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Table 2 Pathogenicity prediction of PTS gene missense variants

From: In silico analysis and the pathogenicity classification of PTS gene variants among Iranian population

Row

Variant

PhD- SNPg

PANTHER PSEP

SNPs & GO

FATHMM-XF

I-Mutant Disease

PolyPhen -2

PROVEAN

Mutation Taster

CADD

SIFT

# of tools with pathogenic prediction

1

c.70C>G (p.His24Asp)

P

Pro Da

D

P

D

Pro Da

De

D

31

Da

10:10

2

c.155A>G (p.Asn52Ser)

P

Pro Da

D

P

D

Pro Da

De

D

25.5

Da

10:10

3

c.200C>T (p.Thr67Met)

P

Pos Da

N

P

D

Pro Da

De

D

31

Da

9:10

4

c.259C>T (p.Pro87Ser)

P

Pro Da

N

P

D

Pos Da

De

D

23.8

T

8:10

5

c.281A>T (p.Asp94Val)

P

Pro Da

N

P

D

Pro Da

De

D

31

Da

9:10

6

c.286G>A (p.Asp96Asn)

P

Pro Da

D

P

D

Pro Da

De

D

31

Da

10:10

7

c.293C>T (p.Pro98Leu)

P

Pro Da

N

P

D

Pos Da

De

D

27.2

Da

9:10

8

c.317C>T (p.Thr106Met)

P

Pro Da

D

P

D

Pro Da

De

D

26.2

Da

10:10

9

c.331G>A (p.Ala111Thr)

P

Pro Da

D

P

D

B

De

D

23.8

T

9:10

10

c.351C>A (p.Asn117Lys)

P

Pro Da

N

P

D

B

N

D

18.26

T

5:10

11

c.367C>T (p.Pro123Ser)

P

Pro Da

N

P

D

Pos Da

De

D

22.8

T

8:10

12

c.373G>A (p.Gly125Arg)

P

Pro Da

N

B

D

B

De

D

23.9

Da

7:10

13

c.400G>A (p.Glu134Lys)

P

Pro Da

D

P

D

Pro Da

De

D

31

Da

10:10

14

c.407A>T (p.Asp136Val)

P

Pro Da

N

P

D

Pos Da

De

D

28.6

Da

9:10

15

c.412A>C (p.Asn138His)

P

Pro Da

N

P

D

Pro Da

De

D

26

Da

9:10

  1. P: pathogenic, Pro Da: probably damaging, Pos Da: possibly damaging, D: disease causing, N: neutral, B: benign, De: deleterious, T: tolerated