VCX3A
Variable charge X-linked 3A
Gene Information Card
| Symbol | VCX3A |
|---|---|
| Full Name | Variable charge X-linked 3A |
| Gene Type | Protein coding |
| Chromosomal Location | Xp22.31 |
| NCBI Gene ID | 51481 ncbi.nlm.nih.gov/gene/51481 |
| Ensembl ID | ENSG00000169057 |
| UniProt ID | Q9H4M9 |
| OMIM ID | 300229 |
| HGNC ID | 12673 |
| Aliases | VCX-3A, VCX3, VCX-3 |
Description
VCX3A (Variable charge X-linked 3A) is a protein-coding gene located on the X chromosome at Xp22.31. It belongs to the VCX/Y gene family, which is characterized by a variable number of tandem repeats encoding a positively charged protein. VCX3A is predominantly expressed in testis and brain, and its function is thought to involve spermatogenesis and neuronal development. The gene is subject to X-inactivation escape and has been implicated in X-linked intellectual disability and male infertility.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| X-linked intellectual disability | VCX3A copy number variation or deletion may disrupt neuronal gene expression networks, contributing to cognitive impairment. | OMIM #300229; case-control studies |
| Male infertility | Reduced VCX3A expression in testis may impair spermatogenesis. | PubMed; expression analysis in azoospermic males |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 12.5 | Medium |
| Brain (cerebral cortex) | 8.3 | Low |
| Prostate | 6.1 | Low |
| Thyroid | 4.7 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK293 | 15.2 | Moderate expression |
| SH-SY5Y | 9.8 | Neuronal cell line |
| NT2/D1 | 11.4 | Testicular embryonal carcinoma |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1A>G | Missense | <0.01% | Uncertain significance; may affect start codon |
| c.124C>T | Nonsense | <0.01% | Predicted loss of function |
Mutation functional classification
Loss of Function (LOF)
Nonsense or frameshift mutations leading to truncated protein; associated with reduced spermatogenesis in model systems.
Gain of Function (GOF)
Not reported for VCX3A.
Dominant Negative (DN)
Not reported for VCX3A.
View complete mutation data：
Gene Ontology (GO)
| • molecular_function (GO:0003674) | • cellular_component (GO:0005575) |
| • biological_process (GO:0008150) |
Protein Summary
VCX3A encodes a small, highly basic protein of approximately 10 kDa. The protein contains a variable number of tandem repeats rich in lysine and arginine, conferring a net positive charge. It is localized to the nucleus and may function in chromatin remodeling or RNA binding. Expression is enriched in testis and brain, suggesting roles in spermatogenesis and neurodevelopment.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| VCX3A Knockout HEK293 Cell Line | EDJ-KQ51321 | Human | 51481 | Details Get a Quote |
| VCX3A Knockout HeLa Cell Line | EDJ-KQ56320 | Human | 51481 | Details Get a Quote |
| VCX3A Knockout A-549 Cell Line | EDJ-KQ64807 | Human | 51481 | Details Get a Quote |
| VCX3A Knockout HCT 116 Cell Line | EDJ-KQ73252 | Human | 51481 | Details Get a Quote |
