ClinVar Genomic variation as it relates to human health

The p.Ala280Val variant in GPD1L has been reported in 1 infant who died suddenly, 2 individuals with Brugada syndrome, and 1 individual with LVNC who also carried a likely pathogenic variant in TTN (Weiss 2002, London 2007, Alder 2016, Methner 2016. Miszalski-Jamka 2017). In vitro functional studies provide some evidence that the p.Ala280Val variant may impact protein function (London 2007, Liu 2009, Valdivia 2009); however, these types of assays may not accurately represent biological function. Furthermore, this variant has also been identified in 0.02% (25/126354) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). Additionally, the alanine (Ala) at position 280 is not conserved, with 3 mammals (opossum, Tasmanian devil, wallaby) and >25 evolutionarily distant species carrying a valine (Val) at this position. These data raise the possibility that this change may be tolerated. Importantly, the validity of the GPD1L association with Brugada syndrome has been formally disputed by a ClinGen expert panel (Hosseini 2018). It had been implicated via a linkage-analysis based study (London 2007) resulting in the identification of the p.Ala280Val variant in a single family, in which it segregated with disease in many members (London 2007). However, this study did not convincingly exclude other genes in the linked region (including SCN5A), leaving it unclear whether the p.Ala280Val variant represented the causal variant. In summary, there is conflicting data for this variant and insufficient evidence supporting an association of the GPD1L gene with Brugada. Therefore, the clinical significance of the p.Ala280Val variant is uncertain. ACMG/AMP Criteria applied: PS3_Supporting, PS4_Supporting, BP4_Strong, BS1_Supporting.

This variant was classified as: Uncertain significance. The available evidence favors the pathogenic nature of this variant, however the currently available data is insufficient to conclusively support its pathogenic nature. Thus this variant is classified as Uncertain significance - favor pathogenic. The following ACMG criteria were applied in classifying this variant: PS3,PP5,BP4.

PM2(s), BS2(s), PP5(noinf)

Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as VUS - 3B. Following criteria are met: 0105 - The mechanism of disease for this gene is not clearly established. Functional analysis of a missense has proven a loss of function consequence, however the pathogenicity of this variant is uncertain (PMID: 17967977, PMID: 19666841). (N) 0107 - This gene is known to be associated with autosomal dominant disease. (N) 0112 - Variants in this gene are known to have reduced penetrance (PMID: 17967977), however only a single example has been observed. (N) 0200 - Variant is predicted to result in a missense amino acid change from an alanine to a valine (exon 6). (N) 0251 - Variant is heterozygous. (N) 0302 - Variant is present in gnomAD v2 <0.001 for a dominant condition (36 heterozygotes, 0 homozygotes). (P) 0309 - An alternative amino acid change at the same position has been observed in gnomAD v2 (12 heterozygotes, 0 homozygotes). (N) 0503 - Missense variant consistently predicted to be tolerated or not conserved in mammals with a minor amino acid change. (B) 0600 - Variant is located in an annotated domain or motif, (NAD_Gly3P_dh_C terminal domain; PDB). (N) 0705 - No comparable variants have previous evidence for pathogenicity. An alternative change (p.Ala280Thr) has been reported as a VUS in a patient who died suddenly (ClinVar). (N) 0808 - Previous reports of pathogenicity are conflicting. This variant has been reported in one large family, and several additional individuals who either died suddenly or had Brugada syndrome. However it has also been reported as a VUS, and as likely benign in an individual with left ventricular hypertrabeculation (ClinVar, PMID: 17967977, PMID: 27435932, PMID: 28798025, PMID: 26743238). (N) 1002 - Moderate functional evidence supporting abnormal protein function. This variant has been functionally proven in transfected HEK293 and COS7 cells to cause a signficant reductions in sodium current and channel formation. It also impairs SCN5A protein localization, and its ability to integrate into the channel (PMID: 17967977, PMID: 19666841). (P) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

Functional studies suggest that p.(A280V) interferes with the trafficking of cardiac SCN5A sodium channels to the plasma membrane and reduces inward sodium current (London et al., 2007; Valdivia et al., 2009); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 22995991, 19745168, 23414114, 17967977, 27435932, 30662450, 30821013, 34426522, 31019026, 31980526, 28798025, 19666841, 31618753)

Criteria: BP4

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 280 of the GPD1L protein (p.Ala280Val). This variant is present in population databases (rs72552291, gnomAD 0.02%). This missense change has been observed in individual(s) with Brugada syndrome (PMID: 17967977, 26743238, 27435932). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 786). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GPD1L protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects GPD1L function (PMID: 17967977, 19666841, 19745168, 20724705). 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.

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

The GPD1L c.839C>T variant is predicted to result in the amino acid substitution p.Ala280Val. This variant was reported in individuals with Brugada syndrome, left ventricular hypertrabeculation, or sudden death (London et al. 2007. PubMed ID: 17967977; Table S1, Adle et al. 2016. PubMed ID: 26743238; Methner et al. 2016. PubMed ID: 27435932; Table S3, Miszalski-Jamka et al. 2017. PubMed ID: 28798025). Functional studies showed that this variant results in reduced enzyme activity, altered SCN5A channel surface expression, and reduces inward sodium current (London et al. 2007. PubMed ID: 17967977; Valdivia et al. 2009. PubMed ID: 19666841; Liu et al. 2009. PubMed ID: 19745168). However, this variant was also reported in unaffected individuals (Table S1, Chen et al. 2018. PubMed ID: 30662450; Campuzano et al. 2019. PubMed ID: 30821013) and documented to co-occur with additional variants which may explain clinical features (Table S3, Miszalski-Jamka et al. 2017. PubMed ID: 28798025; Table S15, Clark et al. 2019. PubMed ID: 31019026; Table S1, Ziats et al. 2020. PubMed ID: 31618753). This variant is reported in 0.020% of alleles in individuals of European (non-Finnish) descent in gnomAD and the majority of labs interpret this variant as uncertain in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/variation/786). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

Variant summary: GPD1L c.839C>T (p.Ala280Val) results in a non-conservative amino acid change located in the Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal domain (IPR006109) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00014 in 248254 control chromosomes (gnomAD). The observed variant frequency is approximately 27 fold of the estimated maximal expected allele frequency for a pathogenic variant in GPD1L causing Brugada Syndrome phenotype (5e-06), suggesting that the variant is benign or has low penetrance. c.839C>T has been reported in the literature in multiple individuals affected with Brugada Syndrome (London_2007, Adler_2016), including a large multi-generation family with several patients (London_2007). This variant has also been reported in a patient with left ventricular hypertrabeculation (Miszalski-Jamka_2017) and in an individual who suffered sudden death by an unknown cause (Methner_2016). These data indicate that the variant may be associated with disease. However, in one of these patients a co-occurrence with another pathogenic variant has also been reported (TTN, p.R10384X), providing supporting evidence for a benign role (Miszalski-Jamka_2017). Multiple publications report experimental evidence evaluating an impact on protein function and demonstrated that the A280V variant caused lower enzyme activity, and resulted in decreased surface expression of SCN5A with lower Na currents (London_2007, Valdivia_2009). Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (2 pathogenic, 2 likely pathogenic, 1 VUS-favor pathogenic). Based on the evidence outlined above, the variant was classified as likely pathogenic.