Scrapie is a lethal neurodegenerative disease of sheep and goats caused by the misfolding of the prion protein. Variants such as M142, D145, S146, H154, Q211, and K222 were experimentally found to increase resistance or extend scrapie incubation period in goats. We aimed to identify polymorphisms in the Afar and Arsi-Bale goat breeds of Ethiopia and computationally assess the effect of variants on prion protein stability. In the present study, four non-synonymous novel polymorphisms G67S, W68R, G69D, and R159H in the first octapeptide repeat and the highly conserved C-terminus globular domain of goat PrP were detected. The resistant genotype, S146, was detected in >50% of the present population. The current study population showed a genetic diversity in Ethiopian goat breeds. In the insilico analysis, the R68 variant was predicted to increase stability while S67, D69, and H159 decrease the stability of prion protein. The new variants in the octapeptide repeat motif were predicted to decrease amyloidogenicity but H159 increased the hotspot sequence amyloidogenic propensity. These novel variants could be the source of conformational flexibility that may trigger the gain or loss of function by prion protein. Further experimental study is required to depict the actual effects of variants on prion protein stability. Prion diseases are lethal neurodegenerative disease of humans and animals caused by the misfolding of prion protein 1. Despite being rare, the diseases are lethal and have resulted in huge animal loss over a course of time in several countries 2. The oldest prion disease is scrapie that affects small ruminants 3,4. Though the exact pathomechanism is not yet known, predisposing genetic variants have been documented in different species 5. A wide range of polymorphisms have been identified in goats either as protective or susceptible alleles. A recent review reported the presence of more than 50 polymorphisms in goat prion protein-coding gene (PRNP) 6. Among the variants, G127S, M142I, H143R, N146S, R154H, Q222K, and S240P are the most common substitutions worldwide 7,8. Similarly, R139S in Algeria 9 , A116V in Tanzania 10 , G134E and Q163P in Turkey 11 and G127A and T193I in Ethiopia 12 were novel (at the time of the report) substitutions discovered in the respective area of study. Alleles such as M142, D145, S146, H154, Q211, and K222 were experimentally found to either extend scrapie incubation period or increase resistance 8,13-16. Experimental studies reported the link between sequence variation in the functional domains of prion protein and scrapie disease development 17,18. Substitutions in the palindrome and glycine-rich motifs were identified to affect amyloid fibril formation 19. Although the C terminal globular domain is often involved in the PrP c to PrP Sc conversion process, octapeptide repeat regions are also known to influence the structural dynamics of prion protein. Insertion or deletion of octapeptide repeat for example, induce disease phenotypes 20. According to the FAOSTAT 2017 report, 3...