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VGLL4 vestigial like family member 4 [ Homo sapiens (human) ]

Gene ID: 9686, updated on 3-Apr-2024

Summary

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Official Symbol
VGLL4provided by HGNC
Official Full Name
vestigial like family member 4provided by HGNC
Primary source
HGNC:HGNC:28966
See related
Ensembl:ENSG00000144560 MIM:618692; AllianceGenome:HGNC:28966
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
VGL-4
Summary
Predicted to enable transcription coactivator binding activity. Involved in negative regulation of Wnt signaling pathway; negative regulation of cell growth; and negative regulation of hippo signaling. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in ovary (RPKM 26.1), thyroid (RPKM 18.5) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
3p25.3-p25.2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (11556067..11721815, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (11551371..11717542, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (11597541..11762013, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19429 Neighboring gene ribosomal protein L13a pseudogene 27 Neighboring gene autophagy related 7 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:11405755-11406954 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:11521898-11522503 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:11574579-11575079 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11586483-11587050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:11587827-11588328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:11588329-11588828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:11616238-11617058 Neighboring gene CSTB pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11624893-11625731 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11634691-11635222 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11635223-11635753 Neighboring gene Sharpr-MPRA regulatory region 8254 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:11642749-11643347 and GRCh37_chr3:11643348-11643945 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11650998-11651770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19431 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11680477-11681428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19433 Neighboring gene Sharpr-MPRA regulatory region 9131 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19434 Neighboring gene TAM41 mitochondrial translocator assembly and maintenance homolog Neighboring gene Sharpr-MPRA regulatory region 5418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11826643-11827198 Neighboring gene FANCD2 pseudogene 2 Neighboring gene CYCS pseudogene 12

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Validation of Osteogenic Properties of Cytochalasin D by High-Resolution RNA-Sequencing in Mesenchymal Stem Cells Derived from Bone Marrow and Adipose Tissues. Samsonraj RM, et al. Stem Cells Dev, 2018 Aug 15. PMID 29882479, Free PMC Article
  2. VGLL4 Selectively Represses YAP-Dependent Gene Induction and Tumorigenic Phenotypes in Breast Cancer. Zhang Y, et al. Sci Rep, 2017 Jul 21. PMID 28733631, Free PMC Article
  3. Downregulation of VGLL4 in the progression of esophageal squamous cell carcinoma. Jiang W, et al. Tumour Biol, 2015 Feb. PMID 25352025
  4. Characterization of genetic variation in the VGLL4 gene in anorexia nervosa. Clarke TK, et al. Psychiatr Genet, 2014 Aug. PMID 24983835, Free PMC Article
  5. Brief report: VGLL4 is a novel regulator of survival in human embryonic stem cells. Tajonar A, et al. Stem Cells, 2013 Dec. PMID 23765749, Free PMC Article

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. VGLL4-TEAD1 promotes vascular smooth muscle cell differentiation from human pluripotent stem cells via TET2.
    Title: VGLL4-TEAD1 promotes vascular smooth muscle cell differentiation from human pluripotent stem cells via TET2.
  2. Biochemical properties of VGLL4 from Homo sapiens and Tgi from Drosophila melanogaster and possible biological implications.
    Title: Biochemical properties of VGLL4 from Homo sapiens and Tgi from Drosophila melanogaster and possible biological implications.
  3. The lncRNA MEG3/miR-16-5p/VGLL4 regulatory axis is involved in etoposide-induced senescence of tumor cells.
    Title: The lncRNA MEG3/miR-16-5p/VGLL4 regulatory axis is involved in etoposide-induced senescence of tumor cells.
  4. HOXB13 suppresses proliferation, migration and invasion, and promotes apoptosis of gastric cancer cells through transcriptional activation of VGLL4 to inhibit the involvement of TEAD4 in the Hippo signaling pathway.
    Title: HOXB13 suppresses proliferation, migration and invasion, and promotes apoptosis of gastric cancer cells through transcriptional activation of VGLL4 to inhibit the involvement of TEAD4 in the Hippo signaling pathway.
  5. VGLL4 inhibits YAP1/TEAD signaling to suppress the epidermal squamous cell carcinoma cancer phenotype.
    Title: VGLL4 inhibits YAP1/TEAD signaling to suppress the epidermal squamous cell carcinoma cancer phenotype.
  6. LINC00641 regulates prostate cancer cell growth and apoptosis via the miR-365a-3p/VGLL4 axis.
    Title: LINC00641 regulates prostate cancer cell growth and apoptosis via the miR-365a-3p/VGLL4 axis.
  7. VGLL4 interacts with STAT3 to function as a tumor suppressor in triple-negative breast cancer
    Title: VGLL4 interacts with STAT3 to function as a tumor suppressor in triple-negative breast cancer.
  8. Identification of VGLL4 as an important regulator of PD-L1 expression and a central role of VGLL4 and YAP in the regulation of tumor immunity.
    Title: Loss of VGLL4 suppresses tumor PD-L1 expression and immune evasion.
  9. our RNA-seq analyses suggest that while the stimulatory effects of CytoD on osteogenesis are pleiotropic and depend on the biological state of the cell type, a small group of genes including VGLL4 may contribute to MSC commitment toward the bone lineage.
    Title: Validation of Osteogenic Properties of Cytochalasin D by High-Resolution RNA-Sequencing in Mesenchymal Stem Cells Derived from Bone Marrow and Adipose Tissues.
  10. Data report that VGLL4 functions as a suppressor of breast tumor (BC) growth and progression. Its low expression correlated with a poor prognosis. Its ectopic expression in BC cell lines reduced cell proliferation, migration, and tumor formation in xenograft mouse model. VGLL4 interacts with TEAD1 via its second TEAD-interacting domain, antagonizing YAP-dependent tumor growth.
    Title: VGLL4 Selectively Represses YAP-Dependent Gene Induction and Tumorigenic Phenotypes in Breast Cancer.
Submit: New GeneRIF Correction See all GeneRIFs (27)

