BCL11A
BCL11 transcription factor A, the group of BAF complex|Zinc fingers C2H2-type
Basic information
Region (hg38): 2:60450519-60554467
Previous symbols: [ "EVI9" ]
Links
Phenotypes
GenCC
Source:
- intellectual disability, autosomal dominant 40 (Definitive), mode of inheritance: AD
- Dias-Logan syndrome (Strong), mode of inheritance: AD
- Dias-Logan syndrome (Moderate), mode of inheritance: AD
- Dias-Logan syndrome (Strong), mode of inheritance: AD
- Dias-Logan syndrome (Strong), mode of inheritance: AD
- Dias-Logan syndrome (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Dias-Logan syndrome | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 24810580; 27453576 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (95 variants)
- Dias-Logan syndrome (45 variants)
- Inborn genetic diseases (23 variants)
- not specified (5 variants)
- BCL11A-related BAFopathy (3 variants)
- Neurodevelopmental delay (3 variants)
- BCL11A-related condition (2 variants)
- Intellectual disability (2 variants)
- Fetal hemoglobin quantitative trait locus 5 (1 variants)
- Global developmental delay (1 variants)
- Postaxial polydactyly;Delayed speech and language development (1 variants)
- Developmental disorder (1 variants)
- See cases (1 variants)
- Microcephaly;Global developmental delay;Profound global developmental delay;Intellectual disability (1 variants)
- Marfanoid habitus and intellectual disability (1 variants)
- BCL11A-related intellectual disability (1 variants)
- Dias-Logan syndrome;Intellectual disability, autosomal dominant 45 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCL11A gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 16 | 24 | ||||
| missense | 66 | 84 | ||||
| nonsense | 11 | |||||
| start loss | 3 | |||||
| frameshift | 22 | 10 | 32 | |||
| inframe indel | 3 | |||||
| splice donor/acceptor (+/-2bp) | 6 | |||||
| splice region ? | 1 | 1 | ||||
| non coding ? | 7 | |||||
| Total | 37 | 23 | 76 | 22 | 12 |
Variants in BCL11A
This is a list of pathogenic ClinVar variants found in the BCL11A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BCL11A | protein_coding | protein_coding | ENST00000335712 | 4 | 102401 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.970 | 0.0300 | 125742 | 0 | 5 | 125747 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.83 | 296 | 549 | 0.539 | 0.0000371 | 5477 |
| Missense in Polyphen | 70 | 164.22 | 0.42627 | 1750 | ||
| Synonymous | 2.10 | 216 | 259 | 0.834 | 0.0000217 | 1646 |
| Loss of Function | 3.98 | 3 | 24.1 | 0.125 | 0.00000110 | 304 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor associated with the BAF SWI/SNF chromatin remodeling complex (By similarity). Repressor of fetal hemoglobin (HbF) level (PubMed:26375765). Involved in brain development (PubMed:27453576). Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. Essential factor in lymphopoiesis required for B- cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity). {ECO:0000250|UniProtKB:Q9QYE3, ECO:0000303|PubMed:26375765, ECO:0000303|PubMed:27453576}.;
- Disease
- DISEASE: Note=Chromosomal aberrations involving BCL11A may be a cause of lymphoid malignancies. Translocation t(2;14)(p13;q32.3) causes BCL11A deregulation and amplification. {ECO:0000269|PubMed:11719382}.; DISEASE: Intellectual developmental disorder with persistence of fetal hemoglobin (IDPFH) [MIM:617101]: An autosomal dominant disorder characterized by delayed psychomotor development, intellectual disability, variable dysmorphic features, including microcephaly, downslanting palpebral fissures, strabismus, and external ear abnormalities, and asymptomatic persistence of fetal hemoglobin. {ECO:0000269|PubMed:27453576}. Note=The disease is caused by mutations affecting the gene represented in this entry. {ECO:0000269|PubMed:27453576}.;
- Pathway
- Prion disease pathway
(Consensus)
Recessive Scores
- pRec
- 0.170
Intolerance Scores
- loftool
- 0.0194
- rvis_EVS
- -1.16
- rvis_percentile_EVS
- 6.17
Haploinsufficiency Scores
- pHI
- 0.669
- hipred
- Y
- hipred_score
- 0.628
- ghis
- 0.586
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bcl11a
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- bcl11ab
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;positive regulation of gene expression;protein sumoylation;negative regulation of dendrite extension;negative regulation of neuron remodeling;cellular response to L-glutamate;negative regulation of dendrite development;negative regulation of branching morphogenesis of a nerve
- Cellular component
- nucleus;nucleoplasm;cytoplasm;postsynaptic density
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein kinase binding;sequence-specific DNA binding;metal ion binding