VWA3B (von Willebrand factor A domain containing 3B)

Gene

• Entrez ID: 200403
• Gene name: Von Willebrand factor A domain containing 3B
• Gene symbol: VWA3B
• Synonyms (NCBI Gene): SCAR22
• Chromosome: 2
• Chromosome location: 2q11.2
• Summary: This gene encodes an intracellular protein that contains a von Willebrand factor type A domain. Intracellular proteins with VWA domains are thought to function in transcription, DNA repair, ribosomal and membrane transport and the proteasome. Mutations in

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs146673560	G>A,C,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic downstream transcript variant, synonymous variant, non coding transcript variant
rs375244468	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, coding sequence variant, missense variant
rs876657414	A>C	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant, genic downstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1488296	hsa-miR-4426	CLIP-seq
MIRT1488297	hsa-miR-4647	CLIP-seq
MIRT1488298	hsa-miR-4662b	CLIP-seq
MIRT1488299	hsa-miR-4666-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA

Other IDs

• MIM: 614884
• HGNC: 28385
• e!Ensembl: ENSG00000168658

Protein

• UniProt ID: Q502W6
• Protein name: von Willebrand factor A domain-containing protein 3B (VWA domain-containing protein 3B)
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13768	VWA_3	140 → 289	von Willebrand factor type A domain	Domain
  PF13768	VWA_3	508 → 658	von Willebrand factor type A domain	Domain
  PF15057	DUF4537	1037 → 1163	Domain of unknown function (DUF4537)	Domain

• Sequence:

  MEKSGPSSTISEQQLQRQEGWINTKTDLAEQSLISSEKWLQLHGLKSNKLTLKQILSQIG
  FPHCEDYVASLGRPVASRYADGLFPQLYRAEDGRVYNLTAKSELIYQFVEHLTQAVESYK
  QRMDWLTSKSRQIFGVILEQCVTIVLDFGGILEGELDLCREALTMVLQEQVAHITEFNII
  RVSQEPVKWQENATPVTEQSIATAISWVEKLTVELTVSEAGRLDALLEAGRDKTIESIYY
  FVVGDVPEESKELLLQRALEIPCPVYTVSFNARGEGTIAFLKDLSAKTHSRFHAFAERTE
  CVEFPAFSTKDGDNVMTWNSRKLKGKLPPGAGVREDVFLVWQEMEEACSTLAQIQRLVAE
  PPKPDVATVDCESETTSVEIASNPEDTWDSKTWLQKYGLKAQKLSLYDVLADCSFRHADG
  VVDIKAKPENESVQTSAETNKKTVHAKYCSRFVHAPWKDGSLVHVNITKEKCKWYSERIH
  TALARIRRRIKWLQDGSQSLFGRLHNDCIYILIDTSHSMKSKLDLVKDKIIQFIQEQLKY
  KSKFNFVKFDGQAVAWREQLAEVNEDNLEQAQSWIRDIKIGSSTNTLSALKTAFADKETQ
  AIYLLTDGRPDQPPETVIDQVKRFQEIPIYTISFNYNDEIANRFLKEVAALTGGEFHFYN
  FGCKDPTPPEAVQNEDLTLLVKEMEQGHSDLEKMQDLYSESLIMDWWYNAEKDGDSKHQK
  EICSMISTPEKCAKPQSDVDSTQTSSLNMLKGPWGLSDQKVQKKKVLHAESTKTSLLRSQ
  MSSLRSSACSERKDGLSNASSRRTALSDKEMSILLAEEWLDDKSSEKVTREGSQVYDHDS
  SDVSSENWLKTYGLVAKKLTLMDALSVAAVPHSSTYVPVLDKHVVSKVFDEVFPLAHVCN
  DTNKMTLINPQGAKLNIYKRKVEQAIQSYEKRLNKIVWRALSQEEKEKLDANKPIQYLEN
  KTVLNQALERLNWPISLKELSMLESEILAGKMYIQQAMELQEAAKKNYANKAPGEQQKLQ
  GNPTKKTKSKRPDPLKGQKVIARCDENGFYFPGVVKKCVSRTQALVGFSYGDTKVVSTSF
  ITPVGGAMPCPLLQVGDYVFAKIVIPKGFDFYVPAIVIALPNKHVATEKFYTVLKCNNRR
  EFCPRSALIKISQNKYALSCSHIKSPPIPEDPEVEDVEARNSAFLFWPLKEADTQDSREP
  RREKPRRKKRPAKQPLQQAAPSDSDGSSHGISSHGSCQGTHPEPRTAHLHFPAAGRLGLS
  SHAIIATPPPRAALPCTLQATHSSKGLRSVPETL

• Sequence length: 1294

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Spinocerebellar ataxia, autosomal recessive 22	Likely pathogenic; Pathogenic	rs546662496, rs876657414	RCV001331743 RCV000211708	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATAXIA, SPINOCEREBELLAR	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar GWAS catalog	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Familial pancreatic carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIAS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VWA3B-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Ataxia, Spinocerebellar	Spinocerebellar Ataxia	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	26157035		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Keratitis	Keratitis	BEFREE	29705009		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 1	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 2	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 4	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 5	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 6 (disorder)	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 7	Spinocerebellar Ataxia	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 22	Spinocerebellar Ataxia	UNIPROT_DG	26157035		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 22	Spinocerebellar Ataxia	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)