VWA3B

von Willebrand factor A domain containing 3B

Basic information

Region (hg38): 2:98087116-98313299

Links

ENSG00000168658 ∙ NCBI:200403 ∙ OMIM:614884 ∙ HGNC:28385 ∙ Uniprot:Q502W6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spinocerebellar ataxia, autosomal recessive 22 (Limited), mode of inheritance: AR
• spinocerebellar ataxia, autosomal recessive 22 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia, autosomal recessive 22	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	26157035

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VWA3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VWA3B 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	6	21
missense			76	15	10	101
nonsense		1		1	2	4
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					3	3
Total	0	1	77	31	21

Variants in VWA3B

This is a list of pathogenic ClinVar variants found in the VWA3B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-98093112-C-T		not specified	Uncertain significance (Apr 18, 2023)
2-98093151-G-T		not specified	Uncertain significance (Jun 26, 2024)
2-98093210-C-T		not specified	Uncertain significance (Sep 03, 2024)
2-98093216-C-A		VWA3B-related disorder	Likely benign (Mar 03, 2022)
2-98093220-A-G		not specified	Uncertain significance (Aug 01, 2024)
2-98093229-A-G		not specified	Uncertain significance (Dec 13, 2023)
2-98093235-A-G		not specified	Uncertain significance (Nov 13, 2024)
2-98093236-C-G		not specified	Uncertain significance (Nov 14, 2024)
2-98093255-A-T		not specified	Uncertain significance (May 28, 2024)
2-98093276-C-T		not specified	Uncertain significance (Jul 19, 2023)
2-98115654-T-C		not specified	Uncertain significance (Jul 14, 2021)
2-98115662-G-A			Likely benign (Jul 31, 2018)
2-98115675-C-T		not specified	Uncertain significance (Apr 04, 2023)
2-98115697-A-G		not specified	Uncertain significance (Jan 23, 2024)
2-98115726-G-A		VWA3B-related disorder	Likely benign (Mar 06, 2020)
2-98115732-G-T		not specified	Uncertain significance (Jun 24, 2022)
2-98119576-T-C		not specified	Uncertain significance (Feb 07, 2023)
2-98119612-C-T		not specified	Uncertain significance (Jun 02, 2023)
2-98119624-G-A		not specified	Uncertain significance (Apr 09, 2024)
2-98119658-T-G		not specified	Uncertain significance (Apr 18, 2023)
2-98119681-G-A		not specified	Likely benign (Oct 01, 2024)
2-98119700-G-A		not specified	Likely benign (Oct 26, 2021)
2-98119714-A-G		not specified	Uncertain significance (Jul 12, 2023)
2-98119714-A-T		not specified	Uncertain significance (May 10, 2024)
2-98119762-C-T		VWA3B-related disorder	Benign (Sep 10, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VWA3B	protein_coding	protein_coding	ENST00000477737	27	226184

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.74e-28	0.144	116831	182	7810	124823	0.0325

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.259	678	697	0.972	0.0000374	8465
Missense in Polyphen		183	182.47	1.0029		2292
Synonymous	0.341	270	277	0.974	0.0000164	2445
Loss of Function	1.97	52	69.7	0.746	0.00000357	832

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0473	0.0469
Ashkenazi Jewish	0.0193	0.0193
East Asian	0.00918	0.00911
Finnish	0.0291	0.0291
European (Non-Finnish)	0.0481	0.0477
Middle Eastern	0.00918	0.00911
South Asian	0.0192	0.0187
Other	0.0332	0.0325

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Spinocerebellar ataxia, autosomal recessive, 22 (SCAR22) [MIM:616948]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAR22 patients manifest variable severity of intellectual disability associated with adult-onset cerebellar ataxia. {ECO:0000269|PubMed:26157035}. Note=The disease may be caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.959
• rvis_EVS: 1.32
• rvis_percentile_EVS: 94.08

Haploinsufficiency Scores

• pHI: 0.0917
• hipred: N
• hipred_score: 0.210

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.195

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vwa3b

Gene ontology

• Cellular component: cytoplasm