CBFA2T3
CBFA2/RUNX1 partner transcriptional co-repressor 3, the group of Zinc fingers MYND-type|A-kinase anchoring proteins
Basic information
Region (hg38): 16:88874858-88977207
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (121 variants)
- not_provided (6 variants)
- Autism (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBFA2T3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005187.6. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | |||||
| missense | 117 | 123 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 117 | 8 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CBFA2T3 | protein_coding | protein_coding | ENST00000268679 | 12 | 102347 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0484 | 0.952 | 125448 | 0 | 8 | 125456 | 0.0000319 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.155 | 428 | 437 | 0.979 | 0.0000318 | 4110 |
| Missense in Polyphen | 93 | 119.59 | 0.77765 | 1101 | ||
| Synonymous | -3.40 | 264 | 202 | 1.30 | 0.0000162 | 1378 |
| Loss of Function | 3.60 | 8 | 28.9 | 0.277 | 0.00000165 | 298 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.000101 | 0.0000995 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000290 | 0.0000265 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000112 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional corepressor which facilitates transcriptional repression via its association with DNA-binding transcription factors and recruitment of other corepressors and histone-modifying enzymes (PubMed:12559562, PubMed:15203199). Can repress the expression of MMP7 in a ZBTB33-dependent manner (PubMed:23251453). Reduces the protein levels and stability of the transcriptinal regulator HIF1A; interacts with EGLN1 and promotes the HIF1A prolyl hydroxylation-dependent ubiquitination and proteasomal degradation pathway (PubMed:25974097). Contributes to inhibition of glycolysis and stimulation of mitochondrial respiration by down-regulating the expression of glycolytic genes including PFKFB3, PFKFB4, PDK1, PFKP, LDHA and HK1 which are direct targets of HIF1A (PubMed:23840896, PubMed:25974097). Regulates the proliferation and the differentiation of erythroid progenitors by repressing the expression of TAL1 target genes (By similarity). Plays a role in granulocyte differentiation (PubMed:15231665). {ECO:0000250|UniProtKB:O54972, ECO:0000269|PubMed:12183414, ECO:0000269|PubMed:15231665, ECO:0000269|PubMed:16966434, ECO:0000269|PubMed:23251453, ECO:0000269|PubMed:23840896, ECO:0000269|PubMed:25974097, ECO:0000303|PubMed:12559562, ECO:0000303|PubMed:15203199}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving CBFA2T3 is found in therapy-related myeloid malignancies. Translocation t(16;21)(q24;q22) that forms a RUNX1-CBFA2T3 fusion protein. {ECO:0000269|PubMed:10995019, ECO:0000269|PubMed:11224496, ECO:0000269|PubMed:9596646}.;
- Pathway
- Hematopoietic Stem Cell Differentiation;ErbB4 signaling events
(Consensus)
Recessive Scores
- pRec
- 0.181
Intolerance Scores
- loftool
- 0.281
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 8.14
Haploinsufficiency Scores
- pHI
- 0.502
- hipred
- Y
- hipred_score
- 0.736
- ghis
- 0.512
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.985
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cbfa2t3
- Phenotype
- immune system phenotype; hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- cbfa2t3
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- response to hypoxia;cell population proliferation;negative regulation of cell population proliferation;granulocyte differentiation;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of glycolytic process;negative regulation of transcription, DNA-templated;regulation of aerobic respiration
- Cellular component
- Golgi membrane;nucleus;nucleoplasm;nucleolus
- Molecular function
- DNA-binding transcription factor activity;transcription corepressor activity;protein binding;metal ion binding