Abstract 19585: Overestimation of Functional Cardiomyopathy Disease Variants in the Human Gene Mutation Database
Introduction: Dilated cardiomyopathy (DM), hypertrophic cardiomyopathy (HCM), and arryhmogenic right ventricular dysplasia (ARVD) have been associated with germline genetic variants. However, uncertainty exists regarding the functional impact of specific variants described in the literature.
Hypothesis: We hypothesized that a substantial fraction of presumed casual variants would be identified as non-disease causing in a normal patient population.
Methods: Missense variants associated with three main subtypes of cardiomyopathy were extracted from Human Gene Mutation Database Professional (HGMD). To assess the prevalence and pathogenicity of these potential disease-causing alleles, the population frequency of each variant was screened in a recently published large-scale exome database of over 60,000 whole exomes (ExAC). In addition, PolyPhen-2 was used to predict the functional impact of amino acid substitution for each missense variant.
Results: In the HGMD, 1,405 missense variants were associated with cardiomyopathy, of which 25% were found in 2 or more samples in the ExAC database. Specifically 121 of 422 (28.7%) DM associated variants, 201 variants of 900 (22.3%) HCM associated variant, and 40 of 83 ARVD (48.2%) associated variants were observed in the ExAC database. Polyphen predicted 331 (23.9%) of variants as benign, 290 (20.6%) as possibly damaging, and 784 (55.8%) as probably damaging. Table 1 presents disease specific Polyphen results.
Conclusions: We observed that a large proportion (25-45%) of cardiomyopathy-associated missense variants predicted as being damaging were indistinguishable from the background in ExAC. Using stringent cutoffs derived from these observations, we estimated more than 50% of previously associated cardiomyopathy variants may be non-functional or non-monogenic causes of cardiomyopathy.
Author Disclosures: K. Lim: None. R. Aplenc: None. J. Rossano: None.
- © 2015 by American Heart Association, Inc.