Use of whole genome sequencing to determine the genetic basis of visceral myopathies including Prune Belly syndrome

Abstract

Objectives/aims: The visceral myopathies (VM) are a group of disorders characterised by poorly contractile or acontractile smooth muscle. They manifest in both the GI and GU tracts, ranging from megacystis to Prune Belly syndrome. We aimed to apply a bespoke virtual genetic panel and describe novel variants associated with this condition using whole genome sequencing data within the Genomics England 100,000 Genomes Project.

Methods: We screened the Genomics England 100,000 Genomes Project rare diseases database for patients with VM-related phenotypes. These patients were screened for sequence variants and copy number variants (CNV) in ACTG2, ACTA2, MYH11, MYLK, LMOD1, CHRM3, MYL9, FLNA and KNCMA1 by analysing whole genome sequencing data. The identified variants were analysed using variant effect predictor online tool, and any possible segregation in other family members and novel missense mutations was modelled using in silico tools. The VM cohort was also used to perform a genome-wide variant burden test in order to identify confirm gene associations in this cohort.

Results: We identified 76 patients with phenotypes consistent with a diagnosis of VM. The range of presentations included megacystis/microcolon hypoperistalsis syndrome, Prune Belly syndrome and chronic intestinal pseudo-obstruction. Of the patients in whom we identified heterozygous ACTG2 variants, 7 had likely pathogenic variants including 1 novel likely pathogenic allele. There were 4 patients in whom we identified a heterozygous MYH11 variant of uncertain significance which leads to a frameshift and a predicted protein elongation. We identified one family in whom we found a heterozygous variant of uncertain significance in KCNMA1 which in silico models predicted to be disease causing and may explain the VM phenotype seen. We did not find any CNV changes in known genes leading to VM-related disease phenotypes. In this phenotype selected cohort, ACTG2 is the largest monogenic cause of VM-related disease accounting for 9% of the cohort, supported by a variant burden test approach, which identified ACTG2 variants as the largest contributor to VM-related phenotypes.

Conclusions: VM are a group of disorders that are not easily classified and may be given different diagnostic labels depending on their phenotype. Molecular genetic analysis of these patients is valuable as it allows precise diagnosis and aids understanding of the underlying disease manifestations. We identified ACTG2 as the most frequent genetic cause of VM. We recommend a nomenclature change to 'autosomal dominant ACTG2 visceral myopathy' for patients with pathogenic variants in ACTG2 and associated VM phenotypes.

Supplementary information: The online version contains supplementary material available at 10.1007/s44162-023-00012-z.

Keywords: ACTG2; MYH11; Prune Belly syndrome; Visceral myopathy; Whole genome sequencing.

Fig. 1

Visceral myopathy cohort and genetic variants identified in this study. A Cohort of 76 patients with visceral myopathy phenotypes including sub-groups CIPO, MMIHS and PBS. B Patients genotype with pathogenic/likely pathogenic variants in ACTG2; VUS in MYH11 and VUS in KCNMA1. C Genotype–phenotype correlations within the identified patients. D Quantile–quantile plot for rare variants associated with visceral myopathy phenotypes following genome-wide variant burden test. Shown are empirically observed quantiles of rare gene effects (AF < 0.001) (y-axis) as a function of quantiles expected from a normal distribution with the same mean and variance as the empirical distribution (x-axis). Variants in ACTG2 were the only statistically significant finding (p = 1.1 × 10⁻.⁷)

Fig. 2

AlphaFold-2 models of KCNMA1 missense variant. A Low-resolution model of KCNMA1 protein structure (NP_002238.2) with region containing amino acid position 1128 boxed. B Wild-type KCNMA1 (NP_002238.2) p.(Arg1128) and C. missense KCNMA1 p.(Arg1128Gln), with likely bond to adjacent leucine (position 1127)