Hypertrophic cardiomyopathy (HCM) is a genetic disease associated with sudden cardiac death. Variants in alpha-actinin-2 (ACTN2), a Z-disc protein that anchors actin thin filaments have been implicated in HCM, yet their structural consequences remain poorly defined. Here, we characterise seventeen HCM-associated ACTN2 variants spanning multiple domains using an integrated and tiered workflow combining high-throughput assays, structural modelling and biophysical approaches. All variants display reduced solubility, with actin-binding domain (ABD) substitutions showing pronounced thermal instability by differential scanning fluorimetry. Modelling of nine variants predicts diverse pathogenic mechanisms including compromised actin-binding, impaired ABD regulatory conformations, disrupted dimerisation interfaces, and perturbed domain architecture. Crystal structures of two rod-domain variants reveal intact dimerisation despite modelling predictions. Actin-binding assays for ABD variants confirm altered actin engagement suggesting that binding dynamics may drive pathogenicity. Limited proteolysis indicates reduced structural stability across variants, while size-exclusion chromatography coupled with multi-angle light scattering or small-angle X-ray scattering (SEC-MALS/SAXS) shows a strong propensity for aggregation. Batch-mode SAXS further demonstrates early aggregation onset in selected ABD variants at elevated temperatures. Collectively, these findings establish that HCM-linked ACTN2 variants compromise protein integrity through multiple mechanisms, highlight the ABD as a hotspot of vulnerability and provide a potential framework for interpreting cardiomyopathy-associated variants.