Identification of a novel C-terminal extension mutation in EPHA2 in a family affected with congenital cataract

• Introduction
• Methods
• Results
• Discussion

Abstract

Purpose: Congenital cataracts occur in 3–4 per 10,000 live births and account for 5% to 20% of pediatric blindness worldwide. With more than 37 genes known to be associated with isolated congenital cataract, whole exome sequencing (WES) was recently introduced as an efficient method for screening all known factors.

Methods: Whole exome analysis in two members of a four-generation pedigree affected with dominant congenital cataract and glaucoma was performed by WES; co-segregation analysis of identified variants in all pedigree members was completed by Sanger sequencing.

Results: Analysis of the WES data identified a novel pathogenic variant in EPHA2, c.2925dupC, p.(Ile976Hisfs*37), that demonstrated complete cosegregation with the phenotype in the pedigree. The mutation occurs in the final amino acid before the stop codon of the normal EPHA2 protein and is predicted to produce a mutant protein with an erroneous C-terminal extension of 35 amino acids. Nine other families have been previously reported with dominant congenital/juvenile cataracts and mutations in EPHA2. Two additional likely loss-of-function variants in genes known to cause dominant congenital cataract were considered and excluded based on control data and cosegregation analysis: a nonsense variant in CYRBB3, c.547G>T, p.(Glu183*), and a splicing variant in CRYBA2, c.446+1G>A.

Conclusions: Identification of a novel pathogenic EPHA2 allele further implicates this gene in congenital cataract. This is only the second EPHA2 mutation that specifically affects the most C-terminal PSD95/Dlg/ZO1 (PDZ)-binding motif and the third pathogenic allele associated with an erroneous C-terminal extension beyond the normal stop codon.

Congenital cataracts occur in 3–4 per 10,000 live births in the United States and account for 5% to 20% of blindness in children worldwide [1]. Congenital cataract can occur as an isolated condition or in association with syndromic anomalies; approximately 10% to 25% are thought to be due to genetic causes [2]. With more than 37 genes known to be associated with nonsyndromic cataract, whole exome sequencing (WES) was recently introduced as an efficient method for screening all known genes, as well as providing the opportunity for novel gene identification [3]. Although this approach offers the advantage of a comprehensive exome and genome examination to identify causative mutations, interpretation of the large volume of identified variants may be complicated, especially for novel changes [4-6].

Autosomal dominant is the most common inheritance pattern for familial nonsyndromic cataracts; however, autosomal recessive and X-linked inheritance has also been reported [7,8]. Interestingly, eight cataract genes have been linked to dominant and recessive patterns of inheritance: CRYAB (OMIM 123590), CRYAA (OMIM 123580), CRYBB1 (OMIM 600929), CRYBB3 (OMIM 123630), GJA8 (OMIM 600897), SIL1 (OMIM 608005), HSF4 (OMIM 602438), and EPHA2 (OMIM 176946) [3,7,9]. Although some genes, such as CRYBB1, show a clear distinction between the two types of alleles with dominant alleles likely having a dominant negative effect (missense, late truncating) and recessive alleles likely resulting in null alleles (early truncating and initiation codon mutations) [10-12], for many genes, such as CRYBB3, there is no obvious distinction between the two types of alleles [3].

The EPHA2 protein belongs to the ephrin receptor group of the protein-tyrosine kinase family, which is important in cell–cell interactions, including effects on neuronal cell migration, cell proliferation, survival, differentiation, and secretion [13,14]. Ephrin receptors are type-I transmembrane proteins; their primary ligand, ephrin, is also membrane bound, and the complex is unique in its ability to generate bidirectional signals into both cells [13,14]. The ephrin receptors and ephrin ligands are divided into two groups, A and B; crossover binding between classes can occur [13,15]. The EphA2 protein contains an extracellular domain and an intracellular domain. The extracellular domain is divided into an N-terminal ligand binding domain, a cysteine-rich domain, and two fibronectin type III repeats; the intracellular domain consists of the juxtamembrane region, a tyrosine kinase domain, a sterile-α-motif (SAM) domain, and a PSD95/Dlg/ZO1 (PDZ)-binding motif [14].

