Mutational spectrum of the AP3B1 gene in an Iraqi family affected with Hermansky–Pudlak syndrome type 2
Egyptian Journal of Medical Human Genetics volume 24, Article number: 41 (2023)
Hermansky–Pudlak syndrome type 2 (HPS2) is a rare autosomal recessive inherited disease present with partial oculocutaneous albinism, nystagmus, prolonged bleeding time, and immunodeficiency.
We aimed at identifying a genetic mutation in an Iraqi family affected by HPS type 2. Here, we applied whole-exome sequencing to identify mutations in the proband. Moreover, we applied Sanger sequencing to confirm the candidate variant. We found a homozygous novel single nucleotide substitution (c.892A > T) in the exon 8 of the AP3B1 gene in the proband.
This study is the first Iraqi case report of a diagnosis of HPS type 2 caused by AP3B1 mutation. Our data expand the spectrum of mutations in AP3B1 gene in HPS type 2 and highlight the importance of molecular prenatal evaluation and relevant genetic counseling.
Hermansky–Pudlak syndrome (HPS), first described in 1959, is a rare autosomal recessive hereditary multi-system disease that comprises a spectrum of different subtypes [1,2,3]. Patients with HPS typically present with tyrosinase-positive oculocutaneous albinism, nystagmus, bleeding diathesis due to platelet function disorder, and systemic complications resulting from abnormal intracellular vesicles trafficking or formation [4,5,6].
Currently, 10 subtypes of HPS (HPS1–HPS10) are described in humans, caused by variants in nine unique genes. Patients with HPS type 2 and HPS type 10 present with various symptoms such as neutropenia, immunodeficiency, and neurological abnormalities in addition to the core features of platelet dysfunction and albinism [7,8,9]. Patients with HPS type 2 absence of the β3A-subunit in the adaptor protein-3 (AP-3) is relevant for sorting of lysosomal [10, 11].
In this study, we performed whole-exome sequencing followed by a Sangar sequencing approach for an Iraqi family with HPS type 2 to identify the underlying genetic defect.
A 9-year-old male born to an Iraqi consanguineous parents (Fig. 1) presented with nystagmus, a tendency to bleed, and platelet dysfunction. The patient also presented with oculocutaneous albinism and recurrent infections of the upper respiratory airways since the first month of life. His parents mentioned that during the first 15 months of life, he had developed normally. We reviewed the entire medical record for the proband. There was evidence of prolonged bleeding. The patient tolerated circumcision with hemorrhagic complications. At the age of 18 months, a tonsillectomy was performed. About 14 days after the tonsillectomy, severe bleeding from the wounds occurred so the boy needed resuscitation. The proband suffered from severe hypoxia and developed severe mental and statomotoric retardation. Measurements of prothrombin time (PT), activated partial thromboplastin time (aPTT), and platelet counts were normal, but he presented with neutropenia (mean peripheral blood polymorphonuclear granulocytes count 0.82 ± 0.45 G/L). Finally, laboratory tests showed neutropenia and prolonged bleeding time. Platelet count was 403 × 103/μL, but bleeding time (Duke method) was extended to 7.5 min (the usual time is about 2–5); The proband was clinically suspected to have HPS type 2. Thus, we applied whole-exome sequencing, which may allow confirmation of a diagnosis of HPS in this family. The studied family had a previous history of two spontaneous abortions.
Whole-exome sequencing test with a focus on HPS genes was performed for the proband. Various known filtering procedures were applied, such as coverage of more than six reads, a minimum quality score of 10, an allele frequency between 75 and 100%, a minor allele frequency (MAF) of ≤ 0.1% in the 1000 Genomes database (https://www.internationalgenome.org/), exome aggregation consortium (ExAC) and the exome variant server (EVS) for the NHLBI exome sequencing project (ESP). Following that, to verify the true positive of whole-exome sequencing identified variant, direct Sanger sequencing using an ABI 3730XL sequencer (Applied Biosystems Inc., Foster City, CA, USA) was performed in the patient and family members.
A novel homozygous potentially pathogenic c.892A > T; p.Arg298Ter mutation in AP3B1 gene (NM_003664.5) associated with HPS type 2 (OMIM#: 608233) was detected. In terms of inheritance, the parents of the patient were both heterozygous carriers for the AP3B1 gene mutation (Fig. 2). This nonsense mutation (c.892A > T; p.Arg298Ter) has not been reported in other patients with HPS type 2, but it is a severe loss-of-function mutation. This mutation describes a substitution mutation at the codon 298 (Arg), which leads to premature termination of the AP3B1 protein (AGA > TGA) (Fig. 2D). Reported mutations in AP3B1 gene are summarized in Table 1 based on Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/index.php). Interestingly, no pathogenic mutations were detected in the other genes in the proband.
