VWA3A

von Willebrand factor A domain containing 3A

Basic information

Region (hg38): 16:22092538-22156964

Links

ENSG00000175267 ∙ NCBI:146177 ∙ ∙ HGNC:27088 ∙ Uniprot:A6NCI4 ∙ 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 VWA3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VWA3A 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				1		1
missense			59	6		65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	59	7	0

Variants in VWA3A

This is a list of pathogenic ClinVar variants found in the VWA3A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-22096897-C-G		not specified	Uncertain significance (Sep 07, 2022)
16-22096906-T-C		not specified	Uncertain significance (May 12, 2024)
16-22100228-G-C		not specified	Uncertain significance (Apr 07, 2023)
16-22100228-G-T		not specified	Uncertain significance (Nov 20, 2023)
16-22100314-G-A		not specified	Uncertain significance (Dec 28, 2023)
16-22100435-G-A		not specified	Likely benign (Dec 19, 2023)
16-22100441-A-G		not specified	Uncertain significance (Aug 02, 2021)
16-22100468-C-T		not specified	Uncertain significance (Jul 20, 2021)
16-22100469-G-A		not specified	Likely benign (Jan 26, 2023)
16-22109548-C-T		not specified	Uncertain significance (Mar 28, 2024)
16-22110896-C-G		not specified	Uncertain significance (Dec 17, 2023)
16-22110897-G-A		not specified	Uncertain significance (May 08, 2024)
16-22110900-G-A		not specified	Uncertain significance (Oct 22, 2021)
16-22110952-C-T		not specified	Uncertain significance (Nov 21, 2022)
16-22115376-C-T		not specified	Uncertain significance (May 30, 2024)
16-22115397-G-A		not specified	Uncertain significance (Jan 24, 2023)
16-22115423-A-T		not specified	Uncertain significance (May 11, 2022)
16-22115453-G-C		not specified	Uncertain significance (Feb 28, 2024)
16-22116814-A-G		not specified	Uncertain significance (Mar 16, 2022)
16-22116834-C-A		not specified	Uncertain significance (Dec 01, 2022)
16-22116848-G-A		not specified	Uncertain significance (Jun 11, 2024)
16-22116850-G-A		not specified	Uncertain significance (Jun 12, 2023)
16-22116859-A-T		not specified	Uncertain significance (Apr 22, 2022)
16-22118936-C-A		not specified	Uncertain significance (Jun 11, 2024)
16-22118984-A-C		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VWA3A	protein_coding	protein_coding	ENST00000389398	33	64429

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.68e-25	0.370	124198	1	457	124656	0.00184

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.714	581	631	0.920	0.0000340	7734
Missense in Polyphen		134	142.57	0.93991		1769
Synonymous	2.00	210	250	0.839	0.0000148	2174
Loss of Function	2.11	49	67.7	0.723	0.00000315	838

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0121	0.0121
Ashkenazi Jewish	0.0000997	0.0000994
East Asian	0.00896	0.00827
Finnish	0.000190	0.000186
European (Non-Finnish)	0.000404	0.000398
Middle Eastern	0.00896	0.00827
South Asian	0.00179	0.00173
Other	0.000678	0.000660

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.831
• rvis_EVS: 1.66
• rvis_percentile_EVS: 96.21

Haploinsufficiency Scores

• pHI: 0.223
• hipred: N
• hipred_score: 0.170
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0469

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vwa3a

Gene ontology

• Cellular component: extracellular region