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 six-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 Bohring-Opitz syndrome have reduced penetrance, or the misclassification of potentially pathogenic variants.

The ASXL1 mutation p.Gly646Trpfs*12 found in a Turkish boy with Bohring‐Opitz Syndrome

“…Taking all this into consideration, we conclude that the p.Gly646Trpfs*12 mutation is a disease‐causing mutation responsible for the patient’s BOS clinical presentation and that, as Carlston et al3 stated, the assumption that pathogenic variants in genes associated with severe, pediatric‐onset, highly penetrant, autosomal dominant conditions have to be absent or extremely rare in public databases has to be taken cautiously.…”

“…In this sense, other mutations present in ExAC (among them the p.Arg404Ter described by Carlston et al3) were previously found to be BOS ‐causing (Table 1). The p.Gly646Trpfs*12 mutation described in our BOS case is one of the two ASXL1 loss of function (LoF) changes especially frequent in ExAC, the other being p.Gly645Valfs*58 (found in 118 individuals).…”

“…Both changes are located in an eight‐nucleotide G‐homopolymer tract and could be over‐represented due to sequencing errors. While these changes were not included in Carlston et al3 analyses, the authors discussed the fact that the p.Gly646Trpfs*12 mutation had been identified in a large series of myeloid malignancies by deep sequencing (confirmed by manual methods in some cases) and had been described as the most common cancer‐associated ASXL1 mutation 5. Besides, 66% of the ExAC carriers of the p.Gly646Trpfs*12 mutation belong to the Cancer Genome Atlas (TCGA) population.…”

“…Heterozygous ASXL1 truncating mutations have been identified as the main cause of BOS 1, 2. A recent publication 3 called the attention to the fact that mutations associated with BOS are also present in the ExAC (Exome Aggregation Consortium) database 4. As ASXL1 is one of the genes most commonly mutated during hematopoietic clonal expansion of cells, the authors hypothesized that the presence of this mutation in public databases could be due to somatic mosaicism, and they could confirm the hypothesis by manual examination of the ExAC WES reads.…”

Genetic literacy series: Primer part 2—Paradigm shifts in epilepsy genetics

“…Of course, there are limitations to using control databases to exclude variants based on the presence in control individuals. Some examples include the inclusion of individuals with related conditions (eg, psychiatric disorders) or who were evaluated prior to the usual age of onset of a given disorder, and the presence of somatic mosaic variants that cause milder or no disease in the control . However, highly penetrant variants causing severe disease should be exceedingly rare if present at all…”