TBX1

protein-coding

T-box transcription factor 1, the group of T-box transcription factors

Gene 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]

Previous symbols:
  • VCF

MANE transcript

NM_001379200.1

Inheritance

AD

ClinVar variants

P:57U:526B:350

Top phenotype

Conotruncal anomaly face syndrome; Tetralogy of Fallot

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr22:19,756,703-19,783,593

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~26.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

conotruncal heart malformationsDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0016581

Submitter: Ambry Genetics

conotruncal heart malformationsSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0016581

Submitter: Labcorp Genetics (formerly Invitae)

DiGeorge syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008564

Submitter: G2P

velocardiofacial syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0008644

Submitter: Ambry Genetics

22q11.2 deletion syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0018923

Submitter: Orphanet

DiGeorge syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0008564

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Conotruncal anomaly face syndrome; Tetralogy of FallotAD

Manifestation: Cardiovascular; Craniofacial; Neurologic

Intervention: Cardiovascular

Rationale: The conditions can include congenital cardiac anomalies, and awareness may allow early identification and management

Refs: 14585638; 16684884; 17273972; 17377518; 19948535; 20937753Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TBX1 variants in ClinVar

12 Conditions Cataloged
DiGeorge syndromeTotal: 801
Cardiovascular phenotypeTotal: 410
not providedTotal: 204
TBX1-related disorderTotal: 53
not specifiedTotal: 48
Velocardiofacial syndromeTotal: 32
Tetralogy of FallotTotal: 25
Conotruncal heart malformationsTotal: 21

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001379200.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
9
clinvar
318
clinvar
1
clinvar
328
missense
2
clinvar
6
clinvar
506
clinvar
29
clinvar
2
clinvar
545
nonsense
10
clinvar
4
clinvar
4
clinvar
18
start loss
0
frameshift
22
clinvar
5
clinvar
6
clinvar
33
splice donor/acceptor (+/-2bp)
3
clinvar
5
clinvar
1
clinvar
9
Total37205263473933

Highest pathogenic variant AF is 0.0000027212438

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001379200.1RefSeqNP_001366129.17MANE Select
ENST00000649276.2EnsemblENSP00000497003.17MANE Select
NM_005992.1RefSeqNP_005983.18Standard
NM_080646.2RefSeqNP_542377.18Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
tbx1Danio rerio

Structure: cardiac muscle cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Heart Development
  • Mesodermal Commitment Pathway
  • FTO Obesity Variant Mechanism

Biological Process

  • angiogenesis
  • blood vessel development
  • cell fate specification
  • neural crest cell migration
  • positive regulation of protein phosphorylation

Molecular Function

  • DNA-binding transcription factor activity, RNA polymerase II-specific
  • DNA-binding transcription factor activity
  • protein homodimerization activity
  • sequence-specific DNA binding

Cellular Component

  • nucleus

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000332710
Coding exons
8
Length
26891
Individuals with no LoFs
125734
Homozygous LoFs
0
Heterozygous LoFs
2
Defined
125736
p
0.00000795
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.7351892200.8600.00001243128
Missense (PolyPhen)85106.820.79571131
Synonymous-3.5513995.01.460.000005971022
Loss of Function3.07214.70.1367.77e-7190

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.00000880.0000088rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Probable transcriptional regulator involved in developmental processes. Is required for normal development of the pharyngeal arch arteries (By similarity). {ECO:0000250}.;
Disease
DISEASE: Note=Haploinsufficiency of the TBX1 gene is responsible for most of the physical malformations present in DiGeorge syndrome (DGS) and velocardiofacial syndrome (VCFS). DGS is characterized by the association of several malformations: hypoplastic thymus and parathyroid glands, congenital conotruncal cardiopathy, and a subtle but characteristic facial dysmorphology. VCFS is marked by the association of congenital conotruncal heart defects, cleft palate or velar insufficiency, facial dysmorpholgy and learning difficulties. It is now accepted that these two syndromes represent two forms of clinical expression of the same entity manifesting at different stages of life.; DISEASE: DiGeorge syndrome (DGS) [MIM:188400]: A congenital syndrome characterized by a wide spectrum of characteristics including parathyroid hypoplasia resulting in hypocalcemia, thymic hypoplasia resulting in T-cell immunodeficiency, defects in the outflow tract of the heart, and craniofacial anomalies. Disturbance of cervical neural crest migration into the derivatives of the pharyngeal arches and pouches can account for the phenotype. {ECO:0000269|PubMed:14585638}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Velocardiofacial syndrome (VCFS) [MIM:192430]: A syndrome characterized by abnormal pharyngeal arch development that results in defective development of the parathyroid glands, thymus, and conotruncal region of the heart. The phenotype is highly variable, with no single clinical feature present in every patient. Affected individuals may present with structural or functional palatal abnormalities, cardiac defects, unique facial characteristics, hypernasal speech, hypotonia, and defective thymic development associated with impaired immune function. In addition, affected individuals may present with learning disabilities, overt developmental delay, and psychiatric disorders. {ECO:0000269|PubMed:14585638, ECO:0000269|PubMed:17273972}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Conotruncal heart malformations (CTHM) [MIM:217095]: A group of congenital heart defects involving the outflow tracts. Examples include truncus arteriosus communis, double-outlet right ventricle and transposition of great arteries. Truncus arteriosus communis is characterized by a single outflow tract instead of a separate aorta and pulmonary artery. In transposition of the great arteries, the aorta arises from the right ventricle and the pulmonary artery from the left ventricle. In double outlet of the right ventricle, both the pulmonary artery and aorta arise from the right ventricle. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.969

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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