ArticlePloS one2012
Identification of functional SNPs in BARD1 gene and in silico analysis of damaging SNPs: based on data procured from dbSNP database.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 43 citations in OpenAlex.
- The association between single nucleotide polymorphisms and ovarian cancer risk: A systematic review and network meta-analysis.Cancer medicine · 2023Pooled it
- BARD1: A Friend or Foe in Pancreatic Ductal Adenocarcinoma?International journal of molecular sciences · 2025Review
- Computational studies on the functional and structural impact of pathogenic mutations in enzymes.Protein science : a publication of the Protein Society · 2025Review
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- Investigation of pathogenic germline variants in gastric cancer and development of "GasCanBase" database.Cancer reports (Hoboken, N.J.) · 2023Article
- Unraveling Extremely DamagingJournal of personalized medicine · 2023Article
- HBD-2 variants and SARS-CoV-2: New insights into inter-individual susceptibility.Frontiers in immunology · 2022Article
- A comprehensive in silico analysis of the deleterious nonsynonymous SNPs of human FOXP2 protein.PloS one · 2022Article
- Computational Insights into the Structural and Functional Impacts of nsSNPs of Bone Morphogenetic Proteins.BioMed research international · 2022Article
- A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy.Scientific reports · 2021Article
- Pathogenic genetic variants from highly connected cancer susceptibility genes confer the loss of structural stability.Scientific reports · 2021Article
- Functional Polymorphisms inJournal of Cancer · 2019Article
- KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses.Scientific reports · 2018Article
- In silico SNP analysis of the breast cancer antigen NY-BR-1.BMC cancer · 2016Article
- Alteration of microRNA expression in cerebrospinal fluid of unconscious patients after traumatic brain injury and a bioinformatic analysis of related single nucleotide polymorphisms.Chinese journal of traumatology = Zhonghua chuang shang za zhi · 2016Article
- Association of three common BARD1 variants with cancer susceptibility: a system review and meta-analysis.International journal of clinical and experimental medicine · 2015Article
- Functional and Structural Consequences of Damaging Single Nucleotide Polymorphisms in Human Prostate Cancer Predisposition Gene RNASEL.BioMed research international · 2015Article
- Article
- Characterization of LGALS3 (galectin-3) as a player in DNA damage response.Cancer biology & therapy · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe BARD1 gene encodes for the BRCA1-associated RING domain (BARD1) protein. Germ line and somatic mutations in BARD1 are found in sporadic breast, ovarian and uterine cancers. There is a plethora of single nucleotide polymorphisms (SNPs) which may or may not be involved in the onset of female cancers. Hence, before planning a larger population study, it is advisable to sort out the possible functional SNPs. To accomplish this goal, data available in the dbSNP database and different computer programs can be used. To the best of our knowledge, until now there has been no such study on record for the BARD1 gene. Therefore, this study was undertaken to find the functional nsSNPs in BARD1.
result2.85% of all SNPs in the dbSNP database were present in the coding regions. SIFT predicted 11 out of 50 nsSNPs as not tolerable and PolyPhen assessed 27 out of 50 nsSNPs as damaging. FastSNP revealed that the rs58253676 SNP in the 3' UTR may have splicing regulator and enhancer functions. In the 5' UTR, rs17489363 and rs17426219 may alter the transcriptional binding site. The intronic region SNP rs67822872 may have a medium-high risk level. The protein structures 1JM7, 3C5R and 2NTE were predicted by PDBSum and shared 100% similarity with the BARD1 amino acid sequence. Among the predicted nsSNPs, rs4986841, rs111367604, rs13389423 and rs139785364 were identified as deleterious and damaging by the SIFT and PolyPhen programs. Additionally, I-Mutant showed a decrease in stability for these nsSNPs upon mutation. Finally, the ExPASy-PROSIT program revealed that the predicted deleterious mutations are contained in the ankyrin ring and BRCT domains.
conclusionUsing the available bioinformatics tools and the data present in the dbSNP database, the four nsSNPs, rs4986841, rs111367604, rs13389423 and rs139785364, were identified as deleterious, reducing the protein stability of BARD1. Hence, these SNPs can be used for the larger population-based studies of female cancers.
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