TBX1 T-box transcription factor 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TBX1provided by HGNC
Official Full Name: T-box transcription factor 1provided by HGNC
Primary source: HGNC:HGNC:11592
See related: Ensembl:ENSG00000184058 MIM:602054; AllianceGenome:HGNC:11592
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: DGS; TGA; VCF; CAFS; CTHM; DGCR; DORV; VCFS; TBX1C; CATCH22
Summary: This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This gene product shares 98% amino acid sequence identity with the mouse ortholog. DiGeorge syndrome (DGS)/velocardiofacial syndrome (VCFS), a common congenital disorder characterized by neural-crest-related developmental defects, has been associated with deletions of chromosome 22q11.2, where this gene has been mapped. Studies using mouse models of DiGeorge syndrome suggest a major role for this gene in the molecular etiology of DGS/VCFS. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]
Expression: Biased expression in testis (RPKM 1.4), prostate (RPKM 1.1) and 13 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q11.21

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (19756703..19783593)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (20133557..20160463)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (19744226..19771116)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

In-silico identification of deleterious non-synonymous SNPs of TBX1 gene: Functional and structural impact towards 22q11.2DS.
Title: In-silico identification of deleterious non-synonymous SNPs of TBX1 gene: Functional and structural impact towards 22q11.2DS.
A regulatory variant impacting TBX1 expression contributes to basicranial morphology in Homo sapiens.
Title: A regulatory variant impacting TBX1 expression contributes to basicranial morphology in Homo sapiens.
Establishment of the Myeloid TBX-Code Reveals Aberrant Expression of T-Box Gene TBX1 in Chronic Myeloid Leukemia.
Title: Establishment of the Myeloid TBX-Code Reveals Aberrant Expression of T-Box Gene TBX1 in Chronic Myeloid Leukemia.
Conserved enhancers control notochord expression of vertebrate Brachyury.
Title: Conserved enhancers control notochord expression of vertebrate Brachyury.
Brachyury positively regulates extracellular matrix synthesis via directly promoting aggrecan transcription in nucleus pulposus.
Title: Brachyury positively regulates extracellular matrix synthesis via directly promoting aggrecan transcription in nucleus pulposus.
SNP-mediated binding of TBX1 to the enhancer element of IL-10 reduces the risk of Behcet's disease.
Title: SNP-mediated binding of TBX1 to the enhancer element of IL-10 reduces the risk of Behçet's disease.
TBX1 functions as a putative oncogene of breast cancer through promoting cell cycle progression.
Title: TBX1 functions as a putative oncogene of breast cancer through promoting cell cycle progression.
Case Report: Unmanipulated Matched Sibling Donor Hematopoietic Cell Transplantation In TBX1 Congenital Athymia: A Lifesaving Therapeutic Approach When Facing a Systemic Viral Infection.
Title: Case Report: Unmanipulated Matched Sibling Donor Hematopoietic Cell Transplantation In TBX1 Congenital Athymia: A Lifesaving Therapeutic Approach When Facing a Systemic Viral Infection.
Relationship Between Severity of T Cell Lymphopenia and Immune Dysregulation in Patients with DiGeorge Syndrome (22q11.2 Deletions and/or Related TBX1 Mutations): a USIDNET Study.
Title: Relationship Between Severity of T Cell Lymphopenia and Immune Dysregulation in Patients with DiGeorge Syndrome (22q11.2 Deletions and/or Related TBX1 Mutations): a USIDNET Study.
T-box transcription factor TBX1, targeted by microRNA-6727-5p, inhibits cell growth and enhances cisplatin chemosensitivity of cervical cancer cells through AKT and MAPK pathways.
Title: T-box transcription factor TBX1, targeted by microRNA-6727-5p, inhibits cell growth and enhances cisplatin chemosensitivity of cervical cancer cells through AKT and MAPK pathways.

Submit: New GeneRIF Correction See all GeneRIFs (61)

