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Table 3 Pathogenicity prediction of PTS gene intronic and synonymous variants. AASS: authentic acceptor splice site, ADSS: authentic donor splice site

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

Row

Variant

VarSeak

MaxEntScan

NNSplice

NetGene2

ASSP

cryp-skip

GENSCAN

# of tools with pathogenic prediction

1

c.84-5G>T

No effect

No effect

No effect

No effect

No effect

No effect

No effect

0:7

2

c.84-3C>G

AASS score ↓

AASS score ↓

AASS loss

AASS loss

AASS loss

AASS loss

AASS loss

7:7

3

c.84-3C>T

No effect

No effect

No effect

AASS loss

AASS score ↓

No effect

No effect

1:7

4

c.163+2T>C

ADSS loss

ADSS loss

ADSS loss

ADSS loss

ADSS loss

ADSS loss

ADSS loss

7:7

5

c.164-36A>G

No effect

No effect

No effect

No effect

No effect

No effect

No effect

0:7

6

c.164-1G>C

AASS loss

AASS loss

AASS loss

AASS loss

AASS loss

AASS loss

AASS loss

7:7

7

c.315-1G>A

AASS loss

AASS loss

AASS loss

AASS loss

AASS loss

AASS loss

AASS loss

7:7

Other variants

8–36

None of the other variants, including c.83+84A>T, c.84-97_84-96del, c.84-7dup, c.84-7del, c.84-6G>T, c.163+14T>C, c.163+92C>T, c.163+136G>T, c.164-97T>C, c.164-92C>G, c.186+122T>C, c.186+132G>T, c.186+166A>G, c.186+169G>C, c.186+184dup, c.187-81A>G, c.187-52G>A, c.243+11G>A, c.243+94T>A, c.243+97C>T, c.243+119G>A, c.243+136A>G, c.243+154C>T, c.312G>A (p.Val104=), c.314+20G>A, c.315-94C>T, c.318G>A (p.Thr106=), c.405T>C (p.Thr135=), c.420G>T (p.Val140=), had an effect on the splicing process