Table 1 In silico prediction of splice site activity for the wild-type and variant sequences.

From: Nonsense-associated altered splicing of MAP3K1 in two siblings with 46,XY disorders of sex development

Program

Default threshold

Score of the wild-type sequence

Score of the variant sequence (c.2254C>T)

Score of c.2254C>A

Score of c.2254C>G

NNSPLICE

0.40

Not recognized as a splice site

1.00

Not recognized as a Splice site

Not recognized as a splice site

ASSP

4.50

Not recognized as a splice site

12.34

Not recognized as a splice site

Not recognized as a splice site

HSF

80.00a

62.92

90.06

No potential alteration of splicing

No potential alteration of splicing

MaxEnt

5.00a

1.09

8.85

0.66

1.20

SpliceRover

No data

Not recognized as a splice site

0.931558

Not recognized as a splice site

Not recognized as a splice site

  1. NNSPLICE, Splice Site Prediction by Neural Network (https://fruitfly.org/seq_tools/splice.html); ASSP, Alternative Splice Site Predictor (https://wangcomputing.com/assp/); HSF, Human Splicing Finder (https://hsf.genomnis.com/home); MaxEntScan (https://hollywood.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html); and SpliceRover (https://bioit2.irc.ugent.be/splicerover/).
  2. aThese thresholds are based on the previous report by Piton et al.38.
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