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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 31.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_144992.5	NP_659429.4	27	yes	-
ENST00000477737.6	ENSP00000417955.1	27	yes	-
NM_001345864.2	NP_001332793.1	21	-	-
ENST00000416277.5	ENSP00000411168.1	9	-	-

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.

• not_specified (209 variants)
• not_provided (41 variants)
• Spinocerebellar_ataxia,_autosomal_recessive_22 (17 variants)
• VWA3B-related_disorder (15 variants)

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. These statistics are base on transcript: NM_144992.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	21	5	28
missense	1	1	183	27	3	215
nonsense		2	3	1	1	7
start loss						0
frameshift		6	7			13
splice donor/acceptor (+/-2bp)		2	3			5
Total	1	11	198	49	9

Highest pathogenic variant AF is 0.000061339204

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
		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

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

Gene ontology

• Cellular component: cytoplasm