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

Associated conditions

Description	Tests
Conotruncal heart malformations MedGen: C1857586 OMIM: 217095 GeneReviews: Not available	Compare labs
DiGeorge syndrome MedGen: C0012236 OMIM: 188400 GeneReviews: 22q11.2 Deletion Syndrome	Compare labs
Tetralogy of Fallot MedGen: C0039685 OMIM: 187500 GeneReviews: Not available	Compare labs
Velocardiofacial syndrome MedGen: C0220704 OMIM: 192430 GeneReviews: 22q11.2 Deletion Syndrome	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2024-06-11) ClinGen Genome Curation Page Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated 2024-06-11) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS of DNA methylation variation within imprinting control regions suggests parent-of-origin association. 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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
NOT enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein dimerization activity	TAS Traceable Author Statement more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in anterior/posterior pattern specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in aorta morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in artery morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in blood vessel development	ISS Inferred from Sequence or Structural Similarity more info
involved_in blood vessel morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell fate specification	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell fate specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to fibroblast growth factor stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to retinoic acid	ISS Inferred from Sequence or Structural Similarity more info
involved_in cochlea morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in coronary artery morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in determination of left/right symmetry	ISS Inferred from Sequence or Structural Similarity more info
involved_in ear morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic cranial skeleton morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic viscerocranium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in enamel mineralization	ISS Inferred from Sequence or Structural Similarity more info
involved_in epithelial cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in face morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in heart development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in inner ear morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in lymph vessel development	ISS Inferred from Sequence or Structural Similarity more info
involved_in mesenchymal cell apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in mesoderm development	ISS Inferred from Sequence or Structural Similarity more info
involved_in middle ear morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in muscle cell fate commitment	ISS Inferred from Sequence or Structural Similarity more info
involved_in muscle organ development	ISS Inferred from Sequence or Structural Similarity more info
involved_in muscle organ morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in muscle tissue morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of mesenchymal cell apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in neural crest cell migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in odontogenesis of dentin-containing tooth	ISS Inferred from Sequence or Structural Similarity more info
involved_in outer ear morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in outflow tract morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in outflow tract septum morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in parathyroid gland development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in pattern specification process	ISS Inferred from Sequence or Structural Similarity more info
involved_in pharyngeal system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of MAPK cascade	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of epithelial cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of mesenchymal cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of tongue muscle cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of animal organ morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in retinoic acid receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in semicircular canal morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in sensory perception of sound	ISS Inferred from Sequence or Structural Similarity more info
involved_in social behavior	ISS Inferred from Sequence or Structural Similarity more info
involved_in soft palate development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in somatic stem cell population maintenance	ISS Inferred from Sequence or Structural Similarity more info
involved_in thymus development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in thyroid gland development	ISS Inferred from Sequence or Structural Similarity more info
involved_in tongue morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in vagus nerve morphogenesis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	ISA Inferred from Sequence Alignment more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: T-box transcription factor TBX1

Names: T-box 1 transcription factor C; Testis-specific T-box protein; brachyury

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_009229.1 RefSeqGene

Range

5001..31891

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_226

mRNA and Protein(s)

NM_001379200.1 → NP_001366129.1 T-box transcription factor TBX1 isoform D

Status: REVIEWED

Source sequence(s)

AC000091

Consensus CDS

CCDS93119.1

UniProtKB/TrEMBL

A0A3B3IS18

Related

ENSP00000497003.1, ENST00000649276.2

Conserved Domains (1) summary

cd20187
Location:118 → 306

T-box_TBX1_10-like; DNA-binding domain of T-box transcription factor 1 and 10, and related T-box proteifactors
NM_005992.1 → NP_005983.1 T-box transcription factor TBX1 isoform B

See identical proteins and their annotated locations for NP_005983.1

Status: REVIEWED

Description

Transcript Variant: This variant (B) contains an alternate exon 9 and an additional exon 10 compared to variant C. It encodes an isoform (B) with the same N-terminal 336 aa, but an unique C-terminus with respect to isoforms A and C.

Source sequence(s)

AF012131

Consensus CDS

CCDS13765.1

UniProtKB/TrEMBL

Q152R5

Related

ENSP00000352483.3, ENST00000359500.7

Conserved Domains (1) summary

pfam00907
Location:112 → 297

T-box; T-box
NM_080646.2 → NP_542377.1 T-box transcription factor TBX1 isoform A

See identical proteins and their annotated locations for NP_542377.1

Status: REVIEWED

Description

Transcript Variant: This variant (A) contains an alternate exon 9 compared to variant C, resulting in an isoform (A) with the same N-terminal 336 aa, but an unique C-terminus with respect to isoforms B and C.

Source sequence(s)

AF012130

Consensus CDS

CCDS13766.1

UniProtKB/Swiss-Prot

C6G493, C6G494, O43435, O43436, Q96RJ2

Related

ENSP00000331176.7, ENST00000329705.11

Conserved Domains (1) summary

cd20187
Location:109 → 297

T-box_TBX1_10-like; DNA-binding domain of T-box transcription factor 1 and 10, and related T-box proteifactors
NM_080647.1 → NP_542378.1 T-box transcription factor TBX1 isoform C

See identical proteins and their annotated locations for NP_542378.1

Status: REVIEWED

Description

Transcript Variant: This variant (C) encodes the longest isoform (C) with the same N-terminal 336 aa, but an unique C-terminus with respect to isoforms A and B.

Source sequence(s)

AF373867

Consensus CDS

CCDS13767.1

UniProtKB/TrEMBL

D9ZGG0

Related

ENSP00000331791.4, ENST00000332710.8

Conserved Domains (1) summary

cd00182
Location:109 → 299

TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...

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_000022.11 Reference GRCh38.p14 Primary Assembly

Range

19756703..19783593

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006724312.3 → XP_006724375.1 T-box transcription factor TBX1 isoform X2

See identical proteins and their annotated locations for XP_006724375.1

UniProtKB/TrEMBL

D9ZGG0

Conserved Domains (1) summary

cd00182
Location:109 → 299

TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...
XM_017028926.2 → XP_016884415.1 T-box transcription factor TBX1 isoform X2

UniProtKB/TrEMBL

D9ZGG0

Conserved Domains (1) summary

cd00182
Location:109 → 299

TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...
XM_017028927.2 → XP_016884416.2 T-box transcription factor TBX1 isoform X1