Table 1.
In silico analysis of GPD1L gene* mutation.
| Protein prediction programmes | Splice site prediction programmes | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| PolyPhen-2a,∗∗ | Mutation Tasterb |
Mutation Assessorc |
I-MUTANT 3.0d | MutPrede | SNPs and GOf | SIFTg | SNAPh | ASSPi
Neural Networkj ESEk |
HSFl |
| Benign (scores: 0.000; 0.001) |
Disease-causing (P: 0.999) |
Neutral | Neutral (RI: 5) |
Deleterious (Pdel: 0.89) |
Neutral (RI: 9) |
Tolerated (SR: 1.0) |
Neutral (RI: 2.0) |
No effect | SRp55 site created SRp40 site broken |
*Refseq transcript accession number NM_015141.3.3; Refseq protein accession number NP_055956.1; uniprot accession number Q8N335.
**Scores relate to predictions based on HumDiv and HumVar models.
b http://www.mutationtaster.org/; P refers to the probability value, which is the probability of the prediction.
d http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant3.0/I-Mutant3.0.cgi; RI refers to reliability index.
e http://mutpred.mutdb.org/; Pdel refers to the probability that the variant is a deleterious mutation.
f http://snps-and-go.biocomp.unibo.it/snps-and-go/; RI refers to reliability index.
g http://sift.jcvi.org/www/SIFT_BLink_submit.html; SR refers to a SeqRep value that corresponds to the fraction of sequences that contain one of the basic amino acids. A low fraction indicates the position is either severely gapped or unalignable and has little information, so it offers poor predictive capability. P refers to the scaled probability that the amino acid change is deleterious (a value less than 0.05 is predicted to be deleterious).
h https://rostlab.org/services/snap/submit; RI refers to reliability index.
k http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi; screened for human U2-type splice donor and acceptor sites above default thresholds.