Variant effect predictor correlation with functional assays is reflective of clinical classification performance

Livesey, Benjamin J.; Marsh, Joseph A.

doi:10.1186/s13059-025-03575-w

Table 2 A summary of the 43 new VEPs including in this analysis and links to the data or source code used to produce predictions

From: Variant effect predictor correlation with functional assays is reflective of clinical classification performance

Predictor	Type	Source	Reference
3Cnet	Clinical-trained	https://github.com/KyoungYeulLee/3Cnet/	[84]
AlphaMissense	Population-tuned	https://zenodo.org/records/8208688	[25]
AlphScore	Clinical-trained	https://zenodo.org/records/6288139	[85]
CADD 1.7 (updated from previous 1.6)	Clinical-trained	https://cadd.bihealth.org/download	[86]
CAPICE	Clinical-trained	https://zenodo.org/records/3928295	[87]
CARP	Population-free	ProteinGym	[88]
CPT-1	Population-free	https://zenodo.org/records/8140323	[28]
DeepSAV	Clinical-trained	http://prodata.swmed.edu/DBSAV/	[89]
DeMaSk	Population-free	https://github.com/Singh-Lab/DeMaSk	[29]
ESCOTT	Population-free	https://zenodo.org/records/10577421	[39]
ESM-1b	Population-free	https://huggingface.co/spaces/ntranoslab/esm_variants	[90]
ESM2	Population-free	https://github.com/facebookresearch/esm	[91]
GEMME	Population-free	https://datadryad.org/stash/dataset/doi:10.5061/dryad.vdncjsz1s	[40]
gMVP	Clinical-trained	https://www.dropbox.com/s/nce1jhg3i7jw1hx/gMVP.csv.gz?dl=0	[92]
iGEMME	Population-free	https://zenodo.org/records/10441521	[39]
InMeRF	Clinical-trained	https://www.med.nagoya-u.ac.jp/neurogenetics/InMeRF/download.html	[93]
LASSIE	Population-tuned	http://compgen.cshl.edu/LASSIE/	[94]
Maverick	Clinical-trained	https://zenodo.org/records/7838659	[95]
MISTIC	Clinical-trained	https://lbgi.fr/mistic/download	[96]
MOIpred	Clinical-trained	https://zenodo.org/records/5620519	[97]
MSA Transformer	Population-free	ProteinGym	[47]
Mutformer	Clinical-trained	https://github.com/WGLab/mutformer?tab=readme-ov-file	[98]
MutScore	Clinical-trained	https://mutscorebatch-wgt7hvakhq-ew.a.run.app/	[99]
mvPPT	Clinical-trained	http://www.mvppt.club/	[49]
PHACT	Population-free	https://zenodo.org/records/11281312	[100]
PHACTboost	Clinical-trained	https://zenodo.org/records/11281312	[101]
PhD_SNPg	Clinical-trained	https://github.com/biofold/PhD-SNPg	[102]
popEVE	Population-tuned	https://pop.evemodel.org/	[38]
ProGen2	Population-free	https://github.com/salesforce/progen	[103]
ProtGPT2	Population-free	ProteinGym	[104]
Rhapsody	Clinical-trained	https://github.com/prody/rhapsody	[105]
RITA	Population-free	ProteinGym	[106]
SaProt	Population-free	https://github.com/westlake-repl/SaProt	[43]
Sequence UNET	Population-free	https://github.com/allydunham/sequence_unet	[107]
SIGMA	Clinical-trained	https://sigma-pred.org/	[108]
SNPred	Clinical-trained	https://www.synapse.org/#!Synapse:syn52137034/files/	[53]
SPRI	Clinical-trained	http://sts.bioe.uic.edu/spri/	[109]
TranceptEVE	Population-free	ProteinGym	[41]
Tranception	Population-free	https://github.com/OATML-Markslab/Tranception	[42]
UNEECON	Population-tuned	https://github.com/yifei-lab/UNEECON	[110]
Unirep (evotuned)	Population-free	ProteinGym	[111]
VESPA	Clinical-trained	https://github.com/Rostlab/VESPA	[48]
Wavenet	Population-free	ProteinGym	[45]

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ISSN: 1474-760X

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