BRCA1 R1699Q variant displaying ambiguous functional abrogation confers intermediate breast and ovarian cancer risk

Abstract

Background Clinical classification of rare sequence changes identified in the breast cancer susceptibility genes BRCA1 and BRCA2 is essential for appropriate genetic counselling of individuals carrying these variants. We previously showed that variant BRCA1 c.5096G>A p. Arg1699Gln in the BRCA1 transcriptional transactivation domain demonstrated equivocal results from a series of functional assays, and proposed that this variant may confer low to moderate risk of cancer. Methods Measures of genetic risk (report of family history, segregation) were assessed for 68 BRCA1 c.5096G>A p.Arg1699Gln (R1699Q) families recruited through family cancer clinics, comparing results with 34 families carrying the previously classified pathogenic BRCA1 c.5095C>T p.Arg1699Trp (R1699W) mutation at the same residue, and to 243 breast cancer families with no BRCA1 pathogenic mutation (BRCA-X). Results Comparison of BRCA1 carrier prediction scores of probands using the BOADICEA risk prediction tool revealed that BRCA1 c.5096G>A p.Arg1699Gln variant carriers had family histories that were less ‘BRCA1-like’ than BRCA1 c.5095C>T p.Arg1699Trp mutation carriers (p<0.00001), but more ‘BRCA1-like’ than BRCA-X families (p=0.0004). Further, modified segregation analysis of the subset of 30 families with additional genotyping showed that BRCA1 c.5096G >A p. Arg1699Gln had reduced penetrance compared with the average truncating BRCA1 mutation penetrance (p=0.0002), with estimated cumulative risks to age 70 of breast or ovarian cancer of 24%. Conclusions Our results provide substantial evidence that the BRCA1 c.5096G>A p.Arg1699Gln (R1699Q) variant, demonstrating ambiguous functional deficiency across multiple assays, is associated with intermediate risk of breast and ovarian cancer, highlighting challenges for risk modelling and clinical management of patients of this and other potential moderate-risk variants.

A High-Throughput Functional Complementation Assay for Classification ofBRCA1Missense Variants

“…The pathogenic 5382insC truncation mutation could not be classifi ed because it scored as neutral in one of three transfection series. This was probably due to technical reasons, as the 5382insC mutation did not restore HR activity in Brca1 -defi cient embryonic stem cells, in contrast with R1699Q, which was recently shown to confer intermediate risk of HBOC ( 32 ).…”

“…We therefore tested complementation of PARP inhibitor sensitivity for a number of BRCA1 mutants and the BRCA1 wild-type control. Given the unexpected neutral effects of the M1400V, L1407P, and M1411T mutations in the PALB2 interaction domain, we decided to include these variants in this series, as well as the R1699Q and V1736A variants that have recently been shown to confer (intermediate) breast and ovarian cancer risk ( 31,32 ). To allow direct comparison of results from different assays, we repeated the cisplatin sensitivity and proliferation assays in parallel to the olaparib sensitivity assay.…”

Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals

“…A nonsense variant, BRCA1 p.Leu63*, was found in a heterozygous individual in 2KJPN [28]. Interestingly, the BRCA1 p.Arg1699Gln variant is known to be one of the genetic risk factors for intermediate breast and ovarian cancers [29], and this variant was found in three heterozygous individuals in 2KJPN (MAF = 0.07%). A missense variant, BRCA1 p.Val271Met (rs80357244), was classified as DM in HGMD and was found in 27 heterozygous individuals (MAF = 0.7%) in 2KJPN.…”

The Role of New Sequencing Technology in Identifying Rare Mutations in New Susceptibility Genes for Cancer

“…1). Much more diverse clinical phenotypes associated with carrying mutations in these genes are now apparent, and there is evidence that some mutations are associated with more moderate risk [31] and/or attenuated disease [32].…”