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Table 2 Putative variants of nine South Indian patients identified by clinical exome sequencing

From: Clinical exome sequencing facilitates the understanding of genetic heterogeneity in Leber congenital amaurosis patients with variable phenotype in southern India

Patient ID Gene Chromosomal locus Exon Variant Class Variants Zygosity MOI Minor allele frequency Functional Prediction Tools ACMG Evidence ACMG Classification SNP id Reference
cDNA_Change Amino acid_Change ExAC 1000G SIFT PP2 Mutation Taster FATHMM
AS01 RPE65 1p31.2 5 Frameshift-ins c.361dup p.Ser121PhefsTer10 Hom AR NA NA NA NA D NA PVS1, PM2, PP3, PP5 Pathogenic rs121918844 13,14,15
AS02 LCA5 6q14.1 7 Frameshift-del c.1062_1068del p.Tyr354Ter Hom AR NA NA NA NA D NA PVS1, PM2, PP3, PP5 Pathogenic NA 17,18
AS03 LCA5 6q14.1 9 Frameshift-del c.1823dela p.Leu608TyrfsTer30 Hom AR NA NA NA NA D NA PVS1, PM2, PP3 Pathogenic NA this study
AS04 CRX 19q13.33 4 Frameshift-del c.848dela p.Met283ArgfsTer88 Het AD NA NA NA NA D NA PVS1, PM2, PP4 Pathogenic NA this study
AS05 PRPH2 6p21.1 2 Missense c.629C > T p.Pro210Leu Hom AR NA NA D (0.03) PoD (0.847) D D PM1,PM2, PP3, PP5 Likely Pathogenic rs61755798 24
AS06 CEP290 12q21.32 23 Missense c.2483G > Ta p.Ser828Ile Hom AR NA NA D (0) PoD (0.731) D T PM2, PP3 Uncertain significance NA this study
AS07 ALMS1 2p13.1 16 Frameshift-del c.11310_11313del p.Glu3771TrpfsTer18 Hom AR 1.67E-05 NA NA NA D NA PVS1, PM2, PP3, PP5 Pathogenic rs747272625 this study
AS08 IFT80 3q25.33 18 Missense c.1936G > T p.Val646Phe Hom AR 5.07E-05 NA D (0) PrD (0.927) D D PM2, PP3 Uncertain significance rs752617502 this study
AS09 RP1 8q12.1 4 Frameshift-del c.3751_3752del p.Val1251PhefsTer9 Hom AR 8.24E-06 NA NA NA D NA PVS1, PM2, PP3 Pathogenic rs745640645 this study
  1. Hom = homozygous; Het = heterozygous; MOI = mode of inheritance; AR = autosomal recessive; AD = autosomal dominant. NA = not available, SIFT (score: 1 to 0); D = deleterious (≤ 0.05); T = tolerated (> 0.05), PP2 (score: 0 to 1); PrD = probably damaging (≥ 0.909); PoD = possibly damaging (≥ 0.447); B = benign (≤ 0.446), mutation taster; D = diseases causing, FATHMM (0 to 1); D = deleterious (> 0.45); T = tolerated (< 0.45), aNovel mutations