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 this gene are associated with Spinocerebellar ataxia, autosomal recessive 22. Alternatively spliced transcript variants have... See more...

Aliases for VWA3B Gene

Aliases for VWA3B Gene

  • Von Willebrand Factor A Domain Containing 3B 2 3 5
  • Von Willebrand Factor A Domain-Containing Protein 3B 3 4
  • VWA Domain-Containing Protein 3B 3 4
  • SCAR22 3

External Ids for VWA3B Gene

Previous GeneCards Identifiers for VWA3B Gene

  • GC02P098703
  • GC02P092468

Summaries for VWA3B Gene

Entrez Gene Summary for VWA3B Gene

  • 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 this gene are associated with Spinocerebellar ataxia, autosomal recessive 22. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, May 2017]

GeneCards Summary for VWA3B Gene

VWA3B (Von Willebrand Factor A Domain Containing 3B) is a Protein Coding gene. Diseases associated with VWA3B include Spinocerebellar Ataxia, Autosomal Recessive 22. An important paralog of this gene is VWA3A.

Additional gene information for VWA3B Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VWA3B Gene

Genomics for VWA3B Gene

GeneHancer (GH) Regulatory Elements for VWA3B Gene

Promoters and enhancers for VWA3B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J098086 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 755.3 +0.4 373 2.3 ZNF24 ZNF133 MNT NKRF NCOA3 IKZF1 CREB1 ZIC2 RFX1 IKZF2 VWA3B ANKRD36 ACTR1B ANKRD36B ENSG00000277701 piR-49423-133
GH02J098088 Promoter 0.4 Ensembl 750.6 +1.8 1785 0.2 IKZF2 VWA3B piR-49423-133
GH02J098245 Promoter 0.3 EPDnew 750.1 +158.3 158298 0.1 VWA3B ATP5F1BP1 piR-31199-170
GH02J098010 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 10.4 -74.5 -74546 3.2 ZNF24 SP1 NR2F6 ETV6 RELA NKRF MLLT1 POLR2A CREM ZBED1 VWA3B C2orf92 ZAP70 TMEM131 lnc-VWA3B-2 piR-60246-091
GH02J097966 Enhancer 1.2 Ensembl ENCODE dbSUPER 9.9 -119.9 -119915 10 NR2F6 JUND ETV6 HLF CREM HNF1A ZBED1 ZNF644 ZBTB33 IKZF1 TMEM131 RNU7-96P ZAP70 VWA3B ANKRD36B C2orf92 lnc-VWA3B-3 lnc-ACTR1B-11
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VWA3B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VWA3B gene promoter:
  • AML1a
  • CBF(2)
  • CBF-A
  • CBF-B
  • CP1A
  • FOXI1
  • FOXO4
  • HFH-3
  • NF-Y
  • NF-YA

Genomic Locations for VWA3B Gene

Genomic Locations for VWA3B Gene
chr2:98,087,116-98,330,681
(GRCh38/hg38)
Size:
243,566 bases
Orientation:
Plus strand
chr2:98,703,579-98,929,762
(GRCh37/hg19)
Size:
226,184 bases
Orientation:
Plus strand

Genomic View for VWA3B Gene

Genes around VWA3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VWA3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VWA3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VWA3B Gene

Proteins for VWA3B Gene

  • Protein details for VWA3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q502W6-VWA3B_HUMAN
    Recommended name:
    von Willebrand factor A domain-containing protein 3B
    Protein Accession:
    Q502W6
    Secondary Accessions:
    • B9EK71
    • Q86T73
    • Q8N2D0
    • Q8N770
    • Q8NA79
    • Q8ND63
    • Q8ND65
    • Q8WW02

    Protein attributes for VWA3B Gene

    Size:
    1294 amino acids
    Molecular mass:
    145748 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC04047.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAD89964.1; Type=Frameshift; Positions=1071, 1087, 1110, 1147, 1153, 1195, 1207; Evidence={ECO:0000305};

    Alternative splice isoforms for VWA3B Gene

neXtProt entry for VWA3B Gene

Post-translational modifications for VWA3B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for VWA3B Gene

Domains & Families for VWA3B Gene

Gene Families for VWA3B Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for VWA3B Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VWA3B Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ54766, moderately similar to Mus musculus inter alpha-trypsin inhibitor, heavy chain 4 (Itih4), mRNA (B7Z7Q7_HUMAN)
  • von Willebrand factor A domain-containing protein 3B (VWA3B_HUMAN)
genes like me logo Genes that share domains with VWA3B: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for VWA3B Gene

Function for VWA3B Gene

Phenotypes From GWAS Catalog for VWA3B Gene

genes like me logo Genes that share phenotypes with VWA3B: view

Human Phenotype Ontology for VWA3B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for VWA3B Gene

Localization for VWA3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for VWA3B Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VWA3B gene
Compartment Confidence
nucleus 3
plasma membrane 1
cytosol 1
mitochondrion 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for VWA3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with VWA3B: view

Pathways & Interactions for VWA3B Gene

PathCards logo

SuperPathways for VWA3B Gene

No Data Available

Interacting Proteins for VWA3B Gene

Gene Ontology (GO) - Biological Process for VWA3B Gene

None

No data available for Pathways by source and SIGNOR curated interactions for VWA3B Gene

Drugs & Compounds for VWA3B Gene

No Compound Related Data Available

Transcripts for VWA3B Gene

mRNA/cDNA for VWA3B Gene

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VWA3B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^
SP1: - - - - -
SP2: - - - -
SP3: -
SP4: - -
SP5:

ExUns: 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29a · 29b
SP1:
SP2: -
SP3: -
SP4: -
SP5:

Relevant External Links for VWA3B Gene

GeneLoc Exon Structure for
VWA3B
ECgene alternative splicing isoforms for
VWA3B

Expression for VWA3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VWA3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VWA3B Gene

This gene is overexpressed in Testis (x34.6).

