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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)