Table 2. Prediction of functional effects of the SNPs.

Metabolites	SNP	Gene	Allele	Residue change	CADD		polyphen 2		Provean		SIFT
					impact	phred score	prediction	score	prediction (cutoff = 0.05)	score	prediction	score
asparagine	rs8012505	ASPG	C > G	S344R	Moderate, modifier	15.87	probably damaging	0.988	Damaging	0.016	Damaging	0.03
proline	rs5747933	PRODH	G > T	T275N	Moderate, modifier	7.274	no data		Tolerated	0.636	Tolerated	0.5
phenyl- alanine	rs118092776	PAH	C > T	R53H	Moderate, modifier	17.68	no data		Damaging	0.007	Damaging	0.01
glycine	rs1047891	CPS1	C > A	T1406N	Moderate, modifier	14.03	benign	0.009	Tolerated	0.235	Tolerated	0.25
formate	rs1801133	MTHFR	C > T	A222V	Moderate	21.9	probably damaging	0.998	Deleterious	−3.76	Damaging	0.05
creatinine	rs820336	MYLK	G > A	intron	Modifier	4.782