Table 1 Rare variants in patients with unilateral high myopia
Variants | Family | Gene (ReIseqID) | Nucleotide acid | Amino acid | REVEL | CADD | ①| ② | ③ | ④ | ⑤ | HSF | ACMG-AMP |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID | Change | Effect | Criteria | ||||||||||
A. Pathogenic variants | |||||||||||||
1 | F13-II:2 | TSPAN12 (NM_012338.3) | c.375G > A | p.Trp125* | / | / | / | / | / | / | DM | / | PVS1;PS1;PM2;PM4;PM6;PP4 |
2 | F15-II:2 | ZEB2 (NM_014795.4) | c.298_300del | p.Asn100del | / | / | / | / | / | / | DM | NSSC | PS1;PS2;PM2;PM4;PM6 |
3 | F14-II:1 | GPR179 (NM_001004334.4) | c.3238C > T | p.Gln1080* | / | / | / | / | / | 17/280534 | DM? | / | PVS1; PM3;PM4; PP1 |
4 | F14-II:1 | GPR179 (NM_001004334.4) | c.3656_3657del | p.Pro1219Argfs*18 | / | / | / | / | / | 51/280988 | DM? | / | PVS1;PM3;PP1 |
5 | F18-II:1 | OPN1LW (NM_020061.6) | LLIAVA | / | / | / | / | / | / | / | DM | SSC | PVS1;PS1;PS2; PS3;PM2;PP1 |
6 | F19-II:1 | FRMD7 (NM_194277.2) | c.910C > T | p.Arg304* | / | / | / | / | / | 1/183050 | DM | / | PVS1;PS1;PM2;PM4;PP1;PP4 |
B. Likely pathogenic variants | |||||||||||||
1 | F2-II:2 | COL2A1 (NM_001844.4) | c.943G > A | p.Gly315Ser | 0.97 | 28.8 | D | PD | D | / | / | SSC | PM5;PM2;PP1;PP3 |
2 | F3-II:2 | COL11A1 (NM_001854.4) | c.2971G > A | p.Gly991Ser | 0.982 | 31 | D | PD | D | / | / | SSC | PM5;PM2;PP1;PP3;PP4 |
3 | F7-II:2 | FBN1 (NM_000138.4) | c.4894C > T | p.Arg1632Cys | 0.602 | 32 | D | PD | D | 1/251312 | / | NSSC | PS2;PM5;PM2;PP3 |
4 | F9-II:1 | FZD4 (NM_012193.3) | c.328_330del | p.Ile110del | / | / | / | / | / | / | / | SSC | PM4;PM2;PP1;PP3;PP4 |
5 | F10-II:1 | FZD4 (NM_012193.3) | c.313A > G | p.Met105Val | 0.511 | 24.9 | T | PD | N | 6/250246 | DM | SSC | PS1;PP1;PP3;PP4 |
6 | F11-II:1 | LRP5 (NM_002335.3) | c.4466C > A | p.Thr1489Lys | 0.751 | 26.7 | D | PB | D | / | / | SSC | PM5;PM2;PP1;PP3;PP4 |
C. Uncertain significance variants | |||||||||||||
1 | F1-II:1 | COL2A1 (NM_001844.4) | c.86-35G > A | / | / | / | / | / | / | / | / | SSC | PM2;PP1;PP3;PP4 |
2 | F4-II:1 | COL11A1 (NM_001854.4) | c.1899 + 3A > G | / | / | / | / | / | / | / | / | SSC | PM6;PP3;PP4 |
3 | F5-II:2 | COL11A1 (NM_001854.4) | c.1630G > T | p.Gly544Trp | 0.95 | 33 | D | PD | D | / | / | NSSC | PM2;PP1;PP3 |
4 | F6-II:2 | COL11A1 (NM_001854.4) | c.2502 + 11G > T | / | / | / | / | / | / | / | / | NSSC | PM2;PP1 |
5 | F8-II:1 | FBN1 (NM_000138.4) | c.7841C > T | p.Ala2614Val | 0.434 | 23.2 | T | PD | N | / | / | NSSC | PM2;PP1 |
6 | F12-II:2 | LRP5 (NM_002335.3) | c.4505C > T | p.Pro1502Leu | 0.743 | 29.4 | D | PD | D | / | / | NSSC | PM2;PP1;PP3;PP4 |
7 | F16-II:2 | PAX6 (NM_000280.5) | c.652A > G | p.Thr218Ala | 0.906 | 23.5 | D | PD | D | / | / | NSSC | PM2;PP1;PP3;PP4 |
8 | F17-II:1 | GPR143 (NM_000273.2) | c.767 + 10C > G | / | / | / | / | / | / | / | / | NSSC | PM2;PP4 |
9 | F20-II:2 | CACNA1F (NM_005183.4) | c.1969G > A | p.Ala657Thr | 0.749 | 24.5 | D | PB | D | 12/168126 | / | NSSC | PM2: PP1; PP3 |