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VWA1 Gene

protein-coding   GIFtS: 50
GCID: GC01P001370

Von Willebrand Factor A Domain Containing 1

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Von Willebrand Factor A Domain Containing 11 2
WARP2 5
Von Willebrand Factor A Domain-Containing Protein 12
Von Willebrand Factor A Domain-Related Protein2

External Ids:    HGNC: 309101   Entrez Gene: 648562   Ensembl: ENSG000001794037   OMIM: 6119015   UniProtKB: Q6PCB03   

Export aliases for VWA1 gene to outside databases

Previous GC identifers: GC01P001457 GC01P001360 GC01P000645


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for VWA1 Gene:
VWA1 belongs to the von Willebrand factor (VWF; MIM 613160) A (VWFA) domain superfamily of extracellular matrix
proteins and appears to play a role in cartilage structure and function (Fitzgerald et al., 2002 (PubMed
12062410)).(supplied by OMIM, Nov 2010)

GeneCards Summary for VWA1 Gene:
VWA1 (von Willebrand factor A domain containing 1) is a protein-coding gene. GO annotations related to this gene include identical protein binding. An important paralog of this gene is MATN4.

UniProtKB/Swiss-Prot: VWA1_HUMAN, Q6PCB0
Function: Promotes matrix assembly (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the VWA1 gene promoter:
         Bach1   AML1a   Pax-5   GR-beta   ATF-2   XBP-1   C/EBPalpha   CRE-BP1   HEN1   ARP-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVWA1 promoter sequence
   Search Chromatin IP Primers for VWA1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VWA1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p36.33   Ensembl cytogenetic band:  1p36.33   HGNC cytogenetic band: 1p36.33

VWA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VWA1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P001370:  view genomic region     (about GC identifiers)

Start:
1,370,241 bp from pter      End:
1,378,262 bp from pter
Size:
8,022 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: VWA1_HUMAN, Q6PCB0 (See protein sequence)
Recommended Name: von Willebrand factor A domain-containing protein 1 precursor  
Size: 445 amino acids; 46804 Da
Subunit: Homodimer or homomultimer. Interacts with HSPG2 (By similarity)
Secondary accessions: A8K692 B3KUA1 E9PB53 Q7L5D7 Q9H6J5
Alternative splicing: 3 isoforms:  Q6PCB0-1   Q6PCB0-2   Q6PCB0-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for VWA1: NX_Q6PCB0

Explore proteomics data for VWA1 at MOPED

Post-translational modifications: 

  • N-glycosylated (By similarity)1
  • Glycosylation2 at Asn264, Thr437, Ser442
  • Modification sites at PhosphoSitePlus

  • See VWA1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_073745.2  NP_954572.2  

    ENSEMBL proteins: 
     ENSP00000463643   ENSP00000423404   ENSP00000417185   ENSP00000464343   ENSP00000385008  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    FN3: Fibronectin type III domain containing

    3 InterPro protein domains:
     IPR003961 Fibronectin_type3
     IPR013783 Ig-like_fold
     IPR002035 VWF_A

    Graphical View of Domain Structure for InterPro Entry Q6PCB0

    ProtoNet protein and cluster: Q6PCB0

    1 Blocks protein domain: IPB002035 Von Willebrand factor type A domain signature

    UniProtKB/Swiss-Prot: VWA1_HUMAN, Q6PCB0
    Similarity: Contains 2 fibronectin type-III domains
    Similarity: Contains 1 VWFA domain


    Find genes that share domains with VWA1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: VWA1_HUMAN, Q6PCB0
    Function: Promotes matrix assembly (By similarity)

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0042802identical protein binding IEA--
         
    Find genes that share ontologies with VWA1           About GenesLikeMe


    Phenotypes:
         5 MGI mutant phenotypes (inferred from 1 allele(MGI details for Vwa1):
     behavior/neurological  integument  muscle  nervous system  skeleton 

    Find genes that share phenotypes with VWA1           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for VWA1

