INTRODUCTION: The aim of this study was to determine the potential genetic cause of retinal capillary hemangioblastoma (RCH) with symptoms of Von Hippel-Lindau (VHL) disease. CASE PRESENTATIONS: Three Iranian families (5 RCH patients) with novel variants are included in this study. The CONCLUSION: The structural information and computational analysis of the identified variants are predicted to induce conformational changes that limit the flexibility of protein VHL interaction interface with Elongin B/C, Elongin C/B, and Cullin-2, which are necessary for hypoxia-inducible factor 1-α binding. The genetic variants identified in Iranian patients with RCH may aid in the molecular confirmation of other patients diagnosed with VHL and their at-risk family members. These pioneering results that include detailed structural and functional analysis of a variant's effect on the VHL protein may serve as a model for future studies.