Table 4. In silico predictions of the PLG identified mutations.

Nucleotide Change	Protein Change	Variant Type	dbSNP v137	NNSPLICE score*	HSF score*	SIFT score (median)	PolyPhen-2 score (sensitivity - specificity)	Align GVGD score	Mutation Taster p-value	PhyloP	Grantham distances
c.12 G>A	p.Lys4Lys	PSSM	rs4252061	1.00–1.00	97.66–97.66	—	—	—	—	0.69	—
c.112 A>G	p.Lys38Glu	Missense	rs73015965	—	—	0.005 (3.37)	0.879 (0.82–0.94)	C55 (GV:0–GD:56.87)	0†	1.78	56
c.781 C>T	p.Arg261Cys	Missense	—	—	—	0 (3.84)	0.999 (0.14–0.99)	C65 (GV:0–GD:179.53)	1	4	180
c.1878-6 T>C	—	PSSM	rs192519670	0.98–0.98	84.28–84.93	—	—	—	—	−0.134	—
c.2134 G>A	p.Gly712Arg	Missense	rs202074006	—	—	0.03 (3.84)	1 (0.00–1.00)	C65 (GV:0–GD:125.13)	0.99	1.25	125

NNSPLICE [0-1]: threshold ≥0.4 and HSF [0-100]: Human Splicing Finder, threshold ≥65. In both programs a splice site effect was considered as potentially deleterious when a variation between the native and the mutation score was more than 10%; SIFT [1-0]: scores less than 0.05 indicate substitutions are predicted as deleterious; Polyphen-2 [0-1]: scores range from 0.000 (most probably benign) to 1 (most probably damaging); Align GDGV [C0-C65]: scores range from Class C0 (less likely deleterious) to Class C65 (most likely deleterious); Mutation Taster [0-1]: from disease causing variants (p-value = 1.0) to might not be disease causing (p-value <0.99); PhyloP [-14.1 to 6.4]: from highly conserved (score >3) to moderately conserved (score 1-3) or poorly conserved (score <1); Grantham distances [0-215]: from highly different physicochemical properties and more probably damaging (score >50) to moderately (score 25-50) or poorly different and most probably tolerated (score <25); PSSM: Potential splicing site mutation.

^*Score native – mutation.

^†This variant is listed as pathogenic in NCBI ClinVar database (http://www.ncbi.nlm.nih.gov/clinvar/). Thus, it is automatically predicted to be disease-causing in Mutation Taster but real probability is shown.