rs28937319 — SCN5A SCN5A Cardiac Sodium Channel Variant 2

Rare loss-of-function missense variant in the cardiac sodium channel Nav1.5 causing congenital sick sinus syndrome through altered channel inactivation kinetics; also reported in association with Brugada syndrome and dilated cardiomyopathy

See your personal result for SCN5A

Upload your DNA data to find out which genotype you carry and what it means for you.

Upload your DNA data

Works with 23andMe, AncestryDNA, and other DNA test exports. Results in under 60 seconds.

SCN5A P1297L — When the Heart's Electrical Starter Fails

Every heartbeat begins in the sinoatrial node (SAN), a cluster of specialized pacemaker cells that fire spontaneously and propagate an electrical impulse through the atria and into the ventricles. That propagation depends on Nav1.511 Nav1.5
The cardiac voltage-gated sodium channel encoded by SCN5A, responsible for the rapid depolarization phase of the cardiac action potential, the sodium channel encoded by SCN5A. The Pro1297Leu variant — a single amino acid change in the tenth transmembrane domain of Nav1.5 — impairs how the channel exits its inactivated state, subtly reducing myocardial excitability in a way that can silence the pacemaker and stall conduction between the SAN and the atrium.

ClinVar classifies this variant with conflicting interpretations: the OMIM submission calls it Pathogenic for sick sinus syndrome 1 (OMIM 608567), while more recent submissions (applying stricter ACMG-AMP criteria) assign uncertain significance for some conditions. For the specific context in which it was discovered — compound heterozygous loss-of-function in pediatric congenital sick sinus syndrome — the evidence is mechanistically well-characterized22 mechanistically well-characterized
Benson DW et al. Congenital sick sinus syndrome caused by recessive mutations in the cardiac sodium channel gene (SCN5A). J Clin Invest 2003;112(7):1019-28. Heterozygous carriers (the genotype seen in genome sequencing reports) are usually asymptomatic or mildly affected, with full disease requiring a second SCN5A loss-of-function allele in trans.

The Mechanism

The Pro1297Leu substitution falls in a region critical for inactivation gating — the process by which Nav1.5 rapidly closes after opening during a cardiac action potential. Gui et al. (2010)33 Gui et al. (2010)
Gui J et al. Multiple loss-of-function mechanisms contribute to SCN5A-related familial sick sinus syndrome. PLoS One 2010;5(6):e10985 showed that P1297L channels reach normal peak current density and traffic normally to the cell surface — the number of channels present is not the problem. Instead, the defect is kinetic: the mutant channel undergoes a negative shift in steady-state inactivation (channels inactivate at lower voltages than normal) and shows reduced voltage-dependence of open-state inactivation (less reliable recovery for the next beat). The practical result is that fewer Nav1.5 channels are available at the moment a pacemaker cell tries to fire, or when the SAN impulse tries to cross into atrial tissue.

A second layer of risk comes from genetic background44 genetic background
The H558R common polymorphism in SCN5A, present in approximately 20-30% of the European population, functions as a modifier allele that can amplify dysfunction of pathogenic missense mutations in the same gene. Gui et al. (2010) showed that carriers of the H558R variant (rs1805124) on the same chromosome as P1297L experience further reduction in channel availability, worsening the electrophysiological phenotype — a mechanism-specific interaction important for interpreting clinical severity.

At the tissue level, Butters et al. (2010)55 Butters et al. (2010)
Butters TD et al. Mechanistic links between Na+ channel (SCN5A) mutations and impaired cardiac pacemaking in sick sinus syndrome. Circ Res 2010;107(1):126-37 used computational modeling to show that loss-of-function SCN5A mutations do not merely slow intrinsic pacemaker rate — they also impair electrical conduction across the SAN-atrium junction, potentially producing SAN exit block and sinus arrest. Vagal (parasympathetic) tone amplifies these bradycardic effects.

The Evidence

The key clinical evidence linking Pro1297Leu to disease comes from a landmark 2003 paper in the Journal of Clinical Investigation. Benson et al.66 Benson et al.
Benson DW, Wang DW, Dyment M et al. Congenital sick sinus syndrome caused by recessive mutations in the cardiac sodium channel gene (SCN5A). J Clin Invest 2003;112(7):1019-28 screened SCN5A in ten pediatric patients from seven families with unexplained congenital SSS. Three probands carried compound heterozygous mutations, one of which was P1298L (the same amino acid substitution, alternate transcript numbering). All six identified mutations showed loss-of-function or gating impairment in biophysical characterization.

Because this variant was identified in compound heterozygosity (paired with a second loss-of-function SCN5A allele), heterozygous single-copy carriers in those families were largely unaffected. This inheritance pattern resembles autosomal recessive more than dominant for congenital SSS. However, the same loss-of-function variant context also appears in dominant SCN5A disorders including Brugada syndrome77 Brugada syndrome
Brugada syndrome: a familial arrhythmia characterized by ST-elevation in right precordial ECG leads and risk of ventricular fibrillation, caused by loss-of-function mutations in SCN5A or associated proteins and dilated cardiomyopathy.

A critical practical finding comes from Chiang et al. (2015)88 Chiang et al. (2015)
Chiang DY et al. Loss-of-Function SCN5A Mutations Associated With Sinus Node Dysfunction, Atrial Arrhythmias, and Poor Pacemaker Capture. Circ Arrhythm Electrophysiol 2015;8(5):1105-12: loss-of-function SCN5A mutations are associated with elevated pacemaker lead capture thresholds — the voltage required to electrically stimulate the heart through an implanted device. Among 11 patients with elevated capture thresholds carrying severe loss-of-function SCN5A mutations, 4 could not achieve atrial capture, and 3 had intermittent loss of ventricular capture after implantation, resulting in 2 fatalities and 1 recurrent syncope.

