# Functional Genomics of Cardiac Sodium Channel Variants

> **NIH NIH R01** · VANDERBILT UNIVERSITY MEDICAL CENTER · 2020 · $732,233

## Abstract

As clinical genetic testing is becoming widely deployed for patients with suspected Mendelian diseases as well
as in the broad population, a major emerging challenge is the accurate prediction of pathogenicity of DNA
variants. Multiple features, including allele frequencies across populations, family history, and functional
studies, are currently being used to assign known or new variants to three broad categories: benign,
pathogenic, or (most commonly) variant of uncertain significance (VUS). We propose here to test the
hypothesis that deploying novel phenotyping methods will improve variant classification, and we will focus here
on SCN5A, encoding the cardiac sodium channel. Despite the fact that this channel plays a critical role in
normal heart function, SCN5A variants are surprisingly common and have been associated with serious and
occasionally life-threatening phenotypes including type 1 Brugada Syndrome (BrS1), type 3 Long QT
Syndrome (LQT3), conduction system disease, heart failure, and atrial fibrillation. In aim 1, we will determine
the utility of phenotyping in the electronic health record (EHR) coupled to functional studies to assess
SCN5A VUS pathogenicity. The Electronic Medical Records and Genomics (eMERGE) network in which we
are participants is completing sequencing of 109 Mendelian disease genes, including SCN5A, in 25,000
subjects with EHRs. We will assess VUS pathogenicity by analyzing SCN5A-related EHR phenotypes in
subjects with and without SCN5A rare variants and establishing in vitro function for newly-detected variants
using multiplexed semi-automated electrophysiologic methods. In aim 2, we will build on preliminary data using
deep mutational scanning (DMS) – a high-throughput method to mutagenize each nucleotide in a target
genomic sequence and establish its functional consequences – to identify SCN5A coding variants with
BrS1 or LQT3 features. In a pilot experiment, we developed a drug challenge that biases survival toward cells
that do not express sodium current at their surface (the BrS phenotype) and against cells that display
enhanced sustained sodium current (LQT3). We then generated all 252 possible non-synonymous or
nonsense single amino acid (aa) variants across a 12aa regon of SCN5A, exposed a pool of cells transfected
with one mutant/cell to the drug challenge, used next-generation sequencing pre- and post-drug challenge to
identify variants with BrS1 and LQT3 features, and validated predictions with conventional patch clamp
methods. We will now scale up to scan larger regions, starting with the 253 aa encoding transmembrane
domain IV, known to harbor dozens of pathogenic variants. Further, we will map DMS results onto a model of
the channel to probe the structural basis of loss and gain of function variants. We will incorporate DMS data
into available and new statistical models to build an improved model of SCN5A variant disease risk. The result
of this work will be new approaches to establish functional co...

## Key facts

- **NIH application ID:** 9861323
- **Project number:** 1R01HL149826-01
- **Recipient organization:** VANDERBILT UNIVERSITY MEDICAL CENTER
- **Principal Investigator:** DAN M RODEN
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $732,233
- **Award type:** 1
- **Project period:** 2020-01-01 → 2023-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9861323

## Citation

> US National Institutes of Health, RePORTER application 9861323, Functional Genomics of Cardiac Sodium Channel Variants (1R01HL149826-01). Retrieved via AI Analytics 2026-05-21 from https://api.ai-analytics.org/grant/nih/9861323. Licensed CC0.

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