Table 1. Predicted impact of APE1 variants on protein structure/function.

APE1genetic variants	Source	Percentageoffrequency	Functionalconsequences	PROVEAN		SIFT		CUPSAT		PolyPhen-2
				Score	Prediction	Score	Prediction	Overallstability	Torsion	Score	Prediction
L104R	ALS	once	Reduced AP endonuclease activity (~40%)[9].Impaired 3′-RNA phosphatase and endoribonuclease activities [15, 20]	−4.925	Deleterious	0.00	Affectedproteinfunction	Stabilizing	Unfavorable	0.987	Probably damaging
D148E	NCBI rs1130408	48.5	Normal AP endonuclease activity [8, 9]. Impaired 3′-RNA phosphatase and endoribonuclease activities [15, 20]	−0.204	Neutral	1.00	Tolerated	Destabilizing	Favorable	0.000	Benign
R237C	Tumor, NCBI rs375526265	once	Reduced 3′ to5′ exonuclease and 3′-damage excision activities; slightly reduced AP-DNA complex stability [8].Reduced incision capacity in proximity of nucleosomes [21]	−7.884	Deleterious	0.00	Affected protein function	Stabilizing	Unfavorable	1.000	Probably damaging
D283G	ALS	once	Reduced AP endonuclease activity (~90%) [9]	−6.910	Deleterious	0.00	Affected protein function	Destabilizing	Unfavorable	1.000	Probably damaging

For PROVEAN software (http://provean.jcvi.org/index.php), a cut-off score ≤ −2.5 is considered as deleterious, while a value greater than that is predicted as neutral. For SIFT modelling software (http://sift.jcvi.org/), a score ≤ 0.05 is considered as deleterious, whereas > 0.05 is predicted as tolerated. As template, the APE1 sequence (NP_001632.2) was used. For the PolyPhen-2 tool (http://genetics.bwh.harvard.edu/pph2/) and PROVEAN model, APE1 UniProtKB sequence (P27695) was used as query. CUPSAT predictions (http://cupsat.tu-bs.de/) were obtained by using the PDB APE1 crystallographic structure (1DE8) and the thermal experimental method. N/A = not available. Once = observed a single time. APE1 sequence entries reported above for computational analyses were identical and corresponded to the wild-type enzyme.