Detection and characterisation of large SERPINC1 deletions in type I inherited antithrombin deficiency

Abstract

Methods routinely used for investigating the molecular basis of antithrombin (AT) deficiency do not detect large SERPINC1 rearrangements. Between 2000 and 2008, 86 probands suspected of having AT-inherited type I deficiency were screened for SERPINC1 mutations in our laboratory. Mutations causally linked to the deficiency were identified by sequencing analysis in 63 probands. We present here results of multiplex ligation-dependent probe amplification (MLPA) analysis performed in 22 of the 23 remaining probands, in whom sequencing had revealed no mutation. Large deletions, present at the heterozygous state, were detected in 10 patients: whole gene deletions in 5 and partial deletions removing either exon 6 (n = 2), exons 1-2 (n = 1) or exons 5-7 (n = 2) in 5 others. Exon 6 partial deletions are a 2,769-bp deletion and a 1,892-bp deletion associated with a 10-bp insertion, both having 5' and/or 3' breakpoints located within Alu repeat elements. In addition, we identified the 5' breakpoint of a previously reported deletion of exons 1-2 within an extragenic Alu repeat. Distinct mutational mechanisms explaining these Alu sequence-related deletions are proposed. Overall, in this series, large deletions detected by MLPA explain almost half of otherwise unexplained type I AT-inherited deficiency cases.

On the sequence-directed nature of human gene mutation: The role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease

“…The 13 bp crossover region (i.e. GCCACCACGCCCG) was also found to contain the CCACCA mutational ‘super-hotspot’ [Picard et al, 2010]. In passing, it should also be appreciated that Alu elements are particularly prone to form non-B DNA structures (e.g.…”

Two case reports of inherited antithrombin deficiency: a novel frameshift mutation and a large deletion including all seven exons detected using two methods

“…Picard et al screened 86 probands with an inherited type I antithrombin deficiency and identified point mutations in 63 of them by direct sequencing. Large deletions were detected by MLPA analysis in 10 of the 23 remaining probands in whom sequencing had revealed no mutations and whole gene deletions were found in 5 of these 10 [12]. Large deletions are relatively more frequent among individuals with a type I antithrombin deficiency than in those with a protein C or protein S deficiency, because the SERPINC1 gene is essentially prone to recombinational events due to a high proportion of Alu repeats [9].…”

“…Thus, we suppose that the aberrant polypeptide caused by 21-22delAA in our patient is not secreted into the peripheral blood but is rather degraded by the cellular proteolytic system, which results in the type I antithrombin deficiency in our patient. The total gene deletion identified in Case 2 is the first report of this type of mutation in Japan, and at least 10 such examples have been reported to date worldwide [12]. Picard et al screened 86 probands with an inherited type I antithrombin deficiency and identified point mutations in 63 of them by direct sequencing.…”

Antithrombin deficiency and its laboratory diagnosis

“…By screening ''mutation negative'' AT deficient cases using the multiplex ligation-dependent probe amplification (MLPA) technique, several gross deletions were identified. The breakpoints are often located within Alu repeat elements (57). Amino acid changes caused by single nucleotide substitutions within the coding region of SER-PINC1 may also lead to type I deficiency.…”