Homozygous splice-site variant in ENPP1 underlies generalized arterial calcification of infancy

ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase 1) plays a critical role by converting extracellular ATP to AMP, generating extracellular PPi, a potential inhibitor of calcification. Pathogenic variants in the ENPP1 cause generalized arterial calcification of infancy (GACI [OMIM 208000]). GACI, is an ultra-rare disease characterized by early-onset calcification of large and medium-sized arteries, leading to severe cardiovascular complications such as heart failure, pulmonary stenosis (PS), hypertension, and more. In this study, we report a novel homozygous splice-site pathogenic variant in ENPP1 (NM_006208, c.2230 + 5G > A; p.Asp701Asnfs*2) residing in C-terminal nuclease-like domain (NLD) of ENPP1 protein in a Pakistani family diagnosed with severe valvular PS and mild right ventricular hypertrophy (RVH). cDNA assays confirmed the skipping of exon 21, and the splice product underwent nonsense-mediated decay. Functional studies on fibroblasts from the patient demonstrated increased calcification and decreased enzymatic activity of ENPP1, recapitulating the hallmarks of GACI. By combining genetic analysis with the in vitro study, we substantiate that ENPP1:c.2230 + 5G > A variant is pathogenic, underscoring its role in the development of GACI.