Characterization of Gene Variants Involved in Synaptic Pathways in Extended Utah ASD Pedigrees

Background: Genes in synaptic pathways have been identified as risk factors for ASD in several large recent studies of Autism Spectrum Disorders (ASD) using exome sequencing in parent-child trios and/or cases and controls.  Study of these gene variants and phenotypic characterization of carriers will be critical to inform future in vitro analyses of synaptic structure and function resulting from specific mutations.

Objectives: We have focused on variants in synaptic genes with significant evidence in previous studies where potentially functional variants also occur in ASD families ascertained in Utah. We describe occurrence in cases and unaffected relatives and give detail on phenotypic characteristics of Utah variant carriers including ASD severity (or evidence of any clinical symptoms if the individual is unaffected), IQ, and reported presence/absence of seizures and other health conditions.

Methods: Our data resource includes 518 individuals from Utah families. The Illumina HumanExome chip was genotyped on 186 with ASD and 332 unaffected relatives, and whole exome sequencing (Agilent SureSelect and Illumina GAIIx) was done on 61 relatives with ASD and 27 unaffected relatives in eight extended high-risk pedigrees. The genes studied in these families include CACNA2D3, SCN2A, TRIO. SHANK3, NRXN1, NRXN2, NRXN3. NLGN1, NLGN2, NLGN3, and NLGN4.  Each gene is involved in synaptic transmission, formation, or function, and each has been implicated in ASD and other psychiatric conditions. For each gene, we describe the occurrence of variants that are likely functional in at least one Utah ASD case.  We give further variant information using available sequence annotation tools (e.g., PolyPhen, Annovar).  We then describe occurrence of the variant in other affected and unaffected family members, and associated phenotypic characteristics.

Results: Multiple variants in synaptic genes were found.  We focus particularly on those where functional variants occurred in both affected and unaffected relatives.  For example, a rare variant in SCN2A (rs2228980) occurred in three families, including three affected cases, three unaffected parents, an unaffected grandparent, and two unaffected siblings.  However, in these families, 8 additional siblings (4 affected and 4 unaffected) did not  carry the variant.  Another example is a rare variant in CACNA2D3 (rs142687394), which occurred in three different families, including three cases, three unaffected parents, and two unaffected siblings.  The variant was not found in five other unaffected siblings.

Conclusions: Variants in genes in this important gene pathway occur in both affected and unaffected relatives in Utah families, suggesting reduced penetrance, even when variants appear to be likely damaging.  We note associations with possible seizures, clinical severity, and lower IQ, but these associations are not universal, suggesting pleiotropy. Characterization of particular variants in synaptic genes will inspire additional in vitro studies of synaptic structure and function resulting from these gene variants.  In addition, our sample includes viably frozen peripheral blood mononuclear cells from many subjects, allowing the potential for the creation of derived neuronal cells for further studies of synaptic function specific to both affected and unaffected individuals.