Case report: a synonymous VHL mutation (c.414A > G, p.Pro138Pro) causes pathogenic familial hemangioblastoma through dysregulated splicing

Abstract

Background: von Hippel-Lindau (VHL) disease is a familial neoplasia syndrome that results from the germline mutation of VHL. Pathogenic VHL mutations include deletion, frameshift, nonsense and missense mutations. Synonymous mutations are expected to be phenotypically silent and their role in VHL disease remains poorly understood. Case presentation: We report a Caucasian male with a family history of pheochromocytoma and the synonymous VHL mutation c.414A > G (p.Pro138Pro). At 47-years, MRI revealed pheochromocytoma in the left adrenal gland and hemangioblastomas in the spine and brain. Pheochromocytoma was treated by adrenalectomy. Radiotherapy, followed by craniotomy and resection were needed to reduce hemangioblastomas to residual lesions. Two of three of the proband's children inherited the mutation and both presented with retinal hemangioblastomas without pheochromocytoma at age 7: one twin needed four laser treatments. Primary skin fibroblasts carrying the heterozygous mutation or wild type VHL were established from the family. Mutant fibroblasts downregulated fulllength VHL mRNA and protein, and upregulated the short VHL mRNA isoform (a result of exon 2 skipping in splicing) at the mRNA level but not at the protein level. Conclusions: Our study shows that the synonymous VHL mutation c.414A > G can within 7 years induce pediatric retinal hemangioblastoma in absence of pheochromocytoma. This highlights the need to include splicing-altering synonymous mutations into the screening for VHL disease. This is also the first report on detecting and validating a synonymous VHL mutation using patient-derived fibroblasts. The mutation c.414A > G translates to p.Pro138Pro, yet it is not functionally silent, because it causes aberrant splicing by skipping exon 2. The reduced but not completely abolished pVHL protein in a loss-of-heterozygosity genetic backdrop may underlie the etiology of VHL disease.

Variant spectrum of von Hippel–Lindau disease and its genomic heterogeneity in Japan

“…2B ). Previously, there were some reports of synonymous variant without amino-acid change (c.414A>G, p.Pro138Pro), which were related with up-regulation of exon 2 skipping splice variants (E1-E3) ( 12 , 13 ). We also investigated for exon 2 skipping in blood RNAs from six individuals with a missense variant in exon 2 as well as five controls with no variants of VHL.…”

“…The design of the VHL primers was on the basis of the article by Liu et al . ( 12 ). The PCR conditions were as follows: initial denaturation at 95°C for 10 min, followed by numerous cycles of denaturation at 95°C for 60 s, annealing at 58°C for 60 s, and elongation at 72°C for 60 s on a C1000 Thermal Cycler (Bio-RAD, CA, USA) (30 cycles for GAPDH , 30 cycles for VHL ).…”

Case Report: Aggressive neural crest tumors in a child with familial von Hippel Lindau syndrome associated with a germline VHL mutation (c.414A>G) and a novel KIF1B gene mutation

“…The former codes for two proteins containing 213 and 160 amino acids, both of which are functional tumor suppressors. The isoform lacking exon 2 codes for a 172 amino acid protein that is believed to lack tumor suppressor properties (6). Evidence suggests that although tumors arise predominantly from missense mutations, splice-altering mutations can also lead to tumor formation (6)(7)(8).…”

Case Report: A Synonymous Mutation in NF1 Located at the Non-canonical Splicing Site Leading to Exon 45 Skipping

“…It is a classic theory that the canonical splice site mutations, located at the splice donor or the splice acceptor, mainly involving frameshift mutations, missense mutations and nonsense mutations, are the causes of the splicing sites disruptions (Mort et al, 2014;Jayasinghe et al, 2018;Kim et al, 2020). Synonymous mutations, also known as silent mutations (Liu et al, 2020), are defined as the base substitution that that don't alter amino acids (Sauna and Kimchi-Sarfaty, 2011). Given the characteristics of the genetic code, synonymous mutations are usually considered nonpathogenic (Zhou et al, 2020).…”