TBX3

gene
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Also known as TBX3-ISOXHL

Summary

TBX3 (T-box transcription factor 3, HGNC:11602) is a protein-coding gene on chromosome 12q24.21, encoding T-box transcription factor TBX3 (O15119). Transcriptional repressor involved in developmental processes. It is haploinsufficient (ClinGen: sufficient evidence).

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 protein is a transcriptional repressor and is thought to play a role in the anterior/posterior axis of the tetrapod forelimb. Mutations in this gene cause ulnar-mammary syndrome, affecting limb, apocrine gland, tooth, hair, and genital development. Alternative splicing of this gene results in three transcript variants encoding different isoforms; however, the full length nature of one variant has not been determined.

Source: NCBI Gene 6926 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): ulnar-mammary syndrome (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 137
  • Clinical variants (ClinVar): 670 total — 22 pathogenic, 14 likely-pathogenic
  • Phenotypes (HPO): 73
  • Cancer driver (intOGen): activating (oncogene-like) across 3 cancer types
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • Transcription factor: yes — 29 downstream targets (CollecTRI)
  • MANE Select transcript: NM_005996

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11602
Approved symbolTBX3
NameT-box transcription factor 3
Location12q24.21
Locus typegene with protein product
StatusApproved
AliasesTBX3-ISO, XHL
Ensembl geneENSG00000135111
Ensembl biotypeprotein_coding
OMIM601621
Entrez6926

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 retained_intron

ENST00000257566, ENST00000349155, ENST00000548503, ENST00000552054

RefSeq mRNA: 2 — MANE Select: NM_005996 NM_005996, NM_016569

CCDS: CCDS9175, CCDS9176

Canonical transcript exons

ENST00000349155 — 7 exons

ExonStartEnd
ENSE00000755589114680879114681146
ENSE00000918022114674165114674835
ENSE00000918024114677580114677656
ENSE00001201415114676313114676470
ENSE00001201439114682812114684175
ENSE00002408640114679505114679651
ENSE00002412265114670255114672302

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 99.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.1712 / max 586.2111, expressed in 1390 samples.

FANTOM5 promoters (15 alternative TSS)

Promoter IDTPM avgSamples expressed
13340912.92971366
1334161.1317307
1334100.8289377
1334150.4351160
1334080.4322182
2069110.3950192
1334070.3846168
2069100.3739208
2069090.2850142
1334050.227695

Top tissues by expression

276 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right adrenal gland cortexUBERON:003582799.13gold quality
right adrenal glandUBERON:000123399.04gold quality
adrenal cortexUBERON:000123598.91gold quality
adrenal tissueUBERON:001830398.88gold quality
left adrenal gland cortexUBERON:003582598.76gold quality
left adrenal glandUBERON:000123498.73gold quality
adrenal glandUBERON:000236998.29gold quality
urethraUBERON:000005797.96gold quality
stromal cell of endometriumCL:000225597.91gold quality
seminal vesicleUBERON:000099897.73gold quality
prostate glandUBERON:000236797.50gold quality
right lobe of thyroid glandUBERON:000111996.99gold quality
right lungUBERON:000216796.23gold quality
left lobe of thyroid glandUBERON:000112095.95gold quality
thyroid glandUBERON:000204695.85gold quality
placentaUBERON:000198795.04gold quality
jejunal mucosaUBERON:000039994.50gold quality
corpus epididymisUBERON:000435993.98gold quality
duodenumUBERON:000211493.69gold quality
tendon of biceps brachiiUBERON:000818893.68gold quality
left ovaryUBERON:000211993.32gold quality
right ovaryUBERON:000211893.05gold quality
penisUBERON:000098993.01gold quality
endometriumUBERON:000129592.97gold quality
vaginaUBERON:000099692.96gold quality
endocervixUBERON:000045892.95gold quality
urinary bladderUBERON:000125592.90gold quality
deciduaUBERON:000245092.79gold quality
nippleUBERON:000203092.78gold quality
right lobe of liverUBERON:000111492.18gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-6701yes38.40
E-MTAB-5061yes11.11
E-ANND-3no0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

29 targets.

TargetRegulation
BGLAPRepression
BMP4
CDH1Repression
CDH17
CDKN1ARepression
CDKN2ARepression
CSF1
FRZBRepression
GATA6
GJA1
GJA5Repression
GJC1
GJC3
HCN4
HNF1BRepression
IBSPRepression
JDP2Unknown
MIR137
NPPARepression
ONECUT1Repression
PTEN
RUNX2Repression
SHISA3Repression
SP7Repression
SPP1
TBX2Repression
TBX3
TNFRSF11A
TP53Unknown

JASPAR motifs

MotifNameFamily
MA1566.1TBX3TBX2-related factors
MA1566.2TBX3TBX2-related factors
MA1566.3TBX3TBX2-related factors

JASPAR matrix evidence (PMIDs): PMID:18829543

Upstream regulators (CollecTRI, top): AP1, CTNNB1, JUNB, MYC, PRDM4, SIRT1, TBX2, TBX3, TCF3, TP53

miRNA regulators (miRDB)

