Protein evolution proceeds via generation of new variants and the combined effects of selection and drift that alter the frequency of individual alleles. Reference-quality pan-genomes allow analysis of abundance of protein sequence variants genome wide. This intra-species protein sequence diversity is generally lower than that observed in inter-species comparisons. It allows identification of the highly variable (HV) sub-families of proteins that stand out for their abundance of amino acid variants. We have initially identified HV protein subfamilies in the plant intracellular immune receptors. Here, we used the pan-genome of soy to find other protein families that show a similarly high level of sequence diversity. They include HV subsets of receptor-like proteins, receptor-like kinases of several families, small molecule and nucleic acid-modifying enzymes, and transporters. Together our results point to plant immune processes as key contributors to genome-wide protein diversity.