Use of machine learning to classify high-risk variants of uncertain significance in lamin A/C cardiac disease

Published:December 24, 2021DOI:


      Variation in lamin A/C results in a spectrum of clinical disease, including arrhythmias and cardiomyopathy. Benign variation is rare, and classification of LMNA missense variants via in silico prediction tools results in a high rate of variants of uncertain significance (VUSs).


      The goal of this study was to use a machine learning (ML) approach for in silico prediction of LMNA pathogenic variation.


      Genetic sequencing was performed on family members with conduction system disease, and patient cell lines were examined for LMNA expression. In silico predictions of conservation and pathogenicity of published LMNA variants were visualized with uniform manifold approximation and projection. K-means clustering was used to identify variant groups with similarly projected scores, allowing the generation of statistically supported risk categories.


      We discovered a novel LMNA variant (c.408C>A:p.Asp136Glu) segregating with conduction system disease in a multigeneration pedigree, which was reported as a VUS by a commercial testing company. Additional familial analysis and in vitro testing found it to be pathogenic, which prompted the development of an ML algorithm that used in silico predictions of pathogenicity for known LMNA missense variants. This identified 3 clusters of variation, each with a significantly different incidence of known pathogenic variants (38.8%, 15.0%, and 6.1%). Three hundred thirty-nine of 415 head/rod domain variants (81.7%), including p.Asp136Glu, were in clusters with highest proportions of pathogenic variants.


      An unsupervised ML method successfully identified clusters enriched for pathogenic LMNA variants including a novel variant associated with conduction system disease. Our ML method may assist in identifying high-risk VUS when familial testing is unavailable.


      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'


      Subscribe to Heart Rhythm
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect


        • Dittmer T.A.
        • Misteli T.
        The lamin protein family.
        Genome Biol. 2011; 12: 222
        • Worman H.J.
        • Bonne G.
        “Laminopathies”: a wide spectrum of human diseases.
        Exp Cell Res. 2007; 313: 2121-2133
        • Crasto S.
        • My I.
        • Di Pasquale E.
        The broad spectrum of LMNA cardiac diseases: from molecular mechanisms to clinical phenotype.
        Front Physiol. 2020; 11: 761
        • Hershberger R.E.
        • Morales A.
        LMNA-related dilated cardiomyopathy.
        in: Adam M.P. Ardinger H.H. Pagon R.A. Wallace S.E. Bean L.J.H. Stephens K. Amemiya A. GeneReviews® [Internet]. University of Washington, Seattle, WA2008
        • Hasselberg N.E.
        • Haland T.F.
        • Saberniak J.
        • et al.
        Lamin A/C cardiomyopathy: young onset, high penetrance, and frequent need for heart transplantation.
        Eur Heart J. 2018; 39: 853-860
        • Jordan E.
        • Peterson L.
        • Ai T.
        • et al.
        Evidence-based assessment of genes in dilated cardiomyopathy.
        Circulation. 2021; 144: 7-19
        • Rosenbaum A.N.
        • Agre K.E.
        • Pereira N.L.
        Genetics of dilated cardiomyopathy: practical implications for heart failure management.
        Nat Rev Cardiol. 2020; 17: 286-297
        • Parks S.B.
        • Kushner J.D.
        • Nauman D.
        • et al.
        Lamin A/C mutation analysis in a cohort of 324 unrelated patients with idiopathic or familial dilated cardiomyopathy.
        Am Heart J. 2008; 156: 161-169
        • James C.A.
        • Jongbloed J.D.H.
        • Hershberger R.E.
        • et al.
        International evidence based reappraisal of genes associated with arrhythmogenic right ventricular cardiomyopathy using the clinical genome resource framework.
        Circ Genom Precis Med. 2021; 14e003273
        • van Rijsingen I.A.
        • Arbustini E.
        • Elliott P.M.
        • et al.
        Risk factors for malignant ventricular arrhythmias in lamin A/C mutation carriers a European cohort study.
        J Am Coll Cardiol. 2012; 59: 493-500
        • Pasotti M.
        • Klersy C.
        • Pilotto A.
        • et al.
        Long-term outcome and risk stratification in dilated cardiolaminopathies.
        J Am Coll Cardiol. 2008; 52: 1250-1260
        • Kumar S.
        • Baldinger S.H.
        • Gandjbakhch E.
        • et al.
        Long-term arrhythmic and nonarrhythmic outcomes of lamin A/C mutation carriers.
        J Am Coll Cardiol. 2016; 68: 2299-2307
        • Marchel M.
        • Madej-Pilarczyk A.
        • Tyminska A.
        • et al.
        Cardiac arrhythmias in muscular dystrophies associated with emerinopathy and laminopathy: a cohort study.
        J Clin Med. 2021; 10: 732
        • Brauch K.M.
        • Chen L.Y.
        • Olson T.M.
        Comprehensive mutation scanning of LMNA in 268 patients with lone atrial fibrillation.
        Am J Cardiol. 2009; 103: 1426-1428
        • Pan H.
        • Richards A.A.
        • Zhu X.
        • et al.
        A novel mutation in LAMIN A/C is associated with isolated early-onset atrial fibrillation and progressive atrioventricular block followed by cardiomyopathy and sudden cardiac death.
        Heart Rhythm. 2009; 6: 707-710
        • Sheikh F.N.
        • Hassan S.A.
        • Alam D.
        • Kundi M.
        • Hassan M.
        Lamin A/C cardiomyopathy with E203K pathogenic mutation.
        Cureus. 2020; 12e7761
        • Lai C.C.
        • Yeh Y.H.
        • Hsieh W.P.
        • et al.
        Whole-exome sequencing to identify a novel LMNA gene mutation associated with inherited cardiac conduction disease.
        PLoS One. 2013; 8e83322
        • Wahbi K.
        • Ben Yaou R.
        • Gandjbakhch E.
        • et al.
        Development and validation of a new risk prediction score for life-threatening ventricular tachyarrhythmias in laminopathies.
        Circulation. 2019; 140: 293-302
        • Captur G.
        • Arbustini E.
        • Syrris P.
        • et al.
        Lamin mutation location predicts cardiac phenotype severity: combined analysis of the published literature.
        Open Heart. 2018; 5e000915
        • Tesson F.
        • Saj M.
        • Uvaize M.M.
        • et al.
        Lamin A/C mutations in dilated cardiomyopathy.
        Cardiol J. 2014; 21: 331-342
        • Richards S.
        • Aziz N.
        • Bale S.
        • et al.
        Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
        Genet Med. 2015; 17: 405-424
        • Hart S.N.
        • Polley E.C.
        • Shimelis H.
        • Yadav S.
        • Couch F.J.
        Prediction of the functional impact of missense variants in BRCA1 and BRCA2 with BRCA-ML.
        NPJ Breast Cancer. 2020; 6: 13
      1. Sallah SR, Ellingford JM, Sergouniotis PI, et al. Improving the clinical interpretation of missense variants in X linked genes using structural analysis [published online ahead of print March 25, 2021]. J Med Genet.

