Table 2 Summary of VPPTs tested in the study

From: Evaluating variant pathogenicity prediction tools to establish African inclusive guidelines for germline genetic testing

Tool	Cut-off	Year developed	Prediction model method
SIFT⁵³	*	2001	MSA
bStatistics⁵⁴	≥500	2009	MSA
LRT⁵⁵	*	2009	MSA
MutPred⁵⁶	≥0.5	2009	MSA + Protein parameters + Supervised ML (built on SIFT)
SiPhy⁵⁷	≥12.17	2009	MSA
phastCons470way-mammalian⁵⁸	≥0.5	2010	MSA
phastCons17way-primate⁵⁸	≥0.5	2010	MSA
phastCons100way-vertebrate⁵⁸	≥0.5	2010	MSA
phyloP470way-mammalian⁵⁸	≥1.6	2010	MSA
phyloP17way-primate⁵⁸	≥1.6	2010	MSA
phyloP100way-vertebrate⁵⁸	≥1.6	2010	MSA
PolyPhen2-DIV⁵⁹	*	2010	MSA + Protein parameters + Supervised ML
PolyPhen2-VAR⁵⁹	*	2010	MSA + Protein parameters + Supervised ML
MutationAssessor⁶⁰	*	2011	MSA
PROVEAN⁶¹	*	2012	MSA
FATHMM⁶²	*	2013	MSA
VEST4⁶³	≥0.5	2013	Supervised ML
CADD⁶⁴	>20	2014	Meta-predictor + Supervised ML + Unsupervised ML
MutationTaster⁶⁵	*	2014	MSA
DANN⁶⁶	≥0.99	2015	Supervised ML + DL (with the same training data set and features as CADD)
fathmm-MKL⁶⁷	*	2015	Supervised ML
GenoCanyon⁶⁸	≥0.5	2015	Unsupervised ML
GM12878_fitcons⁶⁹	≥0.6	2015	Unsupervised ML
h1_fitcons⁶⁹	≥0.6	2015	Unsupervised ML
HUVEC_fitcons⁶⁹	≥0.6	2015	Unsupervised ML
integrated_fitcons⁶⁹	≥0.6	2015	Unsupervised ML
MetaLR⁷⁰	*	2015	Meta-predictor + Supervised ML
MetaSVM⁷⁰	*	2015	Meta-predictor + Supervised ML
BayesDel_addAF⁷¹	*	2016	Meta-predictor + Supervised ML
BayesDel_noAF⁷¹	*	2016	Meta-predictor + Supervised ML
Eigen-PC⁴⁶	≥0	2016	Unsupervised ML
Eigen-raw⁴⁶	≥0	2016	Unsupervised ML
M-CAP⁷²	*	2016	Supervised ML
REVEL⁷³	≥0.5	2016	Meta-predictor + Supervised ML
SIFT-4G⁷⁴	*	2016	MSA
DEOGEN2⁷⁵	*	2017	Supervised ML
LINSIGHT⁷⁶	≥0.6	2017	Unsupervised ML
MPC⁷⁷	≥2	2017	MSA (also combined PolyPhen2)
ClinPred⁷⁸	*	2018	Meta-predictor + Supervised ML + Unsupervised ML
fathmm-XF⁷⁹	*	2018	Supervised ML
PrimateAI⁸⁰	*	2018	Supervised ML + DL
GERP-NR⁸¹	≥4	2020	MSA
GERP-RS⁸¹	≥4	2020	MSA
LIST-S2⁸²	*	2020	MSA
EVE⁸³	≥0.5	2021	Unsupervised ML
MVP⁸⁴	≥0.75	2021	Supervised ML + DL
VARITY-ER⁸⁵	≥0.5	2021	Supervised ML
VARITY-ER-LOO⁸⁵	≥0.5	2021	Supervised ML
VARITY-R⁸⁵	≥0.5	2021	Supervised ML
VARITY-R-LOO⁸⁵	≥0.5	2021	Supervised ML
gMVP⁸⁶	≥0.75	2022	Supervised ML
MetaRNN⁸⁷	*	2022	Meta-predictor + Supervised ML + DL
AlphaMissense⁸⁸	*	2023	Unsupervised ML
ESM1b⁸⁹	*	2023	Unsupervised ML + DL

Tools with the directly predicted classification of variant pathogenicity were marked as *.
DL deep learning, MSA multiple sequence alignment, ML machine learning.

Back to article page

Table 2 Summary of VPPTs tested in the study

Search

Quick links