The major and most well-studied genetic cause of Fragile-X syndrome (FXS) is expansion of a CGG repeat in the 5′-UTR of the FMR1 gene. Routine testing for this expansion is performed globally. Overall, there is a paucity of intragenic variants explaining FXS, a fact which is being addressed by a more systematic application of whole exome (WES) and whole genome (WGS) sequencing, even in the diagnostic setting. Here we report two families comprising probands with a clinical suspicion of FXS and no CGG repeat expansions. Using WES/WGS we identified deleterious variants within the coding region of FMR1 in both families. In a family from Finland we identified a complex indel c.1021-1028delinsTATTGG in exon 11 of FMR1 which gives rise to a frameshift and a premature termination codon (PTC), p.Asn341Tyrfs*7. Follow-up mRNA and protein studies on a cell line from the proband revealed that although the mRNA levels of FMR1 were not altered, Fragile X Mental Retardation 1 Protein (FMRP) was undetectable. Additionally, we identified a variant, c.881-1G > T, affecting the canonical acceptor splice site of exon 10 of FMR1 in an Australian family. Our findings reinforce the importance of intragenic FMR1 variant testing, particularly in cases with clinical features of FXS and no CGG repeat expansions identified.

易碎X综合征（FXS）的主要且研究得最多的遗传原因是FMR1基因5'-UTR中CGG重复序列的扩增。此扩展的例行测试在全球范围内执行。总体而言，缺乏能解释FXS的基因内变体，这一事实正在通过更系统地应用全外显子组（WES）和全基因组（WGS）测序来解决，即使在诊断环境中也是如此。在这里，我们报告了两个家族，其中包括具有临床怀疑的FXS且没有CGG重复扩展的先证者。使用WES / WGS，我们在两个家族的FMR1编码区域内鉴定了有害变体。在芬兰的一个家庭中，我们在FMR1的第11外显子中鉴定出一个复杂的indel c.1021-1028delinsTATTGG。这会导致移码和过早终止密码（PTC），p.Asn341Tyrfs * 7。在先证者的细胞系中进行的后续mRNA和蛋白质研究表明，尽管FMR1的mRNA水平没有改变，但脆性X智力低下1蛋白（FMRP）无法检测到。此外，我们确定了一个变体，c.881-1G> T，它影响了澳大利亚家庭中FMR1外显子10的典型受体剪接位点。我们的发现加强了基因内FMR1变异测试的重要性，尤其是在具有FXS临床特征且未发现CGG重复扩增的情况下。