Hereditary antithrombin deficiency: genes and variants

Genes linked to Hereditary antithrombin deficiency

• SERPINC1: Antithrombin-III

  It neutralizes thrombin and several activated coagulation proteases and is greatly accelerated by heparin-like molecules. Heterozygous deficiency causes a strong inherited predisposition to venous thrombosis and can reduce responsiveness to heparin.

  61 disease-causing and 99 uncertain variants in SERPINC1 are linked to Hereditary antithrombin deficiency.

Known disease-causing variants in Hereditary antithrombin deficiency

Showing 60 of 61.

Uncertain variants in Hereditary antithrombin deficiency that look disease-causing

Which prediction tools work for Hereditary antithrombin deficiency

How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).

• CADD: 91 out of 100
• PolyPhen-2: 91 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• CATVariant: 88 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• SIFT: 86 out of 100
• REVEL: 83 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• phyloP: 80 out of 100

Diseases related to Hereditary antithrombin deficiency

• Tuberous sclerosis, also linked to SERPINC1
• Myocardial infarction, also linked to SERPINC1

Frequently asked questions

Which genes are linked to Hereditary antithrombin deficiency?

In CATVariant, Hereditary antithrombin deficiency is linked to 1 analyzed protein: SERPINC1 (Antithrombin-III).

How many genetic variants are linked to Hereditary antithrombin deficiency?

182 variants: 61 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 99 are of uncertain significance or have conflicting reports.

Which uncertain variants in Hereditary antithrombin deficiency look disease-causing?

5 uncertain variants reach the likely-pathogenic range of the ACMG/AMP points scale on computable evidence, for example SERPINC1 P353S, SERPINC1 M284K, SERPINC1 P439S, SERPINC1 F434C and SERPINC1 L131V. These are leads for expert review, not diagnoses.

Which variant effect predictor works best for Hereditary antithrombin deficiency?

Among tools not trained on clinical labels, CADD separates this disease's known disease-causing variants from harmless ones best (AUROC 0.91, based on 32 disease-causing and 9 harmless variants).

About this data

Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.

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