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Protocols

SNPs&GO specifications

Information


Unique identifier OMICS_02219
Name SNPs&GO
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Input data A sequence structure.
Output data Probabilities for each protein variation to be associated to human diseases.
Computer skills Basic
Stability Stable

Taxon


  • Primates
    • Homo sapiens

Maintainer


This tool is not maintained anymore.

Publications for SNPs&GO

SNPs&GO citations

 (53)
call_split

GATA4 Variants in Individuals With a 46,XY Disorder of Sex Development (DSD) May or May Not Be Associated With Cardiac Defects Depending on Second Hits in Other DSD Genes

2018
PMCID: 5893726
PMID: 29670578
DOI: 10.3389/fendo.2018.00142
call_split See protocol

[…] GATA4 sequence variants were then evaluated for their possible functional significance in silico using prediction software programs, including SIFT, Provean, PolyPhen-2, MutationTaster, MutPred, and SNPs&GO.In all three cases, the involved clinician informed the patient about the genetic results, including information on pathogenic, probably pathogenic, and uncertain findings with regard to the D […]

call_split

Local adaptation in European populations affected the genetics of psychiatric disorders and behavioral traits

2018
Genome Med
PMCID: 5870256
PMID: 29580271
DOI: 10.1186/s13073-018-0532-7
call_split See protocol

[…] alysis based on information related to expression quantitative trait loci (eQTLs) rather than physical positions of SNPs and genes, integrating the eQTL data and GO, constructing associations between SNPs and GO terms, and then performing functional enrichment analysis. An FDR correction was applied to the enrichment results for multiple testing (q < 0.05). To validate the results further, we cond […]

library_books

Genetic analyses in a bonobo (Pan paniscus) with arrhythmogenic right ventricular cardiomyopathy

2018
Sci Rep
PMCID: 5847517
PMID: 29531232
DOI: 10.1038/s41598-018-22334-5

[…] y. While not validated for clinical use, the computer-based algorithms PolyPhen (HumDiv and HumVar) and Mutation Taster classified this variant as probably damaging or disease causing, while SIFT and SNPs&Go classified this variant as tolerated or as a neutral polymorphism.Figure 2The second Lody-specific variant was a synonymous heterozygous c.1506ā€‰Cā€‰>ā€‰T (p.I502I) variant in exon 9 of the JUP gen […]

library_books

Dysregulation of NEUROG2 plays a key role in focal cortical dysplasia

2018
PMCID: 5901021
PMID: 29461643
DOI: 10.1002/ana.25187

[…] osaic mutations when <10% of reads were not aligned to the human genome reference (GRCh38/hg38) and were present only in BTRS. Deleterious effect of mutations was evaluated using SIFT, Polyphen2, and SNPs&GO. […]

library_books

Severe bleeding complications and multiple kidney transplants in a patient with tuberous sclerosis complex caused by a novel TSC2 missense variant

2017
PMCID: 5778681
PMID: 29308833
DOI: 10.3325/cmj.2017.58.416

[…] ce, algorithms of PolyPhen-2, Sorts Intolerant From Tolerant (SIFT), Align-Grantham Variation Grantham Deviation (Align-GVGD), MutationTaster, Single Nucleotide Polymorphism Database & Gene Ontology (SNPs&GO), MutPred, MutationAssessor, and Functional Analysis Through Hidden Markov Models (FATHMM) were applied. For the detection of genomic deletions and duplications, a quantitative analysis of all […]

library_books

Novel mutations in Darier disease and association to self reported disease severity

2017
PLoS One
PMCID: 5640244
PMID: 29028823
DOI: 10.1371/journal.pone.0186356

[…] The pathogenicity of missense and intronic/splice-site variants were assessed using in silico prediction programs. Missense variants were assessed with PolyPhen-2 [], SIFT [] and SNPs&GO [], and the splice-site variants were assessed with ASSP [] and HSF []. A mutation is categorised as benign or pathogenic when the majority of scores from the prediction programs are concordan […]

Citations

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SNPs&GO institution(s)
Identification and annotation of SNPs in the context of structure, function, and disease Long Beach, CA, USA
SNPs&GO funding source(s)
This work has been supported by the European Community through the Marie Curie International Outgoing Fellowship program [PIOF-GA-2009- 237225] and COST BMBS Action TD1101; PRIN 2009 [009WXT45Y] and PON project [PON01_02249] from the Italian Ministry of Research, by a start-up funds from the Department of Pathology at the University of Alabama, Birmingham, and by NIH LM05652, LM GM102365, the NSF CNS-0619926.

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