SCN5A Variant Pathogenicity Index Calculator

SCN5A Variant Pathogenicity Index: Explanation and Clinical Context The SCN5A Variant Pathogenicity Index is a clinically validated tool to estimate the likelihood that a given SCN5A gene variant contributes to arrhythmia disorders, including Brugada Syndrome and Long QT Syndrome type 3. It integrates multiple lines of evidence: variant type (missense, nonsense, frameshift, splice-site, in-frame indel), functional study results, evolutionary conservation across species, and population frequency data from databases such as gnomAD. The total score classifies variants into Pathogenic, Likely Pathogenic, Variant of Uncertain Significance (VUS), or Likely Benign/Benign categories, helping clinicians interpret genetic test results in the context of arrhythmia risk.

This index assists in clinical decision-making, genetic counseling, and family screening for inherited arrhythmia syndromes.