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

EBI GWAS Catalog

Description
A genome-wide association study on common SNPs and rare CNVs in anorexia nervosa.
EBI GWAS Catalog
Common variants in left/right asymmetry genes and pathways are associated with relative hand skill.
EBI GWAS Catalog
Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0121

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coactivator binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in negative regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of Wnt signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of cardiac muscle cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of cell growth IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of hippo signaling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of hippo signaling ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
transcription cofactor vestigial-like protein 4
Names
Vestigial-like 4
vestigial like 4

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.

mRNA and Protein(s)

  1. NM_001128219.3 → NP_001121691.1  transcription cofactor vestigial-like protein 4 isoform a

    See identical proteins and their annotated locations for NP_001121691.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    BU682809, D50911, DA383197, DA386938, DR159250
    Consensus CDS
    CCDS46754.1
    UniProtKB/TrEMBL
    G5E9M7
    Related
    ENSP00000404251.2, ENST00000430365.7
    Conserved Domains (2) summary
    smart00711
    Location:240 → 255
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:14 → 230
    VGLL4; Transcription cofactor vestigial-like protein 4

  2. NM_001128220.3 → NP_001121692.1  transcription cofactor vestigial-like protein 4 isoform c

    See identical proteins and their annotated locations for NP_001121692.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains alternate 5' exon structure and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AK307708, BU682809, D50911
    Consensus CDS
    CCDS46755.1
    UniProtKB/TrEMBL
    Q0H0I7
    Related
    ENSP00000416615.2, ENST00000451674.6
    Conserved Domains (2) summary
    smart00711
    Location:154 → 169
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:6 → 144
    VGLL4; Transcription cofactor vestigial-like protein 4

  3. NM_001128221.3 → NP_001121693.1  transcription cofactor vestigial-like protein 4 isoform d

    See identical proteins and their annotated locations for NP_001121693.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains alternate 5' exon structure and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (d) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AK308761, BU682809, D50911
    Consensus CDS
    CCDS46756.1
    UniProtKB/TrEMBL
    Q0H0I7
    Related
    ENSP00000402878.2, ENST00000424529.6
    Conserved Domains (2) summary
    smart00711
    Location:150 → 165
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:1 → 140
    VGLL4; Transcription cofactor vestigial-like protein 4

  4. NM_001284390.2 → NP_001271319.1  transcription cofactor vestigial-like protein 4 isoform e

    See identical proteins and their annotated locations for NP_001271319.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains alternate 5' exon structure and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (e) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    BC000763, BU682809, D50911, DA383197
    Consensus CDS
    CCDS68343.1
    UniProtKB/TrEMBL
    A0A0A6YYI5
    Related
    ENSP00000413030.2, ENST00000426568.5
    Conserved Domains (2) summary
    smart00711
    Location:239 → 254
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:27 → 229
    VGLL4; Transcription cofactor vestigial-like protein 4

