7 Points - This variant was first reported in 1986 simultaneously on the US (Denver) and Italy (Milano-2). In Italy the was described as part of four members of an Italian family (two with histories of venous thromboembolism) and a consistently borderline low (about 70% of normal) qualitative defect of antithrombin III with normal antigen concentrations (Tripodi et al., 1986; PMID: 3563966) and the specific DNA variant later defined (Olds et al., PMID: 2602168). 7 French individuals from 6 families with type 2 RS deficiency and measured mean antithrombin activity of 65% and normal antigen levels (Alhenc-Gelas et al., 2017; PMID: 28300866) are heterozygote carriers. Additionally, 5 Danish individuals from 2 families with type 2 RS deficiency and measured antithrombin activity of 64% (58-70% range) with 38-45 years in range and 3 with documented VT (at age 16, 18 and 36yo) and 1 with recurrent PE (Kjaergaard et al., 2019; PMID: 30721820) carry the variant in heterozygosity. Finally, a 8yo deceased Spanish heterozygote female (No. 64, Cohort 1) with PE (OCP risk factor) is reported with 60% of antithrombin activity and classified as Type 2 HBS (Morena-Barrio et al., 2019: PMID: 30975910). Another case with overlapping authors was reported with limited detail, but confirmed repeat sampling, so this case was counted instead out of an abundance of caution (Bravo-Pérez et al., 2022; PMID: 34800304). Two heterozygote carriers were not included. First, a single individual (unspecified gender or age) from a Japanese cohort of 173 individuals with DVT is a heterozygote carrier. Normal anti-thrombin measurement (113%) (Miyata et al., 2008; PMID: 18954896). Second, a 20-year-old African female (risk factors: BMI, first trimester pregnancy), heterozygote carrier of this variant with recurrent miscarriages and acute unprovoked idiopathic fatal pulmonary embolism (IFPE). No anti-thrombin measurement, thus not included in final count (Halvorsen et al., 2017; PMID: 28174134).

In the US, a 16yo female proband with DVT, 2 months after OCP initiation and recurrence during pregnancy was evaluated in Denver, Colorado with 54% AT activity; multiple AT assays performed.

REVEL score of 0.88 meets set threshold (>0.6). No splicing disruption prediction per SpliceAI and varSEAK.

Total of 8 meioses amongst 3 families.

The variant is absent in gnomAD (v2.1.1 and v3.1.1). There is good coverage profile across both genomes and exomes in this region.

The first report in Italy included assessment with the proband plasma of the AT affinity to immobilized human alpha-thrombin ion sepharose beads revealing defective binding of the antithrombin III to thrombin-sepharose, locating the variant in the active site responsible for binding and neutralizing thrombin (Olds et al., 1989; PMID: 2602168). ​ ​ This missense variant was also constructed with site-directed mutagenesis into a cell system, expressed (translated using rabbit reticulocytes) and purified to assess impaired complex formation with thrombin through chromatography (Austin et al., 1990; PMID: 2207328) and document the affected residue is essential for proper antithrombin activity. ​