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VGLL1

gene
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Also known as TONDUTDU

Summary

VGLL1 (vestigial like family member 1, HGNC:20985) is a protein-coding gene on chromosome Xq26.3, encoding Transcription cofactor vestigial-like protein 1 (Q99990). May act as a specific coactivator for the mammalian TEFs.

The protein encoded by this gene binds proteins of the TEA domain family of transcription factors (TEFs) through the Vg (vestigial) homology region found in its N-terminus. It may thus function as a specific coactivator for the mammalian TEFs.

Source: NCBI Gene 51442 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 58 total
  • GTEx eGene: eQTL in 5 tissues, sQTL in 0 (q < 0.05)
  • MANE Select transcript: NM_016267
  • Notable: 58 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20985
Approved symbolVGLL1
Namevestigial like family member 1
LocationXq26.3
Locus typegene with protein product
StatusApproved
AliasesTONDU, TDU
Ensembl geneENSG00000102243
Ensembl biotypeprotein_coding
OMIM300583
Entrez51442

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000370634

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 1, TSL 3: 2

ENST00000370634, ENST00000440515, ENST00000456412, ENST00000470358, ENST00000872080, ENST00000872081, ENST00000872082, ENST00001090914, ENST00001132255

RefSeq mRNA: 1 — MANE Select: NM_016267 NM_016267

CCDS: CCDS14658

Canonical transcript exons

ENST00000370634 — 5 exons

ExonStartEnd
ENSE00000677012136548589136549008
ENSE00000677013136550768136550821
ENSE00001029091136532215136532296
ENSE00001453195136535996136536234
ENSE00003843261136556451136556799

Expression profiles

Bgee: expression breadth broad, 93 present calls, max score 97.66.

FANTOM5 (CAGE): breadth broad, TPM avg 3.3478 / max 888.3249, expressed in 210 samples.

Highest expression (Bgee): placenta, amniotic fluid, male germ line stem cell (sensu Vertebrata) in testis, palpebral conjunctiva, urinary bladder.

Genetic regulation across tissues (GTEx eQTL / sQTL)

VGLL1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 5 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

5 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Skin Sun Exposed Lower legeqtl2.0e-04+0.34X:136528693:T:C
Lungeqtl1.2e-02-0.40X:135922481:A:G
Breast Mammary Tissueeqtl2.2e-02+0.35X:135614712:G:A
Prostateeqtl2.5e-02+0.23X:137273454:C:T
Stomacheqtl3.6e-02-0.19X:136320128:G:C

FANTOM5 promoters

7 alternative TSS:

Promoter IDTPM avgSamples expressed
1977062.2455172
1977030.468375
1977070.290666
1977040.180748
1977050.123046
1977080.02405
1977090.01586

