CBFA2T2

CBFA2/RUNX1 partner transcriptional co-repressor 2, the group of Zinc fingers MYND-type

Basic information

Region (hg38): 20:33490075-33650036

Links

ENSG00000078699 ∙ NCBI:9139 ∙ OMIM:603672 ∙ HGNC:1536 ∙ Uniprot:O43439 ∙ 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 CBFA2T2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBFA2T2 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			37	4		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	37	4	0

Variants in CBFA2T2

This is a list of pathogenic ClinVar variants found in the CBFA2T2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-33490277-G-A		not specified	Uncertain significance (May 17, 2023)
20-33574205-C-T		not specified	Uncertain significance (Oct 02, 2023)
20-33574217-G-T		not specified	Uncertain significance (Sep 01, 2021)
20-33574219-A-G		not specified	Likely benign (Nov 25, 2024)
20-33574231-G-A		not specified	Uncertain significance (Jun 22, 2021)
20-33606970-A-G		not specified	Uncertain significance (Jan 29, 2024)
20-33607069-C-T		not specified	Uncertain significance (Dec 05, 2024)
20-33607079-T-A		not specified	Uncertain significance (Sep 16, 2021)
20-33607088-C-T		not specified	Uncertain significance (Jun 22, 2024)
20-33611097-G-A		not specified	Uncertain significance (Apr 06, 2024)
20-33611109-A-G		not specified	Uncertain significance (Sep 06, 2023)
20-33611110-C-A		not specified	Uncertain significance (Aug 12, 2024)
20-33611238-G-A		not specified	Uncertain significance (Mar 25, 2024)
20-33611313-G-A		not specified	Uncertain significance (Mar 28, 2024)
20-33619535-G-A		not specified	Uncertain significance (Mar 11, 2022)
20-33619547-T-C		not specified	Uncertain significance (Nov 15, 2024)
20-33623161-C-T		not specified	Uncertain significance (Jun 03, 2022)
20-33623168-G-C		not specified	Uncertain significance (Feb 18, 2025)
20-33623257-T-C		not specified	Uncertain significance (Jan 22, 2025)
20-33624758-C-T			Likely benign (Jun 01, 2018)
20-33624795-A-G		not specified	Likely benign (Aug 02, 2022)
20-33625011-A-C		not specified	Uncertain significance (Jan 04, 2024)
20-33628373-G-A		not specified	Uncertain significance (Mar 16, 2022)
20-33628434-A-G		not specified	Uncertain significance (Sep 03, 2024)
20-33629720-C-T		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBFA2T2	protein_coding	protein_coding	ENST00000346541	11	159962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00415	125743	0	3	125746	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.48	235	369	0.637	0.0000221	3935
Missense in Polyphen		56	117.06	0.47837		1203
Synonymous	0.196	136	139	0.979	0.00000857	1223
Loss of Function	4.51	3	29.4	0.102	0.00000157	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
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). Via association with PRDM14 is involved in regulation of embryonic stem cell (ESC) pluripotency (PubMed:27281218). Involved in primordial germ cell (PCG) formation. Stabilizes PRDM14 and OCT4 on chromatin in a homooligomerization-dependent manner (By similarity). Can repress the expression of MMP7 in a ZBTB33- dependent manner (PubMed:23251453). May function as a complex with the chimeric protein RUNX1/AML1-CBFA2T1/MTG8 (AML1-MTG8/ETO fusion protein) which is produced in acute myeloid leukemia with the chromosomal translocation t(8;21). May thus be involved in the repression of AML1-dependent transcription and the induction of G- CSF/CSF3-dependent cell growth. May be a tumor suppressor gene candidate involved in myeloid tumors with the deletion of the 20q11 region. Through heteromerization with CBFA2T3/MTG16 may be involved in regulation of the proliferation and the differentiation of erythroid progenitors by repressing the expression of TAL1 target genes (By similarity). Required for the maintenance of the secretory cell lineage in the small intestine. Can inhibit Notch signaling probably by association with RBPJ and may be involved in GFI1-mediated Paneth cell differentiation (By similarity). {ECO:0000250|UniProtKB:O70374, ECO:0000269|PubMed:23251453, ECO:0000303|PubMed:12559562, ECO:0000303|PubMed:15203199}.
• Disease: DISEASE: Note=A chromosomal aberration involving CBFA2T2 is found in childhood precursor B-cell acute lymphoblastic leukemia (pre-B ALL). Translocation t(9;20)(p13;q11) with PAX5. {ECO:0000269|PubMed:26115422}.; DISEASE: Note=A chromosomal aberration involving CBFA2T2 is found in acute myeloid leukemia. Translocation t(20;21)(q11;q22) with RUNX1/AML1. {ECO:0000269|PubMed:20520637}.

Recessive Scores

• pRec: 0.277

Intolerance Scores

• loftool: 0.432
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.31

Haploinsufficiency Scores

• pHI: 0.378
• hipred: Y
• hipred_score: 0.783
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cbfa2t2
• Phenotype: cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; immune system phenotype; digestive/alimentary phenotype; reproductive 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)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of neuron projection development;negative regulation of neuron projection development;negative regulation of Notch signaling pathway;negative regulation of transcription, DNA-templated;intestinal epithelial cell differentiation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity;transcription corepressor activity;protein binding;metal ion binding