Cardiac structural and sarcomere genes associated with cardiomyopathy exhibit marked intolerance of genetic variation

Abstract

Background: The clinical significance of variants in genes associated with inherited cardiomyopathies can be difficult to determine because of uncertainty regarding population genetic variation and a surprising amount of tolerance of the genome even to loss-of-function variants. We hypothesized that genes associated with cardiomyopathy might be particularly resistant to the accumulation of genetic variation.

Methods and results: We analyzed the rates of single nucleotide genetic variation in all known genes from the exomes of >5000 individuals from the National Heart, Lung, and Blood Institute's Exome Sequencing Project, as well as the rates of structural variation from the Database of Genomic Variants. Most variants were rare, with over half unique to 1 individual. Cardiomyopathy-associated genes exhibited a rate of nonsense variants, about 96.1% lower than other Mendelian disease genes. We tested the ability of in silico algorithms to distinguish between a set of variants in MYBPC3, MYH7, and TNNT2 with strong evidence for pathogenicity and variants from the Exome Sequencing Project data. Algorithms based on conservation at the nucleotide level (genomic evolutionary rate profiling, PhastCons) did not perform as well as amino acid-level prediction algorithms (Polyphen-2, SIFT). Variants with strong evidence for disease causality were found in the Exome Sequencing Project data at prevalence higher than expected.

Conclusions: Genes associated with cardiomyopathy carry very low rates of population variation. The existence in population data of variants with strong evidence for pathogenicity suggests that even for Mendelian disease genetics, a probabilistic weighting of multiple variants may be preferred over the single gene causality model.

Figure 1

Plot of missense and nonsense variant rates for all known human gene transcripts calculated from the exomes of 5,379 persons in the NHLBI Exome Sequencing Project. Non-OMIM = genes without known association with a Mendelian disease. OMIM = genes with a known association with a Mendelian disease in the Online Mendelian Inheritance in Man (OMIM) database. Cardiomyopathy = genes with known association with a familial cardiomyopathy. Variant rates are in units of counts per 1,000 base pairs of coding region per transcript per chromosome.

Figure 2

Location of nonsense variants found in the large sarcomeric gene titin (TTN). The structure of 5 known isoforms is displayed at the top of the figure oriented by location on chromosome 2, with the 5′ end of the transcript on the right and the 3′ end on the left. Red arrows depict exons in which clusters of nonsense variants were noted.

Figure 3

Plot of minor allele frequency of non-synonymous coding variants from the NHLBI ESP data set over the distribution of the known exons of A) MYH7 (chromosome 14), B) MYBPC3 (chromosome 11), and C) TNNT2 (chromosome 1). Red arrows denote locations of pathogenic variants from a curated list from clinical experience at our institution and literature reports. X-axis is genomic coordinates in megabases. 5′ and 3′ refer to start and end of transcript, respectively.

Figure 4

Relative distribution of missense variants from the NHLBI ESP and a curated pathogenic variant list in the genes MYH7, MYBPC3, and TNNT2, as scored by A) GERP, B) PhastCons, C) SIFT, and D) Polyphen-2. Grey bars denote variants from NHLBI ESP data, black bars denote variants from the pathogenic list. For panel C, 1 – SIFT score was used to preserve consistency between panels, with far right predicted to be more pathogenic and far left predicted to be less pathogenic.

Figure 5

Receiver operator curves for A) GERP, B) PhastCons, C) SIFT, and D) Polyphen-2 for the classification of collected missense variants from the NHLBI ESP data set and a curated pathogenic missense variant list in the genes MYH7, MYBPC3, and TNNT2. AUC = area under the curve.