Submissions for variant NM_000335.5(SCN5A):c.3997A>G (p.Ile1333Val)

dbSNP: rs199473226

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000183057	SCV000235466	pathogenic	not provided	2013-05-30	criteria provided, single submitter	clinical testing	The Ile1334Val mutation in the SCN5A gene has been reported in two unrelated individuals with LQTS, and it was absent from 2,600 reference alleles (Kapplinger J et al., 2009; Stattin E et al., 2012). Also, the NHLBI Exome Sequencing Project reports Ile1334Val was not observed in approximately 6,500 individuals of European and African American ancestry, indicating it is not a common benign variant in these populations. Although Ile1334Val results in a conservative amino acid substitution of one non-polar amino acid with another, the Ile1334 residue is conserved across species. Mutations in nearby residues (Ala1332Thr, Pro1332Leu, Ser1333Tyr) have been reported in association with LQTS, further supporting the functional importance of this region of the protein. The variant is found in LQT panel(s).
Labcorp Genetics (formerly Invitae), Labcorp	RCV000456774	SCV000545050	uncertain significance	Brugada syndrome	2016-08-24	criteria provided, single submitter	clinical testing	This sequence change replaces isoleucine with valine at codon 1334 of the SCN5A protein (p.Ile1334Val). The isoleucine residue is highly conserved and there is a small physicochemical difference between isoleucine and valine. This variant is present in population databases (rs199473226, ExAC 0.002%). This variant was reported in individuals referred for long QT testing (PMID: 19716085, 23098067). ClinVar contains an entry for this variant (Variation ID: 67847). This variant identified in the SCN5A gene is located in the transmembrane spanning DIII-S4/S5 region of the resulting protein (PMID: 25348405), but it is unclear how this variant impacts the function of this protein. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies. In summary, this variant is a rare missense change with uncertain impact on protein function. It has been reported in both the general population and individuals referred for longQT testing, but the available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics	RCV004017378	SCV004849279	uncertain significance	Cardiovascular phenotype	2016-10-07	criteria provided, single submitter	clinical testing	The c.4000A>G (p.I1334V) alteration is located in exon 23 (coding exon 22) of the SCN5A gene. This alteration results from a A to G substitution at nucleotide position 4000, causing the isoleucine (I) at amino acid position 1334 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Clinical Genetics Laboratory, Skane University Hospital Lund	RCV000183057	SCV005198161	likely pathogenic	not provided	2024-02-29	criteria provided, single submitter	clinical testing
Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust	RCV000058626	SCV000090146	not provided	Congenital long QT syndrome		no assertion provided	literature only	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.