ClinVar Genomic variation as it relates to human health

Converted during submission to Likely pathogenic.

The LMNA c.1003C>T variant is predicted to result in the amino acid substitution p.Arg335Trp. This variant has been reported in many unrelated individuals with dilated cardiomyopathy (Lakdawala et al 2012. PubMed ID: 22464770; Table S1B in Walsh R et al 2016. PubMed ID: 27532257; Sousa A et al 2019. PubMed ID: 30871747; Martins E et al 2019. PubMed ID: 31303467; Zhang Y et al 2021. PubMed ID: 34808346). The c.1003C>T variant was also reported in a family with heart hand syndrome IV, but an additional intronic variant (c.1609-12T>G) was also detected (Zaragoza MV et al 2016. PubMed ID: 27723096). In vivo experimental studies suggest this variant impacts protein function (Zhang Y et al 2021. PubMed ID: 34808346). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic.

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 335 of the LMNA protein (p.Arg335Trp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with dilated cardiomyopathy (PMID: 22224630, 24503780, 27532257, 27723096). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 36473). 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. For these reasons, this variant has been classified as Pathogenic.

Not observed in large population cohorts (gnomAD); 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: 34862408, 22266370, 22464770, 22224630, 24503780, 20474083, 26743238, 23811080, 24846508, 27532257, 30165862, 30871747, 31303467, 29709087, 30847666, 31829210, 30528549, 30078822, 34808346, 27723096, 10939567)

The p.Arg335Trp variant in LMNA (ClinVar ID: 36473) was absent from large popula tion studies and has been reported in 9 individuals with a range of phenotypes, all consistent with a laminopathy (1 individual with Emery-Dreifuss muscular dys trophy (EDMD), 1 individual with acro-osteolysis, atrial fibrillation, hypertrig lyceridemia and autoimmune thyroiditis, 1 individual with hand-heart syndrome IV (HHS-IV), and 5 individuals with DCM with or without arrhythmia) (Drouin 2004, Zafeiriou 2005, Lakdawala 2012, Stallmeyer 2012, Walsh 2016, Nishiuchi 2017, Zar agoza 2017). The variant segregated with disease in 7 individuals (HHS-IV: 3 mem bers of 1 family [Zaragoza 2017], DCM+arrhythmia: 3 members of 3 families [Stall meyer 2012, Nishiuchi 2017, LMM data], EDMD: 1 member of 1 family [Zafeiriou 200 5. In vitro protein modeling provides some evidence that the p.Arg335Trp variant may impact protein function (Bollati 2012). In summary, this variant meets crit eria to be classified as pathogenic for laminopathy in an autosomal dominant man ner. ACMG/AMP Criteria applied: PP1_Strong; PM2; PS4_Moderate; PP3; PS3_Supporti ng.

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM1,PM2,PP3,PP4.

PS4, PP1_strong, PM2, PP3

Variant summary: LMNA c.1003C>T (p.Arg335Trp) results in a non-conservative amino acid change located in the Intermediate filament, rod domain (IPR039008) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250386 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1003C>T has been reported in the literature in multiple individuals affected with Dilated Cardiomyopathy and Heart-Hand syndrome (e.g., Lakdawala_2012, Pugh_2014, Nishiuchi_2017, Zaragoza_2017, Zhang_2022), and the variant has been shown to segregate with Heart-Hand syndrome in at least two families (e.g., Zaragoza_2017, Zhang_2022). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, and found the variant results in abnormal nuclear morphology and contraction as well as defective DNA repair in atrial cardiomyocytes (Zhang_2022). Additionally, when the variant was introduced into a zebrafish model, electrical and structural phenotypes were recapitulated (Zhang_2022). The following publications have been ascertained in the context of this evaluation (PMID: 22464770, 29237675, 24503780, 27723096, 34808346). Multiple submitters have reported clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

The p.R335W pathogenic mutation (also known as c.1003C>T), located in coding exon 6 of the LMNA gene, results from a C to T substitution at nucleotide position 1003. The arginine at codon 335 is replaced by tryptophan, an amino acid with dissimilar properties, and is located in the Coil2 domain. This variant has been reported in multiple individuals with dilated cardiomyopathy (DCM), including one DCM case whose unaffected parents reportedly tested negative for this variant (Lakdawala NK et al. J. Card. Fail., 2012 Apr;18:296-303; Stallmeyer B et al. Genet Test Mol Biomarkers, 2012 Jun;16:543-9; Pugh TJ et al. Genet. Med., 2014 Aug;16:601-8; Martins E et al. Rev Port Cardiol, 2019 06;38:441-447). This variant has also been reported in individuals with other laminopathies, including one family demonstrating co-segregation in family members with Heart-Hand syndrome type IV, whose symptoms included DCM and brachydactyly (Zaragoza MV et al. Clin Genet, 2017 03;91:499-500; Lambert JC et al. Joint Bone Spine, 2019 07;86:525-527). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). 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.