Table 2: Identified variants in the patient and predicted function according to different software
| Genes |
Exon |
Transcript |
Variation |
dbSNP |
gnomAD3 |
PROVEAN |
SIFT |
POLYPHEN |
Mutation Taster |
SNPs & GO |
PANTHER |
| KISS1 |
2 |
NM_002256.3 |
c.58G>A;p.E20K2
|
rs12998 |
0.03257 |
Del |
Dam |
Poss dam |
DC |
N |
Poss dam |
| MAP3K1 |
3 |
NM_005921.1 |
c.743G>A;p.R248Q2
|
rs201579608 |
0.0001499 |
N |
Dam |
Poss dam |
DC |
N |
Prob dam |
| MAP3K1 |
14 |
NM_005921.1 |
c.2845_2847delACA;p.T942del2
|
rs769777412 |
0.0004191 |
ND |
| HSD17B4 |
7 |
NM_000414.3 |
c.420A>T; p.K140N2
|
rs28943589 |
0.007370 |
Del |
Tol |
B |
P |
D |
Poss dam |
| HSD17B4 |
24 |
NM_000414.3 |
c.2182A>G;p.M728V2
|
rs28943594 |
0.01051 |
N |
Tol |
B |
P |
N |
Prob dam |
| CYP21A2 |
7 |
NM_000500.7 |
c.878G>A;p.G293D1
|
|
|
Del |
Dam |
Prob dam |
DC |
D |
Prob dam |
| TSPYL1 |
1 |
NM_003309.3 |
c.527_528insGGT;p.V176dup2
|
rs56100880 |
ND |
ND |
| GATA4 |
6 |
NM_002052.4 |
c.1129A>G;p.S377G2
|
rs3729856 |
0.09643 |
N |
Tol |
B |
P |
D |
Prob B |
| GATA4 |
6 |
NM_002052.4 |
c.1138G>A;p.V380M2
|
rs114868912 |
0.005689 |
N |
Tol |
B |
P |
D |
Prob B |
| DMRT2 |
4 |
NM_181872.4 |
c.815A>G;p.N272S2
|
rs138608089 |
0.001039 |
N |
Tol |
Poss dam |
DC |
|
Poss dam |
| CYP19A1 |
5 |
NM_000103.3 |
c.602C>T;p.T201M2
|
rs28757184 |
0.02471 |
N |
Tol |
B |
P |
N |
Prob B |
| SOX3 |
1 |
NM_005634.2 |
c.307C>A;p.P103T2
|
rs201101913 |
0.006186 |
N |
Dam |
B |
DC |
N |
Prob B |
B, benign; D, disease; Dam, damaging; DC, disease causing; Del, deleterious; N, neutral; ND, not determined; P, polymorphism; Poss, possibly; Prob, probably; Tol, tolerated.
1 Variant found in homozygous state. 2 Variant found in heterozygosis. 3Allelic frequencies correspond to both Exome and Genome analyses.