VWA5B2

von Willebrand factor A domain containing 5B2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 3:184229585-184242329

Links

ENSG00000145198NCBI:90113HGNC:25144Uniprot:Q8N398AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VWA5B2 gene.

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
clinvar
2
missense
74
clinvar
3
clinvar
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)3189336
3-184230595-T-C not specified Uncertain significance (Jan 31, 2022)2274768
3-184230604-G-A not specified Uncertain significance (Nov 07, 2022)2322534
3-184230629-G-A not specified Uncertain significance (Jan 31, 2024)3189316
3-184230754-C-G not specified Uncertain significance (Jun 11, 2021)2406621
3-184230857-G-T not specified Uncertain significance (Mar 20, 2024)3332455
3-184230888-G-A not specified Uncertain significance (Sep 17, 2021)2251957
3-184230893-C-A not specified Uncertain significance (Dec 31, 2023)3189328
3-184230912-C-T not specified Uncertain significance (Nov 29, 2021)2398550
3-184233341-G-T Likely benign (Jun 01, 2022)2654310
3-184233349-C-T not specified Uncertain significance (Apr 12, 2024)3332463
3-184233388-G-T not specified Uncertain significance (Jul 06, 2021)2225585
3-184233393-G-A not specified Uncertain significance (Jun 09, 2022)2222563
3-184233620-T-G not specified Uncertain significance (Aug 17, 2022)2364502
3-184233677-C-T not specified Uncertain significance (Jul 14, 2022)2238899
3-184233700-G-A not specified Uncertain significance (Nov 22, 2023)3189337
3-184234302-C-G not specified Uncertain significance (May 11, 2022)2289288
3-184234305-C-T not specified Uncertain significance (Jul 14, 2021)2231050
3-184234310-C-A not specified Uncertain significance (Sep 01, 2021)2248207
3-184234343-C-G not specified Uncertain significance (Dec 18, 2023)3189338
3-184234368-G-A not specified Uncertain significance (Jan 25, 2023)2463460
3-184234632-G-C not specified Uncertain significance (Feb 15, 2023)2484710
3-184234693-C-T not specified Uncertain significance (Apr 27, 2023)2541419
3-184234750-C-T not specified Uncertain significance (Jul 09, 2021)2230343
3-184234751-G-A not specified Uncertain significance (Jun 10, 2024)3332460

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
VWA5B2protein_codingprotein_codingENST00000426955 1911901
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.25e-71.0000000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.524706510.7220.00003937762
Missense in Polyphen124184.680.671442391
Synonymous1.962352770.8500.00001642820
Loss of Function3.751946.70.4070.00000274525

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Vwa5b2
Phenotype