Copyright: © 2017 by the authors. Licensee: Pirogov University.
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (CC BY).

ORIGINAL RESEARCH

Clarification of the status of some mutations considered pathogenic, by harmless mutations attributes

About authors

1 Bioinformatics Data Processing Department,
Genotek Ltd., Moscow, Russia

2 Lomonosov Moscow State University, Moscow, Russia

3 The Core Facilities Center “Genetic Polymorphism”,
Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia

Correspondence should be addressed: Dmitry O. Korostin
ul. Gubkina, d. 3, Moscow, Russia, 119991; moc.liamg@nitsorok.d

Received: 2016-02-10 Accepted: 2016-02-19 Published online: 2017-01-05
|
  1. Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. Predicting the functional effect of amino acid substitutions and indels. PLoS One. 2012; 7 (10): e46688.
  2. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 2009; 4 (7): 1073–81.
  3. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat. Methods. 2010; 7 (4): 248–9.
  4. Online Mendelian Inheritance in Man, OMIM [Internet]. Baltimore (MD): McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University. c1996–2016. [cited 2016 Feb]. Available from: http://omim.org/.
  5. The Human Gene Mutation Database, HGMD [Internet]. Cardiff (UK): Cardiff University. c2015 – [cited 2016 Feb]. Available from: http://www.hgmd.cf.ac.uk/ac/index.php.
  6. Exome Aggregation Consortium (ExAC) [Internet]. Cambridge (MA). [updated 2016 Jan 17, cited 2016 Feb]. Available from: http://exac.broadinstitute.org/.
  7. Bcftools. Available from: http://samtools.github.io/bcftools/.
  8. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012; 6 (2): 80–92.
  9. dbSNP Short Genetic Variants [Internet]. Available from: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1050171.
  10. ClinVar [Internet]. Available from: http://www.ncbi.nlm.nih.gov/clinvar/variation/45271/.
  11. Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr. Protoc. Hum. Genet. 2013; Chapter 7: Unit 7.20.
  12. Zhang W, Stabile LP, Keohavong P, Romkes M, Grandis JR, Traynor AM, et al. Mutation and polymorphism in the EGFR-TK domain associated with lung cancer. J. Thorac. Oncol. 2006; 1 (7): 635–47.
  13. NM_005228.3(EGFR):c.2361G>A (p.Gln787=) Simple - Variation Report - ClinVar – NCBI. Available from: http://www.ncbi.nlm.nih.gov/clinvar/variation/45271/.
  14. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010; 20 (1): 110–21.
  15. Li Y, Wu G, Zuo J, Gao J, Chang Y, Fang F. Genetic variations of the CDC2L2 gene are associated with type 2 diabetes in a Han Chinese cohort. Diabetes. Metab. Res. Rev. 2007; 23 (6): 455–61.
  16. He M.-L, Chen Y, Chen Q, He Y, Zhao J, Wang J, et al. Multiple gene dysfunctions lead to high cancer-susceptibility: evidences from a whole-exome sequencing study. Am. J. Cancer Res. 2011; 1 (4): 562–73.
  17. Pfützer R, Myers E, Applebaum-Shapiro S, Finch R, Ellis I, Neoptolemos J, et al. Novel cationic trypsinogen (PRSS1) N29T and R122C mutations cause autosomal dominant hereditary pancreatitis. Gut. 2002; 50 (2): 271–2.
  18. Hammoud S, Emery BR, Dunn D, Weiss RB, Carrell DT. Sequence alterations in the YBX2 gene are associated with male factor infertility. Fertil. Steril. 2009; 91 (4): 1090–5.