GeneBe

BCL11A

BCL11 transcription factor A, the group of BAF complex|Zinc fingers C2H2-type

Basic information

Region (hg38): 2:60450520-60554467

Previous symbols: [ "EVI9" ]

Links

ENSG00000119866 ∙ NCBI:53335 ∙ OMIM:606557 ∙ HGNC:13221 ∙ Uniprot:Q9H165 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • 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
  • Dias-Logan syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Intellectual developmental disorder with persistence of fetal hemoglobin (Dias-Logan syndrome)ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic24810580; 27453576

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCL11A gene.

  • not_provided (137 variants)
  • Dias-Logan_syndrome (67 variants)
  • Inborn_genetic_diseases (63 variants)
  • BCL11A-related_disorder (18 variants)
  • not_specified (6 variants)
  • Intellectual_disability (5 variants)
  • Neurodevelopmental_delay (3 variants)
  • BCL11A-related_BAFopathy (3 variants)
  • Congenital_cerebellar_hypoplasia (2 variants)
  • BCL11A-related_intellectual_disability (1 variants)
  • Corpus_callosum,_agenesis_of (1 variants)
  • Global_developmental_delay (1 variants)
  • Cerebellar_vermis_hypoplasia (1 variants)
  • Postaxial_polydactyly (1 variants)
  • Delayed_speech_and_language_development (1 variants)
  • See_cases (1 variants)
  • Marfanoid_habitus_and_intellectual_disability (1 variants)
  • Intellectual_disability,_autosomal_dominant_45 (1 variants)
  • Neurodevelopmental_abnormality (1 variants)
  • Developmental_disorder (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. These statistics are base on transcript: NM_000022893.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
6
clinvar
24
clinvar
2
clinvar
 32
missense
6
clinvar
9
clinvar
130
clinvar
13
clinvar
2
clinvar
 160
nonsense
11
clinvar
6
clinvar
2
clinvar
 19
start loss
2
1
 3
frameshift
25
clinvar
20
clinvar
1
clinvar
 46
splice donor/acceptor (+/-2bp)
2
clinvar
5
clinvar
 7
Total 46 41 139 37 4

Highest pathogenic variant AF is 0.0000110618

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BCL11Aprotein_codingprotein_codingENST00000335712 4102401
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9700.0300125742051257470.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.832965490.5390.00003715477
Missense in Polyphen70164.220.426271750
Synonymous2.102162590.8340.00002171646
Loss of Function3.98324.10.1250.00000110304

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004630.0000462
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.000.00
South Asian0.00003280.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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