Abstract: Objective To identify the pathogenic variant in a Chinese family with X-linked agammaglobulinemia (XLA). Methods A trio family with suspected X-linked agammaglobulinemia was recruited. The pathogenic variant was detected by the whole exome sequencing, and then confirmed by Sanger sequencing. cDNA sequencing was performed to find the abnormal splicing of the BTK variant. Quantitative real-time PCR was conducted to evaluate the mRNA expression of BTK in the patient. Results A novel hemizygous splicing variant (c.240+3A＞C) was identified in the BTK gene from this patient. The variant co-segregated with the phenotype of the family members was not listed in the public databases, such as dbSNP153,ExAC, gnomAD or the Human Gene Mutation Database. Further Sanger sequencing demonstrated that the BTK c.240+3A＞C variant led to a 106 bp from intron 3 of BTK insertion between exon 3 and exon 4 of the BTK transcript. The mRNA expression of BTK in the patient was significantly reduced as compared to a control individual. Conclusions The novel c.240+3A＞C splicing variant in BTK likely results in X-linked agammaglobulinemia in this family.

Key words: X-linked agammaglobulinemia, whole exome sequencing, BTK, pathogenic variant