Top tissues by expression

showing 100 of 252 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
placentaUBERON:000198797.66gold quality
amniotic fluidUBERON:000017395.17gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.15gold quality
palpebral conjunctivaUBERON:000181288.04gold quality
urinary bladderUBERON:000125575.30gold quality
deciduaUBERON:000245075.18gold quality
metanephros cortexUBERON:001053374.02gold quality
lower esophagus mucosaUBERON:003583471.90gold quality
nasal cavity epitheliumUBERON:000538471.73gold quality
minor salivary glandUBERON:000183069.26gold quality
olfactory segment of nasal mucosaUBERON:000538668.86gold quality
mucosa of urinary bladderUBERON:000125968.83silver quality
saliva-secreting glandUBERON:000104466.41gold quality
mouth mucosaUBERON:000372966.23gold quality
buccal mucosa cellCL:000233666.12silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099165.57gold quality
gluteal muscleUBERON:000200064.33gold quality
right lungUBERON:000216764.11gold quality
nasal cavity mucosaUBERON:000182662.14gold quality
triceps brachiiUBERON:000150961.96gold quality
urethraUBERON:000005761.32silver quality
germinal epithelium of ovaryUBERON:000130459.95gold quality
biceps brachiiUBERON:000150759.90gold quality
pituitary glandUBERON:000000759.02gold quality
upper lobe of left lungUBERON:000895258.82gold quality
substantia nigra pars reticulataUBERON:000196658.49gold quality
adult mammalian kidneyUBERON:000008258.33gold quality
upper lobe of lungUBERON:000894858.18gold quality
islet of LangerhansUBERON:000000658.14gold quality
metanephrosUBERON:000008158.11gold quality
adenohypophysisUBERON:000219658.11gold quality
oral cavityUBERON:000016758.07silver quality
vena cavaUBERON:000408758.02gold quality
seminal vesicleUBERON:000099858.01silver quality
lateral globus pallidusUBERON:000247657.97gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450257.75gold quality
esophagus mucosaUBERON:000246957.66gold quality
male germ cellCL:000001556.91silver quality
esophagus squamous epitheliumUBERON:000692056.91gold quality
spermCL:000001956.70silver quality
lateral nuclear group of thalamusUBERON:000273656.54gold quality
epithelium of esophagusUBERON:000197656.42gold quality
quadriceps femorisUBERON:000137756.04gold quality
cerebellar vermisUBERON:000472055.98gold quality
deltoidUBERON:000147655.79gold quality
lungUBERON:000204855.79gold quality
mammary glandUBERON:000191155.62gold quality
thoracic mammary glandUBERON:000520055.59gold quality
vastus lateralisUBERON:000137954.77gold quality
substantia nigra pars compactaUBERON:000196554.22gold quality
kidneyUBERON:000211354.12gold quality
gall bladderUBERON:000211054.03gold quality
trabecular bone tissueUBERON:000248353.97gold quality
pancreasUBERON:000126453.66gold quality
prostate glandUBERON:000236753.33gold quality
parotid glandUBERON:000183153.22gold quality
mammary ductUBERON:000176553.06silver quality
squamous epitheliumUBERON:000691452.85gold quality
endometrium epitheliumUBERON:000481152.22gold quality
body of pancreasUBERON:000115051.91gold quality
Brodmann (1909) area 10UBERON:001354151.59gold quality
pancreatic ductal cellCL:000207951.49silver quality
pleuraUBERON:000097751.48gold quality
parietal pleuraUBERON:000240051.07gold quality
skeletal muscle tissueUBERON:000113450.74gold quality
tonsilUBERON:000237250.74gold quality
visceral pleuraUBERON:000240150.71gold quality
hair follicleUBERON:000207350.53gold quality
cortex of kidneyUBERON:000122550.52gold quality
frontal poleUBERON:000279550.41gold quality
middle frontal gyrusUBERON:000270250.30gold quality
vaginaUBERON:000099650.26gold quality
paraflocculusUBERON:000535150.18gold quality
mucosa of paranasal sinusUBERON:000503050.10silver quality
cranial nerve IIUBERON:000094150.01silver quality
Brodmann (1909) area 46UBERON:000648349.94gold quality
oviduct epitheliumUBERON:000480449.82gold quality
epithelial cell of pancreasCL:000008349.72gold quality
thymusUBERON:000237049.57gold quality
heart right ventricleUBERON:000208049.39gold quality
blood vessel layerUBERON:000479749.29gold quality
cervix squamous epitheliumUBERON:000692249.20gold quality
olfactory bulbUBERON:000226448.92gold quality
choroid plexus epitheliumUBERON:000391148.89gold quality
myocardiumUBERON:000234948.87gold quality
type B pancreatic cellCL:000016948.83gold quality
tibialis anteriorUBERON:000138548.79silver quality
cervix epitheliumUBERON:000480148.64gold quality
cardiac muscle of right atriumUBERON:000337948.55gold quality
CA1 field of hippocampusUBERON:000388148.50gold quality
inferior olivary complexUBERON:000212748.47gold quality
left ventricle myocardiumUBERON:000656648.24gold quality
orbitofrontal cortexUBERON:000416748.20gold quality
upper arm skinUBERON:000426348.06gold quality
nephron tubuleUBERON:000123147.92gold quality
tongue squamous epitheliumUBERON:000691947.92gold quality
kidney epitheliumUBERON:000481947.90gold quality
body of tongueUBERON:001187647.75gold quality
metanephric glomerulusUBERON:000473647.74gold quality
renal glomerulusUBERON:000007447.60gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-MTAB-6701yes1313.31
E-MTAB-10018yes360.84
E-MTAB-3929yes196.62
E-HCAD-10yes13.42
E-ANND-3yes6.00

HPA expression

RNA tissue specificity: Tissue enriched

25 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Placentatissue191.5medium
Urinary bladdertissue21.2not detected
Seminal vesicletissue6.3not detected
Kidneytissue3.5not detected
Breasttissue2.1not detected
Lungtissue2.0not detected
Salivary glandtissue1.6not detected
Vaginatissue1.5not detected
Pituitary glandtissue1.4
Pancreastissue1.4not detected
Prostatetissue1.2not detected
Fallopian tubetissue1.2not detected
Tonsiltissue1.1not detected
Stomach 1tissue0.8not detected
Esophagustissue0.7not detected
Adipose tissuetissue0.6not detected
Gallbladdertissue0.5not detected
Epididymistissue0.4not detected
Duodenumtissue0.2not detected
Thymustissue0.2
Heart muscletissue0.1not detected
Endometrium 1tissue0.1not detected
Spleentissue0.1not detected
Livertissue0.1not detected
Small intestinetissue0.1not detected

Brain sub-regions (HPA Brain Atlas): detected in 16; highest nTPM — Ventromedial nucleus (0.2), Angular gyrus (0.1), Area striata (white matter) (0.1), Dentate gyrus (0.1), Frontal eye field (0.1).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting VGLL1 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

