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    VWA5A von Willebrand factor A domain containing 5A [ Homo sapiens (human) ]

    Gene ID: 4013, updated on 28-Oct-2024

    Summary

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    Official Symbol
    VWA5Aprovided by HGNC
    Official Full Name
    von Willebrand factor A domain containing 5Aprovided by HGNC
    Primary source
    HGNC:HGNC:6658
    See related
    Ensembl:ENSG00000110002 MIM:602929; AllianceGenome:HGNC:6658
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BCSC1; BCSC-1; LOH11CR2A
    Summary
    Located in nucleoplasm. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in colon (RPKM 15.2), gall bladder (RPKM 14.6) and 24 other tissues See more
    Orthologs
    all
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    Genomic context

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    See VWA5A in Genome Data Viewer
    Location:
    11q24.2
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (124115450..124147721)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (124144018..124176287)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (123986157..124018428)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 10 subfamily D member 4 pseudogene Neighboring gene Sharpr-MPRA regulatory region 9541 Neighboring gene olfactory receptor family 10 subfamily N member 1 pseudogene Neighboring gene uncharacterized LOC124902778 Neighboring gene olfactory receptor family 10 subfamily D member 1 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of VWA5A as a novel biomarker for inhibiting metastasis in breast cancer by machine-learning based protein prioritization. Koh J, et al. Sci Rep, 2024 Jan 30. PMID 38291227, Free PMC Article
    2. Molecular cloning and characterization of LOH11CR2A, a new gene within a refined minimal region of LOH at 11q23. Monaco C, et al. Genomics, 1997 Dec 1. PMID 9417908
    3. The BCSC-1 locus at chromosome 11q23-q24 is a candidate tumor suppressor gene. Martin ES, et al. Proc Natl Acad Sci U S A, 2003 Sep 30. PMID 14504409, Free PMC Article
    4. Breast cancer suppressor candidate-1 (BCSC-1) is a melanoma tumor suppressor that down regulates MITF. Anghel SI, et al. Pigment Cell Melanoma Res, 2012 Jul. PMID 22594792
    5. Tumor suppressor function of BCSC-1 in nasopharyngeal carcinoma. Zhou YQ, et al. Cancer Sci, 2009 Oct. PMID 19656157, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of VWA5A as a novel biomarker for inhibiting metastasis in breast cancer by machine-learning based protein prioritization.
      Title: Identification of VWA5A as a novel biomarker for inhibiting metastasis in breast cancer by machine-learning based protein prioritization.
    2. BCSC-1 binds to Sox10, which down regulates MITF, and results in a switch of melanoma cells from a proliferative to a migratory phenotype.
      Title: Breast cancer suppressor candidate-1 (BCSC-1) is a melanoma tumor suppressor that down regulates MITF.
    3. LOH11CR2A, PIG8 and CHEK1 are candidate tumor suppressor genes associated with breast carcinoma and have significant clinical as well as prognostic importance.
      Title: Frequent alterations of LOH11CR2A, PIG8 and CHEK1 genes at chromosomal 11q24.1-24.2 region in breast carcinoma: clinical and prognostic implications.
    4. BCSC-1 suppression might play roles in tumorigenesis of some nasopharyngeal carcinomas
      Title: Tumor suppressor function of BCSC-1 in nasopharyngeal carcinoma.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study of aging.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    von Willebrand factor A domain-containing protein 5A
    Names
    breast cancer suppressor candidate 1
    loss of heterozygosity 11 chromosomal region 2 gene A protein
    loss of heterozygosity, 11, chromosomal region 2, gene A
    ortholog of mouse AW551984

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001130142.2 → NP_001123614.1  von Willebrand factor A domain-containing protein 5A isoform 1

      See identical proteins and their annotated locations for NP_001123614.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AP000818, AY366508, BM990294
      Consensus CDS
      CCDS8444.1
      UniProtKB/Swiss-Prot
      O00534, Q6UN19, Q6UN20, Q9BVF8
      UniProtKB/TrEMBL
      A8K6N3
      Related
      ENSP00000407726.2, ENST00000456829.7
      Conserved Domains (3) summary
      smart00609
      Location:1 → 131
      VIT; Vault protein Inter-alpha-Trypsin domain
      cd01461
      Location:278 → 456
      vWA_interalpha_trypsin_inhibitor; vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to ...
      TIGR03788
      Location:19 → 609
      marine_srt_targ; marine proteobacterial sortase target protein

    2. NM_014622.5 → NP_055437.2  von Willebrand factor A domain-containing protein 5A isoform 1

      See identical proteins and their annotated locations for NP_055437.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) lacks an internal exon in the 5' UTR, as compared to variant 3. Both variants 1 and 3 encode the same isoform 1.
      Source sequence(s)
      AF002672, AP000818, AY366505
      Consensus CDS
      CCDS8444.1
      UniProtKB/Swiss-Prot
      O00534, Q6UN19, Q6UN20, Q9BVF8
      UniProtKB/TrEMBL
      A8K6N3
      Related
      ENSP00000376504.1, ENST00000392748.5
      Conserved Domains (3) summary
      smart00609
      Location:1 → 131
      VIT; Vault protein Inter-alpha-Trypsin domain
      cd01461
      Location:278 → 456
      vWA_interalpha_trypsin_inhibitor; vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to ...
      TIGR03788
      Location:19 → 609
      marine_srt_targ; marine proteobacterial sortase target protein

    3. NM_198315.3 → NP_938057.1  von Willebrand factor A domain-containing protein 5A isoform 2

      See identical proteins and their annotated locations for NP_938057.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks multiple 3' exons, but has an alternate 3' sequence, as compared to variant 3. The resulting isoform (2) has a shorter and different C-terminus, as compared to isoform 1.
      Source sequence(s)
      BC001234
      Consensus CDS
      CCDS8445.1
      UniProtKB/TrEMBL
      B4DHS6, C9JSP8
      Related
      ENSP00000355070.5, ENST00000361352.9
      Conserved Domains (2) summary
      smart00609
      Location:1 → 131
      VIT; Vault protein Inter-alpha-Trypsin domain
      cl00057
      Location:278 → 408
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      124115450..124147721
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011542828.3 → XP_011541130.1  von Willebrand factor A domain-containing protein 5A isoform X1

      UniProtKB/TrEMBL
      A8K6N3
      Conserved Domains (3) summary
      smart00609
      Location:17 → 147
      VIT; Vault protein Inter-alpha-Trypsin domain
      cd01461
      Location:294 → 472
      vWA_interalpha_trypsin_inhibitor; vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to ...
      TIGR03788
      Location:35 → 625
      marine_srt_targ; marine proteobacterial sortase target protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      124144018..124176287
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054368781.1 → XP_054224756.1  von Willebrand factor A domain-containing protein 5A isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O00534.2 GenPept UniProtKB/Swiss-Prot:O00534

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