Bridge the gap. There are very few conditions that I have learned as much about in the last three years as SYNGAP1-related disorders. We just passed the critical milestone of 100 SYNGAPians followed in our clinical trial–grade natural history study (SYNGAP1 ProMMiS). In addition, our study using real-world data across more than 2,500 patient years came online earlier this year. We are becoming more familiar with the range of reflex seizures observed in this condition and the unique fingerprint on the sensory profile that characterize its behavioral features. In a recent publication, we explored another aspect of SYNGAP1 that had been neglected so far. We tried to understand what happens when SYNGAP1 variants run in families and what this means for trial readiness and precision therapies.
Figure 1. Familial variants in SYNGAP1 outline the boundaries of a complex neurodevelopmental disorder. (A) Pedigrees of the five families reported in our study by Harrison et al., including three families with protein-truncating variants (Families 1-3) and two families with inherited missense variants (Families 4-5). Overall, familial presentations account for up to 3% of all SYNGAP1-related disorders. (B) Variant spectrum of familial SYNGAP1 variants mapped to the various SYNGAP1 isoforms. Familial SYNGAP1 variants cluster in exons 1-4, but clinical presentations are not necessarily attenuated in all individuals.
SYNGAP1 ProMMiS. In our publication on familial SYNGAP1 variants spearheaded by Alicia Harrison and Jill McKee, we tried to understand the spectrum of phenotypes in familial presentations of this complex neurodevelopmental disorder with epilepsy. Why is this important for the larger mission of SYNGAP1ProMMiS, our clinical trial readiness study?
Endpoints. Familial cases are helpful in defining outcomes for future SYNGAP1 trials in two ways. First, familial inheritance offers unique insight into the overall range of phenotypes associated with a single SYNGAP1 variant, i.e. which clinical features are determined by the causal variant and which features are variable even between family members with the same variant. For example, the GEFS+ spectrum in SCN1A teaches us about the core features of a given SCN1A variant. Second, the clinical presentations of familial variants are often less severe than de novo variants. Therefore, they provide insight into the attenuated end of the disease spectrum. Both factors—variability and outlining the full spectrum—are key when trying to understand what outcomes for future trials will look like. Here are three observations from our study on five families with inherited SYNGAP1 variants.
1 – Phenotypes. We describe three families with inherited pathogenic SYNGAP1 variants in addition to two families with inherited missense variants of uncertain significance (VUS). Individuals in two families had clinical presentations that were less severe than we would usually observe, particularly with respect to the severity of developmental differences and autism. However, the epilepsy subtypes were characteristic of SYNGAP1-related disorders with a high frequency of absence seizures and eyelid myoclonia. Autism features assessed by the Childhood Autism Rating Scale (CARS) were minimal in 4/5 individuals. Full Scale IQs had been formally tested in both individuals in Family 2 and were 67 and 68, results that are on the threshold between mild intellectual disability and borderline intellectual functioning. Motor scores measured by the GMFM-66 were 80 or above for all individuals beyond the age of eight years, consistent with good functional mobility. However, both individuals in Family 1 showed a pattern more consistent with a typical SYNGAP1 presentation. Formal clinical assessments were available for one individual who had severe autism symptoms (CARS) and a lower gross motor score. In summary, while some familial SYNGAP1 presentations present with attenuated features, this is not universally true. In summary, familial versus sporadic SYNGAP1 is not as clear-cut as Dravet Syndrome versus GEFS+.
2 – Variant spectrum. The SYNGAP1 gene has an unusual feature, as some isoforms do not use the first four exons of the gene. Accordingly, disease-causing variants in exons 1–4 only affect some isoforms, while other SYNGAP1 isoforms would remain unaffected. It is an ongoing question in the field whether individuals with variants in exons 1–4 have a less severe presentation or whether both severe and attenuated presentations are independent of variant location. In our study, all three families had variants in the first four exons. However, as mentioned earlier, the presentation of Family 1 was indistinguishable from the broader SYNGAP1 presentation. In summary, while familial SYNGAP1 variants seem more likely to occur in the first four exons, it remains unclear what the true phenotypic consequences are. Better understanding the “exon 1-4” story, including definite data on isoform expression, remains an ongoing goal of SYNGAP1 ProMMiS and our work at ENDD.
3 – Variant classification. In addition to the three families with inherited pathogenic variants, we identified two families with novel, inherited missense variants. Given that these variants were inherited, they were classified as Variants of Uncertain Significance (VUS). Because the phenotypic range was consistent with the broader SYNGAP1presentation, it is tempting to make a judgement call and consider these variants causative. However, we approached this issue differently. Having been involved with the broader ClinGen effort for the last eight years, we instead asked what it would take for these variants to be formally considered pathogenic or likely pathogenic (or, in contrast, benign or likely benign).
ACMG/AMP. Overall, becoming fluent with ACMG/AMP variant curation criteria is critical for the epilepsy genetics community, as an in-depth understanding of these criteria is the first step to modifying them based on our clinical epilepsy knowledge (as we have already done for SCN1A, SCN2A, SCN3A, and SCN8A). For the two inherited SYNGAP1 variants, the limitations of our current variant curation framework clearly showed. Neither computational predictors (PP3/BP4), case data (PS4), nor variant location in hotspots (PM1) pointed in a clear direction for these variants. Furthermore, there are no functional assays for SYNGAP1 (PS3) that could be used to understand the impact of these variants. In summary, it is worthwhile to improve classification of SYNGAP1 variants through modifications of the ACMG/AMP variant classification framework, as these criteria will ultimately be applied for clinical trials. This is part of our ongoing work within our ClinGen working group.
What you need to know. Familial presentations provide a unique view of the clinical and variant spectrum of SYNGAP1-related disorders. Phenotypic boundaries are not as clear-cut as would be expected from other epilepsy genes where sporadic and familial variants co-exist. However, in contrast to other synapse disorders such as STXBP1-related disorders and DNM1-related disorders, familial presentations account for up to 3% of SYNGAP1-related disorders. Classification of inherited missense variants will be an ongoing challenge, but we can leverage our experience in modifying ACMG/AMP criteria to maximize our clinical and molecular understanding of SYNGAP1, make these criteria more precise, and reduce the VUS burden.
