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Table 4 Computational predictions of the functional significances of 3 non-synonymous SNPs in the TRPM6 and TRPM7 genes

From: Common genetic variants of the ion channel transient receptor potential membrane melastatin 6 and 7 (TRPM6 and TRPM7), magnesium intake, and risk of type 2 diabetes in women

rs#

SNP

Functional Prediction Algorithm

  

PMut Score

[Reliability index]a

PolyPhen scoreb

SIFT Scorec

rs3750425

Val1393Ile

(TRPM6)

0.0250 [9]

(Neutral)

1.026

(Borderline)

0.04

(Intolerant)

rs2274924

Lys1584Glu

(TRPM6)

0.2565 [4]

(Neutral)

0.256

(Benign)

<0.001

(Intolerant)

rs8042919

Thr1482Ile

(TRPM7)

0.7987 [5]

(Pathological)

1.079

(Borderline)

0.03

(Intolerant)

  1. a. The range of the PMut prediction score is from 0 to 1; a score over 0.5 suggests an effect on protein function and a score <0.5 indicates that the substitution is likely neutral. The range of the reliability index is from 0 to 9; the higher the number, the more reliable is the prediction.
  2. b. PolyPhen Scores: 1.49–1.25 are designated as "Potentially damaging to function"; 1.24–1.00, "Borderline"; and <1.00, "Benign".
  3. c. The SIFT scores are limited to the range of 0.0 to 1.0. Variants are classified as "Intolerant" (0.00–0.05), "Potentially intolerant" (0.051–0.10), "Borderline" (0.101–0.20), and "Tolerant" (0.201–1.00).