Mutation screening of ZNF644
has successfully identified 2 novel missense variants (c.725C>T, c.821A>T) in two ethnicities within our US population, thus supporting the original report of a causal candidate gene for high-grade myopia (). The two novel variants from our study (c.725C>T, c.821A>T) localize to a conserved region on the third exon, where Shi et al. [30
] previously identified several mutations. The variants were not seen in 1344 and 100 ethnically matched chromosomes, respectively, confirming their rarity. PolyPhen-2
software predicted c.725C>T to be possibly damaging, while c.821A>T was tolerated. With the additional variant information from our study, exon 3 may be a hotspot for susceptibility for high-grade myopia in multiple ethnicities. The clustering of variants in exon 3 may depict the importance in protein domain structures and gene regulatory functions of ZNF644.
The single nucleotide variant rs12117237
was present in 6 Caucasian case samples, but also present in 5 ethnically matched control DNA samples. Public database dbSNP132
reports this variant’s MAF to be 0.2% in a European population, and our p-value of 0.0015 by Fisher’s exact test suggests presence of the alleles likely did not occur by chance. As a result of sequencing additional family members in three high myopia cases for the variant, we discovered 100% co-segregation of the mutation with the disease phenotype in two of four families. PolyPhen-2
software predicts the amino acid change to be tolerated. The variant could be a common rare variant, and proper functional validation would be important to determine whether it is a risk or a causal allele [31
]. However, the MAF is in line with prevalence rates for high-grade myopia in a general population and a founder mutation effect may be plausible. Clinical information was missing refractive error from the 5 ethnically matched controls who also presented with the variant in the heterozygous state. The prevalence rate of high myopia is estimated to be 4.5% in the US population [32
]. Moreover, a recent study suggests that the rarer a variant, the higher the likelihood that the variant functionally alters the protein – thus rs12117237
may be associated with high-grade myopia in a Caucasian population [34
]. A larger case-control population data set should be tested to understand the true significance of the association of this variant to high-grade myopia in Caucasians.
ZNF644 is a transcription factor that may play a role in protein domain structures or regulatory functions [30
]. Expressed in all tissue types, it follows the trend of ubiquitously expressed genes pathogenic to ocular diseases [35
]. To date, it is widely accepted that transcription factor genes in both humans and mouse can play an important role in mammalian eye growth and development. For example, paired-like homeodomain transcription factors 2 and 3 (PITX2
) have been implicated in Axenfeld-Rieger syndrome and cataracts, respectively [36
]. Microphthalmia transcription factor (Mitf
) is associated with ocular albinism, and paired box 6 (PAX6
) has been associated with retinal degeneration, extreme myopia, and corneal innervation [20
]. However, the true function of ZNF644
remains unclear, and molecular characterization of ZNF644
To the best of our knowledge, this is the first successful study confirming a gene implicated with non-syndromic high-grade myopia determined by exome sequencing. We identified two novel variants in ZNF644
in our cohort, in addition to a known variant that demonstrated association. The discovery of previously unidentified variants is not expected due to genetic heterogeneity present in rare complex disease across multiple populations [47
]. Ethnic group specific alleles due to founder effect may explain why the previously reported variants were only present in the Asian population whereas the variants discovered in this report appear to be specific to the Caucasian and African American ethnicities. Determining pathogenic rare missense variants remains a challenge for complex diseases. Identification of novel variants in separate ethnicities emphasizes the importance and demonstrates the power of current research approaches.