146 targeting TBX3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-428299.9975.366408
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-433-3P99.9869.371203
HSA-MIR-570-3P99.9672.414910
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • Mutations in Tbx3 are responsible for ulnar-mammary syndrome (UMS), an autosomal dominant disorder affecting limb, tooth, hair, apocrine gland and genital development. (PMID:11689487)
  • identification of a variant T-site as the essential TBX2/TBX3-binding element in the human p14(ARF) promoter (PMID:12000749)
  • Results demonstrate the structural consequences of T-box domain protein 3 point mutations observed in Ulnar-Mammary syndrome and Holt-Oram syndrome patients. (PMID:12005433)
  • The results are consistent with the previous finding that UMS is caused by haploinsufficiency of TBX3. (PMID:12116211)
  • Overexpression of TBX3 is associated with breast cancer (PMID:15289316)
  • increased expression of truncated cSHMT, Tbx3 and utrophin in plasma samples obtained from patients at early stages of ovarian cancer and breast cancer (PMID:16049973)
  • A literature review of TBX3 combined with a novel TBX3 mutation in a family with ulnar-mammary syndrome finds an association in mutations that disrupt the TBX3 DNA-binding domain and a higher frequency of severe upper limb malformations and teeth defects. (PMID:16530712)
  • Required for heart and limb formation, and is mutated in ulnar-mammary syndrome. (PMID:16556916)
  • Data show that Tbx3 plays an important role in osteogenic differentiation and proliferation of human mesenchymal stem cells derived from adipose tissue. (PMID:16955224)
  • Nyx2-5 confines recombinant hTBX3 expression to the sinoatrial node & sinus horns in mice. Tbx3 suppresses chamber differentiation–another mechanism by which the Tbx3-positive sinoatrial node is shielded from differentiating into atrial myocardium. (PMID:17234970)
  • TBX3 repression to its targets is dependent on HDAC activity. TBX3 may serve as a biomarker for breast cancer. (PMID:18245468)
  • Fluorescence in situ hybridization did not show major deletions or duplications at chromosome 22q11 as well as the TBX5/TBX3 region at 12q24.1. (PMID:18726671)
  • Tbx2 and Tbx3 may play a dual role during the radial to vertical growth phase transition by both inhibiting senescence via repression of p21(CIP1) expression, and enhancing melanoma invasiveness by decreasing E-cadherin levels. (PMID:18829543)
  • TBX3 mRNA expression was significantly higher in metastatic breast cancer than in non-metastatic tumors. (PMID:19218121)
  • The mRNA and protein expressions of Tbx3 are markedly upregulated in breast cancer cell lines and tissue samples. (PMID:19403417)
  • Studies identified Tbx3 as a key regulator of the SAN phenotype. (PMID:20133910)
  • Tbx3 expression was found to be suppressed by AFLL when the expression of tumor suppressor genes p14 and p53 were activated (PMID:20702496)
  • pathway that up-regulates TBX3 expression and provides additional evidence that increased levels of TBX3 contribute to metastasis. (PMID:20942798)
  • Data show that estrogen signaling expands the pool of functional breast cancer stem-like cells through a paracrine FGF/FGFR/Tbx3 signaling pathway. (PMID:21098263)
  • Study indicate mutation of TBX3 gene in the family. (PMID:21199695)
  • In situ hybridization reveals Tbx3 and Sox4 to co-localize extensively in the embryo including the atrioventricular and outflow tract cushion mesenchyme and a small area of interventricular myocardium. (PMID:21538160)
  • identify a Sp1 element and two CCAAT boxes to be essential for basal TBX3 promoter activity (PMID:21784138)
  • Tbx3 overexpression promotes squamous carcinoma cell survival displaying an epithelial-mesenchymal transition phenotype. (PMID:22154512)
  • TBX3 CPG island methylation predicts progression in bladder cancer. (PMID:22284968)
  • TBX3 promotes human embryonic stem cell proliferation and neuroepithelial differentiation in a differentiation stage-dependent manner. (PMID:22865636)
  • Data show that Tbx3 is up-regulated in tissue samples of head and neck squamous cell cancer (HNSCC) patients and that Tbx3 represses PTEN transcription. (PMID:23082988)
  • the sequence variants within the TBX3 gene promoter did not contribute to VSD etiology. (PMID:23116943)
  • Oncogenic B-RAF(V600E) signaling induces the T-Box3 transcriptional repressor to repress E-cadherin and enhance melanoma cell invasion. (PMID:23190890)
  • TBX3 gene polymorphism is associated in the development of colorectal cancers. (PMID:23266556)
  • Coimmunoprecipitations and immunofluorescence analyses confirmed the L2-TBX2 interaction and revealed that human papillomavirus 16 L2 also interacts with human TBX3, another member of the T-box family. (PMID:23388722)
  • TBX3 exon 2 mutation is rare in most human tumors (PMID:23656610)
  • TBX3 plays a pivotal role in mediating the antiproliferative and promigratory role of TGF-beta1 in breast epithelial cells and skin keratinocytes. (PMID:24025717)
  • TBX3 may play an important role as a reciprocal switch between substrate dependent cell proliferation and tumour invasion. (PMID:24098938)
  • Polymorphisms in several genes involved in the Wnt signaling pathway were associated with hepatic fibrosis or inflammation risk in HCV-infected males. (PMID:24386373)
  • The pleiotropic effects of TBX3 mutations in humans and mice likely result from disrupting at least two molecular functions of this protein: transcriptional regulation and pre-mRNA splicing. (PMID:24675841)
  • An enhancement in TBX3 protein expression both in glomerular and tubular regions. (PMID:25158279)
  • Paracrine WNT signaling is stimulated by estrogen and progesterone, while autocrine WNT signaling is induced by the embryonic T-box transcription factor TBX3 (PMID:25350852)
  • Data show that the down-regulation of T-box transcription factor TBX2 by transforming growth factor beta I (TGF-beta1) is mediated by T-box transcription factor TBX3. (PMID:25371204)
  • this new molecular-grade based on the combination of TBX2 and TBX3 methylation is an excellent marker for predicting progression to muscle-invasive bladder cancer in patients with primary pTaG1/2 bladder cancer. (PMID:25394776)
  • TBX3 gene variants may contribute to indirect inguinal hernia as a rare risk factor by reducing TBX3 levels (PMID:25455105)

