BCL11A
Chr 2ADBCL11 transcription factor A
Also known as: CTIP1, DILOS, EVI9, HBFQTL5, SMARCM1, ZNF856
This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. The corresponding mouse gene is a common site of retroviral integration in myeloid leukemia, and may function as a leukemia disease gene, in part, through its interaction with BCL6. During hematopoietic cell differentiation, this gene is down-regulated. It is possibly involved in lymphoma pathogenesis since translocations associated with B-cell malignancies also deregulates its expression. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Highly missense-constrained (top ~0.1%)
This gene — mechanism propensity
The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).
Literature Evidence
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
References
ClinVar Variant Classifications
96 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 5 | 0 | 0 | 0 | 5 |
Likely Pathogenic | 8 | 1 | 0 | 0 | 9 |
VUS | 2 | 51 | 3 | 1 | 57 |
Likely Benign | 0 | 4 | 0 | 3 | 7 |
Benign | 0 | 0 | 0 | 1 | 1 |
Conflicting | — | 1 | |||
| Total | 15 | 56 | 3 | 5 | 80 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →3 pathogenic / likely-pathogenic (of 4) ClinVar copy-number / structural variants overlap BCL11A — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →
Protein Context — Lollipop Plot
BCL11A · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
Online Study of People Who Have Genetic Changes and Features of Autism: Simons Searchlight
RECRUITINGEvaluation of Safety and Efficacy of CTX001 in Pediatric Participants With Transfusion-Dependent β-Thalassemia (TDT)
ACTIVE NOT RECRUITINGA Gene Transfer Study Inducing Fetal Hemoglobin in Sickle Cell Disease (GRASP, BMT CTN 2001)
ACTIVE NOT RECRUITINGLong-term Follow-up (LTFU) of Patients Treated With Genome-edited Autologous Hematopoietic Stem and Progenitor Cells (HSPC)
ACTIVE NOT RECRUITINGEvaluation of Safety and Efficacy of CTX001 in Pediatric Participants With Severe Sickle Cell Disease (SCD)
ACTIVE NOT RECRUITINGEvaluation of Efficacy and Safety of a Single Dose of CTX001 in Participants With Transfusion-Dependent β-Thalassemia and Severe Sickle Cell Disease
RECRUITINGSafety and Efficacy Evaluation of BRL-101 in Subjects With Transfusion-Dependent β-Thalassemia
ENROLLING BY INVITATIONHematopoietic Stem Cell BCL11A Enhancer Gene Editing for Severe β-Hemoglobinopathies
RECRUITINGGene Transfer for Sickle Cell Disease
ACTIVE NOT RECRUITINGUnraveling the Impact of Thalidomide at Diverse Doses in Transfusion Dependent Beta Thalassemia
RECRUITINGExternal Resources
Links to major genomics databases and tools