ClinVar Genomic variation as it relates to human health

ACMG classification criteria: PS3, PM1, PM6

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 225 of the SCN5A protein (p.Arg225Trp). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with clinical features of autosomal dominant SCN5A-related conditions (PMID: 12574143, 19251209, 19606473, 19716085, 20031634, 20129283, 22885917). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 68032). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects SCN5A function (PMID: 12574143, 25624448). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant disrupts the p.Arg225 amino acid residue in SCN5A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 24815523, 26022185). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

The p.R225W pathogenic mutation (also known as c.673C>T), located in coding exon 5 of the SCN5A gene, results from a C to T substitution at nucleotide position 673. The arginine at codon 225 is replaced by tryptophan, an amino acid with dissimilar properties, and is located in the DI-S4 transmembrane region. This variant was previously described in conjunction with another SCN5A alteration in compound heterozygous siblings, both of whom were diagnosed with severe cardiac conduction disease after birth. One of these siblings also developed severe dilated cardiomyopathy (DCM) and died at 1 year of age (Bezzina CR et al. Circ Res. 2003;92:159-68). In another family, this variant was reported in multiple individuals with progressive cardiac conduction disease (PCCD) and/or Brugada syndrome (BrS), although a relative negative for this alteration also exhibited PCCD (Probst V et al. Circ Cardiovasc Genet. 2009;2:552-7). This alteration has also been reported in sudden cardiac death, BrS, and LQTS cohorts (Kapplinger JD et al. Heart Rhythm. 2009;6(9):1297-303; Kapplinger JD et al. Heart Rhythm. 2010;7:33-46; Lahrouchi N et al. J. Am. Coll. Cardiol. 2017 May;69(17):2134-2145). Multiple in vitro functional analyses indicate that this variant impacts protein function (Bezzina CR et al. Circ. Res. 2003;92:159-68; Moreau A et al. J Gen Physiol. 2015;145:93-106; Strege PR et al. Am. J. Physiol. Gastrointest. Liver Physiol. 2018;314:G494-G503). In addition, based on internal structural assessment, this alteration is predicted to disrupt the voltage sensing motif in voltage sensing domain 1 (Jiang D et al. Cell. 2020;01;180(1):122-134.e10). Other alterations affecting the same amino acid, p.R225Q (c.674G>A) and p.R225P (c.674G>C), have been reported in patients with complex arrhythmias and multifocal ventricular ectopy (Millat G et al. Clin Genet. 2006;70:214-27; Beckermann TM et al. Heart Rhythm. 2014;11:1446-53). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

Variant summary: SCN5A c.673C>T (p.Arg225Trp) results in a non-conservative amino acid change located in the Ion transport domain (IPR005821) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 242066 control chromosomes. c.673C>T has been reported in the literature in multiple individuals affected with autosomal dominant SCN5A-related conditions (examples: Probst_2009) These data indicate that the variant is very likely to be associated with disease. Experimental studies have shown that this missense change disrupts the normal function of the protein (examples: Moreau_2015, Strege_2018). The following publications have been ascertained in the context of this evaluation (PMID: 29167113, 25624448, 20031634). ClinVar contains an entry for this variant (Variation ID: 68032). Based on the evidence outlined above, the variant was classified as pathogenic.

This c.673C>T (p.Arg225Trp) variant has been reported in 7 patients with Brugada syndrome from 2 families [PMID 19251209]. This variant was also reported in two siblings with severe conduction disease compound heterozygous for this variant and p.Trp146* variant [PMID 12574143]. The mother however, who was a carrier for this variant, was clinically asymptomatic with normal ECG. Functional assay showed that this variant affects the sodium channel voltage gating. Variants affecting the same amino acid (p.Arg225Gln and p.Arg225Pro) have been reported in additional patients with arrythmias indicating the functional importance of this amino acid and its position [PMID 16922724, 26733869]. This variant was reported in one heterozygous individuals from Europe (http://exac.broadinstitute.org/variant/3-38655264-G-A). This variant is highly conserved in mammals. While not validated for clinical use, computer-based algorithms predict this p.Arg225Trp change to be deleterious. It is thus classified as a pathogenic variant.

PP3, PM1, PM2_supporting, PS3, PS4_moderate

Reported in association with Long QT syndrome, Brugada syndrome, sudden arrhythmia death syndrome (SADS), and other conduction disorders (Bezzina et al., 2003; Kapplinger et al., 2009; Meregalli et al., 2009; Probst et al., 2009; Kapplinger et al., 2010; Lahrouchi et al., 2017); Observed with a nonsense variant on the opposite allele (in trans) in two infant siblings with severe conduction disease and wide QRS-complexes (Bezzina et al., 2003); Published functional studies demonstrated R225W results in a significant reduction in sodium current amplitude and an alteration in gating pore current, indicating gain of function (Bezzina et al., 2003; Moreau et al., 2015); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Reported in ClinVar as pathogenic/likely pathogenic (ClinVar Variant ID# 68032; ClinVar); This variant is associated with the following publications: (PMID: 26916278, 24136861, 31477192, 31981491, 25637381, 24573164, 25624448, 12574143, 19251209, 19716085, 20031634, 20129283, 29167113, 21167004, 28449774, 16922724, 29728395, 31125670, 30193851, 32048431, 32536774, 30847666, 31447099, 33131149, 26582918, 32746448)

This missense variant replaces arginine with tryptophan at codon 225 of the SCN5A protein. This variant is found within a highly conserved region of the transmembrane domain DI. Rare nontruncating variants in this region (a.a.132-410) have been shown to be significantly overrepresented in individuals with Brugada syndrome (PMID: 32893267). Functional studies have shown that this variant causes a significant reduction in sodium current (PMID: 12574143, 19251209, 25624448). This variant has been reported in in over ten individuals affected with Brugada syndrome (PMID: 19251209, 20031634, 36516610). This variant has been observed in compound heterozygous state with p.Trp156* in the same gene in two siblings affected with severe, early-onset conduction disease (PMID: 12574143). It has been shown that this variant segregates with disease in some of these families (PMID: 12574143, 19251209, 20031634). This variant has also been reported in individuals suspected of having Brugada syndrome (PMID: 20129283) or long QT syndrome (PMID: 19716085), as well as in an individual affected with sudden arrhythmic death syndrome (PMID: 34620408). This variant has been identified in 6/273472 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.

This variant has been reported as associated with Long QT syndrome in the following publications (PMID:19716085). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory.