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Table 5 Gene rank and p-value assigned to causal gene in two Mendelian disorders.

From: Identifying Mendelian disease genes with the Variant Effect Scoring Tool

Disorder/Gene

Mean VEST Rank

Mean VEST score

Fisher Rank

Fisher p-value

Stouffer Rank

Stouffer p-value

All genes

     

Miller syndrome/DHODH

112

0.71

7

11.6e-07

3

1.9e-06

Freeman Sheldon syndrome/MYH3

124

0.67

3

3.7e-14

3

9.3e-07

Dominant model

     

Miller syndrome/DHODH

15

0.71

5

4.4e-08

2

1.9e-06

Freeman Sheldon syndrome/MYH3

12

0.67

3

3.7e-14

2

9.3e-07

Recessive model

     

Miller syndrome/DHODH

12

0.71

4

9.8e-06

2

1.9e-06

Dominant model including truncating

   

Miller syndrome/DHODH

11

0.75

10

7.0e-11

3

2.5e-08

Freeman Sheldon syndrome/MYH3

19

0.67

10

3.8e-14

12

9.3e-07

Recessive model including truncating

   

Miller syndrome/DHODH

9

0.75

10

7.14e-10

3

2.5e-08

  1. Ranks and p-values for the genes underlying Miller syndrome and Freeman Sheldon syndrome for three gene lists: all genes harboring missense mutations, genes with a missense mutation in at least one copy in all disease exomes (dominant model), and genes with a missense mutation in both copies in all disease exomes (recessive model). Genes were ranked using two scoring methods, Fisher's method and Stouffer's Z score.