The Scientific World Journal

Research Article

Comparison of Predictive In Silico Tools on Missense Variants in GJB2, GJB6, and GJB3 Genes Associated with Autosomal Recessive Deafness 1A (DFNB1A)

Table 1

Evaluation of missense variants by predictive in silico tools.


Gene	Missense variants	Clinical significance	SIFT	FATHMM	MutationAssessor	Polyphen-2	CONDEL	MutationTaster	MutPred	Align GVGD	PROVEAN

GJB2 (Cx26)	c.79G>A p.Val27Ile rs2274084	Benign	Tolerated score: 0.21	Damaging score: -5.59	Medium FI score: 2.28 VC score: 2.16 VS score: 2.40	Probably damaging HumDiv score: 1.000 HumVar score: 0.998	Deleterious Calculated Condel score: 0.612278613903	Polymorphism score: 29	hypotheses are absent general score: 0.321	Unclassified Class C25 GV 0.00 GD 29.61	Neutral score: -0.660
	c.101T>C p.Met34Thr rs35887622	Pathogenic	Damaging score: 0.01	Damaging score: -5.41	Medium FI score: 2.315 VC score: 2.43 VS score: 2.20	Benign HumDiv score: 0.038 HumVar score: 0.083	Deleterious Calculated Condel score: 0.58786807751	Disease causing score: 81	hypotheses are absent general score: 0.969	Deleterious Class C65 GV 0.00 GD 81.04	Deleterious score: -3.801
	c.109G>A p.Val37Ile rs72474224	Pathogenic	Tolerated score: 0.34	Damaging score: -5.46	Medium FI score: 2.095 VC score: 2.58 VS score: 1.61	Probably damaging HumDiv score: 1.000 HumVar score: 0.996	Deleterious Calculated Condel score: 0.61487213316	Disease causing score: 29	hypotheses are absent general score: 0.902	Unclassified Class C25 GV 0.00 GD 29.61	Neutral score: -0.857
	c.269T>C p.Leu90Pro rs80338945	Pathogenic	Damaging score: 0	Damaging score: -5.64	Medium FI score: 3.33 VC score: 4.26 VS score: 2.40	Probably damaging HumDiv score: 1.000 HumVar score: 0.996	Deleterious Calculated Condel score: 0.676708483818	Disease causing score: 98	Confident hypotheses: Gain of sheet (P = 0.039) general score:0.915	Deleterious C65 GV 0.00 GD 97.78	Deleterious score: -6.482
	c.341A>G p.Glu114Gly rs2274083	Benign	Tolerated score: 0.16	Damaging score: -4.58	Medium FI score: 2.005 VC score: 2.40 VS score: 161	Benign HumDiv score: 0.001 HumVar score: 0.001	Deleterious Calculated Condel score: 0.556433693212	Polymorphism score: 98	hypotheses are absent general score: 0.232	Deleterious Class C65 GV 0.00 GD 97.85	Neutral score: -0.123
	c.368C>A p.Thr123Asn rs111033188	Benign	Tolerated score: 0.59	Damaging score: -4.42	Neutral FI score: -0.305 VC score: -0.61 VS score: - 0	Benign HumDiv score: 0.000 HumVar score: 0.000	Neutral Calculated Condel score: 0.513276654484	Disease causing score: 53	hypotheses are absent general score: 0.201	Deleterious Class C55 GV 0.00 GD 64.77	Neutral score: 0.797
	c.457G>A p.Val153Ile rs111033186	Benign	Tolerated score: 1	Damaging score: -3.69	Neutral FI score: -0.305 VC score: -0.43 VS score: -0.18	Benign HumDiv score: 0.003 HumVar score: 0.007	Neutral Calculated Condel score: 0.491937780564	Disease causing score: 29	hypotheses are absent general score: 0.488	Unclassified Class C25 GV 0.00 GD 29.61	Neutral score: 0.138

GJB6 (Cx30)	c.301G>A p.Glu101Lys rs571454176	Benign	Тolerated score:0.69	Damaging score: -5.26	Neutral FI score: -0.37 VC score: -0.74 VS score: 0	Benign HumDiv score: 0.193 HumVar score: 0.058	Neutral Calculated Condel score: 0.505405538667	Disease causing Score: 56	Actionable hypotheses: Gain of MoRF binding (P = 0.0064) Gain of ubiquitination at E101 (P = 0.0276) Gain of methylation at E101 (P = 0.0345) general score: 0.506	Deleterious Class C55 GV 0.00 GD 56.87	Neutral score: -1.273

GJB3 (Cx31)	с.580G>A p.Ala194Thr rs121908852	Benign	Тolerated score: 0.91	Damaging score: -3.67	Low FI score: 1.085 VC score: -0.54 VS score: 2.71	Benign HumDiv score: 0.163 HumVar score: 0.110	Deleterious Calculated Condel score: 0.529626647419	Disease causing Score: 58	hypotheses are absent general score: 0.399	Deleterious Class C55 GV 0.00 GD 58.02	Neutral score: 1.636

Note. The correct results (both “true” positive and “true” negative results) are highlighted by bold font.