Table 1

Prediction of effects of missense variants on protein function and stability

Variant	Function prediction			Stability prediction
	SIFT^†	Mutation Taster2^‡	Mutation assessor^§	i-Mutant2.0^¶		MUpro^††		iStable^‡‡
	SIFT^†	Mutation Taster2^‡	Mutation assessor^§	Prediction	DDG value	Prediction	Conf. score	Prediction	Conf. score
c.3329G > A (p.Arg1110Gln)	Deleterious	Disease causing		Decrease	−1.02	Decrease	−0.68	Decrease	0.72
c.4027C > T (p.Leu1343Phe)	Deleterious	Disease causing	Medium	Decrease	−1.23	Decrease	−1	Decrease	0.87

^†SIFT classifies an amino acid substitution as “deleterious” or “tolerated” according to the normalized probability. A substitution is predicted as deleterious if the score is < 0.05 and tolerated if the score is ≥ 0.05.

^‡Mutation Taster2 predicts an alteration as one of 4 possible types: “disease causing,” “disease causing automatic”, “polymorphism,” and “polymorphism automatic.”

^§Mutation assessor outputs the annotations of functional impact of a variant as functional (high, medium), predicted non-functional (low, neutral).

^¶I-Mutant2.0 outputs free energy change value (DDG) between mutant and wild-type protein. Stability decreases if DDG < 0 and increases if DDG > 0.

^††MUpro uses a confidence score between -1 and 1 to predict the effects of mutation on protein stability and measure the confidence of the prediction. A score < 0 means the mutation decreases the protein stability, and the smaller the score, the more confident the prediction. Conversely, a score > 0 means the mutation increases the protein stability, and the bigger the score, the more confident the prediction.

^‡‡iStable outputs the prediction as “stability decrease” or “stability increase.”