CBFA2T3 CBFA2/RUNX1 partner transcriptional co-repressor 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CBFA2T3provided by HGNC
Official Full Name: CBFA2/RUNX1 partner transcriptional co-repressor 3provided by HGNC
Primary source: HGNC:HGNC:1537
See related: Ensembl:ENSG00000129993 MIM:603870; AllianceGenome:HGNC:1537
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ETO2; MTG16; MTGR2; ZMYND4; RUNX1T3
Summary: This gene encodes a member of the myeloid translocation gene family which interact with DNA-bound transcription factors and recruit a range of corepressors to facilitate transcriptional repression. The t(16;21)(q24;q22) translocation is one of the less common karyotypic abnormalities in acute myeloid leukemia. The translocation produces a chimeric gene made up of the 5'-region of the runt-related transcription factor 1 gene fused to the 3'-region of this gene. This gene is also a putative breast tumor suppressor. Alternative splicing results in transcript variants. [provided by RefSeq, Nov 2010]
Expression: Broad expression in spleen (RPKM 6.2), lymph node (RPKM 3.7) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q24.3

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (88874858..88977207, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (94945216..95054578, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (88941266..89043615, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CNS erythroblastic sarcoma: a potential emerging pediatric tumor type characterized by NFIA::RUNX1T1/3 fusions.
Title: CNS erythroblastic sarcoma: a potential emerging pediatric tumor type characterized by NFIA::RUNX1T1/3 fusions.
The transcriptional corepressor CBFA2T3 inhibits all-trans-retinoic acid-induced myeloid gene expression and differentiation in acute myeloid leukemia.
Title: The transcriptional corepressor CBFA2T3 inhibits all-trans-retinoic acid-induced myeloid gene expression and differentiation in acute myeloid leukemia.
Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization.
Title: Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization.
These findings suggest rs13333659 in CBFA2T3 as a risk locus to modulate the decline rate of cerebrospinal fluid amyloid-beta42 peptide preceding the onset of clinical symptoms
Title: Genome-wide association study identifies CBFA2T3 affecting the rate of CSF Aβ(42) decline in non-demented elders.
CBFA2T3 is functional in t(8;21) acute myeloid leukemia cells, a possible RUNX1-RUNX1T1-mediated direct interference of CBFA2T3 corepressor function may be compensated by a higher threshold level of CBFA2T3 expression that is needed to drive the relapse of t(8;21) acute myeloid leukemia.
Title: Myeloid translocation gene CBFA2T3 directs a relapse gene program and determines patient-specific outcomes in AML.
Kaiso modifies MTG16-driven inflammation and tumorigenesis; this suggests that Kaiso deregulation contributes to MTG16-dependent colitis and Colitis-associated carcinoma phenotypes.
Title: Kaiso is required for MTG16-dependent effects on colitis-associated carcinoma.
The here presented transcriptomic subgroup-based approach unified the gene expression profiles of RUNX1-CBFA2T3 and RUNX1-RUNX1T1 acute myeloid leukemia.
Title: RNA-sequencing analysis of core binding factor AML identifies recurrent ZBTB7A mutations and defines RUNX1-CBFA2T3 fusion signature.
Analysis of chromatin immunoprecipitation sequencing data sets for MTGR1 and MTG16 targets indicated that MTGR1 can regulate Wnt and Notch signaling.
Title: Myeloid translocation genes differentially regulate colorectal cancer programs.
CBFA2T3 expression is regulated by Med19 in breast cancer cells.
Title: Med19 promotes breast cancer cell proliferation by regulating CBFA2T3/HEB expression.
specific interference with ETO2-GLIS2 oligomerization reverses the transcriptional activation at enhancers and promotes megakaryocytic differentiation, providing a relevant interface to target in this poor-prognosis pediatric leukemia.
Title: ETO2-GLIS2 Hijacks Transcriptional Complexes to Drive Cellular Identity and Self-Renewal in Pediatric Acute Megakaryoblastic Leukemia.

