Table 2 Different in silico tools used in prediction of missense variants pathogenecity in PCLE1 gene

1-Prediction of deleteriousness of SNP upon nucleotide substitution

FATHMM-MKL:

Predicts noncoding effects by integrating functional annotation information from the ENCODE. Range 0 to 1

Insert chromosome position, genomic position, wild nucleotide, mutated nucleotide, values above 0.5 are predicted to be deleterious

[20]

Varsome:

Depending on pathogenicity score (DANN) conservative score (GERP) and other prediction scores

Submit SNP by its genomic position and its protein position

[21]

Mutation taster:

Submit nucleotide substituents within few nucleotides around

[22]

Trapscore: is a prediction score between 0–1 with Regarding the percentile thresholds above the 90th percentile as possibly damaging and above

Submit SNP by its genomic position according to (GRCh37/hg19) version

[23]

2-The effect of SNP on gene regulation and DNA-chromatin binding

Consite Server

Analyze single sequence option, insert genomic sequence of whole exon 20 and 27 nucleotide sequence individually containing the intron/exon boundaries, select Homo sapiens,

TF score cutoff is 80%

[24]

3- Prediction of nsSNP deleteriousness acc. to ranking scores upon amino acid change

PredictSNP0.1

is a consensus classifier that enables access to the nine best performing prediction tools: SIFT, PolyPhen-1, PolyPhen-2, MAPP, PhD-SNP, SNAP, PredictSNP, and nsSNPAnalyzer

Submission of potein ID Q9P212 and substituents

as R1230H, E1393K

[25]

SNP&GO:

Disease probability (if > 0.5 mutation is predicted Disease)

Submit Protein sequence and amino acid substitutents

[26]

Suspect

Submit Protein sequence and amino acid substitutents

[27]

PROVEAN:

-2.5 is consider as a default threshold, therefore, variants with a score equal to or below -2.5 are considered deleterious

Protein sequence and amino acid substitutents

[28]

FATHMM:

Depend on algorithm combines sequence conservation with pathogenicity weights

protein identifier(Q9P212) and amino acid substitutents

[29]

PANTHER

Protein sequence, substitution and single organism(Homo sapiens)

[30]

4-Prediction of Protein stability change upon amino acid substitution

I-mutant 2.0

Submit the whole amino acid sequence and substituents

as R1230H, E1393K

[31]

Mupro

Submit the whole amino acid sequence and substituents

as R1230H, E1393K

[32]

PremPS

Submit PDB file and substituents

[33]

DynaMut:

DynaMut have implemented a consensus estimate of effect upon mutation on protein folding free energy, regarding the environment characteristics of the wild-type residue (e.g., relative solvent accessibility, residue depth and secondary structure) and used in the development of mCSM-Stability and consensus DUET predictions

Submit PDB file and substituents

[34]

5-Estimation of amino acid conservation

Consurf: predicts the crucial functional regions of a protein by estimating the degree of amino acid conservation. The grade range from 1 to 9 estimates the extent of conservation of the amino acid

Insert protein sequence

[35]

WebLogo: conservation can be calculated at each amino acid position that ranges from zero to 4.3 bits (highy conserved)

MSA* file of PLCE1 uploaded for many organisms with their correspnding ID

[36]

6-Molecular modeling

Modeller9.23 software

[37]

7-Effect of SNP on protein 3D structure: predict the structural changes introduced by an amino acid substitution

Missense 3D

Submit PDB file obtained from and hit the variant site as R1230H

[38]

9-Molecular Geometry visualization

UCSF Chimera

1-structure analysis of wild type and both mutated structures

2-Estimate the wildtype PLCE1 PDB structure deviation than mutated forms by using RMSD attribute

[39]

8- Estimation of protein- protein interactions

Cocomaps

the PDB file of PLCE1 with chain ID B as molecule 1and IQGAP1 with PDB file 3fay by chain A only as molecule 2

[40]

10- Molecular Docking

Auto Dock vina

Using predicted PDB file as a receptor and Pospho-inositide 4,5 diphosphate(Conformer3D_CID_125105.sdf) as a ligand. Docking was carried out with the grid size of 60, 60, and 60 along the X-, Y-, and Z-axis with 0.375 Å spacing

[41]

Patch Dock server

This uses molecular docking algorithm based on structure geometry

Using predicted PDB file as a receptor and Pospho-inositide 4,5 diphosphate(Conformer3D_CID_125105.PDB) as a ligand, Complex Type is protein- small ligand and Clustering RMSD is 1.5 Å

[42]