Genetic progress has lead to an increase in the growth rate, feed efficiency and subsequently, increase the rate of mortality and the prevalence of metabolic diseases such as ascites in broilers. Ascites, as one of the three major metabolic diseases, has caused significant economic losses in the poultry industry. Over the past few years, as the improve growth rate, the incidence of ascites has increased dramatically in chickens. Given that, the importance of this disease as one of the common problems in the poultry industry and also its economic importance duo to bird mortality, it is necessary to study the effective factors in ascites disease. Ascites disease is influenced by genetics and environmental factors. Our previous GWAS study showed that the CCDC141 gene could be a strong candidate associated with heart failure and ascites development in broilers. Therefore, the aim of this study is the structural analysis of some parts of this gene in broilers. To achieve this goal, the cardiac index was evaluated on 120 birds of a population of Arian B-line chicks. Then, the DNA of all samples was extracted using the salting-out method from liver tissue. The target regions of this gene were amplified by polymerase chain reaction (PCR) using appropriate primers. In this study, 3 single nucleotide polymorphisms (SNPs) were identified in the target region of the CCDC141 gene. Further investigation revealed that a mutation located in coding region of exon 19 and two SNP in exon 25 of the CCDC141 gene. Statistical analysis revealed that the missense mutation in exon 19 (rs735294925) has been significantly associated with the right ventricular index (P <0.004).  The missense mutation leads a change of amino acid sequence and can have a dramatic effect on stability, hydrogen bond network, conformational dynamics, activity, and many other physiologically important properties of proteins. The finding suggests that the significant missense mutation (rs735294925) is an effective factor in ascites disease by altering the protein function of the CCDC141 gene. The results of this study can be used to accelerate breeding programs for ascites resistance in broilers.