Protein differential expression in normal tissues from HIPED for VWA3B Gene

This gene is overexpressed in Plasma (42.5) and Platelet (23.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VWA3B Gene



Protein tissue co-expression partners for VWA3B Gene

NURSA nuclear receptor signaling pathways regulating expression of VWA3B Gene:

VWA3B

SOURCE GeneReport for Unigene cluster for VWA3B Gene:

Hs.269977

Evidence on tissue expression from TISSUES for VWA3B Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with VWA3B: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VWA3B Gene

Orthologs for VWA3B Gene

This gene was present in the common ancestor of chordates.

Orthologs for VWA3B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VWA3B 33 32
  • 99.2 (n)
OneToOne
dog
(Canis familiaris)
Mammalia VWA3B 33 32
  • 85.85 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VWA3B 33 32
  • 84.17 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Vwa3b 17 33 33 32
  • 79.02 (n)
rat
(Rattus norvegicus)
Mammalia Vwa3b 32
  • 78.37 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VWA3B 33
  • 49 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VWA3B 33
  • 45 (a)
OneToOne
chicken
(Gallus gallus)
Aves VWA3B 33 32
  • 62.25 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VWA3B 33
  • 47 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vwa3b 32
  • 57.38 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 40 (a)
OneToOne
Species where no ortholog for VWA3B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for VWA3B Gene

ENSEMBL:
Gene Tree for VWA3B (if available)
TreeFam:
Gene Tree for VWA3B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VWA3B: view image

Paralogs for VWA3B Gene

Paralogs for VWA3B Gene

(2) SIMAP similar genes for VWA3B Gene using alignment to 10 proteins:

  • VWA3B_HUMAN
  • B7Z7Q7_HUMAN
  • F8W737_HUMAN
  • F8WBX4_HUMAN
  • F8WD48_HUMAN
  • F8WD56_HUMAN
  • H0YCW7_HUMAN
  • H0YDS6_HUMAN
  • H0YEM4_HUMAN
  • H0YF54_HUMAN
genes like me logo Genes that share paralogs with VWA3B: view

Variants for VWA3B Gene

Sequence variations from dbSNP and Humsavar for VWA3B Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs876657414 pathogenic, Spinocerebellar ataxia, autosomal recessive 22, Spinocerebellar ataxia, autosomal recessive, 22 (SCAR22) [MIM:616948] 98,217,874(+) A/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1558643972 uncertain-significance, not provided 98,181,151(+) A/T 5_prime_UTR_variant, coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1000012104 -- 98,271,586(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000026034 -- 98,188,231(+) G/A intron_variant
rs1000065826 -- 98,180,464(+) T/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for VWA3B Gene

Variant ID Type Subtype PubMed ID
dgv222n21 CNV gain 19592680
dgv4027n100 CNV gain 25217958
dgv4028n100 CNV loss 25217958
dgv4029n100 CNV loss 25217958
dgv6974n54 CNV loss 21841781
esv24326 CNV loss 19812545
esv2672637 CNV deletion 23128226
esv2674476 CNV deletion 23128226
esv2720429 CNV deletion 23290073
esv2760564 CNV loss 21179565
esv3575286 CNV gain 25503493
esv3591723 CNV loss 21293372
esv3591724 CNV loss 21293372
esv3591725 CNV loss 21293372
esv6339 CNV gain 19470904
nsv1002366 CNV gain 25217958
nsv1008152 CNV loss 25217958
nsv10105 CNV loss 18304495
nsv1013728 CNV gain 25217958
nsv1143946 CNV deletion 24896259
nsv437289 CNV loss 16327808
nsv438363 CNV loss 16468122
nsv473302 CNV novel sequence insertion 20440878
nsv517669 CNV loss 19592680
nsv518056 CNV gain 19592680
nsv527817 CNV loss 19592680
nsv582515 CNV loss 21841781
nsv818075 CNV loss 17921354
nsv834309 CNV gain 17160897
nsv953492 CNV duplication 24416366
nsv963671 CNV duplication 23825009
nsv999736 CNV loss 25217958

Variation tolerance for VWA3B Gene

Residual Variation Intolerance Score: 95.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.72; 83.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VWA3B Gene

Human Gene Mutation Database (HGMD)
VWA3B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VWA3B

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VWA3B Gene

Disorders for VWA3B Gene

MalaCards: The human disease database

(1) MalaCards diseases for VWA3B Gene - From: HGMD, OMIM, ClinVar, GTR, and GeneCards

Disorder Aliases PubMed IDs
spinocerebellar ataxia, autosomal recessive 22
  • scar22
- elite association - COSMIC cancer census association via MalaCards
Search VWA3B in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VWA3B_HUMAN
  • 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.

Additional Disease Information for VWA3B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VWA3B: view

No data available for Genatlas for VWA3B Gene

Publications for VWA3B Gene

  1. A homozygous mutation of VWA3B causes cerebellar ataxia with intellectual disability. (PMID: 26157035) Kawarai T … Kaji R (Journal of neurology, neurosurgery, and psychiatry 2016) 2 3 4 56
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 43 56
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 56
  5. Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family. (PMID: 26566883) Rafiullah R … Berkel S (Journal of medical genetics 2016) 4 56

Products for VWA3B Gene

Sources for VWA3B Gene