TBXT (T-box transcription factor T)

Gene

• Entrez ID: 6862
• Gene name: T-box transcription factor T
• Gene symbol: TBXT
• Synonyms (NCBI Gene): SAVA, T, TFT
• Chromosome: 6
• Chromosome location: 6q27
• Summary: The protein encoded by this gene is an embryonic nuclear transcription factor that binds to a specific DNA element, the palindromic T-site. It binds through a region in its N-terminus, called the T-box, and effects transcription of genes required for meso

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs3127334	G>A,C	Risk-factor	Intron variant
rs587777303	T>C	Pathogenic	Missense variant, coding sequence variant

Transcription factors

Transcription factor	Regulation	Reference
POU5F1	Repression	17068183

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	ISS
GO:0000785	Component	Chromatin	IBA
GO:0000785	Component	Chromatin	IDA	21632880
GO:0000785	Component	Chromatin	ISA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA	21632880
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IDA	21632880
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001707	Process	Mesoderm formation	IBA
GO:0001708	Process	Cell fate specification	IBA
GO:0001756	Process	Somitogenesis	IBA
GO:0003007	Process	Heart morphogenesis	IBA
GO:0003007	Process	Heart morphogenesis	IDA	21632880
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0003700	Function	DNA-binding transcription factor activity	NAS	8963900
GO:0003714	Function	Transcription corepressor activity	ISS
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	22611028, 24253444
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007165	Process	Signal transduction	NAS	8963900
GO:0007498	Process	Mesoderm development	TAS	8963900
GO:0008595	Process	Anterior/posterior axis specification, embryo	TAS	8963900
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	21632880
GO:0060379	Process	Cardiac muscle cell myoblast differentiation	IDA	21632880
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	IPI	22164283
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	ISS
GO:0090009	Process	Primitive streak formation	NAS	18593560
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IEA

Other IDs

• MIM: 601397
• HGNC: 11515
• e!Ensembl: ENSG00000164458

Protein

• UniProt ID: O15178
• Protein name: T-box transcription factor T (Brachyury protein) (Protein T)
• Protein function: Involved in the transcriptional regulation of genes required for mesoderm formation and differentiation. Binds to a palindromic T site 5'-TTCACACCTAGGTGTGAA-3' DNA sequence and activates gene transcription when bound to such a site. {ECO:0000250
• PDB: 5QRF, 5QRG, 5QRH, 5QRI, 5QRJ, 5QRK, 5QRL, 5QRM, 5QRN, 5QRO, 5QRP, 5QRQ, 5QRR, 5QRS, 5QRT, 5QRU, 5QRV, 5QRW, 5QRX, 5QRY, 5QRZ, 5QS0, 5QS1, 5QS2, 5QS3, 5QS4, 5QS5, 5QS6, 5QS7, 5QS8, 5QS9, 5QSA, 5QSB, 5QSC, 5QSD, 5QSE, 5QSF, 5QSG, 5QSH, 5QSI, 5QSJ, 5QSK, 5QSL, 5QT0, 6F58, 6F59, 6ZU8, 7HI8, 7HI9, 7ZK2, 7ZKF
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00907	T-box	44 → 219	T-box	Domain

• Tissue specificity: TISSUE SPECIFICITY: Detected in testis, but not in other, normal tissues. Detected in lung tumors (at protein level). {ECO:0000269|PubMed:22611028, ECO:0000269|PubMed:30237576}.
• Sequence:

  MSSPGTESAGKSLQYRVDHLLSAVENELQAGSEKGDPTERELRVGLEESELWLRFKELTN
  EMIVTKNGRRMFPVLKVNVSGLDPNAMYSFLLDFVAADNHRWKYVNGEWVPGGKPEPQAP
  SCVYIHPDSPNFGAHWMKAPVSFSKVKLTNKLNGGGQIMLNSLHKYEPRIHIVRVGGPQR
  MITSHCFPETQFIAVTAYQNEEITALKIKYNPFAKAFLDAKERSDHKEMMEEPGDSQQPG
  YSQWGWLLPGTSTLCPPANPHPQFGGALSLPSTHSCDRYPTLRSHRSSPYPSPYAHRNNS
  PTYSDNSPACLSMLQSHDNWSSLGMPAHPSMLPVSHNASPPTSSSQYPSLWSVSNGAVTP
  GSQAAAVSNGLGAQFFRGSPAHYTPLTHPVSAPSSSGSPLYEGAAAATDIVDSQYDAAAQ
  GRLIASWTPVSPPSM

