Gene Gene information from NCBI Gene database.
Entrez ID 53335
Gene name BCL11 transcription factor A
Gene symbol BCL11A
Synonyms (NCBI Gene)
CTIP1DILOSEVI9HBFQTL5SMARCM1ZNF856
Chromosome 2
Chromosome location 2p16.1
Summary 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, throug
SNPs SNP information provided by dbSNP.
25
SNP ID Visualize variation Clinical significance Consequence
rs11886868 C>T Likely-pathogenic, benign Intron variant
rs761909641 ->G Pathogenic Frameshift variant, coding sequence variant, intron variant
rs768799046 ->G,GGGG,GGGTTTTGAAGGGGGGGGGGGGGGGG Pathogenic Frameshift variant, intron variant, coding sequence variant
rs886037864 T>G Pathogenic Coding sequence variant, genic upstream transcript variant, missense variant, upstream transcript variant, 5 prime UTR variant
rs886037865 C>A Pathogenic Coding sequence variant, genic upstream transcript variant, missense variant, upstream transcript variant, 5 prime UTR variant
miRNA miRNA information provided by mirtarbase database.
113
miRTarBase ID miRNA Experiments Reference
MIRT019481 hsa-miR-148b-3p Microarray 17612493
MIRT019603 hsa-miR-340-5p Sequencing 20371350
MIRT020396 hsa-miR-29c-3p Sequencing 20371350
MIRT026052 hsa-miR-196a-5p Sequencing 20371350
MIRT028335 hsa-miR-32-5p Sequencing 20371350
Transcription factors Transcription factors information provided by TRRUST V2 database.
2
Transcription factor Regulation Reference
FOXQ1 Activation 20145154
SIRT1 Repression 15639232
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
48
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 16704730, 19153051, 29606353
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA 19153051
GO:0001067 Function Transcription regulatory region nucleic acid binding IDA 29606353
GO:0001227 Function DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 16704730, 19153051
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
606557 13221 ENSG00000119866
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9H165
Protein name BCL11 transcription factor A (B-cell CLL/lymphoma 11A) (B-cell lymphoma/leukemia 11A) (BCL-11A) (COUP-TF-interacting protein 1) (Ecotropic viral integration site 9 protein homolog) (EVI-9) (Zinc finger protein 856)
Protein function Transcription factor (PubMed:16704730, PubMed:29606353). Associated with the BAF SWI/SNF chromatin remodeling complex (PubMed:23644491, PubMed:39607926). Binds to the 5'-TGACCA-3' sequence motif in regulatory regions of target genes, including a
PDB 5VTB , 6KI6 , 6U9Q , 8DTN , 8DTU , 8THO , 8TLO , 9B4P , 9BV0
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00096 zf-C2H2 378 399 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 405 427 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 742 764 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 770 792 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 800 823 Zinc finger, C2H2 type Domain
Tissue specificity TISSUE SPECIFICITY: Expressed at high levels in brain, spleen thymus, bone marrow and testis. Expressed in CD34-positive myeloid precursor cells, B-cells, monocytes and megakaryocytes. Expression is tightly regulated during B-cell development. {ECO:000026
Sequence
MSRRKQGKPQHLSKREFSPEPLEAILTDDEPDHGPLGAPEGDHDLLTCGQCQMNFPLGDI
LIFIEHKRKQCNGSLCLEKAVDKPPSPSPIEMKKASNPVEVGIQVTPEDDDCLSTSSRGI
CPKQEHIADKLLHWRGLSSPRSAHGALIPTPGMSAEYAPQGICKDEPSSYTCTTCKQPFT
SAWFLLQHAQNTHGLRIYLESEHGSPLTPRVGIPSGLGAECPSQPPLHGIHIADNNPFNL
LRIPGSVSREASGLAEGRFPPTPPLFSPPPRHHLDPHRIERLGAEEMALATHHPSAFDRV
LRLNPMAMEPPAMDFSRRLRELAGNTSSPPLSPGRPSPMQRLLQPFQPGSKPPFLATPPL
PPLQSAPPPSQPPVKSKSCEFCGKTFKFQSNLVVHRRSHTGEKPYKCNLCDHACTQASKL
KRHMKTH
MHKSSPMTVKSDDGLSTASSPEPGTSDLVGSASSALKSVVAKFKSENDPNLIP
ENGDEEEEEDDEEEEEEEEEEEEELTESERVDYGFGLSLEAARHHENSSRGAVVGVGDES
RALPDVMQGMVLSSMQHFSEAFHQVLGEKHKRGHLAEAEGHRDTCDEDSVAGESDRIDDG
TVNGRGCSPGESASGGLSKKLLLGSPSSLSPFSKRIKLEKEFDLPPAAMPNTENVYSQWL
AGYAASRQLKDPFLSFGDSRQSPFASSSEHSSENGSLRFSTPPGELDGGISGRSGTGSGG
STPHISGPGPGRPSSKEGRRSDTCEYCGKVFKNCSNLTVHRRSHTGERPYKCELCNYACA
QSSKLTRHMKTH
GQVGKDVYKCEICKMPFSVYSTLEKHMKKWHSDRVLNNDIKTE
Sequence length 835
Interactions View interactions
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
116
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
BCL11A-related BAFopathy Pathogenic; Likely pathogenic rs2103845910, rs2103863117, rs1446265434 RCV001533074
RCV001533073
RCV001533072
BCL11A-related disorder Likely pathogenic rs2466269611 RCV003909351
Cerebellar vermis hypoplasia Likely pathogenic; Pathogenic rs1558519119 RCV000779633
Congenital cerebellar hypoplasia Likely pathogenic; Pathogenic rs1558612412, rs1558519119 RCV001257951
RCV001257952
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
BCL11A-related intellectual disability Conflicting classifications of pathogenicity rs2103836035 RCV001563650
Clear cell carcinoma of kidney Benign; Likely benign rs147757821 RCV005908748
Developmental disorder Conflicting classifications of pathogenicity rs1676277997 RCV003127447
Familial cancer of breast Benign; Likely benign rs147757821 RCV005908746
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Adenocarcinoma Associate 37372998
Alcoholism Associate 28981154
alpha Thalassemia Associate 19696200
Alzheimer Disease Associate 30180184
Anemia Hemolytic Associate 29879141
Anemia Sickle Cell Associate 18245381, 18667698, 21068433, 22139998, 22801970, 24667352, 25084696, 25703683, 26393293, 26849705, 26888013, 27077760, 27377501, 27838552, 28280727
View all (16 more)
Apraxias Associate 27120335, 28960836
Arthritis Rheumatoid Associate 24213554
Autism Spectrum Disorder Associate 25938782
Autistic Disorder Associate 30755392, 36807877