ClinVar Genomic variation as it relates to human health

proposed classification - variant undergoing re-assessment, contact laboratory

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 377 of the LMNA protein (p.Arg377Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with cardiomyopathy and muscular dystrophy (PMID: 18646565, 21632249, 21840938, 23183350, 24503780). ClinVar contains an entry for this variant (Variation ID: 48031). 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 expected to disrupt LMNA protein function with a positive predictive value of 95%. This variant disrupts the p.Arg377 amino acid residue in LMNA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 12628721, 12673789, 15053843, 16386954). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

This c.1129C>T (p.Arg377Cys) variant in the LMNA gene has previously been reported in a 49 year old male with a diagnosis and a family history of DCM [PMID 24503780] and was also detected in a 10 y/o female who died of heart failure, with unsteady gait, diagnosed at the age of 7 with DCM [PMID 21632249]. This variant was also detected in a cohort of patients with muscular dystrophy [PMID 18646565] and a cohort of patients with cardiac disease [PMID 23183350]. Additional variants affecting the same amino acid at position 377 (p.Arg377His and p.Arg377Leu) have been reported in patients with cardiomyopathy and muscular dystrophy. Arginine at position 377 of the LMNA protein is highly conserved in mammals and has not been observed in the ExAC database. While not validated for clinical use, the computer-based algorithms SIFT and Polyphen-2 predict this Arg377Cys change to be deleterious. It is thus interpreted as a likely pathogenic variant.

The p.R377C pathogenic mutation (also known as c.1129C>T), located in coding exon 6 of the LMNA gene, results from a C to T substitution at nucleotide position 1129. The arginine at codon 377 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been reported in multiple individuals with laminopathies, including dilated cardiomyopathy (DCM), Emery-Dreifuss muscular dystrophy, and limb girdle muscular dystrophy (Deconinck N et al. Neuromuscul Disord, 2010 Aug;20:517-23; Komaki H et al. Neuromuscul Disord, 2011 Aug;21:563-8; Sylvius N et al. FASEB J, 2011 Nov;25:3966-78; Pugh TJ et al. Genet Med, 2014 Aug;16:601-8; Hasselberg NE et al. Eur Heart J, 2018 Mar;39:853-860; Cotta A et al. J Mol Neurosci, 2019 Dec;69:623-627; Krenn M et al. Eur J Neurol, 2022 Jun;29:1815-1824; Pessente GD et al. Front Cardiovasc Med, 2022 Apr;9:823717). Two other alterations at the same codon, p.R377L (c.1130G>T) and p.R377H (c.1130G>A), have been detected in subjects with DCM, as well as in subjects with varying forms of muscular dystrophy, and have been reported to segregate with disease (Muchir A et al. Hum. Mol. Genet., 2000 May;9:1453-9; Ki CS et al. J. Hum. Genet., 2002;47:225-8; Boriani G et al. Stroke, 2003 Apr;34:901-8; Charniot JC et al. Hum. Mutat., 2003 May;21:473-81; Sébillon P et al. J. Med. Genet., 2003 Aug;40:560-7; Rudnik-Schöneborn S et al. Neurogenetics, 2007 Apr;8:137-42; Verdonschot JAJ et al. Circ Genom Precis Med, 2020 10;13:476-487). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration is predicted to be deleterious by BayesDel in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate a damaging effect via disruption of normal protein folding leading to LMNA aggregation (PMID: 34862408); This variant is associated with the following publications: (PMID: 15678000, 21840938, 20474083, 18035086, 10814726, 12920062, 16407522, 19124654, 18646565, 20576434, 24503780, 23183350, 26060040, 27532257, 23062543, 27506821, 12032588, 16386954, 21483645, 31410651, 31296281, 31447099, 30078822, 34930020, 35387801, 37652022, 34363016, 36548481, 35239206, 21632249, 10939567, 34862408)

ACMG Criteria: PS4, PM2_P, PM5, PM1, PP1, PP5; Variant was found in heterozygous state

Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. LMNA p.Arg377Cys Given the case data and lack of presence in general population databases (reviewed below) we consider this variant as likely disease causing. The variant has been seen in at least five unrelated cases with cardiomyopathy or laminopathy in the literature. There is segregation data on family members in the reported cases. Astejada M. et al., 2008 reported c.1129 C>T in one Japanese individual with muscular dystrophy with nuclear envelopathy. No specific details were provided. Komaki H et al., 2011 reported R377C in one female who died at 7 yo from heart failure. She had an unsteady gate and a CK of 1000 at biopsy. Cardiac involvement included DCM diagnosed at 7 yo with an EF of 32%. She had joint contractures of her ankles and no respiratory dysfunction. Sylvius et al., 2011 reported c.1129C>T in two unrelated individuals. One was diagnosed at 42 yo after having difficulty climbing stairs. (S)he had pelvic and muscle weakness, axial muscle wasting, no contractures cardiomyopathy with CD and ICD and was last examined at age 56. The other patient was diagnosed at age 40 after having difficulty climbing stairs. (S)he also had pelvic muscle weakness with cardiac conduction defects and arrhythmia and their last reported evaluation before publication was at age 67. Van Rijsingen et al., 2013 reported this variant in one individual with this variant in their large cohort of LMNA mutation carriers but no individual data was provided. Similar changes at the same amino acid are summarized below: Charniot et al., 2003 reported a family harboring the R377H variant. 12 family members are positive for the R377H variant in lamin A. Of those, 11/12 have a DCM phenotype. The one unaffected individual is the youngest of the mutation positive family members at 21 yo. 4/10 evaluated mutation positive family members have a muscular phenotype, and 1/10 additional family members has a borderline study at age 33 yo. All of the individuals in their 30s and 40s had a reduced ejection fraction (<55%), while those in their 20s had ejection fractions in the 60s. Complete left bundle branch block was found in 5/8 evaluated individuals 4/8 also had some level of AV block (including two individuals who had both LBBB and AVB. 9/12 individuals had some level of AF and 4 had episodes of VT. Every mutation positive family member over the age of 21 had some form of conduction system disease. Muchir et al., 2000 reported a carribean family with the R377H variant. Eight individuals were evaluated. This family reported musculoskeletal, cardiomyopathy and AV conduction system defects. In silico analysis with PolyPhen-2 predicts the variant to be damaging. The argenine at codon is conserved across species, as are neighboring amino acids. Other variants have been reported in association with disease at this codon 377 and nearby codons. In total the variant has not been seen in individuals from publicly available population datasets. There is no variation at codon 377 listed in the NHLBI Exome Sequencing Project dataset, which currently includes variant calls on Caucasian and African American individuals (as of October 29, 2014).