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To investigate the  U2AF1  gene mutation site, mutation load and co-mutations genes in patients with myelodysplastic syndrome (MDS) and their effects on prognosis. Gene mutation detection by next-generation sequence and related clinical data of 234 MDS patients were retrospectively collected and analyzed for the relationship between the clinical characteristics, treatment efficacy and prognosis of  U2AF1  gene mutation. Among the 234 MDS patients, the  U2AF1  gene mutation rate was 21.7% (51 cases), and the median variant allele frequency was 39.5%. Compared with the wild type, the  U2AF1  mutant had a higher incidence of chromosome 8 aberration, and was positively correlated with the occurrence of  ASXL1 ,  RUNX1 ,  SETBP1  gene mutation, negatively correlated with  SF3B1, NPM1  genes mutation ( p  &lt; 0.05). The most common mutation site of  U2AF1  was S34F (32 cases), while  U2AF1  Q157P site mutations had a higher incidence of chromosome 7 abnormalities ( p  = 0.003). The  U2AF1  gene mutation more frequently coincided with signal pathway related gene mutations ( p  = 0.043) with a trend of shortened overall survival. Among patients with  U2AF1  gene mutations, those with  ASXL1  mutations were prone to develop into acute myeloid leukemia, those with  RUNX1  mutations had an increased risk of relapse, and those with  TET2  mutations had higher 1-year survival rate. Compared with the patient group of lower mutation load (VAF ≤ 40%), the group with higher mutation load of  U2AF1  (VAF &gt; 40%) had a significantly lower 1-year survival rate (46.1% and 80.5%,  p  = 0.027). The criteria of  U2AF1  VAF &gt; 40% is an independent indicator for poor prognosis of MDS patients. VAF &gt; 40% of  U2AF1  is an independent factor of short OS in MDS patients. MDS patients with a mutation in the Q157P site of  U2AF1  and a higher  U2AF1  mutation load suggests poor prognosis, and co-mutated genes in  U2AF1  can affect disease progression and prognosis.

Differential U2AF1 mutation sites, burden and co-mutation genes can predict prognosis in patients with myelodysplastic syndrome