Submit: New GeneRIF Correction See all GeneRIFs (31)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of autistic-like traits in a general population study of young adults. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-146703 (e-PCR)
- UniSTS:175382

RH93203 (e-PCR)
- UniSTS:85277

RH121368 (e-PCR)
- UniSTS:134214

SHGC-64049 (e-PCR)
- UniSTS:34659

SHGC-148155 (e-PCR)
- UniSTS:176231

SHGC-61188 (e-PCR)
- UniSTS:77732

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription corepressor activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within granulocyte differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of glycolytic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of proteasomal ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of aerobic respiration	IDA Inferred from Direct Assay more info	PubMed
involved_in response to hypoxia	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: protein CBFA2T3

Names: CBFA2/RUNX1 translocation partner 3; MTG8-related gene 2; MTG8-related protein 2; core-binding factor, runt domain, alpha subunit 2; translocated to, 3; myeloid translocation gene 8 and 16b; myeloid translocation gene on chromosome 16 protein; zinc finger MYND domain-containing protein 4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029533.1 RefSeqGene

Range

4890..107239

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_005187.6 → NP_005178.4 protein CBFA2T3 isoform 1

See identical proteins and their annotated locations for NP_005178.4

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript, encodes the longer isoform (1) and is also known as MTG16a.

Source sequence(s)

AC092384, BC047019, BP282804

Consensus CDS

CCDS10972.1

UniProtKB/Swiss-Prot

D3DX78, O60615, O60616, O60617, O75081, O75082, O75107, O75108, Q0P5Z6, Q6P5W6

UniProtKB/TrEMBL

B2RBQ7

Related

ENSP00000268679.4, ENST00000268679.9

Conserved Domains (4) summary

pfam01753
Location:556 → 592

zf-MYND; MYND finger

pfam07531
Location:173 → 259

TAFH; NHR1 homology to TAF

pfam08788
Location:379 → 445

NHR2; NHR2 domain like

cl23750
Location:482 → 553

vATP-synt_E; ATP synthase (E/31 kDa) subunit
NM_175931.3 → NP_787127.1 protein CBFA2T3 isoform 2

See identical proteins and their annotated locations for NP_787127.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame coding exon, compared to variant 1. These differences cause translation initiation at a downstream start codon and result in an isoform (2) that lacks an internal segment and has a shorter N-terminus, compared to isoform 1. Variant 2 is also known as MTG16b.

Source sequence(s)

AB010420, AC092384, BE676580

Consensus CDS

CCDS10973.1

UniProtKB/TrEMBL

B2RBQ7

Related

ENSP00000332122.5, ENST00000327483.9

Conserved Domains (4) summary

pfam01753
Location:470 → 506

zf-MYND; MYND finger

pfam07531
Location:87 → 173

TAFH; NHR1 homology to TAF

pfam08788
Location:293 → 359

NHR2; NHR2 domain like

cl23750
Location:396 → 467

vATP-synt_E; ATP synthase (E/31 kDa) subunit

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

88874858..88977207 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005256323.6 → XP_005256380.1 protein CBFA2T3 isoform X1

See identical proteins and their annotated locations for XP_005256380.1

UniProtKB/TrEMBL

B2RBQ7

Conserved Domains (4) summary

pfam01753
Location:531 → 567

zf-MYND; MYND finger

pfam07531
Location:148 → 234

TAFH; NHR1 homology to TAF

pfam08788
Location:354 → 420

NHR2; NHR2 domain like

cl23750
Location:457 → 528

vATP-synt_E; ATP synthase (E/31 kDa) subunit
XM_047434826.1 → XP_047290782.1 protein CBFA2T3 isoform X3

UniProtKB/TrEMBL

B2RBQ7
XM_011523419.4 → XP_011521721.1 protein CBFA2T3 isoform X2

UniProtKB/TrEMBL

B2RBQ7

Conserved Domains (3) summary

pfam07531
Location:173 → 259

TAFH; NHR1 homology to TAF

pfam08788
Location:379 → 445

NHR2; NHR2 domain like

cl23750
Location:482 → 553

vATP-synt_E; ATP synthase (E/31 kDa) subunit

RNA

XR_007064926.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

94945216..95054578 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054314245.1 → XP_054170220.1 protein CBFA2T3 isoform X1

UniProtKB/TrEMBL

B2RBQ7
XM_054314247.1 → XP_054170222.1 protein CBFA2T3 isoform X3

UniProtKB/TrEMBL

B2RBQ7
XM_054314246.1 → XP_054170221.1 protein CBFA2T3 isoform X2

UniProtKB/TrEMBL

B2RBQ7
XM_054314248.1 → XP_054170223.1 protein CBFA2T3 isoform X4

UniProtKB/TrEMBL

H3BNH2