Identification and in silico analysis of functional SNPs of the BRCA1 gene.
TLDR
It is proposed that an nsSNP (rs1800751) could be an important candidate for the breast cancer caused by the BRCA1 gene from a comparison of the stabilizing residues of the native and mutant proteins.About:
This article is published in Genomics.The article was published on 2007-10-01 and is currently open access. It has received 79 citations till now. The article focuses on the topics: Nonsynonymous substitution & Untranslated region.read more
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Journal ArticleDOI
Computational insights of K1444N substitution in GAP-related domain of NF1 gene associated with neurofibromatosis type 1 disease: a molecular modeling and dynamics approach
TL;DR: Evidence of the benefits of the computational tools in predicting the pathogenicity of genetic mutations is provided and the application of MDS and different in silico prediction tools for variant assessment and classification in genetic clinics is suggested.
Book ChapterDOI
Comprehensive in silico screening and molecular dynamics studies of missense mutations in Sjogren-Larsson syndrome associated with the ALDH3A2 gene.
S. Udhaya Kumar,D Thirumal Kumar,Pinky D Mandal,Srivarshini Sankar,Rishin Haldar,Balu Kamaraj,Charles Emmanuel Jebaraj Walter,Ramamoorthy Siva,C. George Priya Doss,Hatem Zayed +9 more
TL;DR: The computational pipeline provided in this study helps to elucidate the potential structural and functional differences between the ALDH3A2 native and mutant homodimeric proteins, and will pave the way for drug discovery against specific targets in the SLS patients.
Journal ArticleDOI
In silico analysis of consequences of non-synonymous SNPs of Slc11a2 gene in Indian bovines.
TL;DR: Five non-synonymous SNPs in Slc11a2 gene were identified as deleterious while tested out for polar interactions with other amino acids in the protein, and from above 5, Y374C, Q385H and N492S showed a change in interaction pattern and were confirmed by an increase in total energy after energy minimizations in case of mutant protein compared to the native.
Journal ArticleDOI
Screening and Evaluation of Deleterious SNPs in APOE Gene of Alzheimer's Disease.
TL;DR: Three single-nucleotide polymorphisms (SNPs) are found to be potentially functional polymorphic associated with APOE gene, namely, rs11542041, rs 11542040, and rs11 542034, which are concluded that are deleterious nsSNPs.
Journal ArticleDOI
Functional genomics based prioritization of potential nsSNPs in EPHX1, GSTT1, GSTM1 and GSTP1 genes for breast cancer susceptibility studies.
TL;DR: It is hypothesized that the 6 identified nsSNPs may alter the detoxification process and elevate carcinogenic metabolite accumulation thus modifies the risk of breast cancer susceptibility in a group of women.
References
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Journal ArticleDOI
dbSNP: the NCBI database of genetic variation
Stephen T. Sherry,Minghong Ward,Michael Kholodov,Jonathan Baker,Lon Phan,Elizabeth M. Smigielski,Karl Sirotkin +6 more
TL;DR: The dbSNP database is a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, and is integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data.
Journal ArticleDOI
A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1
Yoshio Miki,Jeff Swensen,Donna M Shattuck-Eidens,P. Andrew Futreal,Keith D Harshman,Sean V. Tavtigian,Qingyun Liu,Charles Cochran,L. Michelle Bennett,Wei Ding,Russell Bell,Judith Rosenthal,Charles E. Hussey,Thanh Tran,Melody McClure,Cheryl Frye,Tom Hattier,Robert Phelps,Astrid Haugen-Strano,Harold Katcher,Kazuko Yakumo,Zahra Gholami,Daniel Shaffer,Steven Stone,Steven Bayer,Christian Wray,Robert Bogden,Priya Dayananth,John R. Ward,Patricia N. Tonin,Steven A. Narod,Pam K. Bristow,Frank H. Norris,Leah M. Helvering,Paul Morrison,Paul Robert Rosteck,Mei Lai,J. Carl Barrett,Cathryn M. Lewis,Susan L. Neuhausen,Lisa A. Cannon-Albright,David E. Goldgar,Roger W. Wiseman,Alexander Kamb,Mark H. Skolnick +44 more
TL;DR: A strong candidate for the 17q-linked BRCA1 gene, which influences susceptibility to breast and ovarian cancer, has been identified by positional cloning methods.
Journal ArticleDOI
SIFT: predicting amino acid changes that affect protein function
Pauline C. Ng,Steven Henikoff +1 more
TL;DR: SIFT is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study and can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms.
Journal ArticleDOI
Estrogen Resistance Caused by a Mutation in the Estrogen-Receptor Gene in a Man
Eric P. Smith,Jeff Boyd,Graeme R. Frank,Hiroyuki Takahashi,Robert M. Cohen,Bonny Specker,Timothy C. Williams,Dennis B. Lubahn,Kenneth S. Korach +8 more
TL;DR: Disruption of the estrogen receptor in humans need not be lethal and is important for bone maturation and mineralization in men as well as women.
Journal ArticleDOI
Predicting Deleterious Amino Acid Substitutions
Pauline C. Ng,Steven Henikoff +1 more
TL;DR: A tool that uses sequence homology to predict whether a substitution affects protein function is constructed, which may be used to identify plausible disease candidates among the SNPs that cause missense substitutions.
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SIFT: predicting amino acid changes that affect protein function
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