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

Gene ID: 4013, updated on 3-Apr-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, Apr 2022]
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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Location:
11q24.2
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (124115450..124147721)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (124144018..124176287)
105.20220307 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
  • 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. 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
  2. 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
  3. 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
  4. Frequent alterations of LOH11CR2A, PIG8 and CHEK1 genes at chromosomal 11q24.1-24.2 region in breast carcinoma: clinical and prognostic implications. Sinha S, et al. Mol Oncol, 2011 Oct. PMID 21803008, Free PMC Article
  5. Tumor suppressor function of BCSC-1 in nasopharyngeal carcinoma. Zhou YQ, et al. Cancer Sci, 2009 Oct. PMID 19656157

See all (21) 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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_2023_10

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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