Resolving SLC6A1 variable expressivity with deep clinical phenotyping and Drosophila models

Variants in SLC6A1 result in a rare neurodevelopmental disorder characterized by a variable clinical presentation of symptoms including developmental delay, epilepsy, motor dysfunction, and autism spectrum disorder. SLC6A1 haploinsufficiency has been confirmed as the predominant pathway of SLC6A1-related neurodevelopmental disorder (SLC6A1-NDD); however, the molecular mechanism underlying the variable clinical presentation remains unclear. Here, through work of the Undiagnosed Diseases Network, we identify an individual with an inherited p.A334S variant of uncertain significance. To resolve this variant and better understand the variable expressivity associated with SLC6A1, we assess the phenotypes of the proband in comparison with a cohort of 13 individuals diagnosed with SLC6A1-NDD. We then create an allelic series in Drosophila melanogaster to functionally characterize these variants. Informatic clustering based on these clinical findings points to significant clinical overlap between the unsolved individual and confirmed SLC6A1-NDD. We confirm phenotypes in flies expressing SLC6A1 variants consistent with a partial loss-of-function mechanism. We conclude that the p.A334S variant is a hypomorphic allele and begin to elucidate the underlying variability in SLC6A1-NDD. These insights will inform clinical diagnosis, prognosis, intervention, and inform therapeutic design for those living with SLC6A1-NDD.