ClinVar Genomic variation as it relates to human health

Variant summary: SCN5A c.4931G>A (p.Arg1644His) results in a non-conservative amino acid change located in the Ion transport domain (IPR005821) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251476 control chromosomes. c.4931G>A has been reported in the literature in a large family with congenital LQTS (Malan_2016) and in multiple other individuals affected with Long QT Syndrome (example: Westenskow_2004 and Gibbs_2018 etc.). These data indicate that the variant is very likely to be associated with disease. Experimental evidence evaluating an impact on protein function demonstrated the variant causes a sustained, non-inactivating inward current and exhibits prolonged action potential durations and increased recovery from inactivation (Dumaine_1996, Wang_1996, Malan_2016). Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic (n=5) and likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.

Not observed at significant frequency in large population cohorts (gnomAD); Located near the cytoplasmic end of the S4 segment of domain IV; Electrophysiological studies in both Xenopus oocytes and mammalian cell lines have shown that R1644H alters the functional properties of the SCN5A channel (Dumaine et al., 1996; Wang et al., 1996); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 14753626, 10508990, 25904541, 18849657, 26669661, 28721524, 31983221, 8620612, 15840476, 15051636, 19841300, 10973849, 15121794, 11273715, 8541846, 26803770, 28220464, 25661095, 28341781, 28412158, 25294783, 29691127, 28573431, 28265756, 28150151, 19026623, 29766885, 31737537, 32383558, 31057083, 8917568, 35052356, 30369311)

This variant has been previously reported as a heterozygous change in patients with long QT syndrome (PMID: 8541846, 28341781, 19026623, 19841300, 31737537). In vitro functional studies of p.Arg1644His showed increased persistent sodium currents compared to the wild-type channels (PMID: 8620612, 8917568). It is absent from the gnomAD population database and thus is presumed to be rare. The c.4931G>A (p.Arg1644His) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. A different amino acid change at the same codon (c.4930C>T, p.Arg1644Cys) has also been reported in individuals with long QT syndrome (PMID: 16344400, 19716085). Based on the available evidence, the c.4931G>A (p.Arg1644His) variant is classified as Pathogenic.

This missense variant replaces arginine with histidine at codon 1644 of the SCN5A protein. This variant is also known as c.4928G>A (p.Arg1643His) based on a different transcript NM_000335.5. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). This variant is found within a highly conserved region of the transmembrane domain DIV. Rare nontruncating variants in this region have been shown to be significantly overrepresented in individuals with long QT syndrome (PMID: 32893267). Functional studies have shown that this variant causes a persistent late inward current when expressed in human kidney cell line and in Xenopus oocytes (PMID: 8620612, 8917568). Induced pluripotent stem cells derived from a carrier individual exhibited accelerated recovery from inactivation of sodium currents, action potential prolongation, and a high incidence of early after depolarizations (PMID: 26803770). This variant has been reported in over ten unrelated individuals affected with long QT syndrome (PMID: 8541846, 1097384, 15051636, 19026623, 19841300, 21185501, 25294783, 26803770, 27566755, 29691127, 30369311, 32383558, 32893267, 32931730, 35052356), and in individuals affected with Brugada syndrome (PMID: 32893267), dilated cardiomyopathy (PMID: 31983221), and idiopathic ventricular fibrillation (PMID: 31057083). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 1644 of the SCN5A protein (p.Arg1644His). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with long QT syndrome (PMID: 8541846, 10973849, 19026623, 19841300). ClinVar contains an entry for this variant (Variation ID: 9369). 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: 8620612, 8917568). For these reasons, this variant has been classified as Pathogenic.

The p.Arg1644His variant in SCN5A has been reported in at least 7 individuals with long QT syndrome (LQTS) and segregated with disease in >10 affected individuals from 2 families (Wang 1995, Wattanasirichaigoon 1999, Splawski 2000, Westenskow 2004, Millat 1009, Kapa 2009, Malan 2016, Anderson 2017, Nieto-Marin 2018). It was also identified in 1 individual with Brugada syndrome (Yamagata 2017). This variant was absent from large population studies but has been reported in ClinVar as pathogenic by multiple clinical laboratories (Variation ID # 9369). In vitro functional studies and computational prediction tools support an impact on protein function (Wang 1996, Dumaine 1996, Malan 2016). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant LQTS. ACMG/AMP criteria applied: PP1_Strong, PM2, PS3_Moderate, PS4_Moderate, PP3.

