The PNPLA3 rs738409 polymorphism (I148M) is a major determinant of hepatic fat and predisposes to the full spectrum of liver damage in nonalcoholic fatty liver disease (NAFLD). Aim of this study was to evaluate whether additional PNPLA3 coding variants contribute to NAFLD susceptibility, first in individuals with contrasting phenotypes (with early onset NAFLD vs. very low aminotransferases), and then in a large validation cohort. Rare PNPLA3 variants were not detected by sequencing coding regions and intron-exon boundaries either in 142 patients with early-onset NAFLD, nor in 100 healthy individuals with ALT <22/20 IU/ml. Besides rs738409 I148M, the rs2294918 G>A polymorphism (E434K sequence variant) was over-represented in NAFLD (adjusted p=0.01). In 1447 subjects with and without NAFLD, the 148M-434E (p<0.0001), but not the 148M-434K haplotype (p>0.9), was associated with histological NAFLD and steatohepatitis. Both the I148M (p=0.0002) and E434K variants (p=0.044) were associated with serum ALT levels, by interacting each other, in that the 434K hampered the association with liver damage of the 148M allele (p=0.006). The E434K variant did not affect PNPLA3 enzymatic activity, but carriers of the rs2294918 A allele (434K) displayed lower hepatic PNPLA3 mRNA and protein levels (p<0.05).