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Table 4 Prediction of NRG1 variants effects on protein function

From: NRG1 variant effects in patients with Hirschsprung disease

Variant

SIFT

Polyphen2 – HDIV

Polyphen2 – HVAR

LRT

Mutation Taster

Mutation Assessor

FATHMM

CADD

DANN

c.397G > C (p.V133 L)

0.22 (tolerated)

0.029 (benign)

0.02 (benign)

0 (neutral)

Disease causing

0.805 (low)

0 (tolerated)

12.29 (benign)

0.9892 (protein disrupting)

rs7834206

0

0

0

0

0

0

0

0

0.6874 (non-protein disrupting)

rs3735774

0.36 (tolerated)

0.003 (benign)

0.004 (benign)

0

Polymorphism

0.345 (neutral)

0

8.83 (benign)

0.9957 (protein disrupting)

rs75155858

0

0.962 (probably damaging)

0.784 (possibly damaging)

0.004 (neutral)

Polymorphism automatic

0.895 (low)

0.4 (tolerated)

14.6 (benign)

0.9934 (protein disrupting)

Prediction scores interpretation:

Method

Deleterious cut-off

SIFT

< 0.05

Polyphen2 HDIV

> 0.453

Polyphen2 HVAR

> 0.447

LRT

> 0.999

Mutation Taster

D (disease causing) or P (polymorphism)

Mutation Assessor

>  0.65

FATHMM

< −1.5

CADD

> 15

DANN

>  0.98 (protein disrupting)

0.93–0.98 (splice site/promoter region)

<  0.93 (non-protein disrupting)