Lethal Phenotype and Expansion of the Clinical Spectrum of Biallelic Loss of Function Variant in SENP7 Gene Unveiled by Whole Exome Sequencing

Abstract

SUMOylation involves covalent attachment of small ubiquitin-like modifier (SUMO) proteins to specific lysine residues on target proteins and regulates various aspects of their function. Sentrin-specific proteases (SENPs) are key players in both the conjugation reaction of SUMO proteins to their targets and the subsequent deconjugation of SUMO-conjugated substrates. Here, we provide the first comprehensive prenatal description of a lethal syndrome linked to a novel homozygous stop-gain variant in SENP7 c.745C>T; p.(Arg249*) in a consanguineous Egyptian family with a history of three fetal deaths, all presenting with multiple congenital anomalies. Similar anomalies were observed through ultrasound assessment of the current fetus, including arthrogryposis multiplex congenita, CNS malformations, congenital heart disease, and renal anomalies. Singleton exome sequencing (ES) of fetal DNA revealed a SENP7 variant allele, which results in a premature termination codon, and the mutant mRNA is predicted to be degraded by nonsense-mediated decay (NMD). This leads to impaired gene function, particularly disrupting SENP7's isopeptidase activity in deconjugating polySUMO chains. Our findings broaden the molecular spectrum of SENP7 variants and emphasize their essential role in the development of the nervous, musculoskeletal, cardiovascular, and renal systems. This study offers new insights into the genotype-phenotype correlations observed in lethal congenital contracture syndromes and severe embryological abnormalities.

Keywords: CNS malformations; SENP7; SUMO protease; SUMOylation; arthrogryposis multiplex congenita (AMC); fetal phenotyping; prenatal ES; renal anomalies.