Fibromodulin Gene Variants (FMOD) as Potential Biomarkers for Prostate Cancer and Benign Prostatic Hyperplasia

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/ 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.