Acute lymphoid leukemia: genes and variants
Acute lymphoid leukemia is linked to 3 analyzed proteins (PAX5, FLT3 and NBN). 5 DNA variants are known to cause it; 41 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Acute lymphoid leukemia
PAX5: Paired box protein Pax-5
It establishes and maintains B-cell identity by activating B-lineage genes and repressing alternative developmental programs. Somatic loss, mutation, or rearrangement is common in B-cell acute lymphoblastic leukemia, while germline variants can confer leukemia susceptibility and immunodeficiency.
3 disease-causing and 2 uncertain variants in PAX5 are linked to Acute lymphoid leukemia.
FLT3: Receptor-type tyrosine-protein kinase FLT3
Its signaling supports survival and expansion of early hematopoietic progenitors. Internal tandem duplications and kinase-domain mutations produce constitutive activity in acute myeloid leukemia and are important prognostic markers and therapeutic targets.
2 disease-causing and 0 uncertain variants in FLT3 are linked to Acute lymphoid leukemia.
NBN: Nibrin
It recruits and organizes the MRE11-RAD50 complex at DNA double-strand breaks and helps activate ATM-dependent DNA-damage responses. Biallelic loss-of-function variants cause Nijmegen breakage syndrome with microcephaly, immunodeficiency, chromosome instability, and high cancer risk.
0 disease-causing and 36 uncertain variants in NBN are linked to Acute lymphoid leukemia.
Weakly linked (only a few uncertain records): BCR and CDKN2A.
Known disease-causing variants in Acute lymphoid leukemia
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| PAX5 V26G | 26 | Paired | Disease-causing (★) |
| PAX5 P130T | 130 | Paired | Disease-causing (★) |
| PAX5 S134C | 134 | Paired | Disease-causing (★) |
| FLT3 D835Y | 835 | Protein kinase | Disease-causing |
| FLT3 D835V | 835 | Protein kinase | Disease-causing |
Same protein, different disease
- Acute myeloid leukemia is also caused by FLT3 variants; they fall mostly in different places as the Acute lymphoid leukemia variants (7 disease-causing).
Diseases related to Acute lymphoid leukemia
- Gastrointestinal stromal tumor, also linked to FLT3
- Ovarian cancer, also linked to NBN
- Acute myeloid leukemia, also linked to FLT3
- Hereditary breast ovarian cancer syndrome, also linked to NBN
- Multiple myeloma, also linked to FLT3
- Hypothyroidism, also linked to FLT3
- Hepatocellular carcinoma, also linked to FLT3
- Primary myelofibrosis, also linked to FLT3
- Renal cell carcinoma, also linked to FLT3
- Acquired polycythemia vera, also linked to FLT3
- Leukemia, acute lymphoblastic, susceptibility to, 3, also linked to PAX5
Frequently asked questions
Which genes are linked to Acute lymphoid leukemia?
In CATVariant, Acute lymphoid leukemia is linked to 3 analyzed proteins: PAX5 (Paired box protein Pax-5), FLT3 (Receptor-type tyrosine-protein kinase FLT3) and NBN (Nibrin).
How many genetic variants are linked to Acute lymphoid leukemia?
48 variants: 5 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 41 are of uncertain significance or have conflicting reports.
Which uncertain variants in Acute lymphoid leukemia look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
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