June 8, 2022

Genetic Variants in Epilepsy Gene Identified

Article published by Medical Xpress

Featuring the work of former CURE Epilepsy Grantee Dr. Gemma Carvill

Investigators have discovered a new method to determine whether individual genetic variants in the epilepsy-associated gene SZT2 cause a neurodevelopmental disorder, according to a Northwestern Medicine study published in the journal Brain.

Pathogenic variants in SZT2 have been associated with the development of different neurodevelopmental disorders, including early-onset epilepsy and developmental delays. Additionally, the SZT2 protein plays an essential role in the mTORC1 signaling pathway, which helps promote cell growth and proliferation.

Classifying these variants as either likely benign or pathogenic, however, has remained a challenge due the large size of SZT2—it contains more than 3,400 amino acids—as well as its lack of crystal structure and functional domains.

“There are many different amino acids that can be mutated and become missense variants, so it’s very challenging to tell which are pathogenic and which are benign. That’s why high-throughput studies like this are so important,” said Gemma Carvill, Ph.D., assistant professor in The Ken and Ruth Davee Department of Neurology Division of Epilepsy and Clinical Neurophysiology and senior author of the study.

For the current study, Carvill’s team recruited twelve individuals who carried biallelic SZT2 variants of which one or more were classified as variants of uncertain significance.

Using CRISPR-Cas9 genome editing, the investigators engineered cells to contain patient-specific missense SZT2 variants and performed a functional cell assay that separated cells based on whether the mTORC1 signaling pathway was active or inactive.

The investigators then used next-generation sequencing to determine which SZT2 missensevariants retained function and which lost function and were likely to be pathogenic.

Ultimately, they discovered a recurrent in-frame deletion—when one amino acid is deleted out of the protein—and was determined to be a loss-of-function variant and reclassified as likely pathogenic.