VWA5B2

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

Basic information

Region (hg38): 3:184229584-184242329

Links

ENSG00000145198 ∙ NCBI:90113 ∙ ∙ HGNC:25144 ∙ Uniprot:Q8N398 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (55 variants)
• not provided (2 variants)

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		2
missense			53	2		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	4	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)
3-184230888-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)
3-184233388-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)
3-184235208-C-T		not specified	Likely benign (Mar 23, 2022)
3-184236201-A-G		not specified	Uncertain significance (Jan 26, 2023)
3-184236219-C-T		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

Recessive Scores

• pRec: 0.0978

Intolerance Scores

• rvis_EVS: 1.37
• rvis_percentile_EVS: 94.49

Haploinsufficiency Scores

• 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