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SNPeffect specifications


Unique identifier OMICS_00187
Name SNPeffect
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 4.0
Maintained Yes


  • Primates
    • Homo sapiens



  • person_outline Frederic Rousseau
  • person_outline Joost Schymkowitz

Publication for SNPeffect

SNPeffect citations


Phylogenetic and CRISPR/Cas9 Studies in Deciphering the Evolutionary Trajectory and Phenotypic Impacts of Rice ERECTA Genes

Front Plant Sci
PMCID: 5902711
PMID: 29692796
DOI: 10.3389/fpls.2018.00473

[…] iversities within different rice subspecies were calculated using public available PERL script “” as described in .Putative effects of variants in rice ERfs were predicted using SNPeffect 4.0 () against MSU Rice Genome Annotation Project (RGAP) Release 7 database (). The results for OsER2 were further examined manually based on NCBI model. Tajima’s D-value was estimated using […]


Genetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch)

BMC Plant Biol
PMCID: 5670703
PMID: 29100531
DOI: 10.1186/s12870-017-1117-0

[…] sing RealignerTargetCreator and IndelRealigner tools, then filtered and merged, generating a single multi-sample file. Mapped reads were visualized in Tablet []. Variants were then annotated by using SNPEffect v2.0 [] and peach reference genes annotations. For the prediction of candidate genes, the following priorities were considered: i) identification of variants from WGS; ii) genes with functio […]


Spatial distribution of disease associated variants in three dimensional structures of protein complexes

PMCID: 5623905
PMID: 28945216
DOI: 10.1038/oncsis.2017.79

[…] ution of structural parameters to the prediction performance has been a long-discussed issue., Numerous tools have been constructed to assess potential changes caused by SNVs in protein 3D structure: SNPeffect database, for example, ignores the conservation profiles of SNVs and relies on predicted structural features (aggregation, amyloidogenicity, stability) and domain and catalytic site annotati […]


Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co expression network and genome analyses

BMC Genomics
PMCID: 5389088
PMID: 28403814
DOI: 10.1186/s12864-017-3678-6
call_split See protocol

[…] ighly duplicated genomic regions, a maximum read coverage depth for each variable site was set to be two times the mean coverage depth for entire genome. The filtered VCF files were used as input for SNPeffect [] to predict the functional effect of each DNA sequence variant. De novo genome assembly of genomic reads from individual isolates was performed using CLC bio assembly software (QIAGEN). Th […]


Genetic Profiles of South Korean Patients With Glucose 6 Phosphate Dehydrogenase Deficiency

PMCID: 5203987
PMID: 28028996
DOI: 10.3343/alm.2017.37.2.108

[…] tabase at an extremely low frequency, i.e., 1.141×10-5 (, ). For the Class IV mutation, G6PD São Paulo, an in silico analysis using SIFT, PROVEAN, PolyPhen-2, Align-GVGD, and the FoldX implemented in SNPeffect 4.0 predicted a relatively mild effect, consistent with the observed enzyme activity levels. […]


Filaggrin gene mutations and new SNPs in asthmatic patients: a cross sectional study in a Spanish population

PMCID: 4960762
PMID: 27462351
DOI: 10.1186/s13223-016-0137-x
call_split See protocol

[…], dbSNP of the NCBI ( prediction analysis of polymorphisms functional effect was carried out by online platforms ExPASyProSite (, SNPeffect 4.0 ( and PolyPhen-2 prediction of functional effects of human nsSNPs ( […]

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SNPeffect institution(s)
VIB Switch Laboratory, Leuven, Belgium ; Department of Molecular Cell Biology, University of Leuven, Leuven, Belgium ; Vrije Universiteit Brussel, Brussel, Belgium; Vesalius Research Center, VIB, Leuven, Belgium; Vesalius Research Center, University of Leuven, Leuven, Belgium; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Bioinformatics, Centro de Investigacion Principe Felipe (CIPF), Valencia, Spain; Functional Genomics Node (INB) at CIPF, Valencia, Spain
SNPeffect funding source(s)
Supported by Interuniversity Attraction Poles (IAP Network 6/43) of the Belgian Federal Science Policy Office (BelSPo) (VIB Switch laboratory); Flanders Institute for Science and Technology (IWT), Fund for Scientific Research (FWO), Flanders, MICINN projects BIO2008-04212, and RD06/0020/1019 (RTICC, ISCIII) (Dopazo lab, partial) GVA-FEDER (PROMETEO/2010/001, partial).

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