Table 2 MLH1, MSH2 and MSH6 germline variants in Pakistani study participants

Exon 1

c.67delG

p.E23Kfs*13

Frameshift

–

P

1 (3.4)

0

–

Yes

Exon 12

c.1358dup

p.T455Dfs*24

Frameshift

–

P

2 (6.9)

0

–

Yes

Exon 15

c.1672G > T

p.E558*

Nonsense

–

P

1 (3.4)

0

–

Yes

Exon 18

c.2041G > A

p.A681T

Missense

rs63750217

P

1 (3.4)

1 (0.6)

–

Yes

Intron 1

c.116 + 3A > T

–

Intronic

–

LP^c

0

1 (0.6)

0

No

Exon 8

c.655A > G

p.I219V

Missense

rs1799977

B

2 (6.9)

–

–

Yes

Exon 17

c.1913G > T

p.G638 L

Missense

–

B^c

0

2 (1.1)

–

No

Exon 17

c.1919C > T

p.P640L

Missense

–

LP^c

6 (20.7)

2 (1.1)

–

Yes

Exon 17

c.1959G > T

p.L653 L

Silent

rs1800146

B

0

1 (0.6)

–

Yes

Intron 1

c.116 + 4C > A

–

Intronic

–

B^c

0

1 (0.6)

–

No

Intron 13

c.1558 + 14G > A

–

Intronic

rs41562513

B

1 (3.4)

–

–

Yes

Intron 14

c.1668-19A > G

–

Intronic

rs9876116

B

8 (27.6)

55 (30.1)

–

Yes

Intron 17

c.1990-26 T > C

–

Intronic

–

B^c

0

2 (1.1)

–

No

Exon 12

c.1861C > T

p.R621*

Nonsense

–

P

1 (3.4)

0

–

Yes

Exon 16

c.2656G > T

p.E886*

Nonsense

–

P

1 (3.4)

0

0

Yes^d

Intron 5

c.943-1G > C

p.G315Ifs*12

Splice site

–

LP

3 (10.4)

0

–

Yes

Exon 13

c.2120G > A

p.C707Y

Missense

–

LP^c

1 (3.4)

2 (1.1)

2 (2)

No

Exon 6

c.984C > T

p.A328A

Silent

–

LB

2 (6.9)

0

–

Yes

Exon 6

c.944G > T

p.G315 V

Missense

rs202026056

B^c

0

1 (0.6)

–

Yes

Exon 6

c.965G > A

p.G322D

Missense

rs4987188

B

1 (3.4)

10 (5.5)

–

Yes

Exon 6

c.1074G > C

p.E358D

Missense

–

B^c

0

1 (0.6)

–

No

Exon 12

c.1786_1788delAAT

p.N596del

In-frame deletion

–

P

0

1 (0.6)

–

Yes

Exon 13

c.2205C > T

p.I735I

Silent

rs533553381

B

0

5 (2.7)

–

Yes

Intron 1

c.211 + 9C > G

–

Intronic

rs2303426

LB

12 (41.4)

–

–

Yes

Intron 9

c.1511-9A > T

–

Intronic

rs12998837

B

2 (6.9)

–

–

Yes

Intron 10

c.1661 + 12G > A

–

Intronic

rs3732183

B

13 (44.8)

–

–

Yes

Intron 12

c.2006-6 T > C

–

Intronic

rs2303428

B

1 (3.4)

37 (20.2)

–

Yes

Intron 12

c.2006-36_2006-33dup

–

Intronic

rs587779126

B^c

0

5 (2.7)

–

Yes

Exon 3

c.540 T > C

p.D180D

Silent

rs1800935

B

1 (3.4)

–

–

Yes

Exon 4A

c.642C > T

p.Y214Y

Silent

rs1800937

B

1 (3.4)

–

–

Yes

Exon 4G

c.3151G > A

p.V1051I

Missense

–

B^c

1 (3.4)

–

–

Yes

Exon 5

c.3306 T > A

p.T1102 T

Silent

rs2020910

B

1 (3.4)

–

–

Yes

Intron 2

c.457 + 13A > G

–

Intronic

rs1800933

LB

1 (3.4)

–

–

Yes

Intron 2

c.457 + 50 T > A

–

Intronic

–

B^c

3 (10.3)

–

–

No

Intron 2

c.457 + 52 T > A

–

Intronic

rs3136282

B

23 (79.3)

–

–

Yes

Intron 4

c.3172 + 20 T > C

–

Intronic

rs3136335

B

2 (6.9)

–

–

Yes

Intron 5

c.3438 + 14A > T

–

Intronic

rs2020911

B

15 (51.7)

–

–

Yes

Intron 6

c.3556 + 146G > A

–

Intronic

rs7562048

B

1 (3.4)

–

–

Yes

Intron 6

c.3556 + 160 T > C

–

Intronic

rs56320267

B

1 (3.4)

–

–

Yes

Intron 6

c.3556 + 170delT

–

Intronic

–

B^c

1 (3.4)

–

–

No

Intron 6

c.3557–4 dupT

–

Intronic

–

B

1 (3.4)

–

–

Yes

Intron 6

c.3557-40 T > A

–

Intronic

rs189436849

LB

1 (3.4)

–

–

Yes

Intron 9

c.4001 + 26A > G

–

Intronic

–

B^c

1 (3.4)

–

–

No