Objective To detecting the genetic etiology of a family with idiopathic pulmonary arterial hypertension and make gene diagnosis for the patient, so as to guide the targeted treatment and early intervention for the patient and her families. Methods The phenotype information of the family members was reviewed and their peripheral blood was collected for genomic DNA extraction. Exome sequencing was used to screen the mutations and proving the selected mutations by PCR-Sanger sequencing method. The pathogenicity of candidate mutation sites were searched through PubMed and related databases, and analyzed by protein function software. The judgement of pathogenicity was considered by clinical presentations and sequencing results of the patients based on Standards and guidelines for the interpretation of sequence variants revised by ACMG. Results At present, there was only one patient with pulmonary hypertension in this family, and other family members had no clinical manifestations of pulmonary hypertension. The female patient had BMPR2 gene c.1748dupA(p.Asn583Lysfs*6) heterozygous mutant. Her father and second son had BMPR2 gene c.1748dupA(p.Asn583Lysfs*6) heterozygous mutant, but none of the other members of the family had the mutation. Conclusions The heterozygous mutation of c.1748dupA (p.Asn583Lysfs*6) of BMPR2 gene is the genetic cause of the idiopathic pulmonary arterial hypertension patient, and the clinical significance of c.1748dupA(p.Asn583Lysfs*6) is pathogenic. The patient can be further diagnosed as pulmonary hypertension, primary 1 (PPH1) by gene diagnosis, and the mutant is novel and pathogenic for PPH1.