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
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  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.