Factor V deficiency: genes and variants

Genes linked to Factor V deficiency

• F5: Coagulation factor V

  After activation, it serves as an essential cofactor for factor Xa in the prothrombinase complex and greatly accelerates thrombin generation. Deficiency can cause bleeding, whereas factor V Leiden produces activated-protein-C resistance and substantially increases venous-thrombosis risk.

  14 disease-causing and 203 uncertain variants in F5 are linked to Factor V deficiency.

Where Factor V deficiency variants cluster

• F5 Plastocyanin-like 4 (positions 536–684): 4 of 14 disease-causing changes, 4.3× more than its size predicts.
• F5 F5/8 type C 2 (positions 2066–2221): 4 of 14 disease-causing changes, 4.1× more than its size predicts.

Known disease-causing variants in Factor V deficiency

Which prediction tools work for Factor V deficiency

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

• CATVariant: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• PolyPhen-2: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• CADD: 99 out of 100
• REVEL: 99 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• MetaLR: 98 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• phyloP: 96 out of 100
• SIFT: 94 out of 100

Diseases related to Factor V deficiency

• Thrombophilia due to thrombin defect, also linked to F5
• Ischemic stroke, also linked to F5
• Thrombophilia due to activated protein C resistance, also linked to F5
• Pregnancy loss, recurrent, susceptibility to, 1, also linked to F5

Frequently asked questions

Which genes are linked to Factor V deficiency?

In CATVariant, Factor V deficiency is linked to 1 analyzed protein: F5 (Coagulation factor V).

How many genetic variants are linked to Factor V deficiency?

283 variants: 14 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 203 are of uncertain significance or have conflicting reports.

Which uncertain variants in Factor V deficiency look disease-causing?

None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.

Which variant effect predictor works best for Factor V deficiency?

Among tools not trained on clinical labels, CADD separates this disease's known disease-causing variants from harmless ones best (AUROC 0.99, based on 14 disease-causing and 40 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.

Download every variant as CSV · Browse all diseases · Methods · About the Center