EPHA2 expression has been shown in the lens of wild-type mice, with highest expression in the cortical lens fiber cells [16]. Mutations in EPHA2 have been associated with autosomal dominant congenital/juvenile cataract and autosomal recessive congenital cataract. In dominant families, a frameshift mutation and a splicing mutation were associated with congenital cataract (four families) while the age of diagnosis in families with missense mutations ranged from birth to 15 years of age (four families) [17-20]. An additional rare heterozygous missense variant was seen in a family with onset at 17 and 20 years of age as well as two controls with age-related cataracts [20]. In recessive families, homozygous missense mutations were associated with congenital cataracts (two families) [9,21]. In addition, several polymorphisms in EPHA2 have been associated with increased risk for age-related cataracts [16,17,22-24]. We present the identification of a novel EPHA2 pathogenic allele along with two rare variants in other known cataract genes through WES in a single family with dominant congenital cataract with or without glaucoma.

The novel EPHA2 frameshift mutation identified in this family, c.2925dupC, p.(Ile976Hisfs*37), affects the intracellular region of the protein, specifically the potential PDZ-binding motif that encompasses amino acids 973–976 (Figure 1B); this motif is predicted to bind PDZ domain-containing proteins that promote the assembly of multiprotein signaling complexes at the membrane. Other intracellular domains include the sterile alpha motif (SAM), tyrosine kinase domain, and juxtamembrane region that are involved in interactions with signaling proteins and other important functions [27]. The c.2925dupC, p.(Ile976Hisfs*37) mutation disrupts the PDZ-motif and, because of the additional aberrant C-terminal sequence, might affect proper folding and function of other EPHA2 domains as well. This is only the second EPHA2 mutation that specifically affects the potential PDZ-motif and the third pathogenic allele associated with an erroneous C-terminal extension beyond the normal stop codon. The previously reported alleles include frameshift mutation c.2915_2916delTG, p.(Val972Glyfs*40), located four codons upstream of the mutation reported here, which completely removes the potential PDZ-motif sequence (Figure 1B) [18]. In addition, the recurrent splicing mutation c.2826–9G>A, seen in three independent families, was shown to result in an insertion of a 7 bp intronic sequence into the mRNA and, consequently, the addition of 71 novel amino acid residues at the C-terminus; this mutation affects the SAM domain and the PDZ-binding motif [18,20]. Thirty-six residues of the erroneous C-terminal tail are identical between these three mutant alleles. Previous studies demonstrated reduced protein stability and function for the c.2915_2916delTG frameshift and c.2826–9G>A splicing mutations [27]. Interestingly, mutations that extend the length of the mutant protein have been reported in two other genes that cause dominant congenital cataracts, PITX3 and FOXE3 [28,29]. Although the PITX3 mutations disrupt a significant portion of the protein sequence in addition to extending the length of the protein [28,30-32], four dominant FOXE3 mutations occur at or within five amino acids of the stop codon [29,33-35]. Given the evidence of pathogenicity and complete cosegregation in the pedigree, the EPHA2 variant c.2925dupC, p.(Ile976Hisfs*37) was determined to be the pathogenic allele causing the congenital cataract in the family.

The congenital cataract phenotype reported in this family is consistent with the previously reported EPHA2 mutations, but two individuals in the family were also affected with juvenile glaucoma, which has not been reported previously in families with EPHA2 mutations [17-20]. Since glaucoma is reported in up to 30% of eyes following congenital cataract extraction [36,37], particularly when cataracts are removed early in life, it is possible that the glaucoma seen in two family members is simply a result of the cataract surgery. Review of whole exome data for the proband and her daughter for known congenital/juvenile glaucoma genes including CYP1B1 (OMIM 601771), MYOC (OMIM 601652), LTBP2(OMIM 602091), and TDRD7 (OMIM 611258) did not identify any rare/novel coding variants in these genes.

The two other rare likely loss-of-function variants in genes known to cause dominant congenital cataract, a nonsense variant in CRYBB3 and a splicing variant in CRYBA2, were considered and excluded based on the control data and cosegregation analysis. Recessive and dominant missense mutations in CYRBB3 have been reported in association with congenital cataract [3,38], and nonsense mutations in two other members of the CRYBB family, CRYBB1 and CRYBB2, as well as CRYGC and CRYGD, are associated with autosomal dominant congenital cataracts [7]. A missense mutation in CRYBA2 was recently reported to cause autosomal dominant congenital cataract with reduced penetrance [3], and multiple splicing mutations in another crystalline gene, CRYBA1, have been reported in association with autosomal dominant congenital cataracts [7]. Although both alleles have some evidence providing support for possible pathogenicity, both are present in EVS at about twice the frequency of congenital cataracts in the general population, which suggests these alleles are not highly penetrant dominant alleles for congenital cataracts. In addition, cosegregation analysis showed that neither variant was present in all three affected family members (Figure 1A). Based on these data, it was concluded that these variants are either rare polymorphisms or recessive alleles that do not contribute to the cataracts in this family.