VWA5B2
Basic information
Region (hg38): 3:184229585-184242329
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VWA5B2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | |||||
missense | 74 | 77 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 74 | 5 | 0 |
Variants in VWA5B2
This is a list of pathogenic ClinVar variants found in the VWA5B2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-184230590-G-C | not specified | Uncertain significance (Jan 09, 2024) | ||
3-184230595-T-C | not specified | Uncertain significance (Jan 31, 2022) | ||
3-184230604-G-A | not specified | Uncertain significance (Nov 07, 2022) | ||
3-184230629-G-A | not specified | Uncertain significance (Jan 31, 2024) | ||
3-184230754-C-G | not specified | Uncertain significance (Jun 11, 2021) | ||
3-184230857-G-T | not specified | Uncertain significance (Mar 20, 2024) | ||
3-184230888-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
3-184230893-C-A | not specified | Uncertain significance (Dec 31, 2023) | ||
3-184230912-C-T | not specified | Uncertain significance (Nov 29, 2021) | ||
3-184233341-G-T | Likely benign (Jun 01, 2022) | |||
3-184233349-C-T | not specified | Uncertain significance (Apr 12, 2024) | ||
3-184233388-G-T | not specified | Uncertain significance (Jul 06, 2021) | ||
3-184233393-G-A | not specified | Uncertain significance (Jun 09, 2022) | ||
3-184233620-T-G | not specified | Uncertain significance (Aug 17, 2022) | ||
3-184233677-C-T | not specified | Uncertain significance (Jul 14, 2022) | ||
3-184233700-G-A | not specified | Uncertain significance (Nov 22, 2023) | ||
3-184234302-C-G | not specified | Uncertain significance (May 11, 2022) | ||
3-184234305-C-T | not specified | Uncertain significance (Jul 14, 2021) | ||
3-184234310-C-A | not specified | Uncertain significance (Sep 01, 2021) | ||
3-184234343-C-G | not specified | Uncertain significance (Dec 18, 2023) | ||
3-184234368-G-A | not specified | Uncertain significance (Jan 25, 2023) | ||
3-184234632-G-C | not specified | Uncertain significance (Feb 15, 2023) | ||
3-184234693-C-T | not specified | Uncertain significance (Apr 27, 2023) | ||
3-184234750-C-T | not specified | Uncertain significance (Jul 09, 2021) | ||
3-184234751-G-A | not specified | Uncertain significance (Jun 10, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
VWA5B2 | protein_coding | protein_coding | ENST00000426955 | 19 | 11901 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
5.25e-7 | 1.00 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.52 | 470 | 651 | 0.722 | 0.0000393 | 7762 |
Missense in Polyphen | 124 | 184.68 | 0.67144 | 2391 | ||
Synonymous | 1.96 | 235 | 277 | 0.850 | 0.0000164 | 2820 |
Loss of Function | 3.75 | 19 | 46.7 | 0.407 | 0.00000274 | 525 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
Recessive Scores
- pRec
- 0.0978
Intolerance Scores
- loftool
- rvis_EVS
- 1.37
- rvis_percentile_EVS
- 94.49
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.241
- ghis
- 0.419
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.102
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | High | Medium | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Vwa5b2
- Phenotype