CBFB
core-binding factor subunit beta
Basic information
Region (hg38): 16:67028984-67101058
Links
Phenotypes
GenCC
Source:
- cleidocranial dysplasia 2 (Limited), mode of inheritance: AD
- acute myeloid leukemia (Limited), mode of inheritance: Unknown
- cleidocranial dysplasia 2 (Strong), mode of inheritance: AD
- cleidocranial dysplasia 2 (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Cleidocranial dysplasia 2 | 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 | Craniofacial; Musculoskeletal; Neurologic | 36241386 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBFB 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 | 0 | |||||
| missense | 2 | |||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 0 | |||||
| non coding | 5 | |||||
| Total | 0 | 0 | 6 | 0 | 5 |
Variants in CBFB
This is a list of pathogenic ClinVar variants found in the CBFB 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 |
|---|---|---|---|---|---|
| CBFB | protein_coding | protein_coding | ENST00000412916 | 6 | 71943 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.959 | 0.0411 | 125743 | 0 | 2 | 125745 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.71 | 58 | 108 | 0.536 | 0.00000566 | 1222 |
| Missense in Polyphen | 12 | 38.033 | 0.31552 | 396 | ||
| Synonymous | -0.942 | 45 | 37.6 | 1.20 | 0.00000182 | 330 |
| Loss of Function | 3.27 | 1 | 14.4 | 0.0695 | 8.75e-7 | 136 |
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 | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Forms the heterodimeric complex core-binding factor (CBF) with RUNX family proteins (RUNX1, RUNX2, and RUNX3). RUNX members modulate the transcription of their target genes through recognizing the core consensus binding sequence 5'-TGTGGT-3', or very rarely, 5'-TGCGGT-3', within their regulatory regions via their runt domain, while CBFB is a non-DNA-binding regulatory subunit that allosterically enhances the sequence-specific DNA- binding capacity of RUNX. The heterodimers bind to the core site of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, LCK, IL3 and GM-CSF promoters. CBF complexes repress ZBTB7B transcription factor during cytotoxic (CD8+) T cell development. They bind to RUNX-binding sequence within the ZBTB7B locus acting as transcriptional silencer and allowing for cytotoxic T cell differentiation. {ECO:0000250|UniProtKB:Q08024}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving CBFB is associated with acute myeloid leukemia of M4EO subtype. Pericentric inversion inv(16)(p13;q22). The inversion produces a fusion protein that consists of the 165 N-terminal residues of CBF-beta (PEPB2) with the tail region of MYH11. {ECO:0000269|PubMed:8351518}.;
- Pathway
- miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Dual hijack model of Vif in HIV infection;RUNX2 regulates osteoblast differentiation;RUNX2 regulates chondrocyte maturation;RUNX2 regulates bone development;RUNX2 regulates genes involved in cell migration;RUNX2 regulates genes involved in differentiation of myeloid cells;Transcriptional regulation by RUNX2;Regulation of RUNX3 expression and activity;RUNX3 Regulates Immune Response and Cell Migration;Signal Transduction;Gene expression (Transcription);RUNX3 regulates RUNX1-mediated transcription;RUNX3 regulates p14-ARF;Transcriptional regulation by RUNX3;RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;RUNX1 regulates transcription of genes involved in BCR signaling;ATF-2 transcription factor network;Signaling by Nuclear Receptors;Regulation of RUNX1 Expression and Activity;Estrogen-dependent gene expression;RUNX1 regulates transcription of genes involved in differentiation of HSCs;RUNX1 regulates transcription of genes involved in differentiation of myeloid cells;RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs);RUNX1 regulates transcription of genes involved in interleukin signaling;RUNX1 regulates estrogen receptor mediated transcription;RUNX1 regulates transcription of genes involved in WNT signaling;RUNX1 regulates expression of components of tight junctions;ESR-mediated signaling;RUNX1 regulates transcription of genes involved in differentiation of keratinocytes;Transcriptional regulation by RUNX1;AP-1 transcription factor network;Regulation of nuclear SMAD2/3 signaling;Regulation of RUNX2 expression and activity
(Consensus)
Recessive Scores
- pRec
- 0.220
Intolerance Scores
- loftool
- 0.158
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.855
- hipred
- Y
- hipred_score
- 0.752
- ghis
- 0.650
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.557
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cbfb
- Phenotype
- skeleton phenotype; immune system phenotype; vision/eye phenotype; digestive/alimentary phenotype; limbs/digits/tail 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; normal 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); liver/biliary system phenotype; respiratory system phenotype; embryo phenotype; homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- cbfb
- Affected structure
- cardiac muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- has fewer parts of type
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;protein polyubiquitination;osteoblast differentiation;regulation of cytokine-mediated signaling pathway;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;lymphocyte differentiation;myeloid cell differentiation;regulation of Wnt signaling pathway;regulation of intracellular estrogen receptor signaling pathway;negative regulation of CD4-positive, alpha-beta T cell differentiation;positive regulation of CD8-positive, alpha-beta T cell differentiation;regulation of regulatory T cell differentiation;regulation of keratinocyte differentiation;regulation of myeloid cell differentiation;regulation of megakaryocyte differentiation;positive regulation of transcription by RNA polymerase II;cell maturation;regulation of B cell receptor signaling pathway;definitive hemopoiesis;regulation of hematopoietic stem cell differentiation;regulation of bicellular tight junction assembly
- Cellular component
- nucleus;nucleoplasm;membrane;core-binding factor complex
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription coregulator activity;transcription coactivator activity;protein binding;sequence-specific DNA binding