Recent progress in next generation sequencing technologies has enabled us to investigate somatic mutations throughout the coding regions of myelodysplastic syndromes (MDS), and have likely provided us with almost the entire spectrum of driver mutations responsible for this disease. As shown by numerous recent studies, such frequent mutations play an important role in the leukemogenesis of MDS. In the first part of this review, we comprehensively describe the characteristics and frequencies of the most prevalent mutations already confirmed as drivers in MDS. Second, we focus on the associations between karyotypic abnormalities and somatic mutations involving chromosomes 5 and 7. In particular, CSNK1A1 mutations are the most recently identified among the 5q- syndromes. Finally, we summarize recently reported findings on the functional effects of frequent splice factor mutations on splicing defects, which have been clarified by multiple institutions.