The homozygous pathogenic variant of the POMGNT1 gene identified using whole-exome sequencing in Iranian family with congenital hydrocephalus

Egyptian Journal of Medical Human Genetics

Table 4 Outputs of in silico analysis and pathogenic prediction tools

Analysis	Tools and in silico parameters	Score (Criteria)	Result/Classification
Pathogenicity	PMut	0.76	Pathogenic/D
	Mutation Taster	1.00	Disease causing/Class A (NMD)
	CADD-PHRED	36.0	Deleterious/Class A (NMD)
	DANN	1.00	Damaging/Higher Probably
	BayesDel	0.66	Deleterious/Strong
	ACMG rules	PVS1, PM2, PP3	Pathogenic/Class I
Conservation	PhastCons100way_vertebrate	1.000	Conserved/buried residue
	PhastCons30way_mammalian	1.000
	phyloP100way_vertebrate	4.699
	phyloP30way_mammalian	1.026
	SiPhy_29way_logOdds	14.56
Protein stability	I-Mutant 2.0	ΔΔG: − 0.2 kcal/mol	ΔΔG < − 0.5/destabilizing mutation

Abbreviations PMut: Pathogenic Mutation prediction; D: Deleterious; NMD: Nonsense-Mediated mRNA Decay; ACMG/AMP; American College of Medical Genetics and Genomics/Association for Molecular Pathology