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4 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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VCX3B
variable charge X-linked 3B
Chromosome X · Xp22.31
NCBI Gene: 425054Ensembl: ENSG00000205642.11HGNC: HGNC:31838UniProt: Q9H321
11PubMed Papers
3Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
brain developmentnucleusnucleolusrecessive X-linked ichthyosisprostate cancerebv-positive nodal t- and nk-cell lymphoma
✦AI Summary

VCX3B (variable charge X-linked 3B) is an X-linked gene with poorly characterized function. Current evidence suggests potential involvement in spermatogenesis and testicular fibrosis rather than primary cognitive development. VCX3B was identified as a differentially expressed X-linked gene in Klinefelter syndrome (47,XXY) testicular tissue, where it was upregulated in fibrotic compared to non-fibrotic samples, alongside genes involved in extracellular matrix remodeling and TGF-β pathway activation 1. The gene is also located within a large deletion region (4.8 Mb) that includes multiple X-linked genes (ANOS1, VCX2, PNPLA4, VCX, STS, HDHD1, VCX3A, NLGN4X) associated with Kallmann syndrome and ichthyosis 2. Analysis of VCX3B alongside related VCX family members in X-linked ichthyosis patients with normal intelligence suggests the gene does not independently cause intellectual disability 3. While GO annotations indicate nuclear localization and potential brain development involvement, clinical evidence supporting cognitive impairment from VCX3B alone is lacking. The gene's specific role in testicular fibrosis pathogenesis requires further investigation.

Sources cited
1
VCX3B identified as differentially expressed X-linked gene upregulated in fibrotic testicular tissue in Klinefelter syndrome
PMID: 36513788
2
VCX3B located within 4.8 Mb deletion involving multiple X-linked genes in Kallmann syndrome and ichthyosis
PMID: 28122887
3
VCX3B analysis in X-linked ichthyosis patients suggests VCX gene family deletion not solely responsible for mental retardation
PMID: 18076704
⚠Limited data available — This gene has 3 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ3
recessive X-linked ichthyosisOpen Targets
0.01Suggestive
prostate cancerOpen Targets
0.00Suggestive
ebv-positive nodal t- and nk-cell lymphomaOpen 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%CA10Shared pathway100%DNAJC30Shared pathway100%FOXR1Shared pathway100%
Tissue Expression6 tissues
Liver
100%
Ovary
80%
Bone Marrow
40%
Lung
40%
Brain
0%
Heart
0%
Gene Interaction Network
Click a node to explore
VCX3BFOXG1VCYPHGDHCA10DNAJC30FOXR1
PROTEIN STRUCTURE
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AlphaFoldAI-predicted · UniProt Q9H321
View on AlphaFold ↗
RankingsWhere VCX3B stands among ~20K protein-coding genes
  • #16,939of 20,598
    Most Researched11
Genes detectedVCX3B
Sources retrieved4 papers
Response time—
📄 Sources
4
1
Expanding the genetic spectrum of ANOS1 mutations in patients with congenital hypogonadotropic hypogonadism.
PMID: 28122887
Hum Reprod · 2017
1.00
2
Transcriptomic differences between fibrotic and non-fibrotic testicular tissue reveal possible key players in Klinefelter syndrome-related testicular fibrosis.
PMID: 36513788
Sci Rep · 2022
0.75
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
0.50
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
0.25