ClinVar Genomic variation as it relates to human health

The p.Arg321X variant has been reported in at least 5 individuals with DCM, and segregated with disease in at least 3 affected relatives (Zeller 2006, Geiger 20 08, M?ller 2009, Sylvius 2011, Al-Saaidi 2013, Hasselberg 2014). In addition, th is variant has been identified by our laboratory in at least 9 affected members of one family with DCM, including one affected obligate carrier (LMM unpublished data) and has also been reported by other clinical laboratories in ClinVar (Var iation ID 48096). Additionally, the p.Arg312X variant has been identified in 1/8 38 Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad. broadinstitute.org/; dbSNP rs267607554). This variant leads to a premature termi nation codon at position 321, which is predicted to result in a truncated or abs ent protein. In vitro studies show that little to no LMNA protein is present in fibroblasts from patients carrying this variant (Geiger 2008, Al-Saaidi 2013). I n summary, this variant meets criteria to be classified as pathogenic for DCM in an autosomal dominant manner based upon presence in multiple affected individua ls, segregation studies, absence from the general population and functional stud ies. ACMG/AMP Criteria applied: PP1_Strong, PM2, PS4_Moderate, PS3_Moderate (Ric hards 2015).

The c.961C>T (p.R321*) alteration, located in exon 6 (coding exon 6) of the LMNA gene, consists of a C to T substitution at nucleotide position 961. This changes the amino acid from a arginine (R) to a stop codon at amino acid position 321. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This alteration has been reported in unrelated individuals with dilated cardiomyopathy (DCM) with conduction system disease and ventricular arrhythmias, and has been reported to segregate with disease in families (Geiger, 2008; Møller, 2009; Hasselberg, 2014; C. Seidman pers comm; Cuenca, 2016; Walsh, 2017). This variant was also detected in an individual with DCM with features suggesting skeletal muscle involvement (Sylvius, 2011). Functional studies report the mRNA produced by this variant is largely subject to nonsense mediated decay (NMD), while studies also report a skewed ratio of lamin A and lamin C protein which may disrupt lamin polymer stability, and incomplete NMD which may result in dominant negative effect from truncated protein retained in the endoplasmic reticulum, contributing to disease (Geiger, 2008; Al-Saaidi, 2013; Carmosino, 2016). Based on the available evidence, this alteration is classified as pathogenic.

Not observed at significant frequency in large population cohorts (Lek et al., 2016); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Published functional studies demonstrate a damaging effect with inappropriate localization into the endoplasmic reticulum affecting cellular homeostasis mechanisms (Carmosino et al., 2016); Reported in ClinVar (ClinVar Variant ID# 48096; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 27532257, 29237675, 30609406, 16715312, 31977013, 17987279, 24001739, 24058181, 26899768, 27421120, 30319452, 24846508, 21840938, 30402260, 24503780, 29095976, 19875404, 31983221, 31447099, 31402444, 33019804, 30078822)

Variant summary: LMNA c.961C>T (p.Arg321X) results in a premature termination codon, predicted to cause a truncation of the encoded protein, which is a commonly known mechanism for disease. The variant has been shown to induce incomplete nonsense mediated decay resulting in nearly absent/reduced expression of the truncated protein (Al-Saaidi_2013, Carmosino_2016). Truncations downstream of this position have been classified as pathogenic in ClinVar (e.g. c.1057C>T [p.Gln353Ter]; c.1228C>T [p.Gln410Ter]). The variant was absent in 249364 control chromosomes (gnomAD). c.961C>T has been reported in the literature in multiple individuals affected with Dilated Cardiomyopathy (Zeller_2006, Al-Saaidi_2013, Carmosino_2016, Hayashi_2020). These data indicate that the variant is very likely to be associated with disease. Functional evaluation of the protein has shown that the truncated protein is lowly expressed and accumulated within the ER, causing ER stress via the unfolded protein response. This in turn caused abnormal Ca2+ handling via the ER, resulting in a reduced Ca2+ release rate (~25%) compared with wildtype LMNA (Carmosino_2016). The variant is shown to also increase apoptosis by 45% (Carmosino_2016). Six ClinVar submitters have assessed the variant since 2014: all six have classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change creates a premature translational stop signal (p.Arg321*) in the LMNA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LMNA are known to be pathogenic (PMID: 18585512, 18926329). This variant is present in population databases (rs267607554, gnomAD 0.1%). This premature translational stop signal has been observed in individual(s) with dilated cardiomyopathy and/or ventricular arrhythmia (PMID: 17987279, 19875404, 24001739, 24058181, 27421120, 27532257). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 48096). For these reasons, this variant has been classified as Pathogenic.