Implication of GATA4 synonymous variants in congenital heart disease: A comprehensive in-silico approach

Synonymous variations, previously considered as neutral, are recently shown to have a significant impact on mRNA structure and stability thereby affecting protein expression and function. Their role in disease pathogenesis is also emerging. GATA4 is an important transcription factor involved in cardiac development and a well-known candidate gene associated with congenital heart disease (CHD). In the present study, we sought to conduct molecular screening of GATA4 gene in 285 sporadic and non-syndromic CHD cases. We identified four synonymous (c.27C>A, c.822C>T, c.1233G>A and c.1263C>T) and two intronic variants (g.83217T>G & g.85012T>A) in GATA4. Extensive computational analysis using widely acceptable tools i.e., Mfold, Human Splicing Finder (HSF) and Codon Usage bias was performed with a view to understand their putative downstream effects on GATA4 function. Mfold, a mRNA structure prediction tool showed the alterations of the mRNA structure and stability due to synonymous variants. Similarly, HSF also confidently predicted effect on the cis-acting regulatory elements of splicing due to four synonymous and one donor site intronic variants. Additionally, a significant change in 'Relative Synonymous Codon usage (RSCU) frequencies' and 'log ratio of codon usage frequencies' of variant codon was also noted that might affect the rate of translation. This study establishes that the synonymous variants are possibly associated with disease phenotype in CHD patients. Comprehensive computational analysis, using well-established web based tools, is suggestive of their potential downstream molecular effects on the structure, stability and expression of GATA4 protein.