TABLE 2.
Summary and Pathogenicity Analysis of ABCA4 (NM_000350.2) Variants in the Study Cohort
| Patient | cDNA Variant | Protein Variant | Type | Coding Effect | M-CAP | REVEL | Eigen | CADD13 | DANN |
|---|---|---|---|---|---|---|---|---|---|
| 1 | c.3322C>T | p.(R1108C) | Substitution | Missense | 0.797 | 0.89 | 0.81 | 35 | 1.00 |
| c.4139C>T | p.(P1380L) | Substitution | Missense | 0.391 | 0.87 | 0.70 | 28 | 1.00 | |
| 2 | c.4139C>T | p.(P1380L) | Substitution | Missense | 0.391 | 0.87 | 0.70 | 28 | 1.00 |
| c.5714+5G>A | p.(?) | Substitution | ? | - | - | - | - | - | |
| 3 | c.2588G>Ca | p.(G863A) | Substitution | Missense | - | 0.80 | 0.58 | 27 | 1.00 |
| c.5603A>Ta | p.(N1868I) | Substitution | Missense | - | 0.40 | 0.03 | 26 | 0.92 | |
| c.6088C>T | p.(R2030*) | Substitution | Nonsense | - | - | 0.54 | 42 | 1.00 | |
| 4 | c.3322C>T | p.(R1108C) | Substitution | Missense | 0.797 | 0.89 | 0.81 | 35 | 1.00 |
| c.1253T>C | p.(F418S) | Substitution | Missense | 0.582 | 0.93 | 0.81 | 29 | 1.00 | |
| 5 | c.161G>A | p.(C54Y) | Substitution | Missense | - | 0.98 | 0.87 | 29 | 1.00 |
| c.2160+1G>C | p.(?) | Substitution | ? | - | - | - | - | - | |
| 6 | c.768G>T | p.(?) | Substitution | ? | - | - | - | - | - |
| c.4539+2001G>A | p.(?) | Substitution | ? | - | - | - | - | - | |
| 7 | c.3050+5G>A | p.(?) | Substitution | ? | - | - | - | - | - |
| c.4594G>Aa | p.(D1532N) | Substitution | Missense | 0.722 | 0.77 | 0.80 | 28 | 1.00 | |
| c.5603A>Ta | p.(N1868I) | Substitution | Missense | - | 0.40 | 0.03 | 26 | 0.92 | |
| 8 | c.3056C>T | p.(T1019M) | Substitution | Missense | 0.611 | 0.96 | 1.10 | 33 | 1.00 |
| c.3056C>T | p.(T1019M) | Substitution | Missense | 0.611 | 0.96 | 1.10 | 33 | 1.00 | |
| 9 | c.161G>A | p.(C54Y) | Substitution | Missense | - | 0.98 | 0.87 | 29 | 1.00 |
| c.4773+3A>G | p.(?) | Substitution | ? | - | - | - | - | - | |
| 10 | c.4139C>T | p.(P1380L) | Substitution | Missense | 0.391 | 0.87 | 0.70 | 28 | 1.00 |
| c.4594G>Aa | p.(D1532N) | Substitution | Missense | 0.722 | 0.77 | 0.80 | 28 | 1.00 | |
| c.5603A>Ta | p.(N1868I) | Substitution | Missense | - | 0.40 | 0.03 | 26 | 0.92 | |
| 11 | c.302+68C>Ta | p.(?) | Substitution | ? | - | - | - | - | - |
| c.4539+2028C>Ta | p.(?) | Substitution | ? | - | - | - | - | - | |
| c.6148–698_ c.6670del - 4770 bp del | p.(?) | Deletion | ? | - | - | - | - | - | |
| 12 | c.302+68C>Ta | p.(?) | Substitution | ? | - | - | - | - | - |
| c.4539+2028C>Ta | p.(?) | Substitution | ? | - | - | - | - | - | |
| c.6148–698_ c.6670del - 4770 bp del | p.(?) | Deletion | ? | - | - | - | - | - |
a
Variants in cis; predicted pathogenicity: M-CAP (>0.025); REVEL (>0.5), Eigen (>0.5), CADD13 (>20), DANN (>0.97).