients without prior genetic counselling: the DNA-BONus study. Eur J Hum Genet. 2016;24:881–8.
doi: 10.1038/ejhg.2015.196
Heramb C, Wangensteen T, Grindedal EM, Ariansen SL, Lothe S, Heimdal KR, et al. BRCA1 and BRCA2 mutation spectrum - an update on mutation distribution in a large cancer genetics clinic in Norway. Hereditary Cancer Clin Pract. 2018;16:3.
doi: 10.1186/s13053-017-0085-6
Colombo M, Blok MJ, Whiley P, Santamarina M, Gutierrez-Enriquez S, Romero A, et al. Comprehensive annotation of splice junctions supports pervasive alternative splicing at the BRCA1 locus: a report from the ENIGMA consortium. Hum Mol Genet. 2014;23:3666–80.
doi: 10.1093/hmg/ddu075
de Jong LC, Cree S, Lattimore V, Wiggins GAR, Spurdle AB, kConFab I, et al. Nanopore sequencing of full-length BRCA1 mRNA transcripts reveals co-occurrence of known exon skipping events. Breast Cancer Res. 2017;19:127.
doi: 10.1186/s13058-017-0919-1
de la Hoya M, Soukarieh O, Lopez-Perolio I, Vega A, Walker LC, van Ierland Y, et al. Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms. Hum Mol Genet. 2016;25:2256–68.
doi: 10.1093/hmg/ddw094
Davy G, Rousselin A, Goardon N, Castera L, Harter V, Legros A, et al. Detecting splicing patterns in genes involved in hereditary breast and ovarian cancer. Eur J Hum Genet. 2017;25:1147–54.
doi: 10.1038/ejhg.2017.116
Evidence-based Network for the Interpretation of Germline Mutant Alleles. ENIGMA BRCA1/2 Gene Variant Classification Criteria version 2.5.1, 2017. https://enigmaconsortium.org/wp-content/uploads/2018/10/ENIGMA_Rules_2017-06-29-v2.5.1.pdf .
Gelli E, Colombo M, Pinto AM, De Vecchi G, Foglia C, Amitrano S, et al. Usefulness and Limitations of Comprehensive Characterization of mRNA Splicing Profiles in the Definition of the Clinical Relevance of BRCA1/2 Variants of Uncertain Significance. Cancers (Basel). 2019;11:295.
doi: 10.3390/cancers11030295
Houdayer C, Caux-Moncoutier V, Krieger S, Barrois M, Bonnet F, Bourdon V, et al. Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants. Hum Mutat. 2012;33:1228–38.
doi: 10.1002/humu.22101
Walker LC, Whiley PJ, Houdayer C, Hansen TV, Vega A, Santamarina M, et al. Evaluation of a 5-tier scheme proposed for classification of sequence variants using bioinformatic and splicing assay data: inter-reviewer variability and promotion of minimum reporting guidelines. Hum Mutat. 2013;34:1424–31.
doi: 10.1002/humu.22388
Evans DG, Harkness EF, Plaskocinska I, Wallace AJ, Clancy T, Woodward ER, et al. Pathology update to the Manchester Scoring System based on testing in over 4000 families. J Med Genet. 2017;54:674–81.
doi: 10.1136/jmedgenet-2017-104584
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 2016;17:13.
doi: 10.1186/s13059-016-0881-8
Cancer Registry of Norway. Cancer in Norway 2017 - Cancer incidence, mortality, survival and prevalence in Norway. Oslo: Cancer Registry of Norway; 2018.
Kuchenbaecker KB, Hopper JL, Barnes DR, Phillips KA, Mooij TM, Roos-Blom MJ, et al. Risks of breast, ovarian, and contralateral breast cancer for BRCA1 and BRCA2 mutation carriers. JAMA. 2017;317:2402–16.
doi: 10.1001/jama.2017.7112
Li J, Wen WX, Eklund M, Kvist A, Eriksson M, Christensen HN, et al. Prevalence of BRCA1 and BRCA2 pathogenic variants in a large, unselected breast cancer cohort. International journal of cancer. Int J Cancer. 2019;144:1195–204.
doi: 10.1002/ijc.31841
Shakya R, Reid LJ, Reczek CR, Cole F, Egli D, Lin CS, et al. BRCA1 tumor suppression depends on BRCT phosphoprotein binding, but not its E3 ligase activity. Science. 2011;334:525–8.
doi: 10.1126/science.1209909
Campos B, Diez O, Domenech M, Baena M, Balmana J, Sanz J, et al. RNA analysis of eight BRCA1 and BRCA2 unclassified variants identified in breast/ovarian cancer families from Spain. Hum Mutat. 2003;22:337.
doi: 10.1002/humu.9176
Wangensteen T, Felde CN, Ahmed D, Maehle L, Ariansen SL. Diagnostic mRNA splicing assay for variants in BRCA1 and BRCA2 identified two novel pathogenic splicing aberrations. Hered Cancer Clin Pract. 2019;17:14.
doi: 10.1186/s13053-019-0113-9
Park B, Sohn JY, Yoon KA, Lee KS, Cho EH, Lim MC, et al. Characteristics of BRCA1/2 mutations carriers including large genomic rearrangements in high risk breast cancer patients. Breast Cancer Res Treat. 2017;163:139–50.
doi: 10.1007/s10549-017-4142-7
Gaildrat P, Krieger S, Thery JC, Killian A, Rousselin A, Berthet P, et al. The BRCA1 c.5434C->G (p.Pro1812Ala) variant induces a deleterious exon 23 skipping by affecting exonic splicing regulatory elements. J Med Genet. 2010;47:398–403.
doi: 10.1136/jmg.2009.074047
Rave-Harel N, Kerem E, Nissim-Rafinia M, Madjar I, Goshen R, Augarten A, et al. The molecular basis of partial penetrance of splicing mutations in cystic fibrosis. Am J Hum Genet. 1997;60:87–94.
pubmed: 8981951
pmcid: 1712544
Fernandez-Rodriguez J, Castellsague J, Benito L, Benavente Y, Capella G, Blanco I, et al. A mild neurofibromatosis type 1 phenotype produced by the combination of the benign nature of a leaky NF1-splice mutation and the presence of a complex mosaicism. Hum Mutat. 2011;32:705–9.
doi: 10.1002/humu.21500
Sanchez-Sanchez F, Kruetzfeldt M, Najera C, Mittnacht S. A novel constitutional mutation affecting splicing of retinoblastoma tumor suppressor gene intron 23 causes partial loss of pRB activity. Hum Mutat. 2005;25:223.
doi: 10.1002/humu.9305
Moghadasi S, Meeks HD, Vreeswijk MP, Janssen LA, Borg A, Ehrencrona H, et al. The BRCA1 c. 5096G>A p.Arg1699Gln (R1699Q) intermediate risk variant: breast and ovarian cancer risk estimation and recommendations for clinical management from the ENIGMA consortium. J Med Genet. 2018;55:15–20.
doi: 10.1136/jmedgenet-2017-104560