Submissions for variant NM_000335.5(SCN5A):c.280A>G (p.Ile94Val)

gnomAD frequency: 0.00002  dbSNP: rs202114798

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV001557210	SCV000637108	uncertain significance	not provided	2025-01-01	criteria provided, single submitter	clinical testing	This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 94 of the SCN5A protein (p.Ile94Val). This variant is present in population databases (rs202114798, gnomAD 0.007%). This missense change has been observed in individual(s) with SCN5A-related conditions (PMID: 24613995, 33500567, 34930020, 37652022). ClinVar contains an entry for this variant (Variation ID: 463314). 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 tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000608230	SCV000710932	uncertain significance	not specified	2016-07-28	criteria provided, single submitter	clinical testing	The p.Ile94Val variant in SCN5A has not been previously reported in individuals with cardiomyopathy, but has been identified in 1/9808 African chromosomes and 1 /16508 South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http:/ /exac.broadinstitute.org; dbSNP rs202114798). Computational prediction tools and conservation analysis suggest that the p.Ile94Val variant may not impact the pr otein, though this information is not predictive enough to rule out pathogenicit y. Of note, a different variant at this amino acid position (p.Ile94Ser) has bee n identified in 1 individual with Brugada Syndrome (Kapplinger 2010). In summary , the clinical significance of the p.Ile94Val variant is uncertain.
Ambry Genetics	RCV000617922	SCV000738145	uncertain significance	Cardiovascular phenotype	2024-07-09	criteria provided, single submitter	clinical testing	The p.I94V variant (also known as c.280A>G), located in coding exon 2 of the SCN5A gene, results from an A to G substitution at nucleotide position 280. The isoleucine at codon 94 is replaced by valine, an amino acid with highly similar properties, and is located in the N-terminal, cytoplasmic region. This variant was detected in an individual from an irritable bowel syndrome cohort who was reported to have Brugada syndrome pattern on ECG, and in individuals with electronic health record indication of arrhythmia (Beyder A. Gastroenterology. 2014;146(7):1659-1668; Glazer AM et al. Circulation. 2022 03;145(12):877-891). This variant has also been detected in an individual from a control cohort (Kapplinger JD. Circ Cardiovasc Genet. 2015 Aug;8(4):582-95). In vitro studies reported this variant to have peak current density similar to wild type, but some impact to other parameters of channel function (Beyder A. Gastroenterology. 2014;146(7):1659-1668; Glazer AM et al. Circulation. 2022 03;145(12):877-891). This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Color Diagnostics, LLC DBA Color Health	RCV001841463	SCV001341799	uncertain significance	Cardiac arrhythmia	2023-05-09	criteria provided, single submitter	clinical testing	This missense variant replaces isoleucine with valine at codon 94 of the SCN5A protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). A functional study has shown that this variant causes a reduction of channel activity in cell culture (PMID: 24613995), while another in vitro study reported this variant does not change channel function (PMID: 34930020). This variant has been reported in an individual affected with irritable bowel syndrome who showed an Brugada-type ECG (PMID: 24613995), in an individual affected with left ventricular noncompaction (PMID: 33500567), and in three individuals affected with atrial fibrillation, long QT syndrome, and/or premature ventricular contraction (PMID: 34930020). This variant has been identified in 3/249412 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
GeneDx	RCV001557210	SCV001778930	uncertain significance	not provided	2020-02-03	criteria provided, single submitter	clinical testing	Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25904541, 24613995)
Fulgent Genetics, Fulgent Genetics	RCV002491006	SCV002784494	uncertain significance	Brugada syndrome 1; Long QT syndrome 3; Sick sinus syndrome 1; Progressive familial heart block, type 1A; Ventricular fibrillation, paroxysmal familial, type 1; Dilated cardiomyopathy 1E; SUDDEN INFANT DEATH SYNDROME; Atrial fibrillation, familial, 10	2021-10-16	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV001841463	SCV004814460	uncertain significance	Cardiac arrhythmia	2024-09-23	criteria provided, single submitter	clinical testing	This missense variant replaces isoleucine with valine at codon 94 of the SCN5A protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). A functional study has shown that this variant causes a reduction of channel activity in cell culture (PMID: 24613995), while another in vitro study reported this variant does not change channel function (PMID: 34930020). This variant has been reported in an individual affected with irritable bowel syndrome who showed an Brugada-type ECG (PMID: 24613995), in an individual affected with left ventricular noncompaction (PMID: 33500567), and in three individuals affected with atrial fibrillation, long QT syndrome, and/or premature ventricular contraction (PMID: 34930020). This variant has been identified in 3/249412 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV004787881	SCV005398806	uncertain significance	Long QT syndrome 3	2024-09-22	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3B. Following criteria are met: 0103 - Loss of function and gain of function are both known mechanisms of disease in this gene. Loss of function is usually associated with Brugada syndrome 1 (MIM#601144) and sick sinus syndrome 1 (SSS) (MIM#608567), whereas gain of function is usually associated with long QT syndrome 3 (LQTS) (MIM#603830). Dilated cardiomyopathy 1E (DCM) (MIM#601154) can be caused by variants with either a loss of function or gain of function mechanism (PMID: 29798782). (I) 0108 - This gene is associated with both recessive and dominant disease. Most conditions associated with this gene are dominantly inherited; however, SSS is caused by biallelic variants (OMIM). (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 20301690). (I) 0200 - Variant is predicted to result in a missense amino acid change from isoleucine to valine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (3 heterozygotes, 0 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0809 - Previous evidence of pathogenicity for this variant is inconclusive. This variant has been classified as a VUS by multiple clinical laboratories in ClinVar, and has been observed in individuals with dilated cardiomyopathy, long QT syndrome or irritable bowel syndrome (PMID: 34930020, 31983221, 24613995). (I) 1010 - Functional evidence for this variant is inconclusive. Patch clamp studies showed that this variant displayed similar properties to wild type on most measures except for a decrease in slope of the voltage dependence of inactivation (PMID: 24613995). (I) 1206 - This variant has been shown to be paternally inherited (by Sanger analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign