VCX3A Gene

HGNC Family Variable charge X/Y family (VCX, VCY)
Name variable charge, X-linked 3A
Description This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes, and all are expressed exclusively in male germ cells. The X-linked members are clustered on chromosome Xp22 and Y-linked members are two identical copies of the gene within a palindromic region on Yq11. The family members share a high degree of sequence identity, with the exception that a 30-bp unit is tandemly repeated in X-linked members but occurs only once in Y-linked members. The VCX gene cluster is polymorphic in terms of copy number; different individuals may have a different number of VCX genes. VCX/Y genes encode small and highly charged proteins of unknown function. The presence of a putative bipartite nuclear localization signal suggests that VCX/Y members are nuclear proteins. This gene contains 8 repeats of the 30-bp unit. [provided by RefSeq, Jul 2008]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nVCX3A (also referred to as VCX‐A in several studies) has been identified as a noncanonical cap‐binding protein that regulates mRNA stability by inhibiting decapping. In biochemical and cell‐based assays, VCX3A binds to the 5′ end of capped mRNAs and interferes with the decapping activity of hDcp2, thereby protecting transcripts from degradation. This tissue‐specific decapping regulation highlights a posttranscriptional mechanism whereby VCX3A influences gene expression patterns."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nGenetic observations further suggest that VCX3A plays a role in neurodevelopment. In patients with X‐linked ichthyosis who display mental retardation, terminal deletions of Xp22.3 eliminate VCX3A as the sole gene within a critical region, implicating its loss in cognitive deficits. This genetic association supports the hypothesis that proper VCX3A function may be essential for normal intellectual development."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nMoreover, studies in neuronal models reveal that VCX3A is ubiquitously expressed in brain tissues and becomes enriched in distinct cytoplasmic foci that co-localize with RNA granules during differentiation. Its ability to bind a subset of mRNAs involved in neuritogenesis, coupled with functional assays showing that overexpression promotes neurite arborization while knockdown diminishes both primary and secondary neurite projections, emphasizes a role in translational suppression and mRNA transport. Hence, VCX3A contributes to the regulation of neuronal differentiation and morphology, providing a molecular link between RNA metabolism and neurodevelopmental processes."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Xinfu Jiao, Zuoren Wang, Megerditch Kiledjian "}, {"type": "b", "children": [{"type": "t", "text": "Identification of an mRNA-decapping regulator implicated in X-linked mental retardation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2006.10.013"}], "href": "https://doi.org/10.1016/j.molcel.2006.10.013"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17157254"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17157254"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "S A Cuevas-Covarrubias, L M González-Huerta "}, {"type": "b", "children": [{"type": "t", "text": "Analysis of the VCX3A, VCX2 and VCX3B genes shows that VCX3A gene deletion is not sufficient to result in mental retardation in X-linked ichthyosis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Br J Dermatol (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/j.1365-2133.2007.08373.x"}], "href": "https://doi.org/10.1111/j.1365-2133.2007.08373.x"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18076704"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18076704"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Xinfu Jiao, Hongxin Chen, Jianmin Chen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Modulation of neuritogenesis by a protein implicated in X-linked mental retardation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Neurosci (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1523/JNEUROSCI.5954-08.2009"}], "href": "https://doi.org/10.1523/JNEUROSCI.5954-08.2009"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19812318"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19812318"}]}]}]}
Synonyms VCX-8R, VCX-A, VCX8R, VCX3, VCXA
Proteins VCX3_HUMAN
NCBI Gene ID 51481
API
Download Associations
Predicted Functions View VCX3A's ARCHS4 Predicted Functions.
Co-expressed Genes View VCX3A's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View VCX3A's ARCHS4 Predicted Functions.

Functional Associations

VCX3A has 2,062 functional associations with biological entities spanning 8 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 55 datasets.

