Authors :
Presenting Author: Stacey Cohen, MS CGC – Children's Hospital of Philadelphia
Lacey Smith, MS CGC – Boston Children's Hospital; Shridhar Parthasarathy, BA – Children's Hospital of Philadelphia; Emily Bonkowski, MS CGC – St. Jude Children’s Research Hospital; William Hong, MD – Boston Children's Hospital; Kimberly Wiltrout, MD – Boston Children's Hospital; Alexander Ing, MS CGC – Lurie Children’s Hospital of Chicago; Andreas Brunklaus, MD – Royal Hospital for Children; Brendan Burns, PhD – Illumina; Christopher Thompson, PhD – Feinberg School of Medicine, Northwestern University; David Lewis-Smith, MA, MB BChir, MClinRes, MRCP – Royal Victoria Infirmary; Dennis Lal, PhD – Cleveland Clinic; Elizabeth Butler, MS CGC – GeneDx; Jillian McKee, MD PhD – Children's Hospital of Philadelphia; Miriam Meisler, PhD – University of Michigan; Rhonda Lassiter, PhD – Ambry Genetics; Sarah Dugger, CGC, PhD – Invitae Corporation; Samin Sajan, PhD – Illumina; Yanmin Chen, PhD – GeneDx; Jacy Wagnon, PhD – The Ohio State University College of Medicine; Katherine Benson, PhD – Royal College of Surgeons in Ireland; Erin Riggs, MS CGC – Geisinger; Edward Cooper, MD PhD – Baylor College of Medicine; Annapurna Poduri, MD MPH – Boston Children's Hospital; Heather Mefford, MD PhD – St. Jude Children’s Research Hospital; Ingo Helbig, MD – Children's Hospital of Philadelphia
Rationale:
Genetic testing laboratories evaluate the pathogenicity of variants in epilepsy-related sodium channel genes (
SCN1A,
SCN2A,
SCN3A,
SCN8A, and
SCN1B) using multiple types of evidence, such as prior reports of a variant in the medical literature and regions of mutational hotspots. Functional assessments can be incorporated into evidence of pathogenicity under an existing ClinGen Bayesian framework based on assay readout and number of pathogenic and benign validation controls studied. However, this framework has not been tailored to electrophysiological assays that are used to assess abnormalities in sodium channel function.
Methods:
The Clinical Genome Resource (ClinGen) Epilepsy Sodium Channel Variant Curation Expert Panel within the Neurodevelopmental Disorders Clinical Domain Working Group (CDWG) is comprised of a group of experts and curators from clinic, academia, and industry tasked with establishing consensus guidelines for variant classification of the epilepsy-related sodium channel genes. To add existing knowledge of experimental results from electrophysiological assays into formal clinical variant interpretation using the PS3 criterion, we introduce an approach for jointly evaluating multiple measured sodium channel properties within the Bayesian framework of the modified American College of American Genetics guidelines. We annotated electrophysiological assessments of variants in the medical literature using the Functional Epilepsy Nomenclature for Ion Channels (FENICS) for pathogenic variants in
SCN1A (n=38),
SCN2A (n=6),
SCN3A (n=7), and
SCN8A (n=12) and benign variants in
SCN1A (n=23) within this framework to determine specific thresholds for weighting evidence to classify variant pathogenicity.
Results:
By comparison of electrophysiological assessments of 63 pathogenic variants in
SCN1A,
SCN2A,
SCN3A, and
SCN8A against measurements for 23 benign
SCN1A variants, several parameters achieved Strong evidence for variant pathogenicity: peak current density that is 74.2% of less of wildtype (LR=20.0), persistent current of at least 135% of wildtype (LR=21.0), voltage dependence of activation that is shifted at least 2.2 mV different from wildtype (LR=21.0), and voltage dependence of fast inactivation that is shifted at least 4.1 mV from wildtype (LR=19.9). Several parameters achieved Moderate evidence for variant pathogenicity: peak current density that is less than 81.5% of wildtype (LR=5.00), persistent current greater than or equal to 125% of wildtype (LR=5.25), shift in voltage dependence of activation greater than or equal to 2.15 mV from wildtype (absolute value) (LR=5.25), and voltage dependence of fast inactivation shifted by less than or equal to 2.96 mV from wildtype (absolute value) (LR=4.99).
Conclusions:
Variant classification in epilepsy-related sodium channel genes can be refined in a formal framework, and similar concepts can be applied to other ion channel genes. The proposed method is suitable for variant classification in the clinical laboratory setting. Tailored variant classification including functional assessments is essential for correct diagnosis and eligibility for gene-specific clinical trials and therapies.
Funding:
5U24NS120854 and 5U54NS108874.