Cross-species orthologs

14 orthologs

OrganismSymbolGene ID
danio_reriotbx3aENSDARG00000002216
mus_musculusTbx3ENSMUSG00000018604
rattus_norvegicusTbx3ENSRNOG00000008706
drosophila_melanogasterH15FBGN0016660
drosophila_melanogastermidFBGN0261963
drosophila_melanogasterocmFBGN0266083
caenorhabditis_elegansWBGENE00003106
caenorhabditis_elegansWBGENE00004750
caenorhabditis_elegansWBGENE00006545
caenorhabditis_elegansWBGENE00006546
caenorhabditis_elegansWBGENE00006556
caenorhabditis_elegansWBGENE00006557
caenorhabditis_elegansWBGENE00006559
caenorhabditis_elegansWBGENE00044798

Paralogs (16): TBX21 (ENSG00000073861), TBX5 (ENSG00000089225), TBX15 (ENSG00000092607), TBX18 (ENSG00000112837), TBX2 (ENSG00000121068), TBX4 (ENSG00000121075), TBX22 (ENSG00000122145), TBR1 (ENSG00000136535), TBX19 (ENSG00000143178), TBX6 (ENSG00000149922), EOMES (ENSG00000163508), TBXT (ENSG00000164458), TBX20 (ENSG00000164532), TBX10 (ENSG00000167800), MGA (ENSG00000174197), TBX1 (ENSG00000184058)

Protein

Protein identifiers

T-box transcription factor TBX3O15119 (reviewed: O15119)

All UniProt accessions (1): O15119

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional repressor involved in developmental processes. Binds to the palindromic T site 5’-TTCACACCTAGGTGTGAA-3’ DNA sequence, or a half-site, which are present in the regulatory region of several genes. Probably plays a role in limb pattern formation. Required for mammary placode induction, and maintenance of the mammary buds during development. Involved in branching morphogenesis in both developing lungs and adult mammary glands, via negative modulation of target genes; acting redundantly with TBX2. Required, together with TBX2, to maintain cell proliferation in the embryonic lung mesenchyme; perhaps acting downstream of SHH, BMP and TGFbeta signaling. Involved in modulating early inner ear development, acting independently of, and also redundantly with, TBX2 in different subregions of the developing ear. Acts as a negative regulator of PML function in cellular senescence.

Subunit / interactions. Interacts with PML (isoform PML-4).

Subcellular location. Nucleus.

Tissue specificity. Widely expressed.

Disease relevance. Ulnar-mammary syndrome (UMS) [MIM:181450] Characterized by ulnar ray defects, obesity, hypogenitalism, delayed puberty, hypoplasia of nipples and apocrine glands. The disease is caused by variants affecting the gene represented in this entry.

Miscellaneous. Contains an interrupted T-box domain. Contains an interrupted T-box domain. May be produced by joining exon 1 to exon 7 thereby eliminating the T-box.

Isoforms (4)

UniProt IDNamesCanonical?
O15119-1IIyes
O15119-2I
O15119-3III
O15119-4IV

RefSeq proteins (2): NP_005987, NP_057653 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001699TF_T-boxFamily
IPR008967p53-like_TF_DNA-bd_sfHomologous_superfamily
IPR018186TF_T-box_CSConserved_site
IPR022582TBX2/3_TADDomain
IPR036960T-box_sfHomologous_superfamily
IPR046360T-box_DNA-bdDomain
IPR048387TBX2_3_RDDomain

Pfam: PF00907, PF12598, PF20627

UniProt features (43 total): strand 9, modified residue 8, helix 6, compositionally biased region 4, sequence conflict 4, region of interest 4, splice variant 3, DNA-binding region 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
1H6FX-RAY DIFFRACTION1.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O15119-F156.550.23

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (8): 371, 432, 438, 456, 707, 738, 740, 742

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-9856649Transcriptional and post-translational regulation of MITF-M expression and activity
R-HSA-1266738Developmental Biology
R-HSA-9730414MITF-M-regulated melanocyte development

MSigDB gene sets: 576 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, GOBP_CARDIAC_CHAMBER_DEVELOPMENT, GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, E2F_Q4_01, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_MAMMARY_GLAND_MORPHOGENESIS, GOBP_MUSCLE_TISSUE_DEVELOPMENT, BENPORATH_ES_WITH_H3K27ME3, GOBP_CARDIAC_SEPTUM_DEVELOPMENT, GOBP_AXIS_SPECIFICATION, GOBP_GLAND_MORPHOGENESIS, GOBP_VENTRICULAR_SEPTUM_MORPHOGENESIS, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_CARDIAC_CHAMBER_MORPHOGENESIS

