TY - JOUR
T1 - Functional analysis and clinical classification of 462 germline BRCA2 missense variants affecting the DNA binding domain
AU - Hu, Chunling
AU - Huang, Huaizhi
AU - Na, Jie
AU - Lumby, Carolyn
AU - Abozaid, Mohamed
AU - Holdren, Megan A.
AU - Rao, Tara J.
AU - Karam, Rachid
AU - Pesaran, Tina
AU - Weyandt, Jamie D.
AU - Csuy, Christen M.
AU - Seelaus, Christina A.
AU - Young, Colin C.
AU - Fulk, Kelly
AU - Heidari, Zahra
AU - Morais Lyra, Paulo Cilas
AU - Couch, Ronan E.
AU - Persons, Benjamin
AU - Polley, Eric
AU - Gnanaolivu, Rohan D.
AU - Boddicker, Nicholas J.
AU - Monteiro, Alvaro N.A.
AU - Yadav, Siddhartha
AU - Domchek, Susan M.
AU - Richardson, Marcy E.
AU - Couch, Fergus J.
N1 - Publisher Copyright:
© 2024 American Society of Human Genetics
PY - 2024/3/7
Y1 - 2024/3/7
N2 - Variants of uncertain significance (VUSs) in BRCA2 are a common result of hereditary cancer genetic testing. While more than 4,000 unique VUSs, comprised of missense or intronic variants, have been identified in BRCA2, the few missense variants now classified clinically as pathogenic or likely pathogenic are predominantly located in the region encoding the C-terminal DNA binding domain (DBD). We report on functional evaluation of the influence of 462 BRCA2 missense variants affecting the DBD on DNA repair activity of BRCA2 using a homology-directed DNA double-strand break repair assay. Of these, 137 were functionally abnormal, 313 were functionally normal, and 12 demonstrated intermediate function. Comparisons with other functional studies of BRCA2 missense variants yielded strong correlations. Sequence-based in silico prediction models had high sensitivity, but limited specificity, relative to the homology-directed repair assay. Combining the functional results with clinical and genetic data in an American College of Medical Genetics (ACMG)/Association for Molecular Pathology (AMP)-like variant classification framework from a clinical testing laboratory, after excluding known splicing variants and functionally intermediate variants, classified 431 of 442 (97.5%) missense variants (129 as pathogenic/likely pathogenic and 302 as benign/likely benign). Functionally abnormal variants classified as pathogenic by ACMG/AMP rules were associated with a slightly lower risk of breast cancer (odds ratio [OR] 5.15, 95% confidence interval [CI] 3.43–7.83) than BRCA2 DBD protein truncating variants (OR 8.56, 95% CI 6.03–12.36). Overall, functional studies of BRCA2 variants using validated assays substantially improved the variant classification yield from ACMG/AMP models and are expected to improve clinical management of many individuals found to harbor germline BRCA2 missense VUS.
AB - Variants of uncertain significance (VUSs) in BRCA2 are a common result of hereditary cancer genetic testing. While more than 4,000 unique VUSs, comprised of missense or intronic variants, have been identified in BRCA2, the few missense variants now classified clinically as pathogenic or likely pathogenic are predominantly located in the region encoding the C-terminal DNA binding domain (DBD). We report on functional evaluation of the influence of 462 BRCA2 missense variants affecting the DBD on DNA repair activity of BRCA2 using a homology-directed DNA double-strand break repair assay. Of these, 137 were functionally abnormal, 313 were functionally normal, and 12 demonstrated intermediate function. Comparisons with other functional studies of BRCA2 missense variants yielded strong correlations. Sequence-based in silico prediction models had high sensitivity, but limited specificity, relative to the homology-directed repair assay. Combining the functional results with clinical and genetic data in an American College of Medical Genetics (ACMG)/Association for Molecular Pathology (AMP)-like variant classification framework from a clinical testing laboratory, after excluding known splicing variants and functionally intermediate variants, classified 431 of 442 (97.5%) missense variants (129 as pathogenic/likely pathogenic and 302 as benign/likely benign). Functionally abnormal variants classified as pathogenic by ACMG/AMP rules were associated with a slightly lower risk of breast cancer (odds ratio [OR] 5.15, 95% confidence interval [CI] 3.43–7.83) than BRCA2 DBD protein truncating variants (OR 8.56, 95% CI 6.03–12.36). Overall, functional studies of BRCA2 variants using validated assays substantially improved the variant classification yield from ACMG/AMP models and are expected to improve clinical management of many individuals found to harbor germline BRCA2 missense VUS.
KW - BRCA2
KW - cancer
KW - HDR
KW - predisposition genes
KW - variant classification
KW - VUS
UR - http://www.scopus.com/inward/record.url?scp=85186741684&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85186741684&partnerID=8YFLogxK
U2 - 10.1016/j.ajhg.2024.02.002
DO - 10.1016/j.ajhg.2024.02.002
M3 - Article
C2 - 38417439
AN - SCOPUS:85186741684
SN - 0002-9297
VL - 111
SP - 584
EP - 593
JO - American journal of human genetics
JF - American journal of human genetics
IS - 3
ER -