Congenital prothrombin deficiency: genes and variants
Explore variant evidence for Congenital prothrombin deficiency across 1 analyzed protein (F2). Linked ClinVar records include 17 pathogenic or likely pathogenic variants, 34 variants of uncertain significance and 7 with conflicting classifications.
Coverage includes proteins already analyzed in CATVariant, not every gene involved in this condition. Database links are associations, not an assessment of clinical gene–disease validity. Computable evidence prioritizes variants for expert review and does not reclassify them. Source labels are pooled across this disease family.
Data updated 2026-10-10. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Congenital prothrombin deficiency
F2: Prothrombin
After cleavage to thrombin, it converts fibrinogen to fibrin and activates multiple additional coagulation components to amplify clot formation. Deficiency can cause bleeding, whereas the common G20210A variant raises prothrombin levels and increases venous-thrombosis risk.
17 ClinVar pathogenic / likely pathogenic and 41 uncertain variants in F2 have source records linked to Congenital prothrombin deficiency. Association strength is not clinical gene validity.
Where Congenital prothrombin deficiency variants cluster
- F2 Peptidase S1 (positions 364–618): 13 of 17 ClinVar pathogenic / likely pathogenic variants, 1.9× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Congenital prothrombin deficiency
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| F2 R596Q | 596 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F2 R461W | 461 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F2 R500Q | 500 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F2 R581C | 581 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F2 R425C | 425 | Peptidase S1 | Pathogenic / likely pathogenic (★) |
| F2 R596W | 596 | Peptidase S1 | Pathogenic / likely pathogenic (★) |
| F2 V424M | 424 | Peptidase S1 | Pathogenic / likely pathogenic (★) |
| F2 G499E | 499 | Peptidase S1 | Pathogenic / likely pathogenic (★) |
| F2 G332A | 332 | Pathogenic / likely pathogenic (★) | |
| F2 E357G | 357 | Pathogenic / likely pathogenic (★) | |
| F2 R425H | 425 | Peptidase S1 | Pathogenic / likely pathogenic |
| F2 D595E | 595 | Peptidase S1 | Pathogenic / likely pathogenic |
| F2 E352K | 352 | Pathogenic / likely pathogenic | |
| F2 E343K | 343 | Pathogenic / likely pathogenic | |
| F2 V365E | 365 | Peptidase S1 | Pathogenic / likely pathogenic |
| F2 M380T | 380 | Peptidase S1 | Pathogenic / likely pathogenic |
| F2 G601V | 601 | Peptidase S1 | Pathogenic / likely pathogenic |
Diseases related to Congenital prothrombin deficiency
- Heart disease, also linked to F2
- Thrombophilia due to thrombin defect, also linked to F2
- Protein c deficiency, also linked to F2
- Ischemic stroke, also linked to F2
Frequently asked questions
Which genes have records linked to Congenital prothrombin deficiency?
This view contains 1 analyzed proteins: F2. Links come from clinical records and association databases. They do not imply that every listed gene is a validated cause, and missing genes may not yet be analyzed.
What do the clinical classifications mean?
Linked records include 17 pathogenic or likely pathogenic variants, 34 variants of uncertain significance and 7 with conflicting classifications. Labels summarize source records; multi-condition records may not make a separate assertion for this disease. Check the original record and review status.
Does the evidence score change a VUS classification?
No. 0 VUS or conflicting variants reach the likely-pathogenic points range on the computable criteria available here. This is a research prioritization signal, not a clinical classification. Patient, family and other required evidence may be missing.
Can I download the variant evidence?
Download the CSV for all 75 variants in the selected disease scope, including clinical labels, review status, evidence criteria, predictor scores, functional measurements and population frequency where available.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from eligible public CATVariant analyses 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