Genetic Variants of Uncertain Significance: Flies in the Ointment

Abstract

Genetic testing for BRCA1 and BRCA2 mutations in individuals with a personal and family history of breast or ovarian cancer can be an invaluable tool in determining appropriate clinical management. Women with such mutations are at high risk for the development of breast and ovarian cancer, and strategies exist to reduce these risks substantially. Cancer risk models may be used to help determine appropriate candidates for genetic testing, which we recommend for those with greater than a 5% to 10% probability of carrying a mutation. Positive results from genetic testing for BRCA1 and BRCA2 mutations, although difficult for patients and families to hear, provide both a basis for decision making and, for many people, a measure of peace that comes from answering the question, “Why?” Negative results in members of families with known mutations provide tremendous relief, as well as freedom from intensive surveillance and surgery. Negative results, when a family mutation has not been identified, may be frustrating but do suggest a reduced risk of ovarian cancer, because most heritable susceptibility to ovarian cancer is a result of BRCA1 and BRCA2 mutations. However, undergoing genetic testing and being presented with a variant of uncertain significance (VUSs) is a clinically and emotionally difficult situation. Advising individuals with a VUS on surveillance and prophylactic surgery is challenging for providers, confusing to families, and distressing for everyone. VUSs (also termed unclassified variants) are sequence variations in a gene where the effect of the sequence change on the function of the protein is not known. Such sequence variants in the coding regions of BRCA1 or BRCA2 may or may not be associated with an increased risk of breast, ovarian, or other cancers. Many of these variants are single-nucleotide substitutions (also called missense mutations) that result in a single amino acid change. Some, like the one described in this issue of the Journal of Clinical Oncology by Malacrida et al, are in-frame deletions that remove amino acids in multiples of three, and thus do not induce a frame shift in protein translation. Some missense mutations clearly alter the function of BRCA1, such as those that occur in the “ring finger ” domain or induce frame shifts by altering splice sites. However, the functional significance of most of the thousands of missense mutations identified to date in BRCA1 and BRCA2 is not clear. Most VUSs are benign polymorphisms, but determining the functional and thus clinical significance of a specific VUS with certainty is difficult. VUSs are unfortunately a common problem in all types of genetic testing, but are particularly problematic in testing BRCA1 and BRCA2 because of the large size of these genes. Between 10% and 15% of individuals undergoing genetic testing for BRCA1 and BRCA2 mutations will be found to have a VUS. VUSs are even more common in non-white populations, with frequencies as high as 46% in African Americans and 22% in Hispanics. The increased difficulty in categorizing VUSs in these populations occurs because the smaller number of people tested to date limits many of the approaches to classifying VUSs described later herein. Fortunately, there are a number of factors which, if known, provide considerable confidence in determining the clinical significance of a VUS (Table 1). Particularly when taken together, these considerations can be important tools when counseling individuals with a VUS. First, and whenever possible, it is important to determine whether the VUS segregates with breast and ovarian