26 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-4455100.0065.481587
HSA-MIR-1213699.9872.815713
HSA-MIR-548N99.9871.944170
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-211099.9666.681930
HSA-MIR-153-5P99.8973.866317
HSA-MIR-129999.7771.242389
HSA-MIR-3150A-3P99.7664.441640
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-548AV-5P99.6070.842107
HSA-MIR-548K99.6070.842107
HSA-MIR-432899.5771.064094
HSA-MIR-1212399.5271.792990
HSA-MIR-467299.5071.582893
HSA-MIR-805499.4870.812084
HSA-MIR-361299.4566.021333
HSA-MIR-65099.4565.771309
HSA-MIR-452-3P99.0166.251241
HSA-MIR-619-5P98.5764.971988
HSA-MIR-367097.8864.39763
HSA-MIR-431497.5067.301369
HSA-MIR-431-5P96.1666.50652
HSA-MIR-2277-3P91.9462.27299

Functional genomics

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000370634 — one region, missense o/e 0.98.

Literature-anchored findings (GeneRIF, showing 8)

  • VGLL1 expression is associated with a triple-negative basal-like phenotype in breast cancer (PMID:24891455)
  • Novel EWSR1-VGLL1 fusion in a pediatric neuroepithelial neoplasm. (PMID:31925773)
  • A new perspective on the interaction between the Vg/VGLL1-3 proteins and the TEAD transcription factors. (PMID:33060790)
  • VGLL1 phosphorylation and activation promotes gastric cancer malignancy via TGF-beta/ERK/RSK2 signaling. (PMID:33069758)
  • Vestigial-like 1 is a shared targetable cancer-placenta antigen expressed by pancreatic and basal-like breast cancers. (PMID:33087697)
  • Vestigial-like 1 (VGLL1): An ancient co-transcriptional activator linking wing, placenta, and tumor development. (PMID:37004960)
  • VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification. (PMID:38233381)
  • VGLL1 stabilization of cytoplasmic TAZ promotes EGFR expression and maintains tumor initiating cells in breast cancer independent of TEAD. (PMID:38417636)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusVgll1ENSMUSG00000031131
drosophila_melanogastervgFBGN0003975

Paralogs (2): VGLL2 (ENSG00000170162), VGLL3 (ENSG00000206538)

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
LINC00892ncRNA100128420
HTATSF1protein-coding27336
BRS3protein-coding680
MIR934ncRNA100126324
ARHGEF6protein-coding9459
CD40LGprotein-coding959
ADGRG4protein-coding139378

Protein

Protein identifiers

Transcription cofactor vestigial-like protein 1 — Q99990 (reviewed: Q99990)

Alternative names: Protein TONDU

All UniProt accessions (3): H0Y5G3, Q5H916, Q99990

UniProt curated annotations — full annotation on UniProt →

Function. May act as a specific coactivator for the mammalian TEFs.

Subunit / interactions. Interacts with TEFs.

Subcellular location. Nucleus.

Similarity. Belongs to the vestigial family.

RefSeq proteins (1): NP_057351* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006627TDU_repeatRepeat
IPR011520Vg_famFamily

Pfam: PF07545

UniProt features (5 total): compositionally biased region 2, chain 1, region of interest 1, sequence variant 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q99990-F157.780.13

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm

Antibody reliability (HPA): IH supported · IF supported

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 70 (showing top): NKX25_02, MODULE_545, ONDER_CDH1_TARGETS_3_DN, FINAK_BREAST_CANCER_SDPP_SIGNATURE, BRN2_01, SMID_BREAST_CANCER_LUMINAL_A_DN, GOZGIT_ESR1_TARGETS_UP, GNF2_KISS1, BENPORATH_ES_CORE_NINE_CORRELATED, SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_UP, VANTVEER_BREAST_CANCER_ESR1_DN, SMID_BREAST_CANCER_LUMINAL_B_DN, GNF2_TIMP2, GOMF_TRANSCRIPTION_COACTIVATOR_ACTIVITY, LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT

GO Biological Process (4): DNA-templated transcription (GO:0006351), regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (2): transcription coactivator activity (GO:0003713), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

14 GO namespaces:

CategoryTerms
DNA-templated transcription2
regulation of DNA-templated transcription2
gene expression1
RNA biosynthetic process1
regulation of gene expression1
regulation of RNA biosynthetic process1
transcription by RNA polymerase II1
positive regulation of RNA biosynthetic process1
transcription coregulator activity1
positive regulation of DNA-templated transcription1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 8 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

