Lipoid proteinosis (LP) is a rare autosomal recessive disorder caused by mutations in extracellular matrix protein 1 (ECM1), a glycoprotein expressed in skin. Whole-exome sequencing (WES) was used to investigate two Chinese siblings with suggestive clinical features of LP. They shared one known (c.960G>A) and one novel (c.1081G>T) pathogenic variant in ECM1 gene, inherited from their unaffected parents. The novel mutation (c.1081G>T) led to a termination codon at position 361 and caused nonsense-mediated mRNA decay and lost the function. Our finding expands the genetic etiology spectrum of LP.