GO Biological Process (62): negative regulation of transcription by RNA polymerase II (GO:0000122), skeletal system development (GO:0001501), blood vessel development (GO:0001568), in utero embryonic development (GO:0001701), cell fate specification (GO:0001708), heart looping (GO:0001947), outflow tract morphogenesis (GO:0003151), atrioventricular bundle cell differentiation (GO:0003167), endocardial cushion formation (GO:0003272), DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of cell population proliferation (GO:0008284), anterior/posterior axis specification, embryo (GO:0008595), animal organ morphogenesis (GO:0009887), specification of animal organ position (GO:0010159), stem cell population maintenance (GO:0019827), limbic system development (GO:0021761), male genitalia development (GO:0030539), female genitalia development (GO:0030540), negative regulation of epithelial cell differentiation (GO:0030857), mammary gland development (GO:0030879), regulation of protein stability (GO:0031647), luteinizing hormone secretion (GO:0032275), embryonic forelimb morphogenesis (GO:0035115), embryonic hindlimb morphogenesis (GO:0035116), forelimb morphogenesis (GO:0035136), atrioventricular canal development (GO:0036302), embryonic digit morphogenesis (GO:0042733), negative regulation of apoptotic process (GO:0043066), negative regulation of myoblast differentiation (GO:0045662), positive regulation of cell cycle (GO:0045787), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of transcription by RNA polymerase II (GO:0045944), follicle-stimulating hormone secretion (GO:0046884), mesoderm morphogenesis (GO:0048332), semicircular canal morphogenesis (GO:0048752), smooth muscle cell differentiation (GO:0051145), roof of mouth development (GO:0060021), cardiac epithelial to mesenchymal transition (GO:0060317), ventricular septum morphogenesis (GO:0060412)

GO Molecular Function (10): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), sequence-specific DNA binding (GO:0043565), RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (4): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cilium (GO:0005929)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
MITF-M-regulated melanocyte development1
Developmental Biology1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding4
regulation of transcription by RNA polymerase II2
transcription by RNA polymerase II2
system development2
anatomical structure morphogenesis2
regulation of DNA-templated transcription2
genitalia development2
DNA-binding transcription factor activity, RNA polymerase II-specific2
cellular anatomical structure2
negative regulation of DNA-templated transcription1
vasculature development1
anatomical structure development1
chordate embryonic development1
cell fate commitment1
cellular developmental process1
embryonic heart tube morphogenesis1
determination of heart left/right asymmetry1
heart morphogenesis1
bundle of His development1
His-Purkinje system cell differentiation1
endocardial cushion morphogenesis1
anatomical structure formation involved in morphogenesis1
gene expression1
RNA biosynthetic process1
cell population proliferation1
regulation of cell population proliferation1
positive regulation of cellular process1
embryonic axis specification1
tripartite regional subdivision1
anterior/posterior axis specification1
animal organ development1
regionalization1
animal organ morphogenesis1
multicellular organismal process1
maintenance of cell number1
forebrain development1
male sex differentiation1
reproductive system development1
female sex differentiation1
epithelial cell differentiation1

Protein interactions and networks

STRING

2246 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TBX3POU5F1P31359890
TBX3NANOGQ9H9S0874
TBX3KLF4P78338874
TBX3SOX2P48431871
TBX3RBM19Q9Y4C8870
TBX3NKX2-5P52952867
TBX3ESRRBO95718822
TBX3SALL4Q9UJQ4819
TBX3TBX5Q99593802
TBX3GATA4P43694753
TBX3RBM39Q14498745
TBX3GJA5P36382722
TBX3SHOX2O60902716
TBX3HCN4Q9Y3Q4715
TBX3LIFP15018710

IntAct

40 interactions, top by confidence:

ABTypeScore
TLE5TBX3psi-mi:“MI:0915”(physical association)0.560
CA8TBX3psi-mi:“MI:0915”(physical association)0.560
TBX3TLE5psi-mi:“MI:0915”(physical association)0.560
TBX3CA8psi-mi:“MI:0915”(physical association)0.560
TBX3PRR20Dpsi-mi:“MI:0915”(physical association)0.560
TBX3PFDN5psi-mi:“MI:0915”(physical association)0.560
TBX3psi-mi:“MI:0915”(physical association)0.560
TBX3CSF3psi-mi:“MI:0915”(physical association)0.560
TBX3UFSP1psi-mi:“MI:0915”(physical association)0.560
Dlg4TBX3psi-mi:“MI:0407”(direct interaction)0.440
TBX3ANXA5psi-mi:“MI:0915”(physical association)0.400
PB2psi-mi:“MI:0914”(association)0.350
SOX2CBX4psi-mi:“MI:0914”(association)0.350
HNRNPLLTBX3psi-mi:“MI:0914”(association)0.350
AFG3L2TBX3psi-mi:“MI:0914”(association)0.350
AKT1TBX3psi-mi:“MI:2364”(proximity)0.270
BRAFTBX3psi-mi:“MI:2364”(proximity)0.270
SMAD4TBX3psi-mi:“MI:2364”(proximity)0.270
SPOPTBX3psi-mi:“MI:2364”(proximity)0.270
TBX3SPOPpsi-mi:“MI:2364”(proximity)0.270
TBX3PTPN11psi-mi:“MI:2364”(proximity)0.270
TBX3PRR20Dpsi-mi:“MI:0915”(physical association)0.000

BioGRID (93): TBX3 (Two-hybrid), TBX3 (Two-hybrid), TBX3 (Affinity Capture-Western), PLEKHF2 (Two-hybrid), TBX3 (Affinity Capture-MS), TBX3 (Affinity Capture-MS), TBX3 (Affinity Capture-MS), TBX3 (Affinity Capture-MS), TBX3 (Affinity Capture-MS), TBX3 (Affinity Capture-MS), TBX3 (Affinity Capture-MS), TBX3 (Affinity Capture-MS), TBX3 (Affinity Capture-MS), TBX3 (Affinity Capture-MS), TBX3 (Affinity Capture-MS)

ESM2 similar proteins: A4QNP7, A8TSS9, O09100, O15119, O70306, O95935, P55198, P70062, P70063, P70064, P70324, P70325, P81068, Q0VGT2, Q13207, Q25113, Q2I327, Q2MJB4, Q32NI9, Q3SA48, Q3SA49, Q4AE28, Q5UU75, Q60707, Q6GL68, Q6PCL0, Q6YHU8, Q76L87, Q7TST9, Q7ZTU9, Q800Q5, Q861Q9, Q863A2, Q86V15, Q8AX98, Q8AXX2, Q8IVH2, Q8UW76, Q90964, Q90ZB6

Diamond homologs: A1YF56, A2AWL7, D3ZJK7, E1BEA8, O01409, O13161, O15119, O15178, O17212, O43435, O54839, O60806, O70306, O73718, O75333, O95935, O95936, O95947, P20293, P24781, P55965, P56158, P57082, P70323, P70324, P70325, P70326, P70327, P79742, P79777, P79778, P79779, P79944, P80492, P87377, P90971, Q07998, Q13207, Q16650, Q17134

SIGNOR signaling

5 interactions.

AEffectBMechanism
AKT3“up-regulates activity”TBX3phosphorylation
TBX3“down-regulates quantity by repression”CDH1“transcriptional regulation”
AKT“up-regulates activity”TBX3phosphorylation
TBX3“down-regulates quantity by repression”CDKN1A“transcriptional regulation”
TBX3“down-regulates quantity by repression”CDKN2A“transcriptional regulation”

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 3 cancer types — BRCA, COADREAD, DLBCLNOS.

Clinical variants and AI predictions

ClinVar

670 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic22
Likely pathogenic14
Uncertain significance348
Likely benign209
Benign42

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1070549NM_005996.4(TBX3):c.1070_1080del (p.Ala357fs)Pathogenic
1527734GRCh37/hg19 12q24.21(chr12:114995645-115376925)Pathogenic
1706466NM_005996.4(TBX3):c.1587dup (p.Ser530fs)Pathogenic
2131719NM_005996.4(TBX3):c.704dup (p.Arg236fs)Pathogenic
2445206NM_005996.4(TBX3):c.1287_1294dup (p.Glu432fs)Pathogenic
2502305NM_005996.4(TBX3):c.868C>T (p.Arg290Ter)Pathogenic
2635163NM_005996.4(TBX3):c.1141G>T (p.Glu381Ter)Pathogenic
2709083NM_005996.4(TBX3):c.438dup (p.Ala147fs)Pathogenic
31909NM_005996.4(TBX3):c.991C>T (p.Gln331Ter)Pathogenic
3356423NM_005996.4(TBX3):c.657+1G>APathogenic
3653115NM_005996.4(TBX3):c.510G>A (p.Trp170Ter)Pathogenic
3669887NM_005996.4(TBX3):c.1038dup (p.Asp347fs)Pathogenic
4071573NM_005996.4(TBX3):c.389+1G>APathogenic
417720NM_005996.4(TBX3):c.1423C>T (p.Gln475Ter)Pathogenic
4279429GRCh37/hg19 12q24.21(chr12:114686840-115741264)x1Pathogenic
4538442NM_005996.4(TBX3):c.1008dup (p.Ala337fs)Pathogenic
4720369NM_005996.4(TBX3):c.48dup (p.Tyr17fs)Pathogenic
591004NM_005996.4(TBX3):c.1920_1921dup (p.Pro641fs)Pathogenic
7987NM_005996.4(TBX3):c.227del (p.Ile76fs)Pathogenic
7988NM_005996.4(TBX3):c.657+1G>CPathogenic
7989NM_005996.4(TBX3):c.817A>T (p.Lys273Ter)Pathogenic
7990NM_005996.4(TBX3):c.88dup (p.Met30fs)Pathogenic
1709213NM_005996.4(TBX3):c.961dup (p.Ser321fs)Likely pathogenic
2444419NM_005996.4(TBX3):c.1170dup (p.Ala391fs)Likely pathogenic
3061897NM_005996.4(TBX3):c.400C>G (p.Pro134Ala)Likely pathogenic
3064137NM_005996.4(TBX3):c.1921_1922insG (p.Pro641fs)Likely pathogenic
3065230NM_005996.4(TBX3):c.945del (p.Ser316fs)Likely pathogenic
3075717NM_005996.4(TBX3):c.309dup (p.Lys104fs)Likely pathogenic
3353475NM_005996.4(TBX3):c.390-1G>ALikely pathogenic
3382904NM_005996.4(TBX3):c.389+1G>TLikely pathogenic

SpliceAI

1127 predictions. Top by Δscore:

VariantEffectΔscore
12:114672298:AGGCC:Aacceptor_gain1.0000
12:114672299:GGCC:Gacceptor_gain1.0000
12:114672300:GCC:Gacceptor_gain1.0000
12:114672301:CC:Cacceptor_gain1.0000
12:114672301:CCC:Cacceptor_gain1.0000
12:114672302:CC:Cacceptor_gain1.0000
12:114672302:CCTG:Cacceptor_loss1.0000
12:114672303:C:CCacceptor_gain1.0000
12:114672303:CT:Cacceptor_loss1.0000
12:114672308:G:Cacceptor_gain1.0000
12:114672308:G:GCacceptor_gain1.0000
12:114676471:C:CCacceptor_gain1.0000
12:114677575:CTCA:Cdonor_loss1.0000
12:114677576:TCA:Tdonor_loss1.0000
12:114677577:CA:Cdonor_loss1.0000
12:114677578:ACC:Adonor_loss1.0000
12:114677654:TAT:Tacceptor_gain1.0000
12:114677654:TATC:Tacceptor_loss1.0000
12:114677656:TC:Tacceptor_loss1.0000
12:114677657:C:CCacceptor_gain1.0000
12:114677657:C:CGacceptor_loss1.0000
12:114679500:TTTA:Tdonor_loss1.0000
12:114679502:TA:Tdonor_loss1.0000
12:114679504:CCT:Cdonor_loss1.0000
12:114679509:T:Cdonor_gain1.0000
12:114679647:ATAGT:Aacceptor_gain1.0000
12:114679648:TAGT:Tacceptor_gain1.0000
12:114679650:GT:Gacceptor_gain1.0000
12:114679650:GTCT:Gacceptor_loss1.0000
12:114679651:TCTG:Tacceptor_loss1.0000

AlphaMissense

4730 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:114677588:T:AR311S1.000
12:114677588:T:GR311S1.000
12:114677589:C:AR311I1.000
12:114677589:C:GR311T1.000
12:114677595:C:TG309D1.000
12:114677596:C:AG309C1.000
12:114677596:C:GG309R1.000
12:114677601:C:AG307V1.000
12:114677601:C:TG307E1.000
12:114677602:C:GG307R1.000
12:114677602:C:TG307R1.000
12:114677607:T:AD305V1.000
12:114677607:T:CD305G1.000
12:114677607:T:GD305A1.000
12:114677608:C:GD305H1.000
12:114677610:C:AR304L1.000
12:114677610:C:GR304P1.000
12:114677610:C:TR304Q1.000
12:114677611:G:AR304W1.000
12:114677611:G:CR304G1.000
12:114677612:G:CF303L1.000
12:114677612:G:TF303L1.000
12:114677613:A:CF303C1.000
12:114677613:A:GF303S1.000
12:114677614:A:CF303V1.000
12:114677614:A:GF303L1.000
12:114677614:A:TF303I1.000
12:114677616:C:AG302V1.000
12:114677616:C:TG302D1.000
12:114677617:C:AG302C1.000

dbSNP variants (sampled 300 via entrez): RS1000081459 (12:114680153 C>A,T), RS1000092646 (12:114672912 A>G), RS1000352746 (12:114684767 C>T), RS1000372007 (12:114683901 C>A,G,T), RS1000526693 (12:114673154 G>C), RS1000679028 (12:114679007 A>G), RS1000707471 (12:114684933 C>T), RS1000748022 (12:114678009 G>GCATA), RS1000785999 (12:114684967 G>A), RS1000820545 (12:114680154 G>A,C), RS1001196417 (12:114673652 C>T), RS1001217414 (12:114679281 A>G), RS1001248638 (12:114673404 G>T), RS1001251914 (12:114671217 A>C), RS1001348992 (12:114676253 T>A)

Disease associations

OMIM: gene MIM:601621 | disease phenotypes: MIM:181450, MIM:614823

GenCC curated gene-disease

DiseaseClassificationInheritance
ulnar-mammary syndromeDefinitiveAutosomal dominant
heart conduction diseaseLimitedAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
ulnar-mammary syndromeDefinitiveAD

Mondo (6): ulnar-mammary syndrome (MONDO:0008411), breast ductal adenocarcinoma (MONDO:0005590), eccrine porocarcinoma (MONDO:0006189), aortic valve disease 2 (MONDO:0013902), obesity disorder (MONDO:0011122), heart conduction disease (MONDO:0000992)

Orphanet (3): Ulnar-mammary syndrome (Orphanet:3138), Obesity due to melanocortin 4 receptor deficiency (Orphanet:71529), NON RARE IN EUROPE: Non rare obesity (Orphanet:521399)

HPO phenotypes

73 total (30 of 73 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000023Inguinal hernia
HP:0000028Cryptorchidism
HP:0000046Small scrotum
HP:0000049Shawl scrotum
HP:0000054Micropenis
HP:0000089Renal hypoplasia
HP:0000130Abnormality of the uterus
HP:0000144Decreased fertility
HP:0000668Hypodontia
HP:0000768Pectus carinatum
HP:0000813Bicornuate uterus
HP:0000823Delayed puberty
HP:0000882Hypoplastic scapulae
HP:0000889Abnormal clavicle morphology
HP:0000894Short clavicles
HP:0000912Sprengel anomaly
HP:0001162Postaxial hand polydactyly
HP:0001167Abnormal finger morphology
HP:0001231Abnormal fingernail morphology
HP:0001513Obesity
HP:0001601Laryngomalacia
HP:0001607Subglottic stenosis
HP:0001629Ventricular septal defect
HP:0001800Hypoplastic toenails
HP:0002021Pyloric stenosis
HP:0002023Anal atresia
HP:0002025Anal stenosis
HP:0002215Sparse axillary hair
HP:0002221Absent axillary hair

GWAS associations

137 associations (top):