SCN5A: PM1, PM2, PM5, PP1, PP3, PS3:Supporting, PS4:Supporting

The p.R1644H pathogenic mutation (also known as c.4931G>A), located in coding exon 27 of the SCN5A gene, results from a G to A substitution at nucleotide position 4931. The arginine at codon 1644 is replaced by histidine, an amino acid with highly similar properties. This mutation was originally detected in a mother and son affected with long QT syndrome (LQTS) (Wang Q et al. Hum Mol Genet. 1995;4(9):1603-7). Other studies demonstrated disruption of inactivation in channels expressed in a human cell line and in Xenopus oocytes; p.R1644H showed sustained inward current predicted to account for the long QT defect, but findings suggested p.R1644H may be less severe than other alterations studied (Dumaine R et al. Circ Res. 1996;78(5):916-24; Wang DW et al. Proc Natl Acad Sci U.S.A. 1996;93(23):13200-5). In a study of compound mutations as a common cause of severe LQTS, p.R1644H was detected in the father and brother of a child with sudden death who also had a variant in the KCNE1 gene (Westenskow P et al. Circulation. 2004;109(15):1834-41). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. 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.

SCN5A Arg1644His c.4931G>A in exon 28, (NM_198056.2, ENST00000303395) hg19 chr3-38592932-C-T SCICD Classification: Likely pathogenic, based on adequate case data, absence in population datasets, and location in region enriched for disease variants. We do feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). Case data: -1 case of LQTS in our center - at least 3 cases of LQTS published (below) - 3 cases "referred for LQTS genetic testing", phenotypes unavailable (below) LQTS cases in the literature: Wang et al., 1995 (PMID 8541846) - segregated in a mother and son with long QT (recruited in Europe, North America, overlapping authors with Splawski et al so may be redundant) Splawski et al., 2000 (PMID 10973849)- seen in 2 families with long QT (recruited in Europe, North America, overlapping authors with Wang et al so may be redundant) Millat et al., 2009 (PMID 19026623) - seen in 1 male with long QT (study done in France, no overlap with other authors, recruitment location not noted). Cases "referred for LQTS genetic testing": Tester et al., 2005 (PMID 15840476) - Seen in 2 unrelated people referred for long QT testing, Ackerman's long QT testing series (tested in his lab), probably not overlapping with Kapplinger et al. Kapplinger et al., 2009 - seen in 1 patient referred for long QT testing at Familion. Those cases likely overlap with the data in Kapa et al (2009) since these are all from Ackerman's group and use data from his cohort and from the Familion cohort. Of note in considering the cases reported by Kapplinger et al (2009) is the lack of phenotypic data on this cohort, the low yield of 36% (vs. 70% in cohorts with firm diagnoses of long QT), and the lack of clarity regarding which variants were seen with another variant (9% of the cohort had multiple variants). Segregation data: segregated with disease in 2 family members (Wang et al., 1995) Functional data: This residue is located in the S4 voltage sensor transmembrane helix of domain IV of the protein. These region is enriched for variants seen in cases vs controls (https://www.cardioclassifier.org/Classifier). Dumaine et al., 1996 (PMID 8620612): heterologous expression in Xenopus oocytes showed inactivation resistance Wang et al., 1996 (PMID 8917568) - heterologous expression in human HEK 293 tsA-201 cells showed showed sustained inward current and non-zero variance, indicating continued channel gating, at times later than 20 msec. Paralogue data from cardiodb: Several variants at position 1644 in paralogous proteins have been reported to be disease causing. A corresponding Arginine to Histidine substitution was reported to cause cryptogenic focal epilepsy in the SCN1A gene (one de novo case). Arginine to Cysteine substitutions at the corresponding amino acids have also been reported in SCN1A (to cause generalized epilepsy with febrile seizures) and CACNA1A (episodic ataxia 2). Conservation data: Per the lab report, The arginine residue is highly conserved and there is a small physicochemical difference between arginine and histidine. There is no variation at codon 1644 listed in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >140,000 unrelated individuals of African, Asian, European, Latino, and Ashkenazi descent. Per Varsome.org, the average coverage at that site in genomes is mean 32.9x, median 32x, and 93.75% of samples have >20x coverage; in exomes it is mean 96.8x, median 100x, and 100% of samples have >20x coverage.

This variant has been reported as associated with Long QT syndrome in the following publications (PMID:8541846;PMID:10973849;PMID:15051636;PMID:15840476;PMID:19841300;PMID:8620612;PMID:8917568). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory.