Identification and Mapping of a 2,009-bp DNA Deletion in SERPING1 of a Hereditary Angioedema Patient

Abstract

We report a heterozygous, 2,009 base pairs (bps) genomic DNA deletion within the SERPING1 gene that has not previously been reported in a case of type I hereditary angioedema (HAE). The patient is a 28-year-old Han Chinese female living in Hong Kong who has suffered from recurrent angioedema since adolescence, with increasing attack frequency as she entered adulthood; in the past, episodes occurred annually, but now occur every two to three months. The affected areas are not itchy and include common sites such as the left and right forearms, but without throat involvement. The patient also experiences epigastric pain. The patient's mother suffers from similar symptoms. A mutation in the serine protease inhibitor, clade G, member 1 (SERPING1) gene is associated with HAE. Patients with HAE type I commonly carry either a small deletion within SERPING1 or a truncated transcript. We performed a multiplex ligation-dependent probe amplification (MLPA) assay on our indexed patient. Our result suggests a 2,009 bps deletion spanning across exons 5 and 6 within SERPING1. Although earlier literature has described other large DNA deletions encasing exons 5 and 6 in SERPING1, these DNA rearrangements were larger in size between 4 and 6 kbps, and the breakpoint locations were generally not determined due to technical constraints (Pappalardo et al., 2000; Duponchel et al., 2001; Roche et al., 2005; Loules et al., 2018; and Göβwein et al., 2008). Our report describes mapping of this 2,009 bps in SERPING1. Using a combination of molecular techniques, we were able to confirm and locate this large heterozygous genomic DNA deletion that includes both exons 5 and 6 of SERPING1.

Figure 1

Heterozygous deletion of exons 5 and 6 in the patient's genomic DNA was detected by the MLPA assay (a). The mother had an identical MLPA result (data not shown). The patient and her mother's genomic DNA produced heterozygous PCR products, suggesting an approximately 2,000-bp deletion (b) (Lane 1: DNA ladder; Lane 2: negative control; Lane 3: patient; Lane 4: patient's mother; and Lane 5: wild-type control).

Figure 2

Genomic DNA sequence electropherograms of the patient and her mother, in comparison with the reference sequence. The deletion is 2,009 bps in size and encompasses exons 5 and 6. The red arrows locate the 3′ end breakpoint, whereas the red frame illustrates a part of the deleted sequence. The deletion boundaries are noted on the patient strand, as indicated by the nucleotide positions.

Figure 3

NG_009625.1:g.12156_14164del2009 led to the truncation of a 500-amino acid C1-INH protein into a 252-amino acid dysfunctional protein. Please note the above amino acid sequences relate only to the codons and not the mature protein with post-translational modifications.

Figure 4

NG_009625.1:g.12156_14164del2009 in SERPING1 (red brackets), and the nearest Alu element sequences (black arrows) relative to this 2,009 bps deletion. The 5′ end of the deletion breakpoint is 16 bps from the adjacent Alu element, while the 3′ end is approximately 1 kbps away from the nearest Alu sequence. Please note the diagram is not in exact scale.