UMD-Predictor protocols

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Associated diseases

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UMD-Predictor specifications

Information


Unique identifier OMICS_11209
Name UMD-Predictor
Interface Web user interface, Application programming interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


Publication for UMD-Predictor

UMD-Predictor in pipelines

 (2)
2017
PMCID: 5421769
PMID: 28481884
DOI: 10.1371/journal.pone.0175998

[…] (ld) between bi-allelic dpyd variants were measured by d’ and d’/lod calculated on haploview software v4.2., in silico pathogenicity prediction of coding variants was performed with the umd-predictor system []. impact of exonic and intronic variations on splicing signal types was predicted with the human splicing finder system []., blood (5 ml) was immediately placed in an ice-bath, […]

2015
PMCID: 5278624
PMID: 27858732
DOI: 10.3233/JND-150074

[…] recommended by the latest publication on gne myopathy nomenclature []., we used the following predictive algorithms to analyze the pathogenicity of the novel variants associated with gne myopathy: umd-predictor (http://www.umd-hts.eu) [], sift (sort intolerant from tolerant human protein; http://sift.jcvi.org) [] and polyphen-2 (polymorphism phenotyping v2; […]


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UMD-Predictor in publications

 (10)
PMCID: 5946819
PMID: 29741738
DOI: 10.1093/infdis/jiy090

[…] indicating that about 1 in 275 africans are heterozygous for this allele., marquet et al extracted both agmo variants from whole-exome-sequencing data by applying different filters, including a umd-predictor to predict potential pathogenicity. we doubted the predicted deleteriousness of the p.lys234arg variant, since bovine agmo carries an arginine in this position (np_001179902.1)., […]

PMCID: 5643959
PMID: 28832565
DOI: 10.1038/ejhg.2017.124

[…] biosoftware, la rochelle, france) for functional effect prediction with splicesitefinder, maxentscan, nnsplice, genesplicer, human splicing finder, polyphen-2, sift, mutationtaster, align gvgd and umd-predictor., twelve patients per experiment were sequenced using the first panel, while 24 were analyzed simultaneously using the second panel. the first 25 portuguese patients tested […]

PMCID: 5552324
PMID: 28797094
DOI: 10.1371/journal.pone.0182946

[…] college of medical genetics and genomics (acmg) guidelines []. prediction of pathogenicity was performed with sift [], polyphen2 hvar [], human splicing finder (version 3.0) [], mutation taster [], umd-predictor [], provean [] and fathmm []. prioritization of noncoding variants was achieved using gwava (version 1.0) [], cadd (version 1.3) [], spidex [] and genomiser []. to determine whether […]

PMCID: 5421769
PMID: 28481884
DOI: 10.1371/journal.pone.0175998

[…] snp and indel positions are given relative to genome build 37 hg19 (reference = nucleotide a of the translation initiation codon atg)., in silico pathogenicity of coding variants was predicted using umd-predictor system []. the potential impact of exonic and intronic variations on splicing signal types was predicted using human splicing finder system []., in vitro functionality derived from two […]

PMCID: 5040013
PMID: 27647186
DOI: 10.4103/0366-6999.190671

[…] canonical ±1 or 2 splice sites, and single exon or multiexon deletions; (3) novel missense mutations predicted to be disease-causing by a combination of four predictive software programs, including umd-predictor (predicted as pathogenic/probably pathogenic),[] mutation taster (predicted as disease-causing),[] polyphen-2 (predicted as probably/possibly damaging),[] and sift software (j. craig […]


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UMD-Predictor institution(s)
Aix-Marseille Université, GMGF, Marseille, France; Inserm, UMR_S 910, Marseille, France; APHM, Hôpital TIMONE Enfants, Laboratoire de Génétique Moléculaire, Marseille, France
UMD-Predictor funding source(s)
Supported by The European Union Seventh Framework Program (grant no. 305444).

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