Table 3.
In silico prediction of missense changes identified in the FMOD gene.
| Prediction tool | p.(Tyr42Ser) Y42S | p.(Pro24Ala) P24A | Results | Website | Ref. | ||
|---|---|---|---|---|---|---|---|
| Score | Prediction | Score | Prediction | ||||
| SIFT4G predictions | 0.004 | Deleterious | 0.339 | Tolerated | Score range: 0 to 1 (≤0.05 damaging/>0.05 tolerated). | https://sift.bii.a-star.edu.sg/www/SIFTdbSNP.html | [25] |
| PolyPhen-2_HVAR | 0.831 | Probably damaging | <0.01 | Benign | Score range: 0 (benign) to 1 (damaging). Probably damaging, possibly damaging or benign. | http://genetics.bwh.harvard.edu/pph2/index.shtml | [26] |
| PROVEAN | -0.86 | Neutral | -0.56 | Neutral | Default score threshold: -2.5 (≤-2.5 deleterious/>-2.5 neutral). | http://provean.jcvi.org/ | [27] |
| WS-SNPs & GO | 0.280 | Neutral | 0.106 | Neutral | Score range: 0 to 1 (probability score: >0.5 disease-associated). | http://snps.biofold.org/snps-and-go/ | [28] |
| MutPred2 | 0.625 | Possibly pathogenic | 0.209 | Neutral | Score range: 0 to 1 (general pathogenicity score: ≥0.50). | http://mutpred.mutdb.org/#qform | [29] |
| SNAP | 2 | Effect | -54 | Neutral | Score: -100 to 100 (≥1 effect). | http://www.rostlab.org/services/SNAP | [30] |
| FATHMM | 0.52 | Tolerated | 0.67 | Tolerated | Pathogenicity threshold: <0 (dano). >0 (Tolerado). | http://fathmm.biocompute.org.uk/inherited.html | [31] |
| M-CAP | ∗ | ∗ | 0.003 | Benign | Pathogenicity threshold: >0.025. | http://bejerano.stanford.edu/mcap/ | [32] |
| Mutation assessor | 1.04 | Low impact | 0.345 | Neutral | Score cutoff: 0.8 neutral and low impact/1.9 low impact and medium impact/3.5 medium impact and high impact. | http://mutationassessor.org/r3/ | [33] |
| PANTHER-PSEP | 455 | Possibly pathogenic | 91 | Possibly benign | Length of time: >450 my probably damaging/450 my > time > 200 my possibly damaging/<200 my probably benign. | http://www.pantherdb.org/tools/csnpScore.do | [34] |
| Mutation taster | 0.999999999606647-A | Disease causing | 0.999999999606647-P | Polymorphism | Prediction: A. Disease causing: probably deleterious/D. disease causing automatic: deleterious/N. polymorphism: probably harmless/P. polymorphism automatic: harmless. | http://www.mutationtaster.org/ | [35] |
| Revel | 0.168 | Benign | 0.081 | Benign | Score range: 0 to 1 (>0.50 likely disease causing/<0.50 likely benign). | https://sites.google.com/site/revelgenomics/downloads | [36] |
Notes: ∗MCAP-MCAP scoring is not available for some alleles; location 1 : 203317274. Abbreviation: my: millions of years.