Table 1 Significanta 1,5-AG (µg/mL) single SNP results in European ancestry sample, with validation in the African ancestry sample.

From: Rare variants in SLC5A10 are associated with serum 1,5-anhydroglucitol (1,5-AG) in the Atherosclerosis Risk in Communities (ARIC) Study

SNP

Gene

Chr

A1/A2b

Functionc

Amino acid change

GERP, SIFT, Poly-phen2, CADD Predictiond

TOP Med AF

TGP EA Effect AFe

TGP AA Effect AFe

European ancestry (N = 6,589)

African ancestry (N = 2,309)

Effect AF

Beta (SE)

P-value

% Var. Explained

Effect AF

Beta (SE)

P-value

% Var. Explained

rs61741107

SLC5A10

17

G/A

NS

G > E

D,D,D,D

0.004

0.002

0

0.007

−9.31 (0.59)

8.85E-56

2.95

0.0005g

−9.17 (3.95)

0.02

0.26

rs148178887

SLC5A10

17

A/T

NS

N > I

D,D,D,D

0.002

0.005

0

0.004

−10.38 (0.82)

1.13E-36

1.71

0.002g

−9.93 (2.80)

3.83E-04

0.36

rs201046878

SLC5A10/ FAM83G f

17

G/A

NS/If

R > W

D,D,D,D

0.002

0.005

0.002

0.004

−8.33 (0.74)

1.96E-29

1.25

0.002g

−9.93 (2.80)

3.83E-04

0.33

rs200038747

SLC5A10/ FAM83G f

17

C/T

NS/If

R > Q

D,D,D,D

0.002

0.001

0.005

0.002

−9.04 (1.23)

1.69E-13

0.61

0.004

0.25 (1.25)

0.84

0.09

rs117355297

SLC5A10

17

C/T

S

—

T,NA,NA,D

0.022

0.05

0.001

0.04

−2.73 (0.26)

3.85E-26

1.37

0.005

−3.34 (1.12)

2.91E-03

0.2

rs4072037

MUC1

1

C/T

NS

—

T,NA,NA,T

0.60

0.55

0.60

0.54

−0.49 (0.10)

3.74E-07

0.26

0.67

−0.22 (0.18)

0.21

0.1

rs961360

R3HDM1

2

A/G

NS

M > V

D,T,B/P,T

0.22

0.23

0.25

0.15

−0.80 (0.14)

7.82E-09

0.32

0.20

−0.41 (0.21)

0.05

0.3

rs10445686

RAB3GAP1

2

A/G

NS

N > S

D,T,B,T

0.14

0.19

0.02

0.13

−0.79 (0.14)

3.59E-08

0.35

0.03

0.21 (0.49)

0.66

0.04

rs2304371

LCT

2

G/A

S

—

D,NA,NA,T

0.70

0.75

0.41

0.83

0.89 (0.13)

6.74E-12

0.49

0.45

0.39 (0.16)

0.02

0.13

rs3739022

LCT

2

G/A

S

—

T,NA, NAT

0.16

0.15

0.22

0.10

−1.07 (0.17)

1.23E-10

0.51

0.21

−0.48 (0.20)

0.02

0.09

rs1050115

UBXN4

2

A/G

S

—

T,NA,NA,T

0.17

0.21

0.17

0.15

−0.80 (0.14)

5.69E-09

0.35

0.14

−0.61 (0.24)

0.01

0.19

rs9283633

SI

3

T/C

NS

T > A

T,T,B,T

0.58

0.63

0.46

0.61

0.52 (0.10)

2.03E-07

0.33

0.48

0.29 (0.17)

0.09

0.17

rs185053832

MGAM

7

C/A

NS

P > T

D,D,D,D

0.006

0.01

0.001

0.01

−3.30 (0.49)

1.70E-11

0.63

0.0027

−1.26 (3.22)

0.69

0.01

rs17683011

SLC5A1

22

A/G

NS

N > S

T,T,B,T

0.04

0.06

0.003

0.07

−0.96 (0.19)

3.36E-07

0.31

0.02

−0.94 (0.66)

0.15

0.01

rs17683448

SLC5A1

22

C/T

S

—

T,NA,NA,T

0.04

0.06

0.003

0.06

−1.14 (0.21)

5.26E-08

0.38

0.01

−0.97 (0.71)

0.17

0.02

  1. aBonferroni corrected significance threshold = 4.1 × 10−7 (0.05/121,052 SNPs).
  2. bA2 is effect allele.
  3. cNS = nonsynonymous, S = synonymous, I = intron.
  4. dGERP and CADD prediction: D = deleterious, T = tolerated otherwise; Polyphen2 and SIFT prediction: D = probably damaging, P = possibly damaging, B = benign.
  5. eTGP = 1000 genomes allele frequency for Eur (EA) and Afr (AA), AF = allele frequency.
  6. fSLC5A10 and FAM83G are overlapping genes. These variants are missense variants in FAM83G and intronic to SLC5A10.
  7. gVariants have minor allele count <1.
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