Fragile X Syndrome via FMR1 Gene

Fragile X syndrome (FXS) is the most common genetic cause of intellectual disability in males and the second most common cause in females, with a prevalence of 1:4000 males and 1:6000 females. FXS is characterized by developmental delay, moderate to severe intellectual disability and autistic behaviors. FXS is typically diagnosed at around three years of age when developmental delay becomes pronounced. Physical features of FXS include an elongated face, prominent jaw, broad forehead, prominent ears, macroorchidism in males, flat feet and hyperextensible finger joints (Gallagher and Hallahan 2011). Common behaviors associated with FXS include attention deficit hyperactivity disorder (ADHD), trouble sleeping, anxiety, mood disorders and aggression. Autistic-like behaviors seen in FXS patients include preserveration of speech, motor stereotypies such as hand flapping, restricted interests and poor eye contact. Approximately 30-50% of FXS patients meet the diagnostic criteria for autism, although symptoms tend to be less severe than in patients with idiopathic autism (McCary and Roberts 2013; McDuffie et al. 2014). FXS-related conditions, Fragile X Tremor Ataxia Syndrome (FXTAS) and Fragile X Premature Ovarian Insufficiency (FXPOI) have not been reported in patients with point mutations in the FMR1 gene.

The majority of FXS cases are caused by an expansion of the CGG repeat in the 5' UTR of the FMR1 gene which leads to methylation and silencing of the FMR1 locus. Sequence variants in the FMR1 gene itself have also been reported to cause FXS and are inherited in an X-linked recessive manner. Both nonsense and missense variants in FMR1 have been identified in males and females with FXS or intellectual disability (De Boulle et al. 1993; Lugenbeel et al. 1995; Grønskov et al. 2011). FMR1 encodes the fragile-X mental retardation protein (FMRP) which is an RNA binding protein highly expressed in the brain. FMRP binds RNAs and transports them to synapses for local translation (Liu-Yesucevitz et al. 2011). FMRP is predicted to bind to as much as 4% of all mRNA in the brain and acts as a translational repressor. FXS is caused by loss of FMRP and improper translation of neuronal mRNAs (Bagni et al. 2012). FMRP mRNA targets are enriched for genes implicated in intellectual disability and autism spectrum disorders, suggesting a common molecular mechanism (Ascano et al. 2012). Loss of FMRP results in long, thin dendritic spines in the cortex which reduces neuronal contacts and impairs synaptic plasticity.

Traditionally, Fragile X testing has consisted of CGG repeat expansion analysis only, therefore limited data is available for the frequency of FMR1 point mutations in FXS patients. A recent study of male patients with an FXS phenotype who tested negative for repeat expansions in both the FMR1 and AFF2 genes identified possibly pathogenic FMR1 missense mutations in 0.56% (3 of 508) of individuals (Handt et al. 2014).

This test provides full coverage of all coding exons of the FMR1 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Before ordering DNA sequencing of FMR1 gene, we strongly recommend ordering the CGG repeat expansion test first, unless targeted testing can be performed for a known familial sequence variant.