VXN
protein-codingvexin
Gene summary
Predicted to be involved in neuron differentiation. Predicted to be located in nucleus and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
- C8orf46
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to VXN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152765.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 2 | 2 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 | 3 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689978.2 | 6 | MANE Select | |
| Ensembl | ENSP00000302260.3 | 6 | MANE Select | |
| Ensembl | ENSP00000473681.1 | 3 | Standard | |
| Ensembl | ENSP00000430388.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- neurogenesis
- neuron differentiation
Cellular Component
- nucleus
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000305454
- Coding exons
- 6
- Length
- 58522
- Individuals with no LoFs
- 125742
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 125747
- p
- 0.0000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.994 | 91 | 122 | 0.747 | 0.00000749 | 1296 |
| Missense (PolyPhen) | 39 | 51.489 | 0.75744 | 571 | ||
| Synonymous | 0.436 | 44 | 47.8 | 0.920 | 0.00000297 | 432 |
| Loss of Function | 2.00 | 3 | 9.76 | 0.308 | 4.75e-7 | 124 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Required for neurogenesis in the neural plate and retina. Strongly cooperates with neural bHLH factors to promote neurogenesis. {ECO:0000250|UniProtKB:Q8BG31}.;
Intolerance Scores
- RVIS EVS
- -0.21
- RVIS percentile EVS
- 38.28
Essentials
- Essential (gene trap)
- N