Click the + buttons to view associations for VCX3A from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles tissues with high or low expression of VCX3A gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles tissue samples with high or low expression of VCX3A gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles tissues with high or low expression of VCX3A gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
Carcinogenome Chemical Perturbation Carcinogenicity Signatures small molecule perturbations changing expression of VCX3A gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
CCLE Cell Line Gene CNV Profiles cell lines with high or low copy number of VCX3A gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
CellMarker Gene-Cell Type Associations cell types associated with VCX3A gene from the CellMarker Gene-Cell Type Associations dataset.
ChEA Transcription Factor Binding Site Profiles transcription factor binding site profiles with transcription factor binding evidence at the promoter of VCX3A gene from the CHEA Transcription Factor Binding Site Profiles dataset.
ChEA Transcription Factor Targets transcription factors binding the promoter of VCX3A gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
ChEA Transcription Factor Targets 2022 transcription factors binding the promoter of VCX3A gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
CM4AI KOLF21J CRISPRi Gene Perturbation Atlas gene perturbations changing expression of VCX3A gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores cellular components containing VCX3A protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores 2025 cellular components containing VCX3A protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
COMPARTMENTS Text-mining Protein Localization Evidence Scores cellular components co-occuring with VCX3A protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 cellular components co-occuring with VCX3A protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
COSMIC Cell Line Gene CNV Profiles cell lines with high or low copy number of VCX3A gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
COSMIC Cell Line Gene Mutation Profiles cell lines with VCX3A gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
DISEASES Text-mining Gene-Disease Association Evidence Scores diseases co-occuring with VCX3A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 diseases co-occuring with VCX3A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
DisGeNET Gene-Disease Associations diseases associated with VCX3A gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
ENCODE Transcription Factor Binding Site Profiles transcription factor binding site profiles with transcription factor binding evidence at the promoter of VCX3A gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
ENCODE Transcription Factor Targets transcription factors binding the promoter of VCX3A gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
GeneRIF Biological Term Annotations biological terms co-occuring with VCX3A gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
GeneSigDB Published Gene Signatures PubMedIDs of publications reporting gene signatures containing VCX3A from the GeneSigDB Published Gene Signatures dataset.
GEO Signatures of Differentially Expressed Genes for Diseases disease perturbations changing expression of VCX3A gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset.
GEO Signatures of Differentially Expressed Genes for Small Molecules small molecule perturbations changing expression of VCX3A gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset.
GEO Signatures of Differentially Expressed Genes for Viral Infections virus perturbations changing expression of VCX3A gene from the GEO Signatures of Differentially Expressed Genes for Viral Infections dataset.
GO Biological Process Annotations 2015 biological processes involving VCX3A gene from the curated GO Biological Process Annotations 2015 dataset.
GO Biological Process Annotations 2023 biological processes involving VCX3A gene from the curated GO Biological Process Annotations 2023 dataset.
GO Biological Process Annotations 2025 biological processes involving VCX3A gene from the curated GO Biological Process Annotations2025 dataset.
GO Cellular Component Annotations 2015 cellular components containing VCX3A protein from the curated GO Cellular Component Annotations 2015 dataset.
GO Cellular Component Annotations 2023 cellular components containing VCX3A protein from the curated GO Cellular Component Annotations 2023 dataset.
GO Cellular Component Annotations 2025 cellular components containing VCX3A protein from the curated GO Cellular Component Annotations 2025 dataset.
GTEx Tissue Gene Expression Profiles tissues with high or low expression of VCX3A gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset.
GTEx Tissue Gene Expression Profiles 2023 tissues with high or low expression of VCX3A gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
GWAS Catalog SNP-Phenotype Associations 2025 phenotypes associated with VCX3A gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset.
Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles cell lines with high or low expression of VCX3A gene relative to other cell lines from the Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles dataset.
HPA Cell Line Gene Expression Profiles cell lines with high or low expression of VCX3A gene relative to other cell lines from the HPA Cell Line Gene Expression Profiles dataset.
HPA Tissue Gene Expression Profiles tissues with high or low expression of VCX3A gene relative to other tissues from the HPA Tissue Gene Expression Profiles dataset.
HPA Tissue Protein Expression Profiles tissues with high or low expression of VCX3A protein relative to other tissues from the HPA Tissue Protein Expression Profiles dataset.
InterPro Predicted Protein Domain Annotations protein domains predicted for VCX3A protein from the InterPro Predicted Protein Domain Annotations dataset.
JASPAR Predicted Human Transcription Factor Targets 2025 transcription factors regulating expression of VCX3A gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset.
JASPAR Predicted Transcription Factor Targets transcription factors regulating expression of VCX3A gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Transcription Factor Targets dataset.
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles cell lines with high or low copy number of VCX3A gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset.
KnockTF Gene Expression Profiles with Transcription Factor Perturbations transcription factor perturbations changing expression of VCX3A gene from the KnockTF Gene Expression Profiles with Transcription Factor Perturbations dataset.
LOCATE Curated Protein Localization Annotations cellular components containing VCX3A protein in low- or high-throughput protein localization assays from the LOCATE Curated Protein Localization Annotations dataset.
LOCATE Predicted Protein Localization Annotations cellular components predicted to contain VCX3A protein from the LOCATE Predicted Protein Localization Annotations dataset.
PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations gene perturbations changing expression of VCX3A gene from the PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
Rummagene Transcription Factor Associations 2026 transcription factors regulating expression of VCX3A gene from the Rummagene Transcription Factor Associations 2026 dataset.
RummaGEO Drug Perturbation Signatures drug perturbations changing expression of VCX3A gene from the RummaGEO Drug Perturbation Signatures dataset.
RummaGEO Gene Perturbation Signatures gene perturbations changing expression of VCX3A gene from the RummaGEO Gene Perturbation Signatures dataset.
TargetScan Predicted Nonconserved microRNA Targets microRNAs regulating expression of VCX3A gene predicted using nonconserved miRNA seed sequences from the TargetScan Predicted Nonconserved microRNA Targets dataset.
TCGA Signatures of Differentially Expressed Genes for Tumors tissue samples with high or low expression of VCX3A gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset.
TISSUES Experimental Tissue Protein Expression Evidence Scores tissues with high expression of VCX3A protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores dataset.
TISSUES Text-mining Tissue Protein Expression Evidence Scores tissues co-occuring with VCX3A protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores dataset.
TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 tissues co-occuring with VCX3A protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset.