Table 5

- Variants characteristics detected in 12 children with 2 variants: a disease-causing variant plus a VUS or a variant with conflicting pathogenicity.

Pt’s ID	First variant (Disease causing)	Variant effect / Classification	Second variant :(Variant effect/ classification (VUS/ conflicting)	SIFT Score for the VUS ^{^*}	Predictions of functional effect with SIFT	Score after NGS
8^{^#}	c.4092-4093delGT (p.Ser1365CysfsTer12)	Frameshift/ likely pathogenic	c.2426G>A (p.Gly809Asp): missense/VUS	0.2	Tolerated	3
10	c.3443T>C (p.Ileu1148Thr)	Missense/ pathogenic	c.2002A>G (p.Met668Val): missense/ conflicting (VUS/Likely pathogenic)	0.04	Affect protein function	8
18	c.3547-3548delGC (p.Ala1183TyrfsTer2)	Frameshift/ pathogenic	c.2715G>C (p.Glu905Asp): missense/VUS	0.04	Affect protein function	9
24	c.4114C>T (p.Gln1372Ter)	Stop-gain/ pathogenic	c.623C>T (p.Ala208Val) missense/VUS	0.4	Tolerated	5
34	c.2297C>G (p.Thr766Arg)	Missense/ pathogenic	c.2897T>G (p.Val966Gly): missense/VUS	0.06	Affect protein function	6
35	c.1630C>T (p.Gln544Ter)	Stop-gain/ pathogenic	c.2576-44G>T: Intronic variant/VUS	0.05	Affect protein function	5
36	c.2507G>A (p.Gly836Glu)	Missense/ likely pathogenic	c.3892G>A (p.Val1298Ile): missense/ VUS	0.03	Affect protein function	4
37	c.915T>A (p.Cys305Ter)	Stop-gain/ pathogenic	c.347T>C (p.Ile116Thr): missense/ Conflicting (VUS/Likely pathogenic)	0.03	Affect protein function	8
38	c.3694A>C (p.Thr1232Pro)	Missense/ likely pathogenic	c.352G>A (p.Asp118Asn): missense/ conflicting (VUS/Likely benign)	0.04	Affect protein function	4
39	c.3547-3548delGC (P.Ala1183TyrfsTer2)	Frameshift/ pathogenic	c.1318A>G (p.Ser440Gly): missense/ VUS	0.02	Affect protein function	6
40	c.2827G>A (p.Gly943Ser)	Missense/ pathogenic	c.1616C>T (p.Pro539Leu): missesnse/ conflicting (VUS/Likely pathogenic)	0.02	Affect protein function	6
41	c.2807T>A (p.Leu936Ter)	Stop-gain/ pathogenic	c.4125-1G>A (Splice acceptor variant)/ VUS	0.04	Affect protein function	7

Pt’ ID: Patient’s identification, NGS: next-generation sequencing

↵* Scores less than 0.05 are considered deleterious.
↵^# This patient (ID 8) has additional heterozygous variant (13:52536088, rs747432408, c.1870-39T>G, intronic variant, has not been reported before and found in low penetrance in ExAC).