A complex genomic abnormality found in a patient with antithrombin deficiency and autoimmune disease-like symptoms

Abstract

Hereditary antithrombin (AT) deficiency is an autosomal dominant thrombophilic disorder caused by SERPINC1 abnormality. In the present study, we analyzed SERPINC1 in a Japanese patient with AT deficiency and autoimmune disease-like symptoms. Direct sequencing and multiplex ligation-dependent probe amplification revealed that the patient was hemizygous for the entire SERPINC1 deletion. Single nucleotide polymorphism genotyping, gene dose measurement, and long-range polymerase chain reaction (PCR) followed by mapping PCR and direct sequencing of the long-range PCR products revealed that the patient had an approximately 111-kb gene deletion from exon 2 of ZBTB37 to intron 5 of RC3H1, including the entire SERPINC1 in chromosome 1. We also found a 7-bp insertion of an unknown origin in the breakpoint, which may be a combination of three parts with a few base-pair microhomologies, resulting from a replication-based process known as 'fork stalling and template switching'. Because RC3H1, which encodes the protein roquin is involved in the repression of self-immune responses, the autoimmune disease-like symptoms of the patient may have resulted from this gene defect. In conclusion, we identified an entire SERPINC1 deletion together with a large deletion of RC3H1 in an AT-deficient patient with autoimmune disease-like symptoms.

A human immune dysregulation syndrome characterized by severe hyperinflammation with a homozygous nonsense Roquin-1 mutation

“…1a). Similarly, a heterozygous deletion of the last 16 exons of RC3H1 has been detected in a Japanese patient with autoimmune disease-like symptoms with high titers of rheumatoid factors 48 . These observations strengthen the hypothesis that residual function of Roquin-1 may be required for autoimmune antibody generation.…”

SVA retrotransposition in exon 6 of the coagulation factor IX gene causing severe hemophilia B

“…1b) showed PCR products more than 2-kb larger than that of the normal control. We also performed multiplex ligation-dependent probe amplification (MLPA) to analyze the relative gene dosage values for all F9 exons from the patient as previously described [6], and found an absence of intragenic deletions or duplications in the F9 regions targeted by the designed probes (data not shown). These data revealed a large insertion located at the intron 5-exon 6 junction without causative mutation in any other F9 exon, suggesting that the exon 6 insertion is responsible for deficiency of the FIX activity observed in the patient.…”

“…Because a band of the correct size in exon 6 was not observed, we performed long-range PCR amplification using upper and lower primers targeted to exons 5 and 6, respectively. We purified each PCR product and determined its DNA sequence as previously described [6].…”

A novel frameshift mutation leading to inherited type I antithrombin deficiency

“…The mutation profile of the SERPINC1 gene is heterogeneous and mostly comprises point mutations and small deletions/insertions. Some large rearrangements have also been reported [5,6]. We herein identified a novel frameshift mutation in a case of inherited type I AT deficiency.…”