HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
VCX3A
variable charge X-linked 3A
Chromosome X · Xp22.31
NCBI Gene: 51481Ensembl: ENSG00000169059.14HGNC: HGNC:18159UniProt: Q9NNX9
12PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
brain developmentnucleusnucleolusinsomniarecessive X-linked ichthyosisIntellectual disabilityglioma
✦AI Summary

VCX3A is an X-linked cancer/testis antigen with emerging roles in both germ cell development and oncology. VCX3A functions as a DNA methylation-dependent gene, predominantly expressed in testicular tissue and aberrantly activated in multiple cancer types 1. In normal physiology, VCX3A may participate in spermatogenesis, as whole-genome sequencing identified novel VCX3A variants in patients with nonobstructive azoospermia 2. Mechanistically, VCX3A is regulated by histone modifications; in pediatric high-grade gliomas harboring H3.3K27M mutations, decreased H3K27me3 and increased H3K4me3 at the VCX3A promoter drive its upregulation 3. VCX3A knockdown significantly inhibited glioma cell growth, and VCX3A overexpression stimulated HLA gene expression, suggesting immune regulatory functions 3. Clinically, VCX3A is expressed in approximately 20-35% of lung cancers as a potential immunotherapeutic target 4. Deletions encompassing VCX3A occur in X-linked ichthyosis and have been associated with mental retardation in some patients with complex deletions involving multiple genes 5, 6, though VCX3A deletion alone appears insufficient for cognitive phenotypes. VCX3A represents a promising biomarker and therapeutic target in pediatric gliomas and lung cancers.

Sources cited
1
VCX3A is upregulated in H3.3K27M pediatric gliomas through altered histone modifications; knockdown inhibits cell growth; overexpression stimulates HLA genes
PMID: 29453317
2
Novel VCX3A variants identified as potential disease-causing mutations in patients with nonobstructive azoospermia
PMID: 36017582
3
VCX3A is a DNA methylation-dependent X-linked cancer/testis gene with maternal-specific imprinting in early embryos
PMID: 41091706
4
VCX3A is expressed as a cancer/testis antigen in approximately 20% of lung adenocarcinomas and 35% of squamous cell carcinomas
PMID: 24970476
5
VCX3A deletion occurs in X-linked ichthyosis but is not sufficient alone to cause mental retardation
PMID: 18076704
6
VCX3A deletions in complex Xp22.3 rearrangements may contribute to mental retardation in contiguous gene deletion syndromes
PMID: 23791652
Disease Associationsⓘ20
insomniaOpen Targets
0.02Suggestive
recessive X-linked ichthyosisOpen Targets
0.02Suggestive
Intellectual disabilityOpen Targets
0.01Suggestive
gliomaOpen Targets
0.00Suggestive
ichthyosisOpen Targets
0.00Suggestive
cancerOpen Targets
0.00Suggestive
hereditary neuropathy with liability to pressure palsiesOpen Targets
0.00Suggestive
metabolic syndromeOpen Targets
0.00Suggestive
Parkinson diseaseOpen Targets
0.00Suggestive
prostate cancerOpen Targets
0.00Suggestive
small cell osteogenic sarcomaOpen Targets
0.00Suggestive
Cognitive impairmentOpen Targets
0.00Suggestive
partial epilepsyOpen Targets
0.00Suggestive
autismOpen Targets
0.00Suggestive
focal segmental glomerulosclerosisOpen Targets
0.00Suggestive
infertilityOpen Targets
0.00Suggestive
lung adenocarcinomaOpen Targets
0.00Suggestive
mental or behavioural disorderOpen Targets
0.00Suggestive
obesityOpen Targets
0.00Suggestive
StrabismusOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
FOXG1Shared pathway100%VCYShared pathway100%PHGDHShared pathway100%MATCAP1Shared pathway100%FOXR1Shared pathway100%DNAJC30Shared pathway100%
Tissue Expression6 tissues
Bone Marrow
100%
Lung
0%
Ovary
0%
Brain
0%
Heart
0%
Liver
0%
Gene Interaction Network
Click a node to explore
VCX3AFOXG1VCYPHGDHMATCAP1FOXR1DNAJC30
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9NNX9
View on AlphaFold ↗
RankingsWhere VCX3A stands among ~20K protein-coding genes
  • #16,616of 20,598
    Most Researched12
Genes detectedVCX3A
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Histone H3.3K27M Mobilizes Multiple Cancer/Testis (CT) Antigens in Pediatric Glioma.
PMID: 29453317
Mol Cancer Res · 2018
1.00
2
Whole-genome sequencing identifies new candidate genes for nonobstructive azoospermia.
PMID: 36017582
Andrology · 2022
0.90
3
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.
PMID: 18076704
Br J Dermatol · 2008
0.80
4
Xp22.3 interstitial deletion: a recognizable chromosomal abnormality encompassing VCX3A and STS genes in a patient with X-linked ichthyosis and mental retardation.
PMID: 23791652
Gene · 2013
0.70
5
A survey of human cancer-germline genes: Linking X chromosome localization, DNA methylation and sex-biased expression in early embryos.
PMID: 41091706
PLoS Genet · 2025
0.60