Pathogenic variants identification in primary congenital glaucoma patients using whole exome sequencing

Abstract

Primary Congenital Glaucoma (PCG) is a severe form of glaucoma that affects infants and young children that damage and causes vision impairment. Despite being a well-known condition, the genetic basis of PCG, particularly in highly consanguineous populations like the Pashtun community, still needs to be explored. Six consanguineous Pashtun families (PCG-01, PCG-02, PCG-03, PCG-04, PCG-05, & PCG-07) suffering from PCG were recruited for whole exome sequencing. A prioritization strategy was employed to identify variants in known PCG-related genes, primarily focusing on CYP1B1. Sanger sequencing was carried out to validate candidate variants and perform segregation studies in affected individuals, siblings, parents, and controls. Whole exome sequencing revealed four pathogenic homozygous variants in six PCG families. Notably, a novel homozygous mutation, c.9delC (S4Afs9), was identified in the CYP1B1 gene in one family (PCG-07). Additionally, the previously unreported variant c.1168 C > A (p.R390S) was found in two families (PCG-2 and PCG-5). Known mutations, including c.868dupC (p. R290Pfs36) and c.1169G > A (p.R390H), were also detected in PCG-01 and PCG-04 families, respectively. Furthermore, a polymorphism, c.1294 C > G (p.L432V), was observed in family PCG-03. This study identifies novel pathogenic variants associated with PCG in consanguineous Pashtun families, highlighting the role of CYP1B1 mutations in PCG development. The findings contribute to a deeper understanding of the genetic basis of PCG and may aid in genetic counselling and early intervention strategies in affected populations.

Keywords: Consanguineous; Exome sequencing; Pathogenic; Primary congenital Glaucoma; Variants.

Fig. 1

Pedigrees of Six PCG consanguineous families (PCG-01, PCG-02, PCG-03, PCG-04/, PCG-05, & PCG-07). Squares denote males, while circles denote females. Filled squares and circles indicate affected members of the family and hollow symbols indicate unaffected individuals. A double marriage line between individuals represents consanguinity.

Fig. 2

A Novel Frameshift alteration and premature termination of protein due to alteration of codon (p.Ser4Ala fs*10).

Fig. 3

Wild type and mutant (p.R390S) model of CYPB1 protein. (A) superimposition of wild-type CYPB1 (green ribbon) and mutant CYPB1R390S orange ribbon. Wild type and mutant residues re shown in the stick model. (B) superimposed model in hydrophobic representation.

Fig. 4

Wild type and mutant (p.R290P) model of CYPB1 protein.

Fig. 5

Wild type and mutant (p.R390S) model of CYPB1 protein. (A) superimposition of wild-type CYPB1 (green ribbon) and mutant CYPB1R390S orange ribbon. Wild type and mutant residues are shown in the stick model. (B) superimposed model in hydrophobic representation.

Fig. 6

Conservation analysis of CYP1B1 protein (A) Multiple sequence alignment across 8 species indicating the conservation of Arg 390 along with 2D representation (B) 2D representation of wild type and mutant residues.