Pathogenic ASXL1 somatic variants in reference databases complicate germline variant interpretation for Bohring-Opitz Syndrome

Abstract

The clinical interpretation of genetic variants has come to rely heavily on reference population databases such as the Exome Aggregation Consortium (ExAC) database. Pathogenic variants in genes associated with severe, pediatric-onset, highly penetrant, autosomal dominant conditions are assumed to be absent or rare in these databases. Exome sequencing of a 6-year-old female patient with seizures, developmental delay, dysmorphic features, and failure to thrive identified an ASXL1 variant previously reported as causative of Bohring-Opitz syndrome (BOS). Surprisingly, the variant was observed seven times in the ExAC database, presumably in individuals without BOS. Although the BOS phenotype fit, the presence of the variant in reference population databases introduced ambiguity in result interpretation. Review of the literature revealed that acquired somatic mosaicism of ASXL1 variants (including pathogenic variants) during hematopoietic clonal expansion can occur with aging in healthy individuals. We examined all ASXL1 truncating variants in the ExAC database and determined most are likely somatic. Failure to consider somatic mosaicism may lead to the inaccurate assumption that conditions like BOS have reduced penetrance, or the misclassification of potentially pathogenic variants.

Keywords: ASXL1; Bohring-Opitz syndrome; DNMT3A; Exome Aggregation Consortium; Tatton-Brown-Rahman syndrome; clonal hematopoiesis of indeterminate potential; somatic mosaicism; variant interpretation.

Figure 1

Bohring-Opitz syndrome (BOS) patient and BOS-associated variants in the Exome Aggregation Consortium (ExAC) browser. A) From top left: Patient as a newborn with a prominent nevus flammeus, at two months demonstrating her high palate, at one year with protuberant cheeks, at two years tented upper lip can be observed, at three and a half years wearing glasses for myopia, at age six when patient most recently presented in genetics clinic. Note the progressive fading of the nevus flammeus with age. B) Table with BOS-associated variants p.Arg404Ter (observed in our patient as well as Hoischen et al. 2011), p.Leu823Ter (Hoischen et al. 2011), and p.Arg965Ter (Magini et al. 2012). Allele ratio (allele balance or alternate allele frequency), phenotype (if the patient was part of a cancer cohort), sex, and age (rounded to the nearest five year mark) for each individual harboring the BOS-associated variants are listed.

Figure 2

Likely somatic putative truncating variants in the Exome Aggregation Consortium (ExAC) browser excluding variants from cancer cohorts. A) 39 ASXL1 (exons indicated) putative truncating variants after filtering are observed in ExAC, with the number of individuals greater than one listed in parentheses (total = 65 individuals). The bolded variants have been observed in patients with Bohring-Opitz syndrome.Underlined variants are those with an average allele balance equal to or greater than 35%. B) Bar graphs of average allele balances for each variant (medium gray bar = 50%), with average rounded ages associated with each variant listed when available. C) Allele balances for filtered, rare ASXL1 variants. Black bars indicate individuals with putative truncating ASXL1 variants and grey bars indicate 30 randomly selected rare (<10 individuals) synonymous ASXL1 variants in ExAC. The median allele balance of putative truncating ASXL1 variants is 22% (n=65), while the median allele balance for those with rare synonymous ASXL1 variants is 47% (n=70). The difference is significant (Mann-Whitney U Test, p=1.02E-14). D) The median rounded age for individuals with putative truncating ASXL1 variants is 70 (n=60, no age data is available for five individuals), while the median rounded age for those with rare synonymous or missense ASXL1 variants is 55 (n=983). The difference is significant (Mann-Whitney U Test, p=3.98E-11). For the original data see Supp. Table S1.