GeneBe

Data sources

At GeneBe, we believe that providing accurate and up-to-date information is crucial for our users. That's why we continuously update our data sources to ensure that we provide the latest and most reliable information possible. Below is a list of the data sources we currently use to provide our users with the most comprehensive and accurate information.

Please note that the list provided below is not comprehensive and is subject to change. We are continuously adding new data sources to our platform, and some of the sources we use are not yet listed here. We apologize for any inconvenience this may cause, and we are working to update the list regularly.

Pathogenicity Scores and Related Resources

Name Comment Publication or link
AlphaMissense Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/37733863
Apogee2 Pathogenicity score for mitochondria https://pubmed.ncbi.nlm.nih.gov/37598215
BayesDel_noAF Pathogenicity score, precomputed for whole genome https://pubmed.ncbi.nlm.nih.gov/27995669
CADD Pathogenicity score, precomputed for whole genome https://pubmed.ncbi.nlm.nih.gov/24487276
CardioBoost Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/33046849/
ClinVar Reputable source of variant pathogenicity https://pubmed.ncbi.nlm.nih.gov/29165669/
Dann Precomputed for whole genome https://pubmed.ncbi.nlm.nih.gov/25338716/
dbscSNV1_ADA Pathogenicity score for splicing https://pubmed.ncbi.nlm.nih.gov/25416802/
dbscSNV1_RF Pathogenicity score for splicing https://pubmed.ncbi.nlm.nih.gov/25416802/
Deogen2 Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/28498993
Domino Gene annotation data https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630195/
SpliceAI Pathogenicity score for splicing https://pubmed.ncbi.nlm.nih.gov/30661751
Fathmm_mkl Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/23033316
gMVP Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/25552646/
GERP Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/15965027/
GeneCC Gene annotation data https://thegencc.org/
Gnomad exome Population allele frequency source https://pubmed.ncbi.nlm.nih.gov/32461654/
Gnomad genome Population allele frequency source https://pubmed.ncbi.nlm.nih.gov/32461654/
Gnomad mito Population allele frequency source https://pubmed.ncbi.nlm.nih.gov/32461654/
HmtVar Pathogenicity score for mitochondria https://pubmed.ncbi.nlm.nih.gov/30371888
ListS2 Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/32352516
LOVD Reputable source of variant pathogenicity https://pubmed.ncbi.nlm.nih.gov/21520333/
LRT Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/19602639
MaxEntScore We use our implementation. https://pubmed.ncbi.nlm.nih.gov/15285897/
mCAP Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/27776117
MetaLR Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/25552646
MetaRNN Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/36209109/
MetaSVN Pathogenicity score https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4375422/
Mitotip Pathogenicity score for mitochondria https://pubmed.ncbi.nlm.nih.gov/29227991
Mitomap Population allele frequency source https://pubmed.ncbi.nlm.nih.gov/25489354
MPC Pathogenicity score https://doi.org/10.1101/148353
MutationAssessor Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/21727090
MutationTaster Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/24681721
MutPred Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/19734154
PhyploP100_way_vertebrate Conservation score https://pubmed.ncbi.nlm.nih.gov/16024819/
Polyphen Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/20354512
PrimateAI Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/30038395
PROVEAN Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/23056405
REVEL Pathogenicity score https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065685/
Sift Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/26633127
SnpEff Variant consequence predictor https://pubmed.ncbi.nlm.nih.gov/22728672
Topmed Population allele frequency source https://bravo.sph.umich.edu/
UniProt Pathogenicity score https://pubmed.ncbi.nlm.nih.gov/30395287/
VEP Variant consequence predictor https://pubmed.ncbi.nlm.nih.gov/27268795/
Varity_R Pathogenicity score https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8546039/

Some of scores are imported from dbNSFP database https://pubmed.ncbi.nlm.nih.gov/33261662/

Presented list is not exhaustive, as it is continuously expanding with new sources being added constantly.