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Background  Primary hyperoxaluria(PH)is a rare autosomal recessive genetic disease that contains three subtypes (PH1, PH2 and PH3). Approximately 80% of PH patients has been reported as subtype PH1, this subtype of PH has been related to a higher risk of renal failure at any age. Several genetic studies indicate that the variants in gene  AGXT  are responsible for the occurrence of PH1. However, the population heterogeneity of the variants in  AGXT  makes the genetic diagnosis of PH1 more challenging as it is hard to locate each specific variant. It is valuable to have a complete spectrum of  AGXT  variants from different population for early diagnosis and clinical treatments of PH1.    Case presentation  In this study, We performed high-throughput sequencing and genetic analysis of a 6-year-old male PH1 patient from a Chinese family. Two variants (c.346G > A: p.Gly116Arg; c.864G > A: p.Trp288X) of the gene  AGXT  were identified. We found a nonsense variant (c.864G > A: p.Trp288X) that comes from the proband’s mother and has never been reported previously. The other missense variant (c.346G > A: p.Gly116Arg) was inherited from his father and has been found previously in a domain of aminotransferase, which plays an important role in the function of AGT protein. Furthermore, we searched 110 pathogenic variants of  AGXT  that have been reported worldwide in healthy local Chinese population, none of these pathogenic variants was detected in the local genomes.    Conclusions  Our research provides an important diagnosis basis for PH1 on the genetic level by updating the genotype of PH1 and also develops a better understanding of the variants in  AGXT  by broadening the variation database of  AGXT  according to the Chinese reference genome.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12882-021-02276-3.

A novel nonsense variant of the AGXT identified in a Chinese family: special variant research in the Chinese reference genome