Practical Actions

For heterozygous carriers of P1297L without symptoms and no family history of SSS or sudden cardiac death, the immediate clinical priority is a baseline ECG to screen for features suggesting Brugada pattern or conduction slowing. The overlap phenotype between Brugada syndrome and SSS from SCN5A loss-of-function is well described, with individual patients sometimes expressing both.

If bradycardia, syncope, or palpitations develop, electrophysiology referral is warranted. The discovery of P1297L in a symptomatic patient should prompt discussion with the electrophysiologist about the pacemaker capture threshold issue99 pacemaker capture threshold issue
Nav1.5 is expressed in the myocardium beyond just the sinus node; loss-of-function reduces overall myocardial excitability, which can elevate the energy needed to electrically capture (stimulate) cardiac tissue through a pacemaker lead. Careful pre-implantation testing and higher-output device settings are warranted — standard pacemaker settings may be inadequate.

Family cascade testing matters: any first-degree relative who also carries a separate loss-of-function SCN5A variant is at risk for the more severe compound heterozygous phenotype.

Interactions

The H558R polymorphism (rs1805124) is the most clinically relevant interaction: when carried on the same chromosome as P1297L, it significantly worsens channel availability and likely increases the probability of symptomatic bradycardia in heterozygous P1297L carriers. In families where multiple members carry P1297L, the H558R co-segregation should be checked.

Other SCN5A loss-of-function variants (rs45620037, rs7626962) can compound with P1297L to produce the more severe autosomal-recessive SSS phenotype seen in the original Benson et al. families. Standard genome panels and WGS typically report all SCN5A coding variants simultaneously, so compound heterozygosity is detectable.

Genotype Interpretations

What each possible genotype means for this variant.

GG Wild-Type Normal

Standard SCN5A P1297 sequence — no sodium channel loss-of-function from this variant

You carry two copies of the standard SCN5A Pro1297 allele and do not have the P1297L variant. Your cardiac sodium channel Nav1.5 is not impaired by this specific mutation. This is the nearly universal genotype — the A allele is found in approximately 1 in 50,000 people in gnomAD population databases, making this one of the rarest SCN5A missense variants. Other SCN5A variants (Brugada syndrome mutations, Long QT type 3 mutations) are not captured by this result.

AA Homozygous P1297L High Risk

Carries two copies of SCN5A P1297L — homozygous loss-of-function sodium channel variant; severe sinus node dysfunction expected

You carry two copies of the P1297L variant, one on each chromosome 3. This homozygous state doubles the loss-of-function burden on Nav1.5 at this position. While the original Benson et al. (2003) paper identified P1297L in compound heterozygosity (paired with a different SCN5A variant), the same loss-of-function mechanism applies in homozygosity — severe reduction in sodium channel availability affecting sinus node automaticity and SAN-to-atrium conduction. This genotype is effectively absent from population databases (gnomAD shows zero homozygotes) and would be expected to cause symptomatic bradycardia, sinus arrest, or complete SAN block requiring pacemaker therapy. Immediate cardiac evaluation is necessary.

AG P1297L Carrier Carrier

Carries one copy of SCN5A P1297L — loss-of-function sodium channel variant associated with arrhythmia and conduction disease

The Pro1297Leu substitution (c.3890C>T in NM_000335.5, alternate numbering P1298L in some transcripts) lies in the transmembrane domain S6 of repeat IV of Nav1.5 — a region critical for voltage-dependent inactivation gating. Biophysical characterization by Gui et al. (2010, PMID 20539757) showed:

  • Normal peak current density: the mutant channel reaches the cell surface at normal density and conducts normally at peak activation
  • Gating defect: negative shift in steady-state inactivation means more channels are unavailable (inactivated) at resting membrane potentials
  • Kinetic defect: reduced voltage-dependence of open-state inactivation impairs reliable recovery between beats

These combine to reduce the sodium current available for each subsequent cardiac cycle — an effect amplified by the common H558R polymorphism (rs1805124) if co-inherited. In tissue, computational modeling (Butters et al. 2010, PMID 20448214) shows the same functional profile impairs sinoatrial node exit conduction, not only intrinsic pacemaker rate, producing sinus arrest and SAN exit block.

For heterozygous carriers: penetrance for symptomatic SSS as a single-allele condition is low in published family data. However, the same Nav1.5 loss-of- function context appears in Brugada syndrome (ST elevation, arrhythmia risk), and the ClinVar record (VCV000009394) includes pathogenic submissions for Brugada syndrome 1. Periodic ECG monitoring is appropriate, particularly in the setting of fever, flecainide use, or vagal stimulation (which unmask Brugada pattern in susceptible carriers).

Important clinical note: if pacemaker implantation is ever needed, inform the electrophysiologist of this SCN5A variant. Loss-of-function SCN5A mutations are associated with elevated capture thresholds — the energy required to stimulate cardiac tissue through a pacemaker lead — and standard device settings may be insufficient. Two fatalities and serious pacemaker malfunction were reported in SCN5A loss-of-function patients with unrecognized elevated thresholds (Chiang et al. 2015, PMID 26111534).