Mutational analysis of phospholipase C epsilon 1 gene in Egyptian children with steroid-resistant nephrotic syndrome

Egyptian Journal of Medical Human Genetics

Table 5 Prediction of deleteriousness of SNP upon nucleotide substitution

Mutation	Trap Score	Varsome			FATHMML-MKL	Mutation Taster
		GREP	DANN	REVEL
G1120G (Novel)	0.062 benign	- 1.97	0.7419		Coding score 0.2837	0.999999999997818 disease causing
R1230H (Novel)	0.359 deleterious	5.7699 conseved	0.9994	0.605 pathogenic	Coding score 0.9937	0.99999490647148 disease causing
E1393K (Novel)	0.075 benign	5.9699 conseved	0.9986 pathogenic	0.208 benign	Coding score 0.9837	0.99040168642085 disease causing
R1575P rs2274224	0.045 benign	5.53	0.6793	0.079 benign	Coding score 0.05564	0.999999910833424 simple amino acid change, SNP
rs2274225	0.06 benign	5.53	0.5286 benign		Non-coding score 0.27012	0.999999355568395 without splice site change
rs759855980	0.25 benign	1.97	0.6348		Non-coding score 0.21292	0.99999991390954 With splice site change
T2013T	0.004	0.425

Non-coding:( positions in intergenic regions, introns or non-coding genes), coding: (positions within coding-sequence exons). GERP:Genomic Evolutionary Rate Profiling (GERP): It ranges from -12.3 to 6.17, with 6.17 being the most conserved. DANN Score is a pathogenicity scoring methodology from 0 to 1 being highly damaging. REVEL is a new ENSEMBLE method for predicting the pathogenicity of missense variants 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing