Table 1. Summary of the identified pathogenic mutations in LCA patients in this study.
| S.No. | Patient ID | Gene | Reference ID | Identified Variations | Amino Acid Change | SIFT score | Clinical Significance |
| 1 | LCA44–1 | RPE65 | NM_000329.2 | HOM | p.S121F | NA | Pathogenic |
| c.361insT | FS*10 | ||||||
| (Novel) | |||||||
| 2 | LCA74–1 | RPE65 | NM_000329.2 | HOM | p.H313Q | 0.29 | Pathogenic |
| c.939T>A | (Tolerated) | ||||||
| (Novel) | |||||||
| 3 | LCA51–1 | RPE65 | NM_000329.2 | HOM | p.S121L | NA | Pathogenic |
| c.361delT | FS*6 | ||||||
| 4 | LCA72–1 | RPE65 | NM_000329.2 | HOM | p.S121L | NA | Pathogenic |
| c.361delT | FS*6 | ||||||
| 5 | LCA 68–1 | RPE65 | NM_000329.2 | HET | p.A132T | 0.11 | Mild Pathogenic |
| c.394G>A | (Tolerated) | ||||||
| 6 | LCA55–1 | GUCY2D | NM_000180.3 | HOM | p.R1040G | 0.00 | Pathogenic |
| c.3118C>G | (Deleterious) | ||||||
| 7 | LCA–87–1 | GUCY2D | NM_000180.3 | HOM | p.R1040G | 0.00 | Pathogenic |
| c.3118C>G | (Deleterious) | ||||||
| 8 | LCA 84–1 | GUCY2D | NM_000180.3 | HOM | p.S1023_V | NA | Pathogenic |
| c.3068_3069ins | 1025dup | ||||||
| CACTGTGAG | |||||||
| (Novel) | |||||||
| 9. | LCA69–1 | AIPL1 | NM_014336.3 | HOM | p.W278X | NA | Pathogenic |
| c.834G>A | |||||||
| 10 | LCA53–1 | CRX | NM_000554.4 | HET c.196G>A | p.V66I | 0.00 | Mild pathogenic |
| IQCB1 | NM_001023570.2 | HOM c.1465C>T | p.R489X | (Deleterious) | Pathogenic | ||
| NA | |||||||
| 11. | LCA81–1 | RPGRIP1 | NM_020366.3 | HOM | p.R1189X | NA | Pathogenic |
| c.3565C>T |
S.No.1–5: Mutations identified by direct sequencing analysis of RPE65.
S.No.6–11: Mutations identified in Asper chip analysis and confirmed by direction sequencing.
Nucleotide numbering represents cDNA numbering with +1 corresponding at the start of the coding sequence (i.e. from the first A of the translation initiation codon, ATG) in the reference sequence according to nomenclature guidelines (www.hgvs.org/mutnomen).
RPE65 c.361del T mutation was identified in two index LCA cases (LCA51–1 and LCA72–1).
GUCY2D c.3118 C>G mutation was identified in two index LCA cases (LCA55–1 and LCA87–1).
Patient LCA68–1 was found to be with single heterozygous RPE65 mutation which alone may not be conclusive to explain the LCA phenotype.
Patient LCA53–1 carried heterozygous CRX mutation along with homozygous IQCB1 mutation; both together can sufficiently explain the LCA phenotype.
SIFT score ranges from 0 to 1; value between 0.00–0.05 is considered deleterious.
Abbreviation: HOM- Homozygous, HET- Heterozygous, FS- Frame Shift, NA-Not applicable.