VWA2

von Willebrand factor A domain containing 2

Basic information

Region (hg38): 10:114239254-114294489

Links

ENSG00000165816 ∙ NCBI:340706 ∙ OMIM:618281 ∙ HGNC:24709 ∙ Uniprot:Q5GFL6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital anomaly of kidney and urinary tract (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VWA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VWA2 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				15	9	24
missense			7	10	8	25
nonsense						0
start loss						0
frameshift				1		1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	0	7	27	17

Variants in VWA2

This is a list of pathogenic ClinVar variants found in the VWA2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-114248705-T-A		VWA2-related disorder	Benign (Sep 17, 2019)
10-114248760-C-T		VWA2-related disorder	Uncertain significance (Sep 25, 2023)
10-114253700-C-T			Benign (Oct 24, 2018)
10-114254993-G-T		VWA2-related disorder	Likely benign (Nov 17, 2020)
10-114255010-A-T			Benign (Dec 31, 2019)
10-114261198-G-A		VWA2-related disorder	Likely benign (May 22, 2023)
10-114261236-C-T		VWA2-related disorder	Likely benign (Feb 12, 2020)
10-114261281-G-A		VWA2-related disorder	Likely benign (Jun 18, 2019)
10-114272786-A-C		VWA2-related disorder	Likely benign (Dec 11, 2023)
10-114277941-C-T		VWA2-related disorder	Benign (Jul 18, 2018)
10-114277995-C-T		VWA2-related disorder	Likely benign (Feb 22, 2019)
10-114278022-G-A		VWA2-related disorder	Benign (Oct 10, 2018)
10-114278053-A-C		VWA2-related disorder	Benign (Dec 31, 2019)
10-114278756-G-A		VWA2-related disorder	Benign (Oct 13, 2022)
10-114278759-G-A			Benign (Oct 24, 2018)
10-114278774-G-A		VWA2-related disorder	Likely benign (Oct 11, 2021)
10-114278812-G-A		VWA2-related disorder	Uncertain significance (Apr 05, 2024)
10-114284921-C-T		VWA2-related disorder	Likely benign (Feb 10, 2020)
10-114284932-G-A		VWA2-related disorder	Uncertain significance (Jul 28, 2023)
10-114284966-C-T			Benign (Dec 20, 2018)
10-114285935-G-A		VWA2-related disorder	Likely benign (Jun 08, 2018)
10-114285997-G-A			Benign (Dec 20, 2018)
10-114286012-C-T		VWA2-related disorder	Likely benign (May 06, 2024)
10-114286036-C-T			Benign (May 02, 2018)
10-114286037-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VWA2	protein_coding	protein_coding	ENST00000603594	11	52255

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.22e-17	0.00540	125403	2	343	125748	0.00137

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0123	457	456	1.00	0.0000288	4642
Missense in Polyphen		131	127.95	1.0238		1568
Synonymous	-0.0506	201	200	1.00	0.0000132	1580
Loss of Function	0.00627	26	26.0	0.999	0.00000127	304

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00441	0.00441
Ashkenazi Jewish	0.00	0.00
East Asian	0.00382	0.00365
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000572	0.000563
Middle Eastern	0.00382	0.00365
South Asian	0.00198	0.00193
Other	0.00119	0.00114

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.258
• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.24

Haploinsufficiency Scores

• pHI: 0.0699
• hipred: N
• hipred_score: 0.238
• ghis: 0.385

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Vwa2

Gene ontology

• Biological process: growth plate cartilage chondrocyte morphogenesis;calcium-independent cell-matrix adhesion;regulation of insulin receptor signaling pathway;protein homooligomerization
• Cellular component: basement membrane;extracellular space;extracellular matrix;extracellular exosome
• Molecular function: calcium ion binding;protein binding;identical protein binding