Identification and Characterization of a Cryptic Genomic Deletion-Insertion in EYA1 Associated with Branchio-Otic Syndrome
Table 1
Pathogenic prediction by computational tools.
Gene
Mutation
CADD-phred
Exome Variant Server
gnomAD
1000G
MutationTaster
PhastCons scores
Phylop score†
PolyPhen-2 (HumVar score)
PROVEAN (score)‡
SIFT (score)§
Origin
EYA1
p.Arg361Gln c.1082G>A rs145219836
26.7
Not present
0.0005
0.0002
Disease causing (0.999)
0.995
6.162
Benign (0.123)
Neutral (-1.86)
Tolerated (0.114)
I-1
GJB2
p.Phe191Leu c.571T>C rs397516878
27.0
Not present
0.000149
0.0002
Disease causing (0.999)
1
5.159
Possibly damaging (1)
Deleterious (-5.72)
Damaging (0.006)
I-1
TCOF1
p.Q859E c.2575C>G rs201043592
11.16
Not present
0.000107
0.0005
Polymorphism
0.139
1.479
Benign (0.301)
Neutral (-1.56)
Damaging (0.046)
I-2
KARS
p.Y229H c.685T>C rs150529876
15.34
Not present
0.001161
0.0032
Polymorphism
0.006
-0.014
Benign (0.275)
Neutral (0.36)
Tolerated (0.593)
I-2
Note: The values vary between 0 and 1; the closer the value is to 1, the more probable the nucleotide is conserved. †The values between -14 and +6, sites predicted to be conserved are assigned positive scores, while sites predicted to be fast evolving are assigned negative scores. ‡Negative and positive scores indicate deleterious and neutral, respectively, with cut-off score set at -2.5. §The value ranges from 0 (deleterious) to 1 (neutral) with cut-off score set at 0.05.
