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. 2019 Dec 13;43(6):371-381.
doi: 10.3906/biy-1905-18. eCollection 2019.

In silico approach to the analysis of SNPs in the human APAF1 gene

Tuğba Kaman  1 , Ömer Faruk Karasakal  2 , Ebru Özkan Oktay  3 , Korkut Ulucan  4   5 , Muhsin Konuk  4
Affiliations

In silico approach to the analysis of SNPs in the human APAF1 gene

Tuğba Kaman et al. Turk J Biol. .

Abstract

The apoptotic protease activating factor 1 (APAF1) gene encodes a cytoplasmic protein that initiates apoptosis and is a crucial factor in the mitochondria-dependent death pathway. APAF1 is implicated in many pathways such as apoptosis, neurodegenerative diseases, and cancer. The purpose of this study was to predict deleterious/damaging SNPs in the APAF1 gene viain silicoanalysis. To this end, APAF1 missense SNPs were obtained from the NCBI dbSNP database. In silico analysis of the missense SNPs was carried out by using publicly available online software tools. The stabilization and three-dimensional modeling of mutant proteins were also determined by using the I-Mutant 2.0 and Project HOPE webservers, respectively. In total, 772 missense SNPs were found in the APAF1 gene from the NCBI dbSNP database, 18 SNPs of which were demonstrated to be deleterious or damaging. Of those, 13 SNPs had a decreasing effect on protein stability, while the other 5 SNPs had an increasing effect. Based on the modeling results, some dissimilarities of mutant type amino acids from wild-type amino acids such as size, charge, and hydrophobicity were revealed. The SNPs predicted to be deleterious in this study might be used in the selection of target SNPs for genotyping in disease association studies. Therefore, we could suggest that the present study could pave the way for future experimental studies.

Keywords: APAF1; apoptosis; in silico; neurodegenerative diseases; single nucleotide polymorphism (SNP).

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Conflict of interest statement

CONFLICT OF INTEREST: none declared

Figures

Figure 1
Figure 1
Usage of online software tools in SNP analyses (modified from Marwa Mohamed Osman et al., 2016).
Figure 2
Figure 2
Gene–gene interactions of APAF1.
Figure 3
Figure 3
Deleterious or damaging SNPs predicted by online software tools.
Figure 4
Figure 4
Schematic diagram of the APAF1 proteins and association with deleterious SNPs in APAF1 gene.
See this image and copyright information in PMC

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