Table 2. Algorithm agreement for RET uncertain gene variants and predicted pathogenicity.

RET uncertain gene variant	PSAAP Predictiona	MutPred Predictionb	PolyPhe Predictionc	SIFT Predictiond	PMut Predictione
5/5 agreement
A510VR600QK603QE632KA640GV648IY791NE843DR844LR844WR886WR912Q	BenignBenignBenignBenignBenignBenignpathogenicbenignpathogenic pathogenic pathogenic pathogenic	BenignBenignBenignBenignBenignBenigndisruptedBenigndisrupted disrupted disrupted disrupted	BenignBenignBenignBenignBenignBenignprobably damagingbenignprobably damaging probably damaging probably damaging probably damaging	Toleratedtoleratedtoleratedtoleratedtoleratedtoleratedaffects functiontoleratedaffects function affects function affects function affects function	Neutralneutralneutralneutralneutralneutralpathologicalneutralpathological pathological pathological pathological
4/5 agreement
C611SD631GE805KS819IR833CS904CS904F	pathogenic pathogenicbenignpathogenic pathogenic pathogenic pathogenic	disruptedbenigndisrupted disruptedbenignbenignbenign	Probably damaging probably damaging probably damaging probably damaging probably damaging probably damaging probably damaging	Affects function affects function affects function affects function affects function affects function affects function	neutralpathological pathologicalneutralpathological pathological pathological
3/5 agreement
Y606CC531RG533SD631AD631VR635GP841LL881VK907M	pathogenic pathogenic pathogenic pathogenic pathogenic pathogenic pathogenicbenignpathogenic	benignbenignbenignbenignbenignbenignbenigndisruptedbenign	probably damaging probablydamaging probably damaging probably damaging probably damaging probably damaging probably damaging probably damaging probably damaging	toleratedtoleratedaffects function affects function affects functiontoleratedtoleratedaffects function affects function	pathological pathologicalneutralneutralneutral pathological pathologicalneutralneutral
2/5 agreement
C630SD631ES649LH665QR844QM848TI852MK907E	pathogenicbenignpathogenicbenignbenignbenignbenignbenign	benignbenignbenignbenignbenignbenignbenignbenign	probably damaging probably damaging probably damaging probably damaging probably damaging probably damaging probably damaging probably damaging	toleratedtoleratedtoleratedtoleratedtoleratedtoleratedaffects function affects function	Neutralpathologicalneutralpathological pathological pathologicalneutralneutral
1/5 agreement
G321RE511KD631NA641SK666NR770QN777SV778IE818K	benignbenignbenignbenignbenignbenignbenignbenignbenign	benignbenignbenignbenignbenignbenignbenignbenignbenign	benignbenignbenignpossibly damaging probably damaging probably damaging possibly damagingbenignpossibly damaging	toleratedtoleratedtoleratedtoleratedtoleratedtoleratedtoleratedaffects functiontolerated	pathological pathological pathologicalneutralneutralneutralneutralneutralneutral

^aPrimary Sequence Amino Acid Properties (PSAAP) algorithm.

^bAnalyzed with default settings at http://mutdb.org/mutpred.

^cAnalyzed with default settings at http://genetics.bwh.harvard.edu/pph.

^dAnalyzed with default settings at http://sift.jcvi.org.

^eAnalyzed with default settings at http://mmb.pcb.ub.es/PMut.