A novel cardiomyopathy phenotype linked to a CHD7 missense variant.

Loss of function in the chromatin remodeler CHD7 causes CHARGE syndrome, characterized by variable penetrance and diverse abnormalities. However, establishing genotype-phenotype correlations has been challenging, as most CHD7 inactivating mutations are null alleles. Through CHD7 missense variant analysis at potential phosphorylation sites, we identified T730 (T720 in mice) as a critical residue associated with pathogenesis. Using a CHD7 T730 missense variant (Chd7(T720A)) and a frameshift null allele (Chd7(fs)) in a mouse model, we found that Chd7(fs/fs) mice were non-viable, while Chd7(fs/+) mice exhibited haploinsufficiency-related circling behavior. Notably, Chd7(fs/T720A) mice died before postnatal day 2, indicating the Chd7(T720A) allele is hypomorphic. Micro-CT analysis at E18.5 revealed that heterozygous mice primarily exhibited hypertrophic cardiomyopathy (HCM), while homozygous mice developed both HCM and dilated cardiomyopathy (DCM). RNA-seq analysis of neonatal Chd7(T720A/T720A) hearts revealed a disrupted transcriptome, which in males and females was characterized by downregulation of mitochondrial energy metabolism genes and enrichment of ETS family transcription factor targets. We further identified GSK3β, GSK3α, HIPK1, and DYRK2 as candidate kinases for this site, suggesting a regulatory role in CHD7. This missense variant causing developmental heart abnormalities establishes the first genotype-phenotype correlation for CHD7, and offers new insights into CHARGE syndrome pathogenesis.