StudyTraitp-value
GCST000396_6Diastolic blood pressure4.000000e-08
GCST000562_5PR interval3.000000e-17
GCST000919_6Serum prostate-specific antigen levels2.000000e-11
GCST001072_8Blood pressure8.000000e-07
GCST001074_2Blood pressure1.000000e-10
GCST001236_19Blood pressure4.000000e-06
GCST001489_1Percent mammographic density1.000000e-08
GCST001787_10Colorectal cancer4.000000e-07
GCST002456_6PR segment duration8.000000e-13
GCST002535_5PR interval7.000000e-07
GCST002630_14Systolic blood pressure2.000000e-07
GCST002829_18Urate levels in overweight individuals2.000000e-06
GCST003273_7Diastolic blood pressure8.000000e-10
GCST003542_103Night sleep phenotypes2.000000e-06
GCST003598_2QRS duration1.000000e-09
GCST003598_31QRS duration3.000000e-10
GCST003630_1Left ventricular QRS voltage8.000000e-08
GCST003872_15QRS complex (12-leadsum)1.000000e-17
GCST004093_38Prostate-specific antigen levels1.000000e-14
GCST004136_17Methadone dose in opioid dependence2.000000e-06
GCST004184_4Lung function (FVC)1.000000e-09
GCST004280_3Diastolic blood pressure5.000000e-13
GCST004280_72Diastolic blood pressure5.000000e-13
GCST004988_47Breast cancer4.000000e-39
GCST005588_5Idiopathic dilated cardiomyopathy7.000000e-06
GCST005783_4Bone mineral density (lumbar spine) in inflammatory bowel disease1.000000e-06
GCST005905_1Global electrical heterogeneity phenotypes2.000000e-24
GCST005905_2Global electrical heterogeneity phenotypes2.000000e-16
GCST005905_3Global electrical heterogeneity phenotypes1.000000e-14
GCST005978_16Diastolic blood pressure4.000000e-13

EFO canonical traits (24, from GWAS)

EFO IDTrait name
EFO:0006336diastolic blood pressure
EFO:0004462PR interval
EFO:0006335systolic blood pressure
EFO:0006340mean arterial pressure
EFO:0005095PR segment
EFO:0004531urate measurement
EFO:0007741R wave amplitude
EFO:0007742QRS amplitude
EFO:0005054QRS complex
EFO:0007907methadone dose measurement
EFO:0004312vital capacity
EFO:0009094idiopathic dilated cardiomyopathy
EFO:0007701spine bone mineral density
EFO:0004327electrocardiography
EFO:0004329alcohol drinking
EFO:0006527smoking status measurement
EFO:0009270heel bone mineral density
EFO:0004314forced expiratory volume
EFO:0008008lower urinary tract symptom
EFO:0010464beta-aminoisobutyric acid measurement
EFO:0010437triacylglycerol 58:10 measurement
EFO:0007614asthma exacerbation measurement
EFO:0004980appendicular lean mass
EFO:0004532serum gamma-glutamyl transferase measurement

MeSH disease descriptors (3)

DescriptorNameTree numbers
D018270Carcinoma, Ductal, BreastC04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390
D057090Eccrine PorocarcinomaC04.557.470.200.025.500
C536937Ulnar-mammary syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

98 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Tetrachlorodibenzodioxinaffects expression, increases expression7
bisphenol Adecreases methylation, increases expression, decreases expression, affects cotreatment5
Valproic Acidincreases expression, affects cotreatment4
(+)-JQ1 compounddecreases expression, affects expression, increases reaction, increases expression, affects cotreatment3
Benzo(a)pyreneincreases methylation, decreases methylation, increases expression3
Estradiolaffects expression, affects cotreatment, increases expression3
bisphenol Sdecreases methylation, affects cotreatment, decreases expression2
Acetaminophendecreases expression, increases expression2
Tobacco Smoke Pollutionincreases expression2
Tretinoinincreases expression2
aristolochic acid Iincreases expression1
FR900359increases phosphorylation1
dicrotophosincreases expression1
methylmercuric chloridedecreases expression1
propionaldehydeincreases expression1
N(4)-hydroxycytidinedecreases expression1
2-methyl-4-isothiazolin-3-oneincreases expression1
terbufosincreases methylation1
arseniteincreases methylation1
afimoxifenedecreases reaction, increases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
fenvalerateincreases expression1
butyraldehydeincreases expression1
3,4,5,3’,4’-pentachlorobiphenylincreases expression1
potassium chromate(VI)affects cotreatment, increases expression1
coumarindecreases phosphorylation1
enzacameneincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
epigallocatechin gallateincreases expression, affects cotreatment1
pentanalincreases expression1

