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    VGLL3 vestigial like family member 3 [ Homo sapiens (human) ]

    Gene ID: 389136, updated on 10-Mar-2024

    Summary

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    Official Symbol
    VGLL3provided by HGNC
    Official Full Name
    vestigial like family member 3provided by HGNC
    Primary source
    HGNC:HGNC:24327
    See related
    Ensembl:ENSG00000206538 MIM:609980; AllianceGenome:HGNC:24327
    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
    VGL3; VGL-3
    Summary
    Predicted to enable protein C-terminus binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in placenta (RPKM 19.8), fat (RPKM 7.7) and 12 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    3p12.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (86937973..86991149, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (87012305..87065510, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (86987123..87040299, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927518 Neighboring gene MPRA-validated peak4735 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:86925274-86925774 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:86940033-86940783 Neighboring gene uncharacterized LOC105377196 Neighboring gene MPRA-validated peak4737 silencer Neighboring gene MPRA-validated peak4738 silencer Neighboring gene phosphoribosyl pyrophosphate amidotransferase pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20109 Neighboring gene phosphoribosyl pyrophosphate amidotransferase pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 506

    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. Regulation of type I interferon signature by VGLL3 in the fibroblast-like synoviocytes of rheumatoid arthritis patients via targeting the Hippo pathway. Du Y, et al. Arthritis Res Ther, 2022 Aug 8. PMID 35941675, Free PMC Article
    2. Recurrent VGLL3 fusions define a distinctive subset of spindle cell rhabdomyosarcoma with an indolent clinical course and striking predilection for the head and neck. Agaimy A, et al. Genes Chromosomes Cancer, 2022 Dec. PMID 35766997, Free PMC Article
    3. Clinicopathologic and Molecular Study of Hybrid Nerve Sheath Tumors Reveals Their Common Association With Fusions Involving VGLL3. Nihous H, et al. Am J Surg Pathol, 2022 May 1. PMID 35256555
    4. VGLL3 activates inflammatory responses by inducing interleukin-1α secretion. Takakura Y, et al. FASEB J, 2021 Nov. PMID 34679187
    5. Hybrid schwannoma-perineurioma frequently harbors VGLL3 rearrangement. Dickson BC, et al. Mod Pathol, 2021 Jun. PMID 33649458, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Exploring the potential of VGLL3 methylation as a prognostic indicator for intracranial aneurysm with gender-specific considerations.
      Title: Exploring the potential of VGLL3 methylation as a prognostic indicator for intracranial aneurysm with gender-specific considerations.
    2. VGLL3 is a mechanosensitive protein that promotes cardiac fibrosis through liquid-liquid phase separation.
      Title: VGLL3 is a mechanosensitive protein that promotes cardiac fibrosis through liquid-liquid phase separation.
    3. Recurrent VGLL3 fusions define a distinctive subset of spindle cell rhabdomyosarcoma with an indolent clinical course and striking predilection for the head and neck.
      Title: Recurrent VGLL3 fusions define a distinctive subset of spindle cell rhabdomyosarcoma with an indolent clinical course and striking predilection for the head and neck.
    4. Regulation of type I interferon signature by VGLL3 in the fibroblast-like synoviocytes of rheumatoid arthritis patients via targeting the Hippo pathway.
      Title: Regulation of type I interferon signature by VGLL3 in the fibroblast-like synoviocytes of rheumatoid arthritis patients via targeting the Hippo pathway.
    5. VGLL3 increases the dependency of cancer cells on de novo nucleotide synthesis through GART expression.
      Title: VGLL3 increases the dependency of cancer cells on de novo nucleotide synthesis through GART expression.
    6. Clinicopathologic and Molecular Study of Hybrid Nerve Sheath Tumors Reveals Their Common Association With Fusions Involving VGLL3.
      Title: Clinicopathologic and Molecular Study of Hybrid Nerve Sheath Tumors Reveals Their Common Association With Fusions Involving VGLL3.
    7. Hybrid schwannoma-perineurioma frequently harbors VGLL3 rearrangement.
      Title: Hybrid schwannoma-perineurioma frequently harbors VGLL3 rearrangement.
    8. VGLL3 activates inflammatory responses by inducing interleukin-1alpha secretion.
      Title: VGLL3 activates inflammatory responses by inducing interleukin-1α secretion.
    9. Immunometabolic function of the transcription cofactor VGLL3 provides an evolutionary rationale for sexual dimorphism in autoimmunity.
      Title: Immunometabolic function of the transcription cofactor VGLL3 provides an evolutionary rationale for sexual dimorphism in autoimmunity.
    10. A new perspective on the interaction between the Vg/VGLL1-3 proteins and the TEAD transcription factors.
      Title: A new perspective on the interaction between the Vg/VGLL1-3 proteins and the TEAD transcription factors.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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 search for loci interacting with known prostate cancer risk-associated genetic variants.
    EBI GWAS Catalog
    Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ38507, DKFZp686O1845

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    transcription cofactor vestigial-like protein 3
    Names
    colon carcinoma related protein

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001320493.2 → NP_001307422.1  transcription cofactor vestigial-like protein 3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 3' terminal exon, resulting in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC108709, BC094780, DA828655
      Consensus CDS
      CCDS82807.1
      UniProtKB/Swiss-Prot
      A8MV65
      Related
      ENSP00000373199.3, ENST00000383698.3
      Conserved Domains (1) summary
      pfam07545
      Location:82 → 112
      Vg_Tdu; Vestigial/Tondu family

    2. NM_001320494.2 → NP_001307423.1  transcription cofactor vestigial-like protein 3 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AC108709
      Conserved Domains (1) summary
      pfam07545
      Location:42 → 59
      Vg_Tdu; Vestigial/Tondu family

    3. NM_016206.4 → NP_057290.2  transcription cofactor vestigial-like protein 3 isoform 1

      See identical proteins and their annotated locations for NP_057290.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA455617, AC108709, AI379920, BC094780, DA828655, DB319377
      Consensus CDS
      CCDS43110.1
      UniProtKB/Swiss-Prot
      A8MV65, D3DU37, Q504T7
      Related
      ENSP00000381436.2, ENST00000398399.7
      Conserved Domains (1) summary
      pfam07545
      Location:82 → 112
      Vg_Tdu; Vestigial/Tondu family

    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
      86937973..86991149 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006713138.5 → XP_006713201.1  transcription cofactor vestigial-like protein 3 isoform X1

      See identical proteins and their annotated locations for XP_006713201.1

      Conserved Domains (1) summary
      pfam07545
      Location:81 → 111
      Vg_Tdu; Vestigial/Tondu family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      87012305..87065510 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346475.1 → XP_054202450.1  transcription cofactor vestigial-like protein 3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A8MV65.1 GenPept UniProtKB/Swiss-Prot:A8MV65

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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