Table 2 The overview of missense and nonsense variants found in the EFNB1 gene analyzed through MutationTaster, Varsome online tools (obtained on 2th November 2020) and Alamut® Visual software (obtained on 10th November 2020)
Patient 1 | Patient 2 | Patient 4 | Patient 5 and 6 | |
|---|---|---|---|---|
coding DNA level (NM_004429.4) | c.35G>A | c.191G>T | c.451G>A | c.628G>T |
gDNA level | g.815G>A | g.9683 | g.10712 | g.11092 |
chromosomal level (GRCh38) | chrX:68829811G>A | chrX:68838679G>T | chrX:68839708G>A | chrX:68840088G>T |
Protein level (NP_004420.1) | p.Trp12* | p.Cys64Phe | p.Gly151Ser | p.Glu210* |
Exon | 1 | 2 | 3 | 4 |
HGMD (v15.11) no. | Not reported | Not reported | CM041297 | Not reported |
dbSNP rs no. | rs1482772814 | Not reported | rs28936069 | Not reported |
gnomAD (v2.1.1) | Not reported | Not reported | Not reported | Not reported |
1000 Genomes | Not reported | Not reported | Not reported | Not reported |
ACMG classification | Pathogenic | Likely pathogenic | Likely pathogenic | Pathogenic |
SIFT (v6.2.0) | n.d. | Deleterious | Deleterious | n.d. |
PolyPhen-2 (v2) | n.d. | Probably damaging | Probably damaging | n.d. |
DANN (v2014) | 0.9954 | 0.9935 | 0.9989 | 0.9969 |
FATHMM-MKL (dbNSFP v4.1) | Damaging | Damaging | Damaging | Damaging |
LRT (dbNSFP v4.1) | Neutral | Deleterious | Deleterious | Neutral |
BayesDel addAF (v4.1) | Damaging | Damaging | Damaging | Damaging |
BayesDel noAF (v4.1) | Damaging | Damaging | Damaging | Damaging |
MutationTaster (v2013) | Disease causing | Disease causing | Disease causing | Disease causing |