        • Kelly B.J.
        • Fitch J.R.
        • Hu Y.
        • et al.
        Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics.
        Genome Biol. 2015; 16: 6
        • Van der Auwera G.A.
        • Carneiro M.O.
        • Hartl C.
        • et al.
        From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.
        Curr Protoc Bioinformatics. 2013; 43: 11.10.1-11.10.33
        • Cingolani P.
        • Platts A.
        • Wang le L.
        • et al.
        A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
        Fly (Austin). 2012; 6: 80-92
        • Dickel D.E.
        • Barozzi I.
        • Zhu Y.
        • et al.
        Genome-wide compendium and functional assessment of in vivo heart enhancers.
        Nat Commun. 2016; 7: 12923
        • Karczewski K.J.
        • Francioli L.C.
        • Tiao G.
        • et al.
        The mutational constraint spectrum quantified from variation in 141,456 humans.
        Nature. 2020; 581: 434-443
      2. McInnes L, Healy J, Melville J. UMAP: uniform manifold approximation and projection for dimension reduction [published online ahead of print February 9, 2018]. arXiv. arXiv:1802.03426.

        • Pedregosa F.
        • Varoquaux G.
        • Gramfort A.
        • et al.
        Scikit-learn: machine learning in Python.
        J Mach Learn Res. 2011; 12: 2825-2830
        • Dolgin M.
        Nomenclature and Criteria for Diagnosis of Diseases of the Heart and Great Vessels.
        Little, Brown and Co., Boston, MA1994
        • Captur G.
        • Arbustini E.
        • Bonne G.
        • et al.
        Lamin and the heart.
        Heart. 2018; 104: 468-479
        • Kolb T.
        • Maass K.
        • Hergt M.
        • Aebi U.
        • Herrmann H.
        Lamin A and lamin C form homodimers and coexist in higher complex forms both in the nucleoplasmic fraction and in the lamina of cultured human cells.
        Nucleus. 2011; 2: 425-433
        • Garg A.
        • Subramanyam L.
        • Agarwal A.K.
        • et al.
        Atypical progeroid syndrome due to heterozygous missense LMNA mutations.
        J Clin Endocrinol Metab. 2009; 94: 4971-4983
        • Mosbah H.
        • Vatier C.
        • Boccara F.
        • et al.
        Looking at new unexpected disease targets in LMNA-linked lipodystrophies in the light of complex cardiovascular phenotypes: implications for clinical practice.
        Cells. 2020; 9: 765