<p>Apple stem grooving virus (ASGV) is one of the most significant pathogens infecting pome and stone fruit trees worldwide. The ASGV-encoded coat protein (CP) functions to encapsulate the viral genomic RNA and is essential for virus infection, while its genetic variation and pathogenicity remain largely unclear. Here, co-variation of the amino acids for ASGV CP and its implication have been analyzed. The results showed that, based on co-variation at amino acid positions 103 and 108, CP variants clustered into three groups, designated as types E¹⁰³-A¹⁰⁸, E¹⁰³-E¹⁰⁸, and Q¹⁰³-E¹⁰⁸. By using a potato virus X-based pathogenicity system, expression of CP (E¹⁰³-A¹⁰⁸)_ASGV, CP (E¹⁰³-E¹⁰⁸)_ASGV, and CP (Q¹⁰³-E¹⁰⁸)_ASGV led to attenuated disease symptoms and lower virus accumulation of potato virus X (PVX). Notably, type CP (Q¹⁰³-E¹⁰⁸)_ASGV exhibited lower virulence compared with the other two types. Transient expression assay in <i>Nicotiana benthamiana</i> plants demonstrated that the mutant type CP (Q¹⁰³-E¹⁰⁸)_ASGV accumulated in a significantly higher level than the other two types. Especially, in vivo and cell-free degradation assays revealed that the mutation of E¹⁰³ to Q¹⁰³ enhances protein stability probably via facilitating its escape from ubiquitin–26S proteasome pathway-mediated degradation. Furthermore, ASGV CP has been demonstrated to possess activity of viral suppressor for RNA silencing (VSR). Taken together, these results provide insights into understanding of the multiple roles in aspects of genetic variation, pathogenicity of heterologous PVX, protein homeostasis, and VSR activity of ASGV CP.</p>