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

ENSG00000129993 ∙ NCBI:863 ∙ OMIM:603870 ∙ HGNC:1537 ∙ Uniprot:O75081 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CBFA2T3 gene.

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.

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				2	1	3
missense			48	4		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	48	7	1

Variants in CBFA2T3

This is a list of pathogenic ClinVar variants found in the CBFA2T3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-88876980-C-T		not specified	Uncertain significance (Jun 22, 2023)
16-88877004-G-C		not specified	Uncertain significance (Jun 06, 2023)
16-88877025-C-A		not specified	Uncertain significance (Aug 29, 2022)
16-88877025-C-T		not specified	Uncertain significance (Jan 04, 2024)
16-88877026-G-A		not specified	Uncertain significance (Jan 09, 2024)
16-88877104-C-T		not specified	Uncertain significance (Dec 22, 2023)
16-88877122-G-A		not specified	Uncertain significance (Dec 20, 2023)
16-88877125-C-T		not specified	Uncertain significance (Dec 04, 2024)
16-88877143-G-A		not specified	Uncertain significance (Dec 02, 2021)
16-88877209-C-T		not specified	Uncertain significance (Nov 09, 2024)
16-88879325-C-T		not specified	Uncertain significance (Mar 19, 2024)
16-88879330-C-T			Benign (Feb 26, 2018)
16-88879367-G-A		not specified	Uncertain significance (Oct 10, 2023)
16-88879415-T-A		not specified	Uncertain significance (Jun 07, 2024)
16-88879436-C-T		not specified	Uncertain significance (Nov 27, 2023)
16-88880780-G-A		not specified	Uncertain significance (Nov 22, 2023)
16-88881306-C-T		not specified	Uncertain significance (Nov 11, 2024)
16-88881312-C-T		not specified	Uncertain significance (Nov 13, 2024)
16-88881315-C-G		not specified	Uncertain significance (Apr 09, 2024)
16-88881315-C-T		not specified	Uncertain significance (Sep 14, 2022)
16-88881323-C-T		not specified	Likely benign (Feb 05, 2024)
16-88881326-C-T		not specified	Uncertain significance (Oct 25, 2022)
16-88881339-C-T		not specified	Likely benign (Apr 12, 2022)
16-88881342-C-T		not specified	Uncertain significance (May 16, 2023)
16-88881348-C-T		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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