A gain of function SLC4A3 mutation causes short QT syndrome: From molecular analysis to phenotypic expression and novel diagnostic testing.

Background: Congenital short QT syndrome (SQTS) is a genetic disorder characterized by short QT interval in the electrocardiogram (ECG) and a high risk of malignant ventricular tachyarrhythmias.

Methods: We identified, by whole-exome sequencing, a novel missense variant in SLC4A3, encoding for the cardiac anion exchanger 3 (AE3). We characterized the mutant using computational structural modeling and functional transport studies in HEK293 cells. Patients were assessed with resting ECG, 12-lead Holter recordings, and a novel diagnostic test termed here the Ippon test.

Results: We detected a novel heterozygous SLC4A3 variant (p.Arg1016Gly) in a family with six cases of sudden cardiac death and a case of documented polymorphic VT in five generations. Functional analyses in HEK293 cells revealed gain-of-function rather than the loss-of-function suggested for previously identified SQTS-associated SLC4A3 variants. While affected family members exhibited a shorter QTc in resting ECG compared with non-affected members (0.36 ±0.02 vs. 0.38 ±0.03 sec, p=0.0068) or 12-lead Holter (0.35 ±0.02 vs. 0.38 ±0.03 sec, p=0.0013), significant overlap was observed. The sudden heart-rate deceleration provoked by the Ippon test revealed that the QT interval of carriers failed to accommodate in response to the sudden bradycardia, resulting in inappropriately short QTc intervals, leading to a clear distinction between affected and non-affected patients (0.34 ±0.02 vs. 0.37 ±0.01, respectively, p=0.0003).

Conclusions: SLC4A3 p.Arg1016Gly is a novel SQTS-associated variant associated with a gain-of-function effect leading to intracellular acidification. The Ippon test is a new provocation maneuver, uniquely aiding the bedside diagnosis of suspected SQTS with high diagnostic accuracy.