Gene based variations are consequential only if are in the vicinity or within some functionally significant regions of 3-dimensional encoded protein. Information regarding significant structural attributes of many proteins is underway and based on data of polymorphisms identified in different parts of the genes. Oxidized Low Density Lipoprotein Receptor-1 (OLR1) gene was reported to be significantly associated with high fat content in milk. Oxidized Low Density Lipoprotein Receptor-1 (OLR1) is a key cell surface receptor for oxidized low density lipoprotein. In this study, protein structural attributes of OLR1 were constructed by homology modelling and functionally significant regions were identified, which might have a role in fatty acid synthesis. This OLR1 is a 270-residue protein in bovine carrying 52-amino acid-long signal peptide. A Pro-His substitution was noted at 17th position, which enhanced OLR1 protein hydrophilicity for enhanced attachments. A transmembrane helix was identified between 35-67th residue and another functionally significant variant was identified at position 181, which was part of Domain-3. This domain is a functionally active part of the receptor in fat synthesis. Results of the study, illustrated that mutations in functionally significant parts of the OLR1 protein affect the high fat content in the buffalo milk.