Thrombophilia, X-linked, due to factor 9 defect: genes and variants

Genes linked to Thrombophilia, X-linked, due to factor 9 defect

• F9: Coagulation factor IX

  Its activated form combines with factor VIIIa to efficiently activate factor X during coagulation. Pathogenic loss-of-function variants cause X-linked hemophilia B, with bleeding severity determined largely by residual factor IX activity.

  62 disease-causing and 31 uncertain variants in F9 are linked to Thrombophilia, X-linked, due to factor 9 defect.

Where Thrombophilia, X-linked, due to factor 9 defect variants cluster

• F9 EGF-like 1 (positions 93–129): 10 of 62 disease-causing changes, 2.0× more than its size predicts.

Known disease-causing variants in Thrombophilia, X-linked, due to factor 9 defect

Showing 60 of 62.

Uncertain variants in Thrombophilia, X-linked, due to factor 9 defect that look disease-causing

Which prediction tools work for Thrombophilia, X-linked, due to factor 9 defect

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

• phyloP: 93 out of 100
• CATVariant: 92 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• PolyPhen-2: 92 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• CADD: 90 out of 100
• REVEL: 86 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• MetaLR: 83 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• SIFT: 82 out of 100

Same protein, different disease

• Hereditary factor IX deficiency disease is also caused by F9 variants; they fall in the same places as the Thrombophilia, X-linked, due to factor 9 defect variants (157 disease-causing).

Diseases related to Thrombophilia, X-linked, due to factor 9 defect

• Hereditary factor VIII deficiency disease, also linked to F9
• Hereditary factor IX deficiency disease, also linked to F9
• Warfarin sensitivity, X-linked, also linked to F9

Frequently asked questions

Which genes are linked to Thrombophilia, X-linked, due to factor 9 defect?

In CATVariant, Thrombophilia, X-linked, due to factor 9 defect is linked to 1 analyzed protein: F9 (Coagulation factor IX).

How many genetic variants are linked to Thrombophilia, X-linked, due to factor 9 defect?

136 variants: 62 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 31 are of uncertain significance or have conflicting reports.

Which uncertain variants in Thrombophilia, X-linked, due to factor 9 defect look disease-causing?

3 uncertain variants reach the likely-pathogenic range of the ACMG/AMP points scale on computable evidence, for example F9 W431L, F9 A279T and F9 L383P. These are leads for expert review, not diagnoses.

Which variant effect predictor works best for Thrombophilia, X-linked, due to factor 9 defect?

Among tools not trained on clinical labels, phyloP separates this disease's known disease-causing variants from harmless ones best (AUROC 0.93, based on 14 disease-causing and 21 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