Background Several studies have identified different genes that control the final dimension and structure of the mandible. Prognathism of the mandible is thought to correlate with these genes; however, no specific gene has been assigned as a risk factor due to various genome-wide scan results in different races. Previous studies that involved the Han ethnic group in China and Korea suggested matrilin-1 (MATN1) polymorphism as the contributor for mandibular prognathism. To date, no study has

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... conducted to understand the role of MATN1 in Deutero-Malay population. This study aimed to detect MATN1 gene polymorphism in the promoter and exon 5 regions, which is a proposed risk factor in class III skeletal malocclusion with mandibular prognathism in Deutero-Malay population. This was a case-control study with purposive sampling method that involved 47 class III skeletal malocclusion subjects with mandibular prognathism (case group) and 47 class I skeletal relation subjects (control group) performed in the Molecular Genetics Laboratory of Faculty of Medicine, Universitas Padjadjaran, Indonesia. DNA isolated from buccal mucous epithelia and MATN1 gene was amplified using the polymerase chain reaction (PCR) and sequencing technique. Data were then analyzed statistically to observe the frequency of allele/genotype MATN1 in class III skeletal malocclusion and mandibular prognathism patients in comparison with the normal mandibular as well as to identify the risk factor of mandibular prognathism. Result The frequency of the 354 T > C(rs20566) CC genotype gene polymorphism in the case group was significantly higher than in the control group. The odd ratio (OR) value of the case group was also higher than in the control group (χ2 = 4.89; p = 0.027; OR = 6.27). Conclusions Our results show that the polymorphism of 354 T > C in the exon 5 region of the CC genotype MATN1 gene is a risk factor for class III skeletal malocclusion with mandible prognathism in Deutero-Malay population.