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    SwitchGear 3'UTR luciferase reporter plasmidVWA1 3' UTR sequence
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    VWA1_HUMAN, Q6PCB0: Secreted, extracellular space, extracellular matrix, basement membrane (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular2
    plasma membrane2
    endoplasmic reticulum1
    lysosome1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region ----
    GO:0005604basement membrane IEA--
    GO:0005614interstitial matrix IEA--
    GO:0031012extracellular matrix ----
    GO:0070062extracellular vesicular exosome IDA19199708

    Find genes that share ontologies with VWA1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for VWA1
    Interactions:

        Search GeneGlobe Interaction Network for VWA1

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for VWA1 (Q6PCB03 ENSP000004171854) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HSPG2P981603, ENSP000003638274I2D: score=1 STRING: ENSP00000363827
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030198extracellular matrix organization IEA--
    GO:0048266behavioral response to pain IEA--

    Find genes that share ontologies with VWA1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for VWA1



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for VWA1 gene (2 alternative transcripts): 
    NM_022834.4  NM_199121.2  

    Unigene Cluster for VWA1:

    Von Willebrand factor A domain containing 1
    Hs.449009  [show with all ESTs]
    Unigene Representative Sequence: NM_022834
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000495558 ENST00000338660 ENST00000476993(uc001afs.3) ENST00000471398
    ENST00000404702(uc001afr.3)
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    hsa-miR-661 hsa-miR-4271 hsa-miR-509-5p hsa-miR-491-5p hsa-miR-29a* hsa-miR-509-3-5p hsa-miR-1205
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      QuantiFast Probe-based Assays in human, mouse, rat VWA1

    Additional mRNA sequence: 

    AK025868.1 AK075366.1 AK096773.1 AK291557.1 AL137722.1 BC003543.1 BC059409.1 

    15 DOTS entries:

    DT.70103179  DT.318405  DT.121440642  DT.100794894  DT.91839434  DT.100794893  DT.102839750  DT.40280238 
    DT.92416976  DT.95154486  DT.121440594  DT.121440619  DT.95328576  DT.100031242  DT.75183532 

    Selected AceView cDNA sequences (see all 229):

    NM_022834 BQ632835 CA947060 BQ632281 BU501952 BU949634 BQ287948 BU785409 
    BU076065 CB961675 AW271737 CA946702 AJ712426 BQ417404 CB069221 CA842069 
    BU786565 BM272055 AA910436 BQ217368 BU076504 CA776639 CB068494 BQ786908 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for VWA1    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b · 3c
    SP1:        -     -                           
    SP2:                                          
    SP3:        -                                 


    ECgene alternative splicing isoforms for VWA1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    VWA1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCCAGGACAC
    VWA1 Expression
    About this image


    VWA1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Endothelium (Cardiovascular System)    fully expand to see all 3 entries
             Adult Endothelial Cells Blood Brain Barrier
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Adult Endothelial Cells Blood Brain Barrier
     
     Pancreas (Endocrine System)
     
     Spinal Cord (Nervous System)
     
     Prostate (Endocrine System)
    VWA1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VWA1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.449009
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for VWA1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vwa11 , 5 von Willebrand factor A domain containing 11, 5 80.71(n)1
    80.46(a)1
      4 (87.31 cM)5
    2462281  NM_147776.41  NP_680085.31 
     1557681495 
    chicken
    (Gallus gallus)
    Aves VWA11 von Willebrand factor A domain containing 1 62.4(n)
    54.77(a)
      419413  XM_417574.4  XP_417574.3 
    lizard
    (Anolis carolinensis)
    Reptilia VWA16
    von Willebrand factor A domain containing 1
    55(a)
    1 ↔ 1
    AAWZ02039143(6848-8092)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004856931 von Willebrand factor A domain-containing protein 1-like 56.23(n)
    54.29(a)
      100485693  XM_002938850.2  XP_002938896.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5683791 von Willebrand factor A domain-containing protein 1-like 50.67(n)
    39.35(a)
      568379  XM_691704.3  XP_696796.2 


    ENSEMBL Gene Tree for VWA1 (if available)
    TreeFam Gene Tree for VWA1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for VWA1 gene
    MATN42  COL14A12  MATN32  MATN22  VIT2  COL12A12  COCH2  COL20A12  
    VWA22  MATN12  
    1 SIMAP similar gene for VWA1 using alignment to 3 protein entries:     VWA1_HUMAN (see all proteins):
    COL21A1

    Find genes that share paralogs with VWA1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for VWA1 (see all 184)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs9243981,2
    C--1371966(-) TGAGCC/TGTGGG 2 -- int10--------
    rs1129567791,2
    C,F--1372151(+) TACAGG/ACCTCT 2 -- int11Minor allele frequency- A:0.50WA 2
    rs1847821611,2
    C--1372268(+) TGGGGA/GGCCCA 2 -- int10--------
    rs1891685941,2
    C--1372269(+) GGGGGG/TCCCAC 2 -- int10--------
    rs2000555831,2
    C--1372422(+) GCTCCA/GCTGCC 3 P syn1 int10--------
    rs1445690331,2
    C,F--1372441(+) CCGGGG/TCCCTG 3 A S mis1 int11Minor allele frequency- T:0.00NA 4456
    rs2019680751,2
    C--1372537(+) CGGTGA/CGTGCT 3 S R mis1 int10--------
    rs1478148271,2
    C,F--1372554(+) CAGCGC/TATGGG 3 R syn1 int11Minor allele frequency- T:0.00NA 4428
    rs1503710021,2
    F--1372569(+) ACCCAC/TACTGG 3 H syn1 int11Minor allele frequency- T:0.00NA 4442
    rs1403193251,2
    C--1372668(+) GATGGC/TGGCTC 3 G syn1 int10--------

    HapMap Linkage Disequilibrium report for VWA1 (1370241 - 1378262 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for VWA1 (see all 19):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv871787CNV Loss21882294
    dgv12n71CNV Loss21882294
    dgv25n71CNV Loss21882294
    dgv19n71CNV Loss21882294
    dgv10n71CNV Loss21882294
    dgv34n71CNV Loss21882294
    nsv871837CNV Loss21882294
    dgv33n71CNV Loss21882294
    dgv40n71CNV Loss21882294
    dgv20n71CNV Loss21882294

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 611901    OMIM disorders: --


    Find genes that share disorders with VWA1           About GenesLikeMe


    Export disorders for VWA1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for VWA1 gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with VWA1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Is there an evolutionary relationship between WARP (von Willebrand factor A-domain-related protein) and the FACIT and FACIT-like collagens? (PubMed id 14527666)1, 3, 9 Fitzgerald J. and Bateman J.F. (FEBS Lett. 2003)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. WARP is a new member of the von Willebrand factor A-domain superfamily of extracellular matrix proteins. (PubMed id 12062410)1, 3 Fitzgerald J....Bateman J.F. (FEBS Lett. 2002)
    4. The matrilin-3 VWA1 domain modulates interleukin-6 release from primary human chondrocytes. (PubMed id 23523902)1 Klatt A.R....Wagener R. (Osteoarthr. Cartil. 2013)
    5. WARP interacts with collagen VI-containing microfibrils in the pericellular matrix of human chondrocytes. (PubMed id 23300779)1 Hansen U....Fitzgerald J. (PLoS ONE 2012)
    6. Immunocytochemical distribution of WARP (von Willebrand A domain-related protein) in the inner ear. (PubMed id 20971096)1 Duong T....Ishiyama G. (Brain Res. 2011)
    7. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). (PubMed id 19199708)1 Gonzalez-Begne M....Yates J.R. (J. Proteome Res. 2009)
    8. Conformational stability and domain unfolding of the Von Willebrand factor A domains. (PubMed id 17187823)1 Auton M....Moake J. (J. Mol. Biol. 2007)
    9. WARP is a novel multimeric component of the chondrocyte pericellular matrix that interacts with perlecan. (PubMed id 16407285)1 Allen J.M....Fitzgerald J. (J. Biol. Chem. 2006)
    10. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 64856 HGNC: 30910 AceView: WARP Ensembl:ENSG00000179403 euGenes: HUgn64856
    ECgene: VWA1 H-InvDB: VWA1

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for VWA1 Pharmacogenomics, SNPs, Pathways

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