• Sequence length: 435

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Sacral agenesis-abnormal ossification of the vertebral bodies-persistent notochordal canal syndrome	Pathogenic	rs587777303	RCV000114433	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ASTHMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHORDOMA	—	CTD, Orphanet CTD, Orphanet CTD, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly-thin corpus callosum-intellectual disability syndrome	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neural tube defect	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURAL TUBE DEFECT, FOLATE-SENSITIVE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURAL TUBE DEFECTS	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURAL TUBE DEFECTS X-LINKED	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neural tube defects, susceptibility to	Uncertain significance; risk factor	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SACRAL AGENESIS WITH VERTEBRAL ANOMALIES	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SACRAL AGENESIS, ABNORMAL OSSIFICATION OF VERTEBRAL BODIES, PERSISTENT NOTOCHORDAL CANAL SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TBXT-related disorder	Benign; Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acrania	Acrania	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Adenocarcinoma	Adenocarcinoma	BEFREE	22611028		★☆☆☆☆ Found in Text Mining only
AMELOGENESIS IMPERFECTA, HYPOPLASTIC/HYPOMATURATION, X-LINKED 1	Amelogenesis Imperfecta, X-Linked	BEFREE	29358858		★☆☆☆☆ Found in Text Mining only
Anencephaly	Anencephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anorectal atresia	Imperforate anus	GENOMICS_ENGLAND_DG	10204846		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	20977921		★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	22611028		★☆☆☆☆ Found in Text Mining only
Cervical spina bifida aperta	Cervical spina bifida aperta	Orphanet			★☆☆☆☆ Found in Text Mining only
Cervical spina bifida cystica	Cervical spina bifida cystica	Orphanet			★☆☆☆☆ Found in Text Mining only
Cervicothoracic spina bifida aperta	Cervicothoracic Spina Bifida	Orphanet			★☆☆☆☆ Found in Text Mining only
Cervicothoracic spina bifida cystica	Cervicothoracic Spina Bifida	Orphanet			★☆☆☆☆ Found in Text Mining only
Chordoma	Chordoma	LHGDN	18301055		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chordoma	Chordoma	GENOMICS_ENGLAND_DG	19801981, 23064415		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chordoma	Chordoma	ORPHANET_DG	19801981, 23064415		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chordoma	Chordoma	CTD_human_DG	19801981, 23064415		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chordoma	Chordoma	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chordoma	Chordoma	Pubtator	24232574, 24990759, 27248133, 27663388, 27901492, 34837714, 40323130	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chordoma	Chordoma	BEFREE	30664779		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Craniorachischisis	Craniorachischisis	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Diastematomyelia	Diastematomyelia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Exencephaly	Anencephaly	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
familial chordoma	Chordoma	GENOMICS_ENGLAND_DG	19801981, 23064415		★☆☆☆☆ Found in Text Mining only
Graves Disease	Graves Disease	BEFREE	29574428		★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Immune thrombocytopenic purpura	Immune Thrombocytopenic Purpura	BEFREE	26093269		★☆☆☆☆ Found in Text Mining only
Iniencephaly	Anencephaly	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Lipoma	Lipoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Lumbosacral spina bifida aperta	Lumbosacral Spina Bifida Aperta	Orphanet			★☆☆☆☆ Found in Text Mining only
Lumbosacral spina bifida cystica	Lumbosacral Spina Bifida Cystica	Orphanet			★☆☆☆☆ Found in Text Mining only
Meningomyelocele	Meningomyelocele	HPO_DG			★☆☆☆☆ Found in Text Mining only
Multiple lipomata	Multiple Lipomata	HPO_DG			★☆☆☆☆ Found in Text Mining only
Muscular Dystrophies, Limb-Girdle	Limb-Girdle Muscular Dystrophy	BEFREE	16948121		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	27580659, 28490401		★☆☆☆☆ Found in Text Mining only
Neural Tube Defects	Neural Tube Defect	LHGDN	11897834		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neural Tube Defects	Neural Tube Defect	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neurenteric Cyst	Neurenteric Cyst	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Sacral agenesis	Sacral Agenesis	GENOMICS_ENGLAND_DG	10204846		★☆☆☆☆ Found in Text Mining only
Sacral agenesis	Sacral Agenesis	HPO_DG			★☆☆☆☆ Found in Text Mining only
SACRAL AGENESIS WITH VERTEBRAL ANOMALIES	Sacral Agenesis With Vertebral Anomalies	GENOMICS_ENGLAND_DG	24253444		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SACRAL AGENESIS WITH VERTEBRAL ANOMALIES	Sacral Agenesis With Vertebral Anomalies	UNIPROT_DG	24253444		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SACRAL AGENESIS WITH VERTEBRAL ANOMALIES	Sacral Agenesis With Vertebral Anomalies	ORPHANET_DG	24253444		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SACRAL AGENESIS WITH VERTEBRAL ANOMALIES	Sacral Agenesis With Vertebral Anomalies	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sacral agenesis-abnormal ossification of the vertebral bodies-persistent notochordal canal syndrome	Sacral Agenesis-Abnormal Ossification Of The Vertebral Bodies-Persistent Notochordal Canal Syndrome	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spina bifida aperta of cervical spine	Spina Bifida	ORPHANET_DG	15449172		★☆☆☆☆ Found in Text Mining only
Spina Bifida Occulta	Spina bifida occulta	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spinal Cord Myelodysplasia	Spinal Cord Myelodysplasia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	BEFREE	22611028		★☆☆☆☆ Found in Text Mining only
Tethered Cord Syndrome	Primary Tethered cord syndrome	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Thoracolumbosacral spina bifida aperta	Thoracolumbosacral spina bifida aperta	Orphanet			★☆☆☆☆ Found in Text Mining only
Thoracolumbosacral spina bifida cystica	Thoracolumbosacral spina bifida cystica	Orphanet			★☆☆☆☆ Found in Text Mining only
Thyroid Diseases	Thyroid Diseases	BEFREE	31465286		★☆☆☆☆ Found in Text Mining only
Total spina bifida aperta	Spina Bifida Cystica	Orphanet			★☆☆☆☆ Found in Text Mining only
Total spina bifida cystica	Spina Bifida Cystica	Orphanet			★☆☆☆☆ Found in Text Mining only
Upper thoracic spina bifida aperta	Upper Thoracic Spina Bifida Aperta	Orphanet			★☆☆☆☆ Found in Text Mining only
Upper thoracic spina bifida cystica	Upper Thoracic Spina Bifida Cystica	Orphanet			★☆☆☆☆ Found in Text Mining only