License & terms of use
MitImpact is free to use. APOGEE1, APOGEE2 and nAPOGEE are for non-commercial use;
third-party annotations keep their own licences, listed below.
What is licensed how
- MitImpact's own content: the compiled database, MitImpact identifiers, genomic and protein annotation, co-variation, CPD, EVmutation and COVEC values. Licensed under CC BY 4.0: you may share and adapt it for any purpose, including commercial, provided you cite MitImpact (see How to cite) and indicate any changes.
- APOGEE1, APOGEE2 and nAPOGEE scores, probabilities and classes. Licensed under CC BY-NC 4.0: free for non-commercial use with attribution. Commercial use, including use in products, paid services or clinical/diagnostic pipelines offered for a fee, requires a separate licence from us.
- Third-party annotations (predictors, population and clinical databases, identifiers) remain under their providers' terms, summarised in the table below. Our licence does not extend to them; where a provider restricts commercial use, that restriction applies to its columns.
Sources and their licences
"In download" says whether the column is in the CSV download. Sources marked attribution publish no licence of their own; their values are included with credit and will be removed at the provider's request.
| Source | Licence / terms | In download | Cite |
|---|---|---|---|
| MitImpact 4 (MITHRIL V059) |
CC BY 4.0 Original MitImpact content: identifiers, coordinates, codon/amino-acid annotation. EVmutation, I-COMS covariation and CPD are on the website only. |
Yes (some columns) | Giovannetti A et al. MitImpact 4. Nucleic Acids Res 2026, doi:10.1093/nar/gkag1070. |
| COVEC WMV 0.4 |
CC BY 4.0 (MitImpact content) Computed by MitImpact from SIFT, PolyPhen-2 and MutationAssessor outputs. |
Yes | Frousios K et al. Genomics 2013;102:223. |
| APOGEE / APOGEE 2 / nAPOGEE APOGEE 2 (2023), nAPOGEE 1.0.0 |
CC BY-NC 4.0 MitImpact's own predictors. Non-commercial use only; commercial licence on request (computationalbiology@policlinicogemelli.it). |
Yes, non-commercial | Bianco SD et al. APOGEE 2. Nat Commun 2023;14:5058. Castellana S et al. APOGEE. PLoS Comput Biol 2017;13:e1005628. |
| FoldX ΔΔG FoldX 4.0/5.0 |
FoldX academic licence Computed by MitImpact with FoldX under its academic licence (research use only). Website only, not in the download. |
Not exported | Schymkowitz J et al. Nucleic Acids Res 2005;33:W382. |
| SnpEff | MIT (software); output unrestricted Functional effect computed by MitImpact with SnpEff. |
Yes | Cingolani P et al. Fly 2012;6:80. |
| rCRS (NC_012920.1) NC_012920.1 |
NCBI: no restrictions Reference sequence for all coordinates. |
Not a column | Andrews RM et al. Nat Genet 1999;23:147. |
| HGNC | CC0 | Yes | Seal RL et al. Genenames.org: the HGNC resources in 2023. Nucleic Acids Res 2023. |
| Ensembl | No restrictions | Yes | Dyer SC et al. Ensembl 2025. Nucleic Acids Res 2025. |
| UniProt | CC BY 4.0 Attribution required. |
Yes | The UniProt Consortium. Nucleic Acids Res 2025;53:D609. |
| NCBI Gene / RefSeq | NCBI: no restrictions | Yes | Sayers EW et al. Database resources of the NCBI. Nucleic Acids Res (latest). |
| OMIM | Copyright Johns Hopkins University MIM gene numbers only, as cross-references; no OMIM text is included. |
Yes, attribution | OMIM®, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, omim.org. |
| dbSNP build 157 |
Public domain | Yes | Phan L et al. The evolution of dbSNP: 25 years of impact in genomic research. Nucleic Acids Res 2025. |
| ClinVar | NCBI: no restrictions Attribution requested. Not for diagnosis without review by a genetics professional. |
Yes | Landrum MJ et al. Nucleic Acids Res 2018;46:D1062. |
| MITOMAP | CC BY 3.0 Attribution required. Values are shipped as received from MITOMAP. |
Yes | Lott MT et al. Curr Protoc Bioinformatics 2013;44:1.23.1. |
| MitoTIP (MITOMAP) | CC BY 3.0 Attribution required. |
Yes | Sonney S et al. PLoS Comput Biol 2017;13:e1005867. |
| gnomAD v3.1 mtDNA |
CC0 Attribution requested; no attempt to re-identify participants. |
Yes | Laricchia KM et al. Genome Res 2022;32:569. Chen S et al. Nature 2024;625:92. |
| HelixMTdb 20200327 |
No licence published (citation requested) | Yes, attribution | Bolze A et al. bioRxiv 2020, doi:10.1101/798264. Data from HelixMTdb, Helix.com/MITO. |
| ToMMo 61KJPN (jMorp) 61KJPN |
ToMMo Conditions of Use Commercial use needs ToMMo's permission; no re-identification. ToMMo was notified of this redistribution (17 October 2026). |
Yes, non-commercial | Tadaka S et al. Nucleic Acids Res 2024;52:D622. |
| COSMIC v90 |
