Case Report: A Novel Synonymous ARPC1B Gene Mutation Causes a Syndrome of Combined Immunodeficiency, Asthma, and Allergy With Significant Intrafamilial Clinical Heterogeneity

Abstract

Recently, a novel syndrome of combined immune deficiency, infections, allergy, and inflammation has been attributed to mutations in the gene encoding actin-related protein 2/3 complex subunit 1B (ARPC1B), which is a key molecule driving the dynamics of the cytoskeleton. Homozygous mutations in the ARPC1B gene have been found to result in the disruption of the protein structure and cause an autosomal recessive syndrome of combined immune deficiency, impaired T-cell migration and proliferation, increased levels of immunoglobulin E (IgE) and immunoglobulin A (IgA), and thrombocytopenia. To date, only a few individuals have been diagnosed with the ARPC1B deficiency syndrome worldwide. In this case series, we report the wide spectrum of phenotype in 3 siblings of a consanguineous family from Afghanistan with a novel homozygous synonymous pathogenic variant c.783G>A, p. (Ala261Ala) of the ARPC1B gene that causes a similar syndrome but no thrombocytopenia. Targeted RNA studies demonstrated that the variant affects the splicing process of mRNA, resulting in a marked reduction of the levels of primary (normal) RNA transcript of the ARPC1B gene in the affected patients and likely premature termination from the abnormally spliced mRNA. The next generation sequencing (NGS) studies facilitated the diagnosis of this rare combined immunodeficiency and led to the decision to treat the affected patients with hematopoietic cell transplant (HCT) from an human leukocyte antigen (HLA)-matched healthy sibling.

Keywords: Arpc1b; allergy; case report; combined immune deficiency; immunodeficiency; inborn errors of immunity.

Figure 1

Timeline of the clinical events, diagnostic evaluations, and treatment strategies. LRTI, lower respiratory tract infections; HSCT, haematopoietic stem cell transplant; DHR, dihydrorhodamine flow cytometric test; IRAK, interleukin-1 receptor-associated kinase 4; WES, whole exome sequencing.

Figure 2

(A) Schematic overview of the wild-type and mutant gDNA and cDNA of exons 6–8 in the ARPC1B gene (i) Wt gDNA with G nucleotide at the last position of exon 7 (ii) Wt cDNA from mRNA analysis (iii) Mutant gDNA with A to G at the last position of exon 7 Arrows represent cryptic splice site in intron 6–7 with 124 nucleotides upstream from the variant G783A (iv) Mutant cDNA represents the result of variant c.783G>A; exon 7 skipping and partly intron 6–7 retention (29 bp) and the activation of a cryptic splice site with 124 nucleotides upstream in intron 6–7. The using transcript for gDNA and cDNA analysis was ENST00000252725.9. (B) Agarose gel electrophoresis for cDNA analysis for variant c.783G>A in ARPC1B. Reverse transcription (RT)-PCR showed leaky splicing with a weak wild-type band with an expected size of 450 bp and a stronger band of around 400 bp, yielded by the skipping of exon 7 of the ARPC1B gene, for patient II-6 (lane 4). For the heterozygous father I-2 (lane 2), RT–PCR showed a stronger wild-type band and a weaker band for the exon 7 skipped product. For the wild-type homozygous II-5 (lane 3), Control 1 (lane 5), and Control 2 (lane 6) enabled a strong wild-type band. Sequencing of the different cDNA products showed unaltered splicing for the smaller product (upper electropherogram) and skipping of exon 7 of the ARPC1B gene (electropherogram below) for the larger product, leading to a premature stop codon on the protein level. Underline letters represent the amino acids and * the stop codon.