EPILOGCredits & Licenses
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Credits & Licenses
EPILOG combines published resources, prediction tools and curated literature evidence. This page lists what is used, in which version, under which license or terms, and how to cite it. Short source notes are shown at the bottom of each report and variant page and link here.
For research use only. EPILOG provides computational predictions and curated literature evidence. The evaluations are not a clinical classification
and have not been validated for clinical use.
1. Variant effect predictors
| Resource | Used for | Version | License / terms | Citation / link |
|---|---|---|---|---|
| AlphaMissense | Pathogenicity score and class of missense variants (shown as published, values not modified) | Google DeepMind release of 2023-09-19 (amino-acid substitution and hg38 tables) | CC BY 4.0 (the first release, v1, was CC BY-NC-SA 4.0) | Cheng J, Novati G, Pan J, et al. Science 381, eadg7492 (2023), doi:10.1126/science.adg7492. Data: doi:10.5281/zenodo.10813168 |
| REVEL | Pathogenicity score of missense variants (shown as published) | v1.3 (2021-05-03) | Freely available for non-commercial use (authors). The Zenodo record lists ODbL 1.0. | Ioannidis NM, Rothstein JH, Pejaver V, et al. Am J Hum Genet 99, 877–885 (2016), doi:10.1016/j.ajhg.2016.08.016. Scores: doi:10.5281/zenodo.7072866 |
| CADD | CADD PHRED score (retrieved by genomic position, shown as published) | GRCh38-v1.7 | Freely available for non-commercial applications; commercial use requires a license from the University of Washington. © University of Washington, Hudson-Alpha Institute for Biotechnology, Berlin Institute of Health. | Schubach M, Maass T, Nazaretyan L, Röner S, Kircher M. CADD v1.7. Nucleic Acids Res (2023), doi:10.1093/nar/gkad989. cadd.gs.washington.edu |
| SCION | Gain- versus loss-of-function probability (SCN1A, SCN2A, SCN8A) | Repository commit 2ac1384 (2022-11-02), run locally | MIT License | github.com/christianbosselmann/SCION |
| funNCion | Gain- versus loss-of-function probability (SCN1A, SCN2A, SCN8A) | Repository commit 34c129f (2019-11-11), pre-computed table | GNU GPL v2 (repository) | github.com/heyhen/funNCion |
2. Curated functional (patch-clamp) evidence
Every evidence row cites the original study by PMID. Rows taken from external compilations are also labelled with their source. EPILOG expressed the reported parameters as LoF / GoF / Non-specific calls and combined them per study.
| Source label | Description | License / terms |
|---|---|---|
| neXtProt | Patch-clamp results (human channels only) extracted from the literature by neXtProt curators and re-expressed by EPILOG. Gaudet P, Bairoch A, Abriel H. neXtProt ion channels variants portal. Zenodo, 2024, doi:10.5281/zenodo.14356360. | CC BY 4.0 |
| Paper extraction | Electrophysiology results that EPILOG curators extracted from the cited papers (GABRA1, KCNQ2, KCNT1). | See the cited studies |
| SCN Viewer 133 | Electrophysiology results for SCN1A / SCN2A / SCN8A variants compiled in the EPILOG SCN Viewer 133 curation and re-checked against the original papers (human channels only). | See the cited studies |
3. Structures and computed values
| Item | How it is obtained | Version / notes |
|---|---|---|
| Protein structures | AlphaFold 3 predictions of the wild-type and variant proteins. The viewer and reports use the top-ranked model (ranked_0). | Prediction software version to be specified |
| Structure comparison | Calculated by EPILOG: Cα RMSD after Kabsch superposition (all residues and helix/strand residues with pLDDT ≥ 70), TM-score, local metrics within 10 Å of the variant. | Method v2 |
| Predicted ΔΔG | ThermoMPNN, estimated from the wild-type structure (kcal/mol, positive = destabilizing). | Repository commit 370f76e (2026-09-09), MIT License. github.com/Kuhlman-Lab/ThermoMPNN |
| Variant evaluation | Pathogenicity, Functional effect and Concordance are derived automatically from the evidence above. | Rule version v1.2 |
4. Clinical annotations
ClinVar and LitVar2 annotations and links are shown as retrieved from NCBI at the time of data collection.