This nonsense mutation (c.892A > T; p.Arg298Ter) has not been reported in other patients with HPS type 2, but it is a severe loss-of-function mutation. This mutation describes a substitution mutation at the codon 298 (Arg), which leads to premature termination of the AP3B1 protein (AGA > TGA) (Fig. 2D).
This report describes the characteristics of a patient with HPS type 2 due to a novel disease-causing AP3B1 mutation. This study proved that the nonsense AP3B1 variant in the exon 8 (c.892A > T or p.Arg298X) leads to an early termination in amino acid production, which would be expected to affect the AP3B1 protein’s function.
It was suspected that the child had HPS because of the combination of oculocutaneous albinism and increased bleeding tendency. In contrast to other subtypes of HPS, HPS type 2 caused by mutations in the β3A-subunit of the adaptor protein complex AP-3 is characterized by immunodeficiency causing increased susceptibility to infections. All reported HPS type 2 patients had severe neutropenia [11, 12]. The case described here also presented with neutropenia.
Wenham et al. in their publication reported two unrelated individuals with HPS type 2, which were homozygous for different deletions AP3B1 gene mutations. One patient with a homozygous frameshift AP3B1 mutation in the exon 2 (c.153_156del) manifests a severe clinical phenotype with albinism, recurrent respiratory infections, failure to thrive, facial dysplasia, pulmonary fibrosis, and developmental delay. No increased bleeding was seen in the patient; however, it is unclear whether the patient has been challenged by surgery in a mucocutaneous area. In addition, the patient also developed transient hepatosplenomegaly, hypertriglyceridemia, and thrombocytopenia strongly suggestive of hemophagocytic syndrome .
Previously, Enders et al. also introduced a homozygous nonsense AP3B1 mutation in exon 8 causing a stop codon at codon 302 (Arg) in a patient with HPS type 2 who showed a severe clinical phenotype similar to the case reported by Wenham et al. [13, 14]. Besides dysplastic characteristics and developmental retardation, he presented with hepatosplenomegaly and recurrent infections and finally developed a lethal hemophagocytic syndrome. First, an increased bleeding tendency had not been recognized; however, he developed severe mucosal bleeding, after tooth extraction. More assessment showed that the two cases described by Wenham et al. and Enders et al. represent the only HPS type 2 patients developing symptoms indicative bleeding symptoms [7, 8, 10,11,12, 15]. However, there was no insufficient evidence of hemophagocytosis. Interestingly, the case reported in this study revealed a nonsense AP3B1 mutation leading to a β3A protein that represents an altered amino acid sequence, which can be a highlighted new candidate mutation Arg298X in exon 8 for HPS type 2. So far, this variant has not been reported before. In this study, our patient did not develop any signs or symptoms of hemophagocytosis.
Previous studies revealed that HPS type 2 could be a consequence of the AP3B1 gene mutations. In this regard, Jung et al. , in their publication, showed causative homozygous genomic exon deletion of the AP3B1 gene in two patients with HPS type 2. Furthermore, Wenham M, et al., evaluating pathogenic genomic defects in two patients, novel mutations in AP3B1 mutation (c.2078_2165del; p. Glu693fsX13 and c.153_156del; p. Glu52fsX11) and concluded that mutations in AP3B1 gene accounted for HPS type 2 . Subsequently, Nishikawa et al.  reported a Japanese patient with a novel compound heterozygous pathogenic mutation (c.188T > A; p.Met63Lys [exon 2] and c.2546T > A; p. Leu849Ter [exon 22]) in AP3B1 gene related with HPS type 2. In this study, we also investigated the genetic defect of HPS type 2 in an Iraqi family using whole-exome sequencing and presented a novel homozygous AP3B1 c.892A > T mutation that resulted in a premature stop codon.
We have detected a novel nonsense AP3B1 mutation causing HPS type 2 in an Iraqi family. The present study revealed that whole-exome sequencing may be used as an efficient and cost-effective molecular diagnostic strategy for detecting HPS type 2 patients. Moreover, detection of HPS type 2 causing AP3B1 gene mutation may be helpful for surveillance and management in at-risk relatives.
Availability of data and materials
The data that support the findings of this study are available from the corresponding author upon reasonable request.
Activated partial thromboplastin time
Exome sequencing project
Exome aggregation consortium
Exome variant server
Minor allele frequency
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We wish to thank the family members for their participation in this study.
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All procedures performed in this study were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or compare ethical strand.
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Written informed consent was obtained from the parents of the patient for this publication.
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Neissi, M., Al-Badran, A.I. Mutational spectrum of the AP3B1 gene in an Iraqi family affected with Hermansky–Pudlak syndrome type 2. Egypt J Med Hum Genet 24, 41 (2023). https://doi.org/10.1186/s43042-023-00421-1