VWA5A
protein-codingvon Willebrand factor A domain containing 5A
Gene summary
Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
- LOH11CR2A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~32.3 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 VWA5A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001130142.2. 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 | 0 | |||||
| missense | 117 | 9 | 126 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 9 | 9 | ||||
| Total | 0 | 0 | 126 | 9 | 0 | 135 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001123614.1 | 17 | MANE Select | |
| Ensembl | ENSP00000407726.2 | 17 | MANE Select | |
| RefSeq | NP_055437.2 | 17 | Standard | |
| RefSeq | NP_938057.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- nucleus
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000456829
- Coding exons
- 17
- Length
- 32360
- Individuals with no LoFs
- 125598
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 150
- Defined
- 125748
- p
- 0.000597
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.599 | 466 | 431 | 1.08 | 0.0000220 | 5169 |
| Missense (PolyPhen) | 109 | 105.32 | 1.035 | 1349 | ||
| Synonymous | 1.10 | 146 | 164 | 0.891 | 0.00000885 | 1525 |
| Loss of Function | -0.714 | 41 | 36.4 | 1.13 | 0.00000179 | 438 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00062 | 0.00055 | rare |
| Latino/Admixed American | 0.00032 | 0.00032 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0016 | 0.0016 | notable |
| Finnish | 0.00042 | 0.00042 | rare |
| European (Non-Finnish) | 0.00057 | 0.00056 | rare |
| South Asian | 0.00086 | 0.00085 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in tumorigenesis as a tumor suppressor. Altered expression of this protein and disruption of the molecular pathway it is involved in, may contribute directly to or modify tumorigenesis.;
Intolerance Scores
- LoFtool
- 0.993
- RVIS EVS
- 0.65
- RVIS percentile EVS
- 84.15
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.151
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |