B-cell acute lymphoblastic leukemia with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1)

Summary

B-cell acute lymphoblastic leukemia with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1) (MONDO:0600030) is a cancer with 2 GWAS associations across 2 studies and 1 clinical trial. Top therapeutic interventions include fludarabine phosphate. A subtype of B-cell acute lymphoblastic leukemia — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Classification: Cancer
• Prevalence: Unknown (Worldwide) [Orphanet-validated]
• GWAS associations: 2
• Clinical trials: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	B-cell acute lymphoblastic leukemia with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1)
Mondo ID	MONDO:0600030
Orphanet	585956
DOID	DOID:0080649
NCIT	C80347
SNOMED CT	450956008
UMLS	C2698315
MedGen	396324
GARD	0022348
Is cancer (heuristic)	yes

Also known as: B acute lymphoblastic leukaemia with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1) · B acute lymphoblastic leukemia with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1) · B lymphoblastic leukaemia lymphoma with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1) (morphologic abnormality) · B lymphoblastic leukemia lymphoma with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1) (morphologic abnormality) · B-acute lymphoblastic leukaemia with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1) · B-acute lymphoblastic leukemia with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1) · B-lymphoblastic leukemia/lymphoma with t(1;19)(q23;p13.3)

Data availability: 2 GWAS associations (2 studies) · 22 cell lines.

Disease family

This is a subtype of B-cell acute lymphoblastic leukemia. Genetic, therapeutic, and trial evidence is largely curated at the broader-term level — see the parent page for the associated-gene cohort and molecular evidence.

Classification path: disease by etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › hematopoietic and lymphoid system neoplasm › hematopoietic and lymphoid cell neoplasm › lymphoid neoplasm › precursor lymphoblastic lymphoma/leukemia › acute lymphoblastic leukemia › B-cell acute lymphoblastic leukemia › B-cell acute lymphoblastic leukemia with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1)

Related subtypes (15): B-lymphoblastic leukemia/lymphoma MLL rearranged, B-lymphoblastic leukemia/lymphoma with ETV6-RUNX1, B-lymphoblastic leukemia/lymphoma with IL3-IGH, B-lymphoblastic leukemia/lymphoma, BCR-ABL1–like, B-lymphoblastic leukemia/lymphoma with IAMP21, B-lymphoblastic leukemia/lymphoma with t(7;9)(q11.2;p13.2), B-lymphoblastic leukemia/lymphoma with t(17;19), B acute lymphoblastic leukemia with PAX5 P80R mutation, B acute lymphoblastic leukemia with DUX4 rearrangement, B-lymphoblastic leukemia with MEF2D rearrangement, B-lymphoblastic leukemia with MYC rearrangement, B-lymphoblastic leukemia with NUTM1 rearrangement, B-lymphoblastic leukemia with PAX5alt, B-lymphoblastic leukemia with TCF3-HLF fusion, B-lymphoblastic leukemia with ZNF384 rearrangement

Genetics & variants

GWAS landscape

2 GWAS associations across 2 studies. Top hits map to 0 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs2665658	2e-08	BCL11A - RN7SL361P	A	4

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90020048	Lee SHR	2020	40	2,057	Genome-wide association study of susceptibility loci for TCF3-PBX1 acute lymphoblastic leukemia in children.
GCST90020049	Lee SHR	2020	40	1,454	Genome-wide association study of susceptibility loci for TCF3-PBX1 acute lymphoblastic leukemia in children.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	0
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	1

MAF distribution

Bucket	Variants
common (>=0.05)	1
low_freq (0.01-0.05)	0
rare (<0.01)	0
unknown	0

Functional consequences

Consequence	Count
intergenic_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs2665658	2	60599667	A>C	0.37	intergenic_variant	BCL11A - RN7SL361P	2e-08	Tier 4: intronic/intergenic

Genes & proteins

No associated-gene cohort resolved for this disease. Atlas builds the molecular and therapeutic sections — associated genes, protein families, druggability, pathways, interactions, and drug associations — by aggregating over a disease’s associated genes (resolved via GWAS / GenCC / ClinVar / CIViC), and none resolved here. This is expected for antibody-mediated, autoimmune, or otherwise non-gene-defined conditions; the curated evidence for this disease is its clinical features, GWAS susceptibility, and clinical trials (above).

Function

No pathway enrichment — requires an associated-gene cohort.

Therapeutics

No druggable-target or therapeutic data for this disease’s cohort.

Clinical trials & evidence

Clinical trials

Clinical trials: 1.

Phase distribution (across all retrieved trials)

Phase	Trials
PHASE2	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT01028716	PHASE2	TERMINATED	Donor Peripheral Blood Stem Cell Transplant in Treating Patients With Hematologic Malignancies

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
FLUDARABINE PHOSPHATE	4	1