Phenotypic and Genetic Heterogeneity of a Pakistani Cohort of 15 Consanguineous Families Segregating Variants in Leber Congenital Amaurosis-Associated Genes

Abstract

Background: Leber congenital amaurosis (LCA) is a congenital onset severe form of inherited retinal dystrophy (IRD) and a common cause of pediatric blindness. Disease-causing variants in at least 14 genes are reported to predispose LCA phenotype. LCA is inherited as an autosomal recessive disease. It can be an isolated eye disorder or as part of a syndrome, such as Senior Loken or Joubert syndrome. Sequencing studies from consanguineous populations have proven useful for novel variants identification; thus, the present study aimed to explore the genetic heterogeneity of 15 consanguineous Pakistani families, each segregating a severe IRD phenotype using targeted next generation sequencing.

Methods: This study enrolled 15 consanguineous families, each with multiple affected cases of retinal dystrophy phenotype. DNA was extracted from blood samples. Targeted panel sequencing of 344 known genes for IRDs was performed, followed by Sanger sequencing for segregation analysis.

Results: Data analysis revealed a total of eight reported (c.316C>T and c.506G>A in RDH12; c.864dup and c.1012C>T in SPATA7, as well as c.1459T>C, c.1062_1068del, c.1495+1G>A, c.998G>A in the CRB1, LCA5, TULP1, and IFT140 genes, respectively) and four novel homozygous (c.720+1G>T in LCA5, c.196G>C in LRAT, c.620_625del in PRPH2, and c.3411_3414del in CRB1) variants segregating with disease phenotype in each respective family. Furthermore, a novel heterozygous variant of CRB1 gene, i.e., c.1935delC in compound heterozygous condition was found segregating with disease phenotype in one large family with multiple consanguinity loops.

Conclusion: Comprehensive molecular diagnosis of 15 consanguineous Pakistani families led to the identification of a total of 5 novel variants contributing to genetic heterogeneity of LCA-associated genes and helped to provide genetic counseling to the affected families.

Keywords: Leber congenital amaurosis; autosomal recessive; childhood blindness; genetic heterogeneity.

Figure 1

Pedigrees of LCA families with novel variants were identified in this study. Squares and circles symbolize males and females, respectively. Clear symbols indicate unaffected family members while filled symbols indicate patients. Consanguineous marriages are indicated by double lines. The symbol labeled with a red arrow in each pedigree highlights the proband.

Figure 2

Fundus photograph of left and right eye of proband of family RP169 (A) and RP196 (B) showing waxy bone spicule with attenuated vessels, maculopathy, and pigmentary changes with pigmented clumps at retinal pigment epithelium, which are characteristic of LCA phenotype.

Figure 3

Sequence chromatograms for homozygous novel variants were identified in this study. The wild-type or carrier sequence is shown on the left and the mutated sequence is shown on the right side. (A) Deletion of 4 nucleotides (TGTT) in CRB1 gene in family RD022 and RP196. The sequence TGTT, present in normal individuals of the family but deleted in affected ones. (B) Novel splice site variant in LCA5 gene in RD024. (C) Novel missense variant in LRAT gene in family RP166. (D) Novel in frame variant in PRPH2 gene in family RP169.