GO termNSEvidence
nucleoplasmCCdirect assay

Protein interactions and networks

STRING

showing 15 of 572 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
VGLL1TEAD1P28347929
VGLL1WWTR1Q9GZV5778
VGLL1VGLL4Q14135763
VGLL1TEAD4Q15561760
VGLL1YAP1P46937716
VGLL1ACTA1P02568661
VGLL1VGLL3A8MV65492
VGLL1RAD51BO15315491
VGLL1TEAD2Q15562435
VGLL1MEF2AQ02078428
VGLL1MYH1P12882427
VGLL1ERP27Q96DN0417
VGLL1MYOGP15173408
VGLL1GATA2P23769407
VGLL1TEAD3Q99594407

IntAct

Human interaction partners of VGLL1 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

14 partners by confidence:

PartnerInteraction typeMIscoreRecords
TEAD3physical association0.6704
AIRIMphysical association0.5603
CDKN2Dphysical association0.5603
HNRNPFphysical association0.5603
LONRF1physical association0.5603
MEIS2physical association0.5603
PFDN5physical association0.5603
RIPPLY1physical association0.5603
TEAD2physical association0.5603
TEAD4physical association0.5603
TEKT4physical association0.5603
TLE5physical association0.5603
TRIM23physical association0.5603
TSSK3physical association0.5603

BioGRID (20 interactions; top human partners by supporting records): TEAD1 (Two-hybrid; 2 records), TEAD2 (Two-hybrid; 2 records), TEAD3 (Two-hybrid; 2 records), TEAD4 (Two-hybrid; 2 records), AES (Two-hybrid), C1orf109 (Two-hybrid), CDKN2D (Two-hybrid), HNRNPF (Two-hybrid), LONRF1 (Two-hybrid), MEIS2 (Two-hybrid), PFDN5 (Two-hybrid), RIPPLY1 (Two-hybrid), SPPL3 (Positive Genetic), TEKT4 (Two-hybrid), TRIM23 (Two-hybrid)

SIGNOR signaling

1 signaling interactions:

AEffectBMechanism
RPS6KA3“down-regulates activity”VGLL1phosphorylation

Disease & clinical

Genetic variants

Variant evidence for VGLL1: 58 ClinVar records (0 pathogenic / likely pathogenic).

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance28
Likely benign3
Benign0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 38 predictions of 403):

Position(s)EffectΔscoreSites
X:136532297–136532298donor_loss0.99004
X:136536235–136536236donor_loss0.99006
X:136532297donor_loss0.9800
X:136535993–136535995acceptor_loss0.98007
X:136549015donor_gain0.9800
X:136550766–136550767acceptor_loss0.98006
X:136550819donor_gain0.9800
X:136550822–136550823donor_loss0.97004
X:136550822–136550823donor_loss0.96002
X:136548587–136548588acceptor_loss0.95006

AlphaMissense

205 missense substitutions predicted likely pathogenic (of 1,676 scored), across 42 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
H4480.9890.995
D4280.9850.995
F4580.9820.999
D3680.9570.987
F3080.9060.996
F3370.9760.996
W2370.9290.973
E4370.8300.958
I3770.7930.951
C2770.7010.940
G3560.9820.992
V4160.9690.982
R4760.9650.995
A4860.9310.993
Y3260.9260.994
T3160.8930.982
E2260.8060.878
L4950.9000.992
V2850.8830.992
S3950.8820.935

HPA cancer prognostics

RNA cancer specificity: Cancer enriched (Bladder Urothelial Carcinoma)

Disease associations

OMIM: gene MIM:300583 | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, decreases expression, decreases methylation6
trichostatin Aaffects cotreatment, increases expression3
Benzo(a)pyreneincreases expression, increases methylation, affects methylation3
mercuric bromideincreases expression, affects cotreatment2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression2
Vorinostataffects cotreatment, increases expression2
Panobinostataffects cotreatment, increases expression2
Air Pollutantsdecreases expression, increases abundance2
Ethinyl Estradiolaffects expression, decreases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Smokedecreases expression, increases abundance2
p-Chloromercuribenzoic Acidaffects cotreatment, increases expression2
bisphenol Aaffects expression1
ascorbate-2-phosphateaffects binding, affects cotreatment, increases expression1
3,4-dichloroanilinedecreases expression1
sodium arsenitedecreases expression1
4-(2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1-propenyl)benzoic acidaffects cotreatment, increases expression1
cylindrospermopsinincreases expression1
corosolic acidincreases expression1
2-palmitoylglycerolincreases expression1
Chir 99021affects cotreatment, increases expression, affects binding1
dorsomorphinaffects cotreatment, increases expression1
XAV939affects binding, affects cotreatment, increases expression1
LDN 193189affects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
3-(4-pyridyl)-1H-indoleaffects cotreatment, increases expression1
Resveratrolaffects cotreatment, decreases expression1
Amphotericin Bincreases expression1
Ascorbic Acidaffects binding, affects cotreatment, increases expression1
Diethylhexyl Phthalateincreases expression1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.