Characterization of a PNLIP Variant Identified in Amish Pediatric Patients with Congenital Pancreatic Lipase Deficiency

Congenital pancreatic lipase deficiency (CPLD, OMIM #614338) is a rare exocrine pancreatic disorder presenting in late infancy with steatorrhea, fat-soluble vitamin deficiency, and low pancreatic lipase activity. Variants of the pancreatic triglyceride lipase (PNLIP) gene have been linked to CPLD. Six children from four Amish families exhibited CPLD symptoms and two had decreased fecal elastase levels when tested. A novel homozygous PNLIP variant, c.869G>A (p.S290N), was identified in these children. This study aimed to characterize the PNLIP variant to understand its mechanism underlying CPLD. The variant impact was first evaluated using computational modeling. Functional analyses included activity assays, cellular PNLIP partition assessments, and endoplasmic reticulum (ER) stress evaluation in transfected cells. Computational modeling showed that p.Ser290 is highly conserved across species and the variant causes steric hindrance resulting in protein misfolding. Functional assays revealed that the PNLIP variant had a complete loss of activity compared to the wild type (WT), with defects in catalytic function and secretion. Immunoblotting showed reduced PNLIP variant in the medium and increased accumulation in the detergent-insoluble fraction consistent with protein misfolding. Variant-expressing cells had elevated levels of BiP, an ER stress marker, and increased Xbp1 mRNA splicing, suggesting an elevated ER stress and unfolded protein response (UPR). In conclusion, the PNLIP p.S290N variant causes CPLD through a loss-of-function mechanism, characterized by loss of enzymatic activity and defective secretion due to protein misfolding. Further studies are needed to determine whether the misfolding variant protein induces proteotoxicity, potentially increasing the risk of pancreatic injury including chronic pancreatitis.