Abstracts

Rationale: Mutations in the sodium channel alpha-1 subunit gene, SCN1A, are a cause of familial epilepsy syndromes including Dravet syndrome and genetic epilepsy with febrile seizures plus (GEFS+). Distinguishing pathogenic mutations from benign, rare variation is a major challenge in the interpretation of clinical genetic test results, particularly for missense mutations. In this study, we compared SCN1A missense mutations in cases and controls by frequency and location to identify high and low probability regions of pathogenicity. Methods: DNA sequence analysis was performed 409 unrelated patients (52% female; age at testing 6.6±6.6 years) referred for SCN1A genetic testing. Case variants were interpreted with respect to published literature, Transgenomic control individuals (n= more than 75 individuals) and the NHLBI Exome Sequencing Project (ESP) database (n= more than 5,300 individuals). Singleton missense mutations present in the NHLBI ESP database were considered to be rare, benign variants in this analysis. Mutations were characterized as being located in the N terminus (amino acids 1 to 123), interdomain linker (IDL I to II, amino acids 426 to 762; IDL II to III, amino acids 993 to 1213; and IDL III to IV, amino acids 1484 to 1536), transmembrane/linker (domain I, amino acids 124 to 425; domain II, amino acids 763 to 992; domain III, amino acids 1214 to 1483; and domain IV, amino acids 1537 to 1786), or C terminus (amino acids 1787 to 2009). Results: Overall, rare protein-altering variants were far more common (p<0.0001) among cases (15%) than in controls (1%). Missense mutations were the most common type, accounting for 61% of unique mutations identified in cases. Misssense mutations occurred with significantly higher frequency in cases compared to controls in the N-terminal (0.7% vs 0.1%; p=0.01) and the transmembrane domain/linker regions (6.4% vs 0.3%; p<0.0001). No significant differences in the frequency of mutations were observed between cases and controls in the interdomain linker (0.5% vs 0.4%; p=0.7) or the C-terminal regions (0.7% vs 0.2%; p=0.09). Conclusions: Our comparison of rare genetic variation seen in patients referred for SCN1A genetic testing compared to rare variation seen in ostensibly healthy individuals suggests mutation location can aid in the interpretation of novel missense variants identified in clinical genetic testing. Based on this analysis, novel variants in the interdomain linker regions should be viewed as variants of uncertain significance, whereas mutations in transmembrane/linker regions may be considered more confidently to be probable disease-causing mutations.