Table 3 Additional missense variants from the candidate genes as seen in 18 T1D families consisting of 37 T1D cases and 49 unaffected first-degree relatives.

From: Linkage analysis using whole exome sequencing data implicates SLC17A1, SLC17A3, TATDN2 and TMEM131L in type 1 diabetes in Kuwaiti families

Gene/chromosome location/ SNP identifier

Aminoacid change

Global MAF

HomAlt genotypes in T1D family members

HomAlt genotypes in 291 general Kuwaiti population

T1D

Unaffected cases

SIFT

Polyphen

nHet (0/1)

nHomAlt (1/1)

nHomRef (0/0)

nHet (0/1)

nHomAlt (1/1)

nHom ref (0/0)

SLC17A3/Chr6: 25850845/rs56027330

p.G279R

7% (T)

Confirmed in 6 index cases

10 (3.4%)

3

6 (16.2%)

28

13

1 (2.0%)

35

0.16

0

TATDN2/Chr3: 10290952/rs148376271

p.R23H

2% (A)

–

0 (0%)

2

0 (0%)

35

1

0 (0%)

48

0.1

0.802

TATDN2/chr3: 10302056/rs2241314

p.H217R

36% (G)

NA

0 (0%)

5

0 (0%)

32

10

1 (2.0%)

38

0.29

0.09

TATDN2/chr3: 10302172/rs394558

p.V256I

40% (G)

Confirmed in 5 index cases

97 (33.3%)

17

5 (13.5%)

15

19

2 (4.1%)

28

0.05

0.006

TATDN2/chr3: 10311939/rs2075352

p.P358L

18% (T)

 

5 (0.3%)

5

0 (0%)

32

4

0 (0%)

45

0.01

0.059

TMEM131L/Chr4: 154525138/rs36023829

p.T991A

3% (G)

–

0 (0%)

3

0 (0%)

34

2

0 (0%)

47

0.32

0

TMEM131L/Chr4: 154,542,906/rs35018723

p.N1254S

2% (G)

–

0 (0%)

1

0 (0%)

36

1

0 (0%)

48

0.39

0.007

TMEM131L/Chr4: 154548809/rs35543386

p.A1392P

1% (C)

–

0 (0%)

1

0 (0%)

36

2

0 (0%)

47

0.24

0.893

TMEM131L/chr4: 154513627/rs7669418

p.I604V

23% (G)

 

12 (4.1%)

13

0 (0%)

24

12

2 (4.1%)

35

1

0

TMEM131L/chr4:1 54514965/rs17370297

p.M645T

23% (C)

 

12 (4.1%)

13

0 (0%)

24

13

2 (4.1%)

34

0.21

0.257

SLC17A1/chr6:25813150/rs1165196

pT269I

28% (G)

Confirmed in 10 index cases

112 (38.5%)

14

10 (27.0%)

13

16

9 (18.4%)

24

0.26

0.001

SLC17A3/chr6:25862466/rs1165165

p.A100T

22% (T)

Confirmed in 2 index cases

24 (8.3%)

10

2 (5.4%)

25

11

3 (6.1%)

35

0.09

0.018

  1. The SIFT score ranges from 0.0 (deleterious) to 1.0 (tolerated); The minimum passing score is 0.4
  2. Genes are italicized.
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