COSMIC licence (academic, no redistribution) COSMIC's terms cover its identifiers and forbid distribution on free-to-access platforms; not shown on the website or in the download. |
No (licence) | Tate JG et al. Nucleic Acids Res 2019;47:D941. |
| UCSC PhyloP / PhastCons hg38 100-way, 470-way |
Free for any use, credit required | Yes | Pollard KS et al. Genome Res 2010;20:110. Siepel A et al. Genome Res 2005;15:1034. |
| CADD | Free for non-commercial use Commercial use needs a licence from UW CoMotion. |
Yes, non-commercial | Schubach M et al. Nucleic Acids Res 2024;52:D1143. |
| MLC (mitochondrial local constraint) | No licence published | Yes, attribution | Lake NJ et al. Nature 2024;625:146. |
| PolyPhen-2 2.2.2 |
Software free for academic/research use; commercial licence available Computed by MitImpact. The authors' no-redistribution clause covers the code, not predictions; treated as non-commercial. Includes the TransFIC transform. |
Yes, non-commercial | Adzhubei IA et al. Nat Methods 2010;7:248. |
| MutationTaster via dbNSFP |
dbNSFP academic: CC BY-NC-ND 4.0 Taken verbatim from dbNSFP v4.5a (CC BY-NC-ND 4.0: sharing allowed, non-commercial, no modified values). |
Yes, non-commercial | Steinhaus R et al. Nucleic Acids Res 2021;49:W446. Via dbNSFP: Liu X et al. Genome Med 2020;12:103. |
| DEOGEN2 via dbNSFP |
dbNSFP academic: CC BY-NC-ND 4.0 Taken verbatim from dbNSFP v4.5a (CC BY-NC-ND 4.0: sharing allowed, non-commercial, no modified values). |
Yes, non-commercial | Raimondi D et al. Nucleic Acids Res 2017;45:W201. Via dbNSFP: Liu X et al. Genome Med 2020;12:103. |
| SIFT 5.0.3 |
No licence published Includes the TransFIC transform computed by MitImpact. |
Yes, attribution | Ng PC, Henikoff S. Nucleic Acids Res 2003;31:3812. |
| SIFT4G | GPL-3.0 (software); output unrestricted | Yes | Vaser R et al. Nat Protoc 2016;11:1. |
| PROVEAN 1.1 |
GPL-3.0 (software); output unrestricted | Yes | Choi Y et al. PLoS One 2012;7:e46688. |
| MutationAssessor | No licence published Includes the TransFIC transform computed by MitImpact. |
Yes, attribution | Reva B et al. Nucleic Acids Res 2011;39:e118. |
| VEST (CRAVAT) CRAVAT 3.2 |
Free for non-commercial use Commercial use needs a licence from the Karchin lab (Johns Hopkins). |
Yes, non-commercial | Carter H et al. BMC Genomics 2013;14(Suppl 3):S3. |
| CHASM (CRAVAT) CRAVAT 3.2 |
Free for non-commercial use Commercial use needs a licence from the Karchin lab (Johns Hopkins). |
Yes, non-commercial | Carter H et al. Cancer Res 2009;69:6660. |
| Meta-SNP server (PANTHER, PhD-SNP, Meta-SNP) | No licence published | Yes, attribution | Capriotti E et al. BMC Genomics 2013;14(Suppl 3):S6. Capriotti E et al. Bioinformatics 2006;22:2729. Tang H, Thomas PD. Bioinformatics 2016;32:2230. |
| SNPDryad | No licence published | Yes, attribution | Wong KC, Zhang Z. Bioinformatics 2014;30:2112. |
| EFIN | No licence published | Yes, attribution | Zeng S et al. BMC Bioinformatics 2014;15:105. |
| CAROL | No licence published | Yes, attribution | Lopes MC et al. Hum Hered 2012;73:47. |
| Condel | No licence published | Yes, attribution | González-Pérez A, López-Bigas N. Am J Hum Genet 2011;88:440. |
| MToolBox | GPL-3.0 | Yes | Calabrese C et al. Bioinformatics 2014;30:3115. |
| Mitoclass.1 | No licence published | Yes, attribution | Martín-Navarro A et al. Hum Mutat 2017;38:899. |
| LIST-S2 1.10 |
Non-commercial, keep author copyright notice | Yes, non-commercial | Malhis N et al. Nucleic Acids Res 2020;48:W154. |
| ESM1b | No licence published for precomputed scores (code MIT) | Yes, attribution | Brandes N et al. Nat Genet 2023;55:1512. |
| VARITY | No licence published | Yes, attribution | Wu Y et al. Am J Hum Genet 2021;108:1891. |
| AlphaMissense Zenodo v3 (10813168) |
CC BY 4.0 Predictions relicensed from CC BY-NC-SA to CC BY 4.0 on 13 March 2024. |
Yes | Cheng J et al. Science 2023;381:eadg7492. |
| PON-mt-tRNA | No licence published | Yes, attribution | Niroula A, Vihinen M. Nucleic Acids Res 2016;44:2020. |
| mitotRNAdb | CC BY 4.0 (tRNAdb) Human mt-tRNA secondary structures, used only to draw the cloverleaf diagram. |
Not a column | Jühling F et al. Nucleic Acids Res 2009;37:D159. |
Commercial licences and questions
Computational Biology and Bioinformatics LaboratoryFondazione Policlinico Universitario A. Gemelli, IRCCS
Largo Agostino Gemelli, 8 - Rome, Italy 00168
computationalbiology@policlinicogemelli.it
If you are a data provider and want your values removed or credited differently, write to the same address.
The material is provided “as is”, without warranty of any kind. It is intended for research purposes and is not a substitute for professional medical or diagnostic judgement.