VWA3A
protein-codingvon Willebrand factor A domain containing 3A
Gene summary
Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~64.4 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 VWA3A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_173615.5. 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 | 2 | 3 | |||
| missense | 178 | 12 | 190 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 185 | 14 | 0 | 199 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_775886.3 | 33 | MANE Select | |
| Ensembl | ENSP00000374049.5 | 33 | MANE Select | |
| Ensembl | ENSP00000299840.6 | 13 | Standard | |
| Ensembl | ENSP00000457167.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- extracellular region
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000389398
- Coding exons
- 33
- Length
- 64429
- Individuals with no LoFs
- 124198
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 457
- Defined
- 124656
- p
- 0.00184
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.714 | 581 | 631 | 0.920 | 0.0000340 | 7734 |
| Missense (PolyPhen) | 134 | 142.57 | 0.93991 | 1769 | ||
| Synonymous | 2.00 | 210 | 250 | 0.839 | 0.0000148 | 2174 |
| Loss of Function | 2.11 | 49 | 67.7 | 0.723 | 0.00000315 | 838 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.011 | 0.011 | notable |
| Latino/Admixed American | 0.00091 | 0.00090 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.0090 | 0.0083 | notable |
| Finnish | 0.00019 | 0.00019 | rare |
| European (Non-Finnish) | 0.00040 | 0.00040 | rare |
| South Asian | 0.0018 | 0.0017 | notable |
| Other | 0.00068 | 0.00066 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.831
- RVIS EVS
- 1.66
- RVIS percentile EVS
- 96.21
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0469
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |