Table 1 Genotypes of the 14 patients with syndromic ciliopathy
Gene | Patient | Variants | Location | Types | Amino acid substitutions | Allele frequency in east asian a | Prediction | American college of medical genetics and genomics (ACMG) prediction [20] |
|---|---|---|---|---|---|---|---|---|
BBS2 (NM_031885.5) | P1 | c.534 + 1G > T | IVS4 | Splice donor | NA | 1.4*10− 3 | varSEAK: exon skipping | Pathogenic PVS1, PM3, PP3, PP4, PP5 |
c.1814 C > G | Exon15 | Nonsense | p.Ser605Ter | 5.4*10− 5 | MutationTaster: disease causing | Pathogenic PVS1, PM2, PM3, PP3, PP4, PP5 | ||
P2 | c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | |
c.563del | Exon5 | Frameshift | p.Ile188Thrfs*13 | 1.1*10− 4 | MutationTaster: disease causing | Pathogenic PVS1, PM2, PM3, PP3, PP4, PP5 | ||
P3 | c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | |
c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | ||
P4 | c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | |
c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | ||
TTC21B: c.264_267dupTAGA (NM_024753.5) | Exon4 | Nonsense | p.E90Ter | 8.6*10− 4 | MutationTaster: disease causing | Pathogenic PVS1, PM2, PP3, PP5 | ||
P5 | c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | |
c.563del | Exon5 | Frameshift | p.Ile188ThrfsTer13 | Â | Â | Â | ||
P6 | c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | |
c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | ||
P7 | c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | |
c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | ||
P8 | c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | |
c.534 + 1G > T | IVS4 | Splice donor | NA |  |  |  | ||
BBS7 (NM_176824.3) | P9 | c.728G > A | Exon8 | Missense | p.Cys243Tyr | 5.5*10− 4 | Polyphen2: probably damaging SIFT: damaging PROVEAN: deleterious MutationTaster: disease causing | Likely pathogenic PM2, PM3, PP2, PP3, PP4, PP5 |
c.1685_1686del | Exon16 | Frameshift | p.Glu562GlyfsTer4 | Novel | MutationTaster: disease causing | Pathogenic PVS1, PM2, PP3, PP4 | ||
P10 | c.849 + 1G > C | IVS8 | Splice donor | NA | 2.7*10− 4 | varSEAK: exon skipping | Pathogenic PVS1, PM2, PP3, PP4 | |
c.728G > A | Exon8 | Missense | p.Cys243Tyr |  |  |  | ||
ALMS1 (NM_015120.4) | P11 | c.6169_6170dupAT | Exon8 | Frameshift | p.Leu2058PhefsTer17 | 1.6*10− 4 | MutationTaster: disease causing | Pathogenic PVS1, PM2, PM3, PP3, PP4 |
c.7972_7978del | Exon10 | Frameshift | p.Phe2658LeufsTer25 | Novel | MutationTaster: disease causing | Pathogenic PVS1, PM2, PM3, PP3, PP4 | ||
P12 | c.10831_10832del | Exon 16 | Frameshift | p.Arg3611AlafsTer6 | 3.5*10− 4 | MutationTaster: disease causing | Pathogenic PVS1, PM2, PM3, PP3, PP4 | |
c.10290_10291del | Exon 15 | Frameshift | p.Lys3431SerfsTer10 | 0 b | MutationTaster: disease causing | Pathogenic PVS1, PM2, PM3, PP3, PP4 | ||
OFD1 (NM_003611.3) | P13 | c.1972 A > T | Exon 16 | Nonsense | p.Lys658Ter | Novel | MutationTaster: disease causing | Pathogenic PVS1, PM2, PP3, PP4 |
C2CD3 (NM_015531.6) | P14 | c.2720 A > G | Exon15 | Missense | p.Tyr907Cys | Novel | Polyphen2: probably damaging SIFT: damaging PROVEAN: deleterious MutationTaster: disease causing | Likely pathogenic PM1, PM2, PP3, PP4 |
c.1730G > A | Exon10 | Missense | p.Arg577His | 0 | Polyphen2: probably damaging SIFT: tolerated PROVEAN: neutral MutationTaster: disease causing | Likely pathogenic PM1, PM2, PP3, PP4 |