  5. NM_001284391.1 → NP_001271320.1  transcription cofactor vestigial-like protein 4 isoform f

    See identical proteins and their annotated locations for NP_001271320.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains alternate 5' exon structure and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (f) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AC022001, AI809612, AK300344, BU682809, D50911, DA383197
    Consensus CDS
    CCDS68342.1
    UniProtKB/TrEMBL
    A0A024R2F0, A0A9K3Y712, G5E9M9, Q0H0I7
    Related
    ENSP00000404624.1, ENST00000413604.5
    Conserved Domains (2) summary
    smart00711
    Location:175 → 190
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:1 → 165
    VGLL4; Transcription cofactor vestigial-like protein 4

  6. NM_014667.4 → NP_055482.2  transcription cofactor vestigial-like protein 4 isoform b

    See identical proteins and their annotated locations for NP_055482.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains alternate 5' exon structure and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AK130542, BU682809, D50911, DA383197
    Consensus CDS
    CCDS2606.1
    UniProtKB/TrEMBL
    A0A075B6E4
    Related
    ENSP00000273038.3, ENST00000273038.7
    Conserved Domains (2) summary
    smart00711
    Location:234 → 249
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:8 → 223
    VGLL4; Transcription cofactor vestigial-like protein 4

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    11556067..11721815 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449259.1 → XP_047305215.1  transcription cofactor vestigial-like protein 4 isoform X1

  2. XM_024453835.2 → XP_024309603.1  transcription cofactor vestigial-like protein 4 isoform X3

    UniProtKB/TrEMBL
    A0A075B6E4
    Conserved Domains (2) summary
    smart00711
    Location:234 → 249
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:8 → 223
    VGLL4; Transcription cofactor vestigial-like protein 4

  3. XM_024453836.2 → XP_024309604.1  transcription cofactor vestigial-like protein 4 isoform X3

    UniProtKB/TrEMBL
    A0A075B6E4
    Conserved Domains (2) summary
    smart00711
    Location:234 → 249
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:8 → 223
    VGLL4; Transcription cofactor vestigial-like protein 4

  4. XM_047449260.1 → XP_047305216.1  transcription cofactor vestigial-like protein 4 isoform X2

  5. XM_047449261.1 → XP_047305217.1  transcription cofactor vestigial-like protein 4 isoform X4

    UniProtKB/TrEMBL
    A0A024R2F0, A0A9K3Y712, G5E9M9

  6. XM_011534269.2 → XP_011532571.1  transcription cofactor vestigial-like protein 4 isoform X4

    See identical proteins and their annotated locations for XP_011532571.1

    UniProtKB/TrEMBL
    A0A024R2F0, A0A9K3Y712, G5E9M9, Q0H0I7
    Conserved Domains (2) summary
    smart00711
    Location:175 → 190
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:1 → 165
    VGLL4; Transcription cofactor vestigial-like protein 4

  7. XM_047449262.1 → XP_047305218.1  transcription cofactor vestigial-like protein 4 isoform X5

  8. XM_024453837.2 → XP_024309605.1  transcription cofactor vestigial-like protein 4 isoform X7

    UniProtKB/TrEMBL
    E7EQU6
    Related
    ENSP00000394439.1, ENST00000418000.5
    Conserved Domains (1) summary
    pfam15245
    Location:8 → 204
    VGLL4; Transcription cofactor vestigial-like protein 4

  9. XM_047449263.1 → XP_047305219.1  transcription cofactor vestigial-like protein 4 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    11551371..11717542 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348499.1 → XP_054204474.1  transcription cofactor vestigial-like protein 4 isoform X1

  2. XM_054348501.1 → XP_054204476.1  transcription cofactor vestigial-like protein 4 isoform X3

    UniProtKB/Swiss-Prot
    B4DTS7, J3KN68, Q14135, Q7L5V0, Q9BQ78

  3. XM_054348502.1 → XP_054204477.1  transcription cofactor vestigial-like protein 4 isoform X3

    UniProtKB/Swiss-Prot
    B4DTS7, J3KN68, Q14135, Q7L5V0, Q9BQ78

  4. XM_054348500.1 → XP_054204475.1  transcription cofactor vestigial-like protein 4 isoform X2

  5. XM_054348503.1 → XP_054204478.1  transcription cofactor vestigial-like protein 4 isoform X8

  6. XM_054348507.1 → XP_054204482.1  transcription cofactor vestigial-like protein 4 isoform X8

  7. XM_054348504.1 → XP_054204479.1  transcription cofactor vestigial-like protein 4 isoform X5

  8. XM_054348506.1 → XP_054204481.1  transcription cofactor vestigial-like protein 4 isoform X7

  9. XM_054348505.1 → XP_054204480.1  transcription cofactor vestigial-like protein 4 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q14135.4 GenPept UniProtKB/Swiss-Prot:Q14135

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