A novel synonymous variant in the NF1 gene disrupting splicing contributes to Neurofibromatosis pathogenesis

Tao Lin¹Zheyan Chen²Biwen Dong³Haojie Pan³Hai Wang³xianjue zheng³Kaixin Chen³yanan lai³Chenhui Zhang³ye dong³zitong xu³Menmen Lin³XIUJIE XI³shuqi xia³yimin wang⁴Wenhuan Wang⁴Li Xiaoqing⁴Cong Cong Sun⁴Yanjun Hu¹FANG XU¹Jianqiong Zheng¹Fan Jin⁵Hongping Zhang¹Jiayong Zheng^4,6*

• ¹Department of Gynecology and Obstetrics, Wenzhou People's Hospital/Wenzhou Maternal and Child Health Care Hospital, WENZHOU, China
• ²Department of Plastic and Aesthetic Surgery, Wenzhou People's Hospital, wenzhou, China
• ³Department of Reproductive Genetics, Wenzhou People's Hospital/Wenzhou Maternal and Child Health Care Hospital, Wenzhou, Zhejiang Province, China
• ⁴Key Laboratory of Obstetrics and Gynecology, Wenzhou People’s Hospital, Wenzhou, Zhejiang Province, China
• ⁵Department of Reproductive Genetics,Women's Hospital,Zhejiang University School of Medicine, hanzhou, China
• ⁶Department of Reproductive Genetics, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University/Wenzhou Maternal and Child Health Care Hospital, wenzhou, China

Background: Neurofibromatosis type 1 (NF1) is a common autosomal dominant genetic disorder characterized by café-au-lait macules, neurofibromas, and other manifestations. It is caused by variations in the NF1 gene located on chromosome 17q11.2. The gene's complexity and extensive variations often lead to misdiagnoses by conventional detection methods, which adverses to effective diagnosis and treatment strategies.Case presentation: A 26-year-old Chinese woman was admitted to our hospital with multiple café-au-lait spots and cutaneous nodules. She had a family history of NF1, with her mother also showing similar dermatological symptoms. Whole exome sequencing (WES) identified a synonymous variation, NM_001042492.3: c.987A>G (p.K329K), in the NF1 gene. Although synonymous variations are typically considered non-pathogenic, RNA sequencing (RNA-seq) and minigene analysis revealed that this variation caused the partial loss of exon 9, leading to aberrant splicing. These findings were validated through Sanger sequencing, confirming the genetic alteration and its impact on mRNA splicing.The case highlights the critical role of synonymous variations in the NF1 gene that significantly impact splicing and protein function. These findings expand our understanding of NF1's genetic diversity and underscore the importance of comprehensive genetic and RNA analyses to achieve accurate diagnosis and in-depth insight into the molecular underpinnings of NF1.