Factor XI deficiency: genes and variants
Explore variant evidence for Factor XI deficiency across 1 analyzed protein (F11). Linked ClinVar records include 57 pathogenic or likely pathogenic variants, 53 variants of uncertain significance and 16 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 2026-10-21. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Factor XI deficiency
F11: Coagulation factor XI
Its activated form amplifies thrombin generation through the intrinsic coagulation pathway. Deficiency causes hemophilia C with variable bleeding, while reduced factor XI activity is associated with lower thrombosis risk and is being explored as a safer anticoagulation target.
57 ClinVar pathogenic / likely pathogenic and 69 uncertain variants in F11 have source records linked to Factor XI deficiency. Association strength is not clinical gene validity.
Where Factor XI deficiency variants cluster
- F11 Apple 4 (positions 291–374): 12 of 57 ClinVar pathogenic / likely pathogenic variants, 1.6× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Factor XI deficiency
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| F11 G418V | 418 | Peptidase S1 | Pathogenic / likely pathogenic (★★★★) |
| F11 A430V | 430 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 A430T | 430 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 W519C | 519 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 R326C | 326 | Apple 4 | Pathogenic / likely pathogenic (★★) |
| F11 R326H | 326 | Apple 4 | Pathogenic / likely pathogenic (★★) |
| F11 G368R | 368 | Apple 4 | Pathogenic / likely pathogenic (★★) |
| F11 G368E | 368 | Apple 4 | Pathogenic / likely pathogenic (★★) |
| F11 C416Y | 416 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 A430S | 430 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 C500W | 500 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 G573E | 573 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 S575L | 575 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 G591D | 591 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 S594R | 594 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 M1I | 1 | Pathogenic / likely pathogenic (★★) | |
| F11 V516M | 516 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 T593M | 593 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 C56R | 56 | Apple 1 | Pathogenic / likely pathogenic (★★) |
| F11 L190P | 190 | Apple 2 | Pathogenic / likely pathogenic (★★) |
| F11 D222Y | 222 | Apple 3 | Pathogenic / likely pathogenic (★★) |
| F11 C230S | 230 | Apple 3 | Pathogenic / likely pathogenic (★★) |
| F11 F301L | 301 | Apple 4 | Pathogenic / likely pathogenic (★★) |
| F11 T322I | 322 | Apple 4 | Pathogenic / likely pathogenic (★★) |
| F11 G354R | 354 | Apple 4 | Pathogenic / likely pathogenic (★★) |
| F11 T150M | 150 | Apple 2 | Pathogenic / likely pathogenic (★★) |
| F11 P400L | 400 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 G478R | 478 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 A109T | 109 | Pathogenic / likely pathogenic (★★) | |
| F11 P206S | 206 | Apple 3 | Pathogenic / likely pathogenic (★★) |
| F11 S243F | 243 | Apple 3 | Pathogenic / likely pathogenic (★★) |
| F11 E315K | 315 | Apple 4 | Pathogenic / likely pathogenic (★★) |
| F11 E341K | 341 | Apple 4 | Pathogenic / likely pathogenic (★★) |
| F11 R396C | 396 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 V403M | 403 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 K536N | 536 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 P538L | 538 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 E597K | 597 | Peptidase S1 | Pathogenic / likely pathogenic (★★) |
| F11 W519S | 519 | Peptidase S1 | Pathogenic / likely pathogenic (★) |
| F11 C500R | 500 | Peptidase S1 | Pathogenic / likely pathogenic (★) |
| F11 H53Y | 53 | Apple 1 | Pathogenic / likely pathogenic (★) |
| F11 M120T | 120 | Apple 2 | Pathogenic / likely pathogenic (★) |
| F11 C374R | 374 | Apple 4 | Pathogenic / likely pathogenic (★) |
| F11 W425R | 425 | Peptidase S1 | Pathogenic / likely pathogenic (★) |
| F11 C545Y | 545 | Peptidase S1 | Pathogenic / likely pathogenic (★) |
| F11 Y614D | 614 | Peptidase S1 | Pathogenic / likely pathogenic (★) |
| F11 T51P | 51 | Apple 1 | Pathogenic / likely pathogenic (★) |
| F11 L373S | 373 | Apple 4 | Pathogenic / likely pathogenic (★) |
| F11 I454K | 454 | Peptidase S1 | Pathogenic / likely pathogenic (★) |
| F11 V611M | 611 | Peptidase S1 | Pathogenic / likely pathogenic (★) |
| F11 K101R | 101 | Apple 1 | Pathogenic / likely pathogenic (★) |
| F11 H145P | 145 | Apple 2 | Pathogenic / likely pathogenic (★) |
| F11 M1K | 1 | Pathogenic / likely pathogenic | |
| F11 V325F | 325 | Apple 4 | Pathogenic / likely pathogenic |
| F11 W587S | 587 | Peptidase S1 | Pathogenic / likely pathogenic |
| F11 T493I | 493 | Peptidase S1 | Pathogenic / likely pathogenic |
| F11 F460V | 460 | Peptidase S1 | Pathogenic / likely pathogenic |
Uncertain variants prioritized for review in Factor XI deficiency
| Variant | Position | Protein part | Clinical label | Evidence |
|---|---|---|---|---|
| F11 T51I | 51 | Apple 1 | Conflicting reports (★) | +6: 2 other pathogenic changes within 3 positions; T51P at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.76 |
| F11 G591A | 591 | Peptidase S1 | Uncertain (★) | +6: 3 other pathogenic changes within 3 positions; G591D at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.61 |
Which prediction tools work for Factor XI deficiency
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- AlphaMissense: 96 out of 100
- ESM1b (LLR): 94 out of 100
- CATVariant: 91 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 86 out of 100
Frequently asked questions
Which genes have records linked to Factor XI deficiency?
This view contains 1 analyzed proteins: F11. 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 57 pathogenic or likely pathogenic variants, 53 variants of uncertain significance and 16 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. 2 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 130 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.
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