REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
3D protein structures	AlphaFold2	https://alphafold.ebi.ac.uk/
Variant data	ClinVar	https://www.ncbi.nlm.nih.gov/clinvar/
Variant data	gnomAD	https://gnomad.broadinstitute.org/
Variant annotation	dbNSFP	http://database.liulab.science/dbNSFP
Deep mutational scanning data	MaveDB	https://www.mavedb.org/#/
Gain-of-function and loss-of-function pathogenic missense variants	GOF/LOF	https://itanlab.shinyapps.io/goflof/
Pre-computed SIGMA scores	This paper	https://sigma-pred.org/
Software and algorithms
Ensembl Variant Effect Predictor program	McLaren et al.32	https://useast.ensembl.org/info/docs/tools/vep/index.html
SpliceAI	Jaganathan et al.33	https://github.com/Illumina/SpliceAI
FoldX	Schymkowitz et al.34	https://foldxsuite.crg.eu/
DSSP (Dictionary of Secondary Structure of Proteins) program	Kabsch et al.35	http://www.csb.yale.edu/userguides/databases/dssp/dssp_man.html
ProteinVolume	Chen et al.36	https://gmlab.bio.rpi.edu/PVolume.php
R	The R Project for Statistical Computing	https://www.r-project.org/
R scripts for data analysis	This paper	https://github.com/zhq921/SIGMA https://doi.org/10.5281/zenodo.10373120