Cellosaurus cell lines

9 cell lines: 6 cancer cell line, 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_1774TTCancer cell lineFemale
CVCL_5098SNU-81Cancer cell lineMale
CVCL_A7A8SEES3-1V human TBX3, clone1Embryonic stem cellMale
CVCL_A7A9SEES3-1V human TBX3, clone2Embryonic stem cellMale
CVCL_A8L5SEES3-1V human TBX3, clone3Embryonic stem cellMale
CVCL_D1ZAAbcam A-549 TBX3 KOCancer cell lineMale
CVCL_D2DBAbcam HCT 116 TBX3 KOCancer cell lineMale
CVCL_TR77HAP1 TBX3 (-) 1Cancer cell lineMale
CVCL_TR78HAP1 TBX3 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00076362PHASE4COMPLETEDPediatric Hypothalamic Obesity
NCT00079547PHASE4COMPLETEDThe Safety and Effectiveness of Low and High Carbohydrate Diets
NCT00115063PHASE4TERMINATEDLOSS- Louisiana Obese Subjects Study
NCT00134303PHASE4COMPLETEDTrial Comparing Metformin Versus Placebo in Non Alcoholic Steatohepatitis (NASH) Patients Receiving Bariatric Surgery for Obesity
NCT00143936PHASE4COMPLETEDThe Safety and Efficacy of Low and High Carbohydrate Diets
NCT00143962PHASE4COMPLETEDComparison of Two Approaches to Weight Loss Follow-Up Study
NCT00152360PHASE4COMPLETEDThe Effect of Xenical on Weight and Risk Factors
NCT00176306PHASE4COMPLETEDLevofloxacin Pharmacokinetics (PK) in the Severely Obese
NCT00203450PHASE4COMPLETEDZonegran for the Treatment of Weight Gain Associated With Psychotropic Medication Use: A Placebo-Controlled Trial
NCT00205504PHASE4COMPLETEDOral Contraceptives in the Metabolic Syndrome
NCT00229229PHASE4TERMINATEDComparison of 4 Diets in the Management of Overweight Patients With Vascular Disease
NCT00234988PHASE4COMPLETEDA Phase IV, Multi-Center, Open-Label Trial of Sibutramine in Combination With a Hypocaloric Diet in Obese and Overweight Thai Subjects.
NCT00264589PHASE4COMPLETEDExercise Training and Cardiovascular Function in Obesity and in Type 2 Diabetes
NCT00288873PHASE4COMPLETEDCharacterization of Hyperparathyroidism and Vitamin D Deficiency in Obesity
NCT00298857PHASE4TERMINATEDA Pharmacokinetic Study to Compare the Dosing of Valproic Acid in Subjects With Different Body Weights
NCT00315146PHASE4COMPLETEDOptimizing Body Composition for Function in Older Adults
NCT00319202PHASE4TERMINATEDClinical Trial to Assess the Effects of Candesartan on the Carbohydrate Metabolism of Obese Subjects
NCT00327912PHASE4UNKNOWNLaparoscopic Roux-en-Y Gastric Bypass Versus Laparoscopic Biliopancreatic Diversion (BPD)- Duodenal Switch for Superobesity
NCT00352287PHASE4COMPLETEDStudy to Determine the Effects of Human Growth Hormone and Pioglitazone in Overweight, Prediabetic Adults
NCT00353054PHASE4COMPLETEDEffect of Calcium/Vitamin D Supplementation on Body Weight and Fat Loss.
NCT00390637PHASE4COMPLETEDDiet, Obesity and Genes (DiOGenes)
NCT00415688PHASE4COMPLETEDLifestyle Modification for Obesity-Related Type 2 Diabetes
NCT00433641PHASE4COMPLETEDWeight Loss in Response to Sibutramine (MERIDIA) is Influenced by the Inherited Genes
NCT00440375PHASE4COMPLETEDEffects of Rosiglitazone on Bone in Postmenopausal Diabetic Women
NCT00453557PHASE4COMPLETEDMechanism of Growth Hormone Effects on Adipose Tissue
NCT00456885PHASE4COMPLETEDThe Effect of Exenatide on Weight and Hunger in Obese, Healthy Women
NCT00463112PHASE4COMPLETEDEffect of Diet Plus Sibutramine on Hormonal and Metabolic Features in Overweight and Obese Women With PCOS
NCT00512187PHASE4COMPLETEDModerate Weight Loss Makes Obese Patients With Severe Chronic Plaque Psoriasis Responsive to Sub-Optimal Dose of Cyclosporine: an Investigator Blinded, Controlled, Randomized Clinical Trial
NCT00516919PHASE4COMPLETEDStudy of Behavioral Weight Loss Therapy for Obesity and Binge Eating in Monolingual Hispanic Persons
NCT00522470PHASE4COMPLETEDEffects of Rosiglitazone on Serum Ghrelin and Peptide YY Levels
NCT00537810PHASE4COMPLETEDTreatment of Binge Eating in Obese Patients in Primary Care
NCT00538486PHASE4COMPLETEDA Randomized, Double-Blind, Active Control Trial Comparing Effects of Telmisartan, Candesartan and Amlodipine, Alone or Plus Metformin, on Non-Diabetic, Obese Hypertensive Patients
NCT00584389PHASE4TERMINATEDThe Effect of Rimonabant on Energy Expenditure, Fat Metabolism and Body Composition
NCT00585182PHASE4COMPLETEDStudy to Evaluate Weight-based Enoxaparin Dosing in Obese Medical Patients at Risk for DVT
NCT00632840PHASE4COMPLETEDPharmacological Regulation of Fat Transport in Metabolic Syndrome
NCT00636142PHASE4COMPLETEDEffects of Infliximab on Insulin Sensitivity and Beta Cell Function in Insulin Resistant Human Obesity
NCT00675987PHASE4COMPLETEDA Randomized Clinical Trial To Study Losartan On Endothelial Dysfunction and Insulin Resistance In Obese Patients
NCT00694811PHASE4COMPLETEDEffects of Re-Feeding Duration on Weight Maintenance After Weight Loss With Very-Low-Energy Diets (VLEDs)
NCT00699413PHASE4TERMINATEDSupplements for Controlling Resistance to Insulin
NCT00729963PHASE4COMPLETEDSibutramine Versus Continuous Positive Airway Pressure (CPAP)in Obstructive Sleep Apnea (OSA) Patients